Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>
Diff between visNetwork versions 0.2.0 dated 2015-12-21 and 0.2.1 dated 2016-01-31
DESCRIPTION | 12 - MD5 | 86 +++++--- NAMESPACE | 12 + NEWS | 12 + R/dependencies.R | 45 ++++ R/visEdges.R | 1 R/visExport.R |only R/visFit.R | 2 R/visFocus.R | 2 R/visGetPositions.R |only R/visIgraph.R |only R/visIgraphLayout.R |only R/visLegend.R | 24 ++ R/visNetwork.R | 24 ++ R/visNodes.R | 1 R/visOptions.R | 8 R/visPhysics.R | 8 R/visSave.R |only R/visSetData.R |only R/visStabilize.R |only README.md | 10 - inst/doc/Introduction-to-visNetwork.html | 98 +++++----- inst/doc/network/edges.html | 7 inst/doc/network/index.html | 8 inst/doc/network/nodes.html | 7 inst/htmlwidgets/lib/export |only inst/htmlwidgets/lib/vis/vis.map | 2 inst/htmlwidgets/lib/vis/vis.min.css | 2 inst/htmlwidgets/lib/vis/vis.min.js | 44 ++-- inst/htmlwidgets/visNetwork.js | 302 +++++++++++++++++++++++++++---- inst/htmlwidgets/visNetwork.yaml | 2 inst/shiny/src/server/options_server.R | 1 man/visEdges.Rd | 1 man/visExport.Rd |only man/visFit.Rd | 2 man/visFocus.Rd | 2 man/visGetPositions.Rd |only man/visIgraphLayout.Rd |only man/visLegend.Rd | 14 + man/visNetwork-igraph.Rd |only man/visNetwork.Rd | 24 ++ man/visNodes.Rd | 1 man/visPhysics.Rd | 4 man/visSave.Rd |only man/visSetData.Rd |only man/visStabilize.Rd |only man/visStartSimulation.Rd |only man/visStopSimulation.Rd |only 48 files changed, 595 insertions(+), 173 deletions(-)
Title: Java Executable .jar Files for 'RKEEL'
Description: KEEL is a popular Java software for a large number of different knowledge data discovery tasks. Furthermore, 'RKEEL' is a package with a R code layer between R and KEEL, for using KEEL in R code. This package downloads and install the .jar files necessary for 'RKEEL' algorithms execution. For more information about KEEL, see <http://www.keel.es/>.
Author: Jose Moyano [aut, cre], Luciano Sanchez Ramos [aut]
Maintainer: Jose Moyano <i02momuj@uco.es>
Diff between RKEELjars versions 1.0.8 dated 2016-01-29 and 1.0.9 dated 2016-01-31
DESCRIPTION | 8 ++--- MD5 | 4 +- R/zzz.R | 90 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 51 insertions(+), 51 deletions(-)
Title: Metropolis Sampler and Supporting Functions for Estimating
Animal Movement from Archival Tags and Satellite Fixes
Description: Data handling and estimation functions for animal movement
estimation from archival or satellite tags. Helper functions are included
for making image summaries binned by time interval from Markov Chain Monte Carlo
simulations.
Author: Michael D. Sumner [aut, cre],
Simon Wotherspoon [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between tripEstimation versions 0.0-42 dated 2015-02-02 and 0.0-44 dated 2016-01-31
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 7 +++++++ NEWS | 10 +++++++++- R/zzz.r |only README.md | 5 +++++ man/mkLookup.Rd | 2 +- 7 files changed, 33 insertions(+), 12 deletions(-)
More information about tripEstimation at CRAN
Permanent link
Title: Code Examples to Accompany the Book "R for Dummies"
Description: Contains all the code examples in the book "R for Dummies" (1st
edition). You can view the table of contents as well as the sample code for each
chapter.
Author: Andrie de Vries [aut, cre],
Joris Meys [aut]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between rfordummies versions 0.1.1 dated 2015-04-24 and 0.1.2 dated 2016-01-31
rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch01.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch02.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch03.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch04.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch05.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch06.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch07.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch08.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch09.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch10.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch11.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch12.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch13.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch14.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch15.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch16.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch17.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch18.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch19.r |only rfordummies-0.1.1/rfordummies/inst/scripts/1-orig/ch20.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch01.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch02.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch03.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch04.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch05.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch06.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch07.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch08.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch09.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch10.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch11.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch12.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch13.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch14.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch15.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch16.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch17.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch18.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch19.r |only rfordummies-0.1.1/rfordummies/inst/scripts/2-clean/ch20.r |only rfordummies-0.1.2/rfordummies/DESCRIPTION | 14 - rfordummies-0.1.2/rfordummies/MD5 | 140 +++++++------- rfordummies-0.1.2/rfordummies/NAMESPACE | 4 rfordummies-0.1.2/rfordummies/R/chapters-auto.R | 98 ++++----- rfordummies-0.1.2/rfordummies/R/chapters.R | 23 -- rfordummies-0.1.2/rfordummies/R/rfordummies-package.r | 1 rfordummies-0.1.2/rfordummies/inst/cleanscripts.R | 4 rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch01.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch02.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch03.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch04.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch05.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch06.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch07.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch08.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch09.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch10.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch11.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch12.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch13.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch14.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch15.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch16.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch17.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch18.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch19.R |only rfordummies-0.1.2/rfordummies/inst/scripts/1-orig/ch20.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch01.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch02.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch03.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch04.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch05.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch06.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch07.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch08.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch09.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch10.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch11.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch12.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch13.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch14.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch15.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch16.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch17.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch18.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch19.R |only rfordummies-0.1.2/rfordummies/inst/scripts/2-clean/ch20.R |only rfordummies-0.1.2/rfordummies/man/ch01.Rd | 28 +- rfordummies-0.1.2/rfordummies/man/ch02.Rd | 28 +- rfordummies-0.1.2/rfordummies/man/ch03.Rd | 28 +- rfordummies-0.1.2/rfordummies/man/ch04.Rd | 28 +- rfordummies-0.1.2/rfordummies/man/ch05.Rd | 28 +- rfordummies-0.1.2/rfordummies/man/ch06.Rd | 28 +- rfordummies-0.1.2/rfordummies/man/ch07.Rd | 28 +- rfordummies-0.1.2/rfordummies/man/ch08.Rd | 28 +- rfordummies-0.1.2/rfordummies/man/ch09.Rd | 28 +- rfordummies-0.1.2/rfordummies/man/ch10.Rd | 29 +- rfordummies-0.1.2/rfordummies/man/ch11.Rd | 29 +- rfordummies-0.1.2/rfordummies/man/ch12.Rd | 29 +- rfordummies-0.1.2/rfordummies/man/ch13.Rd | 33 +-- rfordummies-0.1.2/rfordummies/man/ch14.Rd | 29 +- rfordummies-0.1.2/rfordummies/man/ch15.Rd | 29 +- rfordummies-0.1.2/rfordummies/man/ch16.Rd | 29 +- rfordummies-0.1.2/rfordummies/man/ch17.Rd | 29 +- rfordummies-0.1.2/rfordummies/man/ch18.Rd | 35 +-- rfordummies-0.1.2/rfordummies/man/ch19.Rd | 29 +- rfordummies-0.1.2/rfordummies/man/ch20.Rd | 29 +- rfordummies-0.1.2/rfordummies/man/elements.Rd | 4 rfordummies-0.1.2/rfordummies/man/rfordummies.Rd | 2 rfordummies-0.1.2/rfordummies/man/saveElements.Rd | 3 rfordummies-0.1.2/rfordummies/man/toc.Rd | 2 111 files changed, 339 insertions(+), 537 deletions(-)
Title: Nonparametric Regression
Description:
Tools are provided for
(1) nonparametric regression (kernel, local linear),
(2) semiparametric regression (single index, additive models), and
(3) quantile regression (linear, kernel).
Author: Jussi Klemela <jussi.klemela@gmail.com>
Maintainer: Jussi Klemela <jussi.klemela@gmail.com>
Diff between regpro versions 0.1.0 dated 2013-10-16 and 0.1.1 dated 2016-01-31
DESCRIPTION | 20 +++++++++--------- MD5 | 50 +++++++++++++++++++++++----------------------- NAMESPACE | 7 ++++++ man/additive.Rd | 6 ++--- man/additive.stage.Rd | 2 - man/copula.trans.Rd | 4 +-- man/emp.distribu.Rd | 2 - man/emp.quantile.Rd | 2 - man/kernesti.der.Rd | 2 - man/kernesti.quantile.Rd | 2 - man/kernesti.regr.Rd | 2 - man/linear.Rd | 2 - man/linear.quan.Rd | 2 - man/loclin.Rd | 2 - man/ma.Rd | 2 - man/pcf.additive.Rd | 2 - man/pcf.kern.quan.Rd | 2 - man/pcf.kernesti.Rd | 2 - man/pcf.kernesti.der.Rd | 2 - man/pcf.kernesti.marg.Rd | 2 - man/pcf.kernesti.slice.Rd | 2 - man/pcf.loclin.Rd | 2 - man/pcf.single.index.Rd | 2 - man/pp.regression.Rd | 2 - man/quantil.emp.Rd | 2 - man/single.index.Rd | 2 - 26 files changed, 68 insertions(+), 61 deletions(-)
Title: Data Analysis in Ecology
Description: Miscellaneous functions for data analysis in ecology, with special emphasis on spatial data.
Author: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Maintainer: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Diff between pgirmess versions 1.6.3 dated 2015-11-04 and 1.6.4 dated 2016-01-31
pgirmess-1.6.3/pgirmess/man/QGIS2sp.Rd |only pgirmess-1.6.3/pgirmess/man/classnum.Rd |only pgirmess-1.6.3/pgirmess/man/cormat.Rd |only pgirmess-1.6.3/pgirmess/man/correlog.Rd |only pgirmess-1.6.3/pgirmess/man/diag2edge.Rd |only pgirmess-1.6.3/pgirmess/man/difshannonbio.Rd |only pgirmess-1.6.3/pgirmess/man/pairsrp.Rd |only pgirmess-1.6.3/pgirmess/man/pave.Rd |only pgirmess-1.6.3/pgirmess/man/pclig.Rd |only pgirmess-1.6.3/pgirmess/man/piankabio.Rd |only pgirmess-1.6.3/pgirmess/man/piankabioboot.Rd |only pgirmess-1.6.3/pgirmess/man/polycirc.Rd |only pgirmess-1.6.3/pgirmess/man/polycirc2.Rd |only pgirmess-1.6.3/pgirmess/man/postxt.Rd |only pgirmess-1.6.3/pgirmess/man/preybiom.Rd |only pgirmess-1.6.3/pgirmess/man/print.mc.Rd |only pgirmess-1.6.3/pgirmess/man/selMod.Rd |only pgirmess-1.6.3/pgirmess/man/shannon.Rd |only pgirmess-1.6.3/pgirmess/man/shannonbio.Rd |only pgirmess-1.6.3/pgirmess/man/shannonbioboot.Rd |only pgirmess-1.6.3/pgirmess/man/siegelp179.Rd |only pgirmess-1.6.3/pgirmess/man/tabcont2categ.Rd |only pgirmess-1.6.3/pgirmess/man/val4symb.Rd |only pgirmess-1.6.3/pgirmess/man/valchisq.Rd |only pgirmess-1.6.3/pgirmess/man/write.delim.Rd |only pgirmess-1.6.4/pgirmess/DESCRIPTION | 8 +-- pgirmess-1.6.4/pgirmess/MD5 | 56 +++++++++++++------------- pgirmess-1.6.4/pgirmess/data/preybiom.rda |binary pgirmess-1.6.4/pgirmess/data/siegelp179.rda |binary pgirmess-1.6.4/pgirmess/man/QGIS2sp.rd |only pgirmess-1.6.4/pgirmess/man/classnum.rd |only pgirmess-1.6.4/pgirmess/man/cormat.rd |only pgirmess-1.6.4/pgirmess/man/correlog.rd |only pgirmess-1.6.4/pgirmess/man/diag2edge.rd |only pgirmess-1.6.4/pgirmess/man/difshannonbio.rd |only pgirmess-1.6.4/pgirmess/man/pairsrp.rd |only pgirmess-1.6.4/pgirmess/man/pave.rd |only pgirmess-1.6.4/pgirmess/man/pclig.rd |only pgirmess-1.6.4/pgirmess/man/piankabio.rd |only pgirmess-1.6.4/pgirmess/man/piankabioboot.rd |only pgirmess-1.6.4/pgirmess/man/polycirc.rd |only pgirmess-1.6.4/pgirmess/man/polycirc2.rd |only pgirmess-1.6.4/pgirmess/man/postxt.rd |only pgirmess-1.6.4/pgirmess/man/preybiom.rd |only pgirmess-1.6.4/pgirmess/man/print.mc.rd |only pgirmess-1.6.4/pgirmess/man/selMod.rd |only pgirmess-1.6.4/pgirmess/man/shannon.rd |only pgirmess-1.6.4/pgirmess/man/shannonbio.rd |only pgirmess-1.6.4/pgirmess/man/shannonbioboot.rd |only pgirmess-1.6.4/pgirmess/man/siegelp179.rd |only pgirmess-1.6.4/pgirmess/man/tabcont2categ.rd |only pgirmess-1.6.4/pgirmess/man/val4symb.rd |only pgirmess-1.6.4/pgirmess/man/valchisq.rd |only pgirmess-1.6.4/pgirmess/man/write.delim.rd |only 54 files changed, 32 insertions(+), 32 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: Functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization and sequential processing.
Author: Jouni Helske <jouni.helske@jyu.fi>
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between KFAS versions 1.1.2 dated 2015-06-26 and 1.2.0 dated 2016-01-31
KFAS-1.1.2/KFAS/R/deviance.KFS.R |only KFAS-1.1.2/KFAS/R/subset.SSModel.R |only KFAS-1.1.2/KFAS/man/coef.KFS.Rd |only KFAS-1.1.2/KFAS/man/deviance.KFS.Rd |only KFAS-1.1.2/KFAS/man/fitted.KFS.Rd |only KFAS-1.2.0/KFAS/ChangeLog | 314 +-- KFAS-1.2.0/KFAS/DESCRIPTION | 9 KFAS-1.2.0/KFAS/MD5 | 171 - KFAS-1.2.0/KFAS/NAMESPACE | 114 - KFAS-1.2.0/KFAS/R/KFAS-defunct.R |only KFAS-1.2.0/KFAS/R/KFAS-package.R | 1190 +++++++----- KFAS-1.2.0/KFAS/R/KFS.R | 1129 ++++++----- KFAS-1.2.0/KFAS/R/SSMarima.R | 138 - KFAS-1.2.0/KFAS/R/SSMcustom.R | 155 - KFAS-1.2.0/KFAS/R/SSMcycle.R | 177 - KFAS-1.2.0/KFAS/R/SSModel.R | 717 +++---- KFAS-1.2.0/KFAS/R/SSMregression.R | 363 +-- KFAS-1.2.0/KFAS/R/SSMseasonal.R | 259 +- KFAS-1.2.0/KFAS/R/SSMtrend.R | 187 - KFAS-1.2.0/KFAS/R/approxSSM.R | 266 +- KFAS-1.2.0/KFAS/R/artransform.R | 34 KFAS-1.2.0/KFAS/R/checkModel.R | 263 +- KFAS-1.2.0/KFAS/R/coef.KFS.R | 160 + KFAS-1.2.0/KFAS/R/extract.SSModel.R | 502 ++--- KFAS-1.2.0/KFAS/R/fitSSM.R | 323 ++- KFAS-1.2.0/KFAS/R/fitted.KFS.R | 75 KFAS-1.2.0/KFAS/R/hatvalues.KFS.R | 94 KFAS-1.2.0/KFAS/R/importanceSSM.R | 284 +- KFAS-1.2.0/KFAS/R/initTheta.R | 52 KFAS-1.2.0/KFAS/R/interval.R | 179 - KFAS-1.2.0/KFAS/R/logLik.SSModel.R | 308 +-- KFAS-1.2.0/KFAS/R/mvInnovations.R | 54 KFAS-1.2.0/KFAS/R/plot.SSModel.R |only KFAS-1.2.0/KFAS/R/predict.SSModel.R | 647 +++--- KFAS-1.2.0/KFAS/R/print.objects.R | 181 - KFAS-1.2.0/KFAS/R/residuals.KFS.R | 223 +- KFAS-1.2.0/KFAS/R/rstandard.KFS.R | 157 - KFAS-1.2.0/KFAS/R/signals.R | 191 +- KFAS-1.2.0/KFAS/R/simHelper.R | 93 KFAS-1.2.0/KFAS/R/simulateSSM.R | 202 +- KFAS-1.2.0/KFAS/R/transformSSM.R | 314 +-- KFAS-1.2.0/KFAS/build/vignette.rds |binary KFAS-1.2.0/KFAS/inst/doc/KFAS.R | 323 ++- KFAS-1.2.0/KFAS/inst/doc/KFAS.Rnw | 1992 +++++++++++---------- KFAS-1.2.0/KFAS/inst/doc/KFAS.pdf |binary KFAS-1.2.0/KFAS/man/Extract.SSModel.Rd | 163 - KFAS-1.2.0/KFAS/man/GlobalTemp.Rd | 44 KFAS-1.2.0/KFAS/man/KFAS-defunct.Rd |only KFAS-1.2.0/KFAS/man/KFAS.Rd | 1002 +++++----- KFAS-1.2.0/KFAS/man/KFS.Rd | 191 +- KFAS-1.2.0/KFAS/man/SSModel.Rd | 428 ++-- KFAS-1.2.0/KFAS/man/alcohol.Rd | 34 KFAS-1.2.0/KFAS/man/approxSSM.Rd | 182 + KFAS-1.2.0/KFAS/man/artransform.Rd | 55 KFAS-1.2.0/KFAS/man/boat.Rd | 93 KFAS-1.2.0/KFAS/man/checkModel.Rd | 85 KFAS-1.2.0/KFAS/man/coef.SSModel.Rd |only KFAS-1.2.0/KFAS/man/fitSSM.Rd | 218 +- KFAS-1.2.0/KFAS/man/fitted.SSModel.Rd |only KFAS-1.2.0/KFAS/man/hatvalues.KFS.Rd | 77 KFAS-1.2.0/KFAS/man/importanceSSM.Rd | 180 - KFAS-1.2.0/KFAS/man/ldl.Rd | 64 KFAS-1.2.0/KFAS/man/logLik.SSModel.Rd | 162 - KFAS-1.2.0/KFAS/man/mvInnovations.Rd | 6 KFAS-1.2.0/KFAS/man/plot.SSModel.Rd |only KFAS-1.2.0/KFAS/man/predict.SSModel.Rd | 28 KFAS-1.2.0/KFAS/man/print.KFS.Rd | 46 KFAS-1.2.0/KFAS/man/print.SSModel.Rd | 34 KFAS-1.2.0/KFAS/man/residuals.KFS.Rd | 4 KFAS-1.2.0/KFAS/man/rstandard.KFS.Rd | 25 KFAS-1.2.0/KFAS/man/sexratio.Rd | 68 KFAS-1.2.0/KFAS/man/signal.Rd | 89 KFAS-1.2.0/KFAS/man/simulateSSM.Rd | 106 - KFAS-1.2.0/KFAS/man/transformSSM.Rd | 40 KFAS-1.2.0/KFAS/src/approx.f95 | 306 +-- KFAS-1.2.0/KFAS/src/filter1step.f95 | 250 +- KFAS-1.2.0/KFAS/src/filter1stepnovar.f95 | 158 - KFAS-1.2.0/KFAS/src/gloglik.f95 | 186 - KFAS-1.2.0/KFAS/src/kfilter.f95 | 182 - KFAS-1.2.0/KFAS/src/kfstheta.f95 | 250 +- KFAS-1.2.0/KFAS/src/ptheta.f95 | 254 +- KFAS-1.2.0/KFAS/src/simgaussian.f95 | 545 ++--- KFAS-1.2.0/KFAS/src/smoothsim.f95 | 206 +- KFAS-1.2.0/KFAS/tests/testthat/testArima.R | 167 - KFAS-1.2.0/KFAS/tests/testthat/testBasics.R | 54 KFAS-1.2.0/KFAS/tests/testthat/testGLM.R | 642 +++--- KFAS-1.2.0/KFAS/tests/testthat/testImportanceSSM.R | 60 KFAS-1.2.0/KFAS/tests/testthat/testNumerical.R | 107 - KFAS-1.2.0/KFAS/tests/testthat/testSimulateSSM.R | 88 KFAS-1.2.0/KFAS/tests/testthat/testStruct.R | 44 KFAS-1.2.0/KFAS/vignettes/KFAS.Rnw | 1992 +++++++++++---------- KFAS-1.2.0/KFAS/vignettes/KFAS.bib | 703 ++++--- 92 files changed, 11569 insertions(+), 9889 deletions(-)
Title: Advanced Forest Plot Using 'grid' Graphics
Description: A forest plot that allows for
multiple confidence intervals per row,
custom fonts for each text element,
custom confidence intervals,
text mixed with expressions, and more.
The aim is to extend the use of forest plots beyond meta-analyses.
This is a more general version of the original 'rmeta' package's forestplot
function and relies heavily on the 'grid' package.
Author: Max Gordon [aut, cre],
Thomas Lumley [aut, ctb]
Maintainer: Max Gordon <max@gforge.se>
Diff between forestplot versions 1.3 dated 2015-11-16 and 1.4 dated 2016-01-31
forestplot-1.3/forestplot/tests/visual_tests |only forestplot-1.4/forestplot/DESCRIPTION | 10 forestplot-1.4/forestplot/MD5 | 101 + forestplot-1.4/forestplot/NAMESPACE | 35 forestplot-1.4/forestplot/NEWS | 7 forestplot-1.4/forestplot/R/forestplot.R | 10 forestplot-1.4/forestplot/R/forestplot_helpers.R | 10 forestplot-1.4/forestplot/build/vignette.rds |binary forestplot-1.4/forestplot/inst/doc/forestplot.html | 4 forestplot-1.4/forestplot/man/HRQoL.Rd | 32 forestplot-1.4/forestplot/man/forestplot-package.Rd | 70 - forestplot-1.4/forestplot/man/forestplot.Rd | 660 ++++++------- forestplot-1.4/forestplot/man/fpColors.Rd | 164 +-- forestplot-1.4/forestplot/man/fpDrawCI.Rd | 362 +++---- forestplot-1.4/forestplot/man/fpLegend.Rd | 98 - forestplot-1.4/forestplot/man/fpTxtGp.Rd | 100 - forestplot-1.4/forestplot/man/getTicks.Rd | 122 +- forestplot-1.4/forestplot/man/heightDetails.xaxis.Rd | 52 - forestplot-1.4/forestplot/man/prFpConvertMultidimArray.Rd | 38 forestplot-1.4/forestplot/man/prFpDrawLegend.Rd | 104 +- forestplot-1.4/forestplot/man/prFpDrawLine.Rd | 104 +- forestplot-1.4/forestplot/man/prFpDrawLines.Rd | 50 forestplot-1.4/forestplot/man/prFpFetchRowLabel.Rd | 70 - forestplot-1.4/forestplot/man/prFpFindWidestGrob.Rd | 44 forestplot-1.4/forestplot/man/prFpGetConfintFnList.Rd | 64 - forestplot-1.4/forestplot/man/prFpGetGraphTicksAndClips.Rd | 132 +- forestplot-1.4/forestplot/man/prFpGetLabels.Rd | 96 - forestplot-1.4/forestplot/man/prFpGetLayoutVP.Rd | 66 - forestplot-1.4/forestplot/man/prFpGetLegendBoxPosition.Rd | 58 - forestplot-1.4/forestplot/man/prFpGetLegendGrobs.Rd | 56 - forestplot-1.4/forestplot/man/prFpGetLines.Rd | 52 - forestplot-1.4/forestplot/man/prFpPrepareLegendMarker.Rd | 46 forestplot-1.4/forestplot/man/prFpPrintLabels.Rd | 56 - forestplot-1.4/forestplot/man/prFpPrintXaxis.Rd | 50 forestplot-1.4/forestplot/man/prFpValidateLabelList.Rd | 40 forestplot-1.4/forestplot/man/prFpXrange.Rd | 90 - forestplot-1.4/forestplot/man/prGetTextGrobCex.Rd | 38 forestplot-1.4/forestplot/man/prGparMerge.Rd | 42 forestplot-1.4/forestplot/man/prGridPlotTitle.Rd | 44 forestplot-1.4/forestplot/man/prListRep.Rd | 46 forestplot-1.4/forestplot/man/prPopulateList.Rd | 62 - forestplot-1.4/forestplot/man/prPushMarginViewport.Rd | 58 - forestplot-1.4/forestplot/tests/forestplot2_vtests.R |only forestplot-1.4/forestplot/tests/vtest_from_vignette.R |only forestplot-1.4/forestplot/vignettes/forestplot_files |only 45 files changed, 1690 insertions(+), 1653 deletions(-)
Title: Calculations for All Common Subsequences
Description: Implements several string comparison algorithms, including calACS
(count all common subsequences), lenACS (calculate the lengths of all common subsequences), and lenLCS
(calculate the length of the longest common subsequence).
Some algorithms differentiate between the more strict
definition of subsequence, where a common subsequence cannot be separated
by any other items, from its looser counterpart, where a common subsequence
can be interrupted by other items. This difference is shown in the suffix of the algorithm (-Strict vs -Loose).
For example, q-w is a common subsequence
of q-w-e-r and q-e-w-r on the looser definition, but not on the more strict
definition. calACSLoose Algorithm from Wang, H. All common subsequences
(2007) IJCAI International Joint Conference on Artificial Intelligence, pp. 635-640.
Author: Alan Gu
Maintainer: Alan Gu <alan.on.ca@gmail.com>
Diff between calACS versions 1.2 dated 2015-12-16 and 2.2.1 dated 2016-01-31
calACS-1.2/calACS/R/calACS.R |only calACS-1.2/calACS/R/calACSstr.R |only calACS-2.2.1/calACS/DESCRIPTION | 23 +++++---- calACS-2.2.1/calACS/MD5 | 38 ++++++++++------ calACS-2.2.1/calACS/NAMESPACE | 5 +- calACS-2.2.1/calACS/R/GeneratePossibleSubsequences.r | 19 ++++++-- calACS-2.2.1/calACS/R/calACSLoose.r | 4 - calACS-2.2.1/calACS/R/calACSStrict.R |only calACS-2.2.1/calACS/R/calACSstrLoose.r | 7 -- calACS-2.2.1/calACS/R/calACSstrStrict.R |only calACS-2.2.1/calACS/R/is.subvector.r | 1 calACS-2.2.1/calACS/R/lenACSStrict.r |only calACS-2.2.1/calACS/R/lenACSstrStrict.r |only calACS-2.2.1/calACS/R/lenLCSStrict.r |only calACS-2.2.1/calACS/R/lenLCSstrStrict.r |only calACS-2.2.1/calACS/R/longestVec.r |only calACS-2.2.1/calACS/man/GeneratePossibleSubsequences.Rd | 8 ++- calACS-2.2.1/calACS/man/calACSLoose.Rd | 8 +-- calACS-2.2.1/calACS/man/calACSStrict.Rd | 19 +++++--- calACS-2.2.1/calACS/man/calACSstrLoose.Rd | 9 +-- calACS-2.2.1/calACS/man/calACSstrStrict.Rd | 20 +++++--- calACS-2.2.1/calACS/man/is.subvector.Rd | 4 + calACS-2.2.1/calACS/man/lenACSStrict.Rd |only calACS-2.2.1/calACS/man/lenACSstrStrict.Rd |only calACS-2.2.1/calACS/man/lenLCSStrict.Rd |only calACS-2.2.1/calACS/man/lenLCSstrStrict.Rd |only calACS-2.2.1/calACS/man/longestVec.Rd |only 27 files changed, 100 insertions(+), 65 deletions(-)
Title: Interface for the 'Box.com API'
Description: An R interface for the remote file hosting service 'Box' (https://
www.box.com/). In addition to uploading and downloading files, this package
includes functions which mirror base R operations for local files, (e.g.
box_load(), box_save(), box_read(), box_setwd(), etc.), as well as 'git'
style functions for entire directories (e.g. box_fetch(), box_push()).
Author: Brendan Rocks [aut, cre]
Maintainer: Brendan Rocks <rocks.brendan@gmail.com>
Diff between boxr versions 0.3.1 dated 2016-01-04 and 0.3.2 dated 2016-01-31
boxr-0.3.1/boxr/R/boxr__internal_progress.R |only boxr-0.3.2/boxr/DESCRIPTION | 12 +-- boxr-0.3.2/boxr/LICENSE | 2 boxr-0.3.2/boxr/MD5 | 25 +++---- boxr-0.3.2/boxr/NEWS.md | 9 ++ boxr-0.3.2/boxr/R/boxr__internal_diff_and_delete.R | 4 - boxr-0.3.2/boxr/R/boxr__internal_diff_and_uldl.R | 4 - boxr-0.3.2/boxr/R/boxr__internal_get.R | 6 - boxr-0.3.2/boxr/R/boxr__internal_update_upload.R | 4 - boxr-0.3.2/boxr/R/boxr_auth.R | 2 boxr-0.3.2/boxr/R/boxr_delete_restore.R | 8 +- boxr-0.3.2/boxr/R/boxr_s3_classes.R | 22 +++---- boxr-0.3.2/boxr/R/boxr_upload_download.R | 4 - boxr-0.3.2/boxr/inst/doc/boxr.html | 66 +++++++++++++-------- 14 files changed, 96 insertions(+), 72 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre]
Maintainer: Jonathan Bartlett <jwb133@googlemail.com>
Diff between smcfcs versions 1.1.1 dated 2015-11-23 and 1.2.0 dated 2016-01-30
DESCRIPTION | 12 +- MD5 | 28 +++--- R/smcfcs.r | 86 +++++++++++++++++---- build/vignette.rds |binary data/ex_compet.rda |binary data/ex_coxquad.rda |binary data/ex_lininter.rda |binary data/ex_linquad.rda |binary data/ex_logisticquad.rda |binary data/ex_poisson.rda |only inst/doc/smcfcs-vignette.R | 2 inst/doc/smcfcs-vignette.Rmd | 6 - inst/doc/smcfcs-vignette.html | 171 +++++++++++++++++++++++------------------- man/ex_poisson.Rd |only man/smcfcs.Rd | 35 +++++--- vignettes/smcfcs-vignette.Rmd | 2 16 files changed, 217 insertions(+), 125 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description:
Contains some auxiliary functions for multiple
imputation which complements existing functionality
in R.
In addition to some utility functions, main features
include plausible value imputation, multilevel
imputation functions, imputation using partial least
squares (PLS) for high dimensional predictors, nested
multiple imputation, and two-way imputation.
Author:
Alexander Robitzsch [aut, cre], Simon Grund [ctb],
Thorsten Henke [ctb]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 1.5-0 dated 2015-11-22 and 1.6-0 dated 2016-01-30
DESCRIPTION | 39 ++--- MD5 | 134 +++++++++--------- NAMESPACE | 233 ++++++++++++++++--------------- R/ARb_utils.R | 6 R/MIwaldtest.R | 4 R/NMIwaldtest.R | 2 R/Rhat.mice.R | 16 +- R/Rsessinfo.R | 2 R/Rutils.R | 4 R/cppfunction.R | 4 R/datalist2mids.R | 8 - R/datlist_create.R |only R/draw.pv.ctt.R | 27 +-- R/glm.cluster.R | 4 R/kernelpls.fit2.R | 2 R/latent.regression.em.R | 24 +-- R/lm.cluster.R | 4 R/load.data.R | 6 R/ma.wtd.statNA.R | 252 ++++++++++++++++++++++++++++------ R/mi.anova.R | 12 - R/mice.1chain.R | 26 +-- R/mice.impute.2l.contextual.norm.R | 6 R/mice.impute.2l.eap.R | 4 R/mice.impute.2l.latentgroupmean.R | 70 +++++++-- R/mice.impute.2l.plausible.values.R | 22 +- R/mice.impute.2l.pls.R | 18 +- R/mice.impute.2l.pls2.R | 8 - R/mice.impute.2lonly.pmm2.R | 4 R/mice.impute.grouped.R | 10 - R/mice.impute.norm3.R | 2 R/mice.impute.pmm4.R | 2 R/mice.impute.pmm5.R | 10 - R/mice.impute.pmm6.R | 4 R/mice.impute.tricube.pmm.R | 2 R/mice.impute.tricube.pmm2.R | 6 R/mice.impute.weighted.norm.R | 6 R/micombine.chisquare.R | 6 R/micombine.cor.R | 12 - R/mids2datlist.R | 16 +- R/mids2mlwin.R | 15 +- R/nested.datlist2datlist.R |only R/nesteddatlist2datlist.R |only R/norm.draw2.R | 4 R/norm.draw3.R | 4 R/pca.covridge.R | 2 R/plausible.value.draw.R | 7 R/plausible.value.imputation.R | 6 R/save.data.R | 10 - R/scale_datlist.R |only R/summary.mipo.nmi.R | 6 R/tw.imputation.R | 11 - R/tw.mcmc.imputation.R | 18 +- R/visitSequence.determine.R | 3 R/write.mice.imputation.R | 32 ++-- R/write.pspp.R | 7 R/zzz.R | 7 inst/NEWS | 32 +++- man/cxxfunction.copy.Rd | 44 ++++- man/datlist_create.Rd |only man/fast.groupmean.Rd | 1 man/lm.cluster.Rd | 7 man/ma.scale2.Rd | 2 man/ma.wtd.statNA.Rd | 106 ++++++++++++-- man/mice.impute.2l.latentgroupmean.Rd | 12 + man/mice.impute.grouped.Rd | 3 man/mice.impute.tricube.pmm.Rd | 6 man/mice.nmi.Rd | 2 man/miceadds-package.Rd | 4 man/mids2datlist.Rd | 27 +++ man/mids2mlwin.Rd | 6 man/scale_datlist.Rd |only 71 files changed, 897 insertions(+), 504 deletions(-)
Title: Analysis of Stable Matchings
Description: Implements structural estimators to correct for
the sample selection bias from observed outcomes in matching
markets. This includes one-sided matching of agents into
groups as well as two-sided matching of students to schools.
The package also contains R code for three matching algorithms:
the deferred-acceptance (or Gale-Shapley) algorithm for
stable marriage and college admissions problems, the
top-trading-cycles algorithm for house allocation and a
partitioning linear programme for the roommates problem.
Author: Thilo Klein
Maintainer: Thilo Klein <thilo@klein.uk>
Diff between matchingMarkets versions 0.1-7 dated 2015-10-11 and 0.2-1 dated 2016-01-30
DESCRIPTION | 29 +++--- MD5 | 65 +++++++------- NAMESPACE | 5 - NEWS.md | 7 + R/RcppExports.R | 5 + R/daa.R | 19 +++- R/mfx.R | 2 R/stabit.R | 59 +++---------- R/stabit2.R |only R/stabsim.R | 9 -- R/stabsim2.R |only README.md | 4 build/vignette.rds |binary data/baac00.RData |binary data/klein15a.RData |binary data/klein15b.RData |binary inst/doc/matching.Rnw | 4 inst/doc/matching.pdf |binary man/daa.Rd | 27 +++--- man/khb.Rd | 4 man/matchingMarkets-package.Rd | 19 ---- man/mce.Rd | 8 - man/mfx.Rd | 6 - man/plp.Rd | 10 +- man/stabit.Rd | 120 ++++++++++----------------- man/stabit2.Rd |only man/stabsim.Rd | 12 -- man/stabsim2.Rd |only man/ttc.Rd | 2 src/RcppExports.cpp | 33 +++++++ src/stabitCpp.cpp | 2 src/stabitCpp2.cpp |only vignettes/Sections/1_Introduction.tex | 14 +-- vignettes/Sections/4_MonteCarloResults.Rnw | 128 ++++++++++++++++++++++++----- vignettes/matching.Rnw | 4 vignettes/matching.bib | 38 ++++++-- 36 files changed, 368 insertions(+), 267 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging
For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of
CppJieba
Maintainer: Qin Wenfeng <mail@qinwenfeng.com>
Diff between jiebaR versions 0.7 dated 2015-12-06 and 0.8 dated 2016-01-30
jiebaR-0.7/jiebaR/R/jiebar.R |only jiebaR-0.7/jiebaR/R/tools.R |only jiebaR-0.7/jiebaR/inst/include/lib/ISegment.hpp |only jiebaR-0.7/jiebaR/inst/include/lib/Limonp |only jiebaR-0.7/jiebaR/inst/include/segtype.hpp |only jiebaR-0.7/jiebaR/man/print.hmmseg.Rd |only jiebaR-0.7/jiebaR/src/segtype.cpp |only jiebaR-0.8/jiebaR/DESCRIPTION | 10 jiebaR-0.8/jiebaR/LICENSE | 2 jiebaR-0.8/jiebaR/MD5 | 124 +- jiebaR-0.8/jiebaR/NAMESPACE | 12 jiebaR-0.8/jiebaR/NEWS | 27 jiebaR-0.8/jiebaR/R/RcppExports.R | 60 - jiebaR-0.8/jiebaR/R/dict_tools.R |only jiebaR-0.8/jiebaR/R/overload.R | 2 jiebaR-0.8/jiebaR/R/print.R | 77 - jiebaR-0.8/jiebaR/R/segment.R | 54 jiebaR-0.8/jiebaR/R/tagger.R | 45 jiebaR-0.8/jiebaR/R/worker.R |only jiebaR-0.8/jiebaR/R/worker_func.R |only jiebaR-0.8/jiebaR/README.md | 5 jiebaR-0.8/jiebaR/build/vignette.rds |binary jiebaR-0.8/jiebaR/inst/include/jiebaR.h | 59 + jiebaR-0.8/jiebaR/inst/include/jiebaRAPI.h | 380 ++++-- jiebaR-0.8/jiebaR/inst/include/lib/DictTrie.hpp | 413 +++---- jiebaR-0.8/jiebaR/inst/include/lib/FullSegment.hpp | 230 +--- jiebaR-0.8/jiebaR/inst/include/lib/HMMModel.hpp |only jiebaR-0.8/jiebaR/inst/include/lib/HMMSegment.hpp | 564 ++-------- jiebaR-0.8/jiebaR/inst/include/lib/Jieba.hpp |only jiebaR-0.8/jiebaR/inst/include/lib/KeywordExtractor.hpp | 343 ++---- jiebaR-0.8/jiebaR/inst/include/lib/LevelSegment.hpp |only jiebaR-0.8/jiebaR/inst/include/lib/MPSegment.hpp | 239 +--- jiebaR-0.8/jiebaR/inst/include/lib/MixSegment.hpp | 200 +-- jiebaR-0.8/jiebaR/inst/include/lib/PosTagger.hpp | 172 +-- jiebaR-0.8/jiebaR/inst/include/lib/PreFilter.hpp |only jiebaR-0.8/jiebaR/inst/include/lib/QuerySegment.hpp | 181 +-- jiebaR-0.8/jiebaR/inst/include/lib/SegmentBase.hpp | 116 -- jiebaR-0.8/jiebaR/inst/include/lib/Simhasher.hpp | 54 jiebaR-0.8/jiebaR/inst/include/lib/TransCode.hpp | 62 - jiebaR-0.8/jiebaR/inst/include/lib/Trie.hpp | 359 +----- jiebaR-0.8/jiebaR/inst/include/lib/limonp |only jiebaR-0.8/jiebaR/inst/include/segtype-v4.hpp |only jiebaR-0.8/jiebaR/man/edit_dict.Rd | 5 jiebaR-0.8/jiebaR/man/new_user_word.Rd |only jiebaR-0.8/jiebaR/man/print.jieba.Rd |only jiebaR-0.8/jiebaR/man/query_threshold.Rd |only jiebaR-0.8/jiebaR/man/segment.Rd | 4 jiebaR-0.8/jiebaR/man/show_dictpath.Rd | 5 jiebaR-0.8/jiebaR/man/tagging.Rd | 3 jiebaR-0.8/jiebaR/man/words_locate.Rd |only jiebaR-0.8/jiebaR/man/worker.Rd | 2 jiebaR-0.8/jiebaR/src/Makevars | 2 jiebaR-0.8/jiebaR/src/Makevars.win | 2 jiebaR-0.8/jiebaR/src/RcppExports.cpp | 212 ++- jiebaR-0.8/jiebaR/src/get_tuple.cpp | 10 jiebaR-0.8/jiebaR/src/init.c | 175 ++- jiebaR-0.8/jiebaR/src/segtype-v4.cpp |only jiebaR-0.8/jiebaR/tests/testthat/CPP_API/DESCRIPTION | 6 jiebaR-0.8/jiebaR/tests/testthat/CPP_API/NAMESPACE | 2 jiebaR-0.8/jiebaR/tests/testthat/CPP_API/R/Rcpps.R | 15 jiebaR-0.8/jiebaR/tests/testthat/CPP_API/man/filecoding.Rd | 2 jiebaR-0.8/jiebaR/tests/testthat/CPP_API/src/Makevars |only jiebaR-0.8/jiebaR/tests/testthat/CPP_API/src/test_api.cpp | 118 +- jiebaR-0.8/jiebaR/tests/testthat/CPP_API/tests/testthat/test-cpp.R | 55 jiebaR-0.8/jiebaR/tests/testthat/C_API/DESCRIPTION | 2 jiebaR-0.8/jiebaR/tests/testthat/C_API/R/Rcpps.R | 15 jiebaR-0.8/jiebaR/tests/testthat/C_API/src/Makevars |only jiebaR-0.8/jiebaR/tests/testthat/C_API/src/test_api.c | 112 + jiebaR-0.8/jiebaR/tests/testthat/C_API/tests/testthat/test-c.R | 73 - 69 files changed, 2133 insertions(+), 2477 deletions(-)
Title: Cognitive Diagnosis Modeling
Description:
Functions for cognitive diagnosis modeling
and multidimensional item response modeling for
dichotomous and polytomous data. This package
enables the estimation of the DINA and DINO model,
the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic
model (GDM), the multidimensional linear compensatory
item response model and the structured latent class
model (SLCA).
Author:
Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 4.6-0 dated 2015-11-04 and 4.7-0 dated 2016-01-30
CDM-4.6-0/CDM/src/gdd__c.cpp |only CDM-4.7-0/CDM/DESCRIPTION | 44 +- CDM-4.7-0/CDM/MD5 | 211 +++++++------- CDM-4.7-0/CDM/NAMESPACE | 299 ++++++++------------ CDM-4.7-0/CDM/R/IRT.anova.R | 2 CDM-4.7-0/CDM/R/IRT.compareModels.R | 2 CDM-4.7-0/CDM/R/IRT.derivedParameters.R | 10 CDM-4.7-0/CDM/R/IRT.irfprobPlot.R | 22 - CDM-4.7-0/CDM/R/IRT.jackknife.gdina.R | 8 CDM-4.7-0/CDM/R/IRT.parameterTable.R |only CDM-4.7-0/CDM/R/IRT.repDesign.R | 2 CDM-4.7-0/CDM/R/IRT.se.din.R | 2 CDM-4.7-0/CDM/R/WaldTest.R |only CDM-4.7-0/CDM/R/cdm.est.calc.accuracy.R | 16 + CDM-4.7-0/CDM/R/confint.din.R | 2 CDM-4.7-0/CDM/R/din.R | 8 CDM-4.7-0/CDM/R/din.deterministic.R | 6 CDM-4.7-0/CDM/R/din.validate.qmatrix.R | 2 CDM-4.7-0/CDM/R/equivalent.dina.R | 2 CDM-4.7-0/CDM/R/equivalent.skillclasses.R | 4 CDM-4.7-0/CDM/R/gdina.R | 53 ++- CDM-4.7-0/CDM/R/gdina.dif.R | 4 CDM-4.7-0/CDM/R/gdina.dif_aux.R | 8 CDM-4.7-0/CDM/R/gdina.postproc.R | 2 CDM-4.7-0/CDM/R/gdina.wald.R | 127 ++++---- CDM-4.7-0/CDM/R/gdina.wald_aux.R |only CDM-4.7-0/CDM/R/gdina_designmatrices.R | 12 CDM-4.7-0/CDM/R/gdina_hogdina_alg.R | 8 CDM-4.7-0/CDM/R/gdina_reduced_skillspace.R | 2 CDM-4.7-0/CDM/R/gdm.R | 11 CDM-4.7-0/CDM/R/gdm_algorithm.R | 6 CDM-4.7-0/CDM/R/gdm_postproc.R | 6 CDM-4.7-0/CDM/R/gdm_preproc.R | 4 CDM-4.7-0/CDM/R/itemfit.sx2.R | 14 CDM-4.7-0/CDM/R/label_significance_level.R |only CDM-4.7-0/CDM/R/mcdina.R | 4 CDM-4.7-0/CDM/R/mcdina.simul.R | 11 CDM-4.7-0/CDM/R/modelfit.cor.R | 14 CDM-4.7-0/CDM/R/modelfit.cor.din.R | 2 CDM-4.7-0/CDM/R/modelfit.cor2.R | 14 CDM-4.7-0/CDM/R/personfit.appropriateness.R | 28 - CDM-4.7-0/CDM/R/plot.din.R | 72 ++-- CDM-4.7-0/CDM/R/plot.gdina.R | 2 CDM-4.7-0/CDM/R/plot.gdm.R | 16 - CDM-4.7-0/CDM/R/plot.slca.R | 2 CDM-4.7-0/CDM/R/print.summary.din.R | 6 CDM-4.7-0/CDM/R/sim.din.R | 6 CDM-4.7-0/CDM/R/sim.gdina.R | 4 CDM-4.7-0/CDM/R/skill.cor.R | 6 CDM-4.7-0/CDM/R/slca.R | 11 CDM-4.7-0/CDM/R/slca.algorithm.R | 8 CDM-4.7-0/CDM/R/summary.gdina.R | 2 CDM-4.7-0/CDM/R/summary.gdina.wald.R |only CDM-4.7-0/CDM/R/summary.gdm.R | 2 CDM-4.7-0/CDM/R/summary.mcdina.R | 2 CDM-4.7-0/CDM/R/summary.slca.R | 2 CDM-4.7-0/CDM/R/zzz.R | 6 CDM-4.7-0/CDM/data/data.Students.rda |binary CDM-4.7-0/CDM/data/data.cdm01.rda |binary CDM-4.7-0/CDM/data/data.cdm02.rda |binary CDM-4.7-0/CDM/data/data.dcm.rda |binary CDM-4.7-0/CDM/data/data.dtmr.rda |binary CDM-4.7-0/CDM/data/data.ecpe.rda |binary CDM-4.7-0/CDM/data/data.fraction1.rda |binary CDM-4.7-0/CDM/data/data.fraction2.rda |binary CDM-4.7-0/CDM/data/data.hr.rda |binary CDM-4.7-0/CDM/data/data.jang.rda |binary CDM-4.7-0/CDM/data/data.melab.rda |binary CDM-4.7-0/CDM/data/data.mg.rda |binary CDM-4.7-0/CDM/data/data.pgdina.rda |binary CDM-4.7-0/CDM/data/data.sda6.rda |binary CDM-4.7-0/CDM/data/data.timss03.G8.su.rda |binary CDM-4.7-0/CDM/data/data.timss07.G4.lee.rda |binary CDM-4.7-0/CDM/data/data.timss11.G4.AUT.part.rda |binary CDM-4.7-0/CDM/data/data.timss11.G4.AUT.rda |binary CDM-4.7-0/CDM/data/fraction.subtraction.data.rda |binary CDM-4.7-0/CDM/data/fraction.subtraction.qmatrix.rda |binary CDM-4.7-0/CDM/data/sim.dina.rda |binary CDM-4.7-0/CDM/data/sim.dino.rda |binary CDM-4.7-0/CDM/data/sim.qmatrix.rda |binary CDM-4.7-0/CDM/inst/NEWS | 25 + CDM-4.7-0/CDM/man/CDM-package.Rd | 189 ++++++------ CDM-4.7-0/CDM/man/IRT.factor.scores.Rd | 4 CDM-4.7-0/CDM/man/IRT.modelfit.Rd | 30 +- CDM-4.7-0/CDM/man/IRT.parameterTable.Rd |only CDM-4.7-0/CDM/man/WaldTest.Rd |only CDM-4.7-0/CDM/man/cdi.kli.Rd | 2 CDM-4.7-0/CDM/man/data.Students.Rd | 8 CDM-4.7-0/CDM/man/data.cdm.Rd | 15 - CDM-4.7-0/CDM/man/data.dcm.Rd | 4 CDM-4.7-0/CDM/man/data.ecpe.Rd | 27 + CDM-4.7-0/CDM/man/data.fraction1.Rd | 4 CDM-4.7-0/CDM/man/data.fraction2.Rd | 4 CDM-4.7-0/CDM/man/data.jang.Rd | 4 CDM-4.7-0/CDM/man/data.mg.Rd | 6 CDM-4.7-0/CDM/man/data.pgdina.Rd | 3 CDM-4.7-0/CDM/man/gdina.wald.Rd | 34 +- CDM-4.7-0/CDM/man/itemfit.sx2.Rd | 2 CDM-4.7-0/CDM/man/modelfit.cor.Rd | 4 CDM-4.7-0/CDM/man/sequential.items.Rd | 8 CDM-4.7-0/CDM/man/sim.gdina.Rd | 2 CDM-4.7-0/CDM/man/slca.Rd | 40 +- CDM-4.7-0/CDM/man/vcov.Rd | 8 CDM-4.7-0/CDM/src/cdm_kli_id_c.cpp | 17 - CDM-4.7-0/CDM/src/din.deterministic.devcrit_c.cpp | 7 CDM-4.7-0/CDM/src/din.jml.devcrit_c.cpp | 7 CDM-4.7-0/CDM/src/gdd_c.cpp |only CDM-4.7-0/CDM/src/irt_predict_c.cpp | 7 CDM-4.7-0/CDM/src/modelfit_cor2_c.cpp | 4 CDM-4.7-0/CDM/src/probs_multcat_items_counts_c.cpp | 14 CDM-4.7-0/CDM/src/slca_cfunctions.cpp | 11 111 files changed, 843 insertions(+), 766 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author:
BIFIE
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between BIFIEsurvey versions 1.7-0 dated 2015-11-04 and 1.8-0 dated 2016-01-30
DESCRIPTION | 20 +- MD5 | 86 ++++----- NAMESPACE | 122 ++++++-------- R/BIFIE.correl.R | 6 R/BIFIE.crosstab.R | 8 R/BIFIE.data.boot.R | 4 R/BIFIE.data.jack.R | 4 R/BIFIE.data.transform.R | 6 R/BIFIE.derivedParameters.R | 16 - R/BIFIE.freq.R | 2 R/BIFIE.hist.R | 8 R/BIFIE.linreg.R | 14 - R/BIFIE.logistreg.R | 8 R/BIFIE.mva.R | 6 R/BIFIE.pathmodel.R | 5 R/BIFIE.twolevelreg.R | 19 +- R/BIFIE.univar.R | 22 +- R/BIFIE.univar.test.R | 5 R/BIFIE.waldtest.R | 2 R/BIFIE_NMI_inference_parameters.R | 2 R/BIFIE_by_helper_pureR.R | 6 R/create_summary_table.R | 9 - R/load.BIFIE.data.R | 2 R/load.BIFIEdata.files.R | 12 - R/save.BIFIE.data.R | 2 R/summary.BIFIE.data.R | 4 R/vcov.BIFIE.survey.R | 2 R/write.BIFIE.data.R | 4 R/zzz.R | 10 - data/data.bifie01.rda |binary data/data.pisaNLD.rda |binary data/data.test1.rda |binary data/data.timss1.ind.rda |binary data/data.timss1.rda |binary data/data.timss2.rda |binary data/data.timss3.rda |binary data/data.timss4.rda |binary data/data.timssrep.rda |binary inst/NEWS | 15 + man/BIFIE.data.Rd | 2 man/BIFIE.derivedParameters.Rd | 2 man/BIFIEsurvey-package.Rd | 4 src/jack_dataprep.cpp | 23 +- src/univar.cpp | 320 ++++++++++++++++++++----------------- 44 files changed, 411 insertions(+), 371 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-15 0.4
2012-11-05 0.3
2008-07-30 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-21 2.0-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-29 1.4
2015-07-30 1.3
2014-03-27 1.2
2013-08-26 1.1-13
2013-04-25 1.1-12
2013-01-17 1.1-11
2012-07-03 1.1-9
2012-07-02 1.1-8
2012-05-22 1.1-7
2012-05-14 1.1-6
2011-12-30 1.1-5
2011-10-23 1.1-4
2011-10-20 1.1-3
2011-10-12 1.1-2
2011-09-05 1.1-1
2011-06-20 1.1
2011-06-03 1.0-4
2011-05-30 1.0-3
2011-05-23 1.0-2
2011-05-18 1.0-1
2011-04-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-08 1.5
2012-04-28 1.4
2011-09-23 1.3
2011-08-05 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-21 1.0.1
2015-12-18 1.0.0
2015-03-12 0.7.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-03 0.9.3
2014-11-15 0.9.2
2014-10-09 0.9.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-19 1.0.7
2015-10-19 1.0.6
2015-05-19 1.0.5
2014-02-12 1.0.3.1
2014-01-12 1.0.3
2013-07-04 1.0.1
2013-03-28 1.0.0
2013-01-01 0.9-9
2011-08-23 0.9-7
2011-08-18 0.9-6
2011-04-05 0.9-5
2011-02-23 0.9-4
2010-12-22 0.9-3
2010-08-26 0.9-2
2010-07-24 0.9-1
2009-11-30 0.9
2009-04-23 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-08 1.1
2014-04-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-06 2.0.0
2015-01-06 1.0.1108
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-22 1.1
2015-02-26 1.0
Title: MCMC Generalised Linear Mixed Models
Description: MCMC Generalised Linear Mixed Models.
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield <j.hadfield@ed.ac.uk>
Diff between MCMCglmm versions 2.22 dated 2015-09-21 and 2.22.1 dated 2016-01-30
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/MCMCglmm.h | 10 +++++++++- src/MCMCglmmcc.h | 10 +++++----- src/cs.h | 14 ++++++++++++++ 5 files changed, 35 insertions(+), 13 deletions(-)
Title: Analytical Tools for Zooarchaeological Data
Description: The analysis and inference of faunal remains recovered from
archaeological sites concerns the field of zooarchaeology. The zooaRch package
provides analytical tools to make inferences on zooarchaeological data.
Functions in this package allow users to read, manipulate, visualize, and
analyze zooarchaeological data.
Author: Erik Otarola-Castillo, Jesse Wolfhagen, Max D. Price
Maintainer: Erik Otarola-Castillo <eotarolacastillo@fas.harvard.edu>
Diff between zooaRch versions 1.1 dated 2015-07-24 and 1.2 dated 2016-01-30
DESCRIPTION | 19 - MD5 | 30 +- NAMESPACE | 2 R/zooaRch.r | 6 build/vignette.rds |binary inst/doc/zooaRch-vignette.html | 539 ++++++++++++++--------------------------- inst/doc/zooaRch-vignette.rmd | 2 man/fuse.func.Rd | 10 man/marjRab.Rd | 2 man/marjRab.fuse.Rd | 2 man/mort.func.Rd | 24 - man/speth83.Rd | 4 man/surv.func.Rd | 30 +- man/winslow.fuse.Rd | 6 man/zooaRch-package.Rd | 8 vignettes/zooaRch-vignette.rmd | 2 16 files changed, 265 insertions(+), 421 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
ADMB
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
CppAD (C++ automatic differentiation), Eigen (templated matrix-vector
library) and CHOLMOD (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through BLAS and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.6.5 dated 2015-12-03 and 1.6.6 dated 2016-01-30
DESCRIPTION | 8 +- MD5 | 22 ++--- NEWS | 22 +++++ R/validation.R | 16 +++- inst/include/TMB.hpp | 7 + inst/include/atomic_macro.hpp | 147 +++++++++++++++++++-------------------- inst/include/atomic_math.hpp | 128 ++++++++++++++++++++++----------- inst/include/cppad/configure.hpp | 2 inst/include/tmbutils/array.hpp | 34 ++++++++- inst/include/tmbutils/vector.hpp | 18 ++-- man/oneStepPredict.Rd | 4 - src/utils.c | 2 12 files changed, 258 insertions(+), 152 deletions(-)
Title: Real-Time Stock Price & Volume in China Market
Description: With this package, users can obtain the real-time price and volume information of stocks in China market, as well as the information of the stock index. This package adopted the API from Sina Finance (http://finance.sina.com.cn/).
Author: Xiaodong Deng
Maintainer: Xiaodong Deng <xd_deng@hotmail.com>
Diff between StockChina versions 0.3 dated 2015-09-18 and 0.3.1 dated 2016-01-30
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/index.CN.R | 3 ++- man/stock.CN.Rd | 6 +++--- 4 files changed, 13 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-29 1.0.1
2015-10-01 1.0
Title: Best Hand Analysis for Poker Variants Including Wildcards
Description: Provides insight into how the best hand for a poker game changes based on the game dealt, players who stay in until the showdown and wildcards added to the base game. At this time the package does not support player tactics, so draw poker variants are not included.
Author: Bradley Shanrock-Solberg
Maintainer: Bradley Shanrock-Solberg <greblosb@gmail.com>
Diff between wildpoker versions 1.0 dated 2015-12-01 and 1.1 dated 2016-01-29
DESCRIPTION | 8 - MD5 | 33 ++-- NAMESPACE | 2 R/deck.R | 77 +++++++--- R/hand.R | 26 ++- R/stats.R | 313 +++++++++++++++++++++++++++++--------------- R/sysdata.rda |binary build/partial.rdb |binary data/wpnotsupported.RData |binary data/wpsupportedgames.RData |binary man/figures/graphftq.png |binary man/figures/graphftqc.png |only man/figures/graphhcdp.png |binary man/figures/graphhcdph.png |only man/wildpoker-package.Rd | 2 man/wpgraphs.Rd | 33 ++++ man/wpnotsupported.Rd | 3 man/wprules.Rd |only man/wpsupportedgames.Rd | 6 19 files changed, 338 insertions(+), 165 deletions(-)
Title: Embedded JavaScript Engine
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between V8 versions 0.9 dated 2015-10-18 and 0.10 dated 2016-01-29
DESCRIPTION | 9 + LICENSE | 2 MD5 | 34 +++---- NAMESPACE | 2 NEWS | 3 R/callback.R |only build/vignette.rds |binary inst/doc/npm.R | 2 inst/doc/npm.html | 75 +++++++++------ inst/doc/v8_intro.R | 24 ++-- inst/doc/v8_intro.Rmd | 58 +++++++++-- inst/doc/v8_intro.html | 238 ++++++++++++++++++++++++++++--------------------- man/JS.Rd | 2 man/V8.Rd | 3 src/Makevars.in | 5 + src/V8.cpp | 57 +++++++++++ src/v8_json.h |only tests |only vignettes/v8_intro.Rmd | 58 +++++++++-- 19 files changed, 388 insertions(+), 184 deletions(-)
Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix
design, along with visualizations of several common set, element and attribute
related tasks.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>
Diff between UpSetR versions 1.0.2 dated 2015-12-18 and 1.0.3 dated 2016-01-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 8 ++++++++ R/MainBar.R | 4 ++-- R/SizeBar.R | 20 ++++++++++---------- inst/doc/attribute.plots.html | 15 +++++++++------ inst/doc/basic.usage.html | 16 ++++++++-------- inst/doc/queries.html | 10 +++++----- 8 files changed, 53 insertions(+), 42 deletions(-)
Title: Supplementary Item Response Theory Models
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), DETECT statistic, local structural
equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 1.9-0 dated 2015-11-04 and 1.10-0 dated 2016-01-29
sirt-1.10-0/sirt/DESCRIPTION | 21 sirt-1.10-0/sirt/MD5 | 554 +++++------ sirt-1.10-0/sirt/NAMESPACE | 536 +++++----- sirt-1.10-0/sirt/R/ARb_utils.R | 32 sirt-1.10-0/sirt/R/IRT.mle.R | 12 sirt-1.10-0/sirt/R/IRT.modelfit.sirt.R | 4 sirt-1.10-0/sirt/R/R2noharm-utility.R | 6 sirt-1.10-0/sirt/R/R2noharm.EAP.R | 9 sirt-1.10-0/sirt/R/anova_sirt.R | 16 sirt-1.10-0/sirt/R/attach.environment.sirt.R | 10 sirt-1.10-0/sirt/R/automatic.recode.R | 16 sirt-1.10-0/sirt/R/brm.irf.R | 4 sirt-1.10-0/sirt/R/brm.sim.R | 2 sirt-1.10-0/sirt/R/btm.R | 52 - sirt-1.10-0/sirt/R/categorize.R | 20 sirt-1.10-0/sirt/R/class.accuracy.rasch.R | 10 sirt-1.10-0/sirt/R/data.prep.R | 8 sirt-1.10-0/sirt/R/data.wide2long.R | 4 sirt-1.10-0/sirt/R/detect.R | 39 sirt-1.10-0/sirt/R/dif.logisticregression.R | 27 sirt-1.10-0/sirt/R/dif.variance.R | 8 sirt-1.10-0/sirt/R/dirichlet.R | 9 sirt-1.10-0/sirt/R/equating.rasch.R | 24 sirt-1.10-0/sirt/R/f1d.irt.R | 10 sirt-1.10-0/sirt/R/fit.adisop.R | 4 sirt-1.10-0/sirt/R/fit.gradedresponse.R | 2 sirt-1.10-0/sirt/R/fit.gradedresponse_alg.R | 2 sirt-1.10-0/sirt/R/fit.isop.R | 2 sirt-1.10-0/sirt/R/fit.logistic.R | 4 sirt-1.10-0/sirt/R/fit.logistic_alg.R | 2 sirt-1.10-0/sirt/R/fuzcluster_alg.R | 14 sirt-1.10-0/sirt/R/gom.em.R | 10 sirt-1.10-0/sirt/R/gom.em.alg.R | 25 sirt-1.10-0/sirt/R/gom.jml.R | 3 sirt-1.10-0/sirt/R/gom.jml_alg.R | 9 sirt-1.10-0/sirt/R/greenyang.reliability.R | 11 sirt-1.10-0/sirt/R/invariance.alignment.aux.R | 2 sirt-1.10-0/sirt/R/invariance.alignment2.R | 25 sirt-1.10-0/sirt/R/isop.dich.R | 4 sirt-1.10-0/sirt/R/isop.poly.R | 8 sirt-1.10-0/sirt/R/latent.regression.em.normal.R | 18 sirt-1.10-0/sirt/R/latent.regression.em.raschtype.R | 20 sirt-1.10-0/sirt/R/lavaan2mirt.R | 2 sirt-1.10-0/sirt/R/lc.2raters.R | 8 sirt-1.10-0/sirt/R/likelihood_adjustment.R | 3 sirt-1.10-0/sirt/R/likelihood_adjustment_aux.R | 4 sirt-1.10-0/sirt/R/linking.haberman.aux.R | 2 sirt-1.10-0/sirt/R/linking.robust.R | 29 sirt-1.10-0/sirt/R/lsdm.R | 11 sirt-1.10-0/sirt/R/lsdm_aux.R | 4 sirt-1.10-0/sirt/R/lsem.estimate.R | 26 sirt-1.10-0/sirt/R/lsem.fitsem.R | 20 sirt-1.10-0/sirt/R/lsem.parameter.summary.R | 12 sirt-1.10-0/sirt/R/lsem.permutationTest.R | 9 sirt-1.10-0/sirt/R/lsem.residualize.R | 16 sirt-1.10-0/sirt/R/marginal.truescore.reliability.R | 4 sirt-1.10-0/sirt/R/matrix_functions.R | 4 sirt-1.10-0/sirt/R/matrixfunctions_sirt.R | 2 sirt-1.10-0/sirt/R/mcmc.2pno.R | 4 sirt-1.10-0/sirt/R/mcmc.2pno.ml.R | 12 sirt-1.10-0/sirt/R/mcmc.2pno.ml_alg.R | 30 sirt-1.10-0/sirt/R/mcmc.2pno.ml_output.R | 11 sirt-1.10-0/sirt/R/mcmc.2pno_alg.R | 16 sirt-1.10-0/sirt/R/mcmc.2pnoh.R | 8 sirt-1.10-0/sirt/R/mcmc.2pnoh_alg.R | 34 sirt-1.10-0/sirt/R/mcmc.3pno.testlet.R | 4 sirt-1.10-0/sirt/R/mcmc.3pno.testlet_alg.R | 38 sirt-1.10-0/sirt/R/mcmc.3pno.testlet_output.R | 6 sirt-1.10-0/sirt/R/mcmc.aux.R | 2 sirt-1.10-0/sirt/R/mcmc.list.descriptives.R | 4 sirt-1.10-0/sirt/R/mcmclist2coda.R | 4 sirt-1.10-0/sirt/R/mirt.wrapper.coef.R | 4 sirt-1.10-0/sirt/R/mirt.wrapper.itemplot.R | 2 sirt-1.10-0/sirt/R/mle.reliability.R | 4 sirt-1.10-0/sirt/R/modelfit.cor.R | 12 sirt-1.10-0/sirt/R/modelfit.cor.poly.R | 4 sirt-1.10-0/sirt/R/nedelsky.irf.R | 2 sirt-1.10-0/sirt/R/nedelsky.latresp.R | 2 sirt-1.10-0/sirt/R/nedelsky.sim.R | 2 sirt-1.10-0/sirt/R/noharm.sirt.R | 2 sirt-1.10-0/sirt/R/normal2.cw.R | 9 sirt-1.10-0/sirt/R/np.dich.R | 54 - sirt-1.10-0/sirt/R/osink.R | 2 sirt-1.10-0/sirt/R/pbivnorm2.R | 11 sirt-1.10-0/sirt/R/personfit.R | 15 sirt-1.10-0/sirt/R/pgenlogis.R | 2 sirt-1.10-0/sirt/R/plausible.values.raschtype.R | 25 sirt-1.10-0/sirt/R/plot.invariance.alignment.R | 8 sirt-1.10-0/sirt/R/plot.isop.R | 34 sirt-1.10-0/sirt/R/plot.lsem.R | 28 sirt-1.10-0/sirt/R/plot.lsem.permutationTest.R | 19 sirt-1.10-0/sirt/R/plot.mcmc.sirt.R | 63 - sirt-1.10-0/sirt/R/plot.rasch.mml.R | 4 sirt-1.10-0/sirt/R/plot.rm.sdt.R | 14 sirt-1.10-0/sirt/R/prmse.subscores.R | 26 sirt-1.10-0/sirt/R/prob.guttman.R | 4 sirt-1.10-0/sirt/R/qmc.nodes.R | 2 sirt-1.10-0/sirt/R/rasch.conquest.R | 42 sirt-1.10-0/sirt/R/rasch.copula.R | 20 sirt-1.10-0/sirt/R/rasch.copula2.R | 24 sirt-1.10-0/sirt/R/rasch.copula2_aux.R | 37 sirt-1.10-0/sirt/R/rasch.copula3.R | 16 sirt-1.10-0/sirt/R/rasch.copula3.covariance.R | 4 sirt-1.10-0/sirt/R/rasch.copula3_aux.R | 5 sirt-1.10-0/sirt/R/rasch.evm.pcm.R | 4 sirt-1.10-0/sirt/R/rasch.evm.pcm_aux.R | 6 sirt-1.10-0/sirt/R/rasch.jml.R | 41 sirt-1.10-0/sirt/R/rasch.jml.biascorr.R | 2 sirt-1.10-0/sirt/R/rasch.mirtlc.R | 24 sirt-1.10-0/sirt/R/rasch.mirtlc_aux.R | 15 sirt-1.10-0/sirt/R/rasch.mml.R | 26 sirt-1.10-0/sirt/R/rasch.mml.npirt.R | 6 sirt-1.10-0/sirt/R/rasch.mml.ramsay.R | 21 sirt-1.10-0/sirt/R/rasch.mml.raschtype.R | 37 sirt-1.10-0/sirt/R/rasch.mml2.R | 40 sirt-1.10-0/sirt/R/rasch.mml2.missing1.R | 12 sirt-1.10-0/sirt/R/rasch.pairwise.R | 6 sirt-1.10-0/sirt/R/rasch.pairwise.itemcluster.R | 2 sirt-1.10-0/sirt/R/rasch.pml.R | 8 sirt-1.10-0/sirt/R/rasch.pml2.R | 2 sirt-1.10-0/sirt/R/rasch.pml2_aux.R | 12 sirt-1.10-0/sirt/R/rasch.pml3.R | 2 sirt-1.10-0/sirt/R/rasch.pml3_aux.R | 12 sirt-1.10-0/sirt/R/rasch.pml_aux.R | 20 sirt-1.10-0/sirt/R/rasch.prox.R | 20 sirt-1.10-0/sirt/R/rasch.va.R | 11 sirt-1.10-0/sirt/R/reliability.nonlinear.sem.R | 15 sirt-1.10-0/sirt/R/rm.facets.R | 10 sirt-1.10-0/sirt/R/rm.facets_PP.R | 2 sirt-1.10-0/sirt/R/rm.facets_alg.R | 20 sirt-1.10-0/sirt/R/rm.hrm.est.tau.item.R | 4 sirt-1.10-0/sirt/R/rm.sdt_alg.R | 8 sirt-1.10-0/sirt/R/rm.smooth.distribution.R | 2 sirt-1.10-0/sirt/R/sia.sirt.R | 2 sirt-1.10-0/sirt/R/sim.rasch.dep.R | 5 sirt-1.10-0/sirt/R/smirt.R | 8 sirt-1.10-0/sirt/R/smirt_alg_comp.R | 16 sirt-1.10-0/sirt/R/smirt_alg_noncomp.R | 4 sirt-1.10-0/sirt/R/smirt_postproc.R | 5 sirt-1.10-0/sirt/R/stratified.cronbach.alpha.R | 15 sirt-1.10-0/sirt/R/summary.R2noharm.R | 4 sirt-1.10-0/sirt/R/summary.btm.R | 2 sirt-1.10-0/sirt/R/summary.fuzcluster.R | 2 sirt-1.10-0/sirt/R/summary.gom.em.R | 2 sirt-1.10-0/sirt/R/summary.invariance.alignment.R | 2 sirt-1.10-0/sirt/R/summary.isop.R | 2 sirt-1.10-0/sirt/R/summary.lsem.R | 4 sirt-1.10-0/sirt/R/summary.lsem.permutationTest.R | 4 sirt-1.10-0/sirt/R/summary.mcmc.sirt.R | 3 sirt-1.10-0/sirt/R/summary.noharm.sirt.R | 2 sirt-1.10-0/sirt/R/summary.rasch.copula.R | 4 sirt-1.10-0/sirt/R/summary.rasch.evm.pcm.R | 2 sirt-1.10-0/sirt/R/summary.rasch.mirtlc.R | 2 sirt-1.10-0/sirt/R/summary.rasch.mml2.R | 14 sirt-1.10-0/sirt/R/summary.rasch.pml.R | 2 sirt-1.10-0/sirt/R/summary.rm.facets.R | 2 sirt-1.10-0/sirt/R/summary.rm.sdt.R | 2 sirt-1.10-0/sirt/R/summary.smirt.R | 2 sirt-1.10-0/sirt/R/tetrachoric2.R | 10 sirt-1.10-0/sirt/R/truescore.irt.R | 4 sirt-1.10-0/sirt/R/unidim.csn.R | 6 sirt-1.10-0/sirt/R/wle.rasch.R | 15 sirt-1.10-0/sirt/R/yen.q3.R | 15 sirt-1.10-0/sirt/R/zzz.R | 6 sirt-1.10-0/sirt/data/data.activity.itempars.rda |binary sirt-1.10-0/sirt/data/data.big5.qgraph.rda |binary sirt-1.10-0/sirt/data/data.big5.rda |binary sirt-1.10-0/sirt/data/data.bs07a.rda |binary sirt-1.10-0/sirt/data/data.eid.rda |binary sirt-1.10-0/sirt/data/data.ess2005.rda |binary sirt-1.10-0/sirt/data/data.g308.rda |binary sirt-1.10-0/sirt/data/data.inv4gr.rda |binary sirt-1.10-0/sirt/data/data.liking.science.rda |binary sirt-1.10-0/sirt/data/data.long.rda |binary sirt-1.10-0/sirt/data/data.lsem01.rda |binary sirt-1.10-0/sirt/data/data.math.rda |binary sirt-1.10-0/sirt/data/data.mcdonald.LSAT6.rda |binary sirt-1.10-0/sirt/data/data.mcdonald.act15.rda |binary sirt-1.10-0/sirt/data/data.mcdonald.rape.rda |binary sirt-1.10-0/sirt/data/data.mixed1.rda |binary sirt-1.10-0/sirt/data/data.ml1.rda |binary sirt-1.10-0/sirt/data/data.ml2.rda |binary sirt-1.10-0/sirt/data/data.noharm18.rda |binary sirt-1.10-0/sirt/data/data.noharmExC.rda |binary sirt-1.10-0/sirt/data/data.pars1.2pl.rda |binary sirt-1.10-0/sirt/data/data.pars1.rasch.rda |binary sirt-1.10-0/sirt/data/data.pirlsmissing.rda |binary sirt-1.10-0/sirt/data/data.pisaMath.rda |binary sirt-1.10-0/sirt/data/data.pisaPars.rda |binary sirt-1.10-0/sirt/data/data.pisaRead.rda |binary sirt-1.10-0/sirt/data/data.pw01.rda |binary sirt-1.10-0/sirt/data/data.ratings1.rda |binary sirt-1.10-0/sirt/data/data.ratings2.rda |binary sirt-1.10-0/sirt/data/data.ratings3.rda |binary sirt-1.10-0/sirt/data/data.raw1.rda |binary sirt-1.10-0/sirt/data/data.read.rda |binary sirt-1.10-0/sirt/data/data.reck21.rda |binary sirt-1.10-0/sirt/data/data.reck61DAT1.rda |binary sirt-1.10-0/sirt/data/data.reck61DAT2.rda |binary sirt-1.10-0/sirt/data/data.reck73C1a.rda |binary sirt-1.10-0/sirt/data/data.reck73C1b.rda |binary sirt-1.10-0/sirt/data/data.reck75C2.rda |binary sirt-1.10-0/sirt/data/data.reck78ExA.rda |binary sirt-1.10-0/sirt/data/data.reck79ExB.rda |binary sirt-1.10-0/sirt/data/data.si01.rda |binary sirt-1.10-0/sirt/data/data.si02.rda |binary sirt-1.10-0/sirt/data/data.si03.rda |binary sirt-1.10-0/sirt/data/data.si04.rda |binary sirt-1.10-0/sirt/data/data.si05.rda |binary sirt-1.10-0/sirt/data/data.si06.rda |binary sirt-1.10-0/sirt/data/data.timss.rda |binary sirt-1.10-0/sirt/data/data.timss07.G8.RUS.rda |binary sirt-1.10-0/sirt/inst/NEWS | 32 sirt-1.10-0/sirt/man/Q3.Rd |only sirt-1.10-0/sirt/man/Q3.testlet.Rd |only sirt-1.10-0/sirt/man/R2noharm.Rd | 2 sirt-1.10-0/sirt/man/brm.sim.Rd | 6 sirt-1.10-0/sirt/man/conf.detect.Rd | 10 sirt-1.10-0/sirt/man/data.activity.itempars.Rd | 4 sirt-1.10-0/sirt/man/data.big5.Rd | 2 sirt-1.10-0/sirt/man/data.read.Rd | 48 sirt-1.10-0/sirt/man/data.reck.Rd | 4 sirt-1.10-0/sirt/man/data.wide2long.Rd | 2 sirt-1.10-0/sirt/man/dif.logistic.regression.Rd | 6 sirt-1.10-0/sirt/man/equating.rasch.Rd | 2 sirt-1.10-0/sirt/man/fit.isop.Rd | 4 sirt-1.10-0/sirt/man/fuzcluster.Rd | 6 sirt-1.10-0/sirt/man/gom.em.Rd | 26 sirt-1.10-0/sirt/man/invariance.alignment.Rd | 4 sirt-1.10-0/sirt/man/isop.Rd | 2 sirt-1.10-0/sirt/man/isop.scoring.Rd | 2 sirt-1.10-0/sirt/man/latent.regression.em.raschtype.Rd | 26 sirt-1.10-0/sirt/man/linking.haberman.Rd | 12 sirt-1.10-0/sirt/man/linking.robust.Rd | 4 sirt-1.10-0/sirt/man/lsem.estimate.Rd | 66 + sirt-1.10-0/sirt/man/mcmc.2pno.Rd | 2 sirt-1.10-0/sirt/man/mcmc.2pno.ml.Rd | 12 sirt-1.10-0/sirt/man/mcmc.2pnoh.Rd | 10 sirt-1.10-0/sirt/man/mcmc.3pno.testlet.Rd | 28 sirt-1.10-0/sirt/man/mcmc.list.descriptives.Rd | 18 sirt-1.10-0/sirt/man/md.pattern.sirt.Rd | 2 sirt-1.10-0/sirt/man/mirt.wrapper.Rd | 6 sirt-1.10-0/sirt/man/nedelsky.sim.Rd | 8 sirt-1.10-0/sirt/man/noharm.sirt.Rd | 14 sirt-1.10-0/sirt/man/person.parameter.rasch.copula.Rd | 2 sirt-1.10-0/sirt/man/personfit.stat.Rd | 4 sirt-1.10-0/sirt/man/pgenlogis.Rd | 4 sirt-1.10-0/sirt/man/plausible.value.imputation.raschtype.Rd | 42 sirt-1.10-0/sirt/man/qmc.nodes.Rd | 16 sirt-1.10-0/sirt/man/rasch.copula.Rd | 20 sirt-1.10-0/sirt/man/rasch.evm.pcm.Rd | 4 sirt-1.10-0/sirt/man/rasch.jml.Rd | 2 sirt-1.10-0/sirt/man/rasch.mirtlc.Rd | 9 sirt-1.10-0/sirt/man/rasch.mml.Rd | 28 sirt-1.10-0/sirt/man/rasch.pairwise.itemcluster.Rd | 6 sirt-1.10-0/sirt/man/rasch.pml.Rd | 6 sirt-1.10-0/sirt/man/rasch.va.Rd | 2 sirt-1.10-0/sirt/man/sim.qm.ramsay.Rd | 2 sirt-1.10-0/sirt/man/sim.rasch.dep.Rd | 4 sirt-1.10-0/sirt/man/sim.raschtype.Rd | 2 sirt-1.10-0/sirt/man/sirt-package.Rd | 474 ++++----- sirt-1.10-0/sirt/man/smirt.Rd | 29 sirt-1.10-0/sirt/man/truescore.irt.Rd | 6 sirt-1.10-0/sirt/man/unidim.test.csn.Rd | 6 sirt-1.10-0/sirt/man/wle.rasch.jackknife.Rd | 8 sirt-1.10-0/sirt/src/eigenvaluessirt.cpp | 4 sirt-1.10-0/sirt/src/evm_comp_matrix_poly.cpp | 28 sirt-1.10-0/sirt/src/evm_eigaux_fcts.h | 12 sirt-1.10-0/sirt/src/evm_eigenvals2.h | 4 sirt-1.10-0/sirt/src/first_eigenvalue_sirt.h | 4 sirt-1.10-0/sirt/src/gooijer_isop.cpp | 12 sirt-1.10-0/sirt/src/matrixfunctions_sirt.cpp | 28 sirt-1.10-0/sirt/src/mle_pcm_group_c.cpp | 12 sirt-1.10-0/sirt/src/noharm_sirt_auxfunctions.cpp | 14 sirt-1.10-0/sirt/src/pbivnorm_rcpp_aux.h | 9 sirt-1.10-0/sirt/src/polychoric2_tetrachoric2_rcpp_aux.cpp | 7 sirt-1.10-0/sirt/src/probs_multcat_items_counts_csirt.cpp | 12 sirt-1.10-0/sirt/src/rm_smirt_mml2_code.cpp | 38 sirt-1.9-0/sirt/man/testlet.yen.q3.Rd |only sirt-1.9-0/sirt/man/yen.q3.Rd |only 280 files changed, 2148 insertions(+), 2069 deletions(-)
Title: R Client for Adobe Analytics API V1.4
Description: Functions for interacting with the Adobe Analytics API V1.4
(https://api.omniture.com/admin/1.4/rest/).
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch <rzwitch+rsitecatalyst@gmail.com>
Diff between RSiteCatalyst versions 1.4.6 dated 2015-09-18 and 1.4.7 dated 2016-01-29
DESCRIPTION | 9 - MD5 | 280 ++++++++++++++++----------------- NAMESPACE | 2 NEWS | 7 R/ApiRequest.R | 1 R/GetActivation.R | 19 +- R/GetAxleStartDate.R | 19 +- R/GetBaseCurrency.R | 19 +- R/GetBaseURL.R | 19 +- R/GetBookmarks.R | 35 ++-- R/GetCalculatedMetrics.R | 25 +- R/GetClassifications.R | 12 - R/GetCustomCalendar.R | 19 +- R/GetDashboards.R | 35 ++-- R/GetDataWarehouseDisplay.R | 19 +- R/GetDefaultPage.R | 19 +- R/GetDiscoverEnabled.R | 19 +- R/GetEVars.R | 15 + R/GetEcommerce.R | 19 +- R/GetElements.R | 21 +- R/GetFeed.R | 25 +- R/GetFeeds.R | 29 ++- R/GetFunctions.R | 15 + R/GetGeoSegmentation.R | 19 +- R/GetGroups.R | 23 +- R/GetIPAddressExclusions.R | 25 +- R/GetIPObfuscation.R | 19 +- R/GetInternalURLFilters.R | 29 ++- R/GetKeyVisitors.R | 23 +- R/GetListVariables.R | 29 ++- R/GetLocalization.R | 19 +- R/GetLogin.R | 19 +- R/GetLogins.R | 21 +- R/GetMarketingChannelExpiration.R | 19 +- R/GetMarketingChannelRules.R | 37 ++-- R/GetMarketingChannels.R | 29 ++- R/GetMetrics.R | 20 +- R/GetMobileAppReporting.R | 23 +- R/GetPaidSearchDetection.R | 23 +- R/GetPermanentTraffic.R | 25 +- R/GetPrivacySettings.R | 27 +-- R/GetProps.R | 17 +- R/GetReportDescription.R | 27 +-- R/GetScheduledSpike.R | 25 +- R/GetSegments.R | 21 +- R/GetSiteTitle.R | 19 +- R/GetSuccessEvents.R | 11 - R/GetTemplate.R | 25 +- R/GetTimeZone.R | 19 +- R/GetTransactionEnabled.R | 19 +- R/GetUniqueVisitorVariable.R | 19 +- R/GetUsageLog.R | 7 R/GetVideoSettings.R | 25 +- R/QueueFallout.R | 46 +++-- R/QueueOvertime.R | 28 ++- R/QueuePathing.R | 50 +++-- R/QueueRanked.R | 62 ++++--- R/QueueSummary.R | 41 ++-- R/QueueTrended.R | 64 ++++--- R/RSiteCatalyst.R | 4 R/SCAuth.R | 13 + man/ApiRequest.Rd | 2 man/BuildClassificationValueSegment.Rd | 4 man/BuildHeader.Rd | 2 man/BuildInnerBreakdownsRecursively.Rd | 4 man/BuildLineItemSegment.Rd | 2 man/BuildRealTimeReportStructure.Rd | 4 man/CancelReport.Rd | 4 man/GetActivation.Rd | 2 man/GetAxleStartDate.Rd | 2 man/GetBaseCurrency.Rd | 2 man/GetBaseURL.Rd | 2 man/GetBookmarks.Rd | 2 man/GetCalculatedMetrics.Rd | 2 man/GetClassifications.Rd | 2 man/GetCustomCalendar.Rd | 2 man/GetDashboards.Rd | 2 man/GetDataWarehouseDisplay.Rd | 2 man/GetDefaultPage.Rd | 2 man/GetDiscoverEnabled.Rd | 2 man/GetEcommerce.Rd | 2 man/GetElements.Rd | 2 man/GetEndpoint.Rd | 12 - man/GetEvars.Rd | 2 man/GetFeed.Rd | 2 man/GetFeeds.Rd | 2 man/GetFunctions.Rd | 2 man/GetGeoSegmentation.Rd | 2 man/GetGroups.Rd | 2 man/GetIPAddressExclusions.Rd | 2 man/GetIPObfuscation.Rd | 2 man/GetInternalURLFilters.Rd | 2 man/GetKeyVisitors.Rd | 2 man/GetListVariables.Rd | 2 man/GetLocalization.Rd | 2 man/GetLogin.Rd | 2 man/GetLogins.Rd | 2 man/GetMarketingChannelExpiration.Rd | 2 man/GetMarketingChannelRules.Rd | 2 man/GetMarketingChannels.Rd | 2 man/GetMetrics.Rd | 2 man/GetMobileAppReporting.Rd | 2 man/GetPaidSearchDetection.Rd | 2 man/GetPermanentTraffic.Rd | 2 man/GetPrivacySettings.Rd | 2 man/GetProps.Rd | 2 man/GetQueue.Rd | 2 man/GetRealTimeReport.Rd | 2 man/GetRealTimeSettings.Rd | 6 man/GetReportDescription.Rd | 2 man/GetReportSuites.Rd | 2 man/GetScheduledSpike.Rd | 2 man/GetSegments.Rd | 2 man/GetSiteTitle.Rd | 2 man/GetSuccessEvents.Rd | 2 man/GetTemplate.Rd | 2 man/GetTimeZone.Rd | 2 man/GetTrackingServer.Rd | 4 man/GetTransactionEnabled.Rd | 2 man/GetUniqueVisitorVariable.Rd | 2 man/GetUsageLog.Rd | 10 - man/GetVersionAccess.Rd | 2 man/GetVideoSettings.Rd | 2 man/JsonQueueRealTimeReport.Rd | 3 man/ParseFallout.Rd | 10 - man/ParseOvertime.Rd | 10 - man/ParsePathing.Rd | 10 - man/ParseRanked.Rd | 10 - man/ParseSummary.Rd | 10 - man/ParseTrended.Rd | 10 - man/QueueFallout.Rd | 3 man/QueueOvertime.Rd | 3 man/QueuePathing.Rd | 3 man/QueueRanked.Rd | 3 man/QueueSummary.Rd | 3 man/QueueTrended.Rd | 2 man/RSiteCatalyst.Rd | 12 - man/SCAuth.Rd | 14 + man/SaveRealTimeSettings.Rd | 14 - man/SubmitJsonQueueReport.Rd | 3 man/ValidateReport.Rd | 2 141 files changed, 1119 insertions(+), 815 deletions(-)
Title: EWAS using Reference-Free DNA Methylation Mixture Deconvolution
Description:
Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types.
The older method (Houseman et al., 2014) is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption.
The newer method (Houseman et al., 2016) is similar to non-negative matrix factorization, with additional constraints and additional utilities.
Author: E. Andres Houseman, Sc.D.
Maintainer: E. Andres Houseman <andres.houseman@oregonstate.edu>
Diff between RefFreeEWAS versions 1.3 dated 2014-07-31 and 2.0 dated 2016-01-29
DESCRIPTION | 16 +++++++++------- MD5 | 19 ++++++++++++++++--- NAMESPACE | 13 ++++++++++++- R/RefFreeCellMix.R |only data/HNSCC.RData |only data/datalist | 1 + man/RefFreeCellMix.Rd |only man/RefFreeCellMixArray.Rd |only man/RefFreeCellMixArrayDevianceBoot.Rd |only man/RefFreeCellMixArrayDevianceBoots.Rd |only man/RefFreeCellMixInitialize.Rd |only man/X.HNSCC.caseStatusAge.Rd |only man/Y.HNSCC.averageBetas.Rd |only man/deviance.RefFreeCellMix.Rd |only man/print.RefFreeCellMix.Rd |only man/projectMix.Rd |only man/summary.RefFreeCellMix.Rd |only 17 files changed, 38 insertions(+), 11 deletions(-)
Title: Tools for Reading and Handling Spatial Objects
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
Author: Roger Bivand [cre, aut],
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Nick Bearman [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Kent Johnson [ctb],
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between maptools versions 0.8-37 dated 2015-09-29 and 0.8-39 dated 2016-01-29
ChangeLog | 36 ++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++++++---- MD5 | 29 +++++++++++++++-------------- R/getKMLcoordinates.R | 3 ++- R/kmlPoints.R | 2 +- build/vignette.rds |binary data/wrld_simpl.rda |binary inst/ChangeLog | 36 ++++++++++++++++++++++++++++++++++++ inst/README | 3 +++ inst/doc/combine_maptools.pdf |binary inst/shapes/Testing.kml |only man/as.ppp.Rd | 4 ++-- man/getKMLcoordinates.Rd | 2 ++ man/kmlPoints.Rd | 6 +++--- man/wrld_simpl.Rd | 2 +- src/pip.c | 19 ------------------- 16 files changed, 107 insertions(+), 45 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.3-1 dated 2016-01-08 and 2.1-0 dated 2016-01-29
jomo-1.3-1/jomo/data/mldata.RData |only jomo-1.3-1/jomo/man/mldata.Rd |only jomo-2.1-0/jomo/DESCRIPTION | 8 - jomo-2.1-0/jomo/MD5 | 124 ++++++++++++++----------- jomo-2.1-0/jomo/R/jomo.MCMCchain.R | 21 ++-- jomo-2.1-0/jomo/R/jomo.R | 21 ++-- jomo-2.1-0/jomo/R/jomo1.MCMCchain.R | 17 --- jomo-2.1-0/jomo/R/jomo1.R | 17 --- jomo-2.1-0/jomo/R/jomo1cat.MCMCchain.R | 21 +++- jomo-2.1-0/jomo/R/jomo1cat.R | 10 +- jomo-2.1-0/jomo/R/jomo1con.MCMCchain.R | 19 +++ jomo-2.1-0/jomo/R/jomo1con.R | 10 +- jomo-2.1-0/jomo/R/jomo1mix.MCMCchain.R | 21 +++- jomo-2.1-0/jomo/R/jomo1mix.R | 10 +- jomo-2.1-0/jomo/R/jomo1ran.MCMCchain.R | 77 ++------------- jomo-2.1-0/jomo/R/jomo1ran.R | 77 ++------------- jomo-2.1-0/jomo/R/jomo1rancat.MCMCchain.R | 24 ++++ jomo-2.1-0/jomo/R/jomo1rancat.R | 13 ++ jomo-2.1-0/jomo/R/jomo1rancathr.MCMCchain.R | 24 ++++ jomo-2.1-0/jomo/R/jomo1rancathr.R | 13 ++ jomo-2.1-0/jomo/R/jomo1rancon.MCMCchain.R | 22 ++++ jomo-2.1-0/jomo/R/jomo1rancon.R | 13 ++ jomo-2.1-0/jomo/R/jomo1ranconhr.MCMCchain.R | 21 +++- jomo-2.1-0/jomo/R/jomo1ranconhr.R | 12 ++ jomo-2.1-0/jomo/R/jomo1ranmix.MCMCchain.R | 24 ++++ jomo-2.1-0/jomo/R/jomo1ranmix.R | 13 ++ jomo-2.1-0/jomo/R/jomo1ranmixhr.MCMCchain.R | 24 ++++ jomo-2.1-0/jomo/R/jomo1ranmixhr.R | 13 ++ jomo-2.1-0/jomo/R/jomo2.MCMCchain.R |only jomo-2.1-0/jomo/R/jomo2.R |only jomo-2.1-0/jomo/R/jomo2com.MCMCchain.R |only jomo-2.1-0/jomo/R/jomo2com.R |only jomo-2.1-0/jomo/R/jomo2hr.MCMCchain.R |only jomo-2.1-0/jomo/R/jomo2hr.R |only jomo-2.1-0/jomo/data/cldata.RData |only jomo-2.1-0/jomo/data/tldata.RData |only jomo-2.1-0/jomo/man/cldata.Rd |only jomo-2.1-0/jomo/man/jomo.MCMCchain.Rd | 38 +++++-- jomo-2.1-0/jomo/man/jomo.Rd | 31 ++++-- jomo-2.1-0/jomo/man/jomo1.MCMCchain.Rd | 31 +++--- jomo-2.1-0/jomo/man/jomo1.Rd | 28 ++--- jomo-2.1-0/jomo/man/jomo1cat.MCMCchain.Rd | 20 ++-- jomo-2.1-0/jomo/man/jomo1cat.Rd | 15 +-- jomo-2.1-0/jomo/man/jomo1con.MCMCchain.Rd | 12 +- jomo-2.1-0/jomo/man/jomo1con.Rd | 5 - jomo-2.1-0/jomo/man/jomo1mix.MCMCchain.Rd | 14 +- jomo-2.1-0/jomo/man/jomo1mix.Rd | 6 - jomo-2.1-0/jomo/man/jomo1ran.MCMCchain.Rd | 20 ++-- jomo-2.1-0/jomo/man/jomo1ran.Rd | 14 +- jomo-2.1-0/jomo/man/jomo1rancat.MCMCchain.Rd | 22 ++-- jomo-2.1-0/jomo/man/jomo1rancat.Rd | 14 +- jomo-2.1-0/jomo/man/jomo1rancathr.MCMCchain.Rd | 21 ++-- jomo-2.1-0/jomo/man/jomo1rancathr.Rd | 13 +- jomo-2.1-0/jomo/man/jomo1rancon.MCMCchain.Rd | 17 +-- jomo-2.1-0/jomo/man/jomo1rancon.Rd | 12 +- jomo-2.1-0/jomo/man/jomo1ranconhr.MCMCchain.Rd | 17 ++- jomo-2.1-0/jomo/man/jomo1ranconhr.Rd | 13 +- jomo-2.1-0/jomo/man/jomo1ranmix.MCMCchain.Rd | 23 ++-- jomo-2.1-0/jomo/man/jomo1ranmix.Rd | 14 +- jomo-2.1-0/jomo/man/jomo1ranmixhr.MCMCchain.Rd | 24 ++-- jomo-2.1-0/jomo/man/jomo1ranmixhr.Rd | 14 +- jomo-2.1-0/jomo/man/jomo2.MCMCchain.Rd |only jomo-2.1-0/jomo/man/jomo2.Rd |only jomo-2.1-0/jomo/man/jomo2com.MCMCchain.Rd |only jomo-2.1-0/jomo/man/jomo2com.Rd |only jomo-2.1-0/jomo/man/jomo2hr.MCMCchain.Rd |only jomo-2.1-0/jomo/man/jomo2hr.Rd |only jomo-2.1-0/jomo/man/sldata.Rd | 8 - jomo-2.1-0/jomo/man/tldata.Rd |only jomo-2.1-0/jomo/src/MCMCjomo2com.c |only jomo-2.1-0/jomo/src/MCMCjomo2hf.c |only jomo-2.1-0/jomo/src/MCMCjomo2hr.c |only jomo-2.1-0/jomo/src/jomo2com.c |only jomo-2.1-0/jomo/src/jomo2hf.c |only jomo-2.1-0/jomo/src/jomo2hr.c |only 75 files changed, 639 insertions(+), 476 deletions(-)
Title: Empirical Bayesian Lasso and Elastic Net Methods for Generalized
Linear Models
Description: Provides empirical Bayesian lasso and elastic net algorithms for variable selection and effect estimation. Key features include sparse variable selection and effect estimation via generalized linear regression models, high dimensionality with p>>n, and significance test for nonzero effects. This package outperforms other popular methods such as lasso and elastic net methods in terms of power of detection, false discovery rate, and power of detecting grouping effects.
Author: Anhui Huang, Dianting Liu
Maintainer: Anhui Huang <a.huang1@umiami.edu>
Diff between EBglmnet versions 4.0 dated 2015-12-01 and 4.1 dated 2016-01-29
DESCRIPTION | 17 - MD5 | 38 ++- R/CVonePair.R |only R/EBelasticNet.BinomialCV.R | 81 ++----- R/EBelasticNet.GaussianCV.R | 76 +------ R/EBlassoNE.BinomialCV.R | 65 +----- R/EBlassoNE.GaussianCV.R | 74 ------- R/EBlassoNEG.BinomialCV.R | 111 ++-------- R/EBlassoNEG.GaussianCV.R | 106 ++-------- R/ijIndex.R |only R/lambdaMax.R |only data |only inst/doc/EBglmnet_intro.R | 164 +++++++++++++++ inst/doc/EBglmnet_intro.Rmd | 331 +++++++++++++++++++++++++++----- inst/doc/EBglmnet_intro.pdf |binary man/BASIS.Rd |only man/EBglmnet-internal.Rd | 9 man/EBglmnet-package.Rd | 35 +-- man/EBglmnet.Rd | 62 +++--- man/cv.EBglmnet.Rd | 91 +++----- src/CVonePara.c |only vignettes/EBglmnet_intro.Rmd | 331 +++++++++++++++++++++++++++----- vignettes/EBglmnet_intro.html | 433 ++++++++++++++++++++++++++++++++++-------- 23 files changed, 1313 insertions(+), 711 deletions(-)
Title: Identifies Signatures Present in a Tumor Sample
Description: Takes sample information in the form of the fraction of mutations
in each of 96 trinucleotide contexts and identifies the weighted combination
of published signatures that, when summed, most closely reconstructs the
mutational profile.
Author: Rachel Rosenthal
Maintainer: Rachel Rosenthal <rachel.rosenthal.14@ucl.ac.uk>
Diff between deconstructSigs versions 1.5.0 dated 2016-01-15 and 1.6.0 dated 2016-01-29
DESCRIPTION | 8 +- MD5 | 39 +++++++------- NAMESPACE | 1 R/datasets.R | 1 R/globalVariables.R | 2 R/mut.to.sigs.input.R | 6 +- R/normalize.data.R | 99 +++++++++++++++++++++++++++++-------- R/plotting.R | 84 ++++++++++++++++++++++++++++--- R/whichSignatures.R | 47 +++++++++++++---- README.md | 43 +++++++++++----- data/randomly.generated.tumors.rda |binary data/signatures.cosmic.rda |binary inst/extdata/makePie.png |binary inst/extdata/plotSignatures.png |binary man/getTriContextFraction.Rd | 2 man/makePie.Rd | 7 +- man/mut.to.sigs.input.Rd | 5 + man/norm.it.Rd | 2 man/plotTumor.Rd |only man/signatures.nature2013.Rd | 3 + man/whichSignatures.Rd | 36 ++++++++++--- 21 files changed, 291 insertions(+), 94 deletions(-)
More information about deconstructSigs at CRAN
Permanent link
Title: Context Driven Exploratory Projection Pursuit
Description: Functions and Data to support Context Driven Exploratory Projection Pursuit.
Author: Mohit Dayal
Maintainer: Mohit Dayal <mohitdayal2000@gmail.com>
Diff between cepp versions 1.0 dated 2012-01-14 and 1.7 dated 2016-01-29
cepp-1.0/cepp/R/PP_Index_sdistribution_1i-3.R |only cepp-1.0/cepp/R/PP_Index_sdistribution_1j-6.R |only cepp-1.0/cepp/R/init.R |only cepp-1.0/cepp/R/norms.R |only cepp-1.0/cepp/R/spatial_quantile_26c.R |only cepp-1.0/cepp/R/spatial_quantile_26d.R |only cepp-1.0/cepp/man/penorms.Rd |only cepp-1.0/cepp/man/sann.Rd |only cepp-1.7/cepp/DESCRIPTION | 15 +++--- cepp-1.7/cepp/MD5 | 47 +++++++++--------- cepp-1.7/cepp/NAMESPACE | 7 +- cepp-1.7/cepp/NEWS |only cepp-1.7/cepp/R/CvM.R |only cepp-1.7/cepp/R/PP_Index_sdistribution_3f_1.R |only cepp-1.7/cepp/R/angles3.R |only cepp-1.7/cepp/R/bases.R | 16 +++--- cepp-1.7/cepp/R/caller.R | 16 +++--- cepp-1.7/cepp/R/geodesic.R | 65 -------------------------- cepp-1.7/cepp/R/points_generator_c.R |only cepp-1.7/cepp/R/search-geodesic.R | 4 - cepp-1.7/cepp/R/spatial_quantile_29c.R |only cepp-1.7/cepp/build |only cepp-1.7/cepp/data/Colon.rda |binary cepp-1.7/cepp/data/olive.rda |binary cepp-1.7/cepp/man/Colon.Rd | 7 +- cepp-1.7/cepp/man/CvM.Rd |only cepp-1.7/cepp/man/bases.Rd | 22 +++++--- cepp-1.7/cepp/man/caller.Rd |only cepp-1.7/cepp/man/cepp-package.Rd | 27 ++++------ cepp-1.7/cepp/man/data-olive.Rd | 26 ++++++---- cepp-1.7/cepp/man/evaluator.Rd | 25 +++++----- cepp-1.7/cepp/man/geodesic.Rd | 20 ++------ cepp-1.7/cepp/man/pp.Rd | 25 ++++------ 33 files changed, 129 insertions(+), 193 deletions(-)
Title: Computes Copula using Ranks and Subsampling
Description: Essentially a discussion tool about estimation of copula using ranks and subsampling.
Author: Jerome Collet
Maintainer: Jerome Collet <jeromepcollet@gmail.com>
Diff between subrank versions 0.9.4 dated 2015-11-06 and 0.9.5 dated 2016-01-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/subrank-package.Rd | 4 ++-- src/Tir.h | 3 +++ src/copc.h | 2 +- 5 files changed, 14 insertions(+), 11 deletions(-)
Title: Neo4j Driver for R
Description: Neo4j, a graph database, allows users to store their data as a property graph. A graph consists of nodes that are connected by relationships; both nodes and relationships can have properties, or key-value pairs. RNeo4j is Neo4j's R driver. It allows users to read and write data from and to Neo4j directly from their R environment by exposing an interface for interacting with nodes, relationships, paths, and more. Most notably, it allows users to retrieve Cypher query results as R data frames, where Cypher is Neo4j's graph query language. Visit <http://www.neo4j.com> to learn more about Neo4j.
Author: Nicole White
Maintainer: Nicole White <nicole@neo4j.com>
Diff between RNeo4j versions 1.6.2 dated 2016-01-11 and 1.6.3 dated 2016-01-29
DESCRIPTION | 10 +++++----- LICENSE | 4 ++-- MD5 | 8 ++++---- R/internal.R | 19 ++++++++++--------- tests/testthat/test-internals.R | 16 ++++++++-------- 5 files changed, 29 insertions(+), 28 deletions(-)
Title: Linear Model with Breakpoint
Description: Exact significance tests for a changepoint in linear or multiple linear regression.
Confidence regions with exact coverage probabilities for the changepoint.
Author: Marc Adams [aut, cre],
authors of R function 'lm' [ctb] (general interface),
authors of 'lm.gls' [ctb] (interface and R code for covariate weights),
U.S. NIST [ctb] (C++ code for TNT::Vector template)
Maintainer: Marc Adams <lm.br.pkg@gmail.com>
Diff between lm.br versions 2.7 dated 2015-07-14 and 2.8 dated 2016-01-29
DESCRIPTION | 14 +++++++------- MD5 | 30 +++++++++++++++--------------- R/lm.br.R | 4 ++-- build/vignette.rds |binary demo/testscript.R | 9 +++++---- inst/doc/lm.br.Rnw | 12 ++++++------ inst/doc/lm.br.pdf |binary man/lm.br.Rd | 4 ++-- man/sl.Rd | 4 ++-- src/R_interface.cpp | 2 +- src/cr.cpp | 14 ++++++++------ src/geo.cpp | 8 ++++---- src/globals.h | 11 ++++++----- src/mle.cpp | 8 ++++---- src/set_theta0.cpp | 11 +++++------ vignettes/lm.br.Rnw | 12 ++++++------ 16 files changed, 73 insertions(+), 70 deletions(-)
Title: Kolmogorov-Zurbenko Adaptive Filters
Description: Time Series Analysis including break detection, spectral analysis, KZ Fourier Transforms.
Author: Brian Close <brian.close@gmail.com> and Igor Zurbenko <IZurbenko@albany.edu>
Maintainer: Brian Close <brian.close@gmail.com>
Diff between kza versions 3.0.0 dated 2013-07-13 and 3.2.0 dated 2016-01-29
kza-3.0.0/kza/aclocal.m4 |only kza-3.0.0/kza/src/Makevars |only kza-3.0.0/kza/src/kz_ma.c |only kza-3.0.0/kza/test |only kza-3.2.0/kza/DESCRIPTION | 10 ++--- kza-3.2.0/kza/MD5 | 41 +++++++--------------- kza-3.2.0/kza/NAMESPACE | 15 +++++++- kza-3.2.0/kza/R/kza.R | 23 ++++++++---- kza-3.2.0/kza/R/kzft.R | 74 +++++++++++++++++++---------------------- kza-3.2.0/kza/cleanup | 2 - kza-3.2.0/kza/configure.ac | 47 ++++++-------------------- kza-3.2.0/kza/man/kza.Rd | 7 ++- kza-3.2.0/kza/man/kzsv.Rd | 7 +++ kza-3.2.0/kza/src/Makevars.in | 1 kza-3.2.0/kza/src/Makevars.win | 5 +- kza-3.2.0/kza/src/ckzft.c | 13 ++++++- kza-3.2.0/kza/src/kz.c | 41 ++++++---------------- kza-3.2.0/kza/src/kza.c | 2 - 18 files changed, 133 insertions(+), 155 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.10.0 dated 2015-10-22 and 1.10.1 dated 2016-01-29
CHANGELOG | 6 ++ DESCRIPTION | 8 +- MD5 | 18 +++--- NAMESPACE | 1 R/kde.R | 14 ++--- R/prelim.R | 28 +++------- R/selector.R | 148 +++++------------------------------------------------ build/vignette.rds |binary inst/doc/kde.pdf |binary man/ks-internal.Rd | 1 10 files changed, 54 insertions(+), 170 deletions(-)
Title: Interactive Model Performance Evaluation
Description: Contains functions for evaluating & comparing the performance of Binary classification models. Functions can be called either statically or interactively (as Shiny Apps).
Author: Anup Nair [aut, cre]
Maintainer: Anup Nair <nairanup50695@gmail.com>
Diff between IMP versions 0.1 dated 2015-12-22 and 1.1 dated 2016-01-29
DESCRIPTION | 9 ++++---- MD5 | 15 +++++++------- R/InternalFunctions.R | 14 +++++++++---- R/ShinyFunctions.R | 19 +++++++++--------- R/custom_funcs.R | 47 ++++++++++++++++++++++++++++++++++++---------- README.md |only man/interPerfMeasures.Rd | 2 - man/staticConfMatrix.Rd | 4 ++- man/staticPerfMeasures.Rd | 8 +++++-- 9 files changed, 80 insertions(+), 38 deletions(-)
Title: Easy Authentication with Google OAuth2 APIs
Description: Create R functions that interact with OAuth2 Google APIs easily,
with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre],
Jennifer Bryan [ctb],
Johann deBoer [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>
Diff between googleAuthR versions 0.1.1 dated 2015-08-19 and 0.2.0 dated 2016-01-29
DESCRIPTION | 20 LICENSE | 2 MD5 | 95 ++- NAMESPACE | 6 NEWS.md |only R/googleAuthR.R | 9 R/googleAuthR_auth.R | 49 + R/googleAuthR_batch.R |only R/googleAuthR_generator.R | 368 +++++++++----- R/googleAuthR_options.R | 14 R/googleAuthR_shiny.R | 157 +++++- R/googleAuthR_utility.R | 69 ++ README.md | 229 ++++++++ build/vignette.rds |binary inst/doc/googleAuthR.Rmd | 241 ++++++++- inst/doc/googleAuthR.html | 1079 ++++++++++++++++++++++++++++-------------- man/Authentication.Rd | 6 man/RFC_convert.Rd | 2 man/applyDataParseFunction.Rd |only man/authReturnCode.Rd | 18 man/check.Url.Rd | 2 man/checkGoogleAPIError.Rd | 7 man/checkTokenAPI.Rd | 2 man/createCode.Rd | 18 man/doBatchRequest.Rd |only man/doHttrRequest.Rd | 7 man/error.message.Rd |only man/gar_api_generator.Rd | 51 + man/gar_auth.Rd | 7 man/gar_auth_service.Rd |only man/gar_batch.Rd |only man/gar_batch_walk.Rd |only man/gar_shiny_getAuthUrl.Rd | 21 man/gar_shiny_getToken.Rd | 20 man/gar_shiny_getUrl.Rd | 19 man/get_google_token.Rd | 7 man/googleAuthR.Rd | 15 man/is.NullOb.Rd |only man/is.error.Rd | 2 man/is_legit_token.Rd | 7 man/is_shiny.Rd | 2 man/loginOutput.Rd | 36 - man/makeBatchRequest.Rd |only man/parseBatchResponse.Rd |only man/postwalk.Rd | 2 man/reactiveAccessToken.Rd | 35 - man/renderLogin.Rd | 54 +- man/replace.kv.Rd | 2 man/retryRequest.Rd |only man/revokeEventObserver.Rd |only man/rmNullObs.Rd |only man/split_vector.Rd |only man/substitute.list.Rd | 2 man/token_exists.Rd | 7 man/with_shiny.Rd | 37 - vignettes/googleAuthR.Rmd | 241 ++++++++- 56 files changed, 2213 insertions(+), 754 deletions(-)
Title: Event-Related Potential (ERP) Data Exploration Made Easy
Description: A set of user-friendly functions to aid in organizing, plotting
and analyzing event-related potential (ERP) data. Provides an easy-to-learn
method to explore ERP data. Should be useful to those without a background
in computer programming, and to those who are new to ERPs (or new to the
more advanced ERP software available). Emphasis has been placed on highly
automated processes using functions with as few arguments as possible.
Expects processed (cleaned) data.
Author: Travis Moore [aut, cre]
Maintainer: Travis Moore <travis.m.moore@vanderbilt.edu>
Diff between erp.easy versions 0.6.3 dated 2015-09-25 and 1.0.0 dated 2016-01-29
DESCRIPTION | 8 +-- MD5 | 29 ++++++----- NAMESPACE | 5 +- NEWS.md |only R/Build.R | 22 ++++----- R/Difference.R | 25 ++++++---- R/Filter.R |only R/GrandavgPlot.R | 38 +++++++++++---- R/Load.R | 127 +++++++++++++++++++++++++++++++--------------------- R/Means.R | 5 +- R/Peaks.R | 30 +++++++++--- man/dif.wave.Rd | 14 +++-- man/erp.filter.Rd |only man/grandaverage.Rd | 2 man/load.data.Rd | 73 ++++++++++++++--------------- man/m.measures.Rd | 2 man/p.measures.Rd | 10 ++-- 17 files changed, 232 insertions(+), 158 deletions(-)
Title: Association Between Methylation and a Phenotype of Interest
Description: Is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. Also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.
Author: Barfield, R., Conneely, K., Kilaru,V
Maintainer: R Barfield <rbarfield01@fas.harvard.edu>
Diff between CpGassoc versions 2.50 dated 2015-01-28 and 2.55 dated 2016-01-29
CpGassoc-2.50/CpGassoc/man/cpg.perm.object.rd |only CpGassoc-2.55/CpGassoc/DESCRIPTION | 16 CpGassoc-2.55/CpGassoc/MD5 | 85 +- CpGassoc-2.55/CpGassoc/NAMESPACE | 13 CpGassoc-2.55/CpGassoc/R/CpGassoc-internal.R |only CpGassoc-2.55/CpGassoc/R/cpg.GC.R | 109 +- CpGassoc-2.55/CpGassoc/R/cpg.assoc.R | 248 +++--- CpGassoc-2.55/CpGassoc/R/cpg.combine.R | 216 ++--- CpGassoc-2.55/CpGassoc/R/cpg.everything.R | 8 CpGassoc-2.55/CpGassoc/R/cpg.everything.character.R | 18 CpGassoc-2.55/CpGassoc/R/cpg.everything.complex.R | 46 - CpGassoc-2.55/CpGassoc/R/cpg.everything.logical.R | 33 CpGassoc-2.55/CpGassoc/R/cpg.everything.matrix.R | 126 +-- CpGassoc-2.55/CpGassoc/R/cpg.everything.numeric.R | 12 CpGassoc-2.55/CpGassoc/R/cpg.length.R | 46 - CpGassoc-2.55/CpGassoc/R/cpg.perm.R | 351 ++++----- CpGassoc-2.55/CpGassoc/R/cpg.qc.R | 146 +-- CpGassoc-2.55/CpGassoc/R/cpg.work.R | 740 ++++++++++---------- CpGassoc-2.55/CpGassoc/R/cpgassocsummary.R | 152 ++-- CpGassoc-2.55/CpGassoc/R/design.NULL.R | 60 - CpGassoc-2.55/CpGassoc/R/design.R | 8 CpGassoc-2.55/CpGassoc/R/design.data.frame.R | 62 - CpGassoc-2.55/CpGassoc/R/manhattan.R | 366 ++++----- CpGassoc-2.55/CpGassoc/R/manhattan.reflect.R | 454 ++++++------ CpGassoc-2.55/CpGassoc/R/plot.cpg.R | 476 ++++++------ CpGassoc-2.55/CpGassoc/R/plot.cpg.perm.R | 508 ++++++------- CpGassoc-2.55/CpGassoc/R/pointsizefunction.R | 12 CpGassoc-2.55/CpGassoc/R/print.cpg.R | 68 - CpGassoc-2.55/CpGassoc/R/print.cpg.gc.R | 26 CpGassoc-2.55/CpGassoc/R/print.cpg.perm.R | 66 - CpGassoc-2.55/CpGassoc/R/print.cpg.perm.gc.R | 8 CpGassoc-2.55/CpGassoc/R/scatterplot.R | 240 +++--- CpGassoc-2.55/CpGassoc/R/sort.cpg.R | 22 CpGassoc-2.55/CpGassoc/R/sort.cpg.perm.R | 8 CpGassoc-2.55/CpGassoc/R/summary.cpg.R | 62 - CpGassoc-2.55/CpGassoc/R/summary.cpg.perm.R | 8 CpGassoc-2.55/CpGassoc/build/vignette.rds |binary CpGassoc-2.55/CpGassoc/data/annotation.rda |binary CpGassoc-2.55/CpGassoc/data/datalist | 6 CpGassoc-2.55/CpGassoc/data/samplecpg.rda |binary CpGassoc-2.55/CpGassoc/data/samplepheno.rda |binary CpGassoc-2.55/CpGassoc/inst/doc/CpGassoc.R | 360 ++++----- CpGassoc-2.55/CpGassoc/inst/doc/CpGassoc.pdf |binary CpGassoc-2.55/CpGassoc/man/CpGassoc-package.Rd | 160 ++-- CpGassoc-2.55/CpGassoc/man/cpg.perm.object.Rd |only 45 files changed, 2680 insertions(+), 2665 deletions(-)
Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery, Thomas Buettner
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesPop versions 6.0-0 dated 2016-01-16 and 6.0-1 dated 2016-01-29
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/get_outputs.R | 8 ++++---- R/predict.pop.R | 36 +++++++++++++++++++++--------------- man/LifeTableMx.Rd | 10 +++++++--- man/bayesPop-package.Rd | 4 ++-- tests/test_functions.R | 4 ++++ 8 files changed, 55 insertions(+), 35 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web APIs for chemical information.
Author: Eduard Szöcs [aut, cre],
Daniel Muench [ctb],
Johannes Ranke [ctb]
Maintainer: Eduard Szöcs <eduardszoecs@gmail.com>
Diff between webchem versions 0.0.4.0 dated 2015-12-09 and 0.0.5.0 dated 2016-01-29
webchem-0.0.4.0/webchem/man/alanwood.Rd |only webchem-0.0.4.0/webchem/man/chemid.Rd |only webchem-0.0.4.0/webchem/man/cid_compinfo.Rd |only webchem-0.0.4.0/webchem/man/cir.Rd |only webchem-0.0.4.0/webchem/man/get_cid.Rd |only webchem-0.0.4.0/webchem/man/pan.Rd |only webchem-0.0.4.0/webchem/man/physprop.Rd |only webchem-0.0.4.0/webchem/man/ppdb.Rd |only webchem-0.0.5.0/webchem/DESCRIPTION | 10 webchem-0.0.5.0/webchem/MD5 | 141 +++--- webchem-0.0.5.0/webchem/NAMESPACE | 16 webchem-0.0.5.0/webchem/NEWS | 52 ++ webchem-0.0.5.0/webchem/R/alanwood.R | 130 +++-- webchem-0.0.5.0/webchem/R/chemid.R | 170 ++++++- webchem-0.0.5.0/webchem/R/chemspider.R | 327 +++++++++++---- webchem-0.0.5.0/webchem/R/cir.R | 48 +- webchem-0.0.5.0/webchem/R/cts.R | 43 - webchem-0.0.5.0/webchem/R/etox.R | 243 +++++++---- webchem-0.0.5.0/webchem/R/pan.R | 62 +- webchem-0.0.5.0/webchem/R/physprop.R | 82 +-- webchem-0.0.5.0/webchem/R/ppdb.R | 171 ++++--- webchem-0.0.5.0/webchem/R/pubchem.R | 116 ++--- webchem-0.0.5.0/webchem/R/utils.R | 149 ++++++ webchem-0.0.5.0/webchem/R/webchem-defunct.R | 17 webchem-0.0.5.0/webchem/R/webchem-deprecated.R | 67 ++- webchem-0.0.5.0/webchem/R/webchem.R |only webchem-0.0.5.0/webchem/R/wikidata.R |only webchem-0.0.5.0/webchem/data/jagst.rda |only webchem-0.0.5.0/webchem/data/lc50.rda |only webchem-0.0.5.0/webchem/data/ppdb_idx.rda |binary webchem-0.0.5.0/webchem/man/aw_query.Rd |only webchem-0.0.5.0/webchem/man/ci_query.Rd |only webchem-0.0.5.0/webchem/man/cir_query.Rd |only webchem-0.0.5.0/webchem/man/cs_compinfo.Rd | 5 webchem-0.0.5.0/webchem/man/cs_convert.Rd | 20 webchem-0.0.5.0/webchem/man/cs_csid_mol.Rd | 2 webchem-0.0.5.0/webchem/man/cs_extcompinfo.Rd | 7 webchem-0.0.5.0/webchem/man/cs_inchi_csid.Rd | 3 webchem-0.0.5.0/webchem/man/cs_inchi_inchikey.Rd | 3 webchem-0.0.5.0/webchem/man/cs_inchi_mol.Rd | 3 webchem-0.0.5.0/webchem/man/cs_inchi_smiles.Rd | 5 webchem-0.0.5.0/webchem/man/cs_inchikey_csid.Rd | 3 webchem-0.0.5.0/webchem/man/cs_inchikey_inchi.Rd | 3 webchem-0.0.5.0/webchem/man/cs_inchikey_mol.Rd | 2 webchem-0.0.5.0/webchem/man/cs_prop.Rd |only webchem-0.0.5.0/webchem/man/cs_smiles_inchi.Rd | 3 webchem-0.0.5.0/webchem/man/cts_compinfo.Rd | 4 webchem-0.0.5.0/webchem/man/cts_convert.Rd | 4 webchem-0.0.5.0/webchem/man/etox_basic.Rd | 8 webchem-0.0.5.0/webchem/man/etox_targets.Rd | 8 webchem-0.0.5.0/webchem/man/etox_tests.Rd | 8 webchem-0.0.5.0/webchem/man/get_csid.Rd | 3 webchem-0.0.5.0/webchem/man/get_etoxid.Rd | 15 webchem-0.0.5.0/webchem/man/get_pcid.Rd |only webchem-0.0.5.0/webchem/man/get_wdid.Rd |only webchem-0.0.5.0/webchem/man/is.cas.Rd | 5 webchem-0.0.5.0/webchem/man/is.inchikey.Rd | 9 webchem-0.0.5.0/webchem/man/is.inchikey_cs.Rd | 2 webchem-0.0.5.0/webchem/man/is.inchikey_format.Rd |only webchem-0.0.5.0/webchem/man/is.smiles.Rd |only webchem-0.0.5.0/webchem/man/jagst.Rd |only webchem-0.0.5.0/webchem/man/lc50.Rd |only webchem-0.0.5.0/webchem/man/pan_query.Rd |only webchem-0.0.5.0/webchem/man/parse_mol.Rd | 2 webchem-0.0.5.0/webchem/man/pc_compinfo.Rd |only webchem-0.0.5.0/webchem/man/pp_query.Rd |only webchem-0.0.5.0/webchem/man/ppdb_buildidx.Rd | 2 webchem-0.0.5.0/webchem/man/ppdb_idx.Rd | 4 webchem-0.0.5.0/webchem/man/ppdb_query.Rd |only webchem-0.0.5.0/webchem/man/wd_ident.Rd |only webchem-0.0.5.0/webchem/man/webchem-defunct.Rd | 10 webchem-0.0.5.0/webchem/man/webchem-deprecated.Rd | 35 + webchem-0.0.5.0/webchem/man/webchem.Rd |only webchem-0.0.5.0/webchem/tests/testthat.R | 10 webchem-0.0.5.0/webchem/tests/testthat/test-alanwood.R | 20 webchem-0.0.5.0/webchem/tests/testthat/test-chemid.R | 20 webchem-0.0.5.0/webchem/tests/testthat/test-chemspider.R | 63 +- webchem-0.0.5.0/webchem/tests/testthat/test-cir.R | 17 webchem-0.0.5.0/webchem/tests/testthat/test-cts.R | 6 webchem-0.0.5.0/webchem/tests/testthat/test-etox.R | 66 ++- webchem-0.0.5.0/webchem/tests/testthat/test-pan.R | 23 - webchem-0.0.5.0/webchem/tests/testthat/test-physprop.R | 17 webchem-0.0.5.0/webchem/tests/testthat/test-ppdb.R | 17 webchem-0.0.5.0/webchem/tests/testthat/test-pubchem.R | 32 - webchem-0.0.5.0/webchem/tests/testthat/test-utils.R | 22 + webchem-0.0.5.0/webchem/tests/testthat/test-wikidata.R |only 86 files changed, 1583 insertions(+), 752 deletions(-)
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph],
Nicolas Muller [aut],
Reto Buergin [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 1.8-11 dated 2015-11-25 and 1.8-11.1 dated 2016-01-29
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/TraMineR.h | 4 ---- 3 files changed, 5 insertions(+), 9 deletions(-)
Title: Java Executable .jar Files for 'RKEEL'
Description: KEEL is a popular Java software for a large number of different knowledge data discovery tasks. Furthermore, 'RKEEL' is a package with a R code layer between R and KEEL, for using KEEL in R code. This package downloads and install the .jar files necessary for 'RKEEL' algorithms execution. For more information about KEEL, see <http://www.keel.es/>.
Author: Jose Moyano [aut, cre], Luciano Sanchez Ramos [aut]
Maintainer: Jose Moyano <i02momuj@uco.es>
Diff between RKEELjars versions 1.0.6 dated 2016-01-26 and 1.0.8 dated 2016-01-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + R/zzz.R | 41 +++++++++++++++++++++++++++++++++++++---- inst/exe/Readme.txt | 2 +- 5 files changed, 47 insertions(+), 13 deletions(-)
Title: Quantitative Linkage Analysis Tools using the Variance
Components Approach
Description:
Calculate the polygenic and major gene models for quantitative trait
linkage analysis using variance components approach. The 0.2.2
release includes bug fixes that allow 'multic' to run properly
on 64-bit systems. The 0.3.0 release includes a fully implemented
sw2mloci() function. As of 0.3.8, Splus version is no longer
supported. Additional documentation and examples can be found
in the inst directory.
Author: Eric Lunde, Mariza de Andrade, Beth Atkinson, Pat Votruba
Maintainer: Pat Votruba <votruba.patrick@mayo.edu>
Diff between multic versions 0.4.3 dated 2015-08-27 and 0.4.3.1 dated 2016-01-29
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- src/Calculate.cpp | 2 +- src/Lib.cpp | 4 ++-- src/Makevars |only src/Model.cpp | 6 +++++- src/Robust_Variance.cpp | 2 +- src/calculateCorrelations.cpp | 4 ++-- src/fixibd.cpp | 7 ++++--- src/fullId.cpp | 12 ++++++------ src/sw2mloci.cpp | 6 +++++- src/validateShareOut.cpp | 12 ++++++------ src/verS.h | 6 +++--- 13 files changed, 51 insertions(+), 41 deletions(-)
Title: Memoisation of Functions
Description: Cache the results of a function so that when you call it
again with the same arguments it returns the pre-computed value.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Kirill Müller [aut]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between memoise versions 0.2.1 dated 2014-04-22 and 1.0.0 dated 2016-01-29
memoise-0.2.1/memoise/NEWS |only memoise-1.0.0/memoise/DESCRIPTION | 28 ++-- memoise-1.0.0/memoise/LICENSE | 2 memoise-1.0.0/memoise/MD5 | 22 +-- memoise-1.0.0/memoise/NAMESPACE | 6 memoise-1.0.0/memoise/NEWS.md |only memoise-1.0.0/memoise/R/memoise.r | 214 ++++++++++++++++++++++++------- memoise-1.0.0/memoise/README.md | 5 memoise-1.0.0/memoise/man/forget.Rd | 3 memoise-1.0.0/memoise/man/has_cache.Rd |only memoise-1.0.0/memoise/man/is.memoised.Rd | 3 memoise-1.0.0/memoise/man/memoise.Rd | 30 +++- memoise-1.0.0/memoise/man/timeout.Rd |only memoise-1.0.0/memoise/tests |only 14 files changed, 240 insertions(+), 73 deletions(-)
Title: Methods and Data for Spatial Epidemiology
Description:
Methods and data for cluster detection and disease mapping.
Author: Cici Chen [ctb],
Albert Y. Kim [aut, cre],
Michelle Ross [ctb],
Jon Wakefield [aut]
Maintainer: Albert Y. Kim <albert@stat.washington.edu>
Diff between SpatialEpi versions 1.2.1 dated 2014-06-05 and 1.2.2 dated 2016-01-28
DESCRIPTION | 33 ++-- MD5 | 14 +- NAMESPACE | 6 R/create_geo_objects.R | 16 -- man/NYleukemia.Rd | 2 man/bayes_cluster.Rd | 2 man/create_geo_objects.Rd | 5 src/RcppExports.cpp | 321 ++++++++++++++++++---------------------------- 8 files changed, 162 insertions(+), 237 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RMySQL versions 0.10.7 dated 2015-10-27 and 0.10.8 dated 2016-01-28
DESCRIPTION | 7 + MD5 | 54 +++++++------- NAMESPACE | 2 man/MySQLConnection-class.Rd | 2 man/MySQLDriver-class.Rd | 2 man/MySQLResult-class.Rd | 2 man/constants.Rd | 2 man/db-meta.Rd | 4 - man/dbApply.Rd | 2 man/dbColumnInfo-MySQLConnection-method.Rd | 2 man/dbConnect-MySQLDriver-method.Rd | 4 - man/dbDataType-MySQLDriver-method.Rd | 2 man/dbEscapeStrings.Rd | 2 man/dbGetInfo-MySQLDriver-method.Rd | 4 - man/dbNextResult.Rd | 2 man/dbQuoteIdentifier-MySQLConnection-character-method.Rd | 2 man/dbReadTable.Rd | 2 man/dbUnloadDriver-MySQLDriver-method.Rd | 2 man/dbWriteTable.Rd | 2 man/isIdCurrent.Rd | 4 - man/make.db.names-MySQLConnection-character-method.Rd | 2 man/mysqlBuildTableDefinition.Rd | 2 man/mysqlClientLibraryVersions.Rd | 2 man/mysqlHasDefault.Rd | 2 man/query.Rd | 4 - man/result-meta.Rd | 4 - man/transactions.Rd | 2 src/S4R.h | 23 ----- 28 files changed, 64 insertions(+), 82 deletions(-)
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.4.2 dated 2015-11-20 and 1.4.3 dated 2016-01-28
NAM-1.4.2/NAM/R/gwas2.R |only NAM-1.4.2/NAM/R/manhattan.R |only NAM-1.4.3/NAM/DESCRIPTION | 8 NAM-1.4.3/NAM/MD5 | 38 +-- NAM-1.4.3/NAM/R/RcppExports.R | 4 NAM-1.4.3/NAM/R/gibbs.R | 154 ++++++++++++ NAM-1.4.3/NAM/R/gwas3c.R |only NAM-1.4.3/NAM/R/manhattan2.R |only NAM-1.4.3/NAM/R/reml.R | 18 + NAM-1.4.3/NAM/R/wrapGE.R |only NAM-1.4.3/NAM/build/vignette.rds |binary NAM-1.4.3/NAM/inst/doc/vignette.Rmd | 15 - NAM-1.4.3/NAM/inst/doc/vignette.html | 413 +++++++++++++++++++++++++--------- NAM-1.4.3/NAM/inst/doc/vignette2.R |only NAM-1.4.3/NAM/inst/doc/vignette2.Rmd |only NAM-1.4.3/NAM/inst/doc/vignette2.html |only NAM-1.4.3/NAM/man/Internals.Rd | 6 NAM-1.4.3/NAM/man/Manhattan.Rd | 5 NAM-1.4.3/NAM/man/NAM-package.Rd | 6 NAM-1.4.3/NAM/man/gibbs.Rd | 10 NAM-1.4.3/NAM/man/gwas.Rd | 21 + NAM-1.4.3/NAM/src/RcppExports.cpp | 13 + NAM-1.4.3/NAM/src/gs.cpp |only NAM-1.4.3/NAM/vignettes/vignette.Rmd | 15 - NAM-1.4.3/NAM/vignettes/vignette2.Rmd |only 25 files changed, 578 insertions(+), 148 deletions(-)
Title: Bayesian QTL Mapping Toolkit
Description: QTL mapping toolkit for inbred crosses and recombinant
inbred lines. Includes maximum likelihood and Bayesian tools.
Author: Charles C. Berry <cberry@ucsd.edu>
Maintainer: Charles C. Berry <cberry@ucsd.edu>
Diff between bqtl versions 1.0-30 dated 2014-01-30 and 1.0-32 dated 2016-01-28
CHANGES | 11 +++++++++++ DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 7 +++++++ R/make.state.matrix.s | 2 +- src/hkreg.c | 2 +- src/lapadj.h | 15 ++------------- src/swapbc1.c | 5 ++--- src/swapf2.c | 8 ++++---- 9 files changed, 41 insertions(+), 35 deletions(-)
Title: Lumped Hydrological Model for Education Purposes
Description: The model, developed at the Vienna University of Technology, is a lumped conceptual rainfall-runoff model, following the structure of the HBV model.
The model runs on a daily or shorter time step and consists of a snow routine, a soil moisture routine and a flow routing routine.
See Parajka, J., R. Merz, G. Bloeschl (2007) Uncertainty and multiple objective calibration in regional water balance modelling: case study in 320 Austrian catchments, Hydrological Processes, 21, 435-446.
Author: Alberto Viglione [aut, cre],
Juraj Parajka [aut]
Maintainer: Alberto Viglione <viglione@hydro.tuwien.ac.at>
Diff between TUWmodel versions 0.1-4 dated 2014-11-10 and 0.1-6 dated 2016-01-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/TUWmodel.R | 4 +++- man/TUWmodel.Rd | 11 ++++++----- src/hbvmodel.f | 15 ++++++++++++--- 5 files changed, 29 insertions(+), 17 deletions(-)
Title: Robust Correlation Estimation and Testing Based on Spatial Signs
Description: Provides the spatial sign correlation and the two-stage spatial sign correlation as well as a one-sample test for the correlation coefficient.
Author: Alexander Duerre [aut, cre],
Daniel Vogel [aut]
Maintainer: Alexander Duerre <alexander.duerre@tu-dortmund.de>
Diff between sscor versions 0.1 dated 2015-06-12 and 0.2 dated 2016-01-28
DESCRIPTION | 8 +-- MD5 | 18 +++++-- NAMESPACE | 10 +++- R/SSCM2Shape.R |only R/Shape2SSCM.R |only R/eigenvaluefunctions.R |only R/sscor.R | 109 +++++++++++++++++++++++++++++------------------- inst |only man/SSCM2Shape.Rd |only man/Shape2SSCM.Rd |only man/evSSCM2evShape.Rd |only man/evShape2evSSCM.Rd |only man/sscor-package.Rd | 3 - man/sscor.Rd | 17 ++++--- 14 files changed, 105 insertions(+), 60 deletions(-)
Title: Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
Description: Renders vector-based 'svg' images into high-quality custom-size bitmap
arrays using 'librsvg'. The resulting bitmap can be written to e.g. 'png', 'jpeg'
or 'webp' format. In addition, the package can convert images directly to various
formats such as pdf or postscript.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between rsvg versions 0.3 dated 2016-01-18 and 0.4 dated 2016-01-28
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- NEWS | 3 +++ configure | 5 +++-- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.1.3 dated 2015-11-28 and 0.1.4 dated 2016-01-28
DESCRIPTION | 8 - MD5 | 79 ++++++---- NAMESPACE | 16 +- NEWS | 21 ++ R/RStoolbox.R | 6 R/RcppExports.R | 8 - R/estimateHaze.R | 42 +++-- R/getMeta.R | 3 R/getValidation.R |only R/ggR.R | 12 + R/internalFunctions.R | 12 + R/radCor.R | 98 +++++++++---- R/rasterCVA.R | 28 ++- R/rasterPCA.R | 4 R/readMeta.R | 13 + R/rescaleImage.R | 52 +++++-- R/rsOpts.R | 4 R/spectralIndices.R | 60 +++++--- R/superClass.R | 233 ++++++++++++++++---------------- R/sysdata.rda |binary R/unsuperClass.R | 3 R/validateMap.R |only README.md | 2 man/estimateHaze.Rd | 9 - man/getValidation.Rd |only man/radCor.Rd | 14 + man/rasterCVA.Rd | 13 + man/rescaleImage.Rd | 22 +-- man/spectralIndices.Rd | 36 +++- man/superClass.Rd | 11 - man/validateMap.Rd |only src/RcppExports.cpp | 33 +++- src/gainOffsetRescale.cpp | 15 +- src/rescaleImage.cpp |only src/spectralIndices.cpp | 32 ++-- tests/testthat.R | 3 tests/testthat/test-0.R |only tests/testthat/test-estimateHaze.R |only tests/testthat/test-gainOffsetRescale.R |only tests/testthat/test-getValidation.R |only tests/testthat/test-ggplot.R | 29 +++ tests/testthat/test-radCor.R |only tests/testthat/test-rasterCVA.R |only tests/testthat/test-rescaleImage.R |only tests/testthat/test-spectralIndices.R | 2 tests/testthat/test-superClass.R | 122 ++++++++++++---- tests/testthat/test-validateMap.R |only 47 files changed, 696 insertions(+), 349 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Lei Huang [aut, cre],
Fabian Scheipl [aut],
Jeff Goldsmith [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip Reiss [aut],
Yakuan Chen [ctb],
Sonja Greven [ctb],
Lan Huo [ctb],
Madan Gopal Kundu [ctb],
Julia Wrobel [ctb],
So Young Park [ctb]
Maintainer: Lei Huang <huangracer@gmail.com>
Diff between refund versions 0.1-13 dated 2015-09-08 and 0.1-14 dated 2016-01-28
DESCRIPTION | 33 +- MD5 | 237 ++++++++-------- NAMESPACE | 7 R/DTI-data.R | 7 R/dt_basis.R | 31 +- R/fbps.R | 444 ++++++++++++++++++------------- R/fosr.perm.R | 5 R/fosr.perm.fit.R | 1 R/fpca.face.R | 3 R/fpca.lfda.R |only R/fpca.sc.R | 4 R/mfpca.sc.R | 2 R/pffr-ff.R | 4 R/pffr-methods.R | 45 +++ R/pffr.R | 46 ++- R/plot.peer.R | 8 R/predict.fbps.R |only R/preprocess.pfr.R | 10 R/pspline.setting.R | 66 ++-- R/select_knots.R |only data/DTI.RData |binary man/DTI.Rd | 9 man/DTI2.Rd | 2 man/PEER.Sim.Rd | 2 man/Predict.matrix.dt.smooth.Rd | 4 man/Predict.matrix.fpc.smooth.Rd | 2 man/Predict.matrix.pcre.random.effect.Rd | 2 man/Predict.matrix.peer.smooth.Rd | 2 man/Predict.matrix.pi.smooth.Rd | 2 man/Xt_siginv_X.Rd | 2 man/af.Rd | 2 man/af_old.Rd | 2 man/amc.Rd | 2 man/bayes_fosr.Rd | 2 man/ccb.fpc.Rd | 2 man/cd4.Rd | 2 man/coef.pffr.Rd | 2 man/coefboot.pffr.Rd | 2 man/coefficients.pfr.Rd | 2 man/create.prep.func.Rd | 2 man/expand.call.Rd | 2 man/f_sum.Rd | 2 man/f_sum2.Rd | 2 man/f_sum4.Rd | 2 man/f_trace.Rd | 2 man/fbps.Rd | 19 - man/ff.Rd | 2 man/ffpc.Rd | 2 man/ffpcplot.Rd | 2 man/fgam.Rd | 2 man/fosr.Rd | 2 man/fosr.perm.Rd | 7 man/fosr.vs.Rd | 2 man/fosr2s.Rd | 2 man/fpc.Rd | 2 man/fpca.face.Rd | 4 man/fpca.lfda.Rd |only man/fpca.sc.Rd | 2 man/fpca.ssvd.Rd | 2 man/fpca2s.Rd | 2 man/fpcr.Rd | 2 man/gasoline.Rd | 2 man/getTF.Rd | 2 man/gibbs_cs_fpca.Rd | 2 man/gibbs_cs_wish.Rd | 2 man/gibbs_mult_fpca.Rd | 2 man/gibbs_mult_wish.Rd | 2 man/gls_cs.Rd | 2 man/lf.Rd | 2 man/lf.vd.Rd | 2 man/lf_old.Rd | 2 man/lofocv.Rd | 2 man/lpeer.Rd | 2 man/lpfr.Rd | 2 man/mfpca.sc.Rd | 2 man/model.matrix.pffr.Rd | 2 man/ols_cs.Rd | 2 man/pcre.Rd | 2 man/peer.Rd | 2 man/peer_old.Rd | 2 man/pffr.Rd | 24 + man/pffr.check.Rd |only man/pffrGLS.Rd | 2 man/pffrSim.Rd | 2 man/pfr.Rd | 2 man/pfr_old.Rd | 2 man/pfr_plot.gam.Rd | 2 man/plot.fosr.Rd | 2 man/plot.fosr.vs.Rd | 2 man/plot.fpcr.Rd | 2 man/plot.lpeer.Rd | 2 man/plot.peer.Rd | 8 man/plot.pffr.Rd | 2 man/plot.pfr.Rd | 2 man/predict.fbps.Rd |only man/predict.fgam.Rd | 2 man/predict.fosr.vs.Rd | 2 man/predict.pffr.Rd | 2 man/predict.pfr.Rd | 2 man/print.summary.pffr.Rd | 2 man/pwcv.Rd | 2 man/qq.pffr.Rd |only man/quadWeights.Rd | 2 man/re.Rd | 2 man/refund-package.Rd | 1 man/residuals.pffr.Rd | 2 man/rlrt.pfr.Rd | 2 man/sff.Rd | 2 man/smooth.construct.dt.smooth.spec.Rd | 14 man/smooth.construct.fpc.smooth.spec.Rd | 2 man/smooth.construct.pcre.smooth.spec.Rd | 2 man/smooth.construct.peer.smooth.spec.Rd | 2 man/smooth.construct.pi.smooth.spec.Rd | 2 man/smooth.construct.pss.smooth.spec.Rd | 2 man/sofa.Rd | 2 man/summary.pffr.Rd | 2 man/summary.pfr.Rd | 2 man/vb_cs_fpca.Rd | 2 man/vb_cs_wish.Rd | 2 man/vb_mult_fpca.Rd | 2 man/vb_mult_wish.Rd | 2 man/vis.fgam.Rd | 2 man/vis.pfr.Rd | 2 123 files changed, 713 insertions(+), 508 deletions(-)
Title: Phenotypic Integration Index
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares <ajesusmp@cibio.up.pt>
Diff between PHENIX versions 1.2 dated 2015-04-29 and 1.2.1 dated 2016-01-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 4 ++++ NEWS | 8 ++++++++ man/PHENIX-package.Rd | 3 +++ 5 files changed, 23 insertions(+), 8 deletions(-)
Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian,
for specifying a banded numerical Jacobian and for allowing
a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between nleqslv versions 2.9.1 dated 2015-11-26 and 3.0 dated 2016-01-28
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 12 +++++++++++- R/nleqslv.R | 10 ++++++++-- R/searchzeros.R | 19 ++++++++++++++++--- man/nleqslv.Rd | 6 +++--- man/searchzeros.Rd | 35 ++++++++++++++++++++++++----------- man/testnslv.Rd | 2 +- src/nleqslv.c | 13 ++++++++----- tests/brdtri.Rout | 12 ++++++------ tests/brdtri.Rout.save | 12 ++++++------ 11 files changed, 97 insertions(+), 52 deletions(-)
Title: Mean-Variance Regularization
Description: This is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data. It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm). Among those are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. Key features include:
(i) Normalization and/or variance stabilization of the data,
(ii) Computation of mean-variance-regularized t-statistics (F-statistics to follow),
(iii) Generation of diverse diagnostic plots,
(iv) Computationally efficient implementation using C/C++ interfacing and an option for parallel computing to enjoy a faster and easier experience in the R environment.
Author: Jean-Eudes Dazard [aut, cre], Hua Xu [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between MVR versions 1.30.2 dated 2015-07-11 and 1.30.3 dated 2016-01-28
DESCRIPTION | 13 +++----- MD5 | 7 ++-- inst/NEWS | 95 ++++++++++++++++++++++++++++++++---------------------------- inst/doc |only src/MVRc.h | 27 +++++------------ 5 files changed, 69 insertions(+), 73 deletions(-)
Title: Computational Methods for Immune Cell-Type Subsets
Description: Provided are Computational methods for Immune Cell-type Subsets, including:(1) DCQ (Digital Cell Quantifier) to infer global dynamic changes in immune cell quantities within a complex tissue; and (2) VoCAL (Variation of Cell-type Abundance Loci) a deconvolution-based method that utilizes transcriptome data to infer the quantities of immune-cell types, and then uses these quantitative traits to uncover the underlying DNA loci.
Author: Yael Steuerman [aut, cre],
Irit Gat-Viks [aut]
Maintainer: Yael Steuerman <yaelsteu@mail.tau.ac.il>
Diff between ComICS versions 1.0.1 dated 2015-12-14 and 1.0.2 dated 2016-01-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/IterativeFilteration.R | 16 ++++++++++++---- R/deconvolution.R | 21 +++++++++++---------- R/helperFunc.R | 11 ++++++----- data/vocalEx.RData |binary 6 files changed, 37 insertions(+), 27 deletions(-)
Title: Tools for CM SAF Netcdf Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing Essential Climate Variables related to the energy and water
cycle of the atmosphere (www.cmsaf.eu). It is a joint cooperation of seven
National Meteorological and Hydrological Services, including the Deutscher
Wetterdienst (DWD).
The cmsaf R-package provides a small collection of R-functions, which are
inspired by the Climate Data Operators (cdo). This gives the opportunity to
analyse and manipulate CM SAF data without the need of installing cdo.
The cmsaf R-package is tested for CM SAF netcdf data, which are structured
in three-dimensional arrays (longitude, latitude, time) on a rectangular grid.
Layered CM SAF data have to be converted with the provided `levbox_mergetime`
function. The cmsaf R-package functions have only minor checks for deviations
from the recommended data structure, and give only few specific error messages.
Thus, there is no warranty of accurate results.
A Windows binary file and scripts for an easy application of the functions are
provided at the CM SAF homepage (http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.6 dated 2016-01-19 and 1.6.1 dated 2016-01-28
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/selpoint.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: TH's Data Archive
Description: Contains data sets used in other packages Torsten Hothorn
maintains.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between TH.data versions 1.0-6 dated 2015-01-05 and 1.0-7 dated 2016-01-28
DESCRIPTION | 12 ++++++------ MD5 | 12 +++++++----- NAMESPACE | 6 ++++++ data/geyser.rda |only data/mammoexp.rda |binary man/GBSG2.Rd | 10 ++++------ man/Westbc.Rd | 1 - man/geyser.Rd |only 8 files changed, 23 insertions(+), 18 deletions(-)
Title: R Interface to X-13-ARIMA-SEATS
Description: Easy-to-use interface to X-13-ARIMA-SEATS, the
seasonal adjustment software by the US Census Bureau. It offers full
access to almost all options and outputs of X-13, including X-11 and SEATS,
automatic ARIMA model search, outlier detection and support for user
defined holiday variables, such as Chinese New Year or Indian Diwali. It
also includes a Shiny-based graphical user interface. Seasonal uses the
X-13 binaries from the 'x13binary' package.
Author: Christoph Sax
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between seasonal versions 1.1.0 dated 2015-10-08 and 1.2.0 dated 2016-01-28
seasonal-1.1.0/seasonal/R/defunct.R |only seasonal-1.1.0/seasonal/man/seasonal-defunct.Rd |only seasonal-1.1.0/seasonal/vignettes/seas.tex |only seasonal-1.2.0/seasonal/DESCRIPTION | 17 seasonal-1.2.0/seasonal/MD5 | 94 ++--- seasonal-1.2.0/seasonal/NAMESPACE | 9 seasonal-1.2.0/seasonal/NEWS | 59 +++ seasonal-1.2.0/seasonal/R/checkX13.R | 11 seasonal-1.2.0/seasonal/R/genhol.R | 19 + seasonal-1.2.0/seasonal/R/identify.R | 2 seasonal-1.2.0/seasonal/R/import.spc.R | 65 ++- seasonal-1.2.0/seasonal/R/inspect-sub.R | 2 seasonal-1.2.0/seasonal/R/plot.R | 8 seasonal-1.2.0/seasonal/R/read_series.R | 3 seasonal-1.2.0/seasonal/R/read_udg.R | 7 seasonal-1.2.0/seasonal/R/seas.R | 8 seasonal-1.2.0/seasonal/R/seasonal-package.R | 52 ++ seasonal-1.2.0/seasonal/R/series.R | 2 seasonal-1.2.0/seasonal/R/startup.R | 31 + seasonal-1.2.0/seasonal/R/x13messages.R | 85 ++-- seasonal-1.2.0/seasonal/README.md | 80 +--- seasonal-1.2.0/seasonal/build/vignette.rds |binary seasonal-1.2.0/seasonal/demo/seas.R | 8 seasonal-1.2.0/seasonal/inst/doc/seas.Rnw | 12 seasonal-1.2.0/seasonal/inst/doc/seas.pdf |binary seasonal-1.2.0/seasonal/man/SPECS.Rd | 4 seasonal-1.2.0/seasonal/man/checkX13.Rd | 7 seasonal-1.2.0/seasonal/man/cpi.Rd | 7 seasonal-1.2.0/seasonal/man/easter.Rd | 9 seasonal-1.2.0/seasonal/man/exp.Rd | 3 seasonal-1.2.0/seasonal/man/final.Rd | 20 - seasonal-1.2.0/seasonal/man/genhol.Rd | 86 ++-- seasonal-1.2.0/seasonal/man/identify.seas.Rd | 4 seasonal-1.2.0/seasonal/man/iip.Rd | 13 seasonal-1.2.0/seasonal/man/import.spc.Rd | 59 ++- seasonal-1.2.0/seasonal/man/import.ts.Rd | 10 seasonal-1.2.0/seasonal/man/inspect.Rd | 28 - seasonal-1.2.0/seasonal/man/na.x13.Rd | 5 seasonal-1.2.0/seasonal/man/out.Rd | 31 - seasonal-1.2.0/seasonal/man/outlier.Rd | 4 seasonal-1.2.0/seasonal/man/plot.seas.Rd | 32 - seasonal-1.2.0/seasonal/man/qs.Rd | 32 - seasonal-1.2.0/seasonal/man/seas.Rd | 135 +++---- seasonal-1.2.0/seasonal/man/seasonal-package.Rd | 67 +++ seasonal-1.2.0/seasonal/man/series.Rd | 417 ++++++++++++------------ seasonal-1.2.0/seasonal/man/static.Rd | 28 - seasonal-1.2.0/seasonal/man/summary.seas.Rd | 26 - seasonal-1.2.0/seasonal/tests |only seasonal-1.2.0/seasonal/vignettes/README.tex | 86 ---- seasonal-1.2.0/seasonal/vignettes/seas.Rnw | 12 50 files changed, 963 insertions(+), 736 deletions(-)
Title: Efficient Iterator for Permutations and Combinations
Description: It helps in 1) generating permutations and combinations with or
without replacement; 2) with distinct items or non-distinct items (multiset);
3) calculating number of combinations or permutations in various situations. All
generated sequences are in lexicographical order (AKA, dictionary order). The
algorithms to generate permutations and combinations are memory efficient. These
iterative algorithms enable users to process all sequences without putting all
results in the memory at the same time. The algorithms are written in C/C++ for
faster performances.
Author: Randy Lai [aut, cre], Martin Broadhurst [aut]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between iterpc versions 0.2.7 dated 2015-04-16 and 0.2.8 dated 2016-01-28
iterpc-0.2.7/iterpc/tests/test-all.R |only iterpc-0.2.8/iterpc/DESCRIPTION | 22 +++-- iterpc-0.2.8/iterpc/MD5 | 37 ++++----- iterpc-0.2.8/iterpc/NAMESPACE | 5 + iterpc-0.2.8/iterpc/R/combination.R | 24 +++--- iterpc-0.2.8/iterpc/R/iterator.R | 65 ++++++++-------- iterpc-0.2.8/iterpc/R/permutation.R | 24 +++--- iterpc-0.2.8/iterpc/R/utilities.R | 47 +++++++++--- iterpc-0.2.8/iterpc/README.md | 9 +- iterpc-0.2.8/iterpc/man/getall.Rd | 6 - iterpc-0.2.8/iterpc/man/getcurrent.Rd | 4 - iterpc-0.2.8/iterpc/man/getlength.Rd | 4 - iterpc-0.2.8/iterpc/man/getnext.Rd | 4 - iterpc-0.2.8/iterpc/man/iter_wrapper.Rd |only iterpc-0.2.8/iterpc/man/iterpc.Rd | 16 +--- iterpc-0.2.8/iterpc/man/multichoose.Rd | 6 - iterpc-0.2.8/iterpc/man/nc_multiset.Rd | 10 +- iterpc-0.2.8/iterpc/man/np_multiset.Rd | 6 - iterpc-0.2.8/iterpc/tests/testthat.R |only iterpc-0.2.8/iterpc/tests/testthat/test-combination.R | 70 +++++++++--------- iterpc-0.2.8/iterpc/tests/testthat/test-permutation.R | 56 +++++++------- 21 files changed, 230 insertions(+), 185 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; and the International Tree Ring Data Bank. Additional
data sources are in the works, including global DEM resources (ETOPO1, ETOPO5,
ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National
Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.3 dated 2016-01-20 and 2.0.4 dated 2016-01-28
DESCRIPTION | 16 ++-- LICENSE |only MD5 | 19 +++-- R/SSURGO_FUNCTIONS.R | 9 +- README.md | 177 +++++++++++++++++++++++++++++++++++++++++++++---- inst/CITATION |only inst/FedDataTester.R | 39 ++++++++-- inst/img |only man/FedData-package.Rd | 49 +++++++++---- 9 files changed, 258 insertions(+), 51 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.2-5 dated 2015-09-16 and 1.3-1 dated 2016-01-28
DESCRIPTION | 10 +- MD5 | 160 ++++++++++++++++++++++--------------------- NAMESPACE | 2 R/bplot.r | 8 +- R/huber.mu.R | 7 + R/km.R | 73 ++++++++++--------- R/one.sample.t.R | 2 R/one.sample.z.R | 2 R/qq.Plot.R | 168 ++++++++++++++++++++++++++++++---------------- R/selftest.sampd.r | 22 +++--- build/vignette.rds |binary data/SexDeterm.rda |only data/savage.rda |only data/simberloff.rda |only man/D.sq.Rd | 2 man/Kullback.rd | 4 - man/MC.test.Rd | 2 man/MS.test.Rd | 2 man/Mode.rd | 4 - man/R.hat.rd | 3 man/SM.temp.moist.Rd | 4 - man/Semiconductor.rd | 4 - man/SexDeterm.Rd |only man/Venn.rd | 10 +- man/aids.rd | 2 man/alfalfa.split.plot.Rd | 2 man/anm.LV.rd | 2 man/anm.cont.pdf.rd | 2 man/anm.mc.bvn.rd | 2 man/anm.samp.design.Rd | 4 - man/asthma.Rd | 2 man/auc.rd | 2 man/baby.walk.Rd | 2 man/bone.rd | 6 - man/boot.ci.M.rd | 2 man/bootstrap.rd | 2 man/bplot.rd | 7 + man/bv.boxplot.Rd | 2 man/chi.plot.Rd | 2 man/ci.boot.rd | 2 man/ci.impt.Rd | 4 - man/ci.median.rd | 2 man/ci.mu.Rd | 2 man/ci.mu.oneside.rd | 4 - man/ci.p.rd | 4 - man/ci.prat.ak.Rd | 4 - man/ci.prat.rd | 4 - man/ci.sigma.rd | 4 - man/ci.strat.rd | 2 man/cliff.env.Rd | 2 man/cliff.sp.rd | 2 man/death.penalty.rd | 4 - man/depression.rd | 2 man/exercise.repeated.Rd | 2 man/garments.rd | 2 man/heart.rd | 2 man/joint.ci.bonf.rd | 2 man/km.Rd | 8 +- man/life.exp.Rd | 2 man/mcmc.norm.hier.rd | 2 man/modlevene.test.Rd | 2 man/moose.sel.Rd | 2 man/one.sample.t.rd | 2 man/paik.rd | 2 man/pairw.anova.Rd | 2 man/pairw.fried.rd | 2 man/pairw.kw.rd | 2 man/partial.R2.rd | 2 man/partial.resid.plot.rd | 2 man/perm.fact.test.rd | 4 - man/polyamine.rd | 2 man/power.z.test.Rd | 4 - man/press.rd | 2 man/prostate.rd | 2 man/pseudo.v.Rd | 4 - man/qq.Plot.Rd | 26 ++++--- man/savage.Rd |only man/see.nlm.rd | 2 man/simberloff.Rd |only man/skew.kurt.rd | 8 +- man/tukey.add.test.rd | 4 - man/veneer.rd | 2 man/wheat.rd | 2 man/whickham.rd | 10 +- 84 files changed, 377 insertions(+), 305 deletions(-)
Title: Perceptual Analysis, Visualization and Organization of Spectral
Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color
from spectral data.
Author: Rafael Maia [aut, cre],
Chad Eliason [aut],
Pierre-Paul Bitton [aut]
Maintainer: Rafael Maia <rm72@zips.uakron.edu>
Diff between pavo versions 0.5-2 dated 2015-06-10 and 0.5-4 dated 2016-01-27
DESCRIPTION | 16 ++++++---- MD5 | 70 ++++++++++++++++++++++++------------------------ NAMESPACE | 31 ++++++++++++++++++++- NEWS | 10 ++++++ R/coldist.R | 6 ++-- R/pavo-package.R | 5 +++ man/aggplot.Rd | 14 ++++----- man/aggspec.Rd | 10 +++--- man/as.rspec.Rd | 3 +- man/bgandilum.Rd | 2 - man/coldist.Rd | 29 +++++++++---------- man/explorespec.Rd | 8 ++--- man/getspec.Rd | 12 ++++---- man/irrad2flux.Rd | 4 +- man/merge.rspec.Rd | 5 ++- man/pavo-package.Rd | 4 +- man/peakshape.Rd | 6 ++-- man/plot.rspec.Rd | 12 ++++---- man/plotsmooth.Rd | 4 +- man/procspec.Rd | 14 ++++----- man/projplot.Rd | 4 +- man/segclass.Rd | 8 ++--- man/sensmodel.Rd | 8 ++--- man/sicalis.Rd | 4 +- man/spec2rgb.Rd | 4 +- man/subset.rspec.Rd | 5 ++- man/summary.rspec.Rd | 48 ++++++++++++++++---------------- man/summary.tcs.Rd | 12 ++++---- man/summary.vismodel.Rd | 2 - man/tcs.Rd | 2 - man/tcsplot.Rd | 19 ++++++------- man/teal.Rd | 6 ++-- man/ttvertex.Rd | 2 - man/vismodel.Rd | 28 +++++++++---------- man/vissyst.Rd | 2 - man/voloverlap.Rd | 24 ++++++++-------- 36 files changed, 246 insertions(+), 197 deletions(-)
Title: '--omics' Data Analysis Toolbox
Description: A collection of functions to analyse '--omics' datasets such as DNA
methylation and gene expression profiles.
Author: Gianluca Campanella [aut, cre]
Maintainer: Gianluca Campanella <gianluca@campanella.org>
Diff between omics versions 0.1-2 dated 2016-01-25 and 0.1-3 dated 2016-01-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/mlm.R | 6 ------ R/mlmer.R | 15 ++++----------- inst/NEWS.Rd | 6 ++++++ 5 files changed, 18 insertions(+), 25 deletions(-)
Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by HTTP verbs
(GET(), POST(), etc). Configuration functions make it easy to control
additional request components (authenticate(), add_headers() and so on).
