Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 2.9.4 dated 2015-03-24 and 2.9.5 dated 2015-06-15
DESCRIPTION | 8 +-- MD5 | 114 ++++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS | 33 ++++++++++++ R/DENSITY.R | 4 - R/esa.R | 1 R/ip.secr.R | 20 +++++-- R/join.R | 98 ++++++++++++++++++++++--------------- R/joinold.R |only R/make.capthist.R | 19 +++++-- R/methods.R | 20 +++---- R/pdot.R | 22 +++++++- R/raster.R | 18 +++--- R/read.traps.R | 11 ++++ R/reduce.R | 2 R/regionN.R | 1 R/score.test.R | 35 +------------ R/secr.fit.R | 90 ++++++++++++++++++++++++---------- R/secr.test.R | 2 R/secrloglik.R | 48 ++++++++++++++---- R/sim.capthist.R | 66 +++++++++++++++++-------- R/sim.popn.R | 79 +++++++++++++++++------------- R/sim.secr.R | 6 +- R/usagePlot.R | 4 - R/utility.R | 43 ++++++++++++++++ build/vignette.rds |binary data/OVpossum.RData |binary data/deermouse.RData |binary data/hornedlizard.RData |binary data/housemouse.RData |binary data/ovenbird.RData |binary data/ovensong.RData |binary data/possum.RData |binary data/secrdemo.RData |binary data/skink.RData |binary data/stoatDNA.RData |binary inst/doc/secr-datainput.R | 10 +-- inst/doc/secr-datainput.pdf |binary inst/doc/secr-manual.pdf |binary inst/doc/secr-overview.R | 26 +++++----- inst/doc/secr-overview.Rmd | 4 + inst/doc/secr-overview.pdf |binary man/DENSITY.Rd | 5 + man/RMarkInput.Rd | 2 man/addTelemetry.Rd | 3 - man/clone.Rd | 2 man/contour.Rd | 5 + man/details.Rd | 3 + man/join.Rd | 8 +++ man/make.capthist.Rd | 6 +- man/raster2.Rd |only man/secr-package.Rd | 9 ++- man/secr.fit.Rd | 1 man/secrtest.Rd | 14 ++--- man/sim.popn.Rd | 8 +-- man/simpopndetails.Rd | 8 +-- src/trapping.c | 3 - src/utils.c | 5 + vignettes/secr-overview.Rmd | 4 + 59 files changed, 556 insertions(+), 315 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.46 dated 2015-03-28 and 1.47 dated 2015-06-15
Changelog | 26 +++++++++ DESCRIPTION | 8 +- MD5 | 28 +++++----- R/Functions.R | 70 +++++++++++++++++++++++-- R/blockwiseModulesC.R | 73 ++++++++++++++++++++------ R/corFunctions.R | 2 R/empiricalBayesLM.R | 106 +++++++++++++++++++++++++-------------- R/smaFunctions.R |only man/WGCNA-package.Rd | 4 - man/blockwiseConsensusModules.Rd | 4 + man/blockwiseIndividualTOMs.Rd | 5 + man/blockwiseModules.Rd | 17 ++++++ man/empiricalBayesLM.Rd | 16 +++++ man/labeledHeatmap.multiPage.Rd | 32 +++++++++++ man/plotCor.Rd |only man/plotMat.Rd |only man/rgcolors.func.Rd |only 17 files changed, 312 insertions(+), 79 deletions(-)
Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species
abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Maintainer: Paulo I. Prado <prado@ib.usp.br>
Diff between sads versions 0.1.10 dated 2014-07-02 and 0.2.1 dated 2015-06-15
sads-0.1.10/sads/R/is.wholenumber.R |only sads-0.1.10/sads/R/pth.R |only sads-0.1.10/sads/R/qth.R |only sads-0.1.10/sads/R/trueLL.R |only sads-0.1.10/sads/man/trueLL.Rd |only sads-0.2.1/sads/DESCRIPTION | 18 - sads-0.2.1/sads/MD5 | 199 ++++++------ sads-0.2.1/sads/NAMESPACE | 18 - sads-0.2.1/sads/NEWS |only sads-0.2.1/sads/R/dbs.R | 15 sads-0.2.1/sads/R/dgs.R | 18 - sads-0.2.1/sads/R/dls.R | 23 - sads-0.2.1/sads/R/dmand.R | 23 - sads-0.2.1/sads/R/dmzsm.R | 24 - sads-0.2.1/sads/R/dpareto.R | 11 sads-0.2.1/sads/R/dpoig.R | 23 - sads-0.2.1/sads/R/dpoilog.R | 26 + sads-0.2.1/sads/R/dpoix.R | 31 - sads-0.2.1/sads/R/dpower.R | 25 - sads-0.2.1/sads/R/drbs.R | 16 sads-0.2.1/sads/R/dvolkov.R | 22 - sads-0.2.1/sads/R/dzipf.R | 19 - sads-0.2.1/sads/R/fitbs.R | 7 sads-0.2.1/sads/R/fitgamma.R | 57 ++- sads-0.2.1/sads/R/fitgeom.R | 2 sads-0.2.1/sads/R/fitgs.R | 6 sads-0.2.1/sads/R/fitlnorm.R | 8 sads-0.2.1/sads/R/fitls.R | 10 sads-0.2.1/sads/R/fitmand.R | 10 sads-0.2.1/sads/R/fitmzsm.R | 6 sads-0.2.1/sads/R/fitnbinom.R | 2 sads-0.2.1/sads/R/fitpareto.R | 10 sads-0.2.1/sads/R/fitpoilog.R | 3 sads-0.2.1/sads/R/fitpower.R | 2 sads-0.2.1/sads/R/fitrad.R | 1 sads-0.2.1/sads/R/fitrbs.R | 4 sads-0.2.1/sads/R/fitsad.R | 12 sads-0.2.1/sads/R/fitvolkov.R | 19 - sads-0.2.1/sads/R/fitweibull.R | 8 sads-0.2.1/sads/R/fitzipf.R | 6 sads-0.2.1/sads/R/octav.R | 15 sads-0.2.1/sads/R/pbs.R | 18 - sads-0.2.1/sads/R/pgs.R | 17 - sads-0.2.1/sads/R/plotprofmle.R | 11 sads-0.2.1/sads/R/pls.R | 17 - sads-0.2.1/sads/R/pmand.R | 29 - sads-0.2.1/sads/R/pmzsm.R | 18 - sads-0.2.1/sads/R/ppareto.R | 17 - sads-0.2.1/sads/R/ppoig.R |only sads-0.2.1/sads/R/ppoilog.R | 14 sads-0.2.1/sads/R/ppoix.R |only sads-0.2.1/sads/R/ppower.R | 25 - sads-0.2.1/sads/R/prbs.R | 15 sads-0.2.1/sads/R/pvolkov.R | 18 - sads-0.2.1/sads/R/pzipf.R | 24 - sads-0.2.1/sads/R/qbs.R | 41 -- sads-0.2.1/sads/R/qgs.R | 7 sads-0.2.1/sads/R/qls.R | 38 -- sads-0.2.1/sads/R/qmand.R | 13 sads-0.2.1/sads/R/qmzsm.R |only sads-0.2.1/sads/R/qpareto.R | 17 - sads-0.2.1/sads/R/qpoig.R |only sads-0.2.1/sads/R/qpoilog.R | 40 -- sads-0.2.1/sads/R/qpoix.R |only sads-0.2.1/sads/R/qpower.R | 36 -- sads-0.2.1/sads/R/qrbs.R | 11 sads-0.2.1/sads/R/qvolkov.R | 23 - sads-0.2.1/sads/R/qzipf.R | 11 sads-0.2.1/sads/R/rsad.R | 4 sads-0.2.1/sads/R/sads-classes.R | 23 + sads-0.2.1/sads/R/sads-methods.R | 513 +++++++++++-------------------- sads-0.2.1/sads/R/updatesad.R |only sads-0.2.1/sads/R/utils.R |only sads-0.2.1/sads/README.md |only sads-0.2.1/sads/build/vignette.rds |binary sads-0.2.1/sads/inst/doc/sads_intro.R | 82 ++-- sads-0.2.1/sads/inst/doc/sads_intro.Rnw | 164 ++++++--- sads-0.2.1/sads/inst/doc/sads_intro.pdf |binary sads-0.2.1/sads/man/ICtab.Rd |only sads-0.2.1/sads/man/birds.Rd | 6 sads-0.2.1/sads/man/dbs.Rd | 16 sads-0.2.1/sads/man/dgs.Rd | 4 sads-0.2.1/sads/man/dls.Rd | 12 sads-0.2.1/sads/man/dman.Rd | 6 sads-0.2.1/sads/man/dmzsm.Rd | 22 - sads-0.2.1/sads/man/dpareto.Rd | 10 sads-0.2.1/sads/man/dpoig.Rd | 45 ++ sads-0.2.1/sads/man/dpoilog.Rd | 26 - sads-0.2.1/sads/man/dpoix.Rd | 50 ++- sads-0.2.1/sads/man/dpower.Rd | 4 sads-0.2.1/sads/man/dtrunc.Rd | 2 sads-0.2.1/sads/man/dvolkov.Rd | 35 +- sads-0.2.1/sads/man/dzipf.Rd | 11 sads-0.2.1/sads/man/fitrad-class.Rd | 9 sads-0.2.1/sads/man/fitrad.Rd | 2 sads-0.2.1/sads/man/fitsad-class.Rd | 9 sads-0.2.1/sads/man/fitsad.Rd | 125 ++++--- sads-0.2.1/sads/man/octav-class.Rd | 8 sads-0.2.1/sads/man/octav.Rd | 4 sads-0.2.1/sads/man/octavpred.Rd | 2 sads-0.2.1/sads/man/plotprofmle.Rd | 2 sads-0.2.1/sads/man/pred.logser.Rd | 2 sads-0.2.1/sads/man/radpred.Rd | 11 sads-0.2.1/sads/man/rsad.Rd | 10 sads-0.2.1/sads/man/sads-package.Rd | 11 sads-0.2.1/sads/man/updatesad.Rd |only sads-0.2.1/sads/src |only sads-0.2.1/sads/vignettes/sads_intro.Rnw | 164 ++++++--- 108 files changed, 1222 insertions(+), 1331 deletions(-)
Title: PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations
Description: A collection of tools for approximating the 'PDQ' functions (respectively, the
cumulative distribution, density, and quantile) of probability distributions via classical
expansions involving moments and cumulants.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between PDQutils versions 0.1.1 dated 2015-02-26 and 0.1.2 dated 2015-06-15
DESCRIPTION | 10 MD5 | 48 +- NAMESPACE | 2 R/PDQutils.r | 33 + R/edgeworth.r | 5 R/gram_charlier.r | 316 ++++++++++++++--- R/moments.r | 9 README.md | 89 ++++- build/vignette.rds |binary inst/doc/PDQutils.R | 26 + inst/doc/PDQutils.Rnw | 868 ++++++++++++++++++++++++------------------------- inst/doc/PDQutils.pdf |binary inst/tests |only man/AS269.Rd | 2 man/NEWS.Rd | 10 man/PDQutils.Rd | 33 + man/cumulant2moment.Rd | 2 man/dapx_edgeworth.Rd | 2 man/dapx_gca.Rd | 132 +++++-- man/moment2cumulant.Rd | 2 man/qapx_cf.Rd | 8 man/rapx_cf.Rd | 8 tests |only vignettes/PDQutils.Rnw | 868 ++++++++++++++++++++++++------------------------- vignettes/PDQutils.bib | 61 +++ 25 files changed, 1514 insertions(+), 1020 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.3 dated 2015-01-28 and 0.4.4 dated 2015-06-15
DESCRIPTION | 11 ++-- MD5 | 80 ++++++++++++++++++----------------- NAMESPACE | 9 +++ R/bundle.R | 14 ++++++ R/cache.R | 90 +++++++++++++++++++++++++-------------- R/cranlike-repositories.R |only R/dependencies.R | 93 +++++++++++++++++++++++++++++++++-------- R/install.R | 16 ++++--- R/library-support.R | 23 +++++++--- R/options.R | 13 ++++- R/packrat-mode.R | 26 ++++++++--- R/packrat.R | 22 ++++++--- R/paths.R | 2 R/pkg.R | 13 ++++- R/restore.R | 62 ++++++++++++++++++++------- R/snapshot.R | 24 ++++++---- R/utils.R | 38 ++++++++++++++-- inst/resources/init-rprofile.R | 2 inst/resources/init.R | 2 man/appDependencies.Rd | 2 man/bundle.Rd | 2 man/clean.Rd | 2 man/disable.Rd | 2 man/init.Rd | 2 man/install.Rd | 2 man/install_github.Rd | 2 man/install_local.Rd | 2 man/migrate.Rd | 2 man/packify.Rd | 2 man/packrat-external.Rd | 2 man/packrat-mode.Rd | 2 man/packrat-options.Rd | 5 +- man/packrat.Rd | 2 man/repos_create.Rd |only man/repos_upload.Rd |only man/repository-management.Rd |only man/restore.Rd | 2 man/search_path.Rd | 2 man/snapshot.Rd | 2 man/snapshotImpl.Rd | 2 man/status.Rd | 2 man/unbundle.Rd | 2 man/unused_packages.Rd | 2 43 files changed, 407 insertions(+), 178 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item functioning and modelling item and person
covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.9 dated 2015-03-29 and 1.10 dated 2015-06-15
mirt-1.10/mirt/DESCRIPTION | 18 mirt-1.10/mirt/MD5 | 245 +- mirt-1.10/mirt/NAMESPACE | 8 mirt-1.10/mirt/NEWS | 113 + mirt-1.10/mirt/R/00-classes.R | 8 mirt-1.10/mirt/R/01-itemclass.R |only mirt-1.10/mirt/R/02-item_methods.R | 2337 +++++++++++++++++---- mirt-1.10/mirt/R/03-estimation.R | 213 + mirt-1.10/mirt/R/DIF.R | 31 mirt-1.10/mirt/R/DTF.R | 309 +- mirt-1.10/mirt/R/EMstep.group.R | 35 mirt-1.10/mirt/R/EMstep.utils.R | 16 mirt-1.10/mirt/R/LoadPars.R | 135 - mirt-1.10/mirt/R/M2.R | 89 mirt-1.10/mirt/R/MDIFF.R |only mirt-1.10/mirt/R/MDISC.R |only mirt-1.10/mirt/R/MHRM.group.R | 10 mirt-1.10/mirt/R/Mixed-methods.R | 2 mirt-1.10/mirt/R/MultipleGroup-methods.R | 15 mirt-1.10/mirt/R/PLCI.mirt.R | 32 mirt-1.10/mirt/R/PrepData.R | 43 mirt-1.10/mirt/R/SE.methods.R | 22 mirt-1.10/mirt/R/SingleGroup-methods.R | 157 - mirt-1.10/mirt/R/averageMI.R | 6 mirt-1.10/mirt/R/bfactor.R | 35 mirt-1.10/mirt/R/boot.mirt.R | 16 mirt-1.10/mirt/R/calcLogLik.R | 12 mirt-1.10/mirt/R/createItem.R | 2 mirt-1.10/mirt/R/expand.table.R | 4 mirt-1.10/mirt/R/expected.item.R | 4 mirt-1.10/mirt/R/expected.test.R | 4 mirt-1.10/mirt/R/extract.group.R | 6 mirt-1.10/mirt/R/extract.item.R | 5 mirt-1.10/mirt/R/fixef.R | 12 mirt-1.10/mirt/R/fscores.R | 44 mirt-1.10/mirt/R/fscores.internal.R | 167 - mirt-1.10/mirt/R/imputeMissing.R | 4 mirt-1.10/mirt/R/itemGAM.R |only mirt-1.10/mirt/R/itemfit.R | 55 mirt-1.10/mirt/R/iteminfo.R | 7 mirt-1.10/mirt/R/itemplot.R | 7 mirt-1.10/mirt/R/itemplot.internal.R | 43 mirt-1.10/mirt/R/key2binary.R | 5 mirt-1.10/mirt/R/marginal_rxx.R |only mirt-1.10/mirt/R/mdirt.R | 2 mirt-1.10/mirt/R/mirt-package.R | 6 mirt-1.10/mirt/R/mirt.R | 123 - mirt-1.10/mirt/R/mirt.model.R | 41 mirt-1.10/mirt/R/mirtCluster.R | 2 mirt-1.10/mirt/R/mixedmirt.R | 29 mirt-1.10/mirt/R/mod2values.R | 4 mirt-1.10/mirt/R/model.elements.R | 130 + mirt-1.10/mirt/R/multipleGroup.R | 42 mirt-1.10/mirt/R/personfit.R | 12 mirt-1.10/mirt/R/probtrace.R | 4 mirt-1.10/mirt/R/randef.R | 6 mirt-1.10/mirt/R/read.mirt.R | 42 mirt-1.10/mirt/R/shinyItemplot.R | 10 mirt-1.10/mirt/R/simdata.R | 18 mirt-1.10/mirt/R/utils.R | 223 +- mirt-1.10/mirt/R/wald.R | 19 mirt-1.10/mirt/build/vignette.rds |binary mirt-1.10/mirt/man/Bock1997.Rd | 2 mirt-1.10/mirt/man/DIF.Rd | 10 mirt-1.10/mirt/man/DTF.Rd | 59 mirt-1.10/mirt/man/DiscreteClass-class.Rd | 2 mirt-1.10/mirt/man/LSAT6.Rd | 6 mirt-1.10/mirt/man/LSAT7.Rd | 2 mirt-1.10/mirt/man/M2.Rd | 25 mirt-1.10/mirt/man/MDIFF.Rd |only mirt-1.10/mirt/man/MDISC.Rd |only mirt-1.10/mirt/man/MixedClass-class.Rd | 2 mirt-1.10/mirt/man/MultipleGroupClass-class.Rd | 2 mirt-1.10/mirt/man/PLCI.mirt.Rd | 8 mirt-1.10/mirt/man/SAT12.Rd | 2 mirt-1.10/mirt/man/Science.Rd | 2 mirt-1.10/mirt/man/SingleGroupClass-class.Rd | 5 mirt-1.10/mirt/man/anova-method.Rd | 4 mirt-1.10/mirt/man/averageMI.Rd | 4 mirt-1.10/mirt/man/bfactor.Rd | 24 mirt-1.10/mirt/man/boot.mirt.Rd | 2 mirt-1.10/mirt/man/coef-method.Rd | 5 mirt-1.10/mirt/man/createItem.Rd | 2 mirt-1.10/mirt/man/deAyala.Rd | 2 mirt-1.10/mirt/man/expand.table.Rd | 4 mirt-1.10/mirt/man/expected.item.Rd | 2 mirt-1.10/mirt/man/expected.test.Rd | 6 mirt-1.10/mirt/man/extract.group.Rd | 4 mirt-1.10/mirt/man/extract.item.Rd | 2 mirt-1.10/mirt/man/fixef.Rd | 10 mirt-1.10/mirt/man/fscores.Rd | 47 mirt-1.10/mirt/man/imputeMissing.Rd | 2 mirt-1.10/mirt/man/itemGAM.Rd |only mirt-1.10/mirt/man/itemfit.Rd | 20 mirt-1.10/mirt/man/iteminfo.Rd | 2 mirt-1.10/mirt/man/itemplot.Rd | 2 mirt-1.10/mirt/man/key2binary.Rd | 5 mirt-1.10/mirt/man/marginal_rxx.Rd |only mirt-1.10/mirt/man/mdirt.Rd | 2 mirt-1.10/mirt/man/mirt-package.Rd | 6 mirt-1.10/mirt/man/mirt.Rd | 121 - mirt-1.10/mirt/man/mirt.model.Rd | 47 mirt-1.10/mirt/man/mirtCluster.Rd | 2 mirt-1.10/mirt/man/mixedmirt.Rd | 14 mirt-1.10/mirt/man/mod2values.Rd | 4 mirt-1.10/mirt/man/multipleGroup.Rd | 36 mirt-1.10/mirt/man/personfit.Rd | 5 mirt-1.10/mirt/man/plot-method.Rd | 9 mirt-1.10/mirt/man/print-method.Rd | 2 mirt-1.10/mirt/man/probtrace.Rd | 2 mirt-1.10/mirt/man/randef.Rd | 4 mirt-1.10/mirt/man/residuals-method.Rd | 14 mirt-1.10/mirt/man/show-method.Rd | 2 mirt-1.10/mirt/man/simdata.Rd | 6 mirt-1.10/mirt/man/summary-method.Rd | 14 mirt-1.10/mirt/man/testinfo.Rd | 2 mirt-1.10/mirt/man/wald.Rd | 8 mirt-1.10/mirt/src/Misc.cpp | 20 mirt-1.10/mirt/src/traceLinePts.cpp | 3 mirt-1.10/mirt/tests/extratests/test-02-wideData.R | 6 mirt-1.10/mirt/tests/tests/test-01-mirtOne.R | 12 mirt-1.10/mirt/tests/tests/test-02-mirtTwo.R | 23 mirt-1.10/mirt/tests/tests/test-03-bfactor.R | 10 mirt-1.10/mirt/tests/tests/test-04-multipleGroup.R | 6 mirt-1.10/mirt/tests/tests/test-07-mixedmirt.R | 6 mirt-1.10/mirt/tests/tests/test-09-mirt.model.R | 45 mirt-1.10/mirt/tests/tests/test-10-extras.R | 14 mirt-1.9/mirt/R/01-itemtypes.R |only mirt-1.9/mirt/R/04-derivatives.R |only 129 files changed, 3998 insertions(+), 1712 deletions(-)
Title: Drawing Graphs with 'grid'
Description: Functions for drawing node-and-edge graphs that have been
laid out by graphviz. This provides an alternative
rendering to that provided by the 'Rgraphviz' package, with
two main advantages: the rendering provided by 'gridGraphviz'
should be more similar to what 'graphviz' itself would draw;
and rendering with 'grid' allows for post-hoc customisations
using the named viewports and grobs that 'gridGraphviz'
produces.
Author: Paul Murrell [cre, aut],
Ashley Noel Hinton [aut]
Maintainer: Paul Murrell <p.murrell@auckland.ac.nz>
Diff between gridGraphviz versions 0.1 dated 2012-03-31 and 0.3 dated 2015-06-15
DESCRIPTION | 29 ++++++-- MD5 | 13 ++- NAMESPACE | 10 ++ R/graph.R | 181 +++++++++++++++++++++++++++++++++++++----------------- R/grobs.R |only R/methods.R |only inst |only man/agopenTrue.Rd |only man/graphWidth.Rd |only man/grid.graph.Rd | 6 + 10 files changed, 169 insertions(+), 70 deletions(-)
Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used
in marketing and micro-econometrics applications.
