Title: Username, Full Name, Email Address, 'GitHub' Username of the
Current User
Description: Look up the username and full name of the current user,
the current user's email address and 'GitHub' username,
using various sources of system and configuration information.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between whoami versions 1.1.0 dated 2015-06-11 and 1.1.1 dated 2015-07-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + R/whoami.R | 1 + 4 files changed, 9 insertions(+), 7 deletions(-)
Title: Sparklines in the 'R' Terminal
Description: A sparkline is a line chart, without axes and labels.
Its goal is to show the general shape of changes over time, or
another quantity. This package is an 'R' implementation
of the original shell project: <http://zachholman.com/spark/>.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between spark versions 1.0.0 dated 2014-10-14 and 1.0.1 dated 2015-07-12
spark-1.0.0/spark/README.md |only spark-1.0.1/spark/DESCRIPTION | 23 ++++++++++++----------- spark-1.0.1/spark/LICENSE | 2 +- spark-1.0.1/spark/MD5 | 22 ++++++++++++---------- spark-1.0.1/spark/NAMESPACE | 4 +++- spark-1.0.1/spark/R/scale.r | 2 ++ spark-1.0.1/spark/R/utils.r | 1 + spark-1.0.1/spark/inst |only spark-1.0.1/spark/man/spark.Rd | 3 ++- spark-1.0.1/spark/man/spark.default.Rd | 3 ++- spark-1.0.1/spark/man/spark.matrix.Rd | 3 ++- spark-1.0.1/spark/man/sparklines.Rd | 3 ++- 12 files changed, 39 insertions(+), 27 deletions(-)
Title: Client Side Load Balancing
Description: Decide which server to connect to,
based on previous response times, and configuration.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between spareserver versions 1.0.0 dated 2014-11-03 and 1.0.1 dated 2015-07-12
spareserver-1.0.0/spareserver/README.md |only spareserver-1.0.1/spareserver/DESCRIPTION | 17 ++++----- spareserver-1.0.1/spareserver/LICENSE | 2 - spareserver-1.0.1/spareserver/MD5 | 26 ++++++++------- spareserver-1.0.1/spareserver/NAMESPACE | 5 +- spareserver-1.0.1/spareserver/R/spare-package.r | 6 ++- spareserver-1.0.1/spareserver/inst |only spareserver-1.0.1/spareserver/man/add_server.Rd | 3 + spareserver-1.0.1/spareserver/man/add_service.Rd | 3 + spareserver-1.0.1/spareserver/man/remove_service.Rd | 3 + spareserver-1.0.1/spareserver/man/server.Rd | 3 + spareserver-1.0.1/spareserver/man/services.Rd | 3 + spareserver-1.0.1/spareserver/man/spare_q.Rd | 3 + spareserver-1.0.1/spareserver/man/spareserver-package.Rd | 3 + 14 files changed, 44 insertions(+), 33 deletions(-)
Title: Query 'R' Versions, Including 'r-release' and 'r-oldrel'
Description: Query the main 'R' 'SVN' repository to find the
versions 'r-release' and 'r-oldrel' refer to, and also all
previous 'R' versions and their release dates.
Author: Gabor Csardi [aut, cre],
Jeroen Ooms [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rversions versions 1.0.1 dated 2015-06-05 and 1.0.2 dated 2015-07-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + R/rversions.R | 2 ++ 4 files changed, 10 insertions(+), 7 deletions(-)
Title: A Collection of Small Text Corpora of Interesting Data
Description: A collection of small text corpora of interesting data.
It contains all data sets from https://github.com/dariusk/corpora.
Some examples:
names of animals: birds, dinosaurs, dogs; foods: beer categories,
pizza toppings; geography: English towns, rivers, oceans;
humans: authors, US presidents, occupations; science: elements,
planets; words: adjectives, verbs, proverbs, US president quotes.