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between httr versions 1.0.0 dated 2015-06-25 and 1.1.0 dated 2016-01-27
httr-1.0.0/httr/R/hmac.r |only httr-1.0.0/httr/inst/cacert.pem |only httr-1.0.0/httr/man/url_ok.Rd |only httr-1.0.0/httr/man/url_success.Rd |only httr-1.1.0/httr/DESCRIPTION | 12 httr-1.1.0/httr/MD5 | 229 +++++++++---------- httr-1.1.0/httr/NAMESPACE | 9 httr-1.1.0/httr/NEWS.md |only httr-1.1.0/httr/R/body.R | 2 httr-1.1.0/httr/R/config.r | 4 httr-1.1.0/httr/R/content-parse.r | 72 +++-- httr-1.1.0/httr/R/content.r | 2 httr-1.1.0/httr/R/handle-url.r | 2 httr-1.1.0/httr/R/handle.r | 19 + httr-1.1.0/httr/R/http-browse.r | 2 httr-1.1.0/httr/R/http-patch.r | 1 httr-1.1.0/httr/R/http-post.r | 1 httr-1.1.0/httr/R/http-put.r | 1 httr-1.1.0/httr/R/httr.r | 1 httr-1.1.0/httr/R/oauth-cache.R | 10 httr-1.1.0/httr/R/oauth-endpoint.r | 49 +++- httr-1.1.0/httr/R/oauth-error.r |only httr-1.1.0/httr/R/oauth-init.R | 56 +++- httr-1.1.0/httr/R/oauth-refresh.R | 20 + httr-1.1.0/httr/R/oauth-server-side.R | 52 +--- httr-1.1.0/httr/R/oauth-signature.r | 19 + httr-1.1.0/httr/R/oauth-token.r | 59 +++- httr-1.1.0/httr/R/progress.R | 10 httr-1.1.0/httr/R/request.R | 7 httr-1.1.0/httr/R/response-status.r | 166 ++++++++----- httr-1.1.0/httr/R/sha1.r |only httr-1.1.0/httr/R/str.R |only httr-1.1.0/httr/R/url-query.r | 7 httr-1.1.0/httr/R/url.r | 15 - httr-1.1.0/httr/R/utils.r | 5 httr-1.1.0/httr/R/zzz.R | 3 httr-1.1.0/httr/README.md | 16 - httr-1.1.0/httr/build/vignette.rds |binary httr-1.1.0/httr/demo/00Index | 2 httr-1.1.0/httr/demo/oauth1-withings.r | 2 httr-1.1.0/httr/demo/oauth1-yahoo.r | 3 httr-1.1.0/httr/demo/oauth2-azure.r |only httr-1.1.0/httr/demo/service-account.R |only httr-1.1.0/httr/inst/doc/api-packages.R | 4 httr-1.1.0/httr/inst/doc/api-packages.Rmd | 27 +- httr-1.1.0/httr/inst/doc/api-packages.html | 38 ++- httr-1.1.0/httr/inst/doc/quickstart.html | 64 ++--- httr-1.1.0/httr/man/BROWSE.Rd | 20 - httr-1.1.0/httr/man/DELETE.Rd | 20 - httr-1.1.0/httr/man/GET.Rd | 21 - httr-1.1.0/httr/man/HEAD.Rd | 21 - httr-1.1.0/httr/man/PATCH.Rd | 20 + httr-1.1.0/httr/man/POST.Rd | 20 + httr-1.1.0/httr/man/PUT.Rd | 20 + httr-1.1.0/httr/man/Token-class.Rd | 2 httr-1.1.0/httr/man/VERB.Rd | 21 - httr-1.1.0/httr/man/add_headers.Rd | 10 httr-1.1.0/httr/man/authenticate.Rd | 10 httr-1.1.0/httr/man/cache_info.Rd | 2 httr-1.1.0/httr/man/config.Rd | 17 - httr-1.1.0/httr/man/content.Rd | 8 httr-1.1.0/httr/man/content_type.Rd | 2 httr-1.1.0/httr/man/cookies.Rd | 2 httr-1.1.0/httr/man/guess_media.Rd | 2 httr-1.1.0/httr/man/handle.Rd | 19 + httr-1.1.0/httr/man/handle_pool.Rd | 2 httr-1.1.0/httr/man/has_content.Rd | 2 httr-1.1.0/httr/man/headers.Rd | 2 httr-1.1.0/httr/man/hmac_sha1.Rd | 4 httr-1.1.0/httr/man/http_condition.Rd | 9 httr-1.1.0/httr/man/http_error.Rd | 54 +--- httr-1.1.0/httr/man/http_status.Rd | 8 httr-1.1.0/httr/man/httr.Rd | 2 httr-1.1.0/httr/man/httr_dr.Rd | 2 httr-1.1.0/httr/man/httr_options.Rd | 2 httr-1.1.0/httr/man/init_oauth1.0.Rd | 7 httr-1.1.0/httr/man/init_oauth2.0.Rd | 16 + httr-1.1.0/httr/man/insensitive.Rd | 2 httr-1.1.0/httr/man/jwt_signature.Rd | 4 httr-1.1.0/httr/man/modify_url.Rd | 4 httr-1.1.0/httr/man/oauth1.0_token.Rd | 11 httr-1.1.0/httr/man/oauth2.0_token.Rd | 27 +- httr-1.1.0/httr/man/oauth_app.Rd | 8 httr-1.1.0/httr/man/oauth_callback.Rd | 2 httr-1.1.0/httr/man/oauth_endpoint.Rd | 6 httr-1.1.0/httr/man/oauth_endpoints.Rd | 4 httr-1.1.0/httr/man/oauth_exchanger.Rd | 2 httr-1.1.0/httr/man/oauth_listener.Rd | 2 httr-1.1.0/httr/man/oauth_service_token.Rd | 6 httr-1.1.0/httr/man/oauth_signature.Rd | 8 httr-1.1.0/httr/man/parse_http_date.Rd | 2 httr-1.1.0/httr/man/parse_media.Rd | 2 httr-1.1.0/httr/man/parse_url.Rd | 2 httr-1.1.0/httr/man/progress.Rd | 2 httr-1.1.0/httr/man/response.Rd | 8 httr-1.1.0/httr/man/revoke_all.Rd | 2 httr-1.1.0/httr/man/safe_callback.Rd | 2 httr-1.1.0/httr/man/set_config.Rd | 6 httr-1.1.0/httr/man/set_cookies.Rd | 10 httr-1.1.0/httr/man/sha1_hash.Rd |only httr-1.1.0/httr/man/sign_oauth.Rd | 2 httr-1.1.0/httr/man/status_code.Rd | 2 httr-1.1.0/httr/man/stop_for_status.Rd |only httr-1.1.0/httr/man/timeout.Rd | 10 httr-1.1.0/httr/man/upload_file.Rd | 2 httr-1.1.0/httr/man/use_proxy.Rd | 14 - httr-1.1.0/httr/man/user_agent.Rd | 10 httr-1.1.0/httr/man/verbose.Rd | 10 httr-1.1.0/httr/man/with_config.Rd | 6 httr-1.1.0/httr/man/write_disk.Rd | 2 httr-1.1.0/httr/man/write_function.Rd | 4 httr-1.1.0/httr/man/write_stream.Rd | 2 httr-1.1.0/httr/tests/testthat/test-body.r | 4 httr-1.1.0/httr/tests/testthat/test-content.R | 18 + httr-1.1.0/httr/tests/testthat/test-encoding.R |only httr-1.1.0/httr/tests/testthat/test-header.r | 4 httr-1.1.0/httr/tests/testthat/test-http-condition.R |only httr-1.1.0/httr/tests/testthat/test-http-error.R |only httr-1.1.0/httr/tests/testthat/test-oauth.R | 4 httr-1.1.0/httr/tests/testthat/test-response.r | 37 +-- httr-1.1.0/httr/tests/testthat/test-ssl.R | 12 httr-1.1.0/httr/tests/testthat/test-url.r | 21 + httr-1.1.0/httr/vignettes/api-packages.Rmd | 27 +- 123 files changed, 990 insertions(+), 661 deletions(-)
Title: Goodness-of-Fit Tests for Copulae
Description: Several GoF tests for Copulae are provided. A new hybrid test is implemented which supports all of the individual tests. Estimation methods for the margins are provided. All the tests support parameter estimation and predefined values. The parameters are estimated by pseudo maximum likelihood but if it fails the estimation switches automatically to inversion of Kendall's tau.
Author: Ostap Okhrin <ostap.okhrin@tu-dresden.de>,
Simon Trimborn <simon.trimborn@wiwi.hu-berlin.de>,
Shulin Zhang <slzhang@swufe.edu.cn>,
Qian M. Zhou <qmzhou@sfu.ca>
Maintainer: Simon Trimborn <simon.trimborn@wiwi.hu-berlin.de>
Diff between gofCopula versions 0.1-1 dated 2015-11-04 and 0.1-2 dated 2016-01-27
DESCRIPTION | 13 ++++++++----- MD5 | 16 ++++++++-------- R/tests_copula_helper.R | 9 ++++++--- man/tests_copula1.Rd | 2 +- man/tests_copula2.Rd | 2 +- man/tests_copula3.Rd | 2 +- man/tests_copula4.Rd | 2 +- man/tests_copula6.Rd | 2 +- man/tests_copula7.Rd | 2 +- 9 files changed, 28 insertions(+), 22 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre],
Yves Rosseel [aut]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.1-1 dated 2015-11-12 and 0.1-2 dated 2016-01-27
DESCRIPTION | 6 ++-- MD5 | 20 ++++++++------ NAMESPACE | 4 +- NEWS | 14 +++++++++- R/blav_object_methods.R | 34 +++++++++++++++++++++++++ R/blav_utils.R | 56 +++++++++++++++++++++++++++++++++++++++++ R/blavaan.R | 13 ++++++++- R/jags2r.R |only R/lav_export_jags.R | 65 +++++++++++++++++++++++++++++++++++++----------- R/margloglik.R | 39 ++++------------------------ R/set_priors.R | 18 +++++++++++-- README |only 12 files changed, 202 insertions(+), 67 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-20 1.2
2013-09-20 1.1
2013-02-08 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-17 2.4
2015-05-21 2.3
2014-03-25 2.2
2012-11-19 2.1.2
2012-11-18 2.1.1
2012-08-20 2.1
2012-03-28 2.0
2011-12-08 0.7
2011-11-24 0.6
2011-08-09 0.5
2010-05-04 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-20 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-19 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-17 1.0-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-07 1.0-3
2012-12-14 1.0-2
2011-06-20 1.0-1
2010-12-16 1.0-0
2005-10-05 0.0-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-15 0.4.6
2015-02-25 0.4.5
2015-01-06 0.4.4
2014-05-13 0.4.2
2013-10-06 0.4
2013-05-13 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-06 0.3.3
2013-12-30 0.3.2
2013-11-14 0.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-31 0.7.2
2014-02-08 0.7.1
2014-01-15 0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-27 0.8.7.0
2015-08-06 0.8.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-15 0.10
Title: Stable Isotope Bayesian Ellipses in R
Description: Fits bi-variate ellipses to stable isotope data using Bayesian
inference with the aim being to describe and compare their isotopic
niche.
Author: Andrew Jackson and Andrew Parnell
Maintainer: Andrew Jackson <a.jackson@tcd.ie>
Diff between SIBER versions 2.0 dated 2015-08-13 and 2.0.1 dated 2016-01-27
DESCRIPTION | 13 - MD5 | 101 +++++------ NAMESPACE | 2 NEWS.md |only R/addEllipse.R | 2 R/bayesianLayman.R | 2 R/communityMetricsML.R | 2 R/createSiberObject.R | 261 ++++++++++++++++------------- R/extractPosteriorMeans.R | 2 R/fitEllipse.R | 2 R/generateSiberCommunity.R | 2 R/generateSiberData.R | 2 R/generateSiberGroup.R | 2 R/groupMetricsML.R | 2 R/plotGroupEllipses.R | 2 R/plotSiberObject.R | 52 ++++- R/posteriorSEA.R | 4 R/siberConvexhull.R | 2 R/siberMVN.R | 2 R/sigmaSEA.R | 2 build/vignette.rds |binary inst/doc/Introduction-to-SIBER.R | 61 ++++++ inst/doc/Introduction-to-SIBER.Rmd | 68 +++++++ inst/doc/Introduction-to-SIBER.html | 110 +++++++++--- inst/extdata/test.group.names.csv |only man/SIBER.Rd | 6 man/addEllipse.Rd | 38 ++-- man/bayesianLayman.Rd | 16 - man/communityMetricsML.Rd | 9 - man/createSiberObject.Rd | 39 ++-- man/demo.siber.data.Rd | 14 - man/ellipseBackTransform.Rd | 18 +- man/extractPosteriorMeans.Rd | 16 - man/fitEllipse.Rd | 17 + man/genCircle.Rd | 8 man/generateSiberCommunity.Rd | 20 +- man/generateSiberData.Rd | 21 +- man/generateSiberGroup.Rd | 15 - man/groupMetricsML.Rd | 11 - man/hullArea.Rd | 6 man/laymanMetrics.Rd | 13 - man/plotCommunityHulls.Rd | 18 +- man/plotGroupEllipses.Rd | 8 man/plotGroupHulls.Rd | 22 +- man/plotSiberObject.Rd | 48 +++-- man/posteriorSEA.Rd | 10 - man/siberConvexhull.Rd | 7 man/siberDensityPlot.Rd | 42 ++-- man/siberEllipses.Rd | 12 - man/siberMVN.Rd | 20 +- man/sigmaSEA.Rd | 11 - vignettes/Introduction-to-SIBER.Rmd | 68 +++++++ vignettes/test-nonnumeric-group-labels.Rmd |only 53 files changed, 765 insertions(+), 466 deletions(-)
Title: Parametric Bootstrap and Kenward Roger Based Methods for Mixed
Model Comparison
Diff between pbkrtest versions 0.4-5 dated 2016-01-20 and 0.4-6 dated 2016-01-27
Description: Test in mixed effects models.
Attention is on mixed effects models as implemented in the
'lme4' package.
This package implements a parametric bootstrap test and a Kenward Roger
modification of F-tests for linear mixed effects models and a parametric bootstrap
test for generalized linear mixed models.
Author: Ulrich Halekoh
Maintainer: Søren Højsgaard
ChangeLog | 6 ++++++
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
inst/doc/pbkrtest-introduction.pdf |binary
4 files changed, 16 insertions(+), 10 deletions(-)
Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. Offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>
Diff between ore versions 1.2.1 dated 2015-08-10 and 1.2.2 dated 2016-01-27
DESCRIPTION | 9 +++++---- LICENCE | 2 +- MD5 | 40 ++++++++++++++++++++-------------------- NAMESPACE | 2 +- NEWS | 11 +++++++++++ R/dict.R | 10 ++++++++-- R/es.R | 20 +++++++++++--------- README.md | 2 +- man/es.Rd | 2 +- man/matches.Rd | 2 +- man/ore.Rd | 2 +- man/ore.dict.Rd | 3 ++- man/ore.ismatch.Rd | 4 ++-- man/ore.lastmatch.Rd | 2 +- man/ore.search.Rd | 2 +- man/ore.split.Rd | 2 +- man/ore.subst.Rd | 2 +- src/match.c | 7 ++++++- tests/testthat/test-10-match.R | 1 + tests/testthat/test-20-dict.R | 1 + tests/testthat/test-25-es.R | 2 ++ 21 files changed, 79 insertions(+), 49 deletions(-)
Title: Laplace Deconvolution with Noisy Discrete Non-Equally Spaced
Observations on a Finite Time Interval
Description: Solves the problem of Laplace deconvolution with noisy discrete
non-equally spaced observations on a finite time interval based on expansions
of the convolution kernel, the unknown function and the observed signal over
Laguerre functions basis. It implements the methodology proposed in the paper
"Laplace deconvolution on the basis of time domain data and its application to
Dynamic Contrast Enhanced imaging" by F. Comte, C-A. Cuenod, M. Pensky and Y.
Rozenholc in ArXiv (http://arxiv.org/abs/1405.7107).
Author: Yves Rozenholc (University Paris Descartes), Marianna Pensky (University
of Central Florida)
Maintainer: Yves Rozenholc <yves.rozenholc@parisdescartes.fr>
Diff between LaplaceDeconv versions 1.0.3 dated 2015-10-31 and 1.0.4 dated 2016-01-27
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 7 ++++++- R/LagLaplaceDeconvolution.R | 11 ++++++----- man/BuildLaguerreSystem.Rd | 14 +++++++------- man/EX_DCEMRI_t0.rda-EX_DCEMRI_t1.rda.Rd | 2 +- man/LagLaplDeconv.Rd | 4 ++-- man/LaguerreLaplaceConvolution.Rd | 12 ++++++------ man/LaplaceConvolution.Rd | 10 +++++----- man/MakeLaguerreMatrix.Rd | 6 +++--- 10 files changed, 48 insertions(+), 42 deletions(-)
Title: Simulation-Based Maximum Likelihood Parameter Estimation
Description: An estimation method that can use computer simulations to
approximate maximum-likelihood estimates even when the likelihood function can not
be evaluated directly. It can be applied whenever it is feasible to conduct many
simulations, but works best when the data is approximately Poisson distributed.
It was originally designed for demographic inference in evolutionary
biology. It has optional support for conducting coalescent simulation using
the 'coala' package.
Author: Paul Staab [aut, cre],
Lisha Mathew [aut],
Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between jaatha versions 3.0.0 dated 2015-12-03 and 3.1.0 dated 2016-01-27
jaatha-3.0.0/jaatha/man/jaatha-package.Rd |only jaatha-3.1.0/jaatha/DESCRIPTION | 8 - jaatha-3.1.0/jaatha/MD5 | 68 +++++----- jaatha-3.1.0/jaatha/NAMESPACE | 5 jaatha-3.1.0/jaatha/NEWS.md | 25 +++ jaatha-3.1.0/jaatha/R/block.R | 29 ++-- jaatha-3.1.0/jaatha/R/boot_jaatha.R | 24 +-- jaatha-3.1.0/jaatha/R/coala_interface.R | 15 +- jaatha-3.1.0/jaatha/R/fit_glm.R | 18 ++ jaatha-3.1.0/jaatha/R/initialization.R | 49 ++++++- jaatha-3.1.0/jaatha/R/jaatha.R | 66 +++++++--- jaatha-3.1.0/jaatha/R/jaatha_log.R | 31 ++-- jaatha-3.1.0/jaatha/R/jaatha_model.R | 25 +++ jaatha-3.1.0/jaatha/R/likelihood.R | 26 +--- jaatha-3.1.0/jaatha/R/par_ranges.R | 12 - jaatha-3.1.0/jaatha/R/simulation_cache.R | 36 ++++- jaatha-3.1.0/jaatha/R/stat_cube.R | 11 - jaatha-3.1.0/jaatha/README.md | 19 +-- jaatha-3.1.0/jaatha/build/vignette.rds |binary jaatha-3.1.0/jaatha/inst/doc/jaatha-evolution.html | 2 jaatha-3.1.0/jaatha/inst/doc/jaatha-intro.html | 76 +++++++----- jaatha-3.1.0/jaatha/man/boot_jaatha.Rd | 9 - jaatha-3.1.0/jaatha/man/get_start_pos.Rd |only jaatha-3.1.0/jaatha/man/jaatha.Rd | 41 +++++- jaatha-3.1.0/jaatha/tests/testthat.R | 2 jaatha-3.1.0/jaatha/tests/testthat/test-block.R | 6 jaatha-3.1.0/jaatha/tests/testthat/test-coala-interface.R | 4 jaatha-3.1.0/jaatha/tests/testthat/test-fit-glm.R | 28 +++- jaatha-3.1.0/jaatha/tests/testthat/test-initialization.R | 31 +++- jaatha-3.1.0/jaatha/tests/testthat/test-jaatha-function.R | 13 +- jaatha-3.1.0/jaatha/tests/testthat/test-jaatha-log.R | 26 +--- jaatha-3.1.0/jaatha/tests/testthat/test-jaatha-model.R | 9 + jaatha-3.1.0/jaatha/tests/testthat/test-likelihood.R | 6 jaatha-3.1.0/jaatha/tests/testthat/test-sim-cache.R | 31 ++++ jaatha-3.1.0/jaatha/tests/testthat/test-stat-cubes.R | 14 +- jaatha-3.1.0/jaatha/tests/testthat/test-zzz-bootstrapping.R | 12 + 36 files changed, 507 insertions(+), 270 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: We provide a set of functions to retrieve information about GIMMS NDVI3g files currently available online; download and re-arrange the bi-monthly datasets according to creation time; import downloaded files from native binary (ENVI) format directly into R based on the widely applied 'raster' package; extract accompanying quality flags and perform quality control; calculate monthly value composites (e.g. maximum value composites, MVC) from the bi-monthly input data; and derive long-term monotonous trends from the Mann-Kendall trend test, optionally featuring pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.5.0 dated 2016-01-15 and 0.5.1 dated 2016-01-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/gimmsControls.R | 1 + R/rasterizeGimms.R | 4 ++-- README.md | 9 +++++++++ 5 files changed, 20 insertions(+), 10 deletions(-)
Title: Balanced and Spatially Balanced Sampling
Description: Select balanced and spatially balanced probability samples in multi-dimensional spaces with any prescribed inclusion probabilities. It contains fast (C++ via Rcpp) implementations of the included sampling methods. The local pivotal method and spatially correlated Poisson sampling (for spatially balanced sampling) are included. Also the cube method (for balanced sampling) and the local cube method (for doubly balanced sampling) are included.
Author: Anton Grafström, Jonathan Lisic
Maintainer: Anton Grafström <anton.grafstrom@gmail.com>
Diff between BalancedSampling versions 1.4 dated 2014-05-02 and 1.5.1 dated 2016-01-27
DESCRIPTION | 14 +- MD5 | 15 +- R/lpm2_kdtree.R |only man/BalancedSampling-package.Rd | 6 man/lpm2_kdtree.Rd |only src/RcppExports.cpp | 274 +++++++++++++++------------------------- src/cube.cpp | 270 ++++++--------------------------------- src/kdtree_lpm.c |only src/kdtree_lpm.h |only src/lpm1.cpp | 6 src/lpm3.c |only 11 files changed, 172 insertions(+), 413 deletions(-)
More information about BalancedSampling at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-10 0.9-0
2014-03-07 0.8-1
2012-11-30 0.7-0
2012-09-05 0.6.3
2012-08-18 0.6.2
2012-07-05 0.6.1
2012-03-01 0.6.0
2012-01-04 0.5.0
2011-09-20 0.4.0
2011-07-06 0.3.0
2011-04-01 0.2.1
2011-03-04 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-18 1.4
2015-11-10 1.3
2015-09-29 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-02 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-30 0.2.0
2013-10-19 0.1.2
2013-09-23 0.1.1
2013-09-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-05 1.3-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-31 0.7.8
2013-10-09 0.7.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-23 2.0-8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-01 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-07 1.1
2015-11-13 1.0
Title: Bootstrap Methods
Description: Supplies bootstrap alternatives to traditional hypothesis-test
and confidence-interval procedures such as one-sample and two-sample
inferences for means, medians, standard deviations, and proportions; simple
linear regression; and more. Suitable for general audiences, including
individual and group users, introductory statistics courses, and more advanced
statistics courses that desire an introduction to bootstrap methods.
Author: Neil A. Weiss
Maintainer: Neil A. Weiss <neil.a.weiss@asu.edu>
Diff between wBoot versions 1.0.1 dated 2015-09-22 and 1.0.3 dated 2016-01-27
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++------ man/boot.one.bca.Rd | 5 ++--- man/boot.one.per.Rd | 6 +++--- man/boot.two.bca.Rd | 5 ++--- man/boot.two.per.Rd | 5 ++--- man/wBoot-package.Rd | 13 +++++++++---- 7 files changed, 32 insertions(+), 30 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics'
Engine 'eBird', 'AntWeb', and 'iDigBio'. Includes functionality for
retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.4.4 dated 2016-01-22 and 0.4.5 dated 2016-01-27
DESCRIPTION | 6 MD5 | 44 ++-- NAMESPACE | 1 NEWS.md |only R/antweb_helpers.R | 5 R/ecoengine_helpers.R | 5 R/methods.r | 17 + R/occ_options.r | 14 - R/plugins.r | 2 R/spocc-package.R | 2 R/zzz.r | 6 inst/doc/spocc_vignette.Rmd | 331 ++++++++++++++++--------------- inst/doc/spocc_vignette.html | 330 ++++++++++++++++-------------- man/occ.Rd | 4 man/occ_options.Rd | 1 man/spocc_capwords.Rd | 4 man/spocc_colClasses.Rd | 2 tests/testthat/test-common_params.R | 15 - tests/testthat/test-geometry.R | 105 +++++++++ tests/testthat/test-has_coords.R |only tests/testthat/test-occ.R | 125 ----------- tests/testthat/test-options.R | 38 +++ tests/testthat/test-paging.R |only tests/testthat/test-taxize-integration.R |only vignettes/spocc_vignette.Rmd | 331 ++++++++++++++++--------------- 25 files changed, 722 insertions(+), 666 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.6.400.2.2 dated 2015-12-16 and 0.6.500.4.0 dated 2016-01-27
RcppArmadillo-0.6.400.2.2/RcppArmadillo/inst/include/armadillo_bits/arma_boost.hpp |only RcppArmadillo-0.6.500.4.0/RcppArmadillo/ChangeLog | 24 RcppArmadillo-0.6.500.4.0/RcppArmadillo/DESCRIPTION | 8 RcppArmadillo-0.6.500.4.0/RcppArmadillo/MD5 | 107 ++-- RcppArmadillo-0.6.500.4.0/RcppArmadillo/configure | 4 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/NEWS.Rd | 19 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |binary RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/RcppArmadillo.h | 7 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/RcppArmadilloConfig.h | 8 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo | 23 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp | 4 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp | 14 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 14 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp | 4 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 4 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_str.hpp |only RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 6 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_bones.hpp | 10 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp | 5 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_bones.hpp | 16 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 251 +--------- RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp | 9 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/debug.hpp | 2 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/eop_aux.hpp | 13 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_bones.hpp | 5 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_meat.hpp | 80 +-- RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/field_meat.hpp | 18 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_accu.hpp | 138 ++++- RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_as_scalar.hpp | 2 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_conv.hpp | 35 + RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_eig_gen.hpp | 79 --- RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_eig_pair.hpp | 8 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_elem.hpp | 29 + RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_kmeans.hpp |only RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_conv_bones.hpp | 15 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_conv_meat.hpp | 207 ++++++-- RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_times_meat.hpp | 2 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/gmm_diag_bones.hpp | 18 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/gmm_diag_meat.hpp | 95 +++ RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/mul_gemm.hpp | 4 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/mul_gemv.hpp | 2 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/mul_herk.hpp | 3 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/mul_syrk.hpp | 2 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/op_dot_bones.hpp | 12 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/op_dot_meat.hpp | 8 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/op_max_meat.hpp | 1 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/op_mean_meat.hpp | 2 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/op_min_meat.hpp | 1 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_each_bones.hpp | 2 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_each_meat.hpp | 72 +- RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_meat.hpp | 64 ++ RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_each_meat.hpp | 44 - RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem2_meat.hpp | 24 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_field_meat.hpp | 2 RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_meat.hpp | 2 56 files changed, 870 insertions(+), 658 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <senz@uw.edu>
Diff between Grace versions 0.1.1 dated 2015-10-01 and 0.2 dated 2016-01-27
DESCRIPTION | 14 ++++----- MD5 | 15 ++++++---- NAMESPACE | 2 - R/cvGrace.R |only R/grace.R | 78 ++++++++++++++++++++++++++++-------------------------- R/grace.test.R |only R/make.L.R | 10 +++++- man/grace.Rd | 51 +++++++++++++---------------------- man/grace.test.Rd |only man/make.L.Rd | 8 +++-- 10 files changed, 91 insertions(+), 87 deletions(-)
Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 1.6 dated 2016-01-12 and 1.7 dated 2016-01-27
DESCRIPTION | 9 +-- MD5 | 122 +++++++++++++++++++++++---------------------- NAMESPACE | 2 R/Arotation.R | 30 +++++------ R/f.rbing.R | 2 R/mediandir.R |only R/mediandir_2.R |only R/mix.vmf.R | 40 +++++++------- R/vmkde.tune.R | 24 ++++---- R/wood.mle.R |only man/Arotation.Rd | 12 ++-- man/Directional-package.Rd | 30 +++++------ man/bic.mixvmf.Rd | 21 +++---- man/circ.cor1.Rd | 16 +++-- man/circ.cor2.Rd | 9 +-- man/circ.summary.Rd | 15 ++--- man/circlin.cor.Rd | 15 ++--- man/conc.test.Rd | 17 +++--- man/dirknn.Rd | 13 ++-- man/embed.circaov.Rd | 13 ++-- man/euclid.Rd | 13 ++-- man/euclid.inv.Rd | 11 ++-- man/f.rbing.Rd | 21 ++++--- man/fb.saddle.Rd | 15 ++--- man/fishkent.Rd | 19 +++---- man/hcf.aov.Rd | 11 ++-- man/hcf.circaov.Rd | 11 ++-- man/het.aov.Rd | 11 ++-- man/het.circaov.Rd | 7 +- man/kent.contour.Rd | 11 ++-- man/kent.datacontour.Rd | 19 +++---- man/lambert.Rd | 11 ++-- man/lambert.inv.Rd | 17 +++--- man/lr.aov.Rd | 11 ++-- man/lr.circaov.Rd | 15 ++--- man/meandir.test.Rd | 19 +++---- man/mediandir.Rd |only man/mediandir_2.Rd |only man/mix.vmf.Rd | 15 ++--- man/mixvmf.contour.Rd | 21 ++++--- man/rayleigh.Rd | 19 +++---- man/rbingham.Rd | 13 ++-- man/rfb.Rd | 11 ++-- man/rmixvmf.Rd | 13 ++-- man/rot.matrix.Rd | 13 ++-- man/rotation.Rd | 17 +++--- man/rvmf.Rd | 21 ++++--- man/rvonmises.Rd | 17 +++--- man/spher.cor.Rd | 15 ++--- man/spher.reg.Rd | 20 ++++--- man/spherconc.tet.Rd | 11 ++-- man/spml.reg.Rd | 31 +++++------ man/tang.conc.Rd | 9 +-- man/vm.kde.Rd | 21 ++++--- man/vmf.Rd | 7 +- man/vmf.contour.Rd | 7 +- man/vmf.da.Rd | 19 +++---- man/vmf.kde.Rd | 17 +++--- man/vmf.kerncontour.Rd | 5 + man/vmfda.pred.Rd | 5 + man/vmfkde.tune.Rd | 21 ++++--- man/vmfkde.tune_2.Rd | 13 ++-- man/vmkde.tune.Rd | 27 +++++---- man/vmkde.tune_2.Rd | 17 +++--- man/wood.mle.Rd |only 65 files changed, 537 insertions(+), 480 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between btergm versions 1.6 dated 2015-12-14 and 1.6.5 dated 2016-01-27
DESCRIPTION | 13 + MD5 | 22 +-- NAMESPACE | 2 R/checkdegeneracy.R |only R/gofmethods.R | 32 ++-- R/gofplot.R | 48 +++--- R/gofstatistics.R | 342 +++++++++++++++++++++++-------------------------- man/btergm-package.Rd | 2 man/btergm.Rd | 2 man/checkdegeneracy.Rd |only man/gofmethods.Rd | 2 man/gofplot.Rd | 15 +- man/gofstatistics.Rd | 13 - 13 files changed, 247 insertions(+), 246 deletions(-)
Title: Generalized Estimating Equation Package
Diff between geepack versions 1.2-0 dated 2014-09-13 and 1.2-0.1 dated 2016-01-27
Description: Generalized estimating equations solver for parameters in
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses.
Author: Søren Højsgaard,
Maintainer: Søren Højsgaard
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
src/famstr.cc | 5 ++---
src/inter.cc | 2 --
src/utils.cc | 5 +----
5 files changed, 10 insertions(+), 16 deletions(-)
Title: Fetch and Analyze Data from WaterML or CUAHSI WaterOneFlow Web
Service
Description: Lets you connect to any CUAHSI WaterOneFlow web service
from any hydroserver. To see list of available hydroservers, see http://
hiscentral.cuahsi.org. The package has five data download functions:
GetServices(): show all public HydroServers from the HIS Central Catalog.
HISCentral_GetSites() and HISCentral_GetSeriesCatalog(): search for sites or
time series from the HIS Central catalog based on geographic bounding box,
server, or keyword. GetVariables(): Show a data.frame with all variables
on the server. GetSites(): Show a data.frame with all sites on the server.
GetSiteInfo(): Show what variables, methods and quality control levels are
available at the specific site. GetValues(): Given a site code, variable code,
start time and endtime, fetch a data.frame of all the observation time series
data values. The data.frame has two columns: time and DataValue. This function
has an optional "daily" parameter, you can set daily="max", daily="min" or
daily="mean" to get aggregated daily values. The GetValues function can also
retrieve WaterML 1 or WaterML 2.0 data from a custom URL or from a local file.
The package also has five data upload functions: AddSites(), AddVariables(),
AddMethods(), AddSources(), and AddValues(). These functions can be used for
uploading data to a HydroServer Lite ODM database via the JSON data upload web
service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>
Diff between WaterML versions 1.5.0 dated 2015-09-21 and 1.6.0 dated 2016-01-26
DESCRIPTION | 42 ++++++++++--------- MD5 | 80 ++++++++++++++++++------------------- NAMESPACE | 2 R/AddMethods.R | 4 - R/AddSites.R | 3 - R/AddSources.R | 4 - R/AddValues.R | 5 +- R/AddVariables.R | 4 - R/GetServices.R | 2 R/GetSiteInfo.R | 2 R/GetSites.R | 2 R/GetValues.R | 15 ++++-- R/GetVariables.R | 2 R/HISCentral_GetSeriesCatalog.R | 2 R/HISCentral_GetSites.R | 2 R/MakeSOAPEnvelope.R | 3 - R/WaterMLVersion.R | 2 README.md | 4 - build/vignette.rds |binary inst/CITATION | 2 inst/doc/WaterML-Tutorial.R | 8 +++ inst/doc/WaterML-Tutorial.Rmd | 13 ++++++ inst/doc/WaterML-Tutorial.html | 11 ++++- man/AddMethods.Rd | 2 man/AddSites.Rd | 2 man/AddSources.Rd | 2 man/AddValues.Rd | 2 man/AddVariables.Rd | 2 man/GetServices.Rd | 2 man/GetSiteInfo.Rd | 2 man/GetSites.Rd | 2 man/GetValues.Rd | 11 +++-- man/GetVariables.Rd | 2 man/HISCentral_GetSeriesCatalog.Rd | 2 man/HISCentral_GetSites.Rd | 2 man/MakeSOAPEnvelope.Rd | 5 +- man/WaterML-package.Rd | 2 man/WaterMLVersion.Rd | 4 - man/WaterOneFlowNamespace.Rd | 2 man/WaterOneFlowVersion.Rd | 2 vignettes/WaterML-Tutorial.Rmd | 13 ++++++ 41 files changed, 166 insertions(+), 109 deletions(-)
Title: Bayesian Regularization for Feed-Forward Neural Networks
Description: Bayesian regularization for feed-forward neural networks.
Author: Paulino Perez Rodriguez, Daniel Gianola
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Diff between brnn versions 0.5 dated 2015-01-08 and 0.6 dated 2016-01-26
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 3 +++ inst/history.txt | 2 ++ src/unix/util_unix.c | 8 ++++---- 5 files changed, 19 insertions(+), 14 deletions(-)
Title: Develop and Run Spatially Explicit Discrete Event Simulation
Models
Description: Easily implement a variety of simulation models, with a focus on
spatially explicit agent based models. These include raster-based,
event-based, and agent-based models. The core simulation components are
built upon a discrete event simulation framework that facilitates
modularity, and easily enables the user to include additional functionality
by running user-built simulation modules. Included are numerous tools to
visualize raster and other maps. The suggested package `fastshp` can be
installed with `install.packages("fastshp", repos="http://rforge.net",
type="source")`.
Author: Alex M Chubaty [aut, cre],
Eliot J B McIntire [aut],
Yong Luo [ctb],
Steve Cumming [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alexander.chubaty@canada.ca>
Diff between SpaDES versions 1.0.1 dated 2015-08-10 and 1.1.0 dated 2016-01-26
SpaDES-1.0.1/SpaDES/inst/figs/SpaDES-overview-diagram.pdf |only SpaDES-1.0.1/SpaDES/inst/figs/plot-area-burned.pdf |only SpaDES-1.0.1/SpaDES/man/simList-extract-methods.Rd |only SpaDES-1.0.1/SpaDES/man/simList-inputs-outputs.Rd |only SpaDES-1.0.1/SpaDES/man/simList-paths.Rd |only SpaDES-1.0.1/SpaDES/tests/testthat/Rplots.pdf |only SpaDES-1.1.0/SpaDES/DESCRIPTION | 41 SpaDES-1.1.0/SpaDES/MD5 | 423 SpaDES-1.1.0/SpaDES/NAMESPACE | 834 - SpaDES-1.1.0/SpaDES/NEWS | 324 SpaDES-1.1.0/SpaDES/R/SELES.R | 540 - SpaDES-1.1.0/SpaDES/R/agent.R | 174 SpaDES-1.1.0/SpaDES/R/check.R | 527 - SpaDES-1.1.0/SpaDES/R/checkpoint.R | 584 - SpaDES-1.1.0/SpaDES/R/environment.R | 400 SpaDES-1.1.0/SpaDES/R/initialize.R | 699 - SpaDES-1.1.0/SpaDES/R/load.R | 731 - SpaDES-1.1.0/SpaDES/R/mapReduce.R | 163 SpaDES-1.1.0/SpaDES/R/misc-methods.R | 1325 +- SpaDES-1.1.0/SpaDES/R/module-dependencies-class.R | 384 SpaDES-1.1.0/SpaDES/R/module-dependencies-methods.R | 529 - SpaDES-1.1.0/SpaDES/R/module-repository.R | 568 - 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SpaDES-1.1.0/SpaDES/inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.Rmd | 88 SpaDES-1.1.0/SpaDES/inst/sampleModules/caribouMovement/caribouMovement.R | 279 SpaDES-1.1.0/SpaDES/inst/sampleModules/fireSpread/fireSpread.R | 336 SpaDES-1.1.0/SpaDES/inst/sampleModules/randomLandscapes/randomLandscapes.R | 214 SpaDES-1.1.0/SpaDES/man/Plot.Rd | 581 - SpaDES-1.1.0/SpaDES/man/SELESagentLocation.Rd | 58 SpaDES-1.1.0/SpaDES/man/SELESnumAgents.Rd | 60 SpaDES-1.1.0/SpaDES/man/SELESprobInit.Rd | 86 SpaDES-1.1.0/SpaDES/man/SELEStransitions.Rd | 62 SpaDES-1.1.0/SpaDES/man/SpaDES-package.Rd | 764 - SpaDES-1.1.0/SpaDES/man/addDepends.Rd | 58 SpaDES-1.1.0/SpaDES/man/adj.Rd | 178 SpaDES-1.1.0/SpaDES/man/append_attr.Rd | 78 SpaDES-1.1.0/SpaDES/man/arrangeViewports.Rd | 48 SpaDES-1.1.0/SpaDES/man/arrangement-class.Rd | 144 SpaDES-1.1.0/SpaDES/man/assignSpaDES.Rd | 65 SpaDES-1.1.0/SpaDES/man/cache.Rd | 82 SpaDES-1.1.0/SpaDES/man/changeObjEnv.Rd | 125 SpaDES-1.1.0/SpaDES/man/checkModule.Rd |only 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SpaDES-1.1.0/SpaDES/tests/testthat/test-load.R | 361 SpaDES-1.1.0/SpaDES/tests/testthat/test-mapReduce.R | 168 SpaDES-1.1.0/SpaDES/tests/testthat/test-module-deps-methods.R | 294 SpaDES-1.1.0/SpaDES/tests/testthat/test-module-template.R | 64 SpaDES-1.1.0/SpaDES/tests/testthat/test-paths.R | 103 SpaDES-1.1.0/SpaDES/tests/testthat/test-save.R | 110 SpaDES-1.1.0/SpaDES/tests/testthat/test-simList.R | 427 SpaDES-1.1.0/SpaDES/tests/testthat/test-simulation.R | 170 SpaDES-1.1.0/SpaDES/tests/testthat/test-spread.R | 88 SpaDES-1.1.0/SpaDES/tests/testthat/test-timeunits.R | 179 SpaDES-1.1.0/SpaDES/tests/testthat/test-updateList.R | 32 SpaDES-1.1.0/SpaDES/vignettes/bibliography.bib | 270 SpaDES-1.1.0/SpaDES/vignettes/i-introduction.Rmd | 651 - SpaDES-1.1.0/SpaDES/vignettes/ii-modules.Rmd | 1591 +-- SpaDES-1.1.0/SpaDES/vignettes/iii-plotting.Rmd | 830 - 224 files changed, 29505 insertions(+), 28351 deletions(-)
Title: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Description: Computes necessary information to meta analyze region-based
tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and
performs meta analysis.
Author: Arie Voorman, Jennifer Brody, Han Chen, Thomas Lumley, Brian Davis
Maintainer: Brian Davis <Brian.Davis281@gmail.com>
Diff between seqMeta versions 1.6.0 dated 2015-06-25 and 1.6.5 dated 2016-01-26
DESCRIPTION | 15 +-- MD5 | 54 +++++------ NAMESPACE | 24 +++++ R/burdenMeta.R | 16 +-- R/check_format_skat.R | 8 - R/coxlr.fit.R | 3 R/pchisqsum2.R | 6 - R/prepAdjust.R | 2 R/prepCox.R | 34 +++---- R/prepScores.R | 70 +++++++-------- R/prepScores2.R | 194 ++++++++++++++++++++++--------------------- R/seqMeta.R | 5 - R/singlesnpMeta.R | 12 +- R/skatMeta.R | 8 - R/skatOMeta.R | 23 ++--- R/utils.R | 4 README.md | 13 ++ build/vignette.rds |binary man/burdenMeta.Rd | 11 +- man/prepCondScores.Rd | 47 +++++----- man/prepScores.Rd | 100 +++++++++++----------- man/prepScores2.Rd | 149 ++++++++++++++++++++------------- man/seqMeta.Rd | 2 man/singlesnpMeta.Rd | 20 ++-- man/skatMeta.Rd | 29 +++--- man/skatOMeta.Rd | 49 +++++----- src/coxfit6.c | 36 ++++++- tests/testthat/test-issue2.R | 36 +++---- 28 files changed, 541 insertions(+), 429 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, and orientation patch count for teeth using scans of enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 0.3 dated 2016-01-13 and 1.0 dated 2016-01-26
DESCRIPTION | 8 +- MD5 | 26 ++++---- NAMESPACE | 3 R/DNE.R | 20 ++---- R/DNE3d.R | 2 R/OPC.R | 13 +++- R/OPC3d.R | 91 +++++++++++++++++------------ R/RFI3d.R | 161 +++++++++++++++++++++++------------------------------ R/molaR_Batch.R |only build/molaR.pdf |binary build/vignette.rds |binary man/OPC.Rd | 4 - man/OPC3d.Rd | 5 - man/RFI3d.Rd | 6 - man/molaR_Batch.Rd |only 15 files changed, 171 insertions(+), 168 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre],
Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.21-1 dated 2015-12-17 and 2.22 dated 2016-01-26
DESCRIPTION | 10 +-- MD5 | 38 ++++++------- NAMESPACE | 8 ++ R/betareg.support.R |only R/lsmeans.R | 128 ++++++++++++++++++++++++++++++-------------- R/ref.grid.R | 24 +++++--- R/summary.R | 14 +++- build/vignette.rds |binary inst/CITATION |only inst/NEWS | 13 ++++ inst/doc/extending.pdf |binary inst/doc/using-lsmeans.R | 114 +++++++++++++++++++++------------------ inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 10 ++- man/contrast.Rd | 25 ++++++-- man/lsmeans-package.Rd | 4 + man/models.Rd | 7 ++ man/summary.Rd | 14 ++++ man/update.Rd | 15 ++++- tests/tests1.Rout.save | 32 ++++++----- vignettes/using-lsmeans.rnw | 10 ++- 21 files changed, 309 insertions(+), 157 deletions(-)
Title: Iterative Bias Reduction
Description: Multivariate smoothing using iterative bias reduction with kernel, thin plate splines, Duchon splines or low rank splines.
Author: Pierre-Andre Cornillon, Nicolas Hengartner, Eric Matzner-Lober
Maintainer: "Pierre-Andre Cornillon" <pierre-andre.cornillon@univ-rennes2.fr>
Diff between ibr versions 2.0-0 dated 2015-10-19 and 2.0-2 dated 2016-01-26
ibr-2.0-0/ibr/tests/testthat/preslrds.rda |only ibr-2.0-0/ibr/tests/testthat/preslrtps.rda |only ibr-2.0-2/ibr/DESCRIPTION | 8 ++++---- ibr-2.0-2/ibr/MD5 | 14 ++++++-------- ibr-2.0-2/ibr/R/plot.ibr.R | 2 +- ibr-2.0-2/ibr/tests/testthat/reslrds.rda |binary ibr-2.0-2/ibr/tests/testthat/reslrtps.rda |binary ibr-2.0-2/ibr/tests/testthat/test_dim2.R | 11 ++--------- ibr-2.0-2/ibr/tests/testthat/test_dim5.R | 11 ++--------- 9 files changed, 15 insertions(+), 31 deletions(-)
Title: High-Dimensional Penalized Regression
Description: Algorithms for lasso and fused-lasso problems: implementation of
the lars algorithm for lasso and fusion penalization and EM-based
algorithms for (logistic) lasso and fused-lasso penalization.
Author: Quentin Grimonprez [aut, cre],
Serge Iovleff [aut]
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Diff between HDPenReg versions 0.92 dated 2015-09-07 and 0.93.1 dated 2016-01-26
HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/EM.cpp |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/EnetPenalty.cpp |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/EnetPenalty.h |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/FusedLasso.cpp |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/Lasso.cpp |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/LassoPenalty.cpp |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/LogisticFusedLasso.cpp |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/LogisticFusedLassoPenalty.cpp |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/LogisticFusedLassoPenalty.h |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/LogisticLasso.cpp |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/LogisticLassoPenalty.cpp |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/LogisticLassoPenalty.h |only HDPenReg-0.92/HDPenReg/src/HDPenReg/lassoModels/makefile |only HDPenReg-0.92/HDPenReg/src/emR.cpp |only HDPenReg-0.92/HDPenReg/src/emR.h |only HDPenReg-0.93.1/HDPenReg/DESCRIPTION | 31 - HDPenReg-0.93.1/HDPenReg/MD5 | 154 ++-- HDPenReg-0.93.1/HDPenReg/NAMESPACE | 7 HDPenReg-0.93.1/HDPenReg/NEWS | 13 HDPenReg-0.93.1/HDPenReg/R/EM.R | 238 ++++--- HDPenReg-0.93.1/HDPenReg/R/HDPenReg-package.R | 15 HDPenReg-0.93.1/HDPenReg/R/LarsPath.R | 163 +++-- HDPenReg-0.93.1/HDPenReg/R/cvEM.R | 192 +++--- HDPenReg-0.93.1/HDPenReg/R/cvlars.R | 80 +- HDPenReg-0.93.1/HDPenReg/R/lars.R | 32 - HDPenReg-0.93.1/HDPenReg/R/predict.R | 4 HDPenReg-0.93.1/HDPenReg/R/simulation.R | 174 ++--- HDPenReg-0.93.1/HDPenReg/TODO |only HDPenReg-0.93.1/HDPenReg/cleanup | 3 HDPenReg-0.93.1/HDPenReg/inst/doc/HDPenReg.pdf |binary HDPenReg-0.93.1/HDPenReg/man/EMcvfusedlasso.Rd | 20 HDPenReg-0.93.1/HDPenReg/man/EMcvlasso.Rd | 40 - HDPenReg-0.93.1/HDPenReg/man/EMfusedlasso.Rd | 26 HDPenReg-0.93.1/HDPenReg/man/EMlasso.Rd | 29 HDPenReg-0.93.1/HDPenReg/man/HDPenReg-package.Rd | 13 HDPenReg-0.93.1/HDPenReg/man/HDcvlars.Rd | 6 HDPenReg-0.93.1/HDPenReg/man/HDfusion.Rd | 14 HDPenReg-0.93.1/HDPenReg/man/HDlars.Rd | 21 HDPenReg-0.93.1/HDPenReg/man/LarsPath-class.Rd | 12 HDPenReg-0.93.1/HDPenReg/man/coef.LarsPath.Rd | 5 HDPenReg-0.93.1/HDPenReg/man/coeff.Rd | 5 HDPenReg-0.93.1/HDPenReg/man/computeCoefficients.Rd | 4 HDPenReg-0.93.1/HDPenReg/man/listToMatrix.Rd |only HDPenReg-0.93.1/HDPenReg/man/plot-methods.Rd | 12 HDPenReg-0.93.1/HDPenReg/man/plot.HDcvlars.Rd | 2 HDPenReg-0.93.1/HDPenReg/man/plotCoefficient.Rd | 7 HDPenReg-0.93.1/HDPenReg/man/predict.LarsPath.Rd | 2 HDPenReg-0.93.1/HDPenReg/man/simul.Rd | 4 HDPenReg-0.93.1/HDPenReg/src/EMPenModels.cpp |only HDPenReg-0.93.1/HDPenReg/src/EMPenModels.h |only HDPenReg-0.93.1/HDPenReg/src/HDPenReg/EMCVmain.cpp |only HDPenReg-0.93.1/HDPenReg/src/HDPenReg/EMmain.cpp |only HDPenReg-0.93.1/HDPenReg/src/HDPenReg/Makefile | 14 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lars.mk | 19 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lars/Cvlars.cpp | 2 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lars/Cvlars.h | 2 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lars/PathState.h | 2 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/larsRmain.cpp |only HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels.mk | 30 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/CV.cpp | 299 ++++----- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/CV.h | 23 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/CVFusedLasso.h | 94 +-- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/CVLasso.h | 50 + HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/EM.h | 144 +++- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/EnetSolver.cpp | 57 - HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/EnetSolver.h | 24 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/FusedLasso.h | 179 +---- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/FusedLassoPenalty.cpp | 147 +--- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/FusedLassoPenalty.h | 138 +--- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/FusedLassoSolver.cpp | 301 +++++---- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/FusedLassoSolver.h | 109 +-- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/IAlgo.h | 18 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/IMeasure.h | 43 - HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/IPenalizedSolver.h | 223 ++++--- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/IPenalty.h | 15 HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/Lasso.h | 161 +---- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/LassoPenalty.h | 106 +-- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/LassoSolver.cpp | 289 +++++---- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/LassoSolver.h | 101 +-- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/LogisticFusedLasso.h | 185 +---- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/LogisticFusedLassoSolver.cpp | 310 +++++----- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/LogisticFusedLassoSolver.h | 131 ++-- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/LogisticLasso.h | 171 +---- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/LogisticLassoSolver.cpp | 266 ++++---- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/LogisticLassoSolver.h | 121 +-- HDPenReg-0.93.1/HDPenReg/src/HDPenReg/lassoModels/PenalizedModels.h | 268 +++----- HDPenReg-0.93.1/HDPenReg/src/Makevars | 18 HDPenReg-0.93.1/HDPenReg/src/larsR.cpp | 221 ------- HDPenReg-0.93.1/HDPenReg/src/larsR.h | 13 89 files changed, 2699 insertions(+), 2923 deletions(-)
Title: Data Checking
Description: Checks column names,
column classes, values, keys, joins, vectors and scalars.
If the user-defined conditions are met the function
returns an invisible copy of the data frame, vector or scalar.
Otherwise the function throws an informative error.
Author: Joe Thorley [aut, cre]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between datacheckr versions 0.0.2 dated 2016-01-04 and 0.1.0 dated 2016-01-26
datacheckr-0.0.2/datacheckr/man/check_data.Rd |only datacheckr-0.0.2/datacheckr/tests/testthat/test-check-data-frame.R |only datacheckr-0.1.0/datacheckr/DESCRIPTION | 21 datacheckr-0.1.0/datacheckr/MD5 | 92 ++- datacheckr-0.1.0/datacheckr/NAMESPACE | 22 datacheckr-0.1.0/datacheckr/NEWS.md | 26 + datacheckr-0.1.0/datacheckr/R/check-colnames.R |only datacheckr-0.1.0/datacheckr/R/check-cols.R |only datacheckr-0.1.0/datacheckr/R/check-data-frame.R |only datacheckr-0.1.0/datacheckr/R/check-data-values.R | 24 datacheckr-0.1.0/datacheckr/R/check-data.R | 108 +--- datacheckr-0.1.0/datacheckr/R/check-data2.R |only datacheckr-0.1.0/datacheckr/R/check-data3.R |only datacheckr-0.1.0/datacheckr/R/check-join.R |only datacheckr-0.1.0/datacheckr/R/check-key.R |only datacheckr-0.1.0/datacheckr/R/check-rows.R |only datacheckr-0.1.0/datacheckr/R/check-scalar.R |only datacheckr-0.1.0/datacheckr/R/check-stop-set.R | 22 datacheckr-0.1.0/datacheckr/R/check-values-values.R |only datacheckr-0.1.0/datacheckr/R/check-values.R |only datacheckr-0.1.0/datacheckr/R/check-vector-value.R | 33 - datacheckr-0.1.0/datacheckr/R/check-vector-values.R | 17 datacheckr-0.1.0/datacheckr/R/check-vector.R |only datacheckr-0.1.0/datacheckr/R/package.R | 3 datacheckr-0.1.0/datacheckr/R/utils.R | 70 ++ datacheckr-0.1.0/datacheckr/README.md | 14 datacheckr-0.1.0/datacheckr/build/vignette.rds |binary datacheckr-0.1.0/datacheckr/inst/doc/datacheckr.R | 32 - datacheckr-0.1.0/datacheckr/inst/doc/datacheckr.Rmd | 38 - datacheckr-0.1.0/datacheckr/inst/doc/datacheckr.html | 46 - datacheckr-0.1.0/datacheckr/inst/doc/nycflights13.R |only datacheckr-0.1.0/datacheckr/inst/doc/nycflights13.Rmd |only datacheckr-0.1.0/datacheckr/inst/doc/nycflights13.html |only datacheckr-0.1.0/datacheckr/man/check_cols.Rd |only datacheckr-0.1.0/datacheckr/man/check_count.Rd |only datacheckr-0.1.0/datacheckr/man/check_data1.Rd |only datacheckr-0.1.0/datacheckr/man/check_data2.Rd |only datacheckr-0.1.0/datacheckr/man/check_data3.Rd |only datacheckr-0.1.0/datacheckr/man/check_data_frame.Rd |only datacheckr-0.1.0/datacheckr/man/check_date.Rd |only datacheckr-0.1.0/datacheckr/man/check_flag.Rd |only datacheckr-0.1.0/datacheckr/man/check_int.Rd |only datacheckr-0.1.0/datacheckr/man/check_join.Rd |only datacheckr-0.1.0/datacheckr/man/check_key.Rd |only datacheckr-0.1.0/datacheckr/man/check_number.Rd |only datacheckr-0.1.0/datacheckr/man/check_rows.Rd |only datacheckr-0.1.0/datacheckr/man/check_scalar.Rd |only datacheckr-0.1.0/datacheckr/man/check_string.Rd |only datacheckr-0.1.0/datacheckr/man/check_time.Rd |only datacheckr-0.1.0/datacheckr/man/check_values.Rd |only datacheckr-0.1.0/datacheckr/man/check_vector.Rd |only datacheckr-0.1.0/datacheckr/man/datacheckr.Rd | 2 datacheckr-0.1.0/datacheckr/man/max_integer.Rd | 3 datacheckr-0.1.0/datacheckr/man/max_nrow.Rd |only datacheckr-0.1.0/datacheckr/man/min_integer.Rd |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-cols.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-count.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-data.R | 190 +++++-- datacheckr-0.1.0/datacheckr/tests/testthat/test-check-data123.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-date.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-flag.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-join.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-key.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-number.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-rows.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-scalar.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-string.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-check-values.R | 248 +++++++++- datacheckr-0.1.0/datacheckr/tests/testthat/test-check-vector.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-data-frame.R |only datacheckr-0.1.0/datacheckr/tests/testthat/test-max-nrow.R |only datacheckr-0.1.0/datacheckr/vignettes/datacheckr.Rmd | 38 - datacheckr-0.1.0/datacheckr/vignettes/nycflights13.Rmd |only 73 files changed, 730 insertions(+), 319 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec versions 4.1.15 dated 2015-07-24 and 4.2.8 dated 2016-01-26
ChemoSpec-4.1.15/ChemoSpec/R/chooseLvls.R |only ChemoSpec-4.1.15/ChemoSpec/R/cleanSTOCSYpeaks.R |only ChemoSpec-4.1.15/ChemoSpec/R/collapseRowsOrCols.R |only ChemoSpec-4.1.15/ChemoSpec/R/corSpectra.R |only ChemoSpec-4.1.15/ChemoSpec/R/covSpectra.R |only ChemoSpec-4.1.15/ChemoSpec/R/covSpectraJS.R |only ChemoSpec-4.1.15/ChemoSpec/R/sortCrossPeaks.R |only ChemoSpec-4.1.15/ChemoSpec/inst/extdata/cS.css |only ChemoSpec-4.1.15/ChemoSpec/inst/extdata/cS_brushNguides.js |only ChemoSpec-4.1.15/ChemoSpec/inst/extdata/cS_controls.js |only ChemoSpec-4.1.15/ChemoSpec/inst/extdata/cS_globals.js |only ChemoSpec-4.1.15/ChemoSpec/inst/extdata/cS_main.js |only ChemoSpec-4.1.15/ChemoSpec/inst/extdata/cS_spectra.js |only ChemoSpec-4.1.15/ChemoSpec/inst/extdata/covSpectraJS.html |only ChemoSpec-4.1.15/ChemoSpec/man/chooseLvls.Rd |only ChemoSpec-4.1.15/ChemoSpec/man/cleanSTOCSYpeaks.Rd |only ChemoSpec-4.1.15/ChemoSpec/man/corSpectra.Rd |only ChemoSpec-4.1.15/ChemoSpec/man/sortCrossPeaks.Rd |only ChemoSpec-4.2.8/ChemoSpec/DESCRIPTION | 10 ChemoSpec-4.2.8/ChemoSpec/MD5 | 50 +-- ChemoSpec-4.2.8/ChemoSpec/NAMESPACE | 11 ChemoSpec-4.2.8/ChemoSpec/NEWS | 24 + ChemoSpec-4.2.8/ChemoSpec/R/check4Gaps.R | 2 ChemoSpec-4.2.8/ChemoSpec/R/files2SpectraObject.R | 189 +------------ ChemoSpec-4.2.8/ChemoSpec/R/hypTestScores.R | 2 ChemoSpec-4.2.8/ChemoSpec/R/sumSpectra.R | 1 ChemoSpec-4.2.8/ChemoSpec/inst/doc/ChemoSpec.R | 35 +- ChemoSpec-4.2.8/ChemoSpec/inst/doc/ChemoSpec.Rnw | 42 +- ChemoSpec-4.2.8/ChemoSpec/inst/doc/ChemoSpec.pdf |binary ChemoSpec-4.2.8/ChemoSpec/man/ChemoSpec-package.Rd | 3 ChemoSpec-4.2.8/ChemoSpec/man/MUD.Rd | 4 ChemoSpec-4.2.8/ChemoSpec/man/files2SpectraObject.Rd | 4 ChemoSpec-4.2.8/ChemoSpec/man/plotSpectraJS.Rd | 2 ChemoSpec-4.2.8/ChemoSpec/vignettes/ChemoSpec.Rnw | 42 +- ChemoSpec-4.2.8/ChemoSpec/vignettes/chemometrics.bib | 14 35 files changed, 140 insertions(+), 295 deletions(-)
Title: Bootstrapped Differences of Time Series
Description: Analyze differences among time series curves with Oleson et al's modified p-value technique.
Author: Michael Seedorff, Jacob Oleson, Grant Brown, Joseph Cavanaugh, and Bob McMurray
Maintainer: Michael Seedorff <michael-seedorff@uiowa.edu>
Diff between bdots versions 0.1.2 dated 2015-09-25 and 0.1.4 dated 2016-01-26
DESCRIPTION | 8 +- MD5 | 30 ++++--- NAMESPACE | 7 + R/doubleGaussFit.r | 22 +++++ R/doubleGaussRefit.r | 32 +++++++- R/logisticFit.r | 19 ++++ R/logisticRefit.r | 29 +++++++ R/subsDelete.r |only R/subsPlot.r | 203 ++++++++++++++++++++++----------------------------- build/vignette.rds |binary inst/doc/bdots.R | 23 ++++- inst/doc/bdots.Rnw | 13 +++ inst/doc/bdots.pdf |binary man/refit.Rd | 15 ++- man/subsDelete.Rd |only man/subsPlot.Rd | 3 vignettes/bdots.Rnw | 13 +++ 17 files changed, 264 insertions(+), 153 deletions(-)
Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods 'kernlab'
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut]
Maintainer: Alexandros Karatzoglou <alexis@ci.tuwien.ac.at>
Diff between kernlab versions 0.9-22 dated 2015-08-05 and 0.9-23 dated 2016-01-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/stringkernel.cpp | 4 ++-- src/svm.cpp | 5 ++--- 4 files changed, 11 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-21 2.1
2013-07-11 2.0
2012-08-21 1.2
2012-05-17 1.1
2012-04-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-07-22 1.5
2011-11-02 1.4
2011-10-12 1.3
2011-09-21 1.2
2011-09-11 1.1
2011-08-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-15 0.73
2013-06-18 0.72
2013-03-30 0.71
2012-12-20 0.60
2012-02-15 0.53
2012-02-13 0.52
2011-11-21 0.51
2011-04-28 0.5
Title: Spectroscopy Related Utilities
Description: Utility functions for spectroscopy. 1. Functions to simulate
spectra for use in teaching or testing. 2. Functions to process files created by
'LoggerPro' and 'SpectraSuite' software.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between SpecHelpers versions 0.1.19 dated 2015-07-16 and 0.2.2 dated 2016-01-26
DESCRIPTION | 16 +++++++++------ MD5 | 46 ++++++++++++++++++++++++++++----------------- NAMESPACE | 26 ++++++++++++++++++++++++- NEWS | 6 +++++ R/CIExyz.R |only R/emSpectrum.R |only R/getGamutValues.R |only R/plot2DNMRspec.R | 2 - R/plotCIEchrom.R |only R/plotNMRspec.R | 33 +++++++++++++++++++------------- R/prepCIEgradient.R |only R/sysdata.rda |only data |only man/CIExyz.Rd |only man/SpecHelpers-package.Rd | 2 - man/avgLambda.Rd | 2 - man/emSpectrum.Rd |only man/gatherCsv.Rd | 2 - man/gatherSpecFiles.Rd | 2 - man/gaussCurve.Rd | 4 ++- man/getGamutValues.Rd |only man/jSeq.Rd | 4 ++- man/lorentzCurve.Rd | 4 ++- man/makeSpec.Rd | 4 ++- man/plot2DNMRspec.Rd | 5 ++-- man/plotCIEchrom.Rd |only man/plotNMRspec.Rd | 33 +++++++++++++++++++++++--------- man/prepCIEgradient.Rd |only man/qMS.Rd | 4 ++- man/txt2csv.Rd | 2 - 30 files changed, 138 insertions(+), 59 deletions(-)
Title: Wrapper Functions for GUESS
Description: Wrapper functions for GUESS, a GPU-enabled sparse Bayesian variable
selection method for linear regression based analysis of possibly
multivariate/correlated outcomes.
Author: Gianluca Campanella [cre],
Benoit Liquet [aut],
Marc Chadeau-Hyam [aut],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb]
Maintainer: Gianluca Campanella <gianluca@campanella.org>
Diff between R2GUESS versions 1.6 dated 2014-11-12 and 1.7 dated 2016-01-26
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- NAMESPACE | 2 +- R/plotcim.R | 2 +- R/plotcim.explore.R | 2 +- inst/CITATION |only 6 files changed, 14 insertions(+), 13 deletions(-)
Title: Interactive Exploration of Contour Data
Description: Interactive tools to explore topographic-like data
sets. Such data sets take the form of a matrix in which the rows and
columns provide location/frequency information, and the matrix elements
contain altitude/response information. Such data is found in cartography,
2D spectroscopy and chemometrics. The functions in this package create
interactive web pages showing the contoured data, possibly with
slices from the original matrix parallel to each dimension. The interactive
behavior is created using the D3.js 'JavaScript' library by Mike Bostock.
Author: Bryan Hanson [aut, cre],
Kristina Mulry [ctb]
Maintainer: Bryan Hanson <hanson@depauw.edu>
Diff between exCon versions 0.1.12 dated 2015-07-16 and 0.1.14 dated 2016-01-26
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- NEWS | 3 +++ R/exCon.R | 4 +++- man/exCon-package.Rd | 2 +- man/exCon.Rd | 11 +++++++---- 7 files changed, 26 insertions(+), 17 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-12 dated 2015-12-04 and 0.2-13 dated 2016-01-26
CHANGELOG | 15 ++ DESCRIPTION | 8 - MD5 | 38 +++---- NAMESPACE | 4 R/01matrix.R | 10 + R/02sequences.R | 24 +--- R/03rules.R | 39 +++++++ R/05read_write.R | 7 - R/30similarity.R | 34 +++++- man/SPcontrol-class.Rd | 2 man/sequencerules-class.Rd | 9 + src/ptree.c | 230 ++++++++++++++++++++++++++++++++++++++------- src/similarity.c | 28 +++++ tests/idlists.Rout.save | 4 tests/ptree.R | 7 + tests/ptree.Rout.save | 29 +++-- tests/similarity.R | 9 + tests/similarity.Rout.save | 28 ++++- tests/zaki.R | 11 +- tests/zaki.Rout.save | 23 ++-- 20 files changed, 445 insertions(+), 114 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, PCA and correlation matrices, cluster analyses, scatter
plots, Likert scales, effects plots of regression models (including interaction
terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.8.4 dated 2015-10-12 and 1.9 dated 2016-01-26
DESCRIPTION | 21 MD5 | 166 - NAMESPACE | 300 +- NEWS | 1332 ++++++------- R/helpfunctions.R | 398 +-- R/sjPlotAncovaLSMeans.R | 38 R/sjPlotAnova.R | 875 ++++---- R/sjPlotClusterAnalysis.R | 1780 ++++++++--------- R/sjPlotCorr.R | 9 R/sjPlotFrequencies.R | 1636 +++++++--------- R/sjPlotGLME.R | 4535 +++++++++++++++++++++++---------------------- R/sjPlotGroupFrequencies.R | 2036 ++++++++------------ R/sjPlotGroupPropTable.R | 39 R/sjPlotInteractions.R | 2983 ++++++++++++++--------------- R/sjPlotLikert.R | 3 R/sjPlotLinreg.R | 249 +- R/sjPlotLinregMultiple.R | 908 ++++----- R/sjPlotOdds.R | 73 R/sjPlotOddsMultiple.R | 2 R/sjPlotPCA.R | 11 R/sjPlotPearsonsChi2Test.R | 3 R/sjPlotPolynomials.R | 2 R/sjPlotPropTable.R | 1131 ++++------- R/sjPlotScatter.R | 703 +++--- R/sjPlotSetTheme.R | 1896 +++++++++--------- R/sjPlotStackFrequencies.R | 963 ++++----- R/sjTabCorr.R | 1021 +++++----- R/sjTabDataFrame.R | 7 R/sjTabFrequencies.R | 136 - R/sjTabItemAnalysis.R | 809 ++++---- R/sjTabLinReg.R | 15 R/sjTabOdds.R | 2 R/sjTabPCA.R | 1189 +++++------ R/sjTabPropTable.R | 388 --- R/sjTabSPSS.R | 10 R/sjTabStackFrq.R | 1039 +++++----- README.md | 124 - man/adjust_plot_range.Rd | 3 man/dist_chisq.Rd | 13 man/dist_f.Rd | 9 man/dist_norm.Rd | 9 man/dist_t.Rd | 9 man/save_plot.Rd | 2 man/sjPlot-package.Rd | 102 - man/sjc.cluster.Rd | 37 man/sjc.dend.Rd | 21 man/sjc.elbow.Rd | 15 man/sjc.grpdisc.Rd | 7 man/sjc.kgap.Rd | 17 man/sjc.qclus.Rd | 67 man/sjp.aov1.Rd | 52 man/sjp.chi2.Rd | 9 man/sjp.corr.Rd | 30 man/sjp.frq.Rd | 214 -- man/sjp.glm.Rd | 47 man/sjp.glmer.Rd | 48 man/sjp.glmm.Rd | 43 man/sjp.gpt.Rd | 23 man/sjp.grpfrq.Rd | 193 - man/sjp.int.Rd | 128 - man/sjp.likert.Rd | 65 man/sjp.lm.Rd | 76 man/sjp.lmer.Rd | 74 man/sjp.lmm.Rd | 35 man/sjp.pca.Rd | 72 man/sjp.poly.Rd | 19 man/sjp.scatter.Rd | 25 man/sjp.setTheme.Rd | 42 man/sjp.stackfrq.Rd | 79 man/sjp.xtab.Rd | 116 - man/sjt.corr.Rd | 57 man/sjt.df.Rd | 49 man/sjt.frq.Rd | 57 man/sjt.glm.Rd | 121 - man/sjt.glmer.Rd | 57 man/sjt.grpmean.Rd | 15 man/sjt.itemanalysis.Rd | 37 man/sjt.lm.Rd | 173 - man/sjt.lmer.Rd | 57 man/sjt.mwu.Rd | 11 man/sjt.pca.Rd | 73 man/sjt.stackfrq.Rd | 65 man/sjt.xtab.Rd | 86 man/view_df.Rd | 17 84 files changed, 14486 insertions(+), 14922 deletions(-)
Title: Sabermetrics Functions for Baseball Analytics
Description: A collection of baseball analytics functions for sabermetrics
purposes. Among these functions include popular metrics such as FIP, wOBA, and
runs created and other advanced metrics.
Author: Peter Xenopoulos, Fernando Crema <www.peterxeno.com>
Maintainer: Peter Xenopoulos <peter.xenopoulos@pomona.edu>
Diff between Sabermetrics versions 1.0 dated 2015-02-06 and 2.0 dated 2016-01-26
Sabermetrics-1.0/Sabermetrics/R/sabermetrics.R |only Sabermetrics-1.0/Sabermetrics/inst |only Sabermetrics-1.0/Sabermetrics/man/eqa.Rd |only Sabermetrics-1.0/Sabermetrics/man/rcBasic.Rd |only Sabermetrics-1.0/Sabermetrics/man/rcBasicSB.Rd |only Sabermetrics-1.0/Sabermetrics/man/rcPX.Rd |only Sabermetrics-1.0/Sabermetrics/man/rcTech.Rd |only Sabermetrics-1.0/Sabermetrics/man/secA.Rd |only Sabermetrics-1.0/Sabermetrics/man/wOBA.Rd |only Sabermetrics-1.0/Sabermetrics/vignettes |only Sabermetrics-2.0/Sabermetrics/DESCRIPTION | 17 ++- Sabermetrics-2.0/Sabermetrics/MD5 | 51 ++++++---- Sabermetrics-2.0/Sabermetrics/R/Sabermetrics.R |only Sabermetrics-2.0/Sabermetrics/man/babip.Rd |only Sabermetrics-2.0/Sabermetrics/man/dice.Rd | 61 ++++++------- Sabermetrics-2.0/Sabermetrics/man/era.Rd |only Sabermetrics-2.0/Sabermetrics/man/eraminus.Rd |only Sabermetrics-2.0/Sabermetrics/man/fip.Rd | 65 +++++++------- Sabermetrics-2.0/Sabermetrics/man/fipminus.Rd |only Sabermetrics-2.0/Sabermetrics/man/fp.Rd |only Sabermetrics-2.0/Sabermetrics/man/handedparkfactors.Rd |only Sabermetrics-2.0/Sabermetrics/man/iso.Rd | 42 ++++----- Sabermetrics-2.0/Sabermetrics/man/lgwSB.Rd |only Sabermetrics-2.0/Sabermetrics/man/linearWeights.Rd |only Sabermetrics-2.0/Sabermetrics/man/log5.Rd | 45 +++++++-- Sabermetrics-2.0/Sabermetrics/man/obp.Rd | 61 ++++++------- Sabermetrics-2.0/Sabermetrics/man/ops.Rd | 47 ++++------ Sabermetrics-2.0/Sabermetrics/man/opsplus.Rd |only Sabermetrics-2.0/Sabermetrics/man/parkfactors.Rd |only Sabermetrics-2.0/Sabermetrics/man/pyth.Rd | 40 ++++++-- Sabermetrics-2.0/Sabermetrics/man/raweqa.Rd |only Sabermetrics-2.0/Sabermetrics/man/sabermetrics-package.Rd | 14 +-- Sabermetrics-2.0/Sabermetrics/man/secavg.Rd |only Sabermetrics-2.0/Sabermetrics/man/slg.Rd | 52 ++++------- Sabermetrics-2.0/Sabermetrics/man/whip.Rd |only Sabermetrics-2.0/Sabermetrics/man/woba.Rd |only Sabermetrics-2.0/Sabermetrics/man/wraa.Rd |only Sabermetrics-2.0/Sabermetrics/man/wrc.Rd |only Sabermetrics-2.0/Sabermetrics/man/wrcplus.Rd |only Sabermetrics-2.0/Sabermetrics/man/wsb.Rd |only Sabermetrics-2.0/Sabermetrics/man/xfip.Rd |only Sabermetrics-2.0/Sabermetrics/man/xfipminus.Rd |only 42 files changed, 279 insertions(+), 216 deletions(-)
Title: A Most Informative Histogram-Like Model
Description: Using the MDL principle, it is possible to estimate
parameters for a histogram-like model. The package contains
the implementation of such an estimation method.
Author: Jouke Witteveen
Maintainer: Jouke Witteveen <j.witteveen@gmail.com>
Diff between histmdl versions 0.4-1 dated 2015-03-16 and 0.5-1 dated 2016-01-26
DESCRIPTION | 9 +++--- MD5 | 10 +++---- NAMESPACE | 4 ++- R/histmdl.R | 65 ++++++++++++++++++++++++------------------------- man/histmdl-package.Rd | 4 +-- man/histmdl.Rd | 43 +++++++------------------------- 6 files changed, 57 insertions(+), 78 deletions(-)
Title: Cox Model for Case-Cohort Data with Stratified
Subcohort-Selection
Description: Contains a function, also called cchs, that calculates Estimator III of Borgan et al (2000), Exposure-stratified Case-cohort Designs. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
Author: E. Jones
Maintainer: E. Jones <r-cchs@outlook.com>
Diff between cchs versions 0.1.0 dated 2015-01-29 and 0.2.0 dated 2016-01-26
cchs-0.1.0/cchs/R/classRelatedFunctions.R |only cchs-0.2.0/cchs/DESCRIPTION | 8 cchs-0.2.0/cchs/MD5 | 22 +- cchs-0.2.0/cchs/NAMESPACE | 1 cchs-0.2.0/cchs/R/argProcessingSubroutines.R | 43 ++-- cchs-0.2.0/cchs/R/cchs-class.R |only cchs-0.2.0/cchs/R/cchs.R | 214 ++++++++++++++---------- cchs-0.2.0/cchs/R/rowManipulationSubroutines.R | 34 ++- cchs-0.2.0/cchs/R/samplingFractionSubroutines.R | 86 +++++---- cchs-0.2.0/cchs/R/tiedEventTimeSubroutines.R | 17 + cchs-0.2.0/cchs/R/utils.R | 14 + cchs-0.2.0/cchs/man/cchs.Rd | 76 ++++---- cchs-0.2.0/cchs/man/cchsData.Rd | 11 - 13 files changed, 302 insertions(+), 224 deletions(-)
Title: Java Executable .jar Files for 'RKEEL'
Description: KEEL is a popular Java software for a large number of different knowledge data discovery tasks. Furthermore, 'RKEEL' is a package with a R code layer between R and KEEL, for using KEEL in R code. This package downloads and install the .jar files necessary for 'RKEEL' algorithms execution. For more information about KEEL, see <http://www.keel.es/>.
Author: Jose Moyano [aut, cre], Luciano Sanchez Ramos [aut]
Maintainer: Jose Moyano <i02momuj@uco.es>
Diff between RKEELjars versions 1.0.4 dated 2016-01-24 and 1.0.6 dated 2016-01-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/getJarList.R | 2 ++ R/zzz.R | 9 ++------- 4 files changed, 10 insertions(+), 13 deletions(-)
Title: Graphical User Interface for Data Mining in R
Description: The R Analytic Tool To Learn Easily (Rattle) provides a
Gnome (RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file
(or via ODBC), transform and explore the data,
build and evaluate models, and export models as PMML (predictive
modelling markup language) or as scores. All of this with knowing little
about R. All R commands are logged and commented through the log tab. Thus they
are available to the user as a script file or as an aide for the user to
learn R or to copy-and-paste directly into R itself.
Rattle also exports a number of utility
functions and the graphical user interface, invoked as rattle(), does
not need to be run to deploy these.
Author: Graham Williams [aut, cph, cre],
Mark Vere Culp [cph],
Ed Cox [ctb],
Anthony Nolan [ctb],
Denis White [cph],
Daniele Medri [ctb],
Akbar Waljee [ctb] (OOB AUC for Random Forest),
Brian Ripley [cph] (Author of original print.summary.nnet),
Jose Magana [ctb] (Contributed the ggpairs plots.)
Maintainer: Graham Williams <Graham.Williams@togaware.com>
Diff between rattle versions 4.0.5 dated 2015-11-24 and 4.1.0 dated 2016-01-26
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/evaluate.R | 8 +++++--- R/rattle.R | 4 ++-- R/transform.R | 7 ++++--- R/zzz.R | 5 +++-- build/vignette.rds |binary data/locationsAUS.RData |binary data/weather.RData |binary data/weatherAUS.RData |binary inst/NEWS | 21 +++++++++++++++++++++ inst/doc/rattle.pdf |binary 12 files changed, 50 insertions(+), 25 deletions(-)
Title: Eye-Tracking Data Analysis
Description: A set of tools that address tasks along the pipeline from raw
data to analysis and visualization for eye-tracking data. Offers several
popular types of analyses, including linear and growth curve time analyses,
onset-contingent reaction time analyses, as well as several non-parametric
bootstrapping approaches.
Author: Jacob Dink [aut, cre],
Brock Ferguson [aut]
Maintainer: Jacob Dink <jacobwdink@gmail.com>
Diff between eyetrackingR versions 0.1.3 dated 2016-01-09 and 0.1.4 dated 2016-01-26
DESCRIPTION | 12 +-- MD5 | 42 +++++------ NEWS.md | 3 R/data_prep.R | 18 +++++ R/onset_contingent_data.R | 82 +++++++++++++++++------ inst/doc/divergence_vignette.Rmd | 4 - inst/doc/divergence_vignette.html | 38 ++++------ inst/doc/growth_curve_analysis_vignette.Rmd | 2 inst/doc/growth_curve_analysis_vignette.html | 19 ++--- inst/doc/onset_contingent_analysis_vignette.R | 2 inst/doc/onset_contingent_analysis_vignette.Rmd | 4 - inst/doc/onset_contingent_analysis_vignette.html | 39 +++++----- inst/doc/preparing_your_data_vignette.Rmd | 2 inst/doc/preparing_your_data_vignette.html | 4 - inst/doc/window_analysis_vignette.Rmd | 2 inst/doc/window_analysis_vignette.html | 20 ++--- man/make_onset_data.Rd | 4 - vignettes/divergence_vignette.Rmd | 4 - vignettes/growth_curve_analysis_vignette.Rmd | 2 vignettes/onset_contingent_analysis_vignette.Rmd | 4 - vignettes/preparing_your_data_vignette.Rmd | 2 vignettes/window_analysis_vignette.Rmd | 2 22 files changed, 182 insertions(+), 129 deletions(-)
More information about distance.sample.size at CRAN
Permanent link
Title: Mixed Models, Particularly Spatial GLMMs
Description: Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroscedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [ctb],
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@univ-montp2.fr>
Diff between spaMM versions 1.7.1 dated 2016-01-21 and 1.7.2 dated 2016-01-25
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/HLfit.R | 8 ++++---- R/HLfit_Internals.R | 2 ++ R/MakeCovEst.R | 4 ++-- inst/NEWS.Rd | 3 ++- man/spaMM.Rd | 2 +- src/spaMM_linear.cpp | 3 ++- 8 files changed, 25 insertions(+), 21 deletions(-)
Title: R Graphics Devices for Vector Graphics Output
Description: Vector Graphics devices for SVG, DrawingML for
Microsoft Word and DrawingML for Microsoft PowerPoint.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between rvg versions 0.0.5 dated 2016-01-06 and 0.0.6 dated 2016-01-25
DESCRIPTION | 8 +- MD5 | 39 ++++++++--- NAMESPACE | 13 +++ NEWS |only R/interactivePointsGrob.R |only R/interactivePolygonGrob.R |only R/interactivePolylineGrob.R |only R/interactiveRectGrob.R |only R/interactiveSegmentsGrob.R |only R/interactiveTextGrob.R |only man/drawDetails.interactivePointsGrob.Rd |only man/drawDetails.interactivePolygonGrob.Rd |only man/drawDetails.interactivePolylineGrob.Rd |only man/drawDetails.interactiveRectGrob.Rd |only man/drawDetails.interactiveSegmentsGrob.Rd |only man/drawDetails.interactiveTextGrob.Rd |only man/interactivePointsGrob.Rd |only man/interactivePolygonGrob.Rd |only man/interactivePolylineGrob.Rd |only man/interactiveRectGrob.Rd |only man/interactiveSegmentsGrob.Rd |only man/interactiveTextGrob.Rd |only src/RcppExports.cpp | 18 ++--- src/a_color.cpp | 4 - src/docx.cpp | 2 src/dsvg.cpp | 50 ++++++++------ src/line_style.cpp | 3 src/pptx.cpp | 2 tests/testthat/test-svg-interactive.R | 97 +++++++++++++++++++++++++++++ tests/testthat/test-svg-lines.R | 4 - 30 files changed, 189 insertions(+), 51 deletions(-)
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate
'API' at http://www.ncdc.noaa.gov/cdo-web/webservices/v2, with functions for
each of the 'API' 'endpoints': data, data categories, data sets, data types,
locations, location categories, and stations. In addition, we have an interface
for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical
Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS',
tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [ctb],
Adam Erickson [ctb],
Nicholas Potter [ctb],
Joseph Stachelek [ctb],
Hart Edmund [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 0.5.0 dated 2015-12-02 and 0.5.2 dated 2016-01-25
DESCRIPTION | 22 +-- LICENSE | 2 MD5 | 116 +++++++++-------- NAMESPACE | 11 + NEWS.md |only R/argo.R |only R/coops.R |only R/gefs.R | 9 - R/ghcnd.R | 12 + R/ncdc_plot.r | 46 +++---- R/rnoaa-package.r | 11 - R/seaice.r | 5 R/storm_shp.R | 3 R/tornadoes.R | 6 R/zzz.r | 5 README.md | 214 ++++++++++++++------------------- inst/doc/homr_vignette.Rmd | 122 ++++++++---------- inst/doc/homr_vignette.html | 124 ++++++++----------- inst/doc/ncdc_vignette.Rmd | 58 ++++---- inst/doc/ncdc_vignette.html | 58 ++++---- inst/doc/ncdc_workflow.Rmd | 91 +++++--------- inst/doc/ncdc_workflow.html | 91 +++++--------- inst/doc/seaice_vignette.Rmd | 50 +++---- inst/doc/seaice_vignette.html | 48 +++---- inst/doc/storms_vignette.Rmd | 12 - inst/doc/storms_vignette.html | 12 - inst/doc/swdi_vignette.Rmd | 94 ++++---------- inst/doc/swdi_vignette.html | 94 ++++---------- inst/vign/figure/seaice1-1.png |only inst/vign/figure/seaice2-1.png |only inst/vign/figure/unnamed-chunk-2-1.png |binary inst/vign/figure/unnamed-chunk-3-1.png |binary inst/vign/figure/unnamed-chunk-4-1.png |binary inst/vign/figure/unnamed-chunk-5-1.png |binary inst/vign/figure/unnamed-chunk-7-1.png |binary inst/vign/figure/unnamed-chunk-8-1.png |binary inst/vign/homr_vignette.md | 122 ++++++++---------- inst/vign/myfile.kmz |binary inst/vign/myfile.zip |binary inst/vign/ncdc_vignette.md | 58 ++++---- inst/vign/ncdc_workflow.md | 91 +++++--------- inst/vign/seaice_vignette.Rmd | 35 +++-- inst/vign/seaice_vignette.md | 50 +++---- inst/vign/storms_vignette.md | 12 - inst/vign/swdi_vignette.md | 94 ++++---------- man/argo.Rd |only man/coops.Rd |only man/gefs.Rd | 5 man/ghcnd.Rd | 13 ++ man/ncdc_plot.Rd | 31 +--- man/rnoaa-package.Rd | 6 tests/testthat/test-coops.R |only tests/testthat/test-gefs.R | 31 ++-- tests/testthat/test-ncdc_locs_cats.r | 2 tests/testthat/test-ncdc_plot.r | 1 tests/testthat/test-seaice.R | 7 - tests/testthat/test-storms.R | 27 ++-- vignettes/homr_vignette.Rmd | 122 ++++++++---------- vignettes/ncdc_vignette.Rmd | 58 ++++---- vignettes/ncdc_workflow.Rmd | 91 +++++--------- vignettes/seaice_vignette.Rmd | 50 +++---- vignettes/storms_vignette.Rmd | 12 - vignettes/swdi_vignette.Rmd | 94 ++++---------- 63 files changed, 961 insertions(+), 1367 deletions(-)
Title: Provides an Interface to the Agent-Based Modelling Platform
NetLogo
Description: Interface to use and access Wilensky's NetLogo (Wilensky 1999) from R using either headless (no GUI) or interactive GUI mode. Provides functions to load models, execute commands, and get values from reporters. Mostly analogous to the NetLogo Mathematica Link https://github.com/NetLogo/Mathematica-Link.
Author: Jan C. Thiele
Maintainer: Jan C. Thiele <rnetlogo@gmx.de>
Diff between RNetLogo versions 1.0-1 dated 2014-10-12 and 1.0-2 dated 2016-01-25
DESCRIPTION | 14 - MD5 | 136 +++++----- NEWS | 4 R/NLCommand.R | 4 R/NLDfToList.R | 2 R/NLDoCommand.R | 6 R/NLDoCommandWhile.R | 4 R/NLDoReport.R | 4 R/NLDoReportWhile.R | 4 R/NLGetAgentSet.R | 40 -- R/NLGetGraph.R | 12 R/NLGetPatches.R | 44 --- R/NLLoadModel.R | 4 R/NLQuit.R | 12 R/NLReport.R | 4 R/NLSetAgentSet.R | 31 -- R/NLSetPatchSet.R | 24 - R/NLSetPatches.R | 33 -- R/NLSourceFromString.R | 4 R/NLStart.R | 5 R/onLoad.R | 31 -- build/vignette.rds |binary inst/NEWS.Rd | 17 + inst/doc/parallelProcessing.R | 2 inst/doc/parallelProcessing.Rnw | 2 inst/doc/parallelProcessing.pdf |binary inst/examples/applications/3dPlot/3dPlot.R | 2 inst/examples/applications/AnalyticComparison/analytic.R | 2 inst/examples/applications/Database/database.R | 2 inst/examples/applications/ExplorativeAnalysis/explorativeAnalysis.R | 2 inst/examples/applications/TimeSlider/timeslieder.R | 2 inst/examples/applications/TimeSlider/timeslieder2.R | 2 inst/examples/code_samples/1-NLStart/NLStart.R | 2 inst/examples/code_samples/10-NLGetPatches/NLGetPatches.R | 4 inst/examples/code_samples/11-NLGetAgentSet/NLGetAgentSet.R | 4 inst/examples/code_samples/12-NLSetPatches/NLSetPatches.R | 4 inst/examples/code_samples/13-NLSetPatchSet/NLSetPatchSet.R | 4 inst/examples/code_samples/14-NLSetAgentSet/NLSetAgentSet.R | 4 inst/examples/code_samples/15-NLGetGraph/NLGetGraph.R | 2 inst/examples/code_samples/16-NLSourceFromText/NLSourceFromText.R | 4 inst/examples/code_samples/2-NLLoadModel/NLLoadModel.R | 2 inst/examples/code_samples/3-NLCommand/NLCommand.R | 2 inst/examples/code_samples/4-NLReport/NLReport.R | 2 inst/examples/code_samples/5-NLQuit/NLQuit.R | 2 inst/examples/code_samples/6-Headless/NLStartQuitMultiple.R | 2 inst/examples/code_samples/7-NLDoCommand_NLDoReport/NLDoCommand_NLDoReport.R | 2 inst/examples/code_samples/8-NLDoCommandWhile_NLDoReportWhile/NLDoCommandReportWhile.R | 2 inst/examples/code_samples/9-NLDfToList/NLDfToList.R | 4 inst/java/RNetLogo.jar |binary inst/quickStartGuide.txt | 4 man/NLCommand.Rd | 2 man/NLDfToList.Rd | 2 man/NLDoCommand.Rd | 2 man/NLDoCommandWhile.Rd | 2 man/NLDoReport.Rd | 2 man/NLDoReportWhile.Rd | 2 man/NLGetAgentSet.Rd | 2 man/NLGetGraph.Rd | 2 man/NLGetPatches.Rd | 2 man/NLLoadModel.Rd | 2 man/NLQuit.Rd | 2 man/NLReport.Rd | 2 man/NLSetAgentSet.Rd | 2 man/NLSetPatchSet.Rd | 2 man/NLSetPatches.Rd | 2 man/NLSourceFromString.Rd | 2 man/NLStart.Rd | 10 man/RNetLogo-package.Rd | 16 - vignettes/parallelProcessing.Rnw | 2 69 files changed, 195 insertions(+), 370 deletions(-)
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: The reproducer R package includes data analysis functions and data
sets (e.g., related to software defect prediction) to streamline reproducible
research in software engineering.
Author: Lech Madeyski [cre, aut, ctb],
Marian Jureczko [ctb] (Data contributor),
Barbara Kitchenham [ctb] (Data contributor),
David Bodgen [ctb] (Data contributor),
Pearl Brereton [ctb] (Data contributor),
Jacky Keung [ctb] (Data contributor),
Stuart Charters [ctb] (Data contributor),
Shirley Gibbs [ctb] (Data contributor),
Amnart Pohthong [ctb] (Data contributor)
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.1.3 dated 2015-05-22 and 0.1.4 dated 2016-01-25
DESCRIPTION | 35 + MD5 | 66 +- NAMESPACE | 3 NEWS.md |only R/MadeyskiKitchenhamMetaAnalysis.R | 4 R/data.R | 243 ++++++++++ R/reproducer.R | 66 +- README.md | 2 data/KitchenhamMadeyskiBudgen16.COCOMO.rda |only data/KitchenhamMadeyskiBudgen16.DiffInDiffData.rda |only data/KitchenhamMadeyskiBudgen16.FINNISH.rda |only data/KitchenhamMadeyskiBudgen16.PolishData.rda |only data/KitchenhamMadeyskiBudgen16.PolishSubjects.rda |only data/KitchenhamMadeyskiBudgen16.SubjectData.rda |only inst/CITATION | 42 - man/Ciolkowski09ESEM.MetaAnalysis.PBRvsCBRorAR.Rd | 3 man/KitchenhamMadeyskiBudgen16.COCOMO.Rd |only man/KitchenhamMadeyskiBudgen16.DiffInDiffData.Rd |only man/KitchenhamMadeyskiBudgen16.FINNISH.Rd |only man/KitchenhamMadeyskiBudgen16.PolishData.Rd |only man/KitchenhamMadeyskiBudgen16.PolishSubjects.Rd |only man/KitchenhamMadeyskiBudgen16.SubjectData.Rd |only man/Madeyski15EISEJ.OpenProjects.Rd | 3 man/Madeyski15EISEJ.PropProjects.Rd | 3 man/Madeyski15EISEJ.StudProjects.Rd | 3 man/Madeyski15SQJ.NDC.Rd | 3 man/MadeyskiKitchenham.MetaAnalysis.PBRvsCBRorAR.Rd | 3 man/boxplotAndDensityCurveOnHistogram.Rd | 2 man/boxplotHV.Rd | 5 man/cloudOfWords.Rd | 2 man/densityCurveOnHistogram.Rd | 2 man/fmt.Rd |only man/printXTable.Rd | 2 man/readExcelSheet.Rd | 2 man/reproduceForestPlotRandomEffects.Rd | 2 man/reproduceMixedEffectsAnalysisWithEstimatedVarianceAndExperimentalDesignModerator.Rd | 2 man/reproduceMixedEffectsAnalysisWithExperimentalDesignModerator.Rd | 2 man/reproduceMixedEffectsForestPlotWithExperimentalDesignModerator.Rd | 2 man/reproduceTableWithEffectSizesBasedOnMeanDifferences.Rd | 2 man/reproduceTableWithPossibleModeratingFactors.Rd | 2 man/reproduceTableWithSourceDataByCiolkowski.Rd | 2 41 files changed, 388 insertions(+), 120 deletions(-)
Title: Classes with Reference Semantics
Description: The R6 package allows the creation of classes with reference
semantics, similar to R's built-in reference classes. Compared to reference
classes, R6 classes are simpler and lighter-weight, and they are not built
on S4 classes so they do not require the methods package. These classes
allow public and private members, and they support inheritance, even when
the classes are defined in different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>
Diff between R6 versions 2.1.1 dated 2015-08-18 and 2.1.2 dated 2016-01-25
DESCRIPTION | 6 - MD5 | 16 ++-- NAMESPACE | 2 NEWS | 13 +++ R/print.R | 98 ++++++++++++++---------- inst/doc/Debugging.html | 6 - inst/doc/Introduction.html | 22 ++--- inst/doc/Performance.html | 178 +++++++++++++++++++++------------------------ inst/doc/Portable.html | 6 - 9 files changed, 186 insertions(+), 161 deletions(-)
Title: Parallel Model-Based Clustering using
Expectation-Gathering-Maximization Algorithm for Finite Mixture
Gaussian Model
Description: Aims to utilize model-based clustering (unsupervised)
for high dimensional and ultra large data, especially in a distributed
manner. The code employs pbdMPI to perform a
expectation-gathering-maximization algorithm
for finite mixture Gaussian
models. The unstructured dispersion matrices are assumed in the
Gaussian models. The implementation is default in the single program
multiple data programming model. The code can be executed
through pbdMPI and independent to most MPI applications.
See the High Performance
Statistical Computing website for more information, documents
and examples.
Author: Wei-Chen Chen [aut, cre],
George Ostrouchov [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pmclust versions 0.1-6 dated 2014-02-03 and 0.1-7 dated 2016-01-25
pmclust-0.1-6/pmclust/vignettes/pmclust-include/jss.bst |only pmclust-0.1-6/pmclust/vignettes/pmclust-include/jss.cls |only pmclust-0.1-7/pmclust/ChangeLog | 8 pmclust-0.1-7/pmclust/DESCRIPTION | 38 ++-- pmclust-0.1-7/pmclust/MD5 | 90 +++++----- pmclust-0.1-7/pmclust/NAMESPACE | 20 ++ pmclust-0.1-7/pmclust/R/000_globalVariables.r |only pmclust-0.1-7/pmclust/R/00_pmclust.r | 4 pmclust-0.1-7/pmclust/R/00_pmclust_internal.r | 2 pmclust-0.1-7/pmclust/R/00_pmclust_internal_dmat.r | 2 pmclust-0.1-7/pmclust/R/01_as_dmat.r | 4 pmclust-0.1-7/pmclust/R/01_as_spmd.r | 4 pmclust-0.1-7/pmclust/R/02_convert_data.r | 2 pmclust-0.1-7/pmclust/R/02_load_balance.r | 6 pmclust-0.1-7/pmclust/demo/dmat_em.r | 4 pmclust-0.1-7/pmclust/demo/dmat_kmeans.r | 4 pmclust-0.1-7/pmclust/demo/ex_MixSim.r | 2 pmclust-0.1-7/pmclust/demo/ex_aecm.r | 2 pmclust-0.1-7/pmclust/demo/ex_apecm.r | 2 pmclust-0.1-7/pmclust/demo/ex_apecma.r | 2 pmclust-0.1-7/pmclust/demo/ex_em.r | 2 pmclust-0.1-7/pmclust/demo/ex_kmeans.r | 2 pmclust-0.1-7/pmclust/demo/gbd_aecm.r | 2 pmclust-0.1-7/pmclust/demo/gbd_apecm.r | 2 pmclust-0.1-7/pmclust/demo/gbd_apecma.r | 2 pmclust-0.1-7/pmclust/demo/gbd_em.r | 2 pmclust-0.1-7/pmclust/demo/gbd_kmeans.r | 2 pmclust-0.1-7/pmclust/demo/io_csv.r | 2 pmclust-0.1-7/pmclust/demo/iris_common.r | 4 pmclust-0.1-7/pmclust/demo/iris_dmat.r | 6 pmclust-0.1-7/pmclust/demo/iris_gbdr.r | 4 pmclust-0.1-7/pmclust/demo/iris_single.r | 6 pmclust-0.1-7/pmclust/inst/CITATION | 10 - pmclust-0.1-7/pmclust/inst/doc/pmclust-guide.Rnw | 24 +- pmclust-0.1-7/pmclust/inst/doc/pmclust-guide.pdf |binary pmclust-0.1-7/pmclust/man/01-pmclust_pkmeans.Rd | 4 pmclust-0.1-7/pmclust/man/50-as.dmat.spmd.Rd | 8 pmclust-0.1-7/pmclust/tests/dmat_em.r | 4 pmclust-0.1-7/pmclust/tests/dmat_kmeans.r | 4 pmclust-0.1-7/pmclust/tests/iris_em_dmat.r | 4 pmclust-0.1-7/pmclust/tests/iris_em_spmd.r | 4 pmclust-0.1-7/pmclust/tests/iris_kmeans_dmat.r | 4 pmclust-0.1-7/pmclust/tests/iris_kmeans_spmd.r | 4 pmclust-0.1-7/pmclust/vignettes/build_pdf.sh | 11 + pmclust-0.1-7/pmclust/vignettes/pmclust-guide.Rnw | 18 +- pmclust-0.1-7/pmclust/vignettes/pmclust-include/01-acknowledgement.tex | 6 pmclust-0.1-7/pmclust/vignettes/pmclust-include/01-introduction.tex | 2 pmclust-0.1-7/pmclust/vignettes/pmclust-include/my_jss.cls |only 48 files changed, 195 insertions(+), 144 deletions(-)
Title: Panel Dynamic OLS Estimation of Cointegrating Vectors
Description: Estimates panel data cointegrating relationships following the estimator of Mark and Sul (2003), <DOI:10.1111/j.1468-0084.2003.00066.x>.
Author: Raad Khraishi [aut, cre]
Maintainer: Raad Khraishi <raadkhraishi+pdolsms@gmail.com>
Diff between pdolsms versions 0.1 dated 2016-01-24 and 0.2 dated 2016-01-25
DESCRIPTION | 6 ++--- MD5 | 6 ++--- R/pdols.R | 51 +++++++++++++++++++++++++++++-------------------- data/marksul2003.RData |binary 4 files changed, 37 insertions(+), 26 deletions(-)
Title: Programming with Big Data --- MPI Profiling Tools
Description: MPI profiling tools.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
Gaurav Sehrawat [aut],
Pragneshkumar Patel [aut],
George Ostrouchov [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdPROF versions 0.2-3 dated 2014-05-26 and 0.3-0 dated 2016-01-25
pbdPROF-0.2-3/pbdPROF/R/benchplot.r |only pbdPROF-0.2-3/pbdPROF/R/grid_plotter.r |only pbdPROF-0.2-3/pbdPROF/R/plot.r |only pbdPROF-0.2-3/pbdPROF/R/plot_fpmpi.r |only pbdPROF-0.2-3/pbdPROF/R/plot_mpiP.r |only pbdPROF-0.2-3/pbdPROF/R/plot_tau.r |only pbdPROF-0.2-3/pbdPROF/R/printing.r |only pbdPROF-0.2-3/pbdPROF/R/read.r |only pbdPROF-0.2-3/pbdPROF/README |only pbdPROF-0.2-3/pbdPROF/man/00_pbdPROF-package.Rd |only pbdPROF-0.2-3/pbdPROF/man/01_profilers.Rd |only pbdPROF-0.2-3/pbdPROF/man/02_classes.Rd |only pbdPROF-0.2-3/pbdPROF/man/12_example.Rd |only pbdPROF-0.2-3/pbdPROF/man/aa_read_prof.Rd |only pbdPROF-0.2-3/pbdPROF/man/bb_print.Rd |only pbdPROF-0.2-3/pbdPROF/man/cc_plot.Rd |only pbdPROF-0.2-3/pbdPROF/man/dd_benchplot.Rd |only pbdPROF-0.2-3/pbdPROF/man/zz_internal.Rd |only pbdPROF-0.2-3/pbdPROF/vignettes/include/05-profiling.tex |only pbdPROF-0.2-3/pbdPROF/vignettes/include/06-plotting.tex |only pbdPROF-0.2-3/pbdPROF/vignettes/include/07-debugging.tex |only pbdPROF-0.2-3/pbdPROF/vignettes/include/jss.bst |only pbdPROF-0.3-0/pbdPROF/ChangeLog | 10 + pbdPROF-0.3-0/pbdPROF/DESCRIPTION | 26 ++-- pbdPROF-0.3-0/pbdPROF/MD5 | 75 +++++------- pbdPROF-0.3-0/pbdPROF/NAMESPACE | 28 +--- pbdPROF-0.3-0/pbdPROF/R/00-classes.r | 38 ++++-- pbdPROF-0.3-0/pbdPROF/R/01-generics.r | 8 - pbdPROF-0.3-0/pbdPROF/R/data.r |only pbdPROF-0.3-0/pbdPROF/R/parse.r | 15 +- pbdPROF-0.3-0/pbdPROF/R/pbdPROF-package.r |only pbdPROF-0.3-0/pbdPROF/R/print.r |only pbdPROF-0.3-0/pbdPROF/R/read.prof.r |only pbdPROF-0.3-0/pbdPROF/README.md |only pbdPROF-0.3-0/pbdPROF/demo/allreduce.fpmpi.r | 5 pbdPROF-0.3-0/pbdPROF/demo/allreduce.mpip.r | 5 pbdPROF-0.3-0/pbdPROF/demo/masterslavePI.fpmpi.r | 5 pbdPROF-0.3-0/pbdPROF/demo/masterslavePI.mpip.r | 5 pbdPROF-0.3-0/pbdPROF/demo/svd.fpmpi.r | 5 pbdPROF-0.3-0/pbdPROF/demo/svd.mpip.r | 5 pbdPROF-0.3-0/pbdPROF/inst/CITATION | 4 pbdPROF-0.3-0/pbdPROF/inst/doc/pbdPROF-guide.Rnw | 26 ++-- pbdPROF-0.3-0/pbdPROF/inst/doc/pbdPROF-guide.pdf |binary pbdPROF-0.3-0/pbdPROF/man/Example-datasets.Rd |only pbdPROF-0.3-0/pbdPROF/man/pbdPROF-package.Rd |only pbdPROF-0.3-0/pbdPROF/man/prof-class.Rd |only pbdPROF-0.3-0/pbdPROF/man/prof-print.Rd |only pbdPROF-0.3-0/pbdPROF/man/profilers.Rd |only pbdPROF-0.3-0/pbdPROF/man/read.prof.Rd |only pbdPROF-0.3-0/pbdPROF/src/Makevars.win | 2 pbdPROF-0.3-0/pbdPROF/vignettes/build_pdf.sh | 12 + pbdPROF-0.3-0/pbdPROF/vignettes/include/00-copyright.tex | 2 pbdPROF-0.3-0/pbdPROF/vignettes/include/02-installation.tex | 2 pbdPROF-0.3-0/pbdPROF/vignettes/include/05-plotting.tex |only pbdPROF-0.3-0/pbdPROF/vignettes/include/06-debugging.tex |only pbdPROF-0.3-0/pbdPROF/vignettes/pbdPROF-guide.Rnw | 26 ++-- 56 files changed, 155 insertions(+), 149 deletions(-)
Title: '--omics' Data Analysis Toolbox
Description: A collection of functions to analyse '--omics' datasets such as DNA
methylation and gene expression profiles.
Author: Gianluca Campanella [aut, cre]
Maintainer: Gianluca Campanella <gianluca@campanella.org>
Diff between omics versions 0.1-1 dated 2015-12-05 and 0.1-2 dated 2016-01-25
DESCRIPTION | 9 +++++---- MD5 | 10 ++++++---- R/mlm.R | 16 +++++++++------- R/mlmer.R | 32 ++++++++++++++++++++------------ inst/NEWS.Rd | 6 ++++++ tests |only 6 files changed, 46 insertions(+), 27 deletions(-)
Title: Multi-Resolution Scanning for Cross-Sample Differences
Description: An implementation of the MRS algorithm for comparison across distributions.
The model is based on a nonparametric process taking the form of a Markov model
that transitions between a "null" and an "alternative" state
on a multi-resolution partition tree of the sample space.
MRS effectively detects and characterizes a variety of underlying differences.
These differences can be visualized using several plotting functions.
Author: Jacopo Soriano and Li Ma
Maintainer: Jacopo Soriano <jsoriano.stat@gmail.com>
Diff between MRS versions 1.0 dated 2015-12-07 and 1.1 dated 2016-01-25
MRS-1.0/MRS/man/MRS-package.Rd |only MRS-1.1/MRS/DESCRIPTION | 10 +++++----- MRS-1.1/MRS/MD5 | 11 +++++------ MRS-1.1/MRS/R/RcppExports.R | 4 ++++ MRS-1.1/MRS/R/mrs.R | 11 +++++++---- MRS-1.1/MRS/src/RcppExports.cpp | 1 + MRS-1.1/MRS/src/helpers.cpp | 18 ++++++++++++------ 7 files changed, 34 insertions(+), 21 deletions(-)
Title: Miscellaneous Tools Set
Description: A collection of miscellaneous methods to simplify various tasks,
including plotting, data.frame and matrix transformations, environment
functions, regular expression methods, and string and logical operations, as
well as numerical and statistical tools. Most of the methods are simple but
useful wrappers of common base R functions, which extend S3 generics or
provide default values for important parameters.
Author: Sven E. Templer
Maintainer: Sven E. Templer <sven.templer@gmail.com>
Diff between miscset versions 0.4 dated 2014-09-04 and 1.0.0 dated 2016-01-25
miscset-0.4/miscset/R/gapply.R |only miscset-0.4/miscset/R/ggplotlist.R |only miscset-0.4/miscset/inst/doc/miscset.Rnw |only miscset-0.4/miscset/inst/doc/miscset.pdf |only miscset-0.4/miscset/man/gapply.Rd |only miscset-0.4/miscset/man/ggplotlist.Rd |only miscset-0.4/miscset/vignettes/figure |only miscset-0.4/miscset/vignettes/framed.sty |only miscset-0.4/miscset/vignettes/miscset.Rnw |only miscset-1.0.0/miscset/DESCRIPTION | 22 ++- miscset-1.0.0/miscset/MD5 | 114 +++++++++-------- miscset-1.0.0/miscset/NAMESPACE | 61 +++++++-- miscset-1.0.0/miscset/NEWS | 62 ++++++++- miscset-1.0.0/miscset/R/RcppExports.R | 8 + miscset-1.0.0/miscset/R/aaa.R | 39 +++-- miscset-1.0.0/miscset/R/ciplot.R |only miscset-1.0.0/miscset/R/confint.R |only miscset-1.0.0/miscset/R/do.rbind.r |only miscset-1.0.0/miscset/R/duplicates.r |only miscset-1.0.0/miscset/R/enpaire.R | 26 +-- miscset-1.0.0/miscset/R/factorNA.r |only miscset-1.0.0/miscset/R/gghcl.R | 15 +- miscset-1.0.0/miscset/R/ggplotGrid.R |only miscset-1.0.0/miscset/R/gregexprind.R | 23 +-- miscset-1.0.0/miscset/R/help.index.R |only miscset-1.0.0/miscset/R/leading0.R | 11 - miscset-1.0.0/miscset/R/lload.R | 11 - miscset-1.0.0/miscset/R/lsall.R | 11 - miscset-1.0.0/miscset/R/mgrepl.R | 64 ++------- miscset-1.0.0/miscset/R/nunique.r |only miscset-1.0.0/miscset/R/p2star.R |only miscset-1.0.0/miscset/R/plotn.R |only miscset-1.0.0/miscset/R/rmall.R | 11 - miscset-1.0.0/miscset/R/scale0.R | 39 ++++- miscset-1.0.0/miscset/R/sort.data.frame.r |only miscset-1.0.0/miscset/R/squarematrix.R | 11 - miscset-1.0.0/miscset/R/strextr.R | 11 - miscset-1.0.0/miscset/R/strpart.R | 11 - miscset-1.0.0/miscset/R/strrev.R | 11 - miscset-1.0.0/miscset/R/textable.R | 157 +++++++++++++++++------- miscset-1.0.0/miscset/README.md | 77 +++++------ miscset-1.0.0/miscset/build/vignette.rds |binary miscset-1.0.0/miscset/inst/doc/miscset.R | 176 ++++++++++++++------------- miscset-1.0.0/miscset/inst/doc/miscset.Rmd |only miscset-1.0.0/miscset/inst/doc/miscset.html |only miscset-1.0.0/miscset/man/ciplot.Rd |only miscset-1.0.0/miscset/man/confint.Rd |only miscset-1.0.0/miscset/man/do.rbind.Rd |only miscset-1.0.0/miscset/man/duplicates.Rd |only miscset-1.0.0/miscset/man/enpaire.Rd | 5 miscset-1.0.0/miscset/man/factorNA.Rd |only miscset-1.0.0/miscset/man/gghcl.Rd | 5 miscset-1.0.0/miscset/man/ggplotGrid.Rd |only miscset-1.0.0/miscset/man/gregexprind.Rd | 20 +-- miscset-1.0.0/miscset/man/help.index.Rd |only miscset-1.0.0/miscset/man/leading0.Rd | 7 - miscset-1.0.0/miscset/man/lload.Rd | 8 - miscset-1.0.0/miscset/man/lsall.Rd | 5 miscset-1.0.0/miscset/man/mgrepl.Rd | 41 ++---- miscset-1.0.0/miscset/man/miscset-package.Rd | 17 +- miscset-1.0.0/miscset/man/ntri.Rd | 6 miscset-1.0.0/miscset/man/nunique.Rd |only miscset-1.0.0/miscset/man/p2star.Rd |only miscset-1.0.0/miscset/man/plotn.Rd |only miscset-1.0.0/miscset/man/rmall.Rd | 5 miscset-1.0.0/miscset/man/scale0.Rd | 23 ++- miscset-1.0.0/miscset/man/sort.Rd |only miscset-1.0.0/miscset/man/squarematrix.Rd | 5 miscset-1.0.0/miscset/man/strextr.Rd | 5 miscset-1.0.0/miscset/man/strpart.Rd | 5 miscset-1.0.0/miscset/man/strrev.Rd | 5 miscset-1.0.0/miscset/man/textable.Rd | 68 +++++++--- miscset-1.0.0/miscset/src/RcppExports.cpp | 14 -- miscset-1.0.0/miscset/src/ntri.cpp | 8 + miscset-1.0.0/miscset/vignettes/miscset.Rmd |only 75 files changed, 740 insertions(+), 483 deletions(-)
Title: 2D and 3D Hive Plots for R
Description: Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Author: Bryan A. Hanson [aut, cre],
Vesna Memisevic [ctb],
Jonathan Chung [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between HiveR versions 0.2.44 dated 2015-07-27 and 0.2.46 dated 2016-01-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 7 +++++-- R/chkHPD.R | 2 ++ inst/doc/HiveR.pdf |binary 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Chi-Square and Exact Tests for Non-Parametric Functional
Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on asymptotic chi-square and exact statistics. These tests were designed to reveal evidence for causality based on functional dependencies. They include asymptotic functional chi-square tests, an exact functional test, a comparative functional chi-square test, and also a comparative chi-square test. The normalized non-constant functional chi-square test was used by the Best Performer NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.2.0 dated 2016-01-24 and 2.2.1 dated 2016-01-25
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 7 +++++++ R/FunChisq.R | 2 +- man/FunChisq-package.Rd | 16 +++++++++++----- man/cp.chisq.test.Rd | 6 ++++-- man/cp.fun.chisq.test.Rd | 6 +++--- 7 files changed, 37 insertions(+), 22 deletions(-)
Title: Object-Oriented Implementation of CRM Designs
Description: Implements a wide range of model-based dose
escalation designs, ranging from classical and modern continual
reassessment methods (CRMs) based on dose-limiting toxicity endpoints to
dual-endpoint designs taking into account a biomarker/efficacy outcome. The
focus is on Bayesian inference, making it very easy to setup a new design
with its own JAGS code. However, it is also possible to implement 3+3
designs for comparison or models with non-Bayesian estimation. The whole
package is written in a modular form in the S4 class system, making it very
flexible for adaptation to new models, escalation or stopping rules.
Author: Daniel Sabanes Bove <sabanesd@roche.com>,
Wai Yin Yeung <w.yeung1@lancaster.ac.uk>,
Giuseppe Palermo <giuseppe.palermo@roche.com>,
Thomas Jaki <jaki.thomas@gmail.com>
Maintainer: Daniel Sabanes Bove <sabanesd@roche.com>
Diff between crmPack versions 0.1.6 dated 2015-12-22 and 0.1.7 dated 2016-01-25
DESCRIPTION | 6 - MD5 | 54 ++++++++-------- R/Rules-methods.R | 2 inst/doc/example.R | 4 - inst/doc/example.Rnw | 6 - inst/doc/example.pdf |binary man/DualResponsesDesign-class.Rd | 2 man/DualResponsesSamplesDesign-class.Rd | 2 man/Effloglog-class.Rd | 4 - man/ExpEff.Rd | 2 man/fit.Rd | 2 man/fitGain.Rd | 2 man/gain.Rd | 4 - man/mcmc.Rd | 2 man/nextBest.Rd | 4 - man/plot-DataDual-ModelEff-method.Rd | 2 man/plot-PseudoDualSimulations-missing-method.Rd | 2 man/plot-PseudoDualSimulationsSummary-missing-method.Rd | 2 man/plot-Samples-ModelEff-method.Rd | 2 man/plotDualResponses.Rd | 4 - man/plotGain.Rd | 4 - man/show-PseudoDualSimulationsSummary-method.Rd | 2 man/simulate-DualResponsesDesign-method.Rd | 2 man/simulate-DualResponsesSamplesDesign-method.Rd | 2 man/stopTrial.Rd | 4 - man/summary-PseudoDualSimulations-method.Rd | 2 man/update-Effloglog-method.Rd | 2 vignettes/example.Rnw | 6 - 28 files changed, 66 insertions(+), 66 deletions(-)
Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++. For customizations or interest in other statistical methodologies for web data analysis please contact <davide.altomare@gmail.com>.
Author: Davide Altomare
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between ChannelAttribution versions 1.4 dated 2016-01-08 and 1.5 dated 2016-01-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/ChannelAttribution-package.Rd | 4 ++-- src/ChannelAttribution.cpp | 4 +++- 4 files changed, 11 insertions(+), 9 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
More information about activpalProcessing at CRAN
Permanent link
Title: Turner Miscellaneous
Description: Miscellaneous data and utility functions
for manipulating data and your R environment.
Author: Stephen Turner <vustephen@gmail.com>
Maintainer: Stephen Turner <vustephen@gmail.com>
Diff between Tmisc versions 0.1.2 dated 2015-11-14 and 0.1.4 dated 2016-01-25
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++++----- NAMESPACE | 5 +++++ R/deseqresult2tbl.R | 2 +- R/lmp.R |only R/lowestnonzero.R |only R/read.cb.R | 14 +++++++++----- R/strSort.R |only man/lmp.Rd |only man/lowestnonzero.Rd |only man/read.cb.Rd | 6 ++++-- man/strSort.Rd |only 12 files changed, 34 insertions(+), 17 deletions(-)
Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape,
precision, and accuracy. This includes graphical methods,
descriptive statistics, and inference tests using standard,
but also non-parametric and robust statistical methods.
Implements distributions for radial error in bivariate normal
variables. Works with files exported by OnTarget PC/TDS or
Taran, as well as with custom data files in text format.
Supports inference from range statistics like extreme spread.
Includes a set of web-based graphical user interfaces.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>
Diff between shotGroups versions 0.6.2 dated 2015-11-12 and 0.7 dated 2016-01-25
shotGroups-0.6.2/shotGroups/man/getMaxParam.Rd |only shotGroups-0.7/shotGroups/DESCRIPTION | 16 shotGroups-0.7/shotGroups/MD5 | 138 +++-- shotGroups-0.7/shotGroups/NAMESPACE | 11 shotGroups-0.7/shotGroups/R/CEPs.R |only shotGroups-0.7/shotGroups/R/analyzeGroup.R | 5 shotGroups-0.7/shotGroups/R/combineData.R | 12 shotGroups-0.7/shotGroups/R/compareGroups.R | 82 +-- shotGroups-0.7/shotGroups/R/draw.R | 54 +- shotGroups-0.7/shotGroups/R/drawGroup.R | 25 shotGroups-0.7/shotGroups/R/efficiency.R |only shotGroups-0.7/shotGroups/R/getBoundingBox.R | 2 shotGroups-0.7/shotGroups/R/getCEP.R | 328 +++---------- shotGroups-0.7/shotGroups/R/getConfEll.R | 16 shotGroups-0.7/shotGroups/R/getHitProb.R | 130 +++-- shotGroups-0.7/shotGroups/R/getMOA.R | 106 ++-- shotGroups-0.7/shotGroups/R/getMaxPairDist.R | 10 shotGroups-0.7/shotGroups/R/getMinBBox.R | 4 shotGroups-0.7/shotGroups/R/getMinCircle.R | 18 shotGroups-0.7/shotGroups/R/groupLocation.R | 14 shotGroups-0.7/shotGroups/R/groupShape.R | 62 +- shotGroups-0.7/shotGroups/R/groupSpread.R | 22 shotGroups-0.7/shotGroups/R/grubbs.R | 64 ++ shotGroups-0.7/shotGroups/R/hoyt.R | 22 shotGroups-0.7/shotGroups/R/maxwell.R | 88 --- shotGroups-0.7/shotGroups/R/mvnEll.R | 12 shotGroups-0.7/shotGroups/R/range2sigma.R |only shotGroups-0.7/shotGroups/R/rayleigh.R | 52 +- shotGroups-0.7/shotGroups/R/readData.R | 14 shotGroups-0.7/shotGroups/R/rice.R | 23 shotGroups-0.7/shotGroups/R/runGUI.R |only shotGroups-0.7/shotGroups/R/simRingCount.R | 2 shotGroups-0.7/shotGroups/build/vignette.rds |binary shotGroups-0.7/shotGroups/data/DF300BLK.rda |binary shotGroups-0.7/shotGroups/data/DF300BLKhl.rda |binary shotGroups-0.7/shotGroups/data/DFcciHV.rda |binary shotGroups-0.7/shotGroups/data/DFcm.rda |binary shotGroups-0.7/shotGroups/data/DFdistr.rda |only shotGroups-0.7/shotGroups/data/DFinch.rda |binary shotGroups-0.7/shotGroups/data/DFlistCm.rda |binary shotGroups-0.7/shotGroups/data/DFsavage.rda |binary shotGroups-0.7/shotGroups/data/DFscar17.rda |binary shotGroups-0.7/shotGroups/data/DFtalon.rda |binary shotGroups-0.7/shotGroups/data/targets.rda |binary shotGroups-0.7/shotGroups/inst/ChangeLog | 58 ++ shotGroups-0.7/shotGroups/inst/doc/shotGroups.R | 34 + shotGroups-0.7/shotGroups/inst/doc/shotGroups.Rnw | 210 ++++++-- shotGroups-0.7/shotGroups/inst/doc/shotGroups.pdf |binary shotGroups-0.7/shotGroups/inst/shinyAnalyzeGroups |only shotGroups-0.7/shotGroups/inst/shinyAngularSize |only shotGroups-0.7/shotGroups/inst/shinyHitProbability |only shotGroups-0.7/shotGroups/inst/shinyRangeStatistics |only shotGroups-0.7/shotGroups/man/DFdistr.Rd |only shotGroups-0.7/shotGroups/man/compareGroups.Rd | 2 shotGroups-0.7/shotGroups/man/efficiency.Rd |only shotGroups-0.7/shotGroups/man/fromMOA.Rd | 13 shotGroups-0.7/shotGroups/man/getCEP.Rd | 31 - shotGroups-0.7/shotGroups/man/getDistance.Rd | 5 shotGroups-0.7/shotGroups/man/getHitProb.Rd | 15 shotGroups-0.7/shotGroups/man/getMOA.Rd | 15 shotGroups-0.7/shotGroups/man/getRayParam.Rd | 7 shotGroups-0.7/shotGroups/man/groupLocation.Rd | 2 shotGroups-0.7/shotGroups/man/groupShape.Rd | 10 shotGroups-0.7/shotGroups/man/groupSpread.Rd | 2 shotGroups-0.7/shotGroups/man/maxwell.Rd | 4 shotGroups-0.7/shotGroups/man/range2sigma.Rd |only shotGroups-0.7/shotGroups/man/runGUI.Rd |only shotGroups-0.7/shotGroups/man/shotGroups-package.Rd | 9 shotGroups-0.7/shotGroups/vignettes/distributions.pdf |binary shotGroups-0.7/shotGroups/vignettes/lit.bib | 138 +++++ shotGroups-0.7/shotGroups/vignettes/normal_cep_bias.png |only shotGroups-0.7/shotGroups/vignettes/normal_cep_no_bias.png |only shotGroups-0.7/shotGroups/vignettes/shotGroups.Rnw | 210 ++++++-- 73 files changed, 1262 insertions(+), 835 deletions(-)
Title: Blinder-Oaxaca Decomposition
Description: An implementation of the Blinder-Oaxaca decomposition for linear regression models.
Author: Marek Hlavac <hlavac@fas.harvard.edu>
Maintainer: Marek Hlavac <hlavac@fas.harvard.edu>
Diff between oaxaca versions 0.1.2 dated 2015-02-18 and 0.1.3 dated 2016-01-25
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ R/oaxaca-internal.R | 10 +++++----- build/vignette.rds |binary inst/CITATION | 6 +++--- inst/ChangeLog | 10 ++++++++-- inst/doc/oaxaca.pdf |binary man/oaxaca.Rd | 4 ++-- man/plot.oaxaca.Rd | 4 ++-- 10 files changed, 36 insertions(+), 28 deletions(-)
Title: Non-Parametric Measures of Actigraphy Data
Description: Computes interday stability (IS), intraday variability (IV) & the relative amplitude (RA) from actigraphy data as described in van Someren et al. (1999). Additionally, it also computes L5 (i.e. the 5 hours with lowest average actigraphy amplitude) and M10 (the 10 hours with highest average amplitude) as well as the respective start times. The flex versions will also compute the L-value for a user-defined number of minutes. IS describes the strength of coupling of a rhythm to supposedly stable zeitgebers. It varies between 0 (Gaussian Noise) and 1 for perfect IS. IV describes the fragmentation of a rhythm, i.e. the frequency and extent of transitions between rest and activity. It is near 0 for a perfect sine wave, about 2 for Gaussian noise and may be even higher when a definite ultradian period of about 2 hrs is present. RA is the relative amplitude of a rhythm. Note that to obtain reliable results, actigraphy data should cover a reasonable number of days.
Author: Christine Blume <christine.blume@sbg.ac.at>
Nayantara Santhi <n.santhi@surrey.ac.uk>
Manuel Schabus <manuel.schabus@sbg.ac.at>
Maintainer: Christine Blume <christine.blume@sbg.ac.at>
Diff between nparACT versions 0.2 dated 2016-01-11 and 0.3 dated 2016-01-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/nparACT_auxfunctions1.R | 10 ++++++---- R/nparACT_auxfunctions2.R | 20 +++++++++++++------- R/nparACT_base.R | 6 +++--- R/nparACT_base_loop.R | 6 +++--- R/nparACT_flex.R | 6 +++--- R/nparACT_flex_loop.R | 6 +++--- 8 files changed, 42 insertions(+), 34 deletions(-)
Title: Implementation of the DetMCD Algorithm (Robust and Deterministic
Estimation of Location and Scatter)
Description: Implementation of DetMCD, a new algorithm for robust and deterministic estimation of location and scatter. The benefits of robust and deterministic estimation are explained in Hubert, M., Rousseeuw, P.J. and Verdonck, T. (2012),"A deterministic algorithm for robust location and scatter", Journal of Computational and Graphical Statistics, Volume 21, Number 3, Pages 618--637.
Author: Vakili Kaveh [aut, cre],
Mia Hubert [ths]
Maintainer: Vakili Kaveh <vakili.kaveh.email@gmail.com>
Diff between DetMCD versions 0.0.2 dated 2015-02-03 and 0.0.3 dated 2016-01-25
DESCRIPTION | 14 +-- MD5 | 14 +-- NAMESPACE | 6 + R/DetMCD.R | 134 ++++++++++++++++++----------- man/DetMCD.Rd | 27 +++++ man/InQn.Rd |only src/DetMCD_1.cpp | 253 ++++++++++++++++++++++++++++++++++++------------------- src/DetMCD_2.cpp | 27 +++++ src/DetMCD_3.cpp |only 9 files changed, 319 insertions(+), 156 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Ilya Shpitser and Judea Pearl, and algorithms for z-identifiability, transportability, z-transportability and meta-transportability of causal effects by Elias Bareinboim and Judea Pearl. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Jin Tian.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.2.0 dated 2015-08-03 and 1.2.2 dated 2016-01-25
causaleffect-1.2.0/causaleffect/R/organizeTerms.R |only causaleffect-1.2.2/causaleffect/DESCRIPTION | 10 - causaleffect-1.2.2/causaleffect/MD5 | 111 +++++++++++-- causaleffect-1.2.2/causaleffect/NAMESPACE | 2 causaleffect-1.2.2/causaleffect/NEWS | 6 causaleffect-1.2.2/causaleffect/R/causal.effect.R | 21 ++ causaleffect-1.2.2/causaleffect/R/deconstruct.R |only causaleffect-1.2.2/causaleffect/R/factorize.R |only causaleffect-1.2.2/causaleffect/R/gather.R |only causaleffect-1.2.2/causaleffect/R/get.expression.R | 2 causaleffect-1.2.2/causaleffect/R/join.R |only causaleffect-1.2.2/causaleffect/R/meta.transport.R | 2 causaleffect-1.2.2/causaleffect/R/organize.terms.R |only causaleffect-1.2.2/causaleffect/R/parse.deconstruct.R |only causaleffect-1.2.2/causaleffect/R/parse.expression.R | 66 ++++--- causaleffect-1.2.2/causaleffect/R/parse.graphml.internal.R | 6 causaleffect-1.2.2/causaleffect/R/parse.graphml.standard.R | 6 causaleffect-1.2.2/causaleffect/R/parse.joint.R | 20 -- causaleffect-1.2.2/causaleffect/R/perm.R |only causaleffect-1.2.2/causaleffect/R/probability.R | 2 causaleffect-1.2.2/causaleffect/R/simplify.R |only causaleffect-1.2.2/causaleffect/R/transport.R | 2 causaleffect-1.2.2/causaleffect/R/wrap.dSep.R |only causaleffect-1.2.2/causaleffect/R/zzaux.effect.R | 2 causaleffect-1.2.2/causaleffect/build |only causaleffect-1.2.2/causaleffect/inst |only causaleffect-1.2.2/causaleffect/vignettes |only 27 files changed, 178 insertions(+), 80 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a Bayesian model in the form of MCMC simulations. Given suitable variables of cost and effectiveness / utility for two or more interventions, This package computes the most cost-effective alternative and produces graphical summaries and probabilistic sensitivity analysis.
Author: Gianluca Baio, Andrea Berardi, Anna Heath
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between BCEA versions 2.1-1 dated 2015-05-06 and 2.2-2 dated 2016-01-25
DESCRIPTION | 13 MD5 | 19 NAMESPACE | 6 R/bcea.R | 6788 +++++++++++++++++++++++++++++----------------------- data/Smoking.RData |binary data/Vaccine.RData |binary man/BCEA-package.Rd | 4 man/Smoking.Rd | 2 man/Vaccine.Rd | 2 man/evppi.Rd | 80 man/info.rank.Rd |only 11 files changed, 4003 insertions(+), 2911 deletions(-)
Title: Helps Manage Outliers in Sample Surveys
Description: At present, the only functionality is the calculation of optimal one-sided winsorizing cutoffs. The main function is optimal.onesided.cutoff.bygroup. It calculates the optimal tuning parameter for one-sided winsorisation, and so calculates winsorised values for a variable of interest. See the help file for this function for more details and an example.
Author: Robert Clark
Maintainer: "Robert Clark" <rclark@uow.edu.au>
Diff between surveyoutliers versions 0.0 dated 2015-12-21 and 0.1 dated 2016-01-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/optimal.onesided.cutoff.R | 11 +++++++---- R/robust.lm.onesided.R | 9 +++++---- 4 files changed, 19 insertions(+), 15 deletions(-)
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Title: A GUI to View, Design and Export Various Graphs of Data
Description: Provides a graphical user interface for viewing and designing various types of graphs of the data. The graphs can be saved in different formats of an image.
Author: Dhammapal Bharne, Vaibhav Vindal
Maintainer: Dhammapal Bharne <dhammapalb@uohyd.ac.in>
Diff between plfMA versions 1.0.1 dated 2015-08-27 and 1.0.2 dated 2016-01-25
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/plfMA.R | 2 ++ man/plfMA-package.Rd |only man/plfMA.Rd | 33 +++++++++++++++++++++++---------- 5 files changed, 33 insertions(+), 17 deletions(-)
Title: Tools for Management of Survey Data and the Presentation of
Analysis Results
Description: One of the aims of this package is to make life easier for
useRs who deal with survey data sets. It provides an
infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) SPSS and
Stata files. Further, it provides functionality to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates, which can be exported to LaTeX and HTML.
Author: Martin Elff (with contributions from Christopher N. Lawrence, Dave Atkins, Jason W. Morgan, Achim Zeileis)
Maintainer: Martin Elff <memisc@elff.eu>
Diff between memisc versions 0.99.3 dated 2016-01-17 and 0.99.3.2 dated 2016-01-25
DESCRIPTION | 8 ++-- MD5 | 24 ++++++------ R/codebook-format-html.R | 12 +++--- build/vignette.rds |binary inst/ChangeLog | 6 +++ inst/NEWS.Rd | 1 inst/NEWS.html | 14 ++++++- inst/doc/anes48.html | 86 ++++++++++++++++++++++++++++++++++++-------- inst/doc/ftable-matrix.Rmd | 2 - inst/doc/items.Rmd | 2 - inst/doc/items.html | 54 ++++++++++++++++++++++----- vignettes/ftable-matrix.Rmd | 2 - vignettes/items.Rmd | 2 - 13 files changed, 161 insertions(+), 52 deletions(-)
Title: Ensemble Forecast Verification for Large Data Sets
Description: Set of tools to simplify application of atomic forecast verification
metrics for (comparative) verification of ensemble forecasts to large data sets.
The forecast metrics are imported from the 'SpecsVerification' package, and
additional forecast metrics are provided with this package. Alternatively,
new user-defined forecast scores can be implemented using the example scores
provided and applied using the functionality of this package.
Author: Jonas Bhend [aut, cre],
Jacopo Ripoldi [ctb],
Claudia Mignani [ctb],
Irina Mahlstein [ctb],
Rebecca Hiller [ctb],
Christoph Spirig [ctb],
Mark Liniger [ctb],
Andreas Weigel [ctb],
Joaqu'in Bedia Jimenez [ctb],
Matteo De Felice [ctb]
Maintainer: Jonas Bhend <jonas.bhend@meteoswiss.ch>
Diff between easyVerification versions 0.1.8 dated 2015-10-15 and 0.2.0 dated 2016-01-25
easyVerification-0.1.8/easyVerification/vignettes/ecoms_forecast_verification.pdf |only easyVerification-0.2.0/easyVerification/DESCRIPTION | 17 +- easyVerification-0.2.0/easyVerification/MD5 | 76 +++++----- easyVerification-0.2.0/easyVerification/NAMESPACE | 4 easyVerification-0.2.0/easyVerification/R/Ens2AFC.R | 34 ++-- easyVerification-0.2.0/easyVerification/R/EnsCorr.R | 13 - easyVerification-0.2.0/easyVerification/R/EnsError.R | 26 +-- easyVerification-0.2.0/easyVerification/R/EnsErrorss.R | 27 +-- easyVerification-0.2.0/easyVerification/R/EnsIgn.R |only easyVerification-0.2.0/easyVerification/R/EnsRoca.R | 23 ++- easyVerification-0.2.0/easyVerification/R/EnsRocss.R | 6 easyVerification-0.2.0/easyVerification/R/EnsSprErr.R | 24 +-- easyVerification-0.2.0/easyVerification/R/FairSprErr.R | 16 +- easyVerification-0.2.0/easyVerification/R/RcppExports.R |only easyVerification-0.2.0/easyVerification/R/convert2prob.R | 67 +++++--- easyVerification-0.2.0/easyVerification/R/count2prob.R | 6 easyVerification-0.2.0/easyVerification/R/easyVerification.R | 2 easyVerification-0.2.0/easyVerification/R/toymodel.R | 6 easyVerification-0.2.0/easyVerification/R/veriApply.R | 23 ++- easyVerification-0.2.0/easyVerification/R/veriUnwrap.R | 24 +-- easyVerification-0.2.0/easyVerification/R/zzz.R | 4 easyVerification-0.2.0/easyVerification/README.md | 14 + easyVerification-0.2.0/easyVerification/build/vignette.rds |binary easyVerification-0.2.0/easyVerification/inst/doc/ecoms_forecast_verification.pdf.asis |only easyVerification-0.2.0/easyVerification/man/Ens2AFC.Rd | 16 +- easyVerification-0.2.0/easyVerification/man/EnsCorr.Rd | 5 easyVerification-0.2.0/easyVerification/man/EnsError.Rd | 12 - easyVerification-0.2.0/easyVerification/man/EnsErrorss.Rd | 13 + easyVerification-0.2.0/easyVerification/man/EnsIgn.Rd |only easyVerification-0.2.0/easyVerification/man/EnsRoca.Rd | 2 easyVerification-0.2.0/easyVerification/man/EnsRocss.Rd | 2 easyVerification-0.2.0/easyVerification/man/EnsSprErr.Rd | 15 - easyVerification-0.2.0/easyVerification/man/FairSprErr.Rd | 10 - easyVerification-0.2.0/easyVerification/man/convert2prob.Rd | 37 +++- easyVerification-0.2.0/easyVerification/man/count2prob.Rd | 2 easyVerification-0.2.0/easyVerification/man/toymodel.Rd | 2 easyVerification-0.2.0/easyVerification/man/veriApply.Rd | 18 ++ easyVerification-0.2.0/easyVerification/man/veriUnwrap.Rd | 6 easyVerification-0.2.0/easyVerification/src |only easyVerification-0.2.0/easyVerification/vignettes/easyVerification.Rmd | 59 +++++-- easyVerification-0.2.0/easyVerification/vignettes/ecoms_forecast_verification.pdf.asis | 2 41 files changed, 371 insertions(+), 242 deletions(-)
More information about easyVerification at CRAN
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More information about VertexSimilarity at CRAN
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Title: Functions for Generating Restricted Permutations of Data
Description: A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.
Author: Gavin L. Simpson [aut, cph, cre],
R Core Team [cph],
Douglas M. Bates [ctb],
Jari Oksanen [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between permute versions 0.8-4 dated 2015-05-19 and 0.9-0 dated 2016-01-24
permute-0.8-4/permute/R/permCheck.R |only permute-0.8-4/permute/R/permuplot.R |only permute-0.8-4/permute/R/permute-deprecated.R |only permute-0.8-4/permute/R/shuffle2.R |only permute-0.8-4/permute/R/shuffleSet2.R |only permute-0.8-4/permute/inst/NEWS.Rd |only permute-0.8-4/permute/man/permCheck-deprecated.Rd |only permute-0.8-4/permute/man/permControl-deprecated.Rd |only permute-0.8-4/permute/man/permute-deprecated.Rd |only permute-0.8-4/permute/tests/test-all.R |only permute-0.9-0/permute/DESCRIPTION | 9 permute-0.9-0/permute/MD5 | 84 ++-- permute-0.9-0/permute/NAMESPACE | 37 -- permute-0.9-0/permute/R/allPerms.R | 14 permute-0.9-0/permute/R/allStrata.R | 10 permute-0.9-0/permute/R/as.matrix.allPerms.R |only permute-0.9-0/permute/R/blocks.R | 13 permute-0.9-0/permute/R/check.R | 27 + permute-0.9-0/permute/R/fixupCall.R | 10 permute-0.9-0/permute/R/getFoo-methods.R | 129 ------- permute-0.9-0/permute/R/how.R | 6 permute-0.9-0/permute/R/nobs-methods.R | 3 permute-0.9-0/permute/R/numPerms.R | 20 - permute-0.9-0/permute/R/permute.R | 15 permute-0.9-0/permute/R/print.how.R | 2 permute-0.9-0/permute/R/print.permutationMatrix.R | 5 permute-0.9-0/permute/R/setFoo-methods.R | 82 ---- permute-0.9-0/permute/R/shuffle-utils.R | 5 permute-0.9-0/permute/R/shuffle.R | 146 +++++-- permute-0.9-0/permute/R/shuffleSet.R | 216 ++++++++--- permute-0.9-0/permute/README.md | 2 permute-0.9-0/permute/build/vignette.rds |binary permute-0.9-0/permute/inst/ChangeLog | 41 ++ permute-0.9-0/permute/inst/NEWS |only permute-0.9-0/permute/inst/doc/permutations.pdf |binary permute-0.9-0/permute/man/allPerms.Rd | 10 permute-0.9-0/permute/man/check.Rd | 10 permute-0.9-0/permute/man/how.Rd | 10 permute-0.9-0/permute/man/shuffleSet.Rd | 20 + permute-0.9-0/permute/tests/Examples/permute-Ex.Rout.save | 258 +++++--------- permute-0.9-0/permute/tests/testthat.R |only permute-0.9-0/permute/tests/testthat/test-allPerms.R | 162 ++++++++ permute-0.9-0/permute/tests/testthat/test-as-methods.R |only permute-0.9-0/permute/tests/testthat/test-blocks.R |only permute-0.9-0/permute/tests/testthat/test-check.R | 11 permute-0.9-0/permute/tests/testthat/test-get-methods.R |only permute-0.9-0/permute/tests/testthat/test-how.R |only permute-0.9-0/permute/tests/testthat/test-nobs.R |only permute-0.9-0/permute/tests/testthat/test-numPerms.R |only permute-0.9-0/permute/tests/testthat/test-permute-fun.R |only permute-0.9-0/permute/tests/testthat/test-set-methods.R |only permute-0.9-0/permute/tests/testthat/test-shuffle-utils.R |only permute-0.9-0/permute/tests/testthat/test-shuffle.R | 10 permute-0.9-0/permute/tests/testthat/test-shuffleSet.R | 43 ++ 54 files changed, 837 insertions(+), 573 deletions(-)
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Title: Codon Usage Bias Fits
Description: Estimating mutation and selection coefficients on synonymous
codon bias usage based on models of ribosome overhead cost (ROC).
Multinomial logistic regression and Markov Chain Monte Carlo are used to
estimate and predict protein production rates with/without the presence
of expressions and measurement errors. Work flows with examples for
simulation, estimation and prediction processes are also provided
with parallelization speedup. The whole framework is tested with
yeast genome and gene expression data of Yassour (2009).
Author: Wei-Chen Chen [aut, cre],
Russell Zaretzki [aut],
William Howell [aut],
Cedric Landerer [aut],
Drew Schmidt [aut],
Michael A. Gilchrist [aut],
Preston Hewgley [ctb],
Students REU13 [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between cubfits versions 0.1-0 dated 2014-05-19 and 0.1-2 dated 2016-01-24
cubfits-0.1-0/cubfits/R/my.pPropType.lognormal_MH.r |only cubfits-0.1-0/cubfits/R/my.pPropTypeNoObs.lognormal_MH.r |only cubfits-0.1-0/cubfits/R/my.pPropTypeNoObs_MH.r |only cubfits-0.1-0/cubfits/R/my.proposeBeta.r |only cubfits-0.1-0/cubfits/data/bInit.rda |only cubfits-0.1-0/cubfits/demo/nsef.appr.r |only cubfits-0.1-0/cubfits/demo/nsef.pred.r |only cubfits-0.1-0/cubfits/demo/nsef.simu.r |only cubfits-0.1-0/cubfits/demo/nsef.train.r |only cubfits-0.1-0/cubfits/demo/rocnsef.appr.r |only cubfits-0.1-0/cubfits/demo/rocnsef.pred.r |only cubfits-0.1-0/cubfits/demo/rocnsef.train.r |only cubfits-0.1-0/cubfits/inst/workflow/nsef |only cubfits-0.1-0/cubfits/inst/workflow/roc/02_plots.txt |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wophi_pm-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wophi_scuo-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wphi_pm-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wphi_scuo-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wphi_wophi_pm-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wphi_wophi_scuo-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/05-subset_tsv.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/s4-ad_wophi_true-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/s4-ad_wphi_true-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code_plot_nps |only cubfits-0.1-0/cubfits/inst/workflow/roc/script/simu_run_2_nps.sh |only cubfits-0.1-0/cubfits/inst/workflow/roc/script/wophi_run_2_nps.sh |only cubfits-0.1-0/cubfits/inst/workflow/roc/script/wphi_run_2_nps.sh |only cubfits-0.1-0/cubfits/inst/workflow/roc/script/wphi_wophi_run_2_nps.sh |only cubfits-0.1-0/cubfits/vignettes/cubfits-include/06-misc.tex |only cubfits-0.1-0/cubfits/vignettes/cubfits-include/jss.bst |only cubfits-0.1-0/cubfits/vignettes/cubfits-include/jss.cls |only cubfits-0.1-2/cubfits/ChangeLog | 25 cubfits-0.1-2/cubfits/DESCRIPTION | 23 cubfits-0.1-2/cubfits/INSTALL | 4 cubfits-0.1-2/cubfits/MD5 | 468 ++++------ cubfits-0.1-2/cubfits/NAMESPACE | 20 cubfits-0.1-2/cubfits/R/000_globalVariables.r |only cubfits-0.1-2/cubfits/R/cedric.convergence.r |only cubfits-0.1-2/cubfits/R/cedric.io.r |only cubfits-0.1-2/cubfits/R/cedric.mapBMatNames.r |only cubfits-0.1-2/cubfits/R/cedric.plotting.r |only cubfits-0.1-2/cubfits/R/data.codon.convert.r | 5 cubfits-0.1-2/cubfits/R/data.convert.r | 14 cubfits-0.1-2/cubfits/R/data.io.r | 2 cubfits-0.1-2/cubfits/R/logan.plotting.r |only cubfits-0.1-2/cubfits/R/my.acceptance.r | 61 - cubfits-0.1-2/cubfits/R/my.adaptive.DrawScale.r | 105 +- cubfits-0.1-2/cubfits/R/my.adaptive.r | 46 cubfits-0.1-2/cubfits/R/my.check.data.r |only cubfits-0.1-2/cubfits/R/my.check.rearrange.r | 14 cubfits-0.1-2/cubfits/R/my.coef.r | 19 cubfits-0.1-2/cubfits/R/my.cubappr.r | 189 ++-- cubfits-0.1-2/cubfits/R/my.cubfits.r | 197 ++-- cubfits-0.1-2/cubfits/R/my.cubpred.r | 236 ++--- cubfits-0.1-2/cubfits/R/my.drawBConditionalAll.r | 18 cubfits-0.1-2/cubfits/R/my.drawBConditionalFit.r | 47 - cubfits-0.1-2/cubfits/R/my.drawPhiConditionalAll.r | 15 cubfits-0.1-2/cubfits/R/my.drawPhiConditionalAllPred.r | 17 cubfits-0.1-2/cubfits/R/my.drawRestrictHP.r |only cubfits-0.1-2/cubfits/R/my.drawbiasPhi.r |only cubfits-0.1-2/cubfits/R/my.fitMultinomOne.r | 6 cubfits-0.1-2/cubfits/R/my.init.r | 8 cubfits-0.1-2/cubfits/R/my.init_param.r | 14 cubfits-0.1-2/cubfits/R/my.logPosteriorAll.r | 45 cubfits-0.1-2/cubfits/R/my.logdmultinomCodOne.r | 18 cubfits-0.1-2/cubfits/R/my.pPropType.logmixture.r | 17 cubfits-0.1-2/cubfits/R/my.pPropType.lognormal_RW.r | 46 cubfits-0.1-2/cubfits/R/my.pPropType.lognormal_bias.r |only cubfits-0.1-2/cubfits/R/my.pPropType.r | 13 cubfits-0.1-2/cubfits/R/my.pPropTypeNoObs.logmixture.r | 2 cubfits-0.1-2/cubfits/R/my.pPropTypeNoObs.lognormal_RW.r | 12 cubfits-0.1-2/cubfits/R/my.pPropTypeNoObs.lognormal_bias.r |only cubfits-0.1-2/cubfits/R/my.pPropTypeNoObs.r | 2 cubfits-0.1-2/cubfits/R/my.proposeB.r |only cubfits-0.1-2/cubfits/R/my.proposePhiAll.r | 46 cubfits-0.1-2/cubfits/R/my.proposePhiAllPred.r | 43 cubfits-0.1-2/cubfits/R/my.proposebiasPhi.r |only cubfits-0.1-2/cubfits/R/my.proposesigmaPhi.r |only cubfits-0.1-2/cubfits/R/plotbin.r | 34 cubfits-0.1-2/cubfits/R/plotmodel.r | 24 cubfits-0.1-2/cubfits/R/prop.bin.roc.r | 66 + cubfits-0.1-2/cubfits/R/prop.model.nse.r |only cubfits-0.1-2/cubfits/R/prop.model.roc.r | 23 cubfits-0.1-2/cubfits/R/simu.orf.r | 44 cubfits-0.1-2/cubfits/R/simu.phi.Obs.r | 7 cubfits-0.1-2/cubfits/R/workflow.create.r | 12 cubfits-0.1-2/cubfits/configure | 4 cubfits-0.1-2/cubfits/configure.ac | 4 cubfits-0.1-2/cubfits/data/b.Init.rda |only cubfits-0.1-2/cubfits/data/control.r | 49 - cubfits-0.1-2/cubfits/data/global.r | 11 cubfits-0.1-2/cubfits/data/plot.r | 11 cubfits-0.1-2/cubfits/demo/00Index | 7 cubfits-0.1-2/cubfits/demo/mSCU.r | 2 cubfits-0.1-2/cubfits/demo/plotbin.r | 4 cubfits-0.1-2/cubfits/demo/roc.appr.r | 4 cubfits-0.1-2/cubfits/demo/roc.pred.r | 18 cubfits-0.1-2/cubfits/demo/roc.simu.r | 11 cubfits-0.1-2/cubfits/demo/roc.train.r | 8 cubfits-0.1-2/cubfits/inst/CITATION | 10 cubfits-0.1-2/cubfits/inst/doc/cubfits-guide.Rnw | 14 cubfits-0.1-2/cubfits/inst/doc/cubfits-guide.pdf |binary cubfits-0.1-2/cubfits/inst/workflow/00_readme.txt | 6 cubfits-0.1-2/cubfits/inst/workflow/param/small_bInit.rda |binary cubfits-0.1-2/cubfits/inst/workflow/roc/00_readme.txt | 4 cubfits-0.1-2/cubfits/inst/workflow/roc/01_code.txt | 13 cubfits-0.1-2/cubfits/inst/workflow/roc/code/00-set_env_simu.r | 48 - cubfits-0.1-2/cubfits/inst/workflow/roc/code/00-set_env_wophi.r | 42 cubfits-0.1-2/cubfits/inst/workflow/roc/code/00-set_env_wphi.r | 49 - cubfits-0.1-2/cubfits/inst/workflow/roc/code/00-set_env_wphi_wophi.r | 48 - cubfits-0.1-2/cubfits/inst/workflow/roc/code/02-get_data.r | 15 cubfits-0.1-2/cubfits/inst/workflow/roc/code/03-get_init-tp.r | 21 cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wophi_pm-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wophi_scuo-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wphi_pm-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wphi_scuo-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wphi_wophi_pm-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wphi_wophi_scuo-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/05-subset-tp.r | 52 - cubfits-0.1-2/cubfits/inst/workflow/roc/code/s1-generate_data.r | 10 cubfits-0.1-2/cubfits/inst/workflow/roc/code/s4-wophi_true-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/s4-wphi_true-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/03-plotdiag_bin_est.r | 45 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/03-plotdiag_init.r | 5 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/05-subset_tsv.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/06-plotsingle_model.r | 120 +- cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/06-plotsingle_prxy.r | 23 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/06-plotsingle_prxy_wci.r | 21 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_EPhi_hist.r | 17 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_accept_hist.r | 2 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_acceptvsEPhi.r | 19 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_bin.r | 111 +- cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_medPhi_EPhi.r | 1 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_scuo_cai.r | 8 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_sigmaW_hist.r | 1 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plottrace_logL-tp.r | 32 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plottrace_param_meanEPhi.r | 26 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plottrace_prior.r | 8 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plottrace_quantile_Phi.r | 21 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/08-plotmulti_wophi_wphi.r | 44 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m6-plot_b_corr.r | 26 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m6-plot_b_corr_negsel.r | 22 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m6-plot_prxy.r | 18 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m6-plot_prxy_wci.r | 18 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m7-plot_bin.r | 92 + cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s1-plotdiag_simu_phi.r | 1 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s2-plotdiag_bin_true.r | 90 + cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s3-plotdiag_bin_est.r | 46 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_b_corr_true.r | 28 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_model_true.r | 55 - cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_mscu.r | 27 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_prxy_true.r | 27 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_prxy_true_wci.r | 31 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_scu_mscu.r | 26 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s7-plotaa_deltat_true.r | 25 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s8-plotmulti_true.r | 67 + cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u0-get_case_main.r | 27 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u2-plot_b_corr.r | 94 +- cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u3-plot_trace.r | 11 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u4-plot_aa_allinone.r | 4 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u5-new_page.r | 5 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u6-adjust_focal_codon.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot_ps |only cubfits-0.1-2/cubfits/inst/workflow/roc/script/simu_run_0.sh | 16 cubfits-0.1-2/cubfits/inst/workflow/roc/script/simu_run_1.sh | 41 cubfits-0.1-2/cubfits/inst/workflow/roc/script/simu_run_2.sh | 36 cubfits-0.1-2/cubfits/inst/workflow/roc/script/simu_run_2_ps.sh |only cubfits-0.1-2/cubfits/inst/workflow/roc/script/wophi_run_0.sh | 14 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wophi_run_1.sh | 21 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wophi_run_2.sh | 26 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wophi_run_2_ps.sh |only cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_run_0.sh | 15 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_run_1.sh | 33 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_run_2.sh | 30 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_run_2_ps.sh |only cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_wophi_run_0.sh | 15 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_wophi_run_1.sh | 48 - cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_wophi_run_2.sh | 30 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_wophi_run_2_ps.sh |only cubfits-0.1-2/cubfits/man/a1_cubfits.Rd | 24 cubfits-0.1-2/cubfits/man/a2_cubappr.Rd | 30 cubfits-0.1-2/cubfits/man/a3_cubpred.Rd | 35 cubfits-0.1-2/cubfits/man/b1_plotbin.Rd | 8 cubfits-0.1-2/cubfits/man/b2_plotmodel.Rd | 4 cubfits-0.1-2/cubfits/man/c0_plot.Rd |only cubfits-0.1-2/cubfits/man/c1_io.Rd |only cubfits-0.1-2/cubfits/man/c2_convergence.Rd |only cubfits-0.1-2/cubfits/man/c9_internal.Rd |only cubfits-0.1-2/cubfits/man/s0_init.function.Rd | 4 cubfits-0.1-2/cubfits/man/s1_fitMultinom.Rd | 6 cubfits-0.1-2/cubfits/man/s2_estimatePhi.Rd | 4 cubfits-0.1-2/cubfits/man/t1_simulation.Rd | 11 cubfits-0.1-2/cubfits/man/t5_scu.Rd | 2 cubfits-0.1-2/cubfits/man/yy_control.Rd | 41 cubfits-0.1-2/cubfits/man/yy_dataset.Rd | 8 cubfits-0.1-2/cubfits/man/yy_yassour_PM.Rd | 4 cubfits-0.1-2/cubfits/src/stable_exp.c | 47 - cubfits-0.1-2/cubfits/vignettes/build_pdf.sh | 11 cubfits-0.1-2/cubfits/vignettes/cubfits-guide.Rnw | 14 cubfits-0.1-2/cubfits/vignettes/cubfits-include/01-copyright.tex | 2 cubfits-0.1-2/cubfits/vignettes/cubfits-include/01-introduction.tex | 17 cubfits-0.1-2/cubfits/vignettes/cubfits-include/02-main_functions.tex | 148 ++- cubfits-0.1-2/cubfits/vignettes/cubfits-include/03-speedup.tex | 190 ++-- cubfits-0.1-2/cubfits/vignettes/cubfits-include/04-workflows.tex | 101 +- cubfits-0.1-2/cubfits/vignettes/cubfits-include/05-utilities.tex | 77 - cubfits-0.1-2/cubfits/vignettes/cubfits-include/06-faq.tex |only cubfits-0.1-2/cubfits/vignettes/cubfits-include/07-misc.tex |only cubfits-0.1-2/cubfits/vignettes/cubfits-include/cubfits.bib | 35 cubfits-0.1-2/cubfits/vignettes/cubfits-include/figure/bayesian_model.pdf |only cubfits-0.1-2/cubfits/vignettes/cubfits-include/figure/workflows.pdf |only cubfits-0.1-2/cubfits/vignettes/cubfits-include/my_jss.cls |only 211 files changed, 2999 insertions(+), 1865 deletions(-)
Title: Programming with Big Data -- Demonstrations and Examples Using
'pbdR' Packages
Description: A set of demos of 'pbdR' packages, together with a useful,
unifying vignette.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut]
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdDEMO versions 0.2-0 dated 2014-02-18 and 0.3-0 dated 2016-01-24
pbdDEMO-0.2-0/pbdDEMO/R/read_sql_csv.R |only pbdDEMO-0.2-0/pbdDEMO/README |only pbdDEMO-0.2-0/pbdDEMO/data/control.rda |only pbdDEMO-0.2-0/pbdDEMO/demo/read_sql.r |only pbdDEMO-0.2-0/pbdDEMO/inst/extra/data/data |only pbdDEMO-0.2-0/pbdDEMO/man/00_pbdDEMO-package.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/01_control.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/05_timer.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/10_mpi.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/20_gbd_dmat.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/21_balance.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/ca_dmat_readsql.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/cb_dmat_readcsv.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/cc_plot.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/da_verify.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/ea_examples.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/eb_nc4.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/zz_demo.internal.Rd |only pbdDEMO-0.2-0/pbdDEMO/vignettes/pbdDEMO-include/applications/a5-ts.tex |only pbdDEMO-0.2-0/pbdDEMO/vignettes/pbdDEMO-include/applications/a6-tbd.tex |only pbdDEMO-0.2-0/pbdDEMO/vignettes/pbdDEMO-include/jss.bst |only pbdDEMO-0.2-0/pbdDEMO/vignettes/pbdDEMO-include/jss.cls |only pbdDEMO-0.3-0/pbdDEMO/COPYING | 711 +++++----- pbdDEMO-0.3-0/pbdDEMO/ChangeLog | 58 pbdDEMO-0.3-0/pbdDEMO/DESCRIPTION | 40 pbdDEMO-0.3-0/pbdDEMO/MD5 | 154 +- pbdDEMO-0.3-0/pbdDEMO/NAMESPACE | 63 pbdDEMO-0.3-0/pbdDEMO/R/gbd_dmat.r | 87 - pbdDEMO-0.3-0/pbdDEMO/R/load_balance.r | 141 + pbdDEMO-0.3-0/pbdDEMO/R/mpi_example.r | 59 pbdDEMO-0.3-0/pbdDEMO/R/ncvar_2d.r | 222 ++- pbdDEMO-0.3-0/pbdDEMO/R/pbdDEMO-package.r |only pbdDEMO-0.3-0/pbdDEMO/R/plot_dmat.r | 25 pbdDEMO-0.3-0/pbdDEMO/R/read_csv.r |only pbdDEMO-0.3-0/pbdDEMO/R/timer.R | 17 pbdDEMO-0.3-0/pbdDEMO/R/treft.r |only pbdDEMO-0.3-0/pbdDEMO/R/verify.R | 137 + pbdDEMO-0.3-0/pbdDEMO/R/zzz.R |only pbdDEMO-0.3-0/pbdDEMO/README.md |only pbdDEMO-0.3-0/pbdDEMO/build/vignette.rds |binary pbdDEMO-0.3-0/pbdDEMO/data/TREFHT.rda |binary pbdDEMO-0.3-0/pbdDEMO/demo/00Index | 8 pbdDEMO-0.3-0/pbdDEMO/demo/dist_iris.r |only pbdDEMO-0.3-0/pbdDEMO/demo/dist_pony.r |only pbdDEMO-0.3-0/pbdDEMO/demo/gbd_dmat.r | 2 pbdDEMO-0.3-0/pbdDEMO/demo/iris_dmat.r | 7 pbdDEMO-0.3-0/pbdDEMO/demo/iris_gbd.r | 8 pbdDEMO-0.3-0/pbdDEMO/demo/nc4_dmat.r | 11 pbdDEMO-0.3-0/pbdDEMO/demo/nc4_gbdc.r | 8 pbdDEMO-0.3-0/pbdDEMO/demo/nc4_par_read_1d.r |only pbdDEMO-0.3-0/pbdDEMO/demo/nc4_par_read_2d.r |only pbdDEMO-0.3-0/pbdDEMO/demo/nc4_par_write_1d.r |only pbdDEMO-0.3-0/pbdDEMO/demo/nc4_par_write_2d.r |only pbdDEMO-0.3-0/pbdDEMO/demo/nc4_parallel.r | 4 pbdDEMO-0.3-0/pbdDEMO/demo/ols_dmat.r | 4 pbdDEMO-0.3-0/pbdDEMO/demo/read_csv.r | 20 pbdDEMO-0.3-0/pbdDEMO/demo/read_ncdf.r | 2 pbdDEMO-0.3-0/pbdDEMO/demo/reblock.r | 2 pbdDEMO-0.3-0/pbdDEMO/demo/sample_stat_dmat.r | 12 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_cov.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_lmfit.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_pca.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/cov.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/lmfit.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/pca.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/CITATION | 4 pbdDEMO-0.3-0/pbdDEMO/inst/doc/pbdDEMO-guide.Rnw | 15 pbdDEMO-0.3-0/pbdDEMO/inst/doc/pbdDEMO-guide.pdf |binary pbdDEMO-0.3-0/pbdDEMO/man/Temperature-at-Reference-Height.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/gbd_dmat.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/load_balance.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/mpi_example.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/ncvar.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/pbdDEMO-package.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/plot_dmat.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/read.csv.ddmatrix.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/timer.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/verify.Rd |only pbdDEMO-0.3-0/pbdDEMO/src |only pbdDEMO-0.3-0/pbdDEMO/vignettes/build_pdf.sh | 5 pbdDEMO-0.3-0/pbdDEMO/vignettes/cover/build_cover.sh | 4 pbdDEMO-0.3-0/pbdDEMO/vignettes/cover/cover.pdf |binary pbdDEMO-0.3-0/pbdDEMO/vignettes/cover/cover.tex | 27 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-guide.Rnw | 15 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/01-introduction.tex | 15 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/03-mpi.tex | 68 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/07-dmat_basic.tex | 4 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/09-reading.tex | 26 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/10-pbdNCDF4.tex | 44 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/applications/a4-Bayes.tex | 13 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/applications/a5-pairwise.tex |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/applications/b1-ts.tex |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/applications/c1-tbd.tex |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/frontmatter/00-acknowledgement.tex | 9 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/frontmatter/00-copyright.tex | 10 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/frontmatter/00-covernote.tex |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/frontmatter/00-warn.tex | 5 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/pbdDEMO.bib | 102 + pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/pics/dist_iris.pdf |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/pics/dist_pony.pdf |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/preamble.tex | 91 - pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/style.tex | 7 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/titlepage.tex | 3 103 files changed, 1441 insertions(+), 840 deletions(-)
Title: Safely Access the RStudio API
Description: Access the RStudio API (if available) and provide informative error
messages when it's not.