The package includes:
Bayes Regression (univariate or multivariate dep var),
Bayes Seemingly Unrelated Regression (SUR),
Binary and Ordinal Probit,
Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit,
Negative Binomial (Poisson) Regression,
Multivariate Mixtures of Normals (including clustering),
Dirichlet Process Prior Density Estimation with normal base,
Hierarchical Linear Models with normal prior and covariates,
Hierarchical Linear Models with a mixture of normals prior and covariates,
Hierarchical Multinomial Logits with a mixture of normals prior
and covariates,
Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates,
Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data,
Bayesian treatment of linear instrumental variables models,
Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as in Rossi et al, JASA (01)),
Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see
Jiang, Manchanda, Rossi 2009)
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric
Methods and Applications (Princeton U Press 2014).
Author: Peter Rossi <perossichi@gmail.com>
Maintainer: Peter Rossi <perossichi@gmail.com>
Diff between bayesm versions 3.0-0 dated 2015-06-12 and 3.0-1 dated 2015-06-15
DESCRIPTION | 8 +++--- MD5 | 44 +++++++++++++++++------------------ man/rbayesBLP.Rd | 2 - src/bayesBLP_rcpp_loop.cpp | 14 +++++------ src/rDPGibbs_rcpp_loop.cpp | 14 +++++------ src/rbprobitGibbs_rcpp_loop.cpp | 2 - src/rhierLinearMixture_rcpp_loop.cpp | 10 +++---- src/rhierLinearModel_rcpp_loop.cpp | 8 +++--- src/rhierMnlDP_rcpp_loop.cpp | 20 +++++++-------- src/rhierMnlRwMixture_rcpp_loop.cpp | 10 +++---- src/rhierNegbinRw_rcpp_loop.cpp | 10 +++---- src/rivDP_rcpp_loop.cpp | 18 +++++++------- src/rivgibbs_rcpp_loop.cpp | 8 +++--- src/rmnlIndepMetrop_rcpp_loop.cpp | 4 +-- src/rmnpGibbs_rcpp_loop.cpp | 4 +-- src/rmvpGibbs_rcpp_loop.cpp | 4 +-- src/rnegbinRw_rcpp_loop.cpp | 4 +-- src/rnmixGibbs_rcpp_loop.cpp | 6 ++-- src/rordprobitGibbs_rcpp_loop.cpp | 8 +++--- src/rscaleUsage_rcpp_loop.cpp | 2 - src/rsurGibbs_rcpp_loop.cpp | 4 +-- src/runiregGibbs_rcpp_loop.cpp | 4 +-- src/runireg_rcpp_loop.cpp | 4 +-- 23 files changed, 106 insertions(+), 106 deletions(-)
Title: Rewrite of gWidgets API for Simplified GUI Construction
Description: Re-implementation of gWidgets API. The API is defined in this
package. A second, toolkit-specific package is required to use it. There
are three in development: 'gWidgets2RGtk2', 'gWidgets2Qt', and 'gWidgets2tcltk'.
Author: John Verzani
Maintainer: John Verzani <jverzani@gmail.com>
Diff between gWidgets2 versions 1.0-5 dated 2014-03-05 and 1.0-6 dated 2015-06-15
gWidgets2-1.0-5/gWidgets2/README.md |only gWidgets2-1.0-6/gWidgets2/DESCRIPTION | 37 gWidgets2-1.0-6/gWidgets2/MD5 | 203 ++-- gWidgets2-1.0-6/gWidgets2/NAMESPACE | 12 gWidgets2-1.0-6/gWidgets2/R/BasicInterface.R | 14 gWidgets2-1.0-6/gWidgets2/R/dialogs.R | 14 gWidgets2-1.0-6/gWidgets2/R/gdf.R | 6 gWidgets2-1.0-6/gWidgets2/R/gedit.R | 12 gWidgets2-1.0-6/gWidgets2/R/gexpandgroup.R | 4 gWidgets2-1.0-6/gWidgets2/R/gfilter.R | 460 ++++++++- gWidgets2-1.0-6/gWidgets2/R/gframe.R | 5 gWidgets2-1.0-6/gWidgets2/R/gnotebook.R | 45 gWidgets2-1.0-6/gWidgets2/R/gpanedgroup.R | 5 gWidgets2-1.0-6/gWidgets2/R/gprogressbar.R | 4 gWidgets2-1.0-6/gWidgets2/R/gtable.R | 4 gWidgets2-1.0-6/gWidgets2/R/guiToolkit.R | 9 gWidgets2-1.0-6/gWidgets2/R/handler-methods.R | 61 + gWidgets2-1.0-6/gWidgets2/R/methods.R | 15 gWidgets2-1.0-6/gWidgets2/inst/examples/ex-gbutton.R | 12 gWidgets2-1.0-6/gWidgets2/inst/examples/ex-gdf.R |only gWidgets2-1.0-6/gWidgets2/inst/examples/ex-gexpandgroup.R |only gWidgets2-1.0-6/gWidgets2/man/S4-classes.Rd | 115 +- gWidgets2-1.0-6/gWidgets2/man/XXX.Rd | 9 gWidgets2-1.0-6/gWidgets2/man/add.Rd | 66 - gWidgets2-1.0-6/gWidgets2/man/call_meth.Rd | 15 gWidgets2-1.0-6/gWidgets2/man/check_deprecated.Rd | 11 gWidgets2-1.0-6/gWidgets2/man/check_return_class.Rd | 13 gWidgets2-1.0-6/gWidgets2/man/dispose.Rd | 16 gWidgets2-1.0-6/gWidgets2/man/editable.Rd | 27 gWidgets2-1.0-6/gWidgets2/man/enabled.Rd | 28 gWidgets2-1.0-6/gWidgets2/man/flatten.Rd | 11 gWidgets2-1.0-6/gWidgets2/man/focus.Rd | 26 gWidgets2-1.0-6/gWidgets2/man/font.Rd | 63 - gWidgets2-1.0-6/gWidgets2/man/gWidgets-handlers.Rd | 471 ++++----- gWidgets2-1.0-6/gWidgets2/man/gWidgets2-S3methods.Rd | 102 +- gWidgets2-1.0-6/gWidgets2/man/gWidgets2-package.Rd | 475 ++++------ gWidgets2-1.0-6/gWidgets2/man/gWidgets2-undocumented.Rd | 16 gWidgets2-1.0-6/gWidgets2/man/gaction.Rd | 55 - gWidgets2-1.0-6/gWidgets2/man/galert.Rd | 31 gWidgets2-1.0-6/gWidgets2/man/gbasicdialog.Rd | 74 - gWidgets2-1.0-6/gWidgets2/man/gbutton.Rd | 143 +-- gWidgets2-1.0-6/gWidgets2/man/gcalendar.Rd | 62 - gWidgets2-1.0-6/gWidgets2/man/gcheckbox.Rd | 92 - gWidgets2-1.0-6/gWidgets2/man/gcheckboxgroup.Rd | 169 +-- gWidgets2-1.0-6/gWidgets2/man/gcombobox.Rd | 140 +- gWidgets2-1.0-6/gWidgets2/man/gconfirm.Rd | 36 gWidgets2-1.0-6/gWidgets2/man/gcontainer.Rd | 29 gWidgets2-1.0-6/gWidgets2/man/gdf.Rd | 74 - gWidgets2-1.0-6/gWidgets2/man/gdfnotebook.Rd | 21 gWidgets2-1.0-6/gWidgets2/man/gedit.Rd | 110 +- gWidgets2-1.0-6/gWidgets2/man/getToolkitWidget.Rd | 51 - gWidgets2-1.0-6/gWidgets2/man/getWithDefault.Rd | 13 gWidgets2-1.0-6/gWidgets2/man/get_index_in_list.Rd | 12 gWidgets2-1.0-6/gWidgets2/man/get_object_from_string.Rd | 16 gWidgets2-1.0-6/gWidgets2/man/gexpandgroup.Rd | 78 - gWidgets2-1.0-6/gWidgets2/man/gfile.Rd | 176 +-- gWidgets2-1.0-6/gWidgets2/man/gfilter.Rd | 164 +-- gWidgets2-1.0-6/gWidgets2/man/gformlayout.Rd | 98 -- gWidgets2-1.0-6/gWidgets2/man/gframe.Rd | 51 - gWidgets2-1.0-6/gWidgets2/man/ggraphics.Rd | 98 +- gWidgets2-1.0-6/gWidgets2/man/ggraphicsnotebook.Rd | 63 - gWidgets2-1.0-6/gWidgets2/man/ggroup.Rd | 127 +- gWidgets2-1.0-6/gWidgets2/man/ghtml.Rd | 75 - gWidgets2-1.0-6/gWidgets2/man/gimage.Rd | 38 gWidgets2-1.0-6/gWidgets2/man/ginput.Rd | 38 gWidgets2-1.0-6/gWidgets2/man/glabel.Rd | 73 - gWidgets2-1.0-6/gWidgets2/man/glayout.Rd | 100 +- gWidgets2-1.0-6/gWidgets2/man/gmenu.Rd | 173 +-- gWidgets2-1.0-6/gWidgets2/man/gmessage.Rd | 35 gWidgets2-1.0-6/gWidgets2/man/gnotebook.Rd | 238 ++--- gWidgets2-1.0-6/gWidgets2/man/gpanedgroup.Rd | 75 - gWidgets2-1.0-6/gWidgets2/man/gprogressbar.Rd | 68 - gWidgets2-1.0-6/gWidgets2/man/gradio.Rd | 169 +-- gWidgets2-1.0-6/gWidgets2/man/gseparator.Rd | 46 gWidgets2-1.0-6/gWidgets2/man/gslider.Rd | 132 +- gWidgets2-1.0-6/gWidgets2/man/gspinbutton.Rd | 119 +- gWidgets2-1.0-6/gWidgets2/man/gstackwidget.Rd | 38 gWidgets2-1.0-6/gWidgets2/man/gstatusbar.Rd | 36 gWidgets2-1.0-6/gWidgets2/man/gtable.Rd | 221 ++-- gWidgets2-1.0-6/gWidgets2/man/gtext.Rd | 220 ++-- gWidgets2-1.0-6/gWidgets2/man/gtimer.Rd | 31 gWidgets2-1.0-6/gWidgets2/man/gtoolbar.Rd | 100 -- gWidgets2-1.0-6/gWidgets2/man/gtoolkit.Rd | 8 gWidgets2-1.0-6/gWidgets2/man/gtree.Rd | 221 ++-- gWidgets2-1.0-6/gWidgets2/man/guiToolkit.Rd | 28 gWidgets2-1.0-6/gWidgets2/man/gvarbrowser.Rd | 165 +-- gWidgets2-1.0-6/gWidgets2/man/gwidget.Rd | 78 - gWidgets2-1.0-6/gWidgets2/man/gwindow.Rd | 146 +-- gWidgets2-1.0-6/gWidgets2/man/icons.Rd | 91 - gWidgets2-1.0-6/gWidgets2/man/installing_gWidgets_toolkits.Rd | 6 gWidgets2-1.0-6/gWidgets2/man/isExtant.Rd | 13 gWidgets2-1.0-6/gWidgets2/man/is_MacOSX.Rd | 9 gWidgets2-1.0-6/gWidgets2/man/is_Windows.Rd | 8 gWidgets2-1.0-6/gWidgets2/man/is_empty.Rd | 10 gWidgets2-1.0-6/gWidgets2/man/methods.Rd | 34 gWidgets2-1.0-6/gWidgets2/man/observer.Rd | 14 gWidgets2-1.0-6/gWidgets2/man/redo.Rd | 14 gWidgets2-1.0-6/gWidgets2/man/short_summary.Rd | 44 gWidgets2-1.0-6/gWidgets2/man/size.Rd | 23 gWidgets2-1.0-6/gWidgets2/man/svalue.Rd | 91 - gWidgets2-1.0-6/gWidgets2/man/tag.Rd | 31 gWidgets2-1.0-6/gWidgets2/man/tooltip.Rd | 22 gWidgets2-1.0-6/gWidgets2/man/undo.Rd | 15 gWidgets2-1.0-6/gWidgets2/man/visible.Rd | 30 104 files changed, 3922 insertions(+), 3573 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.29 dated 2015-02-06 and 1.30 dated 2015-06-15
DESCRIPTION | 10 MD5 | 50 ++-- R/CA.R | 120 ++++++----- R/FAMD.R | 179 ++++++++++++++--- R/HCPC.R | 7 R/MCA.R | 89 +++++--- R/MFA.R | 86 ++++---- R/PCA.R | 174 ++++++++-------- R/condes.r | 3 R/dimdesc.r | 22 +- R/plot.FAMD.R | 43 ++-- R/plot.MCA.R | 5 R/plot.MFA.R | 72 ++++++ R/plot.PCA.R | 2 R/plotellipses.r | 20 + R/summary.MFA.r | 1 R/svd.triplet.R | 88 ++++---- R/tab.disjonctif.R | 31 +- inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary man/FAMD.Rd | 2 man/children.Rd | 2 man/geomorphology.Rd | 3 man/plot.FAMD.Rd | 1 man/plotellipses.Rd | 2 man/poulet.Rd | 18 - 26 files changed, 661 insertions(+), 369 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between rfPermute versions 1.6.2 dated 2015-02-23 and 1.7 dated 2015-06-15
DESCRIPTION | 12 ++++++------ MD5 | 41 +++++++++++++++++++++-------------------- NAMESPACE | 7 +++++-- R/calc.imp.pval.R | 2 -- R/clean.rf.data.R | 7 +++---- R/plot.rfPermute.R | 7 +++---- R/plot.rp.importance.r | 6 +++--- R/proximity.plot.r | 5 ++--- R/rfPermute.R | 12 +++++------- R/rfPermute.default.R | 10 +++++----- R/rfPermute.formula.R | 7 +++---- R/rp.combine.R | 4 ++-- R/rp.importance.R | 5 ++--- inst |only man/calc.imp.pval.Rd | 2 +- man/clean.rf.data.Rd | 2 +- man/plot.rfPermute.Rd | 4 ++-- man/plot.rp.importance.Rd | 5 +++-- man/proximity.plot.Rd | 2 +- man/rfPermute.Rd | 17 +++++++---------- man/rp.combine.Rd | 2 +- man/rp.importance.Rd | 2 +- 22 files changed, 77 insertions(+), 84 deletions(-)
Title: An Improved Evaluation of Kolmogorov's Distribution
Description: Provides an alternative, more efficient evaluation of extreme
probabilities of Kolmogorov's goodness-of-fit measure, Dn, when compared to
the original implementation of Wang, Marsaglia, and Tsang. These
probabilities are used in Kolmogorov-Smirnov tests when comparing two
samples.
