Title: An R Package for Retrieval, Analysis, and Anomaly Calculation of
Daily Hydrologic Time Series Data
Description: This package imports U.S. Geological Survey (USGS) daily hydrologic data from USGS web services, plots the data, addresses some common data problems, and calculates and plots anomalies.
Author: Karen R. Ryberg and Aldo V. Vecchia
Maintainer: Karen R. Ryberg
Diff between waterData versions 1.0.3 dated 2013-12-14 and 1.0.4 dated 2014-11-18
DESCRIPTION | 11 +- MD5 | 45 +++++----- NAMESPACE | 4 NEWS | 8 + R/compAnom.R | 99 +++++++++++++----------- R/waterData-package.R | 4 build/vignette.rds |binary data/exampleWaterData.RData |binary inst/doc/vignette.R | 58 +++++++------- inst/doc/vignette.Rnw | 9 +- inst/doc/vignette.pdf |binary man/badDataSet.Rd | 2 man/cleanUp.Rd | 62 +++++++-------- man/compAnom.Rd | 181 +++++++++++++++++++------------------------- man/fillMiss.Rd | 129 ++++++++++++++----------------- man/importDVs.Rd | 152 +++++++++++++++++------------------- man/plotAnoms.Rd | 22 ++--- man/plotParam.Rd | 39 ++++----- man/q05054000LT.Rd |only man/summaryStats.Rd | 39 ++++----- man/tellMeSiteURL.Rd | 58 ++++++-------- man/tellMeURL.Rd | 124 +++++++++++++----------------- man/waterData-package.Rd | 133 +++++++++++++++----------------- vignettes/vignette.Rnw | 9 +- 24 files changed, 575 insertions(+), 613 deletions(-)
Title: Calculate Indices and Theoretical Properties of Protein
Sequences
Description: Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot XVG output files from GROMACS molecular dynamics package.
Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
Maintainer: Daniel Osorio
Diff between Peptides versions 1.0.1 dated 2014-10-16 and 1.0.2 dated 2014-11-18
Peptides-1.0.1/Peptides/man/AAcomp.Rd |only Peptides-1.0.1/Peptides/man/Boman.Rd |only Peptides-1.0.1/Peptides/man/MW.Rd |only Peptides-1.0.1/Peptides/man/Peptides-package.Rd |only Peptides-1.0.2/Peptides/DESCRIPTION | 15 - Peptides-1.0.2/Peptides/MD5 | 59 +++--- Peptides-1.0.2/Peptides/NAMESPACE | 1 Peptides-1.0.2/Peptides/NEWS |only Peptides-1.0.2/Peptides/R/aacomp.R | 6 Peptides-1.0.2/Peptides/R/aindex.R | 4 Peptides-1.0.2/Peptides/R/boman.R | 2 Peptides-1.0.2/Peptides/R/charge.R | 8 Peptides-1.0.2/Peptides/R/hmoment.R | 44 ++--- Peptides-1.0.2/Peptides/R/hydrophobicity.R | 15 - Peptides-1.0.2/Peptides/R/instaindex.R | 6 Peptides-1.0.2/Peptides/R/membpos.R | 45 +---- Peptides-1.0.2/Peptides/R/mw.R | 4 Peptides-1.0.2/Peptides/R/pI.R | 5 Peptides-1.0.2/Peptides/data/H.RData |binary Peptides-1.0.2/Peptides/data/pKscales.RData |binary Peptides-1.0.2/Peptides/inst/tests/runit.boman.R | 2 Peptides-1.0.2/Peptides/inst/tests/runit.charge.R | 6 Peptides-1.0.2/Peptides/inst/tests/runit.hmoment.R | 4 Peptides-1.0.2/Peptides/inst/tests/runit.mw.R | 2 Peptides-1.0.2/Peptides/inst/tests/runit.pI.R | 4 Peptides-1.0.2/Peptides/man/aacomp.Rd |only Peptides-1.0.2/Peptides/man/aindex.Rd | 5 Peptides-1.0.2/Peptides/man/boman.Rd |only Peptides-1.0.2/Peptides/man/charge.Rd | 36 ++-- Peptides-1.0.2/Peptides/man/h.Rd | 79 +++++++-- Peptides-1.0.2/Peptides/man/hmoment.Rd | 22 +- Peptides-1.0.2/Peptides/man/hydrophobicity.Rd | 180 ++++++++++++++------- Peptides-1.0.2/Peptides/man/membpos.Rd | 38 ++-- Peptides-1.0.2/Peptides/man/mw.Rd |only Peptides-1.0.2/Peptides/man/peptides-package.Rd |only 35 files changed, 347 insertions(+), 245 deletions(-)
Title: Analogue and weighted averaging methods for palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer
function models for prediction of environmental data from species
data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre],
Jari Oksanen [aut]
Maintainer: Gavin L. Simpson
Diff between analogue versions 0.14-0 dated 2014-08-29 and 0.16-0 dated 2014-11-18
analogue-0.14-0/analogue/R/analogue-deprecated.R |only analogue-0.14-0/analogue/R/plot3d.prcurve.R |only analogue-0.14-0/analogue/man/plot3d.prcurve-deprecated.Rd |only analogue-0.14-0/analogue/man/plot3d.prcurve.Rd |only analogue-0.16-0/analogue/DESCRIPTION | 12 - analogue-0.16-0/analogue/MD5 | 33 ++-- analogue-0.16-0/analogue/NAMESPACE | 12 - analogue-0.16-0/analogue/R/Stratiplot.R | 7 - analogue-0.16-0/analogue/R/plot.sppResponse.R | 46 +++--- analogue-0.16-0/analogue/R/rdaFit.R | 4 analogue-0.16-0/analogue/R/tran.R | 13 + analogue-0.16-0/analogue/inst/ChangeLog | 28 ++++ analogue-0.16-0/analogue/inst/NEWS.Rd | 27 +++ analogue-0.16-0/analogue/inst/doc/analogue_methods.pdf |binary analogue-0.16-0/analogue/man/Stratiplot.Rd | 8 + analogue-0.16-0/analogue/man/abernethy.Rd | 3 analogue-0.16-0/analogue/man/plot.sppResponse.Rd |only analogue-0.16-0/analogue/man/sppResponse.prcurve.Rd | 8 + analogue-0.16-0/analogue/man/tran.Rd | 20 ++ analogue-0.16-0/analogue/tests/Examples/analogue-Ex.Rout.save | 68 +--------- 20 files changed, 161 insertions(+), 128 deletions(-)
Title: Time Series Clustering Utilities
Description: This package contains a set of measures of dissimilarity between time series to perform time series clustering. Metrics based on raw data, on generating models and on the forecast behavior are implemented. Some additional utilities related to time series clustering are also provided, such as clustering algorithms and cluster evaluation metrics.
Author: Pablo Montero Manso, José Antonio Vilar
Maintainer: Pablo Montero
Diff between TSclust versions 1.2.2 dated 2014-10-28 and 1.2.3 dated 2014-11-18
ChangeLog | 4 +++ DESCRIPTION | 9 ++++--- MD5 | 55 +++++++++++++++++++++++----------------------- inst |only man/SAX.Rd | 2 + man/TSclust-package.Rd | 13 ++++++++++ man/cluster.evaluation.Rd | 3 ++ man/diss.ACF.Rd | 3 ++ man/diss.AR.LPC.CEPS.Rd | 2 + man/diss.AR.MAH.Rd | 3 ++ man/diss.AR.PIC.Rd | 3 ++ man/diss.CDM.Rd | 2 + man/diss.CID.Rd | 2 + man/diss.COR.Rd | 4 ++- man/diss.CORT.Rd | 3 ++ man/diss.DWT.Rd | 3 ++ man/diss.INT.PER.Rd | 5 +++- man/diss.NCD.Rd | 1 man/diss.PER.Rd | 3 ++ man/diss.PRED.Rd | 3 ++ man/diss.Rd | 4 +++ man/diss.SPEC.GLK.Rd | 3 ++ man/diss.SPEC.ISD.Rd | 3 ++ man/diss.SPEC.LLR.Rd | 2 + man/electricity.Rd | 3 ++ man/interest.rates.Rd | 3 ++ man/paired.tseries.Rd | 3 ++ man/pvalues.clust.Rd | 2 + man/synthetic.tseries.Rd | 3 ++ 29 files changed, 115 insertions(+), 34 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
Diff between secr versions 2.9.0 dated 2014-09-22 and 2.9.1 dated 2014-11-18
secr-2.9.0/secr/inst/extdata/stoatmask.txt |only secr-2.9.0/secr/inst/extdata/temppoly.txt |only secr-2.9.0/secr/inst/extdata/temppolyusage.txt |only secr-2.9.1/secr/DESCRIPTION | 10 secr-2.9.1/secr/MD5 | 166 ++++++------- secr-2.9.1/secr/NAMESPACE | 17 - secr-2.9.1/secr/NEWS | 38 +++ secr-2.9.1/secr/R/D.designdata.R | 23 + secr-2.9.1/secr/R/Dsurface.R | 76 ++++-- secr-2.9.1/secr/R/confint.secr.R | 31 +- secr-2.9.1/secr/R/derivedMS.R | 13 - secr-2.9.1/secr/R/empirical.R | 11 secr-2.9.1/secr/R/esa.R | 31 +- secr-2.9.1/secr/R/fxi.R | 7 secr-2.9.1/secr/R/homerange.R | 36 +- secr-2.9.1/secr/R/join.R | 6 secr-2.9.1/secr/R/methods.R | 28 -- secr-2.9.1/secr/R/par.secr.fit.R | 1 secr-2.9.1/secr/R/pdot.R | 18 - secr-2.9.1/secr/R/plot.mask.r | 22 - secr-2.9.1/secr/R/raster.R |only secr-2.9.1/secr/R/reduce.R | 12 secr-2.9.1/secr/R/regionN.R | 68 +++-- secr-2.9.1/secr/R/score.test.R | 59 ++-- secr-2.9.1/secr/R/secr.design.MS.R | 1 secr-2.9.1/secr/R/secr.fit.R | 246 ++++++++++++-------- secr-2.9.1/secr/R/secrloglik.R | 128 +++++----- secr-2.9.1/secr/R/sim.capthist.R | 8 secr-2.9.1/secr/R/sim.popn.R | 7 secr-2.9.1/secr/R/sim.secr.R | 4 secr-2.9.1/secr/R/snip.R | 9 secr-2.9.1/secr/R/suggest.buffer.R | 4 secr-2.9.1/secr/R/telemetry.R | 3 secr-2.9.1/secr/R/trap.builder.R | 68 +++-- secr-2.9.1/secr/R/utility.R | 97 ++++--- secr-2.9.1/secr/R/writeGPS.R | 10 secr-2.9.1/secr/inst/doc/secr-datainput.pdf |binary secr-2.9.1/secr/inst/doc/secr-densitysurfaces.pdf |binary secr-2.9.1/secr/inst/doc/secr-finitemixtures.pdf |binary secr-2.9.1/secr/inst/doc/secr-manual.pdf |binary secr-2.9.1/secr/inst/doc/secr-noneuclidean.pdf |only secr-2.9.1/secr/inst/doc/secr-overview.pdf |binary secr-2.9.1/secr/inst/doc/secr-parameterisations.pdf |binary secr-2.9.1/secr/inst/doc/secr-polygondetectors.pdf |binary secr-2.9.1/secr/inst/doc/secr-sound.pdf |binary secr-2.9.1/secr/inst/doc/secr-varyingeffort.pdf |binary secr-2.9.1/secr/man/DA.Rd | 2 secr-2.9.1/secr/man/DENSITY.Rd | 2 secr-2.9.1/secr/man/Dsurface.Rd | 3 secr-2.9.1/secr/man/OVpossum.Rd | 2 secr-2.9.1/secr/man/SPACECAP.Rd | 4 secr-2.9.1/secr/man/addTelemetry.Rd | 2 secr-2.9.1/secr/man/closedN.Rd | 7 secr-2.9.1/secr/man/contour.Rd | 10 secr-2.9.1/secr/man/coulombe.Rd | 2 secr-2.9.1/secr/man/details.Rd | 21 + secr-2.9.1/secr/man/detector.Rd | 3 secr-2.9.1/secr/man/empirical.Rd | 4 secr-2.9.1/secr/man/hcov.Rd | 2 secr-2.9.1/secr/man/homerange.Rd | 47 ++- secr-2.9.1/secr/man/make.mask.Rd | 4 secr-2.9.1/secr/man/mask.Rd | 4 secr-2.9.1/secr/man/mask.check.Rd | 4 secr-2.9.1/secr/man/ovenbird.Rd | 4 secr-2.9.1/secr/man/pdot.Rd | 6 secr-2.9.1/secr/man/plot.mask.Rd | 4 secr-2.9.1/secr/man/predictDsurface.Rd | 9 secr-2.9.1/secr/man/print.secr.Rd | 40 ++- secr-2.9.1/secr/man/randomHabitat.Rd | 4 secr-2.9.1/secr/man/reduce.capthist.Rd | 5 secr-2.9.1/secr/man/region.N.Rd | 2 secr-2.9.1/secr/man/secr-package.Rd | 10 secr-2.9.1/secr/man/secr.fit.Rd | 12 secr-2.9.1/secr/man/secrtest.Rd | 4 secr-2.9.1/secr/man/sim.popn.Rd | 20 + secr-2.9.1/secr/man/skink.Rd | 6 secr-2.9.1/secr/man/smooths.Rd | 12 secr-2.9.1/secr/man/snip.Rd | 2 secr-2.9.1/secr/man/strip.legend.Rd | 6 secr-2.9.1/secr/man/transformations.Rd | 4 secr-2.9.1/secr/man/trap.builder.Rd | 18 + secr-2.9.1/secr/man/troubleshooting.Rd | 6 secr-2.9.1/secr/man/userdist.Rd |only secr-2.9.1/secr/man/utility.Rd | 10 secr-2.9.1/secr/man/writeGPS.Rd | 9 secr-2.9.1/secr/src/secr.c | 54 +++- secr-2.9.1/secr/src/utils.c | 4 87 files changed, 997 insertions(+), 635 deletions(-)
Title: Compares the distribution of sister clades through a phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution). DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard
Diff between nodiv versions 0.9.1 dated 2014-11-13 and 0.9.2 dated 2014-11-18
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/General_figure_functions.R | 24 +++++------------------- R/Methods_for_data_objects.R | 12 +++++++++++- R/Methods_for_result_objects.R | 23 ++++++++++++----------- R/Node_based_analysis.R | 28 ---------------------------- R/Prepare_data.R | 37 ++++++++++++++++++++++++++++++++++++- man/nodiv-package.Rd | 4 ++-- man/plotSOS.Rd | 12 +++++++----- man/plot_nodes_phylo.Rd | 5 ++++- man/plot_points.Rd | 11 ++++++++--- 12 files changed, 101 insertions(+), 87 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-18 0.2
Title: Statistical Methods for the Analysis of Case-Control Point Data
Description: Various statistical methods for analyzing case-control point data.
The methods available closely follow those in chapter 6 of Applied Spatial
Statistics for Public Health Data by Waller and Gotway (2004).
Author: Joshua French
Maintainer: Joshua French
Diff between smacpod versions 1.0.0 dated 2014-11-01 and 1.1.1 dated 2014-11-18
smacpod-1.0.0/smacpod/R/Kdest.R |only smacpod-1.0.0/smacpod/R/kd.env.R |only smacpod-1.0.0/smacpod/R/logrr.env.R |only smacpod-1.0.0/smacpod/README.md |only smacpod-1.0.0/smacpod/man/kd.env.Rd |only smacpod-1.0.0/smacpod/man/logrr.env.Rd |only smacpod-1.1.1/smacpod/DESCRIPTION | 8 +- smacpod-1.1.1/smacpod/MD5 | 43 ++++++-------- smacpod-1.1.1/smacpod/NAMESPACE | 2 smacpod-1.1.1/smacpod/R/confenv.kdenv.R | 10 ++- smacpod-1.1.1/smacpod/R/kd.R |only smacpod-1.1.1/smacpod/R/kdest.R |only smacpod-1.1.1/smacpod/R/kdplus.test.R | 14 ++-- smacpod-1.1.1/smacpod/R/lines.cienv.R | 10 +-- smacpod-1.1.1/smacpod/R/logrr.R | 93 ++++++++++++++++++++++++++----- smacpod-1.1.1/smacpod/R/logrr.test.R | 2 smacpod-1.1.1/smacpod/R/qnn.test.R | 8 ++ smacpod-1.1.1/smacpod/R/spscan.test.R | 12 +++- smacpod-1.1.1/smacpod/R/tolenv.renv.R | 2 smacpod-1.1.1/smacpod/man/confenv.Rd | 9 ++- smacpod-1.1.1/smacpod/man/kd.Rd |only smacpod-1.1.1/smacpod/man/kdest.Rd | 10 ++- smacpod-1.1.1/smacpod/man/kdplus.test.Rd | 4 - smacpod-1.1.1/smacpod/man/lines.Rd | 10 +-- smacpod-1.1.1/smacpod/man/logrr.Rd | 44 +++++++++++--- smacpod-1.1.1/smacpod/man/logrr.test.Rd | 2 smacpod-1.1.1/smacpod/man/tolenv.Rd | 2 27 files changed, 198 insertions(+), 87 deletions(-)
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov
Maintainer: Martin Maechler
Diff between robustbase versions 0.91-1 dated 2014-05-01 and 0.92-1 dated 2014-11-18
ChangeLog | 42 DESCRIPTION | 13 MD5 | 170 - NAMESPACE | 48 R/AAA.R | 3 R/OGK.R | 29 R/adjoutlyingness.R | 63 R/anova-glmrob.R | 2 R/anova.lmrob.R | 2 R/biweight-funs.R | 2 R/classPC.R |only R/covMcd.R | 273 +- R/detmcd.R |only R/glmrobMqle.R | 4 R/lmrob.M.S.R | 13 R/lmrob.MM.R | 120 - R/lmrob.R | 47 R/ltsReg.R | 24 R/mc.R | 22 R/nlregrob.R | 25 R/nlrob.R | 317 ++ R/plot.lmrob.R | 3 R/psi-rho-funs.R | 10 R/rrcov.control.R | 17 TODO | 62 build/vignette.rds |binary data/biomassTill.rda |only demo |only inst/doc/lmrob_simulation.R | 41 inst/doc/lmrob_simulation.Rnw | 29 inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.Rnw | 35 inst/doc/psi_functions.pdf |binary inst/xtraR/ex-funs.R | 2 inst/xtraR/test_MCD.R | 332 +- man/M.psi.Rd | 2 man/adjOutlyingness.Rd | 49 man/biomassTill.Rd |only man/classPC.Rd |only man/covMcd.Rd | 104 man/lmrob..D..fit.Rd | 4 man/lmrob..M..fit.Rd | 4 man/lmrob.Rd | 2 man/lmrob.S.Rd | 3 man/lmrob.control.Rd | 92 man/lmrob.fit.Rd | 4 man/ltsReg.Rd | 11 man/mc.Rd | 10 man/milk.Rd | 8 man/nlrob-algos.Rd | 7 man/nlrob.Rd | 46 man/outlierStats.Rd |only man/pkg-internal.Rd | 28 man/rankMM.Rd |only man/rrcov.control.Rd | 31 man/weights.lmrob.Rd | 2 src/eigen.f | 292 +- src/init.c | 2 src/rf-common.f | 209 - src/rffastmcd.f | 1533 ++++++------- src/rfltsreg.f | 532 ++-- src/rllarsbi.f | 332 +- tests/MCD-specials.Rout.save | 181 - tests/MT-tst.R | 4 tests/NAcoef.Rout.save | 46 tests/Rsquared.Rout.save | 62 tests/glmrob-1.R | 9 tests/lmrob-data.Rout.save | 94 tests/lmrob-methods.R | 12 tests/lmrob-methods.Rout.save | 120 - tests/lmrob-outlierStats.R |only tests/lmrob-psifns.R | 2 tests/lmrob-psifns.Rout.save | 182 + tests/mc-strict.R | 69 tests/nlregrob-tst.R | 15 tests/nlrob-tst.R | 153 + tests/poisson-ex.R | 29 tests/tmcd.R | 139 - tests/tmcd.Rout.save | 4823 ++++++++++++++++++++++++++++++++++------- tests/weights.R | 2 tests/weights.Rout.save | 47 vignettes/lmrob_simulation.Rnw | 29 vignettes/psi-GGW.pdf |binary vignettes/psi-Hampel.pdf |binary vignettes/psi-Huber.pdf |binary vignettes/psi-LQQ.pdf |binary vignettes/psi-Welsh.pdf |binary vignettes/psi-bisquare.pdf |binary vignettes/psi-optimal.pdf |binary vignettes/psi_functions.Rnw | 35 90 files changed, 7903 insertions(+), 3207 deletions(-)
Title: Substitution and Indel Distances to Infer Evolutionary
Relationships
Description: sidier is a library and R package for evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
Author: A. Jesus Muñoz Pajares
Maintainer: A.J. Muñoz-Pajares
Diff between sidier versions 2.3 dated 2013-08-09 and 3.0 dated 2014-11-18