Author: Darius Kazemi, Matthew Rothenberg, Karl Swedberg, Matthew Hokanson,
Nathan Lachenmyer, Aaron Marriner, Mark Sample, Casey Kolderup,
Nathaniel Mitchell, Daniel D. Beck, Mike Nowak, Ryan Freebern,
Ross Barclay, Ross Binden, Justin Alford, Cole Willsea,
Andrew Gorman, Javier Arce, Patrick Rodriguez,
Liam Cooke, Will Hankinson, K. Adam White, Garrett Miller, Zac Moody,
Jordan Killpack, Brian Jones, Greg Borenstein, Noah Swartz, Nathan Black,
Russell Horton, Mark Wunsch, Kay Belardinelli, Colin Mitchell,
Michael Dewberry, Joe Mahoney
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rcorpora versions 1.1.0 dated 2015-06-08 and 1.1.1 dated 2015-07-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/corpora.R | 2 ++ build/rcorpora.pdf |binary inst/NEWS.md | 4 ++++ 6 files changed, 16 insertions(+), 9 deletions(-)
Title: Distance Based Ranking Models
Description: Implements distance based probability models for ranking data.
The supported distance metrics include Kendall distance and Weighted Kendall distance.
Mixture models are also supported.
Author: Zhaozhi Qian
Maintainer: Zhaozhi Qian <qianzhaozhi@connect.hku.hk>
Diff between rankdist versions 0.4.1 dated 2015-05-17 and 1.0.0 dated 2015-07-12
DESCRIPTION | 12 - MD5 | 51 ++++--- NAMESPACE | 12 + R/class.R | 102 ++++++++------- R/method.R | 215 +++++++++++++++++++++++++++----- R/rankdist.R | 139 +++++++++++++++++++- R/utils.R | 24 ++- data/apa_obj.rda |binary data/apa_partial_obj.rda |only man/DistanceBlock.Rd |only man/DistanceMatrix.Rd |only man/DistancePair.Rd |only man/GenerateExample.Rd |only man/GenerateExampleTopQ.Rd |only man/HashtoRank.Rd | 2 man/ModelSummary.Rd |only man/MomentsEst.Rd | 2 man/OrderingToRanking.Rd | 6 man/RankControl-class.Rd | 11 - man/RankControlKendall-class.Rd | 13 + man/RankControlPhiComponent-class.Rd | 17 +- man/RankControlWeightedKendall-class.Rd | 8 - man/RankData-class.Rd | 45 ++++-- man/RankDistanceModel.Rd | 6 man/RankInit-class.Rd | 8 - man/RanktoHash.Rd | 2 man/apa_obj.Rd | 2 man/apa_partial_obj.Rd |only src/RcppExports.cpp | 88 ++++--------- src/utils.cpp | 33 ++++ tests/testthat/test_RankData.R |only 31 files changed, 573 insertions(+), 225 deletions(-)
Title: Pretty, Human Readable Formatting of Quantities
Description: Pretty, human readable formatting of quantities.
Time intervals: 1337000 -> 15d 11h 23m 20s.
Vague time intervals: 2674000 -> about a month ago.
Bytes: 1337 -> 1.34 kB.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between prettyunits versions 1.0.0 dated 2014-10-13 and 1.0.2 dated 2015-07-12
prettyunits-1.0.0/prettyunits/README.md |only prettyunits-1.0.2/prettyunits/DESCRIPTION | 13 +++++------ prettyunits-1.0.2/prettyunits/MD5 | 26 +++++++++++----------- prettyunits-1.0.2/prettyunits/NAMESPACE | 3 +- prettyunits-1.0.2/prettyunits/R/time-ago.r | 3 ++ prettyunits-1.0.2/prettyunits/R/time.r | 1 prettyunits-1.0.2/prettyunits/inst |only prettyunits-1.0.2/prettyunits/man/pretty_bytes.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/pretty_dt.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/pretty_ms.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/pretty_sec.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/prettyunits.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/time_ago.Rd | 3 +- prettyunits-1.0.2/prettyunits/man/vague_dt.Rd | 3 +- 14 files changed, 40 insertions(+), 27 deletions(-)
Title: Create Disposable R Packages for Testing
Description: Create disposable R packages for testing.
You can create, install and load multiple R packages with a single
function call, and then unload, uninstall and destroy them with another
function call. This is handy when testing how some R code or an R package
behaves with respect to other packages.