Author: Luis Carvalho
Maintainer: Luis Carvalho <lexcarvalho@gmail.com>
Diff between kolmim versions 0.2 dated 2014-04-20 and 1.0 dated 2015-06-15
DESCRIPTION | 20 ++++++++++---------- MD5 | 9 +++++---- inst |only man/ks.test.imp.Rd | 8 +++++--- man/pkolmim.Rd | 8 +++++--- src/kolmim.c | 13 +++++++------ 6 files changed, 32 insertions(+), 26 deletions(-)
Title: Perform Factorial Analysis from FactoMineR with a Shiny
Application
Description: Perform factorial analysis with a menu and draw graphs interactively thanks to FactoMineR and a Shiny application.
Author: Pauline Vaissie, Astrid Monge, Francois Husson
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>
Diff between Factoshiny versions 1.0 dated 2015-02-20 and 1.0.2 dated 2015-06-15
DESCRIPTION | 8 +- MD5 | 53 ++++++++------ NAMESPACE | 3 R/FAMDshiny.R |only R/HCPCshiny.R | 2 R/print.FAMDshiny.R |only inst/FactoCAapp2/global.R | 3 inst/FactoCAapp2/server.R | 68 +++++++++++++++--- inst/FactoCAapp2/ui.R | 24 +++--- inst/FactoFAMDapp2 |only inst/FactoHCPCapp2/global.R | 29 +++++++ inst/FactoHCPCapp2/server.R | 15 ++-- inst/FactoHCPCapp2/ui.R | 14 ++- inst/FactoHCPCappdf2/global.R | 10 ++ inst/FactoHCPCappdf2/server.R | 17 ++-- inst/FactoHCPCappdf2/ui.R | 14 ++- inst/FactoMCAapp2/global.R | 13 +++ inst/FactoMCAapp2/server.R | 157 ++++++++++++++++++++++++++++++++---------- inst/FactoMCAapp2/ui.R | 46 +++++++----- inst/FactoMFAapp/server.R | 41 +++++++--- inst/FactoMFAapp/ui.R | 15 +++- inst/FactoMFAapp2/global.R | 10 ++ inst/FactoMFAapp2/server.R | 45 ++++++++---- inst/FactoMFAapp2/ui.R | 15 +++- inst/FactoPCAapp2/global.R | 6 + inst/FactoPCAapp2/server.R | 47 +++++++++--- inst/FactoPCAapp2/ui.R | 13 ++- man/FAMDshiny.Rd |only man/print.FAMDshiny.Rd |only 29 files changed, 496 insertions(+), 172 deletions(-)
Title: Construction and Evaluation of Metamodels
Description: Estimation, validation and prediction of models of different types : linear models, additive models, MARS,PolyMARS and Kriging.
Author: D. Dupuy and C. Helbert
Maintainer: C. Helbert <Celine.Helbert@ec-lyon.fr>
Diff between DiceEval versions 1.3 dated 2014-05-27 and 1.4 dated 2015-06-15
DESCRIPTION | 13 ++--- MD5 | 9 ++- R/modelFit.R | 116 ++++++++++++++++++++++++------------------------ R/modelPredict.R | 34 +++++++------- inst |only man/DiceEval-package.Rd | 6 +- 6 files changed, 90 insertions(+), 88 deletions(-)
Title: Designs of Computer Experiments
Description: Space-Filling Designs and Uniformity Criteria.
Author: Jessica Franco, Delphine Dupuy, Olivier Roustant, Guillaume
Damblin and Bertrand Iooss.
Maintainer: Celine Helbert <Celine.Helbert@ec-lyon.fr>
Diff between DiceDesign versions 1.6 dated 2014-05-09 and 1.7 dated 2015-06-15
DiceDesign-1.6/DiceDesign/inst/po |only DiceDesign-1.6/DiceDesign/po |only DiceDesign-1.7/DiceDesign/DESCRIPTION | 8 DiceDesign-1.7/DiceDesign/MD5 | 18 - DiceDesign-1.7/DiceDesign/R/rss3d.R | 99 +++++---- DiceDesign-1.7/DiceDesign/inst/CITATION |only DiceDesign-1.7/DiceDesign/man/DiceDesign-package.Rd | 200 ++++++++++---------- DiceDesign-1.7/DiceDesign/man/coverage.Rd | 76 +++---- DiceDesign-1.7/DiceDesign/man/meshRatio.Rd | 80 ++++---- DiceDesign-1.7/DiceDesign/man/mindist.Rd | 86 ++++---- DiceDesign-1.7/DiceDesign/src/C_StraussDesign.c | 19 + 11 files changed, 298 insertions(+), 288 deletions(-)
Title: Bayesian Bootstrap Predictive Mean Matching - Multiple and
Single Imputation for Discrete Data
Description: Included are two variants of Bayesian Bootstrap
Predictive Mean Matching to multiply impute missing data. The
first variant is a variable-by-variable imputation combining
sequential regression and Predictive Mean Matching (PMM) that
has been extended for unordered categorical data. The Bayesian
Bootstrap allows for generating approximately proper multiple
imputations. The second variant is also based on PMM, but the
focus is on imputing several variables at the same time. The
suggestion is to use this variant, if the missing-data pattern
resembles a data fusion situation, or any other
missing-by-design pattern, where several variables have
identical missing-data patterns. Both variants can be run as
'single imputation' versions, in case the analysis objective is
of a purely descriptive nature.
Author: Florian Meinfelder [aut, cre],
Thorsten Schnapp [aut]
Maintainer: Florian Meinfelder <florian.meinfelder@uni-bamberg.de>
Diff between BaBooN versions 0.1-6 dated 2011-03-26 and 0.2-0 dated 2015-06-15
BaBooN-0.1-6/BaBooN/R/BBPMMcol.R |only BaBooN-0.2-0/BaBooN/DESCRIPTION | 22 BaBooN-0.2-0/BaBooN/MD5 |only BaBooN-0.2-0/BaBooN/NAMESPACE | 11 BaBooN-0.2-0/BaBooN/NEWS |only BaBooN-0.2-0/BaBooN/R/BB.R | 5 BaBooN-0.2-0/BaBooN/R/BBPMM.R |only BaBooN-0.2-0/BaBooN/R/BBPMMrow.R | 640 +++++++++++++-------- BaBooN-0.2-0/BaBooN/R/BBmodstab_glm.R | 72 +- BaBooN-0.2-0/BaBooN/R/BBmodstab_mlog.R | 92 +-- BaBooN-0.2-0/BaBooN/R/MIinference.R | 4 BaBooN-0.2-0/BaBooN/R/PMMC.R |only BaBooN-0.2-0/BaBooN/R/PMMsearch.R | 7 BaBooN-0.2-0/BaBooN/R/classes.R | 7 BaBooN-0.2-0/BaBooN/R/dmi.R |only BaBooN-0.2-0/BaBooN/R/impdiagnosticconversion.R |only BaBooN-0.2-0/BaBooN/R/inbind.R |only BaBooN-0.2-0/BaBooN/R/rowimpprep.R | 163 +++-- BaBooN-0.2-0/BaBooN/man/BBPMMcol.Rd | 104 ++- BaBooN-0.2-0/BaBooN/man/BBPMMrow.Rd | 76 +- BaBooN-0.2-0/BaBooN/man/BaBooN-package.Rd |only BaBooN-0.2-0/BaBooN/man/MIinference.Rd | 40 - BaBooN-0.2-0/BaBooN/man/SummaryImp.Rd | 2 BaBooN-0.2-0/BaBooN/man/SummaryImpprep.Rd | 2 BaBooN-0.2-0/BaBooN/man/dmi.Rd |only BaBooN-0.2-0/BaBooN/man/impdiagnosticconversion.Rd |only BaBooN-0.2-0/BaBooN/man/rowimpprep.Rd | 7 BaBooN-0.2-0/BaBooN/src |only 28 files changed, 790 insertions(+), 464 deletions(-)
Title: Assess Tumor Microsatellite Instability with a Decision Tree
Classifier from Exome Somatic Mutations
Description: A decision tree classifier for detecting microsatellite instability (MSI) in somatic mutation data from whole exome sequencing. MSI is detected based on different mutation rates in all sites as well as in simple sequence repeats. This mechanism can also be applied to sequence data of targeted gene panels with shorter sequence length.