sidier-2.3/sidier/sidier_2.3.tar.gz |only sidier-3.0/sidier/DESCRIPTION | 21 +- sidier-3.0/sidier/MD5 | 86 +++++--- sidier-3.0/sidier/NAMESPACE | 11 - sidier-3.0/sidier/NEWS |only sidier-3.0/sidier/R/BARRIEL.R | 2 sidier-3.0/sidier/R/FindHaplo.R | 45 +++- sidier-3.0/sidier/R/GetHaplo.R | 3 sidier-3.0/sidier/R/HapPerPop.R | 2 sidier-3.0/sidier/R/MCIC.R | 18 - sidier-3.0/sidier/R/NINA.thr.R |only sidier-3.0/sidier/R/SIC.R | 5 sidier-3.0/sidier/R/colour.scheme.R |only sidier-3.0/sidier/R/distance.comb.R | 97 +++++++-- sidier-3.0/sidier/R/double.plot.R |only sidier-3.0/sidier/R/mergeNodes.R |only sidier-3.0/sidier/R/mutation.network.R |only sidier-3.0/sidier/R/mutationSummary.R | 165 +++++++++++++++- sidier-3.0/sidier/R/nt.gap.comb.R | 19 + sidier-3.0/sidier/R/perc.thr.R | 62 ++++-- sidier-3.0/sidier/R/pie.network.R |only sidier-3.0/sidier/R/pop.dist.R | 14 - sidier-3.0/sidier/R/simplify.network.R |only sidier-3.0/sidier/R/single.network.R | 32 ++- sidier-3.0/sidier/R/spatial.plot.R |only sidier-3.0/sidier/R/zero.thr.R |only sidier-3.0/sidier/data |only sidier-3.0/sidier/inst |only sidier-3.0/sidier/man/BARRIEL.Rd | 31 +-- sidier-3.0/sidier/man/Example_Spatial.plot_Alignment.Rd |only sidier-3.0/sidier/man/FIFTH.Rd | 21 +- sidier-3.0/sidier/man/FindHaplo.Rd | 27 +- sidier-3.0/sidier/man/GetHaplo.Rd | 34 ++- sidier-3.0/sidier/man/HapPerPop.Rd | 58 ++++- sidier-3.0/sidier/man/MCIC.Rd | 20 + sidier-3.0/sidier/man/NINA.thr.Rd |only sidier-3.0/sidier/man/SIC.Rd | 27 +- sidier-3.0/sidier/man/alignExample.Rd |only sidier-3.0/sidier/man/colour.scheme.Rd |only sidier-3.0/sidier/man/distance.comb.Rd | 43 +++- sidier-3.0/sidier/man/double.plot.Rd |only sidier-3.0/sidier/man/ex_Coords.Rd |only sidier-3.0/sidier/man/ex_alignment1.Rd |only sidier-3.0/sidier/man/mergeNodes.Rd |only sidier-3.0/sidier/man/mutation.network.Rd |only sidier-3.0/sidier/man/mutationSummary.Rd | 45 ++-- sidier-3.0/sidier/man/nt.gap.comb.Rd | 35 +-- sidier-3.0/sidier/man/perc.thr.Rd | 91 +++----- sidier-3.0/sidier/man/pie.network.Rd |only sidier-3.0/sidier/man/pop.dist.Rd | 27 +- sidier-3.0/sidier/man/sidier-package.Rd | 38 +-- sidier-3.0/sidier/man/simplify.network.Rd |only sidier-3.0/sidier/man/simuEvolution.Rd | 2 sidier-3.0/sidier/man/single.network.Rd | 49 +--- sidier-3.0/sidier/man/spatial.plot.Rd |only sidier-3.0/sidier/man/zero.thr.Rd |only 56 files changed, 789 insertions(+), 341 deletions(-)
Title: rPref
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator, and some
generalizations (database preferences).
Author: Patrick Roocks
Maintainer: Patrick Roocks
Diff between rPref versions 0.2 dated 2014-10-14 and 0.3 dated 2014-11-18
DESCRIPTION | 11 +- MD5 | 55 ++++++------ NAMESPACE | 5 - NEWS | 16 +-- R/base-pref.r | 4 R/complex-pref.r | 42 +++++++-- R/pref-classes.r | 211 +++++++++++++++++++++++++++++++++++++++++------ R/pref-eval.r | 10 +- R/rPref.r | 4 R/show-pref.r |only R/visualize.r | 45 ++++++++-- inst/test/test-hasse.R | 12 +- inst/test/test-psel.R | 22 +++- inst/test/test-strings.R |only man/base_pref.Rd | 6 - man/base_pref_macros.Rd | 2 man/complex_pref.Rd | 15 ++- man/get_btg.Rd | 10 +- man/get_hasse_diag.Rd |only man/plot_front.Rd | 2 man/psel.Rd | 10 +- man/rPref.Rd | 6 - man/show.query.Rd |only src/hasse.cpp | 103 +++++++++------------- src/hasse.h |only src/pref-classes.cpp | 68 +++++++++------ src/pref-classes.h | 20 +++- src/psel-par-top.cpp | 29 +++++- src/psel-par.cpp | 17 +++ src/scalagon.cpp | 19 ++-- src/scalagon.h | 2 31 files changed, 514 insertions(+), 232 deletions(-)
Title: Phylogenetic Linear Regression
Description: the phylolm package provides functions for fitting phylogenetic linear regression models and phylogenetic logistic regression. 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.
Author: Lam Si Tung Ho [aut, cre],
Cecile Ane [aut],
Robert Lachlan [ctb],
Kelsey Tarpinian [ctb]
Maintainer: Lam Si Tung Ho
Diff between phylolm versions 2.1 dated 2014-06-05 and 2.2 dated 2014-11-18
DESCRIPTION | 21 MD5 | 31 - R/OUshifts.R |only R/phyloglm.R | 1033 ++++++++++++++++++++++++------------------- R/phylolm.R | 636 +++++++++++++------------- data |only man/OUshifts-methods.Rd |only man/OUshifts.Rd |only man/flowerSize.Rd |only man/flowerTree.Rd |only man/phyloglm-methods.Rd | 68 +- man/phyloglm.Rd | 181 +++---- man/phylolm-methods.Rd | 106 ++-- man/phylolm-package.Rd | 46 - man/phylolm.Rd | 252 +++++----- man/rTrait.Rd | 102 ++-- man/rbinTrait.Rd | 86 +-- man/three.point.compute.Rd | 126 ++--- man/transf.branch.lengths.Rd | 180 +++---- 19 files changed, 1511 insertions(+), 1357 deletions(-)
Title: Extreme Bounds Analysis (EBA)
Description: An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Author: Marek Hlavac
Maintainer: Marek Hlavac
Diff between ExtremeBounds versions 0.1.4.1 dated 2014-05-23 and 0.1.4.2 dated 2014-11-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/ExtremeBounds-internal.R | 7 ++++--- inst/CITATION | 4 ++-- inst/ChangeLog | 3 +++ inst/doc/ExtremeBounds.pdf |binary man/ExtremeBounds.Rd | 2 +- man/eba.Rd | 2 +- man/hist.eba.Rd | 2 +- man/print.eba.Rd | 2 +- 10 files changed, 26 insertions(+), 22 deletions(-)
Title: Bayesian canonical correlation analysis and group factor
analysis
Description: Variational Bayesian algorithm for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA)
Author: Seppo Virtanen, Eemeli Leppaaho and Arto Klami
Maintainer: Seppo Virtanen
Diff between CCAGFA versions 1.0.3 dated 2013-05-06 and 1.0.4 dated 2014-11-18
DESCRIPTION | 16 - MD5 | 13 - NEWS | 6 R/CCAGFA.R | 456 ++++++++++++++++++++++++++++++++++++-------------- man/CCAGFA-package.Rd | 16 - man/GFA.Rd | 14 + man/getDefaultOpts.Rd | 9 man/gradEuv.Rd |only 8 files changed, 382 insertions(+), 148 deletions(-)
Title: C5.0 Decision Trees and Rule-Based Models
Description: C5.0 decision trees and rule-based models for pattern recognition
Author: Max Kuhn, Steve Weston, Nathan Coulter. C code for C5.0 by R. Quinlan
Maintainer: Max Kuhn
Diff between C50 versions 0.1.0-19 dated 2014-06-07 and 0.1.0-21 dated 2014-11-18
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/predict.C5.0.R | 8 +++++++- 3 files changed, 13 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-06 1.0-1
2014-11-04 1.0
Title: Extraction of Business Financial Information from XBRL Documents
Description:
XBRL is a package suited to extract business financial information from
an Extensible Business Reporting Language (XBRL) instance file and the
associated collection of files that defines its Discoverable Taxonomy
Set (DTS). These files are usually disseminated across different remote
locations.
XBRL documents employ many technologies defined by XML standards, such
as XML Schema, Namespaces, XLink, and XPath, which make the extraction
of information involved. The functions provided by this package
address this complexity, returning data frames containing the enclosed
information readily available to perform analyses.
XBRL has been successfully tested in analyzing 10-K and 10-Q
submissions from USA filing companies that are publicly available at
the EDGAR system of the Securities and Exchange Commission (SEC).
As published taxonomy files (such as
"http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd")
are immutable and are used by most filers, XBRL offers the option of
downloading them only the first time they are referred, keeping a
local cache copy that can be used from then on. This speeds-up the
process, specially on slow connections.
XBRL is not and does not aim to be (at least yet) a validating XBRL
processor.
XBRL is still a work in progress. As such, functions and produced data
frames may change structure in future versions until stabilization.
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso
Diff between XBRL versions 0.99.12 dated 2014-08-11 and 0.99.13 dated 2014-11-18
ChangeLog | 7 +++++++ DESCRIPTION | 11 +++++------ MD5 | 8 ++++---- NAMESPACE | 2 +- src/xbrlProcessFacts.cpp | 3 +++ 5 files changed, 20 insertions(+), 11 deletions(-)
Title: Estimation of spatial tail dependence models
Description: Provides functions implementing the pairwise M-estimator for
parametric models for stable tail dependence functions described in "An
M-estimator of spatial tail dependence"
(Einmahl, J.H.J., Kiriliouk, A., Krajina, A. and Segers, J., 2014).