Author: Hadley Wickham [aut],
JJ Allaire [aut, cre],
Kevin Ushey [ctb],
RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rstudioapi versions 0.4.0 dated 2015-12-09 and 0.5 dated 2016-01-24
rstudioapi-0.4.0/rstudioapi/NEWS |only rstudioapi-0.5/rstudioapi/DESCRIPTION | 7 ++- rstudioapi-0.5/rstudioapi/MD5 | 26 +++++++------- rstudioapi-0.5/rstudioapi/NAMESPACE | 4 +- rstudioapi-0.5/rstudioapi/R/stubs.R | 10 +++++ rstudioapi-0.5/rstudioapi/inst |only rstudioapi-0.5/rstudioapi/man/askForPassword.Rd |only rstudioapi-0.5/rstudioapi/man/callFun.Rd | 6 +-- rstudioapi-0.5/rstudioapi/man/document-mutation.Rd | 20 +++++----- rstudioapi-0.5/rstudioapi/man/document_position.Rd | 2 - rstudioapi-0.5/rstudioapi/man/document_range.Rd | 2 - rstudioapi-0.5/rstudioapi/man/getActiveDocumentContext.Rd | 2 - rstudioapi-0.5/rstudioapi/man/getActiveProject.Rd |only rstudioapi-0.5/rstudioapi/man/getVersion.Rd | 2 - rstudioapi-0.5/rstudioapi/man/hasFun.Rd | 12 +++--- rstudioapi-0.5/rstudioapi/man/isAvailable.Rd | 4 +- 16 files changed, 56 insertions(+), 41 deletions(-)
Title: Examples using 'Rcpp' to Interface R and C++
Description: Examples for Seamless R and C++ integration
The 'Rcpp' package contains a C++ library that facilitates the integration of
R and C++ in various ways. This package provides some usage examples.
Note that the documentation in this package currently does not cover all the
features in the package. It is not even close. On the other hand, the site
<http://gallery.rcpp.org> is regrouping a large number of examples for 'Rcpp'.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppExamples versions 0.1.6 dated 2013-01-16 and 0.1.7 dated 2016-01-24
RcppExamples-0.1.6/RcppExamples/R/RcppParamsExample.R |only RcppExamples-0.1.6/RcppExamples/man/RcppDate.Rd |only RcppExamples-0.1.6/RcppExamples/man/RcppParams.Rd |only RcppExamples-0.1.6/RcppExamples/man/RcppRNGs.Rd |only RcppExamples-0.1.6/RcppExamples/man/RcppResultSet.Rd |only RcppExamples-0.1.6/RcppExamples/man/RcppVector.Rd |only RcppExamples-0.1.6/RcppExamples/src/RcppDataFrame.cpp |only RcppExamples-0.1.6/RcppExamples/src/RcppRNGs.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppDateExample.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppMatrixExample.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppParamsExample.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppStringVectorExample.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppVectorExample.cpp |only RcppExamples-0.1.7/RcppExamples/ChangeLog | 26 ++++ RcppExamples-0.1.7/RcppExamples/DESCRIPTION | 31 ++--- RcppExamples-0.1.7/RcppExamples/MD5 | 58 +++++----- RcppExamples-0.1.7/RcppExamples/NAMESPACE | 11 - RcppExamples-0.1.7/RcppExamples/R/RcppDataFrame.R | 17 +- RcppExamples-0.1.7/RcppExamples/R/RcppDateExample.R | 14 +- RcppExamples-0.1.7/RcppExamples/R/RcppExports.R |only RcppExamples-0.1.7/RcppExamples/R/RcppListExample.R |only RcppExamples-0.1.7/RcppExamples/R/RcppMatrixExample.R | 16 +- RcppExamples-0.1.7/RcppExamples/R/RcppRNGs.R | 17 +- RcppExamples-0.1.7/RcppExamples/R/RcppStringVectorExample.R | 14 +- RcppExamples-0.1.7/RcppExamples/R/RcppVectorExample.R | 18 +-- RcppExamples-0.1.7/RcppExamples/README.md |only RcppExamples-0.1.7/RcppExamples/inst/NEWS.Rd | 13 ++ RcppExamples-0.1.7/RcppExamples/man/RcppDataFrame.Rd | 8 - RcppExamples-0.1.7/RcppExamples/man/RcppDateExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppExamples-package.Rd | 11 - RcppExamples-0.1.7/RcppExamples/man/RcppListExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppMatrixExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppNumericVectorExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppRNGsExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppStringVectorExample.Rd |only RcppExamples-0.1.7/RcppExamples/src/DataFrameExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/DateExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/ListExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/Makevars | 7 - RcppExamples-0.1.7/RcppExamples/src/Makevars.win | 13 +- RcppExamples-0.1.7/RcppExamples/src/MatrixExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/NumericVectorExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/RNGs.cpp |only RcppExamples-0.1.7/RcppExamples/src/RcppExports.cpp |only RcppExamples-0.1.7/RcppExamples/src/StringVectorExample.cpp |only 45 files changed, 153 insertions(+), 121 deletions(-)
Title: Analytical Tools for Radiation Oncology
Description: Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from multiple treatment planning system platforms and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data.
Author: Reid F. Thompson <reid.thompson@gmail.com>
Maintainer: Reid F. Thompson <reid.thompson@gmail.com>
Diff between RadOnc versions 1.1.0 dated 2015-04-22 and 1.1.1 dated 2016-01-24
DESCRIPTION | 10 +-- MD5 | 18 +++--- R/CLASSES.R | 5 - R/DVH.R | 32 ++++++------ R/plot.DVH.R | 6 +- R/read.DVH.R | 133 +++++++++++++++++++++++++++++++++++++++++++++++++-- inst/NEWS.Rd | 36 +++++++++++++ man/plot-methods.Rd | 9 +++ man/read.DVH.Rd | 4 - vignettes/RadOnc.Rnw | 8 +-- 10 files changed, 215 insertions(+), 46 deletions(-)
Title: Programming with Big Data -- Distributed Matrix Methods
Description: A set of classes for managing distributed matrices, and
a collection of methods for computing linear algebra and
statistics. Computation is handled mostly by routines from the
'pbdBASE' package, which itself relies on the 'ScaLAPACK' and
'PBLAS' numerical libraries for distributed computing.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
ZhaoKang Wang [ctb],
Michael Lawrence [ctb],
R Core team [ctb] (some wrappers taken from the base and stats
packages)
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdDMAT versions 0.2-3 dated 2013-12-16 and 0.4-0 dated 2016-01-24
pbdDMAT-0.2-3/pbdDMAT/R/00-ddmatrix_class.R |only pbdDMAT-0.2-3/pbdDMAT/R/02-utility.R |only pbdDMAT-0.2-3/pbdDMAT/R/03-redistributions.R |only pbdDMAT-0.2-3/pbdDMAT/R/a_ddmatrix_utility.R |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_algebra.R |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_condition.R |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_create.R |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_matexp.r |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_r_math.R |only pbdDMAT-0.2-3/pbdDMAT/README |only pbdDMAT-0.2-3/pbdDMAT/data |only pbdDMAT-0.2-3/pbdDMAT/man/00_pbdDMAT-package.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/00_zz_dmatclass.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/00_zzz_control.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/aa_dimensions.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ba_randmat.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/bb_hilb.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/bd_companion.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/bz_diag.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ca_asddm.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ca_asmat.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/cb_distrib.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/cc_redist.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/da_print.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/db_summary.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/dz_extract.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/dz_insert.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ea_comparators.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/eb_type.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ec_nas.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/fa_apply.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/fb_bind.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ia_reductions.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ib_arith.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ib_matmult.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ka_miscmath.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/kb_rounding.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/la_linalg.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/lb_qr.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/lc_chol2inv.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ld_kappa.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/le_norm.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ls_eigen2.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/lz_expm.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ra_scale.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/rb_sweep.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/sa_cov.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/sa_pca.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/sc_lmfit.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/zz_dmat.internal.Rd |only pbdDMAT-0.2-3/pbdDMAT/vignettes/pbdDMAT-include |only pbdDMAT-0.4-0/pbdDMAT/ChangeLog | 93 +--- pbdDMAT-0.4-0/pbdDMAT/DESCRIPTION | 45 +- pbdDMAT-0.4-0/pbdDMAT/MD5 | 263 +++++++---- pbdDMAT-0.4-0/pbdDMAT/NAMESPACE | 323 +++++++------- pbdDMAT-0.4-0/pbdDMAT/R/00-classes.r |only pbdDMAT-0.4-0/pbdDMAT/R/000_globalVariables.r |only pbdDMAT-0.4-0/pbdDMAT/R/01-generics.R | 228 ---------- pbdDMAT-0.4-0/pbdDMAT/R/04-misc.R | 131 ----- pbdDMAT-0.4-0/pbdDMAT/R/accessors.r |only pbdDMAT-0.4-0/pbdDMAT/R/as.ddmatrix.r |only pbdDMAT-0.4-0/pbdDMAT/R/as.matrix.r |only pbdDMAT-0.4-0/pbdDMAT/R/as.vector.r |only pbdDMAT-0.4-0/pbdDMAT/R/constructors.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_[.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_apply.R | 235 ++++++++-- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_arithmetic.R | 98 +++- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_bind.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_chol.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_chol2inv.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_cond.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_cov.R | 102 ++-- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_diag.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_eigen.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_eigen2.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_expm.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_head.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_isdot.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_lm.R | 121 ++++- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_logic.r | 213 ++++----- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_lu.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_math.R |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_matmult.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_misc.R | 445 +------------------- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_na.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_norm.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_prcomp.R | 85 +++ pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_print.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_qr.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_redistribute.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_reductions.R | 286 +++++------- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_round.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_scale.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_sd.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_solve.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_special.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_summary.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_sumstats.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_svd.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_sweep.R | 297 +------------ pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_transpose.r |only pbdDMAT-0.4-0/pbdDMAT/R/dsmatrix |only pbdDMAT-0.4-0/pbdDMAT/R/error_stuff.r |only pbdDMAT-0.4-0/pbdDMAT/R/getLocal.r |only pbdDMAT-0.4-0/pbdDMAT/R/isSymmetric.r |only pbdDMAT-0.4-0/pbdDMAT/R/ownany.r |only pbdDMAT-0.4-0/pbdDMAT/R/pbdDMAT-package.R |only pbdDMAT-0.4-0/pbdDMAT/R/sparsity.r |only pbdDMAT-0.4-0/pbdDMAT/R/test_utils.r |only pbdDMAT-0.4-0/pbdDMAT/R/utils.r |only pbdDMAT-0.4-0/pbdDMAT/R/wrappers.r |only pbdDMAT-0.4-0/pbdDMAT/R/zzz.R | 18 pbdDMAT-0.4-0/pbdDMAT/README.md |only pbdDMAT-0.4-0/pbdDMAT/TODO | 11 pbdDMAT-0.4-0/pbdDMAT/build/vignette.rds |binary pbdDMAT-0.4-0/pbdDMAT/cleanup | 10 pbdDMAT-0.4-0/pbdDMAT/demo/cholesky.r | 2 pbdDMAT-0.4-0/pbdDMAT/demo/matprod.r | 2 pbdDMAT-0.4-0/pbdDMAT/demo/reductions.r | 2 pbdDMAT-0.4-0/pbdDMAT/demo/solve.r | 10 pbdDMAT-0.4-0/pbdDMAT/demo/svd.r | 12 pbdDMAT-0.4-0/pbdDMAT/inst/RNACI |only pbdDMAT-0.4-0/pbdDMAT/inst/doc/pbdDMAT-guide.Rnw | 181 +------- pbdDMAT-0.4-0/pbdDMAT/inst/doc/pbdDMAT-guide.pdf |binary pbdDMAT-0.4-0/pbdDMAT/inst/tests |only pbdDMAT-0.4-0/pbdDMAT/man/Comparators.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/Hilbert.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/accessors.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/arithmetic.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/as.ddmatrix.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/as.matrix.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/as.rowcyclic.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/as.vector.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/binds.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/chol2inv.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/companion.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/condnums.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/control.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/covariance.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-apply.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-chol.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-class.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-constructors.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-eigen.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-lu.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-norm.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-prcomp.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-print.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-scale.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-solve.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-summary.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-sumstats.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-svd.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/diag-constructors.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/eigen2.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/expm.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/extract.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/getLocal.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/headsortails.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/insert.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/isSymmetric.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/isdot.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/lm.fit.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/math.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/matmult.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/na.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/pbdDMAT-package.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/qr.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/redistribute.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/reductions.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/rounding.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/sd.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/sparsity.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/sweep.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/transpose.Rd |only pbdDMAT-0.4-0/pbdDMAT/src |only pbdDMAT-0.4-0/pbdDMAT/tests |only pbdDMAT-0.4-0/pbdDMAT/vignettes/build_pdf.sh | 6 pbdDMAT-0.4-0/pbdDMAT/vignettes/include |only pbdDMAT-0.4-0/pbdDMAT/vignettes/pbdDMAT-guide.Rnw | 181 +------- pbdDMAT-0.4-0/pbdDMAT/vignettes/workingwith-include |only 181 files changed, 1337 insertions(+), 2063 deletions(-)
Title: Programming with Big Data -- Base Wrappers for Distributed
Matrices
Description: An interface to and extensions for the 'PBLAS' and
'ScaLAPACK' numerical libraries. This enables R to utilize
distributed linear algebra for codes written in the 'SPMD' fashion.
This interface is deliberately low-level and mimics the style of
the native libraries it wraps. For a much higher level way of
managing distributed matrices, see the 'pbdDMAT' package.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Ewan Higgs [ctb]
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdBASE versions 0.2-3 dated 2013-12-14 and 0.4-3 dated 2016-01-24
pbdBASE-0.2-3/pbdBASE/R/lm.R |only pbdBASE-0.2-3/pbdBASE/R/utility_blacs.R |only pbdBASE-0.2-3/pbdBASE/R/utility_scalapack.R |only pbdBASE-0.2-3/pbdBASE/R/wrappers_blacs.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_matexp.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_misc.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_p_matexp.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_pblas.R |only pbdBASE-0.2-3/pbdBASE/R/wrappers_plinalg.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_putil.R |only pbdBASE-0.2-3/pbdBASE/R/wrappers_scalapack.R |only pbdBASE-0.2-3/pbdBASE/README |only pbdBASE-0.2-3/pbdBASE/data |only pbdBASE-0.2-3/pbdBASE/man/00_pbdBASE-package.Rd |only pbdBASE-0.2-3/pbdBASE/man/aa_initgrid.Rd |only pbdBASE-0.2-3/pbdBASE/man/aa_z_gridexit.Rd |only pbdBASE-0.2-3/pbdBASE/man/ab_blacs.Rd |only pbdBASE-0.2-3/pbdBASE/man/ab_d_minctxt.Rd |only pbdBASE-0.2-3/pbdBASE/man/ab_z_blacsexit.Rd |only pbdBASE-0.2-3/pbdBASE/man/ab_z_coords.Rd |only pbdBASE-0.2-3/pbdBASE/man/ac_envir.Rd |only pbdBASE-0.2-3/pbdBASE/man/ba_a_ownership.Rd |only pbdBASE-0.2-3/pbdBASE/man/zz_base.internal.Rd |only pbdBASE-0.2-3/pbdBASE/src/Rtools |only pbdBASE-0.2-3/pbdBASE/src/base/R_plm.f |only pbdBASE-0.2-3/pbdBASE/src/base/plinalg.f |only pbdBASE-0.2-3/pbdBASE/src/base/prblas.f |only pbdBASE-0.2-3/pbdBASE/src/base/util |only pbdBASE-0.2-3/pbdBASE/src/base/variance.f |only pbdBASE-0.2-3/pbdBASE/src/base_global.h |only pbdBASE-0.2-3/pbdBASE/src/base_mpi_blac.c |only pbdBASE-0.2-3/pbdBASE/vignettes/pbdBASE-include |only pbdBASE-0.4-3/pbdBASE/ChangeLog | 118 - pbdBASE-0.4-3/pbdBASE/DESCRIPTION | 40 pbdBASE-0.4-3/pbdBASE/MD5 | 263 ++- pbdBASE-0.4-3/pbdBASE/NAMESPACE | 118 + pbdBASE-0.4-3/pbdBASE/R/000_globalVariables.r |only pbdBASE-0.4-3/pbdBASE/R/base_lm.R |only pbdBASE-0.4-3/pbdBASE/R/base_matexp.r |only pbdBASE-0.4-3/pbdBASE/R/base_mpi_blacs.r |only pbdBASE-0.4-3/pbdBASE/R/base_mpi_blacs_reductions.r |only pbdBASE-0.4-3/pbdBASE/R/base_p_matexp.r |only pbdBASE-0.4-3/pbdBASE/R/base_pblas_level3.r |only pbdBASE-0.4-3/pbdBASE/R/base_plinalg.r |only pbdBASE-0.4-3/pbdBASE/R/base_prblas.r |only pbdBASE-0.4-3/pbdBASE/R/base_putil.R |only pbdBASE-0.4-3/pbdBASE/R/base_qr.r |only pbdBASE-0.4-3/pbdBASE/R/base_scalapack.r |only pbdBASE-0.4-3/pbdBASE/R/base_scalapack_utility.r |only pbdBASE-0.4-3/pbdBASE/R/base_variance.r |only pbdBASE-0.4-3/pbdBASE/R/coords.r |only pbdBASE-0.4-3/pbdBASE/R/get_conf.r | 11 pbdBASE-0.4-3/pbdBASE/R/get_lib.r | 2 pbdBASE-0.4-3/pbdBASE/R/misc.r | 38 pbdBASE-0.4-3/pbdBASE/R/pbdBASE-package.r |only pbdBASE-0.4-3/pbdBASE/R/pkg_blacs_apts.r | 4 pbdBASE-0.4-3/pbdBASE/R/utility_blacs.r |only pbdBASE-0.4-3/pbdBASE/R/zzz.r | 13 pbdBASE-0.4-3/pbdBASE/README.md |only pbdBASE-0.4-3/pbdBASE/build/vignette.rds |binary pbdBASE-0.4-3/pbdBASE/cleanup | 10 pbdBASE-0.4-3/pbdBASE/configure | 306 ++-- pbdBASE-0.4-3/pbdBASE/configure.ac | 56 pbdBASE-0.4-3/pbdBASE/inst/CITATION | 4 pbdBASE-0.4-3/pbdBASE/inst/RNACI |only pbdBASE-0.4-3/pbdBASE/inst/doc/pbdBASE-guide.Rnw | 140 - pbdBASE-0.4-3/pbdBASE/inst/doc/pbdBASE-guide.pdf |binary pbdBASE-0.4-3/pbdBASE/man/BASE-Global-Environment.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.crossprod.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.dallreduce.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.descinit.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.dhilbmk.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.dim0.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.indxg2p.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.matexp.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.maxdim.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.minctxt.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.nbd.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.numroc.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.ownany.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.p_matexp_pade_wrap.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.p_matpow_by_squaring_wrap.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdchtri.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdclvar.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdhilbmk.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdmkcpn1.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdmvsum.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdsweep.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.procgrid.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rcolcpy.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rcolcpy2.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rl2blas.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rl2insert.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgecon.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgels.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgemm.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgemr2d.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgeqpf.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgesv.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgesvd.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgetrf.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgetri.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdlange.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdlaprnt.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdorgqr.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdormqr.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdpotrf.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdsyev.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdsyevx.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdtran.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdtrcon.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rrowcpy.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rrowcpy2.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.tri2zero.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.valid_context.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacs-max.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacs-min.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacs-p2p.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacs-sums.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacsexit.Rd |only pbdBASE-0.4-3/pbdBASE/man/coords.Rd |only pbdBASE-0.4-3/pbdBASE/man/coordspair.Rd |only pbdBASE-0.4-3/pbdBASE/man/diag.Rd |only pbdBASE-0.4-3/pbdBASE/man/finalizer.Rd |only pbdBASE-0.4-3/pbdBASE/man/g2l_coord.Rd |only pbdBASE-0.4-3/pbdBASE/man/g2lcoord.Rd |only pbdBASE-0.4-3/pbdBASE/man/gridexit.Rd |only pbdBASE-0.4-3/pbdBASE/man/gridinfo.Rd |only pbdBASE-0.4-3/pbdBASE/man/gridinit.Rd |only pbdBASE-0.4-3/pbdBASE/man/init.grid.Rd |only pbdBASE-0.4-3/pbdBASE/man/l2g_coord.Rd |only pbdBASE-0.4-3/pbdBASE/man/lclgblmat.Rd |only pbdBASE-0.4-3/pbdBASE/man/numroc2.Rd |only pbdBASE-0.4-3/pbdBASE/man/pbdBASE-package.Rd |only pbdBASE-0.4-3/pbdBASE/man/pcoords.Rd |only pbdBASE-0.4-3/pbdBASE/src/Makevars.in | 179 +- pbdBASE-0.4-3/pbdBASE/src/Makevars.win | 69 pbdBASE-0.4-3/pbdBASE/src/base/bprnt.f | 11 pbdBASE-0.4-3/pbdBASE/src/base/bprnt_c.c | 8 pbdBASE-0.4-3/pbdBASE/src/base/expm/matexp.c | 297 ++-- pbdBASE-0.4-3/pbdBASE/src/base/expm/matexp.h | 18 pbdBASE-0.4-3/pbdBASE/src/base/expm/p_matexp.c | 92 - pbdBASE-0.4-3/pbdBASE/src/base/expm/pade_coefs.c | 6 pbdBASE-0.4-3/pbdBASE/src/base/linalg |only pbdBASE-0.4-3/pbdBASE/src/base/stats |only pbdBASE-0.4-3/pbdBASE/src/base/utils |only pbdBASE-0.4-3/pbdBASE/src/base_lm.c | 433 +----- pbdBASE-0.4-3/pbdBASE/src/base_matexp.c | 59 pbdBASE-0.4-3/pbdBASE/src/base_mpi_blacs.c |only pbdBASE-0.4-3/pbdBASE/src/base_mpi_blacs_reductions.c |only pbdBASE-0.4-3/pbdBASE/src/base_p_matexp.c | 48 pbdBASE-0.4-3/pbdBASE/src/base_pblas_level3.c | 78 - pbdBASE-0.4-3/pbdBASE/src/base_plinalg.c | 57 pbdBASE-0.4-3/pbdBASE/src/base_prblas.c | 14 pbdBASE-0.4-3/pbdBASE/src/base_putil.c | 21 pbdBASE-0.4-3/pbdBASE/src/base_qr.c |only pbdBASE-0.4-3/pbdBASE/src/base_scalapack.c | 842 +++++------- pbdBASE-0.4-3/pbdBASE/src/base_scalapack_utility.c | 113 - pbdBASE-0.4-3/pbdBASE/src/base_variance.c | 21 pbdBASE-0.4-3/pbdBASE/src/comm_utils.c |only pbdBASE-0.4-3/pbdBASE/src/coords.c |only pbdBASE-0.4-3/pbdBASE/src/descinit.c |only pbdBASE-0.4-3/pbdBASE/src/export_blacs/pkg_tools.c | 13 pbdBASE-0.4-3/pbdBASE/src/other.c | 68 pbdBASE-0.4-3/pbdBASE/src/pbdBASE.h |only pbdBASE-0.4-3/pbdBASE/src/scalapack.h |only pbdBASE-0.4-3/pbdBASE/src/utils |only pbdBASE-0.4-3/pbdBASE/vignettes/build_pdf.sh | 6 pbdBASE-0.4-3/pbdBASE/vignettes/include |only pbdBASE-0.4-3/pbdBASE/vignettes/pbdBASE-guide.Rnw | 140 - 170 files changed, 1847 insertions(+), 1869 deletions(-)
Title: Medical Risk and Comorbidity Tools for ICD-9-CM Data
Description: Generates risk estimates and comorbidity flags from ICD-9-CM
codes available in administrative medical datasets. The package supports
the Charlson Comorbidity Index, the Elixhauser Comorbidity
classification, the Revised Cardiac Risk Index, and the Risk Stratification
Index. Methods are table-based, fast, and use the 'plyr' package, so
parallelization is possible for large jobs. Also includes a sample of
real ICD-9 data for 100 patients from a publicly available dataset.
Author: Patrick McCormick [aut, cre],
Thomas Joseph [aut]
Maintainer: Patrick McCormick <patrick.mccormick@alum.mit.edu>
Diff between medicalrisk versions 1.1 dated 2015-01-06 and 1.2 dated 2016-01-24
DESCRIPTION | 33 - LICENSE |only MD5 | 102 +-- NAMESPACE | 2 NEWS |only R/data.R | 2 R/icd9cm.R | 9 README.md | 18 build/vignette.rds |binary data/charlson_list.rda |binary data/charlson_weights.rda |binary data/charlson_weights_orig.rda |binary data/elixhauser_list.rda |binary data/icd9cm_list.rda |binary data/rsi_beta_1yrpod.rda |binary data/rsi_beta_30dlos.rda |binary data/rsi_beta_30dpod.rda |binary data/rsi_beta_inhosp.rda |binary data/rsi_sample_data.rda |binary data/rsi_sample_results.rda |binary data/vt_inp_sample.rda |binary inst/doc/advanced.R |only inst/doc/advanced.Rmd |only inst/doc/advanced.html |only inst/doc/medicalrisk.R | 42 - inst/doc/medicalrisk.Rmd | 103 ++- inst/doc/medicalrisk.html | 1087 +++++++++++++++++++++++--------------- inst/sql |only man/charlson_list.Rd | 2 man/charlson_weights.Rd | 10 man/charlson_weights_orig.Rd | 8 man/elixhauser_list.Rd | 2 man/generate_charlson_index_df.Rd | 8 man/generate_comorbidity_df.Rd | 12 man/icd9cm_charlson_deyo.Rd | 13 man/icd9cm_charlson_quan.Rd | 23 man/icd9cm_charlson_romano.Rd | 15 man/icd9cm_elixhauser_ahrq37.Rd | 26 man/icd9cm_elixhauser_quan.Rd | 24 man/icd9cm_list.Rd | 8 man/icd9cm_rcri.Rd | 42 - man/icd9cm_sessler_rsi.Rd | 22 man/melt_icd9list.Rd | 2 man/merge_icd9_dx_and_procs.Rd | 4 man/rsi_beta_1yrpod.Rd | 2 man/rsi_beta_30dlos.Rd | 2 man/rsi_beta_30dpod.Rd | 2 man/rsi_beta_inhosp.Rd | 2 man/rsi_sample_data.Rd | 2 man/rsi_sample_results.Rd | 2 man/sessler_get_single_beta.Rd | 2 man/verify_sessler_rsi.Rd | 4 man/vt_inp_sample.Rd | 10 vignettes/advanced.Rmd |only vignettes/medicalrisk.Rmd | 103 ++- vignettes/medicalrisk.bib |only 56 files changed, 1051 insertions(+), 699 deletions(-)
Title: Ordination and Multivariate Analysis for Ecology
Description: A variety of ordination and community analyses
useful in analysis of data sets in community ecology.
Includes many of the common ordination methods, with
graphical routines to facilitate their interpretation,
as well as several novel analyses.
Author: David W. Roberts <droberts@montana.edu>
Maintainer: David W. Roberts <droberts@montana.edu>
Diff between labdsv versions 1.7-0 dated 2015-05-04 and 1.8-0 dated 2016-01-24
labdsv-1.7-0/labdsv/INDEX |only labdsv-1.7-0/labdsv/man/clustify.Rd |only labdsv-1.8-0/labdsv/DESCRIPTION | 13 labdsv-1.8-0/labdsv/MD5 | 83 +-- labdsv-1.8-0/labdsv/NAMESPACE | 66 +- labdsv-1.8-0/labdsv/R/clustify.R | 3 labdsv-1.8-0/labdsv/R/compspec.R | 4 labdsv-1.8-0/labdsv/R/nmds.R | 22 labdsv-1.8-0/labdsv/R/orddist.R | 2 labdsv-1.8-0/labdsv/R/ordutils.R | 4 labdsv-1.8-0/labdsv/R/pco.R | 22 labdsv-1.8-0/labdsv/R/vegtrans.R | 3 labdsv-1.8-0/labdsv/inst/ChangeLog | 717 ++++++++++++++--------------- labdsv-1.8-0/labdsv/man/compspec.Rd | 12 labdsv-1.8-0/labdsv/man/concov.Rd | 2 labdsv-1.8-0/labdsv/man/const.Rd | 4 labdsv-1.8-0/labdsv/man/dematrify.Rd | 1 labdsv-1.8-0/labdsv/man/dga.Rd | 1 labdsv-1.8-0/labdsv/man/disana.Rd | 2 labdsv-1.8-0/labdsv/man/dsvdis.Rd | 10 labdsv-1.8-0/labdsv/man/envrtest.Rd | 1 labdsv-1.8-0/labdsv/man/euclidify.Rd | 1 labdsv-1.8-0/labdsv/man/homoteneity.Rd | 1 labdsv-1.8-0/labdsv/man/importance.Rd | 6 labdsv-1.8-0/labdsv/man/indval.Rd | 1 labdsv-1.8-0/labdsv/man/isamic.Rd | 2 labdsv-1.8-0/labdsv/man/labdsv.internal.Rd | 1 labdsv-1.8-0/labdsv/man/matrify.Rd | 1 labdsv-1.8-0/labdsv/man/metrify.Rd | 3 labdsv-1.8-0/labdsv/man/nmds.Rd | 3 labdsv-1.8-0/labdsv/man/ordcomp.Rd | 2 labdsv-1.8-0/labdsv/man/orddist.Rd | 3 labdsv-1.8-0/labdsv/man/ordpart.Rd | 1 labdsv-1.8-0/labdsv/man/ordtest.Rd | 3 labdsv-1.8-0/labdsv/man/pca.Rd | 9 labdsv-1.8-0/labdsv/man/plot.nmds.Rd | 15 labdsv-1.8-0/labdsv/man/plot.pca.Rd | 2 labdsv-1.8-0/labdsv/man/plot.pco.Rd | 15 labdsv-1.8-0/labdsv/man/rnddist.Rd | 1 labdsv-1.8-0/labdsv/man/rndtaxa.Rd | 1 labdsv-1.8-0/labdsv/man/spcdisc.Rd | 1 labdsv-1.8-0/labdsv/man/vegtrans.Rd | 2 labdsv-1.8-0/labdsv/src/indval.f | 8 labdsv-1.8-0/labdsv/src/random.c |only 44 files changed, 492 insertions(+), 562 deletions(-)
Title: Chi-Square and Exact Tests for Non-Parametric Functional
Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on asymptotic chi-square and exact statistics. These tests were designed to reveal evidence for causality based on functional dependencies. They include asymptotic functional chi-square tests, an exact functional test, and a comparative functional chi-square test. The normalized non-constant functional chi-square test was used by the Best Performer NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.1.0 dated 2015-06-29 and 2.2.0 dated 2016-01-24
DESCRIPTION | 11 +- MD5 | 20 ++-- NAMESPACE | 1 NEWS | 45 +++++++--- R/CPChisq.R |only R/FunChisq.R | 124 ++++++++++++++++++----------- inst/CITATION | 31 ++++++- man/cp.chisq.test.Rd |only man/cp.fun.chisq.test.Rd | 5 - man/fun.chisq.test.Rd | 27 ++++-- tests/testthat.R | 8 - tests/testthat/test_FunChisq.R | 170 ++++++++++++++++++++++++++++++++++------- 12 files changed, 324 insertions(+), 118 deletions(-)
Title: Quantile Regression for Random Variables on the Unit Interval
Description: Employs a two-parameter family of
distributions for modelling random variables on the (0, 1) interval by
applying the cumulative distribution function (cdf) of one parent
distribution to the quantile function of another.
Author: Yiyun Shou [aut, cre],
Michael Smithson [aut]
Maintainer: Yiyun Shou <yiyun.shou@anu.edu.au>
Diff between cdfquantreg versions 1.0.0 dated 2015-12-27 and 1.0.1 dated 2016-01-24
DESCRIPTION | 8 - MD5 | 41 ++++----- NAMESPACE | 3 NEWS |only R/bugsModel.R | 6 - R/cdfquantreg.R | 4 R/qrBugs.R | 25 +++++ R/qrDistributions.R | 16 +-- R/qrInfluence.R | 22 ++--- R/qrMethod.R | 30 +++--- R/qrPlot.R | 42 ++++++++- inst/doc/IPCCExample.Rmd | 2 inst/doc/IPCCExample.html | 36 ++++---- inst/doc/Smithson_Verkuilen2006Example.R | 14 --- inst/doc/Smithson_Verkuilen2006Example.Rmd | 17 --- inst/doc/Smithson_Verkuilen2006Example.html | 121 ++++++++++++---------------- man/cdfquantreg-package.Rd | 6 - man/dq.Rd | 13 +-- man/influence.cdfqr.Rd | 6 - man/qrBugs.Rd | 16 +++ vignettes/IPCCExample.Rmd | 2 vignettes/Smithson_Verkuilen2006Example.Rmd | 17 --- 22 files changed, 231 insertions(+), 216 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.5-4 dated 2015-09-23 and 2.6-1 dated 2016-01-24
DESCRIPTION | 10 - MD5 | 53 +++-- NAMESPACE | 3 R/ensemble.analogue.R | 320 ++++++++++++++++++---------------- R/ensemble.area.R |only R/ensemble.batch.R | 15 - R/ensemble.centroids.R |only R/ensemble.drop1.R | 5 R/ensemble.ecocrop.R |only R/ensemble.formulae.R | 2 R/ensemble.mean.R | 82 ++++++-- R/ensemble.novel.R |only R/ensemble.raster.R | 118 ++++++------ R/ensemble.test.R | 152 +++++++++++----- R/ensemble.test.gbm.R | 2 R/ensemble.test.nnet.R | 2 R/ensemble.test.splits.R | 37 ++- R/ensemble.zones.R |only R/evaluation.strip.plot.R | 6 R/ordicoeno.R | 2 inst/ChangeLog |only inst/etc/R-logo-old.gif |only inst/etc/R-logo-old.ico |only inst/etc/R-logo.gif |binary inst/etc/R-logo.ico |binary inst/etc/Rcmdr-RMarkdown-Template.Rmd |only inst/etc/Rcmdr-menus.txt | 3 man/ensemble.Rd | 26 +- man/ensemble.analogue.Rd |only man/ensemble.batch.Rd | 13 - man/ensemble.ecocrop.Rd |only man/ensemble.novel.Rd |only man/ensemble.raster.Rd | 16 + man/ensemble.zones.Rd |only 34 files changed, 523 insertions(+), 344 deletions(-)
Title: Tools for Reading Formatted Access Log Files
Description: R is used by a vast array of people for a vast array of purposes
- including web analytics. This package contains functions for consuming and
munging various common forms of request log, including the Common and Combined
Web Log formats and various Amazon access logs.
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between webreadr versions 0.3.0 dated 2015-07-16 and 0.4.0 dated 2016-01-23
DESCRIPTION | 20 ++++-- MD5 | 56 +++++++++++------- NAMESPACE | 3 - NEWS | 17 +++++ R/RcppExports.R | 8 ++ R/bro.R |only R/readers.R | 69 ++++++++++++++++++++++- R/splitters.R | 19 ++++-- R/utilities.R | 8 ++ README.md | 8 +- build/vignette.rds |binary inst/doc/Introduction.Rmd | 9 ++- inst/doc/Introduction.html | 8 +- inst/extdata/app_stats.log |only inst/extdata/conn.log |only inst/extdata/dhcp.log |only inst/extdata/dns.log |only inst/extdata/files.log |only inst/extdata/ftp.log |only inst/extdata/http.log |only inst/extdata/s3.log |only man/read_aws.Rd | 5 + man/read_clf.Rd | 2 man/read_combined.Rd | 2 man/read_s3.Rd |only man/read_squid.Rd | 2 man/split_clf.Rd | 15 +++-- man/split_squid.Rd | 7 +- man/webreadr.Rd | 2 src/RcppExports.cpp | 22 +++++-- src/splitters.cpp | 118 +++++++++++++++++++++++++++++++++------- tests/testthat/test_bro.R |only tests/testthat/test_readers.R | 13 +++- tests/testthat/test_splitters.R |only vignettes/Introduction.Rmd | 9 ++- 35 files changed, 325 insertions(+), 97 deletions(-)
Title: Tables so Beautifully Fine-Tuned You Will Believe It's Magic
Description: The introduction of the broom package has made converting model objects into data
frames as simple as a single function. While the broom package focuses on providing tidy
data frames that can be used in advanced analysis, it deliberately stops short of providing
functionality for reporting models in publication-ready tables. pixiedust provides this
functionality with a programming interface intended to be similar to ggplot2's system of
layers with fine tuned control over each cell of the table. Options for output include
printing to the console and to the common markdown formats (markdown, HTML, and LaTeX).
With a little pixiedust (and happy thoughts) tables can really fly.
Author: Benjamin Nutter [aut, cre]
Maintainer: Benjamin Nutter <nutter@battelle.org>
Diff between pixiedust versions 0.5.0 dated 2015-10-15 and 0.6.1 dated 2016-01-23
pixiedust-0.5.0/pixiedust/vignettes/pixiedust_in_latex.Rmd |only pixiedust-0.6.1/pixiedust/DESCRIPTION | 8 pixiedust-0.6.1/pixiedust/MD5 | 71 - pixiedust-0.6.1/pixiedust/NAMESPACE | 5 pixiedust-0.6.1/pixiedust/NEWS | 48 + pixiedust-0.6.1/pixiedust/R/as.data.frame.dust.R | 140 +-- pixiedust-0.6.1/pixiedust/R/chain.R | 18 pixiedust-0.6.1/pixiedust/R/dust.R | 57 + pixiedust-0.6.1/pixiedust/R/glance_foot.R | 320 +++---- pixiedust-0.6.1/pixiedust/R/medley.R | 130 +- pixiedust-0.6.1/pixiedust/R/perform_function.R | 82 - pixiedust-0.6.1/pixiedust/R/pixie_count.R |only pixiedust-0.6.1/pixiedust/R/pixiedust-pkg.R | 54 - pixiedust-0.6.1/pixiedust/R/print.dust.R | 35 pixiedust-0.6.1/pixiedust/R/print_dust_console.R | 6 pixiedust-0.6.1/pixiedust/R/print_dust_html.R | 37 pixiedust-0.6.1/pixiedust/R/print_dust_latex.R | 529 ++++++++---- pixiedust-0.6.1/pixiedust/R/print_dust_markdown.R | 10 pixiedust-0.6.1/pixiedust/R/pvalString.R | 84 - pixiedust-0.6.1/pixiedust/R/redust.R | 122 +- pixiedust-0.6.1/pixiedust/R/sprinkle.R | 85 + pixiedust-0.6.1/pixiedust/R/sprinkle_colnames.R | 204 ++-- pixiedust-0.6.1/pixiedust/R/sprinkle_print_method.R | 36 pixiedust-0.6.1/pixiedust/R/sprinkle_table.R | 46 - pixiedust-0.6.1/pixiedust/R/tidy_levels_labels.R | 6 pixiedust-0.6.1/pixiedust/R/zzz.R | 6 pixiedust-0.6.1/pixiedust/README.md | 36 pixiedust-0.6.1/pixiedust/inst/doc/advancedMagic.html | 129 +- pixiedust-0.6.1/pixiedust/inst/doc/pixiedust.html | 26 pixiedust-0.6.1/pixiedust/inst/doc/sprinkles.html | 36 pixiedust-0.6.1/pixiedust/inst/sprinkles.csv | 22 pixiedust-0.6.1/pixiedust/man/compoundAssignment.Rd |only pixiedust-0.6.1/pixiedust/man/dust.Rd | 25 pixiedust-0.6.1/pixiedust/man/pixie_count.Rd |only pixiedust-0.6.1/pixiedust/man/print.dust.Rd | 5 pixiedust-0.6.1/pixiedust/man/sprinkle.Rd | 64 + pixiedust-0.6.1/pixiedust/tests/testthat/test-dust.R | 17 pixiedust-0.6.1/pixiedust/tests/testthat/test-pixie_count.R |only pixiedust-0.6.1/pixiedust/tests/testthat/test-sprinkles.R | 12 39 files changed, 1544 insertions(+), 967 deletions(-)
Title: Optimal Partitioning of Similarity Relations
Description: Contains a set of algorithms for creating
partitions and coverings of objects largely based on operations
on (dis)similarity relations (or matrices). There are several
iterative re-assignment algorithms optimizing different
goodness-of-clustering criteria. In addition, there are
covering algorithms 'clique' which derives maximal cliques, and
'maxpact' which creates a covering of maximally compact sets.
Graphical analyses and conversion routines are also included.
Author: David W. Roberts <droberts@montana.edu>
Maintainer: David W. Roberts <droberts@montana.edu>
Diff between optpart versions 2.1-1 dated 2013-09-12 and 2.2-0 dated 2016-01-23
optpart-2.1-1/optpart/INDEX |only optpart-2.1-1/optpart/R/testopt.R |only optpart-2.1-1/optpart/man/testopt.Rd |only optpart-2.2-0/optpart/DESCRIPTION | 14 +-- optpart-2.2-0/optpart/MD5 | 117 ++++++++++++-------------- optpart-2.2-0/optpart/NAMESPACE | 60 +++++++++++-- optpart-2.2-0/optpart/R/bestfit.R | 46 +++++++--- optpart-2.2-0/optpart/R/classmatch.R | 103 ++++++++-------------- optpart-2.2-0/optpart/R/clique.R | 26 ++++- optpart-2.2-0/optpart/R/clustify.R |only optpart-2.2-0/optpart/R/confus.R | 29 +----- optpart-2.2-0/optpart/R/disdiam.R | 74 ++-------------- optpart-2.2-0/optpart/R/maxpact.R | 96 +++++++++++++-------- optpart-2.2-0/optpart/R/mergeclust.R | 8 - optpart-2.2-0/optpart/R/murdoch.R | 4 optpart-2.2-0/optpart/R/neighbor.R | 10 -- optpart-2.2-0/optpart/R/optindval.R | 9 -- optpart-2.2-0/optpart/R/optpart.R | 59 +------------ optpart-2.2-0/optpart/R/optsil.R | 59 ++----------- optpart-2.2-0/optpart/R/opttdev.R | 9 -- optpart-2.2-0/optpart/R/partana.R | 43 +++------ optpart-2.2-0/optpart/R/partition.R | 36 +------- optpart-2.2-0/optpart/R/phi.R | 13 -- optpart-2.2-0/optpart/R/refine.R | 24 ----- optpart-2.2-0/optpart/R/reordclust.R | 8 - optpart-2.2-0/optpart/R/silhouette.R | 18 ++-- optpart-2.2-0/optpart/R/stride.R | 80 +++++++++++------ optpart-2.2-0/optpart/R/tabdev.R | 10 -- optpart-2.2-0/optpart/R/testpart.R | 43 ++------- optpart-2.2-0/optpart/R/typal.R | 9 -- optpart-2.2-0/optpart/man/bestfit.Rd | 3 optpart-2.2-0/optpart/man/classmatch.Rd | 2 optpart-2.2-0/optpart/man/clique.Rd | 14 +-- optpart-2.2-0/optpart/man/clique.test.Rd | 26 +++-- optpart-2.2-0/optpart/man/clustering.Rd | 2 optpart-2.2-0/optpart/man/compare.Rd | 2 optpart-2.2-0/optpart/man/confus.Rd | 2 optpart-2.2-0/optpart/man/consider.Rd | 2 optpart-2.2-0/optpart/man/disdiam.Rd | 16 +-- optpart-2.2-0/optpart/man/extract.Rd | 10 +- optpart-2.2-0/optpart/man/fuzconfus.Rd | 2 optpart-2.2-0/optpart/man/maxpact.Rd | 9 +- optpart-2.2-0/optpart/man/mergeclust.Rd | 2 optpart-2.2-0/optpart/man/murdoch.Rd | 2 optpart-2.2-0/optpart/man/neighbor.Rd | 8 - optpart-2.2-0/optpart/man/optindval.Rd | 2 optpart-2.2-0/optpart/man/optpart.Rd | 2 optpart-2.2-0/optpart/man/optpart.internal.Rd | 2 optpart-2.2-0/optpart/man/opttdev.Rd | 2 optpart-2.2-0/optpart/man/partana.Rd | 3 optpart-2.2-0/optpart/man/partition.Rd | 13 +- optpart-2.2-0/optpart/man/phi.Rd | 8 - optpart-2.2-0/optpart/man/refine.Rd | 2 optpart-2.2-0/optpart/man/reordclust.Rd | 2 optpart-2.2-0/optpart/man/silhouette.Rd | 25 +++-- optpart-2.2-0/optpart/man/slice.Rd | 2 optpart-2.2-0/optpart/man/stride.Rd | 10 -- optpart-2.2-0/optpart/man/tabdev.Rd | 10 +- optpart-2.2-0/optpart/man/testpart.Rd | 5 - optpart-2.2-0/optpart/man/typal.Rd | 9 ++ optpart-2.2-0/optpart/src/permute.f | 9 +- optpart-2.2-0/optpart/src/random.c |only 62 files changed, 529 insertions(+), 686 deletions(-)
Title: Numeric Routines for Optically Stimulated Luminescence Dating
Description: Package for optimizing regular numeric problems in optically stimulated luminescence
dating, such as: equivalent dose calculation, annual dose rate determination, growth curve
fitting, decay curve decomposition, fast-component equivalent dose estimation, statistical
age model optimization, and statistical plot visualization.
Author: Jun Peng [aut, cre], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb], Paul Gilbert [ctb], Ravi Varadhan [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between numOSL versions 1.8 dated 2015-05-05 and 1.9 dated 2016-01-23
numOSL-1.8/numOSL/NEWS |only numOSL-1.9/numOSL/DESCRIPTION | 25 ++++++--- numOSL-1.9/numOSL/MD5 | 43 +++++++--------- numOSL-1.9/numOSL/NAMESPACE | 7 ++ numOSL-1.9/numOSL/R/analyst.R | 47 +++++------------ numOSL-1.9/numOSL/R/calDA.R | 24 ++++++++ numOSL-1.9/numOSL/R/calED.R | 56 ++++++++++---------- numOSL-1.9/numOSL/R/dbED.R | 86 +++++++++++++++++--------------- numOSL-1.9/numOSL/man/analyst.Rd | 25 ++++----- numOSL-1.9/numOSL/man/calDA.Rd | 14 ++--- numOSL-1.9/numOSL/man/calED.Rd | 21 +++---- numOSL-1.9/numOSL/man/dbED.Rd | 16 +++-- numOSL-1.9/numOSL/man/decomp.Rd | 10 +-- numOSL-1.9/numOSL/man/fastED.Rd | 17 ++---- numOSL-1.9/numOSL/man/fitGrowth.Rd | 6 +- numOSL-1.9/numOSL/man/mcFMM.Rd | 8 +- numOSL-1.9/numOSL/man/mcMAM.Rd | 2 numOSL-1.9/numOSL/man/numOSL-package.Rd | 2 numOSL-1.9/numOSL/man/psRadialPlot.Rd | 4 - numOSL-1.9/numOSL/man/reportSAM.Rd | 6 +- numOSL-1.9/numOSL/man/select.Rd | 2 numOSL-1.9/numOSL/src/calED.f90 | 83 +++++++++++++++++++++++++----- numOSL-1.9/numOSL/src/inverse.f90 | 2 23 files changed, 293 insertions(+), 213 deletions(-)
Title: Tree Boosting for Multivariate Outcomes
Description: Fits a multivariate model of decision trees for multiple, continuous outcome variables. A model for each outcome variable is fit separately, selecting predictors that explain covariance in the outcomes. Built on top of 'gbm', which fits an ensemble of decision trees to univariate outcomes.
Author: Patrick Miller [aut, cre]
Maintainer: Patrick Miller <patrick.mil10@gmail.com>
Diff between mvtboost versions 0.4.0 dated 2016-01-16 and 0.4.1 dated 2016-01-23
mvtboost-0.4.0/mvtboost/tests/testthat/Rplots.pdf |only mvtboost-0.4.1/mvtboost/DESCRIPTION | 14 - mvtboost-0.4.1/mvtboost/MD5 | 53 +-- mvtboost-0.4.1/mvtboost/NAMESPACE | 1 mvtboost-0.4.1/mvtboost/R/mvtb_nonlin_test.R | 4 mvtboost-0.4.1/mvtboost/R/mvtb_plots.R | 2 mvtboost-0.4.1/mvtboost/R/mvtb_summary.R | 5 mvtboost-0.4.1/mvtboost/R/mvtboost.R | 2 mvtboost-0.4.1/mvtboost/build/partial.rdb |binary mvtboost-0.4.1/mvtboost/data/wellbeing.RData |binary mvtboost-0.4.1/mvtboost/inst/doc/mvtboost_vignette.R | 4 mvtboost-0.4.1/mvtboost/inst/doc/mvtboost_vignette.Rmd | 38 +- mvtboost-0.4.1/mvtboost/inst/doc/mvtboost_vignette.html | 116 ++++---- mvtboost-0.4.1/mvtboost/inst/doc/mvtboost_wellbeing.R | 4 mvtboost-0.4.1/mvtboost/inst/doc/mvtboost_wellbeing.Rmd | 57 ++-- mvtboost-0.4.1/mvtboost/inst/doc/mvtboost_wellbeing.html | 202 +++++++-------- mvtboost-0.4.1/mvtboost/man/mvtb.Rd | 2 mvtboost-0.4.1/mvtboost/man/mvtb.nonlin.Rd | 2 mvtboost-0.4.1/mvtboost/man/mvtboost-package.Rd | 6 mvtboost-0.4.1/mvtboost/man/summary.mvtb.Rd | 2 mvtboost-0.4.1/mvtboost/man/wellbeing.Rd | 2 mvtboost-0.4.1/mvtboost/tests/testthat/test_plot.R | 2 mvtboost-0.4.1/mvtboost/tests/testthat/test_summary.R | 2 mvtboost-0.4.1/mvtboost/vignettes/mvtboost_vignette.Rmd | 38 +- mvtboost-0.4.1/mvtboost/vignettes/mvtboost_wellbeing.Rmd | 57 ++-- mvtboost-0.4.1/mvtboost/vignettes/wb_cv5.Rdata |binary mvtboost-0.4.1/mvtboost/vignettes/wb_cv5test.Rdata |binary mvtboost-0.4.1/mvtboost/vignettes/wb_nonlin.Rdata |binary 28 files changed, 305 insertions(+), 310 deletions(-)
Title: Fast and Simple MongoDB Client for R
Description: High-level, high-performance MongoDB client based on libmongoc and
jsonlite. Includes support for aggregation, indexing, map-reduce, streaming,
SSL encryption and SASL authentication. The vignette gives a brief overview
of the available methods in the package.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.7 dated 2015-12-09 and 0.8 dated 2016-01-23
DESCRIPTION | 10 +-- MD5 | 36 +++++++------- NEWS | 4 + build/vignette.rds |binary inst/doc/intro.Rmd | 2 inst/doc/intro.html | 20 +++---- src/bson/bson-config.h | 9 +++ src/bson/bson-json.c | 2 src/bson/bson-stdint.h | 2 src/bson/bson-string.c | 2 src/bson/bson-version.h | 6 +- src/mongoc/mongoc-cursor.c | 6 +- src/mongoc/mongoc-gridfs.c | 13 ++++- src/mongoc/mongoc-server-description-private.h | 10 +++ src/mongoc/mongoc-server-description.c | 43 ++++++++++++++++ src/mongoc/mongoc-topology-description-private.h | 1 src/mongoc/mongoc-topology-description.c | 59 +++++++++++++++++++++-- src/mongoc/mongoc-version.h | 6 +- vignettes/intro.Rmd | 2 19 files changed, 182 insertions(+), 51 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-10 dated 2015-12-12 and 1.8-11 dated 2016-01-23
ChangeLog | 35 +++++ DESCRIPTION | 6 MD5 | 31 ++-- R/bam.r | 319 +++++++++++++++++++++++++++++++----------------- R/fast-REML.r | 41 +++--- R/gam.sim.r | 5 R/mgcv.r | 10 - R/misc.r | 29 ++-- R/smooth.r | 35 +++-- man/bam.Rd | 12 + man/bug.reports.mgcv.Rd |only man/jagam.Rd | 4 man/mgcv-parallel.Rd | 9 - src/discrete.c | 235 ++++++++++++++++++++++------------- src/init.c | 8 - src/mat.c | 32 +++- src/mgcv.h | 12 + 17 files changed, 526 insertions(+), 297 deletions(-)
Title: Modelling Actual, Potential and Reference Crop
Evapotranspiration
Description: Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo <danlu.guo@adelaide.edu.au>, Seth Westra <swestra@civeng.adelaide.edu.au>
Maintainer: Danlu Guo <danlu.guo@adelaide.edu.au>
Diff between Evapotranspiration versions 1.7 dated 2015-09-23 and 1.8 dated 2016-01-23
Evapotranspiration-1.7/Evapotranspiration/man/ET.Penpan.Rd |only Evapotranspiration-1.8/Evapotranspiration/DESCRIPTION | 10 Evapotranspiration-1.8/Evapotranspiration/MD5 | 89 Evapotranspiration-1.8/Evapotranspiration/NAMESPACE | 9 Evapotranspiration-1.8/Evapotranspiration/NEWS | 43 Evapotranspiration-1.8/Evapotranspiration/R/Evapotranspiration.R | 1039 ++++- Evapotranspiration-1.8/Evapotranspiration/R/Plotting.R | 1 Evapotranspiration-1.8/Evapotranspiration/R/Reading.R | 1888 ++++++---- Evapotranspiration-1.8/Evapotranspiration/data/E_OBS.RData |binary Evapotranspiration-1.8/Evapotranspiration/data/climatedata.rda |binary Evapotranspiration-1.8/Evapotranspiration/data/constants.RData |binary Evapotranspiration-1.8/Evapotranspiration/data/defaultconstants.RData |only Evapotranspiration-1.8/Evapotranspiration/data/processeddata.RData |binary Evapotranspiration-1.8/Evapotranspiration/man/ET.Abtew.Rd | 79 Evapotranspiration-1.8/Evapotranspiration/man/ET.BlaneyCriddle.Rd | 87 Evapotranspiration-1.8/Evapotranspiration/man/ET.BrutsaertStrickler.Rd | 90 Evapotranspiration-1.8/Evapotranspiration/man/ET.ChapmanAustralian.Rd | 113 Evapotranspiration-1.8/Evapotranspiration/man/ET.GrangerGray.Rd | 103 Evapotranspiration-1.8/Evapotranspiration/man/ET.Hamon.Rd | 61 Evapotranspiration-1.8/Evapotranspiration/man/ET.HargreavesSamani.Rd | 63 Evapotranspiration-1.8/Evapotranspiration/man/ET.JensenHaise.Rd | 78 Evapotranspiration-1.8/Evapotranspiration/man/ET.Linacre.Rd | 61 Evapotranspiration-1.8/Evapotranspiration/man/ET.Makkink.Rd | 81 Evapotranspiration-1.8/Evapotranspiration/man/ET.MattShuttleworth.Rd | 101 Evapotranspiration-1.8/Evapotranspiration/man/ET.McGuinnessBordne.Rd | 63 Evapotranspiration-1.8/Evapotranspiration/man/ET.MortonCRAE.Rd | 116 Evapotranspiration-1.8/Evapotranspiration/man/ET.MortonCRWE.Rd | 116 Evapotranspiration-1.8/Evapotranspiration/man/ET.PenPan.Rd |only Evapotranspiration-1.8/Evapotranspiration/man/ET.Penman.Rd | 115 Evapotranspiration-1.8/Evapotranspiration/man/ET.PenmanMonteith.Rd | 101 Evapotranspiration-1.8/Evapotranspiration/man/ET.PriestleyTaylor.Rd | 93 Evapotranspiration-1.8/Evapotranspiration/man/ET.Rd | 92 Evapotranspiration-1.8/Evapotranspiration/man/ET.Romanenko.Rd | 58 Evapotranspiration-1.8/Evapotranspiration/man/ET.SzilagyiJozsa.Rd | 115 Evapotranspiration-1.8/Evapotranspiration/man/ET.Turc.Rd | 94 Evapotranspiration-1.8/Evapotranspiration/man/ETComparison.Rd | 72 Evapotranspiration-1.8/Evapotranspiration/man/ETForcings.Rd | 49 Evapotranspiration-1.8/Evapotranspiration/man/ETPlot.Rd | 43 Evapotranspiration-1.8/Evapotranspiration/man/E_OBS.Rd | 2 Evapotranspiration-1.8/Evapotranspiration/man/Radiation.Rd | 10 Evapotranspiration-1.8/Evapotranspiration/man/ReadInput_InterpAbnormal.Rd |only Evapotranspiration-1.8/Evapotranspiration/man/ReadInput_InterpMissing.Rd |only Evapotranspiration-1.8/Evapotranspiration/man/ReadInputs.Rd | 134 Evapotranspiration-1.8/Evapotranspiration/man/ReadOBSEvaporation.Rd | 18 Evapotranspiration-1.8/Evapotranspiration/man/climatedata.Rd | 33 Evapotranspiration-1.8/Evapotranspiration/man/constants.Rd | 111 Evapotranspiration-1.8/Evapotranspiration/man/data.Rd | 18 Evapotranspiration-1.8/Evapotranspiration/man/defaultconstants.Rd |only Evapotranspiration-1.8/Evapotranspiration/man/processeddata.Rd |only 49 files changed, 3767 insertions(+), 1682 deletions(-)
More information about Evapotranspiration at CRAN
Permanent link
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly
configurable drop-in replacements for base url() and download.file() with
better performance, support for encryption (https, ftps), gzip compression,
authentication, and other libcurl goodies. The core of the package implements a
framework for performing fully customized requests where data can be processed
either in memory, on disk, or streaming via the callback or connection
interfaces. Some knowledge of libcurl is recommended; for a more-user-friendly
web client see the 'httr' package which builds on this package with http
specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.9.4 dated 2015-11-20 and 0.9.5 dated 2016-01-23
DESCRIPTION | 28 +++++++++++++++------------- LICENSE | 2 +- MD5 | 37 ++++++++++++++++++++----------------- NAMESPACE | 4 +++- NEWS | 3 +++ R/nslooup.R |only build/vignette.rds |binary inst/doc/intro.html | 46 +++++++++++++++++++++++----------------------- man/curl.Rd | 3 ++- man/curl_download.Rd | 2 +- man/curl_escape.Rd | 2 +- man/curl_fetch.Rd | 2 +- man/curl_options.Rd | 2 +- man/form_file.Rd | 2 +- man/handle.Rd | 2 +- man/handle_cookies.Rd | 7 ++----- man/ie_proxy.Rd | 2 +- man/nslookup.Rd |only man/parse_date.Rd | 2 +- man/parse_headers.Rd | 2 +- src/nslookup.c |only 21 files changed, 78 insertions(+), 70 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.6.3 dated 2015-10-23 and 1.7.0 dated 2016-01-23
checkmate-1.6.3/checkmate/R/checkPercentage.r |only checkmate-1.6.3/checkmate/man/checkPercentage.Rd |only checkmate-1.6.3/checkmate/man/checkmate.Rd |only checkmate-1.6.3/checkmate/tests/testthat/test_checkPercentage.r |only checkmate-1.6.3/checkmate/tests/testthat/test_qtest.r |only checkmate-1.6.3/checkmate/tests/testthat/test_qtestr.r |only checkmate-1.7.0/checkmate/DESCRIPTION | 25 checkmate-1.7.0/checkmate/MD5 | 257 ++++---- checkmate-1.7.0/checkmate/NAMESPACE | 89 ++ checkmate-1.7.0/checkmate/R/allMissing.r | 2 checkmate-1.7.0/checkmate/R/anyInfinite.r | 4 checkmate-1.7.0/checkmate/R/anyMissing.r | 2 checkmate-1.7.0/checkmate/R/anyNaN.r | 2 checkmate-1.7.0/checkmate/R/checkAccess.r | 31 - checkmate-1.7.0/checkmate/R/checkArray.r | 42 - checkmate-1.7.0/checkmate/R/checkAtomic.r | 37 - checkmate-1.7.0/checkmate/R/checkAtomicVector.r | 36 - checkmate-1.7.0/checkmate/R/checkCharacter.r | 64 -- checkmate-1.7.0/checkmate/R/checkChoice.r | 31 - checkmate-1.7.0/checkmate/R/checkClass.r | 31 - checkmate-1.7.0/checkmate/R/checkComplex.r | 36 - checkmate-1.7.0/checkmate/R/checkCount.r | 36 - checkmate-1.7.0/checkmate/R/checkDataFrame.r | 41 - checkmate-1.7.0/checkmate/R/checkDataTable.r |only checkmate-1.7.0/checkmate/R/checkDirectory.r | 31 - checkmate-1.7.0/checkmate/R/checkEnvironment.r | 31 - checkmate-1.7.0/checkmate/R/checkFactor.r | 118 +-- checkmate-1.7.0/checkmate/R/checkFile.r | 29 checkmate-1.7.0/checkmate/R/checkFlag.r | 36 - checkmate-1.7.0/checkmate/R/checkFunction.r | 31 - checkmate-1.7.0/checkmate/R/checkInt.r | 36 - checkmate-1.7.0/checkmate/R/checkInteger.r | 36 - checkmate-1.7.0/checkmate/R/checkIntegerish.r | 38 - checkmate-1.7.0/checkmate/R/checkList.r | 54 - checkmate-1.7.0/checkmate/R/checkLogical.r | 36 - checkmate-1.7.0/checkmate/R/checkMatrix.r | 38 - checkmate-1.7.0/checkmate/R/checkNamed.r | 39 - checkmate-1.7.0/checkmate/R/checkNames.r | 40 - checkmate-1.7.0/checkmate/R/checkNull.r | 27 checkmate-1.7.0/checkmate/R/checkNumber.r | 33 - checkmate-1.7.0/checkmate/R/checkNumeric.r | 36 - checkmate-1.7.0/checkmate/R/checkPathForOutput.r | 33 - checkmate-1.7.0/checkmate/R/checkScalar.r | 36 - checkmate-1.7.0/checkmate/R/checkScalarNA.r | 31 - checkmate-1.7.0/checkmate/R/checkSetEqual.r | 31 - checkmate-1.7.0/checkmate/R/checkString.r | 36 - checkmate-1.7.0/checkmate/R/checkSubset.r | 31 - checkmate-1.7.0/checkmate/R/checkVector.r | 36 - checkmate-1.7.0/checkmate/R/helper.r | 26 checkmate-1.7.0/checkmate/R/isIntegerish.r | 2 checkmate-1.7.0/checkmate/R/makeAssertion.r |only checkmate-1.7.0/checkmate/R/makeExpectation.r |only checkmate-1.7.0/checkmate/R/makeTest.r |only checkmate-1.7.0/checkmate/R/qassert.r | 34 - checkmate-1.7.0/checkmate/R/qassertr.r | 17 checkmate-1.7.0/checkmate/R/wfwl.r | 6 checkmate-1.7.0/checkmate/R/zzz.r | 8 checkmate-1.7.0/checkmate/build/vignette.rds |binary checkmate-1.7.0/checkmate/inst/NEWS.md | 17 checkmate-1.7.0/checkmate/inst/README.md | 3 checkmate-1.7.0/checkmate/inst/doc/checkmate.R | 67 ++ checkmate-1.7.0/checkmate/inst/doc/checkmate.Rmd | 248 ++++++-- checkmate-1.7.0/checkmate/inst/doc/checkmate.html | 301 +++++++--- checkmate-1.7.0/checkmate/inst/include |only checkmate-1.7.0/checkmate/man/AssertCollection.Rd | 2 checkmate-1.7.0/checkmate/man/anyInfinite.Rd | 4 checkmate-1.7.0/checkmate/man/anyMissing.Rd | 2 checkmate-1.7.0/checkmate/man/anyNaN.Rd | 2 checkmate-1.7.0/checkmate/man/asInteger.Rd | 2 checkmate-1.7.0/checkmate/man/assert.Rd | 2 checkmate-1.7.0/checkmate/man/checkAccess.Rd | 32 - checkmate-1.7.0/checkmate/man/checkArray.Rd | 80 -- checkmate-1.7.0/checkmate/man/checkAtomic.Rd | 125 +--- checkmate-1.7.0/checkmate/man/checkAtomicVector.Rd | 77 -- checkmate-1.7.0/checkmate/man/checkCharacter.Rd | 70 -- checkmate-1.7.0/checkmate/man/checkChoice.Rd | 28 checkmate-1.7.0/checkmate/man/checkClass.Rd | 20 checkmate-1.7.0/checkmate/man/checkComplex.Rd | 69 -- checkmate-1.7.0/checkmate/man/checkCount.Rd | 44 - checkmate-1.7.0/checkmate/man/checkDataFrame.Rd | 72 -- checkmate-1.7.0/checkmate/man/checkDataTable.Rd |only checkmate-1.7.0/checkmate/man/checkDirectory.Rd | 33 - checkmate-1.7.0/checkmate/man/checkEnvironment.Rd | 63 -- checkmate-1.7.0/checkmate/man/checkFactor.Rd | 73 -- checkmate-1.7.0/checkmate/man/checkFile.Rd | 31 - checkmate-1.7.0/checkmate/man/checkFlag.Rd | 42 - checkmate-1.7.0/checkmate/man/checkFunction.Rd | 67 -- checkmate-1.7.0/checkmate/man/checkInt.Rd | 44 - checkmate-1.7.0/checkmate/man/checkInteger.Rd | 72 -- checkmate-1.7.0/checkmate/man/checkIntegerish.Rd | 71 -- checkmate-1.7.0/checkmate/man/checkList.Rd | 73 -- checkmate-1.7.0/checkmate/man/checkLogical.Rd | 70 -- checkmate-1.7.0/checkmate/man/checkMatrix.Rd | 78 -- checkmate-1.7.0/checkmate/man/checkNamed.Rd | 22 checkmate-1.7.0/checkmate/man/checkNames.Rd | 22 checkmate-1.7.0/checkmate/man/checkNull.Rd | 20 checkmate-1.7.0/checkmate/man/checkNumber.Rd | 43 - checkmate-1.7.0/checkmate/man/checkNumeric.Rd | 71 -- checkmate-1.7.0/checkmate/man/checkPathForOutput.Rd | 32 - checkmate-1.7.0/checkmate/man/checkScalar.Rd | 42 - checkmate-1.7.0/checkmate/man/checkScalarNA.Rd | 40 - checkmate-1.7.0/checkmate/man/checkSetEqual.Rd | 29 checkmate-1.7.0/checkmate/man/checkString.Rd | 42 - checkmate-1.7.0/checkmate/man/checkSubset.Rd | 28 checkmate-1.7.0/checkmate/man/checkVector.Rd | 81 -- checkmate-1.7.0/checkmate/man/checkmate-package.Rd |only checkmate-1.7.0/checkmate/man/coalesce.Rd | 2 checkmate-1.7.0/checkmate/man/makeAssertion.Rd |only checkmate-1.7.0/checkmate/man/makeExpectation.Rd |only checkmate-1.7.0/checkmate/man/makeTest.Rd |only checkmate-1.7.0/checkmate/man/qassert.Rd | 20 checkmate-1.7.0/checkmate/man/qassertr.Rd | 4 checkmate-1.7.0/checkmate/src/all_missing.h | 2 checkmate-1.7.0/checkmate/src/all_nchar.h | 2 checkmate-1.7.0/checkmate/src/any_infinite.h | 2 checkmate-1.7.0/checkmate/src/any_missing.h | 2 checkmate-1.7.0/checkmate/src/any_nan.h | 2 checkmate-1.7.0/checkmate/src/checkmate_init.c |only checkmate-1.7.0/checkmate/src/checks.c | 56 + checkmate-1.7.0/checkmate/src/checks.h | 2 checkmate-1.7.0/checkmate/src/cmessages.h | 2 checkmate-1.7.0/checkmate/src/helper.h | 2 checkmate-1.7.0/checkmate/src/is_integerish.h | 2 checkmate-1.7.0/checkmate/src/qassert.c | 17 checkmate-1.7.0/checkmate/src/qassert.h | 4 checkmate-1.7.0/checkmate/src/which_first.h | 3 checkmate-1.7.0/checkmate/tests/testthat/checkmate.test.include |only checkmate-1.7.0/checkmate/tests/testthat/helper.r | 62 +- checkmate-1.7.0/checkmate/tests/testthat/test_checkDataFrame.r | 28 checkmate-1.7.0/checkmate/tests/testthat/test_checkDataTable.r |only checkmate-1.7.0/checkmate/tests/testthat/test_checkFilesystem.r | 6 checkmate-1.7.0/checkmate/tests/testthat/test_checkNumeric.r | 2 checkmate-1.7.0/checkmate/tests/testthat/test_checkScalarNA.r | 3 checkmate-1.7.0/checkmate/tests/testthat/test_include.r |only checkmate-1.7.0/checkmate/tests/testthat/test_interoperability.r |only checkmate-1.7.0/checkmate/tests/testthat/test_qassert.r |only checkmate-1.7.0/checkmate/tests/testthat/test_qassertr.r |only checkmate-1.7.0/checkmate/vignettes/checkmate.Rmd | 201 ++++-- 138 files changed, 2509 insertions(+), 2155 deletions(-)
Title: A Compression Format Optimized for the Web
Description: A lossless compressed data format that uses a combination of the LZ77
algorithm and Huffman coding. Brotli is similar in speed to deflate (gzip) but
offers more dense compression.
Author: Jeroen Ooms [aut, cre],
Google, Inc [aut, cph] (Brotli C++ library)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between brotli versions 0.4 dated 2015-11-26 and 0.5 dated 2016-01-23
DESCRIPTION | 8 LICENSE |only MD5 | 131 +++--- NEWS |only build/vignette.rds |binary inst/doc/benchmarks.html | 24 - src/Makevars | 9 src/dec/bit_reader.c | 13 src/dec/bit_reader.h | 13 src/dec/context.h | 13 src/dec/decode.c | 13 src/dec/decode.h | 13 src/dec/dictionary.c | 13 src/dec/dictionary.h | 13 src/dec/huffman.c | 13 src/dec/huffman.h | 13 src/dec/port.h | 13 src/dec/prefix.h | 13 src/dec/state.c | 13 src/dec/state.h | 13 src/dec/streams.c | 13 src/dec/streams.h | 13 src/dec/transform.h | 13 src/dec/types.h | 13 src/enc/backward_references.cc | 375 ++++++++--------- src/enc/backward_references.h | 27 - src/enc/bit_cost.h | 58 +- src/enc/block_splitter.cc | 138 ++---- src/enc/block_splitter.h | 34 - src/enc/brotli_bit_stream.cc | 736 ++++++++++++++++++++++------------ src/enc/brotli_bit_stream.h | 125 +++-- src/enc/cluster.h | 190 ++++---- src/enc/command.h | 83 +-- src/enc/compress_fragment.cc |only src/enc/compress_fragment.h |only src/enc/compress_fragment_two_pass.cc |only src/enc/compress_fragment_two_pass.h |only src/enc/context.h | 22 - src/enc/dictionary.cc | 18 src/enc/dictionary.h | 24 - src/enc/dictionary_hash.h | 20 src/enc/encode.cc | 598 ++++++++++++++++++++------- src/enc/encode.h | 64 +- src/enc/encode_parallel.cc | 97 ++-- src/enc/encode_parallel.h | 20 src/enc/entropy_encode.cc | 208 ++++----- src/enc/entropy_encode.h | 52 +- src/enc/entropy_encode_static.h |only src/enc/fast_log.h | 63 -- src/enc/find_match_length.h | 38 - src/enc/hash.h | 317 ++++++++------ src/enc/histogram.cc | 28 - src/enc/histogram.h | 42 - src/enc/literal_cost.cc | 106 ++-- src/enc/literal_cost.h | 20 src/enc/metablock.cc | 182 +++----- src/enc/metablock.h | 42 - src/enc/port.h | 43 - src/enc/prefix.h | 65 +-- src/enc/ringbuffer.h | 75 +-- src/enc/static_dict.cc | 110 ++--- src/enc/static_dict.h | 30 - src/enc/static_dict_lut.h | 20 src/enc/streams.cc | 20 src/enc/streams.h | 20 src/enc/transform.h | 97 ++-- src/enc/types.h | 13 src/enc/utf8_util.cc | 25 - src/enc/utf8_util.h | 24 - src/enc/write_bits.h | 32 - 70 files changed, 2440 insertions(+), 2254 deletions(-)
Title: Fungible Coefficients and Monte Carlo Functions
Description: Functions for computing fungible coefficients and Monte Carlo data.
Author: Niels G. Waller <nwaller@umn.edu> and Jeff Jones <jeff.jones@kornferry.com>
Maintainer: Niels G. Waller <nwaller@umn.edu>
Diff between fungible versions 1.2 dated 2015-12-15 and 1.3 dated 2016-01-23
DESCRIPTION | 8 - MD5 | 8 - inst/CITATION | 4 inst/doc/fungible-manual.pdf |binary man/fungibleR.Rd | 201 ++++++++++++++++++++++++++++++++++++++++--- 5 files changed, 201 insertions(+), 20 deletions(-)
Title: Social Relations Analyses with Roles ("Family SRM")
Description: Social Relations Analysis with roles ("Family SRM") are computed,
using a structural equation modeling approach. Groups ranging from three members
up to an unlimited number of members are supported and the mean structure can
be computed. Means and variances can be compared between different groups of
families and between roles.
Author: Felix Schönbrodt, Lara Stas, Tom Loeys
Maintainer: Felix Schönbrodt <felix@nicebread.de>
Diff between fSRM versions 0.6.1 dated 2014-12-08 and 0.6.4 dated 2016-01-23
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Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
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Title: A Tool Set for Analyzing Political Behavior Data
Description: Provides functions for analyzing political behavior data, including measures of political fragmentation, seat apportionment, and graphical demonstrations.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>
Diff between SciencesPo versions 1.3.8 dated 2015-10-19 and 1.3.9 dated 2016-01-22
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Title: Regression Analysis of Sparse Asynchronous Longitudinal Data
Description: Estimation of regression models for sparse asynchronous longitudinal observations, where time-dependent response and covariates are mismatched and observed intermittently within subjects. Kernel weighted estimating equations are used for generalized linear models with either time-invariant or time-dependent coefficients.
Author: Hongyuan Cao, Donglin Zeng, Jialiang Li, Jason P. Fine, and Shannon T. Holloway
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between AsynchLong versions 1.0 dated 2015-02-22 and 2.0 dated 2016-01-22
DESCRIPTION | 12 +-- MD5 | 51 ++++++++------- NAMESPACE | 11 ++- R/SD.R | 102 +++++++++++++++---------------- R/asynchHK.R |only R/asynchLV.R | 47 +++++++------- R/asynchTD.R | 75 +++++++++++++---------- R/asynchTI.R | 72 +++++++++++----------- R/asynchWLV.R |only R/betaHat.R | 132 ++++++++++++++++++++--------------------- R/distances.R | 141 +++++++++++++++++++++++++++++++++++++++---- R/duFunc.R | 80 ++++++++++++------------ R/kernelAuto.R | 148 +++++++++++++++++++++++++++------------------- R/kernelFixed.R | 66 +++++++++++++++++++- R/optFunc.R | 112 ++++++++++++++++++---------------- R/plotTD.R | 46 +++++++------- R/preprocessX.R | 56 +++++++++-------- R/preprocessY.R | 31 +++++---- R/uFunc.R | 61 +++++++++--------- R/uFuncIden.R | 54 ++++++++-------- R/zzz.R |only man/AsynchLong-package.Rd | 12 ++- man/asynchDataTD.Rd | 2 man/asynchDataTI.Rd | 2 man/asynchHK.Rd |only man/asynchLV.Rd | 2 man/asynchTD.Rd | 2 man/asynchTI.Rd | 5 - man/asynchWLV.Rd |only 29 files changed, 787 insertions(+), 535 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-64 dated 2015-11-21 and 0.1-66 dated 2016-01-22
DESCRIPTION | 10 MD5 | 30 + NAMESPACE | 10 NEWS | 13 R/ICA.BinBin.Grid.Sample.R | 781 +++++++++++++++++++++++++++++++++++++++++- R/MaxEntICABinBin.R |only R/MaxEntSPFBinBin.R |only R/SummaryMaxEntSPFBinBin.R |only R/plot.MaxEntSPF.BinBin.R |only R/plot_MaxEntICABinBin.R |only R/plot_SPPBinBin.R | 1 R/summary_MaxEntICABinBin.R |only man/ICA.BinBin.Grid.Full.Rd | 2 man/ICA.BinBin.Grid.Sample.Rd | 14 man/ICABinBin.Rd | 4 man/MaxEntICABinBin.Rd |only man/MaxEntSPFBinBin.Rd |only man/SPP.BinBin.Rd | 19 - man/plot.MaxEntICABinBin.Rd |only man/plot.MaxEntSPFBinBin.Rd |only man/summary.gen.Rd | 4 21 files changed, 849 insertions(+), 39 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics'
Engine 'eBird', 'AntWeb', and 'iDigBio'. Includes functionality for
retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.4.0 dated 2015-10-02 and 0.4.4 dated 2016-01-22
DESCRIPTION | 31 ++++++-------- LICENSE | 2 MD5 | 85 ++++++++++++++++++++------------------ NAMESPACE | 9 ++-- R/antweb_helpers.R |only R/as.ecoengine.R | 2 R/ecoengine_helpers.R |only R/occ.r | 4 - R/occ2df.R | 17 +------ R/occ_names.R | 80 ++++++++++++++++++------------------ R/occ_names_options.R | 1 R/plugin_helpers.R |only R/plugins.r | 94 +++++-------------------------------------- R/spocc-package.R | 40 ++++++++++++++++-- R/zzz.r | 19 ++++++++ README.md | 79 +++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/spocc_vignette.Rmd | 5 +- inst/doc/spocc_vignette.html | 4 + man/as.antweb.Rd | 6 +- man/as.bison.Rd | 10 ++-- man/as.ecoengine.Rd | 2 man/as.gbif.Rd | 10 ++-- man/as.idigbio.Rd | 4 - man/as.inat.Rd | 2 man/as.vertnet.Rd | 2 man/bbox2wkt.Rd | 2 man/fixnames.Rd | 6 +- man/inspect.Rd | 4 - man/occ.Rd | 20 +++++---- man/occ2df.Rd | 2 man/occ_coverage.Rd | 2 man/occ_names.Rd | 4 - man/occ_names_options.Rd | 2 man/occ_options.Rd | 2 man/spocc-package.Rd | 48 ++++++++++++++++++++- man/spocc_capwords.Rd | 4 - man/spocc_colClasses.Rd | 4 - man/spocc_duplicates.Rd | 20 ++++----- man/spocc_objects.Rd | 6 +- man/spocc_type_sum.Rd | 2 man/wkt.Rd | 2 man/wkt_vis.Rd | 6 +- tests/testthat/test-occ.R | 57 ++++++++++++++++---------- vignettes/spocc_vignette.Rmd | 5 +- 45 files changed, 377 insertions(+), 329 deletions(-)
Title: Statistical Inference for MOdular NEtworks (SIMoNe)
Description: Implements the inference of
co-expression networks based on partial correlation
coefficients from either steady-state or time-course
transcriptomic data. Note that with both type of data this
package can deal with samples collected in different
experimental conditions and therefore not identically
distributed. In this particular case, multiple but related
networks are inferred on one simone run.
Author: Julien Chiquet <julien.chiquet@genopole.cnrs.fr>, Gilles
Grasseau <gilles.grasseau@genopole.cnrs.fr>, Camille
Charbonnier <camille.charbonnier@genopole.cnrs.fr>, Christophe
Ambroise <christophe.ambroise@genopole.cnrs.fr>.
Maintainer: Julien Chiquet <julien.chiquet@genopole.cnrs.fr>
Diff between simone versions 1.0-2 dated 2013-12-16 and 1.0-3 dated 2016-01-22
DESCRIPTION | 33 +++++++++++++++++---------------- MD5 | 12 ++++++------ NAMESPACE | 3 +++ NEWS | 3 +++ R/init.R | 4 ++-- inst/CITATION | 18 +++++++++--------- man/simone.Rd | 2 ++ 7 files changed, 42 insertions(+), 33 deletions(-)
Title: ViennaCL C++ Header Files
Description: ViennaCL is a free open-source linear algebra library
for computations on many-core architectures (GPUs, MIC) and
multi-core CPUs. The library is written in C++ and supports CUDA,
OpenCL, and OpenMP (including switches at runtime).
I have placed these libraries in this package as a more efficient
distribution system for CRAN. The idea is that you can write a package
that depends on the ViennaCL library and yet you do not need to
distribute a copy of this code with your package.
Author: Charles Determan Jr.
Maintainer: Charles Determan Jr <cdetermanjr@gmail.com>
Diff between RViennaCL versions 1.7.0-0 dated 2015-10-31 and 1.7.1-0 dated 2016-01-22
RViennaCL-1.7.0-0/RViennaCL/inst/NEW.Rd |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/matrix_axpy.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/reduction.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/row_wise_reduction.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/vector_axpy.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/templates/matrix_axpy_template.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/templates/reduction_template.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/templates/row_wise_reduction_template.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/templates/vector_axpy_template.hpp |only RViennaCL-1.7.1-0/RViennaCL/DESCRIPTION | 9 RViennaCL-1.7.1-0/RViennaCL/MD5 | 516 ++-- RViennaCL-1.7.1-0/RViennaCL/README.md | 2 RViennaCL-1.7.1-0/RViennaCL/build/partial.rdb |binary RViennaCL-1.7.1-0/RViennaCL/inst/NEWS.Rd |only RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/cpu_ram.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/cuda.hpp | 9 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/mem_handle.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/memory.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/opencl.hpp | 9 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/util.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/circulant_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/compressed_compressed_matrix.hpp | 39 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/compressed_matrix.hpp | 46 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/context.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/coordinate_matrix.hpp | 55 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/detail/matrix_def.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/detail/vector_def.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/common.hpp | 56 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/accelerator/fallback.hpp | 56 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/cpu/fallback.hpp | 56 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ev/cedar.hpp | 35 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ev/cypress.hpp | 59 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ni/barts.hpp | 35 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ni/devastator.hpp | 35 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ni/scrapper.hpp | 35 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/si/tahiti.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/vi/hawaii.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/fallback.hpp | 56 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/ge_gt_540m.hpp | 48 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/ge_gtx_470.hpp | 61 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/ge_gtx_580.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/tesla_c2050.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/k/tesla_k20m.hpp | 76 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/m/ge_gtx_750_ti.hpp | 59 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/tesla/ge_gtx_260.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/matrix_product.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/execute.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/execution_handler.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/forwards.h | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/lazy_program_compiler.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/mapped_objects.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/templates/matrix_product_template.hpp | 46 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/templates/template_base.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/templates/utils.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/tree_parsing.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/utils.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ell_matrix.hpp | 54 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/fft.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/forwards.h | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/hankel_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/hyb_matrix.hpp | 52 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/io/matrix_market.hpp | 37 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/amg.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/amg_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/bicgstab.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/bisect.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/bisect_gpu.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cg.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/circulant_matrix_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/amg_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_calls.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_large.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_large_multi.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_large_onei.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_small.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_util.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/common.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/direct_solve.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/fft_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/ilu_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/iterative_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/matrix_operations_col.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/matrix_operations_prod.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/matrix_operations_row.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/misc_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/nmf_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/scalar_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/sparse_matrix_operations.hpp | 436 ++- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/sparse_matrix_operations_solve.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/spgemm.hpp | 23 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/spgemm_rmerge.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/vector_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/amg/amg_base.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/bisect_kernel_calls.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/bisect_large.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/bisect_small.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/config.hpp | 2 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/gerschgorin.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/structs.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/util.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/block_ilu.hpp | 19 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/chow_patel_ilu.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/common.hpp | 19 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/ilu0.hpp | 15 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/ilut.hpp | 15 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/op_applier.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/op_executor.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/block_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/block_vector.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/fspai.hpp | 33 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/qr.hpp | 9 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/small_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/spai-dynamic.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/spai-static.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/spai.hpp | 25 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/spai_tag.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/sparse_vector.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/direct_solve.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/eig.hpp | 2 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/fft_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/gmres.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/hankel_matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/amg_operations.hpp | 37 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/common.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/direct_solve.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/fft_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/ilu_operations.hpp | 21 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/iterative_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/matrix_operations.hpp | 499 ++-- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/misc_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/nmf_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/scalar_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/sparse_matrix_operations.hpp | 117 - RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/spgemm_vector.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/vector_operations.hpp | 162 + RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/ichol.hpp | 13 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/ilu.hpp | 2 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/ilu_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/inner_prod.hpp | 19 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/iterative_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/jacobi_precond.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/lanczos.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/lu.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/maxmin.hpp | 13 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/misc_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/mixed_precision_cg.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/nmf.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/norm_1.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/norm_2.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/norm_frobenius.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/norm_inf.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/amg_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/bisect_kernel_calls.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/common.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/direct_solve.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/fft_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/ilu_operations.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/iterative_operations.hpp | 4 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/amg.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/bisect.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/compressed_compressed_matrix.hpp | 13 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/compressed_matrix.hpp | 159 + RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/coordinate_matrix.hpp | 24 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/ell_matrix.hpp | 24 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/fft.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/hyb_matrix.hpp | 22 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/ilu.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/iterative.hpp | 20 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/matrix.hpp | 703 ++++-- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/matrix_element.hpp |only RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/matrix_solve.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/nmf.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/scalar.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/scan.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/sliced_ell_matrix.hpp | 24 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/spai.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/svd.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/vector.hpp | 882 ++++++-- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/vector_element.hpp |only RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/matrix_operations.hpp | 579 ++++- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/misc_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/nmf_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/scalar_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/sparse_matrix_operations.hpp | 279 +- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/vandermonde_matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/vector_operations.hpp | 1101 +++++++--- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/power_iter.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/prod.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/qr-method-common.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/qr-method.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/qr.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/row_scaling.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/scalar_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/spai.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/sparse_matrix_operations.hpp | 13 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/sum.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/svd.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/toeplitz_matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/tql2.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/vandermonde_matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/vector_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/matrix.hpp | 63 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/matrix_proxy.hpp | 108 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/meta/enable_if.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/meta/predicate.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/meta/result_of.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/meta/tag_of.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/misc/bandwidth_reduction.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/misc/cuthill_mckee.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/misc/gibbs_poole_stockmeyer.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/backend.hpp | 19 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/command_queue.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/context.hpp | 127 - RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/device.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/device_utils.hpp | 12 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/enqueue.hpp | 23 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/error.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/forwards.h | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/handle.hpp | 9 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/kernel.hpp | 43 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/local_mem.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/platform.hpp | 11 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/program.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/utils.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/range.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scalar.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_axbx.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_elementwise.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_generic_dispatcher.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_matrix_dispatcher.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_matrix_prod.hpp | 23 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_scalar_assign.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_scalar_dispatcher.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_util.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_vector_dispatcher.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/forwards.h | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/io.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/preset.hpp | 386 --- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/slice.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/sliced_ell_matrix.hpp | 43 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/toeplitz_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/adapter.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/entry_proxy.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/matrix_generation.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/matrix_size_deducer.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/random.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/sha1.hpp | 1 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/shared_ptr.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/timer.hpp | 4 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/tools.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/clear.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/context.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/fill.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/handle.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/row_major.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/size.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/start.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/stride.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/vandermonde_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/vector.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/vector_proxy.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/version.hpp | 2 265 files changed, 5198 insertions(+), 3460 deletions(-)
Title: Base Package for Phylogenetic Structures and Comparative Data
Description: Provides a base S4 class for comparative methods, incorporating
one or more trees and trait data.
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler,
Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut
Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara,
Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between phylobase versions 0.8.0 dated 2015-07-24 and 0.8.2 dated 2016-01-22
DESCRIPTION | 15 +++---- MD5 | 92 +++++++++++++++++++++---------------------- NAMESPACE | 2 NEWS.md | 3 + R/phylo4d-methods.R | 2 R/treePlot.R | 6 +- build/vignette.rds |binary man/MRCA.Rd | 4 - man/addData-methods.Rd | 4 - man/ancestors.Rd | 5 +- man/checkPhylo4.Rd | 2 man/edgeLength-methods.Rd | 4 - man/edges-accessors.Rd | 4 - man/extractTree.Rd | 3 - man/formatData.Rd | 2 man/geospiza.Rd | 4 + man/getNode-methods.Rd | 6 +- man/labels-methods.Rd | 3 - man/multiPhylo-class.Rd | 2 man/nTips-methods.Rd | 2 man/nodeId-methods.Rd | 4 - man/owls4.Rd | 4 + man/pdata-class.Rd | 2 man/pdata.Rd | 2 man/phylo4-class.Rd | 2 man/phylo4-methods.Rd | 13 +++--- man/phylo4d-accessors.Rd | 5 +- man/phylo4d-class.Rd | 4 - man/phylo4d-methods.Rd | 5 +- man/phyloXXYY.Rd | 6 ++ man/phylobase-package.Rd | 2 man/phylobase.options.Rd | 3 - man/phylobubbles.Rd | 4 + man/phylomat-class.Rd | 6 +- man/plotOneTree.Rd | 3 - man/print-methods.Rd | 6 ++ man/readNexus.Rd | 2 man/reorder-methods.Rd | 2 man/root-methods.Rd | 2 man/setAs-methods.Rd | 2 man/shortestPath-methods.Rd | 2 man/subset-methods.Rd | 2 man/summary-methods.Rd | 5 +- man/tdata-methods.Rd | 4 - man/tip.data.plot.Rd | 2 man/treePlot-methods.Rd | 3 - man/treeStructure-methods.Rd | 4 + 47 files changed, 150 insertions(+), 116 deletions(-)
Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep [aut, cre],
Emmanuel Paradis [aut],
Alastair Potts [aut]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.0.1 dated 2015-12-14 and 2.0.2 dated 2016-01-22
DESCRIPTION | 13 ++-- MD5 | 28 +++++----- NAMESPACE | 9 +-- NEWS | 10 +++ R/fitch.R | 133 +++++++++++++++++++++++++++++++++++++++++++++++---- R/parsimony.R | 28 +++++++--- R/phyDat.R | 24 ++++++--- R/phylo.R | 37 +++++++++----- README.md | 8 ++- man/bootstrap.pml.Rd | 13 +++- man/parsimony.Rd | 5 + man/phyDat.Rd | 1 src/Makevars | 4 - src/fitch.c | 32 +++++++----- src/ml.c | 44 +++++++++++----- 15 files changed, 296 insertions(+), 93 deletions(-)
Title: Tests of Non-Nested Models
Description: Testing non-nested models via theory supplied by Vuong (1989).
Includes tests of model distinguishability and of model fit that can be applied
to both nested and non-nested models. Also includes functionality to obtain
confidence intervals associated with AIC and BIC. This material is based on work
supported by the National Science Foundation under Grant Number SES-1061334.
Author: Edgar Merkle and Dongjun You
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between nonnest2 versions 0.2 dated 2014-12-04 and 0.3 dated 2016-01-22
DESCRIPTION | 26 +++++++++++++++----------- MD5 | 26 +++++++++++++++++--------- NAMESPACE | 24 +++++++++++++++++++++++- NEWS | 11 +++++++++++ R/icci.R | 11 ++++++++--- R/llcont.R | 21 +++++++++++++++++++-- R/vuongtest.R | 55 +++++++++++++++++++++++++++++++++++++++++-------------- build |only inst |only man/icci.Rd | 4 +++- man/llcont.Rd | 6 ++++-- man/vuongtest.Rd | 4 +++- tests |only vignettes |only 14 files changed, 144 insertions(+), 44 deletions(-)
Title: Tools for the Analysis of Ecosystem Metabolism
Description: A collection of tools for the calculation of freewater metabolism.
Author: Luke Winslow, Jake Zwart, Ryan Batt, Jessica Corman, Hilary Dugan, Paul
Hanson, Aline Jaimes, Jordan Read, Richard Woolway
Maintainer: Luke Winslow <lawinslow@gmail.com>
Diff between LakeMetabolizer versions 1.3.3 dated 2015-05-28 and 1.4.1 dated 2016-01-22
LakeMetabolizer-1.3.3/LakeMetabolizer/README.md |only LakeMetabolizer-1.4.1/LakeMetabolizer/DESCRIPTION | 9 LakeMetabolizer-1.4.1/LakeMetabolizer/MD5 | 79 ++-- LakeMetabolizer-1.4.1/LakeMetabolizer/NAMESPACE | 13 LakeMetabolizer-1.4.1/LakeMetabolizer/R/addNAs.R | 7 LakeMetabolizer-1.4.1/LakeMetabolizer/R/calc.zeng.R | 1 LakeMetabolizer-1.4.1/LakeMetabolizer/R/helper.functions.R | 1 LakeMetabolizer-1.4.1/LakeMetabolizer/R/metab.R | 22 - LakeMetabolizer-1.4.1/LakeMetabolizer/R/metab.bayesian.R | 25 + LakeMetabolizer-1.4.1/LakeMetabolizer/R/metab.mle.R | 77 +++- LakeMetabolizer-1.4.1/LakeMetabolizer/R/metab.ols.R | 3 LakeMetabolizer-1.4.1/LakeMetabolizer/R/o2.at.sat.R | 197 +++++++----- LakeMetabolizer-1.4.1/LakeMetabolizer/demo/fig_timeseries.R | 7 LakeMetabolizer-1.4.1/LakeMetabolizer/man/calc.lw.net.Rd | 10 LakeMetabolizer-1.4.1/LakeMetabolizer/man/calc.zeng.Rd | 6 LakeMetabolizer-1.4.1/LakeMetabolizer/man/get.Ts.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/get.vars.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/getSchmidt.Rd | 8 LakeMetabolizer-1.4.1/LakeMetabolizer/man/has.vars.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/is.day.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/is.night.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/k.read.Rd | 38 +- LakeMetabolizer-1.4.1/LakeMetabolizer/man/k.read.base.Rd | 39 +- LakeMetabolizer-1.4.1/LakeMetabolizer/man/k600.2.kGAS.Rd | 8 LakeMetabolizer-1.4.1/LakeMetabolizer/man/load.all.data.Rd | 6 LakeMetabolizer-1.4.1/LakeMetabolizer/man/load.meta.Rd | 4 LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.Rd | 57 +-- LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.bayesian.Rd | 40 +- LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.bookkeep.Rd | 20 - LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.kalman.Rd | 24 - LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.mle.Rd | 36 +- LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.ols.Rd | 16 LakeMetabolizer-1.4.1/LakeMetabolizer/man/o2.at.sat.Rd | 99 ++++-- LakeMetabolizer-1.4.1/LakeMetabolizer/man/par.to.sw.Rd | 6 LakeMetabolizer-1.4.1/LakeMetabolizer/man/rmv.vars.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/sun.rise.set.Rd | 4 LakeMetabolizer-1.4.1/LakeMetabolizer/man/sw.to.par.Rd | 7 LakeMetabolizer-1.4.1/LakeMetabolizer/man/temp.kalman.Rd | 6 LakeMetabolizer-1.4.1/LakeMetabolizer/man/var.indx.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/wind.scale.Rd | 12 LakeMetabolizer-1.4.1/LakeMetabolizer/src/mleLoop.c | 24 + 41 files changed, 574 insertions(+), 351 deletions(-)
More information about LakeMetabolizer at CRAN
Permanent link
Title: Item Response Models for Multiple Ratings
Description:
Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program.
Author:
Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between immer versions 0.2-0 dated 2015-11-04 and 0.3-0 dated 2016-01-22
DESCRIPTION | 28 +++++++++++++++------------- MD5 | 38 +++++++++++++++++++------------------- R/MHprop_hrm.R | 7 +++++-- R/anova_immer.R | 3 ++- R/immer_HRM.R | 6 +++--- R/immer_cml.R | 1 - R/rtrnorm.R | 2 +- data/data.immer01a.rda |binary data/data.immer01b.rda |binary data/data.immer02.rda |binary data/data.immer03.rda |binary data/data.immer04a.rda |binary data/data.immer04b.rda |binary data/data.immer05.rda |binary data/data.immer06.rda |binary data/data.immer07.rda |binary inst/NEWS | 13 +++++++++++-- man/immer-package.Rd | 4 ++-- man/immer_HRM.Rd | 2 +- man/immer_cml.Rd | 2 +- 20 files changed, 60 insertions(+), 46 deletions(-)
Title: Alternative Implementations of Base R Functions
Description: Alternative implementations of some base R functions, including sort, order, and match. Functions are simplified but can be faster or have other advantages.
Author: Craig Varrichio <canthony427@gmail.com>
Maintainer: Craig Varrichio <canthony427@gmail.com>
Diff between grr versions 0.9 dated 2016-01-19 and 0.9.1 dated 2016-01-22
DESCRIPTION | 11 +++++------ MD5 | 14 +++++++------- R/grr.R | 46 +++++++++++++++++++++++++++++++++++++--------- man/grr.Rd | 11 ++++++++--- man/matches.Rd | 2 ++ man/order2.Rd | 16 ++++++++++++++-- man/sort2.Rd | 17 ++++++++++++++--- src/grr.cpp | 21 +++++++++++---------- 8 files changed, 98 insertions(+), 40 deletions(-)
Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models
on top of static maps from various online sources (e.g Google Maps and Stamen
Maps). It includes tools common to those tasks, including functions for
geolocation and routing.
Author: David Kahle [aut, cre],
Hadley Wickham [aut]
Maintainer: David Kahle <david.kahle@gmail.com>
Diff between ggmap versions 2.6 dated 2015-12-19 and 2.6.1 dated 2016-01-22
DESCRIPTION | 6 +- MD5 | 116 ++++++++++++++++++++++---------------------- NEWS | 10 +++ R/LonLat2XY.R | 30 ++++++----- R/OSM_scale_lookup.R | 5 + R/XY2LonLat.R | 2 R/bb2bbox.R | 13 ++--- R/calc_zoom.r | 14 +++-- R/crime.R | 7 +- R/file_drawer.R | 11 ++-- R/geocode.R | 36 ++++++++----- R/get_cloudmademap.R | 31 ++++++----- R/get_googlemap.R | 122 +++++++++++++++++++++++------------------------ R/get_map.R | 42 ++++++++-------- R/get_navermap.R | 46 +++++++++++------ R/get_openstreetmap.R | 1 R/get_stamenmap.R | 33 ++++++++---- R/ggimage.R | 6 +- R/gglocator.R | 17 ++++-- R/ggplot2.R | 2 R/inset.R | 18 +++--- R/make_bbox.R | 27 +++++----- R/mapdist.R | 2 R/mutate_geocode.R | 8 +-- R/qmap.R | 6 +- R/qmplot.R | 44 +++++++++------- R/revgeocode.R | 25 ++++++--- R/route.R | 6 +- R/theme_inset.R | 36 ++++++------- R/theme_nothing.R | 8 +-- R/wind.R | 19 +++++-- R/zips.R | 9 ++- README.md | 49 +++++++++++++----- man/LonLat2XY.Rd | 9 ++- man/OSM_scale_lookup.Rd | 5 + man/bb2bbox.Rd | 13 ++--- man/calc_zoom.Rd | 14 +++-- man/crime.Rd | 3 - man/file_drawer.Rd | 11 ++-- man/geocode.Rd | 34 +++++++------ man/get_cloudmademap.Rd | 31 ++++++----- man/get_googlemap.Rd | 121 ++++++++++++++++++++++++---------------------- man/get_map.Rd | 42 ++++++++-------- man/get_navermap.Rd | 46 +++++++++++------ man/get_openstreetmap.Rd | 1 man/get_stamenmap.Rd | 33 ++++++++---- man/ggimage.Rd | 6 +- man/gglocator.Rd | 11 +++- man/inset.Rd | 18 +++--- man/make_bbox.Rd | 11 ++-- man/mutate_geocode.Rd | 8 +-- man/qmap.Rd | 6 +- man/qmplot.Rd | 44 +++++++++------- man/revgeocode.Rd | 20 +++++-- man/route.Rd | 4 - man/theme_inset.Rd | 22 ++++---- man/theme_nothing.Rd | 7 +- man/wind.Rd | 9 ++- man/zips.Rd | 12 +++- 59 files changed, 780 insertions(+), 568 deletions(-)
Title: ARTFIMA Model Estimation
Description: Fit and simulate ARTFIMA. Theoretical autocovariance function and spectral density function for stationary ARTFIMA.
Author: A. I. McLeod, Mark M. Meerschaert, Farzad Sabzikar
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Diff between artfima versions 1.1 dated 2015-11-08 and 1.2 dated 2016-01-22
artfima-1.1/artfima/data/Huron.rda |only artfima-1.1/artfima/data/NileMin.rda |only artfima-1.1/artfima/data/Ogden.rda |only artfima-1.1/artfima/data/SeriesA.rda |only artfima-1.1/artfima/man/Huron.Rd |only artfima-1.1/artfima/man/NileMin.Rd |only artfima-1.1/artfima/man/Ogden.Rd |only artfima-1.1/artfima/man/SeriesA.Rd |only artfima-1.2/artfima/DESCRIPTION | 12 - artfima-1.2/artfima/MD5 | 41 ++-- artfima-1.2/artfima/NAMESPACE | 7 artfima-1.2/artfima/NEWS | 16 + artfima-1.2/artfima/R/artSim.R | 3 artfima-1.2/artfima/R/artfima.R | 172 ++++++++++---------- artfima-1.2/artfima/R/informationMatrixARTFIMA.R |only artfima-1.2/artfima/R/print.artfima.R | 21 +- artfima-1.2/artfima/R/sdfartfima.R | 5 artfima-1.2/artfima/build/partial.rdb |binary artfima-1.2/artfima/data/SB32.rda |only artfima-1.2/artfima/inst |only artfima-1.2/artfima/man/SB32.Rd |only artfima-1.2/artfima/man/artfima-package.Rd | 2 artfima-1.2/artfima/man/artfima.Rd | 28 +-- artfima-1.2/artfima/man/informationMatrixARTFIMA.Rd |only artfima-1.2/artfima/man/print.artfima.Rd | 2 artfima-1.2/artfima/man/sdfartfima.Rd | 14 + artfima-1.2/artfima/man/seARTFIMA.Rd |only 27 files changed, 171 insertions(+), 152 deletions(-)
Title: Approximate Bayesian Computation via Random Forests
Description: Performs Approximate Bayesian Computation (ABC) model choice via random forests.
Author: Jean-Michel Marin [aut, cre],
Pierre Pudlo [aut],
Christian P. Robert [ctb],
Arnaud Estoup [ctb]
Maintainer: Jean-Michel Marin <jean-michel.marin@umontpellier.fr>
Diff between abcrf versions 0.9-4 dated 2015-08-18 and 1.1 dated 2016-01-22
DESCRIPTION | 28 +++++++++---------- MD5 | 20 +++++++------ NAMESPACE | 18 ++++++------ R/abcrf.R | 38 ++++++++++++++++++------- R/err.abcrf.R |only R/plot.abcrf.R | 57 +++++++++++++++++++++++++++++++------- R/predict.abcrf.R | 45 +++++++++++++++++++----------- man/abcrf.Rd | 75 +++++++++++++++++++++++++++------------------------ man/err.abcrf.Rd |only man/plot.abcrf.Rd | 33 ++++++++++++---------- man/predict.abcrf.Rd | 44 +++++++++++++++++------------ man/snp.Rd | 12 ++++---- 12 files changed, 228 insertions(+), 142 deletions(-)
Title: Utilities from "Seminar fuer Statistik" ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH
Zurich, quite a few related to graphics; many ported from S-plus times.
Author: Martin Maechler et al.
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.0-28 dated 2015-08-15 and 1.0-29 dated 2016-01-22
DESCRIPTION | 15 ++++--- MD5 | 83 ++++++++++++++++++++++--------------------- NAMESPACE | 17 +++++--- R/loessDemo.R |only R/misc-goodies.R | 66 ++++++++++++++++++++++++++++------ R/prime-numbers-fn.R | 46 ++++++++++++----------- R/sessionInfo-ext.R |only R/str_data.R | 29 +++++++++------ TODO | 37 ++++++++++--------- inst/NEWS.Rd | 22 +++++++++++ man/AsciiToInt.Rd | 2 - man/Deprecated.Rd | 2 - man/axTexpr.Rd | 4 +- man/capture-n-write.Rd | 16 +++++++- man/diagX.Rd | 2 - man/errbar.Rd | 2 - man/hatMat.Rd | 4 +- man/iterate.lin.recursion.Rd | 2 - man/loessDemo.Rd |only man/mult.fig.Rd | 2 - man/n.code.Rd | 2 - man/p.arrows.Rd | 2 - man/p.datum.Rd | 2 - man/p.profileTraces.Rd | 2 - man/p.tachoPlot.Rd | 4 +- man/polyn.eval.Rd | 2 - man/pretty10exp.Rd | 2 - man/printTable2.Rd | 2 - man/prt.DEBUG.Rd | 10 ++--- man/ps.latex.Rd | 2 - man/quadrant.Rd | 2 - man/read.org.table.Rd |only man/rrange.Rd | 17 ++++++-- man/sessionInfoX.Rd |only man/signi.Rd | 2 - man/str_data.Rd | 4 -- man/toLatex.numeric.Rd | 2 - man/u.Datumvonheute.Rd | 4 +- man/u.assign0.Rd | 4 +- man/u.boxplot.x.Rd | 2 - man/u.date.Rd | 6 +-- man/u.datumdecode.Rd | 4 +- man/wrapFormula.Rd | 5 ++ man/xy.grid.Rd | 2 - man/xy.unique.x.Rd | 4 +- 45 files changed, 277 insertions(+), 162 deletions(-)
Title: Global Optimization by Differential Evolution in C++
Description: An efficient C++ based implementation of the 'DEoptim'
function which performs global optimization by differential evolution.
Its creation was motivated by trying to see if the old approximation "easier,
shorter, faster: pick any two" could in fact be extended to achieving all
three goals while moving the code from plain old C to modern C++. The
initial version did in fact do so, but a good part of the gain was due to
an implicit code review which eliminated a few inefficiencies which have
since been eliminated in 'DEoptim'.
Author: Dirk Eddelbuettel extending DEoptim (by David Ardia, Katharine Mullen,
Brian Peterson, Joshua Ulrich) which itself is based on DE-Engine (by Rainer Storn)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDE versions 0.1.4 dated 2015-09-05 and 0.1.5 dated 2016-01-22
ChangeLog | 12 +++++++++++- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/RcppDE.pdf |binary src/devol.cpp | 6 +++--- 6 files changed, 23 insertions(+), 13 deletions(-)
Title: Big Data in-Database Analytics with Teradata Aster
Description: A consistent set of tools to perform in-database analytics
on Teradata Aster Big Data Discovery Platform. toaster (a.k.a 'to Aster')
embraces simple 2-step approach: compute in Aster - visualize and analyze
in R. Its `compute` functions use combination of SQL and
SQL/MR functions running in Aster database - highly scalable parallel
and distributed analytical platform. Then `create` functions visualize
results with boxplots, scatterplots, histograms, heatmaps, word clouds,
maps, or slope graphs. Advanced options such as faceting, coloring,
labeling, and others are supported with most functions.
Author: Gregory Kanevsky [aut, cre],
Nick Switanek [aut]
Maintainer: Gregory Kanevsky <gregory.kanevsky@teradata.com>
Diff between toaster versions 0.4.1 dated 2015-12-23 and 0.4.2 dated 2016-01-22
DESCRIPTION | 6 MD5 | 34 +-- NEWS | 36 ++++ R/computeKmeans.R | 18 +- R/maps.R | 118 ++++++++++--- R/plotting.R | 47 +++-- R/plottingKmeans.R | 2 R/showData.R | 11 - demo/baseball-heatmap.R | 4 man/createBoxplot.Rd | 9 - man/createBubblechart.Rd | 11 + man/createCentroidPlot.Rd | 7 man/createHeatmap.Rd | 8 man/createMap.Rd | 74 +++++--- man/createPopPyramid.Rd | 7 man/showData.Rd | 13 - tests/testthat/test-computeKmeans.R | 307 +++++++++++++++++++++++++++++++----- tests/testthat/test-createMap.R | 19 +- 18 files changed, 569 insertions(+), 162 deletions(-)
Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-
objective test functions which are frequently used for the benchmarking of
(numerical) optimization algorithms. Moreover, it offers a set of convenient
functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between smoof versions 1.1 dated 2015-11-24 and 1.2 dated 2016-01-22
smoof-1.1/smoof/R/filterFunctionByTags.R |only smoof-1.1/smoof/R/makeFunctionByName.R |only smoof-1.1/smoof/man/makeFunctionByName.Rd |only smoof-1.2/smoof/DESCRIPTION | 12 smoof-1.2/smoof/MD5 | 243 +++++----- smoof-1.2/smoof/NAMESPACE | 15 smoof-1.2/smoof/NEWS | 26 + smoof-1.2/smoof/R/conversion.R |only smoof-1.2/smoof/R/filterFunctionsByTags.R |only smoof-1.2/smoof/R/getAvailableTags.R | 3 smoof-1.2/smoof/R/getBoxConstraints.R | 2 smoof-1.2/smoof/R/getID.R |only smoof-1.2/smoof/R/hasConstraints.R | 2 smoof-1.2/smoof/R/makeBBOBFunction.R | 6 smoof-1.2/smoof/R/makeFunctionsByName.R |only smoof-1.2/smoof/R/makeMultiObjectiveFunction.R | 6 smoof-1.2/smoof/R/makeObjectiveFunction.R | 11 smoof-1.2/smoof/R/makeSingleObjectiveFunction.R | 4 smoof-1.2/smoof/R/makeUFFunction.R | 3 smoof-1.2/smoof/R/mof.dtlz1.R | 9 smoof-1.2/smoof/R/mof.dtlz2.R | 9 smoof-1.2/smoof/R/mof.dtlz3.R | 9 smoof-1.2/smoof/R/mof.dtlz4.R | 9 smoof-1.2/smoof/R/mof.dtlz5.R | 9 smoof-1.2/smoof/R/mof.dtlz6.R | 9 smoof-1.2/smoof/R/mof.dtlz7.R | 7 smoof-1.2/smoof/R/mof.zdt1.R | 7 smoof-1.2/smoof/R/mof.zdt2.R | 7 smoof-1.2/smoof/R/mof.zdt3.R | 7 smoof-1.2/smoof/R/mof.zdt4.R | 7 smoof-1.2/smoof/R/mof.zdt6.R | 7 smoof-1.2/smoof/R/plot.autoplot.R | 41 + smoof-1.2/smoof/R/plot.plot.R | 28 - smoof-1.2/smoof/R/shouldBeMinimized.R | 2 smoof-1.2/smoof/R/sof.ackley.R | 7 smoof-1.2/smoof/R/sof.adjiman.R | 6 smoof-1.2/smoof/R/sof.alpine01.R | 7 smoof-1.2/smoof/R/sof.alpine02.R | 9 smoof-1.2/smoof/R/sof.aluffi-pentini.R | 6 smoof-1.2/smoof/R/sof.bartels.conn.R | 6 smoof-1.2/smoof/R/sof.beale.R | 6 smoof-1.2/smoof/R/sof.bent.cigar.R | 6 smoof-1.2/smoof/R/sof.bird.R | 6 smoof-1.2/smoof/R/sof.bohachevsky.n1.R | 7 smoof-1.2/smoof/R/sof.booth.R | 6 smoof-1.2/smoof/R/sof.branin.R | 6 smoof-1.2/smoof/R/sof.brent.R | 6 smoof-1.2/smoof/R/sof.brown.R | 7 smoof-1.2/smoof/R/sof.bukin.n2.R | 6 smoof-1.2/smoof/R/sof.bukin.n4.R | 6 smoof-1.2/smoof/R/sof.bukin.n6.R | 6 smoof-1.2/smoof/R/sof.carrom.table.R | 6 smoof-1.2/smoof/R/sof.chichinadze.R | 6 smoof-1.2/smoof/R/sof.chung.reynolds.R | 7 smoof-1.2/smoof/R/sof.complex.R | 6 smoof-1.2/smoof/R/sof.cosine.mixture.R | 7 smoof-1.2/smoof/R/sof.cross.in.tray.R | 6 smoof-1.2/smoof/R/sof.cube.R | 6 smoof-1.2/smoof/R/sof.deckkers.aarts.R | 6 smoof-1.2/smoof/R/sof.deflected.corrugated.spring.R | 8 smoof-1.2/smoof/R/sof.dixon.price.R | 7 smoof-1.2/smoof/R/sof.double.sum.R | 7 smoof-1.2/smoof/R/sof.drop.wave.R | 7 smoof-1.2/smoof/R/sof.easom.R | 6 smoof-1.2/smoof/R/sof.eggcrate.R | 6 smoof-1.2/smoof/R/sof.eggholder.R | 7 smoof-1.2/smoof/R/sof.el.attar.vidyasagar.dutta.R | 6 smoof-1.2/smoof/R/sof.engvall.R | 6 smoof-1.2/smoof/R/sof.exponential.R | 7 smoof-1.2/smoof/R/sof.freudenstein.roth.R | 6 smoof-1.2/smoof/R/sof.giunta.R | 6 smoof-1.2/smoof/R/sof.goldstein.price.R | 6 smoof-1.2/smoof/R/sof.griewank.R | 7 smoof-1.2/smoof/R/sof.hansen.R | 6 smoof-1.2/smoof/R/sof.himmelblau.R | 6 smoof-1.2/smoof/R/sof.holder.table.n1.R | 6 smoof-1.2/smoof/R/sof.holder.table.n2.R | 6 smoof-1.2/smoof/R/sof.hosaki.R | 6 smoof-1.2/smoof/R/sof.hyper.ellipsoid.R | 7 smoof-1.2/smoof/R/sof.jennrichsampson.R | 6 smoof-1.2/smoof/R/sof.judge.R | 6 smoof-1.2/smoof/R/sof.keane.R | 6 smoof-1.2/smoof/R/sof.kearfott.R | 6 smoof-1.2/smoof/R/sof.leon.R | 6 smoof-1.2/smoof/R/sof.matyas.R | 6 smoof-1.2/smoof/R/sof.mccormick.R | 6 smoof-1.2/smoof/R/sof.michalewicz.R | 8 smoof-1.2/smoof/R/sof.mpm2.R | 24 smoof-1.2/smoof/R/sof.periodic.R | 6 smoof-1.2/smoof/R/sof.powell.sum.R | 7 smoof-1.2/smoof/R/sof.price.n1.R | 6 smoof-1.2/smoof/R/sof.price.n2.R | 6 smoof-1.2/smoof/R/sof.price.n4.R | 4 smoof-1.2/smoof/R/sof.rastrigin.R | 7 smoof-1.2/smoof/R/sof.rosenbrock.R | 7 smoof-1.2/smoof/R/sof.schaffer.function.2.R | 6 smoof-1.2/smoof/R/sof.schaffer.function.4.R | 6 smoof-1.2/smoof/R/sof.schwefel.R | 7 smoof-1.2/smoof/R/sof.shubert.R | 6 smoof-1.2/smoof/R/sof.six.hump.camel.back.function.R | 6 smoof-1.2/smoof/R/sof.sphere.R | 7 smoof-1.2/smoof/R/sof.styblinski.tang.R | 6 smoof-1.2/smoof/R/sof.sum.of.different.powers.R | 7 smoof-1.2/smoof/R/sof.three.hump.camel.R | 6 smoof-1.2/smoof/R/sof.trecanni.R | 6 smoof-1.2/smoof/R/sof.zettl.R | 6 smoof-1.2/smoof/R/visualizeParetoOptimalFront.R | 78 +-- smoof-1.2/smoof/R/zzz.R | 2 smoof-1.2/smoof/man/autoplot.smoof_function.Rd | 7 smoof-1.2/smoof/man/conversion.Rd |only smoof-1.2/smoof/man/filterFunctionsByTags.Rd | 2 smoof-1.2/smoof/man/getID.Rd |only smoof-1.2/smoof/man/makeFunctionsByName.Rd |only smoof-1.2/smoof/man/makeMPM2Function.Rd | 10 smoof-1.2/smoof/man/makeMultiObjectiveFunction.Rd | 9 smoof-1.2/smoof/man/makeSingleObjectiveFunction.Rd | 7 smoof-1.2/smoof/man/plot1DNumeric.Rd | 7 smoof-1.2/smoof/man/plot2DNumeric.Rd | 8 smoof-1.2/smoof/man/visualizeParetoOptimalFront.Rd | 34 - smoof-1.2/smoof/tests/testthat/Rplots.pdf |binary smoof-1.2/smoof/tests/testthat/test_conversion.R |only smoof-1.2/smoof/tests/testthat/test_counting_evaluations.R | 4 smoof-1.2/smoof/tests/testthat/test_helpers.R | 6 smoof-1.2/smoof/tests/testthat/test_logging.R | 30 + smoof-1.2/smoof/tests/testthat/test_makeFunctionByName.R | 33 - smoof-1.2/smoof/tests/testthat/test_makeSingleObjectiveFunction.R | 2 smoof-1.2/smoof/tests/testthat/test_plotting.R | 29 - smoof-1.2/smoof/tests/testthat/test_soofuns.R | 1 128 files changed, 758 insertions(+), 485 deletions(-)
Title: Programming with Big Data -- Scalable Linear Algebra Packages
Description: Utilizing scalable linear algebra packages mainly
including BLACS, PBLAS, and ScaLAPACK in double precision via
pbdMPI based on ScaLAPACK version 2.0.2.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Brian Ripley [ctb] (Solaris & Mac)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdSLAP versions 0.2-0 dated 2014-12-24 and 0.2-1 dated 2016-01-22
pbdSLAP-0.2-0/pbdSLAP/README |only pbdSLAP-0.2-0/pbdSLAP/data |only pbdSLAP-0.2-1/pbdSLAP/ChangeLog | 9 ++ pbdSLAP-0.2-1/pbdSLAP/DESCRIPTION | 14 ++-- pbdSLAP-0.2-1/pbdSLAP/MD5 | 35 +++++----- pbdSLAP-0.2-1/pbdSLAP/R/000_globalVariables.r | 4 - pbdSLAP-0.2-1/pbdSLAP/R/slap_blacs.r | 12 +-- pbdSLAP-0.2-1/pbdSLAP/README.md |only pbdSLAP-0.2-1/pbdSLAP/configure | 2 pbdSLAP-0.2-1/pbdSLAP/configure.ac | 3 pbdSLAP-0.2-1/pbdSLAP/demo/gridinfo.r | 8 +- pbdSLAP-0.2-1/pbdSLAP/inst/CITATION | 14 ++-- pbdSLAP-0.2-1/pbdSLAP/inst/doc/pbdSLAP-guide.Rnw | 19 +++-- pbdSLAP-0.2-1/pbdSLAP/inst/doc/pbdSLAP-guide.pdf |binary pbdSLAP-0.2-1/pbdSLAP/man/slap_gridinfo.Rd | 4 - pbdSLAP-0.2-1/pbdSLAP/src/REDIST/Makefile | 3 pbdSLAP-0.2-1/pbdSLAP/src/REDIST/pigemr.c |only pbdSLAP-0.2-1/pbdSLAP/src/REDIST/pigemr2.c |only pbdSLAP-0.2-1/pbdSLAP/src/REDIST/pitrmr.c |only pbdSLAP-0.2-1/pbdSLAP/src/REDIST/pitrmr2.c |only pbdSLAP-0.2-1/pbdSLAP/vignettes/pbdSLAP-guide.Rnw | 19 +++-- pbdSLAP-0.2-1/pbdSLAP/vignettes/pbdSLAP-include/01-copyright.tex | 2 22 files changed, 83 insertions(+), 65 deletions(-)
Title: Network Generator for Combinatorial Graph Problems
Description: Methods for the generation of a wide range of network geographies,
e.g., grid networks or clustered networks. Useful for the generation of
benchmarking instances for the investigation of, e.g., Vehicle-Routing-Problems
or Travelling Salesperson Problems.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between netgen versions 1.2 dated 2015-11-24 and 1.3 dated 2016-01-22
netgen-1.2/netgen/R/getInstanceOverview.R |only netgen-1.3/netgen/DESCRIPTION | 10 netgen-1.3/netgen/MD5 | 60 +++-- netgen-1.3/netgen/NAMESPACE | 6 netgen-1.3/netgen/NEWS | 15 + netgen-1.3/netgen/R/exportToTSPlibFormat.R | 53 +++- netgen-1.3/netgen/R/filterTSPInstances.R |only netgen-1.3/netgen/R/generateRandomNetwork.R | 2 netgen-1.3/netgen/R/getTSPInstancesOverview.R |only netgen-1.3/netgen/R/getValidEdgeWeightTypes.R |only netgen-1.3/netgen/R/helpers.R | 15 + netgen-1.3/netgen/R/importFromTSPlibFormat.R | 3 netgen-1.3/netgen/R/isEuclidean.R |only netgen-1.3/netgen/R/makeNetwork.R | 41 +++ netgen-1.3/netgen/R/pointMatching.R | 27 +- netgen-1.3/netgen/R/printNetwork.R | 5 netgen-1.3/netgen/R/rescaleNetwork.R | 48 +++- netgen-1.3/netgen/man/exportToTSPlibFormat.Rd | 9 netgen-1.3/netgen/man/filterTSPInstances.Rd |only netgen-1.3/netgen/man/getOptimalPointMatching.Rd | 10 netgen-1.3/netgen/man/getTSPInstancesOverview.Rd |only netgen-1.3/netgen/man/getValidEdgeWeightTypes.Rd |only netgen-1.3/netgen/man/isEuclidean.Rd |only netgen-1.3/netgen/man/isNetwork.Rd |only netgen-1.3/netgen/man/makeNetwork.Rd | 13 - netgen-1.3/netgen/man/quoted.Rd |only netgen-1.3/netgen/man/rescaleNetwork.Rd | 17 - netgen-1.3/netgen/tests/testthat/test_asType.R | 52 ++-- netgen-1.3/netgen/tests/testthat/test_dynamise.R | 46 ++-- netgen-1.3/netgen/tests/testthat/test_generateClusteredNetwork.R | 102 ++++----- netgen-1.3/netgen/tests/testthat/test_generateGridNetwork.R | 32 +- netgen-1.3/netgen/tests/testthat/test_generateRandomNetwork.R | 37 +-- netgen-1.3/netgen/tests/testthat/test_getTSPInstancesOverview.R |only netgen-1.3/netgen/tests/testthat/test_import.R | 1 netgen-1.3/netgen/tests/testthat/test_morphInstances.R | 108 +++++----- netgen-1.3/netgen/tests/testthat/test_plots.R | 90 ++++---- netgen-1.3/netgen/tests/testthat/test_rescaleNetwork.R | 73 +++--- 37 files changed, 514 insertions(+), 361 deletions(-)
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb]
Maintainer: Stefan Schlager <stefan.schlager@uniklinik-freiburg.de>
Diff between Morpho versions 2.3.1 dated 2015-12-15 and 2.3.1.1 dated 2016-01-22
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- R/Morpho-package.R | 4 ++-- R/deform.grid.r | 5 +++-- R/permuvec.r | 2 +- R/vertex.r | 1 + inst/NEWS.Rd | 10 ++++++++++ man/Morpho-package.Rd | 4 ++-- man/deformGrid3d.Rd | 5 ++++- src/CVAdists.cpp | 14 ++++++-------- src/armaGinv.cpp | 3 +-- src/asymPerm.cpp | 21 +++++++++------------ src/covPCA.cpp | 12 ++++-------- src/createL.cpp | 6 ++---- src/edgePlane.cpp | 3 ++- src/meshres.cpp | 17 +++++++++-------- src/permudistArma.cpp | 11 +++++------ src/points2mesh.cpp | 28 +++++++++++----------------- src/tpsfx.cpp | 14 ++++++++------ src/updateNormals.cpp | 20 +++++++++----------- 20 files changed, 112 insertions(+), 114 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.12 dated 2016-01-07 and 1.12.3 dated 2016-01-22
DESCRIPTION | 15 ++++++++++----- MD5 | 31 ++++++++++++++++--------------- R/block.R | 10 ++++++---- R/hooks-md.R | 5 ++++- R/plot.R | 4 +--- build/knitr.pdf |binary inst/doc/docco-classic.html | 2 +- inst/doc/docco-linear.html | 2 +- inst/doc/knit_expand.html | 4 ++-- inst/doc/knit_print.html | 23 +++++++++-------------- inst/doc/knitr-html.html | 2 +- inst/doc/knitr-intro.html | 19 +++++++------------ inst/doc/knitr-markdown.html | 4 ++-- inst/doc/knitr-refcard.pdf |binary tests/testit/knit-tikzDevice.Rnw |only tests/testit/test-hooks.R | 2 +- tests/testit/test-plot.R | 6 ++++++ 17 files changed, 67 insertions(+), 62 deletions(-)
Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text
'scholarly' data, including 'Biomed Central', Public Library of
Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ',
'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality
included for searching for articles, downloading full or partial
text, downloading supplementary materials, converting to various
data formats used in and outside of R.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between fulltext versions 0.1.4 dated 2015-10-02 and 0.1.6 dated 2016-01-22
fulltext-0.1.4/fulltext/tests/testthat/test-ft_get.R |only fulltext-0.1.6/fulltext/DESCRIPTION | 9 fulltext-0.1.6/fulltext/LICENSE | 2 fulltext-0.1.6/fulltext/MD5 | 90 +- fulltext-0.1.6/fulltext/NAMESPACE | 7 fulltext-0.1.6/fulltext/R/europe_pmc_utils.R | 2 fulltext-0.1.6/fulltext/R/ft_browse.R | 3 fulltext-0.1.6/fulltext/R/ft_get_si.R | 320 ++------- fulltext-0.1.6/fulltext/R/ft_get_si_plugins.R |only fulltext-0.1.6/fulltext/R/ft_get_si_utils.R |only fulltext-0.1.6/fulltext/R/ft_search.R | 20 fulltext-0.1.6/fulltext/R/fulltext-package.R | 6 fulltext-0.1.6/fulltext/R/plugins_search.R | 13 fulltext-0.1.6/fulltext/README.md | 123 +-- fulltext-0.1.6/fulltext/build/vignette.rds |binary fulltext-0.1.6/fulltext/inst/doc/fulltext_vignette.Rmd | 529 +++++++--------- fulltext-0.1.6/fulltext/inst/doc/fulltext_vignette.html | 516 +++++++-------- fulltext-0.1.6/fulltext/inst/doc/getting_fulltext.Rmd | 89 +- fulltext-0.1.6/fulltext/inst/doc/getting_fulltext.html | 87 +- fulltext-0.1.6/fulltext/inst/ignore/config.R |only fulltext-0.1.6/fulltext/inst/ignore/elsevier_code.R |only fulltext-0.1.6/fulltext/inst/vign/fulltext_vignette.Rmd | 9 fulltext-0.1.6/fulltext/inst/vign/fulltext_vignette.md | 529 +++++++--------- fulltext-0.1.6/fulltext/inst/vign/getting_fulltext.Rmd | 12 fulltext-0.1.6/fulltext/inst/vign/getting_fulltext.md | 89 +- fulltext-0.1.6/fulltext/man/bmc.Rd | 2 fulltext-0.1.6/fulltext/man/bmc_search.Rd | 2 fulltext-0.1.6/fulltext/man/cache.Rd | 2 fulltext-0.1.6/fulltext/man/chunks.Rd | 2 fulltext-0.1.6/fulltext/man/collect.Rd | 8 fulltext-0.1.6/fulltext/man/eupmc.Rd | 20 fulltext-0.1.6/fulltext/man/extract_tools.Rd | 22 fulltext-0.1.6/fulltext/man/ft_browse.Rd | 4 fulltext-0.1.6/fulltext/man/ft_extract.Rd | 12 fulltext-0.1.6/fulltext/man/ft_extract_corpus.Rd | 2 fulltext-0.1.6/fulltext/man/ft_get.Rd | 2 fulltext-0.1.6/fulltext/man/ft_get_si.Rd | 106 ++- fulltext-0.1.6/fulltext/man/ft_links.Rd | 14 fulltext-0.1.6/fulltext/man/ft_providers.Rd | 2 fulltext-0.1.6/fulltext/man/ft_search.Rd | 14 fulltext-0.1.6/fulltext/man/ft_serialize.Rd | 10 fulltext-0.1.6/fulltext/man/ft_type_sum.Rd | 2 fulltext-0.1.6/fulltext/man/fulltext-package.Rd | 21 fulltext-0.1.6/fulltext/man/pdfx.Rd | 14 fulltext-0.1.6/fulltext/man/pipe.Rd | 2 fulltext-0.1.6/fulltext/tests/testthat/test-ft_get.r |only fulltext-0.1.6/fulltext/tests/testthat/test-ft_get_si.r | 20 fulltext-0.1.6/fulltext/vignettes/fulltext_vignette.Rmd | 529 +++++++--------- fulltext-0.1.6/fulltext/vignettes/getting_fulltext.Rmd | 89 +- 49 files changed, 1580 insertions(+), 1776 deletions(-)
Title: Did You Mean?
Description: Add a "Did You Mean" feature to the R interactive. With this
package, error messages for misspelled input of variable names or package names
suggest what you really want to do in addition to notification of the mistake.
Author: Kosei Abe [aut, cre], Richard Cotton [ctb]
Maintainer: Kosei Abe <mail@recyclebin.jp>
Diff between DYM versions 0.1.1 dated 2015-06-15 and 0.2 dated 2016-01-22
DESCRIPTION | 19 +++---- MD5 | 28 +++++----- NAMESPACE | 6 +- R/DYM.R | 48 +++++++++++++----- R/findSimilarName.R | 49 ++++++++++++++++-- R/getNames.R | 1 R/hooks.R | 2 inst/po/en@quot/LC_MESSAGES/R-DYM.mo |binary inst/po/ja/LC_MESSAGES/R-DYM.mo |binary man/DYM.Rd | 21 +++++++- man/findSimilarName.Rd | 36 +++++++++++-- man/getMissingVariable.Rd | 2 man/getNames.Rd | 2 man/isVariableName.Rd | 2 tests/testthat/test-findSimilarName.R | 89 +++++++++++++++++++++++++++++----- 15 files changed, 237 insertions(+), 68 deletions(-)
Title: Quantitative Analysis Made Accessible
Description: Contains a number of functions that serve
two goals: first, make R more accessible to people migrating from
SPSS by adding a number of functions that behave roughly like their
SPSS equivalents; and second, make a number of slightly more
advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
Diff between userfriendlyscience versions 0.3-0 dated 2015-04-20 and 0.4-0 dated 2016-01-21
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Title: Wrapper for MUMPS Library
Description: Exported class can be used for storing sparse matrix
and solving corresponding linear system with one or many right
hand sides. There is a possibility to do separately symbolic analysis,
LU factorization and system solving.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.0.1.6 dated 2016-01-21 and 5.0.1.7 dated 2016-01-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 8 +++++--- man/rmumps-package.Rd | 2 +- src/rmumps_module.cpp | 22 +++++++++++++++++++--- 5 files changed, 33 insertions(+), 15 deletions(-)
Title: Feature-Based Landscape Analysis of Continuous and Constraint
Optimization Problems
Description: Contains tools and features, which can be used for an exploratory
landscape analysis of continuous optimization problems. Those are able to
quantify rather complex properties, such as the global structure,
separability, etc., of continuous optimization problems.
Author: Pascal Kerschke [aut, cre],
Jan Dagefoerde [aut]
Maintainer: Pascal Kerschke <kerschke@uni-muenster.de>
Diff between flacco versions 1.1 dated 2015-11-26 and 1.2 dated 2016-01-21
DESCRIPTION | 8 +++---- MD5 | 12 +++++----- NEWS | 3 ++ R/feature_ela_local_search.R | 6 ++--- tests/testthat/Rplots.pdf |binary tests/testthat/test-calculateFeatures.R | 36 ++++++++++++++++---------------- tests/testthat/test-ela-Levelset.R | 2 - 7 files changed, 35 insertions(+), 32 deletions(-)
Title: Write Formatted Tables in Excel Workbooks
Description: Some functions are included in this package for writing tables in Excel format suitable for distribution.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@ono.com>
Diff between tablaxlsx versions 1.0.3 dated 2015-12-05 and 1.0.4 dated 2016-01-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/reducir.R | 3 +++ 3 files changed, 9 insertions(+), 6 deletions(-)
Title: Mixed Models, Particularly Spatial GLMMs
Description: Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroskedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [ctb],
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@univ-montp2.fr>
Diff between spaMM versions 1.6.2 dated 2015-11-01 and 1.7.1 dated 2016-01-21
DESCRIPTION | 10 MD5 | 100 ++++----- NAMESPACE | 5 R/HLCor.R | 14 - R/HLFactorList.R | 2 R/HLfit.R | 316 +++++++++++++++++------------- R/HLfit_Internals.R | 338 +++++++++++++++++--------------- R/HLframes.R | 131 +++++++----- R/LevenbergMstep.R | 4 R/MakeCovEst.R | 8 R/SEMbetalambda.R | 22 +- R/auglinmodfit.R | 11 - R/calc.p_v.R | 8 R/corrHLfit.R | 86 ++++++-- R/corrMM.LRT.R | 24 +- R/correlationFns.R | 120 ++++------- R/dispGammaGLM.R |only R/extractors.R | 59 ++++- R/generateName.R | 30 +- R/is.diagonal.R | 19 + R/iterateSmooth.R | 183 ++++++++++------- R/locoptim.R | 7 R/migraineLike.R | 190 +++++++++++++++++- R/multinomial.R | 24 +- R/predict.R | 399 +++++++++++++++++++++++++------------- R/preprocess.R | 48 +++- R/simulate.HL.R | 2 R/summary.HL.R | 144 +++++++------ data/Loaloa.RData |binary data/blackcap.RData |binary data/salamander.RData |binary data/scotlip.RData |binary data/seeds.RData |binary data/wafers.RData |binary data/welding.RData |binary inst/NEWS.Rd | 24 ++ man/HLCor.Rd | 7 man/HLfit.Rd | 2 man/autoregressive.Rd | 7 man/corrHLfit.Rd | 4 man/extractors.Rd | 4 man/multinomial.Rd | 4 man/predict.Rd | 16 - man/raster.Rd | 1 man/spaMM-internal.Rd | 20 + src/RcppExports.cpp | 1 src/spaMM_linear.cpp | 20 + tests/testthat/test-Nugget.R | 2 tests/testthat/test-corrHLfit.txt |only tests/testthat/test-fixedLRT.R | 2 tests/testthat/test-predVar.R | 37 +++ tests/testthat/test-sp-nsp.R | 9 52 files changed, 1571 insertions(+), 893 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions. Includes an intuitive
query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 1.1 dated 2016-01-03 and 1.2 dated 2016-01-21
DESCRIPTION | 8 +-- MD5 | 16 ++++--- NAMESPACE | 2 R/gui.R | 116 +++++++++++++++++++++++++++++++++++++----------------- R/indscal.R |only R/plot.R | 4 - R/provenance.R | 89 ++++++++++++++--------------------------- man/combine.Rd |only man/indscal.Rd | 4 - man/provenance.Rd | 6 +- 10 files changed, 132 insertions(+), 113 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.2.2 dated 2015-11-12 and 2.2.3 dated 2016-01-21
DESCRIPTION | 8 MD5 | 14 - R/autoevenn.R | 4 R/evenn.R | 607 +++++++++++++++++++++++++-------------------------- R/man.evenn.R | 18 - man/autoevenn.Rd | 20 + man/eVenn-package.Rd | 4 man/evenn.Rd | 34 ++ 8 files changed, 370 insertions(+), 339 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help safely and efficiently organize Monte Carlo simulations in R.
The package controls the structure and back-end of Monte Carlo simulations
by utilizing a general generate-analyse-summarise strategy. The functions provided control
common simulation issues such as re-simulating non-convergent results, support parallel
back-end and MPI distributed computations, save and restore temporary files,
aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 0.5 dated 2015-12-22 and 0.6 dated 2016-01-21
SimDesign-0.5/SimDesign/man/check_error.Rd |only SimDesign-0.6/SimDesign/DESCRIPTION | 16 - SimDesign-0.6/SimDesign/MD5 | 19 +- SimDesign-0.6/SimDesign/NAMESPACE | 1 SimDesign-0.6/SimDesign/R/analysis.R | 5 SimDesign-0.6/SimDesign/R/functions.R | 29 +-- SimDesign-0.6/SimDesign/R/runSimulation.R | 165 +++++++++++-------- SimDesign-0.6/SimDesign/R/util.R | 36 ---- SimDesign-0.6/SimDesign/man/analyse.Rd | 21 +- SimDesign-0.6/SimDesign/man/runSimulation.Rd | 113 +++++++------ SimDesign-0.6/SimDesign/tests/tests/test-SimDesign.R | 30 +-- 11 files changed, 228 insertions(+), 207 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny applications without
having to know any JavaScript. Examples include: hiding an element, disabling
an input, resetting an input back to its original value, delaying code execution
by a few seconds, and many more useful functions. 'shinyjs' can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.3.1 dated 2016-01-06 and 0.4.0 dated 2016-01-21
shinyjs-0.3.1/shinyjs/R/jsFunc-text.R |only shinyjs-0.3.1/shinyjs/man/text.Rd |only shinyjs-0.4.0/shinyjs/DESCRIPTION | 8 - shinyjs-0.4.0/shinyjs/MD5 | 90 +++++++------- shinyjs-0.4.0/shinyjs/NAMESPACE | 2 shinyjs-0.4.0/shinyjs/NEWS.md | 20 +++ shinyjs-0.4.0/shinyjs/R/colourInput.R | 46 +++---- shinyjs-0.4.0/shinyjs/R/delay.R | 9 + shinyjs-0.4.0/shinyjs/R/disabled.R | 14 +- shinyjs-0.4.0/shinyjs/R/hidden.R | 18 +- shinyjs-0.4.0/shinyjs/R/inlineCSS.R | 14 +- shinyjs-0.4.0/shinyjs/R/jsFunc-aaa.R | 26 ++++ shinyjs-0.4.0/shinyjs/R/jsFunc-classFuncs.R | 57 +++++--- shinyjs-0.4.0/shinyjs/R/jsFunc-html.R |only shinyjs-0.4.0/shinyjs/R/jsFunc-messageFuncs.R | 27 ++-- shinyjs-0.4.0/shinyjs/R/jsFunc-runjs.R | 20 +-- shinyjs-0.4.0/shinyjs/R/jsFunc-stateFuncs.R | 63 +++++---- shinyjs-0.4.0/shinyjs/R/jsFunc-visibilityFuncs.R | 69 +++++----- shinyjs-0.4.0/shinyjs/R/onevent.R | 29 +++- shinyjs-0.4.0/shinyjs/R/reset.R | 28 +++- shinyjs-0.4.0/shinyjs/R/useShinyjs.R | 17 +- shinyjs-0.4.0/shinyjs/R/utils.R | 8 - shinyjs-0.4.0/shinyjs/README.md | 37 ++++- shinyjs-0.4.0/shinyjs/inst/doc/overview.Rmd | 22 ++- shinyjs-0.4.0/shinyjs/inst/doc/overview.html | 28 +++- shinyjs-0.4.0/shinyjs/inst/examples/basic/app.R | 2 shinyjs-0.4.0/shinyjs/inst/examples/basic/helper-text.R | 4 shinyjs-0.4.0/shinyjs/inst/examples/demo/helpers.R | 8 - shinyjs-0.4.0/shinyjs/inst/examples/demo/server.R | 6 shinyjs-0.4.0/shinyjs/inst/examples/sandbox/helpers.R | 6 shinyjs-0.4.0/shinyjs/inst/examples/sandbox/server.R | 10 - shinyjs-0.4.0/shinyjs/inst/srcjs/shinyjs-default-funcs.js | 15 +- shinyjs-0.4.0/shinyjs/man/classFuncs.Rd | 48 +++---- shinyjs-0.4.0/shinyjs/man/colourInput.Rd | 24 +-- shinyjs-0.4.0/shinyjs/man/delay.Rd | 1 shinyjs-0.4.0/shinyjs/man/disabled.Rd | 14 +- shinyjs-0.4.0/shinyjs/man/hidden.Rd | 18 +- shinyjs-0.4.0/shinyjs/man/html.Rd |only shinyjs-0.4.0/shinyjs/man/inlineCSS.Rd | 14 +- shinyjs-0.4.0/shinyjs/man/messageFuncs.Rd | 19 +- shinyjs-0.4.0/shinyjs/man/onevent.Rd | 12 + shinyjs-0.4.0/shinyjs/man/reset.Rd | 4 shinyjs-0.4.0/shinyjs/man/runjs.Rd | 16 +- shinyjs-0.4.0/shinyjs/man/stateFuncs.Rd | 51 +++---- shinyjs-0.4.0/shinyjs/man/updateColourInput.Rd | 22 +-- shinyjs-0.4.0/shinyjs/man/useShinyjs.Rd | 19 +- shinyjs-0.4.0/shinyjs/man/visibilityFuncs.Rd | 60 ++++----- shinyjs-0.4.0/shinyjs/vignettes/overview.Rmd | 22 ++- 48 files changed, 619 insertions(+), 428 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it),
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk (svn://
svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.13.1.1 dated 2015-12-31 and 0.13.1.2 dated 2016-01-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Rvcg-package.R | 4 ++-- inst/NEWS.Rd | 9 +++++++++ man/Rvcg-package.Rd | 4 ++-- src/Rkdtree.cpp | 4 ++-- src/RvcgKD.h | 4 ++-- 7 files changed, 27 insertions(+), 18 deletions(-)
Title: Response Surface Analysis
Description: Advanced response surface analysis. The main function RSA computes
and compares several nested polynomial regression models (full polynomial,
shifted and rotated squared differences, rising ridge surfaces, basic
squared differences). The package provides plotting functions for 3d
wireframe surfaces, interactive 3d plots, and contour plots. Calculates
many surface parameters (a1 to a4, principal axes, stationary point,
eigenvalues) and provides standard, robust, or bootstrapped standard errors
and confidence intervals for them.
Author: Felix Schönbrodt
Maintainer: Felix Schönbrodt <felix@nicebread.de>
Diff between RSA versions 0.9.8 dated 2015-03-23 and 0.9.9 dated 2016-01-21
DESCRIPTION | 11 ++++++----- MD5 | 49 +++++++++++++++++++++++++------------------------ NAMESPACE | 24 +++++++++++++++++++++++- R/RSA.R | 6 ++++-- R/RSA.ST.R | 18 ++++++++++++++---- R/confint.R | 1 + R/imports.R |only R/modeltree.R | 1 + R/plot.RSA.R | 7 ++++--- inst/CITATION | 4 ++-- inst/NEWS.Rd | 19 +++++++++++++++++++ man/RSA.Rd | 10 ++++++---- man/RSA.ST.Rd | 22 ++++++++++++++++------ man/aictab.Rd | 2 +- man/compare.Rd | 2 +- man/compare2.Rd | 2 +- man/confint.RSA.Rd | 3 ++- man/demoRSA.Rd | 2 +- man/fitted.RSA.Rd | 2 +- man/getPar.Rd | 3 ++- man/modeltree.Rd | 2 +- man/motcon.Rd | 2 +- man/motcon2.Rd | 2 +- man/movieRSA.Rd | 20 ++++++++++---------- man/plotRSA.Rd | 31 +++++++++++++++---------------- man/residuals.RSA.Rd | 2 +- 26 files changed, 159 insertions(+), 88 deletions(-)
Title: Precipitation Intensity, Concentration and Anomaly Analysis
Description: Contains functions to analyze the precipitation
intensity, concentration and anomaly.
Author: Lucas Venezian Povoa [aut, cre],
Jonas Teixeira Nery [ctb]
Maintainer: Lucas Venezian Povoa <lucasvenez@gmail.com>
Diff between precintcon versions 2.1 dated 2015-02-19 and 2.2.1 dated 2016-01-21
precintcon-2.1/precintcon/R/precintcon.trend.test.r |only precintcon-2.1/precintcon/TODO |only precintcon-2.2.1/precintcon/DESCRIPTION | 40 - precintcon-2.2.1/precintcon/MD5 | 202 ++++--- precintcon-2.2.1/precintcon/NAMESPACE | 163 +++--- precintcon-2.2.1/precintcon/R/app.r |only precintcon-2.2.1/precintcon/R/as.annual.r | 71 +- precintcon-2.2.1/precintcon/R/as.daily.r | 197 +++---- precintcon-2.2.1/precintcon/R/as.decade.r | 72 +- precintcon-2.2.1/precintcon/R/as.deciles.r | 86 +-- precintcon-2.2.1/precintcon/R/as.fd.r | 92 +-- precintcon-2.2.1/precintcon/R/as.monthly.r | 64 +- precintcon-2.2.1/precintcon/R/as.precintcon.annual.r | 32 - precintcon-2.2.1/precintcon/R/as.precintcon.daily.r | 44 - precintcon-2.2.1/precintcon/R/as.precintcon.decade.r | 34 - precintcon-2.2.1/precintcon/R/as.precintcon.deciles.r | 28 - precintcon-2.2.1/precintcon/R/as.precintcon.fd.r | 28 - precintcon-2.2.1/precintcon/R/as.precintcon.monthly.r | 46 - precintcon-2.2.1/precintcon/R/as.precintcon.seasonal.r | 45 + precintcon-2.2.1/precintcon/R/as.seasonal.r | 70 +- precintcon-2.2.1/precintcon/R/ci.per.year.r | 68 +- precintcon-2.2.1/precintcon/R/ci.r | 98 +-- precintcon-2.2.1/precintcon/R/cv.r |only precintcon-2.2.1/precintcon/R/deciles.r | 6 precintcon-2.2.1/precintcon/R/ff.index.r |only precintcon-2.2.1/precintcon/R/limits.r | 68 +- precintcon-2.2.1/precintcon/R/pci.r | 67 +- precintcon-2.2.1/precintcon/R/pci.seasonal.r |only precintcon-2.2.1/precintcon/R/pci.supraseasonal.r |only precintcon-2.2.1/precintcon/R/pn.r | 86 +-- precintcon-2.2.1/precintcon/R/pplot.deciles.r | 135 ++--- precintcon-2.2.1/precintcon/R/pplot.histogram.r | 135 ++--- precintcon-2.2.1/precintcon/R/pplot.lorenz.r | 156 +++-- precintcon-2.2.1/precintcon/R/pplot.pci.r | 122 ++-- precintcon-2.2.1/precintcon/R/pplot.pn.r | 139 ++--- precintcon-2.2.1/precintcon/R/pplot.rai.r | 130 ++-- precintcon-2.2.1/precintcon/R/pplot.spi.r | 141 ++--- precintcon-2.2.1/precintcon/R/precintcon.H.r | 42 - precintcon-2.2.1/precintcon/R/precintcon.Z.r | 106 +-- precintcon-2.2.1/precintcon/R/precintcon.b.r | 58 +- precintcon-2.2.1/precintcon/R/precintcon.ci.analysis.r | 106 +-- precintcon-2.2.1/precintcon/R/precintcon.ci.per.year.analysis.r | 60 +- precintcon-2.2.1/precintcon/R/precintcon.classification.r | 104 +-- precintcon-2.2.1/precintcon/R/precintcon.deciles.analysis.r | 72 +- precintcon-2.2.1/precintcon/R/precintcon.fd.r | 206 +++---- precintcon-2.2.1/precintcon/R/precintcon.gamma.r | 108 ++-- precintcon-2.2.1/precintcon/R/precintcon.limits.analysis.r | 58 +- precintcon-2.2.1/precintcon/R/precintcon.ln.a.r | 62 +- precintcon-2.2.1/precintcon/R/precintcon.max.r | 78 +- precintcon-2.2.1/precintcon/R/precintcon.min.r | 80 +-- precintcon-2.2.1/precintcon/R/precintcon.monthly.aggregation.r | 62 +- precintcon-2.2.1/precintcon/R/precintcon.pci.analysis.r | 46 - precintcon-2.2.1/precintcon/R/precintcon.plot.deciles.r | 186 ++---- precintcon-2.2.1/precintcon/R/precintcon.plot.histogram.r | 243 ++++----- precintcon-2.2.1/precintcon/R/precintcon.plot.lorenz.r | 266 +++++----- precintcon-2.2.1/precintcon/R/precintcon.plot.lorenz.ungrouped.r | 132 ++-- precintcon-2.2.1/precintcon/R/precintcon.plot.pci.r | 142 ++--- precintcon-2.2.1/precintcon/R/precintcon.plot.pn.r | 212 +++---- precintcon-2.2.1/precintcon/R/precintcon.plot.rai.r | 216 ++++---- precintcon-2.2.1/precintcon/R/precintcon.plot.spi.r | 186 +++--- precintcon-2.2.1/precintcon/R/precintcon.pn.analysis.r | 34 - precintcon-2.2.1/precintcon/R/precintcon.pn.r | 122 ++-- precintcon-2.2.1/precintcon/R/precintcon.r | 219 ++++---- precintcon-2.2.1/precintcon/R/precintcon.r.squared.r | 44 - precintcon-2.2.1/precintcon/R/precintcon.rai.analysis.r | 82 +-- precintcon-2.2.1/precintcon/R/precintcon.read.data.r | 111 ++-- precintcon-2.2.1/precintcon/R/precintcon.spi.analysis.r | 116 ++-- precintcon-2.2.1/precintcon/R/precintcon.spi.per.year.analysis.r | 44 - precintcon-2.2.1/precintcon/R/precintcon.stat.analysis.r | 150 ++--- precintcon-2.2.1/precintcon/R/rai.r | 69 +- precintcon-2.2.1/precintcon/R/read.data.r | 95 +-- precintcon-2.2.1/precintcon/R/spi.per.year.r | 78 +- precintcon-2.2.1/precintcon/R/spi.r | 74 +- precintcon-2.2.1/precintcon/R/stat.r | 72 +- precintcon-2.2.1/precintcon/R/tii.r |only precintcon-2.2.1/precintcon/R/trend.test.r |only precintcon-2.2.1/precintcon/man/app.Rd |only precintcon-2.2.1/precintcon/man/as.annual.Rd | 92 +-- precintcon-2.2.1/precintcon/man/as.daily.Rd | 218 ++++---- precintcon-2.2.1/precintcon/man/as.decade.Rd | 95 +-- precintcon-2.2.1/precintcon/man/as.deciles.Rd | 106 +-- precintcon-2.2.1/precintcon/man/as.fd.Rd | 118 ++-- precintcon-2.2.1/precintcon/man/as.monthly.Rd | 86 +-- precintcon-2.2.1/precintcon/man/as.seasonal.Rd | 93 +-- precintcon-2.2.1/precintcon/man/ci.Rd | 124 ++-- precintcon-2.2.1/precintcon/man/ci.per.year.Rd | 94 +-- precintcon-2.2.1/precintcon/man/cv.Rd |only precintcon-2.2.1/precintcon/man/daily.Rd | 114 ++-- precintcon-2.2.1/precintcon/man/ff.index.Rd |only precintcon-2.2.1/precintcon/man/limits.Rd | 90 +-- precintcon-2.2.1/precintcon/man/monthly.Rd | 54 +- precintcon-2.2.1/precintcon/man/pci.Rd | 90 +-- precintcon-2.2.1/precintcon/man/pci.seasonal.Rd |only precintcon-2.2.1/precintcon/man/pci.supraseasonal.Rd |only precintcon-2.2.1/precintcon/man/pn.Rd | 108 ++-- precintcon-2.2.1/precintcon/man/pplot.deciles.Rd | 134 ++--- precintcon-2.2.1/precintcon/man/pplot.histogram.Rd | 140 ++--- precintcon-2.2.1/precintcon/man/pplot.lorenz.Rd | 154 ++--- precintcon-2.2.1/precintcon/man/pplot.pci.Rd | 126 ++-- precintcon-2.2.1/precintcon/man/pplot.pn.Rd | 142 ++--- precintcon-2.2.1/precintcon/man/pplot.rai.Rd | 143 ++--- precintcon-2.2.1/precintcon/man/pplot.spi.Rd | 142 ++--- precintcon-2.2.1/precintcon/man/precintcon.Rd | 88 +-- precintcon-2.2.1/precintcon/man/rai.Rd | 99 +-- precintcon-2.2.1/precintcon/man/read.data.Rd | 124 ++-- precintcon-2.2.1/precintcon/man/spi.Rd | 100 +-- precintcon-2.2.1/precintcon/man/spi.per.year.Rd | 104 +-- precintcon-2.2.1/precintcon/man/stat.Rd | 92 +-- precintcon-2.2.1/precintcon/man/tii.Rd |only precintcon-2.2.1/precintcon/man/trend.test.Rd |only 110 files changed, 4959 insertions(+), 4917 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Package also contains tools useful for performing Monte Carlo simulations
for studying the behaviour of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 0.6.1 dated 2015-11-19 and 0.7 dated 2016-01-21
DESCRIPTION | 13 - MD5 | 50 ++- NAMESPACE | 3 NEWS | 11 R/PersonClass.R | 4 R/ShinyGUIClass.R | 9 R/createShinyGUI.R | 18 + R/getPerson.R |only R/mirtCAT.R | 49 ++- R/mirtCAT_preamble.R | 36 ++ R/run_pattern.R | 6 R/server.R | 27 +- R/updateDesign.R | 3 R/util.R | 29 +- R/zzz-methods.R | 1 man/createShinyGUI.Rd | 23 + man/findNextItem.Rd | 8 man/generate.mirt_object.Rd | 40 +-- man/generate_pattern.Rd | 12 man/getPerson.Rd |only man/mirtCAT-package.Rd | 12 man/mirtCAT.Rd | 468 ++++++++++++++++++------------------- man/mirtCAT_preamble.Rd | 23 + man/updateDesign.Rd | 9 tests/GUI-tests/GUI-tests.R | 24 + tests/tests/test-mirtCAT_ordered.R | 5 tests/tests/test-mirtCAT_uni.R | 5 27 files changed, 519 insertions(+), 369 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modelling
item and person covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.14 dated 2015-11-19 and 1.15 dated 2016-01-21
DESCRIPTION | 20 +-- MD5 | 148 ++++++++++++----------- NAMESPACE | 2 NEWS | 23 +++ R/02-item_methods.R | 254 +++++++++++++++++++++++++++++++++++++++- R/03-estimation.R | 42 +++++- R/DIF.R | 1 R/M2.R | 3 R/MDIFF.R | 18 ++ R/MDISC.R | 7 - R/MHRM.group.R | 31 ++-- R/Mixed-methods.R | 3 R/PLCI.mirt.R | 2 R/PrepData.R | 88 ++++++++----- R/SE.methods.R | 15 +- R/SIBTEST.R |only R/SingleGroup-methods.R | 2 R/averageMI.R | 2 R/boot.mirt.R | 2 R/createItem.R | 1 R/empirical_plot.R |only R/empirical_rxx.R | 2 R/expand.table.R | 37 +++-- R/expected.item.R | 6 R/expected.test.R | 14 +- R/extract.group.R | 15 +- R/extract.item.R | 6 R/extract.mirt.R | 135 +++++++++++++-------- R/fixef.R | 6 R/fscores.R | 1 R/imputeMissing.R | 30 ++-- R/itemGAM.R | 2 R/itemfit.R | 13 +- R/iteminfo.R | 3 R/itemplot.R | 1 R/key2binary.R | 1 R/marginal_rxx.R | 4 R/mdirt.R | 1 R/mirt.R | 23 +++ R/mirtCluster.R | 1 R/mod2values.R | 2 R/multipleGroup.R | 4 R/personfit.R | 1 R/probtrace.R | 4 R/randef.R | 9 - R/simdata.R | 12 + R/testinfo.R | 4 R/utils.R | 7 - R/wald.R | 10 - man/MDIFF.Rd | 8 - man/MDISC.Rd | 2 man/PLCI.mirt.Rd | 3 man/SIBTEST.Rd |only man/averageMI.Rd | 3 man/boot.mirt.Rd | 3 man/empirical_plot.Rd |only man/empirical_rxx.Rd | 3 man/expand.table.Rd | 17 +- man/expected.item.Rd | 7 - man/extract.group.Rd | 3 man/extract.mirt.Rd | 36 ++++- man/itemGAM.Rd | 3 man/iteminfo.Rd | 5 man/marginal_rxx.Rd | 3 man/mdirt.Rd | 3 man/mirt.Rd | 23 +++ man/mod2values.Rd | 3 man/multipleGroup.Rd | 2 man/probtrace.Rd | 5 man/simdata.Rd | 10 - man/testinfo.Rd | 3 man/wald.Rd | 3 src/dpars.cpp | 241 +++++++++++++++---------------------- tests/tests/test-01-mirtOne.R | 3 tests/tests/test-02-mirtTwo.R | 4 tests/tests/test-07-mixedmirt.R | 14 +- tests/tests/test-12-gpcm_mats.R |only tests/tests/test-13-grsmIRT.R |only 78 files changed, 974 insertions(+), 454 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 2.1.7-1 dated 2015-10-27 and 3.0.0 dated 2016-01-21
geomorph-2.1.7-1/geomorph/R/compare.modular.partitions.r |only geomorph-2.1.7-1/geomorph/R/morphol.integr.r |only geomorph-2.1.7-1/geomorph/R/phylo.pls.R |only geomorph-2.1.7-1/geomorph/R/plotAllometry.r |only geomorph-2.1.7-1/geomorph/R/trajectory.analysis.r |only geomorph-2.1.7-1/geomorph/src |only geomorph-3.0.0/geomorph/DESCRIPTION | 11 geomorph-3.0.0/geomorph/MD5 | 245 - geomorph-3.0.0/geomorph/NAMESPACE | 47 geomorph-3.0.0/geomorph/NEWS | 37 geomorph-3.0.0/geomorph/R/advanced.procD.lm.r | 364 + geomorph-3.0.0/geomorph/R/arrayspecs.r | 8 geomorph-3.0.0/geomorph/R/bilat.symmetry.r | 397 +- geomorph-3.0.0/geomorph/R/compare.evol.rates.r | 172 geomorph-3.0.0/geomorph/R/compare.multi.evol.rates.r | 129 geomorph-3.0.0/geomorph/R/define.links.r | 2 geomorph-3.0.0/geomorph/R/define.modules.r | 8 geomorph-3.0.0/geomorph/R/define.sliders.r | 2 geomorph-3.0.0/geomorph/R/deprecated.defunct.r |only geomorph-3.0.0/geomorph/R/digit.curves.r | 4 geomorph-3.0.0/geomorph/R/digit.fixed.r | 2 geomorph-3.0.0/geomorph/R/digitize2d.r | 22 geomorph-3.0.0/geomorph/R/digitsurface.r | 8 geomorph-3.0.0/geomorph/R/estimate.missing.r | 20 geomorph-3.0.0/geomorph/R/geomorph.data.frame.r |only geomorph-3.0.0/geomorph/R/geomorph.support.code.r | 2470 +++++++++---- geomorph-3.0.0/geomorph/R/geomorph.utils.R |only geomorph-3.0.0/geomorph/R/globalIntegration.r | 3 geomorph-3.0.0/geomorph/R/gpagen.r | 171 geomorph-3.0.0/geomorph/R/gridPar.R | 1 geomorph-3.0.0/geomorph/R/integration.test.R |only geomorph-3.0.0/geomorph/R/modularity.test.R |only geomorph-3.0.0/geomorph/R/morphol.disparity.r | 140 geomorph-3.0.0/geomorph/R/nested.update.R |only geomorph-3.0.0/geomorph/R/phylo.integration.R |only geomorph-3.0.0/geomorph/R/phylo.modularity.R |only geomorph-3.0.0/geomorph/R/physignal.r | 158 geomorph-3.0.0/geomorph/R/plotAllSpecimens.r | 43 geomorph-3.0.0/geomorph/R/plotGMPhyloMorphoSpace.r | 4 geomorph-3.0.0/geomorph/R/plotRefToTarget.r | 17 geomorph-3.0.0/geomorph/R/plotspec.r | 10 geomorph-3.0.0/geomorph/R/procD.allometry.R |only geomorph-3.0.0/geomorph/R/procD.lm.r | 133 geomorph-3.0.0/geomorph/R/procD.pgls.r | 148 geomorph-3.0.0/geomorph/R/readland.nts.r | 8 geomorph-3.0.0/geomorph/R/readland.tps.r | 2 geomorph-3.0.0/geomorph/R/trajectory.analysis.R |only geomorph-3.0.0/geomorph/R/two.b.pls.r | 236 - geomorph-3.0.0/geomorph/R/warpRefMesh.r | 8 geomorph-3.0.0/geomorph/R/warpRefOutline.r | 6 geomorph-3.0.0/geomorph/data/larvalTails.rda |only geomorph-3.0.0/geomorph/man/advanced.procD.lm.Rd | 123 geomorph-3.0.0/geomorph/man/arrayspecs.Rd | 18 geomorph-3.0.0/geomorph/man/bilat.symmetry.Rd | 118 geomorph-3.0.0/geomorph/man/buildtemplate.Rd | 34 geomorph-3.0.0/geomorph/man/compare.evol.rates.Rd | 75 geomorph-3.0.0/geomorph/man/compare.modular.partitions.Rd | 64 geomorph-3.0.0/geomorph/man/compare.multi.evol.rates.Rd | 86 geomorph-3.0.0/geomorph/man/define.links.Rd | 14 geomorph-3.0.0/geomorph/man/define.modules.Rd | 30 geomorph-3.0.0/geomorph/man/define.sliders.Rd | 40 geomorph-3.0.0/geomorph/man/digit.curves.Rd | 6 geomorph-3.0.0/geomorph/man/digit.fixed.Rd | 20 geomorph-3.0.0/geomorph/man/digitize2d.Rd | 48 geomorph-3.0.0/geomorph/man/digitsurface.Rd | 26 geomorph-3.0.0/geomorph/man/editTemplate.Rd | 10 geomorph-3.0.0/geomorph/man/estimate.missing.Rd | 40 geomorph-3.0.0/geomorph/man/findMeanSpec.Rd | 10 geomorph-3.0.0/geomorph/man/fixed.angle.Rd | 8 geomorph-3.0.0/geomorph/man/geomorph-package.Rd | 14 geomorph-3.0.0/geomorph/man/geomorph.data.frame.Rd |only geomorph-3.0.0/geomorph/man/globalIntegration.Rd | 19 geomorph-3.0.0/geomorph/man/gpagen.Rd | 159 geomorph-3.0.0/geomorph/man/gridPar.Rd | 17 geomorph-3.0.0/geomorph/man/hummingbirds.Rd | 6 geomorph-3.0.0/geomorph/man/integration.test.Rd |only geomorph-3.0.0/geomorph/man/larvalTails.Rd |only geomorph-3.0.0/geomorph/man/modularity.test.Rd |only geomorph-3.0.0/geomorph/man/morphol.disparity.Rd | 82 geomorph-3.0.0/geomorph/man/morphol.integr.Rd | 91 geomorph-3.0.0/geomorph/man/mosquito.Rd | 6 geomorph-3.0.0/geomorph/man/motionpaths.Rd | 4 geomorph-3.0.0/geomorph/man/mshape.Rd | 10 geomorph-3.0.0/geomorph/man/nested.update.Rd |only geomorph-3.0.0/geomorph/man/phylo.integration.Rd |only geomorph-3.0.0/geomorph/man/phylo.modularity.Rd |only geomorph-3.0.0/geomorph/man/phylo.pls.Rd | 64 geomorph-3.0.0/geomorph/man/physignal.Rd | 79 geomorph-3.0.0/geomorph/man/plethShapeFood.Rd | 8 geomorph-3.0.0/geomorph/man/plethodon.Rd | 6 geomorph-3.0.0/geomorph/man/plethspecies.Rd | 2 geomorph-3.0.0/geomorph/man/plot.CR.Rd |only geomorph-3.0.0/geomorph/man/plot.CR.phylo.Rd |only geomorph-3.0.0/geomorph/man/plot.advanced.procD.lm.Rd |only geomorph-3.0.0/geomorph/man/plot.bilat.symmetry.Rd |only geomorph-3.0.0/geomorph/man/plot.evolrate.Rd |only geomorph-3.0.0/geomorph/man/plot.gpagen.Rd |only geomorph-3.0.0/geomorph/man/plot.physignal.Rd |only geomorph-3.0.0/geomorph/man/plot.pls.Rd |only geomorph-3.0.0/geomorph/man/plot.procD.allometry.Rd |only geomorph-3.0.0/geomorph/man/plot.procD.lm.Rd |only geomorph-3.0.0/geomorph/man/plot.trajectory.analysis.Rd |only geomorph-3.0.0/geomorph/man/plotAllSpecimens.Rd | 24 geomorph-3.0.0/geomorph/man/plotAllometry.Rd | 104 geomorph-3.0.0/geomorph/man/plotGMPhyloMorphoSpace.Rd | 28 geomorph-3.0.0/geomorph/man/plotOutliers.Rd | 7 geomorph-3.0.0/geomorph/man/plotRefToTarget.Rd | 58 geomorph-3.0.0/geomorph/man/plotTangentSpace.Rd | 32 geomorph-3.0.0/geomorph/man/plotspec.Rd | 16 geomorph-3.0.0/geomorph/man/print.CR.Rd |only geomorph-3.0.0/geomorph/man/print.CR.phylo.Rd |only geomorph-3.0.0/geomorph/man/print.advanced.procD.lm.Rd |only geomorph-3.0.0/geomorph/man/print.bilat.symmetry.Rd |only geomorph-3.0.0/geomorph/man/print.evolrate.Rd |only geomorph-3.0.0/geomorph/man/print.evolrate1.Rd |only geomorph-3.0.0/geomorph/man/print.gpagen.Rd |only geomorph-3.0.0/geomorph/man/print.morphol.disparity.Rd |only geomorph-3.0.0/geomorph/man/print.physignal.Rd |only geomorph-3.0.0/geomorph/man/print.pls.Rd |only geomorph-3.0.0/geomorph/man/print.procD.allometry.Rd |only geomorph-3.0.0/geomorph/man/print.procD.lm.Rd |only geomorph-3.0.0/geomorph/man/print.trajectory.analysis.Rd |only geomorph-3.0.0/geomorph/man/procD.allometry.Rd |only geomorph-3.0.0/geomorph/man/procD.lm.Rd | 131 geomorph-3.0.0/geomorph/man/procD.pgls.Rd | 107 geomorph-3.0.0/geomorph/man/pupfish.Rd | 13 geomorph-3.0.0/geomorph/man/ratland.Rd | 4 geomorph-3.0.0/geomorph/man/read.morphologika.Rd | 14 geomorph-3.0.0/geomorph/man/read.ply.Rd | 8 geomorph-3.0.0/geomorph/man/readland.nts.Rd | 36 geomorph-3.0.0/geomorph/man/readland.tps.Rd | 30 geomorph-3.0.0/geomorph/man/readmulti.nts.Rd | 24 geomorph-3.0.0/geomorph/man/scallopPLY.Rd | 2 geomorph-3.0.0/geomorph/man/scallops.Rd | 2 geomorph-3.0.0/geomorph/man/summary.CR.Rd |only geomorph-3.0.0/geomorph/man/summary.CR.phylo.Rd |only geomorph-3.0.0/geomorph/man/summary.advanced.procD.lm.Rd |only geomorph-3.0.0/geomorph/man/summary.bilat.symmetry.Rd |only geomorph-3.0.0/geomorph/man/summary.evolrate.Rd |only geomorph-3.0.0/geomorph/man/summary.evolrate1.Rd |only geomorph-3.0.0/geomorph/man/summary.gpagen.Rd |only geomorph-3.0.0/geomorph/man/summary.morphol.disparity.Rd |only geomorph-3.0.0/geomorph/man/summary.physignal.Rd |only geomorph-3.0.0/geomorph/man/summary.pls.Rd |only geomorph-3.0.0/geomorph/man/summary.procD.allometry.Rd |only geomorph-3.0.0/geomorph/man/summary.procD.lm.Rd |only geomorph-3.0.0/geomorph/man/summary.trajectory.analysis.Rd |only geomorph-3.0.0/geomorph/man/trajectory.analysis.Rd | 239 - geomorph-3.0.0/geomorph/man/two.b.pls.Rd | 89 geomorph-3.0.0/geomorph/man/two.d.array.Rd | 12 geomorph-3.0.0/geomorph/man/warpRefMesh.Rd | 24 geomorph-3.0.0/geomorph/man/warpRefOutline.Rd | 18 geomorph-3.0.0/geomorph/man/writeland.tps.Rd | 4 153 files changed, 4387 insertions(+), 3012 deletions(-)
Title: Item Focused Trees for the Identification of Items in
Differential Item Functioning
Description: Item focused recursive partitioning for simultaneous selection of
items and variables that induce Differential Item Functioning (DIF) based on the
Rasch Model or the Logistic Regression Approach for DIF detection.