Author: Mini Huang
Maintainer: Mini Huang <mini.huang@nus.edu.sg>
Diff between MSIseq versions 0.99.1 dated 2014-09-03 and 1.0.0 dated 2015-06-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/MSIseq.classify.R | 16 +++++++++++++--- inst/doc/MSIseq.pdf |binary man/MSIseq-package.Rd | 6 +++--- man/MSIseq.classify.Rd | 4 ++-- vignettes/MSIseq.Rnw | 2 +- 7 files changed, 30 insertions(+), 20 deletions(-)
Title: Fuzzy Stationary Probabilities from a Sequence of Observations
of an Unknown Markov Chain
Description: An implementation of a method for computing fuzzy numbers representing stationary probabilities of an unknown Markov chain,
from which a sequence of observations along time has been obtained. The algorithm is based on the proposal presented by James Buckley
in his book on Fuzzy probabilities (Springer, 2005), chapter 6. Package FuzzyNumbers is used to represent the output probabilities.
Author: Author: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Maintainer: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Diff between FuzzyStatProb versions 2.0 dated 2015-03-18 and 2.0.1 dated 2015-06-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/main.R | 35 ++++++++++++++++++----------------- build/vignette.rds |binary 4 files changed, 25 insertions(+), 24 deletions(-)
Title: Block Diagonal Extraction or Replacement
Description: Several tools for handling block-matrix diagonals and similar constructs are implemented. Block-diagonal matrices can be extracted or removed using two small functions implemented here. In addition, non-square matrices are supported. Block diagonal matrices occur when two dimensions of a data set are combined along one edge of a matrix. For example, trade-flow data in the 'decompr' and 'gvc' packages have each country-industry combination occur along both edges of the matrix.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between diagonals versions 0.2.0 dated 2015-05-29 and 0.3.0 dated 2015-06-15
diagonals-0.2.0/diagonals/R/block_matrix.R |only diagonals-0.2.0/diagonals/R/minus_block_matrix.R |only diagonals-0.2.0/diagonals/R/minus_rectangle_matrix.R |only diagonals-0.2.0/diagonals/R/rectangle_matrix.R |only diagonals-0.2.0/diagonals/inst/doc/diagonals.R |only diagonals-0.2.0/diagonals/inst/doc/diagonals.Rmd |only diagonals-0.2.0/diagonals/inst/doc/diagonals.html |only diagonals-0.2.0/diagonals/inst/doc/network.R |only diagonals-0.2.0/diagonals/inst/doc/network.Rmd |only diagonals-0.2.0/diagonals/inst/doc/network.html |only diagonals-0.2.0/diagonals/man/block_matrix.Rd |only diagonals-0.2.0/diagonals/man/minus_block_matrix.Rd |only diagonals-0.2.0/diagonals/man/minus_rectangle_matrix.Rd |only diagonals-0.2.0/diagonals/man/rectangle_matrix.Rd |only diagonals-0.2.0/diagonals/tests |only diagonals-0.2.0/diagonals/vignettes/diagonals.Rmd |only diagonals-0.2.0/diagonals/vignettes/network.Rmd |only diagonals-0.3.0/diagonals/DESCRIPTION | 6 - diagonals-0.3.0/diagonals/MD5 | 41 +++----- diagonals-0.3.0/diagonals/NAMESPACE | 7 - diagonals-0.3.0/diagonals/NEWS | 8 + diagonals-0.3.0/diagonals/R/diag.R |only diagonals-0.3.0/diagonals/R/diagonals.R | 7 + diagonals-0.3.0/diagonals/R/fatdiag.R |only diagonals-0.3.0/diagonals/R/split_vector.R |only diagonals-0.3.0/diagonals/README.md | 75 ++++++++++------ diagonals-0.3.0/diagonals/build/vignette.rds |binary diagonals-0.3.0/diagonals/inst/doc/fatdiag.R |only diagonals-0.3.0/diagonals/inst/doc/fatdiag.Rmd |only diagonals-0.3.0/diagonals/inst/doc/fatdiag.html |only diagonals-0.3.0/diagonals/man/diag-set.Rd |only diagonals-0.3.0/diagonals/man/fatdiag.Rd |only diagonals-0.3.0/diagonals/man/split_vector.Rd |only diagonals-0.3.0/diagonals/vignettes/fatdiag.Rmd |only 34 files changed, 84 insertions(+), 60 deletions(-)
Title: Mixed Effects Cox Models
Description: Cox proportional hazards models containing Gaussian random
effects, also known as frailty models.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau <therneau@mayo.edu>
Diff between coxme versions 2.2-4 dated 2015-03-03 and 2.2-5 dated 2015-06-15
coxme-2.2-4/coxme/noweb/noweb.Rnw |only coxme-2.2-5/coxme/DESCRIPTION | 7 ++---- coxme-2.2-5/coxme/MD5 | 33 +++++++++++++++++++------------- coxme-2.2-5/coxme/NAMESPACE | 1 coxme-2.2-5/coxme/R/anova.coxme.R | 8 ------- coxme-2.2-5/coxme/R/anova.coxmelist.R |only coxme-2.2-5/coxme/build/vignette.rds |binary coxme-2.2-5/coxme/inst/NEWS.Rd | 6 +++++ coxme-2.2-5/coxme/inst/doc/coxme.R | 22 ++++++++++----------- coxme-2.2-5/coxme/inst/doc/coxme.Rnw | 11 ++++------ coxme-2.2-5/coxme/inst/doc/coxme.pdf |binary coxme-2.2-5/coxme/inst/doc/laplace.pdf |binary coxme-2.2-5/coxme/inst/doc/lmekin.pdf |binary coxme-2.2-5/coxme/inst/doc/variance.pdf |binary coxme-2.2-5/coxme/noweb/all.aux |only coxme-2.2-5/coxme/noweb/all.log |only coxme-2.2-5/coxme/noweb/all.out |only coxme-2.2-5/coxme/noweb/all.pdf |only coxme-2.2-5/coxme/noweb/all.tex |only coxme-2.2-5/coxme/noweb/all.toc |only coxme-2.2-5/coxme/noweb/noweb.sty |only coxme-2.2-5/coxme/vignettes/coxme.Rnw | 11 ++++------ 22 files changed, 52 insertions(+), 47 deletions(-)
Title: Tools for Retrieval and Storage of Functional Genomics Data
Description: Package for the systematic retrieval and storage of
functional genomics data via a MySQL database.
Author: Umesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland
<p.d.moerland@amc.uva.nl>
Maintainer: Umesh Nandal <u.k.nandal@amc.uva.nl>
Diff between compendiumdb versions 1.0.0 dated 2015-04-16 and 1.0.1 dated 2015-06-15
DESCRIPTION | 8 MD5 | 6 inst/doc/compendiumdb.pdf |binary inst/scripts/Perl/parsingSoftFile_forESET.pl | 581 +++++++++++++-------------- 4 files changed, 298 insertions(+), 297 deletions(-)
Title: Computed ABC Analysis
Description: For a given data set, the package provides a novel method of computing precise limits to acquire subsets which are easily interpreted. Closely related to the Lorenz curve, the ABC curve visualizes the data by graphically representing the cumulative distribution function. Based on an ABC analysis the algorithm calculates, with the help of the ABC curve, the optimal limits by exploiting the mathematical properties pertaining to distribution of analyzed items. The data containing positive values is divided into three disjoint subsets A, B and C, with subset A comprising very profitable values, i.e. largest data values ("the important few"), subset B comprising values where the yield equals to the effort required to obtain it, and the subset C comprising of non-profitable values, i.e., the smallest data sets ("the trivial many"). Package is based on Ultsch. A ., Lotsch J.: Computed ABC Analysis for rational Selection of most informative Variables in multivariate Data, PLoS One, 2015.