See http://arxiv.org/abs/1403.1975.
Author: Anna Kiriliouk, Johan Segers
Maintainer: Anna Kiriliouk
Diff between spatialTailDep versions 1.0.1 dated 2014-08-14 and 1.0.2 dated 2014-11-18
DESCRIPTION | 6 +- MD5 | 26 +++++----- NAMESPACE | 1 NEWS | 6 ++ R/gridUtilities.r | 6 +- data/KNMIdata.rda |binary man/AsymVar.Rd | 41 +++++------------ man/KNMIdata.Rd | 23 ++++----- man/Mestimator.Rd | 112 +++++++++++++++++------------------------------ man/pairCoordinates.Rd | 15 ++---- man/selectPairIndices.Rd | 23 ++------- man/spatialTailDep.Rd | 72 ++++++++++-------------------- man/tailInt.Rd | 35 +++++--------- man/tailIntEmp.Rd | 28 +++-------- 14 files changed, 150 insertions(+), 244 deletions(-)
More information about spatialTailDep at CRAN
Permanent link
Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in the Global
Charcoal Database. Main functionalities includes data extraction and sites selection,
transformation and interpolation of the charcoal records as well as compositing.
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez
Diff between paleofire versions 1.1.3 dated 2014-05-22 and 1.1.4 dated 2014-11-18
DESCRIPTION | 23 +++++++---------- MD5 | 31 +++++++++++++++-------- NAMESPACE | 8 ++--- R/pfCompositeLF.R | 4 ++ R/pfDotMap.r | 24 +++++++++++------ R/pfGridding.R | 62 ++++++++++++++++++++++++++++------------------ R/pfPublication.R | 4 ++ R/pfToKml.R |only R/zzz.R | 19 +++----------- build |only inst |only man/1paleofiRe-package.Rd | 5 ++- man/pfCompositeLF.Rd | 2 - man/pfToKml.Rd |only man/plot.pfGridding.Rd | 4 ++ vignettes |only 16 files changed, 107 insertions(+), 79 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data. Including multivariate cumulative incidence models, and
bivariate random effects probit models (Liability models). Also contains
two-stage binomial modelling that can do pairwise odds-ratio dependence
modelling based marginal logistic regression models. This is an alternative
to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst
Diff between mets versions 0.2.8 dated 2014-05-13 and 1.0 dated 2014-11-18
DESCRIPTION | 15 MD5 | 203 +++++----- NAMESPACE | 39 +- NEWS | 22 + R/RcppExports.R |only R/bicomprisk.R | 22 + R/bicomprisksim.R |only R/binomial.twostage.R | 80 ++++ R/biprobit.R | 779 +++++++++++++++++++++++++++++++++--------- R/biprobit.strata.R | 23 - R/biprobit.time.R |only R/bptwin.R | 63 +-- R/bptwin2.R | 2 R/casewise.R | 61 ++- R/claytonakes.R | 14 R/coef.biprobit.R | 2 R/cor.R | 42 +- R/cumh.R | 6 R/divide.conquer.R |only R/event.R | 98 +++++ R/fastpattern.R | 14 R/fastreshape.R | 46 +- R/ipw.R | 116 ++++-- R/jumptimes.R |only R/lifetable.R | 61 ++- R/logLik.biprobit.R | 2 R/methodstwinlm.R | 40 +- R/mets-package.R | 3 R/newbptwin.R |only R/npc.R | 11 R/phreg.R | 53 +- R/phreg.par.R | 99 +++-- R/plot.bptwin.R | 2 R/plotcr.R | 36 + R/predict.biprobit.R |only R/print.biprobit.R | 2 R/print.summary.biprobit.R | 54 ++ R/score.biprobit.R | 2 R/sim.bptwin.R | 2 R/sim.clayton.oakes.R | 7 R/summary.biprobit.R | 171 +++++++-- R/summary.bptwin.R | 19 - R/tetrachor.R |only R/twin.clustertrunc.r |only R/twinlm.R | 12 R/twinlm.time.R | 123 +++--- R/twinlm2.R | 343 ------------------ R/twostage.R | 45 +- R/utils.R | 16 R/vcov.biprobit.R | 2 demo |only man/ClaytonOakes.Rd | 2 man/Dbvn.Rd | 2 man/Event.Rd |only man/Grandom.cif.Rd | 4 man/aalenfrailty.Rd | 2 man/back2timereg.Rd | 2 man/bicomprisk.Rd | 14 man/binomial.twostage.Rd | 5 man/biprobit.Rd |only man/blocksample.Rd | 2 man/bptwin.Rd | 20 - man/casewise.Rd | 4 man/casewise.test.Rd | 17 man/concordance.Rd | 2 man/cor.cif.Rd | 8 man/dermalridges.Rd | 2 man/dermalridgesMZ.Rd | 2 man/divide.conquer.Rd |only man/divide.conquer.timereg.Rd |only man/easy.binomial.twostage.Rd | 4 man/easy.twostage.Rd | 2 man/fast.approx.Rd | 2 man/fast.pattern.Rd | 16 man/fast.reshape.Rd | 8 man/internal.Rd | 4 man/ipw.Rd | 28 + man/lifetable.matrix.Rd | 6 man/mena.Rd | 2 man/mets-package.Rd | 2 man/migr.Rd | 2 man/multcif.Rd | 2 man/np.Rd | 2 man/phreg.Rd | 8 man/plack.cif.Rd | 2 man/printcasewisetest.Rd | 2 man/prt.Rd | 2 man/random.cif.Rd | 8 man/simAalenFrailty.Rd | 2 man/simClaytonOakes.Rd | 7 man/simClaytonOakesWei.Rd | 2 man/summary.cor.Rd | 6 man/test.conc.Rd | 2 man/twin.clustertrunc.Rd |only man/twinbmi.Rd | 2 man/twinlm.Rd | 6 man/twinsim.Rd | 2 man/twinstut.Rd | 2 man/twostage.Rd | 2 src/RcppExports.cpp |only src/binomial-plackett.cpp | 119 ++++++ src/biprobit.cpp | 222 ++++++++--- src/claytonoakes.cpp | 91 ++++ src/cor.cpp | 2 src/fastcox.cpp | 113 +++--- src/fastcox.h | 5 src/plackettMLE.cpp | 78 +++- src/tools.cpp | 9 src/tools.h | 6 109 files changed, 2399 insertions(+), 1221 deletions(-)
Title: Kernel Regression Smoothing with Local or Global Plug-in
Bandwidth
Description: Kernel regression smoothing with adaptive local or global plug-in
bandwidth selection.
Author: Eva Herrmann
Maintainer: Martin Maechler
Diff between lokern versions 1.1-5 dated 2013-11-19 and 1.1-6 dated 2014-11-18
lokern-1.1-5/lokern/data/xSim.rda |only lokern-1.1-6/lokern/ChangeLog | 5 ++++ lokern-1.1-6/lokern/DESCRIPTION | 9 ++++---- lokern-1.1-6/lokern/MD5 | 30 +++++++++++++-------------- lokern-1.1-6/lokern/NAMESPACE | 1 lokern-1.1-6/lokern/R/glkerns.R | 4 +-- lokern-1.1-6/lokern/R/lokerns.R | 3 ++ lokern-1.1-6/lokern/TODO | 16 +++++++++----- lokern-1.1-6/lokern/data/xSim.R |only lokern-1.1-6/lokern/man/KernS-methods.Rd | 24 +++++++++++++-------- lokern-1.1-6/lokern/man/glkerns.Rd | 7 ++++-- lokern-1.1-6/lokern/man/lokerns.Rd | 9 +++++--- lokern-1.1-6/lokern/src/auxkerns.f | 6 ++--- lokern-1.1-6/lokern/src/glkerns.f | 11 ++++------ lokern-1.1-6/lokern/src/lokerns.f | 12 +++++----- lokern-1.1-6/lokern/tests/lok1.R | 2 + lokern-1.1-6/lokern/tests/lok1.Rout.save | 34 ++++++++++++++++++++++++++++--- 17 files changed, 114 insertions(+), 59 deletions(-)
Title: Latent Variable Models
Description: Estimation and simulation of latent variable models
Author: Klaus K. Holst
Maintainer: Klaus K. Holst
Diff between lava versions 1.2.6 dated 2014-05-07 and 1.3 dated 2014-11-18
