Title: Significance Bars for 'ggplot2'
Description: Enrich your ggplots with group-wise comparisons.
This package provides an easy way to indicate if two groups are significantly different.
Commonly this is shown by a bar on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***).
The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation
to the plot.
Author: Constantin Ahlmann-Eltze [aut, cre]
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Diff between ggsignif versions 0.1.0 dated 2017-04-05 and 0.2.0 dated 2017-04-26
DESCRIPTION | 8 ++-- MD5 | 22 ++++++----- NEWS.md |only R/significance_annotation.R | 28 ++++++++------ README.md | 6 +++ build/vignette.rds |binary inst/doc/intro.R | 2 - inst/doc/intro.Rmd | 2 - inst/doc/intro.html | 12 +++--- tests/testthat/Rplots.pdf |binary tests/testthat/test-new.R |only tests/testthat/test-significance_annotation.R | 50 +++++++++++++++++++++++++- vignettes/intro.Rmd | 2 - 13 files changed, 96 insertions(+), 36 deletions(-)
Title: Computes Numeric Fourier Integrals
Description: Computes Fourier integrals of functions of one and two variables using the Fast Fourier transform. The Fourier transforms must be evaluated on a regular grid.
Author: Guillermo Basulto-Elias
Maintainer: Guillermo Basulto-Elias <guillermobasulto@gmail.com>
Diff between fourierin versions 0.1.2 dated 2016-05-22 and 0.2.1 dated 2017-04-26
DESCRIPTION | 15 MD5 | 35 - NAMESPACE | 2 NEWS.md | 8 R/RcppExports.R | 2 R/fourierin.R | 946 ++++++++++++++++++----------------- README.md | 108 --- build/vignette.rds |binary inst/doc/fourierin_details.R | 339 +++++++++++- inst/doc/fourierin_details.Rmd | 371 ++++++++++++- inst/doc/fourierin_details.html | 383 ++++++++++++-- inst/include/fourierin.h | 8 inst/include/fourierin_RcppExports.h | 120 ++-- man/fourierin.Rd | 116 ++-- man/fourierin_1d.Rd | 97 ++- man/fourierin_2d.Rd | 56 +- src/RcppExports.cpp | 210 +++---- src/init.c |only vignettes/fourierin_details.Rmd | 446 ++++++++++------ 19 files changed, 2085 insertions(+), 1177 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre],
Yves Rosseel [aut],
Mauricio Garnier-Villarreal [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.2-3 dated 2017-02-24 and 0.2-4 dated 2017-04-26
blavaan-0.2-3/blavaan/R/lav_export_jags.R |only blavaan-0.2-4/blavaan/DESCRIPTION | 10 - blavaan-0.2-4/blavaan/MD5 | 49 +++--- blavaan-0.2-4/blavaan/NAMESPACE | 4 blavaan-0.2-4/blavaan/NEWS | 5 blavaan-0.2-4/blavaan/R/blav_compare.R | 10 - blavaan-0.2-4/blavaan/R/blav_fit.R | 13 + blavaan-0.2-4/blavaan/R/blav_fit_measures.R | 8 blavaan-0.2-4/blavaan/R/blav_object_inspect.R | 79 +++++++-- blavaan-0.2-4/blavaan/R/blav_object_methods.R | 84 ++++++++-- blavaan-0.2-4/blavaan/R/blav_test.R | 4 blavaan-0.2-4/blavaan/R/blav_utils.R | 203 +++++++++++++++++++++---- blavaan-0.2-4/blavaan/R/blavaan.R | 211 +++++++++++++++++++------- blavaan-0.2-4/blavaan/R/dpriors.R | 30 +++ blavaan-0.2-4/blavaan/R/lav_export_mcmc.R |only blavaan-0.2-4/blavaan/R/lav_export_stan.R |only blavaan-0.2-4/blavaan/R/postpred.R | 14 - blavaan-0.2-4/blavaan/R/set_inits.R | 101 +++++++++++- blavaan-0.2-4/blavaan/R/set_partable.R | 45 ++--- blavaan-0.2-4/blavaan/R/set_priors.R | 118 +++++++++----- blavaan-0.2-4/blavaan/R/set_stancovs.R |only blavaan-0.2-4/blavaan/R/set_stanpars.R |only blavaan-0.2-4/blavaan/inst/stanfuns |only blavaan-0.2-4/blavaan/man/bcfa.Rd | 12 + blavaan-0.2-4/blavaan/man/bgrowth.Rd | 12 + blavaan-0.2-4/blavaan/man/blavaan.Rd | 13 + blavaan-0.2-4/blavaan/man/bsem.Rd | 12 + blavaan-0.2-4/blavaan/man/dpriors.Rd | 45 +++-- 28 files changed, 825 insertions(+), 257 deletions(-)
Title: Simulation-Based Random Variable Objects
Description: Implements simulation-based random variable class and a suite of methods.
Author: Jouni Kerman <jouni@kerman.com>
Maintainer: Jouni Kerman <jouni@kerman.com>
Diff between rv versions 2.3.1 dated 2013-06-26 and 2.3.2 dated 2017-04-26
rv-2.3.1/rv/COPYRIGHTS |only rv-2.3.2/rv/ChangeLog | 6 ++++ rv-2.3.2/rv/DESCRIPTION | 12 ++++---- rv-2.3.2/rv/MD5 | 58 ++++++++++++++++++++-------------------- rv-2.3.2/rv/NAMESPACE | 32 ++++++++++++---------- rv-2.3.2/rv/R/abline_rv.R | 4 +- rv-2.3.2/rv/R/cor_rv.R | 4 +- rv-2.3.2/rv/R/cov_rv.R | 4 +- rv-2.3.2/rv/R/ivplot.R | 6 ---- rv-2.3.2/rv/R/median_rv.R | 4 +- rv-2.3.2/rv/R/rvbern.R | 2 - rv-2.3.2/rv/R/rvbeta.R | 2 - rv-2.3.2/rv/R/rvbinom.R | 2 - rv-2.3.2/rv/R/rvcauchy.R | 2 - rv-2.3.2/rv/R/rvchisq.R | 7 ++-- rv-2.3.2/rv/R/rvexp.R | 2 - rv-2.3.2/rv/R/rvgamma.R | 2 - rv-2.3.2/rv/R/rvhyper.R | 2 - rv-2.3.2/rv/R/rvifelse.R | 2 - rv-2.3.2/rv/R/rvmultinom.R | 2 - rv-2.3.2/rv/R/rvnbeta.R | 2 - rv-2.3.2/rv/R/rvngamma.R | 2 - rv-2.3.2/rv/R/rvpois.R | 2 - rv-2.3.2/rv/R/rvt.R | 4 +- rv-2.3.2/rv/R/rvunif.R | 5 +-- rv-2.3.2/rv/R/simapply_rv.R | 2 - rv-2.3.2/rv/R/unlist_rv.R | 7 ++-- rv-2.3.2/rv/build |only rv-2.3.2/rv/inst/doc/rv-doc.pdf |binary rv-2.3.2/rv/man/median.rv.Rd | 3 +- rv-2.3.2/rv/man/unlist.rv.Rd | 14 +++++---- 31 files changed, 101 insertions(+), 95 deletions(-)
Title: Download Qualtrics Survey Data Directly into R
Description: Qualtrics <https://www.qualtrics.com/about/>
allows users to collect online data through surveys.
This package contains convenience functions to pull
survey results straight into R using the Qualtrics
API. See <https://api.qualtrics.com/> for more
information about the Qualtrics API.
Author: Jasper Ginn
Maintainer: Jasper Ginn <jasperginn@gmail.com>
Diff between qualtRics versions 0.3 dated 2016-11-29 and 1.0 dated 2017-04-26
qualtRics-0.3/qualtRics/R/constructHeader.R |only qualtRics-0.3/qualtRics/README.md |only qualtRics-0.3/qualtRics/man/constructHeader.Rd |only qualtRics-1.0/qualtRics/DESCRIPTION | 14 - qualtRics-1.0/qualtRics/MD5 | 35 ++-- qualtRics-1.0/qualtRics/NAMESPACE | 5 qualtRics-1.0/qualtRics/R/assertions.R |only qualtRics-1.0/qualtRics/R/getSurvey.R | 155 +++++++--------------- qualtRics-1.0/qualtRics/R/getSurveys.R | 23 --- qualtRics-1.0/qualtRics/R/readSurvey.R |only qualtRics-1.0/qualtRics/R/utils.R |only qualtRics-1.0/qualtRics/build/vignette.rds |binary qualtRics-1.0/qualtRics/inst/doc/qualtRics.Rmd | 64 +++++++-- qualtRics-1.0/qualtRics/inst/doc/qualtRics.html | 60 ++++++-- qualtRics-1.0/qualtRics/man/getSurvey.Rd | 30 ++-- qualtRics-1.0/qualtRics/man/getSurveys.Rd | 11 - qualtRics-1.0/qualtRics/man/readSurvey.Rd |only qualtRics-1.0/qualtRics/man/registerApiKey.Rd | 7 qualtRics-1.0/qualtRics/tests |only qualtRics-1.0/qualtRics/vignettes/qualtRics.Rmd | 64 +++++++-- qualtRics-1.0/qualtRics/vignettes/qualtricsdf.png |only 21 files changed, 264 insertions(+), 204 deletions(-)
Title: Hierarchical Multiple Imputation
Description: Runs single level and multilevel imputation models. The user just has to pass the data to the main function and, optionally, his analysis model. Basically the package then translates this analysis model into commands to impute the data according to it with functions from 'mice', 'MCMCglmm' or routines build for this package.