Author: Michael Thrun, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Diff between ABCanalysis versions 1.0.1 dated 2015-04-20 and 1.0.2 dated 2015-06-15
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/ABCanalysis-package.Rd | 3 +++ man/ABCanalysis.Rd | 4 +++- man/ABCcurve.Rd | 3 +++ 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Description: Interface to the API for 'TreeBASE' (http://treebase.org)
from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic
trees (of species, population, or genes) and the data used to create
them.
Author: Carl Boettiger [aut, cre],
Duncan Temple Lang [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between treebase versions 0.0-7.1 dated 2014-02-21 and 0.1.0 dated 2015-06-15
treebase-0.0-7.1/treebase/tests/testthat/metadata.R |only treebase-0.0-7.1/treebase/tests/testthat/treebase.R |only treebase-0.1.0/treebase/DESCRIPTION | 21 +-- treebase-0.1.0/treebase/MD5 | 46 +++---- treebase-0.1.0/treebase/NAMESPACE | 2 treebase-0.1.0/treebase/NEWS | 6 treebase-0.1.0/treebase/README.md | 7 - treebase-0.1.0/treebase/man/cache_treebase.Rd | 23 +-- treebase-0.1.0/treebase/man/clean_data.Rd | 4 treebase-0.1.0/treebase/man/download_metadata.Rd | 21 +-- treebase-0.1.0/treebase/man/drop_nonascii.Rd | 4 treebase-0.1.0/treebase/man/drop_nontrees.Rd | 8 - treebase-0.1.0/treebase/man/dryad_metadata.Rd | 9 - treebase-0.1.0/treebase/man/get_nex.Rd | 29 ++-- treebase-0.1.0/treebase/man/get_study.Rd | 22 +-- treebase-0.1.0/treebase/man/get_study_id.Rd | 12 - treebase-0.1.0/treebase/man/have_branchlength.Rd | 5 treebase-0.1.0/treebase/man/metadata.Rd | 24 ++- treebase-0.1.0/treebase/man/metadata_from_oai.Rd | 12 - treebase-0.1.0/treebase/man/oai_metadata.Rd | 18 +- treebase-0.1.0/treebase/man/phylo_metadata.Rd | 16 +- treebase-0.1.0/treebase/man/search_treebase.Rd | 107 +++++++---------- treebase-0.1.0/treebase/man/show_metadata.Rd | 19 +-- treebase-0.1.0/treebase/man/treebase.Rd | 10 + treebase-0.1.0/treebase/tests/testthat/test_metadata.R |only treebase-0.1.0/treebase/tests/testthat/test_treebase.R |only 26 files changed, 212 insertions(+), 213 deletions(-)
Title: An R Interface to 'figshare'
Description: An interface to 'figshare' (http://figshare.com), a scientific repository to archive and assign 'DOIs' to data, software, figures, and more.
Author: Carl Boettiger [aut, cre],
Scott Chamberlain [aut],
Karthik Ram [aut],
Edmund Hart [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfigshare versions 0.3.6 dated 2014-08-04 and 0.3.7 dated 2015-06-15
rfigshare-0.3.6/rfigshare/build |only rfigshare-0.3.6/rfigshare/inst/doc/README.R |only rfigshare-0.3.6/rfigshare/inst/doc/README.Rmd |only rfigshare-0.3.6/rfigshare/inst/doc/README.html |only rfigshare-0.3.6/rfigshare/inst/doc/vignettes/README.Rmd |only rfigshare-0.3.6/rfigshare/vignettes |only rfigshare-0.3.7/rfigshare/DESCRIPTION | 16 +-- rfigshare-0.3.7/rfigshare/MD5 | 78 ++++++--------- rfigshare-0.3.7/rfigshare/NAMESPACE | 2 rfigshare-0.3.7/rfigshare/NEWS | 3 rfigshare-0.3.7/rfigshare/R/fs_browse.R | 9 - rfigshare-0.3.7/rfigshare/R/fs_object_methods.R | 8 - rfigshare-0.3.7/rfigshare/R/fs_search.R | 8 - rfigshare-0.3.7/rfigshare/README.md | 2 rfigshare-0.3.7/rfigshare/man/fs_add_author.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_add_authors.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_add_categories.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_add_links.Rd | 7 - rfigshare-0.3.7/rfigshare/man/fs_add_tags.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_auth.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_author_ids.Rd | 7 - rfigshare-0.3.7/rfigshare/man/fs_author_search.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_browse.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_cat_to_id.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_category_list.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_create.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_create_author.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_delete.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_details.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_download.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_embed.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_ids.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_image_url.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_make_private.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_make_public.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_new_article.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_search.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_update.Rd | 7 - rfigshare-0.3.7/rfigshare/man/fs_upload.Rd | 3 rfigshare-0.3.7/rfigshare/man/fs_upload_one.Rd | 3 rfigshare-0.3.7/rfigshare/man/plot_to_filename.Rd | 3 rfigshare-0.3.7/rfigshare/man/summary_fs_details.Rd | 3 rfigshare-0.3.7/rfigshare/tests/testthat/test_figshare.R | 8 - 43 files changed, 127 insertions(+), 103 deletions(-)
Title: Application in R for Queueing Analysis and Simulation
Description: Provides functions to compute the main characteristics of the
following queueing models: M/M/1, M/M/s, M/M/1/k, M/M/s/k, M/M/1/Inf/H, M/
M/s/Inf/H, M/M/s/Inf/H with Y replacements, M/M/Inf, Open Jackson Networks
and Closed Jackson Networks. Moreover, it is also possible to simulate
similar queueing models with any type of arrival or service distribution: G/
G/1, G/G/s, G/G/1/k, G/G/s/k, G/G/1/Inf/H, G/G/s/Inf/H, G/G/s/Inf/H with Y
replacements, Open Networks and Closed Networks. Finally, contains functions
for fit data to a statistic distribution.
Author: Borja Varela
Maintainer: Borja Varela <borja.varela.brea@gmail.com>
Diff between arqas versions 1.0 dated 2015-06-01 and 1.1 dated 2015-06-15
DESCRIPTION | 10 ++++---- MD5 | 34 ++++++++++++++-------------- R/1_ModelsHeader.R | 34 +++++++++++++++++----------- R/2_SimpleModels.R | 11 ++++----- R/3_ComplexModels.R | 20 ++++++++-------- R/4_NetworkModels.R | 51 +++++++++++++++++++++++------------------- R/5_SimulateModels.R | 26 +++++++++++++++++++++ R/6_DistributionAnalysis.R | 2 - man/ClosedJacksonNetwork.Rd | 20 +++++++++------- man/M_M_1.Rd | 2 - man/M_M_1_INF_H.Rd | 6 ++-- man/M_M_1_K.Rd | 2 - man/M_M_S.Rd | 2 - man/M_M_S_INF_H_Y.Rd | 14 +++++------ man/M_M_S_K.Rd | 2 - man/OpenJacksonNetwork.Rd | 11 ++++----- man/fitData.Rd | 3 +- man/summary.MarkovianModel.Rd | 7 ++++- 18 files changed, 153 insertions(+), 104 deletions(-)