lava-1.2.6/lava/R/estimate.R |only lava-1.3/lava/DESCRIPTION | 15 - lava-1.3/lava/INDEX | 14 - lava-1.3/lava/MD5 | 353 +++++++++++++------------- lava-1.3/lava/NAMESPACE | 29 +- lava-1.3/lava/NEWS | 28 +- lava-1.3/lava/R/Missing.R | 72 ++++- lava-1.3/lava/R/addattr.R | 4 lava-1.3/lava/R/addhook.R | 1 lava-1.3/lava/R/addvar.R | 17 - lava-1.3/lava/R/assoc.R |only lava-1.3/lava/R/baptize.R | 2 lava-1.3/lava/R/bootstrap.R | 10 lava-1.3/lava/R/cancel.R | 4 lava-1.3/lava/R/categorical.R | 41 ++- lava-1.3/lava/R/children.R | 8 lava-1.3/lava/R/coef.R | 8 lava-1.3/lava/R/compare.R | 38 +- lava-1.3/lava/R/confint.R | 4 lava-1.3/lava/R/constrain.R | 6 lava-1.3/lava/R/correlation.R | 2 lava-1.3/lava/R/covariance.R | 8 lava-1.3/lava/R/curereg.R | 38 +- lava-1.3/lava/R/deriv.R | 6 lava-1.3/lava/R/distribution.R | 179 +++++++++---- lava-1.3/lava/R/dsort.R |only lava-1.3/lava/R/effects.R | 10 lava-1.3/lava/R/endogenous.R | 8 lava-1.3/lava/R/equivalence.R | 2 lava-1.3/lava/R/estimate.default.R | 146 +++++++--- lava-1.3/lava/R/estimate.lvm.R |only lava-1.3/lava/R/estimate.multigroup.R | 5 lava-1.3/lava/R/exogenous.R | 10 lava-1.3/lava/R/finalize.R | 79 ++--- lava-1.3/lava/R/fix.R | 22 - lava-1.3/lava/R/formula.R | 4 lava-1.3/lava/R/functional.R | 4 lava-1.3/lava/R/glmest.R | 66 ++-- lava-1.3/lava/R/gof.R | 15 - lava-1.3/lava/R/graph.R | 13 lava-1.3/lava/R/graph2lvm.R | 2 lava-1.3/lava/R/heavytail.R | 4 lava-1.3/lava/R/iid.R | 13 lava-1.3/lava/R/index.sem.R | 24 + lava-1.3/lava/R/information.R | 10 lava-1.3/lava/R/kill.R | 8 lava-1.3/lava/R/labels.R | 88 +++--- lava-1.3/lava/R/latent.R | 10 lava-1.3/lava/R/lava-package.R | 2 lava-1.3/lava/R/lmers.R |only lava-1.3/lava/R/logLik.R | 10 lava-1.3/lava/R/manifest.R | 8 lava-1.3/lava/R/measurement.R | 2 lava-1.3/lava/R/merge.R | 68 +++-- lava-1.3/lava/R/model.R | 18 - lava-1.3/lava/R/model.frame.R | 4 lava-1.3/lava/R/modelPar.R | 8 lava-1.3/lava/R/modelVar.R | 4 lava-1.3/lava/R/modelsearch.R | 2 lava-1.3/lava/R/moments.R | 4 lava-1.3/lava/R/multinomial.R | 129 ++++++++- lava-1.3/lava/R/multipletesting.R |only lava-1.3/lava/R/nodecolor.R | 4 lava-1.3/lava/R/normal.R | 39 ++ lava-1.3/lava/R/optims.R | 6 lava-1.3/lava/R/ordinal.R | 53 ++- lava-1.3/lava/R/ordreg.R | 16 - lava-1.3/lava/R/parameter.R | 4 lava-1.3/lava/R/parpos.R | 10 lava-1.3/lava/R/pars.R | 4 lava-1.3/lava/R/path.R | 18 - lava-1.3/lava/R/pcor.R | 34 +- lava-1.3/lava/R/plot.R | 51 +-- lava-1.3/lava/R/predict.R | 4 lava-1.3/lava/R/print.R | 29 -- lava-1.3/lava/R/profile.R | 2 lava-1.3/lava/R/randomslope.R | 6 lava-1.3/lava/R/regression.R | 162 ++++++----- lava-1.3/lava/R/residuals.R | 6 lava-1.3/lava/R/score.R | 10 lava-1.3/lava/R/sim.R | 155 +++++++---- lava-1.3/lava/R/subgraph.R | 32 +- lava-1.3/lava/R/subset.R | 2 lava-1.3/lava/R/summary.R | 14 - lava-1.3/lava/R/survival.R | 4 lava-1.3/lava/R/transform.R | 22 - lava-1.3/lava/R/utils.R | 16 - lava-1.3/lava/R/vars.R | 10 lava-1.3/lava/R/vcov.R | 4 lava-1.3/lava/R/weight.R | 2 lava-1.3/lava/R/zclick.R | 2 lava-1.3/lava/R/zcolorbar.R | 40 +- lava-1.3/lava/R/zconfband.R | 5 lava-1.3/lava/R/zgetmplus.R | 6 lava-1.3/lava/R/zimages.R | 86 ++++-- lava-1.3/lava/R/zksmooth.R |only lava-1.3/lava/R/zoperators.R | 15 - lava-1.3/lava/demo/00Index | 2 lava-1.3/lava/inst/doc/reference.pdf |binary lava-1.3/lava/man/By.Rd | 17 - lava-1.3/lava/man/Col.Rd | 22 - lava-1.3/lava/man/Combine.Rd | 6 lava-1.3/lava/man/Expand.Rd | 12 lava-1.3/lava/man/Graph.Rd | 9 lava-1.3/lava/man/Missing.Rd | 59 +++- lava-1.3/lava/man/Model.Rd | 13 lava-1.3/lava/man/PD.Rd | 33 +- lava-1.3/lava/man/Range.lvm.Rd | 6 lava-1.3/lava/man/addvar.Rd | 6 lava-1.3/lava/man/baptize.Rd | 6 lava-1.3/lava/man/blockdiag.Rd | 8 lava-1.3/lava/man/bmd.Rd | 9 lava-1.3/lava/man/bmidata.Rd | 2 lava-1.3/lava/man/bootstrap.Rd | 6 lava-1.3/lava/man/bootstrap.lvm.Rd | 47 +-- lava-1.3/lava/man/brisa.Rd | 2 lava-1.3/lava/man/calcium.Rd | 9 lava-1.3/lava/man/cancel.Rd | 6 lava-1.3/lava/man/children.Rd | 9 lava-1.3/lava/man/click.Rd | 30 +- lava-1.3/lava/man/closed.testing.Rd |only lava-1.3/lava/man/colorbar.Rd | 28 +- lava-1.3/lava/man/compare.Rd | 6 lava-1.3/lava/man/confband.Rd | 36 +- lava-1.3/lava/man/confint.lvmfit.Rd | 61 +--- lava-1.3/lava/man/constrain-set.Rd | 99 +++---- lava-1.3/lava/man/correlation.Rd | 6 lava-1.3/lava/man/covariance.Rd | 81 ++--- lava-1.3/lava/man/curereg.Rd | 24 - lava-1.3/lava/man/devcoords.Rd | 18 - lava-1.3/lava/man/dsort.Rd |only lava-1.3/lava/man/equivalence.Rd | 27 - lava-1.3/lava/man/estimate.default.Rd | 67 ++-- lava-1.3/lava/man/estimate.lvm.Rd | 130 ++++----- lava-1.3/lava/man/eventTime.Rd | 29 +- lava-1.3/lava/man/getMplus.Rd | 9 lava-1.3/lava/man/getSAS.Rd | 16 - lava-1.3/lava/man/gof.Rd | 51 +-- lava-1.3/lava/man/hubble.Rd | 9 lava-1.3/lava/man/hubble2.Rd | 2 lava-1.3/lava/man/iid.Rd | 14 - lava-1.3/lava/man/images.Rd |only lava-1.3/lava/man/indoorenv.Rd | 2 lava-1.3/lava/man/intercept.Rd | 46 +-- lava-1.3/lava/man/internal.Rd | 6 lava-1.3/lava/man/kill.Rd | 11 lava-1.3/lava/man/ksmooth2.Rd |only lava-1.3/lava/man/labels-set.Rd | 29 +- lava-1.3/lava/man/lava-package.Rd | 6 lava-1.3/lava/man/lava.options.Rd | 28 -- lava-1.3/lava/man/lvm.Rd | 20 - lava-1.3/lava/man/makemissing.Rd | 15 - lava-1.3/lava/man/missingdata.Rd | 14 - lava-1.3/lava/man/modelsearch.Rd | 19 - lava-1.3/lava/man/multinomial.Rd | 16 - lava-1.3/lava/man/nldata.Rd | 2 lava-1.3/lava/man/nsem.Rd | 2 lava-1.3/lava/man/op_concat.Rd | 11 lava-1.3/lava/man/op_match.Rd | 6 lava-1.3/lava/man/ordreg.Rd | 17 - lava-1.3/lava/man/org.Rd | 36 +- lava-1.3/lava/man/parpos.Rd | 6 lava-1.3/lava/man/partialcor.Rd | 15 - lava-1.3/lava/man/path.Rd | 60 ++-- lava-1.3/lava/man/pdfconvert.Rd | 14 - lava-1.3/lava/man/plot.lvm.Rd | 59 ++-- lava-1.3/lava/man/plotConf.Rd | 76 ++--- lava-1.3/lava/man/predict.lvm.Rd | 22 - lava-1.3/lava/man/regression-set.Rd | 121 ++++---- lava-1.3/lava/man/revdiag.Rd | 10 lava-1.3/lava/man/scheffe.Rd | 8 lava-1.3/lava/man/semdata.Rd | 2 lava-1.3/lava/man/serotonin.Rd | 44 +-- lava-1.3/lava/man/serotonin2.Rd | 2 lava-1.3/lava/man/sim.Rd | 85 ++++-- lava-1.3/lava/man/subset.lvm.Rd | 14 - lava-1.3/lava/man/timedep.Rd | 25 - lava-1.3/lava/man/toformula.Rd | 10 lava-1.3/lava/man/tr.Rd | 4 lava-1.3/lava/man/trim.Rd | 9 lava-1.3/lava/man/twindata.Rd | 20 - lava-1.3/lava/man/vars.Rd | 65 ++-- lava-1.3/lava/tests/testthat/test-constrain.R | 19 - 183 files changed, 2637 insertions(+), 1933 deletions(-)
Title: Fishery Science Methods and Models in R
Description: Fishery science methods and models from literature and colleague contributions
Author: Gary A. Nelson
Maintainer: Gary A. Nelson
Diff between fishmethods versions 1.6-0 dated 2014-03-10 and 1.7-0 dated 2014-11-18
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++++-------------- R/alk.R | 44 ++++++++++++++++++++++++++++++-------------- R/catchmsy.R |only R/clus.lf.R | 18 ++++++++++-------- R/clus.str.lf.R | 15 ++++++++------- R/convmort.R | 2 +- data/lingcod.rda |only man/alk.Rd | 3 ++- man/catchmsy.Rd |only man/clus.lf.Rd | 3 +-- man/clus.str.lf.Rd | 3 +-- man/clus.vb.fit.Rd | 6 +++--- man/growth.Rd | 2 +- man/irm_cr.Rd | 4 ++-- man/irm_h.Rd | 4 ++-- man/lingcod.Rd |only man/pwpop.Rd | 7 +++++-- man/tag_model_avg.Rd | 5 ++++- 19 files changed, 92 insertions(+), 64 deletions(-)
Title: Companion to Applied Regression
Description:
This package accompanies J. Fox and S. Weisberg, An R Companion to Applied Regression,
Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox
Diff between car versions 2.0-21 dated 2014-08-16 and 2.0-22 dated 2014-11-18