Author: Matthias Speidel [aut, cre] (Institute for Employment Research,
Nuremberg, Germany),
Joerg Drechsler [aut] (Institute for Employment Research, Nuremberg,
Germany),
Shahab Jolani [aut] (Maastricht University, Maastricht, The
Netherlands)
Maintainer: Matthias Speidel <matthias.speidel@googlemail.com>
Diff between hmi versions 0.6.3 dated 2017-03-27 and 0.7.4 dated 2017-04-26
hmi-0.6.3/hmi/R/hmi_imp_binary_multi_2016-12-10.R |only hmi-0.6.3/hmi/R/hmi_imp_binary_single_2017-01-12.R |only hmi-0.6.3/hmi/R/hmi_imp_cat_multi_2017-01-10.R |only hmi-0.6.3/hmi/R/hmi_imp_cat_single_2016-12-23.R |only hmi-0.6.3/hmi/R/hmi_imp_catordered_multi_2017-01-04.R |only hmi-0.6.3/hmi/R/hmi_imp_catordered_single_2016-12-22.R |only hmi-0.6.3/hmi/R/hmi_imp_cont_multi_2017-01-25.R |only hmi-0.6.3/hmi/R/hmi_imp_cont_single_2017-01-18.R |only hmi-0.6.3/hmi/R/hmi_imp_count_multi_2017-01-04.R |only hmi-0.6.3/hmi/R/hmi_imp_count_single_2017-01-05.R |only hmi-0.6.3/hmi/R/hmi_imp_interval_2017-02-05.R |only hmi-0.6.3/hmi/R/hmi_imp_roundedcont_2017-01-31.R |only hmi-0.6.3/hmi/R/hmi_imp_semicont_multi_2017-01-10.R |only hmi-0.6.3/hmi/R/hmi_imp_semicont_single_2016-12-10.R |only hmi-0.6.3/hmi/R/hmi_smallfunctions_2017-02-21.R |only hmi-0.6.3/hmi/R/hmi_wrapper_2017-02-05.R |only hmi-0.6.3/hmi/man/contributions4intervalls.Rd |only hmi-0.6.3/hmi/man/divided_interval.Rd |only 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Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between Anthropometry versions 1.7 dated 2015-12-12 and 1.8 dated 2017-04-26
Anthropometry-1.7/Anthropometry/R/matPercs.R |only Anthropometry-1.7/Anthropometry/man/matPercs.Rd |only Anthropometry-1.8/Anthropometry/DESCRIPTION | 12 +- Anthropometry-1.8/Anthropometry/MD5 | 46 +++++----- Anthropometry-1.8/Anthropometry/NAMESPACE | 3 Anthropometry-1.8/Anthropometry/NEWS | 7 + Anthropometry-1.8/Anthropometry/R/anthrCases.R | 14 ++- Anthropometry-1.8/Anthropometry/R/trimmOutl.R | 14 ++- Anthropometry-1.8/Anthropometry/build/vignette.rds |binary Anthropometry-1.8/Anthropometry/inst/CITATION | 41 ++++---- Anthropometry-1.8/Anthropometry/inst/doc/Anthropometry.R | 6 + Anthropometry-1.8/Anthropometry/inst/doc/Anthropometry.Rnw | 8 + Anthropometry-1.8/Anthropometry/inst/doc/Anthropometry.pdf |binary Anthropometry-1.8/Anthropometry/man/Anthropometry-internalTDDclust.Rd | 2 Anthropometry-1.8/Anthropometry/man/Anthropometry-package.Rd | 10 +- Anthropometry-1.8/Anthropometry/man/TDDclust.Rd | 2 Anthropometry-1.8/Anthropometry/man/computSizesTrimowa.Rd | 5 - Anthropometry-1.8/Anthropometry/man/percentilsArchetypoid.Rd | 6 - Anthropometry-1.8/Anthropometry/man/plotPrototypes.Rd | 2 Anthropometry-1.8/Anthropometry/man/plotTrimmOutl.Rd | 2 Anthropometry-1.8/Anthropometry/man/preprocessing.Rd | 2 Anthropometry-1.8/Anthropometry/man/trimowa.Rd | 7 - Anthropometry-1.8/Anthropometry/src/init.c |only Anthropometry-1.8/Anthropometry/vignettes/AA.pdf |binary Anthropometry-1.8/Anthropometry/vignettes/Anthropometry.Rnw | 8 + Anthropometry-1.8/Anthropometry/vignettes/enumitem.sty |only 26 files changed, 114 insertions(+), 83 deletions(-)
Title: Interface to X12-ARIMA/X13-ARIMA-SEATS and Structure for Batch
Processing of Seasonal Adjustment
Description: The X13-ARIMA-SEATS methodology and software is a widely used software and developed by the US Census Bureau. It can be accessed from R with this R package and X13-ARIMA-SEATS binaries are provided by the R package x13binary.
Author: Alexander Kowarik <alexander.kowarik@statistik.gv.at>, Angelika Meraner
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between x12 versions 1.6.0 dated 2014-11-20 and 1.8.0 dated 2017-04-26
DESCRIPTION | 20 +++++++++--------- MD5 | 30 +++++++++++++-------------- NAMESPACE | 7 +++--- NEWS | 2 + R/class.R | 52 ++++++++++++++++++++--------------------------- R/env_functions.R | 11 +++++++-- R/plot-methods.R | 2 - R/readx12Out.R | 6 ++--- R/x12-methods.R | 4 ++- R/x12work.R | 10 +++++---- R/zzz.R | 7 +++--- README | 11 ++++++--- man/enfn.Rd | 5 ++-- man/x12-methods.Rd | 6 ++--- man/x12BaseInfo-class.Rd | 4 +-- man/x12work.Rd | 6 ++--- 16 files changed, 97 insertions(+), 86 deletions(-)
Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-
objective test functions which are frequently used for the benchmarking of
(numerical) optimization algorithms. Moreover, it offers a set of convenient
functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre],
Pascal Kerschke [ctb]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between smoof versions 1.4 dated 2016-08-03 and 1.5 dated 2017-04-26
DESCRIPTION | 13 MD5 | 358 +++++++++++----------- NAMESPACE | 3 NEWS | 26 + R/RcppExports.R | 2 R/addCountingWrapper.R | 4 R/addLoggingWrapper.R | 6 R/conversion.R | 25 - R/doesCountEvaluations.R | 2 R/filterFunctionsByTags.R | 6 R/getLocalOptimum.R | 7 R/getParamSet.R | 3 R/hasTags.R | 6 R/makeBBOBFunction.R | 51 +-- R/makeFunctionsByName.R | 5 R/makeMultiObjectiveFunction.R | 4 R/makeObjectiveFunction.R | 17 - R/makeSingleObjectiveFunction.R | 8 R/mnof.R |only R/mof.MOP3.R | 4 R/plot.autoplot.R | 16 R/smoof_function.R |only R/snof.R |only R/sof.cosine.mixture.R | 4 R/sof.mpm2.R | 30 + R/zzz.R | 1 inst/CITATION |only man/addCountingWrapper.Rd | 3 man/addLoggingWrapper.Rd | 5 man/autoplot.smoof_function.Rd | 7 man/computeExpectedRunningTime.Rd | 1 man/conversion.Rd | 3 man/doesCountEvaluations.Rd | 1 man/filterFunctionsByTags.Rd | 5 man/getAvailableTags.Rd | 1 man/getDescription.Rd | 1 man/getGlobalOptimum.Rd | 1 man/getID.Rd | 1 man/getLocalOptimum.Rd | 3 man/getLoggedValues.Rd | 1 man/getLowerBoxConstraints.Rd | 1 man/getMeanFunction.Rd | 1 man/getName.Rd | 1 man/getNumberOfEvaluations.Rd | 1 man/getNumberOfObjectives.Rd | 1 man/getNumberOfParameters.Rd | 1 man/getParamSet.Rd | 1 man/getRefPoint.Rd | 1 man/getTags.Rd | 1 man/getUpperBoxConstraints.Rd | 1 man/getWrappedFunction.Rd | 1 man/hasBoxConstraints.Rd | 1 man/hasConstraints.Rd | 1 man/hasGlobalOptimum.Rd | 1 man/hasLocalOptimum.Rd | 1 man/hasOtherConstraints.Rd | 1 man/hasTags.Rd | 1 man/isMultiobjective.Rd | 1 man/isNoisy.Rd | 1 man/isSingleobjective.Rd | 1 man/isSmoofFunction.Rd | 1 man/isVectorized.Rd | 1 man/isWrappedSmoofFunction.Rd | 1 man/makeAckleyFunction.Rd | 1 man/makeAdjimanFunction.Rd | 1 man/makeAlpine01Function.Rd | 1 man/makeAlpine02Function.Rd | 1 man/makeAluffiPentiniFunction.Rd | 1 man/makeBBOBFunction.Rd | 1 man/makeBK1Function.Rd | 1 man/makeBartelsConnFunction.Rd | 1 man/makeBealeFunction.Rd | 1 man/makeBentCigarFunction.Rd | 1 man/makeBiSphereFunction.Rd | 1 man/makeBirdFunction.Rd | 1 man/makeBohachevskyN1Function.Rd | 1 man/makeBoothFunction.Rd | 1 man/makeBraninFunction.Rd | 1 man/makeBrentFunction.Rd | 1 man/makeBrownFunction.Rd | 1 man/makeBukinN2Function.Rd | 1 man/makeBukinN4Function.Rd | 1 man/makeBukinN6Function.Rd | 1 man/makeCarromTableFunction.Rd | 1 man/makeChichinadzeFunction.Rd | 1 man/makeChungReynoldsFunction.Rd | 1 man/makeComplexFunction.Rd | 1 man/makeCosineMixtureFunction.Rd | 1 man/makeCrossInTrayFunction.Rd | 1 man/makeCubeFunction.Rd | 1 man/makeDTLZ1Function.Rd | 1 man/makeDTLZ2Function.Rd | 1 man/makeDTLZ3Function.Rd | 1 man/makeDTLZ4Function.Rd | 1 man/makeDTLZ5Function.Rd | 1 man/makeDTLZ6Function.Rd | 1 man/makeDTLZ7Function.Rd | 1 man/makeDeckkersAartsFunction.Rd | 1 man/makeDeflectedCorrugatedSpringFunction.Rd | 1 man/makeDentFunction.Rd | 1 man/makeDixonPriceFunction.Rd | 1 man/makeDoubleSumFunction.Rd | 1 man/makeEasomFunction.Rd | 1 man/makeEggCrateFunction.Rd | 1 man/makeEggholderFunction.Rd | 1 man/makeElAttarVidyasagarDuttaFunction.Rd | 1 man/makeEngvallFunction.Rd | 1 man/makeExponentialFunction.Rd | 1 man/makeFreudensteinRothFunction.Rd | 1 man/makeFunctionsByName.Rd | 1 man/makeGOMOPFunction.Rd | 1 man/makeGeneralizedDropWaveFunction.Rd | 1 man/makeGiuntaFunction.Rd | 1 man/makeGoldsteinPriceFunction.Rd | 1 man/makeGriewankFunction.Rd | 1 man/makeHansenFunction.Rd | 1 man/makeHimmelblauFunction.Rd | 1 man/makeHolderTableN1Function.Rd | 1 man/makeHolderTableN2Function.Rd | 1 man/makeHosakiFunction.Rd | 1 man/makeHyperEllipsoidFunction.Rd | 1 man/makeJennrichSampsonFunction.Rd | 1 man/makeJudgeFunction.Rd | 1 man/makeKeaneFunction.Rd | 1 man/makeKearfottFunction.Rd | 1 man/makeLeonFunction.Rd | 1 man/makeMOP1Function.Rd | 1 man/makeMOP2Function.Rd | 1 man/makeMOP3Function.Rd | 1 man/makeMOP4Function.Rd | 1 man/makeMOP5Function.Rd | 1 man/makeMOP6Function.Rd | 1 man/makeMOP7Function.Rd | 1 man/makeMPM2Function.Rd | 7 man/makeMatyasFunction.Rd | 1 man/makeMcCormickFunction.Rd | 1 man/makeMichalewiczFunction.Rd | 1 man/makeMultiObjectiveFunction.Rd | 5 man/makePeriodicFunction.Rd | 1 man/makePowellSumFunction.Rd | 1 man/makePriceN1Function.Rd | 1 man/makePriceN2Function.Rd | 1 man/makePriceN4Function.Rd | 1 man/makeRastriginFunction.Rd | 1 man/makeRosenbrockFunction.Rd | 1 man/makeSchafferN2Function.Rd | 1 man/makeSchafferN4Function.Rd | 1 man/makeSchwefelFunction.Rd | 1 man/makeShubertFunction.Rd | 1 man/makeSingleObjectiveFunction.Rd | 9 man/makeSixHumpCamelFunction.Rd | 1 man/makeSphereFunction.Rd | 1 man/makeStyblinkskiTangFunction.Rd | 1 man/makeSumOfDifferentSquaresFunction.Rd | 1 man/makeSwiler2014Function.Rd | 1 man/makeThreeHumpCamelFunction.Rd | 1 man/makeTrecanniFunction.Rd | 1 man/makeUFFunction.Rd | 1 man/makeViennetFunction.Rd | 1 man/makeZDT1Function.Rd | 1 man/makeZDT2Function.Rd | 1 man/makeZDT3Function.Rd | 1 man/makeZDT4Function.Rd | 1 man/makeZDT6Function.Rd | 1 man/makeZettlFunction.Rd | 1 man/mnof.Rd |only man/plot.smoof_function.Rd | 1 man/plot1DNumeric.Rd | 1 man/plot2DNumeric.Rd | 1 man/plot3D.Rd | 1 man/resetEvaluationCounter.Rd | 1 man/shouldBeMinimized.Rd | 1 man/smoof-package.Rd | 2 man/smoof_function.Rd |only man/snof.Rd |only man/violatesConstraints.Rd | 1 man/visualizeParetoOptimalFront.Rd | 1 src/RcppExports.cpp | 58 +-- src/init.c |only tests/testthat/Rplots.pdf |binary tests/testthat/helper_zzz.R | 4 tests/testthat/test_conversion.R | 11 tests/testthat/test_makeMultiObjectiveFunction.R |only tests/testthat/test_makeSingleObjectiveFunction.R | 8 tests/testthat/test_shortcuts.R |only 185 files changed, 429 insertions(+), 439 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
Sami Samhuri [ctb, cph] (Javascript strftime library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 1.0.2 dated 2017-04-18 and 1.0.3 dated 2017-04-26
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 14 ++++++++++++++ R/reactives.R | 17 +++++++++++++++-- R/render-plot.R | 8 +++++--- R/server.R | 6 +++--- R/shiny.R | 2 +- README.md | 2 +- inst/www/shared/shiny.js | 2 +- inst/www/shared/shiny.js.map | 2 +- inst/www/shared/shiny.min.js | 4 ++-- inst/www/shared/shiny.min.js.map | 2 +- man/reactivePoll.Rd | 17 +++++++++++++++-- man/shiny-package.Rd | 2 +- 14 files changed, 77 insertions(+), 35 deletions(-)
Title: Rao-Scott Cochran-Armitage by Slices Trend Test
Description: Performs the Rao-Scott Cochran-Armitage by Slices trend test (RSCABS) used
in analysis of histopathological endpoints, built to be used with either a GUI or by a
command line. The RSCABS method is detailed in "Statistical analysis of
histopathological endpoints" by John Green et. al. (2014) <doi:10.1002/etc.2530>.
Author: Joe Swintek [aut, cre],
Kevin Flynn [ctb]
Maintainer: Joe Swintek <swintek.joe@epa.gov>
Diff between RSCABS versions 0.9.01 dated 2016-12-12 and 0.9.2 dated 2017-04-26
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- R/stepDownRSCABS.R | 11 +++++------ inst/doc/RSCABS.pdf |binary man/runRSCABS.Rd | 3 ++- 5 files changed, 18 insertions(+), 17 deletions(-)
Title: Prediction Rule Ensembles
Description: Derives prediction rule ensembles (PREs). Largely follows the
procedure for deriving PREs as described in Friedman & Popescu (2008;
<DOI:10.1214/07-AOAS148>), with several adjustments and improvements. The
main function pre() derives a prediction rule ensemble. Functions print(),
plot(), coef() and importance() can be used to inspect the generated ensemble.
Function predict() generates predicted values. Functions singeplot() and
pairplot() depict dependence of the output on specified predictor variables.
Function cvpre() performs full cross validation of a pre to calculate the
expected prediction error. Functions interact() and bsnullinteract() can be
used to assess interaction effects of predictor variables.
Author: Marjolein Fokkema [aut, cre]
Maintainer: Marjolein Fokkema <m.fokkema@fsw.leidenuniv.nl>
Diff between pre versions 0.1 dated 2016-12-24 and 0.2 dated 2017-04-26
DESCRIPTION | 29 MD5 | 28 NAMESPACE | 4 NEWS |only R/pre.R | 1510 ++++++++++++++++++++++++++++++++------------------ README |only man/bsnullinteract.Rd | 27 man/coef.pre.Rd | 17 man/cvpre.Rd | 37 - man/importance.Rd | 45 - man/interact.Rd | 57 + man/pairplot.Rd | 58 + man/plot.pre.Rd |only man/pre.Rd | 74 +- man/predict.pre.Rd | 26 man/print.pre.Rd |only man/singleplot.Rd | 45 - 17 files changed, 1262 insertions(+), 695 deletions(-)
Title: Isotonic Proportional Hazards Model
Description: Nonparametric estimation of an isotonic covariate effect for proportional hazards model.
Author: Yunro Chung [cre], Anastasia Ivanova, Michael G. Hudgens and Jason P. Fine
Maintainer: Yunro Chung <ychung@fredhutch.org>
Diff between isoph versions 0.5 dated 2016-01-02 and 1.0 dated 2017-04-26
isoph-0.5/isoph/R/RcppExports.R |only isoph-0.5/isoph/R/isoph.td.R |only isoph-0.5/isoph/R/newton.raphson.R |only isoph-0.5/isoph/src |only isoph-1.0/isoph/DESCRIPTION | 20 +-- isoph-1.0/isoph/MD5 | 28 ++-- isoph-1.0/isoph/NAMESPACE | 9 - isoph-1.0/isoph/R/BTF.R |only isoph-1.0/isoph/R/NR1.R |only isoph-1.0/isoph/R/NR2.R |only isoph-1.0/isoph/R/RPA_ti.R |only isoph-1.0/isoph/R/isoph.R | 21 +-- isoph-1.0/isoph/R/isoph.ti.R | 205 ++++++++++++++++++++++------------- isoph-1.0/isoph/R/picm.R | 3 isoph-1.0/isoph/R/plot.isoph.R | 23 +++ isoph-1.0/isoph/R/print.isoph.R | 6 - isoph-1.0/isoph/man/isoph-package.Rd | 8 - isoph-1.0/isoph/man/isoph.Rd | 21 ++- 18 files changed, 207 insertions(+), 137 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Leslie Pérez Cáceres,
Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 2.2 dated 2017-03-24 and 2.3 dated 2017-04-26
DESCRIPTION | 8 ++++---- MD5 | 33 +++++++++++++++++---------------- NEWS | 11 +++++++++++ R/irace.R | 2 +- R/race-wrapper.R | 4 ++++ R/race.R | 41 +++++++++++++++++++---------------------- R/readConfiguration.R | 4 ++-- R/utils.R | 9 +++++---- R/version.R | 2 +- build/partial.rdb |binary inst/doc/irace-package.Rnw | 2 +- inst/doc/irace-package.pdf |binary man/irace-package.Rd | 4 ++-- tests/testtargeval.R |only tests/testthat.R | 2 +- tests/testtime.R | 3 +-- vignettes/NEWS.txt | 11 +++++++++++ vignettes/irace-package.Rnw | 2 +- 18 files changed, 81 insertions(+), 57 deletions(-)
Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of segments shared identical-by-descent (IBD) by
pedigree members. Using sex specific recombination rates along the human
genome (Kong et. al (2010) <doi:10.1038/nature09525>), phased chromosomes
are simulated for all pedigree members, either by unconditional gene
dropping or conditional on a specified IBD pattern. Additional functions
provide summaries and further analysis of the simulated genomes.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between IBDsim versions 0.9-6 dated 2016-04-28 and 0.9-7 dated 2017-04-26
DESCRIPTION | 19 ++++-- MD5 | 20 ++++--- NAMESPACE | 4 - NEWS | 9 +++ R/alleleSummary.R |only R/ibd.runs.R | 66 +++++++++++++++++++++-- R/map_utils.R | 14 ++--- R/twoLocusIBD.R | 134 +++++++++++++++++++++++++++++++++++++++++------- man/alleleSummary.Rd |only man/oneLocusIBD.Rd |only man/oneLocusJacquard.Rd |only man/twoLocusIBD.Rd | 113 ++++++++++++++++++++++------------------ man/twoLocusJacquard.Rd |only src/init.c |only 14 files changed, 284 insertions(+), 95 deletions(-)
Title: Evolutionary Computation in R
Description: Framework for building evolutionary algorithms for both single- and multi-objective continuous or discrete optimization problems. A set of predefined evolutionary building blocks and operators is included. Moreover, the user can easily set up custom objective functions, operators, building blocks and representations sticking to few conventions. The package allows both a black-box approach for standard tasks (plug-and-play style) and a much more flexible white-box approach where the evolutionary cycle is written by hand.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between ecr versions 1.0.1 dated 2016-09-10 and 2.0.0 dated 2017-04-26
ecr-1.0.1/ecr/R/OptState.getter.R |only ecr-1.0.1/ecr/R/OptState.setter.R |only ecr-1.0.1/ecr/R/autoplotECRResult.R |only ecr-1.0.1/ecr/R/checkOperator.R |only ecr-1.0.1/ecr/R/computeDominatedHypervolume.R |only ecr-1.0.1/ecr/R/doTheEvolution.R |only ecr-1.0.1/ecr/R/ea.oneplusoneGA.R |only ecr-1.0.1/ecr/R/ea.simpleEA.R |only ecr-1.0.1/ecr/R/ecr.package.R |only ecr-1.0.1/ecr/R/eventDispatcher.R |only ecr-1.0.1/ecr/R/getBestIndividual.R |only ecr-1.0.1/ecr/R/getNextGeneration.R |only ecr-1.0.1/ecr/R/makeGenerator.R |only ecr-1.0.1/ecr/R/makePopulation.R |only ecr-1.0.1/ecr/R/mergePopulations.R |only ecr-1.0.1/ecr/R/monitor.console.R |only ecr-1.0.1/ecr/R/monitor.opt.path.logging.R |only ecr-1.0.1/ecr/R/operator.generator.random.binary.R |only ecr-1.0.1/ecr/R/operator.generator.random.permutation.R |only ecr-1.0.1/ecr/R/operator.generator.uniform.float.R |only ecr-1.0.1/ecr/R/operator.recombinator.null.R |only ecr-1.0.1/ecr/R/operator.terminator.max.evaluations.R |only ecr-1.0.1/ecr/R/operator.terminator.max.iter.R |only ecr-1.0.1/ecr/R/operator.terminator.optimum.R |only ecr-1.0.1/ecr/R/operator.termnator.max.time.R |only ecr-1.0.1/ecr/R/optState.R |only ecr-1.0.1/ecr/R/rescalePoints.R |only ecr-1.0.1/ecr/R/setupECRControl.R |only ecr-1.0.1/ecr/R/setupEvolutionaryOperators.R |only ecr-1.0.1/ecr/R/setupTerminators.R |only ecr-1.0.1/ecr/man/OptState.Rd |only ecr-1.0.1/ecr/man/OptStateGetter.Rd |only ecr-1.0.1/ecr/man/autoplot.ecr_single_objective_result.Rd |only ecr-1.0.1/ecr/man/buildInitialPopulation.Rd |only ecr-1.0.1/ecr/man/doTheEvolution.Rd |only ecr-1.0.1/ecr/man/ecrpackage.Rd |only ecr-1.0.1/ecr/man/evolutionary_setters.Rd |only ecr-1.0.1/ecr/man/getAvailableEventNames.Rd |only ecr-1.0.1/ecr/man/getEvaluations.Rd |only ecr-1.0.1/ecr/man/getGenerations.Rd |only ecr-1.0.1/ecr/man/getNextGeneration.Rd |only ecr-1.0.1/ecr/man/getOperatorName.Rd |only ecr-1.0.1/ecr/man/getOperatorParameters.Rd |only ecr-1.0.1/ecr/man/makeGenerator.Rd |only ecr-1.0.1/ecr/man/makeMonitor.Rd |only ecr-1.0.1/ecr/man/makePopulation.Rd |only ecr-1.0.1/ecr/man/mergePopulations.Rd |only ecr-1.0.1/ecr/man/onePlusOneGA.Rd |only ecr-1.0.1/ecr/man/print.ecr_control.Rd |only ecr-1.0.1/ecr/man/registerAction.Rd |only ecr-1.0.1/ecr/man/rescalePoints.Rd |only ecr-1.0.1/ecr/man/selectForMating.Rd |only ecr-1.0.1/ecr/man/selectForSurvival.Rd |only ecr-1.0.1/ecr/man/setupBinaryGenerator.Rd |only ecr-1.0.1/ecr/man/setupBitFlipMutator.Rd |only ecr-1.0.1/ecr/man/setupCloseToOptimumTerminator.Rd |only ecr-1.0.1/ecr/man/setupConsoleMonitor.Rd |only ecr-1.0.1/ecr/man/setupCrossoverRecombinator.Rd |only ecr-1.0.1/ecr/man/setupDominatedHypervolumeSelector.Rd |only ecr-1.0.1/ecr/man/setupECRControl.Rd |only ecr-1.0.1/ecr/man/setupEvolutionaryOperators.Rd |only ecr-1.0.1/ecr/man/setupGaussMutator.Rd |only ecr-1.0.1/ecr/man/setupGreedySelector.Rd |only ecr-1.0.1/ecr/man/setupInsertionMutator.Rd |only ecr-1.0.1/ecr/man/setupIntermediateRecombinator.Rd |only ecr-1.0.1/ecr/man/setupInversionMutator.Rd |only ecr-1.0.1/ecr/man/setupMaximumEvaluationsTerminator.Rd |only ecr-1.0.1/ecr/man/setupMaximumIterationsTerminator.Rd |only ecr-1.0.1/ecr/man/setupMaximumTimeTerminator.Rd |only ecr-1.0.1/ecr/man/setupNondomSelector.Rd |only ecr-1.0.1/ecr/man/setupNullRecombinator.Rd |only ecr-1.0.1/ecr/man/setupOXRecombinator.Rd |only ecr-1.0.1/ecr/man/setupOptPathLoggingMonitor.Rd |only ecr-1.0.1/ecr/man/setupOptState.Rd |only ecr-1.0.1/ecr/man/setupPMXRecombinator.Rd |only ecr-1.0.1/ecr/man/setupPermutationGenerator.Rd |only ecr-1.0.1/ecr/man/setupPolynomialMutator.Rd |only ecr-1.0.1/ecr/man/setupRouletteWheelSelector.Rd |only ecr-1.0.1/ecr/man/setupSBXRecombinator.Rd |only ecr-1.0.1/ecr/man/setupScrambleMutator.Rd |only ecr-1.0.1/ecr/man/setupSimpleSelector.Rd |only ecr-1.0.1/ecr/man/setupSwapMutator.Rd |only ecr-1.0.1/ecr/man/setupTerminators.Rd |only ecr-1.0.1/ecr/man/setupTournamentSelector.Rd |only ecr-1.0.1/ecr/man/setupUniformGenerator.Rd |only ecr-1.0.1/ecr/man/setupUniformMutator.Rd |only ecr-1.0.1/ecr/man/simpleEA.Rd |only ecr-1.0.1/ecr/man/summary.ecr_multi_objective_result.Rd |only ecr-1.0.1/ecr/man/updateOptState.Rd |only ecr-1.0.1/ecr/tests/testthat/Rplots.pdf |only ecr-1.0.1/ecr/tests/testthat/test_ea.R |only ecr-1.0.1/ecr/tests/testthat/test_eventDispatcher.R |only ecr-1.0.1/ecr/tests/testthat/test_fitnessEvaluation.R |only ecr-1.0.1/ecr/tests/testthat/test_optPathLoggingMonitor.R |only ecr-1.0.1/ecr/tests/testthat/test_permutationGenerator.R |only ecr-1.0.1/ecr/tests/testthat/test_recombinators.R |only ecr-1.0.1/ecr/tests/testthat/test_selectors.R |only ecr-1.0.1/ecr/tests/testthat/test_setupStoppingConditions.R |only ecr-1.0.1/ecr/tests/testthat/test_stoppingConditions.R |only ecr-2.0.0/ecr/DESCRIPTION | 39 - ecr-2.0.0/ecr/LICENSE | 2 ecr-2.0.0/ecr/MD5 | 345 +++++------- ecr-2.0.0/ecr/NAMESPACE | 148 ++--- ecr-2.0.0/ecr/NEWS | 10 ecr-2.0.0/ecr/R/Result.R | 136 ---- ecr-2.0.0/ecr/R/approximatePoints.R | 6 ecr-2.0.0/ecr/R/computeAverageHausdorffDistance.R | 69 +- ecr-2.0.0/ecr/R/computeCrowdingDistance.R | 2 ecr-2.0.0/ecr/R/computeHV.R |only ecr-2.0.0/ecr/R/doNondominatedSorting.R | 12 ecr-2.0.0/ecr/R/doTerminate.R | 23 ecr-2.0.0/ecr/R/docs.parallelization.R | 13 ecr-2.0.0/ecr/R/dominates.R | 102 +++ ecr-2.0.0/ecr/R/ecr.R | 233 ++++---- ecr-2.0.0/ecr/R/emoa.as-emoa.R | 139 ++-- ecr-2.0.0/ecr/R/emoa.indicators.R | 30 - ecr-2.0.0/ecr/R/emoa.nsga2.R | 80 +- ecr-2.0.0/ecr/R/emoa.sms-emoa.R | 86 +- ecr-2.0.0/ecr/R/evaluateFitness.R | 67 -- ecr-2.0.0/ecr/R/generateOffspring.R | 218 +++++-- ecr-2.0.0/ecr/R/generators.R |only ecr-2.0.0/ecr/R/getters.R |only ecr-2.0.0/ecr/R/initECRControl.R |only ecr-2.0.0/ecr/R/initPopulation.R |only ecr-2.0.0/ecr/R/logger.default.R |only ecr-2.0.0/ecr/R/makeMonitor.R | 40 - ecr-2.0.0/ecr/R/makeMutator.R | 20 ecr-2.0.0/ecr/R/makeOperator.R | 68 -- ecr-2.0.0/ecr/R/makeOptimizationTask.R | 2 ecr-2.0.0/ecr/R/makeRecombinator.R | 21 ecr-2.0.0/ecr/R/makeSelector.R | 13 ecr-2.0.0/ecr/R/makeTerminator.R | 9 ecr-2.0.0/ecr/R/monitor.default.R |only ecr-2.0.0/ecr/R/operator.mutator.bitflip.R | 43 - ecr-2.0.0/ecr/R/operator.mutator.gauss.R | 48 - ecr-2.0.0/ecr/R/operator.mutator.insertion.R | 26 ecr-2.0.0/ecr/R/operator.mutator.inversion.R | 27 ecr-2.0.0/ecr/R/operator.mutator.polynomial.R | 44 - ecr-2.0.0/ecr/R/operator.mutator.scramble.R | 25 ecr-2.0.0/ecr/R/operator.mutator.swap.R | 30 - ecr-2.0.0/ecr/R/operator.mutator.uniform.R | 36 - ecr-2.0.0/ecr/R/operator.recombinator.crossover.R | 78 -- ecr-2.0.0/ecr/R/operator.recombinator.intermediate.R | 35 - ecr-2.0.0/ecr/R/operator.recombinator.ox.R | 35 - ecr-2.0.0/ecr/R/operator.recombinator.pmx.R | 31 - ecr-2.0.0/ecr/R/operator.recombinator.sbx.R | 47 - ecr-2.0.0/ecr/R/operator.selector.dominatedHypervolume.R | 25 ecr-2.0.0/ecr/R/operator.selector.greedy.R | 18 ecr-2.0.0/ecr/R/operator.selector.k-tournament.R | 34 - ecr-2.0.0/ecr/R/operator.selector.nondom.R | 17 ecr-2.0.0/ecr/R/operator.selector.roulettewheel.R | 33 - ecr-2.0.0/ecr/R/operator.selector.simple.R | 24 ecr-2.0.0/ecr/R/paretoArchive.R |only ecr-2.0.0/ecr/R/registerECRObject.R |only ecr-2.0.0/ecr/R/replace.R |only ecr-2.0.0/ecr/R/select.R |only ecr-2.0.0/ecr/R/setup.R |only ecr-2.0.0/ecr/R/terminators.R |only ecr-2.0.0/ecr/R/transformFitness.R | 1 ecr-2.0.0/ecr/R/utilities.R | 28 ecr-2.0.0/ecr/R/zzz.R | 3 ecr-2.0.0/ecr/build |only ecr-2.0.0/ecr/inst |only ecr-2.0.0/ecr/man/asemoa.Rd | 83 +- ecr-2.0.0/ecr/man/computeAverageHausdorffDistance.Rd | 11 ecr-2.0.0/ecr/man/computeCrowdingDistance.Rd | 1 ecr-2.0.0/ecr/man/computeDistanceFromPointToSetOfPoints.Rd | 1 ecr-2.0.0/ecr/man/computeGenerationalDistance.Rd | 11 ecr-2.0.0/ecr/man/computeInvertedGenerationalDistance.Rd | 11 ecr-2.0.0/ecr/man/doNondominatedSorting.Rd | 7 ecr-2.0.0/ecr/man/dominated.Rd | 5 ecr-2.0.0/ecr/man/dominated_hypervolume.Rd | 29 - ecr-2.0.0/ecr/man/dominates.Rd | 5 ecr-2.0.0/ecr/man/ecr.Rd | 134 +--- ecr-2.0.0/ecr/man/ecr_parallelization.Rd | 14 ecr-2.0.0/ecr/man/ecr_result.Rd | 17 ecr-2.0.0/ecr/man/emoa_indicators.Rd | 39 - ecr-2.0.0/ecr/man/evaluateFitness.Rd | 32 - ecr-2.0.0/ecr/man/generateOffspring.Rd | 62 +- ecr-2.0.0/ecr/man/generators.Rd |only ecr-2.0.0/ecr/man/getFront.Rd |only ecr-2.0.0/ecr/man/getIndividuals.Rd |only ecr-2.0.0/ecr/man/getPopulations.Rd |only ecr-2.0.0/ecr/man/getSize.Rd |only ecr-2.0.0/ecr/man/getStatistics.Rd |only ecr-2.0.0/ecr/man/getSupportedRepresentations.Rd | 1 ecr-2.0.0/ecr/man/initECRControl.Rd |only ecr-2.0.0/ecr/man/initLogger.Rd |only ecr-2.0.0/ecr/man/initParetoArchive.Rd |only ecr-2.0.0/ecr/man/initPopulation.Rd |only ecr-2.0.0/ecr/man/is.supported.Rd | 1 ecr-2.0.0/ecr/man/isEcrOperator.Rd | 1 ecr-2.0.0/ecr/man/makeECRMonitor.Rd |only ecr-2.0.0/ecr/man/makeMutator.Rd | 18 ecr-2.0.0/ecr/man/makeOperator.Rd | 17 ecr-2.0.0/ecr/man/makeOptimizationTask.Rd | 1 ecr-2.0.0/ecr/man/makeRecombinator.Rd | 18 ecr-2.0.0/ecr/man/makeSelector.Rd | 16 ecr-2.0.0/ecr/man/makeTerminator.Rd | 5 ecr-2.0.0/ecr/man/mutBitflip.Rd |only ecr-2.0.0/ecr/man/mutGauss.Rd |only ecr-2.0.0/ecr/man/mutInsertion.Rd |only ecr-2.0.0/ecr/man/mutInversion.Rd |only ecr-2.0.0/ecr/man/mutPolynomial.Rd |only ecr-2.0.0/ecr/man/mutScramble.Rd |only ecr-2.0.0/ecr/man/mutSwap.Rd |only ecr-2.0.0/ecr/man/mutUniform.Rd |only ecr-2.0.0/ecr/man/normalizeFront.Rd |only ecr-2.0.0/ecr/man/nsga2.Rd | 68 +- ecr-2.0.0/ecr/man/plotFront.Rd |only ecr-2.0.0/ecr/man/plotStatistics.Rd |only ecr-2.0.0/ecr/man/recCrossover.Rd |only ecr-2.0.0/ecr/man/recIntermediate.Rd |only ecr-2.0.0/ecr/man/recOX.Rd |only ecr-2.0.0/ecr/man/recPMX.Rd |only ecr-2.0.0/ecr/man/recSBX.Rd |only ecr-2.0.0/ecr/man/reference_point_approximation.Rd | 9 ecr-2.0.0/ecr/man/registerECROperator.Rd |only ecr-2.0.0/ecr/man/replace.Rd |only ecr-2.0.0/ecr/man/selDomHV.Rd |only ecr-2.0.0/ecr/man/selGreedy.Rd |only ecr-2.0.0/ecr/man/selNondom.Rd |only ecr-2.0.0/ecr/man/selRoulette.Rd |only ecr-2.0.0/ecr/man/selSimple.Rd |only ecr-2.0.0/ecr/man/selTournament.Rd |only ecr-2.0.0/ecr/man/select.Rd |only ecr-2.0.0/ecr/man/setup.Rd |only ecr-2.0.0/ecr/man/setupECRDefaultMonitor.Rd |only ecr-2.0.0/ecr/man/smsemoa.Rd | 64 +- ecr-2.0.0/ecr/man/stoppingConditions.Rd |only ecr-2.0.0/ecr/man/toGG.Rd |only ecr-2.0.0/ecr/man/updateLogger.Rd |only ecr-2.0.0/ecr/man/updateParetoArchive.Rd |only ecr-2.0.0/ecr/man/which.dominated.Rd | 12 ecr-2.0.0/ecr/man/wrapChildren.Rd | 1 ecr-2.0.0/ecr/src/computeHypervolume.c | 4 ecr-2.0.0/ecr/src/dominance.c | 4 ecr-2.0.0/ecr/src/eps_ind.c | 6 ecr-2.0.0/ecr/src/init.c |only ecr-2.0.0/ecr/tests/testthat/helper_zzz.R | 10 ecr-2.0.0/ecr/tests/testthat/test_approximatePoints.R | 1 ecr-2.0.0/ecr/tests/testthat/test_dominates.R | 3 ecr-2.0.0/ecr/tests/testthat/test_ecr.R | 284 ++------- ecr-2.0.0/ecr/tests/testthat/test_emoa.R | 66 -- ecr-2.0.0/ecr/tests/testthat/test_emoa_indicators.R | 72 +- ecr-2.0.0/ecr/tests/testthat/test_evaluateFitness.R |only ecr-2.0.0/ecr/tests/testthat/test_initECRControl.R |only ecr-2.0.0/ecr/tests/testthat/test_initPopulation.R |only ecr-2.0.0/ecr/tests/testthat/test_logger.R |only ecr-2.0.0/ecr/tests/testthat/test_mutate.R |only ecr-2.0.0/ecr/tests/testthat/test_mutators.R | 50 + ecr-2.0.0/ecr/tests/testthat/test_normalizeFront.R |only ecr-2.0.0/ecr/tests/testthat/test_paretoArchive.R |only ecr-2.0.0/ecr/tests/testthat/test_plotFront.R |only ecr-2.0.0/ecr/tests/testthat/test_terminators.R |only ecr-2.0.0/ecr/vignettes |only 256 files changed, 1759 insertions(+), 2056 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single PNG
image that can be played back. See <http://canvasxpress.org> for more information.
Author: Isaac Neuhaus [aut, cre],
Connie Brett [ctb]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 0.15.2 dated 2017-04-02 and 0.15.5 dated 2017-04-26
DESCRIPTION | 8 - MD5 | 22 ++-- NEWS.md | 3 build/vignette.rds |binary inst/doc/getting_started.html | 8 - inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 90 ++++++++++++++---- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 4 man/canvasXpress-package.Rd | 2 man/canvasXpress.Rd | 1 man/canvasXpressOutput.Rd | 1 man/cxShinyExample.Rd | 1 man/renderCanvasXpress.Rd | 1 12 files changed, 96 insertions(+), 45 deletions(-)
Title: Local Association Measures
Description: Implements the estimation of local (and global) association measures: Ducher's Z, pointwise mutual information and normalized pointwise mutual information. The significance of local (and global) association is accessed using p-values estimated by permutations. Finally, using local association subgroup analysis, it identifies if the association between variables is dependent on the value of another variable.