Author: Gabor Csardi
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between disposables versions 1.0.0 dated 2014-11-01 and 1.0.1 dated 2015-07-12
disposables-1.0.0/disposables/README.md |only disposables-1.0.1/disposables/DESCRIPTION | 14 +++--- disposables-1.0.1/disposables/LICENSE | 2 disposables-1.0.1/disposables/MD5 | 16 ++++--- disposables-1.0.1/disposables/NAMESPACE | 4 + disposables-1.0.1/disposables/R/disposable.r | 40 +++++++++++------- disposables-1.0.1/disposables/inst |only disposables-1.0.1/disposables/man/dispose_packages.Rd | 8 ++- disposables-1.0.1/disposables/man/make_packages.Rd | 8 ++- 9 files changed, 56 insertions(+), 36 deletions(-)
Title: Colored Terminal Output
Description: Colored terminal output on terminals that support 'ANSI'
color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI'
color support is automatically detected. Colors and highlighting can
be combined and nested. New styles can also be created easily.
This package was inspired by the 'chalk' 'JavaScript' project.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between crayon versions 1.3.0 dated 2015-06-05 and 1.3.1 dated 2015-07-12
DESCRIPTION | 19 +++++++++---------- MD5 | 16 ++++++++-------- NAMESPACE | 7 +++++++ R/disposable.r | 4 ++++ R/machinery.r | 4 ++++ R/string_operations.r | 2 ++ R/style-var.r | 3 +++ inst/NEWS.md | 4 ++++ tests/testthat.R | 8 +++++--- 9 files changed, 46 insertions(+), 21 deletions(-)
Title: R Interface to DSDP Semidefinite Programming Library
Description: R interface to DSDP semidefinite programming library. The DSDP software is a free open source implementation of an interior-point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method.
Author: Zhisu Zhu, Yinyu Ye (DSDP by Steve Benson, Yinyu Ye and Xiong Zhang)
Maintainer: Zhisu Zhu <zhuzhisu@alumni.stanford.edu>
Diff between Rdsdp versions 1.0.2 dated 2015-01-06 and 1.0.3 dated 2015-07-12
DESCRIPTION | 9 +++++---- MD5 | 7 ++++--- NAMESPACE | 3 +++ R/Rdsdp.R | 29 ++++++++++++++++++++--------- tests/test3.R |only 5 files changed, 32 insertions(+), 16 deletions(-)
Title: Process Improvement using Data
Description: A collection of scripts and data files for the statistics text:
"Process Improvement using Data". The package contains code for designed
experiments, data sets and other convenience functions used in the book.
Author: Kevin Dunn [aut, cre]
Maintainer: Kevin Dunn <kevin.dunn@mcmaster.ca>
Diff between pid versions 0.13 dated 2015-07-06 and 0.15 dated 2015-07-12
DESCRIPTION | 8 +-- MD5 | 12 +++-- R/paretoPlot.R | 29 +++++++++--- data/oildoe.rda |only data/solar.rda |only man/oildoe.Rd |only man/paretoPlot.Rd | 31 ++++++++++++- man/pid-package.Rd | 121 ++++++++++++++++++++++++++--------------------------- man/solar.Rd |only 9 files changed, 123 insertions(+), 78 deletions(-)
Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.0 dated 2015-06-16 and 2.1 dated 2015-07-12
DESCRIPTION | 8 +- MD5 | 22 +++--- NAMESPACE | 20 ++++++ R/ThresholdROC-2states.R | 140 +++++++++++++++++++++----------------------- R/diagnostic.R | 2 man/ThresholdROC-package.Rd | 4 - man/diagnostic.Rd | 4 - man/plot-thres2.Rd | 2 man/thres2.Rd | 8 +- man/thres3.Rd | 8 +- man/thresTH2.Rd | 2 man/thresTH3.Rd | 2 12 files changed, 120 insertions(+), 102 deletions(-)
Title: A Tool for Structural Topic Model Visualizations
Description: Generates an interactive visualization of topic correlations/hierarchy in a Structural Topic Model (STM) of Roberts, Stewart, and Tingley. The package performs a hierarchical clustering of topics which are then exported to a JSON object and visualized using D3.