car-2.0-21/car/data/Blackmoor.rda |only car-2.0-21/car/man/Blackmoor.Rd |only car-2.0-22/car/DESCRIPTION | 19 car-2.0-22/car/MD5 | 52 - car-2.0-22/car/NAMESPACE | 51 - car-2.0-22/car/NEWS | 24 car-2.0-22/car/R/Anova.R | 180 ++- car-2.0-22/car/R/Boot.R | 12 car-2.0-22/car/R/avPlots.R | 17 car-2.0-22/car/R/compareCoefs.R | 130 +- car-2.0-22/car/R/densityPlot.R | 7 car-2.0-22/car/R/linearHypothesis.R | 1405 ++++++++++++++--------------- car-2.0-22/car/R/mcPlots.R |only car-2.0-22/car/R/ncvTest.R | 82 - car-2.0-22/car/R/residualPlots.R | 14 car-2.0-22/car/R/scatter3d.R | 150 +-- car-2.0-22/car/R/scatterplot.R | 11 car-2.0-22/car/R/scatterplotMatrix.R | 383 ++++--- car-2.0-22/car/R/scatterplotSmoothers.R | 31 car-2.0-22/car/R/utility-functions.R | 31 car-2.0-22/car/data/Blackmore.rda |only car-2.0-22/car/data/KosteckiDillon.rda |only car-2.0-22/car/inst/doc/embedding.pdf |binary car-2.0-22/car/man/Anova.Rd | 641 ++++++------- car-2.0-22/car/man/Blackmore.Rd |only car-2.0-22/car/man/KosteckiDillon.Rd |only car-2.0-22/car/man/ScatterplotSmoothers.Rd | 6 car-2.0-22/car/man/avPlots.Rd | 12 car-2.0-22/car/man/car-package.Rd | 9 car-2.0-22/car/man/linearHypothesis.Rd | 9 car-2.0-22/car/man/mcPlots.Rd |only 31 files changed, 1765 insertions(+), 1511 deletions(-)
Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Description: This package provides an efficient framework for
high-dimensional linear and diagonal discriminant analysis with
variable selection. The classifier is trained using James-Stein-type
shrinkage estimators and predictor variables are ranked using
correlation-adjusted t-scores (CAT scores). Variable selection error
is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer
Diff between sda versions 1.3.4 dated 2014-07-28 and 1.3.5 dated 2014-11-18
DESCRIPTION | 14 +- MD5 | 12 +- NEWS | 7 + R/sda.ranking.R | 14 +- inst/doc/index.html | 2 inst/doc/sda-khan-data.R | 232 +++++++++++++++++++++++++++++----------------- inst/doc/sda-singh-data.R | 120 +++++++++++++++-------- 7 files changed, 255 insertions(+), 146 deletions(-)
Title: Correlation and Regression Analyses for Randomized Response Data
Description: RRreg provides 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 and as
predictors in a linear regression. 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
Diff between RRreg versions 0.1.3 dated 2014-09-20 and 0.2.0 dated 2014-11-18
DESCRIPTION | 34 ++-- MD5 | 72 +++++---- NAMESPACE | 3 NEWS | 10 + R/RRcheck.R | 21 +- R/RRcor.R | 342 ++++++++++++++++++++++++++++++--------------- R/RRcor.models.R | 82 +++++----- R/RRgen.R | 54 +++++-- R/RRlin.R | 226 ++++++++++++++++-------------- R/RRlog.CDM.R | 2 R/RRlog.FR.R | 4 R/RRlog.Kuk.R | 2 R/RRlog.Mangat.R | 2 R/RRlog.R | 66 +++++--- R/RRlog.SLD.R | 28 +-- R/RRlog.UQTknown.R | 2 R/RRlog.UQTunknown.R | 2 R/RRlog.Warner.R | 2 R/RRreg-package.R | 6 R/RRsimu.R | 353 ++++++++++++++++++++++++++++++----------------- R/RRuni.R | 33 +++- R/RRuni.models.R | 50 ++++++ R/helper_functions.R |only R/powerplot.R |only build/vignette.rds |binary inst/CITATION | 10 - inst/doc/RRreg.R | 16 +- inst/doc/RRreg.Rmd | 35 ++-- inst/doc/RRreg.html | 201 ++++++++++++-------------- man/RRcor.Rd | 48 +++--- man/RRgen.Rd | 11 - man/RRlin.Rd | 18 +- man/RRlog.Rd | 9 - man/RRreg-package.Rd | 5 man/RRsimu.Rd | 44 +++-- man/RRuni.Rd | 6 man/powerplot.Rd |only vignettes/RRreg.Rmd | 35 ++-- vignettes/markdown10.css |only 39 files changed, 1116 insertions(+), 718 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-17 0.1.2
Title: seawater carbonate chemistry with R
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso
Diff between seacarb versions 3.0 dated 2014-04-05 and 3.0.2 dated 2014-11-18
seacarb-3.0.2/seacarb/ChangeLog | 14 + seacarb-3.0.2/seacarb/DESCRIPTION | 34 +- seacarb-3.0.2/seacarb/MD5 | 64 ++--- seacarb-3.0.2/seacarb/R/K0.R | 24 + seacarb-3.0.2/seacarb/R/Ks.R | 214 ++++++++--------- seacarb-3.0.2/seacarb/R/Om.R | 84 +++--- seacarb-3.0.2/seacarb/R/Pcorrect.R | 3 seacarb-3.0.2/seacarb/R/at.R | 162 ++++++------ seacarb-3.0.2/seacarb/R/buffer.R | 10 seacarb-3.0.2/seacarb/R/buffesm.R | 12 seacarb-3.0.2/seacarb/R/carb.R | 31 +- seacarb-3.0.2/seacarb/R/f2pCO2.R | 73 +++-- seacarb-3.0.2/seacarb/R/oa.R | 440 +++++++++++++++++------------------ seacarb-3.0.2/seacarb/R/p2fCO2.R | 69 +++-- seacarb-3.0.2/seacarb/R/p2xCO2.R |only seacarb-3.0.2/seacarb/R/pCa.R | 59 ++-- seacarb-3.0.2/seacarb/R/pHinsi.R | 49 ++- seacarb-3.0.2/seacarb/R/pTA.R | 69 ++--- seacarb-3.0.2/seacarb/R/pgas.R | 43 +-- seacarb-3.0.2/seacarb/R/pmix.R | 67 ++--- seacarb-3.0.2/seacarb/R/ppH.R | 92 +++---- seacarb-3.0.2/seacarb/R/psi.R | 39 +-- seacarb-3.0.2/seacarb/R/vapress.R |only seacarb-3.0.2/seacarb/R/x2pCO2.R |only seacarb-3.0.2/seacarb/man/K0.Rd | 5 seacarb-3.0.2/seacarb/man/buffer.Rd | 17 - seacarb-3.0.2/seacarb/man/buffesm.Rd | 7 seacarb-3.0.2/seacarb/man/carb.Rd | 30 +- seacarb-3.0.2/seacarb/man/f2pCO2.Rd | 25 + seacarb-3.0.2/seacarb/man/p2fCO2.Rd | 18 + seacarb-3.0.2/seacarb/man/p2xCO2.Rd |only seacarb-3.0.2/seacarb/man/psi.Rd | 4 seacarb-3.0.2/seacarb/man/vapress.Rd |only seacarb-3.0.2/seacarb/man/x2pCO2.Rd |only seacarb-3.0/seacarb/R/carbex.R |only seacarb-3.0/seacarb/R/carbm.R |only seacarb-3.0/seacarb/man/carbex.Rd |only seacarb-3.0/seacarb/man/carbm.Rd |only 38 files changed, 963 insertions(+), 795 deletions(-)
Title: Simulating the Evolution of Biological Sequences
Description: A coalescent simulator that allows the rapid simulation of
biological sequences under neutral models of evolution.
Author: Paul Staab [aut, cre, cph],
Zhu Sha [aut, cph],
Dirk Metzler [aut, cph, ths],
Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab
Diff between scrm versions 1.3-2 dated 2014-10-22 and 1.3-3 dated 2014-11-18
DESCRIPTION | 17 ++-- MD5 | 26 +++--- NEWS | 28 ++++-- README.md | 57 +++++++++++-- build/vignette.rds |binary inst/doc/scrm-Arguments.Rmd | 174 ++++++++++++++++++++--------------------- inst/doc/scrm-Arguments.html | 4 inst/doc/scrm-TreesForApe.Rmd | 2 inst/doc/scrm-TreesForApe.html | 4 src/scrm/model.cc | 4 src/scrm/model.h | 8 - src/scrm/param.cc | 24 ++++- vignettes/scrm-Arguments.Rmd | 174 ++++++++++++++++++++--------------------- vignettes/scrm-TreesForApe.Rmd | 2 14 files changed, 302 insertions(+), 222 deletions(-)
Title: STK++ Integration To R Using Rcpp
Description: STK++ (http://www.stkpp.org) is a collection of
C++ classes for statistics, clustering, linear algebra, arrays (with an
Eigen-like API), regression, dimension reduction, etc. The integration of
the library to R is using Rcpp. Some functionalities of the Clustering
project provided by the library are available in the R environment as R
functions.
The rtkpp package includes the header files from the STK++
library (currently version 0.8.2). Thus users do not need to
install STK++ itself in order to use it.
STK++ is licensed under the GNU LGPL version 2 or later. rtkpp
(the stkpp integration into R) is licensed under the
GNU GPL version 2 or later.