Author: Olivier M. F. Martin [aut, cre],
Michel Ducher [aut]
Maintainer: Olivier M. F. Martin <olivmrtn@gmail.com>
Diff between zebu versions 0.1.0 dated 2016-08-21 and 0.1.1 dated 2017-04-26
DESCRIPTION | 18 +++--- MD5 | 46 +++++++++-------- NEWS.md |only R/estimate_prob.R | 4 - R/lassie.R | 3 - R/make_trial_dataset.R |only R/permtest.R | 74 ++++++++++++++++++++++++---- README.md | 6 +- build/vignette.rds |binary inst/doc/zebu.R | 9 ++- inst/doc/zebu.Rmd | 49 +++++++++++------- inst/doc/zebu.html | 122 +++++++++++++++++++++++++---------------------- man/estimate_prob.Rd | 1 man/format.lassie.Rd | 1 man/lassie.Rd | 4 - man/lassie_get.Rd | 1 man/local_association.Rd | 5 - man/permtest.Rd | 23 ++++++-- man/plot.lassie.Rd | 1 man/preprocess.Rd | 1 man/print.lassie.Rd | 1 man/subgroups.Rd | 1 man/trial.Rd | 1 man/write.lassie.Rd | 1 vignettes/zebu.Rmd | 49 +++++++++++------- 25 files changed, 256 insertions(+), 165 deletions(-)
Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other
'dplyr' inspired syntactic style when calculating summary statistics on survey
data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>
Diff between srvyr versions 0.2.0 dated 2016-09-26 and 0.2.1 dated 2017-04-26
srvyr-0.2.0/srvyr/man/mutate_each.Rd |only srvyr-0.2.0/srvyr/vignettes/ignore/my_db.sqlite3 |only srvyr-0.2.1/srvyr/DESCRIPTION | 14 +-- srvyr-0.2.1/srvyr/MD5 | 72 ++++++++--------- srvyr-0.2.1/srvyr/NAMESPACE | 21 ++++ srvyr-0.2.1/srvyr/NEWS.md | 10 ++ srvyr-0.2.1/srvyr/R/manip.r | 72 +++++++++++++++-- srvyr-0.2.1/srvyr/R/summarise.r | 7 + srvyr-0.2.1/srvyr/R/survey_package_functions.R |only srvyr-0.2.1/srvyr/README.md | 2 srvyr-0.2.1/srvyr/build/vignette.rds |binary srvyr-0.2.1/srvyr/inst/doc/srvyr-database.R | 3 srvyr-0.2.1/srvyr/inst/doc/srvyr-database.Rmd | 5 - srvyr-0.2.1/srvyr/inst/doc/srvyr-database.html | 13 +-- srvyr-0.2.1/srvyr/inst/doc/srvyr-vs-survey.Rmd | 2 srvyr-0.2.1/srvyr/inst/doc/srvyr-vs-survey.html | 15 +-- srvyr-0.2.1/srvyr/man/as_survey.Rd | 3 srvyr-0.2.1/srvyr/man/as_survey_design.Rd | 3 srvyr-0.2.1/srvyr/man/as_survey_rep.Rd | 3 srvyr-0.2.1/srvyr/man/as_survey_twophase.Rd | 3 srvyr-0.2.1/srvyr/man/as_tibble.Rd | 1 srvyr-0.2.1/srvyr/man/cascade.Rd | 1 srvyr-0.2.1/srvyr/man/dplyr_single.Rd | 13 +-- srvyr-0.2.1/srvyr/man/group_by.Rd | 1 srvyr-0.2.1/srvyr/man/groups.Rd | 1 srvyr-0.2.1/srvyr/man/pipe.Rd | 1 srvyr-0.2.1/srvyr/man/summarise.Rd | 1 srvyr-0.2.1/srvyr/man/summarise_all.Rd |only srvyr-0.2.1/srvyr/man/survey_mean.Rd | 1 srvyr-0.2.1/srvyr/man/survey_quantile.Rd | 3 srvyr-0.2.1/srvyr/man/survey_ratio.Rd | 1 srvyr-0.2.1/srvyr/man/survey_total.Rd | 1 srvyr-0.2.1/srvyr/man/svychisq.Rd |only srvyr-0.2.1/srvyr/man/tbl_svy.Rd | 2 srvyr-0.2.1/srvyr/man/tbl_vars.Rd | 1 srvyr-0.2.1/srvyr/man/unweighted.Rd | 1 srvyr-0.2.1/srvyr/tests/testthat/test_database.R | 16 +++ srvyr-0.2.1/srvyr/tests/testthat/test_survey_package.r |only srvyr-0.2.1/srvyr/vignettes/srvyr-database.Rmd | 5 - srvyr-0.2.1/srvyr/vignettes/srvyr-vs-survey.Rmd | 2 40 files changed, 195 insertions(+), 105 deletions(-)
Title: Calculate Task Split Half Reliability Estimates
Description: A series of functions to calculate the split
half reliability of RT based tasks. The core function performs a Monte Carlo
procedure to process a user defined number of random splits in order to
provide a better reliability estimate. The current functions target the dot-
probe task, however, can be modified for other tasks.
Author: Sam Parsons [aut, cre]
Maintainer: Sam Parsons <sam.parsons@psy.ox.ac.uk>
Diff between splithalf versions 0.1.0 dated 2017-04-07 and 0.2.0 dated 2017-04-26
DESCRIPTION | 6 +- MD5 | 26 ++++++++---- NAMESPACE | 2 NEWS.md | 9 ++++ R/DPsplithalf.R | 46 +++++++++++++++++----- R/DPsplithalfABM.R |only R/DPsplithalfall.R | 76 ++++++++++++++++++++++++++++++++----- R/TSTsplithalf.R |only R/data.R | 42 ++++++++++++++++++++ R/splithalf.R | 32 ++++++++++++++- README.md | 4 - data/TSTdata.RData |only data/TSTdata_missing.RData |only inst/doc/DPsplithalf-vignette.html | 42 ++++++++++---------- man/DPsplithalf.ABM.Rd |only man/TSTdata.Rd |only man/TSTdata_missing.Rd |only man/TSTsplithalf.Rd |only 18 files changed, 228 insertions(+), 57 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of MUMPS (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.0.1.12-3 dated 2017-03-17 and 5.1.1-1 dated 2017-04-26
rmumps-5.0.1.12-3/rmumps/inst/include/cmumps_c.h |only rmumps-5.0.1.12-3/rmumps/inst/include/cmumps_root.h |only rmumps-5.0.1.12-3/rmumps/inst/include/cmumps_struc.h |only rmumps-5.0.1.12-3/rmumps/inst/include/smumps_c.h |only rmumps-5.0.1.12-3/rmumps/inst/include/smumps_root.h |only rmumps-5.0.1.12-3/rmumps/inst/include/smumps_struc.h |only rmumps-5.0.1.12-3/rmumps/inst/include/zmumps_c.h |only rmumps-5.0.1.12-3/rmumps/inst/include/zmumps_root.h |only rmumps-5.0.1.12-3/rmumps/inst/include/zmumps_struc.h |only rmumps-5.0.1.12-3/rmumps/src/Makevars.win |only rmumps-5.0.1.12-3/rmumps/src/lib/MUMPS_5.0.1 |only rmumps-5.0.1.12-3/rmumps/src/lib/Makefile.win |only rmumps-5.0.1.12-3/rmumps/src/lib/scotch_6.0.4/src/Makefile.win |only rmumps-5.1.1-1/rmumps/DESCRIPTION | 13 rmumps-5.1.1-1/rmumps/MD5 | 586 ++++------ rmumps-5.1.1-1/rmumps/NEWS | 9 rmumps-5.1.1-1/rmumps/inst/examples/random_stm.R | 2 rmumps-5.1.1-1/rmumps/inst/include/dmumps_c.h | 18 rmumps-5.1.1-1/rmumps/inst/include/dmumps_root.h | 8 rmumps-5.1.1-1/rmumps/inst/include/dmumps_struc.h | 54 rmumps-5.1.1-1/rmumps/inst/include/mumps_c_types.h | 6 rmumps-5.1.1-1/rmumps/inst/include/mumps_compat.h | 14 rmumps-5.1.1-1/rmumps/inst/include/rmumps.h | 6 rmumps-5.1.1-1/rmumps/man/Rmumps.Rd | 22 rmumps-5.1.1-1/rmumps/src/Makevars | 13 rmumps-5.1.1-1/rmumps/src/Makevars.omp |only rmumps-5.1.1-1/rmumps/src/lib/MUMPS_5.1.1 |only rmumps-5.1.1-1/rmumps/src/lib/Makefile | 305 ----- rmumps-5.1.1-1/rmumps/src/lib/metis-5.1.0/Makefile |only rmumps-5.1.1-1/rmumps/src/lib/mpi.patch |only rmumps-5.1.1-1/rmumps/src/lib/scotch_6.0.4/src/Makefile | 9 rmumps-5.1.1-1/rmumps/src/lib/scotch_6.0.4/src/Makefile.inc | 4 rmumps-5.1.1-1/rmumps/src/lib/scotch_6.0.4/src/Makefile.inc.macos | 2 rmumps-5.1.1-1/rmumps/src/lib/scotch_6.0.4/src/Makefile.inc.rmumps | 4 rmumps-5.1.1-1/rmumps/src/lib/scotch_6.0.4/src/Makefile.inc.win | 4 rmumps-5.1.1-1/rmumps/src/rmumps_module.cpp | 85 + 36 files changed, 505 insertions(+), 659 deletions(-)
Title: IRT Separate Calibration Linking Methods
Description: Item response theory based methods are used to compute
linking constants and conduct chain linking of unidimensional
or multidimensional tests for multiple groups under a common
item design. The unidimensional methods include the Mean/Mean,
Mean/Sigma, Haebara, and Stocking-Lord methods for dichotomous
(1PL, 2PL and 3PL) and/or polytomous (graded response, partial
credit/generalized partial credit, nominal, and multiple-choice
model) items. The multidimensional methods include the least
squares method and extensions of the Haebara and Stocking-Lord
method using single or multiple dilation parameters for
multidimensional extensions of all the unidimensional
dichotomous and polytomous item response models. The package
also includes functions for importing item and/or ability
parameters from common IRT software, conducting IRT true score
and observed score equating, and plotting item response
curves/surfaces, vector plots, information plots, and comparison
plots for examining parameter drift.