Author: Antonio Coppola, Margaret Roberts, Brandon Stewart, Dustin Tingley
Maintainer: Antonio Coppola <acoppola@college.harvard.edu>
Diff between stmCorrViz versions 1.1 dated 2015-03-02 and 1.2 dated 2015-07-12
DESCRIPTION | 16 ++++++---------- MD5 | 12 ++++++------ NAMESPACE | 3 +++ R/clusterAnalysis.R | 7 +++---- R/stmCorrViz.R | 24 ++++++++++++------------ R/stmJSON.R | 40 ++++++++++++++++++++-------------------- man/stmJSON.Rd | 4 ++-- 7 files changed, 52 insertions(+), 54 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC) and the Generalized Adjustment Criterion (GAC)
are implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut],
Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb],
Antti Hyttinen [ctb], Jonas Peters [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.2-2 dated 2015-06-24 and 2.2-3 dated 2015-07-12
pcalg-2.2-2/pcalg/build |only pcalg-2.2-2/pcalg/inst/doc/pcalgDoc.R |only pcalg-2.2-2/pcalg/inst/doc/pcalgDoc.Rnw |only pcalg-2.2-3/pcalg/DESCRIPTION | 14 pcalg-2.2-3/pcalg/MD5 | 47 pcalg-2.2-3/pcalg/NAMESPACE | 9 pcalg-2.2-3/pcalg/R/Aaux.R | 10 pcalg-2.2-3/pcalg/R/AllClasses.R | 8 pcalg-2.2-3/pcalg/R/gacFuns.R | 262 +-- pcalg-2.2-3/pcalg/R/genRandDAG.R | 241 +- pcalg-2.2-3/pcalg/R/jointIda.R |only pcalg-2.2-3/pcalg/R/lingamFuns.R | 928 +++++------ pcalg-2.2-3/pcalg/R/pcalg.R | 2228 ++++++++++++--------------- pcalg-2.2-3/pcalg/inst/doc/pcalgDoc.pdf |binary pcalg-2.2-3/pcalg/inst/external/N_6_1000.rds |only pcalg-2.2-3/pcalg/man/binCItest.Rd | 10 pcalg-2.2-3/pcalg/man/disCItest.Rd | 38 pcalg-2.2-3/pcalg/man/fci.Rd | 41 pcalg-2.2-3/pcalg/man/fciPlus.Rd | 56 pcalg-2.2-3/pcalg/man/jointIda.Rd | 159 + pcalg-2.2-3/pcalg/man/udag2apag.Rd | 66 pcalg-2.2-3/pcalg/man/udag2pag.Rd | 88 - pcalg-2.2-3/pcalg/tests/test_LINGAM.R | 218 ++ pcalg-2.2-3/pcalg/tests/test_fciPlus.R | 196 +- pcalg-2.2-3/pcalg/tests/test_gSquareBin.R | 207 +- pcalg-2.2-3/pcalg/tests/test_gSquareDis.R | 132 + pcalg-2.2-3/pcalg/tests/test_jointIda.R | 63 27 files changed, 2560 insertions(+), 2461 deletions(-)
Title: Orthogonal Array Package
Description: Interface to D-optimal design generation code of the Orthogonal Array package. Can generate D-optimal designs with specified number of runs and factors. The optimality of the designs is defined in terms of a user specified optimization function based on the D-efficiency and Ds-efficiency.
Author: Pieter Thijs Eendebak
Maintainer: Pieter Thijs Eendebak <pieter.eendebak@gmail.com>
Diff between oapackage versions 2.0.22 dated 2015-06-19 and 2.0.23 dated 2015-07-12
DESCRIPTION | 10 - MD5 | 24 +- R/Doptimize.R | 49 +++-- man/Defficiencies.Rd | 11 - man/Doptimize.Rd | 16 + man/oapackage-package.Rd | 26 +-- src/arrayproperties.h | 2 src/arraytools.cpp | 365 +++++++++++++++++++++++++------------------ src/arraytools.h | 3 src/mathtools.h | 16 + src/oaoptions.cpp | 2 tests/example_Doptimize.R | 23 +- tests/example_design_usage.R | 12 - 13 files changed, 325 insertions(+), 234 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot functions for visualizing hypothesis tests in multivariate linear models. They represents sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions).