Author: Serge Iovleff [aut, cre],
Vincent Kubicki [ctb],
Quentin Grimonprez [ctb],
Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff
Diff between rtkpp versions 0.8.3 dated 2014-10-23 and 0.8.4 dated 2014-11-18
rtkpp-0.8.3/rtkpp/inst/projects/Algebra/src/STK_Givens.cpp |only rtkpp-0.8.3/rtkpp/inst/projects/Algebra/src/STK_IQr.cpp |only rtkpp-0.8.3/rtkpp/inst/projects/Algebra/src/STK_ISymEigen.cpp |only rtkpp-0.8.3/rtkpp/inst/projects/Clustering/include/STK_DataManager.h |only rtkpp-0.8.3/rtkpp/inst/projects/Clustering/include/STK_IDataManager.h |only rtkpp-0.8.3/rtkpp/inst/projects/Regress/src/STK_AdditiveBSplineCoefficients.cpp |only rtkpp-0.8.3/rtkpp/man/CategoricalNames.Rd |only rtkpp-0.8.3/rtkpp/man/diagGaussianNames.Rd |only rtkpp-0.8.3/rtkpp/man/gammaNames.Rd |only rtkpp-0.8.4/rtkpp/.Rinstignore | 18 rtkpp-0.8.4/rtkpp/DESCRIPTION | 15 rtkpp-0.8.4/rtkpp/MD5 | 246 ++--- rtkpp-0.8.4/rtkpp/NAMESPACE | 22 rtkpp-0.8.4/rtkpp/R/ClusterAlgo.R | 42 rtkpp-0.8.4/rtkpp/R/ClusterCategorical.R | 304 ++++-- rtkpp-0.8.4/rtkpp/R/ClusterDiagGaussian.R | 278 +++-- rtkpp-0.8.4/rtkpp/R/ClusterGamma.R | 233 +++-- rtkpp-0.8.4/rtkpp/R/ClusterHeterogeneous.R |only rtkpp-0.8.4/rtkpp/R/ClusterInit.R | 2 rtkpp-0.8.4/rtkpp/R/ClusterModelNames.R | 96 +- rtkpp-0.8.4/rtkpp/R/ClusterPlot.R | 24 rtkpp-0.8.4/rtkpp/R/ClusterStrategy.R | 38 rtkpp-0.8.4/rtkpp/R/IClusterModel.R | 301 +++--- rtkpp-0.8.4/rtkpp/R/global.R | 27 rtkpp-0.8.4/rtkpp/R/rtkpp.R | 170 +++ rtkpp-0.8.4/rtkpp/R/rtkppFlags.R | 11 rtkpp-0.8.4/rtkpp/data/HeartDisease.cat.rda |only rtkpp-0.8.4/rtkpp/data/HeartDisease.cont.rda |only rtkpp-0.8.4/rtkpp/data/HeartDisease.target.rda |only rtkpp-0.8.4/rtkpp/data/birds.rda |binary rtkpp-0.8.4/rtkpp/data/car.rda |binary rtkpp-0.8.4/rtkpp/data/geyser.rda |binary rtkpp-0.8.4/rtkpp/data/titanic.rda |binary rtkpp-0.8.4/rtkpp/inst/NEWS.Rd | 9 rtkpp-0.8.4/rtkpp/inst/makefile | 466 +++++----- rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_Givens.h | 40 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_IQr.h | 145 ++- rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_ISymEigen.h | 76 + rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_Qr.h | 19 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_SymEigen.h | 29 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_lapack_Qr.h | 19 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/include/STK_lapack_SymEigen.h | 21 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/src/STK_Qr.cpp | 37 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/src/STK_SymEigen.cpp | 31 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/src/STK_lapack_Qr.cpp | 31 rtkpp-0.8.4/rtkpp/inst/projects/Algebra/src/STK_lapack_SymEigen.cpp | 21 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_Exponential_bjk.h | 15 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_Exponential_bk.h | 81 - rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bjk.h | 2 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bk.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bjk.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bk.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_b.h | 2 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bj.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bjk.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bk.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_b.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bj.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bjk.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bk.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_s.h | 3 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_sj.h | 3 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_sjk.h | 1 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_sk.h | 3 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/MixturesBridges/STK_IMixtureBridge.h |only rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/MixturesBridges/STK_KernelMixtureBridge.h |only rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/MixturesBridges/STK_MixtureBridge.h | 378 ++++---- rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_Clust_Util.h | 37 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_IMixture.h | 35 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_IMixtureComposer.h | 16 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_IMixtureData.h |only rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_IMixtureManager.h | 24 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_MixtureAlgo.h | 35 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_MixtureComposer.h | 25 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_MixtureData.h |only rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_MixtureFacade.h | 9 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_MixtureManager.h | 133 -- rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_Clust_Util.cpp | 43 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IDataManager.cpp | 12 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IMixture.cpp | 40 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IMixtureComposer.cpp | 29 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IMixtureManager.cpp | 14 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureAlgo.cpp | 50 + rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureComposer.cpp | 32 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureFacade.cpp | 27 rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureInit.cpp | 61 - rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_MixtureStrategy.cpp | 150 +-- rtkpp-0.8.4/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineCoefficients.h | 158 ++- rtkpp-0.8.4/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineRegression.h | 6 rtkpp-0.8.4/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineRegressionPage.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Regress/include/STK_BSplineCoefficients.h | 45 rtkpp-0.8.4/rtkpp/inst/projects/Regress/include/STK_BSplineRegression.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/Regress/include/STK_Regress_Util.h | 22 rtkpp-0.8.4/rtkpp/inst/projects/Regress/src/STK_AdditiveBSplineRegressionPage.cpp | 6 rtkpp-0.8.4/rtkpp/inst/projects/Regress/src/STK_BSplineCoefficients.cpp | 59 - rtkpp-0.8.4/rtkpp/inst/projects/Regress/src/STK_Regress_Util.cpp | 24 rtkpp-0.8.4/rtkpp/inst/projects/Rtkpp/include/STK_ClusterFacade.h | 13 rtkpp-0.8.4/rtkpp/inst/projects/Rtkpp/include/STK_ClusterLauncher.h | 53 - rtkpp-0.8.4/rtkpp/inst/projects/STKernel/include/STK_Integer.h | 24 rtkpp-0.8.4/rtkpp/inst/projects/STKernel/include/STK_Range.h | 11 rtkpp-0.8.4/rtkpp/inst/projects/STKernel/include/STK_String.h | 4 rtkpp-0.8.4/rtkpp/inst/projects/STKernel/src/STK_Integer.cpp | 28 rtkpp-0.8.4/rtkpp/inst/projects/STKernel/src/STK_Range.cpp | 10 rtkpp-0.8.4/rtkpp/inst/projects/Sdk/include/STK_IRunner.h | 2 rtkpp-0.8.4/rtkpp/man/ClusterAlgo-class.Rd | 2 rtkpp-0.8.4/rtkpp/man/ClusterCategorical-class.Rd | 9 rtkpp-0.8.4/rtkpp/man/ClusterDiagGaussian-class.Rd | 9 rtkpp-0.8.4/rtkpp/man/ClusterGamma-class.Rd | 9 rtkpp-0.8.4/rtkpp/man/ClusterHeterogeneous-class.Rd |only rtkpp-0.8.4/rtkpp/man/ClusterModels-class.Rd | 22 rtkpp-0.8.4/rtkpp/man/ClusterStrategy-class.Rd | 6 rtkpp-0.8.4/rtkpp/man/HeartDisease.Rd |only rtkpp-0.8.4/rtkpp/man/IClusterComponent-class.Rd |only rtkpp-0.8.4/rtkpp/man/car.Rd | 14 rtkpp-0.8.4/rtkpp/man/clusterAlgo.Rd | 3 rtkpp-0.8.4/rtkpp/man/clusterCategorical.Rd | 4 rtkpp-0.8.4/rtkpp/man/clusterCategoricalNames.Rd |only rtkpp-0.8.4/rtkpp/man/clusterDiagGaussian.Rd | 9 rtkpp-0.8.4/rtkpp/man/clusterDiagGaussianNames.Rd |only rtkpp-0.8.4/rtkpp/man/clusterGamma.Rd | 8 rtkpp-0.8.4/rtkpp/man/clusterGammaNames.Rd |only rtkpp-0.8.4/rtkpp/man/clusterHeterogeneous.Rd |only rtkpp-0.8.4/rtkpp/man/clusterInit.Rd | 2 rtkpp-0.8.4/rtkpp/man/clusterStrategy.Rd | 21 rtkpp-0.8.4/rtkpp/man/extract-methods.Rd | 12 rtkpp-0.8.4/rtkpp/man/initialize-methods.Rd | 52 - rtkpp-0.8.4/rtkpp/man/missingValues-methods.Rd |only rtkpp-0.8.4/rtkpp/man/plot-ClusterGamma-method.Rd | 2 rtkpp-0.8.4/rtkpp/man/plot-ClusterHeterogeneous-method.Rd |only rtkpp-0.8.4/rtkpp/man/print-methods.Rd | 21 rtkpp-0.8.4/rtkpp/man/show-methods.Rd | 24 rtkpp-0.8.4/rtkpp/man/summary-methods.Rd | 12 rtkpp-0.8.4/rtkpp/src/Makevars | 17 rtkpp-0.8.4/rtkpp/src/STK_ClusterFacade.cpp | 16 rtkpp-0.8.4/rtkpp/src/STK_ClusterLauncher.cpp | 260 +++-- rtkpp-0.8.4/rtkpp/src/clusterMixture.cpp | 18 rtkpp-0.8.4/rtkpp/tests/clusterDiagGaussianLikelihood.R | 8 rtkpp-0.8.4/rtkpp/tests/clusterGammaLikelihood.R | 8 138 files changed, 3057 insertions(+), 2055 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
here: http://rootsystemml.github.io/
Author: Guillaume Lobet
Maintainer: Guillaume Lobet
Diff between rsml versions 1.0 dated 2014-10-23 and 1.2 dated 2014-11-18
DESCRIPTION | 12 + MD5 | 94 ++++++------- NAMESPACE | 36 +++++ R/node_functions.R | 7 + R/plant_functions.R | 78 ++++++++++- R/root_functions.R | 96 +++++++++++-- R/rsmlToList.R | 8 + R/rsmlToPlant.R | 283 ++++++++++++++++++++++------------------- data/anagallis.rda |binary data/lupin.rda |binary man/addChildToRoot.Rd | 8 + man/addNodeToRoot.Rd | 7 - man/addRootToPlant.Rd | 7 - man/anagallis.Rd | 2 man/coords.Rd | 7 - man/getInsertionAngle.Rd | 8 + man/getInsertionPosition.Rd | 8 + man/latLength.Rd | 6 man/length.plant.Rd | 6 man/length.root.Rd | 7 - man/lupin.Rd | 2 man/maize.Rd | 2 man/meanInsertionAngle.Rd | 7 - man/meanInsertionAnglePlant.Rd | 6 man/meanInterbranch.Rd | 7 - man/meanInterbranchPlant.Rd | 6 man/nChild.Rd | 7 - man/nLatRoot.Rd | 6 man/nNode.Rd | 7 - man/nPrimRoot.Rd | 6 man/nRoot.Rd | 6 man/node.Rd | 5 man/plant.Rd | 5 man/plot.plant.Rd | 11 + man/primLength.Rd | 6 man/print.node.Rd | 6 man/print.plant.Rd | 6 man/root.Rd | 8 + man/rsmlToList.Rd | 7 - man/rsmlToPlant.Rd | 13 + man/summary.plant.Rd | 7 - man/totalLength.Rd | 7 - man/xrange.Rd | 7 - man/xrangePlant.Rd | 6 man/yrange.Rd | 7 - man/yrangePlant.Rd | 6 man/zrange.Rd | 7 - man/zrangePlant.Rd | 6 48 files changed, 623 insertions(+), 239 deletions(-)
Title: Rcpp Bindings for Annoy, a Library for Approximate Nearest
Neighbors
Description: Annoy is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the Rcpp and BH
packages, exposing the same interface as the original Python wrapper to
Annoy. See https://github.com/spotify/annoy for more on Annoy. Annoy is
released under Version 2.0 of the Apache License. Also included is a small
Windows port of mmap which is release under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
Diff between RcppAnnoy versions 0.0.2 dated 2014-11-16 and 0.0.3 dated 2014-11-18
ChangeLog | 25 +++++++++++++ DESCRIPTION | 12 +++--- MD5 | 11 +++--- README.md | 9 ++++ inst/include/annoylib.h | 87 +++++++++++++++++++++++++----------------------- inst/include/mman.h |only src/annoy.cpp | 75 ++++++++++++++++++++++------------------- 7 files changed, 133 insertions(+), 86 deletions(-)
Title: Fit Latent Markov models in basic versions
Description: Fit certain versions of the Latent Markov model for longitudinal categorical data.