Author: Moritz Berger
Maintainer: Moritz Berger <moritz.berger@stat.uni-muenchen.de>
Diff between DIFtree versions 1.1.0 dated 2015-10-14 and 2.0.1 dated 2016-01-21
DESCRIPTION | 12 MD5 | 38 ++ NAMESPACE | 20 + R/DIFtree-internal.R | 251 +++++++++---------- R/DIFtree.R | 601 ++++++++--------------------------------------- R/DIFtree.default.R |only R/data_sim.R | 9 R/designlists_logistic.R |only R/get_endnodes.R |only R/info_summary.R |only R/infos_summary.R |only R/one_prediction.R |only R/plot.DIFtree.R | 228 ++++++++--------- R/predict.DIFtree.R | 165 +++++++----- R/prepareX.R |only R/ptree.R |only R/summary.DIFtree.R |only R/tree_Logistic.R |only R/tree_Rasch.R |only R/tree_dif.R |only R/tree_nudif.R |only R/tree_udif.R |only R/whole_prediction.R |only man/DIFtree.Rd | 88 ++++-- man/data_sim.Rd | 20 + man/plot.DIFtree.Rd | 48 ++- man/predict.DIFtree.Rd | 43 ++- man/summary.DIFtree.Rd |only 28 files changed, 634 insertions(+), 889 deletions(-)
Title: Wrapper for MUMPS Library
Description: Exported class can be used for storing sparse matrix
and solving corresponding linear system with one or many right
hand sides. There is a possibility to do separately symbolic analysis,
LU factorization and system solving.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.0.1.4 dated 2015-12-17 and 5.0.1.6 dated 2016-01-21
rmumps-5.0.1.4/rmumps/build |only rmumps-5.0.1.4/rmumps/configure |only rmumps-5.0.1.4/rmumps/inst/MUMPS_5.0.1 |only rmumps-5.0.1.4/rmumps/inst/Makefile |only rmumps-5.0.1.4/rmumps/inst/Makefile.mumps |only rmumps-5.0.1.4/rmumps/inst/Makefile.win |only rmumps-5.0.1.4/rmumps/inst/compiler_options.in |only rmumps-5.0.1.4/rmumps/inst/compiler_options.in.win |only rmumps-5.0.1.4/rmumps/inst/metis-5.1.0 |only rmumps-5.0.1.6/rmumps/DESCRIPTION | 11 rmumps-5.0.1.6/rmumps/MD5 | 865 +++++++++----------- rmumps-5.0.1.6/rmumps/NEWS | 16 rmumps-5.0.1.6/rmumps/cleanup | 6 rmumps-5.0.1.6/rmumps/configure.win | 16 rmumps-5.0.1.6/rmumps/inst/examples/random_matrix.R | 2 rmumps-5.0.1.6/rmumps/man/Rmumps.Rd | 10 rmumps-5.0.1.6/rmumps/man/rmumps-package.Rd | 4 rmumps-5.0.1.6/rmumps/src/Makevars | 13 rmumps-5.0.1.6/rmumps/src/Makevars.win | 7 rmumps-5.0.1.6/rmumps/src/lib |only rmumps-5.0.1.6/rmumps/src/rmumps_module.cpp | 8 21 files changed, 470 insertions(+), 488 deletions(-)
Title: Provides the Standard Distribution Functions for the Triangle
Distribution
Description: Provides the "r, q, p, and d" distribution functions for the triangle distribution.
Author: Rob Carnell
Maintainer: Rob Carnell <bertcarnell@gmail.com>
Diff between triangle versions 0.8 dated 2013-02-22 and 0.10 dated 2016-01-21
ChangeLog | 9 +++++++++ DESCRIPTION | 22 +++++++++------------- MD5 | 9 +++++---- NAMESPACE | 2 ++ man/triangle-package.Rd |only man/triangle.Rd | 4 ++-- 6 files changed, 27 insertions(+), 19 deletions(-)
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between tree versions 1.0-36 dated 2015-06-29 and 1.0-37 dated 2016-01-21
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- src/grow.c | 2 ++ src/treefix.c | 1 + 5 files changed, 15 insertions(+), 8 deletions(-)
Title: Supplementary Distributions
Description: Ten distributions supplementing those built into R.
Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi
squared, Spearman's rho, maximum F ratio, the Pearson product
moment correlation coefficiant, Johnson distributions, normal
scores and generalized hypergeometric distributions. In
addition two random number generators of George Marsaglia are
included.
Author: Bob Wheeler <bwheelerg@gmail.com>
Maintainer: ORPHANED
Diff between SuppDists versions 1.1-9.1 dated 2013-10-30 and 1.1-9.2 dated 2016-01-21
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 2 ++ src/dists.cc | 19 +++++++++++++------ 4 files changed, 23 insertions(+), 14 deletions(-)
Title: Programming with Big Data -- Interface to ZeroMQ
Description: 'ZeroMQ' is a well-known library for high-performance
asynchronous messaging in scalable, distributed applications. This
package provides high level R wrapper functions to easily utilize
'ZeroMQ'. We mainly focus on interactive client/server programming
frameworks. For convenience, a minimal 'ZeroMQ' library (4.1.0 rc1)
is shipped with 'pbdZMQ', which can be used if no system installation
of 'ZeroMQ' is available. A few wrapper functions compatible with
'rzmq' are also provided.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
Christian Heckendorf [aut] (file transfer),
George Ostrouchov [aut] (Mac OSX),
Whit Armstrong [ctb] (some functions are modified from the rzmq package
for backwards compatibility),
Brian Ripley [ctb] (C code of shellexec, and Solaris),
R Core team [ctb] (some functions are modified from the R source code)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdZMQ versions 0.2-0 dated 2015-12-16 and 0.2-1 dated 2016-01-21
ChangeLog | 7 +++ DESCRIPTION | 9 ++-- MD5 | 64 +++++++++++++++++------------- NAMESPACE | 11 ++++- R/111_control.r | 21 +++++++++ R/111_pbd_opt.r |only R/222_export_env.r | 4 - R/222_export_opt.r | 61 +++++++++------------------- R/R_zmq_message.r | 6 +- R/R_zmq_poll.r |only R/R_zmq_sendrecv.r | 6 +- R/R_zmq_sendrecv_multipart.r |only R/R_zmq_socket.r | 34 +++++++++++++++ README.md | 1 demo/00Index | 3 + demo/mpclient.r |only demo/mpserver.r |only demo/mspoller.r |only demo/taskvent.r | 3 - demo/wuserver.r | 1 inst/CITATION | 8 ++- inst/doc/pbdZMQ-guide.pdf |binary man/a0_b_control.Rd | 1 man/a0_b_pbd_opt.Rd |only man/a0_c_options.Rd | 32 ++------------- man/a1_socket.Rd | 11 ++++- man/b0_sendrecv.Rd | 2 man/b2_sendrecv_multipart.Rd |only man/b3_poll.Rd |only man/zz_zmq_control.Rd | 5 ++ src/Makevars.in | 2 src/R_zmq.h | 8 +++ src/R_zmq_poll.c |only src/R_zmq_sendrecv.c | 2 src/R_zmq_socket.c | 39 +++++++++++++++++- src/zzz.c | 7 +++ vignettes/pbdZMQ-include/01-copyright.tex | 2 vignettes/pbdZMQ-include/03-example.tex | 10 ++++ 38 files changed, 240 insertions(+), 120 deletions(-)
Title: Programming with Big Data -- Interface to MPI
Description: An efficient interface to MPI by utilizing S4
classes and methods with a focus on Single Program/Multiple Data ('SPMD')
parallel programming style, which is intended for batch parallel
execution.
Author: Wei-Chen Chen [aut, cre],
George Ostrouchov [aut],
Drew Schmidt [aut],
Pragneshkumar Patel [aut],
Hao Yu [aut],
Christian Heckendorf [ctb] (FreeBSD),
Brian Ripley [ctb] (Windows HPC Pack 2012),
R Core team [ctb] (some functions are modified from the base packages)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdMPI versions 0.3-0 dated 2015-12-18 and 0.3-1 dated 2016-01-21
ChangeLog | 6 +++++ DESCRIPTION | 10 ++++----- MD5 | 18 +++++++++-------- NAMESPACE | 5 +++- R/111_pbd_opt.r |only R/222_export_env.r | 31 ++++++++++++++---------------- inst/doc/pbdMPI-guide.pdf |binary man/11_d_pbd_opt.Rd |only man/ww_comm_as_gbd.Rd | 2 - man/zz_spmd_control.Rd | 2 - vignettes/pbdMPI-include/01-copyright.tex | 2 - 11 files changed, 42 insertions(+), 34 deletions(-)
Title: Client for the Captricity API
Description: Get text from images of text using Captricity Optical Character
Recognition (OCR) API. Captricity allows you to get text from handwritten
forms --- think surveys --- and other structured paper documents. And it can
output data in form a delimited file keeping field information intact. For more
information, read https://shreddr.captricity.com/developer/overview/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between captr versions 0.1.3 dated 2015-12-14 and 0.1.4 dated 2016-01-21
DESCRIPTION | 6 +++--- MD5 | 23 ++++++++++++++++------- NAMESPACE | 4 ++++ NEWS | 6 ++++++ R/create_batch.R | 13 ++++++++----- R/list_batch_files.R |only R/list_batches.R |only R/list_docs.R |only R/list_jobs.R |only R/user_profile.R |only build/vignette.rds |binary inst/doc/using_captr.html | 4 ++-- man/create_batch.Rd | 7 +++++-- man/list_batch_files.Rd |only man/list_batches.Rd |only man/list_docs.Rd |only man/list_jobs.Rd |only 17 files changed, 44 insertions(+), 19 deletions(-)
Title: Client for Various 'CrossRef' 'APIs'
Description: Client for various 'CrossRef' 'APIs', including 'metadata' search
with their old and newer search 'APIs', get 'citations' in various formats
(including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs'
to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to
full text of articles when available.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Ted Hart [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rcrossref versions 0.3.4 dated 2015-07-10 and 0.5.0 dated 2016-01-20
DESCRIPTION | 22 +- LICENSE | 2 MD5 | 121 ++++++----- NAMESPACE | 17 + R/cr_agency.r | 4 R/cr_citation_count.r | 1 R/cr_cn.r | 114 +++++++--- R/cr_ft_links.R | 29 +- R/cr_ft_text.R | 166 +++++++++++---- R/cr_fundref.r | 189 ++++++++++++----- R/cr_journals.r | 159 ++++++++++---- R/cr_licenses.R | 49 +++- R/cr_members.r | 187 ++++++++++++----- R/cr_prefixes.r | 123 ++++++++--- R/cr_search_free.r | 5 R/cr_types.R |only R/cr_works.R | 235 ++++++++++++++++----- R/crosscite.R | 6 R/filters.R |only R/id_converter.R |only R/rcrossref-package.R | 39 +++ R/requestor.R |only R/zzz.R | 87 +++---- README.md | 177 ++++++++-------- build/vignette.rds |binary inst/doc/crossref_filters.Rmd | 8 inst/doc/crossref_filters.html | 40 +++ inst/examples/MairChamberlain2014RJournal.txt | 285 ++++++++++++++++++-------- inst/ignore |only inst/vign/crossref_filters.Rmd | 8 inst/vign/crossref_filters.md | 8 man/GET_agency_id.Rd |only man/as.tdmurl.Rd | 4 man/cr_agency.Rd | 8 man/cr_citation-defunct.Rd | 2 man/cr_citation_count.Rd | 2 man/cr_cn.Rd | 58 +++-- man/cr_ft_links.Rd | 18 - man/cr_ft_text.Rd | 71 +++++- man/cr_fundref.Rd | 95 ++++++-- man/cr_journals.Rd | 53 ++++ man/cr_licenses.Rd | 24 +- man/cr_members.Rd | 58 ++++- man/cr_prefixes.Rd | 72 ++++-- man/cr_r.Rd | 2 man/cr_search.Rd | 2 man/cr_search_free.Rd | 4 man/cr_types.Rd |only man/cr_works.Rd | 71 +++++- man/crosscite.Rd | 15 - man/extract_xpdf.Rd | 2 man/filters.Rd |only man/get_styles.Rd | 2 man/id_converter.Rd |only man/pmid2doi.Rd | 2 man/rcrossref-defunct.Rd | 6 man/rcrossref-package.Rd | 50 ++++ tests/testthat/test_cr_cn.R | 16 + tests/testthat/test_cr_ft_links.R | 6 tests/testthat/test_cr_fundref.R | 9 tests/testthat/test_cr_members.R | 11 - tests/testthat/test_cr_members_cursor.R |only tests/testthat/test_cr_prefixes.R | 12 + tests/testthat/test_cr_types.R |only tests/testthat/test_cr_works.R | 83 +++++++ tests/testthat/test_cr_works_cursor.R |only vignettes/crossref_filters.Rmd | 8 67 files changed, 2046 insertions(+), 801 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on 'Lapack' and level-3 'BLAS'.
The 'RcppEigen' package includes the header files from the 'Eigen' C++
template library (currently version 3.2.7). Thus users do not need to
install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel and Romain Francois;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.2.5.1 dated 2015-09-24 and 0.3.2.7.0 dated 2016-01-20
ChangeLog | 28 - DESCRIPTION | 12 MD5 | 130 ++--- README.md | 2 build/vignette.rds |binary inst/NEWS.Rd | 25 inst/doc/RcppEigen-Introduction.pdf |binary inst/include/Eigen/SparseCore | 2 inst/include/Eigen/src/Cholesky/LDLT.h | 2 inst/include/Eigen/src/Cholesky/LLT.h | 2 inst/include/Eigen/src/CholmodSupport/CholmodSupport.h | 10 inst/include/Eigen/src/Core/Array.h | 15 inst/include/Eigen/src/Core/ArrayBase.h | 4 inst/include/Eigen/src/Core/CwiseBinaryOp.h | 3 inst/include/Eigen/src/Core/CwiseUnaryOp.h | 2 inst/include/Eigen/src/Core/DenseBase.h | 14 inst/include/Eigen/src/Core/DenseStorage.h | 255 ++++++---- inst/include/Eigen/src/Core/DiagonalProduct.h | 3 inst/include/Eigen/src/Core/GeneralProduct.h | 10 inst/include/Eigen/src/Core/MapBase.h | 2 inst/include/Eigen/src/Core/MathFunctions.h | 2 inst/include/Eigen/src/Core/Matrix.h | 15 inst/include/Eigen/src/Core/MatrixBase.h | 9 inst/include/Eigen/src/Core/PlainObjectBase.h | 30 + inst/include/Eigen/src/Core/Redux.h | 5 inst/include/Eigen/src/Core/Ref.h | 9 inst/include/Eigen/src/Core/SelfCwiseBinaryOp.h | 10 inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 1 inst/include/Eigen/src/Core/arch/SSE/MathFunctions.h | 8 inst/include/Eigen/src/Core/products/TriangularMatrixMatrix_MKL.h | 4 inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h | 9 inst/include/Eigen/src/Core/util/ForwardDeclarations.h | 3 inst/include/Eigen/src/Core/util/MKL_support.h | 32 + inst/include/Eigen/src/Core/util/Macros.h | 20 inst/include/Eigen/src/Core/util/XprHelper.h | 8 inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h | 23 inst/include/Eigen/src/Geometry/AlignedBox.h | 2 inst/include/Eigen/src/Geometry/AngleAxis.h | 6 inst/include/Eigen/src/Geometry/Quaternion.h | 4 inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h | 4 inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h | 3 inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h | 3 inst/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h | 21 inst/include/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h | 48 + inst/include/Eigen/src/OrderingMethods/Amd.h | 5 inst/include/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h | 4 inst/include/Eigen/src/SparseCore/CompressedStorage.h | 6 inst/include/Eigen/src/SparseCore/SparseCwiseBinaryOp.h | 4 inst/include/Eigen/src/SparseCore/SparseMatrix.h | 5 inst/include/Eigen/src/SparseCore/SparseMatrixBase.h | 35 - inst/include/Eigen/src/SparseCore/SparseUtil.h | 1 inst/include/Eigen/src/SparseCore/SparseVector.h | 1 inst/include/Eigen/src/SparseLU/SparseLU.h | 4 inst/include/Eigen/src/SparseLU/SparseLUImpl.h | 2 inst/include/Eigen/src/SparseLU/SparseLU_Memory.h | 4 inst/include/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h | 8 inst/include/Eigen/src/SparseLU/SparseLU_column_bmod.h | 4 inst/include/Eigen/src/SparseLU/SparseLU_kernel_bmod.h | 4 inst/include/Eigen/src/SparseLU/SparseLU_panel_bmod.h | 8 inst/include/Eigen/src/SparseLU/SparseLU_pivotL.h | 7 inst/include/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h | 2 inst/include/unsupported/Eigen/src/IterativeSolvers/DGMRES.h | 4 inst/include/unsupported/Eigen/src/IterativeSolvers/GMRES.h | 3 inst/include/unsupported/Eigen/src/IterativeSolvers/MINRES.h | 3 inst/unitTests/runit.sparse.R | 5 src/fastLm.cpp | 2 66 files changed, 613 insertions(+), 308 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. 2014, "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189.
Author: Qingzhao Yu
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 2.0-1 dated 2015-12-02 and 2.0-2 dated 2016-01-20
mma-2.0-1/mma/man/data.org2.Rd |only mma-2.0-2/mma/DESCRIPTION | 8 mma-2.0-2/mma/MD5 | 24 +- mma-2.0-2/mma/NAMESPACE | 3 mma-2.0-2/mma/R/mma.r | 316 ++++++++++------------------------ mma-2.0-2/mma/man/boot.med.binx.Rd | 2 mma-2.0-2/mma/man/boot.med.contx.Rd | 4 mma-2.0-2/mma/man/data.org.Rd | 52 +++-- mma-2.0-2/mma/man/med.binx.Rd | 2 mma-2.0-2/mma/man/med.contx.Rd | 4 mma-2.0-2/mma/man/mma-package.Rd | 2 mma-2.0-2/mma/man/mma.Rd | 7 mma-2.0-2/mma/man/summary.med_iden.Rd |only mma-2.0-2/mma/man/summary.mma.Rd | 7 14 files changed, 159 insertions(+), 272 deletions(-)
Title: Joint Random Forest (JRF) for the Simultaneous Estimation of
Multiple Related Networks
Description: Simultaneous estimation of multiple related networks.
Author: Francesca Petralia Developer [aut, cre],
Pei Wang Developer [aut],
Zhidong Tu Developer [aut],
Won-min Song Developer [aut],
Adele Cutler Developer [ctb],
Leo Breiman Developer [ctb],
Andy Liaw Developer [ctb],
Matthew Wiener Developer [ctb]
Maintainer: Francesca Petralia Developer <francesca.petralia@mssm.edu>
Diff between JRF versions 0.1-2 dated 2015-12-03 and 0.1-3 dated 2016-01-20
JRF-0.1-2/JRF/R/importance.R |only JRF-0.1-2/JRF/man/importance.Rd |only JRF-0.1-3/JRF/DESCRIPTION | 6 - JRF-0.1-3/JRF/MD5 | 14 +- JRF-0.1-3/JRF/NAMESPACE | 2 JRF-0.1-3/JRF/R/JRF.R | 183 +++++++++++++++++++++-------------- JRF-0.1-3/JRF/R/JRF_permutation.R |only JRF-0.1-3/JRF/man/JRF.Rd | 119 ++++------------------ JRF-0.1-3/JRF/man/JRF_permutation.Rd |only JRF-0.1-3/JRF/src/regTree.c | 1 10 files changed, 149 insertions(+), 176 deletions(-)
Title: Interface Between R and the OpenStreetMap-Based Routing Service
OSRM
Description: An interface between R and the OSRM API. OSRM is a routing
service based on OpenStreetMap data. See <http://project-osrm.org/> for more
information. A public API exists but one can run its own instance. This package
allows to compute distances (travel time and kilometric distance) between points
and travel time matrices.
Author: Timothée Giraud [cre, aut]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between osrm versions 1.1 dated 2015-11-06 and 2.0.0 dated 2016-01-20
osrm-1.1/osrm/NEWS |only osrm-1.1/osrm/R/osrmTableErrors.R |only osrm-1.1/osrm/R/osrmTableOD.R |only osrm-1.1/osrm/inst |only osrm-1.1/osrm/man/osrmTableErrors.Rd |only osrm-1.1/osrm/man/osrmTableOD.Rd |only osrm-2.0.0/osrm/DESCRIPTION | 14 - osrm-2.0.0/osrm/MD5 | 30 +-- osrm-2.0.0/osrm/NAMESPACE | 2 osrm-2.0.0/osrm/R/osrmTable.R | 255 +++++++++++++++++++++++++------- osrm-2.0.0/osrm/R/osrmViaroute.R | 33 +--- osrm-2.0.0/osrm/R/osrmViarouteGeom.R | 73 ++++----- osrm-2.0.0/osrm/R/package.R | 17 +- osrm-2.0.0/osrm/R/zzz.R | 2 osrm-2.0.0/osrm/README.md | 11 - osrm-2.0.0/osrm/man/osrm.Rd | 17 +- osrm-2.0.0/osrm/man/osrmTable.Rd | 60 +++++-- osrm-2.0.0/osrm/man/osrmViaroute.Rd | 16 -- osrm-2.0.0/osrm/man/osrmViarouteGeom.Rd | 34 +--- 19 files changed, 363 insertions(+), 201 deletions(-)
Title: Access to the Gitlab API
Description: Provides R functions to access the API of the project and
repository management web application gitlab. For many common tasks (repository
file access, issue assignment and status, commenting) convenience wrappers
are provided, and in addition the full API can be used by specifying request
locations. Gitlab is open-source software and can be self-hosted or used on
gitlab.com.
Author: Jirka Lewandowski [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between gitlabr versions 0.5.1 dated 2015-10-27 and 0.6.2 dated 2016-01-20
DESCRIPTION | 24 ++++---- MD5 | 22 ++++--- NAMESPACE | 8 ++ R/gitlab_api.R | 11 ++- R/gitlabr-package.R | 2 R/magrittr_extensions.R | 19 ++++++ R/projects_and_repos.R | 109 ++++++++++++++++++++++++++++++++++++++ man/branches.Rd |only man/create_merge_request.Rd |only man/get_file.Rd | 13 +++- man/gitlab.Rd | 6 +- man/pipe_into.Rd |only man/push_file.Rd |only vignettes/quick-start-gitlabr.Rmd | 10 ++- 14 files changed, 193 insertions(+), 31 deletions(-)
Title: Inference and Analysis for Generalized Quadratic Diffusions
Description: Tools for performing inference and analysis on a class of quadratic diffusion processes for both scalar and bivariate diffusion systems. For scalar diffusions, a module is provided for solving first passage time problems for both time-homogeneous and time-inhomogeneous GQDs.
Author: Etienne A.D. Pienaar [aut, cre],
Melvin M. Varughese [ctb]
Maintainer: Etienne A.D. Pienaar <etiennead@gmail.com>
Diff between DiffusionRgqd versions 0.1.1 dated 2015-10-13 and 0.1.2 dated 2016-01-20
DiffusionRgqd-0.1.1/DiffusionRgqd/man/figures/desktop.ini |only DiffusionRgqd-0.1.2/DiffusionRgqd/DESCRIPTION | 11 DiffusionRgqd-0.1.2/DiffusionRgqd/MD5 | 106 ++++++--- DiffusionRgqd-0.1.2/DiffusionRgqd/NAMESPACE | 3 DiffusionRgqd-0.1.2/DiffusionRgqd/NEWS.md | 26 +- DiffusionRgqd-0.1.2/DiffusionRgqd/R/BiGQD.density.R | 85 ++++--- DiffusionRgqd-0.1.2/DiffusionRgqd/R/BiGQD.mcmc.R | 46 ++-- DiffusionRgqd-0.1.2/DiffusionRgqd/R/BiGQD.mle.R | 26 +- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.density.R | 111 ++++++---- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.dic.R | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.estimates.R | 65 +++-- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.mcmc.R | 51 +++- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.mle.R | 35 ++- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.plot.R | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/README.md | 35 +++ DiffusionRgqd-0.1.2/DiffusionRgqd/build |only DiffusionRgqd-0.1.2/DiffusionRgqd/data/SDEsim5.txt |only DiffusionRgqd-0.1.2/DiffusionRgqd/demo |only DiffusionRgqd-0.1.2/DiffusionRgqd/inst |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/BiGQD.density.Rd | 51 +++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/BiGQD.mcmc.Rd | 45 +++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/BiGQD.mle.Rd | 45 +++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/DiffusionRgqd-package.Rd | 6 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.TIpassage.Rd | 6 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.aic.Rd | 2 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.density.Rd | 40 ++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.dic.Rd | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.estimates.Rd | 15 + DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.mcmc.Rd | 38 ++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.mle.Rd | 42 ++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.passage.Rd | 6 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.plot.Rd | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.remove.Rd | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/man/SDEsim1.Rd | 2 DiffusionRgqd-0.1.2/DiffusionRgqd/man/SDEsim2.Rd | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/man/SDEsim4.Rd | 5 DiffusionRgqd-0.1.2/DiffusionRgqd/man/SDEsim5.Rd |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/BivEqn1.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/BivEqn2.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/BivEqn3.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/SDEsim5.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/ScalarEqn1.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/ScalarEqn2.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/ScalarEqn3.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/TransDens1.png |binary DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/TransDens2.png |binary DiffusionRgqd-0.1.2/DiffusionRgqd/vignettes |only 47 files changed, 665 insertions(+), 262 deletions(-)
Title: Bindings to the CommonMark Reference Implementation
Description: The CommonMark specification defines a rationalized version of markdown
syntax. This package uses the libcmark reference implementation for converting
markdown text into various formats including html, latex and groff man. In
addition it exposes the markdown parse tree in xml format.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between commonmark versions 0.6 dated 2016-01-03 and 0.7 dated 2016-01-20
DESCRIPTION | 6 MD5 | 22 NEWS | 7 src/cmark/blocks.c | 6 src/cmark/cmark.h | 20 src/cmark/cmark_version.h | 4 src/cmark/commonmark.c | 57 src/cmark/html.c | 2 src/cmark/iterator.c | 3 src/cmark/node.c | 16 src/cmark/render.c | 20 src/cmark/scanners.c |26864 +++++++++++++++++----------------------------- 12 files changed, 10561 insertions(+), 16466 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.3.0 dated 2016-01-19 and 1.3.1 dated 2016-01-20
DESCRIPTION | 8 ++--- MD5 | 16 +++++------ NEWS | 3 ++ build/vignette.rds |binary inst/doc/discreteBPCP.R | 6 ++-- inst/doc/discreteBPCP.Rnw | 63 ++++++++++++++++++++++++++++++++------------- inst/doc/discreteBPCP.pdf |binary man/bpcp-package.Rd | 4 +- vignettes/discreteBPCP.Rnw | 63 ++++++++++++++++++++++++++++++++------------- 9 files changed, 110 insertions(+), 53 deletions(-)
Title: Univariate Outlier Detection
Description: Detect outliers in one-dimensional data.
Author: Mark van der Loo <mark.vanderloo@gmail.com>
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between extremevalues versions 2.3.1 dated 2015-07-14 and 2.3.2 dated 2016-01-20
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS | 4 ++++ inst/CITATION | 6 +++--- 4 files changed, 15 insertions(+), 11 deletions(-)
Title: Tools Inspired by Stata to Manipulate Tabular Data
Description: A set of tools inspired by Stata to explore data.frames (summarize,
tabulate, xtile, pctile, binscatter, elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>
Diff between statar versions 0.5.0 dated 2016-01-01 and 0.6.0 dated 2016-01-20
statar-0.5.0/statar/R/tag.R |only statar-0.5.0/statar/man/tag.Rd |only statar-0.6.0/statar/DESCRIPTION | 6 +-- statar-0.6.0/statar/MD5 | 31 ++++++++++--------- statar-0.6.0/statar/NAMESPACE | 4 +- statar-0.6.0/statar/R/fill_gap.R |only statar-0.6.0/statar/R/is.panel.R | 39 ++++++++++++++----------- statar-0.6.0/statar/R/statar.R | 1 statar-0.6.0/statar/R/sum_up.R | 20 ++++++------ statar-0.6.0/statar/R/tab.R | 13 ++++---- statar-0.6.0/statar/README.md | 4 +- statar-0.6.0/statar/inst/doc/panel-data.Rmd | 29 +++++++++++++----- statar-0.6.0/statar/inst/doc/panel-data.html | 33 +++++++++++++++------ statar-0.6.0/statar/man/fill_gap.Rd |only statar-0.6.0/statar/man/is.panel.Rd | 19 ++++++------ statar-0.6.0/statar/man/sum_up.Rd | 4 +- statar-0.6.0/statar/man/tab.Rd | 4 +- statar-0.6.0/statar/tests/testthat/test_fill.R |only statar-0.6.0/statar/vignettes/panel-data.Rmd | 29 +++++++++++++----- 19 files changed, 144 insertions(+), 92 deletions(-)
Title: Using Percolation and Conductance to Find Information Flow
Certainty in a Direct Network
Description: To find the certainty of dominance interactions with indirect interactions being considered.
Author: Kevin Fujii [aut],
Jian Jin [aut, cre],
Aaron Shev [aut],
Brianne Beisner [aut],
Brenda McCowan [aut, cph],
Hsieh Fushing [aut, cph]
Maintainer: Jian Jin <jinjian.pku@gmail.com>
Diff between Perc versions 0.1.0 dated 2015-10-22 and 0.1.1 dated 2016-01-20
DESCRIPTION | 8 ++--- MD5 | 18 +++++++----- R/as.conflictmat.R | 11 ++++--- R/conductance.R | 5 ++- R/findAllRankOrder.R | 70 ++++++++++++++++++++++++++++++++++-------------- R/sim.rank.order.R | 61 +++++++---------------------------------- build/vignette.rds |binary man/getAllCosts.Rd |only man/getAllRankOrder.Rd |only man/getBestRankOrder.Rd |only man/getSimOutput.Rd |only vignettes/Perc.Rmd | 20 ++++++------- 12 files changed, 96 insertions(+), 97 deletions(-)
Title: Parametric Bootstrap and Kenward Roger Based Methods for Mixed
Model Comparison
Diff between pbkrtest versions 0.4-4 dated 2015-12-12 and 0.4-5 dated 2016-01-20
Description: Test in mixed effects models.
Attention is on mixed effects models as implemented in the
lme4 package.
The package implements a parametric bootstrap test and a Kenward-Roger
modification of F-tests for linear mixed effects models and a parametric bootstrap
test for generalized linear mixed models.
Author: Ulrich Halekoh
Maintainer: Søren Højsgaard
ChangeLog | 19
DESCRIPTION | 12
MD5 | 46 +-
R/KR-Sigma-G.R | 346 ++++++++--------
R/KR-Sigma-G2.R | 306 +++++++-------
R/KR-across-versions.R | 40 -
R/KR-init-modcomp.R | 128 +++---
R/KR-linearAlgebra.R | 120 ++---
R/KR-modcomp.R | 540 +++++++++++++-------------
R/KR-vcovAdj.R | 155 -------
R/KR-vcovAdj0.R | 232 +++++------
R/KR-vcovAdj15.R |only
R/KR-vcovAdj16.R |only
R/PB-anova.R | 110 ++---
R/PB-modcomp.R | 764 ++++++++++++++++++-------------------
R/PB-refdist.R | 281 +++++--------
R/PB-utils.R | 76 +--
R/getKR.R | 24 -
R/get_ddf_Lb.R | 338 ++++++++--------
R/modelCoercion.R | 344 ++++++++--------
build/vignette.rds |binary
inst/doc/pbkrtest-introduction.pdf |binary
man/KRmodcomp.Rd | 2
man/pbkrtest-internal.Rd | 2
man/vcovAdj.Rd | 53 +-
25 files changed, 1893 insertions(+), 2045 deletions(-)
Title: Automatic Differentiation of Multivariate Operations
Description: An object that supports automatic differentiation
of matrix- and multidimensional-valued functions with
respect to multidimensional independent variables.
Automatic differentiation is via 'forward accumulation'.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between madness versions 0.1.0 dated 2015-12-15 and 0.2.0 dated 2016-01-20
DESCRIPTION | 27 +++++---- MD5 | 42 ++++++++++----- NAMESPACE | 3 + R/diag.r |only R/eigen.r |only R/madness_pkg.r | 15 +++++ R/matwise.r | 79 +---------------------------- R/max.r |only R/norm.r |only R/reshape.r | 36 ------------- R/theta.r | 1 R/to_objective.r |only R/twomoments.r | 82 ++++++++++++++++++++++-------- README.md | 70 ++++++++++++++++++++++--- build |only inst/doc |only man/NEWS.Rd | 21 +++++++ man/eigen.Rd |only man/matwise.Rd | 38 +------------- man/max.Rd |only man/norm.Rd |only man/reshapes.Rd | 11 ---- man/to_objective.Rd |only man/todiag.Rd |only man/twomoments.Rd | 22 ++++++-- tests/testthat/test-basic.r | 103 ++++++++++++++++++++++++++++++++++---- tests/testthat/test-correctness.r | 46 ++++++++++++++++ vignettes |only 28 files changed, 367 insertions(+), 229 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers.
Author: Jordan Read [aut, cre],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut],
Emily Read [aut],
Luke Winslow [aut]
Maintainer: Jordan Read <jread@usgs.gov>
Diff between geoknife versions 1.0.0 dated 2015-10-04 and 1.1.3 dated 2016-01-20
geoknife-1.0.0/geoknife/R/loadOutput.R |only geoknife-1.1.3/geoknife/DESCRIPTION | 20 - geoknife-1.1.3/geoknife/MD5 | 177 +++++----- geoknife-1.1.3/geoknife/NAMESPACE | 3 geoknife-1.1.3/geoknife/R/01-webdata-obj.R | 18 - geoknife-1.1.3/geoknife/R/02-webgeom-obj.R | 28 + geoknife-1.1.3/geoknife/R/03-geojob-obj.R | 6 geoknife-1.1.3/geoknife/R/04-webprocess-obj.R | 42 +- geoknife-1.1.3/geoknife/R/06-simplegeom-obj.R | 38 +- geoknife-1.1.3/geoknife/R/07-datagroup-obj.R | 6 geoknife-1.1.3/geoknife/R/algorithm-webprocess.R | 13 geoknife-1.1.3/geoknife/R/attribute-webgeom.R | 5 geoknife-1.1.3/geoknife/R/check.R | 2 geoknife-1.1.3/geoknife/R/download-geojob.R | 5 geoknife-1.1.3/geoknife/R/email-geojob.R | 5 geoknife-1.1.3/geoknife/R/gcontent.R |only geoknife-1.1.3/geoknife/R/geoknife-generic.R | 7 geoknife-1.1.3/geoknife/R/geom-webgeom.R | 36 +- geoknife-1.1.3/geoknife/R/inputs-webprocess.R | 27 + geoknife-1.1.3/geoknife/R/parseTimeseries.R | 28 - geoknife-1.1.3/geoknife/R/processInputsToXML.R | 17 geoknife-1.1.3/geoknife/R/query-webdata-times.R | 18 - geoknife-1.1.3/geoknife/R/query-webdata-variables.R | 8 geoknife-1.1.3/geoknife/R/query-webdata.R | 42 +- geoknife-1.1.3/geoknife/R/query-webgeom.R | 2 geoknife-1.1.3/geoknife/R/query-webprocess.R | 2 geoknife-1.1.3/geoknife/R/result.R |only geoknife-1.1.3/geoknife/R/setJobState.R | 6 geoknife-1.1.3/geoknife/R/setProcessInputs.R | 6 geoknife-1.1.3/geoknife/R/show-webdata.R | 4 geoknife-1.1.3/geoknife/R/start-geojob.R | 48 +- geoknife-1.1.3/geoknife/R/times-webdata.R | 77 +++- geoknife-1.1.3/geoknife/R/url-generic.R | 60 ++- geoknife-1.1.3/geoknife/R/values-webgeom.R | 39 +- geoknife-1.1.3/geoknife/R/variables-webdata.R | 27 - geoknife-1.1.3/geoknife/R/version-generic.R | 33 + geoknife-1.1.3/geoknife/README.md | 18 - geoknife-1.1.3/geoknife/build/vignette.rds |binary geoknife-1.1.3/geoknife/demo/prism_subset.R | 8 geoknife-1.1.3/geoknife/inst/CITATION | 2 geoknife-1.1.3/geoknife/inst/doc/geoknife.html | 69 +-- geoknife-1.1.3/geoknife/man/XML-method.Rd | 4 geoknife-1.1.3/geoknife/man/abstract-datagroup.Rd | 2 geoknife-1.1.3/geoknife/man/algorithm-webprocess.Rd | 7 geoknife-1.1.3/geoknife/man/attribute.Rd | 4 geoknife-1.1.3/geoknife/man/bufferPoint.Rd | 2 geoknife-1.1.3/geoknife/man/canStart.Rd | 8 geoknife-1.1.3/geoknife/man/cancel-methods.Rd | 2 geoknife-1.1.3/geoknife/man/check-geojob.Rd | 2 geoknife-1.1.3/geoknife/man/datagroup-class.Rd | 5 geoknife-1.1.3/geoknife/man/datagroup-methods.Rd | 2 geoknife-1.1.3/geoknife/man/download.Rd | 4 geoknife-1.1.3/geoknife/man/email-method.Rd | 4 geoknife-1.1.3/geoknife/man/fetchGML_IDs.Rd | 2 geoknife-1.1.3/geoknife/man/gcontent.Rd |only geoknife-1.1.3/geoknife/man/geojob-class.Rd | 5 geoknife-1.1.3/geoknife/man/geojob-methods.Rd | 4 geoknife-1.1.3/geoknife/man/geoknife-methods.Rd | 32 - geoknife-1.1.3/geoknife/man/geom.Rd | 9 geoknife-1.1.3/geoknife/man/getJobState.Rd | 2 geoknife-1.1.3/geoknife/man/inputs-webprocess.Rd | 14 geoknife-1.1.3/geoknife/man/parseTimeseries.Rd | 5 geoknife-1.1.3/geoknife/man/query.Rd | 5 geoknife-1.1.3/geoknife/man/result-methods.Rd | 10 geoknife-1.1.3/geoknife/man/setJobState.Rd | 8 geoknife-1.1.3/geoknife/man/simplegeom-class.Rd | 20 - geoknife-1.1.3/geoknife/man/simplegeom-methods.Rd | 7 geoknife-1.1.3/geoknife/man/start-methods.Rd | 11 geoknife-1.1.3/geoknife/man/successful-methods.Rd | 3 geoknife-1.1.3/geoknife/man/times-webdata.Rd | 2 geoknife-1.1.3/geoknife/man/times_query-method.Rd | 4 geoknife-1.1.3/geoknife/man/url.Rd | 26 - geoknife-1.1.3/geoknife/man/values.Rd | 14 geoknife-1.1.3/geoknife/man/variables-webdata.Rd | 4 geoknife-1.1.3/geoknife/man/variables_query-method.Rd | 4 geoknife-1.1.3/geoknife/man/version.Rd | 4 geoknife-1.1.3/geoknife/man/waitUntilFinished.Rd | 4 geoknife-1.1.3/geoknife/man/webdata-class.Rd | 5 geoknife-1.1.3/geoknife/man/webdata-methods.Rd | 4 geoknife-1.1.3/geoknife/man/webgeom-class.Rd | 10 geoknife-1.1.3/geoknife/man/webgeom-methods.Rd | 24 + geoknife-1.1.3/geoknife/man/webprocess-class.Rd | 12 geoknife-1.1.3/geoknife/man/webprocess-methods.Rd | 2 geoknife-1.1.3/geoknife/tests/testthat/test-geoknife_com.R | 4 geoknife-1.1.3/geoknife/tests/testthat/test-geoknife_setters.R | 4 geoknife-1.1.3/geoknife/tests/testthat/test-geoknife_xml_parser.R | 1 geoknife-1.1.3/geoknife/tests/testthat/test-processErrors.R | 15 geoknife-1.1.3/geoknife/tests/testthat/test-times_webdata.R |only geoknife-1.1.3/geoknife/tests/testthat/test-waitUntilFinished.R | 4 geoknife-1.1.3/geoknife/tests/testthat/test-webdata_object.R | 3 geoknife-1.1.3/geoknife/tests/testthat/test-webprocess_input.R | 27 + geoknife-1.1.3/geoknife/tests/testthat/test-webprocess_object.R | 14 92 files changed, 788 insertions(+), 538 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an
abstraction for a value that may be available at some point in the future.
The state of a future can either be unresolved or resolved. As soon as it is
resolved, the value is available. Futures are useful constructs in for instance
concurrent evaluation, e.g. parallel processing and distributed processing on
compute clusters. The purpose of this package is to provide a lightweight
interface for using futures in R. Functions 'future()' and 'value()' exist for
creating futures and requesting their values, e.g.
'f <- future({ mandelbrot(c(0.28,0), side=2) })' and 'v <- value(f)'.
The 'resolve()' function can be used to check if a future is resolved or not.
An infix assignment operator '%<=%' exists for creating futures whose values
are accessible by the assigned variables (as promises), e.g.
'v %<=% { mandelbrot(c(0.28,0), side=2) }'.
This package implements synchronous "lazy" and "eager" futures, and asynchronous
"multicore", "multisession" and ad hoc "cluster" futures. Additional types of
futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.10.0 dated 2015-12-30 and 0.11.0 dated 2016-01-20
future-0.10.0/future/R/MulticoreFuture.R |only future-0.11.0/future/DESCRIPTION | 31 - future-0.11.0/future/MD5 | 113 ++- future-0.11.0/future/NAMESPACE | 115 ++- future-0.11.0/future/NEWS | 28 future-0.11.0/future/R/ClusterFuture-class.R |only future-0.11.0/future/R/Future-class.R | 71 ++ future-0.11.0/future/R/FutureRegistry.R | 17 future-0.11.0/future/R/LazyFuture-class.R | 5 future-0.11.0/future/R/MulticoreFuture-class.R |only future-0.11.0/future/R/MultisessionFuture-class.R |only future-0.11.0/future/R/availableCores.R | 240 ++++---- future-0.11.0/future/R/cluster.R |only future-0.11.0/future/R/eager.R | 8 future-0.11.0/future/R/flapply.R |only future-0.11.0/future/R/future.R | 5 future-0.11.0/future/R/futureAssign_OP.R | 4 future-0.11.0/future/R/futureCall.R |only future-0.11.0/future/R/futureOf.R | 10 future-0.11.0/future/R/globals.R | 210 ++++--- future-0.11.0/future/R/multicore.R | 138 +++- future-0.11.0/future/R/multisession.R |only future-0.11.0/future/R/plan.R | 64 +- future-0.11.0/future/R/utils.R | 46 + future-0.11.0/future/demo/mandelbrot.R | 44 + future-0.11.0/future/inst/doc/future-issues.html | 10 future-0.11.0/future/inst/doc/future-issues.md.rsp | 385 ++++++------ future-0.11.0/future/inst/doc/future.html | 70 +- future-0.11.0/future/inst/doc/future.md.rsp | 596 ++++++++++---------- future-0.11.0/future/man/ClusterFuture-class.Rd |only future-0.11.0/future/man/MulticoreFuture-class.Rd | 12 future-0.11.0/future/man/availableCores.Rd | 123 ++-- future-0.11.0/future/man/cluster.Rd |only future-0.11.0/future/man/eager.Rd | 139 ++-- future-0.11.0/future/man/future.Rd | 116 +-- future-0.11.0/future/man/futureAssign.Rd | 10 future-0.11.0/future/man/injectNextStrategy.Rd |only future-0.11.0/future/man/lazy.Rd | 12 future-0.11.0/future/man/multicore.Rd | 175 +++-- future-0.11.0/future/man/multisession.Rd |only future-0.11.0/future/man/plan.Rd | 21 future-0.11.0/future/man/requestCore.Rd | 66 +- future-0.11.0/future/man/resolve.Rd | 80 +- future-0.11.0/future/man/supportsMulticore.Rd | 40 - future-0.11.0/future/man/usedCores.Rd | 40 - future-0.11.0/future/tests/FutureRegistry.R | 17 future-0.11.0/future/tests/availableCores.R | 28 future-0.11.0/future/tests/cluster.R |only future-0.11.0/future/tests/demo.R | 39 - future-0.11.0/future/tests/dotdotdot.R | 92 +-- future-0.11.0/future/tests/flapply.R |only future-0.11.0/future/tests/future.R | 3 future-0.11.0/future/tests/futureAssign_OP.R | 207 +++--- future-0.11.0/future/tests/futureCall.R |only future-0.11.0/future/tests/futures.R | 132 ++-- future-0.11.0/future/tests/globals,tricky.R | 177 +---- future-0.11.0/future/tests/lazy.R | 4 future-0.11.0/future/tests/multicore.R | 154 ++--- future-0.11.0/future/tests/multisession.R |only future-0.11.0/future/tests/plan.R | 2 future-0.11.0/future/tests/resolve.R | 11 future-0.11.0/future/tests/rng.R | 61 +- future-0.11.0/future/tests/sessions.R |only future-0.11.0/future/tests/utils.R | 81 ++ future-0.11.0/future/vignettes/future-issues.md.rsp | 385 ++++++------ future-0.11.0/future/vignettes/future.md.rsp | 596 ++++++++++---------- 66 files changed, 2802 insertions(+), 2231 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; and the International Tree Ring Data Bank. Additional
data sources are in the works, including global DEM resources (ETOPO1, ETOPO5,
ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National
Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky <bocinsky@gmail.com>
Dylan Beaudette <Dylan.Beaudette@ca.usda.gov>
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.2 dated 2015-12-03 and 2.0.3 dated 2016-01-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/GHCN_FUNCTIONS.R | 4 ++-- R/SSURGO_FUNCTIONS.R | 2 ++ README.md | 2 +- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Correlational Class Analysis
Description: Perform a correlational class analysis of the data, resulting in a partition of the data into separate modules.
Author: Andrei Boutyline
Maintainer: Andrei Boutyline <andrei.boutyline@gmail.com>
Diff between corclass versions 0.1 dated 2013-12-10 and 0.1.1 dated 2016-01-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 8 ++++++++ R/cca.R | 24 ++++++++++++++---------- man/corclass-package.Rd | 6 +++--- man/plot.cca.Rd | 2 +- 6 files changed, 35 insertions(+), 23 deletions(-)
Title: Randomization for Clinical Trials
Description: This tool enables the user to choose a randomization procedure
based on sound scientific criteria. It comprises the generation of
randomization sequences as well the assessment of randomization procedures
based on carefully selected criteria. Furthermore, randomizeR provides a
function for the comparison of randomization procedures.
Author: Thi Mui Pham [ctb],
David Schindler [aut],
Diane Uschner [aut, cre]
Maintainer: Diane Uschner <duschner@ukaachen.de>
Diff between randomizeR versions 1.0 dated 2015-09-09 and 1.1.0 dated 2016-01-19
DESCRIPTION | 33 - MD5 | 203 +++++----- NAMESPACE | 21 - R/abcdPar.R |only R/abcdSeq.R |only R/assess.R | 54 ++ R/bbcdPar.R |only R/bbcdSeq.R |only R/bsdPar.R | 9 R/chenPar.R |only R/chenSeq.R |only R/chronBias.R | 23 - R/combinedBias.R |only R/compare.R | 15 R/corGuess.R | 2 R/doublyT.R | 4 R/gbcdPar.R |only R/gbcdSeq.R |only R/mpPar.R | 5 R/randPar.R | 64 +++ R/randSeq.R | 50 ++ R/randomizeROverview.R | 15 R/randomizeRPackage.R | 1 R/rpbrPar.R | 12 R/rpbrSeq.R | 9 R/rtbdPar.R | 50 +- R/rtbdSeq.R | 8 R/saveAssess.R | 6 R/saveRand.R | 32 + R/testDec.R | 2 R/util.R | 3 build/vignette.rds |binary inst/doc/comparison-example.pdf |binary inst/doc/randomizeR-refCard.Rnw |only inst/doc/randomizeR-refCard.pdf |only man/K.Rd | 2 man/N.Rd | 2 man/a.Rd |only man/abcdPar.Rd |only man/abcdRand.Rd |only man/assess.Rd | 43 +- man/bbcdPar.Rd |only man/bbcdRand.Rd |only man/blocks.Rd | 2 man/bsdPar.Rd | 16 man/bsdRand.Rd | 4 man/cash-assessment-method.Rd | 2 man/cash-comparison-method.Rd | 2 man/cash-endpoint-method.Rd | 2 man/cash-issue-method.Rd | 2 man/cash-randPar-method.Rd | 2 man/cash-randSeq-method.Rd | 2 man/chenPar.Rd |only man/chenRand.Rd |only man/chronBias.Rd | 45 +- man/coin.Rd | 2 man/combineBias.Rd |only man/compare.Rd | 24 - man/corGuess.Rd | 17 man/crPar.Rd | 16 man/createParam.Rd | 18 man/createSeq.Rd | 2 man/doublyT.Rd | 2 man/doublyTValues.Rd | 5 man/ebcPar.Rd | 16 man/gbcdPar.Rd |only man/gbcdRand.Rd |only man/genNcps.Rd | 3 man/generateAllSequences.Rd | 53 ++ man/generateRandomSequences.Rd | 115 ++++- man/getCorGuesses.Rd | 3 man/getDesign.Rd | 46 +- man/getExpectation.Rd | 26 - man/getProbabilities.Rd | 25 - man/getRandomizationList.Rd | 3 man/hadaPar.Rd | 18 man/imbal.Rd | 18 man/issue.Rd | 25 - man/method.Rd | 2 man/mpPar.Rd | 16 man/mti.Rd | 2 man/mu.Rd | 2 man/normEndp.Rd | 8 man/overview.Rd | 33 + man/pbrPar.Rd | 20 man/plot.Rd | 3 man/plotSeq.Rd |only man/randBlocks.Rd | 2 man/randPar-class.Rd | 2 man/randPar.Rd | 14 man/randSeq-class.Rd | 4 man/randomizeR-package.Rd | 22 - man/rarPar.Rd | 16 man/ratio.Rd | 2 man/rho.Rd |only man/rpbrPar.Rd | 16 man/rtbdPar.Rd | 16 man/saveAssess.Rd | 7 man/saveRand.Rd | 7 man/seed.Rd | 2 man/selBias.Rd | 38 - man/setPower.Rd | 22 - man/sigma.Rd | 2 man/summary.Rd | 7 man/tbdPar.Rd | 18 man/type.Rd | 4 man/udPar.Rd | 16 tests/testthat/OnlyOnce/test_empiricalVsTheoreticalFrequency.R | 55 ++ tests/testthat/test_combineBias.R |only tests/testthat/test_lengthOfSequences.R | 24 - tests/testthat/test_mti.R | 6 tests/testthat/test_nrOfSequences.R | 32 + tests/testthat/test_seedGenSeq.R | 17 tests/testthat/test_sequenceProbability.R | 11 vignettes/randomizeR-refCard.Rnw |only 115 files changed, 1121 insertions(+), 511 deletions(-)
Title: Benchmarking and Rescaling R2 using Noise Percentile Analysis
Description: Provides the tools needed to benchmark the R2 value corresponding to a certain acceptable noise level while also providing a rescaling function based on that noise level yielding a new value of R2 we refer to as R2k which is independent of both the number of degrees of freedom and the noise distribution function.
Author: Joseph G Kreke, PhD; Harris, Inc.
Sangeet Khemlani, PhD; Naval Research Laboratory.
Greg Trafton, PhD; Naval Research Laboratory.
Maintainer: Joseph G Kreke <jkreke2@gmail.com>
Diff between pAnalysis versions 1.0 dated 2015-11-18 and 2.0 dated 2016-01-19
pAnalysis-1.0/pAnalysis/R/Percentile_Analysis_Functions.R |only pAnalysis-2.0/pAnalysis/DESCRIPTION | 8 ++++---- pAnalysis-2.0/pAnalysis/MD5 | 6 +++--- pAnalysis-2.0/pAnalysis/R/Percentile_Analysis_Functions_v2.R |only pAnalysis-2.0/pAnalysis/build/partial.rdb |binary 5 files changed, 7 insertions(+), 7 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
Siem Heisterkamp [ctb] (Author fixed sigma),
Bert Van Willigen [ctb] (Programmer fixed sigma),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-123 dated 2016-01-17 and 3.1-124 dated 2016-01-19
ChangeLog | 19 DESCRIPTION | 10 MD5 | 44 - NAMESPACE | 6 R/VarCorr.R | 29 - R/gls.R | 30 - R/gnls.R | 69 +- R/lme.R | 1203 ++++++++++++++++++++++++------------------------ R/newFunc.R | 42 - R/nlme.R | 576 +++++++++++----------- man/VarCorr.Rd | 9 man/glsControl.Rd | 4 man/gnlsControl.Rd | 4 man/lmeControl.Rd | 4 man/nlmeControl.Rd | 4 src/corStruct.c | 2 src/gnls.c | 4 src/nlme.c | 4 src/nlmefit.c | 2 src/nls.c | 2 tests/anova.gls.R | 7 tests/nlme.R | 5 tests/sigma-fixed-etc.R | 10 23 files changed, 1055 insertions(+), 1034 deletions(-)
Title: Statistical Object Oriented Data Analysis of RDP-Based Taxonomic
Trees from Human Microbiome Data
Description: Tools to model, compare, and visualize populations of taxonomic tree objects.
Author: Patricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between HMPTrees versions 1.2 dated 2013-09-16 and 1.3 dated 2016-01-19
HMPTrees-1.2/HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.R |only HMPTrees-1.3/HMPTrees/DESCRIPTION | 23 +++--- HMPTrees-1.3/HMPTrees/MD5 | 32 ++++----- HMPTrees-1.3/HMPTrees/NAMESPACE | 4 + HMPTrees-1.3/HMPTrees/NEWS | 11 ++- HMPTrees-1.3/HMPTrees/R/checkTreeValidHelp.R | 7 -- HMPTrees-1.3/HMPTrees/R/compareTwoDataSets.R | 35 ++++------ HMPTrees-1.3/HMPTrees/R/generateTree.R | 7 -- HMPTrees-1.3/HMPTrees/R/getMLEandLoglike.R | 2 HMPTrees-1.3/HMPTrees/R/pairedCompareTwoDataSets.R |only HMPTrees-1.3/HMPTrees/R/plotTree.R | 2 HMPTrees-1.3/HMPTrees/R/transformHMPTreetoHMP.R | 12 +-- HMPTrees-1.3/HMPTrees/R/traverseTree.R | 11 +-- HMPTrees-1.3/HMPTrees/build |only HMPTrees-1.3/HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.Rnw | 2 HMPTrees-1.3/HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.pdf |binary HMPTrees-1.3/HMPTrees/man/HMPTrees-package.Rd | 7 -- HMPTrees-1.3/HMPTrees/man/pairedCompareTwoDataSets.Rd |only HMPTrees-1.3/HMPTrees/vignettes/Creating-Data-From-RDP-Tutorial.Rnw | 2 19 files changed, 81 insertions(+), 76 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.2.6 dated 2015-07-02 and 1.3.0 dated 2016-01-19
DESCRIPTION | 10 - MD5 | 24 +-- NEWS | 8 - R/bpcp2sample.R | 138 ++++++++++++----- R/kmciFunctions.R | 355 ++++++++++++++++++++++------------------------ build |only inst/CITATION | 2 inst/doc/discreteBPCP.R |only inst/doc/discreteBPCP.Rnw |only inst/doc/discreteBPCP.pdf |only man/bpcp-package.Rd | 4 man/bpcpControl.Rd | 6 man/kmciALL.Rd | 6 man/plot.kmciLR.Rd | 2 tests |only vignettes |only 16 files changed, 310 insertions(+), 245 deletions(-)
Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap standard errors on various network estimation routines, such as EBICglasso() from the 'qgraph' package and IsingFit() from the 'IsingFit' package.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between bootnet versions 0.1 dated 2015-03-02 and 0.2 dated 2016-01-19
DESCRIPTION | 14 - MD5 | 23 +- NAMESPACE | 19 +- R/bootTable.R | 117 ++++++++---- R/bootnet.R | 307 +++++++++++++++++++++++++++++---- R/bootstrapIncreasesEdges.R |only R/comparePlot.R |only R/estimateNetwork.R | 1 R/evenMoreTests.R |only R/plotMethod.R | 405 ++++++++++++++++++++++++++++++++++++++++---- R/summaryMethod.R | 159 ++++++++++++++--- man/bootnet.Rd | 78 ++++++-- man/plot.bootnet.Rd | 49 ++++- man/summary.bootnet.Rd | 13 + 14 files changed, 999 insertions(+), 186 deletions(-)
Title: R API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export and Engage API. The R functions allow for event and profile data export as well as for segmentation, retention and addiction analysis. Results are always parsed into convenient R objects. Furthermore it is possible to load and update profiles.
Author: Meinhard Ploner
Maintainer: Meinhard Ploner <meinhard.ploner@prosiebensat1digital.de>
Diff between RMixpanel versions 0.1-3 dated 2016-01-14 and 0.2-1 dated 2016-01-19
RMixpanel-0.1-3/RMixpanel/R/mixpanelGetPeople.R |only RMixpanel-0.1-3/RMixpanel/R/mixpanelGetPeopleCount.R |only RMixpanel-0.2-1/RMixpanel/DESCRIPTION | 12 ++--- RMixpanel-0.2-1/RMixpanel/MD5 | 18 ++++---- RMixpanel-0.2-1/RMixpanel/NAMESPACE | 1 RMixpanel-0.2-1/RMixpanel/R/mixpanelGetProfiles.R |only RMixpanel-0.2-1/RMixpanel/R/mixpanelGetProfilesCount.R |only RMixpanel-0.2-1/RMixpanel/R/mixpanelUpdateProfile.R |only RMixpanel-0.2-1/RMixpanel/README.md | 33 ++++++++++++--- RMixpanel-0.2-1/RMixpanel/build/partial.rdb |binary RMixpanel-0.2-1/RMixpanel/man/RMixpanel-package.Rd | 6 -- RMixpanel-0.2-1/RMixpanel/man/mixpanelGetSegmentation.Rd | 2 RMixpanel-0.2-1/RMixpanel/man/mixpanelUpdateProfile.Rd |only 13 files changed, 48 insertions(+), 24 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.6.0 dated 2015-11-04 and 3.6.1 dated 2016-01-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 +++++++ R/Deriv.R | 9 +++++---- man/Deriv-package.Rd | 4 ++-- tests/testthat/test_Deriv.R | 9 +++++++++ 6 files changed, 32 insertions(+), 15 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: The qgraph package can be used to visualize data as networks as well as provides an interface for visualizing weighted graphical models.
Author: Sacha Epskamp, Giulio Costantini, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.3.1 dated 2015-03-10 and 1.3.2 dated 2016-01-19
qgraph-1.3.1/qgraph/R/Jaccard.R |only qgraph-1.3.2/qgraph/DESCRIPTION | 13 - qgraph-1.3.2/qgraph/MD5 | 30 ++-- qgraph-1.3.2/qgraph/NAMESPACE | 19 ++ qgraph-1.3.2/qgraph/NEWS | 10 + qgraph-1.3.2/qgraph/R/PLOT.R | 19 ++ qgraph-1.3.2/qgraph/R/centrality.R | 233 +++++++++++++++++++------------- qgraph-1.3.2/qgraph/R/centralityTable.R | 2 qgraph-1.3.2/qgraph/R/clusteringTable.R | 2 qgraph-1.3.2/qgraph/R/cor_auto.R | 6 qgraph-1.3.2/qgraph/R/drawNode.R | 37 ++++- qgraph-1.3.2/qgraph/R/makeBW.R |only qgraph-1.3.2/qgraph/R/qgraph.R | 9 - qgraph-1.3.2/qgraph/R/qgraphAnnotate.R | 3 qgraph-1.3.2/qgraph/R/qgraphBoot.R |only qgraph-1.3.2/qgraph/R/qgraphGUI.R | 2 qgraph-1.3.2/qgraph/man/centrality.Rd | 8 - qgraph-1.3.2/qgraph/man/makeBW.Rd |only 18 files changed, 259 insertions(+), 134 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb],
Martin Maechler [ctb],
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.0-3 dated 2015-07-22 and 1.0-4 dated 2016-01-19
DESCRIPTION | 8 - MD5 | 49 +++--- NAMESPACE | 2 R/mvt.R | 173 ++++++++++++---------- R/noisy-root.R |only R/tvpack.R | 38 ++-- build/vignette.rds |binary inst/NEWS | 12 + inst/doc/MVT_Rnews.pdf |binary inst/include/mvtnorm.h | 6 man/algorithms.Rd | 17 +- man/pmvnorm.Rd | 6 man/pmvt.Rd | 31 ++-- man/qmvnorm.Rd | 18 +- man/qmvt.Rd | 18 +- src/C_FORTRAN_interface.c | 10 - src/miwa.c | 242 +++++++++++++++---------------- src/mvtnorm-init.c | 2 src/mvtnorm.h | 6 src/tvpack.f | 8 - tests/Examples/mvtnorma-Ex.Rout.save | 267 +++++++++++++++++++---------------- tests/bugfix-tests.R | 5 tests/bugfix-tests.Rout.save | 47 +++--- tests/regtest-TVPACK.R | 10 - tests/regtest-TVPACK.Rout.save | 22 +- tests/test-noisy-root.R |only tests/test-noisy-root.Rout.save |only 27 files changed, 538 insertions(+), 459 deletions(-)
Title: Tools for CM SAF Netcdf Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing Essential Climate Variables related to the energy and water
cycle of the atmosphere (www.cmsaf.eu). It is a joint cooperation of seven
National Meteorological and Hydrological Services, including the Deutscher
Wetterdienst (DWD).
The cmsaf R-package provides a small collection of R-functions, which are
inspired by the Climate Data Operators (cdo). This gives the opportunity to
analyse and manipulate CM SAF data without the need of installing cdo.
The cmsaf R-package is tested for CM SAF netcdf data, which are structured
in three-dimensional arrays (longitude, latitude, time) on a rectangular grid.
Layered CM SAF data have to be converted with the provided `levbox_mergetime`
function. The cmsaf R-package functions have only minor checks for deviations
from the recommended data structure, and give only few specific error messages.
Thus, there is no warranty of accurate results.
A Windows binary file and scripts for an easy application of the functions are
provided at the CM SAF homepage (http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.5 dated 2015-07-30 and 1.6 dated 2016-01-19
DESCRIPTION | 8 +-- MD5 | 94 ++++++++++++++++++++++++-------------------- NAMESPACE | 8 +++ R/box_mergetime.R | 31 ++++++++------ R/change_att.R | 4 - R/cmsaf.add.R | 4 - R/cmsaf.addc.R |only R/cmsaf.div.R | 108 ++++++++++++++++++++++++--------------------------- R/cmsaf.divc.R |only R/cmsaf.mul.R | 100 ++++++++++++++++++++++------------------------- R/cmsaf.mulc.R |only R/cmsaf.sub.R | 92 ++++++++++++++++++++----------------------- R/cmsaf.subc.R |only R/dayrange.R | 28 +++++-------- R/divdpm.R | 28 +++++-------- R/extract.period.R | 28 +++++-------- R/fldmax.R | 4 - R/fldmean.R | 31 +++++--------- R/fldmin.R | 31 +++++--------- R/get_time.R | 55 ++++++++++++++++++------- R/levbox_mergetime.R | 25 +++++++---- R/mon.anomaly.R | 44 +++++++++----------- R/monmean.R | 26 +++++------- R/monsum.R | 28 +++++-------- R/muldpm.R | 4 - R/multimonmean.R | 26 +++++------- R/multimonsum.R | 28 +++++-------- R/ncinfo.R | 20 +++------ R/read_nc.R |only R/seas.anomaly.R | 24 ++++------- R/seasmean.R | 28 +++++-------- R/sellonlatbox.R | 15 +------ R/selmon.R | 10 +--- R/selperiod.R | 10 +--- R/selpoint.R | 49 +++++++++++++---------- R/seltime.R | 12 +---- R/selyear.R | 10 +--- R/timmean.R | 4 - R/trend.R | 10 +--- R/wfldmean.R | 15 +------ R/year.anomaly.R | 10 +--- R/yearmean.R | 10 +--- R/yearsum.R | 10 +--- R/ymonmean.R | 10 +--- R/ymonsum.R | 12 +---- R/yseasmean.R | 10 +--- man/cmsaf.addc.Rd |only man/cmsaf.divc.Rd |only man/cmsaf.mulc.Rd |only man/cmsaf.subc.Rd |only man/muldpm.Rd | 2 man/read_nc.Rd |only man/selpoint.Rd | 16 +++++-- 53 files changed, 519 insertions(+), 603 deletions(-)
Title: Covariance Matrix Adaptation Evolution Strategy
Description: Pure R implementation of the Covariance Matrix Adaptation -
Evolution Strategy (CMA-ES) with optional restarts (IPOP-CMA-ES).
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between cmaesr versions 1.0 dated 2016-01-19 and 1.0.1 dated 2016-01-19
DESCRIPTION | 10 +++++----- MD5 | 7 ++++--- NEWS |only R/cmaes.R | 16 +++++++++------- man/cmaes.Rd | 4 ++-- 5 files changed, 20 insertions(+), 17 deletions(-)
Title: Binary Logic
Description: Convert to binary numbers (Base2). Shift, rotate, summary. Based on logical vector.
Author: Daniel Dörrhöfer <ddo@openmailbox.org>
Maintainer: Daniel Dörrhöfer <ddo@openmailbox.org>
Diff between binaryLogic versions 0.2.6 dated 2015-12-18 and 0.3.2 dated 2016-01-19
DESCRIPTION | 6 - MD5 | 12 +- R/binOperators.R | 20 ++- README.md | 220 ++++++++++++++++++++++--------------- man/switchEndianess.Rd | 12 +- tests/testthat/test-BinaryS3.R | 17 ++ tests/testthat/test-binOperators.R | 4 7 files changed, 179 insertions(+), 112 deletions(-)
Title: European Commission Annual Macro-Economic (AMECO) Database
Description: Annual macro-economic database provided by the European Commission.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between ameco versions 0.1 dated 2015-10-23 and 0.2 dated 2016-01-19
DESCRIPTION | 11 ++++++----- MD5 | 22 ++++++++++++---------- NAMESPACE | 3 ++- R/data.R | 2 +- README.md | 16 ++++++++++++++-- data/ameco.RData |binary inst/doc/ameco_dataset.R | 2 +- inst/doc/ameco_dataset.Rmd | 4 ++-- inst/doc/ameco_dataset.html | 14 +++++++------- man/ameco.Rd | 4 ++-- tests |only vignettes/ameco_dataset.Rmd | 4 ++-- 12 files changed, 49 insertions(+), 33 deletions(-)
Title: A Stable Isotope Mixing Model
Description: Fits a stable isotope mixing model via JAGS in R. The package allows for any number of isotopes or sources, as well as concentration dependencies.
Author: Andrew Parnell
Maintainer: Andrew Parnell <andrew.parnell@ucd.ie>
Diff between simmr versions 0.2 dated 2015-08-17 and 0.3 dated 2016-01-19
DESCRIPTION | 13 MD5 | 35 + NAMESPACE | 3 R/combine_sources.R |only R/compare_groups.R | 12 R/compare_sources.R |only R/plot.simmr_input.R | 39 + R/plot.simmr_output.R | 151 ++++--- README.md |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/simmr.R | 98 +++-- inst/doc/simmr.Rmd | 129 ++++-- inst/doc/simmr.html | 919 +++++++++++++++++------------------------------ man/combine_sources.Rd |only man/compare_groups.Rd | 2 man/compare_sources.Rd |only man/plot.simmr_input.Rd | 81 ++-- man/plot.simmr_output.Rd | 9 man/simmr_mcmc.Rd | 18 vignettes/simmr.Rmd | 129 ++++-- 21 files changed, 786 insertions(+), 852 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-1 dated 2015-07-23 and 1.4-2 dated 2016-01-19
DESCRIPTION | 8 +- MD5 | 24 +++---- build/vignette.rds |binary data/cholesterol.rda |binary data/litter.rda |binary inst/NEWS | 4 + inst/doc/chfls1.pdf |binary inst/doc/generalsiminf.pdf |binary inst/doc/multcomp-examples.pdf |binary tests/Examples/multcomp-Ex.Rout.save | 115 +++++++++++++++++------------------ tests/regtest-Tukey.Rout.save | 14 ++-- tests/regtest-interface.Rout.save | 16 ++-- tests/regtest-mmm.Rout.save | 14 ++-- 13 files changed, 99 insertions(+), 96 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
http://ec.europa.eu/eurostat/ together with search and manipulation
utilities.
Author: Lahti Leo [aut, cre],
Biecek Przemyslaw [aut],
Kainu Markus [aut],
Huovari Janne [aut]
Maintainer: Lahti Leo <louhos@googlegroups.com>
Diff between eurostat versions 1.0.16 dated 2015-03-27 and 1.2.13 dated 2016-01-19
eurostat-1.0.16/eurostat/inst/doc/eurostat_tutorial.html |only eurostat-1.0.16/eurostat/vignettes/NUTS_2010_60M_SH |only eurostat-1.0.16/eurostat/vignettes/NUTS_2010_60M_SH.zip |only eurostat-1.0.16/eurostat/vignettes/eurostat_tutorial.md |only eurostat-1.0.16/eurostat/vignettes/figure |only eurostat-1.2.13/eurostat/DESCRIPTION | 20 - eurostat-1.2.13/eurostat/LICENSE | 4 eurostat-1.2.13/eurostat/MD5 | 179 +++++--------- eurostat-1.2.13/eurostat/NAMESPACE | 6 eurostat-1.2.13/eurostat/R/clean_eurostat_cache.R | 13 - eurostat-1.2.13/eurostat/R/data_countries.R |only eurostat-1.2.13/eurostat/R/dic_order.R |only eurostat-1.2.13/eurostat/R/eurostat-package.R | 4 eurostat-1.2.13/eurostat/R/eurostat_url.R | 12 eurostat-1.2.13/eurostat/R/eurotime2date.R | 45 ++- eurostat-1.2.13/eurostat/R/eurotime2num.R | 42 ++- eurostat-1.2.13/eurostat/R/get_eurostat.R | 140 ++++++---- eurostat-1.2.13/eurostat/R/get_eurostat_dic.R | 44 +-- eurostat-1.2.13/eurostat/R/get_eurostat_raw.R | 20 - eurostat-1.2.13/eurostat/R/get_eurostat_toc.R | 11 eurostat-1.2.13/eurostat/R/label_eurostat.R | 79 ++++-- eurostat-1.2.13/eurostat/R/search_eurostat.R | 36 +- eurostat-1.2.13/eurostat/R/set_eurostat_toc.R | 19 - eurostat-1.2.13/eurostat/R/tidy_eurostat.R | 117 ++++++--- eurostat-1.2.13/eurostat/R/utils.R |only eurostat-1.2.13/eurostat/README.md | 7 eurostat-1.2.13/eurostat/build/vignette.rds |binary eurostat-1.2.13/eurostat/data |only eurostat-1.2.13/eurostat/inst/CITATION | 8 eurostat-1.2.13/eurostat/inst/doc/eurostat_tutorial.R | 14 + eurostat-1.2.13/eurostat/inst/doc/eurostat_tutorial.Rmd | 55 +++- eurostat-1.2.13/eurostat/inst/doc/eurostat_tutorial.pdf |only eurostat-1.2.13/eurostat/man/clean_eurostat_cache.Rd | 6 eurostat-1.2.13/eurostat/man/dic_order.Rd |only eurostat-1.2.13/eurostat/man/eu_countries.Rd |only eurostat-1.2.13/eurostat/man/eurostat-package.Rd | 6 eurostat-1.2.13/eurostat/man/eurostat_url.Rd | 10 eurostat-1.2.13/eurostat/man/eurotime2date.Rd | 19 - eurostat-1.2.13/eurostat/man/eurotime2num.Rd | 18 - eurostat-1.2.13/eurostat/man/get_eurostat.Rd | 80 ++++-- eurostat-1.2.13/eurostat/man/get_eurostat_dic.Rd | 29 +- eurostat-1.2.13/eurostat/man/get_eurostat_raw.Rd | 22 - eurostat-1.2.13/eurostat/man/get_eurostat_toc.Rd | 14 - eurostat-1.2.13/eurostat/man/label_eurostat.Rd | 46 ++- eurostat-1.2.13/eurostat/man/search_eurostat.Rd | 36 +- eurostat-1.2.13/eurostat/man/set_eurostat_toc.Rd | 12 eurostat-1.2.13/eurostat/man/tidy_eurostat.Rd | 35 +- eurostat-1.2.13/eurostat/tests/testthat/test-all.R | 73 +++++ eurostat-1.2.13/eurostat/vignettes/2015-RJournal |only eurostat-1.2.13/eurostat/vignettes/eurostat_tutorial.Rmd | 55 +++- eurostat-1.2.13/eurostat/vignettes/eurostat_tutorial.html |only eurostat-1.2.13/eurostat/vignettes/fig |only eurostat-1.2.13/eurostat/vignettes/main.R | 10 eurostat-1.2.13/eurostat/vignettes/tmp |only 54 files changed, 831 insertions(+), 515 deletions(-)
Title: Diversity-Dependent Diversification
Description:
Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439.
Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence.
See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.
Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 3.0 dated 2015-11-13 and 3.1 dated 2016-01-19
DESCRIPTION | 10 - MD5 | 62 ++++----- NAMESPACE | 4 R/bd_ML.R | 2 R/bd_loglik.R | 78 +++++------- R/dd_KI_ML.R | 2 R/dd_KI_loglik.R | 317 ++++++++++++++++++++++++++++++++++++++++++++++++- R/dd_KI_sim.R | 4 R/dd_LR.R | 2 R/dd_ML.R | 2 R/dd_MS_ML.R | 2 R/dd_MS_loglik.R | 237 ++++++++++++++++++++++++++++++++++++ R/dd_SR_ML.R | 2 R/dd_SR_loglik.R | 298 ++++++++++++++++++++++++++++++++++++++++++++-- R/dd_loglik.R | 212 +++++++++++++++++++++++++++++++- R/dd_loglik_M.R | 310 +++++++++++++++++++++++++++++++++++++---------- R/dd_loglik_bw_rhs.R | 4 R/dd_logliknorm_rhs2.R | 2 R/dd_sim.R | 2 man/DDD-internal.Rd | 20 +++ man/DDD-package.Rd | 8 - man/bd_ML.Rd | 4 man/bd_loglik.Rd | 4 man/dd_KI_ML.Rd | 4 man/dd_KI_loglik.Rd | 8 - man/dd_LR.Rd | 4 man/dd_ML.Rd | 6 man/dd_MS_ML.Rd | 2 man/dd_MS_loglik.Rd | 8 - man/dd_SR_ML.Rd | 7 - man/dd_SR_loglik.Rd | 10 - man/dd_loglik.Rd | 12 - 32 files changed, 1439 insertions(+), 210 deletions(-)
Title: Statistical Analysis of Amplicon Data of the Same Sample to
Identify Artefacts
Description: Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts. The AmpliconDuo package, whereas amplicon duo from here on refers to the two amplicon data sets of a split sample, is intended to help interpret the obtained read frequency distribution across split samples, and to filter the false positive reads.
Author: Anja Lange [aut, cre], Daniel Hoffmann [aut]
Maintainer: Anja Lange <anja.lange@uni-due.de>
Diff between AmpliconDuo versions 1.0 dated 2014-03-20 and 1.1 dated 2016-01-19
DESCRIPTION | 13 -- MD5 | 22 +-- R/plotORdensity.R | 275 ++++++++++++++++++++++---------------------- data/ampliconfreqs.long.rda |binary data/ampliconfreqs.rda |binary data/amplicons.rda |binary data/site.f.rda |binary man/AmpliconDuo-package.Rd | 12 - man/ampliconfreqs.Rd | 6 man/ampliconfreqs.long.Rd | 6 man/plotAmpliconduo.Rd | 2 man/plotAmpliconduo.set.Rd | 2 12 files changed, 167 insertions(+), 171 deletions(-)
Title: Thermoluminescence Glow Curve Deconvolution
Description: Deconvolving first-order and general-order thermoluminescence glow
curves using a modified Levenberg-Marquardt algorithm. It provides the
possibility of setting constraints or fixing any of parameters. It offers
an interactive way to initialize parameters by clicking with a mouse on a
plot at positions where peak maxima should be located. The optimal estimate
is obtained by "trial-and-error". It also provides routines for simulating
first-order, second-order, and general-order glow peaks (or glow curves).
Author: Jun Peng [aut, cre], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb], Linda R. Petzold [ctb], Alan C. Hindmarsh [ctb], R. Woodrow Setzer [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between tgcd versions 1.7 dated 2015-09-16 and 1.8 dated 2016-01-19
DESCRIPTION | 12 ++++----- MD5 | 10 +++---- R/simPeak.R | 4 +-- man/simPeak.Rd | 17 ++++++++----- src/qeOTOR.f90 | 50 ++++++++++++++++++++------------------ src/simPeak.f90 | 72 ++++++++++++++++++++++++++++---------------------------- 6 files changed, 87 insertions(+), 78 deletions(-)
More information about SubpathwayLNCE at CRAN
Permanent link
Title: Multi-States Semi-Markov Models
Description: Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model.
Author: Agnieszka Listwon-Krol, Philippe Saint-Pierre
Maintainer: Agnieszka Listwon-Krol <agnieszka.krol@isped.u-bordeaux2.fr>
Diff between SemiMarkov versions 1.4.2 dated 2015-08-04 and 1.4.3 dated 2016-01-19
DESCRIPTION | 8 +- MD5 | 6 - R/SemiMarkov.r | 184 +++++++++++++++++++++++++----------------------------- man/semiMarkov.Rd | 2 4 files changed, 95 insertions(+), 105 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided.
'CCTZ' is a C++ library for translating between absolute and civil times
using the rules of a time zone.
The 'CCTZ' source code, released under the Apache 2.0 License, is included in
this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.0.2 dated 2015-12-02 and 0.0.3 dated 2016-01-19
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- inst/include/src/cctz.h | 10 +++++----- inst/include/src/cctz_libc.h | 4 ---- src/cctz_fmt.cc | 21 +++++++++++++++++++++ src/cctz_if.cc | 4 +--- src/cctz_info.cc | 24 ++++++++++++++++++++---- src/cctz_libc.cc | 33 +++++++++++++++++++++++++-------- 9 files changed, 89 insertions(+), 36 deletions(-)
Title: Easily Tidy Data with `spread()` and `gather()` Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.3.1 dated 2015-09-10 and 0.4.0 dated 2016-01-18
tidyr-0.3.1/tidyr/man/seq_range.Rd |only tidyr-0.3.1/tidyr/tests/testthat/test-matrixToDataFrame.R |only tidyr-0.4.0/tidyr/DESCRIPTION | 9 - tidyr-0.4.0/tidyr/MD5 | 112 +++++++------ tidyr-0.4.0/tidyr/NAMESPACE | 16 + tidyr-0.4.0/tidyr/R/RcppExports.R | 12 - tidyr-0.4.0/tidyr/R/complete.R | 18 +- tidyr-0.4.0/tidyr/R/expand.R | 113 ++++++++++---- tidyr-0.4.0/tidyr/R/extract.R | 8 tidyr-0.4.0/tidyr/R/fill.R | 28 ++- tidyr-0.4.0/tidyr/R/gather.R | 48 +++-- tidyr-0.4.0/tidyr/R/id.R |only tidyr-0.4.0/tidyr/R/nest.R | 67 ++++++-- tidyr-0.4.0/tidyr/R/separate.R | 24 ++ tidyr-0.4.0/tidyr/R/seq.R |only tidyr-0.4.0/tidyr/R/spread.R | 74 ++++++--- tidyr-0.4.0/tidyr/R/unite.R | 14 + tidyr-0.4.0/tidyr/R/unnest.R | 71 ++++++-- tidyr-0.4.0/tidyr/R/utils.R | 10 + tidyr-0.4.0/tidyr/README.md | 2 tidyr-0.4.0/tidyr/build/vignette.rds |binary tidyr-0.4.0/tidyr/inst/doc/tidy-data.html | 96 +++++------ tidyr-0.4.0/tidyr/man/complete.Rd | 25 +-- tidyr-0.4.0/tidyr/man/complete_.Rd | 4 tidyr-0.4.0/tidyr/man/expand.Rd | 54 +++++- tidyr-0.4.0/tidyr/man/expand_.Rd | 2 tidyr-0.4.0/tidyr/man/extract.Rd | 6 tidyr-0.4.0/tidyr/man/extract_.Rd | 2 tidyr-0.4.0/tidyr/man/extract_numeric.Rd | 2 tidyr-0.4.0/tidyr/man/fill.Rd | 15 + tidyr-0.4.0/tidyr/man/fill_.Rd | 7 tidyr-0.4.0/tidyr/man/full_seq.Rd |only tidyr-0.4.0/tidyr/man/gather.Rd | 13 + tidyr-0.4.0/tidyr/man/gather_.Rd | 10 - tidyr-0.4.0/tidyr/man/nest.Rd | 24 ++ tidyr-0.4.0/tidyr/man/nest_.Rd | 7 tidyr-0.4.0/tidyr/man/pipe.Rd | 2 tidyr-0.4.0/tidyr/man/replace_na.Rd | 2 tidyr-0.4.0/tidyr/man/separate.Rd | 15 + tidyr-0.4.0/tidyr/man/separate_.Rd | 9 - tidyr-0.4.0/tidyr/man/spread.Rd | 44 +++-- tidyr-0.4.0/tidyr/man/spread_.Rd | 28 +-- tidyr-0.4.0/tidyr/man/unite.Rd | 5 tidyr-0.4.0/tidyr/man/unite_.Rd | 2 tidyr-0.4.0/tidyr/man/unnest.Rd | 22 +- tidyr-0.4.0/tidyr/man/unnest_.Rd | 9 - tidyr-0.4.0/tidyr/src/RcppExports.cpp | 29 ++- tidyr-0.4.0/tidyr/src/fill.cpp | 92 +++++++++++ tidyr-0.4.0/tidyr/src/matrixToDataFrame.cpp | 3 tidyr-0.4.0/tidyr/src/melt.cpp | 33 ++-- tidyr-0.4.0/tidyr/tests/testthat/test-expand.R | 23 ++ tidyr-0.4.0/tidyr/tests/testthat/test-extract.R | 8 tidyr-0.4.0/tidyr/tests/testthat/test-fill.R | 58 ++++++- tidyr-0.4.0/tidyr/tests/testthat/test-gather.R | 19 ++ tidyr-0.4.0/tidyr/tests/testthat/test-id.R |only tidyr-0.4.0/tidyr/tests/testthat/test-nest.R | 27 +++ tidyr-0.4.0/tidyr/tests/testthat/test-separate.R | 8 tidyr-0.4.0/tidyr/tests/testthat/test-spread.R | 102 ++++++++++++ tidyr-0.4.0/tidyr/tests/testthat/test-unite.R | 18 ++ tidyr-0.4.0/tidyr/tests/testthat/test-unnest.R | 37 ++++ 60 files changed, 1118 insertions(+), 370 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Hans-Juergen Auinger <auinger@tum.de>
Diff between synbreed versions 0.11-22 dated 2015-10-06 and 0.11-29 dated 2016-01-18
DESCRIPTION | 12 +++---- MD5 | 40 +++++++++++++------------ NAMESPACE | 2 - R/add.pedigree.r |only R/codeGeno.r | 65 +++++++++++++++++++++++++---------------- R/create.gpData.r | 1 R/create.pedigree.r | 44 ++++++++++++--------------- R/discard.markers.r | 17 ++++++++-- R/gpMod.r | 4 +- R/kinship.r | 23 ++++++++------ R/plot.genMap.r | 2 - R/plot.pedigree.r | 5 +-- R/predict.gpMod.r | 10 ++---- R/read.write.vcf.r | 4 +- R/summary.relationshipMatrix.r | 4 +- man/add.pedigree.Rd |only man/create.pedigree.Rd | 31 ++++++++++--------- man/discard.individuals.Rd | 7 +++- man/discard.markers.Rd | 5 ++- man/kinship.Rd | 12 ++++--- man/plot.pedigree.Rd | 30 +++++++++++------- man/predict.gpMod.Rd | 56 ++++++++++++++++++----------------- 22 files changed, 210 insertions(+), 164 deletions(-)
Title: Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
Description: Renders vector-based 'svg' images into high-quality custom-size bitmap
arrays using 'librsvg'. The resulting bitmap can be written to e.g. 'png', 'jpeg'
or 'webp' format. In addition, the package can convert images directly to various
formats such as pdf or postscript.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between rsvg versions 0.2 dated 2016-01-15 and 0.3 dated 2016-01-18
DESCRIPTION | 17 +++++----- MD5 | 13 ++++--- NAMESPACE | 6 +++ NEWS |only R/rsvg.R | 99 +++++++++++++++++++++++++++++++++++++++++++++++++++--------- configure | 2 - man/rsvg.Rd | 41 ++++++++++++++++++++---- src/rsvg.c | 82 +++++++++++++++++++++++++++++++++++++++++++++++-- 8 files changed, 221 insertions(+), 39 deletions(-)
Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: Previously an R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/>, and from version 0.8-0 an R
interface to the 'Spectra' library <http://yixuan.cos.name/spectra/>
to solve large scale eigenvalue/vector problems.
It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the 'eigs()' function which does the similar job as in 'Matlab',
'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. Matrices can be given in either dense
or sparse form.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.9-0 dated 2015-11-18 and 0.10-0 dated 2016-01-18
DESCRIPTION | 18 LICENSE | 2 MD5 | 31 - README.md | 8 inst/NEWS.Rd | 9 inst/include/Spectra/CompInfo.h |only inst/include/Spectra/GenEigsSolver.h | 348 ++++++++--------- inst/include/Spectra/LinAlg/DoubleShiftQR.h | 291 +++++++------- inst/include/Spectra/LinAlg/TridiagEigen.h | 120 ++++- inst/include/Spectra/LinAlg/UpperHessenbergEigen.h | 52 +- inst/include/Spectra/LinAlg/UpperHessenbergQR.h | 194 ++++----- inst/include/Spectra/MatOp/DenseGenComplexShiftSolve.h | 30 - inst/include/Spectra/MatOp/DenseGenMatProd.h | 14 inst/include/Spectra/MatOp/DenseGenRealShiftSolve.h | 22 - inst/include/Spectra/MatOp/DenseSymShiftSolve.h | 22 - inst/include/Spectra/MatOp/SparseGenMatProd.h | 14 inst/include/Spectra/SymEigsSolver.h | 331 ++++++++-------- 17 files changed, 822 insertions(+), 684 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and NIST curves P-256, P-384 and P-521.
Cryptographic signatures can either be created and verified manually or via x509
certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA
for asymmetric (public key) encryption. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.9 dated 2016-01-13 and 0.9.1 dated 2016-01-18
DESCRIPTION | 6 +++--- MD5 | 28 +++++++++++++++------------- NAMESPACE | 1 + R/askpass.R |only R/read.R | 2 +- R/rsa.R | 2 +- R/signing.R | 2 +- configure | 2 +- inst/doc/bignum.html | 24 ++++++++++++------------ inst/doc/crypto_hashing.html | 4 ++-- inst/doc/secure_rng.html | 18 +++++++++--------- man/askpass.Rd |only man/read_key.Rd | 2 +- man/rsa_encrypt.Rd | 2 +- man/signatures.Rd | 2 +- src/ssl.c | 8 +++++++- 16 files changed, 56 insertions(+), 47 deletions(-)
Title: Visualisation of Oceanographic Data and Model Output
Description: Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between OceanView versions 1.0.3 dated 2015-03-04 and 1.0.4 dated 2016-01-18
OceanView |only 1 file changed
Title: Latin Hypercube Samples
Description: Provides a number of methods for creating and augmenting Latin Hypercube Samples.
Author: Rob Carnell [aut, cre]
Maintainer: Rob Carnell <bertcarnell@gmail.com>
Diff between lhs versions 0.12 dated 2016-01-15 and 0.13 dated 2016-01-18
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- inst/unitTests/runit_augmentLHS.r | 28 ++++++++++++++++++++++++---- inst/unitTests/runit_geneticLHS.r | 23 ++++++++++++++++++----- inst/unitTests/runit_optAugmentLHS.r | 14 ++++++++++++-- inst/unitTests/runit_optSeededLHS.r | 21 ++++++++++++++++++--- inst/unitTests/runit_optimumLHS.r | 28 ++++++++++++++++++++++++---- inst/unitTests/runit_randomLHS.r | 2 +- 9 files changed, 112 insertions(+), 31 deletions(-)
Title: Advanced Tables for Markdown/HTML
Description: Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While allowing
advanced layout, the underlying css-structure is simple in order to maximize
compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package
also contains a few text formatting functions that help outputting text
compatible with HTML/'LaTeX'.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between htmlTable versions 1.3 dated 2015-04-21 and 1.5 dated 2016-01-18
htmlTable-1.3/htmlTable/tests/visual_tests/htmlTable_markdown.Rmd |only htmlTable-1.3/htmlTable/tests/visual_tests/pandoc_v1.13_bug.md |only htmlTable-1.5/htmlTable/DESCRIPTION | 24 htmlTable-1.5/htmlTable/MD5 | 104 + htmlTable-1.5/htmlTable/NAMESPACE | 13 htmlTable-1.5/htmlTable/NEWS | 16 htmlTable-1.5/htmlTable/R/htmlTable.R | 121 +- htmlTable-1.5/htmlTable/R/htmlTable_helpers.R | 114 +- htmlTable-1.5/htmlTable/R/htmlTable_render.R | 48 htmlTable-1.5/htmlTable/R/interactiveTable.R |only htmlTable-1.5/htmlTable/R/txtFrmt.R | 33 htmlTable-1.5/htmlTable/build/vignette.rds |binary htmlTable-1.5/htmlTable/inst/doc/general.html | 196 +-- htmlTable-1.5/htmlTable/inst/doc/tables.R | 6 htmlTable-1.5/htmlTable/inst/doc/tables.html | 190 ++- htmlTable-1.5/htmlTable/inst/examples/interactiveTable_example.R |only htmlTable-1.5/htmlTable/inst/html_components |only htmlTable-1.5/htmlTable/inst/javascript |only htmlTable-1.5/htmlTable/man/SCB.Rd | 10 htmlTable-1.5/htmlTable/man/htmlTable.Rd | 570 ++++------ htmlTable-1.5/htmlTable/man/interactiveTable.Rd |only htmlTable-1.5/htmlTable/man/outputInt.Rd | 5 htmlTable-1.5/htmlTable/man/prAddCells.Rd | 65 - htmlTable-1.5/htmlTable/man/prAddSemicolon2StrEnd.Rd | 18 htmlTable-1.5/htmlTable/man/prAttr4RgroupAdd.Rd | 26 htmlTable-1.5/htmlTable/man/prConvertDfFactors.Rd |only htmlTable-1.5/htmlTable/man/prGetAlign.Rd | 20 htmlTable-1.5/htmlTable/man/prGetCgroupHeader.Rd | 122 -- htmlTable-1.5/htmlTable/man/prGetRgroupLine.Rd | 87 - htmlTable-1.5/htmlTable/man/prGetRowlabelPos.Rd | 43 htmlTable-1.5/htmlTable/man/prGetScriptString.Rd |only htmlTable-1.5/htmlTable/man/prGetStyle.Rd | 33 htmlTable-1.5/htmlTable/man/prGetThead.Rd | 175 +-- htmlTable-1.5/htmlTable/man/prMergeClr.Rd | 15 htmlTable-1.5/htmlTable/man/prPrepareAlign.Rd | 58 - htmlTable-1.5/htmlTable/man/prPrepareCgroup.Rd | 59 - htmlTable-1.5/htmlTable/man/prPrepareColors.Rd | 11 htmlTable-1.5/htmlTable/man/prPrepareCss.Rd | 30 htmlTable-1.5/htmlTable/man/prSkipRownames.Rd | 14 htmlTable-1.5/htmlTable/man/prTblNo.Rd | 31 htmlTable-1.5/htmlTable/man/pvalueFormatter.Rd | 5 htmlTable-1.5/htmlTable/man/splitLines4Table.Rd | 4 htmlTable-1.5/htmlTable/man/tblNoLast.Rd | 15 htmlTable-1.5/htmlTable/man/tblNoNext.Rd | 15 htmlTable-1.5/htmlTable/man/txtInt.Rd | 24 htmlTable-1.5/htmlTable/man/txtMergeLines.Rd | 30 htmlTable-1.5/htmlTable/man/txtPval.Rd | 52 htmlTable-1.5/htmlTable/man/txtRound.Rd | 46 htmlTable-1.5/htmlTable/tests/testInteractive.R |only htmlTable-1.5/htmlTable/tests/testthat/test-htmlTable.R | 106 - htmlTable-1.5/htmlTable/tests/testthat/test-htmlTable_cgroup.R |only htmlTable-1.5/htmlTable/tests/testthat/test-htmlTable_rgroup_tspanner.R | 80 + htmlTable-1.5/htmlTable/tests/testthat/test-interactiveTable.R |only htmlTable-1.5/htmlTable/tests/testthat/test-txtFrmt.R | 25 htmlTable-1.5/htmlTable/tests/testthat/test-txtMergeLines.R |only htmlTable-1.5/htmlTable/tests/visual_tests/htmlTable_vtests.R | 4 htmlTable-1.5/htmlTable/tests/visual_tests/pandoc_test.Rmd | 16 htmlTable-1.5/htmlTable/tests/visual_tests/word_test.Rmd |only htmlTable-1.5/htmlTable/tests/visual_tests/word_test.html |only htmlTable-1.5/htmlTable/vignettes/custom.css | 2 60 files changed, 1417 insertions(+), 1264 deletions(-)
Title: Estimation and Fit Diagnostics for Generalized Exponential
Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized
Exponential Random Graph Models via Gibbs sampling or Metropolis
Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson
<jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A.
Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between GERGM versions 0.6.2 dated 2015-12-20 and 0.7.4 dated 2016-01-18
DESCRIPTION | 12 MD5 | 57 ++-- NAMESPACE | 3 R/Convert_Simulated_Networks_To_Observed_Scale.R | 90 ++++-- R/Estimate_GERGM.R | 262 +++++-------------- R/GERGM_Class.R | 15 - R/GOF.R | 20 - R/Helper_Functions.R | 12 R/Log_Likelihood_and_MPLE_Objective.R | 33 +- R/MCMCMLE.R | 302 ++++++++++++----------- R/Optimize_Proposal_Variance.R |only R/Package_Documentation.R | 22 + R/Parse_Formula_Object.R | 11 R/Prepare_Covariates.R | 2 R/Run_MPLE.R |only R/Simulate_GERGM.R | 73 +++-- R/Symmetrize_Network.R |only R/Thin_Statistic_Samples.R | 2 R/Update_Lambda_Estimates.R |only R/gergm.R | 178 ++++++------- R/hysteresis.R |only R/hysteresis_parallel.R |only R/hysteresis_plot.R |only R/parallel_gergm.R |only R/simulate_networks.R | 84 ++---- R/single_gergm_specification.R |only R/zzz.R |only README.md | 4 man/gergm.Rd | 16 + man/hysteresis.Rd |only man/hysteresis_plot.Rd |only man/parallel_gergm.Rd |only src/Metropolis_Hastings_Sampler.cpp | 80 ++---- tests/testthat/test_experimental_features.R | 86 +++--- tests/testthat/test_gergm.R | 37 +- tests/testthat/test_hysteresis.R |only tests/testthat/test_parallel_gergm.R |only 37 files changed, 693 insertions(+), 708 deletions(-)
Title: Extensible Package for Parallel, Batch Training of Base Learners
for Ensemble Modeling
Description: Extensible S4 classes and methods for batch training of regression and classification algorithms such as Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines, K-Nearest Neighbors, Penalized Regression (L1/L2), and Bayesian Additive Regression Trees. These algorithms constitute a set of 'base learners', which can subsequently be combined together to form ensemble predictions. This package provides cross-validation wrappers to allow for downstream application of ensemble integration techniques, including best-error selection. All base learner estimation objects are retained, allowing for repeated prediction calls without the need for re-training. For large problems, an option is provided to save estimation objects to disk, along with prediction methods that utilize these objects. This allows users to train and predict with large ensembles of base learners without being constrained by system RAM.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.mahani@sentrana.com>
Diff between EnsembleBase versions 0.7.1 dated 2015-01-05 and 1.0.0 dated 2016-01-18
ChangeLog | 10 + DESCRIPTION | 13 - MD5 | 34 ++-- NAMESPACE | 16 +- R/aaa.R | 2 R/baselearners.R | 244 +++++++++++++++++++++++++++---- R/regression_bart.R |only R/regression_gbm.R | 6 R/regression_knn.R | 6 R/regression_nnet.R | 6 R/regression_penreg.R |only R/regression_rf.R | 6 R/regression_svm.R | 6 man/ALL.Regression.Config-class.Rd | 16 +- man/ALL.Regression.FitObj-class.Rd | 6 man/BaseLearner.CV.Batch.FitObj-class.Rd | 1 man/BaseLearner.Fit-methods.Rd | 8 + man/Regression.CV.Batch.Fit.Rd | 22 ++ man/make.configs.Rd | 14 + 19 files changed, 346 insertions(+), 70 deletions(-)
Title: Copula Based Bivariate Beta-Binomial Model for Diagnostic Test
Accuracy Studies
Description: Modelling of sensitivity and specificity on their natural scale
using copula based bivariate beta-binomial distribution to yield marginal mean sensitivity
and specificity. The intrinsic negative correlation between sensitivity and
specificity is modelled using a copula function. A forest plot can be obtained
for categorical covariates or for the model with intercept only.
Author: Victoria N Nyaga [aut, cre]
Maintainer: Victoria N Nyaga <victoria.nyaga@outlook.com>
Diff between CopulaDTA versions 0.0.1 dated 2015-12-03 and 0.0.2 dated 2016-01-18
CopulaDTA-0.0.1/CopulaDTA/man/fitcopula.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/forestplot.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/ft.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/printcopula.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/summarycopula.Rd |only CopulaDTA-0.0.1/CopulaDTA/man/tracecopula.Rd |only CopulaDTA-0.0.2/CopulaDTA/DESCRIPTION | 14 CopulaDTA-0.0.2/CopulaDTA/MD5 | 50 - CopulaDTA-0.0.2/CopulaDTA/NAMESPACE | 20 CopulaDTA-0.0.2/CopulaDTA/R/classes.R |only CopulaDTA-0.0.2/CopulaDTA/R/data.R | 2 CopulaDTA-0.0.2/CopulaDTA/R/fit.R | 619 +++----------------- CopulaDTA-0.0.2/CopulaDTA/R/methods.R |only CopulaDTA-0.0.2/CopulaDTA/R/model.R |only CopulaDTA-0.0.2/CopulaDTA/R/plot.R | 83 +- CopulaDTA-0.0.2/CopulaDTA/R/print.R | 90 +- CopulaDTA-0.0.2/CopulaDTA/R/summary.R | 55 - CopulaDTA-0.0.2/CopulaDTA/R/traceplot.R | 26 CopulaDTA-0.0.2/CopulaDTA/R/utils.R | 57 + CopulaDTA-0.0.2/CopulaDTA/inst/CITATION | 27 CopulaDTA-0.0.2/CopulaDTA/man/ascus.Rd | 3 CopulaDTA-0.0.2/CopulaDTA/man/cdtafit-class.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/cdtamodel-class.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/cdtamodel.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/fit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/fit.cdtamodel.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/forestplot.cdtafit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/omega.to.ktau.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/plot.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/prep.data.Rd | 5 CopulaDTA-0.0.2/CopulaDTA/man/print.cdtafit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/show.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/summary.cdtafit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/telomerase.Rd | 3 CopulaDTA-0.0.2/CopulaDTA/man/traceplot.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/traceplot.cdtafit.Rd |only CopulaDTA-0.0.2/CopulaDTA/man/waic.Rd | 38 - 37 files changed, 344 insertions(+), 748 deletions(-)
Title: Calculate the Assortativity Coefficient of Weighted and Binary
Networks
Description: Functions to calculate the assortment of vertices in social networks. This can be measured on both weighted and binary networks, with discrete or continuous vertex values.
Author: Damien Farine <dfarine@orn.mpg.de>
Maintainer: Damien Farine <dfarine@orn.mpg.de>
Diff between assortnet versions 0.11 dated 2016-01-07 and 0.12 dated 2016-01-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/assortment.continuous.R | 2 +- R/assortment.discrete.R | 2 +- man/assortnet-package.Rd | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from http://www.r-inla.org. It is recommended the testing version, which can be downloaded by running: source("http://www.math.ntnu.no/inla/givemeINLA-testing.R"). A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the abn website.
Author: Fraser Ian Lewis [aut], Marta Pittavino [cre, ctb], Reinhard Furrer [ctb]
Maintainer: Marta Pittavino <marta.pittavino@math.uzh.ch>
Diff between abn versions 0.86 dated 2015-12-28 and 1.0 dated 2016-01-18
abn-0.86/abn/data/pigs1par.RData |only abn-0.86/abn/inst/doc/abn_v0.85.R |only abn-0.86/abn/inst/doc/abn_v0.85.Rnw |only abn-0.86/abn/inst/doc/abn_v0.85.pdf |only abn-0.86/abn/man/pigs.1par.rd |only abn-0.86/abn/man/var33.rd |only abn-0.86/abn/vignettes/abn_v0.85.Rnw |only abn-1.0/abn/ChangeLog | 3 abn-1.0/abn/DESCRIPTION | 8 abn-1.0/abn/MD5 | 43 abn-1.0/abn/build/vignette.rds |binary abn-1.0/abn/data/pigs.vienna.RData |only abn-1.0/abn/inst/bootstrapping_example/10KBootstrapping.R |only abn-1.0/abn/inst/bootstrapping_example/10Kbootstrapping.bash |only abn-1.0/abn/inst/bootstrapping_example/MargPlots_PigsData.pdf |only abn-1.0/abn/inst/bootstrapping_example/Pigs_PostBootPlots.pdf |only abn-1.0/abn/inst/bootstrapping_example/inits.R |only abn-1.0/abn/inst/bootstrapping_example/initsearch.bash |only abn-1.0/abn/inst/bootstrapping_example/jags_pigs_script.R |only abn-1.0/abn/inst/bootstrapping_example/pigs_model.bug |only abn-1.0/abn/inst/bootstrapping_example/pigs_post_params.R |only abn-1.0/abn/inst/doc/abn_v1.0.R |only abn-1.0/abn/inst/doc/abn_v1.0.Rnw |only abn-1.0/abn/inst/doc/abn_v1.0.pdf |only abn-1.0/abn/man/pigs.vienna.Rd |only abn-1.0/abn/man/var33.Rd |only abn-1.0/abn/vignettes/Bootstrapping.png |only abn-1.0/abn/vignettes/ComparisonOfNetworkScore.pdf |only abn-1.0/abn/vignettes/DAG_cycle.pdf |only abn-1.0/abn/vignettes/MargPlots_PigsData.pdf |only abn-1.0/abn/vignettes/PigsArea.png |only abn-1.0/abn/vignettes/Pigs_PostBootPlots.pdf |only abn-1.0/abn/vignettes/Summary.png |only abn-1.0/abn/vignettes/abn.bib | 694 +++++++++- abn-1.0/abn/vignettes/abn_v1.0.Rnw |only abn-1.0/abn/vignettes/abn_v10-newfile.pdf |only abn-1.0/abn/vignettes/map1_10var.dot |only abn-1.0/abn/vignettes/map_1par.dot |only abn-1.0/abn/vignettes/plbinaryNode.png |only abn-1.0/abn/vignettes/postbootpigs.pdf |only 40 files changed, 698 insertions(+), 50 deletions(-)
Title: Tools for Cycling Data Analysis
Description: A suite of functions for analysing cycling data.
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Diff between cycleRtools versions 1.1.0 dated 2016-01-16 and 1.1.1 dated 2016-01-18
cycleRtools-1.1.0/cycleRtools/java/Tests.java |only cycleRtools-1.1.0/cycleRtools/tests |only cycleRtools-1.1.1/cycleRtools/DESCRIPTION | 10 +-- cycleRtools-1.1.1/cycleRtools/MD5 | 29 ++------- cycleRtools-1.1.1/cycleRtools/NEWS | 5 + cycleRtools-1.1.1/cycleRtools/R/Wbal.R | 3 cycleRtools-1.1.1/cycleRtools/build/vignette.rds |binary cycleRtools-1.1.1/cycleRtools/inst/doc/cycling_data_analysis.R | 4 + cycleRtools-1.1.1/cycleRtools/inst/doc/cycling_data_analysis.Rmd | 20 ++++-- cycleRtools-1.1.1/cycleRtools/inst/doc/cycling_data_analysis.html | 32 ++++++++-- cycleRtools-1.1.1/cycleRtools/man/Wbal.Rd | 2 cycleRtools-1.1.1/cycleRtools/vignettes/cycling_data_analysis.Rmd | 20 ++++-- 12 files changed, 84 insertions(+), 41 deletions(-)
Title: Plotting Multi-Dimensional Data - Using 'rgl'
Description: The 'rgl' implementation of plot3D functions.
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between plot3Drgl versions 1.0 dated 2014-03-17 and 1.0.1 dated 2016-01-18
DESCRIPTION | 17 ++++----- MD5 | 23 ++++++------ NAMESPACE | 6 ++- R/arrowsrgl.R | 75 +++++++++++++++++---------------------- R/imagergl.R | 73 +++++++++++++++++++++----------------- R/plot2Drgl.R | 100 +++++++++++++++++++++++++++++++++++++++++++++-------- R/plot3Drgl.R | 53 ++++++++++++++++++++++------ R/plotrgl.R | 85 +++++++++++++++++++++++++++++---------------- R/plotrglcolkey.R |only R/scatterrgl.R | 60 ++++++++++++++++++++++--------- build/vignette.rds |binary man/imagergl.Rd | 77 +++++++++++++++++++++++++++++++--------- man/persp3Drgl.Rd | 6 +-- 13 files changed, 387 insertions(+), 188 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full
Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.6.0 dated 2015-11-13 and 0.7.0 dated 2016-01-18
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Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyse data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskar.hansson@fhi.no>
Diff between strvalidator versions 1.5.2 dated 2015-08-31 and 1.6.0 dated 2016-01-18
strvalidator-1.5.2/strvalidator/R/compact.r |only strvalidator-1.5.2/strvalidator/man/compact.Rd |only strvalidator-1.5.2/strvalidator/man/strValidator-package.Rd |only strvalidator-1.6.0/strvalidator/DESCRIPTION | 16 strvalidator-1.6.0/strvalidator/MD5 | 386 strvalidator-1.6.0/strvalidator/NAMESPACE | 78 strvalidator-1.6.0/strvalidator/NEWS | 102 strvalidator-1.6.0/strvalidator/R/addColor.r | 12 strvalidator-1.6.0/strvalidator/R/addData.r | 33 strvalidator-1.6.0/strvalidator/R/addData_gui.r | 66 strvalidator-1.6.0/strvalidator/R/addDye_gui.r | 9 strvalidator-1.6.0/strvalidator/R/addMarker.r | 9 strvalidator-1.6.0/strvalidator/R/addMarker_gui.r | 10 strvalidator-1.6.0/strvalidator/R/addSize.r | 10 strvalidator-1.6.0/strvalidator/R/addSize_gui.r | 10 strvalidator-1.6.0/strvalidator/R/calculateAT.r | 119 strvalidator-1.6.0/strvalidator/R/calculateAT6.r | 39 strvalidator-1.6.0/strvalidator/R/calculateAT6_gui.r | 8 strvalidator-1.6.0/strvalidator/R/calculateAT_gui.r | 34 strvalidator-1.6.0/strvalidator/R/calculateAllele.r |only strvalidator-1.6.0/strvalidator/R/calculateBalance.r | 67 strvalidator-1.6.0/strvalidator/R/calculateBalance_gui.r | 113 strvalidator-1.6.0/strvalidator/R/calculateConcordance_gui.r | 2 strvalidator-1.6.0/strvalidator/R/calculateDropout.r | 196 strvalidator-1.6.0/strvalidator/R/calculateDropout_gui.r | 73 strvalidator-1.6.0/strvalidator/R/calculateHeight.r | 11 strvalidator-1.6.0/strvalidator/R/calculateHeight_gui.r | 21 strvalidator-1.6.0/strvalidator/R/calculateLb.r |only strvalidator-1.6.0/strvalidator/R/calculateLb_gui.r |only strvalidator-1.6.0/strvalidator/R/calculatePullup_gui.r | 2 strvalidator-1.6.0/strvalidator/R/calculateRatio.r |only strvalidator-1.6.0/strvalidator/R/calculateRatio_gui.r |only strvalidator-1.6.0/strvalidator/R/calculateResultType_gui.r | 2 strvalidator-1.6.0/strvalidator/R/calculateSpike.r |only strvalidator-1.6.0/strvalidator/R/calculateSpike_gui.r |only strvalidator-1.6.0/strvalidator/R/calculateStutter.r | 18 strvalidator-1.6.0/strvalidator/R/calculateStutter_gui.r | 15 strvalidator-1.6.0/strvalidator/R/checkSubset.r | 18 strvalidator-1.6.0/strvalidator/R/checkSubset_gui.r | 49 strvalidator-1.6.0/strvalidator/R/colConvert.r |only strvalidator-1.6.0/strvalidator/R/columns.r | 52 strvalidator-1.6.0/strvalidator/R/columns_gui.r | 50 strvalidator-1.6.0/strvalidator/R/cropData_gui.r | 68 strvalidator-1.6.0/strvalidator/R/detectKit.r | 52 strvalidator-1.6.0/strvalidator/R/editData_gui.r | 327 strvalidator-1.6.0/strvalidator/R/filterProfile.r | 185 strvalidator-1.6.0/strvalidator/R/filterProfile_gui.r | 48 strvalidator-1.6.0/strvalidator/R/filterSpike_gui.r |only strvalidator-1.6.0/strvalidator/R/generateEPG.r | 659 strvalidator-1.6.0/strvalidator/R/generateEPG_gui.r | 154 strvalidator-1.6.0/strvalidator/R/getKit.r | 5 strvalidator-1.6.0/strvalidator/R/ggsave_gui.r | 14 strvalidator-1.6.0/strvalidator/R/globals.R | 23 strvalidator-1.6.0/strvalidator/R/heightToPeak.r | 89 strvalidator-1.6.0/strvalidator/R/hooks.r | 7 strvalidator-1.6.0/strvalidator/R/import.r | 66 strvalidator-1.6.0/strvalidator/R/import_gui.r | 178 strvalidator-1.6.0/strvalidator/R/modelDropout_gui.r | 9 strvalidator-1.6.0/strvalidator/R/plotAT_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotBalance_gui.r | 355 strvalidator-1.6.0/strvalidator/R/plotCapillary_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotDistribution_gui.r | 59 strvalidator-1.6.0/strvalidator/R/plotDropout_gui.r | 8 strvalidator-1.6.0/strvalidator/R/plotKit_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotPeaks_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotPrecision_gui.r | 20 strvalidator-1.6.0/strvalidator/R/plotPullup_gui.r | 20 strvalidator-1.6.0/strvalidator/R/plotRatio_gui.r |only strvalidator-1.6.0/strvalidator/R/plotResultType_gui.r | 3 strvalidator-1.6.0/strvalidator/R/plotStutter_gui.r | 23 strvalidator-1.6.0/strvalidator/R/readPanelsFile.r | 3 strvalidator-1.6.0/strvalidator/R/scrambleAlleles.r |only strvalidator-1.6.0/strvalidator/R/slim.r | 13 strvalidator-1.6.0/strvalidator/R/slim_gui.r | 18 strvalidator-1.6.0/strvalidator/R/strvalidator-package.r | 49 strvalidator-1.6.0/strvalidator/R/strvalidator.r | 265 strvalidator-1.6.0/strvalidator/R/tableBalance.r | 10 strvalidator-1.6.0/strvalidator/R/tableBalance_gui.r | 7 strvalidator-1.6.0/strvalidator/R/tablePrecision_gui.r | 2 strvalidator-1.6.0/strvalidator/R/trim.r | 27 strvalidator-1.6.0/strvalidator/R/trim_gui.r | 28 strvalidator-1.6.0/strvalidator/inst/extdata/database.txt | 2 strvalidator-1.6.0/strvalidator/inst/extdata/database_readme.txt | 4 strvalidator-1.6.0/strvalidator/inst/extdata/kit.txt | 9518 +++++----- strvalidator-1.6.0/strvalidator/man/addColor.Rd | 4 strvalidator-1.6.0/strvalidator/man/addData.Rd | 6 strvalidator-1.6.0/strvalidator/man/addData_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/addDye_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/addMarker.Rd | 2 strvalidator-1.6.0/strvalidator/man/addMarker_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/addSize.Rd | 2 strvalidator-1.6.0/strvalidator/man/addSize_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/blockAT.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateAT.Rd | 6 strvalidator-1.6.0/strvalidator/man/calculateAT6.Rd | 11 strvalidator-1.6.0/strvalidator/man/calculateAT6_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateAT_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateAllele.Rd |only strvalidator-1.6.0/strvalidator/man/calculateBalance.Rd | 6 strvalidator-1.6.0/strvalidator/man/calculateBalance_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateCapillary.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateCapillary_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateConcordance.Rd | 6 strvalidator-1.6.0/strvalidator/man/calculateConcordance_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateDropout.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateDropout_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateHeight.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateHeight_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateHeterozygous.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateHeterozygous_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateLb.Rd |only strvalidator-1.6.0/strvalidator/man/calculateLb_gui.Rd |only strvalidator-1.6.0/strvalidator/man/calculateMixture.Rd | 10 strvalidator-1.6.0/strvalidator/man/calculateMixture_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateOL.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateOL_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateOverlap.Rd | 6 strvalidator-1.6.0/strvalidator/man/calculateOverlap_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculatePeaks.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculatePeaks_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculatePullup.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculatePullup_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateRatio.Rd |only strvalidator-1.6.0/strvalidator/man/calculateRatio_gui.Rd |only strvalidator-1.6.0/strvalidator/man/calculateResultType.Rd | 2 strvalidator-1.6.0/strvalidator/man/calculateResultType_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateSpike.Rd |only strvalidator-1.6.0/strvalidator/man/calculateSpike_gui.Rd |only strvalidator-1.6.0/strvalidator/man/calculateStutter.Rd | 4 strvalidator-1.6.0/strvalidator/man/calculateStutter_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/checkDataset.Rd | 2 strvalidator-1.6.0/strvalidator/man/checkSubset.Rd | 13 strvalidator-1.6.0/strvalidator/man/checkSubset_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/colConvert.Rd |only strvalidator-1.6.0/strvalidator/man/colNames.Rd | 2 strvalidator-1.6.0/strvalidator/man/columns.Rd | 24 strvalidator-1.6.0/strvalidator/man/columns_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/combineBinsAndPanels.Rd | 6 strvalidator-1.6.0/strvalidator/man/combine_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/cropData_gui.Rd | 6 strvalidator-1.6.0/strvalidator/man/detectKit.Rd | 6 strvalidator-1.6.0/strvalidator/man/editData_gui.Rd | 8 strvalidator-1.6.0/strvalidator/man/export.Rd | 4 strvalidator-1.6.0/strvalidator/man/export_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/filterProfile.Rd | 6 strvalidator-1.6.0/strvalidator/man/filterProfile_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/generateEPG.Rd | 19 strvalidator-1.6.0/strvalidator/man/generateEPG_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/getDb.Rd | 2 strvalidator-1.6.0/strvalidator/man/getKit.Rd | 6 strvalidator-1.6.0/strvalidator/man/ggsave_gui.Rd | 7 strvalidator-1.6.0/strvalidator/man/guessProfile.Rd | 2 strvalidator-1.6.0/strvalidator/man/guessProfile_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/heightToPeak.Rd | 2 strvalidator-1.6.0/strvalidator/man/import.Rd | 9 strvalidator-1.6.0/strvalidator/man/import_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/listObjects.Rd | 2 strvalidator-1.6.0/strvalidator/man/makeKit_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/modelDropout_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotAT_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotBalance_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotCapillary_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotDistribution_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotDropout_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/plotKit_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotPeaks_gui.Rd | 6 strvalidator-1.6.0/strvalidator/man/plotPrecision_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotPullup_gui.Rd | 2 strvalidator-1.6.0/strvalidator/man/plotRatio_gui.Rd |only strvalidator-1.6.0/strvalidator/man/plotResultType_gui.Rd | 6 strvalidator-1.6.0/strvalidator/man/plotStutter_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/readBinsFile.Rd | 2 strvalidator-1.6.0/strvalidator/man/readPanelsFile.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref1.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref11.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref2.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref3.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref4.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref51.Rd | 2 strvalidator-1.6.0/strvalidator/man/ref52.Rd | 2 strvalidator-1.6.0/strvalidator/man/saveObject.Rd | 4 strvalidator-1.6.0/strvalidator/man/scrambleAlleles.Rd |only strvalidator-1.6.0/strvalidator/man/set1.Rd | 2 strvalidator-1.6.0/strvalidator/man/set2.Rd | 2 strvalidator-1.6.0/strvalidator/man/set3.Rd | 2 strvalidator-1.6.0/strvalidator/man/set4.Rd | 2 strvalidator-1.6.0/strvalidator/man/set5.Rd | 2 strvalidator-1.6.0/strvalidator/man/slim.Rd | 2 strvalidator-1.6.0/strvalidator/man/slim_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/sortMarker.Rd | 4 strvalidator-1.6.0/strvalidator/man/strvalidator-package.Rd |only strvalidator-1.6.0/strvalidator/man/strvalidator.Rd | 42 strvalidator-1.6.0/strvalidator/man/tableBalance.Rd | 2 strvalidator-1.6.0/strvalidator/man/tableBalance_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/tableCapillary.Rd | 4 strvalidator-1.6.0/strvalidator/man/tableCapillary_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/tablePrecision.Rd | 2 strvalidator-1.6.0/strvalidator/man/tablePrecision_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/tableStutter.Rd | 2 strvalidator-1.6.0/strvalidator/man/tableStutter_gui.Rd | 4 strvalidator-1.6.0/strvalidator/man/trim.Rd | 6 strvalidator-1.6.0/strvalidator/man/trim_gui.Rd | 4 strvalidator-1.6.0/strvalidator/tests/testthat/test-calculateBalance.r | 1852 + strvalidator-1.6.0/strvalidator/tests/testthat/test-calculateDropout.r | 55 strvalidator-1.6.0/strvalidator/tests/testthat/test-calculateLb.r |only strvalidator-1.6.0/strvalidator/tests/testthat/test-filterProfile.r | 154 strvalidator-1.6.0/strvalidator/tests/testthat/test-tableBalance.r | 5 207 files changed, 9787 insertions(+), 6684 deletions(-)
Title: Automatic Marking of R Assignments
Description: Automatic marking of R assignments for students and teachers based
on 'testthat' test suites.
Author: Mans Magnusson, Oscar Pettersson
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between markmyassignment versions 0.3.0 dated 2015-12-28 and 0.4.0 dated 2016-01-18
markmyassignment-0.3.0/markmyassignment/man/stop_if_circular_calls.Rd |only markmyassignment-0.4.0/markmyassignment/DESCRIPTION | 12 - markmyassignment-0.4.0/markmyassignment/MD5 | 89 ++++---- markmyassignment-0.4.0/markmyassignment/R/assertion_funcions.R | 8 markmyassignment-0.4.0/markmyassignment/R/expectations.R | 20 ++ markmyassignment-0.4.0/markmyassignment/R/mark_my_assignment.R | 94 ++++++--- markmyassignment-0.4.0/markmyassignment/R/mark_my_file.R | 19 + markmyassignment-0.4.0/markmyassignment/R/reporter.R | 2 markmyassignment-0.4.0/markmyassignment/R/set_assignment.R | 53 ++++- markmyassignment-0.4.0/markmyassignment/README.md | 99 +--------- markmyassignment-0.4.0/markmyassignment/build |only markmyassignment-0.4.0/markmyassignment/inst/doc |only markmyassignment-0.4.0/markmyassignment/inst/extdata/example_assignment07_pkgs.yml |only markmyassignment-0.4.0/markmyassignment/inst/extdata/example_assignment08_bad_pkgs.yml |only markmyassignment-0.4.0/markmyassignment/inst/extdata/example_lab_file_messy.R |only markmyassignment-0.4.0/markmyassignment/man/StudentReporter-class.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/assert_function_arguments_in_API.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/assignment_yml_ok.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/cached_tasks.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/check_assignment_file.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/check_existance_tasks.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/check_installed_packages.Rd |only markmyassignment-0.4.0/markmyassignment/man/cheer.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/delete_circular_calls.Rd |only markmyassignment-0.4.0/markmyassignment/man/directories.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_function_arguments.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_function_code.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_package.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_self_contained.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/expect_tidy_code.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/find_expr.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/function_code.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/get_file.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/get_mark_my_reporter.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/get_tests.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/has_function_arguments.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/is_self_contained.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/mark_my_dir.Rd | 5 markmyassignment-0.4.0/markmyassignment/man/mark_my_file.Rd | 6 markmyassignment-0.4.0/markmyassignment/man/path_type.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/read_assignment_yml.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/run_test_suite.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/show_tasks.Rd | 4 markmyassignment-0.4.0/markmyassignment/man/temp_folder_check_create.Rd | 1 markmyassignment-0.4.0/markmyassignment/man/use_package.Rd | 1 markmyassignment-0.4.0/markmyassignment/tests/testthat/test-mark_my_assignment.R | 18 - markmyassignment-0.4.0/markmyassignment/tests/testthat/test-mark_my_file.R | 51 +++-- markmyassignment-0.4.0/markmyassignment/tests/testthat/test-set_assignment.R | 13 + markmyassignment-0.4.0/markmyassignment/vignettes |only 49 files changed, 311 insertions(+), 207 deletions(-)
More information about markmyassignment at CRAN
Permanent link
Title: MA Birk's Functions
Description: This is a compilation of functions that I found useful to make.
It currently includes a couple of functions to work with converting units of
measurement, and some miscellaneous wrapper functions to make R code shorter and
faster to write.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between birk versions 1.3.0 dated 2015-02-01 and 2.0.0 dated 2016-01-18
birk-1.3.0/birk/R/Q10calc.R |only birk-1.3.0/birk/man/Q10calc.Rd |only birk-2.0.0/birk/DESCRIPTION | 15 - birk-2.0.0/birk/MD5 | 34 +- birk-2.0.0/birk/NAMESPACE | 8 birk-2.0.0/birk/NEWS | 20 + birk-2.0.0/birk/R/birk.R | 6 birk-2.0.0/birk/R/conv_dim.R |only birk-2.0.0/birk/R/conv_unit.R | 369 +++++++++++++++++++++---------- birk-2.0.0/birk/R/range_seq.R | 7 birk-2.0.0/birk/R/se.R | 3 birk-2.0.0/birk/R/summ_stat.R |only birk-2.0.0/birk/R/which.closest.R |only birk-2.0.0/birk/man/birk.Rd | 6 birk-2.0.0/birk/man/conv_dim.Rd |only birk-2.0.0/birk/man/conv_unit.Rd | 62 ++--- birk-2.0.0/birk/man/conv_unit_options.Rd | 5 birk-2.0.0/birk/man/geom_mean.Rd | 3 birk-2.0.0/birk/man/range_seq.Rd | 3 birk-2.0.0/birk/man/se.Rd | 3 birk-2.0.0/birk/man/summ_stat.Rd |only birk-2.0.0/birk/man/which.closest.Rd |only 22 files changed, 360 insertions(+), 184 deletions(-)
Title: Randomization Inference Tools
Description: Tools for randomization inference.
Author: Jake Bowers <jwbowers@illinois.edu>, Mark Fredrickson
<mark.m.fredrickson@gmail.com>, and Ben Hansen <ben.hansen@umich.edu>
Maintainer: Jake Bowers <jwbowers@illinois.edu>
Diff between RItools versions 0.1-12 dated 2014-07-24 and 0.1-13 dated 2016-01-17
RItools-0.1-12/RItools/inst/tests |only RItools-0.1-12/RItools/tests/zzz.R |only RItools-0.1-13/RItools/DESCRIPTION | 21 - RItools-0.1-13/RItools/MD5 | 50 +- RItools-0.1-13/RItools/NAMESPACE | 58 +- RItools-0.1-13/RItools/NEWS | 7 RItools-0.1-13/RItools/R/data.R |only RItools-0.1-13/RItools/R/plot.xbal.R | 41 + RItools-0.1-13/RItools/R/print.xbal.R | 77 +++ RItools-0.1-13/RItools/R/ritools-package.R |only RItools-0.1-13/RItools/R/utils.R | 40 + RItools-0.1-13/RItools/R/xBalance.R | 233 +++++++++++ RItools-0.1-13/RItools/R/xBalanceEngine.R | 131 +++--- RItools-0.1-13/RItools/R/xtable.xbal.R | 76 +++ RItools-0.1-13/RItools/inst/doc/RItools.pdf |only RItools-0.1-13/RItools/man/balanceplot.Rd | 139 +++--- RItools-0.1-13/RItools/man/formula.xbal.Rd |only RItools-0.1-13/RItools/man/nuclearplants.Rd | 114 ++--- RItools-0.1-13/RItools/man/plot.xbal.Rd | 87 +--- RItools-0.1-13/RItools/man/print.xbal.Rd | 115 ++--- RItools-0.1-13/RItools/man/subset.xbal.Rd | 28 - RItools-0.1-13/RItools/man/xBalance.Rd | 326 ++++++++------- RItools-0.1-13/RItools/man/xtable.xbal.Rd | 122 ++--- RItools-0.1-13/RItools/tests/naImputeTests.Rout.save | 32 - RItools-0.1-13/RItools/tests/testthat |only RItools-0.1-13/RItools/tests/testthat.R |only RItools-0.1-13/RItools/tests/xBalanceTests.Rout.save | 374 ++++++++---------- RItools-0.1-13/RItools/tests/xBalanceTests2.Rout.save | 64 +-- 28 files changed, 1274 insertions(+), 861 deletions(-)
Title: Methods in Structural Reliability
Description: Various reliability analysis methods for: 1) computing
failure probability (probability that the output of a numerical
model exceeds a threshold); 2) computing the size of a sample
to estimate a quantile with a confidence level.
Author: Nicolas BOUSQUET, Gilles DEFAUX, Bertrand IOOSS, Vincent MOUTOUSSAMY,
Clement WALTER
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between mistral versions 2.0.0 dated 2016-01-05 and 2.0.1 dated 2016-01-17
DESCRIPTION | 6 - MD5 | 36 +++++------ R/AKMCS.R | 128 ++++++++++++++++++++-------------------- R/IRW.R | 2 R/MP.R | 6 + R/MetaIS.R | 11 ++- R/MonteCarlo.R | 25 +++---- R/S2MART.R | 4 - R/SubsetSimulation.R | 4 - man/AKMCS.Rd | 12 ++- man/IRW.Rd | 2 man/MP.Rd | 6 + man/MetaIS.Rd | 11 ++- man/MonteCarlo.Rd | 25 +++---- man/S2MART.Rd | 4 - man/SubsetSimulation.Rd | 4 - tests/AKMCS.R | 152 ++++++++++++++++++++++++------------------------ tests/MetaIS.R | 140 ++++++++++++++++++++++---------------------- tests/MonteCarlo.R | 146 +++++++++++++++++++++++----------------------- 19 files changed, 368 insertions(+), 356 deletions(-)
Title: Tools for Management of Survey Data and the Presentation of
Analysis Results
Description: One of the aims of this package is to make life easier for
useRs who deal with survey data sets. It provides an
infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) SPSS and
Stata files. Further, it provides functionality to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates, which can be exported to LaTeX and HTML.
Author: Martin Elff (with contributions from Christopher N. Lawrence, Dave Atkins, Jason W. Morgan, Achim Zeileis)
Maintainer: Martin Elff <memisc@elff.eu>
Diff between memisc versions 0.97 dated 2015-03-08 and 0.99.3 dated 2016-01-17
memisc-0.97/memisc/R/Termplot.R |only memisc-0.97/memisc/R/bucket.R |only memisc-0.97/memisc/R/panel-errbars.R |only memisc-0.97/memisc/R/paste-and-draw.R |only memisc-0.97/memisc/R/predictionFrame.R |only memisc-0.97/memisc/R/simulate.R |only memisc-0.97/memisc/R/unzip.R |only memisc-0.97/memisc/R/varpredict.R |only memisc-0.97/memisc/demo |only memisc-0.97/memisc/inst/doc/anes48.Rnw |only memisc-0.97/memisc/inst/doc/anes48.pdf |only memisc-0.97/memisc/man/Termplot.Rd |only memisc-0.97/memisc/man/buckets.Rd |only memisc-0.97/memisc/man/errbars.Rd |only memisc-0.97/memisc/man/predictionFrame.Rd |only memisc-0.97/memisc/man/simulation.Rd |only memisc-0.97/memisc/man/trimws.Rd |only memisc-0.97/memisc/man/unzip.Rd |only memisc-0.97/memisc/vignettes/anes48.Rnw |only memisc-0.99.3/memisc/DESCRIPTION | 32 memisc-0.99.3/memisc/MD5 | 155 ++-- memisc-0.99.3/memisc/NAMESPACE | 129 +++ memisc-0.99.3/memisc/R/AllClasses.R | 9 memisc-0.99.3/memisc/R/AllGenerics.R | 3 memisc-0.99.3/memisc/R/HTML.R |only memisc-0.99.3/memisc/R/aaa.R | 10 memisc-0.99.3/memisc/R/applyTemplate.R | 25 memisc-0.99.3/memisc/R/cases.R | 201 +++-- memisc-0.99.3/memisc/R/codebook-format-html.R |only memisc-0.99.3/memisc/R/codebook-methods.R | 121 ++- memisc-0.99.3/memisc/R/collect.R | 6 memisc-0.99.3/memisc/R/dataset-methods.R | 247 ++++--- memisc-0.99.3/memisc/R/format-html-dataframe.R |only memisc-0.99.3/memisc/R/format-html-ftable-matrix.R |only memisc-0.99.3/memisc/R/format-html-ftable.R |only memisc-0.99.3/memisc/R/format-html-matrix.R |only memisc-0.99.3/memisc/R/format-html-other.R |only memisc-0.99.3/memisc/R/ftable-matrix.R |only memisc-0.99.3/memisc/R/html-tools.R |only memisc-0.99.3/memisc/R/import-internal-spss-syntax.R | 501 ++++++++++---- memisc-0.99.3/memisc/R/import-internal-stata.R | 6 memisc-0.99.3/memisc/R/importer-methods.R | 38 - memisc-0.99.3/memisc/R/item-methods.R | 108 --- memisc-0.99.3/memisc/R/item-more-methods-datetime.R |only memisc-0.99.3/memisc/R/mtable-format-delim.R |only memisc-0.99.3/memisc/R/mtable-format-html.R |only memisc-0.99.3/memisc/R/mtable-format-latex.R |only memisc-0.99.3/memisc/R/mtable-format-print.R |only memisc-0.99.3/memisc/R/mtable-manip.R |only memisc-0.99.3/memisc/R/mtable-tools-format.R |only memisc-0.99.3/memisc/R/mtable.R | 645 ++----------------- memisc-0.99.3/memisc/R/percentages.R |only memisc-0.99.3/memisc/R/relabel.R |only memisc-0.99.3/memisc/R/rename.R | 56 - memisc-0.99.3/memisc/R/spss-portable-methods.R | 2 memisc-0.99.3/memisc/R/spss-syntax-methods.R | 26 memisc-0.99.3/memisc/R/spss-sysfile-methods.R | 2 memisc-0.99.3/memisc/R/toLatex-dataframe.R |only memisc-0.99.3/memisc/R/toLatex-ftable-matrix.R |only memisc-0.99.3/memisc/R/tolatex-ftable.R | 44 - memisc-0.99.3/memisc/R/trimws.R | 7 memisc-0.99.3/memisc/R/value-filters.R | 34 - memisc-0.99.3/memisc/R/wild-codes.R |only memisc-0.99.3/memisc/R/zzz.R | 1 memisc-0.99.3/memisc/build/vignette.rds |binary memisc-0.99.3/memisc/inst/ChangeLog | 249 +++++++ memisc-0.99.3/memisc/inst/NEWS.Rd | 120 +++ memisc-0.99.3/memisc/inst/NEWS.html |only memisc-0.99.3/memisc/inst/doc/anes48.R | 302 ++------ memisc-0.99.3/memisc/inst/doc/anes48.Rmd |only memisc-0.99.3/memisc/inst/doc/anes48.html |only memisc-0.99.3/memisc/inst/doc/ftable-matrix.R |only memisc-0.99.3/memisc/inst/doc/ftable-matrix.Rmd |only memisc-0.99.3/memisc/inst/doc/ftable-matrix.html |only memisc-0.99.3/memisc/inst/doc/items.R |only memisc-0.99.3/memisc/inst/doc/items.Rmd |only memisc-0.99.3/memisc/inst/doc/items.html |only memisc-0.99.3/memisc/inst/doc/mtable-html.R |only memisc-0.99.3/memisc/inst/doc/mtable-html.Rmd |only memisc-0.99.3/memisc/inst/doc/mtable-html.html |only memisc-0.99.3/memisc/inst/gles |only memisc-0.99.3/memisc/man/00memisc.Rd | 22 memisc-0.99.3/memisc/man/cases.Rd | 10 memisc-0.99.3/memisc/man/codebook.Rd | 9 memisc-0.99.3/memisc/man/collect.Rd | 6 memisc-0.99.3/memisc/man/dataSets.Rd | 30 memisc-0.99.3/memisc/man/dataset-manip.Rd |only memisc-0.99.3/memisc/man/format_html.Rd |only memisc-0.99.3/memisc/man/format_html.codebook.Rd |only memisc-0.99.3/memisc/man/format_html.ftable.Rd |only memisc-0.99.3/memisc/man/ftable-matrices.Rd |only memisc-0.99.3/memisc/man/html.Rd |only memisc-0.99.3/memisc/man/importers.Rd | 4 memisc-0.99.3/memisc/man/items.Rd | 19 memisc-0.99.3/memisc/man/mtable-format-delim.Rd |only memisc-0.99.3/memisc/man/mtable-format-html.Rd |only memisc-0.99.3/memisc/man/mtable-format-latex.Rd |only memisc-0.99.3/memisc/man/mtable-format-print.Rd |only memisc-0.99.3/memisc/man/mtable.Rd | 160 ++-- memisc-0.99.3/memisc/man/percentages.Rd |only memisc-0.99.3/memisc/man/query.Rd | 4 memisc-0.99.3/memisc/man/styles.Rd | 10 memisc-0.99.3/memisc/man/toLatexExtra.Rd | 72 +- memisc-0.99.3/memisc/man/wild.codes.Rd |only memisc-0.99.3/memisc/src/readfixed.c | 9 memisc-0.99.3/memisc/src/rofile.c | 13 memisc-0.99.3/memisc/vignettes/anes48.Rmd |only memisc-0.99.3/memisc/vignettes/ftable-matrix.Rmd |only memisc-0.99.3/memisc/vignettes/items.Rmd |only memisc-0.99.3/memisc/vignettes/mtable-html.Rmd |only 110 files changed, 1859 insertions(+), 1588 deletions(-)
Title: Client for the YouTube API
Description: Get comments posted on YouTube videos, information on how many
times a video has been liked, search for videos with particular content, and
much more. You can also scrape captions from a few videos. To learn more about
the YouTube API, see https://developers.google.com/youtube/v3/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 0.1 dated 2015-11-16 and 0.2 dated 2016-01-17
DESCRIPTION | 8 ++--- MD5 | 41 ++++++++++++++++++++--------- NAMESPACE | 6 ++++ NEWS |only R/get_comments.R | 27 +++++++++++++------ R/get_related_videos.R |only R/get_stats.R | 11 +++---- R/list_abuse_report_reasons.R |only R/list_guidecats.R |only R/list_langs.R |only R/list_regions.R |only R/list_videocats.R |only R/tuber.R | 42 ++++++++++++++++++++++++++++++ R/yt_search.R | 54 +++++++++++++++++++++++++++++---------- R/yt_topic_search.R | 3 +- build/vignette.rds |binary inst/doc/tuber-ex.html | 4 +- man/get_comments.Rd | 13 +++++++-- man/get_stats.Rd | 4 +- man/list_abuse_report_reasons.Rd |only man/list_guidecats.Rd |only man/list_langs.Rd |only man/list_regions.Rd |only man/list_videocats.Rd |only man/tuber_GET.Rd |only man/tuber_POST.Rd |only man/yt_get_related_videos.Rd |only man/yt_search.Rd | 42 +++++++++++++++++++++++++++--- man/yt_topic_search.Rd | 3 -- 29 files changed, 199 insertions(+), 59 deletions(-)
Title: R Commander Plug-in for University Level Applied Statistics
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [aut]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between RcmdrPlugin.NMBU versions 1.8.3 dated 2015-07-27 and 1.8.5 dated 2016-01-17
DESCRIPTION | 10 MD5 | 10 R/NMBU.GUI.Data.R | 4 R/NMBU.GUI.Models.R | 2 R/NMBU.RcmdrPlugin.NMBU.R | 1 R/NMBU.Utilities.R | 1442 +++++++++++++++++++++++----------------------- 6 files changed, 749 insertions(+), 720 deletions(-)
More information about RcmdrPlugin.NMBU at CRAN
Permanent link
Title: Inference on Single Binomial Proportion and Bayesian
Computations
Description: Abundant statistical literature has revealed the importance of constructing and evaluating various methods for constructing confidence intervals (CI) for single binomial proportion (p). We comprehensively provide procedures in frequentist (approximate with or without adding pseudo counts or continuity correction or exact) and in Bayesian cultures. Evaluation procedures for CI warrant active computational attention and required summaries pertaining to four criterion (coverage probability, expected length, p-confidence, p-bias, and error) are implemented.
Author: M.Subbiah, V.Rajeswaran
Maintainer: Rajeswaran Viswanathan <v.rajeswaran@gmail.com>
Diff between proportion versions 1.1.0 dated 2015-12-13 and 1.2.0 dated 2016-01-17
DESCRIPTION | 8 ++--- MD5 | 36 +++++++++++----------- R/102.Confidence_base_n_Graph.R | 44 +++++++++++++-------------- R/104.ConfidenceIntervals_BASE_n_x_Graph.R | 16 +++++----- R/112.ConfidenceIntervals_ADJ_n_Graph.R | 36 +++++++++++----------- R/113.ConfidenceIntervals_ADJ_n_x.R | 12 +++---- R/122.ConfidenceIntervals_CC_n_Graph.R | 32 ++++++++++---------- R/123.ConfidenceIntervals_CC_n_x.R | 12 +++---- R/202.CoverageProb_BASE_All_Graph.R | 46 +++++++++++------------------ R/213.CoverageProb_ADJ_All_Graph.R | 28 ++++++++--------- R/222.CoverageProb_CC_All_Graph.R | 30 +++++++++--------- R/224.CoverageProb_GENERAL_GIVEN_p.R | 9 +---- R/225.CoverageProb_GENERAL_SIMULATEDp.R | 17 +++++----- R/326.Expec_Leng_GENERAL_SIMULATEDp.R | 2 - R/327.Expec_Leng_GENERAL_GIVENp.R | 2 - R/402.p-Confidence_p-Bias_BASE_All_Graph.R | 3 - R/412.p-Confidence_p-Bias_ADJ_All_Graph.R | 3 - R/422.p-Confidence_p-Bias_CC_All_Graph.R | 3 - vignettes/proportion.Rmd | 43 ++++++++++++++++----------- 19 files changed, 188 insertions(+), 194 deletions(-)
Title: Search and Extract Data from the OECD
Description: Search and extract data from the OECD.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between OECD versions 0.2.0 dated 2015-12-04 and 0.2.2 dated 2016-01-17
DESCRIPTION | 11 MD5 | 28 +- NAMESPACE | 16 - R/main.R | 430 +++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/oecd_vignette_main.R | 120 +++++----- inst/doc/oecd_vignette_main.Rmd | 338 +++++++++++++++--------------- inst/doc/oecd_vignette_main.pdf |binary man/browse_metadata.Rd | 47 ++-- man/get_data_structure.Rd | 45 ++-- man/get_dataset.Rd | 107 ++++----- man/get_datasets.Rd | 57 ++--- man/search_dataset.Rd | 67 +++--- tests |only vignettes/oecd_vignette_main.Rmd | 338 +++++++++++++++--------------- 15 files changed, 807 insertions(+), 797 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
Siem Heisterkamp [ctb] (Author fixed sigma),
Bert Van Willigen [ctb] (Programmer fixed sigma),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-122 dated 2015-08-19 and 3.1-123 dated 2016-01-17
nlme-3.1-122/nlme/tests/nlme.Rout.save |only nlme-3.1-123/nlme/ChangeLog | 18 nlme-3.1-123/nlme/DESCRIPTION | 14 nlme-3.1-123/nlme/MD5 | 129 ++-- nlme-3.1-123/nlme/NAMESPACE | 14 nlme-3.1-123/nlme/R/VarCorr.R | 41 - nlme-3.1-123/nlme/R/corStruct.R | 10 nlme-3.1-123/nlme/R/gls.R | 340 ++++++----- nlme-3.1-123/nlme/R/gnls.R | 103 ++- nlme-3.1-123/nlme/R/lmList.R | 33 - nlme-3.1-123/nlme/R/lme.R | 482 ++++++++-------- nlme-3.1-123/nlme/R/nlme.R | 279 ++++----- nlme-3.1-123/nlme/R/reStruct.R | 19 nlme-3.1-123/nlme/R/simulate.R | 241 +++----- nlme-3.1-123/nlme/README | 22 nlme-3.1-123/nlme/inst/po/de/LC_MESSAGES/R-nlme.mo |binary nlme-3.1-123/nlme/inst/po/de/LC_MESSAGES/nlme.mo |binary nlme-3.1-123/nlme/inst/po/en@quot/LC_MESSAGES/R-nlme.mo |binary nlme-3.1-123/nlme/inst/po/en@quot/LC_MESSAGES/nlme.mo |binary nlme-3.1-123/nlme/inst/po/fr/LC_MESSAGES/R-nlme.mo |binary nlme-3.1-123/nlme/inst/po/fr/LC_MESSAGES/nlme.mo |binary nlme-3.1-123/nlme/inst/po/ko/LC_MESSAGES/R-nlme.mo |binary nlme-3.1-123/nlme/inst/po/ko/LC_MESSAGES/nlme.mo |binary nlme-3.1-123/nlme/inst/po/pl/LC_MESSAGES/R-nlme.mo |binary nlme-3.1-123/nlme/inst/po/pl/LC_MESSAGES/nlme.mo |binary nlme-3.1-123/nlme/man/VarCorr.Rd | 35 - nlme-3.1-123/nlme/man/anova.lme.Rd | 89 +- nlme-3.1-123/nlme/man/bdf.Rd | 5 nlme-3.1-123/nlme/man/glsControl.Rd | 14 nlme-3.1-123/nlme/man/gnlsControl.Rd | 13 nlme-3.1-123/nlme/man/lmeControl.Rd | 46 - nlme-3.1-123/nlme/man/nlmeControl.Rd | 17 nlme-3.1-123/nlme/man/predict.lme.Rd | 24 nlme-3.1-123/nlme/man/predict.nlme.Rd | 55 + nlme-3.1-123/nlme/man/simulate.lme.Rd | 68 +- nlme-3.1-123/nlme/po/R-de.po | 41 - nlme-3.1-123/nlme/po/R-fr.po | 33 - nlme-3.1-123/nlme/po/R-ko.po | 21 nlme-3.1-123/nlme/po/R-nlme.pot | 16 nlme-3.1-123/nlme/po/R-pl.po | 58 + nlme-3.1-123/nlme/po/de.po | 20 nlme-3.1-123/nlme/po/fr.po | 20 nlme-3.1-123/nlme/po/ko.po | 20 nlme-3.1-123/nlme/po/nlme.pot | 22 nlme-3.1-123/nlme/po/pl.po | 20 nlme-3.1-123/nlme/src/init.c | 21 nlme-3.1-123/nlme/src/nlme.c | 23 nlme-3.1-123/nlme/src/nlmefit.c | 199 ++++-- nlme-3.1-123/nlme/src/nlmefit.h | 15 nlme-3.1-123/nlme/src/rs.f | 160 ++--- nlme-3.1-123/nlme/tests/anova.gls.R | 24 nlme-3.1-123/nlme/tests/coef.R | 11 nlme-3.1-123/nlme/tests/coef.Rout.save |only nlme-3.1-123/nlme/tests/contrMat.R | 43 + nlme-3.1-123/nlme/tests/data.frame.R | 7 nlme-3.1-123/nlme/tests/deparse.R | 49 + nlme-3.1-123/nlme/tests/gls.R | 10 nlme-3.1-123/nlme/tests/lme.R | 57 + nlme-3.1-123/nlme/tests/lme.Rout.save | 203 ++++-- nlme-3.1-123/nlme/tests/missing.R | 4 nlme-3.1-123/nlme/tests/missing.Rout.save | 12 nlme-3.1-123/nlme/tests/nlme.R | 28 nlme-3.1-123/nlme/tests/nlme2.R | 62 +- nlme-3.1-123/nlme/tests/predict.lme.R | 70 ++ nlme-3.1-123/nlme/tests/sigma-fixed-etc.R |only nlme-3.1-123/nlme/tests/update.R | 20 nlme-3.1-123/nlme/tests/updateLme.R | 25 67 files changed, 2088 insertions(+), 1337 deletions(-)
Title: Novel Methods for Parallel Coordinates
Description: New approaches to parallel coordinates plots for
multivariate data visualization, including applications to clustering,
outlier hunting and regression diagnostics. Includes general functions
for multivariate nonparametric density and regression estimation,
using parallel computation.
Author: Norm Matloff <normmatloff@gmail.com> and Yingkang Xie
<yingkang.xie@gmail.com>
Maintainer: Norm Matloff <normmatloff@gmail.com>
Diff between freqparcoord versions 1.0.0 dated 2014-03-23 and 1.0.1 dated 2016-01-17
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 4 +++- man/prgeng.Rd | 2 ++ 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include combinatorial search (all possible subset regression), productivity evaluation using distance measures: DDF (directional distance function), DEA (data envelopment analysis), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 1.8 dated 2015-12-18 and 1.9 dated 2016-01-17
DJL-1.8/DJL/R/DJL-internal.R |only DJL-1.8/DJL/R/aps.reg.R |only DJL-1.8/DJL/man/aps.reg.Rd |only DJL-1.9/DJL/DESCRIPTION | 6 +++--- DJL-1.9/DJL/MD5 | 13 ++++++------- DJL-1.9/DJL/NAMESPACE | 4 ++-- DJL-1.9/DJL/NEWS | 13 +++++++++++++ DJL-1.9/DJL/R/ma.aps.reg.R |only DJL-1.9/DJL/man/ma.aps.reg.Rd |only DJL-1.9/DJL/man/target.spec.dea.Rd | 6 ++++-- 10 files changed, 28 insertions(+), 14 deletions(-)
Title: Sustainable Transport Planning
Description: Functionality and data access tools for transport planning,
including origin-destination analysis, route allocation and modelling travel
patterns.