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.0-15 dated 2015-04-18 and 1.0-16 dated 2015-07-12
DESCRIPTION | 17 MD5 | 142 +-- NAMESPACE | 6 NEWS | 3 build/vignette.rds |binary data/Adopted.RData |binary data/Bees.rda |binary data/FootHead.rda |binary data/Headache.RData |binary data/Hernior.RData |binary data/MockJury.RData |binary data/NLSY.RData |binary data/Oslo.RData |binary data/Plastic.rda |binary data/Pottery2.RData |binary data/Probe1.RData |binary data/Probe2.RData |binary data/RatWeight.RData |binary data/ReactTime.RData |binary data/Rohwer.rda |binary data/RootStock.rda |binary data/Sake.RData |binary data/Skulls.RData |binary data/SocGrades.RData |binary data/VocabGrowth.rda |binary data/WeightLoss.RData |binary data/schooldata.RData |binary inst/doc/HE-examples.R | 1096 +++++++++++++-------------- inst/doc/repeated.R | 1266 ++++++++++++++++---------------- man/MockJury.Rd | 2 man/heplot-package.Rd | 4 vignettes/fig/plot-Ortho-fm1.pdf |binary vignettes/fig/plot-Ortho-fm3.pdf |binary vignettes/fig/plot-grades-can-class.pdf |binary vignettes/fig/plot-grades-can-gpa.pdf |binary vignettes/fig/plot-grades-can-sex.pdf |binary vignettes/fig/plot-grades-pairs.pdf |binary vignettes/fig/plot-hern-can-age.pdf |binary vignettes/fig/plot-hern-can-build.pdf |binary vignettes/fig/plot-hern-can-cardiac.pdf |binary vignettes/fig/plot-hern-can-pstat.pdf |binary vignettes/fig/plot-hern-pairs.pdf |binary vignettes/fig/plot-jury-can1.pdf |binary vignettes/fig/plot-jury-mod1-HE.pdf |binary vignettes/fig/plot-jury-mod1-pairs.pdf |binary vignettes/fig/plot-jury-mod2-HE.pdf |binary vignettes/fig/plot-jury-mod3-eff.pdf |binary vignettes/fig/plot-obk-HE1.pdf |binary vignettes/fig/plot-obk-HE2.pdf |binary vignettes/fig/plot-obk-HE3.pdf |binary vignettes/fig/plot-obk2-HE1.pdf |binary vignettes/fig/plot-obk2-HE2.pdf |binary vignettes/fig/plot-ortho-HE.pdf |binary vignettes/fig/plot-ortho-nonlin-HE.pdf |binary vignettes/fig/plot-ortho-xyplot1.pdf |binary vignettes/fig/plot-ortho-xyplot2.pdf |binary vignettes/fig/plot-plastic2.pdf |binary vignettes/fig/plot-rohwer-HE1.pdf |binary vignettes/fig/plot-rohwer-HE2.pdf |binary vignettes/fig/plot-rohwer-HE3.pdf |binary vignettes/fig/plot-rohwer-HE4.pdf |binary vignettes/fig/plot-skulls-HE-pairs.pdf |binary vignettes/fig/plot-skulls-bwplot.pdf |binary vignettes/fig/plot-skulls-can2.pdf |binary vignettes/fig/plot-skulls4.pdf |binary vignettes/fig/plot-voc1.pdf |binary vignettes/fig/plot-voc4.pdf |binary vignettes/fig/plot-voc8.pdf |binary vignettes/fig/plot-wl-HE1.pdf |binary vignettes/fig/plot-wl-HE2.pdf |binary vignettes/fig/plot-wl-HE3.pdf |binary vignettes/fig/plot-wl-means.pdf |binary 72 files changed, 1271 insertions(+), 1265 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 0.1.5.2 dated 2015-06-10 and 0.2.0 dated 2015-07-12
DESCRIPTION | 12 ++-- MD5 | 22 ++++---- NEWS.md | 13 +++++ R/ggMarginal.R | 96 +++++++++++++++++++++++++------------- R/plotCount.R | 7 +- build/vignette.rds |binary inst/doc/overview.R | 5 + inst/doc/overview.Rmd | 53 +++++++++++--------- inst/doc/overview.html | 35 +++++++------ inst/examples/ggMarginal/server.R | 28 ++++++++++- inst/examples/ggMarginal/ui.R | 12 +++- man/plotCount.Rd | 6 +- 12 files changed, 195 insertions(+), 94 deletions(-)
Title: Compound Poisson Linear Models
Description: Likelihood-based and Bayesian methods for various compound Poisson linear models.