Author: Francesco Bartolucci, Silvia Pandolfi - University of Perugia (IT) -, and Fulvia Pennoni - University of Milano Bicocca
Maintainer: Francesco Bartolucci
Diff between LMest versions 1.0 dated 2012-11-28 and 2.0 dated 2014-11-18
LMest-1.0/LMest/R/aggr_data.R |only LMest-1.0/LMest/data/data_criminal.rda |only LMest-1.0/LMest/man/aggr_data.Rd |only LMest-1.0/LMest/man/data_criminal.Rd |only LMest-2.0/LMest/DESCRIPTION | 17 - LMest-2.0/LMest/MD5 | 116 +++++++++-- LMest-2.0/LMest/NAMESPACE | 4 LMest-2.0/LMest/R/blkdiag.R |only LMest-2.0/LMest/R/bootstrap_lm_cov_latent.R |only LMest-2.0/LMest/R/complk.R | 14 - LMest-2.0/LMest/R/deconding.R |only LMest-2.0/LMest/R/draw_lm_basic.R | 8 LMest-2.0/LMest/R/draw_lm_cov_latent.R |only LMest-2.0/LMest/R/draw_lm_mixed.R |only LMest-2.0/LMest/R/est_lm_basic.R | 262 +++++++++++++++++-------- LMest-2.0/LMest/R/est_lm_cov_latent.R |only LMest-2.0/LMest/R/est_lm_cov_manifest.R |only LMest-2.0/LMest/R/est_lm_mixed.R |only LMest-2.0/LMest/R/est_multilogit.R |only LMest-2.0/LMest/R/expit.R |only LMest-2.0/LMest/R/expit1.R |only LMest-2.0/LMest/R/lk_ar_rho.R |only LMest-2.0/LMest/R/lk_comp_latent.R |only LMest-2.0/LMest/R/lk_obs.R | 77 +++++-- LMest-2.0/LMest/R/lk_obs_latent.R |only LMest-2.0/LMest/R/lk_obs_manifest.R |only LMest-2.0/LMest/R/lk_obs_mixed.R |only LMest-2.0/LMest/R/lk_sta.R |only LMest-2.0/LMest/R/logit1.R |only LMest-2.0/LMest/R/marg_param.R |only LMest-2.0/LMest/R/print.LMbasic.R |only LMest-2.0/LMest/R/print.LMlatent.R |only LMest-2.0/LMest/R/print.LMmanifest.R |only LMest-2.0/LMest/R/print.LMmixed.R |only LMest-2.0/LMest/R/prob_multilogit.R |only LMest-2.0/LMest/R/prob_post_cov.R |only LMest-2.0/LMest/R/prod_array.R |only LMest-2.0/LMest/R/rec1.R |only LMest-2.0/LMest/R/rec3.R |only LMest-2.0/LMest/R/recursions.R | 72 +++++- LMest-2.0/LMest/R/sq.R |only LMest-2.0/LMest/R/stationary.R |only LMest-2.0/LMest/R/summary.LMbasic.R |only LMest-2.0/LMest/R/summary.LMlatent.R |only LMest-2.0/LMest/R/summary.LMmanifest.R |only LMest-2.0/LMest/R/summary.LMmixed.R |only LMest-2.0/LMest/R/trans_par.R |only LMest-2.0/LMest/data/data_SRHS.rda |only LMest-2.0/LMest/data/data_criminal_sim.rda |only LMest-2.0/LMest/man/LMest-package.Rd | 13 - LMest-2.0/LMest/man/blkdiag.Rd |only LMest-2.0/LMest/man/bootstrap_lm_basic.Rd | 2 LMest-2.0/LMest/man/bootstrap_lm_cov_latent.Rd |only LMest-2.0/LMest/man/complk.Rd | 2 LMest-2.0/LMest/man/data_SRHS.Rd |only LMest-2.0/LMest/man/data_criminal_sim.Rd |only LMest-2.0/LMest/man/deconding.Rd |only LMest-2.0/LMest/man/draw_lm_basic.Rd | 2 LMest-2.0/LMest/man/draw_lm_cov_latent.Rd |only LMest-2.0/LMest/man/draw_lm_mixed.Rd |only LMest-2.0/LMest/man/est_lm_basic.Rd | 31 +- LMest-2.0/LMest/man/est_lm_cov_latent.Rd |only LMest-2.0/LMest/man/est_lm_cov_manifest.Rd |only LMest-2.0/LMest/man/est_lm_mixed.Rd |only LMest-2.0/LMest/man/est_multilogit.Rd |only LMest-2.0/LMest/man/expit.Rd |only LMest-2.0/LMest/man/expit1.Rd |only LMest-2.0/LMest/man/invglob.Rd | 4 LMest-2.0/LMest/man/lk_ar_rho.Rd |only LMest-2.0/LMest/man/lk_comp_latent.Rd |only LMest-2.0/LMest/man/lk_obs.Rd | 9 LMest-2.0/LMest/man/lk_obs_latent.Rd |only LMest-2.0/LMest/man/lk_obs_manifest.Rd |only LMest-2.0/LMest/man/lk_obs_mixed.Rd |only LMest-2.0/LMest/man/lk_sta.Rd |only LMest-2.0/LMest/man/logit1.Rd |only LMest-2.0/LMest/man/long2wide.Rd | 7 LMest-2.0/LMest/man/marg_param.Rd |only LMest-2.0/LMest/man/print.LMbasic.Rd |only LMest-2.0/LMest/man/print.LMlatent.Rd |only LMest-2.0/LMest/man/print.LMmanifest.Rd |only LMest-2.0/LMest/man/print.LMmixed.Rd |only LMest-2.0/LMest/man/prob_multilogit.Rd |only LMest-2.0/LMest/man/prob_post_cov.Rd |only LMest-2.0/LMest/man/prod_array.Rd |only LMest-2.0/LMest/man/rec1.Rd |only LMest-2.0/LMest/man/rec3.Rd |only LMest-2.0/LMest/man/recursions.Rd | 5 LMest-2.0/LMest/man/sq.Rd |only LMest-2.0/LMest/man/stationary.Rd |only LMest-2.0/LMest/man/summary.LMbasic.Rd |only LMest-2.0/LMest/man/summary.LMlatent.Rd |only LMest-2.0/LMest/man/summary.LMmanifest.Rd |only LMest-2.0/LMest/man/summary.LMmixed.Rd |only LMest-2.0/LMest/man/trans_par.Rd |only LMest-2.0/LMest/src |only 96 files changed, 461 insertions(+), 184 deletions(-)
Title: Probabilistic Species Co-occurrence Analysis in R
Description: This R package applies the probabilistic model of species co-occurrence (Veech 2013) to a set of species distributed among a set of survey or sampling sites. The algorithm calculates the observed and expected frequencies of co-occurrence between each pair of species. The expected frequency is based on the distribution of each species being random and independent of the other species. The analysis returns the probabilities that a more extreme (either low or high) value of co-occurrence could have been obtained by chance. The package also includes functions for visualizing species co-occurrence results and preparing data for downstream analyses.
Author: Daniel M. Griffith, Joseph A. Veech, and Charles J. Marsh
Maintainer: Daniel M. Griffith
Diff between cooccur versions 1.1 dated 2014-05-06 and 1.2 dated 2014-11-18
DESCRIPTION | 6 ++-- MD5 | 16 +++++------ R/cooccur.R | 74 +++++++++++++++++++++++++++++++++++++--------------- R/obs.v.exp.R | 4 +- R/pair.R | 2 - R/plot.cooccur.R | 46 ++++++++++++++++++++++++-------- R/summary.cooccur.R | 4 ++ man/cooccur.Rd | 5 ++- man/pair.Rd | 2 - 9 files changed, 111 insertions(+), 48 deletions(-)
Title: Boolean Binary Response Models
Description: This package implements a
partial-observability procedure for testing Boolean
hypotheses that generalizes the binary response GLM as
outlined in Braumoeller (2003).
Author: Jason W. Morgan
Maintainer: Jason W. Morgan
Diff between boolean3 versions 3.1.5 dated 2014-06-25 and 3.1.6 dated 2014-11-18
DESCRIPTION | 8 - MD5 | 66 +++++++-------- NAMESPACE | 2 NEWS | 4 R/boolean-package.R | 4 R/optim.R | 3 R/predprob.R | 185 ++++++++++++++++++++++---------------------- R/utils.R | 42 ++++++--- man/boolboot.Rd | 2 man/boolean-class.Rd | 2 man/boolean.Rd | 2 man/boolean3-package.Rd | 6 - man/boolfit-class.Rd | 2 man/boolprep.Rd | 2 man/boolprob-class.Rd | 2 man/boolprob.Rd | 2 man/boolprof-class.Rd | 2 man/boolprof.Rd | 2 man/boolsum-class.Rd | 2 man/coef.boolean.Rd | 2 man/logLik.boolean.Rd | 2 man/model.matrix.boolean.Rd | 2 man/nobs.boolean.Rd | 2 man/plot.boolprob.Rd | 2 man/plot.boolprof.Rd | 2 man/predict.boolean.Rd | 13 ++- man/print.boolboot.Rd | 2 man/print.boolean.Rd | 2 man/print.boolprob.Rd | 2 man/print.boolprof.Rd | 2 man/print.boolsum.Rd | 2 man/summary.boolboot.Rd | 2 man/summary.boolean.Rd | 2 man/vcov.boolean.Rd | 2 34 files changed, 205 insertions(+), 176 deletions(-)