Author: Robin Lovelace [aut, cre],
Richard Ellison [aut],
Barry Rowlingson [aut] (Author of overline),
Nick Bearman [aut] (Co-author of gclip)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.1.0 dated 2016-01-15 and 0.1.1 dated 2016-01-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/introducing-stplanr.html | 8 ++++---- src/spatialnetworks.cpp | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release. For further examples and documentation, please
proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 1.0.6.1 dated 2015-10-12 and 2.0.1 dated 2016-01-16
ggtern-1.0.6.1/ggtern/R/TRL-line.R |only ggtern-1.0.6.1/ggtern/R/aaa.R |only ggtern-1.0.6.1/ggtern/R/clip-polygons.R |only ggtern-1.0.6.1/ggtern/R/data.R |only ggtern-1.0.6.1/ggtern/R/element_ternary.R |only ggtern-1.0.6.1/ggtern/R/geom-Lline.R |only ggtern-1.0.6.1/ggtern/R/geom-Rline.R |only ggtern-1.0.6.1/ggtern/R/geom-Tline.R |only ggtern-1.0.6.1/ggtern/R/geom-confidence.R |only ggtern-1.0.6.1/ggtern/R/geom-errorbarL.R |only ggtern-1.0.6.1/ggtern/R/geom-errorbarR.R |only ggtern-1.0.6.1/ggtern/R/geom-errorbarT.R |only ggtern-1.0.6.1/ggtern/R/geom-polygon-tern.R |only ggtern-1.0.6.1/ggtern/R/geom-segment.R |only ggtern-1.0.6.1/ggtern/R/geom-smooth.R |only ggtern-1.0.6.1/ggtern/R/geom.R |only ggtern-1.0.6.1/ggtern/R/ggsave.R |only ggtern-1.0.6.1/ggtern/R/ggtern-build.R |only ggtern-1.0.6.1/ggtern/R/ggtern.R |only ggtern-1.0.6.1/ggtern/R/global.R |only ggtern-1.0.6.1/ggtern/R/kde2d-weighted.R |only ggtern-1.0.6.1/ggtern/R/labs-new.R |only ggtern-1.0.6.1/ggtern/R/labs-pcnt.R |only ggtern-1.0.6.1/ggtern/R/log-ratio-trans.R |only ggtern-1.0.6.1/ggtern/R/mahalanobis.R |only ggtern-1.0.6.1/ggtern/R/multiplot.R |only ggtern-1.0.6.1/ggtern/R/panel.R |only ggtern-1.0.6.1/ggtern/R/point-in-sequence.R |only ggtern-1.0.6.1/ggtern/R/scales.R |only ggtern-1.0.6.1/ggtern/R/stat-Lline.R |only ggtern-1.0.6.1/ggtern/R/stat-Rline.R |only ggtern-1.0.6.1/ggtern/R/stat-Tline.R |only ggtern-1.0.6.1/ggtern/R/stat-smooth.R |only ggtern-1.0.6.1/ggtern/R/statnew.R |only ggtern-1.0.6.1/ggtern/R/tern-clockwise.R |only ggtern-1.0.6.1/ggtern/R/tern-render.R |only ggtern-1.0.6.1/ggtern/R/tern-stop.R |only ggtern-1.0.6.1/ggtern/R/theme-arrowbaseline.R |only ggtern-1.0.6.1/ggtern/R/theme-convenience.R |only ggtern-1.0.6.1/ggtern/man/approved_geometries.Rd |only ggtern-1.0.6.1/ggtern/man/clipPolygons.Rd |only ggtern-1.0.6.1/ggtern/man/coord.Rd |only ggtern-1.0.6.1/ggtern/man/coord_tern.Rd |only ggtern-1.0.6.1/ggtern/man/data.Rd |only ggtern-1.0.6.1/ggtern/man/data_Feldspar.Rd |only ggtern-1.0.6.1/ggtern/man/data_USDA.Rd |only ggtern-1.0.6.1/ggtern/man/element_ternary.Rd |only ggtern-1.0.6.1/ggtern/man/enforceTernaryCoordinates.Rd |only ggtern-1.0.6.1/ggtern/man/expandRange.Rd |only ggtern-1.0.6.1/ggtern/man/expandTern.Rd |only ggtern-1.0.6.1/ggtern/man/geom_TLRline.Rd |only ggtern-1.0.6.1/ggtern/man/geom_errorbarTLR.Rd |only ggtern-1.0.6.1/ggtern/man/geom_polygon_tern.Rd |only ggtern-1.0.6.1/ggtern/man/geom_segment.Rd |only ggtern-1.0.6.1/ggtern/man/geomconfidence.Rd |only ggtern-1.0.6.1/ggtern/man/getBreaks.Rd |only ggtern-1.0.6.1/ggtern/man/ggtern-labels.Rd |only ggtern-1.0.6.1/ggtern/man/ggtern-package.Rd |only ggtern-1.0.6.1/ggtern/man/ggtern.multi.Rd |only ggtern-1.0.6.1/ggtern/man/iflasttern.Rd |only ggtern-1.0.6.1/ggtern/man/logratio.Rd |only ggtern-1.0.6.1/ggtern/man/mahalanobis.Rd |only ggtern-1.0.6.1/ggtern/man/notransform.Rd |only ggtern-1.0.6.1/ggtern/man/point.in.sequence.Rd |only ggtern-1.0.6.1/ggtern/man/print.Rd |only ggtern-1.0.6.1/ggtern/man/scale_TLR_continuous.Rd |only ggtern-1.0.6.1/ggtern/man/showhidegrid.Rd |only ggtern-1.0.6.1/ggtern/man/stat_interpolate_tern.Rd |only ggtern-1.0.6.1/ggtern/man/stat_smooth_tern.Rd |only ggtern-1.0.6.1/ggtern/man/suppressColours.Rd |only ggtern-1.0.6.1/ggtern/man/ternLimitsForCoord.Rd |only ggtern-1.0.6.1/ggtern/man/tern_dep.Rd |only ggtern-1.0.6.1/ggtern/man/tern_stop.Rd |only ggtern-1.0.6.1/ggtern/man/ternary_transformations.Rd |only ggtern-1.0.6.1/ggtern/man/theme_arrowbaseline.Rd |only ggtern-1.0.6.1/ggtern/man/theme_bw.Rd |only ggtern-1.0.6.1/ggtern/man/theme_classic.Rd |only ggtern-1.0.6.1/ggtern/man/theme_custom.Rd |only ggtern-1.0.6.1/ggtern/man/theme_gray.Rd |only ggtern-1.0.6.1/ggtern/man/theme_minimal.Rd |only ggtern-1.0.6.1/ggtern/man/theme_rgbg.Rd |only ggtern-1.0.6.1/ggtern/man/theme_rgbw.Rd |only ggtern-1.0.6.1/ggtern/man/undoCartesian.Rd |only ggtern-2.0.1/ggtern/DESCRIPTION | 68 ggtern-2.0.1/ggtern/MD5 | 253 +-- ggtern-2.0.1/ggtern/NAMESPACE | 445 ++++- ggtern-2.0.1/ggtern/NEWS | 15 ggtern-2.0.1/ggtern/R/aes.R | 25 ggtern-2.0.1/ggtern/R/calc-kde2d-weighted.R |only ggtern-2.0.1/ggtern/R/calc-mahalanobis-distance.R |only ggtern-2.0.1/ggtern/R/calc-tern-tlr2xy.R |only ggtern-2.0.1/ggtern/R/coord-tern.R | 1406 +++++++---------- ggtern-2.0.1/ggtern/R/depreciated.R |only ggtern-2.0.1/ggtern/R/doc-data.R |only ggtern-2.0.1/ggtern/R/doc-theme-convenience.R |only ggtern-2.0.1/ggtern/R/geom-Xisoprop.R |only ggtern-2.0.1/ggtern/R/geom-Xline.R |only ggtern-2.0.1/ggtern/R/geom-confidence-tern.R |only ggtern-2.0.1/ggtern/R/geom-density-tern.R | 102 - ggtern-2.0.1/ggtern/R/geom-errorbarX.R |only ggtern-2.0.1/ggtern/R/geom-interpolate-tern.R | 68 ggtern-2.0.1/ggtern/R/geom-mask.R |only ggtern-2.0.1/ggtern/R/geom-smooth-tern.R |only ggtern-2.0.1/ggtern/R/gg-internal.R | 75 ggtern-2.0.1/ggtern/R/ggtern-constructor.R |only ggtern-2.0.1/ggtern/R/ggtern-package.R | 34 ggtern-2.0.1/ggtern/R/labels-new.R |only ggtern-2.0.1/ggtern/R/labels-percent.R |only ggtern-2.0.1/ggtern/R/modifications-gridExtra.R |only ggtern-2.0.1/ggtern/R/onLoad.R | 52 ggtern-2.0.1/ggtern/R/plot-build.R |only ggtern-2.0.1/ggtern/R/plot-construction.R | 79 ggtern-2.0.1/ggtern/R/plot.R |only ggtern-2.0.1/ggtern/R/position-.R |only ggtern-2.0.1/ggtern/R/position-jitter-tern.R |only ggtern-2.0.1/ggtern/R/position-nudge-tern.R |only ggtern-2.0.1/ggtern/R/save.R |only ggtern-2.0.1/ggtern/R/scales-.R |only ggtern-2.0.1/ggtern/R/scales-tern.R |only ggtern-2.0.1/ggtern/R/stat-confidence-tern.R |only ggtern-2.0.1/ggtern/R/stat-density-tern.R | 163 + ggtern-2.0.1/ggtern/R/stat-interpolate-tern.R | 203 -- ggtern-2.0.1/ggtern/R/stat-smooth-tern.R |only ggtern-2.0.1/ggtern/R/strip-unapproved.R | 183 +- ggtern-2.0.1/ggtern/R/tern-limits.R | 86 - ggtern-2.0.1/ggtern/R/theme-arrowlength.R | 35 ggtern-2.0.1/ggtern/R/theme-clockwise.R |only ggtern-2.0.1/ggtern/R/theme-defaults.R | 686 +++++--- ggtern-2.0.1/ggtern/R/theme-elements.R | 182 +- ggtern-2.0.1/ggtern/R/theme-gridsontop.R |only ggtern-2.0.1/ggtern/R/theme-legend-position.R |only ggtern-2.0.1/ggtern/R/theme-noarrows.R | 9 ggtern-2.0.1/ggtern/R/theme-novar-tern.R | 31 ggtern-2.0.1/ggtern/R/theme-rotate.R |only ggtern-2.0.1/ggtern/R/theme-showgrid.R | 82 ggtern-2.0.1/ggtern/R/theme-showlabels.R | 15 ggtern-2.0.1/ggtern/R/theme-showsecondary.R | 22 ggtern-2.0.1/ggtern/R/theme-showtitles.R | 9 ggtern-2.0.1/ggtern/R/theme-ticksoutside.R | 12 ggtern-2.0.1/ggtern/R/theme.R | 122 - ggtern-2.0.1/ggtern/R/utilities-help.R | 104 - ggtern-2.0.1/ggtern/R/utilities.R | 594 +------ ggtern-2.0.1/ggtern/build/partial.rdb |binary ggtern-2.0.1/ggtern/data/Fragments.RData |only ggtern-2.0.1/ggtern/man/aes.Rd | 2 ggtern-2.0.1/ggtern/man/approved_layers.Rd |only ggtern-2.0.1/ggtern/man/calc_mahalanobis_distance.Rd |only ggtern-2.0.1/ggtern/man/convenience_functions.Rd | 62 ggtern-2.0.1/ggtern/man/coord-tern.Rd |only ggtern-2.0.1/ggtern/man/data_sets_Feldspar.Rd |only ggtern-2.0.1/ggtern/man/data_sets_Fragments.Rd |only ggtern-2.0.1/ggtern/man/data_sets_USDA.Rd |only ggtern-2.0.1/ggtern/man/geom_Xisoprop.Rd |only ggtern-2.0.1/ggtern/man/geom_Xline.Rd |only ggtern-2.0.1/ggtern/man/geom_confidence_tern.Rd |only ggtern-2.0.1/ggtern/man/geom_density_tern.Rd | 72 ggtern-2.0.1/ggtern/man/geom_errorbarX.Rd |only ggtern-2.0.1/ggtern/man/geom_interpolate_tern.Rd | 94 - ggtern-2.0.1/ggtern/man/geom_mask.Rd |only ggtern-2.0.1/ggtern/man/geom_smooth_tern.Rd | 104 - ggtern-2.0.1/ggtern/man/ggplot.Rd |only ggtern-2.0.1/ggtern/man/ggplotGrob.Rd |only ggtern-2.0.1/ggtern/man/ggplot_build.Rd | 28 ggtern-2.0.1/ggtern/man/ggplot_gtable.Rd | 4 ggtern-2.0.1/ggtern/man/ggsave.Rd | 58 ggtern-2.0.1/ggtern/man/ggtern.Rd | 14 ggtern-2.0.1/ggtern/man/ggtern_labels.Rd |only ggtern-2.0.1/ggtern/man/ggtern_package.Rd |only ggtern-2.0.1/ggtern/man/ggtern_themes.Rd |only ggtern-2.0.1/ggtern/man/kde2d.weighted.Rd | 14 ggtern-2.0.1/ggtern/man/label_formatter.Rd |only ggtern-2.0.1/ggtern/man/modification-gridExtra.Rd |only ggtern-2.0.1/ggtern/man/overloaded.Rd | 93 - ggtern-2.0.1/ggtern/man/plotconstruction.Rd |only ggtern-2.0.1/ggtern/man/position_jitter_tern.Rd |only ggtern-2.0.1/ggtern/man/position_nudge_tern.Rd |only ggtern-2.0.1/ggtern/man/scale_tern_continuous.Rd |only ggtern-2.0.1/ggtern/man/stat_density_tern.Rd | 89 - ggtern-2.0.1/ggtern/man/strip_unapproved.Rd | 12 ggtern-2.0.1/ggtern/man/suffix_arrow.Rd | 10 ggtern-2.0.1/ggtern/man/tern_limits.Rd | 47 ggtern-2.0.1/ggtern/man/ternary-transformation.Rd |only ggtern-2.0.1/ggtern/man/theme_clockwise.Rd | 8 ggtern-2.0.1/ggtern/man/theme_complete.Rd | 43 ggtern-2.0.1/ggtern/man/theme_elements.Rd | 134 - ggtern-2.0.1/ggtern/man/theme_gridsontop.Rd |only ggtern-2.0.1/ggtern/man/theme_novar_tern.Rd | 14 ggtern-2.0.1/ggtern/man/theme_showgrid.Rd |only ggtern-2.0.1/ggtern/man/theme_showlabels.Rd | 11 ggtern-2.0.1/ggtern/man/theme_showprimary.Rd | 30 ggtern-2.0.1/ggtern/man/theme_showtitles.Rd | 6 ggtern-2.0.1/ggtern/man/themearrowlength.Rd | 43 ggtern-2.0.1/ggtern/man/themelegendposition.Rd |only ggtern-2.0.1/ggtern/man/themerotate.Rd |only ggtern-2.0.1/ggtern/man/themeshowhidearrows.Rd | 2 ggtern-2.0.1/ggtern/man/themeticksoutside.Rd | 7 ggtern-2.0.1/ggtern/man/transform_position_tern.Rd |only ggtern-2.0.1/ggtern/man/undocumented.Rd | 151 - ggtern-2.0.1/ggtern/man/zzz-depreciated.Rd |only 199 files changed, 3172 insertions(+), 3140 deletions(-)
Title: Tools for Cycling Data Analysis
Description: A suite of functions for analysing cycling data.
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Diff between cycleRtools versions 1.0.4 dated 2015-12-01 and 1.1.0 dated 2016-01-16
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Title: Subgroup Discovery Algorithms for R
Description: Implementation of some algorithms for the data mining task called
"subgroup discovery" without package dependencies. It also provide a Shiny App
for make the analysis easier. The algorithms works with data sets provided in
KEEL or ARFF format files or data.frame objects. If you want more information about KEEL format, please
refer to < http://www.keel.es > .
Author: Angel M. Garcia [aut, cre],
Pedro Gonzalez [aut, cph],
Cristobal J. Carmona [aut, cph],
Francisco Charte [ctb]
Maintainer: Angel M. Garcia <amgv0009@red.ujaen.es>
Diff between SDR versions 0.6.0.0 dated 2015-07-19 and 0.7.0.0 dated 2016-01-16
SDR-0.6.0.0/SDR/README.md |only SDR-0.6.0.0/SDR/vignettes/Interfaz1.png |only SDR-0.6.0.0/SDR/vignettes/Interfaz2.png |only SDR-0.6.0.0/SDR/vignettes/MESDIFSchema.png |only SDR-0.6.0.0/SDR/vignettes/NMEEFSchema.png |only SDR-0.7.0.0/SDR/DESCRIPTION | 21 SDR-0.7.0.0/SDR/LICENSE | 44 SDR-0.7.0.0/SDR/MD5 | 110 SDR-0.7.0.0/SDR/NAMESPACE | 21 SDR-0.7.0.0/SDR/NEWS.md |only SDR-0.7.0.0/SDR/R/Difuso.R | 476 +- SDR-0.7.0.0/SDR/R/FuGePSD.R |only SDR-0.7.0.0/SDR/R/MESDIF.R | 1097 ++-- SDR-0.7.0.0/SDR/R/NMEEFSD.R | 1529 +++--- SDR-0.7.0.0/SDR/R/PackageDoc.R | 63 SDR-0.7.0.0/SDR/R/QualityMeasures.R | 303 - SDR-0.7.0.0/SDR/R/SDIGA.R | 1399 +++--- SDR-0.7.0.0/SDR/R/Utils.R | 1448 +++--- SDR-0.7.0.0/SDR/R/datasets.R | 4 SDR-0.7.0.0/SDR/R/ga.R | 4012 +++++++++--------- SDR-0.7.0.0/SDR/R/leerDatos.R | 2013 ++++++--- SDR-0.7.0.0/SDR/R/read_arff.R |only SDR-0.7.0.0/SDR/build/vignette.rds |binary SDR-0.7.0.0/SDR/data/carTra.rda |binary SDR-0.7.0.0/SDR/data/carTst.rda |binary SDR-0.7.0.0/SDR/data/germanTra.rda |binary SDR-0.7.0.0/SDR/data/germanTst.rda |binary SDR-0.7.0.0/SDR/data/habermanTra.rda |binary SDR-0.7.0.0/SDR/data/habermanTst.rda |binary SDR-0.7.0.0/SDR/inst/doc/SDRpackage.R | 5 SDR-0.7.0.0/SDR/inst/doc/SDRpackage.Rmd | 87 SDR-0.7.0.0/SDR/inst/doc/SDRpackage.pdf |binary SDR-0.7.0.0/SDR/inst/shiny/server.R | 1346 +++--- SDR-0.7.0.0/SDR/inst/shiny/ui.R | 338 - SDR-0.7.0.0/SDR/inst/shiny/www/bootstrap.css |only SDR-0.7.0.0/SDR/inst/shiny/www/load.js | 4 SDR-0.7.0.0/SDR/inst/shiny/www/page2.md |only SDR-0.7.0.0/SDR/man/FUGEPSD.Rd |only SDR-0.7.0.0/SDR/man/FuGePSD_Mutation.Rd |only SDR-0.7.0.0/SDR/man/FuGePSD_crossover.Rd |only SDR-0.7.0.0/SDR/man/MESDIF.Rd | 11 SDR-0.7.0.0/SDR/man/NMEEF_SD.Rd | 4 SDR-0.7.0.0/SDR/man/Pop.evaluate.Rd |only SDR-0.7.0.0/SDR/man/Pop.fuzzyReasoningMethod.Rd |only SDR-0.7.0.0/SDR/man/Rule.addLabel.Rd |only SDR-0.7.0.0/SDR/man/Rule.addVariable.Rd |only SDR-0.7.0.0/SDR/man/Rule.changeLabel.Rd |only SDR-0.7.0.0/SDR/man/Rule.clearAntecedent.Rd |only SDR-0.7.0.0/SDR/man/Rule.compatibility.Rd |only SDR-0.7.0.0/SDR/man/Rule.deleteVariable.Rd |only SDR-0.7.0.0/SDR/man/Rule.evaluate.Rd |only SDR-0.7.0.0/SDR/man/Rule.exchangeVariables.Rd |only SDR-0.7.0.0/SDR/man/Rule.toCANVectorRepresentation.Rd |only SDR-0.7.0.0/SDR/man/SDIGA.Rd | 4 SDR-0.7.0.0/SDR/man/addKeelRegister.Rd |only SDR-0.7.0.0/SDR/man/changeTargetVariable.Rd | 11 SDR-0.7.0.0/SDR/man/createNewRule.Rd |only SDR-0.7.0.0/SDR/man/improvedTable.Rd |only SDR-0.7.0.0/SDR/man/keelFromARFF.Rd |only SDR-0.7.0.0/SDR/man/keelFromDataFrame.Rd |only SDR-0.7.0.0/SDR/man/modifyFuzzyCrispIntervals.Rd | 4 SDR-0.7.0.0/SDR/man/parseTime.Rd |only SDR-0.7.0.0/SDR/man/print.keel.Rd |only SDR-0.7.0.0/SDR/man/printFuGePSDParameters.Rd |only SDR-0.7.0.0/SDR/man/read.keel.Rd | 24 SDR-0.7.0.0/SDR/man/save.keel.Rd |only SDR-0.7.0.0/SDR/man/summary.keel.Rd |only SDR-0.7.0.0/SDR/man/tokenCompetition.Rd |only SDR-0.7.0.0/SDR/man/tournamentSelection.Rd |only SDR-0.7.0.0/SDR/man/writeRuleFile.Rd |only SDR-0.7.0.0/SDR/man/writeTestQMFile.Rd |only SDR-0.7.0.0/SDR/vignettes/Interfaz1.PNG |only SDR-0.7.0.0/SDR/vignettes/Interfaz2.PNG |only SDR-0.7.0.0/SDR/vignettes/MESDIFSchema.PNG |only SDR-0.7.0.0/SDR/vignettes/NMEEFSchema.PNG |only SDR-0.7.0.0/SDR/vignettes/SDRpackage.Rmd | 87 SDR-0.7.0.0/SDR/vignettes/salida.tex |only SDR-0.7.0.0/SDR/vignettes/testQualityMeasures.txt |only 78 files changed, 8114 insertions(+), 6351 deletions(-)
Title: An Algorithm to Infer Relatedness
Description: Inference of relatedness coefficients from a bi-allelic genotype matrix using a Maximum Likelihood estimation.
Author: Fabien Laporte
Maintainer: Fabien Laporte <fabien.laporte@moulon.inra.fr>
Diff between Relatedness versions 1.2 dated 2015-11-03 and 1.3 dated 2016-01-16
DESCRIPTION | 6 MD5 | 18 +- R/RelCoef.R | 248 +++++++++++++++++++-------------------- R/RelCoefLine.R |only R/RelComb.R |only R/Relatedness-internal.R | 281 +++++++++++++++------------------------------ data/Delta.rda |only man/Delta.Rd |only man/RelCoef.Rd | 20 +-- man/RelCoefLine.Rd |only man/RelComb.Rd |only man/Relatedness-package.Rd | 2 src/BoucleEMacc.c | 33 ----- 13 files changed, 250 insertions(+), 358 deletions(-)
Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch <ivan.marin@uv.es>
Maintainer: Ivan Marin-Franch <ivan.marin@uv.es>
Diff between visualFields versions 0.4.2 dated 2015-01-28 and 0.4.3 dated 2016-01-16
DESCRIPTION | 10 +- MD5 | 166 +++++++++++++++++++++++------------------------ NAMESPACE | 13 ++- R/tdrank.R | 3 R/tdranknv.R | 5 - R/vfdemographics.R | 1 R/vflayout.R | 36 ++++++++++ data/csplocmap.rda |binary data/saplocmap.rda |binary data/vfidefault.rda |binary data/vfsettings.rda |binary inst/news.txt | 9 +- man/ageLinearModel.Rd | 2 man/bebie.Rd | 6 - man/colormapgraph.Rd | 2 man/createviewport.Rd | 2 man/csplocmap.Rd | 2 man/fdplocmap.Rd | 2 man/filterReliability.Rd | 2 man/getnv.Rd | 2 man/ghpostd.Rd | 2 man/ghranktd.Rd | 2 man/gloperc.Rd | 2 man/hist_poplr.Rd | 2 man/lidLensArtifact.Rd | 2 man/loadvfcsv.Rd | 2 man/loadvfxml.Rd | 2 man/loadvfxmlbatch.Rd | 2 man/locperc.Rd | 2 man/nvcspsgalpha.Rd | 2 man/nvsapdefault.Rd | 2 man/pdpmap.Rd | 2 man/pdpmapghr.Rd | 2 man/pdval.Rd | 2 man/pdvalghr.Rd | 2 man/poplr.Rd | 2 man/poplr_cstat.Rd | 2 man/poplr_pstat.Rd | 2 man/progols.Rd | 2 man/quad2Dfit.Rd | 2 man/ringmapgraph.Rd | 2 man/saplocmap.Rd | 2 man/sdnv.Rd | 2 man/sdnvghr.Rd | 2 man/setnv.Rd | 2 man/stimLoc.Rd | 2 man/tdpmap.Rd | 2 man/tdrank.Rd | 2 man/tdrankadjperc.Rd | 2 man/tdrankglm.Rd | 2 man/tdranknv.Rd | 2 man/tdrankperc.Rd | 2 man/tdval.Rd | 2 man/vf91016csp1vf.Rd | 2 man/vf91016left.Rd | 2 man/vf91016right.Rd | 2 man/vfShafi2011.Rd | 2 man/vfcolormap.Rd | 2 man/vfdemographics.Rd | 2 man/vfenv.Rd | 2 man/vfgrayscale.Rd | 2 man/vfidefault.Rd | 2 man/vfindex.Rd | 2 man/vfindexpmap.Rd | 2 man/vfiperc.Rd | 2 man/vflayout.Rd | 2 man/vflayout_legoplot.Rd | 2 man/vflayout_poplr.Rd | 2 man/vflayoutghr.Rd | 2 man/vfobject.Rd | 2 man/vfplot.Rd | 2 man/vfplot_poplr.Rd | 2 man/vfplotloc.Rd | 2 man/vfsegmentcoord.Rd | 2 man/vfselectvisit.Rd | 2 man/vfsettings.Rd | 2 man/vfsort.Rd | 2 man/vfstats.Rd | 2 man/vfstatspmap.Rd | 2 man/xmlblock.Rd | 2 man/xmldevval.Rd | 2 man/xmlitem.Rd | 2 man/xmlvfval.Rd | 2 man/xmlvfxy.Rd | 2 84 files changed, 214 insertions(+), 177 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.5.2 dated 2016-01-08 and 0.5.4 dated 2016-01-16
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- R/lin.ratio.R | 2 +- R/vardchangannual.R | 4 ++++ R/vardchanges.R | 11 ++++++++--- R/vardcros.R | 6 +++--- R/vardom.R | 4 ++-- R/vardomh.R | 4 ++-- R/variance_est.R | 23 ++++++++++++----------- inst/CITATION | 4 ++-- inst/NEWS | 8 ++++++++ man/lin.ratio.Rd | 9 ++++++--- man/vardchangannual.Rd | 6 ++++-- man/vardchanges.Rd | 3 ++- man/vardom.Rd | 5 +++-- man/vardomh.Rd | 12 ++++++++---- man/vardpoor-package.Rd | 4 ++-- 17 files changed, 87 insertions(+), 58 deletions(-)
Title: R Ultimate Multilabel Dataset Repository
Description: Large collection of multilabel datasets along with the functions
needed to export them to several formats, to make partitions, and to obtain
bibliographic information.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>
Diff between mldr.datasets versions 0.3.1 dated 2015-11-24 and 0.3.15 dated 2016-01-16
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/export.R | 29 +++++++++++++++++------------ R/kfolds.R | 8 +++++--- R/utils.R | 24 +++++++++++++----------- README.md | 8 ++++++-- man/write.mldr.Rd | 4 ++-- 7 files changed, 53 insertions(+), 40 deletions(-)
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for multi-
label data sets along with an interactive Shiny application to ease their use.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>
Diff between mldr versions 0.3.18 dated 2015-12-05 and 0.3.22 dated 2016-01-16
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/mldr.R | 10 +++++----- README.md | 20 +++++++++++++++++++- build/vignette.rds |binary inst/CITATION | 8 ++++++-- inst/doc/mldr.pdf |binary 7 files changed, 40 insertions(+), 18 deletions(-)
Title: Power Analysis for Generalised Linear Mixed Models by Simulation
Description: Calculate power for generalised linear mixed models, using
simulation. Designed to work with models fit using the 'lme4' package.
Author: Peter Green, Catriona MacLeod
Maintainer: Peter Green <greenp@landcareresearch.co.nz>
Diff between simr versions 1.0.0 dated 2015-11-01 and 1.0.1 dated 2016-01-16
DESCRIPTION | 11 +++--- MD5 | 26 ++++++++++---- NAMESPACE | 3 + NEWS.md |only R/getData.R | 19 +++++++--- R/glm.R | 28 +++------------ R/glmm.R | 2 - R/modify.R | 19 +++++++++- build/vignette.rds |only inst |only tests/testthat/test_binomial.R |only vignettes/examples.Rmd | 72 +++++++++++++++++++++++------------------ vignettes/fromscratch.Rmd | 14 +++++-- 13 files changed, 116 insertions(+), 78 deletions(-)
Title: Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
Description: Used primarily for estimates of allele frequency surfaces from point estimates.
It can also place individuals of unknown origin back onto the geographic map with great accuracy.
Additionally, it can place admixed individuals by estimating contributing fractions at each
location on a map. Lastly, it can rank SNPs by their ability to differentiate populations.
See "Fast Spatial Ancestry via Flexible Allele Frequency Surfaces" (John Michael Ranola, John
Novembre, Kenneth Lange) in Bioinformatics 2014 for more info.
Author: John Michael O Ranola, John Novembre, and Kenneth Lange
Maintainer: John Michael O. Ranola <ranolaj@uw.edu>
Diff between OriGen versions 1.3.1 dated 2015-09-09 and 1.4.3 dated 2016-01-16
DESCRIPTION | 11 MD5 | 32 R/OriGen-internal.R | 459 ++- data/LocationsTrialDataSmall.txt.gz |binary data/MicrosatTrialDataSmall.txt.gz |binary man/CalcFractionsMultiLoglik.Rd |only man/FitAdmixedModelFindUnknowns.Rd | 59 man/FitMultinomialAdmixedModelFindUnknowns.Rd |only man/FitMultinomialModel.Rd | 68 man/FitMultinomialModelFindUnknowns.Rd | 65 man/FitOriGenModel.Rd | 9 man/FitOriGenModelFindUnknowns.Rd | 8 man/GenerateHeatMaps.Rd | 63 man/PlotAdmixedSurface.Rd | 38 man/PlotAlleleFrequencySurface.Rd | 51 man/PlotAlleleFrequencySurfaceOld.Rd | 8 man/PlotUnknownHeatMap.Rd | 8 src/OriGen.f90 | 3128 +++++++++++++++----------- 18 files changed, 2452 insertions(+), 1555 deletions(-)
Title: Tree Boosting for Multivariate Outcomes
Description: Fits a multivariate model of decision trees for multiple,
continuous outcome variables. A model for each outcome variable is fit
separately, selecting predictors that explain that explain covariance in
multiple outcomes. Package is built on top of 'gbm', which fits an ensemble
of decision trees to univariate outcomes.
Author: Patrick Miller [aut, cre]
Maintainer: Patrick Miller <patrick.mil10@gmail.com>
Diff between mvtboost versions 0.3 dated 2015-09-24 and 0.4.0 dated 2016-01-16
DESCRIPTION | 18 ++-- MD5 | 76 ++++++++++---------- NAMESPACE | 4 - R/mvtb_nonlin_test.R | 25 +++--- R/mvtb_plots.R | 62 +++++++++------- R/mvtb_summary.R | 40 ++++++---- R/mvtboost.R | 141 +++++++++++++++++++------------------ build/partial.rdb |binary build/vignette.rds |binary data/wellbeing.RData |binary inst/doc/mvtboost_vignette.R | 4 - inst/doc/mvtboost_vignette.Rmd | 14 ++- inst/doc/mvtboost_vignette.html | 28 +++---- inst/doc/mvtboost_wellbeing.R | 21 ++++- inst/doc/mvtboost_wellbeing.Rmd | 67 +++++++++++------ inst/doc/mvtboost_wellbeing.html | 93 +++++++++++++----------- man/addalpha.Rd | 2 man/colorRampPaletteAlpha.Rd | 2 man/gbm.ri.Rd | 8 +- man/mvtb.Rd | 147 +++++++++++++++++++-------------------- man/mvtb.cluster.Rd | 26 +++--- man/mvtb.covex.Rd |only man/mvtb.heat.Rd | 24 +++--- man/mvtb.nonlin.Rd | 27 +++---- man/mvtb.perspec.Rd | 26 +++--- man/mvtb.ri.Rd | 16 ++-- man/mvtb.uncomp.Rd | 2 man/mvtboost-package.Rd | 8 -- man/plot.mvtb.Rd | 18 ++-- man/predict.mvtb.Rd | 10 +- man/print.mvtb.Rd | 2 man/summary.mvtb.Rd | 2 man/wellbeing.Rd | 28 ++++++- tests/testthat/Rplots.pdf |binary tests/testthat/test_params.R | 20 +++++ tests/testthat/test_plot.R | 2 tests/testthat/test_summary.R | 46 +++++++----- vignettes/mvtboost_vignette.Rmd | 14 ++- vignettes/mvtboost_wellbeing.Rmd | 67 +++++++++++------ vignettes/wb_cv5test.Rdata |only 40 files changed, 622 insertions(+), 468 deletions(-)
Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions are to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich;
Yulia R. Gel;
Xingyu Wang;
Calvin Chu
Maintainer: Vyacheslav Lyubchich <lyubchic@umces.edu>
Diff between funtimes versions 2.0 dated 2015-08-08 and 2.1 dated 2016-01-16
DESCRIPTION | 19 ++++++++++--------- MD5 | 14 +++++++------- R/CWindowCluster.R | 4 ++-- R/q.tails.R | 8 ++++---- man/CWindowCluster.Rd | 27 ++++++++++++++------------- man/i.tails.Rd | 8 ++++++-- man/q.tails.Rd | 7 +++++-- man/sync.test.Rd | 4 ++-- 8 files changed, 50 insertions(+), 41 deletions(-)
Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery, Thomas Buettner
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesPop versions 5.4-0 dated 2015-07-18 and 6.0-0 dated 2016-01-16
bayesPop-5.4-0/bayesPop/data/vwBaseYear2008.R |only bayesPop-5.4-0/bayesPop/data/vwBaseYear2008.txt |only bayesPop-6.0-0/bayesPop/ChangeLog | 15 bayesPop-6.0-0/bayesPop/DESCRIPTION | 16 bayesPop-6.0-0/bayesPop/MD5 | 51 - bayesPop-6.0-0/bayesPop/NAMESPACE | 10 bayesPop-6.0-0/bayesPop/R/adjustments.R | 1 bayesPop-6.0-0/bayesPop/R/aggregate.R | 16 bayesPop-6.0-0/bayesPop/R/get_outputs.R | 91 +- bayesPop-6.0-0/bayesPop/R/plot_functions.R | 6 bayesPop-6.0-0/bayesPop/R/predict.pop.R | 382 +++++++- bayesPop-6.0-0/bayesPop/data/vwBaseYear2015.R |only bayesPop-6.0-0/bayesPop/data/vwBaseYear2015.txt |only bayesPop-6.0-0/bayesPop/inst/ex-data/Pop/predictions/prediction.rda |binary bayesPop-6.0-0/bayesPop/inst/ex-data/Pop/predictions/totpop_country218.rda |binary bayesPop-6.0-0/bayesPop/inst/ex-data/Pop/predictions/totpop_country528.rda |binary bayesPop-6.0-0/bayesPop/man/LifeTableMx.Rd | 28 bayesPop-6.0-0/bayesPop/man/age.specific.migration.Rd |only bayesPop-6.0-0/bayesPop/man/bayesPop-package.Rd | 6 bayesPop-6.0-0/bayesPop/man/expressions.Rd | 19 bayesPop-6.0-0/bayesPop/man/get.pop.Rd | 48 - bayesPop-6.0-0/bayesPop/man/pop.aggregate.Rd | 9 bayesPop-6.0-0/bayesPop/man/pop.map.Rd | 5 bayesPop-6.0-0/bayesPop/man/predict.pop.Rd | 35 bayesPop-6.0-0/bayesPop/man/specific_expressions.Rd | 4 bayesPop-6.0-0/bayesPop/man/vwBaseYear.Rd | 22 bayesPop-6.0-0/bayesPop/src/projection_functions.c | 449 +++++++--- bayesPop-6.0-0/bayesPop/tests/run_tests.R | 3 bayesPop-6.0-0/bayesPop/tests/test_functions.R | 72 + 29 files changed, 965 insertions(+), 323 deletions(-)
Title: Evaluate Treatment Selection Biomarkers
Description: Evaluate the performance of markers used to guide treatment selection decisions. Package includes functions to plot risk curves, evaluate marker performance, assess model calibration, and compare markers.
Author: Marshall Brown and Holly Janes
Maintainer: Marshall Brown <mdbrown@fhcrc.org>
Diff between TreatmentSelection versions 1.1.2 dated 2014-06-16 and 1.2.0 dated 2016-01-15
TreatmentSelection-1.1.2/TreatmentSelection/inst/example/tutorial_files |only TreatmentSelection-1.2.0/TreatmentSelection/DESCRIPTION | 10 TreatmentSelection-1.2.0/TreatmentSelection/MD5 | 45 - TreatmentSelection-1.2.0/TreatmentSelection/NAMESPACE | 16 TreatmentSelection-1.2.0/TreatmentSelection/NEWS | 4 TreatmentSelection-1.2.0/TreatmentSelection/R/calibrate.trtsel.R | 2 TreatmentSelection-1.2.0/TreatmentSelection/R/compare.trtsel.R | 2 TreatmentSelection-1.2.0/TreatmentSelection/R/eval.trtsel.R | 5 TreatmentSelection-1.2.0/TreatmentSelection/R/get.plot.ci.R | 2 TreatmentSelection-1.2.0/TreatmentSelection/R/get.plot.ci_disc.R | 2 TreatmentSelection-1.2.0/TreatmentSelection/R/get.summary.measures.case.control.R | 6 TreatmentSelection-1.2.0/TreatmentSelection/R/get.summary.measures.stratified.case.control.R | 12 TreatmentSelection-1.2.0/TreatmentSelection/R/myplotcompare.trtsel_disc.R | 13 TreatmentSelection-1.2.0/TreatmentSelection/R/plot.trtsel.R | 6 TreatmentSelection-1.2.0/TreatmentSelection/R/predcurvePLOT_gg.R | 4 TreatmentSelection-1.2.0/TreatmentSelection/R/trteffectPLOT_gg_disc.R | 18 TreatmentSelection-1.2.0/TreatmentSelection/R/trteffectPLOTcompare_gg_disc.R | 33 TreatmentSelection-1.2.0/TreatmentSelection/README.md | 2 TreatmentSelection-1.2.0/TreatmentSelection/inst/example/checkSubCohortEstimation.R |only TreatmentSelection-1.2.0/TreatmentSelection/inst/example/tutorial.Rmd | 6 TreatmentSelection-1.2.0/TreatmentSelection/inst/example/tutorial.html | 367 +++++----- TreatmentSelection-1.2.0/TreatmentSelection/man/TreatmentSelection-package.Rd | 4 TreatmentSelection-1.2.0/TreatmentSelection/man/plot.trtsel.Rd | 5 23 files changed, 331 insertions(+), 233 deletions(-)
More information about TreatmentSelection at CRAN
Permanent link
Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology, used to identify distinct perspectives existing within a group.
This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see http://qmethod.org).
A single function runs the full analysis. Each step can be run separately using the corresponding functions: for automatic flagging of Q-sorts (manual flagging is optional), for statement scores, for distinguishing and consensus statements, and for general characteristics of the factors.
Additional functions are available to import and export data, to print and plot, to import raw data from individual *.CSV files, and to make printable cards.
The package also offers functions to print Q cards and to generate Q distributions for study administration.
The package uses principal components and it allows manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
See further details in the package documentation, and in the web pages below, which include a cookbook, guidelines for more advanced analysis (how to perform manual flagging or change the sign of factors), data management, and a beta graphical user interface for online and offline use.
Author: Aiora Zabala [aut, cre] (Main author),
Maximilian Held [aut] (Author of additional data management functions)
Maintainer: Aiora Zabala <aiora.zabala@gmail.com>
Diff between qmethod versions 1.3.1 dated 2015-05-05 and 1.4.0 dated 2016-01-15
DESCRIPTION | 15 +++++++++------ MD5 | 40 ++++++++++++++++++++++++++++++---------- NAMESPACE | 19 +++++++++++++++++-- R/export.pqmethod.R |only R/loa.and.flags.R |only R/make.distribution.R |only R/qbstep.R |only R/qdc.R | 2 +- R/qfcharact.R | 6 +++--- R/qflag.R | 3 ++- R/qfsi.R |only R/qindtest.R |only R/qmb.plot.R |only R/qmb.summary.R |only R/qmboots.R |only R/qmethod.R | 5 ++--- R/qpcrustes.R |only R/qzscores.R | 16 ++++++++-------- man/export.pqmethod.Rd |only man/loa.and.flags.Rd |only man/make.distribution.Rd |only man/qbstep.Rd |only man/qfsi.Rd |only man/qindtest.Rd |only man/qmb.plot.Rd |only man/qmb.summary.Rd |only man/qmboots.Rd |only man/qmethod-package.Rd | 6 ++---- man/qmethod.Rd | 6 ++++-- man/qpcrustes.Rd |only man/qzscores.Rd | 2 +- 31 files changed, 79 insertions(+), 41 deletions(-)
Title: Probability and Statistics with R, Second Edition
Description: Functions and data sets for the text Probability and Statistics
with R, Second Edition.
Author: Alan T. Arnholt
Maintainer: Alan T. Arnholt <arnholtat@appstate.edu>
Diff between PASWR2 versions 1.0 dated 2014-11-21 and 1.0.2 dated 2016-01-15
DESCRIPTION | 15 - MD5 | 218 +++++++++--------- NAMESPACE | 46 +++ R/AgainStart.R | 43 +-- R/binogen.R | 74 +++--- R/checkingplots.R | 6 R/cisim.R | 2 R/ntester.R | 110 ++++----- R/srs.R | 62 ++--- R/wilcoxeTEST.R | 594 +++++++++++++++++++++++++------------------------- README.md | 39 ++- man/AGGRESSION.Rd | 13 - man/APPLE.Rd | 9 man/APTSIZE.Rd | 19 - man/BABERUTH.Rd | 33 +- man/BAC.Rd | 23 + man/BATTERY.Rd | 9 man/BIOMASS.Rd | 13 - man/BODYFAT.Rd | 21 - man/CALCULUS.Rd | 9 man/CARS2004.Rd | 7 man/CHIPS.Rd | 11 man/CIRCUIT.Rd | 19 - man/COSAMA.Rd | 15 - man/COWS.Rd | 11 man/DEPEND.Rd | 9 man/DROSOPHILA.Rd | 17 - man/ENGINEER.Rd | 13 - man/EPIDURAL.Rd | 7 man/EPIDURALF.Rd | 7 man/EURD.Rd | 5 man/FAGUS.Rd | 7 man/FCD.Rd | 5 man/FERTILIZE.Rd | 5 man/FOOD.Rd | 5 man/FORMULA1.Rd | 15 - man/GD.Rd | 9 man/GLUCOSE.Rd | 5 man/GRADES.Rd | 5 man/GROCERY.Rd | 13 - man/HARDWATER.Rd | 9 man/HOUSE.Rd | 5 man/HSWRESTLER.Rd | 10 man/HUBBLE.Rd | 9 man/INSURQUOTES.Rd | 7 man/JANKA.Rd | 5 man/KINDER.Rd | 9 man/LEDDIODE.Rd | 5 man/LOSTR.Rd | 9 man/MILKCARTON.Rd | 9 man/NC2010DMG.Rd | 9 man/PAMTEMP.Rd | 15 - man/PASWR2-package.Rd | 3 man/PHENYL.Rd | 7 man/PHONE.Rd | 7 man/RAT.Rd | 5 man/RATBP.Rd | 11 man/REFRIGERATOR.Rd | 9 man/ROACHEGGS.Rd | 9 man/SALINITY.Rd | 5 man/SATFRUIT.Rd | 7 man/SBIQ.Rd | 5 man/SCHIZO.Rd | 5 man/SCORE.Rd | 5 man/SDS4.Rd | 11 man/SIGN.test.Rd | 14 - man/SIMDATAST.Rd | 5 man/SIMDATAXT.Rd | 5 man/SOCCER.Rd | 5 man/STATTEMPS.Rd | 7 man/STSCHOOL.Rd | 5 man/SUNDIG.Rd | 5 man/SUNFLOWER.Rd | 9 man/SURFACESPAIN.Rd | 11 man/SWIMTIMES.Rd | 7 man/TENNIS.Rd | 5 man/TESTSCORES.Rd | 7 man/TIRE.Rd | 13 - man/TIREWEAR.Rd | 15 - man/TITANIC3.Rd | 9 man/TOE.Rd | 7 man/TOP20.Rd | 11 man/URLADDRESS.Rd | 13 - man/VIT2005.Rd | 9 man/WAIT.Rd | 5 man/WASHER.Rd | 5 man/WATER.Rd | 7 man/WCST.Rd | 7 man/WEIGHTGAIN.Rd | 9 man/WHEATSPAIN.Rd | 13 - man/WHEATUSA2004.Rd | 11 man/WOOL.Rd | 7 man/bino.gen.Rd | 6 man/checking.plots.Rd | 23 + man/cisim.Rd | 10 man/eda.Rd | 4 man/interval.plot.Rd | 4 man/ksdist.Rd | 3 man/ksldist.Rd | 3 man/multiplot.Rd | 4 man/normarea.Rd | 6 man/nsize.Rd | 8 man/ntester.Rd | 14 - man/oneway.plots.Rd | 8 man/srs.Rd | 7 man/tsum.test.Rd | 21 + man/twoway.plots.Rd | 9 man/wilcoxe.test.Rd | 15 - man/z.test.Rd | 42 +-- man/zsum.test.Rd | 49 ++-- 110 files changed, 1189 insertions(+), 1011 deletions(-)
Title: Hypothesis Testing and Power Calculations for Comparing
Metagenomic Samples from HMP
Description: Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.
Author: Patricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between HMP versions 1.3.1 dated 2013-05-08 and 1.4.2 dated 2016-01-15
DESCRIPTION | 24 +++------ MD5 | 109 +++++++++++++++++++++-------------------- NAMESPACE | 5 + NEWS | 18 ++++++ R/Barchart.data.R | 4 - R/C.alpha.multinomial.R | 5 - R/DM.MoM.R | 6 +- R/Data.filter.R | 9 +-- R/Dirichlet.multinomial.R | 7 +- R/LLDM.R |only R/MC.Xdc.statistics.R | 21 +++---- R/MC.Xmc.statistics.R | 21 +++---- R/MC.Xmcupo.statistics.R | 27 ++++------ R/MC.Xoc.statistics.R | 21 +++---- R/MC.Xsc.statistics.R | 12 +--- R/MC.ZT.statistics.R | 23 +++----- R/Multinomial.R | 7 +- R/T.statistics.R | 4 - R/Xdc.statistics.Hnull.Ha.R | 7 +- R/Xdc.statistics.MoM.R | 7 -- R/Xdc.statistics.R | 4 - R/Xmc.sevsample.R | 18 +++--- R/Xmc.statistics.Hnull.Ha.R | 11 +--- R/Xmc.statistics.R | 24 ++++----- R/Xmcupo.effectsize.R | 2 R/Xmcupo.sevsample.R | 39 +++++++------- R/Xmcupo.statistics.Hnull.Ha.R | 13 ++-- R/Xmcupo.statistics.R | 24 +++------ R/Xoc.statistics.Hnull.Ha.R | 9 +-- R/Xoc.statistics.MoM.R | 9 +-- R/Xoc.statistics.R | 4 - R/Xsc.onesample.R | 2 R/Xsc.statistics.R | 7 +- R/Z.statistics.R | 2 R/formatDataSets.R |only R/kullbackLeiber.R |only R/loglikDM.R | 11 ---- R/pioest.R | 2 R/weirMoM.R | 20 ++----- man/C.alpha.multinomial.Rd | 6 -- man/Data.filter.Rd | 3 - man/Dirichlet.multinomial.Rd | 2 man/HMP-internal.Rd | 1 man/HMP-package.Rd | 3 - man/MC.Xdc.statistics.Rd | 17 +++--- man/MC.Xmc.statistics.Rd | 10 ++- man/MC.Xmcupo.statistics.Rd | 14 ++--- man/MC.Xoc.statistics.Rd | 17 +++--- man/MC.Xsc.statistics.Rd | 12 ++-- man/Xdc.sevsample.Rd | 7 -- man/Xmc.sevsample.Rd | 8 --- man/Xmcupo.effectsize.Rd | 5 + man/Xmcupo.sevsample.Rd | 11 ---- man/Xoc.sevsample.Rd | 6 -- man/Xsc.onesample.Rd | 6 -- man/formatDataSets.Rd |only man/kullbackLeiber.Rd |only man/pioest.Rd | 5 + 58 files changed, 312 insertions(+), 359 deletions(-)
Title: Binary Graph Analysis Tools
Description: Tools to analyze binary graph objects.
Author: Terrence Brooks, Berkley Shands, Skye Buckner-Petty, Patricio S. La Rosa, Elena Deych, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between bingat versions 1.1 dated 2014-06-24 and 1.2.2 dated 2016-01-15
DESCRIPTION | 17 +++++----- MD5 | 68 ++++++++++++++++++++++++------------------ NAMESPACE | 6 ++- NEWS | 24 ++++++++++++++ R/estGStar.R | 4 +- R/estLogLik.R | 2 - R/estMLE.R | 4 +- R/full2lt.R | 2 - R/gaConsensus.R |only R/getGibbsMixture.R | 8 ++-- R/getLoglikeMixture.R | 8 +++- R/glmReg.R | 11 ++---- R/glrtPvalue.R | 76 +++++++++++++++++++++++------------------------ R/glrtReg.R | 6 +-- R/graphNetworkPlot.R | 6 +-- R/lrtPvalue.R |only R/pairedPvalue.R |only R/plotHeatmap.R |only R/plotMDS.R |only R/testGoF.R | 23 +++++++++----- man/BinGAT-package.Rd | 19 +++++++++-- man/braingraphs.Rd | 4 +- man/calcDistance.Rd | 2 - man/estGStar.Rd | 5 +-- man/estLogLik.Rd | 6 +-- man/estMLE.Rd | 7 +--- man/estTau.Rd | 6 +-- man/gaConsensus.Rd |only man/getGibbsMixture.Rd | 13 ++++---- man/getLoglikeMixture.Rd | 5 +-- man/getNumEdges.Rd | 2 - man/getNumNodes.Rd | 4 +- man/glrtPvalue.Rd | 30 ++++++------------ man/graphNetworkPlot.Rd | 2 - man/lrtPvalue.Rd |only man/pairedPvalue.Rd |only man/plotHeatmap.Rd |only man/plotMDS.Rd |only man/rGibbs.Rd | 4 +- man/testGoF.Rd | 13 ++++---- 40 files changed, 218 insertions(+), 169 deletions(-)
Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes. Now extended to include multivariate and unsupervised forests.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.0.5 dated 2015-12-24 and 2.0.7 dated 2016-01-15
DESCRIPTION | 8 - MD5 | 60 ++++---- R/data.utilities.R | 6 R/factor.utilities.R | 2 R/find.interaction.R | 2 R/generic.impute.rfsrc.R | 2 R/generic.predict.rfsrc.R | 314 +++++++++++++++++++++++----------------------- R/impute.rfsrc.R | 2 R/max.subtree.R | 2 R/plot.competing.risk.R | 2 R/plot.rfsrc.R | 2 R/plot.survival.R | 2 R/plot.variable.R | 2 R/predict.rfsrc.R | 2 R/print.rfsrc.R | 2 R/rf2rfz.R | 2 R/rfsrc.R | 268 +++++++++++++++++++-------------------- R/rfsrc.news.R | 2 R/rfsrcSyn.R | 2 R/stat.split.R | 2 R/utilities.R | 2 R/var.select.R | 2 R/vimp.R | 2 R/zzz.R | 2 configure.ac | 2 inst/NEWS | 20 +- inst/doc/rsf-Rnews.pdf |binary man/predict.rfsrc.Rd | 2 man/rfsrc.Rd | 57 +++++--- src/randomForestSRC.c | 143 ++++++++++++-------- src/randomForestSRC.h | 10 - 31 files changed, 484 insertions(+), 444 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Sustainable Transport Planning
Description: Functionality and data access tools for transport planning,
including origin-destination analysis, route allocation and modelling travel
patterns.
Author: Robin Lovelace [aut, cre],
Richard Ellison [aut],
Barry Rowlingson [aut] (Author of overline),
Nick Bearman [aut] (Co-author of gclip)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.0.2 dated 2015-11-02 and 0.1.0 dated 2016-01-15
stplanr-0.0.2/stplanr/R/distance-decay-functions.R |only stplanr-0.0.2/stplanr/R/recat-NTS.R |only stplanr-0.0.2/stplanr/inst/doc/cycling-routing-stplanr.R |only stplanr-0.0.2/stplanr/inst/doc/cycling-routing-stplanr.Rmd |only stplanr-0.0.2/stplanr/inst/doc/cycling-routing-stplanr.html |only stplanr-0.0.2/stplanr/inst/doc/flow-data-with-R.R |only stplanr-0.0.2/stplanr/inst/doc/flow-data-with-R.Rmd |only stplanr-0.0.2/stplanr/inst/doc/flow-data-with-R.html |only stplanr-0.0.2/stplanr/man/age_recat.Rd |only stplanr-0.0.2/stplanr/man/dd_logcub.Rd |only stplanr-0.0.2/stplanr/man/dd_loglin.Rd |only stplanr-0.0.2/stplanr/man/dd_logsqrt.Rd |only stplanr-0.0.2/stplanr/vignettes/cycling-routing-stplanr.Rmd |only stplanr-0.0.2/stplanr/vignettes/flow-data-with-R.Rmd |only stplanr-0.1.0/stplanr/DESCRIPTION | 29 + stplanr-0.1.0/stplanr/LICENSE | 4 stplanr-0.1.0/stplanr/MD5 | 151 +++++----- stplanr-0.1.0/stplanr/NAMESPACE | 68 +++- stplanr-0.1.0/stplanr/NEWS |only stplanr-0.1.0/stplanr/R/RcppExports.R |only stplanr-0.1.0/stplanr/R/SpatialLinesNetwork.R |only stplanr-0.1.0/stplanr/R/catchmentArea.R | 146 +++++++++ stplanr-0.1.0/stplanr/R/crs-funs.R |only stplanr-0.1.0/stplanr/R/data.r | 44 ++ stplanr-0.1.0/stplanr/R/geo-functions.R | 75 ++++ stplanr-0.1.0/stplanr/R/gps.R | 31 -- stplanr-0.1.0/stplanr/R/gtfs.R |only stplanr-0.1.0/stplanr/R/load-stats19.R |only stplanr-0.1.0/stplanr/R/loadABS.R | 22 + stplanr-0.1.0/stplanr/R/od-funs.R | 68 +++- stplanr-0.1.0/stplanr/R/osrmfunctions.R |only stplanr-0.1.0/stplanr/R/overline.R | 1 stplanr-0.1.0/stplanr/R/routes.R | 56 ++- stplanr-0.1.0/stplanr/R/stplanr-package.R | 19 + stplanr-0.1.0/stplanr/R/toptail.R |only stplanr-0.1.0/stplanr/README.md | 96 ++---- stplanr-0.1.0/stplanr/build/vignette.rds |binary stplanr-0.1.0/stplanr/data/cents.rda |binary stplanr-0.1.0/stplanr/data/zones.rda |only stplanr-0.1.0/stplanr/inst/doc/introducing-stplanr.R | 6 stplanr-0.1.0/stplanr/inst/doc/introducing-stplanr.Rmd | 12 stplanr-0.1.0/stplanr/inst/doc/introducing-stplanr.html | 135 +++----- stplanr-0.1.0/stplanr/inst/extdata/beartransit-ca-us.zip |only stplanr-0.1.0/stplanr/inst/extdata/sydroads.zip |only stplanr-0.1.0/stplanr/man/SpatialLinesNetwork-class.Rd |only stplanr-0.1.0/stplanr/man/SpatialLinesNetwork.Rd |only stplanr-0.1.0/stplanr/man/bbox_scale.Rd | 2 stplanr-0.1.0/stplanr/man/buff_geo.Rd |only stplanr-0.1.0/stplanr/man/calc_catchment.Rd | 2 stplanr-0.1.0/stplanr/man/calc_catchment_sum.Rd | 2 stplanr-0.1.0/stplanr/man/calc_moving_catchment.Rd | 2 stplanr-0.1.0/stplanr/man/calc_network_catchment.Rd |only stplanr-0.1.0/stplanr/man/cents.Rd | 13 stplanr-0.1.0/stplanr/man/crs_select_aeq.Rd |only stplanr-0.1.0/stplanr/man/cyclestreet_pat.Rd | 2 stplanr-0.1.0/stplanr/man/decode_gl.Rd |only stplanr-0.1.0/stplanr/man/dl_stats19.Rd |only stplanr-0.1.0/stplanr/man/find_network_nodes.Rd |only stplanr-0.1.0/stplanr/man/flow.Rd | 5 stplanr-0.1.0/stplanr/man/flowlines.Rd | 2 stplanr-0.1.0/stplanr/man/format_stats19_ac.Rd |only stplanr-0.1.0/stplanr/man/format_stats19_ca.Rd |only stplanr-0.1.0/stplanr/man/format_stats19_ve.Rd |only stplanr-0.1.0/stplanr/man/gclip.Rd | 2 stplanr-0.1.0/stplanr/man/graphhopper_pat.Rd | 2 stplanr-0.1.0/stplanr/man/gsection.Rd | 2 stplanr-0.1.0/stplanr/man/gtfs2sldf.Rd |only stplanr-0.1.0/stplanr/man/islines.Rd | 2 stplanr-0.1.0/stplanr/man/line2df.Rd | 4 stplanr-0.1.0/stplanr/man/line2points.Rd |only stplanr-0.1.0/stplanr/man/line2route.Rd | 3 stplanr-0.1.0/stplanr/man/lineLabels.Rd | 2 stplanr-0.1.0/stplanr/man/locate2spdf.Rd |only stplanr-0.1.0/stplanr/man/mapshape.Rd | 55 ++- stplanr-0.1.0/stplanr/man/mapshape_available.Rd |only stplanr-0.1.0/stplanr/man/nearest2spdf.Rd |only stplanr-0.1.0/stplanr/man/od2line.Rd | 2 stplanr-0.1.0/stplanr/man/onewaygeo.Rd | 2 stplanr-0.1.0/stplanr/man/onewayid.Rd | 2 stplanr-0.1.0/stplanr/man/overline.Rd | 2 stplanr-0.1.0/stplanr/man/plot-SpatialLinesNetwork-ANY-method.Rd |only stplanr-0.1.0/stplanr/man/read_stats19_ac.Rd |only stplanr-0.1.0/stplanr/man/read_stats19_ca.Rd |only stplanr-0.1.0/stplanr/man/read_stats19_ve.Rd |only stplanr-0.1.0/stplanr/man/read_table_builder.Rd | 2 stplanr-0.1.0/stplanr/man/route_cyclestreet.Rd | 12 stplanr-0.1.0/stplanr/man/route_graphhopper.Rd | 13 stplanr-0.1.0/stplanr/man/routes_fast.Rd | 2 stplanr-0.1.0/stplanr/man/routes_slow.Rd | 7 stplanr-0.1.0/stplanr/man/stplanr-package.Rd | 2 stplanr-0.1.0/stplanr/man/sum_network_routes.Rd |only stplanr-0.1.0/stplanr/man/summary-SpatialLinesNetwork-method.Rd |only stplanr-0.1.0/stplanr/man/table2matrix.Rd |only stplanr-0.1.0/stplanr/man/toptail.Rd |only stplanr-0.1.0/stplanr/man/toptail_buff.Rd |only stplanr-0.1.0/stplanr/man/toptailgs.Rd |only stplanr-0.1.0/stplanr/man/viaroute.Rd |only stplanr-0.1.0/stplanr/man/viaroute2sldf.Rd |only stplanr-0.1.0/stplanr/man/weightfield.Rd |only stplanr-0.1.0/stplanr/man/writeGeoJSON.Rd | 2 stplanr-0.1.0/stplanr/man/zones.Rd |only stplanr-0.1.0/stplanr/src |only stplanr-0.1.0/stplanr/tests/testthat/test-od2line.R | 2 stplanr-0.1.0/stplanr/vignettes/introducing-stplanr.Rmd | 12 104 files changed, 722 insertions(+), 405 deletions(-)
Title: A Social Media Search and Analytic Tool
Description: Social media search and analytic tool that takes one or multiple URL(s) and returns the information about the popularity and reach of the URL(s) on social media. The function get_socialmedia() retrieves the number of shares, likes, pins, and hits on Facebook (www.facebook.com), Pinterest (www.pinterest.com), StumbleUpon (www.stumbleupon.com), LinkedIn (www.linkedin.com), and Reddit (www.reddit.com). The package also includes dedicated functions for each social network platform and a function to resolve shortened URLs.
Author: Marco Toledo Bastos
Maintainer: Marco Toledo Bastos <marco@toledobastos.com>
Diff between SocialMediaMineR versions 0.1 dated 2014-06-25 and 0.2 dated 2016-01-15
SocialMediaMineR-0.1/SocialMediaMineR/R/get_twitter.R |only SocialMediaMineR-0.1/SocialMediaMineR/man/get_twitter.Rd |only SocialMediaMineR-0.2/SocialMediaMineR/ChangeLog | 5 + SocialMediaMineR-0.2/SocialMediaMineR/DESCRIPTION | 12 +-- SocialMediaMineR-0.2/SocialMediaMineR/MD5 | 38 ++++------ SocialMediaMineR-0.2/SocialMediaMineR/NAMESPACE | 4 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_facebook.R | 6 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_linkedin.R | 8 +- SocialMediaMineR-0.2/SocialMediaMineR/R/get_pinterest.R | 6 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_reddit.R | 6 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_socialmedia.R | 21 ++--- SocialMediaMineR-0.2/SocialMediaMineR/R/get_stumbleupon.R | 6 - SocialMediaMineR-0.2/SocialMediaMineR/R/get_url.R | 2 SocialMediaMineR-0.2/SocialMediaMineR/man/SocialMediaMineR-package.Rd | 7 - SocialMediaMineR-0.2/SocialMediaMineR/man/get_facebook.Rd | 4 - SocialMediaMineR-0.2/SocialMediaMineR/man/get_linkedin.Rd | 2 SocialMediaMineR-0.2/SocialMediaMineR/man/get_pinterest.Rd | 4 - SocialMediaMineR-0.2/SocialMediaMineR/man/get_reddit.Rd | 2 SocialMediaMineR-0.2/SocialMediaMineR/man/get_socialmedia.Rd | 9 +- SocialMediaMineR-0.2/SocialMediaMineR/man/get_stumbleupon.Rd | 2 SocialMediaMineR-0.2/SocialMediaMineR/man/get_url.Rd | 4 - 21 files changed, 71 insertions(+), 77 deletions(-)
More information about SocialMediaMineR at CRAN
Permanent link
Title: Relative Survival
Description: Various functions for relative survival analysis.
Author: Maja Pohar Perme [aut, cre], Klemen Pavlic [ctb]
Maintainer: Maja Pohar Perme <maja.pohar@mf.uni-lj.si>
Diff between relsurv versions 2.0-6 dated 2015-08-14 and 2.0-7 dated 2016-01-15
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++----- NAMESPACE | 15 ++++++++------- R/Rcode.r | 8 ++++---- R/rsdiff.r | 28 ++++++++++++++-------------- R/slopop1930_2014.r |only inst |only man/rsdiff.Rd |only man/rssurv.Rd | 2 +- 9 files changed, 39 insertions(+), 35 deletions(-)
Title: Phylogenetics for the Environmental Sciences
Description: Eco-phylogenetic and community phylogenetic analyses.
Keeps community ecological and phylogenetic data matched up and
comparable using 'comparative.comm' objects. Wrappers for common
community phylogenetic indices ('pez.shape', 'pez.evenness',
'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation
of Cavender-Bares (2004) correlation of phylogenetic and
ecological matrices ('fingerprint.regression'). Phylogenetic
Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives &
Helmus (2011) and Rafferty & Ives (2013). Simulation of null
assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').
Author: William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares,
Anthony R. Ives, Caroline Tucker, Steve C. Walker, Matthew R. Helmus
Maintainer: William D. Pearse <will.pearse@gmail.com>
Diff between pez versions 1.1-0 dated 2015-08-06 and 1.1-1 dated 2016-01-15
DESCRIPTION | 8 ++--- MD5 | 30 ++++++++++--------- NEWS | 10 ++++++ R/comparative.comm.R | 2 - R/eco.scape.R | 10 +++++- R/metrics.R | 13 +++++--- R/pglmm.R | 29 ++++++++++++++---- R/scape.R | 55 ++++++++++++++++++----------------- build/vignette.rds |binary inst/CITATION | 6 ++- inst/doc/pez-pglmm-overview.R |only inst/doc/pez-pglmm-overview.Rnw |only inst/doc/pez-pglmm-overview.pdf |only man/eco.scape.Rd | 6 +++ man/pez.metrics.Rd | 10 +++++- man/pglmm.Rd | 18 ++++++++--- man/scape.Rd | 61 +++++++++++++++------------------------ vignettes/pez-pglmm-overview.Rnw |only 18 files changed, 155 insertions(+), 103 deletions(-)
Title: Elastic Functional Data Analysis
Description: Functions to support functional data analysis using the square root velocity framework.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.5.1 dated 2015-11-16 and 1.6.0 dated 2016-01-15
DESCRIPTION | 13 +-- MD5 | 78 ++++++++++++++++----- NAMESPACE | 17 ++++ NEWS | 8 +- R/align_fPCA.R | 6 - R/calc_shape_dist.R |only R/curve_functions.R |only R/curve_geodesic.R |only R/curve_karcher_cov.R |only R/curve_karcher_mean.R |only R/curve_pair_align.R |only R/curve_principal_directions.R |only R/curve_srvf_align.R |only R/curve_to_q.R |only R/f_to_srvf.R | 8 +- R/fdasrvf-package.r | 17 ++++ R/image_funcs.R |only R/optimum.reparam.R | 8 +- R/pair_align_image.R |only R/q_to_curve.R |only R/reparam_curve.R |only R/reparam_image.R |only R/resamplecurve.R |only R/sample_shapes.R |only R/srsf_to_f.R | 8 +- R/time_warping.R | 22 +++--- R/utility_functions.R | 136 +++++++++++++++++++++++++++++++++----- README.md | 4 + data/datalist |only data/mpeg7.RData |only man/align_fPCA.Rd | 6 + man/beta.Rd |only man/calc_shape_dist.Rd |only man/curve_geodesic.Rd |only man/curve_karcher_cov.Rd |only man/curve_karcher_mean.Rd |only man/curve_pair_align.Rd |only man/curve_principal_directions.Rd |only man/curve_srvf_align.Rd |only man/curve_to_q.Rd |only man/f_to_srvf.Rd | 8 +- man/fdasrvf.Rd | 2 man/optimum.reparam.Rd | 8 +- man/pair_align_image.Rd |only man/q_to_curve.Rd |only man/reparam_curve.Rd |only man/reparam_image.Rd |only man/resamplecurve.Rd |only man/sample_shapes.Rd |only man/srsf_to_f.Rd | 8 +- man/time_warping.Rd | 16 ++-- src/Makevars | 6 + src/Makevars.win | 13 ++- src/fdaqmap |only src/gropt/incl/def.h | 17 ---- 55 files changed, 292 insertions(+), 117 deletions(-)
More information about deconstructSigs at CRAN
Permanent link
Title: Actigraphy Data Analysis
Description: Functional linear modeling and analysis for actigraphy data.
Author: William Shannon, Tao Li, Hong Xian, Jia Wang, Elena Deych, Carlos Gonzalez
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between Actigraphy versions 1.2 dated 2012-10-30 and 1.3.2 dated 2016-01-15
DESCRIPTION | 23 +- MD5 | 66 +++--- NAMESPACE | 4 R/Ftest.R | 22 +- R/cat_flm_plot.R | 26 +- R/cont_flm_plot.R | 16 - R/fda.matchid.R | 24 +- R/fda.smoothdata.R | 5 R/flm_cate.R | 7 R/flm_ftest.R | 12 - build |only inst/doc/Categorical-FDA-Tutorial.R |only inst/doc/Categorical-FDA-Tutorial.Rnw | 89 ++++----- inst/doc/Categorical-FDA-Tutorial.pdf |binary inst/doc/Continuous-FDA-Tutorial.R |only inst/doc/Continuous-FDA-Tutorial.Rnw | 90 ++++----- inst/doc/Continuous-FDA-Tutorial.pdf |binary inst/doc/Figures-from-Referenced-Paper.R |only inst/doc/Figures-from-Referenced-Paper.Rnw | 273 +++++++++++++--------------- inst/doc/Figures-from-Referenced-Paper.pdf |binary man/Actigraphy-internal.Rd | 5 man/Actigraphy-package.Rd | 35 +-- man/act_29pt.Rd | 10 - man/act_8pt.Rd | 10 - man/cat_flm_plot.Rd | 69 +++---- man/clinic_29pt_ahi.Rd | 8 man/clinic_29pt_bmi.Rd | 8 man/clinic_8pt.Rd | 8 man/cont_flm_plot.Rd | 59 ++---- man/fda.matchid.Rd | 64 +++--- man/fda.smoothdata.Rd | 45 ++-- man/flm_cate.Rd | 36 +-- man/weekday.Rd | 10 - vignettes/Categorical-FDA-Tutorial.Rnw | 89 ++++----- vignettes/Continuous-FDA-Tutorial.Rnw | 90 ++++----- vignettes/Figures-from-Referenced-Paper.Rnw | 273 +++++++++++++--------------- 36 files changed, 741 insertions(+), 735 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains also functions scABEL.ad() and sampleN.scABEL.ad() to iteratively
adjust alpha in order to maintain the consumer risk in ABEL studies
and adapt the sample size for the loss in power.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate
power and sample size for the BE decision via the FDA procedure for
highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances)
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.3-02 dated 2015-12-02 and 1.3-3 dated 2016-01-15
DESCRIPTION | 11 +++++++---- MD5 | 23 ++++++++++++++--------- NAMESPACE | 10 ++++++---- NEWS | 10 ++++++++++ R/power_scABEL2.R |only R/sampleN.scABEL.ad.R |only R/samplesize_RSABE.R | 3 ++- R/samplesize_scABEL.R | 3 ++- R/scABEL.R | 26 ++++++++++++++++++++++++++ R/scABEL.ad.R |only man/sampleN.RSABE.Rd | 12 +++++++----- man/sampleN.scABEL.Rd | 12 +++++++----- man/sampleN.scABEL.ad.Rd |only man/scABEL.Rd | 4 ++-- man/scABEL.ad.Rd |only 15 files changed, 83 insertions(+), 31 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.1.0 dated 2015-11-13 and 1.1.1 dated 2016-01-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + R/statistics.R | 4 +++- man/PRESS.Rd | 3 +++ 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using gnm, with
support for convenient printing, plots, and jackknife/bootstrap
standard errors. For complex survey data, models can be fitted from
design objects from the 'survey' package. Currently supported models
include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative
layer effect model (Xie), and several association models: Goodman's
row-column association models of the RC(M) and RC(M)-L families
with one or several dimensions; two skew-symmetric association
models proposed by Yamaguchi and by van der Heijden & Mooijaart.
Author: Milan Bouchet-Valat [aut, cre],
Heather Turner [ctb]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between logmult versions 0.6.2 dated 2015-04-22 and 0.6.3 dated 2016-01-15
logmult-0.6.2/logmult/R/permn.R |only logmult-0.6.2/logmult/R/regtype.R |only logmult-0.6.2/logmult/tests/lambda.R.rkward_autosave |only logmult-0.6.3/logmult/DESCRIPTION | 21 - logmult-0.6.3/logmult/MD5 | 65 ++-- logmult-0.6.3/logmult/NAMESPACE | 18 + logmult-0.6.3/logmult/NEWS | 16 logmult-0.6.3/logmult/R/hmskew.R | 6 logmult-0.6.3/logmult/R/hmskewL.R | 20 - logmult-0.6.3/logmult/R/jackboot.R | 3 logmult-0.6.3/logmult/R/maor.R | 37 +- logmult-0.6.3/logmult/R/plot.assoc.R | 122 ++----- logmult-0.6.3/logmult/R/ras.R |only logmult-0.6.3/logmult/R/rc.R | 11 logmult-0.6.3/logmult/R/rcL.R | 12 logmult-0.6.3/logmult/R/rcL.trans.R | 8 logmult-0.6.3/logmult/R/summary.assoc.R | 5 logmult-0.6.3/logmult/R/svygnm.R |only logmult-0.6.3/logmult/R/tools.R | 12 logmult-0.6.3/logmult/R/unidiff.R | 7 logmult-0.6.3/logmult/R/yrcskew.R | 82 ++--- logmult-0.6.3/logmult/man/hmskewL.Rd | 6 logmult-0.6.3/logmult/man/maor.Rd | 11 logmult-0.6.3/logmult/man/plot.assoc.Rd | 19 - logmult-0.6.3/logmult/man/ras.Rd |only logmult-0.6.3/logmult/man/rcL.Rd | 2 logmult-0.6.3/logmult/man/summary.assoc.Rd | 4 logmult-0.6.3/logmult/man/summary.unidiff.Rd | 4 logmult-0.6.3/logmult/man/svygnm.Rd |only logmult-0.6.3/logmult/man/unidiff.Rd | 5 logmult-0.6.3/logmult/tests/Clogg-Shihadeh1994.R | 4 logmult-0.6.3/logmult/tests/Rplots.pdf |only logmult-0.6.3/logmult/tests/Wong2010-4.7.R | 4 logmult-0.6.3/logmult/tests/hmskewL.R | 9 logmult-0.6.3/logmult/tests/maor.R | 227 +++++++++++++- logmult-0.6.3/logmult/tests/ras.R |only logmult-0.6.3/logmult/tests/supplementary.R | 2 logmult-0.6.3/logmult/tests/vanderHeijden-Mooijaart1995.R | 5 38 files changed, 523 insertions(+), 224 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: We provide a set of functions to retrieve information about GIMMS NDVI3g files currently available online; download and re-arrange the bi-monthly datasets according to creation time; import downloaded files from native binary (ENVI) format directly into R based on the widely applied 'raster' package; extract accompanying quality flags and perform quality control; calculate monthly value composites (e.g. maximum value composites, MVC) from the bi-monthly input data; and derive long-term monotonous trends from the Mann-Kendall trend test, optionally featuring pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.4.0 dated 2015-12-18 and 0.5.0 dated 2016-01-15
DESCRIPTION | 17 +---- MD5 | 34 +++++----- NEWS | 10 +-- R/downloadGimms.R | 20 ++++-- R/gimmsControls.R | 17 +++++ R/monthlyComposite.R | 26 ++++--- R/monthlyIndices.R | 160 ++++++++++++++++++++++++------------------------ R/rasterizeGimms.R | 55 ++++++++++++---- R/rearrangeFiles.R | 17 ++--- R/significantTau.R | 9 +- R/updateInventory.R | 124 +++++++++++++++++++------------------ man/downloadGimms.Rd | 6 + man/monthlyComposite.Rd | 20 +++--- man/monthlyIndices.Rd | 6 - man/rasterizeGimms.Rd | 42 +++++++----- man/rearrangeFiles.Rd | 17 ++--- man/significantTau.Rd | 9 +- man/updateInventory.Rd | 22 +++--- 18 files changed, 341 insertions(+), 270 deletions(-)
Title: Models and Data Sets for the Study of Species-Area Relationships
Description: Hierarchical models for the analysis of species-area
relationships (SARs) by combining several data sets and covariates;
with a global data set combining individual SAR studies;
as described in Solymos and Lele
(2012, Global Ecology and Biogeography 21, 109-120).
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between sharx versions 1.0-4 dated 2014-05-19 and 1.0-5 dated 2016-01-15
DESCRIPTION | 19 +- MD5 | 20 +- NAMESPACE | 21 +- R/hsarx.R | 422 +++++++++++++++++++++++++-------------------------- R/sie.R | 101 ++++++------ inst/CITATION | 40 ++-- inst/ChangeLog | 39 ++-- man/hsarx.Rd | 164 +++++++++---------- man/sardata.Rd | 108 ++++++------- man/sharx-package.Rd | 50 +++--- man/sie.Rd | 136 ++++++++-------- 11 files changed, 564 insertions(+), 556 deletions(-)
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrmtools versions 0.0-3 dated 2015-11-10 and 0.0-4 dated 2016-01-15
qrmtools-0.0-3/qrmtools/data |only qrmtools-0.0-3/qrmtools/inst/doc/VaR_ES_estimators.R |only qrmtools-0.0-3/qrmtools/inst/doc/VaR_ES_estimators.Rmd |only qrmtools-0.0-3/qrmtools/inst/doc/VaR_ES_estimators.html |only qrmtools-0.0-3/qrmtools/man/SnP_500.Rd |only qrmtools-0.0-3/qrmtools/vignettes/VaR_ES_estimators.Rmd |only qrmtools-0.0-4/qrmtools/DESCRIPTION | 8 - qrmtools-0.0-4/qrmtools/MD5 | 32 +--- qrmtools-0.0-4/qrmtools/NAMESPACE | 12 + qrmtools-0.0-4/qrmtools/R/VaR_bounds.R | 87 ++++++----- qrmtools-0.0-4/qrmtools/R/zzz.R | 9 - qrmtools-0.0-4/qrmtools/build/vignette.rds |binary qrmtools-0.0-4/qrmtools/inst/doc/ARMA_GARCH_VaR.html | 20 +- qrmtools-0.0-4/qrmtools/inst/doc/VaR_bounds.R | 84 +++++++---- qrmtools-0.0-4/qrmtools/inst/doc/VaR_bounds.Rmd | 90 ++++++++---- qrmtools-0.0-4/qrmtools/inst/doc/VaR_bounds.html | 119 ++++++++++------ qrmtools-0.0-4/qrmtools/man/Black_Scholes.Rd | 4 qrmtools-0.0-4/qrmtools/man/VaR_bounds.Rd | 25 +-- qrmtools-0.0-4/qrmtools/src/VaR_bounds.c | 73 +++++---- qrmtools-0.0-4/qrmtools/vignettes/VaR_bounds.Rmd | 90 ++++++++---- 20 files changed, 407 insertions(+), 246 deletions(-)
Title: Modified Maximum Contrast Method
Description: An implementation of modified maximum contrast methods
and the maximum contrast method: Functions 'mmcm.mvt' and
'mcm.mvt' give P-value by using randomized quasi-Monte Carlo
method with 'pmvt' function of package 'mvtnorm', and
'mmcm.resamp' gives P-value by using a permutation method.
Author: Kengo NAGASHIMA and Yasunori SATO
Maintainer: Kengo NAGASHIMA <nshi@chiba-u.jp>
Diff between mmcm versions 1.2-5 dated 2014-09-10 and 1.2-6 dated 2016-01-15
DESCRIPTION | 18 +++++------ MD5 | 25 ++++++++-------- NAMESPACE | 3 + NEWS | 80 ++++++++++++++++++++-------------------------------- NEWS.md |only R/mcm.mvt.R | 1 R/mmcm.mvt.R | 1 R/mmcm.resamp.R | 14 +++++---- R/print.mmcm.R | 3 + man/mcm.mvt.Rd | 3 + man/mmcm-package.Rd | 3 + man/mmcm.mvt.Rd | 3 + man/mmcm.resamp.Rd | 5 +-- man/print.mmcm.Rd | 3 + 14 files changed, 79 insertions(+), 83 deletions(-)
Title: Latin Hypercube Samples
Description: Provides a number of methods for creating and augmenting Latin Hypercube Samples.
Author: Rob Carnell [aut, cre]
Maintainer: Rob Carnell <bertcarnell@gmail.com>
Diff between lhs versions 0.10 dated 2012-07-13 and 0.12 dated 2016-01-15
ChangeLog | 7 +++++++ DESCRIPTION | 23 ++++++++++++----------- MD5 | 21 ++++++++++++++++----- NAMESPACE | 2 ++ R/geneticLHS.R | 17 ++++++++++++----- build |only inst/doc/augmentLHS_Example.R |only inst/unitTests |only man/geneticLHS.Rd | 5 +++-- tests |only 10 files changed, 52 insertions(+), 23 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories, a method for
variable selection based on the SVD, Bézier lines with arrows complementing the
ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.1 dated 2015-03-04 and 1.3 dated 2016-01-15
DESCRIPTION | 23 - MD5 | 186 ++++++----- NAMESPACE | 23 + NEWS | 15 R/RcppExports.R | 138 ++++---- R/bezierArrowGradient.R | 1 R/bezierArrowSmpl.R | 1 R/bezier_private_functions.R | 42 +- R/descriptionStats.R | 2 R/docx_document.R |only R/figCaptionNo.R | 3 R/getDescriptionStatsBy.R | 59 ++- R/getPval.R | 7 R/getSvdMostInfluential.R | 2 R/mergeDesc.R | 1 R/private_functions.R | 4 R/transitionClass.R | 473 ++++++++++++++++++----------- R/transitionClass_helpers.R | 269 +++++++++++++--- R/transitionPlot.R | 1 R/transitionPlot_helpers.R | 2 build/vignette.rds |binary inst/doc/Descriptives.R | 6 inst/doc/Descriptives.html | 154 +++++---- inst/doc/Transition-class.R | 4 inst/doc/Transition-class.html | 92 +++-- inst/doc/transitionPlot.R | 8 inst/doc/transitionPlot.html | 113 +++--- inst/examples/transitionClass_example.R |only inst/extdata |only inst/rmarkdown |only man/Gmisc-deprecated.Rd | 8 man/Gmisc-package.Rd | 76 ++-- man/Transition-class.Rd | 42 ++ man/bezierArrowGradient.Rd | 101 +++--- man/bezierArrowSmpl.Rd | 79 ++-- man/calculateLinesAndArrow.Rd | 54 +-- man/copyAllNewAttributes.Rd | 21 - man/describeFactors.Rd | 93 ++--- man/describeMean.Rd | 87 ++--- man/describeMedian.Rd | 70 +--- man/describeProp.Rd | 80 ++-- man/docx_document.Rd |only man/fastDoCall.Rd | 47 +- man/figCapNo.Rd | 35 -- man/figCapNoLast.Rd | 15 man/figCapNoNext.Rd | 15 man/getAbsoluteWidth.Rd | 33 -- man/getBezierAdj4Arrw.Rd | 13 man/getDescriptionStatsBy.Rd | 241 ++++++-------- man/getGridVal.Rd | 14 man/getPval.Rd | 53 +-- man/getSvdMostInfluential.Rd | 77 ++-- man/getVectorAngle.Rd | 10 man/gnrlBezierPoints.Rd | 15 man/htmlTable_latex.Rd | 13 man/insertRowAndKeepAttr.Rd | 18 - man/isHorizontal.Rd | 4 man/mergeDesc.Rd | 60 +-- man/mergeLists.Rd | 16 man/mergeLists_internal.Rd | 6 man/prCaptionFix.Rd |only man/prConvertShowMissing.Rd | 12 man/prDescGetAndValidateDefaultRef.Rd | 10 man/prDescGetMissing.Rd | 47 +- man/prFtpHeaderStyle.Rd |only man/prFtpOtherChanges.Rd |only man/prFtpOtherRemoval.Rd |only man/prFtpScriptRemoval.Rd |only man/prGetStatistics.Rd | 77 ++-- man/prGetTextGrobCex.Rd | 4 man/prGridPlotTitle.Rd | 21 - man/prPasteVec.Rd | 8 man/prPushMarginViewport.Rd | 18 - man/prSetMaxWidth.Rd |only man/prTcMatchClr.Rd |only man/prTcPlotArrows.Rd | 33 -- man/prTcPlotBoxColumn.Rd | 17 - man/prTcValidateAndPrepClr.Rd | 20 - man/prTpGetBoxPositions.Rd | 23 - man/prTpGetBoxPropClr.Rd | 14 man/prTpGetBoxSizedTextGrob.Rd | 12 man/prTpGetColors.Rd | 25 - man/prTpPlotArrows.Rd | 38 +- man/prTpPlotBox.Rd | 20 - man/prTpPlotBoxes.Rd | 206 +++++------- man/transitionPlot.Rd | 246 ++++++--------- man/validateAndConvertVectorInputs.Rd | 21 - src/Makevars.win | 2 src/RcppExports.cpp | 46 +- tests/testthat/Rplots.pdf |only tests/testthat/test-bezier.R | 100 ++++-- tests/testthat/test-docx_document.R |only tests/testthat/test-figCapNo.R | 22 - tests/testthat/test-fig_caption.R |only tests/testthat/test-getDescriptionStats.R | 76 +++- tests/testthat/test-transitionClass.R | 209 +++++------- tests/visual_tests/FTP_test |only tests/visual_tests/Full_test_suite.Rmd |only tests/visual_tests/Highlighting_test.Rmd |only tests/visual_tests/MathJax_test.Rmd |only tests/visual_tests/Max_width_test.Rmd |only tests/visual_tests/transitionClass_vtest.R |only 102 files changed, 2361 insertions(+), 1991 deletions(-)
Title: Convert Data from and to 'geoJSON' or 'topoJSON'
Description: Convert data to 'geoJSON' or 'topoJSON' from various R classes,
including vectors, lists, data frames, shape files, and spatial classes.
'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos', but
rather aims to be a high level client to simplify conversions of data from and
to 'geoJSON' and 'topoJSON'.
Author: Scott Chamberlain [aut, cre],
Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonio versions 0.1.4 dated 2015-08-12 and 0.1.6 dated 2016-01-15
DESCRIPTION | 23 +++--- LICENSE | 2 MD5 | 121 +++++++++++++++++--------------- NAMESPACE | 5 + NEWS | 20 +++++ R/as.json.R | 13 ++- R/as.location.R | 6 - R/construction.R | 4 - R/geojson_json.R | 2 R/geojson_list.R | 5 - R/geojson_sp.R |only R/geojsonio-package.R | 3 R/lint.R | 15 ++- R/mapgist.R | 48 ++++++------ R/mapleaflet.R | 6 - R/pipe.R |only R/startup.R |only R/validate.R | 4 - R/zzz.r | 24 ++---- README.md | 12 +-- build/vignette.rds |binary inst/doc/geojsonio_vignette.Rmd | 5 - inst/doc/geojsonio_vignette.html | 5 - inst/img/unnamed-chunk-18-1.png |binary inst/img/unnamed-chunk-20-1.png |binary inst/vign/figure/unnamed-chunk-17-1.png |binary inst/vign/geojsonio_vignette.Rmd | 3 inst/vign/geojsonio_vignette.md | 5 - man/as.json.Rd | 13 +++ man/as.location.Rd | 2 man/bounds.Rd | 4 - man/canada_cities.Rd | 10 +- man/centroid.Rd | 2 man/file_to_geojson.Rd | 8 +- man/geojson-add.Rd | 10 +- man/geojson_json.Rd | 7 + man/geojson_list.Rd | 2 man/geojson_read.Rd | 8 +- man/geojson_sp.Rd |only man/geojson_style.Rd | 32 ++++---- man/geojson_write.Rd | 4 - man/geojsonio.Rd | 20 ++--- man/lint.Rd | 7 + man/map_gist.Rd | 2 man/map_leaf.Rd | 2 man/pipe.Rd | 4 - man/pretty.Rd | 2 man/projections.Rd | 3 man/states.Rd | 4 - man/topojson_read.Rd | 4 - man/us_cities.Rd | 10 +- man/validate.Rd | 2 tests/testthat/test-as.json.R | 38 ++++++---- tests/testthat/test-as.location.R | 13 +++ tests/testthat/test-file_to_geojson.R | 87 ++++++++++++++--------- tests/testthat/test-geojson_sp.R |only tests/testthat/test-geojson_write.R | 38 ++++++---- tests/testthat/test-lint.R | 115 +++++++++++++++++++++++++++--- tests/testthat/test-map_gist.R | 8 +- tests/testthat/test-mapleaflet.R |only tests/testthat/test-onload.R | 11 ++ tests/testthat/test-pretty.R |only tests/testthat/test-spatial_methods.R |only tests/testthat/test-validate.R |only tests/testthat/us_cities.rds |only tests/testthat/us_citites_two_row.rds |only vignettes/geojsonio_vignette.Rmd | 5 - 67 files changed, 519 insertions(+), 289 deletions(-)
Title: An Interface to the DescribeDisplay GGobi Plugin
Description: Produce publication quality graphics from output of GGobi's
describe display plugin.
Author: Di Cook [aut, cre],
Hadley Wickham [aut],
Andreas Buja [aut],
Barret Schloerke [aut]
Maintainer: Di Cook <dicook@monash.edu>
Diff between DescribeDisplay versions 0.2.4 dated 2013-07-18 and 0.2.5 dated 2016-01-15
DescribeDisplay-0.2.4/DescribeDisplay/R/DescribeDisplay-package.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/axis-geom.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/axis-grob.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/data.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot-barchart.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot-parcoords.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot-scatmat.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot-timeseries.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/ggplot.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/plots.r |only DescribeDisplay-0.2.4/DescribeDisplay/R/utils.r |only DescribeDisplay-0.2.4/DescribeDisplay/ggobi-xml |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/barchart.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/histogram.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/parcoord.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/plot1d.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/scatmat.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/timeseries.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/tour1d.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/tour2d.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/tour2x1d.r |only DescribeDisplay-0.2.4/DescribeDisplay/inst/examples/xyplot.r |only DescribeDisplay-0.2.4/DescribeDisplay/load.r |only DescribeDisplay-0.2.4/DescribeDisplay/write-xml.rnw |only DescribeDisplay-0.2.5/DescribeDisplay/DESCRIPTION | 42 ++- DescribeDisplay-0.2.5/DescribeDisplay/LICENSE |only DescribeDisplay-0.2.5/DescribeDisplay/MD5 | 114 +++++----- DescribeDisplay-0.2.5/DescribeDisplay/NAMESPACE | 46 +++- DescribeDisplay-0.2.5/DescribeDisplay/NEWS | 12 + DescribeDisplay-0.2.5/DescribeDisplay/R/DescribeDisplay-package.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/axis-geom.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/axis-grob.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/data.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot-barchart.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot-parcoords.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot-scatmat.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot-timeseries.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/ggplot.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/plots.R |only DescribeDisplay-0.2.5/DescribeDisplay/R/utils.R |only DescribeDisplay-0.2.5/DescribeDisplay/README.md |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/barchart.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/histogram.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/parcoord.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/plot1d.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/scatmat.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/timeseries.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/tour1d.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/tour2d.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/tour2x1d.R |only DescribeDisplay-0.2.5/DescribeDisplay/inst/examples/xyplot.R |only DescribeDisplay-0.2.5/DescribeDisplay/man/addbrush.Rd | 31 +- DescribeDisplay-0.2.5/DescribeDisplay/man/axesGrob.Rd | 12 - DescribeDisplay-0.2.5/DescribeDisplay/man/axesViewport.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/compact_pcp.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/compact_scatmat.Rd | 12 - DescribeDisplay-0.2.5/DescribeDisplay/man/compact_timeseries.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_clean_plot.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_defaults.Rd | 13 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_edges.Rd | 15 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_example.Rd | 9 DescribeDisplay-0.2.5/DescribeDisplay/man/dd_load.Rd | 23 +- DescribeDisplay-0.2.5/DescribeDisplay/man/dd_plot_class.Rd | 11 DescribeDisplay-0.2.5/DescribeDisplay/man/dd_points.Rd | 15 - DescribeDisplay-0.2.5/DescribeDisplay/man/dd_tour_axes.Rd | 11 DescribeDisplay-0.2.5/DescribeDisplay/man/ddpanelGrob.Rd | 22 + DescribeDisplay-0.2.5/DescribeDisplay/man/describedisplayreshape.Rd | 9 DescribeDisplay-0.2.5/DescribeDisplay/man/geom_axis.Rd | 10 DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.barplot.Rd | 20 - DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.dd.Rd | 16 - DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.ddplot.Rd | 24 +- DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.histogram.Rd | 20 - DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.parcoords.Rd | 25 +- DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.scatmat.Rd | 21 - DescribeDisplay-0.2.5/DescribeDisplay/man/ggplot.timeseries.Rd | 20 - DescribeDisplay-0.2.5/DescribeDisplay/man/plot.dd.Rd | 44 +-- DescribeDisplay-0.2.5/DescribeDisplay/man/plot.ddplot.Rd | 26 +- DescribeDisplay-0.2.5/DescribeDisplay/man/range01.Rd | 11 DescribeDisplay-0.2.5/DescribeDisplay/man/removehiddens.Rd | 11 DescribeDisplay-0.2.5/DescribeDisplay/man/zeeThemAll.Rd | 8 DescribeDisplay-0.2.5/DescribeDisplay/tests |only 81 files changed, 406 insertions(+), 299 deletions(-)
More information about DescribeDisplay at CRAN
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Title: Community Dynamics Metrics
Description: A toolbox of ecological community dynamics metrics that are
explicitly temporal. Functions fall into two categories: temporal diversity
indices and community stability metrics. The diversity indices are temporal
analogs to traditional diversity indices such as richness and rank-abundance
curves. Specifically, functions are provided to calculate species turnover, mean
rank shifts, and lags in community similarity between time points. The community
stability metrics calculate overall stability and patterns of species covariance
and synchrony over time.
Author: Lauren Hallett [aut],
Sydney K. Jones [aut],
Andrew A. MacDonald [aut],
Dan F. B. Flynn [aut],
Peter Slaughter [aut],
Julie Ripplinger [aut],
Scott L. Collins [aut],
Corinna Gries [aut],
Matthew B. Jones [aut, cre]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between codyn versions 1.0.0 dated 2015-10-20 and 1.0.1 dated 2016-01-15
DESCRIPTION | 24 +++--- MD5 | 105 +++++++++++++++--------------- NAMESPACE | 2 NEWS | 10 ++ R/rank_shift.R | 1 R/rate_change.R | 2 R/synchrony.R | 4 - R/temporal_torus_translation.R | 2 R/turnover.R | 3 R/utilities.R | 29 +++++++- R/variance_ratio.R | 53 +++++++++++---- README.md | 3 build/vignette.rds |binary inst/CITATION |only inst/doc/Community_Stability_Metrics.html | 52 +++++++------- inst/doc/Temporal_Diversity_Indices.html | 28 ++------ inst/doc/codyn_overview.html | 4 - inst/tests/test_community_stability.R | 10 ++ inst/tests/test_rank_shift.R | 9 ++ inst/tests/test_rate_change.R | 22 ++++++ inst/tests/test_synchrony.R | 13 +++ inst/tests/test_turnover.R | 10 ++ inst/tests/test_utilities.R | 41 +++++++++-- inst/tests/test_variance_ratio.R | 24 ++++++ man/check_multispp.Rd |only man/check_names.Rd | 2 man/check_numeric.Rd | 2 man/check_single.Rd | 2 man/check_single_onerep.Rd | 2 man/check_sppvar.Rd |only man/codyn.Rd | 12 +-- man/collins08.Rd | 4 - man/community_stability.Rd | 4 - man/genRand.Rd | 2 man/get_lag_i.Rd | 2 man/get_lagged_distances.Rd | 4 - man/get_slope.Rd | 2 man/getintersect.Rd | 2 man/getturnover.Rd | 2 man/knz_001d.Rd | 6 - man/mean_rank_shift.Rd | 16 ++-- man/meanrank.Rd | 2 man/rate_change.Rd | 22 +++--- man/rate_change_interval.Rd | 14 ++-- man/stability_onerep.Rd | 2 man/synch_onerep.Rd | 4 - man/synchrony.Rd | 6 - man/temporal_torus_translation.Rd | 6 - man/temporal_torus_translation_CI.Rd | 6 - man/transpose_community.Rd | 2 man/turnover.Rd | 9 +- man/turnover_allyears.Rd | 2 man/variance_ratio.Rd | 66 ++++++++++++------ man/variance_ratio_longformdata.Rd | 2 man/variance_ratio_matrixdata.Rd | 2 55 files changed, 428 insertions(+), 232 deletions(-)
Title: API Client Library for 'Wikidata'
Description: An API client for the Wikidata <http://wikidata.org/> store of
semantic data.
Author: Oliver Keyes [aut, cre], Christian Graul [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between WikidataR versions 1.0.0 dated 2015-06-01 and 1.0.1 dated 2016-01-14
DESCRIPTION | 16 ++++++++++------ MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 2 +- NEWS | 3 +++ R/WikidataR.R | 3 +++ R/prints.R | 6 ++++++ R/utils.R | 6 +++--- README.md | 11 ++++++----- build/vignette.rds |binary inst/doc/Introduction.Rmd | 8 +++----- inst/doc/Introduction.html | 9 ++++----- man/WikidataR.Rd | 5 +++-- man/find_item.Rd | 4 +++- man/get_item.Rd | 4 +++- man/get_random.Rd | 4 +++- man/print.find_item.Rd | 4 ++-- man/print.find_property.Rd | 4 ++-- man/print.wikidata.Rd | 4 ++-- vignettes/Introduction.Rmd | 8 +++----- 19 files changed, 78 insertions(+), 59 deletions(-)
Title: Estimation of the Structural Topic Model
Description: The Structural Topic Model (STM) allows researchers
to estimate topic models with document-level covariates.
The package also includes tools for model selection, visualization,
and estimation of topic-covariate regressions.
Author: Margaret E. Roberts, Brandon M. Stewart and Dustin Tingley
Maintainer: Brandon Stewart <bms4@princeton.edu>
Diff between stm versions 1.1.0 dated 2015-07-27 and 1.1.3 dated 2016-01-14
stm-1.1.0/stm/vignettes/vignetteBib.bib |only stm-1.1.3/stm/DESCRIPTION | 8 stm-1.1.3/stm/LICENSE | 4 stm-1.1.3/stm/MD5 | 228 +- stm-1.1.3/stm/NAMESPACE | 93 stm-1.1.3/stm/R/RcppExports.R | 30 stm-1.1.3/stm/R/STMconvergence.R | 86 stm-1.1.3/stm/R/STMestep.R | 152 - stm-1.1.3/stm/R/STMfunctions.R | 348 +-- stm-1.1.3/stm/R/STMinit.R | 341 +-- stm-1.1.3/stm/R/STMlncpp.R | 32 stm-1.1.3/stm/R/STMmnreg.R | 292 +- stm-1.1.3/stm/R/STMmu.R | 194 - stm-1.1.3/stm/R/STMoptbeta.R | 28 stm-1.1.3/stm/R/STMreport.R | 114 - stm-1.1.3/stm/R/STMsigma.R | 30 stm-1.1.3/stm/R/checkBeta.R | 74 stm-1.1.3/stm/R/checkFactors.R | 174 - stm-1.1.3/stm/R/cloud.R | 104 - stm-1.1.3/stm/R/convertCorpus.R |only stm-1.1.3/stm/R/dmr.R | 404 +-- stm-1.1.3/stm/R/estimateEffect.R | 286 +- stm-1.1.3/stm/R/exclusivity.R | 38 stm-1.1.3/stm/R/findThoughts.R | 106 - stm-1.1.3/stm/R/findTopic.R | 36 stm-1.1.3/stm/R/heldout.R | 148 - stm-1.1.3/stm/R/jeffreyskappa.R | 324 +-- stm-1.1.3/stm/R/labelTopics.R | 220 +- stm-1.1.3/stm/R/manyTopics.R | 134 - stm-1.1.3/stm/R/multiSTM.R | 846 ++++---- stm-1.1.3/stm/R/parseFormulas.R | 88 stm-1.1.3/stm/R/permute.R | 192 - stm-1.1.3/stm/R/plot.STM.R | 496 ++-- stm-1.1.3/stm/R/plot.estimateEffect.R | 186 - stm-1.1.3/stm/R/plot.searchK.R | 54 stm-1.1.3/stm/R/plotModels.R | 38 stm-1.1.3/stm/R/plotQuote.R | 56 stm-1.1.3/stm/R/plotRemoved.R | 122 - stm-1.1.3/stm/R/plotTopicLoess.R | 98 stm-1.1.3/stm/R/plottingutilfns.R | 564 ++--- stm-1.1.3/stm/R/prepDocuments.R | 196 - stm-1.1.3/stm/R/produce_cmatrix.R | 196 - stm-1.1.3/stm/R/readCorpus.R | 125 - stm-1.1.3/stm/R/residuals.R | 70 stm-1.1.3/stm/R/s.R | 46 stm-1.1.3/stm/R/sageLabels.R | 198 - stm-1.1.3/stm/R/searchK.R | 62 stm-1.1.3/stm/R/selectModel.R | 130 - stm-1.1.3/stm/R/semanticCoherence.R | 106 - stm-1.1.3/stm/R/simBetas.R | 24 stm-1.1.3/stm/R/spectral.R | 542 ++--- stm-1.1.3/stm/R/stm.R | 463 ++-- stm-1.1.3/stm/R/stm.control.R | 370 +-- stm-1.1.3/stm/R/summary.STM.R | 32 stm-1.1.3/stm/R/tau.R | 74 stm-1.1.3/stm/R/textProcessor.R | 274 +- stm-1.1.3/stm/R/thetaPosterior.R | 318 +-- stm-1.1.3/stm/R/toLDAvis.R | 32 stm-1.1.3/stm/R/topicCorr.R | 88 stm-1.1.3/stm/R/topicLasso.R | 170 - stm-1.1.3/stm/R/topicQuality.R | 38 stm-1.1.3/stm/R/writeLdac.R | 28 stm-1.1.3/stm/R/zzz.R | 14 stm-1.1.3/stm/build/vignette.rds |binary stm-1.1.3/stm/data/datalist | 6 stm-1.1.3/stm/data/gadarian.RData |binary stm-1.1.3/stm/data/gadarianFit.RData |binary stm-1.1.3/stm/data/poliblog5k.RData |binary stm-1.1.3/stm/inst/CITATION | 46 stm-1.1.3/stm/inst/NEWS.Rd | 280 +- stm-1.1.3/stm/inst/doc/stmVignette.R | 519 ++--- stm-1.1.3/stm/inst/doc/stmVignette.Rnw | 1512 +++++++------- stm-1.1.3/stm/inst/doc/stmVignette.pdf |binary stm-1.1.3/stm/man/checkBeta.rd | 100 stm-1.1.3/stm/man/checkResiduals.Rd | 100 stm-1.1.3/stm/man/cloud.Rd | 98 stm-1.1.3/stm/man/convertCorpus.Rd |only stm-1.1.3/stm/man/estimateEffect.Rd | 152 - stm-1.1.3/stm/man/findThoughts.Rd | 130 - stm-1.1.3/stm/man/findTopic.Rd | 74 stm-1.1.3/stm/man/gadarian.Rd | 85 stm-1.1.3/stm/man/heldout.Rd | 116 - stm-1.1.3/stm/man/labelTopics.Rd | 123 - stm-1.1.3/stm/man/manyTopics.Rd | 277 +- stm-1.1.3/stm/man/multiSTM.Rd | 280 +- stm-1.1.3/stm/man/permutationTest.Rd | 168 - stm-1.1.3/stm/man/plot.MultimodDiagnostic.Rd | 192 - stm-1.1.3/stm/man/plot.STM.Rd | 196 - stm-1.1.3/stm/man/plot.STMpermute.Rd | 124 - stm-1.1.3/stm/man/plot.estimateEffect.Rd | 386 +-- stm-1.1.3/stm/man/plot.searchK.Rd | 74 stm-1.1.3/stm/man/plot.topicCorr.Rd | 112 - stm-1.1.3/stm/man/plotModels.Rd | 126 - stm-1.1.3/stm/man/plotQuote.Rd | 116 - stm-1.1.3/stm/man/plotRemoved.Rd | 78 stm-1.1.3/stm/man/plotTopicLoess.Rd | 96 stm-1.1.3/stm/man/poliblog5k.Rd | 78 stm-1.1.3/stm/man/prepDocuments.Rd | 140 - stm-1.1.3/stm/man/readCorpus.Rd | 118 - stm-1.1.3/stm/man/s.Rd | 68 stm-1.1.3/stm/man/sageLabels.Rd | 112 - stm-1.1.3/stm/man/searchK.Rd | 172 - stm-1.1.3/stm/man/selectModel.Rd | 284 +- stm-1.1.3/stm/man/stm-package.Rd | 132 - stm-1.1.3/stm/man/stm.Rd | 362 +-- stm-1.1.3/stm/man/summary.STM.Rd | 48 stm-1.1.3/stm/man/textProcessor.Rd | 200 - stm-1.1.3/stm/man/thetaPosterior.Rd | 98 stm-1.1.3/stm/man/toLDAvis.Rd | 124 - stm-1.1.3/stm/man/topicCorr.Rd | 110 - stm-1.1.3/stm/man/topicLasso.Rd | 184 - stm-1.1.3/stm/man/topicQuality.Rd | 118 - stm-1.1.3/stm/man/writeLdac.Rd | 80 stm-1.1.3/stm/vignettes/apsr.bst | 2756 +++++++++++++-------------- stm-1.1.3/stm/vignettes/extracted.bib |only stm-1.1.3/stm/vignettes/natbib.bst | 2576 ++++++++++++------------- stm-1.1.3/stm/vignettes/stmVignette.Rnw | 1512 +++++++------- 117 files changed, 12597 insertions(+), 12605 deletions(-)
Title: An API Client for Wikimedia Traffic Data
Description: Pageview data from the 'Wikimedia' sites, such as
'Wikipedia' (https://www.wikipedia.org/), from entire projects to per-article
levels of granularity, through the new RESTful API and data source (https://
wikimedia.org/api/rest_v1/?doc).
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between pageviews versions 0.1.1 dated 2015-11-25 and 0.2.0 dated 2016-01-14
DESCRIPTION | 15 ++++++++------ MD5 | 30 ++++++++++++++-------------- NAMESPACE | 3 +- NEWS | 11 ++++++++++ R/query.R | 6 +++-- R/timestamps.R |only R/utils.R | 7 ++++++ README.md | 12 +++++++---- build/vignette.rds |binary inst/doc/Accessing_Wikimedia_pageviews.Rmd | 9 ++++---- inst/doc/Accessing_Wikimedia_pageviews.html | 5 ++-- man/article_pageviews.Rd | 6 +++-- man/pageview_timestamps.Rd |only man/pageviews.Rd | 2 - man/project_pageviews.Rd | 6 +++-- man/top_articles.Rd | 3 +- vignettes/Accessing_Wikimedia_pageviews.Rmd | 9 ++++---- 17 files changed, 81 insertions(+), 43 deletions(-)
Title: Dynamic Extensions for Network Objects
Description: Simple interface routines to facilitate the handling of network objects with complex intertemporal data. This is a part of the "statnet" suite of packages for network analysis.
Author: Carter T. Butts [aut],
Ayn Leslie-Cook [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut, cre],
Zack Almquist [ctb],
David R. Hunter [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Steven M. Goodreau [ctb],
Jeffrey Horner [ctb],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamic versions 0.8.1 dated 2015-10-07 and 0.9.0 dated 2016-01-14
ChangeLog | 6 DESCRIPTION | 10 - MD5 | 30 ++-- R/extract.R | 7 + R/utilities.R | 22 +-- build/vignette.rds |binary data/McFarland_cls33_10_16_96.rda |binary inst/doc/networkDynamic.R | 222 +++++++++++++++++++++++++----------- inst/doc/networkDynamic.Rnw | 135 +++++++++++++++++++-- inst/doc/networkDynamic.pdf |binary man/as.data.frame.networkDynamic.Rd | 18 +- man/classrooms.Rd | 8 - tests/converter_tests.R | 8 - tests/network_tests.R | 24 +++ tests/tea_tests.R | 7 + vignettes/networkDynamic.Rnw | 135 +++++++++++++++++++-- 16 files changed, 490 insertions(+), 142 deletions(-)
More information about networkDynamic at CRAN
Permanent link
Title: Tests for General Factorial Designs
Description: Implemented are the Wald-type statistic,
a permuted version thereof as well as the ANOVA-type statistic
for general factorial designs, even with non-normal error terms
and/or heteroscedastic variances, for crossed designs with an
arbitrary number of factors and nested designs with up to three factors.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@uni-ulm.de>
Diff between GFD versions 0.1.2 dated 2015-11-18 and 0.1.4 dated 2016-01-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GFD-function.R | 4 +++- man/GFD.Rd | 4 +++- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <daniel.bowman@unc.edu>
Diff between rNOMADS versions 2.1.6 dated 2015-11-13 and 2.1.7 dated 2016-01-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ R/ReadGrib.R | 8 ++++++-- 4 files changed, 17 insertions(+), 9 deletions(-)
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information: http://upwell.pfeg.noaa.gov/erddap/information.html.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rerddap versions 0.3.0 dated 2015-10-09 and 0.3.4 dated 2016-01-14
DESCRIPTION | 13 +- LICENSE | 2 MD5 | 100 ++++++++--------- NAMESPACE | 9 - NEWS | 18 +++ R/cache_delete.R | 6 - R/cache_details.R | 8 - R/cache_list.R | 11 - R/grid.R | 205 ++---------------------------------- R/info.R | 2 R/ncdf_helpers.R | 54 --------- R/rerddap-package.r | 11 + R/search.R | 22 +-- R/search_adv.R | 52 ++++++++- R/version.R | 7 - R/zzz.r | 28 +++- README.md | 107 +++++++++++------- build/vignette.rds |binary inst/doc/rerddap_vignette.Rmd | 133 ++++++++++++++--------- inst/doc/rerddap_vignette.html | 133 ++++++++++++++--------- inst/vign/rerddap_vignette.Rmd | 6 - inst/vign/rerddap_vignette.md | 133 ++++++++++++++--------- man/cache_delete.Rd | 8 - man/cache_details.Rd | 7 - man/cache_list.Rd | 13 +- man/convert_time.Rd | 4 man/convert_units.Rd | 4 man/disk.Rd | 2 man/ed_search.Rd | 2 man/ed_search_adv.Rd | 25 ++-- man/eurl.Rd | 2 man/fipscounty.Rd | 4 man/griddap.Rd | 71 +++++------- man/info.Rd | 4 man/institutions.Rd | 2 man/ioos_categories.Rd | 2 man/key_words.Rd | 4 man/keywords.Rd | 2 man/longnames.Rd | 2 man/rerddap-package.Rd | 13 +- man/servers.Rd | 2 man/standardnames.Rd | 2 man/tabledap.Rd | 2 man/type_sum.Rd | 2 man/variablenames.Rd | 2 man/version.Rd | 9 - tests/testthat/test-ed_search.R | 7 + tests/testthat/test-ed_search_adv.R | 13 +- tests/testthat/test-griddap.r | 2 tests/testthat/test-info.R | 8 - vignettes/rerddap_vignette.Rmd | 133 ++++++++++++++--------- 51 files changed, 718 insertions(+), 695 deletions(-)
Title: Smooth Multivariate Interpolation for Gridded and Scattered Data
Description: Smooth multivariate interpolation for gridded and scattered data
with possibly large datasets. The code for scattered data is taken from the
'SHEPPACK' Fortran package.
Author: Yves Deville <deville.yves@alpestat.com> Yann Richet
<yann.richet@irsn.fr>. Fortran codes by William Thacker, Manjula Iyer
Jingwei Zhang, Laynet Watson, Jeffrey Birch, Manjula Iyer, Michael Berry
and Robert Renka. Fortran codes by Alain Hebert.
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between smint versions 0.4.0 dated 2015-06-12 and 0.4.2 dated 2016-01-14
ChangeLog | 19 ++++++++++++ DESCRIPTION | 8 ++--- MD5 | 63 ++++++++++++++++++++--------------------- NAMESPACE | 8 +++-- R/GridInt.R | 5 +-- R/gridIntCard.R | 2 - README.md |only inst/doc/smintGuide.pdf |binary man/Grid.Rd | 3 + man/ShepFun1.Rd | 3 + man/apply_Grid.Rd | 3 + man/array_Grid.Rd | 3 + man/as.Grid.Rd | 3 + man/as.Grid.default.Rd | 3 + man/boundary_Grid.Rd | 3 + man/branin.Rd | 3 + man/cardinalBasis_ceschino.Rd | 3 + man/cardinalBasis_lagrange.Rd | 3 + man/cardinalBasis_natSpline.Rd | 3 + man/checkX.Rd | 3 + man/closest.Rd | 3 + man/drop_Grid.Rd | 3 + man/interp_Grid.Rd | 3 + man/interp_ceschino.Rd | 3 + man/qsheppInt.Rd | 3 + man/randGrid.Rd | 3 + man/range_Grid.Rd | 3 + man/round_levels.Rd | 3 + man/sampleIn.Rd | 3 + man/scale_Grid.Rd | 3 + man/smint-package.Rd | 4 +- man/subset_Grid.Rd | 3 + src/gridInt.c | 47 ++++++++++++++++-------------- 33 files changed, 137 insertions(+), 88 deletions(-)
Title: R API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export API. The R functions allow for event and profile data export as well as for segmentation, retention and addiction analysis. Results are always parsed into convenient R objects.
Author: Meinhard Ploner
Maintainer: Meinhard Ploner <meinhard.ploner@prosiebensat1digital.de>
Diff between RMixpanel versions 0.1-2 dated 2015-11-25 and 0.1-3 dated 2016-01-14
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 20 ++++++++++---------- NAMESPACE | 4 +++- R/eventsJson2RMatrix.R | 9 ++++++--- R/mixpanelGetData.R | 2 +- R/mixpanelGetSegmentation.R | 5 +++-- README.md | 2 +- build/partial.rdb |binary man/mixpanelGetProfiles.Rd | 4 ++-- man/mixpanelGetSegmentation.Rd | 3 ++- 11 files changed, 34 insertions(+), 27 deletions(-)
Title: North Symbols and Scale Bars for Maps Created with 'ggplot2' or
'ggmap'
Description: Adds north symbols (18 options) and scale bars in kilometers to
maps in geographic or metric coordinates created with 'ggplot2' or 'ggmap'.
Author: Oswaldo Santos Baquero [aut, cre]
Maintainer: Oswaldo Santos Baquero <oswaldosant@gmail.com>
Diff between ggsn versions 0.2.0 dated 2015-08-22 and 0.3.0 dated 2016-01-14
DESCRIPTION | 12 +++++++----- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 8 ++++++-- NEWS | 8 ++++++++ R/blank.R | 5 +++-- R/ggsn-package.R | 9 +++++---- R/north.R | 5 +++-- R/north2.R | 5 +++-- R/scalebar.R | 34 ++++------------------------------ inst/extdata/sp.dbf |binary man/blank.Rd | 9 +++++---- man/ggsn-package.Rd | 8 ++++---- man/north.Rd | 7 ++++--- man/north2.Rd | 7 ++++--- man/northSymbols.Rd | 2 +- man/scalebar.Rd | 36 +++++------------------------------- 16 files changed, 77 insertions(+), 108 deletions(-)
Title: Calculation of Average Population Attributable Fractions and
Confidence Intervals
Description: Average population attributable fractions are calculated for a set of risk factors (either binary or ordinal valued) for both prospective and case-control designs. Confidence intervals are found by Monte Carlo simulation. The method can be applied to either prospective or case control designs, provided an estimate of disease prevalence is provided. In addition to an exact calculation of AF, an approximate calculation, based on randomly sampling permutations has been implemented to ensure the calculation is computationally tractable when the number of risk factors is large.
Author: John Ferguson [aut, cre]
Maintainer: John Ferguson <john.ferguson@nuigalway.ie>
Diff between averisk versions 1.0 dated 2015-10-29 and 1.0.1 dated 2016-01-14
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/main.R | 16 +++++++++++++++- 3 files changed, 20 insertions(+), 6 deletions(-)
Title: Batch Effect Removal (in Phenotype Prediction using Gene Data)
Description: Various tools dealing with batch effects, in particular enabling the
removal of discrepancies between training and test sets in prediction scenarios.
The following batch effect removal methods are implemented: FAbatch, ComBat, (f)SVA,
mean-centering, standardization, Ratio-A and Ratio-G. For each of these we provide
an additional function which enables a posteriori ('addon') batch effect removal
in independent batches ('test data'). Here, the (already batch effect adjusted)
training data is not altered. For evaluating the success of batch effect adjustment
several metrics are provided. Moreover, the package implements a plot for the
visualization of batch effects using principal component analysis. The main functions
of the package are ba() and baaddon() which enable batch effect removal and addon
batch effect removal, respectively, with one of the seven methods mentioned above.
Another important function is bametric() which is a wrapper function for all implemented
methods for evaluating the success of batch effect removal.
Author: Roman Hornung, David Causeur
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between bapred versions 0.2 dated 2015-12-02 and 0.3 dated 2016-01-14
DESCRIPTION | 6 +++--- MD5 | 31 ++++++++++++++++--------------- inst |only man/avedist.Rd | 2 +- man/ba.Rd | 2 +- man/baaddon.Rd | 2 +- man/bametric.Rd | 2 +- man/bapred-package.Rd | 2 +- man/diffexprm.Rd | 2 +- man/fabatch.Rd | 2 +- man/fabatchaddon.Rd | 2 +- man/kldist.Rd | 2 +- man/meancenteraddon.Rd | 2 +- man/ratioaaddon.Rd | 2 +- man/ratiogaddon.Rd | 2 +- man/sepscore.Rd | 2 +- man/standardizeaddon.Rd | 2 +- 17 files changed, 33 insertions(+), 32 deletions(-)
Title: Tools for ABC Analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage.
Author: Matt Nunes [aut, cre],
Dennis Prangle [aut]
Maintainer: Matt Nunes <m.nunes@lancaster.ac.uk>
Diff between abctools versions 1.0.3 dated 2015-07-15 and 1.0.4 dated 2016-01-14
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++--------------- R/saABC.R | 2 +- R/semiauto.abc.R | 6 ++++-- man/AS.select.Rd | 7 ++++++- man/AS.test.Rd | 7 ++++++- man/abctools-package.Rd | 14 ++++++++++---- man/coal.Rd | 3 +++ man/cov.pi.Rd | 4 ++++ man/mc.ci.Rd | 4 ++++ man/mincrit.Rd | 8 +++++++- man/nn.ent.Rd | 3 +++ man/saABC.Rd | 5 ++++- man/selectsumm.Rd | 7 ++++++- man/semiauto.abc.Rd | 6 +++++- man/stage2.Rd | 7 ++++++- 16 files changed, 90 insertions(+), 35 deletions(-)
Title: Hidden Markov Models for Life Sequences and Other Multivariate,
Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent)
Markov models and mixture hidden Markov models for social
sequence data and other categorical time series. Also some more restricted
versions of these type of models are available: Markov models, mixture
Markov models, and latent class models. The package supports models for one or
multiple subjects with one or multiple parallel sequences (channels). External
covariates can be added to explain cluster membership in mixture models. The
package provides functions for evaluating and comparing models, as well as
functions for easy plotting of multichannel sequence data and hidden Markov
models. Models are estimated using maximum likelihood via the EM algorithm and/or
direct numerical maximization with analytical gradients.
All main algorithms are written in C++ with support for parallel computation.
Author: Jouni Helske, Satu Helske
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between seqHMM versions 1.0.3-1 dated 2015-12-30 and 1.0.4 dated 2016-01-14
DESCRIPTION | 8 MD5 | 140 +-- NEWS | 18 R/HMMplot.R | 839 +++++++++++----------- R/SSPlotter.R | 852 +++++++++++----------- R/build_hmm.R | 83 +- R/build_lcm.R | 74 + R/build_mhmm.R | 51 - R/build_mm.R | 11 R/build_mmm.R | 60 + R/fit_model.R | 58 - R/forwardBackward.R | 17 R/gridplot.R | 36 R/hidden_paths.R | 17 R/import_seqdef.R | 7 R/logLik.hmm.R | 11 R/logLik.mhmm.R | 11 R/mHMMplotgrid.R | 108 +- R/mc_to_sc.R | 51 - R/mc_to_sc_data.R | 67 + R/mssplot.R | 8 R/plot.hmm.R | 23 R/posterior_probs.R | 14 R/separate_mhmm.R | 4 R/seqHMM-package.R | 6 R/simulate_hmm.R | 4 R/simulate_mhmm.R | 53 - R/simulate_pars.R | 3 R/ssp.R | 59 + R/ssplot.R | 49 - R/ssplotM.R | 2 R/trim_hmm.R | 8 build/vignette.rds |binary data/biofam3c.rda |binary data/colorpalette.rda |binary data/hmm_biofam.rda |binary data/hmm_mvad.rda |binary data/mhmm_biofam.rda |binary data/mhmm_mvad.rda |binary inst/doc/seqHMM.R | 698 +++++++++--------- inst/doc/seqHMM.Rnw | 1768 +++++++++++++++++++++++------------------------ inst/doc/seqHMM.pdf |binary man/TraMineR_imports.Rd | 12 man/build_hmm.Rd | 83 +- man/build_lcm.Rd | 72 + man/build_mhmm.Rd | 49 - man/build_mm.Rd | 11 man/build_mmm.Rd | 173 ++-- man/fit_model.Rd | 59 - man/forward_backward.Rd | 17 man/gridplot.Rd | 36 man/hidden_paths.Rd | 17 man/logLik.hmm.Rd | 11 man/logLik.mhmm.Rd | 11 man/mc_to_sc.Rd | 36 man/mc_to_sc_data.Rd | 66 + man/mssplot.Rd | 8 man/plot.hmm.Rd | 2 man/posterior_probs.Rd | 14 man/separate_mhmm.Rd | 3 man/seqHMM-deprecated.Rd | 52 - man/seqHMM.Rd | 6 man/simulate_hmm.Rd | 4 man/simulate_mhmm.Rd | 61 - man/simulate_pars.Rd | 5 man/ssp.Rd | 58 - man/ssplot.Rd | 61 - man/trim_model.Rd | 8 src/log_EM.cpp | 2 vignettes/references.bib | 81 +- vignettes/seqHMM.Rnw | 1768 +++++++++++++++++++++++------------------------ 71 files changed, 4223 insertions(+), 3781 deletions(-)
Title: Extra Map Databases
Description: Supplement to maps package, providing the larger and/or
higher-resolution databases.
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapdata versions 2.2-5 dated 2015-08-03 and 2.2-6 dated 2016-01-14
mapdata-2.2-5/mapdata/src/Makefile |only mapdata-2.2-6/mapdata/DESCRIPTION | 8 ++++---- mapdata-2.2-6/mapdata/MD5 | 9 ++++++--- mapdata-2.2-6/mapdata/cleanup |only mapdata-2.2-6/mapdata/configure |only mapdata-2.2-6/mapdata/configure.ac |only mapdata-2.2-6/mapdata/src/Makefile.in |only mapdata-2.2-6/mapdata/src/Makefile.win | 1 + 8 files changed, 11 insertions(+), 7 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.0.77 dated 2015-11-20 and 1.0.78 dated 2016-01-14
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS | 3 R/rng.R | 210 +++++++++++++++++++++++++++++++++++------------------ man/adaBayes.Rd | 9 +- man/qmle.Rd | 2 man/rng.Rd | 109 ++++++++++++++++++++++----- man/setModel.Rd | 38 +++++++-- man/spectralcov.Rd | 1 9 files changed, 279 insertions(+), 115 deletions(-)
Title: Change-Point Estimation using Shape-Restricted Splines
Description: In a scatterplot where the response variable is Gaussian, Poisson or binomial, we consider the case in which the mean function is smooth with a change-point, which is a mode, an inflection point or a jump point. The main routine estimates the mean curve and the change-point as well using shape-restricted B-splines. An optional subroutine delivering a bootstrap confidence interval for the change-point is incorporated in the main routine.
Author: Xiyue Liao and Mary C Meyer
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between ShapeChange versions 1.1 dated 2015-11-15 and 1.2 dated 2016-01-14
DESCRIPTION | 12 - MD5 | 12 - NAMESPACE | 2 R/ShapeChange.R | 421 ++++++++++++++++++++++++++++++++------------- man/ShapeChange-package.Rd | 6 man/changept.Rd | 28 +- man/ip.Rd | 2 7 files changed, 332 insertions(+), 151 deletions(-)
Title: Population Viability Analysis with Data Cloning
Description: Likelihood based population viability analysis in the
presence of observation error and missing data.
The package can be used to fit, compare, predict,
and forecast various growth model types using data cloning.
Author: Khurram Nadeem, Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between PVAClone versions 0.1-2 dated 2014-05-19 and 0.1-4 dated 2016-01-14
DESCRIPTION | 15 MD5 | 62 ++-- NAMESPACE | 38 +- R/bevertonholt.R | 696 +++++++++++++++++++++++----------------------- R/fancyPVAmodel.R | 42 +- R/generateMCMC.R | 104 +++--- R/gompertz.R | 692 +++++++++++++++++++++++---------------------- R/internals.R | 38 +- R/modelselection.R | 238 +++++++-------- R/pva-class.R | 52 +-- R/pva-methods.R | 94 ++---- R/pva.R | 124 ++++---- R/ricker.R | 611 ++++++++++++++++++++-------------------- R/thetalogistic.R | 678 ++++++++++++++++++++++---------------------- R/thetalogistic_D.R | 724 ++++++++++++++++++++++++------------------------ data/paurelia.rda |binary data/redstart.rda |binary data/songsparrow.rda |binary inst/ChangeLog | 52 ++- man/PVAClone-package.Rd | 120 +++---- man/fancyPVAmodel.Rd | 60 +-- man/generateLatent.Rd | 98 +++--- man/growthmodels.Rd | 256 ++++++++-------- man/internals.Rd | 116 +++---- man/model.select.Rd | 314 ++++++++++---------- man/paurelia.Rd | 58 +-- man/pva-class.Rd | 125 ++++---- man/pva-methods.Rd | 38 +- man/pva.Rd | 295 +++++++++---------- man/pvamodel-class.Rd | 126 ++++---- man/redstart.Rd | 90 ++--- man/songsparrow.Rd | 78 ++--- 32 files changed, 3029 insertions(+), 3005 deletions(-)
Title: Extension to ggplot2
Description: The R package '\href{http://docs.ggplot2.org/current/}{ggplot2}'
is a plotting system based on the grammar of graphics. '\href{https://
ggobi.github.io/ggally}{GGally}' extends 'ggplot2' by adding several functions to
reduce the complexity of combining geoms with transformed data. Some of these
functions include a pairwise plot matrix, a scatterplot plot matrix, a parallel
coordinates plot, a survival plot, and several functions to plot networks.
Author: Barret Schloerke [aut, cre] (author for ggpairs and ggally_*.
contributor for all functions.),
Jason Crowley [aut] (ggparcoord),
Di Cook [aut, ths] (ggscatmat, gglyph),
Heike Hofmann [ths],
Hadley Wickham [ths],
Francois Briatte [aut] (ggcorr, ggnet, ggnet2),
Moritz Marbach [aut] (ggnet, ggnet2),
Edwin Thoen [aut] (ggsurv),
Amos Elberg [aut] (ggnetworkmap)
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between GGally versions 1.0.0 dated 2015-12-30 and 1.0.1 dated 2016-01-14
GGally-1.0.0/GGally/man/set_to_blank_list_if_blank.Rd |only GGally-1.0.1/GGally/DESCRIPTION | 24 GGally-1.0.1/GGally/MD5 | 105 +- GGally-1.0.1/GGally/NEWS | 16 GGally-1.0.1/GGally/R/find-combo.R | 6 GGally-1.0.1/GGally/R/gg-plots.R | 130 +-- GGally-1.0.1/GGally/R/gglyph.R | 8 GGally-1.0.1/GGally/R/ggmatrix.R | 4 GGally-1.0.1/GGally/R/ggmatrix_print.R | 30 GGally-1.0.1/GGally/R/ggpairs.R | 86 +- GGally-1.0.1/GGally/R/ggpairs_add.R | 2 GGally-1.0.1/GGally/R/ggpairs_getput.R | 34 GGally-1.0.1/GGally/R/ggpairs_internal_plots.R | 2 GGally-1.0.1/GGally/R/ggparcoord.R | 167 ++-- GGally-1.0.1/GGally/R/ggscatmat.R | 83 +- GGally-1.0.1/GGally/build/vignette.rds |binary GGally-1.0.1/GGally/inst/doc/gglyph.Rmd | 8 GGally-1.0.1/GGally/inst/doc/gglyph.html | 292 ++------ GGally-1.0.1/GGally/inst/doc/ggmatrix.Rmd | 8 GGally-1.0.1/GGally/inst/doc/ggmatrix.html | 452 ++++-------- GGally-1.0.1/GGally/inst/doc/ggnetworkmap.R | 1 GGally-1.0.1/GGally/inst/doc/ggnetworkmap.Rmd | 10 GGally-1.0.1/GGally/inst/doc/ggnetworkmap.html | 342 ++------- GGally-1.0.1/GGally/inst/doc/ggpairs.Rmd | 9 GGally-1.0.1/GGally/inst/doc/ggpairs.html | 498 ++++---------- GGally-1.0.1/GGally/inst/doc/ggscatmat.Rmd | 9 GGally-1.0.1/GGally/inst/doc/ggscatmat.html | 276 ++----- GGally-1.0.1/GGally/man/add_and_overwrite_aes.Rd | 2 GGally-1.0.1/GGally/man/getPlot.Rd | 2 GGally-1.0.1/GGally/man/gg-add.Rd | 2 GGally-1.0.1/GGally/man/ggally_density.Rd | 2 GGally-1.0.1/GGally/man/ggally_ratio.Rd | 6 GGally-1.0.1/GGally/man/ggfluctuation2.Rd | 2 GGally-1.0.1/GGally/man/ggpairs.Rd | 20 GGally-1.0.1/GGally/man/ggparcoord.Rd | 14 GGally-1.0.1/GGally/man/ggscatmat.Rd | 2 GGally-1.0.1/GGally/man/glyphs.Rd | 7 GGally-1.0.1/GGally/man/print.ggmatrix.Rd | 5 GGally-1.0.1/GGally/man/putPlot.Rd | 6 GGally-1.0.1/GGally/tests/testthat/test-gg-plots.R | 6 GGally-1.0.1/GGally/tests/testthat/test-gglyph.R | 4 GGally-1.0.1/GGally/tests/testthat/test-ggmatrix.R | 18 GGally-1.0.1/GGally/tests/testthat/test-ggmatrix_getput.R | 2 GGally-1.0.1/GGally/tests/testthat/test-ggnet.R | 15 GGally-1.0.1/GGally/tests/testthat/test-ggnet2.R | 17 GGally-1.0.1/GGally/tests/testthat/test-ggnetworkmap.R | 13 GGally-1.0.1/GGally/tests/testthat/test-ggpairs.R | 82 +- GGally-1.0.1/GGally/tests/testthat/test-ggparcoord.R | 30 GGally-1.0.1/GGally/tests/testthat/test-ggscatmat.R | 8 GGally-1.0.1/GGally/vignettes/gglyph.Rmd | 8 GGally-1.0.1/GGally/vignettes/ggmatrix.Rmd | 8 GGally-1.0.1/GGally/vignettes/ggnetworkmap.Rmd | 10 GGally-1.0.1/GGally/vignettes/ggpairs.Rmd | 9 GGally-1.0.1/GGally/vignettes/ggscatmat.Rmd | 9 54 files changed, 1116 insertions(+), 1795 deletions(-)
Title: Tools Developed for Structured Sufficient Dimension Reduction
(sSDR)
Description: Performs structured OLS (sOLS) and structured SIR (sSIR).
Author: Yang Liu <zjubioly@gmail.com>, Francesca Chiaromonte, Bing Li
Maintainer: Yang Liu <zjubioly@gmail.com>
Diff between sSDR versions 1.0.0 dated 2015-10-01 and 1.1.0 dated 2016-01-14
DESCRIPTION | 10 +++++----- MD5 | 7 ++++--- NAMESPACE | 1 + R/sSDR.R | 41 +++++++++++++++++++++++++++++++++++++++++ man/sOLS.comp.d.Rd |only 5 files changed, 51 insertions(+), 8 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate.
Author: Chung-hong Chan [aut],
Geoffrey CH Chan [aut],
Thomas J. Leeper [aut, cre],
Christopher Gandrud [aut],
Ista Zahn [aut]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between rio versions 0.2 dated 2015-05-07 and 0.3.0 dated 2016-01-14
rio-0.2/rio/tests/testthat/errors.R |only rio-0.2/rio/tests/testthat/identical.R |only rio-0.2/rio/tests/testthat/noheader.csv |only rio-0.2/rio/tests/testthat/test_header.R |only rio-0.3.0/rio/DESCRIPTION | 21 +-- rio-0.3.0/rio/MD5 | 46 ++++--- rio-0.3.0/rio/NAMESPACE | 12 + rio-0.3.0/rio/NEWS | 48 +++++++ rio-0.3.0/rio/R/export.R | 25 ++-- rio-0.3.0/rio/R/import.R | 160 ++++++++++++++++++-------- rio-0.3.0/rio/R/set_class.R | 5 rio-0.3.0/rio/R/utils.R | 102 +++++++++++++++- rio-0.3.0/rio/README.md | 9 + rio-0.3.0/rio/inst/doc/rio.R | 4 rio-0.3.0/rio/inst/doc/rio.Rmd | 5 rio-0.3.0/rio/inst/doc/rio.html | 13 +- rio-0.3.0/rio/inst/examples |only rio-0.3.0/rio/man/convert.Rd | 3 rio-0.3.0/rio/man/import.Rd | 8 - rio-0.3.0/rio/po |only rio-0.3.0/rio/tests/test-all.R | 3 rio-0.3.0/rio/tests/testthat/test_convert.R |only rio-0.3.0/rio/tests/testthat/test_errors.R |only rio-0.3.0/rio/tests/testthat/test_export.R |only rio-0.3.0/rio/tests/testthat/test_guess.R | 1 rio-0.3.0/rio/tests/testthat/test_identical.R |only rio-0.3.0/rio/tests/testthat/test_import.R |only rio-0.3.0/rio/tests/testthat/test_remote.R |only rio-0.3.0/rio/tests/testthat/test_set_class.R |only rio-0.3.0/rio/vignettes/rio.Rmd | 5 30 files changed, 357 insertions(+), 113 deletions(-)
Title: Hierarchical Models Made Easy with Data Cloning
Description: S4 classes around infrastructure provided by the
coda and dclone packages to make package development easy as a breeze
with data cloning for hierarchical models.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between dcmle versions 0.2-4 dated 2013-10-01 and 0.3-0 dated 2016-01-14
dcmle-0.2-4/dcmle/R/dcexample.R |only dcmle-0.2-4/dcmle/man/dcexample.Rd |only dcmle-0.3-0/dcmle/DESCRIPTION | 25 dcmle-0.3-0/dcmle/MD5 | 23 dcmle-0.3-0/dcmle/NAMESPACE | 124 ++- dcmle-0.3-0/dcmle/R/dcmle-classes.R | 427 ++++++------ dcmle-0.3-0/dcmle/R/dcmle-graphics.R | 265 ++++---- dcmle-0.3-0/dcmle/R/dcmle-methods.R | 993 ++++++++++++++---------------- dcmle-0.3-0/dcmle/R/dcmle.R | 43 - dcmle-0.3-0/dcmle/R/zzz.R | 4 dcmle-0.3-0/dcmle/inst/ChangeLog | 52 + dcmle-0.3-0/dcmle/man/dcCodaMCMC-class.Rd | 167 ++--- dcmle-0.3-0/dcmle/man/dcmle-package.Rd | 15 dcmle-0.3-0/dcmle/tests |only 14 files changed, 1120 insertions(+), 1018 deletions(-)
Title: Plotting ggplot2 Graphics in an XKCD Style
Description: Plotting ggplot2 graphs using the XKCD style.
Author: Emilio Torres-Manzanera
Maintainer: Emilio Torres-Manzanera <torres@uniovi.es>
Diff between xkcd versions 0.0.4 dated 2014-12-15 and 0.0.5 dated 2016-01-13
xkcd-0.0.4/xkcd/vignettes/xkcd-intro-008.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-011.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-012.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-015.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-016.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-017.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-018.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-021.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-022.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-CaritasSpain.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-angles.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-facetcity.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-facetvs.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-motherday.png |only xkcd-0.0.4/xkcd/vignettes/xkcd-intro-twoman.png |only xkcd-0.0.5/xkcd/DESCRIPTION | 17 ++-- xkcd-0.0.5/xkcd/MD5 | 71 +++++++----------- xkcd-0.0.5/xkcd/NAMESPACE | 3 xkcd-0.0.5/xkcd/NEWS | 51 +----------- xkcd-0.0.5/xkcd/R/xkcdaxis.R | 5 - xkcd-0.0.5/xkcd/R/xkcdline.R | 9 +- xkcd-0.0.5/xkcd/build/vignette.rds |binary xkcd-0.0.5/xkcd/inst/doc/xkcd-intro.R | 14 --- xkcd-0.0.5/xkcd/inst/doc/xkcd-intro.Rnw | 24 +----- xkcd-0.0.5/xkcd/inst/doc/xkcd-intro.pdf |binary xkcd-0.0.5/xkcd/man/theme_xkcd.Rd | 3 xkcd-0.0.5/xkcd/man/xkcd-package.Rd | 3 xkcd-0.0.5/xkcd/man/xkcdaxis.Rd | 3 xkcd-0.0.5/xkcd/man/xkcdline.Rd | 3 xkcd-0.0.5/xkcd/man/xkcdman.Rd | 3 xkcd-0.0.5/xkcd/man/xkcdrect.Rd | 3 xkcd-0.0.5/xkcd/vignettes/gr1.pdf |binary xkcd-0.0.5/xkcd/vignettes/gr1.png |binary xkcd-0.0.5/xkcd/vignettes/graxis.png |binary xkcd-0.0.5/xkcd/vignettes/grbar.png |binary xkcd-0.0.5/xkcd/vignettes/grcaritas.png |binary xkcd-0.0.5/xkcd/vignettes/grfonts.png |binary xkcd-0.0.5/xkcd/vignettes/grhelp.png |binary xkcd-0.0.5/xkcd/vignettes/grhomosapiens.png |binary xkcd-0.0.5/xkcd/vignettes/grmotherday.png |binary xkcd-0.0.5/xkcd/vignettes/grnofonts.png |binary xkcd-0.0.5/xkcd/vignettes/grsevan.png |binary xkcd-0.0.5/xkcd/vignettes/grstickfigure.png |binary xkcd-0.0.5/xkcd/vignettes/xkcd-intro.Rnw | 24 +----- 44 files changed, 77 insertions(+), 159 deletions(-)
Title: Twitter Collector and Export to 'SQLite', 'postGIS' and 'GIS'
Format
Description: This is an improved implementation of the package 'StreamR' to capture tweets and store it into a SQLite and 'postGIS' data base. The package simplifies the configuration task to capture tweets and facilitates its store into a 'PostGIS' database. Also exports tweets to 'GIS' format.
Author: Pau Aragó
Maintainer: Pau Aragó <parago@uji.es>
Diff between tweet2r versions 0.3 dated 2015-12-28 and 0.4.1 dated 2016-01-13
ChangeLog | 11 +++++++++++ DESCRIPTION | 14 ++++++-------- MD5 | 17 +++++++++-------- NAMESPACE | 2 +- R/t2gis.R | 16 +++++++++++----- R/t2pgis.R | 4 +++- R/t2sqlite.R | 2 +- R/tweet2r.R | 7 ++----- README.md |only man/tweet2r.Rd | 2 +- 10 files changed, 45 insertions(+), 30 deletions(-)
Title: Range Ancestral State Estimation for Phylogeography and
Comparative Analyses
Description: The rase package primarily implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., & Crawford, F. W. (2015). Historical Biogeography Using Species Geographical Ranges. Systematic biology, 64(6), 1059-1073. It also includes Bayesian inference of ancestral states under a Brownian Motion model of character evolution and Maximum Likelihood estimation of rase for n-dimensional data. Visualizing functions in 3D are implemented using the rgl package.
Author: Ignacio Quintero [aut, cre],
Forrest W. Crawford [aut],
Petr Keil [aut]
Maintainer: Ignacio Quintero <ignacio.quintero@yale.edu>
Diff between rase versions 0.2-21 dated 2015-11-09 and 0.2-22 dated 2016-01-13
rase-0.2-21/rase/man/random_rase3d.Rd |only rase-0.2-22/rase/DESCRIPTION | 12 +++---- rase-0.2-22/rase/MD5 | 15 ++++----- rase-0.2-22/rase/NAMESPACE | 5 --- rase-0.2-22/rase/R/rase_source.r | 50 --------------------------------- rase-0.2-22/rase/README.md | 19 ++++++------ rase-0.2-22/rase/man/bm_ase.Rd | 2 - rase-0.2-22/rase/man/point.like.bm.Rd | 2 - rase-0.2-22/rase/man/ranges.like.bm.Rd | 2 - 9 files changed, 27 insertions(+), 80 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and NIST curves P-256, P-384 and P-521.
Cryptographic signatures can either be created and verified manually or via x509
certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA
for asymmetric (public key) encryption. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut],
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between openssl versions 0.8 dated 2015-12-14 and 0.9 dated 2016-01-13
openssl-0.8/openssl/inst/doc/intro.Rmd |only openssl-0.8/openssl/inst/doc/intro.html |only openssl-0.9/openssl/DESCRIPTION | 8 +-- openssl-0.9/openssl/LICENSE | 2 openssl-0.9/openssl/MD5 | 27 +++++------ openssl-0.9/openssl/NEWS | 4 + openssl-0.9/openssl/R/cert.R | 6 -- openssl-0.9/openssl/R/hash.R | 5 -- openssl-0.9/openssl/inst/doc/bignum.html | 54 +++++++++++------------ openssl-0.9/openssl/inst/doc/crypto_hashing.html | 27 ++++++----- openssl-0.9/openssl/inst/doc/secure_rng.html | 32 ++++++------- openssl-0.9/openssl/man/certificates.Rd | 2 openssl-0.9/openssl/man/hash.Rd | 5 -- openssl-0.9/openssl/src/Makevars.win | 7 +- openssl-0.9/openssl/src/ssl.c | 44 +++++++++++------- openssl-0.9/openssl/src/win32 |only 16 files changed, 119 insertions(+), 104 deletions(-)
Title: Functions for Optimal Non-Bipartite Matching
Description: Perform non-bipartite matching and matched randomization. A
"bipartite" matching utilizes two separate groups, e.g. smokers being
matched to nonsmokers or cases being matched to controls. A "non-bipartite"
matching creates mates from one big group, e.g. 100 hospitals being
randomized for a two-arm cluster randomized trial or 5000 children who
have been exposed to various levels of secondhand smoke and are being
paired to form a greater exposure vs. lesser exposure comparison. At the
core of a non-bipartite matching is a N x N distance matrix for N potential
mates. The distance between two units expresses a measure of similarity or
quality as mates (the lower the better). The 'gendistance()' and
'distancematrix()' functions assist in creating this. The 'nonbimatch()'
function creates the matching that minimizes the total sum of distances
between mates; hence, it is referred to as an "optimal" matching. The
'assign.grp()' function aids in performing a matched randomization. Note
bipartite matching can be performed using the prevent option in
'gendistance()'.
Author: Cole Beck [aut, cre], Bo Lu [aut], Robert Greevy [aut]
Maintainer: Cole Beck <cole.beck@vanderbilt.edu>
Diff between nbpMatching versions 1.4.5 dated 2015-05-14 and 1.5.0 dated 2016-01-13
DESCRIPTION | 12 ++++------ MD5 | 20 ++++++++-------- NAMESPACE | 2 + R/distancematrix.R | 45 ++++++++++++++++++-------------------- R/gendistance.R | 27 ++++++++++++---------- R/make.phantoms.R | 8 +++--- R/nbpmatching-package.R | 12 ++++++++++ R/nonbimatch.R | 25 ++++++++++++++++----- man/gendistance.Rd | 17 ++++++++++---- man/make.phantoms.Rd | 4 +-- tests/testthat/test-gendistance.R | 2 - 11 files changed, 104 insertions(+), 70 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, and orientation patch count for teeth using scans of enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 0.2 dated 2015-12-11 and 0.3 dated 2016-01-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/DNE.R | 23 +++++++++++++---------- R/DNE3d.R | 2 +- R/compute_energy_per_face.R | 2 +- build/molaR.pdf |binary man/DNE.Rd | 11 +++++++---- vignettes/molaR_vignette.Rmd | 11 +++++++---- 8 files changed, 39 insertions(+), 30 deletions(-)
Title: Zoo of Geometric Objects
Description: Geometric objects defined in geozoo can be simulated or displayed in the R package tourr.
Author: Barret Schloerke [aut, cre],
Di Cook [ths],
Hadley Wickham [ths]
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between geozoo versions 0.4.3 dated 2014-01-03 and 0.5.0 dated 2016-01-13
geozoo-0.4.3/geozoo/R/cross.polytope.r |only geozoo-0.4.3/geozoo/R/cube.r |only geozoo-0.4.3/geozoo/R/mobius.r |only geozoo-0.4.3/geozoo/R/parametric.r |only geozoo-0.4.3/geozoo/R/print.r |only geozoo-0.4.3/geozoo/R/simplex.r |only geozoo-0.4.3/geozoo/R/sphere.r |only geozoo-0.4.3/geozoo/R/torus.r |only geozoo-0.4.3/geozoo/R/xml.r |only geozoo-0.5.0/geozoo/DESCRIPTION | 36 ++++++---- geozoo-0.5.0/geozoo/MD5 | 79 ++++++++++++----------- geozoo-0.5.0/geozoo/NAMESPACE | 6 + geozoo-0.5.0/geozoo/NEWS | 22 +++++- geozoo-0.5.0/geozoo/R/cross.polytope.R |only geozoo-0.5.0/geozoo/R/cube.R |only geozoo-0.5.0/geozoo/R/geozoo.R |only geozoo-0.5.0/geozoo/R/mobius.R |only geozoo-0.5.0/geozoo/R/parametric.R |only geozoo-0.5.0/geozoo/R/print.R |only geozoo-0.5.0/geozoo/R/simplex.R |only geozoo-0.5.0/geozoo/R/sphere.R |only geozoo-0.5.0/geozoo/R/torus.R |only geozoo-0.5.0/geozoo/R/xml.R |only geozoo-0.5.0/geozoo/README.md |only geozoo-0.5.0/geozoo/man/boy.surface.Rd | 13 ++- geozoo-0.5.0/geozoo/man/conic.spiral.Rd | 25 ++++--- geozoo-0.5.0/geozoo/man/conic.spiral.nautilus.Rd | 26 ++++--- geozoo-0.5.0/geozoo/man/cross.cap.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/cross.polytope.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/cube.dotline.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/cube.face.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/cube.iterate.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/cube.solid.grid.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/cube.solid.random.Rd | 19 +++-- geozoo-0.5.0/geozoo/man/dini.surface.Rd | 21 +++--- geozoo-0.5.0/geozoo/man/ellipsoid.Rd | 23 +++--- geozoo-0.5.0/geozoo/man/enneper.surface.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/klein.fig.eight.Rd | 21 +++--- geozoo-0.5.0/geozoo/man/mobius.Rd | 16 ++-- geozoo-0.5.0/geozoo/man/mobius.experiment.Rd | 16 ++-- geozoo-0.5.0/geozoo/man/print.geozoo.Rd | 14 ++-- geozoo-0.5.0/geozoo/man/print.geozooNoScale.Rd |only geozoo-0.5.0/geozoo/man/roman.surface.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/simplex.Rd | 17 ++-- geozoo-0.5.0/geozoo/man/sphere.hollow.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/sphere.solid.grid.Rd | 20 +++-- geozoo-0.5.0/geozoo/man/sphere.solid.random.Rd | 19 +++-- geozoo-0.5.0/geozoo/man/torus.Rd | 21 +++--- geozoo-0.5.0/geozoo/man/torus.flat.Rd | 19 +++-- geozoo-0.5.0/geozoo/man/write.xml.Rd | 16 ++-- geozoo-0.5.0/geozoo/tests |only 51 files changed, 357 insertions(+), 260 deletions(-)
Title: Methods for Reading dChip Files
Description: Functions for reading DCP and CDF.bin files generated by the dChip software.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between dChipIO versions 0.1.4 dated 2016-01-12 and 0.1.5 dated 2016-01-13
DESCRIPTION | 8 +++--- MD5 | 19 ++++++++-------- NEWS | 8 ++++++ R/readCdfBin.R | 29 ++++++++++++++---------- R/readCdfBinHeader.R | 39 ++++++++++++--------------------- R/readDcp.R | 51 +++++++++++++++++++------------------------ R/readDcpHeader.R | 56 +++++++++++++++++++---------------------------- R/readDcpRectangle.R | 6 +++-- R/utils.R |only man/readCdfBin.Rd | 48 ++++++++++++++++++++-------------------- man/readDcp.Rd | 60 +++++++++++++++++++++++++-------------------------- 11 files changed, 158 insertions(+), 166 deletions(-)
Title: Wegener Center Climate Uncertainty Explorer
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary 'NetCDF' format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global Circulation Models, as the 'CMIP5' simulations, can be read in the same way as Regional Climate Models, as e.g. the 'CORDEX' or 'ENSEMBLES' simulations. The package has been developed at the 'Wegener Center for Climate and Global Change' at the University of Graz, Austria.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik <thomas.mendlik@uni-graz.at>
Diff between wux versions 2.1-1 dated 2015-09-17 and 2.2-0 dated 2016-01-13
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- R/InitModelDictionary.R | 4 ++-- R/ReadGridFile.R | 20 +++++++++++++------- R/ReadNetCdf.R | 26 +++++++++++++++++--------- R/ReadNetCdfTimeData.R | 18 ++++++++++++------ R/landmask.R | 12 +++++++++--- R/models2wuxAggregateTemporal.R | 19 ++++++++++++++----- R/models2wuxGetFilenames.R | 4 ++-- R/models2wuxGetParameterShortName.R | 17 ++++++++++++++--- 11 files changed, 98 insertions(+), 52 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-13 0.14.8
2016-01-07 0.14.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-05 0.4
2014-12-29 0.3
2014-05-18 0.2
2014-01-05 0.1
Title: Tools for Semantic Vector Spaces
Description: Various tools for semantic vector spaces, such as
correspondence analysis (simple, multiple and discriminant), latent
semantic analysis, probabilistic latent semantic analysis, non-negative
matrix factorization, latent class analysis and EM clustering. Furthermore,
there are specialized distance measures, plotting functions and some helper
functions.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between svs versions 1.0.3 dated 2015-10-18 and 1.1.0 dated 2016-01-13
DESCRIPTION | 13 - MD5 | 36 ++-- NAMESPACE | 6 R/svs.r | 349 ++++++++++++++++++++++++++++++++++++--------- man/MI.Rd |only man/cd_plot.Rd | 7 man/centers_ca.Rd | 10 + man/dist_chisquare.Rd | 6 man/dist_cosine.Rd | 6 man/dist_wrt.Rd | 6 man/dist_wrt_centers.Rd | 10 + man/fast_E_M.Rd | 3 man/fast_lca.Rd |only man/fast_mca.Rd | 2 man/fast_psa.Rd | 5 man/freq_ca.Rd | 5 man/outerec.Rd |only man/pc_plot.Rd | 6 man/pmi.Rd |only man/svs-package.Rd | 11 + man/weighting_functions.Rd | 18 +- 21 files changed, 398 insertions(+), 101 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks: 1) Reading and writing
data between R and other statistical software packages like 'SPSS', 'SAS' or
'Stata' and working with labelled data; this includes easy ways to get and set
label attributes, to convert labelled vectors into factors (and vice versa),
or to deal with multiple declared missing values etc. 2) Data transformation
tasks like recoding, dichotomizing or grouping variables, setting and replacing
missing values. 3) Convenient functions to perform frequently used statistical
tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.3 dated 2015-11-23 and 1.4 dated 2016-01-13
DESCRIPTION | 8 - MD5 | 38 +++-- NAMESPACE | 4 NEWS | 14 ++ R/efc.R | 64 ++++----- R/is_empty.R | 90 ++++++++----- R/overdisp.R |only R/std_b.R | 3 R/to_dummy.R |only R/to_value.R | 195 +++++++++++++++--------------- README.md | 20 +-- man/efc.Rd | 71 +++++----- man/get_label.Rd | 160 ++++++++++++------------ man/get_labels.Rd | 324 +++++++++++++++++++++++++------------------------- man/is_empty.Rd | 94 +++++++------- man/overdisp.Rd |only man/set_label.Rd | 228 +++++++++++++++++------------------ man/set_labels.Rd | 292 ++++++++++++++++++++++----------------------- man/sjmisc-package.Rd | 4 man/to_dummy.Rd |only man/to_factor.Rd | 208 ++++++++++++++++---------------- man/to_value.Rd | 3 22 files changed, 933 insertions(+), 887 deletions(-)
Title: Similarity Regression Functions
Description: Functions for performing Bayesian `similarity regression',
specialised for modelling the association between a HPO-encoded phenotype
and binary genotype. A `no association' model is compared with one in which
the log odds of having a rare genotype is linked to the semantic similarity
between patient phenotype and a latent characteristic phenotype. The method
estimates the probability of an association together with an HPO-coded phenotype
characteristic of the disease.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between SimReg versions 1.2 dated 2015-09-15 and 1.3 dated 2016-01-13
SimReg-1.2/SimReg/R/imports.R |only SimReg-1.2/SimReg/man/as.row.leaves.Rd |only SimReg-1.2/SimReg/man/get.term.term.matrix.Rd |only SimReg-1.2/SimReg/man/get.two.term.marginals.Rd |only SimReg-1.2/SimReg/man/hpo.plot.marginal.freqs.Rd |only SimReg-1.2/SimReg/man/leaf.term.pair.marginal.matrix.Rd |only SimReg-1.2/SimReg/man/sim.reg.Rd |only SimReg-1.2/SimReg/man/sim.reg.full.summary.Rd |only SimReg-1.2/SimReg/man/sim.reg.summary.Rd |only SimReg-1.2/SimReg/man/single.term.marginals.plot.Rd |only SimReg-1.2/SimReg/man/two.term.marginals.plot.Rd |only SimReg-1.3/SimReg/DESCRIPTION | 25 SimReg-1.3/SimReg/MD5 | 46 - SimReg-1.3/SimReg/NAMESPACE | 58 + SimReg-1.3/SimReg/R/functions.R | 145 +++- SimReg-1.3/SimReg/R/plots.R | 521 +++++----------- SimReg-1.3/SimReg/R/simReg.R | 231 +++---- SimReg-1.3/SimReg/build |only SimReg-1.3/SimReg/inst |only SimReg-1.3/SimReg/man/SimReg-package.Rd | 28 SimReg-1.3/SimReg/man/as_row_leaves.Rd |only SimReg-1.3/SimReg/man/full_names.Rd |only SimReg-1.3/SimReg/man/log_odds_trace.Rd |only SimReg-1.3/SimReg/man/phi_plot.Rd |only SimReg-1.3/SimReg/man/prune_sim_mat.Rd |only SimReg-1.3/SimReg/man/sim_reg.Rd |only SimReg-1.3/SimReg/man/sim_reg_summary.Rd |only SimReg-1.3/SimReg/man/term_marginals.Rd |only SimReg-1.3/SimReg/man/term_marginals_from_phi_vec.Rd |only SimReg-1.3/SimReg/man/term_pair_marginals.Rd |only SimReg-1.3/SimReg/man/term_pair_marginals_plot.Rd |only SimReg-1.3/SimReg/src/DeltaLikelihood.cpp | 4 SimReg-1.3/SimReg/src/RcppExports.cpp | 11 SimReg-1.3/SimReg/src/RcppExports.h | 16 SimReg-1.3/SimReg/vignettes |only 35 files changed, 511 insertions(+), 574 deletions(-)
Title: Sample Size Computations Controlling the Type-II Generalized
Family-Wise Error Rate
Description: The significance of mean difference tests in clinical trials is established if at least r null hypotheses are rejected among m that are simultaneously tested. This package enables one to compute necessary sample sizes for single-step (Bonferroni) and step-wise procedures (Holm and Hochberg). These three procedures control the q-generalized family-wise error rate (probability of making at least q false rejections). Sample size is computed (for these single-step and step-wise procedures) in a such a way that the r-power (probability of rejecting at least r false null hypotheses, i.e. at least r significant endpoints among m) is above some given threshold, in the context of tests of difference of means for two groups of continuous endpoints (variables). Various types of structure of correlation are considered. It is also possible to analyse data (i.e., actually test difference in means) when these are available. The case r equals 1 is treated in separate functions that were used in Lafaye de Micheaux et al. (2014) <doi:10.1080/10543406.2013.860156>.
Author: Pierre Lafaye de Micheaux, Benoit Liquet and Jeremie Riou
Maintainer: Pierre Lafaye de Micheaux <lafaye@dms.umontreal.ca>
Diff between rPowerSampleSize versions 1.0 dated 2015-11-28 and 1.0.1 dated 2016-01-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/indivne.rm.ssc.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
More information about rPowerSampleSize at CRAN
Permanent link
Title: Hierarchical Modeling and Frequency Method Checking on
Overdispersed Gaussian, Poisson, and Binomial Data
Description: We utilize approximate Bayesian machinery to fit two-level conjugate hierarchical models on overdispersed Gaussian, Poisson, and Binomial data and evaluates whether the resulting approximate Bayesian interval estimates for random effects meet the nominal confidence levels via frequency coverage evaluation. The data that Rgbp assumes comprise observed sufficient statistic for each random effect, such as an average or a proportion of each group, without population-level data. The approximate Bayesian tool equipped with the adjustment for density maximization produces approximate point and interval estimates for model parameters including second-level variance component, regression coefficients, and random effect. For the Binomial data, the package provides an option to produce posterior samples of all the model parameters via the acceptance-rejection method. The package provides a quick way to evaluate coverage rates of the resultant Bayesian interval estimates for random effects via a parametric bootstrapping, which we call frequency method checking.
Author: Joseph Kelly, Hyungsuk Tak, and Carl Morris
Maintainer: Joseph Kelly <josephkelly@post.harvard.edu>
Diff between Rgbp versions 1.1.0 dated 2015-08-04 and 1.1.1 dated 2016-01-13
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ R/br.R | 27 +++++++++---------- R/coverage.R | 78 +++++++++++++++++++++++++++---------------------------- R/gbp.R | 12 ++++---- R/gr.R | 14 ++++----- R/pr.R | 18 ++++++------ man/coverage.Rd | 2 - man/gbp.Rd | 12 ++++---- man/print.gbp.Rd | 4 +- 10 files changed, 96 insertions(+), 95 deletions(-)
Title: Hydrology and Climate Forecasting
Description: Focuses on data processing and visualization in hydrology and
climate forecasting. Main function includes data extraction, data downscaling, data
resampling, gap filler of precipitation, bias correction of forecasting data, flexible
time series plot, and spatial map generation. It is a good pre-processing and
post-processing tool for hydrological and hydraulic modellers.
Author: Yuanchao Xu [aut, cre]
Maintainer: Yuanchao Xu <xuyuanchao37@gmail.com>
Diff between hyfo versions 1.3.4 dated 2015-12-05 and 1.3.6 dated 2016-01-13
DESCRIPTION | 10 +- MD5 | 42 +++++----- NAMESPACE | 2 NEWS | 23 +++++- R/array_dimension.R | 4 - R/biasCorrect(generic).R | 4 - R/getEnsemble.R | 3 R/getPreciBar(generic).R | 4 - R/getSpatialMap.R | 2 R/multi-biasCorrect(generic).R | 4 - R/ncdf.R | 157 +++++++++++++++++++++++++---------------- R/startup.R | 2 README.md | 16 ++++ inst/doc/hyfo.pdf |binary man/downscaleNcdf.Rd | 5 - man/getFrcEnsem.Rd | 3 man/getNcdfVar.Rd | 5 - man/getPreciBar.Rd | 2 man/getPreciBar_comb.Rd | 2 man/getSpatialMap_comb.Rd | 2 man/loadNcdf.Rd | 5 - man/writeNcdf.Rd | 12 +-- 22 files changed, 189 insertions(+), 120 deletions(-)
Title: Functional Clustering Algorithms
Description: Unified framework to cluster functional data according to one of seven models. All models are based on the projection of the curves onto a basis. The main function funcit() calls wrapper functions for the existing algorithms, so that input parameters are the same. A list is returned with each entry representing the same or extended output for the corresponding method. Method specific as well as general visualization tools are available.