Author: Wayne Zhang
Maintainer: Wayne Zhang <actuary_zhang@hotmail.com>
Diff between cplm versions 0.7-2 dated 2014-03-10 and 0.7-3 dated 2015-07-12
DESCRIPTION | 10 - MD5 | 26 ++-- NAMESPACE | 68 +++++----- NEWS | 9 + R/cpglmm.R | 6 R/gini.R | 298 +++++++++++++++++++++++------------------------ data/AutoClaim.RData |binary data/ClaimTriangle.RData |binary data/FineRoot.RData |binary man/bcplm.Rd | 1 man/cpglmm.Rd | 1 man/cplm-package.Rd | 2 src/cpglmm.c | 5 vignettes/literatur.bib | 5 14 files changed, 226 insertions(+), 205 deletions(-)
Title: Bootstrapped Confidence Intervals for (Negative) Likelihood
Ratio Tests
Description: Computes appropriate confidence intervals for the likelihood ratio tests commonly used in medicine/epidemiology. It is particularly useful when the sensitivity or specificity in the sample is 100%. Note that this does not perform the test on nested models--for that, see 'epicalc::lrtest'.
Author: Keith A. Marill and Ari B. Friedman
Maintainer: Ari B. Friedman <abfriedman@gmail.com>
Diff between bootLR versions 0.9 dated 2014-05-27 and 1.0 dated 2015-07-12
DESCRIPTION | 20 ++--- MD5 | 24 +++---- NAMESPACE | 3 NEWS |only R/bootLR.R | 146 ++++++++++++++++++++++++++++++------------- inst |only man/BayesianLR.test.Rd | 97 ++++++++++++++++------------ man/bca.Rd | 19 ++--- man/confusionStatistics.Rd | 25 ++----- man/drawMaxedOut.Rd | 28 ++++---- man/medianConsistentlyOne.Rd | 28 ++++---- man/print.lrtest.Rd | 22 ++++-- man/run.BayesianLR.test.Rd | 44 +++++------- man/sequentialGridSearch.Rd | 37 ++++------ 14 files changed, 282 insertions(+), 211 deletions(-)
Title: GUI Implementing Bayesian Working Memory Models
Description: A GUI R implementation of hierarchical Bayesian models of working memory, used for analyzing change detection data.
Author: R. D. Morey <richarddmorey@gmail.com>
Maintainer: R. D. Morey <richarddmorey@gmail.com>
Diff between WMCapacity versions 0.9.6.6 dated 2011-11-24 and 0.9.6.7 dated 2015-07-12
DESCRIPTION | 16 MD5 | 23 NAMESPACE | 30 NEWS |only R/analysistab.R | 1512 +++++++++++------------ R/datatab.R | 1414 +++++++++++----------- R/diagnosticstab.R | 1136 ++++++++--------- R/gui_functions.R | 488 +++---- R/modeltab.R | 3312 ++++++++++++++++++++++++++-------------------------- R/savetab.R | 22 R/wommbat.R | 172 +- man/wommbatGUI.Rd | 109 - man/wommbatNoGUI.Rd | 60 13 files changed, 4145 insertions(+), 4149 deletions(-)
Title: Sequential and Batch Change Detection Using Parametric and
Nonparametric Methods
Description: Sequential and batch change detection for univariate data streams, using the change point model framework. Functions are provided to allow nonparametric distribution-free change detection in the mean, variance, or general distribution of a given sequence of observations. Parametric change detection methods are also provided for Gaussian, Bernoulli and Exponential sequences. Both the batch (Phase I) and sequential (Phase II) settings are supported, and the sequences may contain either a single or multiple change points.