Author: Jonathan P. Weeks <weeksjp@gmail.com>
Maintainer: Jonathan P. Weeks <weeksjp@gmail.com>
Diff between plink versions 1.5-0 dated 2017-04-07 and 1.5-1 dated 2017-04-26
DESCRIPTION | 8 ++-- MD5 | 10 ++--- NAMESPACE | 2 - R/plot.R | 98 +------------------------------------------------- inst/NEWS | 9 ++++ inst/doc/plink-UD.pdf |binary 6 files changed, 21 insertions(+), 106 deletions(-)
Title: Multilevel Model Intraclass Correlation for Slope Heterogeneity
Description: A function and vignettes for computing an intraclass correlation
described in Aguinis & Culpepper (2015) <doi:10.1177/1094428114563618>.
This package quantifies the share of variance in a dependent variable that
is attributed to group heterogeneity in slopes.
Author: Steven Andrew Culpepper [aut, cph, cre],
Herman Aguinis [aut, cph]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between iccbeta versions 1.0 dated 2014-11-25 and 1.0.1 dated 2017-04-26
DESCRIPTION | 33 +++++--- MD5 | 25 ++++-- NAMESPACE | 12 +-- NEWS.md |only R/RcppExports.R | 101 ++++++++++++++++++++++----- R/datasets-docs.R |only R/iccbeta-internal.R |only README.md |only inst/CITATION | 25 +++--- man/Hofmann.Rd | 140 ++++++++++++++++++-------------------- man/icc_beta.Rd | 180 ++++++++++++++++++++++++++----------------------- man/iccbeta-package.Rd | 163 ++++++++++++++++++++++---------------------- man/simICCdata.Rd | 120 ++++++++++++++++---------------- src/RcppExports.cpp | 22 ++--- src/icc_beta.cpp | 91 +++++++++++++++++++++--- src/init.c |only 16 files changed, 533 insertions(+), 379 deletions(-)
Title: Bayesian 4 Parameter Item Response Model
Description: Estimate Barton & Lord's (1981) <doi:10.1002/j.2333-8504.1981.tb01255.x>
four parameter IRT model with lower and upper asymptotes using Bayesian
formulation described by Culpepper (2016) <doi:10.1007/s11336-015-9477-6>.
Author: Steven Andrew Culpepper [aut, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between fourPNO versions 1.0.3 dated 2015-12-16 and 1.0.4 dated 2017-04-26
DESCRIPTION | 23 + MD5 | 42 +-- NAMESPACE | 20 + NEWS.md |only R/RcppExports.R | 514 ++++++++++++++++++++++++----------------- R/fourPNO-internal.R | 257 ++++++++++---------- README.md |only inst/CITATION | 24 + man/Gibbs_2PNO.Rd | 139 +++++------ man/Gibbs_4PNO.Rd | 171 ++++++------- man/Total_Tabulate.Rd | 55 ++-- man/Y_4pno_simulate.Rd | 71 ++--- man/fourPNO-package.Rd |only man/kappa_initialize.Rd | 47 +-- man/min2LL_4pno.Rd | 75 ++--- man/rmvnorm.Rd | 58 ++-- man/update_2pno.Rd | 89 +++---- man/update_WKappaZ_NA.Rd | 101 +++----- man/update_ab_NA.Rd | 75 ++--- man/update_ab_norestriction.Rd | 75 ++--- man/update_theta.Rd | 71 ++--- src/RcppExports.cpp | 98 +++---- src/fourpno_101315.cpp | 202 +++++++++++----- src/init.c |only 24 files changed, 1211 insertions(+), 996 deletions(-)
Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy "And" Gate (DINA)
cognitive diagnostic model parameters using the Gibbs sampler described
by Culpepper (2015) <doi:10.3102/1076998615595403>.
Author: Steven Andrew Culpepper [aut, cph, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between dina versions 1.0.1 dated 2015-10-28 and 1.0.2 dated 2017-04-26
DESCRIPTION | 29 ++- MD5 | 30 ++-- NAMESPACE | 14 + NEWS.md |only R/RcppExports.R | 363 +++++++++++++++++++++++++++++++++++++------------- R/dina-internal.R | 259 ++++++++++++++++++----------------- README.md |only inst |only man/DINA_Gibbs.Rd | 288 ++++++++++++++++++++------------------- man/DINAsim.Rd | 188 ++++++++++++------------- man/dina-package.Rd | 51 +++---- man/rDirichlet.Rd | 41 ++--- man/rmultinomial.Rd | 41 ++--- man/update_alpha.Rd | 70 ++++----- man/update_sg.Rd | 69 ++++----- src/DINAcpp101315.cpp | 261 ++++++++++++++++++++++++++++++----- src/RcppExports.cpp | 50 +++--- src/init.c |only 18 files changed, 1075 insertions(+), 679 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-08 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-09 1.1-3
2013-05-16 1.1-0
2013-03-22 1.0-1
2012-07-25 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-14 0.4.2
2015-06-12 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-26 0.4-19
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-12 1.1.1
2016-02-24 1.1
2015-02-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-09 1.4.7
2017-01-02 1.4.6
2015-03-04 1.4.1
2014-11-26 1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-31 0.9-43
2010-03-09 0.9-42
2009-12-10 0.9-41
2009-10-13 0.9-40
2008-05-02 0.9-38
2008-01-11 0.9-37
2007-10-28 0.9-35
2007-08-25 0.9-34
2007-07-13 0.9-33
2007-07-12 0.9-32
2007-04-20 0.9-31
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-29 0.1.7
2014-02-20 0.1.5
2013-02-04 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-03 2.16
2015-10-21 2.12
2015-09-28 2.11
2013-05-21 2.7
2013-03-12 2.3
2013-02-07 2.1
2012-10-02 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-31 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-02 1.4
2013-12-20 1.3
2013-03-16 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-22 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-14 1.1.1
2012-04-17 1.1
2009-06-03 1.0
Title: : Disease-Gene-Variant Relations Mining from the Public
Databases and Literature
Description: Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature from the public databases including HPO (Human Phenotype Ontology, <http://human-phenotype-ontology.github.io/about.html>), Orphanet <http://www.orpha.net/consor/cgi-bin/index.php>, OMIM (Online Mendelian Inheritance in Man, <http://www.omim.org>), ClinVar <http://www.ncbi.nlm.nih.gov/clinvar>, and UniProt (Universal Protein Resource, <http://www.uniprot.org>) and PubMed abstracts. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. UniProt focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the UniProt are manually curated from UniProtKB/Swiss-Prot. Additionally, PubMed provides the primary and latest source of the information. Text mining was employed to capture the information from PubMed abstracts.
Author: Zongfu Cao <caozongfu@gmail.com>; Lei Wang <isan.wong@gmail.com>
Maintainer: Zongfu Cao <caozongfu@gmail.com>
Diff between VarfromPDB versions 2.1.11 dated 2016-10-31 and 2.2.6 dated 2017-04-26
VarfromPDB-2.1.11/VarfromPDB/inst/doc/VarfromPDB.pdf |only VarfromPDB-2.2.6/VarfromPDB/DESCRIPTION | 23 +- VarfromPDB-2.2.6/VarfromPDB/MD5 | 54 ++--- VarfromPDB-2.2.6/VarfromPDB/NAMESPACE | 4 VarfromPDB-2.2.6/VarfromPDB/R/extract_clinvar.R | 102 +++------- VarfromPDB-2.2.6/VarfromPDB/R/extract_genes_orphanet.R | 6 VarfromPDB-2.2.6/VarfromPDB/R/extract_omim.R | 9 VarfromPDB-2.2.6/VarfromPDB/R/extract_pubmed.R | 86 +++++--- VarfromPDB-2.2.6/VarfromPDB/R/extract_uniprot.R | 7 VarfromPDB-2.2.6/VarfromPDB/R/genes_add_pubmed.R | 38 +++ VarfromPDB-2.2.6/VarfromPDB/R/genes_compile.R | 17 + VarfromPDB-2.2.6/VarfromPDB/R/localPDB.R | 138 ++++++++++---- VarfromPDB-2.2.6/VarfromPDB/R/pheno_extract_HPO.R | 4 VarfromPDB-2.2.6/VarfromPDB/R/variants_compile.R | 109 +++++++---- VarfromPDB-2.2.6/VarfromPDB/build |only VarfromPDB-2.2.6/VarfromPDB/inst/doc/VarfromPDB.R |only VarfromPDB-2.2.6/VarfromPDB/inst/doc/VarfromPDB.Rmd |only VarfromPDB-2.2.6/VarfromPDB/inst/doc/VarfromPDB.html |only VarfromPDB-2.2.6/VarfromPDB/man/aa.Rd | 3 VarfromPDB-2.2.6/VarfromPDB/man/extract_clinvar.Rd | 14 - VarfromPDB-2.2.6/VarfromPDB/man/extract_genes_orphanet.Rd | 2 VarfromPDB-2.2.6/VarfromPDB/man/extract_omim.Rd | 7 VarfromPDB-2.2.6/VarfromPDB/man/extract_pubmed.Rd | 13 - VarfromPDB-2.2.6/VarfromPDB/man/extract_uniprot.Rd | 2 VarfromPDB-2.2.6/VarfromPDB/man/genes_add_pubmed.Rd | 27 +- VarfromPDB-2.2.6/VarfromPDB/man/genes_compile.Rd | 4 VarfromPDB-2.2.6/VarfromPDB/man/grep_split.Rd | 2 VarfromPDB-2.2.6/VarfromPDB/man/localPDB.Rd | 10 - VarfromPDB-2.2.6/VarfromPDB/man/pheno_extract_HPO.Rd | 2 VarfromPDB-2.2.6/VarfromPDB/man/variants_compile.Rd | 5 VarfromPDB-2.2.6/VarfromPDB/vignettes |only 31 files changed, 406 insertions(+), 282 deletions(-)
Title: Trust Region Optimization for Nonlinear Functions with Sparse
Hessians
Description: Trust region algorithm for nonlinear optimization. Efficient when
the Hessian of the objective function is sparse (i.e., relatively few nonzero
cross-partial derivatives). See Braun, M. (2014) <doi:10.18637/jss.v060.i04>.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun <braunm@smu.edu>
Diff between trustOptim versions 0.8.5 dated 2015-02-04 and 0.8.6 dated 2017-04-26
DESCRIPTION | 24 ++++--- MD5 | 39 +++++------ NAMESPACE | 5 - NEWS | 8 ++ R/RcppExports.R | 2 R/binary.R | 61 ++++++++---------- R/callTrust.R | 81 ++++++++++++++---------- R/trustOptim.R | 15 ++-- build/vignette.rds |binary inst/doc/trustOptim-demo.R | 6 - inst/doc/trustOptim-demo.html | 137 ++++++++++++++++++++++++----------------- inst/doc/trustOptim-quick.R | 2 inst/doc/trustOptim-quick.html | 100 +++++++++++++++++------------ man/binary-data.Rd | 3 man/binary.Rd | 3 man/trust.optim.Rd | 24 ++++++- man/trustOptim.Rd | 3 src/Makevars.win | 8 +- src/RcppExports.cpp | 44 +++++-------- src/init.c |only vignettes/trustOptim.bib | 46 +------------ 21 files changed, 332 insertions(+), 279 deletions(-)
Title: SEER and Atomic Bomb Survivor Data Analysis Tools
Description: Creates SEER (Surveillance, Epidemiology and End Results) and A-bomb data binaries
from ASCII sources and provides tools for estimating SEER second cancer risks.