Author: Christina Yassouridis [aut, cre],
Dominik Ernst [ctb],
Madison Giacofci [ctb],
Sophie Lambert-Lacroix [ctb],
Guillemette Marot [ctb],
Franck Picard [ctb],
Nicoleta Serban [ctb],
Huijing Jiang [ctb],
Gareth James [ctb],
Catherine Sugar [ctb],
Hans-Georg Mueller [ctb],
Jie Peng [ctb],
Chiou Jeng-Min [ctb],
Pai-Ling Li [ctb]
Maintainer: Christina Yassouridis <c_ya02@yahoo.de>
Diff between funcy versions 0.8.3 dated 2015-10-19 and 0.8.4 dated 2016-01-13
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NEWS.md | 43 ++++++++++++++++++++-------- R/plot.R | 6 ++- R/plotFSCM.R | 79 ++++++++++++++++++++++++++++++---------------------- R/xecute.R | 3 - src/la/clapack.h | 4 +- src/la/uselapack.cc | 2 + 8 files changed, 98 insertions(+), 61 deletions(-)
Title: Doubly Robust Generalized Estimating Equations
Description: Fit restricted mean models for the conditional association
between an exposure and an outcome, given covariates. Three methods
are implemented: O-estimation, where a nuisance model for the
association between the covariates and the outcome is used;
E-estimation where a nuisance model for the association
between the covariates and the exposure is used, and doubly robust (DR)
estimation where both nuisance models are used. In DR-estimation,
the estimates will be consistent when at least one of the nuisance
models is correctly specified, not necessarily both.
Author: Johan Zetterqvist <johan.zetterqvist@ki.se> , Arvid Sjölander <arvid.sjolander@ki.se> with contributions from Alexander Ploner.
Maintainer: Johan Zetterqvist <johan.zetterqvist@ki.se>
Diff between drgee versions 1.1.3 dated 2015-06-12 and 1.1.4 dated 2016-01-13
drgee-1.1.3/drgee/R/clogitRes.R |only drgee-1.1.4/drgee/DESCRIPTION | 13 drgee-1.1.4/drgee/MD5 | 50 - drgee-1.1.4/drgee/NAMESPACE | 9 drgee-1.1.4/drgee/NEWS | 120 ++- drgee-1.1.4/drgee/R/condit.R |only drgee-1.1.4/drgee/R/drFit.R | 34 - drgee-1.1.4/drgee/R/dreFit.R | 529 ++++++++-------- drgee-1.1.4/drgee/R/dreFitCond.R | 44 - drgee-1.1.4/drgee/R/drgee.R | 330 +++++----- drgee-1.1.4/drgee/R/drgeeData.R | 1060 ++++++++++++++++----------------- drgee-1.1.4/drgee/R/eFit.R | 67 -- drgee-1.1.4/drgee/R/findRoots.R | 43 - drgee-1.1.4/drgee/R/gee.R | 272 ++++---- drgee-1.1.4/drgee/R/geeFit.R | 93 +- drgee-1.1.4/drgee/R/geeFitCond.R | 171 ++--- drgee-1.1.4/drgee/R/oFit.R | 82 +- drgee-1.1.4/drgee/R/robVcov.R | 67 +- drgee-1.1.4/drgee/inst/CITATION | 47 + drgee-1.1.4/drgee/man/drgee-package.Rd | 88 +- drgee-1.1.4/drgee/man/drgee.Rd | 617 +++++++++---------- drgee-1.1.4/drgee/man/drgeeData.Rd | 313 ++++----- drgee-1.1.4/drgee/man/findRoots.Rd | 110 +-- drgee-1.1.4/drgee/man/gee.Rd | 208 +++--- drgee-1.1.4/drgee/man/robVcov.Rd | 98 +-- drgee-1.1.4/drgee/src |only 26 files changed, 2273 insertions(+), 2192 deletions(-)
Title: Profile Output Processing Tools for R
Description: Tools for examining Rprof profile output.
Author: Luke Tierney and Riad Jarjour
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between proftools versions 0.99-0 dated 2016-01-05 and 0.99-2 dated 2016-01-13
proftools-0.99-0/proftools/vignettes/Rprof.cg |only proftools-0.99-0/proftools/vignettes/proftools.R |only proftools-0.99-0/proftools/vignettes/proftools.pdf |only proftools-0.99-0/proftools/vignettes/proftools.tex |only proftools-0.99-2/proftools/DESCRIPTION | 9 +++++---- proftools-0.99-2/proftools/MD5 | 13 +++++++------ proftools-0.99-2/proftools/build |only proftools-0.99-2/proftools/inst/doc |only proftools-0.99-2/proftools/man/annotateSource.Rd | 2 +- proftools-0.99-2/proftools/vignettes/jsslogo.jpg |only 10 files changed, 13 insertions(+), 11 deletions(-)
Title: Statistical Matching
Description: Integration of two data sources referred to the same target population which share a number of common variables (aka data fusion). Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio <madorazi@istat.it>
Diff between StatMatch versions 1.2.3 dated 2015-01-29 and 1.2.4 dated 2016-01-13
StatMatch-1.2.3/StatMatch/R/Frechet.bounds.cat.R |only StatMatch-1.2.3/StatMatch/R/RANDwNND.hotdeck.r |only StatMatch-1.2.4/StatMatch/DESCRIPTION | 8 StatMatch-1.2.4/StatMatch/MD5 | 34 - StatMatch-1.2.4/StatMatch/NAMESPACE | 5 StatMatch-1.2.4/StatMatch/NEWS | 8 StatMatch-1.2.4/StatMatch/R/Fbwidths.by.x.R | 121 ++-- StatMatch-1.2.4/StatMatch/R/Frechet.bounds.cat.2.R |only StatMatch-1.2.4/StatMatch/R/RANDwNND.hotdeck.R |only StatMatch-1.2.4/StatMatch/R/comb.samples.R | 285 +++++----- StatMatch-1.2.4/StatMatch/R/pBayes.R |only StatMatch-1.2.4/StatMatch/build/vignette.rds |binary StatMatch-1.2.4/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.R | 78 +- StatMatch-1.2.4/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.Rnw | 105 +-- StatMatch-1.2.4/StatMatch/inst/doc/Statistical_Matching_with_StatMatch.pdf |binary StatMatch-1.2.4/StatMatch/man/Fbwidths.by.x.Rd | 29 - StatMatch-1.2.4/StatMatch/man/Frechet.bounds.cat.Rd | 8 StatMatch-1.2.4/StatMatch/man/comb.samples.Rd | 6 StatMatch-1.2.4/StatMatch/man/pBayes.Rd |only StatMatch-1.2.4/StatMatch/man/pw.assoc.Rd | 4 StatMatch-1.2.4/StatMatch/vignettes/Statistical_Matching_with_StatMatch.Rnw | 105 +-- 21 files changed, 450 insertions(+), 346 deletions(-)
Title: Sensitivity Indices with Dependent Inputs
Description: Sensitivity indices with dependent correlated inputs, using a
method based on PLS regression.
Author: A. Bouvier [aut], J.-P. Gauchi [aut, cre], E. Volatier [ctb]
Maintainer: Annie Bouvier <annie.bouvier@jouy.inra.fr>
Diff between sivipm versions 1.1-2 dated 2015-10-28 and 1.1-3 dated 2016-01-13
DESCRIPTION | 8 +- MD5 | 52 +++++++++---------- NAMESPACE | 5 + NEWS | 12 ++++ R/allmono.R | 2 R/class-sivip.R | 35 +++++++++--- R/factorsplit.R | 2 R/fastregpls2.R | 7 +- R/polynome.R | 2 R/regpls2.R | 24 +++++--- R/sivipm.R | 60 ++++++++++++++------- R/vect2poly.R | 2 inst/doc/Vignette.pdf |binary man/sivip-class.Rd | 15 ++--- man/sivipboot.Rd | 2 man/sivipm.Rd | 33 +++++------- src/bouclen.c | 24 ++++++++ tests/exX18Y14.R | 4 - tests/exX18Y14.Rout.save | 38 +++++++++---- tests/exX18Y2.R | 8 +- tests/exX18Y2.Rout.save | 123 ++++++++++++++++++++++++--------------------- tests/exXY180.R | 2 tests/exXY180.Rout.save | 22 +++++--- tests/excornell0.R | 14 ++--- tests/excornell0.Rout.save | 102 +++++++++++++++++++++---------------- tests/excornell1.R | 10 ++- tests/excornell1.Rout.save | 62 +++++++++++++++++++--- 27 files changed, 424 insertions(+), 246 deletions(-)
Title: Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Description: In the field of stratified sampling design, this package
offers an approach for the determination of the best
stratification of a sampling frame, the one that ensures the
minimum sample cost under the condition to satisfy precision
constraints in a multivariate and multidomain case. This
approach is based on the use of the genetic algorithm: each
solution (i.e. a particular partition in strata of the sampling
frame) is considered as an individual in a population; the
fitness of all individuals is evaluated applying the
Bethel-Chromy algorithm to calculate the sampling size
satisfying precision constraints on the target estimates.
Functions in the package allows to: (a) analyse the obtained
results of the optimisation step; (b) assign the new strata
labels to the sampling frame; (c) select a sample from the new
frame accordingly to the best allocation.
Functions for the execution of the genetic algorithm are a modified
version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Daniela Pagliuca, Egon Willighagen,
Diego Zardetto
Maintainer: Giulio Barcaroli <barcarol@istat.it>
Diff between SamplingStrata versions 1.0-4 dated 2015-08-25 and 1.1 dated 2016-01-13
DESCRIPTION | 13 ++-- MD5 | 31 ++++++----- NAMESPACE | 3 - NEWS | 14 +++++ R/buildStrataDF.R | 7 +- R/optimizeStrata.R | 67 ++++++++++++++++-------- R/plotSamprate.R |only R/rbgaV2.R | 17 +++++- R/recode.R |only R/strataGenalg.R | 8 +- build/vignette.rds |binary inst/doc/SamplingStrataVignette.R | 93 +++++++++++++++++++++++++++++++++ inst/doc/SamplingStrataVignette.Rnw | 97 +++++++++++++++++++++++++++++++++-- inst/doc/SamplingStrataVignette.pdf |binary inst/doc/tuneParameters.pdf |binary man/plotSamprate.Rd |only man/swissmunicipalities.Rd | 4 - vignettes/SamplingStrataVignette.Rnw | 97 +++++++++++++++++++++++++++++++++-- 18 files changed, 389 insertions(+), 62 deletions(-)
More information about SamplingStrata at CRAN
Permanent link
Title: Plotting Multi-Dimensional Data
Description: Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between plot3D versions 1.0-2 dated 2014-11-07 and 1.1 dated 2016-01-13
DESCRIPTION | 16 ++++---- MD5 | 94 +++++++++++++++++++++++++-------------------------- NAMESPACE | 1 R/Contour.R | 1 R/Image.R | 90 +++++++++++++++++++++++++++++++++--------------- R/arrows3D.R | 25 +++++++------ R/box3D.R | 65 +++++++++++++++++++++-------------- R/colorlegend.R | 43 +++++++++++++++++------ R/contour3D.R | 5 +- R/functions.R | 37 ++++++++++++-------- R/hist3D.R | 81 ++++++++++++++++++++++++++++++++++--------- R/image3D.R | 8 ++-- R/isosurf3D.R | 24 ++++++++----- R/paintit.R | 81 ++++++++++++++++++++++++++----------------- R/persp3D.R | 41 +++++++++++++--------- R/persp3Db.R | 4 +- R/plot.struct.R | 20 +++------- R/plot2D.R | 25 +++++++------ R/poly3D.R | 41 ++++++++++++++-------- R/polygon3D.R | 22 +++++++---- R/ribbon3D.R | 28 +++++++++------ R/scatter.R | 16 +++++--- R/scatter3D.R | 19 +++++++--- R/segments3D.R | 18 +++++---- R/slice3D.R | 24 +++++++++---- R/slicecont3D.R | 21 +++++++---- R/sphere.R | 20 +++++++--- R/surf3D.R | 20 ++++++---- R/text3D.R | 28 +++++++++------ R/voxel3D.R | 11 +++-- build/vignette.rds |binary data/Hypsometry.rda |binary data/Oxsat.rda |binary inst/doc/plot3D.R | 90 ++++++++++++++++++++++++++++++++++++++++++++++++ inst/doc/plot3D.rnw | 72 +++++++++++++++++++++++++++++++++++++++ man/Image.Rd | 29 +++++++++++++-- man/Oxsat.Rd | 2 - man/arrows3D.Rd | 48 ++++++++++++++------------ man/colorkey.Rd | 8 +++- man/colors.Rd | 2 - man/image3D.Rd | 13 ++++--- man/persp3D.Rd | 33 +++++++++++------ man/plot3D.Rd | 2 - man/plotdev.Rd | 11 ++++- man/scatter.Rd | 30 ++++++++++------ man/slice3D.Rd | 14 ++++--- man/surf3D.Rd | 15 +++++--- vignettes/plot3D.rnw | 72 +++++++++++++++++++++++++++++++++++++++ 48 files changed, 952 insertions(+), 418 deletions(-)
Title: Helper Functions for QCA in R
Description: Helper functions for Qualitative Comparative Analysis: evaluate and
plot Boolean formulae on fuzzy set score data, apply Boolean operations, compute
consistency and coverage measures.
Author: Jirka Lewandowski <jirka.lewandowski@wzb.eu> [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between QCAtools versions 0.1 dated 2015-01-07 and 0.2.1 dated 2016-01-13
DESCRIPTION | 18 +++++++++++------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 26 ++++++++++++++------------ R/QCAtools-package.r | 6 +++++- R/boolean.R | 4 ++-- R/xyplot.R | 7 ++++--- README.md | 4 ++-- man/QCAtools.Rd | 2 +- man/boolean.Rd | 3 ++- man/consistency.Rd | 8 +++++--- man/evaluate_dnf.Rd | 5 +++-- man/format_dnf.Rd | 2 +- man/formula_to_function.Rd | 3 ++- man/plot.qca.Rd | 5 +++-- man/xyplot.Rd | 5 +++-- 15 files changed, 72 insertions(+), 54 deletions(-)
More information about ontologySimilarity at CRAN
Permanent link
Title: An R Package for Multiple Break-Point Detection via the
Cross-Entropy Method
Description: Implements the Cross-Entropy (CE) method, which is a model based stochastic optimization technique to estimate both the number and their corresponding locations of break-points in continuous and discrete measurements (Priyadarshana and Sofronov (2015), Priyadarshana and Sofronov (2012a), Priyadarshana and Sofronov (2012b)).
Author: Priyadarshana W.J.R.M. and Georgy Sofronov
Maintainer: Priyadarshana W.J.R.M. <mjayawardana@swin.edu.au>
Diff between breakpoint versions 1.1 dated 2014-12-21 and 1.2 dated 2016-01-13
breakpoint-1.1/breakpoint/R/CE.Normal.R |only breakpoint-1.1/breakpoint/R/ce.4betaNB.R |only breakpoint-1.1/breakpoint/R/ce.simNormalNB.R |only breakpoint-1.1/breakpoint/man/CE.Normal.Rd |only breakpoint-1.2/breakpoint/DESCRIPTION | 22 +- breakpoint-1.2/breakpoint/MD5 | 89 ++++++-- breakpoint-1.2/breakpoint/NAMESPACE | 5 breakpoint-1.2/breakpoint/NEWS |only breakpoint-1.2/breakpoint/R/AIC.MeanNormal.R |only breakpoint-1.2/breakpoint/R/AIC.MeanVarNormal.R |only breakpoint-1.2/breakpoint/R/AICnb.R |only breakpoint-1.2/breakpoint/R/AICzinb.R |only breakpoint-1.2/breakpoint/R/BIC.MeanNormal.R |only breakpoint-1.2/breakpoint/R/BIC.MeanVarNormal.R |only breakpoint-1.2/breakpoint/R/CE.NB.Init.R |only breakpoint-1.2/breakpoint/R/CE.NB.R | 131 ++++++++---- breakpoint-1.2/breakpoint/R/CE.Normal.Init.Mean.R |only breakpoint-1.2/breakpoint/R/CE.Normal.Init.MeanVar.R |only breakpoint-1.2/breakpoint/R/CE.Normal.Mean.R |only breakpoint-1.2/breakpoint/R/CE.Normal.MeanVar.R |only breakpoint-1.2/breakpoint/R/CE.ZINB.Init.R |only breakpoint-1.2/breakpoint/R/CE.ZINB.R | 131 ++++++++---- breakpoint-1.2/breakpoint/R/betaIntEst.R |only breakpoint-1.2/breakpoint/R/breakpoint-internal.R |only breakpoint-1.2/breakpoint/R/ce.4betaNB.AIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.4betaNB.AIC.R |only breakpoint-1.2/breakpoint/R/ce.4betaNB.BIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.4betaNB.BIC.R |only breakpoint-1.2/breakpoint/R/ce.4betaZINB.AIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.4betaZINB.AIC.R |only breakpoint-1.2/breakpoint/R/ce.4betaZINB.BIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.4betaZINB.BIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.Mean.AIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.Mean.BIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.MeanVar.AIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.MeanVar.BIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.Init.mBIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.MeanAIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.MeanBIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.MeanVar.AIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.MeanVar.BIC.R |only breakpoint-1.2/breakpoint/R/ce.sim4beta.R | 7 breakpoint-1.2/breakpoint/R/ce.simNormalNB.AIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.simNormalNB.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simNormalNB.BIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.simNormalNB.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simNormalZINB.AIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.simNormalZINB.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simNormalZINB.BIC.Init.R |only breakpoint-1.2/breakpoint/R/ce.simNormalZINB.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.Mean.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.Mean.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.MeanVar.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.MeanVar.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.Init.mBIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.MeanAIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.MeanBIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.MeanVar.AIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.MeanVar.BIC.R |only breakpoint-1.2/breakpoint/R/ce.simnormal.R | 9 breakpoint-1.2/breakpoint/R/llhood.MeanNormal.R |only breakpoint-1.2/breakpoint/R/llhood.MeanVarNormal.R |only breakpoint-1.2/breakpoint/R/loglik.MeanNormal.R |only breakpoint-1.2/breakpoint/R/loglik.MeanVarNormal.R |only breakpoint-1.2/breakpoint/R/profilePlot.R | 3 breakpoint-1.2/breakpoint/data/ch1.GM03563.rda |binary breakpoint-1.2/breakpoint/man/CE.NB.Init.Rd |only breakpoint-1.2/breakpoint/man/CE.NB.Rd | 49 ++-- breakpoint-1.2/breakpoint/man/CE.Normal.Init.Mean.Rd |only breakpoint-1.2/breakpoint/man/CE.Normal.Init.MeanVar.Rd |only breakpoint-1.2/breakpoint/man/CE.Normal.Mean.Rd |only breakpoint-1.2/breakpoint/man/CE.Normal.MeanVar.Rd |only breakpoint-1.2/breakpoint/man/CE.ZINB.Init.Rd |only breakpoint-1.2/breakpoint/man/CE.ZINB.Rd | 38 ++- breakpoint-1.2/breakpoint/man/breakpoint-package.Rd | 19 - breakpoint-1.2/breakpoint/man/ch1.GM03563.Rd | 6 breakpoint-1.2/breakpoint/man/profilePlot.Rd | 16 - 77 files changed, 365 insertions(+), 160 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-29 0.1.1
2015-04-02 0.1.0
Title: Using GPUs in Statistical Genomics
Description: Can be used to carry out
permutation resampling inference in the context of RNA
microarray studies.
Author: Ivo D. Shterev, Sin-Ho Jung, Stephen L. George and Kouros Owzar
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>
Diff between permGPU versions 0.14.7 dated 2016-01-07 and 0.14.8 dated 2016-01-13
DESCRIPTION | 12 +++++++----- MD5 | 10 +++++----- NEWS | 4 ++++ man/permGPU-package.Rd | 5 +++-- man/permgpu.Rd | 4 ++-- man/scoregpu.Rd | 4 ++-- 6 files changed, 23 insertions(+), 16 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of a joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Multivariate joint frailty models for two types of recurrent events and a terminal event.
7) Joint models for longitudinal data and a terminal event.
8) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.8.2 dated 2015-12-08 and 2.8.3 dated 2016-01-13
DESCRIPTION | 8 +++---- MD5 | 26 ++++++++++++---------- NEWS | 6 +++++ R/epoce.R | 3 +- R/prediction.R | 2 - R/print.trivPenal.R | 2 - man/frailtyPenal.Rd | 2 - man/frailtypack-package.Rd | 6 ++--- man/num.id.Rd | 17 +++++++-------- src/aresidusMartingale.f90 | 51 +++++++++++++++++++++++---------------------- src/epoce.f90 |only src/epoce_log.f90 |only src/epoce_long.f90 | 8 +++---- src/joint_longi.f90 | 18 +++++++-------- src/prediction_tri.f90 | 12 +++++----- 15 files changed, 87 insertions(+), 74 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.4-3 dated 2015-12-06 and 1.4-4 dated 2016-01-13
DESCRIPTION | 11 ++-- MD5 | 44 ++++++++-------- NAMESPACE | 1 NEWS | 16 +++++ R/AbdFreqCount.R | 4 - R/CommunityProfile.R | 4 - R/Coverage.R | 2 R/DivEst.R | 10 ++- R/DivPart.R | 3 - R/DivProfile.R | 121 +++++++++++++++++++++++++++++++++++++++++---- R/Shannon.R | 18 +++--- R/SpeciesDistribution.R | 4 - R/Tsallis.R | 19 ++----- R/rCommunity.R | 6 -- build/vignette.rds |binary inst/doc/entropart.R | 2 inst/doc/entropart.Rnw | 6 +- inst/doc/entropart.pdf |binary man/DivEst.Rd | 4 - man/DivProfile.Rd | 29 +++++++++- man/SpeciesDistribution.Rd | 4 - vignettes/entropart.Rnw | 6 +- vignettes/entropart.bib | 10 +++ 23 files changed, 238 insertions(+), 86 deletions(-)
Title: Generate Cofeature Matrices
Description: Generate cofeature (feature by sample) matrices. The package
utilizes ggplot2::geom_tile() to generate the matrix allowing for easy
additions from the base matrix.
Author: Fong Chun Chan [aut, cre]
Maintainer: Fong Chun Chan <fongchunchan@gmail.com>
Diff between cofeatureR versions 1.0.0 dated 2015-12-23 and 1.0.1 dated 2016-01-13
DESCRIPTION | 10 ++--- MD5 | 6 +-- R/plot_cofeature_mat.R | 9 ++--- README.md | 87 ++++++++++++++++++++++++++++++++++++++----------- 4 files changed, 81 insertions(+), 31 deletions(-)
Title: A MediaWiki API Wrapper
Description: A wrapper for the MediaWiki API, aimed particularly at the
Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve
page text, information about users or the history of pages, and elements of
the category tree.
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between WikipediR versions 1.2.0 dated 2015-05-17 and 1.3.0 dated 2016-01-13
DESCRIPTION | 12 +++++++----- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 3 ++- NEWS | 9 +++++++++ R/categories.R | 7 +++++-- R/metadata.R | 7 +++++-- R/query.R | 13 +++++++------ README.md | 6 ++++-- build/vignette.rds |binary man/categories_in_page.Rd | 3 ++- man/page_backlinks.Rd | 2 +- man/page_content.Rd | 2 +- man/page_external_links.Rd | 2 +- man/page_info.Rd | 3 ++- man/page_links.Rd | 7 +++++-- man/pages_in_category.Rd | 18 +++++++++++------- man/query.Rd | 2 +- man/random_page.Rd | 2 +- man/recent_changes.Rd | 2 +- man/revision_content.Rd | 3 ++- man/revision_diff.Rd | 3 ++- man/user_contributions.Rd | 6 ++++-- man/user_information.Rd | 2 +- 23 files changed, 96 insertions(+), 62 deletions(-)
Title: Access and Plot CanVec and CanVec+ Data for Rapid Basemap
Creation in Canada
Description: Provides an interface to the National Topographic System (NTS), which is
the way in which a number of freely available Canadian datasets
are organized. CanVec and CanVec+ datasets, which include all data used
to create Canadian topographic maps, are two such datasets that are useful
in creating vector-based maps for locations across Canada. This packages searches
CanVec data by location, plots it using pretty defaults, and exports it to
human-readable shapefiles for use in another GIS.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rcanvec versions 0.1.3 dated 2015-10-18 and 0.1.4 dated 2016-01-13
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/nts.R | 4 +++- README.md |only man/rcanvec-package.Rd | 9 +-------- 5 files changed, 12 insertions(+), 16 deletions(-)
Title: Body Mass Estimation Equations for Vertebrates
Description: Estimation equations are from a variety of sources but are, in general, based on regressions between skeletal measurements (e.g., femoral circumference) and body mass in living taxa.
Author: Nicolas E. Campione
Maintainer: Nicolas E. Campione <nicolas.campione@geo.uu.se>
Diff between MASSTIMATE versions 1.2 dated 2014-05-19 and 1.3 dated 2016-01-13
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ NAMESPACE | 1 + R/QE.R | 27 +++++++++++++++++++++++---- R/bipeds.R | 20 ++++++++++++++++++-- R/cQE.R | 22 ++++++++++++++++++++-- R/quadrupeds.R | 30 +++++++++++++++++++++++++----- README.md |only man/MASSTIMATE-package.Rd | 12 +++++++----- man/QE.Rd | 30 +++++++++++++++++++++--------- man/bipeds.Rd | 19 ++++++++++++------- man/cQE.Rd | 39 ++++++++++++++++++++++++--------------- man/dinosbip.Rd | 4 ++-- man/quadrupeds.Rd | 15 ++++++++++----- 14 files changed, 180 insertions(+), 72 deletions(-)
Title: R Interface to 'lp_solve' Version 5.5.2.0
Description: The lpSolveAPI package provides an R interface to 'lp_solve',
a Mixed Integer Linear Programming (MILP) solver with support for pure
linear, (mixed) integer/binary, semi-continuous and special ordered sets
(SOS) models.
Author: lp_solve <http://lpsolve.sourceforge.net/>,
Kjell Konis <kjell.konis@me.com>.
Maintainer: Kjell Konis <kjell.konis@me.com>
Diff between lpSolveAPI versions 5.5.2.0-14 dated 2014-11-12 and 5.5.2.0-17 dated 2016-01-13
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- NAMESPACE | 21 ++++++++++++++++----- R/lp.control.q | 4 ++-- 4 files changed, 29 insertions(+), 18 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/1.10.4/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
Sami Samhuri [ctb, cph] (Javascript strftime library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 0.12.2 dated 2015-08-05 and 0.13.0 dated 2016-01-12
shiny-0.12.2/shiny/inst/www/shared/jqueryui/1.10.4 |only shiny-0.13.0/shiny/DESCRIPTION | 37 shiny-0.13.0/shiny/LICENSE | 2 shiny-0.13.0/shiny/MD5 | 417 ++-- shiny-0.13.0/shiny/NAMESPACE | 30 shiny-0.13.0/shiny/NEWS | 82 shiny-0.13.0/shiny/R/app.R | 114 + shiny-0.13.0/shiny/R/bootstrap-layout.R | 192 ++ shiny-0.13.0/shiny/R/bootstrap.R | 179 +- shiny-0.13.0/shiny/R/conditions.R |only shiny-0.13.0/shiny/R/graph.R | 25 shiny-0.13.0/shiny/R/htmltools.R | 1 shiny-0.13.0/shiny/R/image-interact-opts.R | 5 shiny-0.13.0/shiny/R/imageutils.R | 9 shiny-0.13.0/shiny/R/input-select.R | 11 shiny-0.13.0/shiny/R/input-text.R | 10 shiny-0.13.0/shiny/R/jqueryui.R | 2 shiny-0.13.0/shiny/R/middleware-shiny.R | 36 shiny-0.13.0/shiny/R/middleware.R | 2 shiny-0.13.0/shiny/R/modules.R |only shiny-0.13.0/shiny/R/progress.R | 8 shiny-0.13.0/shiny/R/react.R | 24 shiny-0.13.0/shiny/R/reactive-domains.R | 2 shiny-0.13.0/shiny/R/reactives.R | 222 +- shiny-0.13.0/shiny/R/render-plot.R | 48 shiny-0.13.0/shiny/R/render-table.R |only shiny-0.13.0/shiny/R/server.R | 468 +++-- shiny-0.13.0/shiny/R/shiny.R | 221 ++ shiny-0.13.0/shiny/R/shinyui.R | 88 - shiny-0.13.0/shiny/R/shinywrappers.R | 45 shiny-0.13.0/shiny/R/showcase.R | 2 shiny-0.13.0/shiny/R/update-input.R | 23 shiny-0.13.0/shiny/R/utils.R | 321 +++ shiny-0.13.0/shiny/README.md | 2 shiny-0.13.0/shiny/build |only shiny-0.13.0/shiny/inst/doc |only shiny-0.13.0/shiny/inst/staticdocs/index.r | 20 shiny-0.13.0/shiny/inst/template |only shiny-0.13.0/shiny/inst/tests/test-modules.R |only shiny-0.13.0/shiny/inst/tests/test-reactivity.r | 26 shiny-0.13.0/shiny/inst/tests/test-stacks.R |only shiny-0.13.0/shiny/inst/tests/test-staticdocs.R | 2 shiny-0.13.0/shiny/inst/tests/test-stop-app.R |only shiny-0.13.0/shiny/inst/tests/test-ui.R |only shiny-0.13.0/shiny/inst/tests/test-utils.R | 28 shiny-0.13.0/shiny/inst/www/shared/bootstrap/css/bootstrap-theme.css | 147 + 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shiny-0.13.0/shiny/inst/www/shared/jqueryui/README |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/images |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/index.html |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/jquery-ui.css |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/jquery-ui.js |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/jquery-ui.min.css |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/jquery-ui.min.js |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/jquery-ui.structure.css |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/jquery-ui.structure.min.css |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/jquery-ui.theme.css |only shiny-0.13.0/shiny/inst/www/shared/jqueryui/jquery-ui.theme.min.css |only shiny-0.13.0/shiny/inst/www/shared/selectize/css/selectize.bootstrap3.css | 12 shiny-0.13.0/shiny/inst/www/shared/selectize/js/selectize.min.js | 6 shiny-0.13.0/shiny/inst/www/shared/shiny.js | 299 +++ shiny-0.13.0/shiny/inst/www/shared/shiny.js.map | 2 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Title: Repulsive Text and Label Geoms for 'ggplot2'
Description:
Provides text and label geoms for 'ggplot2' that help to avoid overlapping
text labels. Labels repel away from each other and away from the data
points.
Author: Kamil Slowikowski [aut, cre]
Maintainer: Kamil Slowikowski <kslowikowski@fas.harvard.edu>
Diff between ggrepel versions 0.3 dated 2016-01-09 and 0.4 dated 2016-01-12
ggrepel-0.3/ggrepel/R/utils.R |only ggrepel-0.4/ggrepel/DESCRIPTION | 8 ggrepel-0.4/ggrepel/MD5 | 44 +-- ggrepel-0.4/ggrepel/NEWS | 26 ++ ggrepel-0.4/ggrepel/R/RcppExports.R | 8 ggrepel-0.4/ggrepel/R/geom-label-repel.R | 102 ++++--- ggrepel-0.4/ggrepel/R/geom-text-repel.R | 128 ++++------ ggrepel-0.4/ggrepel/R/ggrepel-package.R | 16 + ggrepel-0.4/ggrepel/README.md | 19 + ggrepel-0.4/ggrepel/inst/doc/ggrepel.R | 43 --- ggrepel-0.4/ggrepel/inst/doc/ggrepel.Rmd | 60 ++++ ggrepel-0.4/ggrepel/inst/doc/ggrepel.html | 79 ++++-- ggrepel-0.4/ggrepel/man/geom_text_repel.Rd | 28 +- ggrepel-0.4/ggrepel/man/ggrepel.Rd | 16 + ggrepel-0.4/ggrepel/man/intersect_line_rectangle.Rd | 4 ggrepel-0.4/ggrepel/src/RcppExports.cpp | 13 + ggrepel-0.4/ggrepel/src/repel_boxes.cpp | 119 +++++---- ggrepel-0.4/ggrepel/vignettes/figures/ggrepel/animated.gif |only ggrepel-0.4/ggrepel/vignettes/figures/ggrepel/geom_label_repel-1.png |binary ggrepel-0.4/ggrepel/vignettes/figures/ggrepel/geom_text_repel-1.png |binary ggrepel-0.4/ggrepel/vignettes/figures/ggrepel/geom_text_repel_options-1.png |binary ggrepel-0.4/ggrepel/vignettes/figures/ggrepel/volcano-1.png |only ggrepel-0.4/ggrepel/vignettes/genes.txt.bz2 |only ggrepel-0.4/ggrepel/vignettes/ggrepel.Rmd | 60 ++++ ggrepel-0.4/ggrepel/vignettes/ggrepel.md | 87 +++++- 25 files changed, 559 insertions(+), 301 deletions(-)
Title: Interface Between GRASS 7 Geographical Information System and R
Description: Interpreted interface between GRASS 7 geographical
information system and R, based on starting R from within the GRASS GIS
environment, or running free-standing R in a temporary GRASS location;
the package provides facilities for using all GRASS commands from the
R command line. This package may not be used for GRASS 6, for which
spgrass6 should be used.
Author: Roger Bivand [cre, aut],
Rainer Krug [ctb],
Markus Neteler [ctb],
Sebastian Jeworutzki [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass7 versions 0.1-3 dated 2015-10-12 and 0.1-4 dated 2016-01-12
ChangeLog | 1107 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 11 MD5 | 14 R/AAA.R | 18 R/rgrass.R | 2 R/vect_link.R | 76 ++- R/xml1.R | 49 -- inst/ChangeLog | 41 ++ 8 files changed, 1224 insertions(+), 94 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for doing parallel programming with 'Rcpp'.
For example, the parallelFor() function can be used to convert the work of
a standard serial "for" loop into a parallel one and the parallelReduce()
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut, cre],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between RcppParallel versions 4.3.14 dated 2015-06-02 and 4.3.15 dated 2016-01-12
RcppParallel-4.3.14/RcppParallel/NEWS |only RcppParallel-4.3.15/RcppParallel/DESCRIPTION | 10 +++++----- RcppParallel-4.3.15/RcppParallel/MD5 | 6 +++--- RcppParallel-4.3.15/RcppParallel/inst/NEWS |only RcppParallel-4.3.15/RcppParallel/src/Makevars | 10 +++++++--- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Model-Based Clustering for Multivariate Partial Ranking Data
Description: Implementation of a model-based clustering algorithm for
ranking data. Multivariate rankings as well as partial rankings are taken
into account. This algorithm is based on an extension of the Insertion
Sorting Rank (ISR) model for ranking data, which is a meaningful and
effective model parametrized by a position parameter (the modal ranking,
quoted by mu) and a dispersion parameter (quoted by pi). The heterogeneity
of the rank population is modelled by a mixture of ISR, whereas conditional
independence assumption is considered for multivariate rankings.
Author: Quentin Grimonprez, Julien Jacques
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Diff between Rankcluster versions 0.92.9 dated 2014-07-25 and 0.93.1 dated 2016-01-12
DESCRIPTION | 22 MD5 | 102 - NAMESPACE | 2 R/RankDistance.R | 266 ++- R/RankFunctions.R | 146 +- R/Rankcluster-package.R | 6 R/conversion.R | 400 ++--- R/criteria.R | 18 R/data.R | 8 R/mixtureSEM.R | 304 ++-- R/rankclust.R | 88 - R/resultClass.R | 395 ++--- R/test.R | 410 ++--- build/vignette.rds |binary data/APA.rda |binary data/big4.rda |binary data/eurovision.rda |binary data/quiz.rda |binary data/sports.rda |binary data/words.rda |binary inst/doc/Rankcluster.pdf |binary man/APA.Rd | 14 man/Output-class.Rd | 3 man/Rankclust-class.Rd | 4 man/Rankcluster-package.Rd | 10 man/big4.Rd | 14 man/convertRank.Rd | 3 man/criteria.Rd | 3 man/distCayley.Rd | 5 man/distHamming.Rd | 5 man/distKendall.Rd | 5 man/distSpearman.Rd | 5 man/eurovision.Rd | 18 man/frequence.Rd | 3 man/getter-methods.Rd | 5 man/khi2.Rd | 7 man/kullback.Rd | 9 man/probability.Rd | 11 man/quiz.Rd | 18 man/rankclust.Rd | 14 man/show-methods.Rd | 3 man/simulISR.Rd | 3 man/sports.Rd | 12 man/summary-methods.Rd | 5 man/unfrequence.Rd | 3 man/words.Rd | 10 src/RankCluster.cpp | 3148 ++++++++++++++++++++++----------------------- src/functions.cpp | 909 ++++++------ src/functions.h | 4 src/run.cpp | 229 +-- src/runFunctions.cpp | 4 src/test.cpp | 7 52 files changed, 3365 insertions(+), 3295 deletions(-)
Title: Visually Assessing the Specificity and Informativeness of Primer
Pairs
Description: Identifies potential target sequences for a given set of primers
and generates taxonomically annotated phylogenetic trees with the predicted
amplification products.
Author: Jim Hester
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between primerTree versions 1.0.1 dated 2014-06-09 and 1.0.3 dated 2016-01-12
DESCRIPTION | 16 ++++++----- MD5 | 54 +++++++++++++++++++++------------------- NAMESPACE | 17 ++++++++++-- R/filterResults.R |only R/plot.R | 4 +- R/primerTree.R | 17 ++++++++---- R/search.R | 10 +++++-- R/sequence.R | 6 ++-- man/accession2gi.Rd | 3 +- man/bryophytes_trnL.Rd | 3 +- man/clustalo.Rd | 3 +- man/filter_seqs.Rd |only man/get_sequence.Rd | 3 +- man/get_sequences.Rd | 3 +- man/get_taxonomy.Rd | 3 +- man/gi2taxid.Rd | 3 +- man/identify.primerTree_plot.Rd | 3 +- man/layout_tree_ape.Rd | 3 +- man/mammals_16S.Rd | 3 +- man/plot.primerTree.Rd | 3 +- man/plot_tree.Rd | 15 +++++------ man/plot_tree_ranks.Rd | 9 +++--- man/primerTree.Rd | 3 +- man/primer_search.Rd | 3 +- man/search_primer_pair.Rd | 29 +++++++++++---------- man/seq_lengths.Rd |only man/seq_lengths.primerTree.Rd |only man/summary.primerTree.Rd | 3 +- man/tree_from_alignment.Rd | 8 ++++- src/read_dna.c | 8 ++--- 30 files changed, 143 insertions(+), 92 deletions(-)
Title: Multiple Comparisons Using Normal Approximation
Description: Multiple contrast tests and simultaneous confidence
intervals based on normal approximation. With implementations for
binomial proportions in a 2xk setting (risk difference and odds ratio),
poly-3-adjusted tumour rates, biodiversity indices (multinomial data)
and expected values under lognormal assumption. Approximative power
calculation for multiple contrast tests of binomial and Gaussian data.
Author: Frank Schaarschmidt [aut, cre], Daniel Gerhard [aut], Martin Sill [aut]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>
Diff between MCPAN versions 1.1-15 dated 2013-10-10 and 1.1-20 dated 2016-01-12
DESCRIPTION | 13 ++++++------- MD5 | 23 +++++++++++++---------- NAMESPACE | 41 ++++++++++++++++++++++++++++++++++++++++- R/multinomORci.R |only R/powerbinom.R | 14 +++++++------- R/powermcpn.R | 18 +++++++++--------- R/powermcpt.R | 19 ++++++++++--------- man/MCPAN-package.Rd | 6 +++--- man/binomORci.Rd | 4 ++-- man/multinomORci.Rd |only man/powerbinom.Rd | 4 +++- man/powermcpn.Rd | 4 +++- man/powermcpt.Rd | 1 + man/print.multinomORci.Rd |only 14 files changed, 97 insertions(+), 50 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [aut],
Joerg Bendix [aut]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.3.1 dated 2015-10-06 and 0.4.0 dated 2016-01-12
hsdar-0.3.1/hsdar/data/endmember_spectra.RData |only hsdar-0.3.1/hsdar/man/endmember_spectra.Rd |only hsdar-0.4.0/hsdar/ChangeLog | 34 hsdar-0.4.0/hsdar/DESCRIPTION | 13 hsdar-0.4.0/hsdar/MD5 | 118 +- hsdar-0.4.0/hsdar/NAMESPACE | 6 hsdar-0.4.0/hsdar/R/AAAClasses.R | 13 hsdar-0.4.0/hsdar/R/USGS_speclib.R |only hsdar-0.4.0/hsdar/R/blockwise_functions.R | 6 hsdar-0.4.0/hsdar/R/caret_createDataPartition.R |only hsdar-0.4.0/hsdar/R/caret_featurePlot.R |only hsdar-0.4.0/hsdar/R/caret_gafs.R |only hsdar-0.4.0/hsdar/R/caret_parameters.R |only hsdar-0.4.0/hsdar/R/caret_preProcess.R |only hsdar-0.4.0/hsdar/R/caret_rfe.R |only hsdar-0.4.0/hsdar/R/caret_safs.R |only hsdar-0.4.0/hsdar/R/caret_sbf.R |only hsdar-0.4.0/hsdar/R/caret_train.R |only hsdar-0.4.0/hsdar/R/caret_utils.R |only hsdar-0.4.0/hsdar/R/getFiniteNri.R |only hsdar-0.4.0/hsdar/R/nri.R | 7 hsdar-0.4.0/hsdar/R/nri_attributes.R |only hsdar-0.4.0/hsdar/R/nri_index.R |only hsdar-0.4.0/hsdar/R/nri_methods.R | 4 hsdar-0.4.0/hsdar/R/speclib.R | 16 hsdar-0.4.0/hsdar/R/speclib_bandnames.R | 9 hsdar-0.4.0/hsdar/R/speclib_index.R | 40 hsdar-0.4.0/hsdar/R/speclib_mask.R | 1 hsdar-0.4.0/hsdar/R/speclib_raster-methods.R |only hsdar-0.4.0/hsdar/R/speclib_spectra.R | 125 ++ hsdar-0.4.0/hsdar/build/hsdar.pdf |only hsdar-0.4.0/hsdar/build/vignette.rds |binary hsdar-0.4.0/hsdar/data/spectral_data.RData |binary hsdar-0.4.0/hsdar/inst/doc/References.pdf |binary hsdar-0.4.0/hsdar/inst/doc/hsdar-intro.Rnw | 172 +-- hsdar-0.4.0/hsdar/inst/doc/hsdar-intro.pdf |binary hsdar-0.4.0/hsdar/man/DistMat3D-methods.Rd | 4 hsdar-0.4.0/hsdar/man/Nri-class.Rd | 1 hsdar-0.4.0/hsdar/man/USGS.Rd |only hsdar-0.4.0/hsdar/man/applySpeclib.Rd | 4 hsdar-0.4.0/hsdar/man/attributes_speclib.Rd | 15 hsdar-0.4.0/hsdar/man/bdri.Rd | 2 hsdar-0.4.0/hsdar/man/caret_createDataPartition-methods.Rd |only hsdar-0.4.0/hsdar/man/caret_createFolds-methods.Rd |only hsdar-0.4.0/hsdar/man/caret_createResample-methods.Rd |only hsdar-0.4.0/hsdar/man/caret_featurePlot-methods.Rd |only hsdar-0.4.0/hsdar/man/caret_gafs.Rd |only hsdar-0.4.0/hsdar/man/caret_preProcess-methods.Rd |only hsdar-0.4.0/hsdar/man/caret_rfe.Rd |only hsdar-0.4.0/hsdar/man/caret_safs.Rd |only hsdar-0.4.0/hsdar/man/caret_setPredictor.Rd |only hsdar-0.4.0/hsdar/man/caret_setResponse.Rd |only hsdar-0.4.0/hsdar/man/caret_sfb.Rd |only hsdar-0.4.0/hsdar/man/caret_showCaretParameters.Rd |only hsdar-0.4.0/hsdar/man/caret_train-methods.Rd |only hsdar-0.4.0/hsdar/man/cor.test.normalized.ratio.index.Rd | 2 hsdar-0.4.0/hsdar/man/cut.specfeat.Rd | 2 hsdar-0.4.0/hsdar/man/define.features.Rd | 2 hsdar-0.4.0/hsdar/man/dist_speclib.Rd | 32 hsdar-0.4.0/hsdar/man/feature_properties.Rd | 2 hsdar-0.4.0/hsdar/man/getNRI.Rd | 2 hsdar-0.4.0/hsdar/man/glm.normalized.ratio.index.Rd | 2 hsdar-0.4.0/hsdar/man/normalized.ratio.index-methods.Rd | 7 hsdar-0.4.0/hsdar/man/normalized.ratio.index.best.perfomance.Rd | 2 hsdar-0.4.0/hsdar/man/plot.glm.normalized.ratio.index.Rd | 11 hsdar-0.4.0/hsdar/man/rededge.Rd | 2 hsdar-0.4.0/hsdar/man/specfeat.Rd | 4 hsdar-0.4.0/hsdar/man/speclib.Rd | 1 hsdar-0.4.0/hsdar/man/spectra.Rd | 31 hsdar-0.4.0/hsdar/man/spectral_data.Rd | 10 hsdar-0.4.0/hsdar/man/subset_speclib.Rd | 8 hsdar-0.4.0/hsdar/man/t.test.nri.Rd | 6 hsdar-0.4.0/hsdar/man/unmix.Rd | 40 hsdar-0.4.0/hsdar/vignettes/hsdar-intro.Rnw | 172 +-- hsdar-0.4.0/hsdar/vignettes/hsdar-intro.tex | 564 ++++------ hsdar-0.4.0/hsdar/vignettes/hsdar.bib | 8 76 files changed, 871 insertions(+), 629 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new
approach to the statistical analysis of multi-valued data, we consider
histogram-valued data, i.e., data described by univariate histograms. The
methods and the basic statistics for histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., a Euclidean metric
between quantile functions. The package contains unsupervised classification
techniques, least square regression and tools for histogram-valued data and for
histogram time series.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unina2.it>
Diff between HistDAWass versions 0.1.3 dated 2015-07-16 and 0.1.4 dated 2016-01-12
HistDAWass-0.1.3/HistDAWass/data/datalist |only HistDAWass-0.1.4/HistDAWass/DESCRIPTION | 24 - HistDAWass-0.1.4/HistDAWass/MD5 | 185 ++++------ HistDAWass-0.1.4/HistDAWass/NAMESPACE | 2 HistDAWass-0.1.4/HistDAWass/R/Met_HTS.R | 12 HistDAWass-0.1.4/HistDAWass/R/Met_MatH.R | 35 - HistDAWass-0.1.4/HistDAWass/R/Met_distributionH.R | 4 HistDAWass-0.1.4/HistDAWass/R/Plotting_with_ggplot.R | 7 HistDAWass-0.1.4/HistDAWass/R/Utility.R | 31 - HistDAWass-0.1.4/HistDAWass/man/Age_Pyramids_2014.Rd | 8 HistDAWass-0.1.4/HistDAWass/man/Agronomique.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/BLOOD.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/BloodBRITO.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/Center.cell.MatH-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/China_Month.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/China_Seas.Rd | 6 HistDAWass-0.1.4/HistDAWass/man/DouglasPeucker.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/HTS-class.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/HTS.exponential.smoothing.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/HTS.moving.averages.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/HTS.predict.knn.Rd | 18 HistDAWass-0.1.4/HistDAWass/man/HistDAWass-package.Rd | 16 HistDAWass-0.1.4/HistDAWass/man/MatH-class.Rd | 5 HistDAWass-0.1.4/HistDAWass/man/OzoneFull.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/OzoneH.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/RetHTS.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/ShortestDistance.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/TMatH-class.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/TdistributionH-class.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/WH.1d.PCA.Rd | 20 - 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HistDAWass-0.1.4/HistDAWass/man/WH_2d_Kohonen_maps.Rd | 26 - HistDAWass-0.1.4/HistDAWass/man/WH_adaptive.kmeans.Rd | 16 HistDAWass-0.1.4/HistDAWass/man/WH_adaptive_fcmeans.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/WH_fcmeans.Rd | 8 HistDAWass-0.1.4/HistDAWass/man/WH_hclust.Rd | 10 HistDAWass-0.1.4/HistDAWass/man/WH_kmeans.Rd | 14 HistDAWass-0.1.4/HistDAWass/man/WassSqDistH-methods.Rd | 6 HistDAWass-0.1.4/HistDAWass/man/checkEmptyBins-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/compP-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/compQ-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/crwtransform-methods.Rd | 3 HistDAWass-0.1.4/HistDAWass/man/data2hist.Rd | 14 HistDAWass-0.1.4/HistDAWass/man/distributionH-class.Rd | 6 HistDAWass-0.1.4/HistDAWass/man/dotpW-methods.Rd | 5 HistDAWass-0.1.4/HistDAWass/man/extract-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/get.MatH.main.info-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/get.MatH.ncols-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/get.MatH.nrows-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/get.MatH.rownames-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/get.MatH.stats-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/get.MatH.varnames-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/get.distr-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/get.histo-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/get.m-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/get.s-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/is.registeredMH-methods.Rd | 8 HistDAWass-0.1.4/HistDAWass/man/kurtH-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/meanH-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/minus.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/plot-HTS.Rd | 10 HistDAWass-0.1.4/HistDAWass/man/plot-MatH.Rd | 14 HistDAWass-0.1.4/HistDAWass/man/plot-TdistributionH.Rd | 8 HistDAWass-0.1.4/HistDAWass/man/plot-distributionH.Rd | 8 HistDAWass-0.1.4/HistDAWass/man/plotPredVsObs.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/plot_errors.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/plus-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/rQQ-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/register-methods.Rd | 10 HistDAWass-0.1.4/HistDAWass/man/registerMH-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/show-MatH-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/show-distributionH-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/skewH-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/stations_coordinates.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/stdH-methods.Rd | 4 HistDAWass-0.1.4/HistDAWass/man/subsetHTS-methods.Rd | 2 HistDAWass-0.1.4/HistDAWass/man/times-methods.Rd | 2 94 files changed, 409 insertions(+), 405 deletions(-)
Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze
randomized response (RR) survey designs (e.g., Warner, S. L. (1965).
Randomized response: A survey technique for eliminating evasive answer
bias. Journal of the American Statistical Association, 60, 63–69).
Besides univariate estimates of true proportions, RR variables can be used
for correlations, as dependent variable in a logistic regression (with or
without random effects), as predictors in a linear regression, or as
dependent variable in a beta-binomial ANOVA. For simulation and bootstrap
purposes, RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck <dheck@mail.uni-mannheim.de>
Diff between RRreg versions 0.6.0 dated 2015-12-14 and 0.6.1 dated 2016-01-12
DESCRIPTION | 8 MD5 | 14 R/RRlog.R | 5 R/RRreg-package.R | 1 inst/CITATION | 10 inst/doc/RRreg.Rmd | 2 inst/doc/RRreg.html | 952 +++++++++++++++++----------------------------------- vignettes/RRreg.Rmd | 2 8 files changed, 345 insertions(+), 649 deletions(-)
Title: UCA Rcmdr Plug-in
Description: Some extension to Rcmdr (R Commander) made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrPlugin.UCA versions 2.0-4 dated 2015-06-10 and 2.0-5 dated 2016-01-12
ChangeLog | 10 ++++++++-- DESCRIPTION | 13 ++++++++----- MD5 | 11 ++++++----- R/RcmdrPlugin.UCA.R | 4 ++-- man/RcmdrPlugin.UCA-package.Rd | 4 ++-- man/RcmdrPlugin.UCA.es-package.Rd | 4 ++-- po/R-RcmdrPlugin.UCA-es.mo |only 7 files changed, 28 insertions(+), 18 deletions(-)
More information about RcmdrPlugin.UCA at CRAN
Permanent link
Title: Parametric Network Enrichment Analysis
Description: Includes functions and examples to compute Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.2.3 dated 2015-12-19 and 1.2.4 dated 2016-01-12
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/yeast.Rd | 17 +++++++++++++++++ 3 files changed, 23 insertions(+), 6 deletions(-)
Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 1.5 dated 2015-11-23 and 1.6 dated 2016-01-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++++----- R/dirknn.R |only R/dirknn.tune.R |only R/rot.matrix.R | 5 ++--- man/bic.mixvmf.Rd | 2 +- man/dirknn.Rd |only man/dirknn.tune.Rd |only man/rmixvmf.Rd | 6 ++---- man/spher.reg.Rd | 4 ++-- 10 files changed, 20 insertions(+), 19 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan versions 2.3-2 dated 2015-11-19 and 2.3-3 dated 2016-01-12
DESCRIPTION | 8 +-- MD5 | 56 +++++++++++++-------------- R/anosim.R | 9 ++-- R/bioenv.default.R | 4 - R/estaccumR.R | 2 R/gdispweight.R | 1 R/metaMDS.R | 8 +++ R/mrpp.R | 4 - R/ordiareatest.R | 4 - R/rarefy.R | 19 ++++----- R/renyiaccum.R | 1 R/specpool.R | 23 ++++++----- R/treedist.R | 5 ++ R/treedive.R | 6 ++ R/treeheight.R | 23 ++++++++++- R/tsallisaccum.R | 1 R/zzz.R | 2 inst/NEWS.Rd | 54 ++++++++++++++++++++++++++ inst/doc/FAQ-vegan.pdf |binary inst/doc/NEWS.html | 66 ++++++++++++++++++++++++++++++++ inst/doc/decision-vegan.pdf |binary inst/doc/diversity-vegan.pdf |binary inst/doc/intro-vegan.pdf |binary src/monoMDS.f | 12 ++++- vignettes/FAQ-vegan.pdf |binary vignettes/NEWS.html | 66 ++++++++++++++++++++++++++++++++ vignettes/decision-vegan.tex | 18 ++++---- vignettes/diversity-vegan.tex | 86 +++++++++++++++++++++--------------------- vignettes/intro-vegan.tex | 66 ++++++++++++++++++-------------- 29 files changed, 395 insertions(+), 149 deletions(-)
Title: Estimating Local Gaussian Parameters
Description: Computational routines for estimating and visualizing local Gaussian parameters. Local Gaussian parameters are useful for characterizing and testing for non-linear dependence within bivariate data. See e.g. Tjostheim and Hufthammer, Local Gaussian correlation: A new measure of dependence, Journal of Econometrics, 2013, Volume 172 (1), pages 33-48.
Author: Tore Selland Kleppe <tore.kleppe@uis.no>
Maintainer: Tore Selland Kleppe <tore.kleppe@uis.no>
Diff between localgauss versions 0.34 dated 2014-12-09 and 0.35 dated 2016-01-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/localgauss.R | 19 ++++++++++++------- src/Makevars | 1 - 4 files changed, 19 insertions(+), 15 deletions(-)
Title: Interface to the iDigBio Data API
Description: An interface to iDigBio's search API that allows downloading
specimen records. Searches are returned as a data.frame. Other functions
such as the metadata end points return lists of information. iDigBio is a US
project focused on digitizing and serving museum specimen collections on the
web. See <https://www.idigbio.org> for information on iDigBio.
Author: Francois Michonneau [aut, cph],
Matthew Collins [aut, cre],
Scott Chamberlain [ctb]
Maintainer: Matthew Collins <mcollins@acis.ufl.edu>
Diff between ridigbio versions 0.3.2 dated 2016-01-04 and 0.3.3 dated 2016-01-12
DESCRIPTION | 17 ++--- MD5 | 54 ++++++++-------- NAMESPACE | 2 man/build_field_lists.Rd | 2 man/idig_GET.Rd | 4 - man/idig_POST.Rd | 4 - man/idig_check.Rd | 2 man/idig_check_error.Rd | 4 - man/idig_count_media.Rd | 2 man/idig_count_records.Rd | 4 - man/idig_meta_fields.Rd | 2 man/idig_parse.Rd | 2 man/idig_search.Rd | 3 man/idig_search_media.Rd | 20 +++--- man/idig_search_records.Rd | 34 +++++----- man/idig_top_media.Rd | 2 man/idig_top_records.Rd | 12 +-- man/idig_url.Rd | 2 man/idig_validate.Rd | 4 - man/idig_version.Rd | 2 man/idig_view_media.Rd | 2 man/idig_view_records.Rd | 2 man/ridigbio.Rd | 10 +-- tests/testthat/test-idig_search_records.R | 39 +++++++----- tests/testthat/test-idig_top_media.R | 97 +++++++++++++++++------------- tests/testthat/test-idig_top_records.R | 95 +++++++++++++++++------------ tests/testthat/test-idig_view_media.R | 31 +++++---- tests/testthat/test-idig_view_records.R | 32 +++++---- 28 files changed, 267 insertions(+), 219 deletions(-)
Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Description: Low level functions for implementing
maximum likelihood estimating procedures for
complex models using data cloning and Bayesian
Markov chain Monte Carlo methods.
Sequential and parallel MCMC support
for JAGS, WinBUGS and OpenBUGS.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between dclone versions 2.0-0 dated 2013-09-30 and 2.1-1 dated 2016-01-12
DESCRIPTION | 26 ++++---- MD5 | 26 ++++---- NAMESPACE | 88 +++++++++++++++++---------- R/bugs.fit.R | 40 ++++++------ R/bugs.parfit.R | 30 ++++----- R/chisq.diag.mcmc.list.R | 12 +-- R/mclapplySB.R | 4 - R/pairs.mcmc.list.R | 12 +-- R/parDosa.R | 24 +++---- R/parLapplySB.R | 4 - R/parLapplySLB.R | 6 - R/snowWrapper.R | 16 ++-- inst/ChangeLog | 152 ++++++++++++++++++++++++++++++----------------- man/ovenbird.Rd | 2 14 files changed, 253 insertions(+), 189 deletions(-)
Title: AMCE Estimator for Conjoint Experiments
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Author: Anton Strezhnev, Elissa Berwick, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev <astrezhnev@fas.harvard.edu>
Diff between cjoint versions 2.0.1 dated 2015-10-17 and 2.0.3 dated 2016-01-12
DESCRIPTION | 8 MD5 | 14 NAMESPACE | 2 R/cjoint.R | 1608 ++++++++++++++++++++++++++++++---------------------- R/onAttach.R |only inst/CITATION |only man/amce.Rd | 60 + man/plot.amce.Rd | 63 +- man/summary.amce.Rd | 64 +- 9 files changed, 1087 insertions(+), 732 deletions(-)
Title: Detection of Outliers in Circular-Circular Regression
Description: Detection of outliers in circular-circular regression models, modifying its and estimating of models parameters.
Author: Azade Ghazanfarihesari, Majid Sarmad- Ferdowsi University Of Mashhad
Maintainer: Azade Ghazanfarihesari <azade_ghazanfari@yahoo.com>
Diff between CircOutlier versions 3.1.4 dated 2016-01-05 and 3.2.3 dated 2016-01-12
CircOutlier-3.1.4/CircOutlier/R/DMCE.R |only CircOutlier-3.1.4/CircOutlier/man/CircOutlier-package.Rd |only CircOutlier-3.2.3/CircOutlier/DESCRIPTION | 12 +- CircOutlier-3.2.3/CircOutlier/MD5 | 33 +++--- CircOutlier-3.2.3/CircOutlier/NAMESPACE | 4 CircOutlier-3.2.3/CircOutlier/R/DMCEE.R |only CircOutlier-3.2.3/CircOutlier/R/Huberized.R | 45 ++++---- CircOutlier-3.2.3/CircOutlier/R/MCE.R | 7 - CircOutlier-3.2.3/CircOutlier/R/Predict.R | 52 +++++----- CircOutlier-3.2.3/CircOutlier/R/mce_1.R | 11 +- CircOutlier-3.2.3/CircOutlier/data/DMCE.rda |only CircOutlier-3.2.3/CircOutlier/data/wind.rda |binary CircOutlier-3.2.3/CircOutlier/data/wind2.rda |only CircOutlier-3.2.3/CircOutlier/man/DMCE.Rd | 77 ++++----------- CircOutlier-3.2.3/CircOutlier/man/DMCEE.Rd |only CircOutlier-3.2.3/CircOutlier/man/Huberized.Rd | 1 CircOutlier-3.2.3/CircOutlier/man/MCE.Rd | 4 CircOutlier-3.2.3/CircOutlier/man/Predict.Rd | 6 - CircOutlier-3.2.3/CircOutlier/man/mce_1.Rd | 4 CircOutlier-3.2.3/CircOutlier/man/wind.Rd | 6 - CircOutlier-3.2.3/CircOutlier/man/wind2.Rd |only 21 files changed, 115 insertions(+), 147 deletions(-)
Title: Optimal Discriminating Designs
Description: A collection of functions for numerical construction of optimal discriminating designs. At the current moment T-optimal designs (which maximize the lower bound for the power of F-test for regression model discrimination), KL-optimal designs (for lognormal errors) and their robust analogues can be calculated with the package.
Author: Roman Guchenko [aut, cre]
Maintainer: Roman Guchenko <RomanGuchenko@yandex.ru>
Diff between rodd versions 0.1-1 dated 2014-12-13 and 0.2-1 dated 2016-01-11
DESCRIPTION | 9 +-- MD5 | 62 +++++++++++++++++---------- NAMESPACE | 6 ++ R/KLD.R |only R/KLD.new.R |only R/KLopt.lnorm.R |only R/KLp.R |only R/Tfs.R | 7 +-- R/Tp.R | 15 +++--- R/evaluate.local.maximums.lnorm.R |only R/evaluate.weights.1.R | 87 +++++++++++++++++++------------------- R/evaluate.weights.1.lnorm.R |only R/evaluate.weights.2.R | 13 +---- R/evaluate.weights.2.lnorm.R |only R/g.R |only R/klopt.lnorm.main.R |only R/mu.R |only R/num.deriv.R | 2 R/plot.KLopt.lnorm.R |only R/plot.tpopt.R | 15 +++--- R/print.KLopt.lnorm.R |only R/print.tpopt.R | 23 ++++------ R/psi.R | 7 +-- R/psi.lnorm.R |only R/psi.lnorm.new.R |only R/psi.lnorm_1.R |only R/psi_1.R | 15 +++--- R/second.order.num.deriv.R | 2 R/summary.KLopt.lnorm.R |only R/summary.tpopt.R | 41 ++++++++--------- R/topt.R | 27 ++++++----- R/tpopt.R | 11 ++-- R/w_.R | 11 ++-- man/KLopt.lnorm.Rd |only man/plot.KLopt.lnorm.Rd |only man/plot.tpopt.Rd | 2 man/print.KLopt.lnorm.Rd |only man/print.tpopt.Rd | 2 man/rodd-package.Rd | 4 + man/summary.KLopt.lnorm.Rd |only man/summary.tpopt.Rd | 2 man/tpopt.Rd | 46 ++++++++++++++++++++ 42 files changed, 238 insertions(+), 171 deletions(-)
Title: Dynamic (Longitudinal) Network Datasets
Description: A collection of dynamic network data sets from various sources and multiple authors represented as 'networkDynamic'-formatted objects.
Author: Skye Bender-deMoll [cre],
Martina Morris [ctb],
Li Wang [ctb],
Gerhard van de Bunt [ctb],
Goele Bossaert [ctb],
Nadine Meidert [ctb],
SocioPatterns.org [ctb],
Tore Opsahi [ctb],
Radoslaw Michalski, (et al) [ctb],
Allison Davis, (et. al.) [ctb],
C.E. Priebe, (et. al.) [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamicData versions 0.1.0 dated 2014-02-07 and 0.2.1 dated 2016-01-11
ChangeLog |only DESCRIPTION | 39 ++++++++++++++---- LICENSE | 2 MD5 | 21 +++++++--- data/concurrencyComparisonNets.rda |binary data/datalist |only data/davisActorsDyn.rda |only data/davisDyn.rda |only data/enronEmails.rda |only data/manufacturingEmails.rda |only man/concurrencyComparisonNets.Rd | 77 ++++++++++++++++++++----------------- man/davisDyn.Rd |only man/enronEmails.Rd |only man/hospital.Rd | 4 - man/manufacturingEmails.Rd |only man/networkDynamicData-package.Rd | 19 ++++----- 16 files changed, 100 insertions(+), 62 deletions(-)
More information about networkDynamicData at CRAN
Permanent link
Title: Tools for Analyzing Finite Mixture Models
Description: A collection of R functions for analyzing finite mixture models. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
Author: Derek Young [aut, cre],
Tatiana Benaglia [aut],
Didier Chauveau [aut],
David Hunter [aut],
Ryan Elmore [ctb],
Thomas Hettmansperger [ctb],
Hoben Thomas [ctb],
Fengjuan Xuan [ctb]
Maintainer: Derek Young <derek.young@uky.edu>
Diff between mixtools versions 1.0.3 dated 2015-04-19 and 1.0.4 dated 2016-01-11
DESCRIPTION | 13 +- MD5 | 42 +++--- NAMESPACE | 13 +- NEWS | 9 + R/multmixmodelsel.R | 2 R/mvnpEM.R |only build/vignette.rds |binary inst/doc/mixtools.pdf |binary man/multmixmodel.sel.Rd | 2 man/mvnpEM.Rd |only man/normalmixEM.Rd | 300 +++++++++++++++++++++++----------------------- man/normalmixMMlc.Rd | 309 +++++++++++++++++++++++------------------------- man/npMSL.Rd | 8 - man/plot.mixEM.Rd | 161 ++++++++++++------------- man/plot.mvnpEM.Rd |only man/plotFDR.Rd | 10 - man/post.beta.Rd | 126 ++++++++++--------- man/print.mvnpEM.Rd |only man/regmixEM.mixed.Rd | 196 +++++++++++++++--------------- man/spEMsymloc.Rd | 2 man/spEMsymlocN01.Rd | 4 man/summary.mvnpEM.Rd |only man/summary.npEM.Rd | 6 man/wquantile.Rd | 6 src/mvwkde.c |only 25 files changed, 618 insertions(+), 591 deletions(-)
Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between mefa versions 3.2-6 dated 2015-11-22 and 3.2-7 dated 2016-01-11
DESCRIPTION | 8 MD5 | 212 +++---- NAMESPACE | 180 +++--- R/aggregate.mefa.R | 114 +-- R/aoplot.R | 2 R/aoplot.default.R | 36 - R/as.array.mefa.R | 18 R/as.data.frame.mefa.R | 24 R/as.data.frame.stcs.R | 22 R/as.list.mefa.R | 20 R/as.matrix.mefa.R | 12 R/as.mefa.R | 12 R/as.mefa.array.R | 36 - R/as.mefa.default.R | 38 - R/as.mefa.list.R | 40 - R/as.stcs.R | 12 R/as.stcs.default.R | 6 R/boxplot.mefa.R | 68 +- R/boxplot.stcs.R | 12 R/cdrop.R | 38 - R/coercionMethodsForMefa4.R | 110 +-- R/dim.mefa.R | 16 R/dimnames.mefa.R | 22 R/extract.mefa.R | 182 +++--- R/fill.na.R | 46 - R/image.dist.R | 60 +- R/image.mefa.R | 90 +-- R/image.stcs.R | 14 R/is.dist.R | 6 R/is.mefa.R | 12 R/is.stcs.R | 12 R/label.R | 28 R/mat2list.R | 26 R/mefa.R | 132 ++-- R/mefaCheck.R | 116 +-- R/mefaCompare.R | 90 +-- R/mefaCrosstab.R | 76 +- R/mefaNestedless.R | 40 - R/mefaTables.R | 112 +-- R/mefadocs.R | 32 - R/mefalogo.R | 82 +- R/mefaweb.R | 12 R/melt.R | 12 R/melt.mefa.R | 230 +++---- R/mfill.R | 4 R/msr.R | 28 R/mss.R | 36 - R/mtr.R | 34 - R/mts.R | 36 - R/plot.mefa.R | 152 ++--- R/plot.stcs.R | 12 R/print.mefa.R | 58 - R/print.summary.mefa.R | 58 - R/qvector.R | 22 R/rdrop.R | 38 - R/rep.data.frame.R | 6 R/report.R | 12 R/report.mefa.R | 534 +++++++++--------- R/samp.R | 4 R/samp.default.R | 20 R/segm.R | 4 R/segm.default.R | 20 R/stack.dist.R | 46 - R/stcs.R | 172 ++--- R/summary.mefa.R | 46 - R/summary.stcs.R | 18 R/taxa.R | 4 R/taxa.default.R | 18 R/vec2dist.R | 24 R/xtab.R | 4 R/xtab.default.R | 10 R/zzz.R | 22 build/vignette.rds |binary demo/00Index | 2 demo/mefa.R | 488 ++++++++-------- inst/CITATION | 38 - inst/ChangeLog | 824 ++++++++++++++------------- inst/SampleReport | 80 +- inst/doc/mefa.R | 732 ++++++++++++------------ inst/doc/mefa.Rnw | 1304 ++++++++++++++++++++++---------------------- inst/doc/mefa.pdf |binary man/aggregate.mefa.Rd | 172 ++--- man/aoplot.Rd | 92 +-- man/as.mefa.Rd | 204 +++--- man/dolina.Rd | 118 +-- man/fill.na.Rd | 86 +- man/image.dist.Rd | 84 +- man/label.Rd | 90 +-- man/mat2list.Rd | 138 ++-- man/mefa.Rd | 298 +++++----- man/mefaCheck.Rd | 86 +- man/mefaCrosstab.Rd | 94 +-- man/mefaNestedless.Rd | 70 +- man/mefaTables.Rd | 96 +-- man/mefadocs.Rd | 50 - man/mefalogo.Rd | 84 +- man/mefaweb.Rd | 58 - man/melt.mefa.Rd | 144 ++-- man/plot.mefa.Rd | 212 +++---- man/qvector.Rd | 86 +- man/rep.data.frame.Rd | 80 +- man/report.mefa.Rd | 154 ++--- man/stack.dist.Rd | 136 ++-- man/stcs.Rd | 176 ++--- tests/tests.R | 4 vignettes/mefa.Rnw | 1304 ++++++++++++++++++++++---------------------- vignettes/mefa.bib | 452 +++++++-------- 107 files changed, 5979 insertions(+), 5967 deletions(-)
Title: Pacific Decadal Oscillation Index
Description: Monthly Pacific Decadal Oscillation (PDO) index
values from January 1900 to present.
Author: Joe Thorley [aut, cre],
Nathan Mantua [aut, dtc],
Steven R. Hare [aut, dtc]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between rpdo versions 0.1.0 dated 2015-10-19 and 0.1.1 dated 2016-01-11
DESCRIPTION | 16 +++++++++------- MD5 | 20 +++++++++++++------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/data.R | 31 +++---------------------------- README.md | 38 ++++++++++++++++++-------------------- build |only data/pdo.rda |binary inst |only man/pdo.Rd | 33 ++++----------------------------- tests |only vignettes |only 12 files changed, 53 insertions(+), 91 deletions(-)
Title: Semi-Supervised Generalized Structural Equation Modeling
Description: Conducts a semi-gSEM statistical analysis (semi-supervised generalized structural equation modeling) on a data frame of coincident observations of multiple predictive or intermediate variables and a final continuous, outcome variable, via two functions sgSEMp1() and sgSEMp2(), representing fittings based on two statistical principles. Principle 1 determines all sensible univariate relationships in the spirit of the Markovian process. The relationship between each pair of variables, including predictors and the final outcome variable, is determined with the Markovian property that the value of the current predictor is sufficient in relating to the next level variable, i.e., the relationship is independent of the specific value of the preceding-level variables to the current predictor, given the current value. Principle 2 resembles the multiple regression principle in the way multiple predictors are considered simultaneously. Specifically, the relationship of the first-level predictors (such as Time and irradiance etc) to the outcome variable (such as, module degradation or yellowing) is fit by a supervised additive model. Then each significant intermediate variable is taken as the new outcome variable and the other variables (except the final outcome variable) as the predictors in investigating the next-level multivariate relationship by a supervised additive model. This fitting process is continued until all sensible models are investigated.
Author: Junheng Ma <jxm216@case.edu>, Nicholas Wheeler <nrw16@case.edu>, Yifan Xu <ethan.yifanxu@case.edu>, Wenyu Du <wxd97@case.edu>, Abdulkerim Gok <axg515@case.edu>, Jiayang Sun <jiayang.sun@case.edu>
Maintainer: Junheng Ma <jxm216@case.edu>
Diff between gSEM versions 0.4.3.3 dated 2015-12-23 and 0.4.3.4 dated 2016-01-11
DESCRIPTION | 10 +- MD5 | 30 +++---- R/acrylic.R | 17 ++-- R/cf.R | 5 - R/gSEM.R | 7 + R/genInit.R | 2 R/nlsR2.R | 1 R/path.R | 3 R/plot.sgSEMp2.R | 198 ++++++++++++++++++++++++---------------------------- R/plotAll.R | 1 R/sgSEMp2.R | 194 +++++++++++++++++++++++++++----------------------- man/gSEM.Rd | 6 - man/genInit.Rd | 3 man/path.Rd | 3 man/plot.sgSEMp2.Rd | 4 - man/sgSEMp2.Rd | 15 +++ 16 files changed, 256 insertions(+), 243 deletions(-)
Title: Permutation Significance for Random Forests
Description: Estimate False Discovery Rates (FDRs) for importance metrics from
random forest runs.
Author: Ankur Chakravarthy
Maintainer: Ankur Chakravarthy <ankur.chakravarthy.10@ucl.ac.uk>
Diff between pRF versions 1.1 dated 2015-11-05 and 1.2 dated 2016-01-11
DESCRIPTION | 15 +++++++++------ MD5 | 6 +++--- NAMESPACE | 19 +++++++++++-------- R/AC_pRF.R | 15 +++++++++++---- 4 files changed, 34 insertions(+), 21 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-13 0.3.2
2013-11-26 0.3.1
Title: Unit Root and Cointegration Tests for Time Series Data
Description: Unit root and cointegration tests encountered in applied
econometric analysis are implemented.
Author: Bernhard Pfaff [aut, cre],
Eric Zivot [ctb],
Matthieu Stigler [ctb]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between urca versions 1.2-8 dated 2013-06-06 and 1.2-9 dated 2016-01-11
DESCRIPTION | 26 +++++++++++++------------- MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 42 ++++++++++++++++++++---------------------- R/internal.R | 4 ++-- data/Raotbl1.rda |binary data/Raotbl2.rda |binary data/Raotbl3.rda |binary data/Raotbl4.rda |binary data/Raotbl5.rda |binary data/Raotbl6.rda |binary data/Raotbl7.rda |binary data/UKconinc.rda |binary data/UKconsumption.rda |binary data/UKpppuip.rda |binary data/denmark.rda |binary data/ecb.rda |binary data/finland.rda |binary data/npext.rda |binary data/nporg.rda |binary 19 files changed, 53 insertions(+), 55 deletions(-)
Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle. Additional
code contributions from Edzer Pebesma.
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between lgcp versions 1.3-13 dated 2015-11-19 and 1.3-14 dated 2016-01-11
DESCRIPTION | 10 +++--- MD5 | 24 +++++++-------- NAMESPACE | 16 +++++----- R/MultitypeSpatialOnlyPlusParameters.R | 10 +++--- R/gridFunctionMethods.R | 32 ++++++++++----------- R/lgcp.R | 5 +-- R/lgcpMethods.R | 50 ++++++++++++++++----------------- R/lgcpStructures.R | 18 +++++------ build/vignette.rds |binary data/wpopdata.rda |binary data/wtowncoords.rda |binary data/wtowns.rda |binary inst/doc/lgcp.pdf |binary 13 files changed, 83 insertions(+), 82 deletions(-)
Title: Interface to Climatic Research Unit Time-Series Version 3.21
Data
Description: Functions for reading in and manipulating CRU TS3.21: Climatic Research Unit (CRU) Time-Series (TS) Version 3.21 data.
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between cruts versions 0.1 dated 2015-07-11 and 0.2 dated 2016-01-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 16 ++++++++-------- R/cruts.R | 3 ++- R/import-export.R | 6 +++--- 5 files changed, 21 insertions(+), 20 deletions(-)
Title: R Wrapper Around the Telegram Bot API
Description: R wrapper around the Telegram Bot API (http://core.telegram.org/bots/api) to access Telegram's messaging facilities with ease (e.g. you send messages, images, files from R to your smartphone).
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Diff between telegram versions 0.3.0 dated 2015-12-29 and 0.4.0 dated 2016-01-11
DESCRIPTION | 8 - MD5 | 27 +++- NAMESPACE | 4 R/TGBot.R | 292 ++++++++++++++++++++++++++++++++++++-------- R/telegram-package.r | 4 README.md | 9 + man/TGBot.Rd | 35 ++--- man/bot_token.Rd | 8 - man/forwardMessage.Rd |only man/getFile.Rd |only man/getMe.Rd |only man/getUpdates.Rd |only man/getUserProfilePhotos.Rd |only man/sendAudio.Rd |only man/sendDocument.Rd |only man/sendLocation.Rd |only man/sendMessage.Rd |only man/sendPhoto.Rd |only man/sendSticker.Rd |only man/sendVideo.Rd |only man/sendVoice.Rd |only 21 files changed, 305 insertions(+), 82 deletions(-)
Title: Robust Fitting of Linear Model
Description: Robust fitting of linear model which can take response in matrix form.
Author: Oleg Yegorov <egorov@smedx.com>
Maintainer: Oleg Yegorov <egorov@smedx.com>
Diff between rlm versions 1.1 dated 2015-02-21 and 1.2 dated 2016-01-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + R/rlm.r | 10 +++++----- src/IWLS.cpp | 16 ++++++++-------- 5 files changed, 22 insertions(+), 21 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-29 1.6.9
2014-08-25 1.6.8
2014-06-16 1.6.7
2011-09-02 1.6.6
2011-01-10 1.6.5
2010-07-30 1.6.2
2010-07-30 1.6.3
2010-05-17 1.6.1
2006-07-10 1.6
Title: Soil Physical Analysis
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between soilphysics versions 2.4 dated 2015-06-26 and 3.0 dated 2016-01-11
DESCRIPTION | 11 ++++--- MD5 | 27 ++++++++++--------- NAMESPACE | 3 -- NEWS | 7 +++++ R/criticalmoisture.R | 2 - R/iwc.R | 4 +- R/llwr.R | 51 +++++++++++++++++------------------- data/skp1994.rda |binary inst |only man/fitlbc.Rd | 2 - man/fitsoilwater4.Rd | 4 +- man/iwc.Rd | 8 ++--- man/llwr.Rd | 46 ++++++++++++++++---------------- man/skp1994.Rd | 8 ++--- man/soilphysics-package.Rd | 63 +++++---------------------------------------- 15 files changed, 97 insertions(+), 139 deletions(-)
Title: Neo4j Driver for R
Description: Neo4j, a graph database, allows users to store their data as a property graph. A graph consists of nodes that are connected by relationships; both nodes and relationships can have properties, or key-value pairs. RNeo4j is Neo4j's R driver. It allows users to read and write data from and to Neo4j directly from their R environment by exposing an interface for interacting with nodes, relationships, paths, and more. Most notably, it allows users to retrieve Cypher query results as R data frames, where Cypher is Neo4j's graph query language. Visit <http://www.neo4j.com> to learn more about Neo4j.
Author: Nicole White
Maintainer: Nicole White <nicole@neo4j.com>
Diff between RNeo4j versions 1.6.1 dated 2015-11-30 and 1.6.2 dated 2016-01-11
DESCRIPTION | 8 ++++---- MD5 | 11 +++++++---- R/internal.R | 22 ++++++++++++++++++---- man/getConstraint.Rd | 2 +- man/getIndex.Rd | 2 +- tests/test.sh |only tests/test_all.sh |only tests/testthat/test-internals.R |only 8 files changed, 31 insertions(+), 14 deletions(-)
Title: Tools for Analysis, Design, and Operation of Water Supply
Storages
Description: Measure single-storage water supply system performance using resilience,
reliability, and vulnerability metrics; assess storage-yield-reliability
relationships; determine no-fail storage with sequent peak analysis; optimize
release decisions for water supply, hydropower, and multi-objective reservoirs
using deterministic and stochastic dynamic programming; evaluate inflow
persistence using the Hurst coefficient.
Author: Sean Turner [aut, cre],
Jia Yi Ng [aut],
Stefano Galelli [aut]
Maintainer: Sean Turner <swd.turner@gmail.com>
Diff between reservoir versions 1.1.0 dated 2016-01-04 and 1.1.1 dated 2016-01-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/reservoir.R | 4 +++- R/sequent_peak_analysis.R | 4 ++-- man/Rippl.Rd | 2 +- man/reservoir.Rd | 4 +++- 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.9.0-1 dated 2015-11-27 and 0.9.2-0 dated 2016-01-11
quanteda-0.9.0-1/quanteda/R/distance.R |only quanteda-0.9.2-0/quanteda/DESCRIPTION | 19 quanteda-0.9.2-0/quanteda/MD5 | 194 +- quanteda-0.9.2-0/quanteda/NAMESPACE | 17 quanteda-0.9.2-0/quanteda/NEWS | 40 quanteda-0.9.2-0/quanteda/R/RcppExports.R | 4 quanteda-0.9.2-0/quanteda/R/converters.R | 19 quanteda-0.9.2-0/quanteda/R/corpus.R | 25 quanteda-0.9.2-0/quanteda/R/dfm-classes.R | 136 - quanteda-0.9.2-0/quanteda/R/dfm-main.R | 23 quanteda-0.9.2-0/quanteda/R/dfm-methods.R | 247 --- quanteda-0.9.2-0/quanteda/R/dfm-weighting.R |only quanteda-0.9.2-0/quanteda/R/dictionaries.R | 129 - quanteda-0.9.2-0/quanteda/R/plots.R | 2 quanteda-0.9.2-0/quanteda/R/selectFeatures.R |only quanteda-0.9.2-0/quanteda/R/similarity.R |only quanteda-0.9.2-0/quanteda/R/stopwords.R | 451 ----- quanteda-0.9.2-0/quanteda/R/textfile.R | 89 - quanteda-0.9.2-0/quanteda/R/textmodel-generics.R | 11 quanteda-0.9.2-0/quanteda/R/textmodel-wordfish.R | 109 + quanteda-0.9.2-0/quanteda/R/textmodel-wordscores.R | 11 quanteda-0.9.2-0/quanteda/R/toLower.R | 6 quanteda-0.9.2-0/quanteda/R/tokenize.R | 4 quanteda-0.9.2-0/quanteda/R/wordstem.R | 20 quanteda-0.9.2-0/quanteda/build/vignette.rds |binary quanteda-0.9.2-0/quanteda/data/LBGexample.RData |binary quanteda-0.9.2-0/quanteda/inst/doc/LitVignette.R | 4 quanteda-0.9.2-0/quanteda/inst/doc/LitVignette.Rmd | 4 quanteda-0.9.2-0/quanteda/inst/doc/LitVignette.html | 17 quanteda-0.9.2-0/quanteda/inst/doc/quickstart.html | 1088 +++++++++++++- quanteda-0.9.2-0/quanteda/inst/extdata |only quanteda-0.9.2-0/quanteda/man/LBGexample.Rd | 2 quanteda-0.9.2-0/quanteda/man/applyDictionary.Rd | 18 quanteda-0.9.2-0/quanteda/man/cbind.dfm.Rd | 2 quanteda-0.9.2-0/quanteda/man/changeunits.Rd | 10 quanteda-0.9.2-0/quanteda/man/collocations.Rd | 46 quanteda-0.9.2-0/quanteda/man/convert.Rd | 36 quanteda-0.9.2-0/quanteda/man/corpus.Rd | 137 - 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quanteda-0.9.2-0/quanteda/man/textmodel.Rd | 44 quanteda-0.9.2-0/quanteda/man/textmodel_ca.Rd | 4 quanteda-0.9.2-0/quanteda/man/textmodel_fitted-class.Rd | 2 quanteda-0.9.2-0/quanteda/man/textmodel_wordfish.Rd | 104 - quanteda-0.9.2-0/quanteda/man/textmodel_wordscores.Rd | 32 quanteda-0.9.2-0/quanteda/man/texts.Rd | 6 quanteda-0.9.2-0/quanteda/man/tf.Rd |only quanteda-0.9.2-0/quanteda/man/tfidf.Rd |only quanteda-0.9.2-0/quanteda/man/toLower.Rd | 12 quanteda-0.9.2-0/quanteda/man/tokenize.Rd | 70 quanteda-0.9.2-0/quanteda/man/topfeatures.Rd | 2 quanteda-0.9.2-0/quanteda/man/trim.Rd | 18 quanteda-0.9.2-0/quanteda/man/ukimmigTexts.Rd | 2 quanteda-0.9.2-0/quanteda/man/weight.Rd | 66 quanteda-0.9.2-0/quanteda/man/wordlists.Rd | 2 quanteda-0.9.2-0/quanteda/man/wordstem.Rd | 24 quanteda-0.9.2-0/quanteda/src/RcppExports.cpp | 7 quanteda-0.9.2-0/quanteda/src/wordfish.cpp | 16 quanteda-0.9.2-0/quanteda/tests/testthat/testConvert.R |only quanteda-0.9.2-0/quanteda/tests/testthat/testSimilarity.R |only quanteda-0.9.2-0/quanteda/vignettes/LitVignette.Rmd | 4 quanteda-0.9.2-0/quanteda/vignettes/Users |only 103 files changed, 2393 insertions(+), 1918 deletions(-)
Title: Testing Workbench for Precision-Recall Curves
Description: A testing workbench for evaluating Precision-Recall curves under various conditions.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between prcbench versions 0.1.0 dated 2016-01-08 and 0.2.0 dated 2016-01-11
DESCRIPTION | 15 +- MD5 | 18 +-- R/main_benchmark.R | 44 ++++++-- README.md | 96 +++++++++++++---- inst/doc/introduction.R | 2 inst/doc/introduction.Rmd | 41 +++---- inst/doc/introduction.html | 66 +++++++----- man/run_benchmark.Rd | 7 + tests/testthat/test_main_benchmark.R | 190 ++++++++++++++++++++++++----------- vignettes/introduction.Rmd | 41 +++---- 10 files changed, 337 insertions(+), 183 deletions(-)
Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Description: Screens and sorts phylogenetic trees in both traditional and
extended Newick format. Allows for the fast and flexible screening (within
a tree) of Exclusive clades that comprise only the target taxa and/or Non-
Exclusive clades that includes a defined portion of non-target taxa.
Author: Timothy Stephens [aut, cre, trl] (R port),
Debashish Bhattacharya [aut],
Mark Ragan [aut],
Cheong Xin Chan [aut, cph] (Original Perl implementation)
Maintainer: Timothy Stephens <timothy.stephens1@uqconnect.edu.au>
Diff between PhySortR versions 1.0.3 dated 2015-12-21 and 1.0.5 dated 2016-01-11
DESCRIPTION | 16 ++- MD5 | 10 +- NAMESPACE | 12 +- man/PhySortR.Rd | 68 +++++++------- man/convert.eNewick.Rd | 52 +++++------ man/sortTrees.Rd | 228 ++++++++++++++++++++++++------------------------- 6 files changed, 195 insertions(+), 191 deletions(-)
Title: Non-Parametric Measures of Actigraphy Data
Description: Computes interday stability (IS), intraday variability (IV) & the relative amplitude (RA) from actigraphy data as described in van Someren et al. (1999). Additionally, it also computes L5 (i.e. the 5 hours with lowest average actigraphy amplitude) and M10 (the 10 hours with highest average amplitude) as well as the respective start times. The flex versions will also compute the L-value for a user-defined number of minutes. IS describes the strength of coupling of a rhythm to supposedly stable zeitgebers. It varies between 0 (Gaussian Noise) and 1 for perfect IS. IV describes the fragmentation of a rhythm, i.e. the frequency and extent of transitions between rest and activity. It is near 0 for a perfect sine wave, about 2 for Gaussian noise and may be even higher when a definite ultradian period of about 2 hrs is present. RA is the relative amplitude of a rhythm. Note that to obtain reliable results, actigraphy data should cover a reasonable number of days.
Author: Christine Blume <christine.blume@sbg.ac.at>
Nayantara Santhi <n.santhi@surrey.ac.uk>
Manuel Schabus <manuel.schabus@sbg.ac.at>
Maintainer: Christine Blume <christine.blume@sbg.ac.at>
Diff between nparACT versions 0.1 dated 2015-10-22 and 0.2 dated 2016-01-11
DESCRIPTION | 10 ++++---- MD5 | 31 +++++++++++++------------- NAMESPACE | 4 +-- R/nparACT-internal.R |only R/nparACT_auxfunctions1.R | 4 +-- R/nparACT_auxfunctions2.R | 54 ++++++++++++++++++++++++++++++---------------- R/nparACT_base.R | 21 +++++++++++------ R/nparACT_base_loop.R | 27 ++++++++++++++++------- R/nparACT_flex.R | 17 ++++++++++---- R/nparACT_flex_loop.R | 23 ++++++++++++++----- data/sleepstudy.rda |binary man/nparACT-package.Rd | 6 ++--- man/nparACT_base.Rd | 2 - man/nparACT_base_loop.Rd | 2 - man/nparACT_flex.Rd | 2 - man/nparACT_flex_loop.Rd | 2 - man/sleepstudy.Rd | 6 ++--- 17 files changed, 133 insertions(+), 78 deletions(-)
Title: Aligned Rank Transform
Description: The Aligned Rank Transform for nonparametric
factorial ANOVAs as described by J. O. Wobbrock,
L. Findlater, D. Gergle, & J. J. Higgins, "The Aligned
Rank Transform for nonparametric factorial analyses
using only ANOVA procedures", CHI 2011.
Author: Matthew Kay [aut, cre],
Jacob O. Wobbrock [aut]
Maintainer: Matthew Kay <mjskay@uw.edu>
Diff between ARTool versions 0.9.5 dated 2015-06-01 and 0.10.0 dated 2016-01-11
DESCRIPTION | 21 + MD5 | 62 +++-- NAMESPACE | 36 ++- NEWS |only R/anova.art.R | 296 +++++++++++++++++------- R/art.R | 382 +++++++++++++++++++++++--------- R/artlm.R | 137 +++++++---- R/data.R |only R/flat.anova.R |only R/global.variables.R |only R/internal.R | 135 ++++++----- build |only data/Higgins1990Table1.RData |binary data/Higgins1990Table1.art.RData |binary data/Higgins1990Table5.RData |binary data/Higgins1990Table5.art.RData |binary data/HigginsABC.RData |binary data/HigginsABC.art.RData |binary data/InteractionTestData.RData |only inst/doc |only man/Higgins1990Table1.Rd | 81 +++--- man/Higgins1990Table1.art.Rd | 67 ++--- man/Higgins1990Table5.Rd | 92 ++++--- man/Higgins1990Table5.art.Rd | 67 ++--- man/HigginsABC.Rd | 72 +++--- man/HigginsABC.art.Rd | 85 +++---- man/InteractionTestData.Rd |only man/anova.art.Rd | 176 +++++++------- man/art.Rd | 252 ++++++++++++--------- man/artlm.Rd | 108 ++++----- man/summary.art.Rd | 82 +++--- tests/testthat/test.anova.art.R |only tests/testthat/test.art.R | 38 ++- tests/testthat/test.artlm.R | 32 ++ tests/testthat/test.parse.art.formula.R | 51 ++++ vignettes |only 36 files changed, 1399 insertions(+), 873 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.2 dated 2015-11-15 and 0.12.3 dated 2016-01-10
ChangeLog | 62 ++++++++++++ DESCRIPTION | 8 - MD5 | 74 +++++++-------- README.md | 14 +- build/Rcpp.pdf |binary build/vignette.rds |binary inst/NEWS.Rd | 32 ++++++ inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/doc/Rcpp-unitTests.pdf |binary inst/doc/Rcpp.bib | 8 - inst/include/Rcpp/Module.h | 15 ++- inst/include/Rcpp/String.h | 28 +++++ inst/include/Rcpp/Vector.h | 2 inst/include/Rcpp/config.h | 4 inst/include/Rcpp/internal/Proxy_Iterator.h | 2 inst/include/Rcpp/macros/interface.h | 11 ++ inst/include/Rcpp/vector/Matrix.h | 44 ++++++++- inst/include/Rcpp/vector/MatrixColumn.h | 41 ++++++++ inst/include/Rcpp/vector/MatrixRow.h | 121 +++++++++++++++++++++++++ inst/include/Rcpp/vector/const_generic_proxy.h | 2 inst/include/Rcpp/vector/const_string_proxy.h | 2 inst/include/Rcpp/vector/proxy.h | 7 + inst/include/Rcpp/vector/traits.h | 2 inst/unitTests/cpp/Matrix.cpp | 73 +++++++++++++++ inst/unitTests/cpp/Vector.cpp | 18 +++ inst/unitTests/cpp/wrap.cpp | 23 ++++ inst/unitTests/runit.Matrix.R | 39 ++++++++ inst/unitTests/runit.Vector.R | 12 ++ inst/unitTests/runit.wrap.R | 12 ++ src/attributes.cpp | 17 +++ vignettes/Rcpp.bib | 8 - 38 files changed, 610 insertions(+), 71 deletions(-)
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal .
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.5.0.1 dated 2015-12-01 and 1.6 dated 2016-01-10
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- NAMESPACE | 3 +++ R/Rsomoclu.R | 24 +++++++++++++++++++++++- data/rgbs.txt.gz |binary man/Rsomoclu.kohonen.Rd |only man/Rsomoclu.train.Rd | 10 +++++++++- src/Makefile.in | 8 ++++---- src/Rsomoclu.cpp | 28 ++++++++++++++++------------ src/configure | 20 ++++++++++---------- src/training.cpp | 4 +++- tests/R_interface_test.R | 9 +++++++++ 12 files changed, 93 insertions(+), 44 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.8 dated 2016-01-09 and 1.9 dated 2016-01-10
DESCRIPTION | 9 ++++----- MD5 | 5 +++-- man/cit-package.Rd | 4 ++-- src/Makevars.win |only 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Species Distribution Modeling
Description: Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites.
Author: Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between dismo versions 1.0-12 dated 2015-03-15 and 1.0-15 dated 2016-01-10
DESCRIPTION | 10 ++-- MD5 | 104 ++++++++++++++++++++++++------------------------ NAMESPACE | 5 +- R/Mahalanobis.R | 2 R/Mahalanobis.predict.R | 2 R/bioclim.R | 2 R/bioclim.plot.R | 2 R/bioclim.predict.R | 6 +- R/circles.R | 33 ++++++++++----- R/circles.predict.R | 11 ++--- R/convHull.R | 2 R/dcEvaluate.R | 8 +-- R/density.R | 2 R/diversity.R | 6 +- R/domain.R | 2 R/domain.predict.R | 2 R/ecocrop.R | 2 R/ecolim.R | 4 - R/errorDetect.R | 2 R/evaluate.R | 10 ++-- R/gbif.R | 70 ++++++++++++++++++-------------- R/gbm.fixed.R | 2 R/gbm.interactions.R | 7 +-- R/gbm.perspec.R | 4 - R/gbm.plot.R | 6 +- R/gbm.plot.fits.R | 6 +- R/gbm.simplify.R | 23 ++++------ R/gbm.step.R | 2 R/geoDist.R | 2 R/geocode.R | 5 +- R/gmap.R | 6 +- R/gridSample.R | 4 - R/hullls.R | 2 R/kauc.R | 2 R/maxent.R | 8 +-- R/maxent.predict.R | 4 - R/mess.R | 6 +- R/nicheEquivelancy.R | 6 +- R/nullRandom.R | 14 +++--- R/pairs.R | 9 ++-- R/pointValues.R | 4 - R/precision.R | 4 - R/randomPoints.R | 6 +- R/response.R | 6 +- R/voronoi.R | 2 R/voronoiHull.R | 6 +- build/vignette.rds |binary inst/doc/brt.pdf |binary inst/doc/sdm.R | 6 +- inst/doc/sdm.Rnw | 12 +---- inst/doc/sdm.pdf |binary man/circles.Rd | 23 ++++------ vignettes/sdm.Rnw | 12 +---- 53 files changed, 250 insertions(+), 236 deletions(-)
Title: A Collection of Handy, Useful Functions
Description: A set of little functions that have been found useful to do little
odds and ends such as plotting the results of K-means clustering, substituting
special text characters, viewing parts of a data.frame, constructing formulas
from text and building design and response matrices.
Author: Jared P. Lander
Maintainer: Jared P. Lander <packages@jaredlander.com>
Diff between useful versions 1.1.9 dated 2015-09-22 and 1.2.0 dated 2016-01-10
DESCRIPTION | 16 ++-- LICENSE | 2 MD5 | 129 +++++++++++++++++++------------------- NAMESPACE | 4 - NEWS.md |only R/formatters.r | 11 +-- R/subMultiple.r | 6 + R/tsPlot.r | 12 +-- README.md | 2 man/ComputeHartigan.Rd | 3 man/FitKMeans.Rd | 4 - man/ForceDataFrame.Rd | 2 man/MapToInterval.Rd | 4 - man/PlotHartigan.Rd | 4 - man/WhichCorner.Rd | 3 man/binary.flip.Rd | 4 - man/bottomleft.Rd | 4 - man/bottomright.Rd | 4 - man/build.formula.Rd | 4 - man/build.x.Rd | 20 ++--- man/build.y.Rd | 3 man/cart2pol.Rd | 4 - man/classdf.Rd | 2 man/colsToFront.Rd | 5 - man/compare.list.Rd | 4 - man/constant.Rd | 3 man/corner.Rd | 4 - man/find.case.Rd | 2 man/fortify.acf.Rd | 4 - man/fortify.kmeans.Rd | 4 - man/fortify.ts.Rd | 4 - man/indexToPosition.Rd | 3 man/interval.check.Rd | 3 man/left.Rd | 4 - man/lower.case.Rd | 2 man/mixed.case.Rd | 2 man/moveToFront.Rd | 5 - man/multiple.Rd | 8 +- man/multiple.comma.Rd | 6 + man/multiple.dollar.Rd | 6 + man/multiple.identity.Rd | 6 + man/multiple_format.Rd | 8 +- man/numeric.case.Rd | 4 - man/plot.Rd | 2 man/plot.acf.Rd | 4 - man/plot.kmeans.Rd | 4 - man/plotTimesSeries.Rd | 4 - man/pol2cart.Rd | 12 ++- man/positionToIndex.Rd | 3 man/reclass.Rd | 5 - man/right.Rd | 4 - man/shift.column.Rd | 4 - man/simple.impute.Rd | 3 man/simple.impute.data.frame.Rd | 3 man/simple.impute.default.Rd | 3 man/simple.impute.tbl_df.Rd | 3 man/subMultiple.Rd | 15 ++-- man/subOut.Rd | 4 - man/subSpecials.Rd | 8 +- man/topleft.Rd | 4 - man/topright.Rd | 4 - man/ts.plotter.Rd | 4 - man/upper.case.Rd | 2 man/useful.Rd | 2 man/vplayout.Rd | 8 +- tests/testthat/test-subMultiple.R | 4 + 66 files changed, 261 insertions(+), 182 deletions(-)
Title: Student Growth Percentiles & Percentile Growth Trajectories
Description: Functions to calculate student growth percentiles and percentile growth projections/trajectories for students using large scale,
longitudinal assessment data. Functions use quantile regression to estimate the conditional density associated
with each student's achievement history. Percentile growth projections/trajectories are calculated using the coefficient matrices derived from
the quantile regression analyses and specify what percentile growth is required for students to reach future achievement targets.
Author: Damian W. Betebenner [aut, cre],
Adam R. Van Iwaarden [aut],
Ben Domingue [aut],
Yi Shang [aut],
Jonathan Weeks [ctb],
John Stewart [ctb],
Jinnie Choi [ctb],
Xin Wei [ctb],
Hi Shin Shim [ctb],
Xiaoyuan Tan [ctb] (Arizona Department of Education),
Carrie Giovannini [ctb] (Arizona Department of Education),
Sarah Polasky [ctb] (Arizona State University),
Rebecca Gau [ctb] (Arizona Charter School Association),
Jeffrey Dean [ctb] (University of Arkansas),
William Bonk [ctb] (Colorado Department of Education),
Marie Huchton [ctb] (Colorado Department of Education),
Allison Timberlake [ctb] (Georgia Department of Education),
Qi Qin [ctb] (Georgia Department of Education),
Melissa Fincher [ctb] (Georgia Department of Education),
Kiran Athota [ctb] (Georgia Department of Education),
Travis Allen [ctb] (Georgia Department of Education),
Glenn Hirata [ctb] (Hawaii Department of Education),
Glenn Nochi [ctb] (Hawaii Department of Education),
Joshua Lee [ctb] (Hawaii Department of Education),
Ayaka Nukui [ctb] (Idaho Department of Education),
Carissa Miller [ctb] (Idaho Department of Education),
Matthew Raimondi [ctb] (Elgin Area School District U46 (Illinois)),
Wes Bruce [ctb] (Indiana Department of Education),
Robert Hochsegang [ctb] (Indiana Department of Education),
Tony Moss [ctb] (Kansas State Department of Education),
Xuewen Sheng [ctb] (Kansas State Department of Education),
Kathy Flanagan [ctb] (Massachusetts Department of Elementary and Secondary Education),
Robert Lee [ctb] (Massachusetts Department of Elementary and Secondary Education),
Ji Zeng [ctb] (Michigan Department of Education),
Steve Viger [ctb] (Michigan Department of Education),
Joe DeCastra [ctb] (Mississippi Department of Education),
Ken Thompson [ctb] (Mississippi Department of Education),
Soo Yeon Cho [ctb] (Missouri Department of Education),
Jeff Halsell [ctb] (Clark County School District, Nevada),
Selcuk Ozdemir [ctb] (Washoe County School District, Nevada),
Roger Silva [ctb] (Nevada Department of Education),
Deb Wiswell [ctb] (New Hampshire Department of Education),
Katya Levitan-Reiner [ctb] (New Haven Public Schools),
Catherine McCaslin [ctb] (New Haven Public Schools),
Joshua Marland [ctb] (New York Education Department),
W Joshua Rew [ctb] (Oregon Department of Education),
Jason Becker [ctb] (Rhode Island Department of Education),
Jessica Bailey [ctb] (Rhode Island Department of Education),
Ana Karantonis [ctb] (Rhode Island Department of Education),
Deborah Jonas [ctb] (Virginia Department of Education),
Juan D'Brot [ctb] (West Virginia Department of Education),
Nate Hixson [ctb] (West Virginia Department of Education),
Deb Came [ctb] (Washington Office of Superintendent of Public Instruction),
Ashley Colburn [ctb] (Washington Office of Superintendent of Public Instruction),
Nick Hassell [ctb] (Washington Office of Superintendent of Public Instruction),
Krissy Johnson [ctb] (Washington Office of Superintendent of Public Instruction),
Daniel Bush [ctb] (Wisconsin Department of Education),
Justin Meyer [ctb] (Wisconsin Department of Education),
Joseph Newton [ctb] (Wisconsin Department of Education),
Nick Stroud [ctb] (Wisconsin Department of Education),
John Paul [ctb] (Wyoming Department of Education),
Michael Flicek [ctb] (Michael Flicek Projects LLC working with Wyoming Department of Education),
Phyllis Clay [ctb] (Albuquerque Public Schools),
Peter Kinyua [ctb] (Albuquerque Public Schools),
Brendan Houng [ctb] (University of Melbourne, Australia, NAPLAN),
Leslie Rosale [ctb] (Ministry of Education, Guatemala),
Nathan Wall [ctb] (eMetric working with Nevada Department of Education and South Dakota Department of Education),
Narek Sahakyan [ctb] (World Class Instruction and Design (WIDA))
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGP versions 1.2-0.0 dated 2014-01-28 and 1.4-0.0 dated 2016-01-10
DESCRIPTION | 79 - MD5 | 182 +-- NAMESPACE | 18 R/abcSGP.R | 61 - R/analyzeSGP.R | 1893 ++++++++++++++++++++++++------------ R/as.splineMatrix.R | 6 R/baselineSGP.R | 95 + R/bubblePlot.R | 268 ++--- R/bubblePlot_Styles.R | 128 +- R/capwords.R | 45 R/checkConfig.R | 4 R/checkSGP.R | 129 +- R/checksplineMatrix.R | 8 R/combineSGP.R | 330 +++--- R/convertScaleScore.R |only R/convertTime.R |only R/createKnotsBoundaries.R | 22 R/createLongCutscores.R |only R/createUniqueLongData.R |only R/csemScoreSimulator.R | 53 - R/ddcast.R |only R/equateSGP.R |only R/getAchievementLevel.R | 66 + R/getCohortDataInfo.R | 17 R/getHighNeedStatus.R | 4 R/getJSON.R |only R/getKnotsBoundaries.R | 111 +- R/getMaxOrderForProgression.R | 20 R/getMyLabel.R |only R/getNewCutscores.R |only R/getPanelData.R | 461 +++++++- R/getPanelDataVnames.R | 79 + R/getPercentileTableNames.R | 22 R/getPreferredSGP.R | 31 R/getSGPBaselineConfig.R | 7 R/getSGPConfig.R | 547 ++++++++++ R/getSGPtNames.R |only R/getStateAbbreviation.R | 11 R/getTableNameYear.R |only R/getTargetAchievementLevels.R |only R/getTargetInitialStatus.R | 58 - R/getTargetName.R | 32 R/getTargetSGP.R | 166 ++- R/getTargetSGPContentArea.R | 17 R/getTargetSGPLevel.R |only R/getTargetScaleScore.R | 266 +++-- R/getTimeShiftIndex.R |only R/getVersion.R |only R/getYearsContentAreasGrades.R | 25 R/getsplineMatrices.R | 6 R/gofSGP.R | 366 +++++-- R/growthAchievementPlot.R | 382 +++---- R/is.SGP.R | 4 R/is.splineMatrix.R | 4 R/linkagePlot.R |only R/mergeSGP.R | 6 R/outputSGP.R | 561 ++++++---- R/piecewiseTransform.R |only R/prepareSGP.R | 151 +- R/rliSGP.R |only R/splineMatrix-class.R | 4 R/sqliteSGP.R | 153 +- R/startParallel.R | 67 - R/stopParallel.R | 9 R/studentGrowthPercentiles.R | 1136 +++++++++++++--------- R/studentGrowthPlot.R | 1788 ++++++++++++++++++++-------------- R/studentGrowthPlot_Styles.R | 1984 ++++++++++++++++++++------------------ R/studentGrowthProjections.R | 648 +++++++++--- R/summarizeSGP.R | 511 ++++----- R/summarizeSGP_Utilities.R |only R/testSGP.R | 2053 ++++++++++++++++++++++++++++------------ R/transformScaleScore.R |only R/unfoldstudentGrowthPlots.R |only R/unique.splineMatrix.R | 8 R/updateSGP.R | 289 ++++- R/visualizeSGP.R | 523 ++++++---- R/yearIncrement.R | 10 R/zzz.R | 2 data/SGPstateData.rda |binary inst/CITATION | 16 inst/NEWS | 25 man/SGP-class.Rd | 2 man/SGP-package.Rd | 20 man/SGPstateData.Rd | 3 man/abcSGP.Rd | 105 +- man/analyzeSGP.Rd | 133 +- man/baselineSGP.Rd | 12 man/bubblePlot_Styles.Rd | 3 man/capwords.Rd | 4 man/combineSGP.Rd | 22 man/gofSGP.Rd | 4 man/growthAchievementPlot.Rd | 54 - man/outputSGP.Rd | 11 man/prepareSGP.Rd | 6 man/rliSGP.Rd |only man/studentGrowthPercentiles.Rd | 372 +++---- man/studentGrowthPlot.Rd | 16 man/studentGrowthPlot_Styles.Rd | 13 man/studentGrowthProjections.Rd | 75 + man/summarizeSGP.Rd | 14 man/testSGP.Rd | 37 man/updateSGP.Rd | 85 + man/visualizeSGP.Rd | 15 103 files changed, 10827 insertions(+), 6146 deletions(-)
Title: Extra Themes, Scales and Geoms for 'ggplot2'
Description: Some extra themes, geoms, and scales for 'ggplot2'.
Provides 'ggplot2' themes and scales that replicate the look of plots
by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata',
'Excel', and 'The Wall Street Journal', among others.
Provides 'geoms' for Tufte's box plot and range frame.
Author: Jeffrey B. Arnold [aut, cre],
Gergely Daroczi [ctb],
Bo Werth [ctb],
Brian Weitzner [ctb],
Joshua Kunst [ctb],
Baptise Auguie [ctb],
Bob Rudis [ctb],
Hadley Wickham [ctb, cph] (Code from the ggplot2 package.),
Justin Talbot [ctb] (Code from the labeling package)
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between ggthemes versions 3.0.0 dated 2015-12-20 and 3.0.1 dated 2016-01-10
ggthemes-3.0.0/ggthemes/data |only ggthemes-3.0.1/ggthemes/DESCRIPTION | 21 ggthemes-3.0.1/ggthemes/MD5 | 93 - ggthemes-3.0.1/ggthemes/NEWS | 7 ggthemes-3.0.1/ggthemes/R/banking.R | 41 ggthemes-3.0.1/ggthemes/R/base.R | 1 ggthemes-3.0.1/ggthemes/R/calc.R | 4 ggthemes-3.0.1/ggthemes/R/colorblind.R | 2 ggthemes-3.0.1/ggthemes/R/economist.R | 47 ggthemes-3.0.1/ggthemes/R/excel.R | 25 ggthemes-3.0.1/ggthemes/R/few.R | 11 ggthemes-3.0.1/ggthemes/R/fivethirtyeight.R | 10 ggthemes-3.0.1/ggthemes/R/gdocs.R | 1 ggthemes-3.0.1/ggthemes/R/geom-rangeframe.R | 1 ggthemes-3.0.1/ggthemes/R/geom-tufteboxplot.R | 4 ggthemes-3.0.1/ggthemes/R/ggthemes-data.R | 636 +++++++++- ggthemes-3.0.1/ggthemes/R/hc.R | 47 ggthemes-3.0.1/ggthemes/R/igray.R | 9 ggthemes-3.0.1/ggthemes/R/pander.R | 210 ++- ggthemes-3.0.1/ggthemes/R/scale-tufte.R | 140 -- ggthemes-3.0.1/ggthemes/R/shapes.R | 2 ggthemes-3.0.1/ggthemes/R/show.R | 3 ggthemes-3.0.1/ggthemes/R/solarized.R | 75 - ggthemes-3.0.1/ggthemes/R/stat-fivenumber.R | 3 ggthemes-3.0.1/ggthemes/R/stata.R | 130 +- ggthemes-3.0.1/ggthemes/R/tableau.R | 100 + ggthemes-3.0.1/ggthemes/R/theme-foundation.R | 16 ggthemes-3.0.1/ggthemes/R/theme-map.R | 18 ggthemes-3.0.1/ggthemes/R/tufte.R | 14 ggthemes-3.0.1/ggthemes/R/utils.R | 3 ggthemes-3.0.1/ggthemes/R/wsj.R | 59 ggthemes-3.0.1/ggthemes/inst/doc/ggthemes.html | 12 ggthemes-3.0.1/ggthemes/man/bank_slopes.Rd | 12 ggthemes-3.0.1/ggthemes/man/geom_tufteboxplot.Rd | 2 ggthemes-3.0.1/ggthemes/man/hc_pal.Rd | 8 ggthemes-3.0.1/ggthemes/man/range_breaks.Rd | 2 ggthemes-3.0.1/ggthemes/man/scale_colour_gradient2_tableau.Rd | 17 ggthemes-3.0.1/ggthemes/man/scale_colour_gradient_tableau.Rd | 23 ggthemes-3.0.1/ggthemes/man/tableau_div_gradient_pal.Rd | 9 ggthemes-3.0.1/ggthemes/man/theme_economist.Rd | 3 ggthemes-3.0.1/ggthemes/man/theme_excel.Rd | 8 ggthemes-3.0.1/ggthemes/man/theme_foundation.Rd | 9 ggthemes-3.0.1/ggthemes/man/theme_pander.Rd | 19 ggthemes-3.0.1/ggthemes/man/theme_stata.Rd | 10 ggthemes-3.0.1/ggthemes/man/theme_wsj.Rd | 2 ggthemes-3.0.1/ggthemes/man/tremmel_shape_pal.Rd | 2 ggthemes-3.0.1/ggthemes/man/wsj_pal.Rd | 16 ggthemes-3.0.1/ggthemes/tests |only 48 files changed, 1389 insertions(+), 498 deletions(-)
Title: Desirability Functions for Ranking, Selecting, and Integrating
Data
Description: Functions for (1) ranking, selecting, and prioritising genes,
proteins, and metabolites from high dimensional biology experiments, (2)
multivariate hit calling in high content screens, and (3) combining data
from diverse sources.
Author: Stanley E. Lazic
Maintainer: Stanley E. Lazic <stan.lazic@cantab.net>
Diff between desiR versions 1.1 dated 2015-09-16 and 1.2 dated 2016-01-10
DESCRIPTION | 8 ++++---- MD5 | 21 ++++++++++++--------- R/d.low.R | 2 +- R/d.rank.R |only R/des.line.R | 13 ++++++++++--- inst/CITATION |only inst/doc/Gene_ranking.Rmd | 28 ++++++++++++++-------------- inst/doc/Gene_ranking.pdf |binary man/d.low.Rd | 2 +- man/d.rank.Rd |only man/des.line.Rd | 2 +- vignettes/Gene_ranking.Rmd | 28 ++++++++++++++-------------- vignettes/Gene_ranking.html | 34 +++++++++++++++++----------------- 13 files changed, 74 insertions(+), 64 deletions(-)
Title: Plots Coefficients from Fitted Models
Description: Plots the coefficients from model objects. This very quickly shows the user the point estimates and confidence intervals for fitted models.
Author: Jared P. Lander
Maintainer: Jared P. Lander <packages@jaredlander.com>
Diff between coefplot versions 1.2.0 dated 2013-05-12 and 1.2.4 dated 2016-01-10
coefplot-1.2.0/coefplot/README |only coefplot-1.2.0/coefplot/inst |only coefplot-1.2.0/coefplot/man/collidev.Rd |only coefplot-1.2.0/coefplot/man/pos_dodgev.Rd |only coefplot-1.2.4/coefplot/DESCRIPTION | 22 coefplot-1.2.4/coefplot/LICENSE |only coefplot-1.2.4/coefplot/MD5 | 92 +-- coefplot-1.2.4/coefplot/NAMESPACE | 24 coefplot-1.2.4/coefplot/NEWS | 16 coefplot-1.2.4/coefplot/R/buildPlottingFrame.r | 6 coefplot-1.2.4/coefplot/R/coefPredMatching.r | 15 coefplot-1.2.4/coefplot/R/coefplot.r | 86 ++- coefplot-1.2.4/coefplot/R/dodging.r | 280 +++++----- coefplot-1.2.4/coefplot/R/extractCoef.r | 129 ++++ coefplot-1.2.4/coefplot/R/multiplot.r | 11 coefplot-1.2.4/coefplot/R/position.r |only coefplot-1.2.4/coefplot/README.md |only coefplot-1.2.4/coefplot/man/buildModelCI.Rd | 22 coefplot-1.2.4/coefplot/man/buildModelCI.default.Rd | 78 +- coefplot-1.2.4/coefplot/man/buildPlotting.default.Rd | 116 +--- coefplot-1.2.4/coefplot/man/coefplot.Rd | 46 - coefplot-1.2.4/coefplot/man/coefplot.data.frame.Rd |only coefplot-1.2.4/coefplot/man/coefplot.default.Rd | 163 ++--- coefplot-1.2.4/coefplot/man/coefplot.glm.Rd | 25 coefplot-1.2.4/coefplot/man/coefplot.lm.Rd | 25 coefplot-1.2.4/coefplot/man/coefplot.rxGlm.Rd | 26 coefplot-1.2.4/coefplot/man/coefplot.rxLinMod.Rd | 25 coefplot-1.2.4/coefplot/man/coefplot.rxLogit.Rd | 25 coefplot-1.2.4/coefplot/man/doRegex.Rd | 19 coefplot-1.2.4/coefplot/man/extract.coef.Rd | 23 coefplot-1.2.4/coefplot/man/extract.coef.cv.glmnet.Rd |only coefplot-1.2.4/coefplot/man/extract.coef.default.Rd | 24 coefplot-1.2.4/coefplot/man/extract.coef.glm.Rd | 22 coefplot-1.2.4/coefplot/man/extract.coef.glmnet.Rd |only coefplot-1.2.4/coefplot/man/extract.coef.lm.Rd | 22 coefplot-1.2.4/coefplot/man/extract.coef.maxLik.Rd |only coefplot-1.2.4/coefplot/man/extract.coef.rxGlm.Rd | 19 coefplot-1.2.4/coefplot/man/extract.coef.rxLinMod.Rd | 19 coefplot-1.2.4/coefplot/man/extract.coef.rxLogit.Rd | 19 coefplot-1.2.4/coefplot/man/get.assign.Rd | 16 coefplot-1.2.4/coefplot/man/get.assign.glm.Rd | 16 coefplot-1.2.4/coefplot/man/get.assign.lm.Rd | 16 coefplot-1.2.4/coefplot/man/getCoefsFromPredictors.Rd | 22 coefplot-1.2.4/coefplot/man/getCoefsFromPredictors.default.Rd | 29 - coefplot-1.2.4/coefplot/man/getCoefsFromPredictors.rxGlm.Rd | 28 - coefplot-1.2.4/coefplot/man/getCoefsFromPredictors.rxLinMod.Rd | 28 - coefplot-1.2.4/coefplot/man/getCoefsFromPredictors.rxLogit.Rd | 28 - coefplot-1.2.4/coefplot/man/getCoefsFromPredictorsRevo.Rd | 28 - coefplot-1.2.4/coefplot/man/matchCoefs.Rd | 19 coefplot-1.2.4/coefplot/man/matchCoefs.default.Rd | 17 coefplot-1.2.4/coefplot/man/multiplot.Rd | 206 ++----- coefplot-1.2.4/coefplot/man/position_dodgev.Rd | 55 + 52 files changed, 969 insertions(+), 938 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 2.14.0 dated 2015-10-25 and 3.0.0 dated 2016-01-09
aroma.affymetrix-2.14.0/aroma.affymetrix/man/bgAdjustGcrma.AffymetrixCelFile.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/bgAdjustGcrma.AffymetrixCelSet.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/bgAdjustOptical.AffymetrixCelFile.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/bgAdjustRma.AffymetrixCelFile.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/nbrOfArrays.AffymetrixCnChpSet.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/nbrOfArrays.CnagCfhSet.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/nbrOfArrays.DChipDcpSet.Rd |only aroma.affymetrix-3.0.0/aroma.affymetrix/DESCRIPTION | 15 aroma.affymetrix-3.0.0/aroma.affymetrix/MD5 | 283 ++-- aroma.affymetrix-3.0.0/aroma.affymetrix/NAMESPACE | 10 aroma.affymetrix-3.0.0/aroma.affymetrix/NEWS | 28 aroma.affymetrix-3.0.0/aroma.affymetrix/R/999.DEPRECATED.R | 41 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AbstractProbeSequenceNormalization.R | 216 +-- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AdditiveCovariatesNormalization.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffyGenePDInfo.writeCdf.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.MONOCELL.R | 9 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.R | 32 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.UNIQUE.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.getSubsetOfCellIndices.R | 12 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.getSubsetOfUnits.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.writeCdfByExcludingCells.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.BG.R | 652 ---------- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.R | 70 - aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.allocateFromCdf.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.createFrom.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.normalizeAffine.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.normalizeQuantile.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelSet.BG.R | 172 -- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelSet.NORM.R | 43 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelSet.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R | 168 +- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCnChpFile.R | 13 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCnChpSet.R | 31 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCnChpSet.extras.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCsvGenomeInformation.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixFileSet.getIdentifier.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixNetAffxCsvFile.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixPgfFile.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixTsvFile.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.R | 291 ++-- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AromaChipTypeAnnotationFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AromaUfcFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ChipEffectFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ChipEffectFile.fromDataFile.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ChipEffectNnn.extractChromosomalDataFrame.R | 30 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnChipEffectFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnChipEffectSet.importFromApt.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnChipEffectSet.importFromDChip.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnProbeAffinityFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnagCfhFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnagCfhSet.R | 33 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipDcpSet.R | 31 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipDcpSet.extras.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipGenomeInformation.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipQuantileNormalization.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipSnpInformation.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ExonChipEffectFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ExonRmaPlm.calculateWeights.R | 12 aroma.affymetrix-3.0.0/aroma.affymetrix/R/FirmaFile.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/FirmaModel.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/FragmentEquivalentClassNormalization.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/FragmentLengthNormalization.R | 245 ++- aroma.affymetrix-3.0.0/aroma.affymetrix/R/GcContentNormalization.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/GcRmaBackgroundCorrection.R | 362 +++++ aroma.affymetrix-3.0.0/aroma.affymetrix/R/GenericReporter.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/GenomeInformation.AFFX.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/LimmaBackgroundCorrection.R | 148 +- aroma.affymetrix-3.0.0/aroma.affymetrix/R/MatNormalization.R | 190 +- aroma.affymetrix-3.0.0/aroma.affymetrix/R/MatSmoothing.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/OpticalBackgroundCorrection.R | 159 +- aroma.affymetrix-3.0.0/aroma.affymetrix/R/Package.XTRA.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ParameterCelFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ParameterCelSet.R | 8 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ProbeLevelModel.calculateResiduals.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ProbeLevelModel.calculateWeights.R | 10 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ProbeLevelModel.fit.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ProbeLevelTransform3.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/QualityAssessmentFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/QuantileNormalization.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ReseqCrosstalkCalibration.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ResidualFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/RmaBackgroundCorrection.R | 183 ++ aroma.affymetrix-3.0.0/aroma.affymetrix/R/RmaPlm.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ScaleNormalization.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ScaleNormalization3.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SmoothMultiarrayModel.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SmoothMultiarrayModel.fit.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SnpChipEffectFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SnpChipEffectSet.exportTotalAndFracB.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SnpInformation.R | 9 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SnpProbeAffinityFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SpatialRowColumnNormalization.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/Transform.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/UflSnpInformation.R | 31 aroma.affymetrix-3.0.0/aroma.affymetrix/R/UgpGenomeInformation.R | 11 aroma.affymetrix-3.0.0/aroma.affymetrix/R/UnitModel.fitCnProbes.R | 54 aroma.affymetrix-3.0.0/aroma.affymetrix/R/UnitTypeScaleNormalization.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/WeightsFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/bpmapCluster2Cdf.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/createExonByTranscriptCdf.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/env2Cdf.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/findByCdf2.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/profileCGH.writeRegions.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/randomSeed.R |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/annotationData/dataSets/HapMap,testSet/all,fullnames.txt.md5 |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/annotationData/genomes/Human/Human,chromosomes.txt.md5 |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/annotationData/samples/HapMap270.saf.md5 |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/21.doASCRMAv2,CalMaTe.R | 75 - aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/futures |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R | 119 - aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/12.doGCRMA_vs_gcrma.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R | 119 - aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,extractAndWrite.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R | 58 aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,TumorNormalPair.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/ChipEffectSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/CnagCfhSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/CrlmmParametersSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/DChipDcpSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/FirmaSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/GcRmaBackgroundCorrection.Rd | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/man/LimmaBackgroundCorrection.Rd | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/man/Non-documented_objects.Rd | 10 aroma.affymetrix-3.0.0/aroma.affymetrix/man/ParameterCelSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/ResidualSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/RmaBackgroundCorrection.Rd | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/WeightsSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/calculateParametersGsb.AffymetrixCelSet.Rd | 10 aroma.affymetrix-3.0.0/aroma.affymetrix/man/getHeader.AffymetrixCelFile.Rd | 1 aroma.affymetrix-3.0.0/aroma.affymetrix/man/randomSeed.Rd |only aroma.affymetrix-3.0.0/aroma.affymetrix/tests/AffymetrixCdfFile.R | 9 aroma.affymetrix-3.0.0/aroma.affymetrix/tests/AffymetrixCelFile.R |only aroma.affymetrix-3.0.0/aroma.affymetrix/tests/AffymetrixCelSet.R | 15 140 files changed, 2112 insertions(+), 2197 deletions(-)
More information about aroma.affymetrix at CRAN
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Title: Phonetic Spelling Algorithms
Description: Provides a collection of phonetic algorithms including
Soundex, Metaphone, NYSIIS, Caverphone, and others.
Author: "James P. Howard, II" <jh@jameshoward.us>
Maintainer: "James P. Howard, II" <jh@jameshoward.us>
Diff between phonics versions 0.5.4 dated 2015-12-27 and 0.6.2 dated 2016-01-09
DESCRIPTION | 8 +++---- MD5 | 41 ++++++++++++++++++++++++---------------- NAMESPACE | 4 +++ R/RcppExports.R | 4 +-- R/caverphone.R | 2 - R/lein.R | 2 - R/mra.R |only R/nysiis.R | 2 - R/rogerroot.R |only R/statcan.R | 2 - README.md | 4 +++ man/caverphone.Rd | 5 ++-- man/lein.Rd | 5 ++-- man/metaphone.Rd | 5 ++-- man/mra.Rd |only man/nysiis.Rd | 3 +- man/rogerroot.Rd |only man/soundex.Rd | 5 ++-- man/statcan.Rd | 5 ++-- src/metaphone.cpp | 2 - src/soundex.cpp | 2 - tests/testthat/mra-compare.csv |only tests/testthat/mra-encode.csv |only tests/testthat/rogerroot.csv |only tests/testthat/test-mra.R |only tests/testthat/test-rogerroot.R |only 26 files changed, 62 insertions(+), 39 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.6 dated 2016-01-08 and 1.1.7 dated 2016-01-09
DESCRIPTION | 6 +- MD5 | 4 - R/GDM_Table_Funcs.R | 134 ++++++++++++++++++++++++++-------------------------- 3 files changed, 72 insertions(+), 72 deletions(-)
Title: Eye-Tracking Data Analysis
Description: A set of tools that address tasks along the pipeline from raw
data to analysis and visualization for eye-tracking data. Offers several
popular types of analyses, including linear and growth curve time analyses,
onset-contingent reaction time analyses, as well as several non-parametric
bootstrapping approaches.
Author: Jacob Dink [aut, cre],
Brock Ferguson [aut]
Maintainer: Jacob Dink <jacobwdink@gmail.com>
Diff between eyetrackingR versions 0.1.2 dated 2016-01-08 and 0.1.3 dated 2016-01-09
eyetrackingR-0.1.2/eyetrackingR/tests/testthat/clust_dat_output_lm.txt |only eyetrackingR-0.1.3/eyetrackingR/DESCRIPTION | 6 eyetrackingR-0.1.3/eyetrackingR/MD5 | 26 - eyetrackingR-0.1.3/eyetrackingR/NEWS.md | 3 eyetrackingR-0.1.3/eyetrackingR/inst/doc/divergence_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/inst/doc/growth_curve_analysis_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/inst/doc/onset_contingent_analysis_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/inst/doc/preparing_your_data_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/inst/doc/window_analysis_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/tests/testthat/tb_output_between_subj.txt | 193 ++++++--- eyetrackingR-0.1.3/eyetrackingR/tests/testthat/tb_output_interaction.txt | 197 ++++++---- eyetrackingR-0.1.3/eyetrackingR/tests/testthat/tb_output_within_subj.txt | 175 +++++--- eyetrackingR-0.1.3/eyetrackingR/tests/testthat/tclust_tb_anal.txt |only eyetrackingR-0.1.3/eyetrackingR/tests/testthat/test_analyze_time_bins.R | 67 +-- eyetrackingR-0.1.3/eyetrackingR/tests/testthat/test_cluster_analysis.R | 39 + 15 files changed, 458 insertions(+), 268 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 2.10.0 dated 2015-12-07 and 2.10.2 dated 2016-01-09
secr-2.10.0/secr/vignettes/secr-datainput.html |only secr-2.10.0/secr/vignettes/secr-overview.html |only secr-2.10.2/secr/DESCRIPTION | 12 - secr-2.10.2/secr/MD5 | 72 ++++----- secr-2.10.2/secr/NAMESPACE | 2 secr-2.10.2/secr/NEWS | 26 +++ secr-2.10.2/secr/R/LLsurface.secr.R | 2 secr-2.10.2/secr/R/discretize.R | 51 +++++- secr-2.10.2/secr/R/join.R | 32 +--- secr-2.10.2/secr/R/make.capthist.R | 39 +++-- secr-2.10.2/secr/R/mask.check.R | 20 +- secr-2.10.2/secr/R/methods.R | 43 ++++- secr-2.10.2/secr/R/par.secr.fit.R | 5 secr-2.10.2/secr/R/pdot.R | 4 secr-2.10.2/secr/R/pmixProfileLL.R | 17 +- secr-2.10.2/secr/R/secr.design.MS.R | 8 - secr-2.10.2/secr/R/secr.fit.R | 7 secr-2.10.2/secr/R/secrloglik.R | 4 secr-2.10.2/secr/R/sim.capthist.R | 137 ++++++++++++------ secr-2.10.2/secr/R/sim.popn.R | 1 secr-2.10.2/secr/R/sim.secr.R | 11 + secr-2.10.2/secr/R/utility.R | 64 ++++++++ secr-2.10.2/secr/R/verify.R | 1 secr-2.10.2/secr/build/vignette.rds |binary secr-2.10.2/secr/inst/doc/secr-manual.pdf |binary secr-2.10.2/secr/inst/doc/secr-overview.R | 19 -- secr-2.10.2/secr/man/Parallel.Rd | 17 ++ secr-2.10.2/secr/man/contour.Rd | 2 secr-2.10.2/secr/man/discretize.Rd | 16 +- secr-2.10.2/secr/man/secr-package.Rd | 4 secr-2.10.2/secr/man/smooths.Rd | 4 secr-2.10.2/secr/src/detectfn.c | 155 +++++++++++++++++--- secr-2.10.2/secr/src/polygon.c | 23 +-- secr-2.10.2/secr/src/secr.c | 185 ++++++++++++------------- secr-2.10.2/secr/src/secr.h | 17 +- secr-2.10.2/secr/src/sighting.c | 115 ++++++++++----- secr-2.10.2/secr/src/trapping.c | 15 +- secr-2.10.2/secr/src/utils.c | 46 +++++- 38 files changed, 789 insertions(+), 387 deletions(-)
Title: Empirical Bayes Estimation and Inference in R
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models
and some other density estimation and regression methods based on convex
optimization.
Author: Roger Koenker [aut, cre],
Jiaying Gu [ctb],
Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between REBayes versions 0.58 dated 2015-09-21 and 0.61 dated 2016-01-09
DESCRIPTION | 6 +++--- MD5 | 25 +++++++++++++------------ R/Bmix.R | 4 ++-- R/GLmix.R | 50 +++++++++++++++++++++++++++++++++----------------- R/KWDual.R | 2 +- R/Weibullmix.R | 5 +++-- R/predict.R | 1 - demo/00Index | 3 ++- demo/GLmix0.R |only inst/ChangeLog | 18 ++++++++++++++++++ man/Bmix.Rd | 2 +- man/GLmix.Rd | 9 ++++++--- man/KWDual.Rd | 2 +- man/medde.Rd | 4 ++-- 14 files changed, 85 insertions(+), 46 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.1.4 dated 2015-12-15 and 3.1.8 dated 2016-01-09
DESCRIPTION | 8 MD5 | 122 ++++++------- NAMESPACE | 12 + R/Methods-aux.R | 2 R/RCauto.R | 6 R/RFfit.R | 11 - R/RMmodels.R | 358 +++++++++++++++++++-------------------- R/basic.fctns.R | 3 R/convert.R | 23 +- R/fitgauss.R | 118 +++++++------ R/generatemodels.R | 31 ++- R/getNset.R | 18 + R/kriging.R | 76 ++++---- R/rf-plots.R | 20 +- R/rf.R | 5 configure.ac | 5 inst/CITATION | 2 inst/doc/multivariate_jss.pdf |binary man/Bayesian.Rd | 1 man/GaussianFields.Rd | 99 ++++++++-- man/RFboxcox.Rd | 2 man/RFgetModelInfo.Rd | 1 man/RFinterpolate.Rd | 2 man/RFloglikelihood.Rd | 10 - man/RFoptions.Rd | 12 - man/RMintern.Rd | 22 -- man/RMmatrix.Rd | 2 man/RMmodelsMultivariate.Rd | 28 ++- man/RMmodelsTrend.Rd | 3 man/RMmppplus.Rd | 12 - man/papers.jss14.Rd | 1 man/plot-method.Rd | 1 src/Huetchen.cc | 7 src/InternalCov.cc | 10 - src/KeyInfo.cc | 4 src/MLE.cc | 51 +++-- src/Makevars.in | 11 - src/Primitive.cc | 31 +++ src/RF.h | 146 +++++++--------- src/Specific.cc | 2 src/circulant.cc | 58 ++++-- src/direct.cc | 32 +-- src/extremes.cc | 8 src/families.cc | 13 + src/gauss.cc | 69 ++++++- src/gausslikeli.cc | 193 ++++++++------------- src/getNset.cc | 69 ++++--- src/hyperplan.cc | 4 src/initNerror.cc | 49 ++--- src/nugget.cc | 2 src/plusmalS.cc | 3 src/rf_interfaces.cc | 380 ++++++++++++++++++++++-------------------- src/sequential.cc | 4 src/shape_processes.h | 1 src/spectral.cc | 2 src/startGetNset.cc | 3 src/tbm.cc | 2 src/trend.cc | 13 - src/userinterfaces.cc | 2 src/variogramAndCo.cc | 73 +++++--- src/variogramAndCo.h | 12 - src/win_linux_aux.cc | 4 62 files changed, 1291 insertions(+), 983 deletions(-)
Title: Phylogenetic Linear Regression
Description: Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.
Author: Lam Si Tung Ho [aut, cre],
Cecile Ane [aut],
Robert Lachlan [ctb],
Kelsey Tarpinian [ctb],
Rachel Feldman [ctb]
Maintainer: Lam Si Tung Ho <lamho86@gmail.com>
Diff between phylolm versions 2.3 dated 2015-09-11 and 2.4 dated 2016-01-09
DESCRIPTION | 11 +++--- MD5 | 24 +++++++++----- NAMESPACE | 3 + R/OUshifts.R | 73 ++++++++++++++++++++++++++++++------------- R/testingTreeWithQuartetCF.r |only README.md | 13 +++++++ data/guidetree.rda |only data/quartetCF.rda |only man/OUshifts.Rd | 9 ++++- man/guidetree.Rd |only man/phyloglm.Rd | 2 - man/phylolm-package.Rd | 11 +++--- man/phylolm.Rd | 4 +- man/quartetCF.Rd |only man/stepwise.test.tree.Rd |only man/test.one.species.tree.Rd |only man/test.tree.preparation.Rd |only 17 files changed, 105 insertions(+), 45 deletions(-)
Title: LaTeX Wrappers for R Users
Description: Provides the functionality to write LaTeX code from within R
without having to learn LaTeX. Functionality also exists to create HTML
and Markdown code. While the functionality still exists to write
complete documents with lazyWeave, it is generally easier to do so with
with markdown and knitr. lazyWeave's main strength now is the ability
to design custom and complex tables for reporting results.
Author: Benjamin Nutter
Maintainer: Benjamin Nutter <nutter@battelle.org>
Diff between lazyWeave versions 3.0.0 dated 2015-07-27 and 3.0.1 dated 2016-01-09
DESCRIPTION | 8 MD5 | 162 +++--- NAMESPACE | 90 +-- NEWS | 119 ++-- R/catconttable.R | 418 +++++++-------- R/cattable.R | 462 ++++++++--------- R/conttable.R | 390 +++++++------- R/is.significant.R | 74 +- R/lazy.build.R | 286 +++++----- R/lazy.citation.R | 116 ++-- R/lazy.counter.R | 276 +++++----- R/lazy.figure.R | 324 ++++++------ R/lazy.file.end.R | 44 - R/lazy.file.start.R | 262 ++++----- R/lazy.footnote.R | 154 ++--- R/lazy.insert.code.R | 80 +-- R/lazy.label.R | 54 +- R/lazy.landscape.R | 70 +- R/lazy.link.R | 118 ++-- R/lazy.list.R | 344 ++++++------- R/lazy.matrix.R | 282 +++++----- R/lazy.page.break.R | 68 +- R/lazy.page.number.R | 70 +- R/lazy.ref.R | 108 ++-- R/lazy.section.R | 352 ++++++------- R/lazy.table.R | 924 +++++++++++++++++------------------ R/lazy.text.R | 298 +++++------ R/lazy.text.format.R | 126 ++-- R/lazy.toc.R | 152 ++--- R/lazy.verbatim.end.R | 28 - R/lazy.verbatim.start.R | 78 +- R/lazy.write.R | 148 ++--- R/lazyWeave.R | 80 +-- R/mantel.test.R | 288 +++++----- R/map.size.R | 114 ++-- R/print.ctable.R | 242 ++++----- R/pvalString.R | 166 +++--- R/setHtmlOptions.R | 114 ++-- R/split_ctable.R | 56 +- R/univ.R | 350 ++++++------- R/write.ctable.r | 678 ++++++++++++------------- R/write.univ.R | 218 ++++---- R/zzz.R | 36 - README.md | 54 +- man/ComparisonTable.Rd | 396 +++++++-------- man/Delivery.rd | 68 +- man/Scout.rd | 48 - man/WritePrintCtable.Rd | 240 ++++----- man/is_significant.Rd | 76 +- man/lazy.build.Rd | 92 +-- man/lazy.citation.Rd | 86 +-- man/lazy.counter.Rd | 154 ++--- man/lazy.figure.Rd | 150 ++--- man/lazy.file.end.Rd | 36 - man/lazy.file.start.Rd | 156 ++--- man/lazy.footnote.Rd | 102 +-- man/lazy.insert.code.Rd | 72 +- man/lazy.landscape.Rd | 62 +- man/lazy.link.Rd | 68 +- man/lazy.list.Rd | 148 ++--- man/lazy.matrix.Rd | 174 +++--- man/lazy.page.break.Rd | 64 +- man/lazy.page.number.Rd | 58 +- man/lazy.ref.Rd | 82 +-- man/lazy.section.Rd | 160 +++--- man/lazy.table.Rd | 366 ++++++------- man/lazy.text.Rd | 136 ++--- man/lazy.text.format.Rd | 94 +-- man/lazy.toc.Rd | 104 +-- man/lazy.verbatim.start.Rd | 72 +- man/lazy.write.Rd | 72 +- man/lazyWeave.Rd | 88 +-- man/mantel.test.Rd | 126 ++-- man/map.size.Rd | 82 +-- man/pvalString.Rd | 106 ++-- man/setHtmlOptions.Rd | 122 ++-- man/univ.Rd | 184 +++--- man/write.univ.Rd | 224 ++++---- tests/testthat.R | 6 tests/testthat/test-is.significant.R | 28 - tests/testthat/test-lazy.citation.R | 48 - tests/testthat/test-lazy.counter.R | 4 82 files changed, 6620 insertions(+), 6615 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.7 dated 2015-10-28 and 1.8 dated 2016-01-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/C_CIT_V12.R | 4 +++- man/cit-package.Rd | 4 ++-- 4 files changed, 12 insertions(+), 10 deletions(-)
Title: Gaussian Approximation of Bayesian Binary Regression Models
Description: The main functions compute the expectation propagation approximation of a Bayesian probit/logit models with Gaussian prior. More information can be found in Chopin and Ridgway (2015). More models and priors should follow.
Author: James Ridgway
Maintainer: James Ridgway <james.ridgway@ensae.fr>
Diff between EPGLM versions 1.1 dated 2015-09-18 and 1.1.1 dated 2016-01-09
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/function.cpp | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Eye-Tracking Data Analysis
Description: A set of tools that address tasks along the pipeline from raw
data to analysis and visualization for eye-tracking data. Offers several
popular types of analyses, including linear and growth curve time analyses,
onset-contingent reaction time analyses, as well as several non-parametric
bootstrapping approaches.
Author: Jacob Dink [aut, cre],
Brock Ferguson [aut]
Maintainer: Jacob Dink <jacobwdink@gmail.com>
Diff between eyetrackingR versions 0.1.1 dated 2015-11-16 and 0.1.2 dated 2016-01-08
DESCRIPTION | 18 LICENSE | 2 MD5 | 63 +- NAMESPACE | 5 NEWS.md |only R/eyetrackingR.R | 21 R/helpers.R | 65 ++ R/onset_contingent_data.R | 14 R/time_cluster_data.R | 241 ++++++---- R/time_sequence_data.R | 505 +++++++++++++---------- R/time_spline_data.R | 152 ++++-- README.md | 16 build/vignette.rds |binary inst/doc/divergence_vignette.R | 106 +++- inst/doc/divergence_vignette.Rmd | 193 +++++--- inst/doc/divergence_vignette.html | 292 ++++++++----- inst/doc/growth_curve_analysis_vignette.html | 25 - inst/doc/onset_contingent_analysis_vignette.html | 25 - inst/doc/preparing_your_data_vignette.html | 10 inst/doc/window_analysis_vignette.html | 26 - man/analyze_boot_splines.Rd | 9 man/analyze_time_bins.Rd | 28 - man/analyze_time_clusters.Rd | 24 - man/make_boot_splines_data.Rd | 28 - man/make_time_cluster_data.Rd | 31 - man/plot.bin_analysis.Rd | 8 man/plot.time_cluster_data.Rd | 8 man/simulate_eyetrackingr_data.Rd | 9 tests/testthat/clust_dat_output_lm.txt |only tests/testthat/tb_output_between_subj.txt |only tests/testthat/tb_output_interaction.txt |only tests/testthat/tb_output_within_subj.txt |only tests/testthat/test_analyze_time_bins.R | 112 ++++- tests/testthat/test_cluster_analysis.R | 62 +- vignettes/divergence_vignette.Rmd | 193 +++++--- 35 files changed, 1439 insertions(+), 852 deletions(-)
Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++. For customizations or interest in other statistical methodologies for web data analysis please contact <davide.altomare@gmail.com>.
Author: Davide Altomare
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between ChannelAttribution versions 1.3 dated 2015-12-03 and 1.4 dated 2016-01-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/ChannelAttribution-package.Rd | 4 ++-- src/ChannelAttribution.cpp | 14 +++++++------- 4 files changed, 15 insertions(+), 15 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Fast Multivariate Normal Methods
Description: Provides computationally efficient tools related to
the multivariate normal distribution. The main functionalities are:
simulating multivariate normal random vectors, evaluating multivariate
normal densities and Mahalanobis distances. These tools are very efficient
thanks to the use of C++ code and of the OpenMP API.
Author: Matteo Fasiolo, using the C++ parallel RNG of Thijs van den Berg and
Ziggurat algorithm of Jens Maurer and Steven Watanabe (boost)
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between mvnfast versions 0.1.3 dated 2014-08-20 and 0.1.4 dated 2016-01-08
DESCRIPTION | 20 +++++++++++------ MD5 | 28 ++++++++++++------------ R/maha.R | 2 - R/ms.R | 2 - R/rmvn.R | 4 +-- build/vignette.rds |binary inst/CITATION | 6 ++--- inst/COPYRIGHTS | 2 - inst/doc/mvnfast.R | 7 ------ inst/doc/mvnfast.html | 56 ++++++++++++++++++++++++++++++++----------------- man/dmvn.Rd | 32 +++++++++++----------------- man/maha.Rd | 33 +++++++++++----------------- man/ms.Rd | 57 ++++++++++++++++++++------------------------------ man/rmvn.Rd | 55 +++++++++++++++++++----------------------------- src/mvnfast.h | 2 - 15 files changed, 144 insertions(+), 162 deletions(-)
Title: Cryptic Transcription Analysis in Yeast
Description: Calculates cryptic scores for genes using the ratio
(Cheung et al., 2008), the 3' enrichment method
(DeGennaro et al., 2013) and the probabilistic
method. It also provide methods to estimates
cryptic transcription start sites.
Author: Nicole Uwimana, Benjamin Haibe-Kains, Francois Robert
Maintainer: Nicole Uwimana <nicole.uwimana@gmail.com>
Diff between yCrypticRNAs versions 0.99.0 dated 2015-12-11 and 0.99.1 dated 2016-01-08
DESCRIPTION | 21 +++--- MD5 | 28 ++++---- NAMESPACE | 2 R/coverageDataSet.R | 27 +++++--- R/cryptic_transcripts_methods.R | 8 +- R/initiation_points_methods.R | 132 +++++++++++++++++++++++++++++----------- R/utils.R | 24 +++++-- inst/doc/yCrypticRNAs.R | 6 - inst/doc/yCrypticRNAs.Rmd | 6 - inst/doc/yCrypticRNAs.html | 10 +-- man/bam_to_reads.Rd | 6 + man/zscore_score.Rd | 2 src/bedFile.cpp | 14 ++-- tests/yCrypticRNAs_tests.R | 7 +- vignettes/yCrypticRNAs.Rmd | 6 - 15 files changed, 197 insertions(+), 102 deletions(-)
Title: An Algorithm for Morphometric Characters Selection and
Statistical Validation in Morphological Taxonomy
Diff between VARSEDIG versions 1.0 dated 2016-01-05 and 1.1 dated 2016-01-08
Description: An algorithm which identifies the morphometric features that significantly discriminate two taxa and validates the morphological distinctness between them via a Monte-Carlo test, polar coordinates and overlap of the area under the density curve.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NAMESPACE | 2 +-
R/VARSEDIG.R | 24 +++++-------------------
man/VARSEDIG.Rd | 6 +++---
5 files changed, 18 insertions(+), 32 deletions(-)
Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences
on websites (i.e., clickstream). A click can be represented by a number,
character or string. Clickstreams can be modeled as zero- (only computes
occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>
Diff between clickstream versions 1.1.5 dated 2015-07-07 and 1.1.6 dated 2016-01-08
DESCRIPTION | 14 +++++--- MD5 | 64 ++++++++++++++++++------------------- NAMESPACE | 3 + NEWS | 7 ++++ R/Clickstream.r | 20 +++++++---- R/Fitting.r | 12 ++++-- R/MarkovChain.r | 44 ++++++++++--------------- R/Pattern.r | 6 +-- R/clickstream-package.R | 2 - inst/CITATION | 8 ++-- man/MarkovChain-class.Rd | 4 +- man/Pattern-class.Rd | 3 + man/absorbingStates-methods.Rd | 5 +- man/as.transactions.Rd | 4 +- man/clickstream-package.Rd | 4 +- man/clusterClickstreams.Rd | 10 +++-- man/fitMarkovChain.Rd | 4 +- man/frequencies.Rd | 4 +- man/predict-methods.Rd | 7 ++-- man/predict.ClickstreamClusters.Rd | 4 +- man/print.ClickstreamClusters.Rd | 4 +- man/print.Clickstreams.Rd | 4 +- man/print.MarkovChainSummary.Rd | 4 +- man/randomClicks-methods.Rd | 7 ++-- man/randomClickstreams.Rd | 4 +- man/readClickstreams.Rd | 4 +- man/show-methods.Rd | 5 +- man/states-methods.Rd | 5 +- man/summary-methods.Rd | 4 +- man/summary.ClickstreamClusters.Rd | 4 +- man/summary.Clickstreams.Rd | 4 +- man/transientStates-methods.Rd | 5 +- man/writeClickstreams.Rd | 4 +- 33 files changed, 166 insertions(+), 121 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.5.0 dated 2016-01-07 and 0.5.2 dated 2016-01-08
DESCRIPTION | 10 ++--- MD5 | 36 ++++++++++---------- R/lin.ratio.R | 4 +- R/vardchangannual.R | 9 ++--- R/vardchanges.R | 83 ++++++++++++++++++++++++++++-------------------- R/vardchangespoor.R | 3 + R/vardcros.R | 20 ++++++----- R/vardom.R | 10 ++++- R/vardomh.R | 12 ++++-- inst/CITATION | 4 +- inst/NEWS | 4 ++ man/lin.ratio.Rd | 7 ++-- man/vardchangannual.Rd | 43 +++++++++++------------- man/vardchanges.Rd | 19 +++++----- man/vardcros.Rd | 8 +--- man/vardcrospoor.Rd | 4 -- man/vardom.Rd | 6 ++- man/vardomh.Rd | 8 +++- man/vardpoor-package.Rd | 4 +- 19 files changed, 165 insertions(+), 129 deletions(-)
Title: Manipulate, Validate and Resolve 'IP' Addresses
Description: A toolkit for manipulating, validating and testing 'IP' addresses and
ranges, along with datasets relating to 'IP' addresses. While it primarily has
support for the 'IPv4' address space, more extensive 'IPv6' support is intended.
Author: Bob Rudis <bob@rudis.net> [aut, cre],
Oliver Keyes <ironholds@gmail.com> [aut]
Maintainer: Bob Rudis <bob@rudis.net>
Diff between iptools versions 0.2.1 dated 2015-07-23 and 0.3.0 dated 2016-01-08
iptools-0.2.1/iptools/INSTALL |only iptools-0.2.1/iptools/cleanup |only iptools-0.2.1/iptools/configure |only iptools-0.2.1/iptools/configure.in |only iptools-0.2.1/iptools/src/Makevars.in |only iptools-0.3.0/iptools/DESCRIPTION | 34 - iptools-0.3.0/iptools/MD5 | 68 +-- iptools-0.3.0/iptools/NAMESPACE | 7 iptools-0.3.0/iptools/R/RcppExports.R | 30 + iptools-0.3.0/iptools/R/iptools.R | 1 iptools-0.3.0/iptools/R/is.R |only iptools-0.3.0/iptools/R/zzz.R |only iptools-0.3.0/iptools/README | 43 +- iptools-0.3.0/iptools/build/vignette.rds |binary iptools-0.3.0/iptools/inst/doc/introduction_to_iptools.Rmd | 3 iptools-0.3.0/iptools/inst/doc/introduction_to_iptools.html | 6 iptools-0.3.0/iptools/inst/doc/iptools_datasets.html | 4 iptools-0.3.0/iptools/man/hostname_to_ip.Rd | 3 iptools-0.3.0/iptools/man/iana_assignments.Rd | 2 iptools-0.3.0/iptools/man/iana_ports.Rd | 2 iptools-0.3.0/iptools/man/iana_special_assignments.Rd | 2 iptools-0.3.0/iptools/man/ip_classify.Rd | 5 iptools-0.3.0/iptools/man/ip_in_range.Rd | 3 iptools-0.3.0/iptools/man/ip_numeric.Rd | 2 iptools-0.3.0/iptools/man/ip_random.Rd | 2 iptools-0.3.0/iptools/man/ip_to_hostname.Rd | 3 iptools-0.3.0/iptools/man/iptools.Rd | 2 iptools-0.3.0/iptools/man/iptools_refresh.Rd | 3 iptools-0.3.0/iptools/man/is_checks.Rd |only iptools-0.3.0/iptools/man/range_boundaries.Rd | 3 iptools-0.3.0/iptools/man/range_generate.Rd | 3 iptools-0.3.0/iptools/man/validate_range.Rd | 3 iptools-0.3.0/iptools/man/xff_extract.Rd | 3 iptools-0.3.0/iptools/src/Makevars.win |only iptools-0.3.0/iptools/src/RcppExports.cpp | 11 iptools-0.3.0/iptools/src/asio_bindings.cpp | 231 ++++++++++-- iptools-0.3.0/iptools/src/asio_bindings.h | 32 + iptools-0.3.0/iptools/src/iptools.cpp | 46 ++ iptools-0.3.0/iptools/tests/testthat/test_is.R |only iptools-0.3.0/iptools/vignettes/introduction_to_iptools.Rmd | 3 40 files changed, 437 insertions(+), 123 deletions(-)
Title: Hierarchical Inference Testing
Description: Hierarchical inference testing (HIT) for (generalized) linear
models with correlated covariates applicable to high-dimensional settings.
Author: Jonas Klasen [aut, cre]
Maintainer: Jonas Klasen <qtcat@gmx.de>
Diff between hit versions 0.2-0 dated 2015-12-04 and 0.2-1 dated 2016-01-08
DESCRIPTION | 8 - MD5 | 19 +- NAMESPACE | 1 NEWS.md | 11 - R/hit.R | 341 +++++++++++++++++++++++++++------------------- README.md | 1 man/hit.Rd | 68 ++++----- man/opt.penalty.Rd |only man/samp1.lasso.Rd | 27 +-- man/samp2.sigHierarchy.Rd | 8 - tests/testthat/test_hit.R | 6 11 files changed, 272 insertions(+), 218 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.3.2 dated 2015-12-02 and 1.4 dated 2016-01-08
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++++--------- NAMESPACE | 3 +++ NEWS | 19 ++++++++++++------- R/HelpersMG-package.R | 10 ++++++---- R/MHalgoGen.R | 6 +++--- R/as.mcmc.mcmcComposite.R | 1 + R/dmnbinom.R |only R/merge.mcmcComposite.R | 3 +-- R/modifyVector.R |only R/summary.mcmcComposite.R | 4 +--- R/which2D.R |only man/HelpersMG-package.Rd | 10 ++++++---- man/dmnbinom.Rd |only man/modifyVector.Rd |only man/which2D.Rd |only 16 files changed, 52 insertions(+), 36 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.5 dated 2015-12-07 and 1.1.6 dated 2016-01-08
gdm-1.1.5/gdm/src/Gdm4Rlib.cpp |only gdm-1.1.5/gdm/src/Gdm4Rlib.h |only gdm-1.1.6/gdm/DESCRIPTION | 8 +- gdm-1.1.6/gdm/MD5 | 14 ++-- gdm-1.1.6/gdm/NAMESPACE | 8 +- gdm-1.1.6/gdm/R/GDM_Table_Funcs.R | 48 ++++++++++---- gdm-1.1.6/gdm/man/formatsitepair.Rd | 2 gdm-1.1.6/gdm/man/plot.gdm.Rd | 123 +++++++++++++++++++----------------- gdm-1.1.6/gdm/src/Gdmlib.cpp |only gdm-1.1.6/gdm/src/Gdmlib.h |only 10 files changed, 118 insertions(+), 85 deletions(-)
Title: Fire Weather Index System and Fire Behaviour Prediction System
Calculations
Description: Provides three functions to calculate the outputs of the two main components of the Canadian Forest Fire Danger Rating System (CFFDRS): the Fire Weather Index (FWI) System and the Fire Behaviour Prediction (FBP) System.
Author: Xianli Wang, Alan Cantin, Marc-Andre Parisien, Mike Wotton, Kerry Anderson, and Mike Flannigan
Maintainer: Alan Cantin <Alan.Cantin@Canada.ca>
Diff between fwi.fbp versions 1.5 dated 2014-07-03 and 1.7 dated 2016-01-08
DESCRIPTION | 18 +++++++++--------- MD5 | 17 +++++++++-------- R/fbp.r | 7 ++++++- R/fwi.r | 6 ++++++ R/fwiBAT.r | 4 ++++ man/fbp.Rd | 9 +-------- man/fwi.Rd | 8 +------- man/fwi.fbp-deprecated.Rd |only man/fwi.fbp-package.Rd | 15 ++++----------- man/fwiBAT.Rd | 8 +------- 10 files changed, 41 insertions(+), 51 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between embryogrowth versions 6.1.1 dated 2015-10-16 and 6.2 dated 2016-01-08
DESCRIPTION | 8 +- MD5 | 121 ++++++++++++++++++++-------------------- NAMESPACE | 2 NEWS | 16 ++++- R/GRTRN_MHmcmc.R | 15 ++++ R/TSP.list.R | 17 +++-- R/embryogrowth-package.R | 8 +- R/fonctionMCMC.R | 6 - R/info.nests.R | 114 +++++++++++++++++++++++++++++-------- R/plot.NestsResult.R | 11 +-- R/plotR_hist.R | 2 R/stages.R |only data/TSP.list.rda |binary data/stages.rda |only man/ChangeSSM.Rd | 18 ++--- man/FormatNests.Rd | 2 man/GRTRN_MHmcmc.Rd | 18 ++--- man/GenerateAnchor.Rd | 6 - man/GenerateConstInc.Rd | 6 - man/GenerateTest.Rd | 4 - man/MovingIncubation.Rd | 6 - man/STRN.Rd | 45 -------------- man/STRN_MHmcmc.Rd | 2 man/STSRE_NestingArea.Rd | 20 +++--- man/STSRE_TSD.Rd | 11 +-- man/TRN_MHmcmc_p.Rd | 8 +- man/TSP.list.Rd | 26 ++++---- man/TestParallel.Rd | 2 man/dydt.Gompertz.Rd | 8 +- man/dydt.exponential.Rd | 10 +-- man/dydt.linear.Rd | 8 +- man/embryogrowth-package.Rd | 44 +++++++------- man/hist.Nests.Rd | 4 - man/hist.NestsResult.Rd | 4 - man/info.nests.Rd | 23 +++---- man/likelihoodR.Rd | 10 +-- man/logLik.NestsResult.Rd | 2 man/logLik.tsd.Rd | 2 man/nest.Rd | 4 - man/plot.NestsResult.Rd | 35 +++++------ man/plot.tsd.Rd | 8 +- man/plotR.Rd | 24 +++---- man/plotR_hist.Rd | 2 man/plot_transition.Rd | 10 +-- man/predict.tsd.Rd | 15 ++-- man/resultNest_4p.Rd | 14 ++-- man/resultNest_4p_transition.Rd | 8 +- man/resultNest_4p_weight.Rd | 16 ++--- man/resultNest_6p.Rd | 16 ++--- man/resultNest_newp.Rd | 12 +-- man/result_mcmc_4p.Rd | 18 ++--- man/result_mcmc_4p_weight.Rd | 28 ++++----- man/result_mcmc_6p.Rd | 20 +++--- man/result_mcmc_newp.Rd | 26 ++++---- man/searchR.Rd | 32 +++++----- man/stages.Rd |only man/summary.Nests.Rd | 2 man/switch.transition.Rd | 2 man/tempConst.Rd | 18 ++--- man/tsd.Rd | 63 ++++++++++---------- man/tsd_MHmcmc.Rd | 19 +++--- man/tsd_MHmcmc_p.Rd | 15 ++-- man/weightmaxentropy.Rd | 12 +-- 63 files changed, 547 insertions(+), 481 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.4.3 dated 2015-09-27 and 4.4.4 dated 2016-01-08
DESCRIPTION | 6 - MD5 | 54 +++++------ NEWS | 13 ++ R/earth.R | 10 -- inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/earth.times.bat | 2 inst/slowtests/test.big.R | 4 inst/slowtests/test.big.Rout.save | 12 +- inst/slowtests/test.big.bat | 2 inst/slowtests/test.cv.bat | 2 inst/slowtests/test.earthc.mak | 6 - inst/slowtests/test.earthc.out.save | 143 +++++++++++++++--------------- inst/slowtests/test.full.Rout.save | 14 +- inst/slowtests/test.full.bat | 2 inst/slowtests/test.glm.bat | 2 inst/slowtests/test.incorrect.bat | 2 inst/slowtests/test.mods.bat | 2 inst/slowtests/test.plotd.bat | 2 inst/slowtests/test.pmethod.cv.bat | 2 inst/slowtests/test.varmod.Rout.save | 4 inst/slowtests/test.varmod.bat | 2 inst/slowtests/test.varmod.mgcv.Rout.save | 2 inst/slowtests/test.varmod.mgcv.bat | 2 inst/slowtests/test.weights.R | 20 ++++ inst/slowtests/test.weights.Rout.save | 58 +++++++++++- inst/slowtests/test.weights.bat | 2 src/earth.c | 28 ++--- 28 files changed, 247 insertions(+), 151 deletions(-)
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.5.0 dated 2014-04-30 and 0.5.1 dated 2016-01-08
DESCRIPTION | 14 - MD5 | 71 +++--- NAMESPACE | 5 NEWS | 114 +++++---- R/accessors.R | 102 ++++---- R/fortify.R | 8 R/plot.R | 502 +++++++++++++++++++++---------------------- R/print.R | 26 +- build |only data/TopGear.RData |binary man/AIC.seqModel.Rd | 96 +++----- man/coef.seqModel.Rd | 102 +++----- man/coefPlot.Rd | 123 ++++------ man/corHuber.Rd | 135 +++++------ man/critPlot.Rd | 89 +++---- man/diagnosticPlot.Rd | 246 +++++++++------------ man/fitted.seqModel.Rd | 95 +++----- man/fortify.seqModel.Rd | 153 +++++-------- man/getScale.Rd | 85 +++---- man/grplars.Rd | 394 +++++++++++++++------------------- man/lambda0.Rd | 128 ++++------- man/perry.seqModel.Rd | 167 ++++++-------- man/plot.seqModel.Rd | 70 ++---- man/predict.seqModel.Rd | 128 ++++------- man/residuals.seqModel.Rd | 101 +++----- man/rlars.Rd | 364 ++++++++++++++----------------- man/robustHD-deprecated.Rd | 75 +++--- man/robustHD-package.Rd | 69 ----- man/sparseLTS.Rd | 521 ++++++++++++++++++++------------------------- man/standardize.Rd | 71 ++---- man/tsBlocks.Rd | 44 +-- man/tslars.Rd | 290 +++++++++++-------------- man/tslarsP.Rd | 351 +++++++++++++----------------- man/winsorize.Rd | 151 +++++-------- man/wt.Rd | 64 ++--- src/corHuber.cpp | 2 src/fastLasso.cpp | 2 37 files changed, 2263 insertions(+), 2695 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.3-0 dated 2015-12-15 and 1.3-1 dated 2016-01-08
DESCRIPTION | 8 ++--- MD5 | 60 ++++++++++++++++++++--------------------- R/jomo1.MCMCchain.R | 12 ++++++-- R/jomo1.R | 12 ++++++-- R/jomo1ran.MCMCchain.R | 12 ++++++-- R/jomo1ran.R | 12 ++++++-- R/jomo1rancat.MCMCchain.R | 7 +++- R/jomo1rancat.R | 7 +++- R/jomo1rancathr.MCMCchain.R | 8 ++++- R/jomo1rancathr.R | 8 ++++- R/jomo1rancon.MCMCchain.R | 7 +++- R/jomo1rancon.R | 7 +++- R/jomo1ranconhr.MCMCchain.R | 8 ++++- R/jomo1ranconhr.R | 8 ++++- R/jomo1ranmix.MCMCchain.R | 7 +++- R/jomo1ranmix.R | 7 +++- R/jomo1ranmixhr.MCMCchain.R | 8 ++++- R/jomo1ranmixhr.R | 8 ++++- inst/CITATION | 2 - man/jomo1rancat.MCMCchain.Rd | 8 ++--- man/jomo1rancat.Rd | 8 ++--- man/jomo1rancathr.MCMCchain.Rd | 9 ++---- man/jomo1rancathr.Rd | 10 ++---- man/jomo1rancon.MCMCchain.Rd | 5 +-- man/jomo1rancon.Rd | 8 ++--- man/jomo1ranconhr.MCMCchain.Rd | 7 +--- man/jomo1ranconhr.Rd | 6 +--- man/jomo1ranmix.MCMCchain.Rd | 6 +--- man/jomo1ranmix.Rd | 6 +--- man/jomo1ranmixhr.MCMCchain.Rd | 10 ++---- man/jomo1ranmixhr.Rd | 10 ++---- 31 files changed, 173 insertions(+), 128 deletions(-)
Title: Bayesian Meta-Analysis and Meta-Regression
Description: Provides a collection of functions for conducting meta-analyses under Bayesian context in R. The package includes functions for computing various effect size or outcome measures (e.g. odds ratios, mean difference and incidence rate ratio) for different types of data based on MCMC simulations. Users are allowed to fit fixed- and random-effects models with different priors to the data. Meta-regression can be carried out if effects of additional covariates are observed. Furthermore, the package provides functions for creating posterior distribution plots and forest plot to display main model output. Traceplots and some other diagnostic plots are also available for assessing model fit and performance.