Author: Gordon J. Ross
Maintainer: Gordon J. Ross <gordon@gordonjross.co.uk>
Diff between cpm versions 2.0 dated 2015-06-05 and 2.1 dated 2015-07-12
DESCRIPTION | 12 +++++------- MD5 | 24 ++++++++++++------------ NAMESPACE | 3 ++- man/changeDetected.Rd | 2 +- man/cpmPackage.Rd | 18 +++++++++++------- man/cpmReset.Rd | 2 +- man/detectChangePoint.Rd | 14 ++++++++------ man/detectChangePointBatch.Rd | 12 +++++++----- man/getBatchThreshold.Rd | 12 +++++++----- man/getStatistics.Rd | 2 +- man/makeChangePointModel.Rd | 12 +++++++----- man/processObservation.Rd | 2 +- man/processStream.Rd | 9 +++++---- 13 files changed, 68 insertions(+), 56 deletions(-)
Title: Correct for Verification Bias in Diagnostic Accuracy & Agreement
Description: A standard test is observed on all specimens. We treat the second test (or sampled test) as being conducted on only a stratified sample of specimens. Verification Bias is this situation when the specimens for doing the second (sampled) test is not under investigator control. We treat the total sample as stratified two-phase sampling and use inverse probability weighting. We estimate diagnostic accuracy (category-specific classification probabilities; for binary tests reduces to specificity and sensitivity, and also predictive values) and agreement statistics (percent agreement, percent agreement by category, Kappa (unweighted), Kappa (quadratic weighted) and symmetry tests (reduces to McNemar's test for binary tests)). See: Katki HA, Li Y, Edelstein DW, Castle PE. Estimating the agreement and diagnostic accuracy of two diagnostic tests when one test is conducted on only a subsample of specimens. Stat Med. 2012 Feb 28; 31(5): 10.1002/sim.4422.
Author: Hormuzd A. Katki and David W. Edelstein
Maintainer: Hormuzd Katki <katkih@mail.nih.gov>
Diff between CompareTests versions 1.0 dated 2011-04-04 and 1.1 dated 2015-07-12
DESCRIPTION | 27 - MD5 |only NAMESPACE |only NEWS |only R/CompareTests.R | 638 +++++++++++++++++++++++++------------------- man/CompareTests-package.Rd | 14 man/CompareTests.Rd | 118 +++++--- man/fulltable.Rd | 10 man/specimens.Rd | 6 9 files changed, 454 insertions(+), 359 deletions(-)
Title: Interface for FAME Time Series Database
Description: Read and write FAME databases.
Author: Jeff Hallman <jeffrey.j.hallman@frb.gov>
Maintainer: Jeff Hallman <jeffrey.j.hallman@frb.gov>
Diff between fame versions 2.18 dated 2011-12-30 and 2.21 dated 2015-07-12
fame-2.18/fame/COPYRIGHTS |only fame-2.21/fame/DESCRIPTION | 16 ++--- fame-2.21/fame/MD5 | 30 ++++----- fame-2.21/fame/NAMESPACE | 8 +- fame-2.21/fame/NEWS | 18 +++++ fame-2.21/fame/R/fame.R | 103 +++++++++++++++++++++++---------- fame-2.21/fame/R/windows/zzz.R | 2 fame-2.21/fame/configure | 4 - fame-2.21/fame/configure.ac | 4 - fame-2.21/fame/inst/COPYRIGHTS |only fame-2.21/fame/man/fameAddAttribute.Rd | 4 - fame-2.21/fame/man/fameIsScalar.Rd | 9 +- fame-2.21/fame/man/lowLevelFame.Rd | 39 ++++++++++-- fame-2.21/fame/man/tifToFameName.Rd | 8 +- fame-2.21/fame/src/chli.c | 1 fame-2.21/fame/src/fame.c | 8 ++ fame-2.21/fame/src/fame.h | 2 17 files changed, 182 insertions(+), 74 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. 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 1.2.3 dated 2015-06-29 and 1.3.2 dated 2015-07-12
DESCRIPTION | 11 ++-- MD5 | 12 ++-- NAMESPACE | 2 R/GetValues.R | 98 ++++++++++++++++++++++++++++++++++++++-- R/HISCentral_GetSeriesCatalog.R | 3 - R/WaterMLVersion.R |only man/GetValues.Rd | 8 ++- man/WaterMLVersion.Rd |only 8 files changed, 118 insertions(+), 16 deletions(-)
Title: Parameterized Queries Extension for RODBC
Description: An extension for RODBC package adding support for parameterized
queries.