Author: Tao Ding, Gianluca Baio
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between bmeta versions 0.1.1 dated 2015-11-20 and 0.1.2 dated 2016-01-08
DESCRIPTION | 10 MD5 | 16 NAMESPACE | 2 R/bmeta.R | 3965 +++++++++++++++++++++++++++----------------------- man/acf.plot.Rd | 10 man/bmeta-package.Rd | 4 man/bmeta.Rd | 4 man/funnel.plot.Rd | 23 man/posterior.plot.Rd | 20 9 files changed, 2267 insertions(+), 1787 deletions(-)
Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd
Ed)"
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The
Statistical Sleuth: A Course in Methods of Data Analysis (3rd
ed)", Cengage Learning.
Author: Original by F.L. Ramsey and D.W. Schafer,
modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin
A. Turlach, vignettes contributed by Nicholas Horton, Linda Loi,
Kate Aloisio and Ruobing Zhang
Maintainer: Berwin A Turlach <Berwin.Turlach@gmail.com>
Diff between Sleuth3 versions 0.1-8 dated 2015-02-17 and 1.0-1 dated 2016-01-08
DESCRIPTION | 22 +- MD5 | 393 +++++++++++++++++++----------------- build |only data/case0101.rda |binary data/case0102.rda |binary data/case0201.rda |binary data/case0202.rda |binary data/case0301.rda |binary data/case0302.rda |binary data/case0401.rda |binary data/case0402.rda |binary data/case0501.rda |binary data/case0502.rda |binary data/case0601.rda |binary data/case0602.rda |binary data/case0701.rda |binary data/case0702.rda |binary data/case0801.rda |binary data/case0802.rda |binary data/case0901.rda |binary data/case0902.rda |binary data/case1001.rda |binary data/case1002.rda |binary data/case1101.rda |binary data/case1102.rda |binary data/case1201.rda |binary data/case1202.rda |binary data/case1301.rda |binary data/case1302.rda |binary data/case1401.rda |binary data/case1402.rda |binary data/case1501.rda |binary data/case1502.rda |binary data/case1601.rda |binary data/case1602.rda |binary data/case1701.rda |binary data/case1702.rda |binary data/case1801.rda |binary data/case1802.rda |binary data/case1803.rda |binary data/case1901.rda |binary data/case1902.rda |binary data/case2001.rda |binary data/case2002.rda |binary data/case2101.rda |binary data/case2102.rda |binary data/case2201.rda |binary data/case2202.rda |binary data/ex0112.rda |binary data/ex0116.rda |binary data/ex0125.rda |binary data/ex0126.rda |binary data/ex0127.rda |binary data/ex0211.rda |binary data/ex0218.rda |binary data/ex0221.rda |binary data/ex0222.rda |binary data/ex0223.rda |binary data/ex0321.rda |binary data/ex0323.rda |binary data/ex0327.rda |binary data/ex0330.rda |binary data/ex0331.rda |binary data/ex0332.rda |binary data/ex0333.rda |binary data/ex0428.rda |binary data/ex0429.rda |binary data/ex0430.rda |binary data/ex0431.rda |binary data/ex0432.rda |binary data/ex0518.rda |binary data/ex0523.rda |binary data/ex0524.rda |binary data/ex0525.rda |binary data/ex0623.rda |binary data/ex0624.rda |binary data/ex0721.rda |binary data/ex0722.rda |binary data/ex0724.rda |binary data/ex0725.rda |binary data/ex0726.rda |binary data/ex0727.rda |binary data/ex0728.rda |binary data/ex0729.rda |binary data/ex0730.rda |binary data/ex0816.rda |binary data/ex0817.rda |binary data/ex0820.rda |binary data/ex0822.rda |binary data/ex0823.rda |binary data/ex0824.rda |binary data/ex0825.rda |binary data/ex0826.rda |binary data/ex0828.rda |binary data/ex0829.rda |binary data/ex0914.rda |binary data/ex0915.rda |binary data/ex0918.rda |binary data/ex0920.rda |binary data/ex0921.rda |binary data/ex0923.rda |binary data/ex1014.rda |binary data/ex1026.rda |binary data/ex1027.rda |binary data/ex1028.rda |binary data/ex1029.rda |binary data/ex1030.rda |binary data/ex1031.rda |binary data/ex1033.rda |binary data/ex1111.rda |binary data/ex1120.rda |binary data/ex1122.rda |binary data/ex1123.rda |binary data/ex1124.rda |binary data/ex1125.rda |binary data/ex1217.rda |binary data/ex1220.rda |binary data/ex1221.rda |binary data/ex1222.rda |binary data/ex1223.rda |binary data/ex1225.rda |binary data/ex1317.rda |binary data/ex1319.rda |binary data/ex1320.rda |binary data/ex1321.rda |binary data/ex1416.rda |binary data/ex1417.rda |binary data/ex1419.rda |binary data/ex1420.rda |binary data/ex1507.rda |binary data/ex1509.rda |binary data/ex1514.rda |binary data/ex1515.rda |binary data/ex1516.rda |binary data/ex1517.rda |binary data/ex1518.rda |binary data/ex1519.rda |binary data/ex1605.rda |binary data/ex1611.rda |binary data/ex1612.rda |binary data/ex1613.rda |binary data/ex1614.rda |binary data/ex1615.rda |binary data/ex1620.rda |binary data/ex1708.rda |binary data/ex1715.rda |binary data/ex1716.rda |binary data/ex1914.rda |binary data/ex1916.rda |binary data/ex1917.rda |binary data/ex1918.rda |binary data/ex1919.rda |binary data/ex1921.rda |binary data/ex1922.rda |binary data/ex1923.rda |binary data/ex2011.rda |binary data/ex2012.rda |binary data/ex2015.rda |binary data/ex2016.rda |binary data/ex2017.rda |binary data/ex2018.rda |binary data/ex2019.rda |binary data/ex2113.rda |binary data/ex2115.rda |binary data/ex2116.rda |binary data/ex2117.rda |binary data/ex2118.rda |binary data/ex2119.rda |binary data/ex2120.rda |binary data/ex2216.rda |binary data/ex2220.rda |binary data/ex2222.rda |binary data/ex2223.rda |binary data/ex2224.rda |binary data/ex2225.rda |binary data/ex2226.rda |binary data/ex2414.rda |binary inst/doc/Sleuth3-manual.pdf |binary inst/doc/chapter01-HortonMosaic.Rnw |only inst/doc/chapter01-HortonMosaic.pdf |only inst/doc/chapter02-HortonMosaic.Rnw |only inst/doc/chapter02-HortonMosaic.pdf |only inst/doc/chapter03-HortonMosaic.Rnw |only inst/doc/chapter03-HortonMosaic.pdf |only inst/doc/chapter04-HortonMosaic.Rnw |only inst/doc/chapter04-HortonMosaic.pdf |only inst/doc/chapter05-HortonMosaic.Rnw |only inst/doc/chapter05-HortonMosaic.pdf |only inst/doc/chapter06-HortonMosaic.Rnw |only inst/doc/chapter06-HortonMosaic.pdf |only inst/doc/chapter07-HortonMosaic.Rnw |only inst/doc/chapter07-HortonMosaic.pdf |only inst/doc/chapter08-HortonMosaic.Rnw |only inst/doc/chapter08-HortonMosaic.pdf |only inst/doc/chapter09-HortonMosaic.Rnw |only inst/doc/chapter09-HortonMosaic.pdf |only inst/doc/chapter10-HortonMosaic.Rnw |only inst/doc/chapter10-HortonMosaic.pdf |only inst/doc/chapter11-HortonMosaic.Rnw |only inst/doc/chapter11-HortonMosaic.pdf |only inst/doc/chapter12-HortonMosaic.Rnw |only inst/doc/chapter12-HortonMosaic.pdf |only inst/doc/chapter13-HortonMosaic.Rnw |only inst/doc/chapter13-HortonMosaic.pdf |only vignettes |only 205 files changed, 230 insertions(+), 185 deletions(-)
Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd
Ed)"
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The
Statistical Sleuth: A Course in Methods of Data Analysis (2nd
ed)", Duxbury.
Author: Original by F.L. Ramsey and D.W. Schafer,
modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin
A. Turlach, vignettes contributed by Nicholas Horton, Kate Aloisio
and Ruobing Zhang
Maintainer: Berwin A Turlach <Berwin.Turlach@gmail.com>
Diff between Sleuth2 versions 1.0-7 dated 2012-09-12 and 2.0-3 dated 2016-01-08
Sleuth2-1.0-7/Sleuth2/LICENSE.GPL-2 |only Sleuth2-1.0-7/Sleuth2/LICENSE.GPL-3 |only Sleuth2-2.0-3/Sleuth2/DESCRIPTION | 32 - Sleuth2-2.0-3/Sleuth2/GPL-2 |only Sleuth2-2.0-3/Sleuth2/GPL-3 |only Sleuth2-2.0-3/Sleuth2/MD5 | 335 +++++++------- Sleuth2-2.0-3/Sleuth2/build |only Sleuth2-2.0-3/Sleuth2/data/case0101.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0102.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0201.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0202.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0301.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0302.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0401.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0402.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0501.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0502.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0601.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0602.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0701.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0702.rda |binary Sleuth2-2.0-3/Sleuth2/data/case0801.rda |binary 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|binary Sleuth2-2.0-3/Sleuth2/data/case2002.rda |binary Sleuth2-2.0-3/Sleuth2/data/case2101.rda |binary Sleuth2-2.0-3/Sleuth2/data/case2102.rda |binary Sleuth2-2.0-3/Sleuth2/data/case2201.rda |binary Sleuth2-2.0-3/Sleuth2/data/case2202.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0112.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0116.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0211.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0221.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0222.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0223.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0321.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0323.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0327.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0328.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0331.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0332.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0333.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0428.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0429.rda |binary Sleuth2-2.0-3/Sleuth2/data/ex0430.rda |binary 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Title: Analysis of Large-Scale Pharmacogenomic Data
Description: Contains a set of functions to perform large-scale analysis of pharmacogenomic data.
Author: Petr Smirnov, Zhaleh Safikhani, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Diff between PharmacoGx versions 1.1.2 dated 2015-11-15 and 1.1.4 dated 2016-01-08
PharmacoGx-1.1.2/PharmacoGx/man/GWC.Rd |only PharmacoGx-1.1.4/PharmacoGx/DESCRIPTION | 13 PharmacoGx-1.1.4/PharmacoGx/MD5 | 170 +- PharmacoGx-1.1.4/PharmacoGx/NAMESPACE | 3 PharmacoGx-1.1.4/PharmacoGx/R/GWC.R | 35 PharmacoGx-1.1.4/PharmacoGx/R/LogLogisticRegression.R | 89 - PharmacoGx-1.1.4/PharmacoGx/R/PharmacoSetClass.R | 611 ++++++---- PharmacoGx-1.1.4/PharmacoGx/R/combineTest.R | 44 PharmacoGx-1.1.4/PharmacoGx/R/computeAUC.R | 1 PharmacoGx-1.1.4/PharmacoGx/R/computeDrugSensitivity.R | 4 PharmacoGx-1.1.4/PharmacoGx/R/computeIC50.R | 24 PharmacoGx-1.1.4/PharmacoGx/R/connectivityScore.R | 70 - PharmacoGx-1.1.4/PharmacoGx/R/corWeighted.R | 4 PharmacoGx-1.1.4/PharmacoGx/R/downloadPSet.R | 2 PharmacoGx-1.1.4/PharmacoGx/R/downloadSignatures.R | 1 PharmacoGx-1.1.4/PharmacoGx/R/drugDoseResponseCurve.R | 7 PharmacoGx-1.1.4/PharmacoGx/R/drugPerturbationSig.R | 16 PharmacoGx-1.1.4/PharmacoGx/R/drugSensitivitySig.R | 46 PharmacoGx-1.1.4/PharmacoGx/R/geneDrugPerturbation.R | 86 - PharmacoGx-1.1.4/PharmacoGx/R/intersectList.R | 5 PharmacoGx-1.1.4/PharmacoGx/R/intersectPSets.R | 41 PharmacoGx-1.1.4/PharmacoGx/R/rankGeneDrugPerturbation.R | 198 +-- PharmacoGx-1.1.4/PharmacoGx/R/rankGeneDrugSensitivity.R | 18 PharmacoGx-1.1.4/PharmacoGx/R/signatureClass.R | 26 PharmacoGx-1.1.4/PharmacoGx/R/summarizeSensitivityProfiles.R | 52 PharmacoGx-1.1.4/PharmacoGx/R/unionList.R | 5 PharmacoGx-1.1.4/PharmacoGx/build/vignette.rds |binary PharmacoGx-1.1.4/PharmacoGx/data/CCLEsmall.rda |binary PharmacoGx-1.1.4/PharmacoGx/inst/doc/CreatingPharmacoSet.pdf |binary PharmacoGx-1.1.4/PharmacoGx/inst/doc/PharmacoGx.R | 6 PharmacoGx-1.1.4/PharmacoGx/inst/doc/PharmacoGx.Rnw | 4 PharmacoGx-1.1.4/PharmacoGx/inst/doc/PharmacoGx.pdf |binary PharmacoGx-1.1.4/PharmacoGx/man/CCLEsmall.Rd | 2 PharmacoGx-1.1.4/PharmacoGx/man/CMAPsmall.Rd | 2 PharmacoGx-1.1.4/PharmacoGx/man/GDSCsmall.Rd | 2 PharmacoGx-1.1.4/PharmacoGx/man/HDAC_genes.Rd | 4 PharmacoGx-1.1.4/PharmacoGx/man/LogLogisticRegression.Rd | 40 PharmacoGx-1.1.4/PharmacoGx/man/PharmacoSet-class.Rd | 50 PharmacoGx-1.1.4/PharmacoGx/man/PharmacoSet.Rd | 10 PharmacoGx-1.1.4/PharmacoGx/man/availablePSets.Rd | 4 PharmacoGx-1.1.4/PharmacoGx/man/cellInfo-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/cellInfo.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/cellNames-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/cellNames.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/checkPSetStructure.Rd | 3 PharmacoGx-1.1.4/PharmacoGx/man/computeAUC.Rd | 9 PharmacoGx-1.1.4/PharmacoGx/man/computeIC50.Rd | 6 PharmacoGx-1.1.4/PharmacoGx/man/connectivityScore.Rd | 9 PharmacoGx-1.1.4/PharmacoGx/man/dateCreated.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/downloadPSet.Rd | 5 PharmacoGx-1.1.4/PharmacoGx/man/downloadPertSig.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/drugDoseResponseCurve.Rd | 26 PharmacoGx-1.1.4/PharmacoGx/man/drugInfo-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/drugInfo.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/drugNames-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/drugNames.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/drugPerturbationSig.Rd | 3 PharmacoGx-1.1.4/PharmacoGx/man/drugSensitivitySig.Rd | 15 PharmacoGx-1.1.4/PharmacoGx/man/featureInfo-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/featureInfo.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/featureNames.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/gwc.Rd |only PharmacoGx-1.1.4/PharmacoGx/man/intersectList.Rd | 3 PharmacoGx-1.1.4/PharmacoGx/man/intersectPSet.Rd | 16 PharmacoGx-1.1.4/PharmacoGx/man/molecularProfiles-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/molecularProfiles.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/pSetName.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/pertNumber-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/pertNumber.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/phenoInfo-set.Rd | 11 PharmacoGx-1.1.4/PharmacoGx/man/phenoInfo.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/sensNumber-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/sensNumber.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/sensitivityInfo-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/sensitivityInfo.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/sensitivityMeasures.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/sensitivityProfiles-set.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/sensitivityProfiles.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/show-PharmacoSet-method.Rd | 7 PharmacoGx-1.1.4/PharmacoGx/man/show-PharmacoSig-method.Rd | 2 PharmacoGx-1.1.4/PharmacoGx/man/showSigAnnot.Rd | 2 PharmacoGx-1.1.4/PharmacoGx/man/sub-PharmacoSet-method.Rd | 2 PharmacoGx-1.1.4/PharmacoGx/man/subsetTo.Rd | 3 PharmacoGx-1.1.4/PharmacoGx/man/summarizeMolecularProfiles.Rd | 3 PharmacoGx-1.1.4/PharmacoGx/man/summarizeSensitivityProfiles.Rd | 5 PharmacoGx-1.1.4/PharmacoGx/man/unionList.Rd | 3 PharmacoGx-1.1.4/PharmacoGx/vignettes/PharmacoGx.Rnw | 4 87 files changed, 1167 insertions(+), 847 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the md5, sha-1, sha-256,
crc32, xxhash and murmurhash algorithms) permitting easy comparison of R
language objects, as well as a function 'hmac()' to create hash-based
message authentication code.
The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1
and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2,
and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1, sha-256 and aes, this package uses small standalone
implementations that were provided by Christophe Devine. For crc32, code
from the zlib library is used. For sha-512, an implementation by Aaron
D. Gifford is used. For xxhash, the implementation by Yann Collet is used.
For murmurhash, an implementation by Shane Day is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely
tested) libraries such as OpenSSL should be used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu and Thierry Onkelinx.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.8 dated 2014-12-31 and 0.6.9 dated 2016-01-08
ChangeLog | 44 ++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 16 ++++++++------ MD5 | 25 +++++++++++++++------- NAMESPACE | 14 ++++++++++++ R/digest.R | 34 ++++++++++++++++++++++++------- R/sha1.R |only README.md | 8 ++++--- build |only inst/doc |only man/digest.Rd | 21 +++++++++++++------ man/hmac.Rd | 11 +++++++--- man/sha1.rd |only src/digest.c | 57 +++++++++++++++++++++------------------------------- tests/num2hexTest.R |only tests/sha1Test.R |only vignettes |only 16 files changed, 163 insertions(+), 67 deletions(-)
Title: Class and Methods Definitions for Packages 'aws', 'adimpro',
'fmri' and 'dti'
Description: The package defines method extract and provides OpenMP support needed in several packages.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between awsMethods versions 1.0-3 dated 2014-03-05 and 1.0-3.1 dated 2016-01-08
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/utilities.r | 6 +++--- src/Makevars.in | 2 +- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.21 dated 2015-11-10 and 0.5.22 dated 2016-01-07
DESCRIPTION | 8 MD5 | 62 + NAMESPACE | 2 R/cleanTreatment.R |only R/deviationFact.R |only R/effectTreatmentC.R |only R/effectTreatmentN.R |only R/indicatorTreatment.R |only R/isBadTreatment.R |only R/outOfSample.R |only R/prevalenceFact.R |only R/utils.R |only R/vtreat.R | 1398 +++++++--------------------------------- R/vtreatImpl.R |only README.md | 87 +- build/vignette.rds |binary inst/doc/vtreat.html | 272 +++---- inst/doc/vtreatOverfit.R | 5 inst/doc/vtreatOverfit.Rmd | 7 inst/doc/vtreatOverfit.html | 162 ++-- man/catScore.Rd | 2 man/designTreatmentsC.Rd | 11 man/designTreatmentsN.Rd | 11 man/designTreatmentsZ.Rd | 12 man/hold1OutMeans.Rd | 2 man/mkCrossFrameCExperiment.Rd |only man/mkCrossFrameNExperiment.Rd |only man/pressStatOfBestLinearFit.Rd | 2 man/vtreat-package.Rd | 8 tests/testthat/testBO.R | 2 tests/testthat/testCar.R | 2 tests/testthat/testDataTable.R | 2 tests/testthat/testNoY.R | 30 tests/testthat/testParallel.R | 2 tests/testthat/testStability.R |only tests/testthat/testUniqValue.R |only tests/testthat/testW1.R | 49 + tests/testthat/testWeirdTypes.R | 2 tests/testthat/testZW.R | 2 39 files changed, 658 insertions(+), 1484 deletions(-)
Title: Data Structures and Handling for Neuroimaging Data
Description: A collection of data structures that represent
volumetric brain imaging data. The focus is on basic data handling for 3D
and 4D neuroimaging data. In addition, there are function to read and write
NIFTI files and limited support for reading AFNI files.
Author: Bradley R. Buchsbaum
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between neuroim versions 0.0.4 dated 2015-07-02 and 0.0.6 dated 2016-01-07
neuroim-0.0.4/neuroim/man/as.vector-BrainData-ANY-method.Rd |only neuroim-0.0.6/neuroim/DESCRIPTION | 27 neuroim-0.0.6/neuroim/MD5 | 430 +++++----- neuroim-0.0.6/neuroim/NAMESPACE | 31 neuroim-0.0.6/neuroim/R/AFNI_IO.R | 134 +++ neuroim-0.0.6/neuroim/R/AllClass.R | 174 +++- neuroim-0.0.6/neuroim/R/AllGeneric.R | 131 ++- neuroim-0.0.6/neuroim/R/Axis.R | 3 neuroim-0.0.6/neuroim/R/BinaryIO.R | 16 neuroim-0.0.6/neuroim/R/BrainData.R | 2 neuroim-0.0.6/neuroim/R/BrainFileDescriptor.R | 95 -- neuroim-0.0.6/neuroim/R/BrainMetaInfo.R | 114 ++ neuroim-0.0.6/neuroim/R/BrainRegion3D.R | 18 neuroim-0.0.6/neuroim/R/BrainSlice.R | 13 neuroim-0.0.6/neuroim/R/BrainSpace.R | 42 neuroim-0.0.6/neuroim/R/BrainSurface.R |only neuroim-0.0.6/neuroim/R/BrainVector.R | 24 neuroim-0.0.6/neuroim/R/BrainVolume.R | 26 neuroim-0.0.6/neuroim/R/Display.R | 151 +++ neuroim-0.0.6/neuroim/R/FREESURFER_IO.R |only neuroim-0.0.6/neuroim/R/SparseBrainVector.R | 15 neuroim-0.0.6/neuroim/R/common.R | 24 neuroim-0.0.6/neuroim/R/conncomp.R | 11 neuroim-0.0.6/neuroim/R/neuroim.R | 1 neuroim-0.0.6/neuroim/build/vignette.rds |binary neuroim-0.0.6/neuroim/man/AFNIFileDescriptor-class.Rd | 2 neuroim-0.0.6/neuroim/man/AFNIMetaInfo-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet1D-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet2D-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet3D-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet4D-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet5D-class.Rd | 2 neuroim-0.0.6/neuroim/man/Base-class.Rd | 2 neuroim-0.0.6/neuroim/man/BaseMetaInfo-class.Rd | 2 neuroim-0.0.6/neuroim/man/BaseSource-class.Rd | 2 neuroim-0.0.6/neuroim/man/BinaryReader-class.Rd | 2 neuroim-0.0.6/neuroim/man/BinaryReader.Rd | 2 neuroim-0.0.6/neuroim/man/BinaryWriter-class.Rd | 2 neuroim-0.0.6/neuroim/man/BootstrapSearchlight.Rd | 2 neuroim-0.0.6/neuroim/man/BrainBucket-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainBucketSource-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainData-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainFileDescriptor-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainFileSource-class.Rd | 11 neuroim-0.0.6/neuroim/man/BrainMetaInfo-class.Rd | 12 neuroim-0.0.6/neuroim/man/BrainSlice-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainSlice.Rd | 10 neuroim-0.0.6/neuroim/man/BrainSource-class.Rd | 4 neuroim-0.0.6/neuroim/man/BrainSpace-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainSpace.Rd | 2 neuroim-0.0.6/neuroim/man/BrainSurface-class.Rd |only neuroim-0.0.6/neuroim/man/BrainSurfaceSource-class.Rd |only neuroim-0.0.6/neuroim/man/BrainSurfaceVector-class.Rd |only neuroim-0.0.6/neuroim/man/BrainSurfaceVectorSource-class.Rd |only neuroim-0.0.6/neuroim/man/BrainVector-class.Rd | 8 neuroim-0.0.6/neuroim/man/BrainVectorSource-class.Rd | 4 neuroim-0.0.6/neuroim/man/BrainVectorSource.Rd | 2 neuroim-0.0.6/neuroim/man/BrainVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainVolume.Rd | 4 neuroim-0.0.6/neuroim/man/BrainVolumeSource-class.Rd | 10 neuroim-0.0.6/neuroim/man/ClusteredBrainVolume-class.Rd | 3 neuroim-0.0.6/neuroim/man/ColumnReader-class.Rd |only neuroim-0.0.6/neuroim/man/ColumnReader.Rd |only neuroim-0.0.6/neuroim/man/DenseBrainVector-class.Rd | 2 neuroim-0.0.6/neuroim/man/DenseBrainVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/FileMetaInfo-class.Rd | 4 neuroim-0.0.6/neuroim/man/FreeSurferSurfaceGeometryMetaInfo-class.Rd |only neuroim-0.0.6/neuroim/man/FreesurferAsciiSurfaceFileDescriptor-class.Rd |only neuroim-0.0.6/neuroim/man/IndexLookupVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/Kernel-class.Rd | 2 neuroim-0.0.6/neuroim/man/Kernel.Rd | 2 neuroim-0.0.6/neuroim/man/Layer-class.Rd | 6 neuroim-0.0.6/neuroim/man/Layer.Rd | 6 neuroim-0.0.6/neuroim/man/LogicalBrainVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/MNI_SPACE_1MM.Rd | 2 neuroim-0.0.6/neuroim/man/NIMLSurfaceDataMetaInfo-class.Rd |only neuroim-0.0.6/neuroim/man/NIMLSurfaceDataMetaInfo.Rd |only neuroim-0.0.6/neuroim/man/NIMLSurfaceFileDescriptor-class.Rd |only neuroim-0.0.6/neuroim/man/NIfTIFileDescriptor-class.Rd | 2 neuroim-0.0.6/neuroim/man/NIfTIMetaInfo-class.Rd | 2 neuroim-0.0.6/neuroim/man/NamedAxis-class.Rd | 2 neuroim-0.0.6/neuroim/man/NullMetaInfo-class.Rd | 2 neuroim-0.0.6/neuroim/man/ROIVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/ROIVolume.Rd | 2 neuroim-0.0.6/neuroim/man/RandomSearchlight.Rd | 2 neuroim-0.0.6/neuroim/man/RegionCube.Rd | 12 neuroim-0.0.6/neuroim/man/RegionSphere.Rd | 4 neuroim-0.0.6/neuroim/man/RegionSquare.Rd | 16 neuroim-0.0.6/neuroim/man/Searchlight.Rd | 2 neuroim-0.0.6/neuroim/man/SparseBrainVector-class.Rd | 5 neuroim-0.0.6/neuroim/man/SparseBrainVectorSource-class.Rd | 2 neuroim-0.0.6/neuroim/man/SparseBrainVolume-class.Rd | 10 neuroim-0.0.6/neuroim/man/SurfaceDataMetaInfo-class.Rd |only neuroim-0.0.6/neuroim/man/SurfaceDataMetaInfo.Rd |only neuroim-0.0.6/neuroim/man/SurfaceGeometryMetaInfo-class.Rd |only neuroim-0.0.6/neuroim/man/SurfaceGeometryMetaInfo.Rd |only neuroim-0.0.6/neuroim/man/addDim-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.array-BrainData-method.Rd | 2 neuroim-0.0.6/neuroim/man/as.list-methods.Rd | 16 neuroim-0.0.6/neuroim/man/as.logical-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.mask-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.matrix-BrainData-method.Rd | 2 neuroim-0.0.6/neuroim/man/as.matrix-methods.Rd | 16 neuroim-0.0.6/neuroim/man/as.numeric-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.raster-methods.Rd | 8 neuroim-0.0.6/neuroim/man/as.sparse-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.vector-BrainData-method.Rd |only neuroim-0.0.6/neuroim/man/axes-methods.Rd | 2 neuroim-0.0.6/neuroim/man/axisToIndex-methods.Rd | 2 neuroim-0.0.6/neuroim/man/bounds-methods.Rd | 2 neuroim-0.0.6/neuroim/man/close-methods.Rd | 2 neuroim-0.0.6/neuroim/man/clusterCenters-methods.Rd | 2 neuroim-0.0.6/neuroim/man/concat-methods.Rd | 13 neuroim-0.0.6/neuroim/man/connComp-methods.Rd | 2 neuroim-0.0.6/neuroim/man/connComp3D.Rd | 6 neuroim-0.0.6/neuroim/man/coordToGrid-methods.Rd | 2 neuroim-0.0.6/neuroim/man/coordToIndex-methods.Rd | 2 neuroim-0.0.6/neuroim/man/coords-methods.Rd | 8 neuroim-0.0.6/neuroim/man/dataFile-methods.Rd | 4 neuroim-0.0.6/neuroim/man/dataFileMatches-methods.Rd | 4 neuroim-0.0.6/neuroim/man/dataReader-methods.Rd | 5 neuroim-0.0.6/neuroim/man/dim-BrainData-method.Rd | 2 neuroim-0.0.6/neuroim/man/dim-BrainSpace-method.Rd | 2 neuroim-0.0.6/neuroim/man/dim-FileMetaInfo-method.Rd | 2 neuroim-0.0.6/neuroim/man/dropDim-methods.Rd | 5 neuroim-0.0.6/neuroim/man/eachSeries-methods.Rd | 8 neuroim-0.0.6/neuroim/man/eachSlice-methods.Rd | 2 neuroim-0.0.6/neuroim/man/eachVolume-methods.Rd | 34 neuroim-0.0.6/neuroim/man/fileMatches-methods.Rd | 4 neuroim-0.0.6/neuroim/man/fill-methods.Rd | 3 neuroim-0.0.6/neuroim/man/gridToCoord-methods.Rd | 6 neuroim-0.0.6/neuroim/man/gridToIndex-methods.Rd | 2 neuroim-0.0.6/neuroim/man/headerFile-methods.Rd | 4 neuroim-0.0.6/neuroim/man/headerFileMatches-methods.Rd | 4 neuroim-0.0.6/neuroim/man/image-methods.Rd | 4 neuroim-0.0.6/neuroim/man/imageGrid.Rd | 4 neuroim-0.0.6/neuroim/man/indexToCoord-methods.Rd | 2 neuroim-0.0.6/neuroim/man/indexToGrid-methods.Rd | 6 neuroim-0.0.6/neuroim/man/indices-methods.Rd | 8 neuroim-0.0.6/neuroim/man/internal-methods.Rd | 5 neuroim-0.0.6/neuroim/man/inverseTrans-methods.Rd | 2 neuroim-0.0.6/neuroim/man/length-methods.Rd | 2 neuroim-0.0.6/neuroim/man/loadBucket.Rd | 2 neuroim-0.0.6/neuroim/man/loadData-methods.Rd | 13 neuroim-0.0.6/neuroim/man/loadFSSurface.Rd |only neuroim-0.0.6/neuroim/man/loadSurface.Rd |only neuroim-0.0.6/neuroim/man/loadVector.Rd | 2 neuroim-0.0.6/neuroim/man/loadVolume.Rd | 7 neuroim-0.0.6/neuroim/man/loadVolumeList.Rd | 2 neuroim-0.0.6/neuroim/man/lookup-methods.Rd | 8 neuroim-0.0.6/neuroim/man/makeVector.Rd | 2 neuroim-0.0.6/neuroim/man/makeVolume.Rd | 2 neuroim-0.0.6/neuroim/man/map-methods.Rd | 2 neuroim-0.0.6/neuroim/man/mapToColors.Rd |only neuroim-0.0.6/neuroim/man/matchAnatomy2D.Rd | 2 neuroim-0.0.6/neuroim/man/matchAnatomy3D.Rd | 2 neuroim-0.0.6/neuroim/man/matrixToVolumeList.Rd | 2 neuroim-0.0.6/neuroim/man/mergePartitions-methods.Rd | 2 neuroim-0.0.6/neuroim/man/names-methods.Rd | 2 neuroim-0.0.6/neuroim/man/ndim-methods.Rd | 3 neuroim-0.0.6/neuroim/man/neuroim.Rd | 6 neuroim-0.0.6/neuroim/man/numClusters-methods.Rd | 2 neuroim-0.0.6/neuroim/man/origin-methods.Rd | 3 neuroim-0.0.6/neuroim/man/overlay-methods.Rd | 2 neuroim-0.0.6/neuroim/man/partition-methods.Rd | 2 neuroim-0.0.6/neuroim/man/permMat-methods.Rd | 2 neuroim-0.0.6/neuroim/man/pick-methods.Rd | 2 neuroim-0.0.6/neuroim/man/print-AxisSet2D-method.Rd | 2 neuroim-0.0.6/neuroim/man/print-AxisSet3D-method.Rd | 2 neuroim-0.0.6/neuroim/man/print-NamedAxis-method.Rd | 2 neuroim-0.0.6/neuroim/man/print-methods.Rd | 2 neuroim-0.0.6/neuroim/man/readAFNIHeader.Rd | 2 neuroim-0.0.6/neuroim/man/readColumns-methods.Rd |only neuroim-0.0.6/neuroim/man/readElements-methods.Rd | 2 neuroim-0.0.6/neuroim/man/readHeader.Rd | 2 neuroim-0.0.6/neuroim/man/readMetaInfo-methods.Rd | 10 neuroim-0.0.6/neuroim/man/render-methods.Rd |only neuroim-0.0.6/neuroim/man/renderSlice-methods.Rd |only neuroim-0.0.6/neuroim/man/scaleSeries-methods.Rd | 6 neuroim-0.0.6/neuroim/man/series-methods.Rd | 12 neuroim-0.0.6/neuroim/man/seriesIter.Rd | 15 neuroim-0.0.6/neuroim/man/show-AxisSet1D-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-AxisSet2D-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-AxisSet3D-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-AxisSet4D-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BaseMetaInfo-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BrainSpace-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BrainVector-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BrainVectorSource-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BrainVolume-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-FileMetaInfo-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-NamedAxis-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-NullMetaInfo-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-ROIVolume-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-SparseBrainVector-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-SurfaceDataMetaInfo-method.Rd |only neuroim-0.0.6/neuroim/man/show-SurfaceGeometryMetaInfo-method.Rd |only neuroim-0.0.6/neuroim/man/slice-methods.Rd | 2 neuroim-0.0.6/neuroim/man/sliceData.Rd |only neuroim-0.0.6/neuroim/man/space-methods.Rd | 3 neuroim-0.0.6/neuroim/man/spacing-methods.Rd | 2 neuroim-0.0.6/neuroim/man/splitFill-methods.Rd | 5 neuroim-0.0.6/neuroim/man/splitReduce-methods.Rd | 11 neuroim-0.0.6/neuroim/man/splitScale-methods.Rd | 5 neuroim-0.0.6/neuroim/man/stripExtension-methods.Rd | 4 neuroim-0.0.6/neuroim/man/sub-BrainBucket-index-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-ROIVolume-numeric-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVector-missing-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVector-missing-numeric-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVector-numeric-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVector-numeric-numeric-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-matrix-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-missing-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-missing-numeric-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-numeric-missing-missing-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-numeric-numeric-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-sub-BrainBucket-index-missing-method.Rd | 2 neuroim-0.0.6/neuroim/man/subVector-methods.Rd |only neuroim-0.0.6/neuroim/man/takeSeries-methods.Rd | 2 neuroim-0.0.6/neuroim/man/takeVolume-methods.Rd | 8 neuroim-0.0.6/neuroim/man/tesselate-methods.Rd | 2 neuroim-0.0.6/neuroim/man/trans-methods.Rd | 4 neuroim-0.0.6/neuroim/man/values-methods.Rd | 2 neuroim-0.0.6/neuroim/man/voxels-methods.Rd | 2 neuroim-0.0.6/neuroim/man/writeElements-methods.Rd | 2 neuroim-0.0.6/neuroim/man/writeVector-methods.Rd | 7 neuroim-0.0.6/neuroim/man/writeVolume-methods.Rd | 9 neuroim-0.0.6/neuroim/tests/runit-BrainVector.R | 37 neuroim-0.0.6/neuroim/tests/runit-connComp3D.R |only 231 files changed, 1484 insertions(+), 718 deletions(-)
Title: Stable Isotope Mixing Model
Description: Estimates diet contributions from isotopic sources using JAGS.
Includes estimation of concentration dependence and measurement error.
Author: Jake Ferguson and Jack Hopkins
Maintainer: Jake Ferguson <troutinthemilk@gmail.com>
Diff between IsotopeR versions 0.5.1 dated 2015-11-10 and 0.5.2 dated 2016-01-07
IsotopeR-0.5.1/IsotopeR/vignettes/Fig1.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig10.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig11.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig12.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig13.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig14.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig15.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig16.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig17.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig18.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig19.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig2.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig20.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig21.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig22.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig3.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig4.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig5.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig6.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig7.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig8.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig9.png |only IsotopeR-0.5.1/IsotopeR/vignettes/IsoScreen.png |only IsotopeR-0.5.1/IsotopeR/vignettes/IsotopeR.Rnw.backup |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-IsotopeR.eps |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-IsotopeR.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-Load_Previous_Run.eps |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-Load_Previous_Run.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-New_Run.eps |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-New_Run.png |only IsotopeR-0.5.2/IsotopeR/DESCRIPTION | 8 IsotopeR-0.5.2/IsotopeR/MD5 | 77 - IsotopeR-0.5.2/IsotopeR/NAMESPACE | 3 IsotopeR-0.5.2/IsotopeR/NEWS | 6 IsotopeR-0.5.2/IsotopeR/R/IsotopeRgui.R | 86 - IsotopeR-0.5.2/IsotopeR/R/Plot_jags.R | 2 IsotopeR-0.5.2/IsotopeR/inst/doc/IsotopeR.Rnw | 555 ++++------ IsotopeR-0.5.2/IsotopeR/inst/doc/IsotopeR.pdf |binary IsotopeR-0.5.2/IsotopeR/man/IsoWrapper.Rd | 18 IsotopeR-0.5.2/IsotopeR/vignettes/Figures |only IsotopeR-0.5.2/IsotopeR/vignettes/IsotopeR.Rnw | 257 ++-- 41 files changed, 498 insertions(+), 514 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.2-1 dated 2015-12-09 and 1.2-2 dated 2016-01-07
DESCRIPTION | 8 MD5 | 30 +- R/g.analyse.R | 1 R/g.calibrate.R | 29 ++ R/g.dotorcomma.R | 66 +++-- R/g.extractheadervars.R | 2 R/g.getbout.R | 2 R/g.getmeta.R | 76 +++++- R/g.inspectfile.R | 368 +++++++++++++++++--------------- R/g.part1.R | 547 ++++++++++++++++++++++++------------------------ R/g.part4.R | 11 R/g.report.part2.R | 2 R/g.shell.GGIR.R | 475 ++++++++++++++++++----------------------- inst/NEWS.Rd | 6 man/GGIR-package.Rd | 4 man/g.part4.Rd | 5 16 files changed, 855 insertions(+), 777 deletions(-)
Title: Tools for Analysis of Diversity and Similarity in Biological
Systems
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
Author: Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak <pietrzak.20@osu.edu>
Diff between divo versions 0.1.1 dated 2015-02-03 and 0.1.2 dated 2016-01-07
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 5 ++++- R/divo.R | 2 +- build/vignette.rds |binary inst/DivO_DP.py | 2 +- inst/DivO_EnvCheck.py | 2 +- inst/DivO_Overlap.py | 2 +- inst/doc/divo-Manual.Rnw | 2 +- inst/doc/divo-Manual.pdf |binary inst/doc/divo-Vignette.Rnw | 2 +- inst/doc/divo-Vignette.pdf |binary vignettes/divo-Manual.Rnw | 2 +- vignettes/divo-Vignette.Rnw | 2 +- 14 files changed, 29 insertions(+), 26 deletions(-)
Title: General Purpose Interface to 'Elasticsearch'
Description: Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java'
Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' 'API'
(<https://www.elastic.co/products/elasticsearch>), including functions for
setting connection details to 'Elasticsearch' instances, loading bulk data,
searching for documents with both 'HTTP' query variables and 'JSON' based body
requests. In addition, 'elastic' provides functions for interacting with 'APIs'
for 'indices', documents, nodes, clusters, an interface to the cat 'API', and
more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between elastic versions 0.5.0 dated 2015-07-02 and 0.6.0 dated 2016-01-07
elastic-0.5.0/elastic/R/mlt.R |only elastic-0.5.0/elastic/man/mlt.Rd |only elastic-0.5.0/elastic/tests/test-all.R |only elastic-0.6.0/elastic/DESCRIPTION | 26 + elastic-0.6.0/elastic/LICENSE | 2 elastic-0.6.0/elastic/MD5 | 193 ++++++++------ elastic-0.6.0/elastic/NAMESPACE | 13 elastic-0.6.0/elastic/NEWS.md | 83 ++++++ elastic-0.6.0/elastic/R/Search.R | 65 ++-- elastic-0.6.0/elastic/R/Search_uri.R | 38 +- elastic-0.6.0/elastic/R/alias.R | 17 - elastic-0.6.0/elastic/R/cat.r | 97 ++++--- elastic-0.6.0/elastic/R/cluster.R | 94 ++++++- elastic-0.6.0/elastic/R/connect.R | 123 +++++---- elastic-0.6.0/elastic/R/count.r | 5 elastic-0.6.0/elastic/R/defunct.R |only elastic-0.6.0/elastic/R/docs_bulk.r | 227 ++++++++++++++--- elastic-0.6.0/elastic/R/docs_create.R | 2 elastic-0.6.0/elastic/R/docs_delete.R | 2 elastic-0.6.0/elastic/R/docs_get.r | 4 elastic-0.6.0/elastic/R/docs_mget.r | 9 elastic-0.6.0/elastic/R/documents.R | 16 - elastic-0.6.0/elastic/R/elastic-package.r | 23 + elastic-0.6.0/elastic/R/explain.R | 11 elastic-0.6.0/elastic/R/field_stats.R |only elastic-0.6.0/elastic/R/httr-verbs.R | 138 ++++++++-- elastic-0.6.0/elastic/R/index.R | 79 +++-- elastic-0.6.0/elastic/R/mapping.R | 61 ++-- elastic-0.6.0/elastic/R/msearch.R |only elastic-0.6.0/elastic/R/nodes.R | 20 - elastic-0.6.0/elastic/R/parsers.r | 1 elastic-0.6.0/elastic/R/percolater.R |only elastic-0.6.0/elastic/R/search_body.R | 18 - elastic-0.6.0/elastic/R/search_shards.R | 2 elastic-0.6.0/elastic/R/searchapis.R | 21 - elastic-0.6.0/elastic/R/tokenizer_set.R | 2 elastic-0.6.0/elastic/R/validate.R |only elastic-0.6.0/elastic/R/zzz.r | 10 elastic-0.6.0/elastic/README.md | 89 +++--- elastic-0.6.0/elastic/build/vignette.rds |binary elastic-0.6.0/elastic/inst/doc/elastic_intro.Rmd | 40 +- elastic-0.6.0/elastic/inst/doc/elastic_intro.html | 40 +- elastic-0.6.0/elastic/inst/doc/search.Rmd | 56 +--- elastic-0.6.0/elastic/inst/doc/search.html | 56 +--- elastic-0.6.0/elastic/inst/examples/msearch_eg1.json |only elastic-0.6.0/elastic/inst/examples/msearch_eg2.json |only elastic-0.6.0/elastic/inst/examples/test1.csv |only elastic-0.6.0/elastic/inst/examples/test1_id.csv |only elastic-0.6.0/elastic/inst/examples/test2.csv |only elastic-0.6.0/elastic/inst/examples/test2_id.csv |only elastic-0.6.0/elastic/inst/examples/test3.csv |only elastic-0.6.0/elastic/inst/examples/test3_id.csv |only elastic-0.6.0/elastic/inst/vign/elastic_intro.Rmd | 15 - elastic-0.6.0/elastic/inst/vign/elastic_intro.md | 40 +- elastic-0.6.0/elastic/inst/vign/search.md | 56 +--- elastic-0.6.0/elastic/man/Search.Rd | 167 +++++++----- elastic-0.6.0/elastic/man/Search_uri.Rd | 44 ++- elastic-0.6.0/elastic/man/alias.Rd | 13 elastic-0.6.0/elastic/man/cat.Rd | 75 ++--- elastic-0.6.0/elastic/man/cluster.Rd | 82 +++++- elastic-0.6.0/elastic/man/connect.Rd | 26 + elastic-0.6.0/elastic/man/count.Rd | 7 elastic-0.6.0/elastic/man/docs_bulk.Rd | 80 +++++ elastic-0.6.0/elastic/man/docs_create.Rd | 4 elastic-0.6.0/elastic/man/docs_delete.Rd | 4 elastic-0.6.0/elastic/man/docs_get.Rd | 4 elastic-0.6.0/elastic/man/docs_mget.Rd | 10 elastic-0.6.0/elastic/man/documents.Rd | 18 - elastic-0.6.0/elastic/man/elastic-defunct.Rd |only elastic-0.6.0/elastic/man/elastic.Rd | 24 + elastic-0.6.0/elastic/man/es_auth.Rd | 2 elastic-0.6.0/elastic/man/es_parse.Rd | 2 elastic-0.6.0/elastic/man/explain.Rd | 8 elastic-0.6.0/elastic/man/field_stats.Rd |only elastic-0.6.0/elastic/man/index.Rd | 52 ++- elastic-0.6.0/elastic/man/index_status-defunct.Rd |only elastic-0.6.0/elastic/man/mapping.Rd | 45 +-- elastic-0.6.0/elastic/man/mapping_delete-defunct.Rd |only elastic-0.6.0/elastic/man/mlt-defunct.Rd |only elastic-0.6.0/elastic/man/msearch.Rd |only elastic-0.6.0/elastic/man/nodes-defunct.Rd |only elastic-0.6.0/elastic/man/nodes.Rd | 19 - elastic-0.6.0/elastic/man/percolate.Rd |only elastic-0.6.0/elastic/man/ping.Rd | 2 elastic-0.6.0/elastic/man/preference.Rd | 18 - elastic-0.6.0/elastic/man/scroll.Rd | 4 elastic-0.6.0/elastic/man/search_body.Rd | 20 - elastic-0.6.0/elastic/man/search_shards.Rd | 4 elastic-0.6.0/elastic/man/searchapis.Rd | 11 elastic-0.6.0/elastic/man/tokenizer_set.Rd | 4 elastic-0.6.0/elastic/man/units-distance.Rd | 12 elastic-0.6.0/elastic/man/units-time.Rd | 8 elastic-0.6.0/elastic/man/validate.Rd |only elastic-0.6.0/elastic/tests/other/test-mlt.R | 19 - elastic-0.6.0/elastic/tests/testthat/helper-elastic.R |only elastic-0.6.0/elastic/tests/testthat/test-alias.R | 10 elastic-0.6.0/elastic/tests/testthat/test-cat.R | 66 ++-- elastic-0.6.0/elastic/tests/testthat/test-cluster.R | 16 - elastic-0.6.0/elastic/tests/testthat/test-connect.R | 4 elastic-0.6.0/elastic/tests/testthat/test-count.R | 10 elastic-0.6.0/elastic/tests/testthat/test-docs.R | 41 --- elastic-0.6.0/elastic/tests/testthat/test-explain.R | 10 elastic-0.6.0/elastic/tests/testthat/test-indices.R | 64 +--- elastic-0.6.0/elastic/tests/testthat/test-mappings.R | 110 ++++---- elastic-0.6.0/elastic/tests/testthat/test-msearch.R |only elastic-0.6.0/elastic/tests/testthat/test-nodes.R | 4 elastic-0.6.0/elastic/tests/testthat/test-ping.R | 5 elastic-0.6.0/elastic/tests/testthat/test-search.R | 22 - elastic-0.6.0/elastic/tests/testthat/test-search_uri.R | 13 elastic-0.6.0/elastic/vignettes/elastic_intro.Rmd | 40 +- elastic-0.6.0/elastic/vignettes/search.Rmd | 56 +--- 111 files changed, 1796 insertions(+), 1257 deletions(-)
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between rJava versions 0.9-7 dated 2015-07-29 and 0.9-8 dated 2016-01-07
rJava-0.9-7/rJava/jri/REngine/REngine.jar |only rJava-0.9-7/rJava/jri/REngine/Rserve.jar |only rJava-0.9-8/rJava/DESCRIPTION | 6 rJava-0.9-8/rJava/MD5 | 102 rJava-0.9-8/rJava/NEWS | 8 rJava-0.9-8/rJava/R/zzz.R.in | 14 rJava-0.9-8/rJava/configure | 12 rJava-0.9-8/rJava/configure.ac | 12 rJava-0.9-8/rJava/inst/javadoc/ArrayDimensionException.html | 4 rJava-0.9-8/rJava/inst/javadoc/ArrayWrapper.html | 4 rJava-0.9-8/rJava/inst/javadoc/ArrayWrapper_Test.html | 4 rJava-0.9-8/rJava/inst/javadoc/DummyPoint.html | 4 rJava-0.9-8/rJava/inst/javadoc/FlatException.html | 4 rJava-0.9-8/rJava/inst/javadoc/NotAnArrayException.html | 4 rJava-0.9-8/rJava/inst/javadoc/NotComparableException.html | 4 rJava-0.9-8/rJava/inst/javadoc/ObjectArrayException.html | 4 rJava-0.9-8/rJava/inst/javadoc/PrimitiveArrayException.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaArrayIterator.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaArrayTools.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaArrayTools_Test.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaClassLoader.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaComparator.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaImport.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaTools.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaTools_Test.TestException.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaTools_Test.html | 4 rJava-0.9-8/rJava/inst/javadoc/RectangularArrayBuilder.html | 4 rJava-0.9-8/rJava/inst/javadoc/RectangularArrayBuilder_Test.html | 4 rJava-0.9-8/rJava/inst/javadoc/RectangularArrayExamples.html | 4 rJava-0.9-8/rJava/inst/javadoc/RectangularArraySummary.html | 4 rJava-0.9-8/rJava/inst/javadoc/TestException.html | 4 rJava-0.9-8/rJava/inst/javadoc/allclasses-frame.html | 4 rJava-0.9-8/rJava/inst/javadoc/allclasses-noframe.html | 4 rJava-0.9-8/rJava/inst/javadoc/constant-values.html | 4 rJava-0.9-8/rJava/inst/javadoc/deprecated-list.html | 4 rJava-0.9-8/rJava/inst/javadoc/help-doc.html | 4 rJava-0.9-8/rJava/inst/javadoc/index-all.html | 4 rJava-0.9-8/rJava/inst/javadoc/index.html | 2 rJava-0.9-8/rJava/inst/javadoc/overview-tree.html | 4 rJava-0.9-8/rJava/inst/javadoc/package-frame.html | 4 rJava-0.9-8/rJava/inst/javadoc/package-summary.html | 4 rJava-0.9-8/rJava/inst/javadoc/package-tree.html | 4 rJava-0.9-8/rJava/inst/javadoc/serialized-form.html | 4 rJava-0.9-8/rJava/inst/jri/JRIEngine.jar |binary rJava-0.9-8/rJava/inst/jri/REngine.jar |binary rJava-0.9-8/rJava/jri/configure | 4294 ++++------ rJava-0.9-8/rJava/jri/configure.ac | 7 rJava-0.9-8/rJava/jri/tools/config.guess | 1246 +- rJava-0.9-8/rJava/jri/tools/config.sub | 605 + rJava-0.9-8/rJava/jri/tools/install-sh | 708 + rJava-0.9-8/rJava/src/rJava.h | 2 53 files changed, 3957 insertions(+), 3205 deletions(-)
Title: Applied Geochemistry EDA
Description: Geological Survey of Canada (GSC) functions for exploratory data analysis with applied geochemical data, with special application to the estimation of background ranges and identification of outliers, 'anomalies', to support mineral exploration and environmental studies. Additional functions are provided to support analytical data QA/QC, ANOVA for investigations of field sampling and analytical variability, and utility tasks. NOTE: function caplot() for concentration-area plots employs package 'akima', however, 'akima' is only licensed for not-for-profit use. Therefore, not-for-profit users of 'rgr' will have to independently make package 'akima' available through library(....); and use of function caplot() by for-profit users will fail.
Author: Robert G. Garrett
Maintainer: Robert G. Garrett <robert.garrett@canada.ca>
Diff between rgr versions 1.1.11 dated 2015-05-04 and 1.1.13 dated 2016-01-07
rgr-1.1.11/rgr/inst/doc/What_is_in_rgr_1-1-11.pdf |only rgr-1.1.11/rgr/inst/doc/rgr_Overview_1-1-11.pdf |only rgr-1.1.11/rgr/inst/doc/rgr_func_list_1-1-11.pdf |only rgr-1.1.11/rgr/man/rgr_1.1.11-package.Rd |only rgr-1.1.13/rgr/DESCRIPTION | 10 +- rgr-1.1.13/rgr/MD5 | 82 +++++++++++----------- rgr-1.1.13/rgr/NAMESPACE | 10 +- rgr-1.1.13/rgr/R/ad.plot3.R | 41 ++++++----- rgr-1.1.13/rgr/R/ad.plot4.R | 2 rgr-1.1.13/rgr/R/caplot.R | 35 ++------- rgr-1.1.13/rgr/R/gx.hist.R | 6 + rgr-1.1.13/rgr/R/gx.mf.R |only rgr-1.1.13/rgr/R/gx.rma.R | 66 +++++++++++------ rgr-1.1.13/rgr/R/gx.t.test.R |only rgr-1.1.13/rgr/R/inset.R | 5 - rgr-1.1.13/rgr/R/shape.R | 5 + rgr-1.1.13/rgr/R/shape.alt.R |only rgr-1.1.13/rgr/data/ad.test.rda |binary rgr-1.1.13/rgr/data/crm.test.new.rda |binary rgr-1.1.13/rgr/data/crm.test.rda |binary rgr-1.1.13/rgr/data/fix.test.asis.rda |binary rgr-1.1.13/rgr/data/fix.test.rda |binary rgr-1.1.13/rgr/data/kola.c.rda |binary rgr-1.1.13/rgr/data/kola.o.rda |binary rgr-1.1.13/rgr/data/ms.data1.rda |binary rgr-1.1.13/rgr/data/ms.data2.rda |binary rgr-1.1.13/rgr/data/ms.data3.rda |binary rgr-1.1.13/rgr/data/ogrady.mat2open.rda |binary rgr-1.1.13/rgr/data/ogrady.rda |binary rgr-1.1.13/rgr/data/sind.mat2open.rda |binary rgr-1.1.13/rgr/data/sind.rda |binary rgr-1.1.13/rgr/data/triples.test1.rda |binary rgr-1.1.13/rgr/data/triples.test2.rda |binary rgr-1.1.13/rgr/inst/doc/What_is_in_rgr_1-1-13.pdf |only rgr-1.1.13/rgr/inst/doc/rgr_Overview_1-1-13.pdf |only rgr-1.1.13/rgr/inst/doc/rgr_func_list_1-1-13.pdf |only rgr-1.1.13/rgr/man/ad.plot3.Rd | 10 +- rgr-1.1.13/rgr/man/ad.plot4.Rd | 2 rgr-1.1.13/rgr/man/caplot.Rd | 14 +-- rgr-1.1.13/rgr/man/gx.hist.Rd | 10 +- rgr-1.1.13/rgr/man/gx.mf.Rd |only rgr-1.1.13/rgr/man/gx.mvalloc.Rd | 4 - rgr-1.1.13/rgr/man/gx.mvalloc.closed.Rd | 4 - rgr-1.1.13/rgr/man/gx.rma.Rd | 3 rgr-1.1.13/rgr/man/gx.t.test.Rd |only rgr-1.1.13/rgr/man/inset.Rd | 2 rgr-1.1.13/rgr/man/rgr_1.1.13-package.Rd |only rgr-1.1.13/rgr/man/shape.Rd | 6 - rgr-1.1.13/rgr/man/shape.alt.Rd |only 49 files changed, 172 insertions(+), 145 deletions(-)
Title: A Toolbox for the Analysis of Proteomics Data
Description: Tools for the statistical analysis and visualization of (relative and absolute) quantitative (LFQ,TMT,HRM) Proteomics data.
Author: Erik Ahrne
Maintainer: Erik Ahrne <erik.ahrne@unibas.ch>
Diff between SafeQuant versions 2.2.1 dated 2016-01-05 and 2.2.2 dated 2016-01-07
SafeQuant-2.2.1/SafeQuant/exec/commitToTPPServer.sh |only SafeQuant-2.2.1/SafeQuant/exec/createDocumentation.sh |only SafeQuant-2.2.1/SafeQuant/inst/version/TODO.txt |only SafeQuant-2.2.2/SafeQuant/DESCRIPTION | 6 SafeQuant-2.2.2/SafeQuant/MD5 | 25 +- SafeQuant-2.2.2/SafeQuant/README.md | 15 - SafeQuant-2.2.2/SafeQuant/exec/mFuzzClustering.R | 128 +++++++++-- SafeQuant-2.2.2/SafeQuant/inst/manuals/SafeQuant-man.pdf |binary SafeQuant-2.2.2/SafeQuant/inst/testData |only SafeQuant-2.2.2/SafeQuant/tests/initTestSession.R | 32 +- SafeQuant-2.2.2/SafeQuant/tests/testExpressionAnalysis.R | 52 ++-- SafeQuant-2.2.2/SafeQuant/tests/testIdentificationAnalysis.R | 10 SafeQuant-2.2.2/SafeQuant/tests/testParser.R | 2 SafeQuant-2.2.2/SafeQuant/tests/testTMT.R | 8 SafeQuant-2.2.2/SafeQuant/tests/testTargeted.R | 2 15 files changed, 184 insertions(+), 96 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.11 dated 2015-08-14 and 1.12 dated 2016-01-07
DESCRIPTION | 35 +++++--- MD5 | 149 +++++++++++++++++++------------------- NAMESPACE | 4 + R/block.R | 103 ++++++++++++++++++-------- R/cache.R | 5 - R/citation.R | 12 ++- R/defaults.R | 1 R/engine.R | 65 +++++++++++++--- R/header.R | 2 R/highlight.R | 3 R/hooks-extra.R | 2 R/hooks-html.R | 43 +++++++--- R/hooks-latex.R | 36 ++++----- R/hooks-md.R | 68 ++++++++++++----- R/hooks-rst.R | 4 - R/hooks-textile.R | 3 R/hooks.R | 23 +++++ R/output.R | 16 +++- R/pandoc.R | 4 - R/plot.R | 43 ++++++++++ R/rocco.R | 12 +-- R/spin.R | 5 + R/table.R | 99 +++++++++++++++++++------ R/template.R | 2 R/themes.R | 2 R/utils-base64.R | 2 R/utils-conversion.R | 50 ++++++++++++ R/utils-sweave.R | 4 - R/utils.R | 81 +++++++++++++++++--- README.md | 5 - build/knitr.pdf |binary build/vignette.rds |binary inst/doc/docco-classic.html | 2 inst/doc/docco-linear.html | 2 inst/doc/knit_expand.html | 4 - inst/doc/knit_print.html | 124 ++++++++++++++++++------------- inst/doc/knitr-intro.html | 87 ++++++++++++++-------- inst/doc/knitr-markdown.html | 4 - inst/doc/knitr-refcard.pdf |binary inst/examples/knitr-beamer.Rnw | 2 inst/examples/knitr-graphics.Rnw | 24 +++--- inst/examples/knitr-listings.Rnw | 2 inst/examples/knitr-manual.Rnw | 7 + inst/examples/knitr-manual.bib | 8 +- inst/examples/knitr-manual.lyx | 34 ++++++-- inst/examples/knitr-minimal.Rnw | 2 inst/examples/knitr-packages.bib | 56 +++++++------- inst/examples/knitr-spin.html | 2 inst/examples/knitr-subfloats.Rnw | 4 - inst/examples/knitr-themes.Rnw | 4 - inst/examples/knitr-twocolumn.Rnw | 4 - inst/examples/upload-github.R | 11 +- man/all_patterns.Rd | 52 ------------- man/asis_output.Rd | 5 + man/chunk_hook.Rd | 2 man/hook_plot.Rd | 8 +- man/include_graphics.Rd |only man/kable.Rd | 7 + man/knit2html.Rd | 5 + man/knit_engines.Rd | 7 - man/knit_hooks.Rd | 7 - man/knit_patterns.Rd | 7 - man/knit_theme.Rd | 5 - man/knit_watch.Rd |only man/opts_chunk.Rd | 7 - man/opts_hooks.Rd |only man/opts_knit.Rd | 7 - man/opts_template.Rd | 7 - man/output_hooks.Rd | 8 +- man/rand_seed.Rd | 2 man/spin.Rd | 5 + man/write_bib.Rd | 12 ++- tests/testit/test-hooks.R | 15 +++ tests/testit/test-output.R | 28 +++++++ tests/testit/test-plot.R | 13 +++ tests/testit/test-table.R | 6 + tests/testit/test-utils.R | 8 ++ 77 files changed, 976 insertions(+), 513 deletions(-)
Title: Image Processing Library Based on CImg
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R.
Author: Simon Barthelme [aut, cre],
Antoine Cecchi [ctb]
Maintainer: Simon Barthelme <simon.barthelme@gipsa-lab.fr>
Diff between imager versions 0.14 dated 2015-09-18 and 0.15 dated 2016-01-07
imager-0.14/imager/man/subim.Rd |only imager-0.15/imager/DESCRIPTION | 18 imager-0.15/imager/MD5 | 206 +-- imager-0.15/imager/NAMESPACE | 13 imager-0.15/imager/NEWS | 11 imager-0.15/imager/R/RcppExports.R | 118 -- imager-0.15/imager/R/cimg_class.R | 1509 +++----------------------- imager-0.15/imager/R/conversions.R |only imager-0.15/imager/R/coordinates.R |only imager-0.15/imager/R/imgen.R |only imager-0.15/imager/R/interpolation.R | 44 imager-0.15/imager/R/splitcombine.R |only imager-0.15/imager/R/stencils.R |only imager-0.15/imager/R/utils.R | 435 +++++++ imager-0.15/imager/README.md | 3 imager-0.15/imager/inst/include/CImg.h | 11 imager-0.15/imager/man/FFT.Rd | 6 imager-0.15/imager/man/add.colour.Rd | 2 imager-0.15/imager/man/as.cimg.Rd | 6 imager-0.15/imager/man/as.cimg.array.Rd | 4 imager-0.15/imager/man/as.cimg.data.frame.Rd | 4 imager-0.15/imager/man/as.cimg.function.Rd | 34 imager-0.15/imager/man/as.data.frame.cimg.Rd | 4 imager-0.15/imager/man/as.raster.cimg.Rd | 4 imager-0.15/imager/man/at.Rd | 2 imager-0.15/imager/man/autocrop.Rd | 2 imager-0.15/imager/man/blur_anisotropic.Rd | 4 imager-0.15/imager/man/boats.Rd | 2 imager-0.15/imager/man/boxblur.Rd | 2 imager-0.15/imager/man/boxblur_xy.Rd | 4 imager-0.15/imager/man/bucketfill.Rd | 6 imager-0.15/imager/man/capture.plot.Rd | 4 imager-0.15/imager/man/center.stencil.Rd | 4 imager-0.15/imager/man/channels.Rd | 2 imager-0.15/imager/man/cimg.Rd | 4 imager-0.15/imager/man/cimg.dimensions.Rd | 2 imager-0.15/imager/man/cimg.extract.Rd | 29 imager-0.15/imager/man/cimg2im.Rd | 4 imager-0.15/imager/man/convolve.Rd | 6 imager-0.15/imager/man/correlate.Rd | 6 imager-0.15/imager/man/deriche.Rd | 2 imager-0.15/imager/man/diffusion_tensors.Rd | 2 imager-0.15/imager/man/displacement.Rd | 2 imager-0.15/imager/man/display.Rd | 6 imager-0.15/imager/man/display_list.Rd | 2 imager-0.15/imager/man/distance_transform.Rd | 4 imager-0.15/imager/man/erode.Rd | 6 imager-0.15/imager/man/extract_patches.Rd | 4 imager-0.15/imager/man/frames.Rd | 2 imager-0.15/imager/man/get.locations.Rd | 5 imager-0.15/imager/man/get.stencil.Rd | 4 imager-0.15/imager/man/get_gradient.Rd | 2 imager-0.15/imager/man/get_hessian.Rd | 2 imager-0.15/imager/man/grayscale.Rd | 2 imager-0.15/imager/man/haar.Rd | 4 imager-0.15/imager/man/idply.Rd | 4 imager-0.15/imager/man/iiply.Rd | 7 imager-0.15/imager/man/ilply.Rd | 4 imager-0.15/imager/man/im2cimg.Rd | 2 imager-0.15/imager/man/im_split.Rd | 4 imager-0.15/imager/man/imager.Rd | 2 imager-0.15/imager/man/imager.colourspaces.Rd | 2 imager-0.15/imager/man/imager.combine.Rd | 21 imager-0.15/imager/man/imager.replace.Rd |only imager-0.15/imager/man/imappend.Rd | 2 imager-0.15/imager/man/imdirac.Rd | 8 imager-0.15/imager/man/imdraw.Rd | 6 imager-0.15/imager/man/imfill.Rd | 12 imager-0.15/imager/man/imgradient.Rd | 6 imager-0.15/imager/man/imhessian.Rd | 4 imager-0.15/imager/man/imnoise.Rd | 9 imager-0.15/imager/man/imrotate.Rd | 2 imager-0.15/imager/man/imsharpen.Rd | 3 imager-0.15/imager/man/imshift.Rd | 2 imager-0.15/imager/man/imsplit.Rd | 6 imager-0.15/imager/man/imsub.Rd |only imager-0.15/imager/man/imwarp.Rd | 10 imager-0.15/imager/man/interp.Rd | 2 imager-0.15/imager/man/isoblur.Rd | 2 imager-0.15/imager/man/label.Rd | 5 imager-0.15/imager/man/liply.Rd | 4 imager-0.15/imager/man/load.image.Rd | 6 imager-0.15/imager/man/medianblur.Rd | 2 imager-0.15/imager/man/mirror.Rd | 2 imager-0.15/imager/man/pad.Rd | 2 imager-0.15/imager/man/periodic.part.Rd | 5 imager-0.15/imager/man/permute_axes.Rd | 2 imager-0.15/imager/man/pixel.grid.Rd | 12 imager-0.15/imager/man/pixel.index.Rd | 4 imager-0.15/imager/man/play.Rd | 2 imager-0.15/imager/man/plot.cimg.Rd | 2 imager-0.15/imager/man/renorm.Rd | 4 imager-0.15/imager/man/resize.Rd | 2 imager-0.15/imager/man/resize_uniform.Rd | 4 imager-0.15/imager/man/rotate_xy.Rd | 2 imager-0.15/imager/man/save.image.Rd | 2 imager-0.15/imager/man/selectSimilar.Rd | 6 imager-0.15/imager/man/squeeze.Rd | 2 imager-0.15/imager/man/stencil.cross.Rd | 4 imager-0.15/imager/man/sub-.cimg.Rd | 2 imager-0.15/imager/man/threshold.Rd | 18 imager-0.15/imager/man/vanvliet.Rd | 12 imager-0.15/imager/man/warp.Rd | 2 imager-0.15/imager/man/watershed.Rd | 12 imager-0.15/imager/src/Makevars.win | 2 imager-0.15/imager/src/filtering.cpp | 81 - imager-0.15/imager/src/morphology.cpp | 15 imager-0.15/imager/src/transformations.cpp | 22 108 files changed, 1183 insertions(+), 1741 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits and imputation of censored data.
Author: Clifford Anderson-Bergman; the Eigen team for Eigen library included(for C++ matrix operations); uses Marloes Maathuis's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.3.2 dated 2016-01-05 and 1.3.3 dated 2016-01-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 10 ++++++++++ src/icenReg_files/experimentalCode.cpp | 2 ++ src/icenReg_files/ic_sp_ch.cpp | 7 +++++-- src/icenReg_files/regressionTransforms.cpp | 2 +- 6 files changed, 28 insertions(+), 13 deletions(-)
Title: Kinship-Adjusted Survival SNP-Set Analysis
Description: SNP-set association testing for censored phenotypes in the presence of intrafamilial correlation.
Author: Martin Leclerc and Lajmi Lakhal Chaieb
Maintainer: Martin Leclerc <martin.leclerc.5@ulaval.ca>
Diff between gyriq versions 1.0.1 dated 2015-11-23 and 1.0.2 dated 2016-01-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/gyriq.R | 15 +++++++++++++-- R/testGyriq.R | 11 +++++++++++ man/gyriq-package.Rd | 15 +++++++++++++-- man/testGyriq.Rd | 11 +++++++++++ src/kernel_func.c | 7 ++++++- 7 files changed, 64 insertions(+), 15 deletions(-)
Title: Variable Selection Deviation Measures and Instability Tests for
High-Dimensional Generalized Linear Models
Description: Variable selection deviation (VSD) measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
Author: Ying Nan <nanx0006@gmail.com>, Yanjia Yu <yuxxx748@umn.edu>, Yuhong Yang <yyang@stat.umn.edu>, Yi Yang <yi.yang6@mcgill.ca>
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Diff between glmvsd versions 1.3 dated 2015-07-25 and 1.4 dated 2016-01-07
ChangeLog | 6 + DESCRIPTION | 14 +-- MD5 | 30 +++---- NAMESPACE | 4 R/binomialfit.R | 24 ++--- R/gaussianfit.R | 24 ++--- R/glmvsd.R | 208 +++++++++++++++++++++++++++----------------------- R/logitARM.R | 90 +++++++++++---------- R/logitIC.R | 54 ++++++------ R/lsARM.R | 95 +++++++++++----------- R/lsIC.R | 6 - R/modelfit.R | 36 ++++---- R/stability.test.R | 103 ++++++++++++------------ R/tools.R | 11 -- man/glmvsd.Rd | 16 ++- man/stability.test.Rd | 8 + 16 files changed, 381 insertions(+), 348 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.31.4 dated 2015-10-09 and 1.31.5 dated 2016-01-07
DESCRIPTION | 10 MD5 | 32 +- NAMESPACE | 3 R/AovSum.r | 192 +++++++++-------- R/CA.R | 2 R/FAMD.R | 2 R/MFA.R | 2 R/catdes.r | 2 R/condes.r | 4 R/plot.FAMD.R | 5 R/plot.MFA.R | 14 - R/plotellipses.r | 48 ++-- R/summary.CA.r | 2 inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary man/plot.MFA.Rd | 2 man/plotellipses.Rd | 6 17 files changed, 175 insertions(+), 151 deletions(-)
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between dynRB versions 0.5 dated 2015-12-24 and 0.6 dated 2016-01-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/unitTests/test_dynRB_VPa.R | 17 ----------------- man/dynRB-package.Rd | 4 ++-- tests/testthat/test_dynRB_VPa.R | 17 ----------------- 5 files changed, 9 insertions(+), 43 deletions(-)
Title: Arps Decline Curve Analysis in R
Description: Functions for Arps decline-curve analysis on oil and gas data. Includes exponential, hyperbolic, harmonic, and hyperbolic-to-exponential models as well as the preceding with initial curtailment. Functions included for computing rate, cumulative production, instantaneous decline, EUR, time to economic limit, and performing least-squares best fits.
Author: Derrick Turk [aut, cre, cph]
Maintainer: Derrick Turk <dwt@terminusdatascience.com>
Diff between aRpsDCA versions 1.0.1 dated 2015-06-22 and 1.0.2 dated 2016-01-07
DESCRIPTION | 9 +++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 ++ R/arps.R | 6 ++++-- R/bestfit.R | 2 +- R/curtail.R | 2 +- R/eur.R | 2 +- R/s3.R | 2 +- README.md | 9 +++++---- tests/fit_and_plot.R | 2 +- tests/fit_and_plot_from_Np.R | 2 +- 11 files changed, 32 insertions(+), 26 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.4.8 dated 2015-12-23 and 0.5.0 dated 2016-01-07
DESCRIPTION | 8 - MD5 | 34 ++--- NAMESPACE | 1 R/lin.ratio.R | 8 - R/vardchangannual.R |only R/vardchanges.R | 302 +++++++++++++++++++++++++++++++----------------- R/vardchangespoor.R | 51 +++++--- R/vardcros.R | 37 +++-- R/vardom.R | 4 inst/CITATION | 6 inst/COPYING | 2 inst/NEWS | 4 man/lin.ratio.Rd | 9 - man/vardchangannual.Rd |only man/vardchanges.Rd | 43 ++++++ man/vardchangespoor.Rd | 23 ++- man/vardcros.Rd | 8 - man/vardcrospoor.Rd | 1 man/vardpoor-package.Rd | 4 19 files changed, 364 insertions(+), 181 deletions(-)
Title: Estimating Mixed Graphical Models
Description: Estimation of Mixed Graphical model using L1-regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between mgm versions 1.1-3 dated 2016-01-06 and 1.1-4 dated 2016-01-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/mgm-package.Rd | 2 +- src/mMRFSampler_Ccore.cpp | 7 ++++++- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between OUwie versions 1.46 dated 2015-09-05 and 1.48 dated 2016-01-07
DESCRIPTION | 10 - MD5 | 22 +-- NAMESPACE | 6 R/OUwie.R | 10 - R/OUwie.boot.R | 33 +++- R/OUwie.sim.R | 28 +++ R/OUwie.slice.R | 11 - R/hOUwie.R |only R/pathLike.R |only R/varcov.ou.R | 207 +++++++++++++++------------- R/weight.mat.R | 385 ++++++++++++++++++++++++++++------------------------- man/OUwie.sim.Rd | 5 man/OUwie.slice.Rd | 3 13 files changed, 404 insertions(+), 316 deletions(-)
Title: Multi-Model Inference
Description: Model selection and model averaging based on information criteria
(AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń <kamil.barton@go2.pl>
Diff between MuMIn versions 1.15.1 dated 2015-07-03 and 1.15.6 dated 2016-01-07
MuMIn-1.15.1/MuMIn/R/glm-link-new.R |only MuMIn-1.15.1/MuMIn/R/predict-new.R |only MuMIn-1.15.6/MuMIn/DESCRIPTION | 19 MuMIn-1.15.6/MuMIn/MD5 | 63 - MuMIn-1.15.6/MuMIn/NAMESPACE | 14 MuMIn-1.15.6/MuMIn/NEWS | 373 ++++++----- MuMIn-1.15.6/MuMIn/R/Weights.R | 1 MuMIn-1.15.6/MuMIn/R/arm.glm.R | 24 MuMIn-1.15.6/MuMIn/R/coefTable.R | 159 ++++ MuMIn-1.15.6/MuMIn/R/coeffs.R | 14 MuMIn-1.15.6/MuMIn/R/dredge.R | 168 ++--- MuMIn-1.15.6/MuMIn/R/get.models.R | 14 MuMIn-1.15.6/MuMIn/R/makeArgs.R | 91 +- MuMIn-1.15.6/MuMIn/R/model.avg.R | 34 - MuMIn-1.15.6/MuMIn/R/modify.model.selection.R | 65 +- MuMIn-1.15.6/MuMIn/R/pdredge.R | 150 ++-- MuMIn-1.15.6/MuMIn/R/rbind.model.selection.R | 33 - MuMIn-1.15.6/MuMIn/R/substitution.R | 66 +- MuMIn-1.15.6/MuMIn/R/utils-misc.R | 9 MuMIn-1.15.6/MuMIn/R/utils-models.R | 135 +++- MuMIn-1.15.6/MuMIn/data/Beetle.rda |binary MuMIn-1.15.6/MuMIn/data/Cement.rda |binary MuMIn-1.15.6/MuMIn/data/GPA.rda |binary MuMIn-1.15.6/MuMIn/man/MuMIn-package.Rd | 6 MuMIn-1.15.6/MuMIn/man/data-Beetle.Rd | 65 -- MuMIn-1.15.6/MuMIn/man/data-GPA.Rd | 10 MuMIn-1.15.6/MuMIn/man/dredge.Rd | 116 +-- MuMIn-1.15.6/MuMIn/man/exprApply.Rd | 8 MuMIn-1.15.6/MuMIn/man/par.avg.Rd | 4 MuMIn-1.15.6/MuMIn/man/std.coef.Rd | 5 MuMIn-1.15.6/MuMIn/man/subset.model.selection.Rd | 2 MuMIn-1.15.6/MuMIn/man/supported-classes.Rd | 13 MuMIn-1.15.6/MuMIn/tests/classes.R | 732 ++++++++++------------- MuMIn-1.15.6/MuMIn/tests/gam-smooth-consitency.R |only 34 files changed, 1364 insertions(+), 1029 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.3 dated 2015-10-03 and 1.4 dated 2016-01-07
hisse-1.3/hisse/tests |only hisse-1.4/hisse/DESCRIPTION | 10 +++++----- hisse-1.4/hisse/MD5 | 9 +++------ hisse-1.4/hisse/R/hisseNull4.R | 4 ++-- hisse-1.4/hisse/R/plotHisse.R | 2 ++ 5 files changed, 12 insertions(+), 13 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized Singular Value Decomposition of a matrix pair,
using Lapack routines.
Author: Berend Hasselman [cre, aut],
Lapack authors [aut, cph]
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between geigen versions 1.8 dated 2015-11-02 and 1.9 dated 2016-01-07
DESCRIPTION | 8 MD5 | 32 +- NEWS | 5 R/gsvd.R | 43 ++ inst/COPYRIGHTS | 11 man/geigen.Rd | 2 man/gqz.Rd | 2 man/gsvd.Rd | 2 src/dggsvd3.f |only src/dggsvp3.f |only src/xdggsvd.f | 9 src/xzggsvd.f | 7 src/zggesall.f | 16 - src/zggevall.f | 8 src/zggevsdeps.f | 50 +-- src/zggsvdall.f | 761 +++++++++++++++++-------------------------------- tests/tgsvd4.R | 12 tests/tgsvd4.Rout.save | 39 +- 18 files changed, 424 insertions(+), 583 deletions(-)
Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between corHMM versions 1.17 dated 2015-10-29 and 1.18 dated 2016-01-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ancRECON.R | 9 ++++++--- 3 files changed, 12 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-22 0.3.0
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between dunn.test versions 1.3.1 dated 2015-10-08 and 1.3.2 dated 2016-01-06
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/dunn.test.R | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Conover-Iman Test of Multiple Comparisons Using Rank Sums
Description: Computes the Conover-Iman test (1979) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. conover.test makes k(k-1)/2 multiple pairwise comparisons based on Conover-Iman t-test-statistic of the rank differences. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Conover-Iman test may be understood as a test for median difference. conover.test accounts for tied ranks. The Conover-Iman test is strictly valid if and only if the corresponding Kruskal-Wallis null hypothesis is rejected.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between conover.test versions 1.1.0 dated 2015-09-26 and 1.1.1 dated 2016-01-06
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/conover.test.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Dynamic Model Averaging
Description: Dynamic model averaging for binary and continuous
outcomes.
Author: Tyler H. McCormick, Adrian Raftery, David Madigan
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between dma versions 1.2-2 dated 2014-11-06 and 1.2-3 dated 2016-01-06
ChangeLog |only DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- NAMESPACE | 3 +++ R/logistic.dma.default.R | 7 ++++--- man/dma-package.Rd | 4 ++-- 6 files changed, 19 insertions(+), 14 deletions(-)
Title: Visualization of Spatial and Spatio-Temporal Objects in Google
Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>
Diff between plotKML versions 0.5-4 dated 2015-12-24 and 0.5-5 dated 2016-01-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- demo/plotKML.R | 3 ++- inst/doc/jss1079.pdf |binary man/plotKML.Rd | 3 ++- 5 files changed, 12 insertions(+), 10 deletions(-)
Title: Estimating Mixed Graphical Models
Description: Estimation of Mixed Graphical model using L1-regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between mgm versions 1.1-2 dated 2015-09-03 and 1.1-3 dated 2016-01-06
DESCRIPTION | 11 - MD5 | 22 +- NAMESPACE | 2 R/mgmfit.R | 13 - R/mgmsampler.R | 39 +++- R/potts_parameter.R | 56 ++---- README.md | 10 + man/mgm-package.Rd | 12 - man/mgmfit.Rd | 3 man/mgmsampler.Rd | 15 + src/RcppExports.cpp | 2 src/mMRFSampler_Ccore.cpp | 378 +++++++++++++++++++++++----------------------- 12 files changed, 293 insertions(+), 270 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. These functions are
mainly for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm. In addition, a collection of functions are
provided for drawing vector diagrams in 2D and 3D.
Author: Michael Friendly [aut, cre], John Fox [aut], Georges Monette [ctb], Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 0.6.0 dated 2015-12-14 and 0.7.0 dated 2016-01-06
matlib-0.6.0/matlib/R/showEqn.R |only matlib-0.6.0/matlib/man/is_square_matrix.Rd |only matlib-0.6.0/matlib/man/is_symmetric_matrix.Rd |only matlib-0.7.0/matlib/DESCRIPTION | 17 ++-- matlib-0.7.0/matlib/MD5 | 58 ++++++++------- matlib-0.7.0/matlib/NAMESPACE | 8 +- matlib-0.7.0/matlib/NEWS |only matlib-0.7.0/matlib/R/arrows3d.R | 40 ++++++---- matlib-0.7.0/matlib/R/corner.R | 77 +++++++++++++++++++-- matlib-0.7.0/matlib/R/gsorth.R | 1 matlib-0.7.0/matlib/R/is_square.R | 17 ++++ matlib-0.7.0/matlib/R/matlib.R | 3 matlib-0.7.0/matlib/R/mpower.R | 2 matlib-0.7.0/matlib/R/regvec3d.R |only matlib-0.7.0/matlib/R/showeqn.R |only matlib-0.7.0/matlib/R/vectors.R | 11 ++- matlib-0.7.0/matlib/R/vectors3d.R | 52 +++++++++----- matlib-0.7.0/matlib/README.md | 10 +- matlib-0.7.0/matlib/inst/doc/gramreg.html | 40 +++++----- matlib-0.7.0/matlib/man/Proj.Rd | 8 +- matlib-0.7.0/matlib/man/arc.Rd |only matlib-0.7.0/matlib/man/arrows3d.Rd | 23 +++--- matlib-0.7.0/matlib/man/cone3d.Rd | 2 matlib-0.7.0/matlib/man/corner.Rd | 11 +-- matlib-0.7.0/matlib/man/is_square.Rd |only matlib-0.7.0/matlib/man/matlib.Rd | 3 matlib-0.7.0/matlib/man/mpower.Rd | 2 matlib-0.7.0/matlib/man/plot.regvec3d.Rd |only matlib-0.7.0/matlib/man/point_on_line.Rd | 18 +++- matlib-0.7.0/matlib/man/regvec3d.Rd |only matlib-0.7.0/matlib/man/showEqn.Rd | 2 matlib-0.7.0/matlib/man/vectors.Rd | 8 +- matlib-0.7.0/matlib/man/vectors3d.Rd | 42 ++++++++--- matlib-0.7.0/matlib/vignettes/eigen-ex1.Rmd | 3 matlib-0.7.0/matlib/vignettes/linear-equations.Rmd | 2 35 files changed, 315 insertions(+), 145 deletions(-)
Title: Download Google Sheets Using Just the URL
Description: Simple package to download Google Sheets using just the sharing
link. Spreadsheets can be downloaded as a data frame, or as plain text to parse
manually. Google Sheets is the new name for Google Docs Spreadsheets.
Author: Max Conway [aut, cre]
Maintainer: Max Conway <conway.max1@gmail.com>
Diff between gsheet versions 0.1.0 dated 2015-03-10 and 0.2.1 dated 2016-01-06
DESCRIPTION | 17 ++++++++++------- MD5 | 18 +++++++++--------- NAMESPACE | 3 ++- R/gsheet2tbl.R | 18 ++++++++++-------- R/gsheet2text.R | 17 +++++++++++++---- README.md | 24 ++++++++++++++++++++---- man/gsheet2tbl.Rd | 19 ++++++++++--------- man/gsheet2text.Rd | 11 +++++++---- tests/testthat/test-gsheet2tbl.R | 7 +++---- tests/testthat/test-gsheet2text.R | 6 ++++++ 10 files changed, 90 insertions(+), 50 deletions(-)
Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation, manipulation and simulation of multistate
data - the Lexis suite of functions, which includes interfaces to
mstate, etm and cmprsk packages.
Also contains functions for Age-Period-Cohort modeling and a
function for interval censored data and some useful functions for
tabulation and plotting, as well some epidemiological datasets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <bxc@steno.dk>
Diff between Epi versions 1.1.71 dated 2015-09-17 and 2.0 dated 2016-01-06
Epi-1.1.71/Epi/inst/doc/sim-Lexis.rnw |only Epi-1.1.71/Epi/vignettes/sim-Lexis.rnw |only Epi-2.0/Epi/CHANGES | 10 ++++ Epi-2.0/Epi/DESCRIPTION | 16 +++--- Epi-2.0/Epi/MD5 | 36 ++++++++------- Epi-2.0/Epi/NAMESPACE | 9 +++ Epi-2.0/Epi/R/factorize.R | 2 Epi-2.0/Epi/R/foreign.R | 2 Epi-2.0/Epi/R/lexis.R | 77 +++++++++++++++++++++++++++++++++ Epi-2.0/Epi/R/simLexis.R | 39 +++++++++------- Epi-2.0/Epi/build/vignette.rds |binary Epi-2.0/Epi/inst/doc/index.html | 4 - Epi-2.0/Epi/inst/doc/sim-Lexis.pdf |binary Epi-2.0/Epi/inst/doc/simLexis.R |only Epi-2.0/Epi/inst/doc/simLexis.pdf |only Epi-2.0/Epi/inst/doc/simLexis.rnw |only Epi-2.0/Epi/man/Lexis.Rd | 2 Epi-2.0/Epi/man/N2Y.Rd | 28 +++++++++--- Epi-2.0/Epi/man/Ns.Rd | 30 +++++++----- Epi-2.0/Epi/man/rbind.Lexis.Rd |only Epi-2.0/Epi/man/subset.Lexis.Rd | 14 +++--- Epi-2.0/Epi/vignettes/index.html |only Epi-2.0/Epi/vignettes/simLexis.rnw |only 23 files changed, 200 insertions(+), 69 deletions(-)
Title: Modeling Framework for Cellular Communities in their
Environments
Description: Can be used for simulation of organisms living in
communities. Each organism is represented individually and genome scale
metabolic models determine the uptake and release of compounds. Biological
processes such as movement, diffusion, chemotaxis and kinetics are available
along with data analysis techniques.
Author: Eugen Bauer [aut],
Johannes Zimmermann [aut, cre]
Maintainer: Johannes Zimmermann <j.zimmermann@iem.uni-kiel.de>
Diff between BacArena versions 1.0 dated 2015-12-08 and 1.0.1 dated 2016-01-06
BacArena-1.0.1/BacArena/DESCRIPTION | 10 BacArena-1.0.1/BacArena/MD5 | 26 +- BacArena-1.0.1/BacArena/NAMESPACE | 12 BacArena-1.0.1/BacArena/NEWS |only BacArena-1.0.1/BacArena/R/Arena.R | 141 ++++++++++- BacArena-1.0.1/BacArena/R/Stuff.R | 32 +- BacArena-1.0.1/BacArena/R/Substance.R | 2 BacArena-1.0.1/BacArena/README.md | 24 + BacArena-1.0.1/BacArena/build/vignette.rds |binary BacArena-1.0.1/BacArena/inst/doc/BacArena-Introduction.R | 2 BacArena-1.0.1/BacArena/inst/doc/BacArena-Introduction.Rmd | 4 BacArena-1.0.1/BacArena/inst/doc/BacArena-Introduction.pdf |only BacArena-1.0.1/BacArena/man/findFeeding.Rd |only BacArena-1.0.1/BacArena/man/openArena.Rd |only BacArena-1.0.1/BacArena/vignettes/BacArena-Introduction.Rmd | 4 BacArena-1.0.1/BacArena/vignettes/BacArena-Introduction.html |only BacArena-1.0/BacArena/inst/doc/BacArena-Introduction.html |only 17 files changed, 211 insertions(+), 46 deletions(-)
Title: WordNet Interface
Description: An interface to WordNet using the Jawbone Java API to WordNet.
WordNet (<http://wordnet.princeton.edu/>) is a large lexical database of
English. Nouns, verbs, adjectives and adverbs are grouped into sets of
cognitive synonyms (synsets), each expressing a distinct concept. Synsets
are interlinked by means of conceptual-semantic and lexical relations.
Please note that WordNet(R) is a registered tradename. Princeton
University makes WordNet available to research and commercial users
free of charge provided the terms of their license
(<http://wordnet.princeton.edu/wordnet/license/>) are followed, and
proper reference is made to the project using an appropriate
citation (<http://wordnet.princeton.edu/wordnet/citing-wordnet/>).
Author: Ingo Feinerer [aut],
Kurt Hornik [aut, cre],
Mike Wallace [ctb, cph] (Jawbone Java WordNet API library)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between wordnet versions 0.1-10 dated 2014-09-01 and 0.1-11 dated 2016-01-06
DESCRIPTION | 8 ++++---- LICENSE | 7 +++++-- MD5 | 10 +++++----- build/vignette.rds |binary inst/CITATION | 46 +++++++++++++++------------------------------- inst/doc/wordnet.pdf |binary 6 files changed, 29 insertions(+), 42 deletions(-)
Title: Spherical k-Means Clustering
Description: Algorithms to compute spherical k-means partitions.
Features several methods, including a genetic and a fixed-point
algorithm and an interface to the CLUTO vcluster program.
Author: Kurt Hornik [aut, cre],
Ingo Feinerer [aut],
Martin Kober [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between skmeans versions 0.2-7 dated 2015-06-24 and 0.2-8 dated 2016-01-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/CITATION | 34 ++++++++++++++-------------------- 3 files changed, 19 insertions(+), 25 deletions(-)
Title: Simulations to Predict the Number of RAD and GBS Loci
Description: Provides a number of functions to simulate restriction enzyme digestion, library construction and fragments size selection to predict the number of loci expected from most of the Restriction site Associated DNA (RAD) and Genotyping By Sequencing (GBS) approaches. SimRAD estimates the number of loci expected from a particular genome depending on the protocol type and parameters allowing to assess feasibility, multiplexing capacity and the amount of sequencing required.
Author: Olivier Lepais [aut, cre],
Jason Weir [aut]
Maintainer: Olivier Lepais <olepais@st-pee.inra.fr>
Diff between SimRAD versions 0.95 dated 2014-11-24 and 0.96 dated 2016-01-06
DESCRIPTION | 18 +++++++++--------- MD5 | 18 +++++++++--------- NAMESPACE | 4 +++- man/SimRAD-package.Rd | 6 +++--- man/adapt.select.Rd | 2 +- man/exclude.seqsite.Rd | 2 +- man/insilico.digest.Rd | 2 +- man/ref.DNAseq.Rd | 2 +- man/sim.DNAseq.Rd | 2 +- man/size.select.Rd | 2 +- 10 files changed, 30 insertions(+), 28 deletions(-)
Title: Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Models
Description: We provide a graphical user interface for interactive Markov chain
Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a
posterior sample. The interface is powered by RStudio's Shiny web application
framework and works with the output of MCMC programs written in any programming
language (and has extended functionality for Stan models fit using the rstan
package and the No-U-Turn sampler).
Author: Jonah Gabry [aut, cre],
Stan Development Team [ctb],
Michael Andreae [ctb],
Michael Betancourt [ctb],
Bob Carpenter [ctb],
Yuanjun Gao [ctb],
Andrew Gelman [ctb],
Ben Goodrich [ctb],
Daniel Lee [ctb],
Dongying Song [ctb],
Rob Trangucci [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between shinystan versions 2.0.1 dated 2015-09-17 and 2.1.0 dated 2016-01-06
shinystan-2.0.1/shinystan/inst/ShinyStan/server_files/utilities/update_multiparam_selectize.R |only shinystan-2.0.1/shinystan/inst/doc/deploying-shinyStan.Rmd |only shinystan-2.0.1/shinystan/inst/doc/deploying-shinyStan.html |only shinystan-2.0.1/shinystan/inst/doc/using-shinyStan.Rmd |only shinystan-2.0.1/shinystan/inst/doc/using-shinyStan.html |only shinystan-2.0.1/shinystan/vignettes/deploying-shinyStan.Rmd |only shinystan-2.0.1/shinystan/vignettes/using-shinyStan.Rmd |only shinystan-2.1.0/shinystan/DESCRIPTION | 30 +- shinystan-2.1.0/shinystan/MD5 | 132 +++++----- shinystan-2.1.0/shinystan/NAMESPACE | 2 shinystan-2.1.0/shinystan/R/array2shinystan.R | 2 shinystan-2.1.0/shinystan/R/as.shinystan.R | 21 + shinystan-2.1.0/shinystan/R/chains2shinystan.R | 24 - shinystan-2.1.0/shinystan/R/convenience.R | 2 shinystan-2.1.0/shinystan/R/deploy_shinystan.R | 33 +- shinystan-2.1.0/shinystan/R/eight_schools.R | 2 shinystan-2.1.0/shinystan/R/generate_quantity.R | 8 shinystan-2.1.0/shinystan/R/launch_shinystan.R | 3 shinystan-2.1.0/shinystan/R/launch_shinystan_demo.R | 3 shinystan-2.1.0/shinystan/R/mcmc2shinystan.R | 2 shinystan-2.1.0/shinystan/R/misc.R | 2 shinystan-2.1.0/shinystan/R/model_code.R | 4 shinystan-2.1.0/shinystan/R/notes.R | 15 + shinystan-2.1.0/shinystan/R/rename_model.R | 2 shinystan-2.1.0/shinystan/R/retrieve.R | 2 shinystan-2.1.0/shinystan/R/shinystan-class.R | 2 shinystan-2.1.0/shinystan/R/shinystan-package.R | 19 - shinystan-2.1.0/shinystan/R/sso_info.R | 4 shinystan-2.1.0/shinystan/R/stan2shinystan.R | 7 shinystan-2.1.0/shinystan/R/stanreg2shinystan.R | 41 ++- shinystan-2.1.0/shinystan/R/update_sso.R | 15 + shinystan-2.1.0/shinystan/R/zzz.R | 2 shinystan-2.1.0/shinystan/build/vignette.rds |binary shinystan-2.1.0/shinystan/inst/ShinyStan/css/ShinyStan.css | 26 + shinystan-2.1.0/shinystan/inst/ShinyStan/css/ShinyStan_datatables.css | 16 - shinystan-2.1.0/shinystan/inst/ShinyStan/ggplot_fns.rda |binary shinystan-2.1.0/shinystan/inst/ShinyStan/ggplot_fns_old.rda |only shinystan-2.1.0/shinystan/inst/ShinyStan/global.R | 1 shinystan-2.1.0/shinystan/inst/ShinyStan/global_utils.R | 48 ++- shinystan-2.1.0/shinystan/inst/ShinyStan/helper_functions/hmc_diagnostics_helpers.R | 10 shinystan-2.1.0/shinystan/inst/ShinyStan/helper_functions/shinystan_helpers.R | 3 shinystan-2.1.0/shinystan/inst/ShinyStan/helper_functions/summary_stats_helpers.R | 2 shinystan-2.1.0/shinystan/inst/ShinyStan/html/citation.html | 4 shinystan-2.1.0/shinystan/inst/ShinyStan/server.R | 68 ++--- shinystan-2.1.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/ppcheck_helpers.R | 2 shinystan-2.1.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/rstanarm.R |only shinystan-2.1.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/diagnostics.R | 70 ++--- shinystan-2.1.0/shinystan/inst/ShinyStan/server_files/pages/estimate/ui/multiparam_selectize.R | 45 +++ shinystan-2.1.0/shinystan/inst/ShinyStan/server_files/utilities/extract_sso.R | 2 shinystan-2.1.0/shinystan/inst/ShinyStan/server_files/utilities/make_param_list_with_groups_sort.R | 27 -- shinystan-2.1.0/shinystan/inst/ShinyStan/ui.R | 55 ++-- shinystan-2.1.0/shinystan/inst/ShinyStan/ui_files/about.R | 4 shinystan-2.1.0/shinystan/inst/ShinyStan/ui_files/diagnostics_customize.R | 6 shinystan-2.1.0/shinystan/inst/ShinyStan/ui_files/pp_navlist.R | 6 shinystan-2.1.0/shinystan/inst/ShinyStan/ui_files/pp_navlist_rstanarm.R |only shinystan-2.1.0/shinystan/inst/doc/deploy_shinystan.Rmd |only shinystan-2.1.0/shinystan/inst/doc/deploy_shinystan.html |only shinystan-2.1.0/shinystan/inst/doc/shinystan-package.Rmd |only shinystan-2.1.0/shinystan/inst/doc/shinystan-package.html |only shinystan-2.1.0/shinystan/man/as.shinystan.Rd | 17 - shinystan-2.1.0/shinystan/man/deploy_shinystan.Rd | 37 +- shinystan-2.1.0/shinystan/man/eight_schools.Rd | 2 shinystan-2.1.0/shinystan/man/generate_quantity.Rd | 6 shinystan-2.1.0/shinystan/man/launch_shinystan.Rd | 17 - shinystan-2.1.0/shinystan/man/launch_shinystan_demo.Rd | 15 - shinystan-2.1.0/shinystan/man/model_code.Rd | 8 shinystan-2.1.0/shinystan/man/notes.Rd | 9 shinystan-2.1.0/shinystan/man/rename_model.Rd | 3 shinystan-2.1.0/shinystan/man/retrieve.Rd | 11 shinystan-2.1.0/shinystan/man/shinystan-class.Rd | 6 shinystan-2.1.0/shinystan/man/shinystan-package.Rd | 47 +-- shinystan-2.1.0/shinystan/man/sso_info.Rd | 4 shinystan-2.1.0/shinystan/man/update_sso.Rd | 7 shinystan-2.1.0/shinystan/vignettes/deploy_shinystan.Rmd |only shinystan-2.1.0/shinystan/vignettes/shinystan-package.Rmd |only 75 files changed, 562 insertions(+), 401 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny applications without
having to know any JavaScript. Examples include: hiding an element, disabling
an input, resetting an input back to its original value, delaying code execution
by a few seconds, and many more useful functions. 'shinyjs' can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.3.0 dated 2015-12-30 and 0.3.1 dated 2016-01-06
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- inst/doc/overview.html | 6 +++--- inst/srcjs/shinyjs-default-funcs.js | 2 +- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre],
Alexey Stukalov [ctb],
Matt Denwood [ctb]
Maintainer: Martyn Plummer <plummerm@iarc.fr>
Diff between rjags versions 4-4 dated 2015-10-22 and 4-5 dated 2016-01-06
rjags-4-4/rjags/src/jags.cc.orig |only rjags-4-4/rjags/src/parallel.cc.orig |only rjags-4-5/rjags/DESCRIPTION | 8 +- rjags-4-5/rjags/INSTALL | 109 +++++++++++++++++++++-------------- rjags-4-5/rjags/MD5 | 10 +-- rjags-4-5/rjags/configure | 63 ++++++++++++++------ rjags-4-5/rjags/configure.ac | 43 ++++++++----- 7 files changed, 144 insertions(+), 89 deletions(-)
Title: Self Contained Units of Source Code
Description: Provides modules as an organizational unit for source code. Modules
enforce to be more rigorous when defining dependencies and have
a local search path. They can be used as a sub unit within packages
or in scripts.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between modules versions 0.1.0 dated 2015-12-19 and 0.2.0 dated 2016-01-06
DESCRIPTION | 15 - LICENSE | 26 +- MD5 | 37 +- NAMESPACE | 5 NEWS | 26 +- R/getSearchPath.R |only R/modfun.R |only R/module-class.R | 40 +-- R/module-coercion.R | 46 ++- R/module-helper.R | 115 +++++---- R/module.R | 259 +++++++++++--------- inst/doc/modulesInR.R | 47 ++- inst/doc/modulesInR.Rmd | 110 +++++--- inst/doc/modulesInR.html | 95 ++++--- man/modfun.Rd |only man/module.Rd | 38 ++- man/utilityFunctions.Rd |only tests/testthat.R | 8 tests/testthat/test-model-coercion.R | 55 +++- tests/testthat/test-modfun.R |only tests/testthat/test-module.R | 434 +++++++++++++++++++---------------- vignettes/modulesInR.Rmd | 110 +++++--- 22 files changed, 873 insertions(+), 593 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Description: Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals, and generation of similarity matrices.
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKmisc versions 0.99 dated 2015-06-29 and 0.991 dated 2016-01-06
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- NAMESPACE | 3 ++- NEWS | 6 ++++++ R/simCorVars.R |only man/simCorVars.Rd |only 6 files changed, 17 insertions(+), 8 deletions(-)
Title: Implementation of the 'Lights Out' Puzzle Game
Description: Lights Out is a puzzle game consisting of a grid of lights
that are either on or off. Pressing any light will toggle it and its
adjacent lights. The goal of the game is to switch all the lights off. This
package provides an interface to play the game on different board sizes,
both through the command line or with a visual application. Puzzles can
also be solved using the automatic solver included. View a demo
online at http://daattali.com/shiny/lightsout/.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between lightsout versions 0.2 dated 2016-01-04 and 0.2.1 dated 2016-01-06
DESCRIPTION | 7 ++++--- MD5 | 4 ++-- inst/doc/overview.html | 6 +++--- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main
function is ggMarginal(), which can be used to add marginal
histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ggExtra versions 0.3.1 dated 2015-11-07 and 0.3.4 dated 2016-01-06
DESCRIPTION | 8 +++++--- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 2 +- NEWS.md | 12 ++++++++++++ R/ggMarginal.R | 5 +++++ R/runExample.R | 5 +++++ inst/doc/overview.html | 6 +++--- inst/examples/ggMarginal/ui.R | 11 ++++++----- inst/examples/ggMarginal/www/style.css | 6 +++--- man/ggExtra.Rd | 4 ++-- man/ggMarginal.Rd | 9 +++++---- man/plotCount.Rd | 8 ++++---- man/print.ggExtraPlot.Rd | 2 +- man/removeGrid.Rd | 2 +- man/rotateTextX.Rd | 2 +- man/runExample.Rd | 2 +- 16 files changed, 70 insertions(+), 44 deletions(-)
Title: Avoid the Typical Working Directory Pain When Using 'knitr'
Description: An extension of 'knitr' that adds flexibility in several
ways. One common source of frustration with 'knitr' is that it assumes
the directory where the source file lives should be the working directory,
which is often not true. 'ezknitr' addresses this problem by giving you
complete control over where all the inputs and outputs are, and adds several
other convenient features to make rendering markdown/HTML documents easier.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ezknitr versions 0.3.0 dated 2015-12-08 and 0.3.1 dated 2016-01-06
DESCRIPTION | 9 +++++---- MD5 | 11 ++++++----- NEWS.md |only README.md | 35 ++++++++++++++++++++--------------- inst/doc/overview.Rmd | 10 ++++++---- inst/doc/overview.html | 15 ++++++++------- vignettes/overview.Rmd | 10 ++++++---- 7 files changed, 51 insertions(+), 39 deletions(-)
Title: Implementation of the Dynamic TOPMODEL Hydrological Model
Description: A native R implementation and enhancement of the Dynamic TOPMODEL
semi-distributed hydrological model. Includes some pre-processsing and
output routines.
Author: Peter Metcalfe, Keith Beven and Jim Freer
Maintainer: Peter Metcalfe <p.metcalfe@lancaster.ac.uk>
Diff between dynatopmodel versions 1.0 dated 2014-05-13 and 1.1 dated 2016-01-06
dynatopmodel-1.0/dynatopmodel/R/AddParam.R |only dynatopmodel-1.0/dynatopmodel/R/Addupslope.areas.R |only dynatopmodel-1.0/dynatopmodel/R/AdjacencyMatrix.R |only dynatopmodel-1.0/dynatopmodel/R/AggregateLayer.R |only dynatopmodel-1.0/dynatopmodel/R/ArrowsPts.R |only dynatopmodel-1.0/dynatopmodel/R/Bearing.R |only dynatopmodel-1.0/dynatopmodel/R/BufferLines.R |only dynatopmodel-1.0/dynatopmodel/R/BuildReachRaster.R |only dynatopmodel-1.0/dynatopmodel/R/Catchment3dOverview.R |only dynatopmodel-1.0/dynatopmodel/R/CellBoundingPoly.R |only dynatopmodel-1.0/dynatopmodel/R/CellExtent.R |only dynatopmodel-1.0/dynatopmodel/R/CheckAllParams.R |only dynatopmodel-1.0/dynatopmodel/R/CheckClass.R |only dynatopmodel-1.0/dynatopmodel/R/CheckClassAndNotNull.R |only dynatopmodel-1.0/dynatopmodel/R/CheckNotNull.R |only dynatopmodel-1.0/dynatopmodel/R/CheckParams.R |only dynatopmodel-1.0/dynatopmodel/R/CloneLayer.R |only dynatopmodel-1.0/dynatopmodel/R/ConnectLines.R |only dynatopmodel-1.0/dynatopmodel/R/CopyVals.R |only dynatopmodel-1.0/dynatopmodel/R/DEMFromRaster.R |only dynatopmodel-1.0/dynatopmodel/R/DEMToRaster.R |only dynatopmodel-1.0/dynatopmodel/R/DisplayObservedFlows.R |only dynatopmodel-1.0/dynatopmodel/R/DistanceMatrix.R |only dynatopmodel-1.0/dynatopmodel/R/DoUpdateBaseFlows.R |only dynatopmodel-1.0/dynatopmodel/R/DownslopeFlowAllocations.R |only dynatopmodel-1.0/dynatopmodel/R/DrawDirectedLine.R |only dynatopmodel-1.0/dynatopmodel/R/DrawDirectedLineSegments.R |only dynatopmodel-1.0/dynatopmodel/R/DriveName.R |only dynatopmodel-1.0/dynatopmodel/R/DropNormal.R |only dynatopmodel-1.0/dynatopmodel/R/ExpandPoly.R |only dynatopmodel-1.0/dynatopmodel/R/FindNext.R |only dynatopmodel-1.0/dynatopmodel/R/FixNullOrLt.R |only dynatopmodel-1.0/dynatopmodel/R/Get3dTransformedDRN.R |only dynatopmodel-1.0/dynatopmodel/R/GetCRS.R |only dynatopmodel-1.0/dynatopmodel/R/GetCoords.R |only dynatopmodel-1.0/dynatopmodel/R/GetLineID.R |only dynatopmodel-1.0/dynatopmodel/R/GetNextDownslopeCell.R |only dynatopmodel-1.0/dynatopmodel/R/GetSaturated.R |only dynatopmodel-1.0/dynatopmodel/R/GetSpatialOutput.R |only dynatopmodel-1.0/dynatopmodel/R/GetTimeSeriesInputRange.R |only dynatopmodel-1.0/dynatopmodel/R/GetUserResponse.R |only dynatopmodel-1.0/dynatopmodel/R/HighlightCell.R |only dynatopmodel-1.0/dynatopmodel/R/HighlightCell3d.R |only dynatopmodel-1.0/dynatopmodel/R/HighlightCells.R |only dynatopmodel-1.0/dynatopmodel/R/InitialiseChannelFlows.R |only dynatopmodel-1.0/dynatopmodel/R/IntercellDists.R |only dynatopmodel-1.0/dynatopmodel/R/IntersectionAngle.R |only dynatopmodel-1.0/dynatopmodel/R/KMLLineToSpatialPolygonsDataFrame.R |only dynatopmodel-1.0/dynatopmodel/R/Last.R |only dynatopmodel-1.0/dynatopmodel/R/LineCentroid.R |only dynatopmodel-1.0/dynatopmodel/R/LineLengths.R |only dynatopmodel-1.0/dynatopmodel/R/LineToIntersection.R |only dynatopmodel-1.0/dynatopmodel/R/LogEvent.R |only dynatopmodel-1.0/dynatopmodel/R/MapCell.R |only dynatopmodel-1.0/dynatopmodel/R/MapCells.R |only dynatopmodel-1.0/dynatopmodel/R/MatchClass.R |only dynatopmodel-1.0/dynatopmodel/R/MatrixFromRaster.R |only dynatopmodel-1.0/dynatopmodel/R/MatrixToArrayIndex.R |only dynatopmodel-1.0/dynatopmodel/R/MergeLines.R |only dynatopmodel-1.0/dynatopmodel/R/MergeLinesList.R |only dynatopmodel-1.0/dynatopmodel/R/MergePolys.R |only dynatopmodel-1.0/dynatopmodel/R/NearestLineToPoint.R |only dynatopmodel-1.0/dynatopmodel/R/NearestLinesToPoint.R |only dynatopmodel-1.0/dynatopmodel/R/NearestPts.R |only dynatopmodel-1.0/dynatopmodel/R/NearestSegmentToPoint.R |only dynatopmodel-1.0/dynatopmodel/R/NullOrLt.R |only dynatopmodel-1.0/dynatopmodel/R/Plot3dContours.R |only dynatopmodel-1.0/dynatopmodel/R/PlotDemADrn.R |only dynatopmodel-1.0/dynatopmodel/R/PlotGroupings.R |only dynatopmodel-1.0/dynatopmodel/R/PlotPerpsDemObject.R |only dynatopmodel-1.0/dynatopmodel/R/PolygonFromExtent.R |only dynatopmodel-1.0/dynatopmodel/R/ProjectSpatial.R |only dynatopmodel-1.0/dynatopmodel/R/ReadDischargeData.R |only dynatopmodel-1.0/dynatopmodel/R/RecombineShapes.R |only dynatopmodel-1.0/dynatopmodel/R/ResetFluxes.R |only dynatopmodel-1.0/dynatopmodel/R/ResetStorages.R |only dynatopmodel-1.0/dynatopmodel/R/RunSummary.R |only dynatopmodel-1.0/dynatopmodel/R/RunTOPMODEL.R |only dynatopmodel-1.0/dynatopmodel/R/SetFigWindow.R |only dynatopmodel-1.0/dynatopmodel/R/ShowAllocation.R |only dynatopmodel-1.0/dynatopmodel/R/SlopeGDAL.R |only dynatopmodel-1.0/dynatopmodel/R/SnapExtent.R |only dynatopmodel-1.0/dynatopmodel/R/SpatialLinesDataFrameToIgraph.R |only dynatopmodel-1.0/dynatopmodel/R/SpatialSequence.R |only dynatopmodel-1.0/dynatopmodel/R/StoresEmpty.R |only dynatopmodel-1.0/dynatopmodel/R/StoresFull.R |only dynatopmodel-1.0/dynatopmodel/R/UniqueExcludingNAs.R |only dynatopmodel-1.0/dynatopmodel/R/VectProd.R |only dynatopmodel-1.0/dynatopmodel/R/WeightedAverage.R |only dynatopmodel-1.0/dynatopmodel/R/WeightedRandomSelection.R |only dynatopmodel-1.0/dynatopmodel/R/WriteShapefile.R |only dynatopmodel-1.0/dynatopmodel/R/add.disc.R |only dynatopmodel-1.0/dynatopmodel/R/add.layers.R |only dynatopmodel-1.0/dynatopmodel/R/add.legend.R |only dynatopmodel-1.0/dynatopmodel/R/add.nearest.gauge.R |only dynatopmodel-1.0/dynatopmodel/R/aggregate.obs.R |only dynatopmodel-1.0/dynatopmodel/R/aggregate.qobs.R |only dynatopmodel-1.0/dynatopmodel/R/aggregate.xts.R |only dynatopmodel-1.0/dynatopmodel/R/allocate.PE.R |only dynatopmodel-1.0/dynatopmodel/R/allocate.rain.R |only dynatopmodel-1.0/dynatopmodel/R/apply.params.R |only dynatopmodel-1.0/dynatopmodel/R/apply.set.R |only dynatopmodel-1.0/dynatopmodel/R/approx.pe.ts.R |only dynatopmodel-1.0/dynatopmodel/R/area.notNA.R |only dynatopmodel-1.0/dynatopmodel/R/as.SpatialLines.R |only dynatopmodel-1.0/dynatopmodel/R/as.SpatialLines1.R |only dynatopmodel-1.0/dynatopmodel/R/as.SpatialLinesList.R |only dynatopmodel-1.0/dynatopmodel/R/as.SpatialPolygonsDataFrame.R |only dynatopmodel-1.0/dynatopmodel/R/asPOSIXct.R |only dynatopmodel-1.0/dynatopmodel/R/build.calib.set.R |only dynatopmodel-1.0/dynatopmodel/R/build.flow.dist.matrix.R |only dynatopmodel-1.0/dynatopmodel/R/build.hru.spatial.R |only dynatopmodel-1.0/dynatopmodel/R/build.hru.table.R |only dynatopmodel-1.0/dynatopmodel/R/build.reach.raster.R |only dynatopmodel-1.0/dynatopmodel/R/build.reaches.R |only dynatopmodel-1.0/dynatopmodel/R/calc.persp.matrix.R |only dynatopmodel-1.0/dynatopmodel/R/calib.names.R |only dynatopmodel-1.0/dynatopmodel/R/cells.to.poly.R |only dynatopmodel-1.0/dynatopmodel/R/centroid.R |only dynatopmodel-1.0/dynatopmodel/R/check.and.fix.input.R |only dynatopmodel-1.0/dynatopmodel/R/check.cols.R |only dynatopmodel-1.0/dynatopmodel/R/check.obs.R |only dynatopmodel-1.0/dynatopmodel/R/check.time.intervals.R |only dynatopmodel-1.0/dynatopmodel/R/chunk.R |only dynatopmodel-1.0/dynatopmodel/R/clean.disc.R |only dynatopmodel-1.0/dynatopmodel/R/clean.up.dirs.R |only dynatopmodel-1.0/dynatopmodel/R/combine.groupings.R |only dynatopmodel-1.0/dynatopmodel/R/compassRose.R |only dynatopmodel-1.0/dynatopmodel/R/convert.to.specific.discharges.R |only dynatopmodel-1.0/dynatopmodel/R/create.proj.R |only dynatopmodel-1.0/dynatopmodel/R/current.input.R |only dynatopmodel-1.0/dynatopmodel/R/current.storage.R |only dynatopmodel-1.0/dynatopmodel/R/def.chan.par.R |only dynatopmodel-1.0/dynatopmodel/R/def.disp.par.R |only dynatopmodel-1.0/dynatopmodel/R/def.hsu.par.R |only dynatopmodel-1.0/dynatopmodel/R/def.run.par.R |only dynatopmodel-1.0/dynatopmodel/R/delete.NULLs.R |only dynatopmodel-1.0/dynatopmodel/R/dens.R |only dynatopmodel-1.0/dynatopmodel/R/densify.R |only dynatopmodel-1.0/dynatopmodel/R/determine.reaches.R |only dynatopmodel-1.0/dynatopmodel/R/disaggregate.xts.R |only dynatopmodel-1.0/dynatopmodel/R/disc.catch.R |only dynatopmodel-1.0/dynatopmodel/R/disc.dir.name.R |only 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|only dynatopmodel-1.1/dynatopmodel/R/read_obs.r |only dynatopmodel-1.1/dynatopmodel/R/results.r |only dynatopmodel-1.1/dynatopmodel/R/root_zone.R |only dynatopmodel-1.1/dynatopmodel/R/route_ovf.r |only dynatopmodel-1.1/dynatopmodel/R/routing.r |only dynatopmodel-1.1/dynatopmodel/R/unsat_zone.R |only dynatopmodel-1.1/dynatopmodel/R/update_subsurface.r |only dynatopmodel-1.1/dynatopmodel/R/upslope_area.r |only dynatopmodel-1.1/dynatopmodel/R/weighted.average.r |only dynatopmodel-1.1/dynatopmodel/R/xts_util.r |only dynatopmodel-1.1/dynatopmodel/data/brompton.rda |only dynatopmodel-1.1/dynatopmodel/data/datalist |only dynatopmodel-1.1/dynatopmodel/man/NSE.Rd |only dynatopmodel-1.1/dynatopmodel/man/aggregate_obs.Rd |only dynatopmodel-1.1/dynatopmodel/man/approx.pe.ts.Rd | 100 +- dynatopmodel-1.1/dynatopmodel/man/brompton.Rd |only dynatopmodel-1.1/dynatopmodel/man/build_chans.Rd |only dynatopmodel-1.1/dynatopmodel/man/build_layers.Rd |only dynatopmodel-1.1/dynatopmodel/man/build_routing_table.Rd |only dynatopmodel-1.1/dynatopmodel/man/discretise.Rd |only dynatopmodel-1.1/dynatopmodel/man/disp.par.Rd |only dynatopmodel-1.1/dynatopmodel/man/disp_output.Rd |only dynatopmodel-1.1/dynatopmodel/man/dynatopmodel.Rd |only dynatopmodel-1.1/dynatopmodel/man/run.dtm.Rd | 231 +++--- dynatopmodel-1.1/dynatopmodel/man/time_at_peak.Rd |only dynatopmodel-1.1/dynatopmodel/man/time_to_peak.Rd |only dynatopmodel-1.1/dynatopmodel/man/upslope.area.Rd | 63 - 339 files changed, 337 insertions(+), 600 deletions(-)
Title: Cluster Ensembles
Description: CLUster Ensembles.
Author: Kurt Hornik [aut, cre],
Walter Böhm [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between clue versions 0.3-50 dated 2015-06-14 and 0.3-51 dated 2016-01-06
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- build/vignette.rds |binary data/CKME.rda |binary data/Cassini.rda |binary data/GVME.rda |binary data/GVME_Consensus.rda |binary data/Kinship82.rda |binary data/Kinship82_Consensus.rda |binary data/Phonemes.rda |binary inst/CITATION | 42 +++++++++++++----------------------------- inst/doc/clue.pdf |binary 12 files changed, 27 insertions(+), 43 deletions(-)
Title: Basic Non-Compartmental Pharmacokinetics
Description: Estimation of pharmacokinetic parameters using non-compartmental theory.
Author: Thomas Jaki <jaki.thomas@gmail.com> and Martin J. Wolfsegger
<wolfseggerm@gmx.at>
Maintainer: Thomas Jaki <jaki.thomas@gmail.com>
Diff between PK versions 1.3-2 dated 2013-08-09 and 1.3-3 dated 2016-01-06
DESCRIPTION | 13 +++++-------- MD5 | 8 ++++---- NAMESPACE | 12 ++++++++++++ inst/CITATION | 4 ++-- inst/NEWS | 5 +++++ 5 files changed, 28 insertions(+), 14 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package provides the Mann-Kendall Trend Test,
seasonal Mann-Kendall Test,
correlated seasonal Mann-Kendall Test,
partial Mann-Kendall Trend test,
(Seasonal) Sen's slope, partial correlation trend test and
change-point test after Pettitt.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 0.0.2 dated 2015-11-12 and 0.1.0 dated 2016-01-06
trend-0.0.2/trend/COPYING |only trend-0.1.0/trend/DESCRIPTION | 8 ++-- trend-0.1.0/trend/MD5 | 47 ++++++++++++++------------- trend-0.1.0/trend/NAMESPACE | 10 +---- trend-0.1.0/trend/R/cs.test.R |only trend-0.1.0/trend/R/csmk.test.R | 19 ++++++++++ trend-0.1.0/trend/R/mk.test.R | 18 ++++++++++ trend-0.1.0/trend/R/multivar.MK.test.R | 17 +++++++++ trend-0.1.0/trend/R/partial.cor.trend.test.R | 17 +++++++++ trend-0.1.0/trend/R/pettitt.test.R | 18 ++++++++++ trend-0.1.0/trend/R/print.trend.test.R | 17 +++++++++ trend-0.1.0/trend/R/sea.sens.slope.R | 17 +++++++++ trend-0.1.0/trend/R/sens.slope.R | 20 ++++++++++- trend-0.1.0/trend/R/smk.test.R | 19 ++++++++++ trend-0.1.0/trend/R/summary.trend.test.R | 17 +++++++++ trend-0.1.0/trend/R/wm.test.R |only trend-0.1.0/trend/build/vignette.rds |binary trend-0.1.0/trend/inst/NEWS.Rd | 17 +++++++++ trend-0.1.0/trend/inst/doc/trend.R | 18 +++++----- trend-0.1.0/trend/inst/doc/trend.Rnw | 2 + trend-0.1.0/trend/inst/doc/trend.pdf |binary trend-0.1.0/trend/man/cs.test.Rd |only trend-0.1.0/trend/man/pettitt.test.Rd | 1 trend-0.1.0/trend/man/trend-package.Rd | 37 +++++++++++++-------- trend-0.1.0/trend/man/wm.test.Rd |only trend-0.1.0/trend/src/pettitt.f90 | 2 - trend-0.1.0/trend/vignettes/trend.Rnw | 2 + 27 files changed, 263 insertions(+), 60 deletions(-)
Title: An Information About Deputies and Votings in Polish Diet from
Seventh to Eighth Term of Office
Description: Set of functions that access information about deputies and votings
in Polish diet from webpage <http://www.sejm.gov.pl/>. The package was developed
as a result of an internship in MI2 Group - <http://mi2.mini.pw.edu.pl/>,
Faculty of Mathematics and Information Science, Warsaw University of Technology.
Author: Piotr Smuda [aut, cre],
Przemyslaw Biecek [aut],
Tomasz Mikolajczyk [ctb]
Maintainer: Piotr Smuda <piotrsmuda@gmail.com>
Diff between sejmRP versions 1.2 dated 2015-10-23 and 1.3 dated 2016-01-06
DESCRIPTION | 20 +- MD5 | 174 +++++++++--------- NAMESPACE | 3 R/create_database.R | 66 +++--- R/deputies_add_new.R | 15 - R/deputies_create_table.R | 17 + R/deputies_get_data.R | 12 - R/deputies_get_ids.R | 14 - R/deputies_update_table.R | 19 + R/get_counter_table.R | 2 R/get_deputies_table.R | 8 R/get_filtered_votes.R | 41 +++- R/get_statements_table.R | 11 - R/get_votes_table.R | 9 R/get_votings_table.R | 11 - R/remove_database.R | 1 R/safe_html.R | 6 R/safe_readHTMLTable.R |only R/statements_create_table.R | 30 ++- R/statements_get_statements_data.R | 10 - R/statements_get_statements_table.R | 2 R/statements_update_table.R | 44 +++- R/votes_create_table.R | 28 +- R/votes_get_clubs_links.R | 6 R/votes_get_results.R | 16 + R/votes_match_deputies_ids.R | 17 + R/votes_update_table.R | 43 ++-- R/votings_create_table.R | 26 +- R/votings_get_meetings_links.R | 16 - R/votings_get_meetings_table.R | 10 - R/votings_get_votings_links.R | 6 R/votings_get_votings_table.R | 2 R/votings_update_table.R | 44 ++-- man/create_database.Rd | 37 ++- man/deputies_add_new.Rd | 10 - man/deputies_create_table.Rd | 8 man/deputies_get_data.Rd | 7 man/deputies_get_ids.Rd | 9 man/deputies_update_table.Rd | 8 man/get_deputies_table.Rd | 7 man/get_filtered_votes.Rd | 19 + man/get_statements_table.Rd | 8 man/get_votes_table.Rd | 7 man/get_votings_table.Rd | 10 - man/remove_database.Rd | 3 man/safe_html.Rd | 5 man/safe_readHTMLTable.Rd |only man/statements_create_table.Rd | 7 man/statements_get_statement.Rd | 5 man/statements_get_statements_data.Rd | 13 - man/statements_get_statements_table.Rd | 7 man/statements_update_table.Rd | 8 man/votes_create_table.Rd | 15 - man/votes_get_clubs_links.Rd | 9 man/votes_get_results.Rd | 6 man/votes_match_deputies_ids.Rd | 17 + man/votes_update_table.Rd | 17 - man/votings_create_table.Rd | 14 - man/votings_get_date.Rd | 5 man/votings_get_meetings_links.Rd | 15 - man/votings_get_meetings_table.Rd | 13 - man/votings_get_votings_links.Rd | 9 man/votings_get_votings_table.Rd | 7 man/votings_update_table.Rd | 13 - tests/testthat/test_!remove_database.R | 2 tests/testthat/test_create_database.R | 2 tests/testthat/test_deputies_create_table.R | 2 tests/testthat/test_deputies_get_data.R | 12 - tests/testthat/test_deputies_get_ids.R | 6 tests/testthat/test_deputies_update_table.R | 2 tests/testthat/test_get_deputies_table.R | 6 tests/testthat/test_get_filtered_table.R | 18 - tests/testthat/test_get_statements_table.R | 6 tests/testthat/test_get_votes_table.R | 6 tests/testthat/test_get_votings_table.R | 6 tests/testthat/test_statements_create_table.R | 2 tests/testthat/test_statements_get_statement.R | 2 tests/testthat/test_statements_get_statements_table.R | 2 tests/testthat/test_statements_update_table.R | 2 tests/testthat/test_votings_create_table.R | 3 tests/testthat/test_votings_get_date.R | 2 tests/testthat/test_votings_get_meetings_links.R | 4 tests/testthat/test_votings_get_meetings_table.R | 2 tests/testthat/test_votings_get_votings_links.R | 4 tests/testthat/test_votings_update_table.R | 3 tests/testthat/test_vottes_create_table.R | 4 tests/testthat/test_vottes_match_deputies_ids.R | 12 - tests/testthat/test_vottes_update_table.R | 4 vignettes/INSTRUCTION.Rmd | 105 ++++++---- 89 files changed, 713 insertions(+), 553 deletions(-)
Title: Tools for Working with Rotation Data
Description: Tools for working with rotational data, including
simulation from the most commonly used distributions on SO(3),
methods for different Bayes, mean and median type estimators for
the central orientation of a sample, confidence/credible
regions for the central orientation based on those estimators and
a novel visualization technique for rotation data. Most recently,
functions to identify potentially discordant (outlying) values
have been added.
Author: Bryan Stanfill <bstanfill2003@gmail.com>, Heike Hofmann
<hofmann@iastate.edu>, Ulrike Genschel <ulrike@iastate.edu>
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>
Diff between rotations versions 1.4 dated 2015-10-14 and 1.5 dated 2016-01-06
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 14 +++++++------- NAMESPACE | 3 ++- R/plot.R | 4 ++-- build/vignette.rds |binary inst/doc/rotations-intro.pdf |binary man/plot.SO3.Rd | 5 ++--- 8 files changed, 18 insertions(+), 18 deletions(-)
Title: A Survey Monkey R Client
Description: Programmatic access to the Survey Monkey API <https://developer.surveymonkey.com/>, which currently provides extensive functionality for monitoring surveys and retrieving survey results and some functionality for creating new surveys and data collectors.
Author: Thomas J. Leeper [aut, cre],
Kevin Little [ctb],
Stephan Renatus [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between Rmonkey versions 0.2.11 dated 2015-03-31 and 0.3.1 dated 2016-01-06
DESCRIPTION | 23 ++++++++---- MD5 | 56 +++++++++++++++---------------- NAMESPACE | 6 ++- NEWS | 22 +++++++++++- R/collectors.r | 7 ++- R/createcollector.r | 7 ++- R/createsurvey.r | 19 ++++++---- R/getresponses.r | 86 +++++++++++++++++++++++++++++++++--------------- R/respondentlist.r | 7 ++- R/responsecounts.r | 7 ++- R/smlogin.r | 2 - R/surveydetails.r | 26 ++++++++++++-- R/surveylist.r | 7 ++- R/templates.r | 7 ++- R/userdetails.r | 7 ++- README.md | 26 ++++++++++---- man/Rmonkey-package.Rd | 4 +- man/collectors.Rd | 4 +- man/createcollector.Rd | 4 +- man/createsurvey.Rd | 13 +++---- man/getresponses.Rd | 18 +++++++--- man/respondentlist.Rd | 4 +- man/responsecounts.Rd | 4 +- man/sm_login.Rd | 4 +- man/sm_response_list.Rd | 7 ++- man/surveydetails.Rd | 27 +++++++++++---- man/surveylist.Rd | 4 +- man/templates.Rd | 4 +- man/userdetails.Rd | 4 +- 29 files changed, 274 insertions(+), 142 deletions(-)
Title: Graphical User Interface for FactoMineR
Description: Rcmdr Plugin for the 'FactoMineR' package.
Author: Francois Husson, Julie Josse, Sebastien Le
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between RcmdrPlugin.FactoMineR versions 1.5-0 dated 2014-08-28 and 1.6-0 dated 2016-01-06
DESCRIPTION | 10 +++++----- MD5 | 4 +++- inst/po/sl |only po/R-sl.po |only 4 files changed, 8 insertions(+), 6 deletions(-)
More information about RcmdrPlugin.FactoMineR at CRAN
Permanent link
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Description: The Kruskal and Wallis one-way analysis of variance by ranks
or van der Waerden's normal score test can be employed,
if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the omnibus test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
(such as Nemenyi's test, Dunn's test, Conover's test,
van der Waerden's test). Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test
or the Quade-test. The consequent post-hoc pairwise
multiple comparison tests according to Nemenyi, Conover and Quade
are also provided in this package. Finally Durbin's test for
a two-way balanced incomplete block design (BIBD) is also given
in this package.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMR versions 4.0 dated 2015-12-07 and 4.1 dated 2016-01-06
DESCRIPTION | 8 ++--- MD5 | 48 ++++++++++++++++---------------- NAMESPACE | 1 R/dunn.test.control.R | 2 - R/durbin.test.R | 2 - R/jonckheere.test.R | 2 - R/posthoc.durbin.test.R | 2 - R/posthoc.friedman.conover.R | 2 - R/posthoc.friedman.nemenyi.test.R | 6 ++-- R/posthoc.kruskal.conover.R | 2 - R/posthoc.kruskal.dunn.test.R | 2 - R/posthoc.kruskal.nemenyi.test.R | 29 +++++++++++-------- R/posthoc.quade.test.R | 2 - R/posthoc.vanWaerden.test.R | 2 - R/print.PMCMR.R | 10 +++--- R/vanWaerden.test.R | 2 - build/vignette.rds |binary inst/NEWS.Rd | 15 ++++++++++ inst/doc/PMCMR.R | 52 +++++++++++++++++------------------ inst/doc/PMCMR.Rnw | 9 +++--- inst/doc/PMCMR.pdf |binary man/PMCMR-package.Rd | 4 +- man/posthoc.friedman.nemenyi.test.Rd | 22 +++++++++++++- man/posthoc.kruskal.nemenyi.test.Rd | 8 ----- vignettes/PMCMR.Rnw | 9 +++--- 25 files changed, 137 insertions(+), 104 deletions(-)
Title: Multivariate Meshes and Histograms in Arbitrary Dimensions
Description: Define, manipulate and plot meshes on simplices, spheres, balls, rectangles and tubes.
Directional and other multivariate histograms are provided.
Author: John P. Nolan
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between mvmesh versions 1.1 dated 2015-08-21 and 1.2 dated 2016-01-06
DESCRIPTION | 12 +- MD5 | 24 +++-- NAMESPACE | 13 +-- R/mvhist.R | 52 ++++++++++-- R/mvmesh-methods.R | 49 +++++++---- R/mvmesh.R | 205 ++++++++++++++++++++++++++++++++++++++++++-------- demo/00Index | 3 demo/mvhist.R | 25 +++++- demo/mvmesh.R | 2 demo/mvmeshmisc.R |only man/mvhist.Rd | 11 ++ man/mvmesh-geom.Rd | 5 + man/mvmesh-package.Rd | 26 +++--- man/mvmeshmisc.Rd |only 14 files changed, 327 insertions(+), 100 deletions(-)
Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The
base classes and methods are inspired by the python code found in
the 'ObsPy' python toolbox <http://github.com/obsypy/obspy>. Additional classes and
methods support data returned by web services provided by the 'IRIS DMC'
<http://service.iris.edu/>.
Author: Jonathan Callahan [aut, cre],
Rob Casey [aut],
Mary Templeton [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between IRISSeismic versions 1.0.5 dated 2015-07-21 and 1.0.7 dated 2016-01-06
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/Class-IrisClient.R | 20 +++++++++++--------- R/Class-Trace.R | 2 +- R/spectralUtils.R | 9 +++++---- build/vignette.rds |binary inst/doc/IRISSeismic-intro.pdf |binary man/IRISSeismic-package.Rd | 5 +++++ man/butterworth.Rd | 4 ++-- 9 files changed, 37 insertions(+), 29 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang, and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-62 dated 2015-11-23 and 6.0-64 dated 2016-01-06
.Rinstignore | 1 DESCRIPTION | 11 +++---- MD5 | 37 ++++++++++++++------------ R/adaptive.R | 2 + R/confusionMatrix.R | 3 +- R/dummyVar.R | 2 - R/modelLookup.R | 40 ++++++++-------------------- R/nearZeroVar.R | 42 +++++++++++++++++------------- R/preProcess.R | 14 +++++++++- R/predict.train.R | 47 ++++++++++++++++------------------ R/train.default.R | 4 ++ build/vignette.rds |binary inst/NEWS.Rd | 19 +++++++++++++ inst/models/models.RData |binary man/nearZeroVar.Rd | 10 ++++--- man/preProcess.Rd | 3 +- man/trainControl.Rd | 6 ++-- tests/testthat/preProcess_methods.R | 32 +++++++++++++++++++++++ tests/testthat/test_Dummies.R |only tests/testthat/test_confusionMatrix.R | 2 - tests/testthat/test_glmnet_varImp.R |only vignettes/algorithm.tex |only 22 files changed, 170 insertions(+), 105 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level aroma.* packages
part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 2.14.0 dated 2015-10-21 and 3.0.0 dated 2016-01-06
DESCRIPTION | 17 - MD5 | 72 ++-- NAMESPACE | 11 NEWS | 13 R/999.DEPRECATED.R | 61 ---- R/AromaMicroarrayDataSet.ATTRS.R | 4 R/AromaMicroarrayTabularBinaryFile.R | 4 R/AromaTabularBinaryFile.R | 4 R/AromaTabularBinarySet.ATTRS.R | 5 R/AromaTransform.R | 9 R/AromaUflFile.R | 3 R/AromaUgpFile.R | 3 R/AromaUnitChromosomeTabularBinaryFile.R | 15 - R/AromaUnitGcContentFile.R | 7 R/CopyNumberChromosomalModel.plotChromosomesLayers.R | 2 R/CopyNumberChromosomalModel.plotFitLayers.R | 2 R/CopyNumberChromosomalModel.plotSampleLayers.R | 2 R/CopyNumberSegmentationModel.R | 283 ++++++++++--------- R/ProbePositionEffects.R | 6 R/SampleAnnotationFile.R | 5 R/TextUnitNamesFile.R | 4 R/findAnnotationData.R | 2 R/mergeBoxplotStats.list.R | 12 man/AromaMicroarrayDataSet.Rd | 2 man/AromaTabularBinarySet.Rd | 2 man/AromaUnitCallSet.Rd | 2 man/AromaUnitFracBCnBinarySet.Rd | 2 man/AromaUnitGenotypeCallSet.Rd | 2 man/AromaUnitPscnBinarySet.Rd | 2 man/AromaUnitSignalBinarySet.Rd | 2 man/AromaUnitTotalCnBinarySet.Rd | 2 man/Non-documented_objects.Rd | 11 man/RawMirroredAlleleBFractions.Rd | 2 man/RawSequenceReads.Rd | 2 man/SegmentedAlleleBFractions.Rd | 2 man/SegmentedCopyNumbers.Rd | 2 man/mergeBoxplotStats.list.Rd | 36 +- 37 files changed, 290 insertions(+), 327 deletions(-)
Title: Integration of Functions Over Simplices
Description: Provides methods to integrate functions over m-dimensional simplices
in n-dimensional Euclidean space. There are exact methods for polynomials and
adaptive methods for integrating an arbitrary function. Dirichlet probabilities
are calculated in certain cases.
Author: John P. Nolan, with parts based on code by Alan Genz
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between SimplicialCubature versions 1.0 dated 2014-09-24 and 1.1 dated 2016-01-05
DESCRIPTION | 19 +++-- MD5 | 22 +++--- NAMESPACE | 5 - R/SimplicialCubature.R | 125 ++++++++++++++++++++++++-------------- R/adsimp.R | 26 +++++-- R/grnmol.R | 2 demo |only man/CanonicalSimplex.Rd | 24 ++++--- man/SimplicialCubature-package.Rd | 23 +++--- man/adaptIntegrateSimplex.Rd | 25 +++++-- man/adsimp.Rd | 13 ++- man/integrateSimplexPolynomial.Rd | 2 12 files changed, 181 insertions(+), 105 deletions(-)
More information about SimplicialCubature at CRAN
Permanent link
Title: Stochastic Gradient Descent for Scalable Estimation
Description: A fast and flexible set of tools for large scale estimation. It
features many stochastic gradient methods, built-in models, visualization
tools, automated hyperparameter tuning, model checking, interval estimation,
and convergence diagnostics.
Author: Dustin Tran [aut, cre],
Panos Toulis [aut],
Tian Lian [ctb],
Ye Kuang [ctb],
Edoardo Airoldi [ctb]
Maintainer: Dustin Tran <dustin@cs.columbia.edu>
Diff between sgd versions 1.0 dated 2015-09-23 and 1.1 dated 2016-01-05
DESCRIPTION | 10 ++++----- MD5 | 22 +++++++++++--------- R/data-winequality.R |only R/plot.sgd.R | 6 ++--- R/sgd.R | 49 ++++++++++++++++++++++++++++++++------------- data |only demo/00Index | 1 demo/bench-logistic-wine.R |only inst/doc/sgd-jss.pdf |binary man/sgd.Rd | 33 ++++++++++++++++++++++-------- man/winequality.Rd |only src/Makevars.win | 2 - src/sgd.cpp | 18 ++++++++-------- src/sgd/base_sgd.h | 3 +- 14 files changed, 94 insertions(+), 50 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided by this package to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Joel de Guzman [cph] (Boost),
Eric Niebler [cph] (Boost),
Thomas Heller [cph] (Boost),
John Fletcher [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.8.2 dated 2015-11-27 and 2.9.0 dated 2016-01-05
DESCRIPTION | 16 MD5 | 49 - NAMESPACE | 2 R/pairs.R | 2 R/stan_csv.R | 6 R/stan_demo.R | 13 R/stan_plot.R | 2 R/stan_plot_options.R | 15 R/stanfit-class.R | 12 R/stanmodel-class.R | 296 +++--- build/vignette.rds |binary inst/NEWS | 10 inst/doc/rstan_vignette.pdf |binary inst/include/rstan/filtered_values.hpp |only inst/include/rstan/rstan_writer.hpp | 19 inst/include/rstan/stan_args.hpp | 60 - inst/include/rstan/stan_fit.hpp | 93 +- inst/include/rstan/sum_values.hpp |only inst/include/rstan/values.hpp |only man/rstan.Rd | 4 man/stan.Rd | 9 man/stan_demo.Rd | 8 man/stan_plot.Rd | 13 man/stanfit-method-plot.Rd | 19 man/stanmodel-class.Rd | 1 man/stanmodel-method-vb.Rd |only src/lang__grammars__indexes_grammar_inst.cpp |only tools/stan-functions.txt | 1236 +++++++++++++-------------- 28 files changed, 997 insertions(+), 888 deletions(-)
Title: Extract the Colors from Images
Description: A pure R implementation of the median cut algorithm.
Extracts the dominant colors from an image, and turns them into
a scale for use in plots or for fun!
Author: Joel Carlson
Maintainer: Joel Carlson <jnkcarlson@gmail.com>
Diff between RImagePalette versions 0.1.0 dated 2015-12-29 and 0.1.1 dated 2016-01-05
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 3 +++ R/quantizeImage.R |only R/scale_image.R | 11 ++++++++++- README.md | 31 +++++++++++++++++++++++++++++-- man/quantize_image.Rd |only 7 files changed, 52 insertions(+), 11 deletions(-)
Title: Profile Output Processing Tools for R
Description: Tools for examining Rprof profile output.
Author: Luke Tierney and Riad Jarjour
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between proftools versions 0.1-0 dated 2013-10-03 and 0.99-0 dated 2016-01-05
DESCRIPTION | 8 - MD5 | 49 +++++- NAMESPACE | 21 ++ R/plot.R |only R/prof.R |only R/proftools.R | 295 +++++++++++++++++++++-------------------- R/treemap.R |only README | 32 ++++ inst/samples/Rprof-dg.out |only inst/samples/Rprof-rec.out |only inst/samples/Rprof-rec0.out |only inst/samples/Rprof-rec1.out |only inst/samples/bootlmEx.R |only inst/samples/dg.R |only inst/samples/loops.R |only inst/samples/rec.R |only inst/samples/rec0.R |only inst/samples/rec1.R |only inst/samples/rw.R |only man/annotateSource.Rd |only man/callTreeGraphs.Rd |only man/filterProfileData.Rd |only man/flatProfile.Rd | 3 man/hotPaths.Rd |only man/plot.proftools_profData.Rd |only man/plotProfileCallGraph.Rd | 12 + man/printProfileCallGraph.Rd | 10 + man/profileCallGraph2Dot.Rd | 16 +- man/profileExpr.Rd |only man/proftools-package.Rd |only man/styles.Rd | 8 - man/summaries.Rd |only man/utils.Rd |only man/writeCallGrindFile.Rd |only vignettes |only 35 files changed, 286 insertions(+), 168 deletions(-)
Title: Mathematical Morphology in Any Number of Dimensions
Description: Provides tools for performing mathematical morphology operations,
such as erosion and dilation, on data of arbitrary dimensionality. Can also
be used for finding connected components, resampling, filtering, smoothing
and other image processing-style operations.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between mmand versions 1.2.0 dated 2015-08-06 and 1.3.0 dated 2016-01-05
mmand-1.2.0/mmand/src/Makevars.win |only mmand-1.3.0/mmand/DESCRIPTION | 18 +- mmand-1.3.0/mmand/MD5 | 107 ++++++++---- mmand-1.3.0/mmand/NAMESPACE | 7 mmand-1.3.0/mmand/NEWS | 17 + mmand-1.3.0/mmand/R/components.R |only mmand-1.3.0/mmand/R/kernels.R | 43 +++- mmand-1.3.0/mmand/R/morph.R | 91 +++++++--- mmand-1.3.0/mmand/README.md | 77 +++++++- mmand-1.3.0/mmand/inst/COPYRIGHTS |only mmand-1.3.0/mmand/man/binarise.Rd | 2 mmand-1.3.0/mmand/man/binary.Rd | 4 mmand-1.3.0/mmand/man/components.Rd |only mmand-1.3.0/mmand/man/display.Rd | 2 mmand-1.3.0/mmand/man/filters.Rd | 18 +- mmand-1.3.0/mmand/man/gameOfLife.Rd | 3 mmand-1.3.0/mmand/man/gaussianSmooth.Rd | 8 mmand-1.3.0/mmand/man/kernels.Rd | 36 ++-- mmand-1.3.0/mmand/man/morph.Rd | 2 mmand-1.3.0/mmand/man/morphology.Rd | 4 mmand-1.3.0/mmand/man/neighbourhood.Rd | 2 mmand-1.3.0/mmand/man/resample.Rd | 2 mmand-1.3.0/mmand/man/sampleKernelFunction.Rd | 3 mmand-1.3.0/mmand/man/symmetric.Rd |only mmand-1.3.0/mmand/man/threshold.Rd | 4 mmand-1.3.0/mmand/src/Array.cpp | 44 +++- mmand-1.3.0/mmand/src/Array.h | 80 +++++++- mmand-1.3.0/mmand/src/Componenter.cpp |only mmand-1.3.0/mmand/src/Componenter.h |only mmand-1.3.0/mmand/src/Kernel.cpp | 10 - mmand-1.3.0/mmand/src/Kernel.h | 14 - mmand-1.3.0/mmand/src/Makevars | 2 mmand-1.3.0/mmand/src/Morpher.cpp | 37 ++-- mmand-1.3.0/mmand/src/Morpher.h | 6 mmand-1.3.0/mmand/src/Resampler.cpp | 8 mmand-1.3.0/mmand/src/Resampler.h | 16 - mmand-1.3.0/mmand/src/lemon |only mmand-1.3.0/mmand/src/main.cpp | 57 +++++- mmand-1.3.0/mmand/tests/testthat/fan_components_box.rds |only mmand-1.3.0/mmand/tests/testthat/fan_components_diamond.rds |only mmand-1.3.0/mmand/tests/testthat/fan_sobel_filtered.rds |only mmand-1.3.0/mmand/tests/testthat/sobel_kernel_2d.rds |only mmand-1.3.0/mmand/tests/testthat/test-05-kernels.R | 4 mmand-1.3.0/mmand/tests/testthat/test-10-morph.R | 8 mmand-1.3.0/mmand/tests/testthat/test-25-components.R |only 45 files changed, 531 insertions(+), 205 deletions(-)
Title: Methods in Structural Reliability
Description: Various reliability analysis methods for: 1) computing
failure probability (probability that the output of a numerical
model exceeds a threshold); 2) computing the size of a sample
to estimate a quantile with a confidence level.
Author: Nicolas BOUSQUET, Gilles DEFAUX, Bertrand IOOSS, Vincent MOUTOUSSAMY,
Clement WALTER
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between mistral versions 1.1-1 dated 2014-11-25 and 2.0.0 dated 2016-01-05
mistral-1.1-1/mistral/R/FindInDatabase.R |only mistral-1.1-1/mistral/R/getSeedBelowThreshold.R |only mistral-2.0.0/mistral/DESCRIPTION | 23 mistral-2.0.0/mistral/MD5 | 82 mistral-2.0.0/mistral/NAMESPACE | 87 mistral-2.0.0/mistral/R/AKMCS.R | 884 ++++----- mistral-2.0.0/mistral/R/FORM.R | 488 ++--- mistral-2.0.0/mistral/R/IRW.R |only mistral-2.0.0/mistral/R/LSVM.R |only mistral-2.0.0/mistral/R/MP.R |only mistral-2.0.0/mistral/R/MRM.R | 1343 ++++++-------- mistral-2.0.0/mistral/R/MetaIS.R | 1246 +++++++----- mistral-2.0.0/mistral/R/MonotonicQuantileEstimation.R |only mistral-2.0.0/mistral/R/MonteCarlo.R | 323 ++- mistral-2.0.0/mistral/R/S2MART.R | 487 +++-- mistral-2.0.0/mistral/R/SMART.R | 950 ++++----- mistral-2.0.0/mistral/R/SVMLinearMonotone.R |only mistral-2.0.0/mistral/R/SubsetSimulation.R | 459 ++-- mistral-2.0.0/mistral/R/UtoX.R | 9 mistral-2.0.0/mistral/R/WilksFormula.R | 165 - mistral-2.0.0/mistral/R/generateWithAR.R | 81 mistral-2.0.0/mistral/R/limitFunction.R | 72 mistral-2.0.0/mistral/R/modelLSVM.R |only mistral-2.0.0/mistral/R/plotLSVM.R |only mistral-2.0.0/mistral/R/runifSphere.R | 31 mistral-2.0.0/mistral/R/testConvexity.R |only mistral-2.0.0/mistral/R/trainModel.R | 220 +- mistral-2.0.0/mistral/R/updateLSVM.R |only mistral-2.0.0/mistral/data |only mistral-2.0.0/mistral/man/AKMCS.Rd | 368 ++- mistral-2.0.0/mistral/man/ComputeDistributionParameter.Rd | 2 mistral-2.0.0/mistral/man/FORM.Rd | 51 mistral-2.0.0/mistral/man/IRW.Rd |only mistral-2.0.0/mistral/man/LSVM.Rd |only mistral-2.0.0/mistral/man/MP.Rd |only mistral-2.0.0/mistral/man/MRM.Rd | 208 +- mistral-2.0.0/mistral/man/MetaIS.Rd | 424 ++-- mistral-2.0.0/mistral/man/Mistral-package.Rd | 11 mistral-2.0.0/mistral/man/MonotonicQuantileEstimation.Rd |only mistral-2.0.0/mistral/man/MonteCarlo.Rd | 214 +- mistral-2.0.0/mistral/man/S2MART.Rd | 283 +- mistral-2.0.0/mistral/man/SMART.Rd | 287 +- mistral-2.0.0/mistral/man/SubsetSimulation.Rd | 245 +- mistral-2.0.0/mistral/man/UtoX.Rd | 14 mistral-2.0.0/mistral/man/kiureghian.Rd |only mistral-2.0.0/mistral/man/modelLSVM.Rd |only mistral-2.0.0/mistral/man/plotLSVM.Rd |only mistral-2.0.0/mistral/man/testConvexity.Rd |only mistral-2.0.0/mistral/man/updateLSVM.Rd |only mistral-2.0.0/mistral/man/waarts.Rd |only mistral-2.0.0/mistral/tests |only 51 files changed, 4791 insertions(+), 4266 deletions(-)
Title: The All-Configurations, Maximum-Interaction F-Test for Hidden
Additivity
Description: Computes the ACMIF test and Bonferroni-adjusted p-value of interaction in two-factor studies. Produces corresponding interaction plot and analysis of variance tables and p-values from several other tests of non-additivity.
Author: Jason A. Osborne, Christopher T. Franck and Bongseog Choi
Maintainer: Jason A. Osborne <jaosborn@ncsu.edu>
Diff between hiddenf versions 1.3 dated 2015-04-09 and 2.0 dated 2016-01-05
hiddenf-1.3/hiddenf/R/Malikfunction.R |only hiddenf-1.3/hiddenf/R/anova.hiddenf.R |only hiddenf-1.3/hiddenf/R/hiddenf.R |only hiddenf-1.3/hiddenf/R/plot.hiddenf.R |only hiddenf-1.3/hiddenf/R/print.hiddenf.R |only hiddenf-1.3/hiddenf/R/summary.hiddenf.R |only hiddenf-1.3/hiddenf/man/Malikfunction.Rd |only hiddenf-1.3/hiddenf/man/anova.hiddenf.Rd |only hiddenf-1.3/hiddenf/man/hiddenf.Rd |only hiddenf-1.3/hiddenf/man/plot.hiddenf.Rd |only hiddenf-1.3/hiddenf/man/print.hiddenf.Rd |only hiddenf-1.3/hiddenf/man/summary.hiddenf.Rd |only hiddenf-2.0/hiddenf/DESCRIPTION | 11 +- hiddenf-2.0/hiddenf/MD5 | 83 +++++++++--------- hiddenf-2.0/hiddenf/NAMESPACE | 14 ++- hiddenf-2.0/hiddenf/R/HiddenF.R |only hiddenf-2.0/hiddenf/R/KKSAPvalue.R | 119 ++++++++++++++------------- hiddenf-2.0/hiddenf/R/MalikPvalue.R | 80 ++++++++---------- hiddenf-2.0/hiddenf/R/MalikTab.R | 34 +++---- hiddenf-2.0/hiddenf/R/MandelPvalue.R | 46 +++++----- hiddenf-2.0/hiddenf/R/TukeyPvalue.R | 27 +++--- hiddenf-2.0/hiddenf/R/additivityPvalues.R | 57 ++++++------ hiddenf-2.0/hiddenf/R/anova.HiddenF.R |only hiddenf-2.0/hiddenf/R/anovaprint.r |only hiddenf-2.0/hiddenf/R/computePSS.R | 8 - hiddenf-2.0/hiddenf/R/makemtx.fcn.R | 10 +- hiddenf-2.0/hiddenf/R/maketall.fcn.R | 40 ++++----- hiddenf-2.0/hiddenf/R/plot.HiddenF.R |only hiddenf-2.0/hiddenf/R/print.HiddenF.R |only hiddenf-2.0/hiddenf/R/rconfig.fcn.R | 94 ++++++++++----------- hiddenf-2.0/hiddenf/R/rkconfig.fcn.R | 114 ++++++++++++------------- hiddenf-2.0/hiddenf/R/summary.HiddenF.R |only hiddenf-2.0/hiddenf/data/Boik.mtx.rda |binary hiddenf-2.0/hiddenf/data/Graybill.mtx.rda |binary hiddenf-2.0/hiddenf/data/cjejuni.mtx.rda |binary hiddenf-2.0/hiddenf/data/cnv1.mtx.rda |binary hiddenf-2.0/hiddenf/data/cnvall.mtx.rda |binary hiddenf-2.0/hiddenf/man/Boik.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/Graybill.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/HiddenF.Rd |only hiddenf-2.0/hiddenf/man/KKSAPvalue.Rd | 8 - hiddenf-2.0/hiddenf/man/MalikPvalue.Rd | 11 +- hiddenf-2.0/hiddenf/man/MalikTab.Rd | 10 -- hiddenf-2.0/hiddenf/man/MandelPvalue.Rd | 6 - hiddenf-2.0/hiddenf/man/TukeyPvalue.Rd | 2 hiddenf-2.0/hiddenf/man/additivityPvalues.Rd | 4 hiddenf-2.0/hiddenf/man/anova.HiddenF.Rd |only hiddenf-2.0/hiddenf/man/cjejuni.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/cnv1.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/cnvall.mtx.Rd | 2 hiddenf-2.0/hiddenf/man/hiddenf-package.Rd | 36 +------- hiddenf-2.0/hiddenf/man/plot.HiddenF.Rd |only hiddenf-2.0/hiddenf/man/print.HiddenF.Rd |only hiddenf-2.0/hiddenf/man/summary.HiddenF.Rd |only 54 files changed, 405 insertions(+), 419 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol
Maintainer: Vincent Plagnol <v.plagnol@ucl.ac.uk>
Diff between ExomeDepth versions 1.1.6 dated 2015-09-04 and 1.1.8 dated 2016-01-05
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 4 ++-- inst/doc/ExomeDepth-vignette.Rnw | 11 +++++++++-- inst/doc/ExomeDepth-vignette.pdf |binary vignettes/.install_extras |only vignettes/ExomeDepth-vignette.Rnw | 11 +++++++++-- 7 files changed, 28 insertions(+), 14 deletions(-)
Title: Detecting of Outliers in Circular Regression
Description: Detecting of outliers in circular-circular regression models, modifying its and estimating of models parameters.
Author: Azade Ghazanfarihesari, Majid Sarmad- Ferdowsi University Of Mashhad
Maintainer: Azade Ghazanfarihesari <azade_ghazanfari@yahoo.com>
Diff between CircOutlier versions 3.1.3 dated 2015-06-09 and 3.1.4 dated 2016-01-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 3 ++- R/Predict.R | 1 - man/CircOutlier-package.Rd | 2 +- man/DMCE.Rd | 2 +- man/MCE.Rd | 2 +- man/mce_1.Rd | 2 +- 8 files changed, 16 insertions(+), 16 deletions(-)
Title: The Chopthin Resampler
Description: Resampling is a standard step in particle filtering and in
sequential Monte Carlo. This package implements the chopthin resampler, which
keeps a bound on the ratio between the largest and the smallest weights after
resampling.