Author: Mateusz Zoltak [aut, cre],
Brian Ripley [aut],
Michael Lapsley [aut]
Maintainer: Mateusz Zoltak <zozlak@zozlak.org>
Diff between RODBCext versions 0.2.3 dated 2014-07-29 and 0.2.5 dated 2015-07-12
DESCRIPTION | 10 ++-- MD5 | 32 +++++++------- NAMESPACE | 2 NEWS | 23 ++++++++-- R/sqlExecute.R | 34 +++++++++++++-- R/sqlPrepare.R | 4 + README.md | 5 +- build/vignette.rds |binary inst/doc/Parameterized_SQL_queries.Rmd | 25 ++++++----- inst/doc/Parameterized_SQL_queries.html | 69 +++++++++++++++++--------------- man/odbcFetchRows.Rd | 3 - man/sqlExecute.Rd | 16 +++++-- man/sqlFetchMore.Rd | 3 - man/sqlPrepare.Rd | 3 - src/RODBC.c | 17 ++++--- src/RODBCext.c | 10 ++-- vignettes/Parameterized_SQL_queries.Rmd | 25 ++++++----- 17 files changed, 172 insertions(+), 109 deletions(-)
Title: Gene and Splice Site Annotation Using Annotation Data from
Ensembl and UCSC Genome Browsers
Description: The packge contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between refGenome versions 1.3.0 dated 2014-09-18 and 1.5.3 dated 2015-07-12
refGenome-1.3.0/refGenome/src/ptr_pair_list.h |only refGenome-1.3.0/refGenome/src/refGenome.c |only refGenome-1.5.3/refGenome/ChangeLog | 8 refGenome-1.5.3/refGenome/DESCRIPTION | 10 refGenome-1.5.3/refGenome/MD5 | 58 - refGenome-1.5.3/refGenome/NAMESPACE | 8 refGenome-1.5.3/refGenome/NEWS | 38 refGenome-1.5.3/refGenome/R/refGenome.r | 803 ++++++++----------- refGenome-1.5.3/refGenome/build/vignette.rds |binary refGenome-1.5.3/refGenome/inst/doc/readGTF.R |only refGenome-1.5.3/refGenome/inst/doc/readGTF.Rnw |only refGenome-1.5.3/refGenome/inst/doc/readGTF.pdf |only refGenome-1.5.3/refGenome/inst/doc/refGenome.R | 171 ++-- refGenome-1.5.3/refGenome/inst/doc/refGenome.Rnw | 513 +++++++++--- refGenome-1.5.3/refGenome/inst/doc/refGenome.pdf |binary refGenome-1.5.3/refGenome/man/ensemblGenome-class.Rd | 15 refGenome-1.5.3/refGenome/man/overlapJuncs.Rd | 18 refGenome-1.5.3/refGenome/man/readGtf.Rd |only refGenome-1.5.3/refGenome/man/refExons-class.Rd | 6 refGenome-1.5.3/refGenome/man/refGenome-class.Rd | 51 - refGenome-1.5.3/refGenome/man/refGenome-package.Rd | 2 refGenome-1.5.3/refGenome/man/ucscGenome-class.Rd | 8 refGenome-1.5.3/refGenome/man/unifyJuncs.Rd | 10 refGenome-1.5.3/refGenome/man/unifyRanges.Rd |only refGenome-1.5.3/refGenome/src/Makevars | 1 refGenome-1.5.3/refGenome/src/Makevars.win | 1 refGenome-1.5.3/refGenome/src/data_frame.h |only refGenome-1.5.3/refGenome/src/extptr.h |only refGenome-1.5.3/refGenome/src/grange.h |only refGenome-1.5.3/refGenome/src/gtf.h |only refGenome-1.5.3/refGenome/src/range_partition.h |only refGenome-1.5.3/refGenome/src/refGenome.cpp |only refGenome-1.5.3/refGenome/src/refGenome.h | 88 -- refGenome-1.5.3/refGenome/src/tokenize.h |only refGenome-1.5.3/refGenome/tests/test-all.R | 33 refGenome-1.5.3/refGenome/tests/test_unify_ranges.r |only refGenome-1.5.3/refGenome/vignettes/readGTF.Rnw |only refGenome-1.5.3/refGenome/vignettes/refGenome.Rnw | 513 +++++++++--- 38 files changed, 1519 insertions(+), 836 deletions(-)