Author: Axel Gandy and F. Din-Houn Lau
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between chopthin versions 0.2 dated 2015-12-07 and 0.2.1 dated 2016-01-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/NEWS.Rd | 6 ++++++ src/chopthin_internal.h | 1 + tests/testthat/test-chopthin_exact.R | 2 +- 5 files changed, 16 insertions(+), 9 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Aimee
Teo Broman
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between broman versions 0.59-5 dated 2015-08-05 and 0.62-1 dated 2016-01-05
broman-0.59-5/broman/R/loadfile.R |only broman-0.59-5/broman/README.md |only broman-0.59-5/broman/man/attachfile.Rd |only broman-0.59-5/broman/man/loadfile.Rd |only broman-0.59-5/broman/tests/testthat/test-attachload.R |only broman-0.62-1/broman/DESCRIPTION | 9 broman-0.62-1/broman/MD5 | 195 +++++++++--------- broman-0.62-1/broman/NAMESPACE | 10 broman-0.62-1/broman/R/add_commas.R | 1 broman-0.62-1/broman/R/arrowlocator.R | 1 broman-0.62-1/broman/R/cf.R | 1 broman-0.62-1/broman/R/compare_rows.R | 1 broman-0.62-1/broman/R/convert2hex.R | 2 broman-0.62-1/broman/R/dotplot.R |only broman-0.62-1/broman/R/exit.R | 1 broman-0.62-1/broman/R/fac2num.R |only broman-0.62-1/broman/R/fisher.R | 2 broman-0.62-1/broman/R/grayplot.R | 22 +- broman-0.62-1/broman/R/help.R | 1 broman-0.62-1/broman/R/histlines.R | 1 broman-0.62-1/broman/R/holmans_triangle.R | 4 broman-0.62-1/broman/R/jiggle.R |only broman-0.62-1/broman/R/kbdate.R | 1 broman-0.62-1/broman/R/manyboxplot.R | 1 broman-0.62-1/broman/R/maxabs.R |only broman-0.62-1/broman/R/mypairs.R | 1 broman-0.62-1/broman/R/myround.R | 1 broman-0.62-1/broman/R/normalize.R | 1 broman-0.62-1/broman/R/objectsizes.R | 1 broman-0.62-1/broman/R/openfile.R | 3 broman-0.62-1/broman/R/pastedot.R | 2 broman-0.62-1/broman/R/permtest.R | 1 broman-0.62-1/broman/R/pushbullet.R | 2 broman-0.62-1/broman/R/qr.R | 1 broman-0.62-1/broman/R/revrainbow.R | 1 broman-0.62-1/broman/R/rmvn.R | 1 broman-0.62-1/broman/R/runningmean.R | 2 broman-0.62-1/broman/R/simp.R | 1 broman-0.62-1/broman/R/strwidth2xlim.R | 1 broman-0.62-1/broman/R/util.R | 1 broman-0.62-1/broman/R/venn_diagram.R | 1 broman-0.62-1/broman/R/winsorize.R | 1 broman-0.62-1/broman/inst/README.md | 1 broman-0.62-1/broman/inst/STATUS.txt | 31 ++ broman-0.62-1/broman/man/add_commas.Rd | 2 broman-0.62-1/broman/man/arrowlocator.Rd | 11 - broman-0.62-1/broman/man/attrnames.Rd | 2 broman-0.62-1/broman/man/brocolors.Rd | 2 broman-0.62-1/broman/man/bromanversion.Rd | 3 broman-0.62-1/broman/man/cf.Rd | 3 broman-0.62-1/broman/man/chisq.Rd | 3 broman-0.62-1/broman/man/colwalpha.Rd | 2 broman-0.62-1/broman/man/compare_rows.Rd | 2 broman-0.62-1/broman/man/convert2hex.Rd | 3 broman-0.62-1/broman/man/done.Rd | 2 broman-0.62-1/broman/man/dotplot.Rd |only broman-0.62-1/broman/man/errors2pushbullet.Rd | 2 broman-0.62-1/broman/man/excel_fig.Rd | 2 broman-0.62-1/broman/man/exit.Rd | 2 broman-0.62-1/broman/man/fac2num.Rd |only broman-0.62-1/broman/man/fisher.Rd | 3 broman-0.62-1/broman/man/grayplot.Rd | 5 broman-0.62-1/broman/man/h.Rd | 3 broman-0.62-1/broman/man/hex2dec.Rd | 3 broman-0.62-1/broman/man/histlines.Rd | 5 broman-0.62-1/broman/man/jiggle.Rd |only broman-0.62-1/broman/man/kbdate.Rd | 3 broman-0.62-1/broman/man/lenuniq.Rd | 2 broman-0.62-1/broman/man/make.Rd | 3 broman-0.62-1/broman/man/manyboxplot.Rd | 5 broman-0.62-1/broman/man/maxabs.Rd |only broman-0.62-1/broman/man/mypairs.Rd | 3 broman-0.62-1/broman/man/myround.Rd | 3 broman-0.62-1/broman/man/normalize.Rd | 3 broman-0.62-1/broman/man/note.Rd | 2 broman-0.62-1/broman/man/objectsizes.Rd | 5 broman-0.62-1/broman/man/openfile.Rd | 3 broman-0.62-1/broman/man/paired.perm.test.Rd | 11 - broman-0.62-1/broman/man/paste..Rd | 3 broman-0.62-1/broman/man/paste00.Rd | 3 broman-0.62-1/broman/man/perm.test.Rd | 13 - broman-0.62-1/broman/man/plot_crayons.Rd | 2 broman-0.62-1/broman/man/pushbullet_devices.Rd | 2 broman-0.62-1/broman/man/qqline2.Rd | 5 broman-0.62-1/broman/man/qr2.Rd | 5 broman-0.62-1/broman/man/quantileSE.Rd | 5 broman-0.62-1/broman/man/revrainbow.Rd | 3 broman-0.62-1/broman/man/rmvn.Rd | 3 broman-0.62-1/broman/man/runningmean.Rd | 5 broman-0.62-1/broman/man/runningratio.Rd | 3 broman-0.62-1/broman/man/simp.Rd | 3 broman-0.62-1/broman/man/stop_sending_errors.Rd | 2 broman-0.62-1/broman/man/strwidth2lines.Rd | 4 broman-0.62-1/broman/man/strwidth2xlim.Rd | 9 broman-0.62-1/broman/man/switchv.Rd | 3 broman-0.62-1/broman/man/theme_karl.Rd | 3 broman-0.62-1/broman/man/triarrow.Rd | 5 broman-0.62-1/broman/man/trilines.Rd | 5 broman-0.62-1/broman/man/triplot.Rd | 3 broman-0.62-1/broman/man/tripoints.Rd | 3 broman-0.62-1/broman/man/venn.Rd | 3 broman-0.62-1/broman/man/winsorize.Rd | 3 broman-0.62-1/broman/man/xlimlabel.Rd | 9 broman-0.62-1/broman/src/count_close.c |only broman-0.62-1/broman/src/count_close.h |only broman-0.62-1/broman/tests/testthat/test-fac2num.R |only broman-0.62-1/broman/tests/testthat/test-maxabs.R |only 107 files changed, 285 insertions(+), 232 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-
of-design-space plots and similar graphics for exploring the properties of
experimental designs. The design region is explored via random sampling, which
allows for more flexibility than traditional variance dispersion graphs. A
formula interface is leveraged to provide access to complex model formulae.
Graphics can be constructed simultaneously for multiple experimental designs
and/or multiple model formulae. Instead of using pointwise optimization to
find the minimum and maximum scaled prediction variance curves, which can be
inaccurate and time consuming, this package uses quantile regression as an
alternative.
Author: Pieter Schoonees [aut, cre, cph], Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between vdg versions 1.1.2 dated 2015-10-26 and 1.1.3 dated 2016-01-05
DESCRIPTION | 27 +++++++++++++++------------ MD5 | 28 ++++++++++++++-------------- NAMESPACE | 2 +- build/vignette.rds |binary inst/CITATION | 2 +- man/GJ54.Rd | 2 +- man/LHS.Rd | 5 +++-- man/meanspv.Rd | 4 ++-- man/plot.spv.Rd | 23 ++++++++++++----------- man/print.spv.Rd | 4 ++-- man/runif_sphere.Rd | 6 ++++-- man/sampler.Rd | 10 +++++----- man/spv.Rd | 9 +++++---- man/stdrange.Rd | 2 +- man/vdg-package.Rd | 24 ++++++++++++------------ 15 files changed, 78 insertions(+), 70 deletions(-)
Title: GAMLSS Data
Description: Data for GAMLSS models.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby <r.rigby@londonmet.ac.uk>
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.data versions 4.3-0 dated 2015-07-16 and 4.3-2 dated 2016-01-05
DESCRIPTION | 8 ++--- MD5 | 74 +++++++++++++++++++++++++----------------------- data/CD4.rda |binary data/LGAclaims.rda |binary data/Mums.rda |binary data/VictimsOfCrime.rda |binary data/acidity.rda |binary data/aep.rda |binary data/aids.rda |binary data/alveolar.rda |binary data/computer.rda |binary data/datalist | 3 + data/db.rda |binary data/dbbmi.rda |binary data/fabric.rda |binary data/film30.rda |binary data/film90.rda |binary data/glass.rda |binary data/glasses.RData |only data/hodges.rda |binary data/hodges1.rda |binary data/lice.rda |binary data/margolin.rda |binary data/meta.rda |only data/mvi.rda |binary data/mviBig.rda |binary data/parzen.rda |binary data/polio.rda |binary data/rent.rda |binary data/rent99.polys.rda |binary data/rent99.rda |binary data/respInf.rda |only data/species.rda |binary data/stylo.rda |binary data/tensile.rda |binary data/tse.rda |binary data/usair.rda |binary data/vas5.rda |binary man/glasses.Rd |only man/meta.Rd |only man/respInf.Rd |only 41 files changed, 47 insertions(+), 38 deletions(-)
Title: Unimodal Additive Hazards Model
Description: Nonparametric estimation of a unimodal or U-shape covariate effect under additive hazards model.
Author: Yunro Chung [cre], Anastasia Ivanova, Michael G. Hudgens and Jason P. Fine
Maintainer: Yunro Chung <yunro@live.unc.edu>
Diff between uniah versions 0.3 dated 2015-12-28 and 0.4 dated 2016-01-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/print.uniah.R | 4 ++-- R/uniah.R | 24 ++++++++++++------------ R/uniah.ti.known.R | 10 +++++----- R/uniah.ti.unknown.R | 9 +++++---- man/uniah-package.Rd | 4 ++-- man/uniah.Rd | 18 +++++++++--------- 8 files changed, 46 insertions(+), 45 deletions(-)
Title: Time Delay Estimation for Stochastic Time Series of
Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between timedelay versions 1.0.0 dated 2015-07-20 and 1.0.1 dated 2016-01-05
timedelay-1.0.0/timedelay/R/logprofilelikelihood.R |only timedelay-1.0.0/timedelay/man/logprofilelikelihood.Rd |only timedelay-1.0.1/timedelay/DESCRIPTION | 11 timedelay-1.0.1/timedelay/MD5 | 18 timedelay-1.0.1/timedelay/NAMESPACE | 6 timedelay-1.0.1/timedelay/R/bayesian.R | 269 ++++++------ timedelay-1.0.1/timedelay/R/entirelogprofilelikelihood.R | 37 + timedelay-1.0.1/timedelay/man/bayesian.Rd | 65 -- timedelay-1.0.1/timedelay/man/entirelogprofilelikelihood.Rd | 22 timedelay-1.0.1/timedelay/man/simple.Rd | 2 timedelay-1.0.1/timedelay/man/timedelay-package.Rd | 98 +--- 11 files changed, 249 insertions(+), 279 deletions(-)
Title: Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis.
Author: Keurcien Luu, Michael G.B. Blum
Maintainer: Keurcien Luu <keurcien.luu@imag.fr>
Diff between pcadapt versions 2.1 dated 2015-12-18 and 2.1.1 dated 2016-01-05
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- inst/doc/pcadapt.Rmd | 30 +++++++----------------------- inst/doc/pcadapt.html | 34 ++++++++++------------------------ man/pcadapt-package.Rd | 4 ++-- vignettes/pcadapt.Rmd | 30 +++++++----------------------- 6 files changed, 36 insertions(+), 82 deletions(-)
Title: Least-Squares Bilinear Clustering for Three-Way Data
Description: Functions for performing least-squares bilinear clustering of
three-way data. The method uses the bilinear decomposition (or biadditive
model) to model two-way matrix slices while clustering over the third way.
Up to four different types of clusters are included, one for each term of the
bilinear decomposition. In this way, matrices are clustered simultaneously on
(a subset of) their overall means, row margins, column margins and row-column
interactions. The orthogonality of the bilinear model results in separability of
the joint clustering problem into four separate ones. Three of these subproblems
are specific k-means problems, while a special algorithm is implemented for the
interactions. Plotting methods are provided, including biplots for the low-rank
approximations of the interactions.
Author: Pieter Schoonees [aut, cre], Patrick Groenen [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between lsbclust versions 1.0.3 dated 2015-08-14 and 1.0.4 dated 2016-01-05
DESCRIPTION | 31 +++++++++-------- MD5 | 76 ++++++++++++++++++++++---------------------- NAMESPACE | 5 +- R/T3Clusf.R |only R/plot.col.kmeans.R | 2 - R/plot.int.lsbclust.R | 7 +--- R/plot.ovl.kmeans.R | 20 +++++++++-- R/plot.row.kmeans.R | 2 - data/dcars.rda |binary data/lov.rda |binary data/supermarkets.rda |binary inst/CITATION | 2 - man/ClustMeans.Rd | 2 - man/KMeansW.Rd | 14 ++++---- man/LossMat.Rd | 2 - man/T3Clusf.Rd |only man/bicomp.Rd | 10 ++--- man/cmat.Rd | 2 - man/dcars.Rd | 12 +++--- man/genproc.Rd | 4 +- man/indarr.Rd | 4 +- man/int.lsbclust.Rd | 10 ++--- man/lov.Rd | 30 ++++++++--------- man/lsbclust-package.Rd | 2 - man/lsbclust.Rd | 16 ++++----- man/lsbclusttoclue.Rd | 2 - man/orc.lsbclust.Rd | 18 +++++----- man/plot.bicomp.Rd | 6 +-- man/plot.col.kmeans.Rd | 2 - man/plot.int.lsbclust.Rd | 40 +++++++++++------------ man/plot.lsbclust.Rd | 4 +- man/plot.ovl.kmeans.Rd | 2 - man/plot.row.kmeans.Rd | 2 - man/plot.step.lsbclust.Rd | 4 +- man/print.lsbclust.Rd | 2 - man/sim.lsbclust.Rd | 2 - man/step.lsbclust.Rd | 32 +++++++++--------- man/summary.int.lsbclust.Rd | 2 - man/summary.lsbclust.Rd | 2 - man/supermarkets.Rd | 6 +-- 40 files changed, 197 insertions(+), 182 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting, displaying and checking GAMLSS Models.
Author: Mikis Stasinopoulos [aut, cre, cph],
Bob Rigby [aut],
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss versions 4.3-6 dated 2015-09-03 and 4.3-7 dated 2016-01-05
gamlss-4.3-6/gamlss/R/histSmo-6-03-12.R |only gamlss-4.3-7/gamlss/DESCRIPTION | 8 +-- gamlss-4.3-7/gamlss/MD5 | 36 +++++++-------- gamlss-4.3-7/gamlss/NAMESPACE | 22 ++++++++- gamlss-4.3-7/gamlss/R/cy.R | 21 ++++++++- gamlss-4.3-7/gamlss/R/gamlss.R | 43 +++++++++--------- gamlss-4.3-7/gamlss/R/histSmo.R |only gamlss-4.3-7/gamlss/R/lo_new.R | 54 +++++++++++++---------- gamlss-4.3-7/gamlss/R/pb_03-02-2014.R | 2 gamlss-4.3-7/gamlss/R/pb_goingtozero.R | 21 ++++++++- gamlss-4.3-7/gamlss/R/pb_new.R | 37 +++++++++++++++- gamlss-4.3-7/gamlss/R/pbm_new.R | 73 +++++++++++++++++++++++++++++++- gamlss-4.3-7/gamlss/R/random.R | 50 ++++++++++++++++++++- gamlss-4.3-7/gamlss/R/re_gamlss_lme.R | 12 +++-- gamlss-4.3-7/gamlss/R/term.plot-new.R | 44 +++++++++++++------ gamlss-4.3-7/gamlss/inst/doc/NEWS.txt | 42 ++++++++++++------ gamlss-4.3-7/gamlss/man/histSmo.Rd | 54 ++++++++++++++++------- gamlss-4.3-7/gamlss/man/lo.Rd | 7 +-- gamlss-4.3-7/gamlss/man/ps.Rd | 8 +++ gamlss-4.3-7/gamlss/man/random.Rd | 2 20 files changed, 400 insertions(+), 136 deletions(-)
Title: Constrained Dual Scaling for Detecting Response Styles
Description: This is an implementation of constrained dual scaling for
detecting response styles in categorical data, including utility functions. The
procedure involves adding additional columns to the data matrix representing the
boundaries between the rating categories. The resulting matrix is then doubled
and analyzed by dual scaling. One-dimensional solutions are sought which provide
optimal scores for the rating categories. These optimal scores are constrained
to follow monotone quadratic splines. Clusters are introduced within which the
response styles can vary. The type of response style present in a cluster can
be diagnosed from the optimal scores for said cluster, and this can be used to
construct an imputed version of the data set which adjusts for response styles.
Author: Pieter Schoonees [aut, cre]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between cds versions 1.0.2 dated 2015-08-15 and 1.0.3 dated 2016-01-05
DESCRIPTION | 30 ++++++++++--------- MD5 | 76 ++++++++++++++++++++++++------------------------- NAMESPACE | 2 - R/G.start.R | 39 ++++++++++++++----------- R/cds.R | 28 ++++++++++++------ inst/CITATION | 2 - man/G.start.Rd | 8 +++-- man/Lfun.G.upd.Rd | 4 +- man/Lfun.Rd | 2 - man/addbounds.Rd | 4 +- man/approxloads.Rd | 2 - man/calc.wt.bubbles.Rd | 4 +- man/cds-package.Rd | 2 - man/cds.Rd | 16 +++++++--- man/cds.sim.Rd | 8 ++--- man/cdstoclue.Rd | 2 - man/clean.scales.Rd | 2 - man/create.ind.Rd | 2 - man/create.rs.Rd | 2 - man/createcdsdata.Rd | 4 +- man/datsim.Rd | 2 - man/gen.cop.Rd | 8 ++--- man/genPCA.Rd | 2 - man/group.ALS.Rd | 2 - man/indmat.Rd | 2 - man/ispline.Rd | 2 - man/orthprocr.Rd | 2 - man/plot.cds.Rd | 2 - man/plot.cdslist.Rd | 2 - man/print.cds.Rd | 2 - man/print.cdsdata.Rd | 2 - man/rcormat.Rd | 2 - man/rcovmat.Rd | 2 - man/sensory.Rd | 5 +-- man/sensory.aux.Rd | 3 + man/simpca.Rd | 2 - man/trQnorm.Rd | 2 - man/trRnorm.Rd | 2 - man/updateG.Rd | 2 - 39 files changed, 161 insertions(+), 126 deletions(-)
Title: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS
Proteomics Data
Description: Determination of absolute protein quantities is necessary for multiple applications, such as mechanistic modeling of biological systems. Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics can measure relative protein abundance on a system-wide scale. To estimate absolute quantitative information using these relative abundance measurements requires additional information such as heavy-labeled references of known concentration. Multiple methods have been using different references and strategies; some are easily available whereas others require more effort on the users end. Hence, we believe the field might benefit from making some of these methods available under an automated framework, which also facilitates validation of the chosen strategy. We have implemented the most commonly used absolute label-free protein abundance estimation methods for LC-MS/MS modes quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, we used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. Our open-source software is written in the statistical programming language R and validated and demonstrated on a synthetic sample.
Author: George Rosenberger, Hannes Roest, Christina Ludwig, Ruedi Aebersold, Lars Malmstroem
Maintainer: George Rosenberger <rosenberger@imsb.biol.ethz.ch>
Diff between aLFQ versions 1.3.2 dated 2014-09-29 and 1.3.3 dated 2016-01-05
aLFQ-1.3.2/aLFQ/data/aa.index.rda |only aLFQ-1.3.2/aLFQ/man/aa.index.Rd |only aLFQ-1.3.3/aLFQ/DESCRIPTION | 18 +-- aLFQ-1.3.3/aLFQ/MD5 | 18 +-- aLFQ-1.3.3/aLFQ/NAMESPACE | 108 +++++++++++----------- aLFQ-1.3.3/aLFQ/R/ALF.R | 2 aLFQ-1.3.3/aLFQ/R/apexFeatures.R | 7 - aLFQ-1.3.3/aLFQ/inst/CITATION | 2 aLFQ-1.3.3/aLFQ/man/ALF.Rd | 2 aLFQ-1.3.3/aLFQ/man/aLFQ.package.Rd | 12 +- aLFQ-1.3.3/aLFQ/tests/Examples/aLFQ-Ex.Rout.save | 109 ----------------------- 11 files changed, 88 insertions(+), 190 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.4.22 dated 2015-10-27 and 1.4.23 dated 2016-01-05
DESCRIPTION | 8 +- MD5 | 10 +- R/invgauss.R | 143 +++++++++++++++++++++++++++++------------- inst/NEWS | 5 + man/invgauss.Rd | 4 - tests/statmod-Tests.Rout.save | 10 +- 6 files changed, 121 insertions(+), 59 deletions(-)
Title: Plant Root System Markup Language (RSML) File Processing
Description: Read and analyse Root System Markup Language (RSML) files, used to
store plant root system architecture data. More information can be found
at the address <http://rootsystemml.github.io/>.
Author: Guillaume Lobet
Maintainer: Guillaume Lobet <guillaume.lobet@ulg.ac.be>
Diff between rsml versions 1.2 dated 2014-11-18 and 1.3 dated 2016-01-05
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/plant_functions.R | 17 ++++++++++++++--- R/root_functions.R | 3 +++ R/rsmlToList.R | 4 ++-- 6 files changed, 31 insertions(+), 15 deletions(-)
Title: SAGA Geoprocessing and Terrain Analysis in R
Description: Provides access to geocomputing and terrain analysis
functions of the geographical information system (GIS) 'SAGA' (System for
Automated Geoscientific Analyses) from within R by running the command
line version of SAGA. This package furthermore provides several R functions
for handling ASCII grids, including a flexible framework for applying local
functions (including predict methods of fitted models) and focal functions to
multiple grids. SAGA GIS is available under GPLv2 / LGPLv2 licence from
http://sourceforge.net/projects/saga-gis/.
Author: Alexander Brenning and Donovan Bangs
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between RSAGA versions 0.94-4 dated 2015-11-05 and 0.94-5 dated 2016-01-05
DESCRIPTION | 10 +-- MD5 | 14 ++-- R/RSAGA-core.R | 4 - R/RSAGA-modules.R | 128 ++++++++++++++++++++++++++++++++++++------ R/RSAGA-package.R | 2 inst/doc/RSAGA-landslides.pdf |binary man/RSAGA-package.Rd | 2 man/rsaga.import.gdal.Rd | 94 +++++++++++++++++++++++++++++- 8 files changed, 219 insertions(+), 35 deletions(-)
Title: PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations
Description: A collection of tools for approximating the 'PDQ' functions
(respectively, the cumulative distribution, density, and quantile) of
probability distributions via classical expansions involving moments and
cumulants.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between PDQutils versions 0.1.2 dated 2015-06-15 and 0.1.3 dated 2016-01-05
DESCRIPTION | 16 +++++++++------- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 10 +++++++++- R/PDQutils.r | 13 ++++++++++++- R/gram_charlier.r | 4 ++-- README.md | 5 ++++- build/vignette.rds |binary inst/doc/PDQutils.R | 2 +- inst/doc/PDQutils.Rnw | 2 +- inst/doc/PDQutils.pdf |binary man/AS269.Rd | 39 ++++++++++++++++++++------------------- man/NEWS.Rd | 17 +++++++++++------ man/PDQutils.Rd | 42 +++++++++++++++++++++--------------------- man/cumulant2moment.Rd | 2 +- man/dapx_edgeworth.Rd | 10 +++++----- man/dapx_gca.Rd | 32 ++++++++++++++++---------------- man/moment2cumulant.Rd | 2 +- man/qapx_cf.Rd | 26 +++++++++++++------------- man/rapx_cf.Rd | 8 ++++---- vignettes/PDQutils.Rnw | 2 +- 20 files changed, 150 insertions(+), 120 deletions(-)
Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 <doi:10.1002/sim.2897> or Baker and Jackson, 2008 <doi:10.1007/s10729-007-9041-8>) or mixtures of normals (Beath, 2014 <doi:10.1002/jrsm.1114>).
Author: Ken Beath [aut, cre], Ben Bolker [aut], R Development Core Team [aut]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between metaplus versions 0.7-5 dated 2015-11-02 and 0.7-6 dated 2016-01-05
DESCRIPTION | 15 MD5 | 24 - NAMESPACE | 4 R/metaplus.R | 5 R/mymle.R | 308 +++++++++---------- R/profilenorm.metaplus.R | 260 +++++++++------- R/profilet.metaplus.R | 743 ++++++++++++++++++++++++++++++++--------------- data/cdp.RData |binary inst/NEWS | 10 man/metaplus-package.Rd | 24 - man/metaplus.Rd | 100 ++++++ man/outlierProbs.Rd | 65 ++-- man/testOutliers.Rd | 2 13 files changed, 979 insertions(+), 581 deletions(-)
Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, randomForest, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between visreg versions 2.2-0 dated 2015-04-22 and 2.2-1 dated 2016-01-05
DESCRIPTION | 8 +++--- MD5 | 25 +++++++++++--------- NAMESPACE | 4 ++- NEWS | 8 ++++++ R/Response.R | 47 ++++++++++---------------------------- R/Terms.R | 6 +--- R/setupF.R | 10 ++++---- R/setupV.R | 7 +++-- R/setupV2.R | 6 ++-- R/visreg2d.R | 1 R/visregPlot.R | 7 +++-- R/visregPred.R |only R/visregResid.R |only inst/tests/nonstandard-packages.R |only tests/visreg-mlm.R | 1 15 files changed, 61 insertions(+), 69 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.filesets versions 2.9.0 dated 2015-10-20 and 2.10.0 dated 2016-01-05
R.filesets-2.10.0/R.filesets/DESCRIPTION | 16 R.filesets-2.10.0/R.filesets/MD5 | 79 +- R.filesets-2.10.0/R.filesets/NAMESPACE | 3 R.filesets-2.10.0/R.filesets/NEWS | 24 R.filesets-2.10.0/R.filesets/R/Arguments.EXTRAS.R | 21 R.filesets-2.10.0/R.filesets/R/ChecksumFile.R | 14 R.filesets-2.10.0/R.filesets/R/GenericDataFile.R | 334 +++------- R.filesets-2.10.0/R.filesets/R/GenericDataFileSet.PARALLEL.R | 18 R.filesets-2.10.0/R.filesets/R/GenericDataFileSet.R | 79 -- R.filesets-2.10.0/R.filesets/R/GenericDataFileSet.getChecksum.R | 2 R.filesets-2.10.0/R.filesets/R/GenericTabularFileSet.R | 5 R.filesets-2.10.0/R.filesets/R/TabularTextFile.R | 2 R.filesets-2.10.0/R.filesets/R/fullname.R | 10 R.filesets-2.10.0/R.filesets/R/utils.R |only R.filesets-2.10.0/R.filesets/man/ChecksumFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/GenericDataFile.Rd | 2 R.filesets-2.10.0/R.filesets/man/GenericDataFileSet.Rd | 1 R.filesets-2.10.0/R.filesets/man/GenericTabularFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/Non-documented_objects.Rd | 3 R.filesets-2.10.0/R.filesets/man/RDataFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/RdsFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/TabularTextFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/anyNA.GenericDataFileSet.Rd | 4 R.filesets-2.10.0/R.filesets/man/compareChecksum.GenericDataFile.Rd | 2 R.filesets-2.10.0/R.filesets/man/extract.GenericDataFileSet.Rd | 2 R.filesets-2.10.0/R.filesets/man/getChecksum.GenericDataFile.Rd | 7 R.filesets-2.10.0/R.filesets/man/hasBeenModified.GenericDataFile.Rd | 6 R.filesets-2.10.0/R.filesets/man/readChecksum.GenericDataFile.Rd | 3 R.filesets-2.10.0/R.filesets/man/validateChecksum.GenericDataFile.Rd | 3 R.filesets-2.10.0/R.filesets/man/writeChecksum.GenericDataFile.Rd | 2 R.filesets-2.10.0/R.filesets/tests/ChecksumFile.R |only R.filesets-2.10.0/R.filesets/tests/GenericDataFile.R | 143 ++++ R.filesets-2.10.0/R.filesets/tests/GenericDataFileSet,dsApply.R | 10 R.filesets-2.10.0/R.filesets/tests/GenericDataFileSet,sortBy.R | 5 R.filesets-2.10.0/R.filesets/tests/GenericDataFileSet.R | 75 ++ R.filesets-2.10.0/R.filesets/tests/RDataFileSet.R |only R.filesets-2.10.0/R.filesets/tests/RdsFileSet.R | 2 R.filesets-2.10.0/R.filesets/tests/TabularTextFile,extend.R | 35 - R.filesets-2.10.0/R.filesets/tests/TabularTextFile.R | 6 R.filesets-2.10.0/R.filesets/tests/TabularTextFileSet.R | 8 R.filesets-2.10.0/R.filesets/tests/fullname.R |only R.filesets-2.10.0/R.filesets/tests/readDataFrame.R | 5 R.filesets-2.9.0/R.filesets/man/seq.GenericDataFileSet.Rd |only 43 files changed, 519 insertions(+), 422 deletions(-)
Title: Tools to Evaluate DNA Profile Evidence
Description: Tools to determine DNA profile Weight of Evidence.
For further information see the likeLTD guide provided,
or Balding, D.J. (2013) <doi: 10.1073/pnas.1219739110>.
Author: David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Maintainer: Christopher Steele <c.steele.11@ucl.ac.uk>
Diff between likeLTD versions 6.0.1 dated 2015-12-18 and 6.0.2 dated 2016-01-05
DESCRIPTION | 10 +-- MD5 | 12 ++-- build/vignette.rds |binary inst/doc/likeLTDguide.pdf |binary inst/doc/usage.pdf |binary src/gammaDist.cpp | 10 +-- src/maximizePeaks.cpp | 117 ++++++++++++++++++++-------------------------- 7 files changed, 67 insertions(+), 82 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits and imputed cross-validation. Includes functions for fitting both the univariate and bivariate NPMLE.
Author: Clifford Anderson-Bergman; the Eigen team for Eigen library included(for C++ matrix operations); uses Marloes Maathuis's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.3.1 dated 2015-12-10 and 1.3.2 dated 2016-01-05
icenReg-1.3.1/icenReg/build |only icenReg-1.3.1/icenReg/data/essIncData.RData |only icenReg-1.3.1/icenReg/data/essIncData_small.RData |only icenReg-1.3.1/icenReg/inst |only icenReg-1.3.1/icenReg/man/ICNPMLE.Rd |only icenReg-1.3.1/icenReg/man/abs_inv.Rd |only icenReg-1.3.1/icenReg/man/essIncData.Rd |only icenReg-1.3.1/icenReg/man/essIncData_small.Rd |only icenReg-1.3.1/icenReg/man/icenReg_cv.Rd |only icenReg-1.3.1/icenReg/man/optCliq.Rd |only icenReg-1.3.1/icenReg/man/simBVCen.Rd |only icenReg-1.3.1/icenReg/vignettes |only icenReg-1.3.2/icenReg/DESCRIPTION | 14 ++-- icenReg-1.3.2/icenReg/MD5 | 63 +++++++------------ icenReg-1.3.2/icenReg/NAMESPACE | 12 +-- icenReg-1.3.2/icenReg/R/Utilities.R | 1 icenReg-1.3.2/icenReg/R/referenceClasses.R | 11 +++ icenReg-1.3.2/icenReg/R/user_functions.R | 35 ++++++---- icenReg-1.3.2/icenReg/data/IR_diabetes.RData |only icenReg-1.3.2/icenReg/man/IR_diabetes.Rd |only icenReg-1.3.2/icenReg/man/diag_baseline.Rd | 17 +---- icenReg-1.3.2/icenReg/man/diag_covar.Rd | 28 +++----- icenReg-1.3.2/icenReg/man/getFitEsts.Rd | 4 - icenReg-1.3.2/icenReg/man/getSCurves.Rd | 57 +++++++++-------- icenReg-1.3.2/icenReg/man/ic_par.Rd | 26 ++++--- icenReg-1.3.2/icenReg/man/ic_sp.Rd | 49 +++++++------- icenReg-1.3.2/icenReg/man/imputeCens.Rd | 10 +-- icenReg-1.3.2/icenReg/man/miceData.Rd | 14 ++-- icenReg-1.3.2/icenReg/man/predict.icenReg_fit.Rd | 7 +- icenReg-1.3.2/icenReg/man/simIC_weib.Rd | 26 ++++--- icenReg-1.3.2/icenReg/man/unpublishedRdFiles |only icenReg-1.3.2/icenReg/src/icenReg_files/ic_par.cpp | 4 - icenReg-1.3.2/icenReg/src/icenReg_files/ic_sp_ch.cpp | 4 - 33 files changed, 193 insertions(+), 189 deletions(-)
Title: Interface to the iDigBio Data API
Description: An interface to iDigBio's search API that allows downloading
specimen records. Searches are returned as a data.frame. Other functions
such as the metadata end points return lists of information. iDigBio is a US
project focused on digitizing and serving museum specimen collections on the
web. See <https://www.idigbio.org> for information on iDigBio.
Author: Francois Michonneau [aut, cph],
Matthew Collins [aut, cre],
Scott Chamberlain [ctb]
Maintainer: Matthew Collins <mcollins@acis.ufl.edu>
Diff between ridigbio versions 0.3.1 dated 2015-08-31 and 0.3.2 dated 2016-01-04
DESCRIPTION | 8 +- LICENSE | 2 MD5 | 20 +++--- R/ridigbio.R | 6 + man/ridigbio.Rd | 8 ++ tests/testthat/test-base.R | 39 +++++++----- tests/testthat/test-idig_count_media.R | 34 +++++++--- tests/testthat/test-idig_count_records.R | 34 ++++++---- tests/testthat/test-idig_meta_fields.R | 80 ++++++++++++++++--------- tests/testthat/test-idig_search_media.R | 69 +++++++++++++--------- tests/testthat/test-idig_search_records.R | 94 +++++++++++++++++------------- 11 files changed, 244 insertions(+), 150 deletions(-)
Title: Functional Programming Tools
Description: Make your pure functions purr with the 'purrr' package. This
package completes R's functional programming tools with missing features
present in other programming languages.
Author: Hadley Wickham [aut, cre],
Lionel Henry [ctb],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between purrr versions 0.1.0 dated 2015-09-28 and 0.2.0 dated 2016-01-04
purrr-0.1.0/purrr/R/RcppExports.R |only purrr-0.1.0/purrr/R/zip.R |only purrr-0.1.0/purrr/man/cross2.Rd |only purrr-0.1.0/purrr/man/map_call.Rd |only purrr-0.1.0/purrr/man/zip_n.Rd |only purrr-0.1.0/purrr/src/RcppExports.cpp |only purrr-0.1.0/purrr/tests/testthat/test-zip.R |only purrr-0.2.0/purrr/DESCRIPTION | 13 purrr-0.2.0/purrr/MD5 | 177 +++++++----- purrr-0.2.0/purrr/NAMESPACE | 59 +++- purrr-0.2.0/purrr/R/along.R |only purrr-0.2.0/purrr/R/arrays.R | 6 purrr-0.2.0/purrr/R/at-depth.R | 7 purrr-0.2.0/purrr/R/coercion.R | 29 + purrr-0.2.0/purrr/R/composition.R | 41 +- purrr-0.2.0/purrr/R/cross.R | 93 +++--- purrr-0.2.0/purrr/R/dmap.R |only purrr-0.2.0/purrr/R/every-some.R | 4 purrr-0.2.0/purrr/R/flatten.R | 75 +++-- purrr-0.2.0/purrr/R/invoke.R | 142 ++++++--- purrr-0.2.0/purrr/R/keep.R | 4 purrr-0.2.0/purrr/R/lmap.R | 24 - purrr-0.2.0/purrr/R/map-vector.R | 36 -- purrr-0.2.0/purrr/R/map.R | 262 ++++++++++++------ purrr-0.2.0/purrr/R/negate.R | 2 purrr-0.2.0/purrr/R/objects.R | 14 purrr-0.2.0/purrr/R/output.R |only purrr-0.2.0/purrr/R/partial.R | 2 purrr-0.2.0/purrr/R/reduce.R | 53 +++ purrr-0.2.0/purrr/R/rerun.R | 12 purrr-0.2.0/purrr/R/rows.R | 196 +++++++++---- purrr-0.2.0/purrr/R/set_names.R |only purrr-0.2.0/purrr/R/split_by.R | 6 purrr-0.2.0/purrr/R/transpose.R |only purrr-0.2.0/purrr/R/utils.R | 108 +++++-- purrr-0.2.0/purrr/README.md | 21 - purrr-0.2.0/purrr/man/accumulate.Rd |only purrr-0.2.0/purrr/man/along.Rd |only purrr-0.2.0/purrr/man/array-coercion.Rd | 8 purrr-0.2.0/purrr/man/as_function.Rd |only purrr-0.2.0/purrr/man/as_vector.Rd | 14 purrr-0.2.0/purrr/man/at_depth.Rd | 25 - purrr-0.2.0/purrr/man/bare-type-predicates.Rd | 6 purrr-0.2.0/purrr/man/by_row.Rd | 83 +++-- purrr-0.2.0/purrr/man/by_slice.Rd | 44 +-- purrr-0.2.0/purrr/man/compose.Rd | 2 purrr-0.2.0/purrr/man/conditional-map.Rd | 37 +- purrr-0.2.0/purrr/man/contains.Rd | 4 purrr-0.2.0/purrr/man/cross_n.Rd |only purrr-0.2.0/purrr/man/detect.Rd | 4 purrr-0.2.0/purrr/man/dmap.Rd |only purrr-0.2.0/purrr/man/every.Rd | 4 purrr-0.2.0/purrr/man/flatmap.Rd | 49 --- purrr-0.2.0/purrr/man/flatten.Rd | 58 ++- purrr-0.2.0/purrr/man/get-attr.Rd |only purrr-0.2.0/purrr/man/head_while.Rd | 4 purrr-0.2.0/purrr/man/invoke.Rd | 92 +++++- purrr-0.2.0/purrr/man/is_empty.Rd | 2 purrr-0.2.0/purrr/man/is_formula.Rd | 2 purrr-0.2.0/purrr/man/keep.Rd | 2 purrr-0.2.0/purrr/man/lift.Rd | 42 +- purrr-0.2.0/purrr/man/lmap.Rd | 22 - purrr-0.2.0/purrr/man/map.Rd | 61 ++-- purrr-0.2.0/purrr/man/map2.Rd | 91 ++++-- purrr-0.2.0/purrr/man/negate.Rd | 4 purrr-0.2.0/purrr/man/null-default.Rd |only purrr-0.2.0/purrr/man/partial.Rd | 2 purrr-0.2.0/purrr/man/pipe.Rd | 2 purrr-0.2.0/purrr/man/prepend.Rd | 2 purrr-0.2.0/purrr/man/rbernoulli.Rd | 2 purrr-0.2.0/purrr/man/rdunif.Rd | 4 purrr-0.2.0/purrr/man/reduce.Rd | 4 purrr-0.2.0/purrr/man/rerun.Rd | 2 purrr-0.2.0/purrr/man/safely.Rd |only purrr-0.2.0/purrr/man/scalar-type-predicates.Rd | 4 purrr-0.2.0/purrr/man/set_names.Rd |only purrr-0.2.0/purrr/man/slice_rows.Rd | 2 purrr-0.2.0/purrr/man/splice.Rd | 2 purrr-0.2.0/purrr/man/split_by.Rd | 23 - purrr-0.2.0/purrr/man/transpose.Rd |only purrr-0.2.0/purrr/man/type-predicates.Rd | 7 purrr-0.2.0/purrr/man/update_list.Rd | 6 purrr-0.2.0/purrr/man/when.Rd | 4 purrr-0.2.0/purrr/src/fast-copy.cpp | 167 +++++------ purrr-0.2.0/purrr/src/fast-copy.h | 8 purrr-0.2.0/purrr/src/flatten.c |only purrr-0.2.0/purrr/src/map.c |only purrr-0.2.0/purrr/src/map.h |only purrr-0.2.0/purrr/src/rows-data.cpp |only purrr-0.2.0/purrr/src/rows-data.h |only purrr-0.2.0/purrr/src/rows-formatter.cpp |only purrr-0.2.0/purrr/src/rows-formatter.h |only purrr-0.2.0/purrr/src/rows.cpp | 276 ++++--------------- purrr-0.2.0/purrr/src/transpose.c |only purrr-0.2.0/purrr/src/utils.cpp | 63 ++++ purrr-0.2.0/purrr/src/utils.h | 15 + purrr-0.2.0/purrr/src/vector.c |only purrr-0.2.0/purrr/src/vector.h |only purrr-0.2.0/purrr/tests/testthat/test-dmap.R |only purrr-0.2.0/purrr/tests/testthat/test-flatten.R |only purrr-0.2.0/purrr/tests/testthat/test-invoke.R |only purrr-0.2.0/purrr/tests/testthat/test-map.R | 55 +-- purrr-0.2.0/purrr/tests/testthat/test-map2.R |only purrr-0.2.0/purrr/tests/testthat/test-map_n.R |only purrr-0.2.0/purrr/tests/testthat/test-output.R |only purrr-0.2.0/purrr/tests/testthat/test-predicates.R |only purrr-0.2.0/purrr/tests/testthat/test-recycle_args.R |only purrr-0.2.0/purrr/tests/testthat/test-rerun.R |only purrr-0.2.0/purrr/tests/testthat/test-rows.R | 241 +++++++++++++++- purrr-0.2.0/purrr/tests/testthat/test-transpose.R |only purrr-0.2.0/purrr/tests/testthat/test-update-list.R |only 111 files changed, 1825 insertions(+), 1112 deletions(-)
Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for
reproducible model validation, calibration and comparison.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <nanx@uchicago.edu>
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between hdnom versions 2.1 dated 2015-10-27 and 3.0 dated 2016-01-04
hdnom-2.1/hdnom/R/hdnom.calibrate.R |only hdnom-2.1/hdnom/R/hdnom.models.R |only hdnom-2.1/hdnom/R/hdnom.nomogram.R |only hdnom-2.1/hdnom/R/hdnom.validate.R |only hdnom-3.0/hdnom/DESCRIPTION | 15 hdnom-3.0/hdnom/MD5 | 147 ++- hdnom-3.0/hdnom/NAMESPACE | 64 + hdnom-3.0/hdnom/NEWS.md | 38 hdnom-3.0/hdnom/R/1.hdnom.models.R |only hdnom-3.0/hdnom/R/10.hdnom.compare.calibrate.R |only hdnom-3.0/hdnom/R/2.hdnom.nomogram.R |only hdnom-3.0/hdnom/R/3.hdnom.validate.R |only hdnom-3.0/hdnom/R/4.hdnom.calibrate.R |only hdnom-3.0/hdnom/R/5.hdnom.external.validate.R |only hdnom-3.0/hdnom/R/6.hdnom.external.calibrate.R |only hdnom-3.0/hdnom/R/7.hdnom.kmplot.R |only hdnom-3.0/hdnom/R/8.hdnom.logrank.R |only hdnom-3.0/hdnom/R/9.hdnom.compare.validate.R |only hdnom-3.0/hdnom/R/hdnom-package.R | 7 hdnom-3.0/hdnom/README.md | 10 hdnom-3.0/hdnom/TODO | 9 hdnom-3.0/hdnom/build/vignette.rds |binary hdnom-3.0/hdnom/inst/doc/hdnom.R | 104 +- hdnom-3.0/hdnom/inst/doc/hdnom.Rmd | 373 ++++++-- hdnom-3.0/hdnom/inst/doc/hdnom.html | 451 ++++++++-- hdnom-3.0/hdnom/man/glmnet.basesurv.Rd | 6 hdnom-3.0/hdnom/man/glmnet.calibrate.internal.pred.Rd | 12 hdnom-3.0/hdnom/man/glmnet.external.calibrate.internal.pred.Rd |only hdnom-3.0/hdnom/man/glmnet.external.validate.internal.Rd |only hdnom-3.0/hdnom/man/glmnet.survcurve.Rd | 6 hdnom-3.0/hdnom/man/glmnet.tune.alpha.Rd | 4 hdnom-3.0/hdnom/man/glmnet.validate.internal.Rd | 8 hdnom-3.0/hdnom/man/hdcox.aenet.Rd | 15 hdnom-3.0/hdnom/man/hdcox.alasso.Rd | 15 hdnom-3.0/hdnom/man/hdcox.enet.Rd | 11 hdnom-3.0/hdnom/man/hdcox.flasso.Rd | 15 hdnom-3.0/hdnom/man/hdcox.lasso.Rd | 11 hdnom-3.0/hdnom/man/hdcox.mcp.Rd | 9 hdnom-3.0/hdnom/man/hdcox.mnet.Rd | 9 hdnom-3.0/hdnom/man/hdcox.scad.Rd | 9 hdnom-3.0/hdnom/man/hdcox.snet.Rd | 9 hdnom-3.0/hdnom/man/hdnom-package.Rd | 9 hdnom-3.0/hdnom/man/hdnom.calibrate.Rd | 45 hdnom-3.0/hdnom/man/hdnom.calibrate.internal.true.Rd | 8 hdnom-3.0/hdnom/man/hdnom.compare.calibrate.Rd |only hdnom-3.0/hdnom/man/hdnom.compare.validate.Rd |only hdnom-3.0/hdnom/man/hdnom.external.calibrate.Rd |only hdnom-3.0/hdnom/man/hdnom.external.calibrate.internal.true.Rd |only hdnom-3.0/hdnom/man/hdnom.external.validate.Rd |only hdnom-3.0/hdnom/man/hdnom.kmplot.Rd |only hdnom-3.0/hdnom/man/hdnom.logrank.Rd |only hdnom-3.0/hdnom/man/hdnom.nomogram.Rd | 11 hdnom-3.0/hdnom/man/hdnom.validate.Rd | 50 - hdnom-3.0/hdnom/man/hdnom.varinfo.Rd |only hdnom-3.0/hdnom/man/kmplot.Rd |only hdnom-3.0/hdnom/man/ncvreg.basesurv.Rd | 6 hdnom-3.0/hdnom/man/ncvreg.calibrate.internal.pred.Rd | 12 hdnom-3.0/hdnom/man/ncvreg.external.calibrate.internal.pred.Rd |only hdnom-3.0/hdnom/man/ncvreg.external.validate.internal.Rd |only hdnom-3.0/hdnom/man/ncvreg.survcurve.Rd | 6 hdnom-3.0/hdnom/man/ncvreg.tune.gamma.Rd | 4 hdnom-3.0/hdnom/man/ncvreg.tune.gamma.alpha.Rd | 4 hdnom-3.0/hdnom/man/ncvreg.validate.internal.Rd | 8 hdnom-3.0/hdnom/man/penalized.basesurv.Rd | 6 hdnom-3.0/hdnom/man/penalized.calibrate.internal.pred.Rd | 10 hdnom-3.0/hdnom/man/penalized.external.calibrate.internal.pred.Rd |only hdnom-3.0/hdnom/man/penalized.external.validate.internal.Rd |only hdnom-3.0/hdnom/man/penalized.survcurve.Rd | 6 hdnom-3.0/hdnom/man/penalized.validate.internal.Rd | 8 hdnom-3.0/hdnom/man/plot.hdnom.calibrate.Rd | 8 hdnom-3.0/hdnom/man/plot.hdnom.compare.calibrate.Rd |only hdnom-3.0/hdnom/man/plot.hdnom.compare.validate.Rd |only hdnom-3.0/hdnom/man/plot.hdnom.external.calibrate.Rd |only hdnom-3.0/hdnom/man/plot.hdnom.external.validate.Rd |only hdnom-3.0/hdnom/man/plot.hdnom.nomogram.Rd | 8 hdnom-3.0/hdnom/man/plot.hdnom.validate.Rd | 21 hdnom-3.0/hdnom/man/predict.hdcox.model.Rd |only hdnom-3.0/hdnom/man/print.hdcox.model.Rd |only hdnom-3.0/hdnom/man/print.hdnom.calibrate.Rd | 8 hdnom-3.0/hdnom/man/print.hdnom.compare.calibrate.Rd |only hdnom-3.0/hdnom/man/print.hdnom.compare.validate.Rd |only hdnom-3.0/hdnom/man/print.hdnom.external.calibrate.Rd |only hdnom-3.0/hdnom/man/print.hdnom.external.validate.Rd |only hdnom-3.0/hdnom/man/print.hdnom.nomogram.Rd | 8 hdnom-3.0/hdnom/man/print.hdnom.validate.Rd | 8 hdnom-3.0/hdnom/man/smart.Rd | 2 hdnom-3.0/hdnom/man/smarto.Rd | 2 hdnom-3.0/hdnom/man/summary.hdnom.calibrate.Rd | 8 hdnom-3.0/hdnom/man/summary.hdnom.compare.calibrate.Rd |only hdnom-3.0/hdnom/man/summary.hdnom.compare.validate.Rd |only hdnom-3.0/hdnom/man/summary.hdnom.external.calibrate.Rd |only hdnom-3.0/hdnom/man/summary.hdnom.external.validate.Rd |only hdnom-3.0/hdnom/man/summary.hdnom.validate.Rd | 8 hdnom-3.0/hdnom/vignettes/aenetfit.rds |binary hdnom-3.0/hdnom/vignettes/hdnom.Rmd | 373 ++++++-- hdnom-3.0/hdnom/vignettes/hdnom.bib | 10 96 files changed, 1431 insertions(+), 583 deletions(-)
Title: Testing Goodness-of-Fit with the Kernel Density Estimator
Description: Tests of goodness-of-fit based on a kernel smoothing of the data.
Author: Jose M. Pavia
Maintainer: Jose M. Pavia <Jose.M.Pavia@uv.es>
Diff between GoFKernel versions 2.0-6 dated 2015-08-04 and 2.1-0 dated 2016-01-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GoFKernel.r | 40 +++++++++++++++++++++++++++++----------- man/density.reflected.Rd | 8 +++++--- 4 files changed, 41 insertions(+), 21 deletions(-)
Title: Compare Groups, Analytically and Graphically
Description: Comprehensive data analysis software, and the name "cg" stands for "compare groups." Its genesis and evolution are driven by common needs to compare administrations, conditions, etc. in medicine research and development. The current version provides comparisons of unpaired samples, i.e. a linear model with one factor of at least two levels. It also provides comparisons of two paired samples. Good data graphs, modern statistical methods, and useful displays of results are emphasized.
Author: Bill Pikounis [aut, cre, cph], John Oleynick [aut], Eva Ye [ctb]
Maintainer: Bill Pikounis <cg@billpikounis.net>
Diff between cg versions 1.0-2 dated 2014-12-31 and 1.0-3 dated 2016-01-04
DESCRIPTION | 18 MD5 | 24 NAMESPACE | 34 R/p00ReadInOneFactorData.R | 5 R/p02DescriptiveOneFactorData.R | 2326 +++++++++++++++++------------------ R/p03FormalOneFactorData.R | 2 R/p05SampleSizeOneFactorData.R | 2 R/utilities.R | 11 R/version.R | 2 inst/NEWS | 5 man/cg-package.Rd | 14 man/prepare.Rd | 16 man/prepareCGPairedDifferenceData.Rd | 7 13 files changed, 1254 insertions(+), 1212 deletions(-)
Title: Estimation of Temporal Ordering of Cancer Abnormalities
Description: This is a package with functions for timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.
Author: Elizabeth Purdom
Maintainer: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Diff between cancerTiming versions 3.0.0 dated 2015-04-13 and 3.1.3 dated 2016-01-04
DESCRIPTION | 10 +++--- MD5 | 12 ++++--- NAMESPACE | 7 +++- R/eventTimingList.R | 74 ++++++++++++++++++++++++++------------------- R/mut2seg.R |only man/eventTimingOverList.Rd | 21 ++++++++++++ man/labelSeg.Rd | 2 - man/mut2Seg.Rd |only 8 files changed, 83 insertions(+), 43 deletions(-)
Title: Coarse Approximation Linear Function
Description: Contains a greedy algorithm for coarse approximation linear function.
Author: Stephanie Lane [aut, cre], Clark Jeffries [aut], Diana Perkins [aut]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between CALF versions 0.1 dated 2015-11-15 and 0.1.1 dated 2016-01-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/CALF.R | 4 ++-- man/CALF-package.Rd | 2 +- man/CaseControl.Rd | 2 +- man/calf.Rd | 2 +- 7 files changed, 16 insertions(+), 16 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.95.1435 dated 2015-12-28 and 0.95.1441 dated 2016-01-04
DESCRIPTION | 10 +++--- MD5 | 24 ++++++++-------- R/device.R | 6 ++-- inst/NEWS | 8 ++++- inst/doc/WebGL.html | 77 +++++++++++++++++++++++++++------------------------- inst/doc/rgl.html | 13 +++++--- src/Device.h | 4 +- src/api.cpp | 4 +- src/api.h | 2 - src/device.cpp | 4 +- src/pixmap.cpp | 9 ++++-- src/rglview.cpp | 58 ++++++++++++++++++++++++++------------- src/rglview.h | 4 +- 13 files changed, 129 insertions(+), 94 deletions(-)
Title: A Very Basic Templating Engine
Description: Replace parameters in strings and/or text files with specified
values.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between infuser versions 0.2.1 dated 2015-09-30 and 0.2.2 dated 2016-01-04
DESCRIPTION | 12 +++++++----- MD5 | 21 +++++++++++---------- NAMESPACE | 2 +- R/core.R | 31 +++++++++++++++++++------------ man/infuse.Rd | 16 ++++++++-------- man/print.infuse.Rd | 2 +- man/print_requested_params.Rd | 2 +- man/read_template.Rd | 2 +- man/trim.Rd | 2 +- man/variables_requested.Rd | 2 +- tests/testthat/test_core_functionality.R | 17 +++++++++++++++++ vignettes |only 12 files changed, 68 insertions(+), 41 deletions(-)
Title: Multiple Hot-Deck Imputation
Description: Performs multiple hot-deck imputation of categorical and continuous variables in a data frame.
Author: Skyler Cranmer, Jeff Gill, Natalie Jackson, Andreas Murr, Dave Armstrong
Maintainer: Dave Armstrong <dave@quantoid.net>
Diff between hot.deck versions 1.0 dated 2014-09-15 and 1.1 dated 2016-01-04
DESCRIPTION | 10 +++--- MD5 | 24 ++++++++-------- NAMESPACE | 1 R/hd2amelia.R |only R/hot.deck.R | 14 ++++----- R/scaleContinuous.R | 55 +++++++++++++++++++++++++------------- build/vignette.rds |binary inst/doc/Using_Hot_Deck_Data.R | 22 +++++++++------ inst/doc/Using_Hot_Deck_Data.Rnw | 15 ++++++---- inst/doc/Using_Hot_Deck_Data.pdf |binary man/hd2amelia.Rd |only man/hot.deck-package.Rd | 8 ++--- man/hot.deck.Rd | 2 - vignettes/Using_Hot_Deck_Data.Rnw | 15 ++++++---- 14 files changed, 102 insertions(+), 64 deletions(-)
Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between dotwhisker versions 0.2.0.2 dated 2015-12-23 and 0.2.0.3 dated 2016-01-04
DESCRIPTION | 6 MD5 | 8 R/dwplot.R | 12 + man/dwplot.Rd | 4 vignettes/kl2007_examples.Rmd | 361 +++++++++++++++++++++++++++++++++++++++++- 5 files changed, 372 insertions(+), 19 deletions(-)
Title: Gradient Boosting
Description: Functional gradient descent algorithm for a variety of convex and nonconvex loss functions, for both classical and robust regression and classification problems. HingeBoost is implemented for binary and multi-class classification, with unequal misclassification costs for binary case. The algorithm can fit linear and nonlinear classifiers.
Author: Zhu Wang [aut, cre],
Torsten Hothorn [ctb]
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between bst versions 0.3-11 dated 2015-12-19 and 0.3-12 dated 2016-01-04
DESCRIPTION | 11 MD5 | 40 + NEWS | 10 R/mbst.R | 2 R/mhingebst.R | 984 ++++++++++++++++++++--------------------- R/rmbst.R | 3 R/simdata.R | 6 build/vignette.rds |binary inst/doc/khan.R | 170 +++++-- inst/doc/khan.Rnw | 138 +++++ inst/doc/khan.pdf |binary inst/doc/mcl.R |only inst/doc/mcl.Rnw |only inst/doc/mcl.pdf |only inst/doc/pros.pdf |binary inst/doc/static_khan.pdf |only inst/doc/static_khan.pdf.asis |only inst/doc/static_mcl.pdf |only inst/doc/static_mcl.pdf.asis |only man/ex1data.Rd | 9 man/mhingebst.Rd | 2 man/rmbst.Rd | 5 vignettes/khan.Rnw | 138 +++++ vignettes/mcl.Rnw |only vignettes/static_khan.pdf.asis |only vignettes/static_mcl.pdf.asis |only 26 files changed, 921 insertions(+), 597 deletions(-)
Title: Basic Unix Process Control
Description: Wrappers for fork()/waitpid() meant to allow R users to quickly
and easily fork child processes and wait for them to finish.
Author: Daniel Robertson
Maintainer: Daniel Robertson <danlrobertson89@gmail.com>
Diff between bfork versions 0.1.1 dated 2016-01-04 and 0.1.2 dated 2016-01-04
bfork-0.1.1/bfork/configure |only bfork-0.1.1/bfork/configure.ac |only bfork-0.1.1/bfork/man/waitall.Rd |only bfork-0.1.1/bfork/src/Makevars.in |only bfork-0.1.1/bfork/src/config.h.in |only bfork-0.1.2/bfork/DESCRIPTION | 10 +++--- bfork-0.1.2/bfork/MD5 | 26 ++++++--------- bfork-0.1.2/bfork/NAMESPACE | 2 - bfork-0.1.2/bfork/R/bfork.R | 4 +- bfork-0.1.2/bfork/README.md | 8 ++-- bfork-0.1.2/bfork/cleanup | 2 - bfork-0.1.2/bfork/man/bfork-package.Rd | 4 +- bfork-0.1.2/bfork/man/fork.Rd | 4 +- bfork-0.1.2/bfork/man/wait.Rd | 45 ++++++++++++++++----------- bfork-0.1.2/bfork/man/waitpid.Rd |only bfork-0.1.2/bfork/src/fork.c | 1 bfork-0.1.2/bfork/tests/testthat/test-fork.R | 2 - 17 files changed, 57 insertions(+), 51 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-03 2.1-3
2012-09-28 2.1-2
2012-08-23 2.1-1
2012-08-15 2.0
2012-06-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-14 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-23 0.7-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-07 0.0.2
2015-07-22 0.0.1
Title: Just Let it Simmer
Description: Discrete-Event Simulation (DES) package for R.
Author: Bart Smeets [aut],
Iñaki Ucar [aut, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between simmer versions 3.1.1 dated 2015-12-16 and 3.1.2 dated 2016-01-04
DESCRIPTION | 6 - LICENSE | 2 MD5 | 73 +++++++++++----------- R/RcppExports.R | 4 + R/plot.R | 47 +++----------- R/simulator.R | 56 +++++++++++------ R/utils.R | 13 +++- R/wrap.R | 7 +- TODO | 4 - build/vignette.rds |binary inst/doc/introduction.R | 4 - inst/doc/introduction.Rmd | 4 - inst/doc/introduction.html | 75 ++++++++++++----------- inst/doc/terminology.html | 4 - inst/doc/trajectories.html | 50 +++++++-------- man/get_mon_arrivals.Rd | 6 + man/get_mon_attributes.Rd | 2 man/get_mon_resources.Rd | 2 src/RcppExports.cpp | 12 +++ src/activity.cpp | 2 src/activity.h | 18 +---- src/entity.cpp | 25 ++++++- src/entity.h | 96 +++++++++++++++++++----------- src/simmer_rcpp.cpp | 52 +++++++++++----- src/simulator.h | 44 ++++++------- src/stats.h | 75 +++++++++-------------- tests/testthat.R | 3 tests/testthat/test-convenience-funcs.R |only tests/testthat/test-plot.R | 4 - tests/testthat/test-simmer-generator.R | 28 -------- tests/testthat/test-simmer-resource.R | 21 +++--- tests/testthat/test-simmer.R | 38 ++++++----- tests/testthat/test-simulation-1.R | 16 +++-- tests/testthat/test-trajectory-rollback.R | 18 +++-- tests/testthat/test-trajectory-timeout.R | 12 +++ tests/testthat/test-trajectory.R | 40 ++++++------ tests/testthat/test-wrap.R | 2 vignettes/introduction.Rmd | 4 - 38 files changed, 466 insertions(+), 403 deletions(-)
Title: Niche Estimation
Diff between EnvNicheR versions 1.0 dated 2013-07-09 and 1.3 dated 2016-01-04
Description: A plot overlying the niche of multiple species is obtained, to determine the niche conditions which favor a higher species richness, to create boxplots with the range of environmental variables of the species, to obtain a list of species in an area of the niche selected by the user and to estimate niche overlap among the species. It uses an output file of the software ModestR, which is available at the web site www.ipez.es/ModestR.
Author: Cástor Guisande González
Maintainer: Cástor Guisande González
EnvNicheR-1.0/EnvNicheR/EnvNicheR-Ex.R |only
EnvNicheR-1.0/EnvNicheR/R/niche.R |only
EnvNicheR-1.0/EnvNicheR/man/niche.Rd |only
EnvNicheR-1.3/EnvNicheR/DESCRIPTION | 19 +++++++--------
EnvNicheR-1.3/EnvNicheR/MD5 | 19 +++++++++------
EnvNicheR-1.3/EnvNicheR/NAMESPACE | 16 +++++++++---
EnvNicheR-1.3/EnvNicheR/R/Niche.R |only
EnvNicheR-1.3/EnvNicheR/R/NicheOverlap.R |only
EnvNicheR-1.3/EnvNicheR/R/OverlapTaxa.R |only
EnvNicheR-1.3/EnvNicheR/data/Carnivores.RData |binary
EnvNicheR-1.3/EnvNicheR/data/Polar.coordinates.RData |only
EnvNicheR-1.3/EnvNicheR/man/Carnivores.Rd | 24 +++++++++----------
EnvNicheR-1.3/EnvNicheR/man/Niche.Rd |only
EnvNicheR-1.3/EnvNicheR/man/NicheOverlap.Rd |only
EnvNicheR-1.3/EnvNicheR/man/OverlapTaxa.Rd |only
EnvNicheR-1.3/EnvNicheR/man/Polar.coordinates.Rd |only
16 files changed, 45 insertions(+), 33 deletions(-)
Title: Automated Runs and Evaluations of Ecological Niche Models
Description: Automatically partitions data into evaluation bins, executes ecological niche models across a range of settings, and calculates a variety of evaluation statistics. Current version only implements ENMs with Maxent (Phillips et al. 2006).
Author: Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A. Boria, Jamie M. Kass, Maria Uriarte and Robert P. Anderson
Maintainer: Robert Muscarella <bob.muscarella@gmail.com>
Diff between ENMeval versions 0.2.0 dated 2015-09-11 and 0.2.1 dated 2016-01-04
DESCRIPTION | 13 ++++++------- MD5 | 8 ++++---- NAMESPACE | 3 ++- NEWS | 4 ++++ R/tuning.R | 6 +++--- 5 files changed, 19 insertions(+), 15 deletions(-)
Title: Statistical Tests for Cryptographic Randomness
Description: Performs cryptographic randomness tests on a sequence of random integers or bits. Included tests are greatest common divisor, birthday spacings, book stack, adaptive chi-square, topological binary, and three random walk tests. Tests except greatest common divisor and birthday spacings are not covered by standard test suites. In addition to the chi-square goodness-of-fit test, results of Anderson-Darling, Kolmogorov-Smirnov, and Jarque-Bera tests are also generated by some of the cryptographic randomness tests.
Author: Haydar Demirhan
Maintainer: Haydar Demirhan <haydarde@hacettepe.edu.tr>
Diff between CryptRndTest versions 1.1.5 dated 2015-09-01 and 1.2.1 dated 2016-01-04
CryptRndTest-1.1.5/CryptRndTest/R/CryptRndTest-internal.R |only CryptRndTest-1.2.1/CryptRndTest/DESCRIPTION | 10 CryptRndTest-1.2.1/CryptRndTest/MD5 | 52 + CryptRndTest-1.2.1/CryptRndTest/NAMESPACE | 46 + CryptRndTest-1.2.1/CryptRndTest/R/GCD.test.R | 145 ---- CryptRndTest-1.2.1/CryptRndTest/R/GCD.test.default.R |only CryptRndTest-1.2.1/CryptRndTest/R/GCD.test.main.R |only CryptRndTest-1.2.1/CryptRndTest/R/Random.walk.G.R | 2 CryptRndTest-1.2.1/CryptRndTest/R/adaptive.chi.square.R | 55 - CryptRndTest-1.2.1/CryptRndTest/R/adaptive.chi.square.default.R |only CryptRndTest-1.2.1/CryptRndTest/R/adaptive.chi.square.main.R |only CryptRndTest-1.2.1/CryptRndTest/R/birthday.spacings.R | 11 CryptRndTest-1.2.1/CryptRndTest/R/birthday.spacings.default.R |only CryptRndTest-1.2.1/CryptRndTest/R/birthday.spacings.main.R |only CryptRndTest-1.2.1/CryptRndTest/R/book.stack.R | 59 - CryptRndTest-1.2.1/CryptRndTest/R/book.stack.default.R |only CryptRndTest-1.2.1/CryptRndTest/R/book.stack.main.R |only CryptRndTest-1.2.1/CryptRndTest/R/check.R |only CryptRndTest-1.2.1/CryptRndTest/R/dogumGunuAraliklari.R | 2 CryptRndTest-1.2.1/CryptRndTest/R/print.CryptRndTest.R |only CryptRndTest-1.2.1/CryptRndTest/R/random.walk.tests.R | 60 -- CryptRndTest-1.2.1/CryptRndTest/R/random.walk.tests.default.R |only CryptRndTest-1.2.1/CryptRndTest/R/random.walk.tests.main.R |only CryptRndTest-1.2.1/CryptRndTest/R/topological.binary.R | 23 CryptRndTest-1.2.1/CryptRndTest/R/topological.binary.default.R |only CryptRndTest-1.2.1/CryptRndTest/R/topological.binary.main.R |only CryptRndTest-1.2.1/CryptRndTest/man/CryptRndTest-internal.Rd | 13 CryptRndTest-1.2.1/CryptRndTest/man/CryptRndTest-package.Rd | 200 +++--- CryptRndTest-1.2.1/CryptRndTest/man/GCD.test.Rd | 235 +++---- CryptRndTest-1.2.1/CryptRndTest/man/adaptive.chi.square.Rd | 154 ++--- CryptRndTest-1.2.1/CryptRndTest/man/birthday.spacings.Rd | 196 +++--- CryptRndTest-1.2.1/CryptRndTest/man/book.stack.Rd | 148 ++-- CryptRndTest-1.2.1/CryptRndTest/man/print.CryptRndTest.Rd |only CryptRndTest-1.2.1/CryptRndTest/man/random.walk.tests.Rd | 300 +++++----- CryptRndTest-1.2.1/CryptRndTest/man/topological.binary.Rd | 128 ++-- 35 files changed, 784 insertions(+), 1055 deletions(-)
Title: Tools for Analysis, Design, and Operation of Water Supply
Storages
Description: Measure single-storage water supply system performance using resilience,
reliability, and vulnerability metrics; assess storage-yield-reliability
relationships; determine no-fail storage with sequent peak analysis; optimize
release decisions for water supply, hydropower, and multi-objective reservoirs
using deterministic and stochastic dynamic programming; evaluate inflow
persistence using the Hurst coefficient.
Author: Sean Turner [aut, cre],
Jia Yi Ng [aut],
Stefano Galelli [aut]
Maintainer: Sean Turner <swd.turner@gmail.com>
Diff between reservoir versions 1.0.0 dated 2015-07-23 and 1.1.0 dated 2016-01-04
reservoir-1.0.0/reservoir/R/dynamic_prog.R |only reservoir-1.0.0/reservoir/R/stoch_dyanamic_prog.R |only reservoir-1.0.0/reservoir/data/example_reservoir_data.RData |only reservoir-1.0.0/reservoir/man/ResX_inflow.ts.Rd |only reservoir-1.1.0/reservoir/DESCRIPTION | 25 +- reservoir-1.1.0/reservoir/MD5 | 57 +++-- reservoir-1.1.0/reservoir/NAMESPACE | 9 reservoir-1.1.0/reservoir/R/Data.R | 14 - reservoir-1.1.0/reservoir/R/dp.R |only reservoir-1.1.0/reservoir/R/dp_hydro.R |only reservoir-1.1.0/reservoir/R/dp_multi.R |only reservoir-1.1.0/reservoir/R/dp_supply.R |only reservoir-1.1.0/reservoir/R/hurst_basic.R | 4 reservoir-1.1.0/reservoir/R/res_rel_vul.R | 122 ++++-------- reservoir-1.1.0/reservoir/R/reservoir.R | 57 +++-- reservoir-1.1.0/reservoir/R/sdp.R |only reservoir-1.1.0/reservoir/R/sdp_hydro.R |only reservoir-1.1.0/reservoir/R/sdp_multi.R |only reservoir-1.1.0/reservoir/R/sdp_supply.R |only reservoir-1.1.0/reservoir/R/sequent_peak_analysis.R | 51 +++-- reservoir-1.1.0/reservoir/R/simres.R |only reservoir-1.1.0/reservoir/R/sry_storage.R | 66 +++--- reservoir-1.1.0/reservoir/R/sry_yield.R | 74 ++++--- reservoir-1.1.0/reservoir/data/resX.RData |only reservoir-1.1.0/reservoir/inst |only reservoir-1.1.0/reservoir/man/Hurst.Rd | 7 reservoir-1.1.0/reservoir/man/Rippl.Rd | 20 - reservoir-1.1.0/reservoir/man/dp.Rd | 10 reservoir-1.1.0/reservoir/man/dp_hydro.Rd |only reservoir-1.1.0/reservoir/man/dp_multi.Rd |only reservoir-1.1.0/reservoir/man/dp_supply.Rd |only reservoir-1.1.0/reservoir/man/resX.Rd |only reservoir-1.1.0/reservoir/man/reservoir.Rd | 65 ++++-- reservoir-1.1.0/reservoir/man/rrv.Rd | 30 +- reservoir-1.1.0/reservoir/man/sdp.Rd | 4 reservoir-1.1.0/reservoir/man/sdp_hydro.Rd |only reservoir-1.1.0/reservoir/man/sdp_multi.Rd |only reservoir-1.1.0/reservoir/man/sdp_supply.Rd |only reservoir-1.1.0/reservoir/man/simRes.Rd |only reservoir-1.1.0/reservoir/man/storage.Rd | 17 - reservoir-1.1.0/reservoir/man/yield.Rd | 25 +- 41 files changed, 360 insertions(+), 297 deletions(-)
Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of
Markov Chain Monte Carlo simulations, as well as for graphically display
results from full MCMC analysis. The package also facilitates the graphical
interpretation of models by providing flexible functions to plot the
results against observed variables.
Author: Xavier Fernández i MarÃn <xavier.fim@gmail.com>
Maintainer: Xavier Fernández i MarÃn <xavier.fim@gmail.com>
Diff between ggmcmc versions 0.7.2 dated 2015-09-03 and 0.7.3 dated 2016-01-04
DESCRIPTION | 10 +++-- MD5 | 74 ++++++++++++++++++++++---------------------- NAMESPACE | 2 - NEWS | 15 ++++++++ R/ggs.R | 1 R/ggs_geweke.R | 2 - R/ggs_pairs.R | 33 ++++++++++--------- man/ac.Rd | 2 - man/calc_bin.Rd | 2 - man/ci.Rd | 2 - man/get_family.Rd | 2 - man/ggmcmc.Rd | 2 - man/ggs.Rd | 2 - man/ggs_Rhat.Rd | 2 - man/ggs_autocorrelation.Rd | 2 - man/ggs_caterpillar.Rd | 2 - man/ggs_chain.Rd | 2 - man/ggs_compare_partial.Rd | 2 - man/ggs_crosscorrelation.Rd | 2 - man/ggs_density.Rd | 2 - man/ggs_geweke.Rd | 4 +- man/ggs_histogram.Rd | 2 - man/ggs_pairs.Rd | 13 ++++--- man/ggs_ppmean.Rd | 2 - man/ggs_ppsd.Rd | 2 - man/ggs_rocplot.Rd | 2 - man/ggs_running.Rd | 2 - man/ggs_separation.Rd | 2 - man/ggs_traceplot.Rd | 2 - man/gl_unq.Rd | 2 - man/radon.Rd | 2 - man/roc_calc.Rd | 2 - man/s.Rd | 2 - man/s.binary.Rd | 2 - man/s.y.rep.Rd | 2 - man/sde0f.Rd | 2 - man/y.Rd | 2 - man/y.binary.Rd | 2 - 38 files changed, 116 insertions(+), 96 deletions(-)
Title: Generate Random Data Sets
Description: Generates random data sets including: data.frames, lists,
and vectors.
Author: Tyler Rinker [aut, cre],
Josh O'Brien [ctb],
Ananda Mahto [ctb],
Matthew Sigal [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between wakefield versions 0.2.0 dated 2015-12-02 and 0.2.1 dated 2016-01-04
DESCRIPTION | 17 - MD5 | 198 +++++++++--------- NAMESPACE | 2 NEWS | 12 + R/year.R | 16 - README.md | 390 ++++++++++++++++--------------------- data/animal_list.rda |binary data/grady_augmented.rda |binary data/languages.rda |binary data/name_neutral.rda |binary data/presidential_debates_2012.rda |binary data/state_populations.rda |binary inst/CITATION | 4 man/age.Rd | 60 ++--- man/animal.Rd | 61 ++--- man/animal_list.Rd | 2 man/answer.Rd | 62 ++--- man/area.Rd | 62 ++--- man/as_integer.Rd | 2 man/car.Rd | 62 ++--- man/children.Rd | 62 ++--- man/coin.Rd | 62 ++--- man/color.Rd | 61 ++--- man/date_stamp.Rd | 62 ++--- man/death.Rd | 61 ++--- man/dice.Rd | 61 ++--- man/dna.Rd | 61 ++--- man/dob.Rd | 60 ++--- man/dummy.Rd | 61 ++--- man/education.Rd | 61 ++--- man/employment.Rd | 61 ++--- man/eye.Rd | 61 ++--- man/grade.Rd | 61 ++--- man/grade_level.Rd | 62 ++--- man/grady_augmented.Rd | 2 man/group.Rd | 62 ++--- man/hair.Rd | 62 ++--- man/height.Rd | 61 ++--- man/hour.Rd | 2 man/id.Rd | 2 man/income.Rd | 62 ++--- man/internet_browser.Rd | 64 ++---- man/interval.Rd | 2 man/iq.Rd | 62 ++--- man/language.Rd | 62 ++--- man/languages.Rd | 2 man/letter.Rd | 59 ++--- man/level.Rd | 60 ++--- man/likert.Rd | 61 ++--- man/lorem_ipsum.Rd | 60 ++--- man/marital.Rd | 62 ++--- man/military.Rd | 62 ++--- man/minute.Rd | 2 man/month.Rd | 62 ++--- man/name.Rd | 62 ++--- man/name_neutral.Rd | 2 man/normal.Rd | 60 ++--- man/peek.Rd | 2 man/plot.tbl_df.Rd | 2 man/political.Rd | 62 ++--- man/presidential_debates_2012.Rd | 2 man/print.available.Rd | 2 man/print.variable.Rd | 2 man/probs.Rd | 2 man/r_data.Rd | 2 man/r_data_frame.Rd | 2 man/r_dummy.Rd | 2 man/r_insert.Rd | 2 man/r_list.Rd | 2 man/r_na.Rd | 2 man/r_sample.Rd | 2 man/r_sample_binary.Rd | 2 man/r_sample_factor.Rd | 2 man/r_sample_integer.Rd | 2 man/r_sample_logical.Rd | 2 man/r_sample_ordered.Rd | 2 man/r_sample_replace.Rd | 2 man/r_series.Rd | 2 man/race.Rd | 62 ++--- man/relate.Rd | 2 man/religion.Rd | 64 ++---- man/sat.Rd | 62 ++--- man/second.Rd | 2 man/sentence.Rd | 62 ++--- man/seriesname.Rd | 2 man/sex.Rd | 60 ++--- man/sex_inclusive.Rd | 60 ++--- man/smokes.Rd | 62 ++--- man/speed.Rd | 61 ++--- man/state.Rd | 62 ++--- man/state_populations.Rd | 2 man/string.Rd | 62 ++--- man/table_heat.Rd | 2 man/time_stamp.Rd | 2 man/valid.Rd | 62 ++--- man/variables.Rd | 2 man/varname.Rd | 2 man/wakefield.Rd | 2 man/year.Rd | 69 ++---- man/zip_code.Rd | 62 ++--- 100 files changed, 1601 insertions(+), 2133 deletions(-)
Title: Historical and Contemporary Boundaries of the United States of
America
Description: The boundaries for geographical units in the United States of
America contained in this package include state, county, congressional
district, and zip code tabulation area. Contemporary boundaries are provided
by the U.S. Census Bureau (public domain). Historical boundaries for the
years from 1629 to 2000 are provided form the Newberry Library's 'Atlas of
Historical County Boundaries' (licensed CC BY-NC-SA). Additional high
resolution data is provided in the 'USAboundariesData' package;
this package provides an interface to access that data.
Author: Lincoln Mullen [aut, cre],
Dr. William M. Scholl Center for American History and Culture, The
Newberry Library [cph],
United States Census Bureau [cph]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between USAboundaries versions 0.1.1 dated 2014-12-24 and 0.2.0 dated 2016-01-04
USAboundaries-0.1.1/USAboundaries/R/datasets.R |only USAboundaries-0.1.1/USAboundaries/R/fortify_boundaries.R |only USAboundaries-0.2.0/USAboundaries/DESCRIPTION | 50 ++- USAboundaries-0.2.0/USAboundaries/MD5 | 60 ++-- USAboundaries-0.2.0/USAboundaries/NAMESPACE | 16 - USAboundaries-0.2.0/USAboundaries/NEWS |only USAboundaries-0.2.0/USAboundaries/R/census-bureau.R |only USAboundaries-0.2.0/USAboundaries/R/filters.R |only USAboundaries-0.2.0/USAboundaries/R/historical-atlas-county-boundaries.R |only USAboundaries-0.2.0/USAboundaries/R/install-data-pkg.R |only USAboundaries-0.2.0/USAboundaries/R/state_codes.R |only USAboundaries-0.2.0/USAboundaries/R/us_boundaries.R | 87 +++--- USAboundaries-0.2.0/USAboundaries/R/us_congressional.R |only USAboundaries-0.2.0/USAboundaries/R/us_counties.R |only USAboundaries-0.2.0/USAboundaries/R/us_states.R |only USAboundaries-0.2.0/USAboundaries/R/usboundaries-package.r | 39 +- USAboundaries-0.2.0/USAboundaries/README.md | 142 +++++++--- USAboundaries-0.2.0/USAboundaries/build/vignette.rds |binary USAboundaries-0.2.0/USAboundaries/data/cb_2014_us_cd114_20m.rda |only USAboundaries-0.2.0/USAboundaries/data/cb_2014_us_county_20m.rda |only USAboundaries-0.2.0/USAboundaries/data/cb_2014_us_state_20m.rda |only USAboundaries-0.2.0/USAboundaries/data/datalist | 4 USAboundaries-0.2.0/USAboundaries/data/hist_us_counties.rda |binary USAboundaries-0.2.0/USAboundaries/data/hist_us_states.rda |binary USAboundaries-0.2.0/USAboundaries/data/state_codes.rda |only USAboundaries-0.2.0/USAboundaries/inst/doc/usboundaries.R | 26 - USAboundaries-0.2.0/USAboundaries/inst/doc/usboundaries.Rmd | 59 ++-- USAboundaries-0.2.0/USAboundaries/inst/doc/usboundaries.html | 112 +++++-- USAboundaries-0.2.0/USAboundaries/man/USAboundaries.Rd | 29 +- USAboundaries-0.2.0/USAboundaries/man/census_boundaries.Rd |only USAboundaries-0.2.0/USAboundaries/man/hist_us_counties.Rd | 14 USAboundaries-0.2.0/USAboundaries/man/hist_us_states.Rd | 14 USAboundaries-0.2.0/USAboundaries/man/install_data_package.Rd |only USAboundaries-0.2.0/USAboundaries/man/state_codes.Rd |only USAboundaries-0.2.0/USAboundaries/man/us_boundaries.Rd | 51 ++- USAboundaries-0.2.0/USAboundaries/man/us_congressional.Rd |only USAboundaries-0.2.0/USAboundaries/man/us_counties.Rd |only USAboundaries-0.2.0/USAboundaries/man/us_states.Rd |only USAboundaries-0.2.0/USAboundaries/tests/testthat/test-us_boundaries.R | 51 +-- USAboundaries-0.2.0/USAboundaries/tests/testthat/test-us_congressional.R |only USAboundaries-0.2.0/USAboundaries/tests/testthat/test-us_counties.R |only USAboundaries-0.2.0/USAboundaries/tests/testthat/test-us_states.R |only USAboundaries-0.2.0/USAboundaries/vignettes/usboundaries.Rmd | 59 ++-- 43 files changed, 493 insertions(+), 320 deletions(-)
Title: N-Gram Based Text Categorization
Description: Text categorization based on n-grams.
Author: Kurt Hornik [aut, cre],
Johannes Rauch [aut],
Christian Buchta [aut],
Ingo Feinerer [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between textcat versions 1.0-3 dated 2015-06-02 and 1.0-4 dated 2016-01-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/textcat.R | 4 ++-- data/ECIMCI_profiles.rda |binary data/TC_byte_profiles.rda |binary data/TC_char_profiles.rda |binary inst/CITATION | 38 ++++++++++++++++---------------------- 7 files changed, 27 insertions(+), 33 deletions(-)
Title: Dynamic Updating Methods for Player Ratings Estimation
Description: Implements schemes for estimating player or
team skill based on dynamic updating. Implemented methods include
Elo, Glicko and Stephenson. Contains pdf documentation of a
reproducible analysis using approximately two million chess
matches.
Author: Alec Stephenson and Jeff Sonas.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between PlayerRatings versions 1.0-0 dated 2012-07-26 and 1.0-1 dated 2016-01-04
DESCRIPTION | 21 - MD5 | 14 NAMESPACE | 2 build |only inst/doc/AFLRatings.R |only inst/doc/AFLRatings.pdf |binary inst/doc/ChessRatings.pdf |binary inst/doc/MathSport.pdf |binary inst/doc/sweave/ChessRatings.Rnw | 732 +++++++++++++++++++-------------------- 9 files changed, 389 insertions(+), 380 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg.
Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 3.0.1 dated 2015-12-04 and 3.0.2 dated 2016-01-04
DESCRIPTION | 8 MD5 | 16 inst/NEWS.Rd | 9 man/map.Rd | 14 src/world.gon | 1399 ++--- src/world.gonstats | 2 src/world.line |12841 +++++++++++++++++++++++++--------------------------- src/world.linestats | 2 src/world.name | 24 9 files changed, 7143 insertions(+), 7172 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function
fitting with an emphasis on splines, spatial data and spatial
statistics. The major methods include cubic, and thin plate splines,
Kriging and compact covariances for large data sets. The splines and
Kriging methods are supporting by functions that can determine the
smoothing parameter (nugget and sill variance) by cross validation
and also by restricted maximum likelihood. For Kriging there is
an easy to function that also estimates the correlation scale (range).
A major feature is that
any covariance function implemented in R and following a simple fields
format can be used for spatial prediction. There are also many useful
functions for plotting and
working with spatial data as images. This package also contains an
implementation of sparse matrix methods for large spatial data sets and
currently requires the sparse matrix (spam) package.
Use help(fields) to get started and for an
overview. The fields source code is deliberately commented and
provides useful explanations of numerical details in addition to the
manual pages. The commented source code can be viewed by expanding the
source code .tar.gz file and looking in R subdirectory.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>
Diff between fields versions 8.3-5 dated 2015-10-15 and 8.3-6 dated 2016-01-04
DESCRIPTION | 6 MD5 | 536 +++++++++++++++++----------------- R/BD.R | 2 R/ChicagoO3.R | 2 R/Exponential.R | 2 R/ExponentialUpper.R | 2 R/Krig.family.R | 4 R/Matern.R | 2 R/RMprecip.R | 2 R/SUBSCRIPTING.spatial.design.R | 2 R/US.R | 2 R/add.image.R | 2 R/arrow.plot.R | 2 R/as.image.R | 2 R/as.surface.R | 2 R/bisection.search.R | 2 R/bplot.family.R | 2 R/cat.matrix.R | 2 R/cat.to.list.R | 2 R/ceiling2.R | 2 R/coef.Krig.R | 2 R/colorbar.plot.R | 2 R/cover.design.R | 2 R/cubic.cov.R | 2 R/describe.R | 2 R/discretize.image.R | 2 R/double.exp.R | 2 R/drape.color.R | 2 R/drape.plot.R | 2 R/dyadic.2check.R | 2 R/dyadic.check.R | 2 R/evlpoly.R | 2 R/evlpoly2.R | 2 R/exp.earth.cov.R | 2 R/exp.image.cov.R | 2 R/exp.simple.cov.R | 2 R/fast.1way.R | 2 R/fastTps.family.R | 2 R/fields.color.picker.R | 2 R/fields.convert.grid.R | 2 R/fields.derivative.poly.R | 2 R/fields.diagonalize.R | 2 R/fields.diagonalize2.R | 2 R/fields.duplicated.matrix.R | 2 R/fields.mkpoly.R | 2 R/fields.rdist.near.R | 2 R/fields.style.R | 2 R/fields.x.to.grid.R | 2 R/find.upcross.R | 2 R/fitted.Krig.R | 2 R/flame.R | 2 R/gauss.cov.R | 2 R/gcv.Krig.R | 2 R/image.family.R | 6 R/image.plot.R | 2 R/image.smooth.R | 2 R/in.poly.R | 2 R/interp.surface.R | 2 R/interp.surface.grid.R | 2 R/mKrig.MLE.R | 2 R/mKrig.R | 2 R/make.surface.grid.R | 2 R/matern.image.cov.R | 2 R/minimax.crit.R | 2 R/minitri.R | 2 R/parse.grid.list.R | 2 R/plot.Krig.R | 2 R/plot.spatial.design.R | 2 R/plot.spatialProcess.R | 2 R/plot.sreg.R | 2 R/plot.surface.R | 2 R/plot.vgram.matrix.R | 2 R/poly.image.R | 2 R/predict.Krig.R | 2 R/predict.interp.surface.R | 2 R/predict.sreg.R | 2 R/predictDerivative.Krig.R | 2 R/predictSE.R | 2 R/predictSEUsingKrigA.R | 2 R/predictSurface.Krig.R | 2 R/predictSurface.family.R | 2 R/predictSurfaceSE.family.R | 4 R/print.Krig.R | 2 R/print.spatial.design.R | 2 R/print.sreg.R | 2 R/print.summary.Krig.R | 2 R/print.summary.spatial.design.R | 2 R/print.summary.spatialProcess.R | 2 R/print.summary.sreg.R | 2 R/printGCVWarnings.R | 2 R/qr.q2ty.R | 2 R/qr.yq2.R | 2 R/qsreg.family.R | 6 R/quickPrint.R | 2 R/quilt.plot.R | 2 R/rad.cov.R | 2 R/rad.image.cov.R | 2 R/rad.simple.cov.R | 2 R/radbas.constant.R | 2 R/rat.diet.R | 2 R/rdist.R | 2 R/rdist.earth.R | 2 R/rdist.earth.vec.R | 2 R/rdist.vec.R | 2 R/residuals.Krig.R | 2 R/ribbon.plot.R | 2 R/set.panel.R | 2 R/setup.image.smooth.R | 2 R/sim.Krig.R | 2 R/sim.Krig.approx.R | 2 R/sim.mKrig.approx.R | 2 R/sim.rf.R | 2 R/smooth.2d.R | 2 R/spam_2lz.R | 2 R/splint.R | 2 R/sreg.family.R | 18 - R/stationary.image.cov.R | 2 R/stationary.taper.cov.R | 2 R/stats.R | 2 R/stats.bin.R | 2 R/summary.Krig.R | 2 R/summary.ncdf.R | 2 R/summary.spatial.design.R | 2 R/summary.spatialProcess.R | 2 R/summary.sreg.R | 2 R/summaryGCV.Krig.R | 2 R/summaryGCV.sreg.R | 2 R/supportsArg.R | 2 R/surface.family.R | 10 R/test.for.zero.R | 24 - R/tim.colors.R | 2 R/transformx.R | 2 R/unrollZGrid.R | 2 R/unscale.R | 2 R/vgram.matrix.R | 2 R/wendland.family.R | 2 R/wendland.image.cov.R | 2 R/world.R | 2 R/xline.R | 2 R/yline.R | 2 man/BD.Rd | 2 man/CO.Rd | 2 man/Exponential.Rd | 2 man/Krig.Amatrix.Rd | 2 man/Krig.Rd | 2 man/Krig.engine.default.Rd | 2 man/Krig.null.function.Rd | 2 man/RMprecip.Rd | 2 man/US.Rd | 2 man/US.dat.Rd | 2 man/Wendland.Rd | 2 man/add.image.Rd | 2 man/arrow.plot.Rd | 2 man/as.image.Rd | 2 man/as.surface.Rd | 2 man/bplot.Rd | 2 man/bplot.xy.Rd | 2 man/colorbar.plot.Rd | 2 man/cover.design.Rd | 2 man/drape.plot.Rd | 2 man/exp.cov.Rd | 2 man/fields-internal.Rd | 2 man/fields-stuff.Rd | 2 man/fields.Rd | 2 man/fields.grid.Rd | 2 man/fields.hints.Rd | 2 man/fields.tests.Rd | 50 ++- man/flame.Rd | 2 man/gcv.Krig.Rd | 2 man/grid.list.Rd | 2 man/image.cov.Rd | 2 man/image.plot.Rd | 2 man/image.smooth.Rd | 2 man/image2lz.Rd | 2 man/interp.surface.Rd | 2 man/lennon.Rd | 2 man/minitri.Rd | 2 man/ozone.Rd | 2 man/ozone2.Rd | 2 man/plot.Krig.Rd | 2 man/plot.surface.Rd | 2 man/predict.Krig.Rd | 2 man/predictSE.Krig.Rd | 2 man/predictSurface.Rd | 2 man/print.Krig.Rd | 2 man/pushpin.Rd | 2 man/qsreg.Rd | 2 man/quilt.plot.Rd | 2 man/rat.diet.Rd | 2 man/rdist.Rd | 2 man/rdist.earth.Rd | 2 man/ribbon.plot.Rd | 2 man/set.panel.Rd | 2 man/sim.Krig.Rd | 2 man/sim.rf.Rd | 2 man/smooth.2d.Rd | 2 man/spam2lz.Rd | 2 man/splint.Rd | 2 man/sreg.Rd | 2 man/stats.Rd | 2 man/stats.bin.Rd | 2 man/summary.Krig.Rd | 2 man/summary.ncdf.Rd | 2 man/surface.Krig.Rd | 2 man/tim.colors.Rd | 2 man/transformx.Rd | 2 man/vgram.Rd | 2 man/vgram.matrix.Rd | 2 man/world.Rd | 2 man/xline.Rd | 2 man/yline.Rd | 2 src/css.f | 2 src/csstr.f | 2 src/cvrf.f | 2 src/dchold.f | 2 src/dcopy.f | 2 src/ddfind.f | 2 src/ddot.f | 2 src/dlv.f | 2 src/dmaket.f | 2 src/drdfun.f | 2 src/dsetup.f | 2 src/evlpoly.f | 2 src/evlpoly2.f | 2 src/expfn.f | 2 src/ifind.f | 2 src/igpoly.f | 2 src/inpoly.f | 2 src/mltdrb.f | 2 src/mltdtd.f | 2 src/multW.f | 2 src/multeb.f | 2 src/multrb.f | 2 src/radbas.f | 2 src/radfn2.f | 2 src/radfun.f | 2 src/rcss.f | 2 src/rcssr.f | 2 src/rcsswt.f | 2 src/rdist.f | 2 src/sortm.f | 2 tests/Krig.Z.test.Rout.save | 100 +++--- tests/Krig.se.W.Rout.save | 22 - tests/Krig.se.grid.test.Rout.save | 6 tests/Krig.se.test.Rout.save | 38 +- tests/Krig.test.Rout.save | 162 +++++----- tests/Krig.test.W.Rout.save | 50 +-- tests/KrigGCVREML.test.Rout.save | 34 +- tests/Likelihood.test.Rout.save | 48 +-- tests/REMLest.test.Rout.save | 30 - tests/Tps.test.Rout.save | 56 +-- tests/Wend.test.Rout.save | 26 - tests/cov.test.Rout.save | 30 - tests/derivative.test.Rout.save | 88 ++--- tests/diag.multiply.test.Rout.save | 12 tests/diagonal2.test.R | 26 - tests/diagonal2.test.Rout.save | 25 - tests/evlpoly.test.Rout.save | 12 tests/fastTpsPredict.test.Rout.save | 26 - tests/mKrig.MLE.test.Rout.save | 14 tests/mKrig.Z.Rout.save | 26 - tests/mKrig.parameters.test.Rout.save | 64 ++-- tests/mKrig.se.test.Rout.save | 50 +-- tests/mKrig.test.Rout.save | 104 +++--- tests/misc.test.Rout.save | 14 tests/spam.test.Rout.save | 38 +- tests/sreg.test.Rout.save | 24 - tests/test.cov.Rout.save | 126 +++---- tests/vgram.test.Rout.save | 14 269 files changed, 1201 insertions(+), 1190 deletions(-)
Title: Interface for the 'Box.com API'
Description: An R interface for the remote file hosting service 'Box' (https://
www.box.com/). In addition to uploading and downloading files, this package
includes functions which mirror base R operations for local files, (e.g.
box_load(), box_save(), box_read(), box_setwd(), etc.), as well as 'git'
style functions for entire directories (e.g. box_fetch(), box_push()).
Author: Brendan Rocks [aut, cre]
Maintainer: Brendan Rocks <rocks.brendan@gmail.com>
Diff between boxr versions 0.2.9 dated 2015-08-20 and 0.3.1 dated 2016-01-04
DESCRIPTION | 27 - MD5 | 96 ++--- NAMESPACE | 13 NEWS.md |only R/boxr__internal_diff_and_delete.R | 336 +++++++++--------- R/boxr__internal_diff_and_uldl.R | 302 ++++++++-------- R/boxr__internal_dir_comparison.R | 48 +- R/boxr__internal_get.R |only R/boxr__internal_misc.R | 131 +++++-- R/boxr__internal_progress.R |only R/boxr__internal_update_upload.R | 114 +++--- R/boxr__internal_verb_exit.R | 4 R/boxr_add_description.R |only R/boxr_auth.R | 97 +++-- R/boxr_delete_restore.R | 243 ++++++------- R/boxr_dir_verbs.R | 684 ++++++++++++++++++------------------- R/boxr_file_versions.R | 122 +++--- R/boxr_misc.R | 410 ++++++++++------------ R/boxr_read.R | 249 +++++++------ R/boxr_s3_classes.R | 585 +++++++++++++++++++------------ R/boxr_save_load.R | 119 +++--- R/boxr_search.R |only R/boxr_source.R | 2 R/boxr_upload_download.R | 454 ++++++++++-------------- R/boxr_write.R |only R/zzz.R | 2 build/vignette.rds |binary inst/doc/boxr.Rmd | 35 + inst/doc/boxr.html | 39 +- man/boxGet.Rd |only man/box_add_description.Rd |only man/box_auth.Rd | 20 - man/box_auth_on_attach.Rd | 2 man/box_delete_file.Rd | 13 man/box_dir_create.Rd | 9 man/box_dir_diff.Rd | 82 ++-- man/box_dl.Rd | 65 ++- man/box_fetch.Rd | 45 +- man/box_fresh_auth.Rd |only man/box_ls.Rd | 4 man/box_previous_versions.Rd | 10 man/box_read.Rd | 73 ++- man/box_save.Rd | 36 + man/box_search.Rd |only man/box_setwd.Rd | 10 man/box_source.Rd | 6 man/box_upload_new.Rd | 5 man/box_write.Rd |only man/boxr-package.Rd | 10 man/boxr_S3_classes.Rd |only man/boxr_options.Rd | 6 man/create_loc_dir_df.Rd | 6 man/dirTreeRecursive.Rd | 10 man/downloadDirFiles.Rd | 10 vignettes/boxr.Rmd | 35 + 55 files changed, 2452 insertions(+), 2117 deletions(-)
Title: Climate Data from Wang and Dillon
Description: This is the data companion package to the package tempcycles.
This package includes the metadata, linear, and cycling parameters from
"Recent geographic convergence in diurnal and annual temperature cycling
flattens global thermal profiles", Wang & Dillon, Nature Climate Change,
4, 988-992 (2014). doi:10.1038/nclimate2378.
Author: George Wang [aut, cre]
Maintainer: George Wang <biogeek@gmail.com>
Diff between tempcyclesdata versions 1.0.0 dated 2016-01-01 and 1.0.1 dated 2016-01-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/data.R | 2 ++ data/tempcyclesdata.rda |binary man/tempcyclesdata.Rd | 2 ++ 5 files changed, 11 insertions(+), 7 deletions(-)
More information about tempcyclesdata at CRAN
Permanent link
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, shared objects, vignettes, or function documentation. It is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.8.0 dated 2015-09-16 and 2.9.0 dated 2016-01-03
StanHeaders-2.8.0/StanHeaders/inst/include/src/msinttypes.h |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/interface_callbacks/writer/csv.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/interface_callbacks/writer/filtered_values.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/interface_callbacks/writer/messages.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/interface_callbacks/writer/noop.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/interface_callbacks/writer/sum_values.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/interface_callbacks/writer/values.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/io/mcmc_writer.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/arguments/arg_variational_eta_adagrad.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/diagnose.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_adapt.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_nuts.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_static_hmc.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/init/init_windowed_adapt.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/print_progress.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/mcmc/run_markov_chain.hpp |only StanHeaders-2.8.0/StanHeaders/inst/include/src/stan/services/optimization |only StanHeaders-2.8.0/StanHeaders/inst/include/stan/math/rev/core/chainable.hpp |only StanHeaders-2.9.0/StanHeaders/DESCRIPTION | 8 StanHeaders-2.9.0/StanHeaders/MD5 | 292 +++--- StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/interface_callbacks/writer/base_writer.hpp | 100 ++ StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/interface_callbacks/writer/noop_writer.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/interface_callbacks/writer/stream_writer.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/io/json/json_data_handler.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/io/json/json_handler.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/io/json/json_parser.hpp | 6 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/io/stan_csv_reader.hpp | 3 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/ast.hpp | 355 +++++--- StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/ast_def.cpp | 203 ++++ StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/generator.hpp | 166 +++ StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar.hpp | 3 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar_def.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar_def.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar_inst.cpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar.hpp | 13 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_def.hpp | 186 +++- StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar.hpp | 20 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar_def.hpp | 78 + StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar_def.hpp | 3 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/lang/parser.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/base_hmc.hpp | 29 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp | 31 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp | 12 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/dense_e_point.hpp | 17 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/diag_e_metric.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/diag_e_point.hpp | 17 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/ps_point.hpp | 20 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/unit_e_metric.hpp | 12 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/base_integrator.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/base_leapfrog.hpp | 28 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/expl_leapfrog.hpp | 20 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_dense_e_nuts.hpp | 12 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_diag_e_nuts.hpp | 12 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_unit_e_nuts.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/base_nuts.hpp | 15 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/dense_e_nuts.hpp | 13 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/diag_e_nuts.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/unit_e_nuts.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_dense_e_static_hmc.hpp | 12 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_diag_e_static_hmc.hpp | 12 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_unit_e_static_hmc.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/static/base_static_hmc.hpp | 15 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/static/dense_e_static_hmc.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/static/diag_e_static_hmc.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/mcmc/hmc/static/unit_e_static_hmc.hpp | 14 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/model/indexing |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/model/indexing.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/model/model_header.hpp | 1 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/optimization/bfgs.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/optimization/lbfgs_update.hpp | 3 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/arg_variational.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/arg_variational_adapt.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/arg_variational_adapt_engaged.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/arg_variational_adapt_iter.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/arg_variational_eta.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/argument.hpp | 28 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/argument_parser.hpp | 111 +- StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/argument_probe.hpp | 5 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/categorical_argument.hpp | 64 - StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/list_argument.hpp | 72 - StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/singleton_argument.hpp | 42 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/unvalued_argument.hpp | 24 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/arguments/valued_argument.hpp | 32 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/init/initialize_state.hpp | 152 +-- StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/io/write_error_msg.hpp | 37 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/mcmc/sample.hpp | 20 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/mcmc/warmup.hpp | 15 StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/optimize |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/sample |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/services/variational |only StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/variational/advi.hpp | 394 ++++++--- StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/variational/families/normal_fullrank.hpp | 431 +++++++--- StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/variational/families/normal_meanfield.hpp | 359 ++++++-- StanHeaders-2.9.0/StanHeaders/inst/include/src/stan/version.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/unit_vector_constrain.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/fwd/mat/functor/gradient.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/fwd/mat/functor/jacobian.hpp | 9 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_mix.hpp | 9 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/memory/stack_alloc.hpp | 6 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/mix/mat/functor/derivative.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/mix/mat/functor/grad_hessian.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/mix/mat/functor/grad_tr_mat_times_hessian.hpp | 12 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/mix/mat/functor/gradient_dot_vector.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/mix/mat/functor/hessian.hpp | 18 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/mix/mat/functor/hessian_times_vector.hpp | 20 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/mix/mat/functor/partial_derivative.hpp | 6 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor.hpp | 9 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor_corr.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_corr_matrix.hpp | 12 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_cov_matrix.hpp | 9 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_lower_triangular.hpp | 9 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_definite.hpp | 9 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_semidefinite.hpp | 9 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_spsd_matrix.hpp | 9 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_symmetric.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/err/check_unit_vector.hpp | 5 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form_diag.hpp | 18 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_array_1d.hpp | 20 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_array_2d.hpp | 11 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_matrix.hpp | 24 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_row_vector.hpp | 24 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/fun/to_vector.hpp | 22 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/fun/unit_vector_constrain.hpp | 75 - StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/fun/unit_vector_free.hpp | 25 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_log.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_rng.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_log.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_rng.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_log.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_rng.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_log.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_log.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_rng.hpp | 9 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_log.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_rng.hpp | 11 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/prim/scal/meta/OperandsAndPartials.hpp | 5 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/arr/functor/coupled_ode_system.hpp | 227 ++--- StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/chainable_alloc.hpp | 11 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/chainablestack.hpp | 5 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/empty_nested.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/gevv_vvv_vari.hpp | 1 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/grad.hpp | 10 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/nested_size.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/print_stack.hpp | 3 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/recover_memory.hpp | 3 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/recover_memory_nested.hpp | 1 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/set_zero_all_adjoints.hpp | 2 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/var.hpp | 7 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/core/vari.hpp | 58 + StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/mat/fun/log_softmax.hpp | 7 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/mat/fun/unit_vector_constrain.hpp |only StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/mat/functor/gradient.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/rev/mat/functor/jacobian.hpp | 8 StanHeaders-2.9.0/StanHeaders/inst/include/stan/math/version.hpp | 2 StanHeaders-2.9.0/StanHeaders/man/StanHeaders-package.Rd | 4 158 files changed, 2926 insertions(+), 1545 deletions(-)
Title: A Platform for the Study of Macroecology of Life History Traits
Description: Tools for easy generation of (life-history) traits maps based on
species range (extent-of-occurrence) maps.
Author: Mihai Valcu [aut, cre],
James Dale [aut],
Joan Maspons [ctb]
Maintainer: Mihai Valcu <valcu@orn.mpg.de>
Diff between rangeMapper versions 0.2-8 dated 2014-10-27 and 0.3-0 dated 2016-01-03
rangeMapper-0.2-8/rangeMapper/R/MapSummary-methods.R |only rangeMapper-0.2-8/rangeMapper/data/wrens.csv.gz |only rangeMapper-0.2-8/rangeMapper/inst/GUI/bootstrap-switch.html |only rangeMapper-0.2-8/rangeMapper/inst/GUI/functions.R |only rangeMapper-0.2-8/rangeMapper/inst/GUI/tooltip.js |only rangeMapper-0.2-8/rangeMapper/man/00_rangeMap-class.Rd |only rangeMapper-0.2-8/rangeMapper/man/00_rangeMapper.Rd |only rangeMapper-0.2-8/rangeMapper/man/01_rangeMapStart-class.Rd |only rangeMapper-0.2-8/rangeMapper/man/02_rangeMapStart.Rd |only rangeMapper-0.2-8/rangeMapper/man/03_rangeFiles.Rd |only rangeMapper-0.2-8/rangeMapper/man/04_rangeMapBbox.Rd |only rangeMapper-0.2-8/rangeMapper/man/05_gridSize.Rd |only rangeMapper-0.2-8/rangeMapper/man/06_canvas.Rd |only rangeMapper-0.2-8/rangeMapper/man/07_assemblageFetch.Rd |only rangeMapper-0.2-8/rangeMapper/man/07_range.fetch.Rd |only rangeMapper-0.2-8/rangeMapper/man/07_rangeMapProcess.Rd |only rangeMapper-0.2-8/rangeMapper/man/07_rangeTraits.Rd |only rangeMapper-0.2-8/rangeMapper/man/07_vertices.Rd |only rangeMapper-0.2-8/rangeMapper/man/08_bioSave.Rd |only rangeMapper-0.2-8/rangeMapper/man/09_SpatialPixelsRangeMap-class.Rd |only rangeMapper-0.2-8/rangeMapper/man/10_metadataUpdate.Rd |only rangeMapper-0.2-8/rangeMapper/man/10_rangeMapSave.Rd |only rangeMapper-0.2-8/rangeMapper/man/11_MapPlot-methods.Rd |only rangeMapper-0.2-8/rangeMapper/man/12_rangeMapRemove.Rd |only rangeMapper-0.2-8/rangeMapper/man/13_rangeMapExport.Rd |only rangeMapper-0.2-8/rangeMapper/man/99_wrens.Rd |only rangeMapper-0.3-0/rangeMapper/DESCRIPTION | 45 rangeMapper-0.3-0/rangeMapper/MD5 | 144 +- rangeMapper-0.3-0/rangeMapper/NAMESPACE | 180 +-- rangeMapper-0.3-0/rangeMapper/NEWS | 55 - rangeMapper-0.3-0/rangeMapper/R/AAA.R | 57 - rangeMapper-0.3-0/rangeMapper/R/AllClasses.R | 353 ++---- rangeMapper-0.3-0/rangeMapper/R/GUI.R | 31 rangeMapper-0.3-0/rangeMapper/R/MapCanvas-methods.R | 527 +++++----- rangeMapper-0.3-0/rangeMapper/R/MapExport-methods.R | 47 rangeMapper-0.3-0/rangeMapper/R/MapFetch-methods.R | 170 ++- rangeMapper-0.3-0/rangeMapper/R/MapPlot-methods.R | 140 ++ rangeMapper-0.3-0/rangeMapper/R/MapProcess-methods.R | 510 +++------ rangeMapper-0.3-0/rangeMapper/R/MapRemove-methods.R | 113 +- rangeMapper-0.3-0/rangeMapper/R/MapSave-methods.R | 416 ++++--- rangeMapper-0.3-0/rangeMapper/R/MapShow-methods.R |only rangeMapper-0.3-0/rangeMapper/R/assemblageFetch-methods.R | 111 +- rangeMapper-0.3-0/rangeMapper/R/bioSave-methods.R | 162 +-- rangeMapper-0.3-0/rangeMapper/R/metadataUpdate-methods.R | 129 +- rangeMapper-0.3-0/rangeMapper/R/projectINI-methods.R | 68 - rangeMapper-0.3-0/rangeMapper/R/rangeFiles-methods.R | 37 rangeMapper-0.3-0/rangeMapper/R/rangeMapper-package.R |only rangeMapper-0.3-0/rangeMapper/R/rangeMapper-ramp.R |only rangeMapper-0.3-0/rangeMapper/R/style.R |only rangeMapper-0.3-0/rangeMapper/R/utils-spatial.R | 231 ++++ rangeMapper-0.3-0/rangeMapper/R/utils.R | 103 + rangeMapper-0.3-0/rangeMapper/build |only rangeMapper-0.3-0/rangeMapper/data/wrens.csv |only rangeMapper-0.3-0/rangeMapper/inst/GUI/server.R | 93 - rangeMapper-0.3-0/rangeMapper/inst/GUI/ui.R | 253 ---- rangeMapper-0.3-0/rangeMapper/inst/doc |only rangeMapper-0.3-0/rangeMapper/inst/extdata/wrens/vector/Troglodytes_sissonii.shp |binary rangeMapper-0.3-0/rangeMapper/inst/extdata/wrens/vector/Troglodytes_sissonii.shx |binary rangeMapper-0.3-0/rangeMapper/inst/extdata/wrens/vector/Troglodytes_tanneri.dbf |binary rangeMapper-0.3-0/rangeMapper/inst/extdata/wrens/vector/Troglodytes_tanneri.shp |binary rangeMapper-0.3-0/rangeMapper/inst/extdata/wrens/vector/Troglodytes_tanneri.shx |binary rangeMapper-0.3-0/rangeMapper/inst/extdata/wrens/vector_combined/make.R |only rangeMapper-0.3-0/rangeMapper/inst/extdata/wrens/vector_combined/wrens.dbf |binary rangeMapper-0.3-0/rangeMapper/inst/extdata/wrens/vector_combined/wrens.shp |binary rangeMapper-0.3-0/rangeMapper/inst/extdata/wrens/vector_combined/wrens.shx |binary rangeMapper-0.3-0/rangeMapper/man/View_rmap.Rd |only rangeMapper-0.3-0/rangeMapper/man/WKT2SpatialPolygonsDataFrame.Rd | 83 - rangeMapper-0.3-0/rangeMapper/man/as.rmap.frame.data.table.Rd |only rangeMapper-0.3-0/rangeMapper/man/assemblageFetch.Rd |only rangeMapper-0.3-0/rangeMapper/man/bio.save.Rd |only rangeMapper-0.3-0/rangeMapper/man/canvas.save.Rd |only rangeMapper-0.3-0/rangeMapper/man/global.bbox.save.Rd |only rangeMapper-0.3-0/rangeMapper/man/gridSize.save.Rd |only rangeMapper-0.3-0/rangeMapper/man/metadata.update.Rd |only rangeMapper-0.3-0/rangeMapper/man/palette_rangemap.Rd |only rangeMapper-0.3-0/rangeMapper/man/plot-SpatialPixelsRangeMap-missing-method.Rd |only rangeMapper-0.3-0/rangeMapper/man/plot-rmap.frame-missing-method.Rd |only rangeMapper-0.3-0/rangeMapper/man/processRanges.Rd |only rangeMapper-0.3-0/rangeMapper/man/ramp.Rd |only rangeMapper-0.3-0/rangeMapper/man/rangeFetch.Rd |only rangeMapper-0.3-0/rangeMapper/man/rangeMap.export.Rd |only rangeMapper-0.3-0/rangeMapper/man/rangeMap.fetch.Rd |only rangeMapper-0.3-0/rangeMapper/man/rangeMap.save.Rd |only rangeMapper-0.3-0/rangeMapper/man/rangeMap.start.Rd |only rangeMapper-0.3-0/rangeMapper/man/rangeMapProjInfo.Rd |only rangeMapper-0.3-0/rangeMapper/man/rangeMapper.Rd |only rangeMapper-0.3-0/rangeMapper/man/rangeOverlay.Rd |only rangeMapper-0.3-0/rangeMapper/man/rangeTraits.Rd |only rangeMapper-0.3-0/rangeMapper/man/rm.rangeMapper.Rd |only rangeMapper-0.3-0/rangeMapper/man/selectShpFiles.Rd |only rangeMapper-0.3-0/rangeMapper/man/tables-SQLiteConnection-method.Rd |only rangeMapper-0.3-0/rangeMapper/man/tables-methods.Rd |only rangeMapper-0.3-0/rangeMapper/man/theme_rangemap.Rd |only rangeMapper-0.3-0/rangeMapper/man/wrens.Rd |only rangeMapper-0.3-0/rangeMapper/tests |only rangeMapper-0.3-0/rangeMapper/vignettes |only 96 files changed, 2197 insertions(+), 1861 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions. Includes an intuitive
query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 1.0 dated 2015-12-10 and 1.1 dated 2016-01-03
DESCRIPTION | 9 +++---- MD5 | 32 +++++++++++++------------ NAMESPACE | 2 + R/documentation.R | 25 ------------------- R/gui.R |only R/kde.R | 5 +++ R/minsorting.R | 5 +-- R/plot.R | 55 +++++++++++++++++++++++++++++-------------- R/provenance.R | 57 ++++++++++++++++++++++++++++++--------------- data/Namib.rda |binary data/endmembers.rda |binary man/GPA.Rd |only man/minsorting.Rd | 5 +-- man/plot.KDE.Rd | 2 - man/plot.ternary.Rd | 3 -- man/procrustes.Rd | 10 +++---- man/provenance.Rd | 34 ++++++++++---------------- man/read.distributional.Rd | 12 ++++----- 18 files changed, 134 insertions(+), 122 deletions(-)
Title: Fast and Versatile Non-Negative Matrix Factorization
Description: This is a package for Non-Negative Linear Models (NNLM). It implements
fast sequential coordinate descent algorithms for non-negative linear regression
and non-negative matrix factorization (NMF). It supports mean square error and Kullback-Leibler divergence loss.
Many other features are also implemented, including missing value imputation, domain knowledge integration,
designable W and H matrices and multiple forms of regularizations.
Author: Xihui Lin [aut, cre],
Paul C Boutros [aut]
Maintainer: Xihui Lin <xihuil.silence@gmail.com>
Diff between NNLM versions 0.4.0 dated 2015-12-26 and 0.4.1 dated 2016-01-03
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NEWS | 5 +++ R/nnmf.R | 19 ++++++++---- inst/doc/Fast-And-Versatile-NMF.Rmd | 8 ++--- inst/doc/Fast-And-Versatile-NMF.html | 52 +++++++++++++++++------------------ man/nnmf.Rd | 19 ++++++++---- src/nnlm.h | 5 --- vignettes/Fast-And-Versatile-NMF.Rmd | 8 ++--- 9 files changed, 79 insertions(+), 63 deletions(-)
Title: Study Design and Data Analysis in the Presence of Error-Prone
Diagnostic Tests and Self-Reported Outcomes
Description: We consider studies in which information from error-prone
diagnostic tests or self-reports are gathered sequentially to determine the
occurrence of a silent event. Using a likelihood-based approach
incorporating the proportional hazards assumption, we provide functions to
estimate the survival distribution and covariate effects. We also provide
functions for power and sample size calculations for this setting.
Author: Xiangdong Gu and Raji Balasubramanian
Maintainer: Xiangdong Gu <ustcgxd@gmail.com>
Diff between icensmis versions 1.3.0 dated 2015-10-14 and 1.3.1 dated 2016-01-03
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/powerfuncs.cpp | 13 +++++++++++-- 3 files changed, 16 insertions(+), 7 deletions(-)
Title: Sampling Variance Estimation
Description: Functions to calculate some point estimators and estimating their variance under unequal probability sampling without replacement. Single and two stage sampling designs are considered. Some approximations for the second order inclusion probabilities are also available (sample and population based).
Author: Emilio Lopez Escobar [aut, cre, cph] <emilio@numerika.mx>,
Ernesto Barrios Zamudio [ctb] <ebarrios@itam.mx>,
Juan Francisco Munoz Rosas [ctb] <jfmunoz@go.ugr.es>
Maintainer: Emilio Lopez Escobar <emilio@numerika.mx>
Diff between samplingVarEst versions 0.9-9 dated 2014-05-13 and 1.0-1 dated 2016-01-03
ChangeLog | 12 ++++ DESCRIPTION | 16 +++-- MD5 | 36 +++++++----- R/Est_EmpDistFunc_Hajek.r |only R/Est_EmpDistFunc_NHT.r |only README | 7 +- inst/CITATION | 5 + man/Est_EmpDistFunc_Hajek.rd |only man/Est_EmpDistFunc_NHT.rd |only man/Est_Ratio.rd | 2 man/VE_EB_HT_Ratio.rd | 2 man/VE_EB_SYG_Ratio.rd | 2 man/VE_Jk_B_Ratio.rd | 2 man/VE_Jk_CBS_HT_Ratio.rd | 2 man/VE_Jk_CBS_SYG_Ratio.rd | 2 man/VE_Jk_EB_SW2_Ratio.rd | 2 man/VE_Jk_Tukey_Ratio.rd | 2 man/VE_Lin_HT_Ratio.rd | 120 +++++++++++++++++++++--------------------- man/VE_Lin_SYG_Ratio.rd | 2 man/samplingVarEst-package.rd | 4 + src/Est_EmpDistFunc_Hajek.c |only src/Est_EmpDistFunc_NHT.c |only 22 files changed, 121 insertions(+), 97 deletions(-)
More information about samplingVarEst at CRAN
Permanent link
Title: Robust Linear Mixed Effects Models
Description: A method to fit linear mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <koller.manuel@gmail.com>
Diff between robustlmm versions 1.7-6 dated 2015-08-30 and 1.8 dated 2016-01-03
DESCRIPTION | 8 +- MD5 | 30 ++++----- NAMESPACE | 3 R/DAS-scale.R | 38 ++++++++++-- R/rlmer.R | 49 ++++++++++++---- build/vignette.rds |binary inst/doc/ggplot.theme.R | 5 - inst/doc/rlmer.pdf |binary tests/compare-methods.Rout.save | 20 +++--- vignettes/figs/fig-ex-penicillin-qq-ranef.pdf |binary vignettes/figs/fig-ex-penicillin-qq-resid.pdf |binary vignettes/figs/fig-ex-penicillin-raw.pdf |binary vignettes/figs/fig-ex-penicillin-robustness-weights.pdf |binary vignettes/figs/fig-ex-penicillin-ta.pdf |binary vignettes/figs/fig-ex-sleepstudy-raw.pdf |binary vignettes/figs/fig-ex-smoothedHuber.pdf |binary 16 files changed, 102 insertions(+), 51 deletions(-)
Title: Rainbow Plots, Bagplots and Boxplots for Functional Data
Description: Functions and data sets for functional data display and outlier detection.
Author: Han Lin Shang and Rob J Hyndman
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>
Diff between rainbow versions 3.3 dated 2015-04-15 and 3.4 dated 2016-01-03
ChangeLog | 131 ------ DESCRIPTION | 10 MD5 | 26 - NAMESPACE | 14 R/fbag.R | 128 +++--- R/plot.fds.R | 11 build/vignette.rds |binary inst/doc/rainbow.R | 20 - inst/doc/rainbow.Rnw | 63 +-- inst/doc/rainbow.pdf |binary man/SVDplot.Rd | 2 man/rainbow-package.Rd | 4 vignettes/Shang.bib | 969 ++++++++++++++++++++++++------------------------- vignettes/rainbow.Rnw | 63 +-- 14 files changed, 675 insertions(+), 766 deletions(-)
Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping structures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.8.9 dated 2015-11-29 and 1.9.1 dated 2016-01-03
forestFloor-1.8.9/forestFloor/src/multiClass.cpp |only forestFloor-1.9.1/forestFloor/DESCRIPTION | 14 forestFloor-1.9.1/forestFloor/MD5 | 58 - forestFloor-1.9.1/forestFloor/NAMESPACE | 36 - forestFloor-1.9.1/forestFloor/NEWS |only forestFloor-1.9.1/forestFloor/R/convolute_ff.R | 3 forestFloor-1.9.1/forestFloor/R/forestFloor_randomForest_multiClass.R | 71 -- forestFloor-1.9.1/forestFloor/R/plot.forestFloor_multiClass.R | 103 ++- forestFloor-1.9.1/forestFloor/R/plot.forestFloor_regression.R | 77 +- forestFloor-1.9.1/forestFloor/R/plot_simplex3.R | 5 forestFloor-1.9.1/forestFloor/R/print.forestFloor_multiClass.R |only forestFloor-1.9.1/forestFloor/R/show3d.R | 24 forestFloor-1.9.1/forestFloor/R/vec.plot.R | 50 + forestFloor-1.9.1/forestFloor/man/append.overwrite.alists.Rd | 12 forestFloor-1.9.1/forestFloor/man/as.numeric.factor.Rd | 13 forestFloor-1.9.1/forestFloor/man/box.outliers.Rd | 10 forestFloor-1.9.1/forestFloor/man/convolute_ff.Rd | 29 forestFloor-1.9.1/forestFloor/man/convolute_ff2.Rd | 25 forestFloor-1.9.1/forestFloor/man/convolute_grid.Rd | 68 +- forestFloor-1.9.1/forestFloor/man/fcol.Rd | 104 ++- forestFloor-1.9.1/forestFloor/man/forestFloor-package.Rd | 15 forestFloor-1.9.1/forestFloor/man/forestFloor.Rd | 54 - forestFloor-1.9.1/forestFloor/man/plot.forestFloor.Rd | 309 ++++------ forestFloor-1.9.1/forestFloor/man/plot_simplex3.Rd | 80 +- forestFloor-1.9.1/forestFloor/man/print.forestFloor.Rd | 6 forestFloor-1.9.1/forestFloor/man/recTree.Rd | 61 - forestFloor-1.9.1/forestFloor/man/show3d.Rd | 43 - forestFloor-1.9.1/forestFloor/man/vec.plot.Rd | 39 - forestFloor-1.9.1/forestFloor/tests/allExamples.R |only forestFloor-1.9.1/forestFloor/tests/rfPermute_supported.R | 72 +- forestFloor-1.9.1/forestFloor/tests/testBinaryClass.R | 21 forestFloor-1.9.1/forestFloor/tests/testMultiClass.cpp.R | 20 32 files changed, 742 insertions(+), 680 deletions(-)
Title: Time Series Clustering with Dynamic Time Warping Distance
Description: Time series clustering using different techniques related to the
Dynamic Time Warping distance and its corresponding lower bounds. Additionally,
an implementation of k-Shape clustering is available, and the package can be
easily extended with custom distance measures and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 1.3.0 dated 2015-12-11 and 2.0.0 dated 2016-01-03
dtwclust-1.3.0/dtwclust/R/dtwclust-plot.R |only dtwclust-1.3.0/dtwclust/man/plot-methods.Rd |only dtwclust-2.0.0/dtwclust/DESCRIPTION | 24 dtwclust-2.0.0/dtwclust/MD5 | 117 + dtwclust-2.0.0/dtwclust/NAMESPACE | 11 dtwclust-2.0.0/dtwclust/R/DBA.R | 112 + dtwclust-2.0.0/dtwclust/R/NCCc.R | 5 dtwclust-2.0.0/dtwclust/R/SBD.R | 375 ++-- dtwclust-2.0.0/dtwclust/R/TADPole.R | 189 -- dtwclust-2.0.0/dtwclust/R/all_cent.R | 442 ++--- dtwclust-2.0.0/dtwclust/R/dtw-lb.R | 200 +- dtwclust-2.0.0/dtwclust/R/dtwclust-classes.R | 177 ++ dtwclust-2.0.0/dtwclust/R/dtwclust-methods.R |only dtwclust-2.0.0/dtwclust/R/dtwclust.R | 1471 +++++++++---------- dtwclust-2.0.0/dtwclust/R/dtwdistfun.R | 379 ++-- dtwclust-2.0.0/dtwclust/R/kcca-list.R | 104 - dtwclust-2.0.0/dtwclust/R/lb-improved.R | 201 +- dtwclust-2.0.0/dtwclust/R/lb-keogh.R | 159 +- dtwclust-2.0.0/dtwclust/R/pkg.R | 293 ++- dtwclust-2.0.0/dtwclust/R/reinterpolate.R | 2 dtwclust-2.0.0/dtwclust/R/shape-extraction.R | 79 - dtwclust-2.0.0/dtwclust/R/utils.R | 347 ++-- dtwclust-2.0.0/dtwclust/R/zscore.R | 5 dtwclust-2.0.0/dtwclust/README.md | 142 + dtwclust-2.0.0/dtwclust/inst/NEWS.Rd |only dtwclust-2.0.0/dtwclust/inst/dtwclust-examples.R |only dtwclust-2.0.0/dtwclust/man/DBA.Rd | 29 dtwclust-2.0.0/dtwclust/man/NCCc.Rd | 4 dtwclust-2.0.0/dtwclust/man/SBD.Rd | 16 dtwclust-2.0.0/dtwclust/man/TADPole.Rd | 6 dtwclust-2.0.0/dtwclust/man/clusterSim.Rd |only dtwclust-2.0.0/dtwclust/man/dtw_lb.Rd | 31 dtwclust-2.0.0/dtwclust/man/dtwclust-class.Rd | 40 dtwclust-2.0.0/dtwclust/man/dtwclust-methods.Rd |only dtwclust-2.0.0/dtwclust/man/dtwclust-package.Rd | 34 dtwclust-2.0.0/dtwclust/man/dtwclust.Rd | 337 ++-- dtwclust-2.0.0/dtwclust/man/dtwclustControl-class.Rd |only dtwclust-2.0.0/dtwclust/man/dtwclustFamily-class.Rd |only dtwclust-2.0.0/dtwclust/man/lb_improved.Rd | 6 dtwclust-2.0.0/dtwclust/man/lb_keogh.Rd | 6 dtwclust-2.0.0/dtwclust/man/randIndex.Rd |only dtwclust-2.0.0/dtwclust/man/shape_extraction.Rd | 26 dtwclust-2.0.0/dtwclust/man/zscore.Rd | 4 dtwclust-2.0.0/dtwclust/src/pairs.c | 87 - dtwclust-2.0.0/dtwclust/src/runminmax.c |only dtwclust-2.0.0/dtwclust/tests |only 46 files changed, 3032 insertions(+), 2428 deletions(-)
Title: Bindings to the CommonMark Reference Implementation
Description: The CommonMark specification defines a rationalized version of markdown
syntax. This package uses the libcmark reference implementation for converting
markdown text into various formats including html, latex and groff man. In
addition it exposes the markdown parse tree in xml format.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between commonmark versions 0.5 dated 2015-09-01 and 0.6 dated 2016-01-03
commonmark-0.5/commonmark/src/cmark/bench.h |only commonmark-0.6/commonmark/DESCRIPTION | 17 commonmark-0.6/commonmark/LICENSE | 2 commonmark-0.6/commonmark/MD5 | 55 commonmark-0.6/commonmark/NAMESPACE | 2 commonmark-0.6/commonmark/NEWS | 3 commonmark-0.6/commonmark/man/commonmark.Rd | 2 commonmark-0.6/commonmark/src/cmark/blocks.c | 148 commonmark-0.6/commonmark/src/cmark/chunk.h | 12 commonmark-0.6/commonmark/src/cmark/cmark.h | 122 commonmark-0.6/commonmark/src/cmark/cmark_ctype.c | 12 commonmark-0.6/commonmark/src/cmark/cmark_version.h | 4 commonmark-0.6/commonmark/src/cmark/commonmark.c | 34 commonmark-0.6/commonmark/src/cmark/houdini_html_u.c | 11 commonmark-0.6/commonmark/src/cmark/html.c | 44 commonmark-0.6/commonmark/src/cmark/inlines.c | 19 commonmark-0.6/commonmark/src/cmark/iterator.c | 4 commonmark-0.6/commonmark/src/cmark/latex.c | 80 commonmark-0.6/commonmark/src/cmark/main.c | 9 commonmark-0.6/commonmark/src/cmark/man.c | 22 commonmark-0.6/commonmark/src/cmark/node.c | 165 commonmark-0.6/commonmark/src/cmark/node.h | 10 commonmark-0.6/commonmark/src/cmark/render.c | 9 commonmark-0.6/commonmark/src/cmark/render.h | 1 commonmark-0.6/commonmark/src/cmark/scanners.c | 8038 ++++++++----------- commonmark-0.6/commonmark/src/cmark/scanners.h | 13 commonmark-0.6/commonmark/src/cmark/utf8.c | 9 commonmark-0.6/commonmark/src/cmark/utf8.h | 6 commonmark-0.6/commonmark/src/cmark/xml.c | 24 29 files changed, 4246 insertions(+), 4631 deletions(-)
Title: Segmentation Methods for Array CGH Analysis
Description: cghseg is an R package dedicated to the analysis of CGH
profiles using segmentation models.
Author: Franck Picard, Mark Hoebeke, Emilie Lebarbier, Vincent Miele,
Guillem Rigaill, Stephane Robin
Maintainer: ORPHANED
Diff between cghseg versions 1.0.2 dated 2013-11-12 and 1.0.2-1 dated 2016-01-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 3 +++ src/Segmentation_ibp.cc | 1 + src/Segmentation_mean.cc | 2 +- src/compactEM_init.cc | 5 ++--- 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Tools for Simulation Studies in Parallel
Description: Tools for setting up ("design"), conducting, and evaluating
large-scale simulation studies with graphics and tables, including
parallel computations.
Author: Marius Hofert and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between simsalapar versions 1.0-7 dated 2015-12-22 and 1.0-8 dated 2016-01-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/graphics.R | 25 ++++++++++++++++--------- man/mayplot.Rd | 23 ++++++++++++----------- 4 files changed, 35 insertions(+), 27 deletions(-)
Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Description: Provides tools for importing and working with
bibliographic references. It greatly enhances the 'bibentry' class by
providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references,
supports 'UTF-8' encoding, and can be easily searched by any field, by date
ranges, and by various formats for name lists (author by last names,
translator by full names, etc.). Entries can be updated, combined, sorted,
printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files
can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez',
'CrossRef', and 'Zotero' are provided for importing references and
references can be created from locally stored 'PDF' files using 'Poppler'. Includes
functions for citing and generating a bibliography with hyperlinks for
documents prepared with 'RMarkdown' or 'RHTML'.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>
Diff between RefManageR versions 0.8.63 dated 2015-06-09 and 0.10.5 dated 2016-01-02
RefManageR-0.10.5/RefManageR/DESCRIPTION | 14 RefManageR-0.10.5/RefManageR/LICENSE | 4 RefManageR-0.10.5/RefManageR/MD5 | 148 +++---- RefManageR-0.10.5/RefManageR/NAMESPACE | 202 +++++----- RefManageR-0.10.5/RefManageR/R/04InternalFunctions.R | 161 ++++---- RefManageR-0.10.5/RefManageR/R/05makeBibLatex.R | 69 +-- RefManageR-0.10.5/RefManageR/R/07makeBibLatexAuthoryear.R | 54 +- RefManageR-0.10.5/RefManageR/R/08asBibEntry.R | 1 RefManageR-0.10.5/RefManageR/R/09sort.R | 2 RefManageR-0.10.5/RefManageR/R/BibEntryAddOp.R | 2 RefManageR-0.10.5/RefManageR/R/BibEntryCombineOp.R | 3 RefManageR-0.10.5/RefManageR/R/BibEntryDollarExtract.R | 3 RefManageR-0.10.5/RefManageR/R/BibEntryExtractOp.R | 13 RefManageR-0.10.5/RefManageR/R/BibEntryReplaceBibEntry.R | 4 RefManageR-0.10.5/RefManageR/R/BibEntryReplaceOp.R | 1 RefManageR-0.10.5/RefManageR/R/GetDOIs.R | 4 RefManageR-0.10.5/RefManageR/R/NamesAssign.R | 1 RefManageR-0.10.5/RefManageR/R/ReadBib.R | 16 RefManageR-0.10.5/RefManageR/R/ReadCrossRef.R | 8 RefManageR-0.10.5/RefManageR/R/ReadGS.R | 4 RefManageR-0.10.5/RefManageR/R/ReadPDFs.R | 7 RefManageR-0.10.5/RefManageR/R/ReadPDFsSupport.R | 171 ++++---- RefManageR-0.10.5/RefManageR/R/ReadPubMed.R | 25 - RefManageR-0.10.5/RefManageR/R/RefManageR-package.R | 4 RefManageR-0.10.5/RefManageR/R/WriteBib.R | 2 RefManageR-0.10.5/RefManageR/R/asdataframe.R | 12 RefManageR-0.10.5/RefManageR/R/format.R | 10 RefManageR-0.10.5/RefManageR/R/open.BibEntry.R | 5 RefManageR-0.10.5/RefManageR/R/print.R | 2 RefManageR-0.10.5/RefManageR/R/rmdCite.R | 11 RefManageR-0.10.5/RefManageR/README.md | 37 + RefManageR-0.10.5/RefManageR/build/vignette.rds |binary RefManageR-0.10.5/RefManageR/inst/NEWS | 18 RefManageR-0.10.5/RefManageR/inst/doc/TestAlphabetic.html | 18 RefManageR-0.10.5/RefManageR/inst/doc/TestHtml.html | 106 ++--- RefManageR-0.10.5/RefManageR/inst/doc/TestRmd.html | 4 RefManageR-0.10.5/RefManageR/inst/doc/manual.pdf |binary RefManageR-0.10.5/RefManageR/man/BibEntry.Rd | 260 ++++++------- RefManageR-0.10.5/RefManageR/man/BibOptions.Rd | 256 ++++++------ RefManageR-0.10.5/RefManageR/man/Cite.Rd | 228 +++++------ RefManageR-0.10.5/RefManageR/man/FindBibEntry.Rd | 26 - RefManageR-0.10.5/RefManageR/man/GetBibEntryWithDOI.Rd | 74 +-- RefManageR-0.10.5/RefManageR/man/GetDOIs.Rd | 86 ++-- RefManageR-0.10.5/RefManageR/man/GetPubMedByID.Rd | 88 ++-- RefManageR-0.10.5/RefManageR/man/GetPubMedRelated.Rd | 118 ++--- RefManageR-0.10.5/RefManageR/man/LookupPubMedID.Rd | 86 ++-- RefManageR-0.10.5/RefManageR/man/ReadBib.Rd | 89 ++-- RefManageR-0.10.5/RefManageR/man/ReadCrossRef.Rd | 124 +++--- RefManageR-0.10.5/RefManageR/man/ReadGS.Rd | 144 +++---- RefManageR-0.10.5/RefManageR/man/ReadPDFs.Rd | 114 ++--- RefManageR-0.10.5/RefManageR/man/ReadPubMed.Rd | 114 ++--- RefManageR-0.10.5/RefManageR/man/ReadZotero.Rd | 148 +++---- RefManageR-0.10.5/RefManageR/man/RefManageR-package.Rd | 158 +++---- RefManageR-0.10.5/RefManageR/man/SearchBib.Rd | 246 ++++++------ RefManageR-0.10.5/RefManageR/man/UpdateFieldName.Rd | 66 +-- RefManageR-0.10.5/RefManageR/man/WriteBib.Rd | 104 ++--- RefManageR-0.10.5/RefManageR/man/as.BibEntry.Rd | 116 ++--- RefManageR-0.10.5/RefManageR/man/as.data.frame.BibEntry.Rd | 72 +-- RefManageR-0.10.5/RefManageR/man/c.BibEntry.Rd | 82 ++-- RefManageR-0.10.5/RefManageR/man/cash-.BibEntry.Rd | 76 +-- RefManageR-0.10.5/RefManageR/man/cash-set-.BibEntry.Rd | 94 ++-- RefManageR-0.10.5/RefManageR/man/head.BibEntry.Rd | 70 +-- RefManageR-0.10.5/RefManageR/man/levels.BibEntry.Rd | 70 +-- RefManageR-0.10.5/RefManageR/man/merge.BibEntry.Rd | 162 ++++---- RefManageR-0.10.5/RefManageR/man/names.BibEntry.Rd | 68 +-- RefManageR-0.10.5/RefManageR/man/open.BibEntry.Rd | 94 ++-- RefManageR-0.10.5/RefManageR/man/print.BibEntry.Rd | 140 +++---- RefManageR-0.10.5/RefManageR/man/sort.BibEntry.Rd | 152 +++---- RefManageR-0.10.5/RefManageR/man/sub-sub-.BibEntry.Rd | 104 ++--- RefManageR-0.10.5/RefManageR/man/sub-subset-.BibEntry.Rd | 72 +-- RefManageR-0.10.5/RefManageR/man/subset-.BibEntry.Rd | 130 +++--- RefManageR-0.10.5/RefManageR/man/toBiblatex.Rd | 174 ++++---- RefManageR-0.10.5/RefManageR/man/unlist.BibEntry.Rd | 110 ++--- RefManageR-0.10.5/RefManageR/tests/testthat/test-sort.R | 2 RefManageR-0.8.63/RefManageR/inst/Rmd/TestPandoc.Rmd |only RefManageR-0.8.63/RefManageR/inst/pdf |only 76 files changed, 2784 insertions(+), 2679 deletions(-)
Title: Procedures to Generate Patterns under Computerized Adaptive
Testing
Description: Generation of response patterns under dichotomous and polytomous computerized adaptive testing (CAT) framework.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@ulg.ac.be>
Diff between catR versions 3.5 dated 2015-09-27 and 3.6 dated 2016-01-02
DESCRIPTION | 8 +- MD5 | 20 ++--- NEWS | 22 +++++ R/Pi.R | 199 +++++++++++++++++++++++++++++--------------------- R/genDichoMatrix.R | 5 - man/eapSem.Rd | 2 man/genDichoMatrix.Rd | 8 -- man/genPolyMatrix.Rd | 2 man/nextItem.Rd | 4 - man/randomCAT.Rd | 2 man/thetaEst.Rd | 2 11 files changed, 164 insertions(+), 110 deletions(-)
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Can calculate various string distances based on edits
(damerau-levenshtein, hamming, levenshtein, optimal sting alignment), qgrams (q-
gram, cosine, jaccard distance) or heuristic metrics (jaro, jaro-winkler). An
implementation of soundex is provided as well. Distances can be computed between
character vectors while taking proper care of encoding or between integer
vectors representing generic sequences.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.4 dated 2015-10-26 and 0.9.4.1 dated 2016-01-02
DESCRIPTION | 21 ++++++------ MD5 | 50 ++++++++++++++--------------- NAMESPACE | 2 - NEWS | 6 +++ R/doc_parallel.R | 4 +- R/stringsim.R | 14 +++++--- man/amatch.Rd | 18 +++++----- man/phonetic.Rd | 26 +++++++-------- man/printable_ascii.Rd | 4 +- man/qgrams.Rd | 8 ++-- man/seq_amatch.Rd | 16 ++++----- man/seq_dist.Rd | 18 +++++----- man/seq_qgrams.Rd | 2 - man/seq_sim.Rd | 4 +- man/stringdist-encoding.Rd | 18 +++++----- man/stringdist-metrics.Rd | 64 +++++++++++++++++++------------------- man/stringdist-package.Rd | 10 ++--- man/stringdist-parallelization.Rd | 15 +++----- man/stringdist.Rd | 14 ++++---- man/stringsim.Rd | 20 +++++++---- src/Rstringdist.c | 33 ++++++++++++++----- src/dl.c | 8 ++-- src/lv.c | 9 +++-- src/osa.c | 4 +- src/utils.h | 6 ++- tests/testthat/testStringdist.R | 18 ++++++++++ 26 files changed, 233 insertions(+), 179 deletions(-)
Title: Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal
Testing
Description: Fast and accurate trisomy prediction in non-invasive prenatal
testing.
Author: Dirk de Weerd, Lennart Johansson
Maintainer: Lennart Johansson <l.johansson@umcg.nl>
Diff between NIPTeR versions 1.0.0 dated 2015-11-06 and 1.0.1 dated 2016-01-02
DESCRIPTION | 12 +++---- MD5 | 56 +++++++++++++++++----------------- R/best_fit_beta.R | 12 +++++++ R/bin_sample.R | 16 +++++++++ R/chi_correction.R | 11 ++++++ R/control_group.R | 32 +++++++++++++++++++ R/diagnose_control_group.R | 6 +++ R/gc_correct.R | 10 ++++++ R/ncv_calculation.R | 7 ++++ R/prepare_ncv_template.R | 9 +++++ R/regression.R | 7 ++++ R/z_score.R | 7 ++++ build/vignette.rds |binary inst/doc/NIPTeR.Rmd | 5 +++ inst/doc/NIPTeR.html | 8 +++- man/add_samples_controlgroup.Rd | 12 +++++++ man/as_control_group.Rd | 11 ++++++ man/bin_bam_sample.Rd | 16 +++++++++ man/calculate_ncv_score.Rd | 8 ++++ man/calculate_z_score.Rd | 8 ++++ man/chi_correct.Rd | 11 ++++++ man/diagnose_control_group.Rd | 6 +++ man/gc_correct.Rd | 11 ++++++ man/match_control_group.Rd | 15 +++++++++ man/perform_regression.Rd | 7 ++++ man/prepare_ncv.Rd | 10 ++++++ man/remove_duplicates_controlgroup.Rd | 6 +++ man/remove_sample_controlgroup.Rd | 7 ++++ vignettes/NIPTeR.Rmd | 5 +++ 29 files changed, 295 insertions(+), 36 deletions(-)
Title: R for Amplicon-Sequencing-Based Microbial-Ecology
Description: Characterizing environmental microbiota diversity using amplicon-based next generation sequencing (NGS) data. Functions are developed to manipulate operational taxonomic unit (OTU) table, perform descriptive and inferential statistics, and generate publication-quality plots.
Author: Wen Chen, Joshua Simpson, C. Andre Levesque
Maintainer: Wen Chen <Wen.Chen@agr.gc.ca>
Diff between RAM versions 1.2.1.2 dated 2015-12-01 and 1.2.1.3 dated 2016-01-02
ChangeLog | 7 DESCRIPTION | 16 LICENSE | 2 MD5 | 198 ++++++------ NAMESPACE | 12 NEWS | 23 + R/assist.ado.R | 28 - R/core.R | 716 +++++++++++++++++++++---------------------- R/group.Taxa.R | 99 ++---- R/group_CLUST.R | 234 +++++++------- R/metadata.R | 721 +++++++++++++++++++++----------------------- R/ordination_functions.R | 8 R/phylo_taxonomy.R | 214 ++++++------- R/plot_misc.R | 107 ++---- R/process_data.R | 2 R/summary.R | 5 R/validation_functions.R | 36 +- build/RAM.pdf |binary man/ITS1_and_ITS2.Rd | 12 man/LCA.OTU.Rd | 42 +- man/META.clust.Rd | 54 +-- man/OTU.diversity.Rd | 52 +-- man/OTU.ord.Rd | 106 +++--- man/OTU.rarefy.Rd | 15 man/OTU.recap.Rd | 38 +- man/OTU.subsets.Rd | 35 -- man/RAM-package.Rd | 50 +-- man/RAM.dates.Rd | 15 man/RAM.factors.Rd | 65 +-- man/RAM.input.formatting.Rd | 17 - man/RAM.pal.Rd | 6 man/RAM.plotting.Rd | 98 ++--- man/RAM.rank.formatting.Rd | 20 - man/Taxa.ord.Rd | 118 +++---- man/alignment.Rd | 8 man/assist.NB.Rd | 49 +- man/assist.ado.Rd | 86 ++--- man/assist.ordination.Rd | 47 +- man/col.splitup.Rd | 52 +-- man/combine.OTU.Rd | 14 man/core.OTU.Rd | 35 +- man/core.OTU.rank.Rd | 36 +- man/core.Taxa.Rd | 51 +-- man/correlation.Rd | 89 ++--- man/data.clust.Rd | 75 ++-- man/data.revamp.Rd | 82 ++--- man/dissim.Rd | 92 ++--- man/dissim.heatmap.Rd | 101 +++--- man/dissim.plot.Rd | 122 +++---- man/diversity.indices.Rd | 61 +-- man/envis.NB.Rd | 53 +-- man/factor.abundance.Rd | 50 +-- man/filter.META.Rd | 39 +- man/filter.OTU.Rd | 22 - man/filter.Taxa.Rd | 26 - man/fread.OTU.Rd | 42 +- man/fread.meta.Rd | 16 man/get.rank.Rd | 56 +-- man/group.OTU.Rd | 56 +-- man/group.Taxa.bar.Rd | 82 ++--- man/group.Taxa.box.Rd | 34 +- man/group.abund.Taxa.Rd | 39 +- man/group.abundance.Rd | 52 +-- man/group.abundance.meta.Rd | 51 +-- man/group.diversity.Rd | 84 ++--- man/group.heatmap.Rd | 76 ++-- man/group.heatmap.simple.Rd | 100 +++--- man/group.indicators.Rd | 118 +++---- man/group.rich.Rd | 28 - man/group.spatial.Rd | 68 +--- man/group.spec.Rd | 29 - man/group.temporal.Rd | 51 +-- man/group.venn.Rd | 55 +-- man/location.formatting.Rd | 10 man/match.data.Rd | 27 - man/meta.Rd | 25 - man/network_data.Rd | 32 - man/pcoa.plot.Rd | 176 +++++----- man/percent.classified.Rd | 18 - man/phylo_taxonomy.Rd | 71 ++-- man/phylog_taxonomy.Rd | 72 ++-- man/read.OTU.Rd | 51 +-- man/read.meta.Rd | 14 man/reset.META.Rd | 23 - man/sample.locations.Rd | 83 ++--- man/sample.map.Rd | 49 +- man/sample.sites.Rd | 38 +- man/seq_var.Rd | 126 +++---- man/shared.OTU.Rd | 25 - man/shared.Taxa.Rd | 25 - man/tax.abund.Rd | 79 ++-- man/tax.fill.Rd | 69 +--- man/tax.split.Rd | 72 +--- man/theme_ggplot.Rd | 9 man/top.groups.plot.Rd | 54 +-- man/transpose.LCA.Rd | 9 man/transpose.OTU.Rd | 11 man/valid.OTU.Rd | 11 man/valid.taxonomy.Rd | 42 +- man/write.data.Rd | 21 - 100 files changed, 3250 insertions(+), 3390 deletions(-)
Title: Isotonic Proportional Hazards Model
Description: Nonparametric estimation of an isotonic covariate effect for proprotional hazards model.
Author: Yunro Chung [cre], Anastasia Ivanova, Michael G. Hudgens and Jason P. Fine
Maintainer: Yunro Chung <yunro@live.unc.edu>
Diff between isoph versions 0.4 dated 2015-11-22 and 0.5 dated 2016-01-02
DESCRIPTION | 12 +++-- MD5 | 24 ++++++----- NAMESPACE | 2 R/RcppExports.R |only R/isoph.R | 38 +++++++++++++----- R/isoph.td.R | 63 +++++++++++++++++++++++++----- R/isoph.ti.R | 104 +++++++++++++++++++++++++++++++++++++++++---------- R/newton.raphson.R |only R/picm.R | 9 ---- R/plot.isoph.R | 17 ++++---- R/print.isoph.R | 8 ++- man/isoph-package.Rd | 6 +- man/isoph.Rd | 46 ++++++++++------------ src/BTFft.cpp |only src/RcppExports.cpp |only 15 files changed, 227 insertions(+), 102 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.3.1 dated 2015-12-21 and 3.4.0 dated 2016-01-01
DESCRIPTION | 15 ++++++++------- MD5 | 15 ++++++++------- NEWS | 6 ++++++ R/admin1.R | 20 +++++++++++++++++--- R/startup_messages.R |only inst/doc/f-world-bank-data.html | 4 ++-- inst/doc/h-creating-your-own-maps.html | 2 +- inst/doc/i-creating-admin1-maps.html | 8 ++------ man/admin1_choropleth.Rd | 14 +++++++++++++- 9 files changed, 57 insertions(+), 27 deletions(-)
Title: The Transfer Entropy Package
Description: Estimates the transfer entropy from one time series to another, where each time series consists of continuous random variables. The transfer entropy is an extension of mutual information which takes into account the direction of information flow, under the assumption that the underlying processes can be described by a Markov model. Two estimation methods are provided. The first calculates transfer entropy as the difference of mutual information. Mutual information is estimated using the Kraskov method, which builds on a nearest-neighbor framework (see package references). The second estimation method estimate transfer entropy via the a generalized correlation sum.
Author: ANN Library: David Mount, Sunil Arya (see src/ann_1.1.2/Copyright.txt).
Transfer Entropy Packge: Ghazaleh Haratinezhad Torbati, Glenn Lawyer.
Maintainer: Ghazaleh Haratinezhad Torbati <ghazaleh@mpi-inf.mpg.de>
Diff between TransferEntropy versions 1.1 dated 2015-12-30 and 1.2 dated 2016-01-01
DESCRIPTION | 17 +++++++---------- MD5 | 8 ++++---- build/partial.rdb |binary inst/COPYRIGHTS | 4 ++-- src/Makevars.win | 2 +- 5 files changed, 14 insertions(+), 17 deletions(-)
More information about TransferEntropy at CRAN
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More information about tempcyclesdata at CRAN
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Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.2.1 dated 2015-11-27 and 1.2.2 dated 2016-01-01
DESCRIPTION | 7 +++---- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/wrappers.R | 7 ++++--- build/vignette.rds |binary data/exrates.RData |binary inst/doc/article.pdf |binary inst/doc/heavytails.pdf |binary man/svsample2.Rd | 5 ++++- 9 files changed, 23 insertions(+), 16 deletions(-)
Title: Tools Inspired by Stata to Manipulate Tabular Data
Description: A set of tools inspired by Stata to explore data.frames (summarize,
tabulate, xtile, pctile, binscatter, elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>
Diff between statar versions 0.4.0 dated 2015-12-30 and 0.5.0 dated 2016-01-01
statar-0.4.0/statar/R/fill_gap.R |only statar-0.4.0/statar/R/group.R |only statar-0.4.0/statar/R/set.R |only statar-0.4.0/statar/R/setna.R |only statar-0.4.0/statar/R/setpanel.R |only statar-0.4.0/statar/man/discard.Rd |only statar-0.4.0/statar/man/discard_if.Rd |only statar-0.4.0/statar/man/fill_gap.Rd |only statar-0.4.0/statar/man/group.Rd |only statar-0.4.0/statar/man/keep.Rd |only statar-0.4.0/statar/man/keep_if.Rd |only statar-0.4.0/statar/man/setdiscard.Rd |only statar-0.4.0/statar/man/setkeep.Rd |only statar-0.4.0/statar/man/setna.Rd |only statar-0.5.0/statar/DESCRIPTION | 6 statar-0.5.0/statar/MD5 | 73 ++--- statar-0.5.0/statar/NAMESPACE | 21 - statar-0.5.0/statar/R/count.R | 2 statar-0.5.0/statar/R/is.panel.R |only statar-0.5.0/statar/R/tlead-tlag.R | 18 - statar-0.5.0/statar/R/utils.R | 339 ++++++++++++++++++++------ statar-0.5.0/statar/README.md | 14 - statar-0.5.0/statar/build/vignette.rds |binary statar-0.5.0/statar/inst/doc/panel-data.Rmd | 74 ----- statar-0.5.0/statar/inst/doc/panel-data.html | 71 ----- statar-0.5.0/statar/inst/doc/vector.Rmd | 6 statar-0.5.0/statar/inst/doc/vector.html | 8 statar-0.5.0/statar/man/count.Rd | 5 statar-0.5.0/statar/man/elapsed.Rd | 4 statar-0.5.0/statar/man/find_duplicates.Rd | 2 statar-0.5.0/statar/man/is.panel.Rd | 41 +-- statar-0.5.0/statar/man/join.Rd | 2 statar-0.5.0/statar/man/pctile.Rd | 2 statar-0.5.0/statar/man/stat_binmean.Rd | 6 statar-0.5.0/statar/man/statar.Rd | 2 statar-0.5.0/statar/man/sum_up.Rd | 2 statar-0.5.0/statar/man/tab.Rd | 4 statar-0.5.0/statar/man/tag.Rd | 3 statar-0.5.0/statar/man/tempname.Rd | 2 statar-0.5.0/statar/man/tlead-tlag.Rd | 16 - statar-0.5.0/statar/man/winsorize.Rd | 3 statar-0.5.0/statar/man/xtile.Rd | 4 statar-0.5.0/statar/tests/testthat/test_lag.R | 4 statar-0.5.0/statar/vignettes/panel-data.Rmd | 74 ----- statar-0.5.0/statar/vignettes/vector.Rmd | 6 45 files changed, 414 insertions(+), 400 deletions(-)
Title: Tools for Preprocessing Combinations
Description: Preprocessing is often the most time-consuming phase in knowledge
discovery and preprocessing transformations interdependent in unexpected
ways. This package helps to make preprocessing faster and more effective. It
provides an S4 framework for creating and testing preprocessing combinations
for classification, clustering and outlier detection. The framework supports
user-defined and domain-specific preprocessors and preprocessing phases.
Default preprocessors can be used for low variance removal, missing value
imputation, scaling, outlier removal, noise smoothing, feature selection and
class imbalance correction.
Author: Markus Vattulainen
Maintainer: Markus Vattulainen <markus.vattulainen@gmail.com>
Diff between preprocomb versions 0.1.0 dated 2015-10-11 and 0.2.0 dated 2016-01-01
preprocomb-0.1.0/preprocomb/R/03BaseClass.R |only preprocomb-0.1.0/preprocomb/man/prc.Rd |only preprocomb-0.2.0/preprocomb/DESCRIPTION | 21 - preprocomb-0.2.0/preprocomb/MD5 | 46 +- preprocomb-0.2.0/preprocomb/NAMESPACE | 7 preprocomb-0.2.0/preprocomb/R/00Utils.R | 124 ------ preprocomb-0.2.0/preprocomb/R/01DataClass.R | 50 +- preprocomb-0.2.0/preprocomb/R/02PhaseClass.R | 3 preprocomb-0.2.0/preprocomb/R/03PreprocessorClass.R |only preprocomb-0.2.0/preprocomb/R/04GridClass.R | 158 +++++--- preprocomb-0.2.0/preprocomb/R/05PredictionControlClass.R | 191 +++++----- preprocomb-0.2.0/preprocomb/R/06PreProCombClass.R | 94 ++-- preprocomb-0.2.0/preprocomb/R/07AnalysisComponent.R |only preprocomb-0.2.0/preprocomb/R/08DefaultPreprocessorsAndPhases.R |only preprocomb-0.2.0/preprocomb/man/GridClass-class.Rd | 2 preprocomb-0.2.0/preprocomb/man/PreprocessorClass-class.Rd | 4 preprocomb-0.2.0/preprocomb/man/getpreprocessors.Rd | 4 preprocomb-0.2.0/preprocomb/man/getprogrammaticprediction.Rd |only preprocomb-0.2.0/preprocomb/man/initializedataclassobject.Rd |only preprocomb-0.2.0/preprocomb/man/prepro.Rd |only preprocomb-0.2.0/preprocomb/man/preprocomb.Rd | 20 - preprocomb-0.2.0/preprocomb/man/preprodefault.Rd |only preprocomb-0.2.0/preprocomb/man/setgrid.Rd | 6 preprocomb-0.2.0/preprocomb/man/setphase.Rd | 3 preprocomb-0.2.0/preprocomb/man/setpreprocessor.Rd | 25 - preprocomb-0.2.0/preprocomb/man/showrules.Rd |only preprocomb-0.2.0/preprocomb/man/testpreprocessors.Rd | 2 preprocomb-0.2.0/preprocomb/man/transformdata.Rd | 2 preprocomb-0.2.0/preprocomb/tests |only 29 files changed, 379 insertions(+), 383 deletions(-)
More information about MPLikelihoodWB at CRAN
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Title: Analyze Cricketers Based on ESPN Cricinfo Statsguru
Description: Tools for analyzing performances of cricketers based on stats in
ESPN Cricinfo Statsguru. The toolset can be used for analysis of Tests,ODIs
and Twenty20 matches of both batsmen and bowlers.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between cricketr versions 0.0.11 dated 2015-12-30 and 0.0.12 dated 2016-01-01
DESCRIPTION | 6 +- MD5 | 84 +++++++++++++++++++------------------- man/batsman4s.Rd | 7 ++- man/batsman4s6s.Rd | 6 ++ man/batsman6s.Rd | 6 ++ man/batsmanAvgRunsGround.Rd | 5 +- man/batsmanAvgRunsOpposition.Rd | 4 + man/batsmanContributionWonLost.Rd | 5 +- man/batsmanDismissals.Rd | 5 +- man/batsmanMeanStrikeRate.Rd | 5 +- man/batsmanMovingAverage.Rd | 5 +- man/batsmanPerfBoxHist.Rd | 6 ++ man/batsmanPerfForecast.Rd | 5 +- man/batsmanPerfHomeAway.Rd | 6 ++ man/batsmanRunsFreqPerf.Rd | 5 +- man/batsmanRunsLikelihood.Rd | 5 +- man/batsmanRunsPredict.Rd | 6 +- man/batsmanRunsRanges.Rd | 5 +- man/batsmanScoringRateODTT.Rd | 6 +- man/battingPerf3d.Rd | 5 +- man/bowlerAvgWktsGround.Rd | 5 +- man/bowlerAvgWktsOpposition.Rd | 5 +- man/bowlerContributionWonLost.Rd | 5 +- man/bowlerEconRate.Rd | 6 ++ man/bowlerHistWickets.Rd | 6 ++ man/bowlerMovingAverage.Rd | 4 + man/bowlerPerfForecast.Rd | 5 +- man/bowlerPerfHomeAway.Rd | 5 +- man/bowlerWktRateTT.Rd | 5 +- man/bowlerWktsFreqPercent.Rd | 5 +- man/bowlerWktsRunsPlot.Rd | 5 +- man/checkBatsmanInForm.Rd | 5 +- man/checkBowlerInForm.Rd | 5 +- man/clean.Rd | 3 - man/cleanBowlerData.Rd | 3 - man/relativeBatsmanSR.Rd | 8 ++- man/relativeBatsmanSRODTT.Rd | 10 +++- man/relativeBowlingER.Rd | 9 ++-- man/relativeBowlingERODTT.Rd | 11 +++- man/relativeBowlingPerf.Rd | 11 +++- man/relativeRunsFreqPerf.Rd | 9 ++-- man/relativeRunsFreqPerfODTT.Rd | 12 +++-- man/relativeWktRateTT.Rd | 9 ++-- 43 files changed, 231 insertions(+), 107 deletions(-)
Title: Bayesian Non- and Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 1.0.5 dated 2015-07-08 and 1.1.0 dated 2016-01-01
ChangeLog | 4 DESCRIPTION | 8 MD5 | 20 - R/bnpglm.R | 125 +++++++-- man/BNSP-package.Rd | 8 man/bnpglm.Rd | 306 +++++++++++++++++----- man/simD.rd | 3 src/OneResLtnt.c | 509 +++++++++++++++++++++++++------------ src/other.functions.h | 687 ++++++++++++++++++++++++++++++++++++++------------ src/pdfs.h | 194 +++++++++++++- src/sampling.h | 105 ++++++- 11 files changed, 1513 insertions(+), 456 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.9.1 dated 2015-12-31 and 0.9.2 dated 2016-01-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/render.R | 2 +- inst/NEWS | 5 +++++ 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Models and Tests for Departure from Hardy-Weinberg Equilibrium
and Independence Between Loci
Description: Fits models for genotypic disequilibria, as described in
Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986).
Contrast terms are available that account for first order interactions
between loci. Also implements, for a single locus in a single
population, a conditional exact test for Hardy-Weinberg equilibrium.
Author: John Maindonald, with \code{hwexact()} from Randall Johnson.
Maintainer: John Maindonald <John.Maindonald@anu.edu.au>
Diff between hwde versions 0.66 dated 2015-09-14 and 0.67 dated 2016-01-01
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- build/vignette.rds |binary man/MendelABC.Rd | 4 +--- 4 files changed, 9 insertions(+), 11 deletions(-)