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch <radivot@ccf.org>
Diff between SEERaBomb versions 2016.2 dated 2016-11-11 and 2017.1 dated 2017-04-26
DESCRIPTION | 8 +-- MD5 | 53 ++++++++++++--------- NAMESPACE | 4 - NEWS | 28 +++++++++++ R/canc2py.R |only R/esd.R |only R/mapTrts.R | 17 ++++-- R/mkSEER.R | 1 R/msd.R | 7 ++ R/pickFields.R | 5 +- R/riskVsAge.R |only R/seerSet.R | 7 ++ inst/doc/examples/mkDataBinaries.R | 12 +++- inst/doc/examples/registryDiffs.R | 5 +- inst/doc/papers/leukemia2016/APL.R | 4 - inst/doc/papers/leukemia2016/PYnMDSvsDBs.R | 10 ++-- inst/doc/papers/leukemia2016/amlAbombAge.R | 10 ++-- inst/doc/papers/leukemia2016/amlMDScomputing.R | 4 - inst/doc/papers/leukemia2016/aveAge.R | 4 - inst/doc/papers/leukemia2016/consort.R | 4 - inst/doc/papers/leukemia2016/incidAllFirsts.R | 62 ++++++++++++++----------- inst/doc/papers/leukemia2016/mkExcelDemo.R | 4 - inst/doc/papers/leukemia2016/setup.R | 6 +- inst/doc/papers/leukemia2016/specificFirst.R | 6 +- inst/doc/papers/leukemiaRes2016/CLLcomputing.R | 4 - man/canc2py.Rd |only man/esd.Rd |only man/fillPYM.Rd | 2 man/pickFields.Rd | 5 +- man/riskVsAge.Rd |only src/SEERaBomb_init.c |only 31 files changed, 171 insertions(+), 101 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
Ruben Arslan [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
Eli Grey [ctb, cph] (FileSaver library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 1.4 dated 2017-03-24 and 1.5 dated 2017-04-26
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ R/html_document.R | 10 +++++----- R/html_fragment.R | 5 +++-- R/shiny.R | 2 +- R/shiny_prerendered.R | 2 +- inst/NEWS | 11 +++++++++++ inst/rmd/fragment/default.html | 10 ++++++++++ man/html_document.Rd | 8 ++++---- man/html_document_base.Rd | 8 ++++---- man/html_fragment.Rd | 7 +++++-- man/html_notebook.Rd | 8 ++++---- man/slidy_presentation.Rd | 8 ++++---- 13 files changed, 67 insertions(+), 42 deletions(-)
Title: R Client for the eBird Database of Bird Observations
Description: A programmatic client for the eBird database, including functions
for searching for bird observations by geographic location (latitude,
longitude), eBird hotspots, location identifiers, by notable sightings, by
region, and by taxonomic name.
Author: Rafael Maia [aut],
Scott Chamberlain [aut],
Andy Teucher [aut],
Sebastian Pardo [aut, cre]
Maintainer: Sebastian Pardo <sebpardo@gmail.com>
Diff between rebird versions 0.3.0 dated 2016-03-23 and 0.4.0 dated 2017-04-26
DESCRIPTION | 12 ++++----- MD5 | 46 ++++++++++++++++++------------------- NEWS.md | 8 ++++++ R/ebirdfreq.R | 18 +++++--------- R/ebirdtaxonomy.R | 2 - R/zzz.R | 2 - build/vignette.rds |binary inst/doc/rebird_vignette.html | 4 +-- man/ebirdfreq.Rd | 12 ++++----- man/ebirdgeo.Rd | 7 ++--- man/ebirdhotspot.Rd | 7 ++--- man/ebirdloc.Rd | 7 ++--- man/ebirdnotable.Rd | 7 ++--- man/ebirdregion.Rd | 7 ++--- man/ebirdregioncheck.Rd | 7 ++--- man/ebirdtaxonomy.Rd | 9 +++---- man/getlatlng.Rd | 7 ++--- man/nearestobs.Rd | 7 ++--- man/rebird-package.Rd | 3 -- tests/testthat/test-ebirdfreq.R | 4 +-- tests/testthat/test-ebirdgeo.R | 2 - tests/testthat/test-ebirdhotspot.R | 2 - tests/testthat/test-ebirdloc.R | 8 +++--- tests/testthat/test-ebirdnotable.R | 2 - 24 files changed, 92 insertions(+), 98 deletions(-)
Title: Automatic Differentiation of Multivariate Operations
Description: An object that supports automatic differentiation
of matrix- and multidimensional-valued functions with
respect to multidimensional independent variables.
Automatic differentiation is via 'forward accumulation'.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between madness versions 0.2.1 dated 2017-04-14 and 0.2.2 dated 2017-04-26
DESCRIPTION | 21 ++++---- MD5 | 98 +++++++++++++++++++-------------------- NAMESPACE | 4 + R/AllClass.r | 3 + R/Ops.r | 9 ++- R/coerce.r | 8 +-- R/det.r | 4 + R/diag.r | 20 ++++--- R/eigen.r | 4 + R/madness_pkg.r | 9 +++ R/matwise.r | 11 ++-- R/norm.r | 10 ++- R/reshape.r | 30 ++++++++++- R/solve.r | 9 +-- R/sums.r | 23 ++++----- R/to_objective.r | 1 inst/doc/introducing_madness.pdf |binary man/NEWS.Rd | 8 +++ man/accessor-methods.Rd | 15 ++--- man/arithops.Rd | 87 +++++++++++++++++----------------- man/as.Rd | 11 +--- man/as.madness.Rd | 2 man/bind.Rd | 13 ++--- man/blockrep.Rd | 1 man/colsums.Rd | 21 ++------ man/det.Rd | 10 +-- man/eigen.Rd | 10 +-- man/elwise.Rd | 13 ++--- man/extract-methods.Rd | 4 + man/madness-class.Rd | 12 ++-- man/madness-pkg.Rd | 12 ++-- man/marithops.Rd | 23 +++------ man/matrix.trace.Rd | 3 - man/matwise.Rd | 8 +-- man/max.Rd | 4 - man/norm.Rd | 9 +-- man/numderiv.Rd | 5 - man/outer.Rd | 22 +++----- man/reshapes.Rd | 31 ++++-------- man/setter-methods.Rd | 9 +-- man/show-methods.Rd | 1 man/solve.Rd | 15 +---- man/sumprod.Rd | 9 +-- man/theta.Rd | 7 +- man/to_objective.Rd | 2 man/todiag.Rd | 17 ++---- man/twomoments.Rd | 7 +- man/vcov.madness.Rd | 7 +- man/vec.Rd | 16 +++--- tests/testthat/test-basic.r | 15 +++++ 50 files changed, 359 insertions(+), 334 deletions(-)
Title: Choice Item Response Theory
Description: Jointly model the accuracy of cognitive responses and item choices
within a bayesian hierarchical framework as described by Culpepper and
Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package
contains the datasets used within the analysis of the paper.
Author: Steve Culpepper [aut, cph],
James Balamuta [aut, cre, ctb, com, cph]
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between cIRT versions 1.2.0 dated 2016-04-13 and 1.2.1 dated 2017-04-26
DESCRIPTION | 17 +- MD5 | 59 +++---- NAMESPACE | 13 + NEWS.md | 5 R/RcppExports.R | 67 +++++--- R/cIRT-package.R | 15 + build/vignette.rds |binary inst/doc/Estimating-the-Model-in-the-Paper.html | 189 +++++++++++------------- inst/doc/Package-Overview.html | 13 - inst/doc/Simulation-Study-with-cIRT.html | 85 +++++----- man/Generate_Choice.Rd | 1 man/Total_Tabulate.Rd | 1 man/TwoPLChoicemcmc.Rd | 7 man/cIRT.Rd | 7 man/cIRT_package.Rd | 19 +- man/center_matrix.Rd | 10 - man/choice_matrix.Rd | 1 man/direct_sum.Rd | 2 man/payout_matrix.Rd | 1 man/probitHLM.Rd | 7 man/riwishart.Rd | 7 man/rmvnorm.Rd | 8 - man/rwishart.Rd | 8 - man/survey_data.Rd | 1 man/trial_matrix.Rd | 1 src/RcppExports.cpp | 82 +++++----- src/armadillo_manipulations.cpp | 17 +- src/init.c |only src/project_source.cpp | 47 +++-- src/rgens.cpp | 21 +- src/total_cpp.cpp | 15 + 31 files changed, 376 insertions(+), 350 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-02 2.16.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-23 3010.78
2012-12-10 2160.77
2009-09-29 2100.76
2009-04-16 290.75
2008-10-27 270.74
2008-10-23 270.73
2007-10-08 260.72
2007-10-02 260.71
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-29 0.18
2016-03-09 0.17
2014-11-19 0.15
2014-11-09 0.13
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-25 1.2.2
2013-01-18 1.2.1
2010-01-03 1.2.0
2007-07-29 1.1.0
2006-10-18 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-15 1.0-4
2013-10-05 1.0-3
2013-07-30 1.0-2
2013-06-27 1.0-1
2013-06-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-24 1.1.1
2013-10-22 1.1.0
2012-08-04 1.0.1
2012-03-26 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-27 0.2
2016-05-22 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-08 0.8.4
2013-12-23 0.8.2
2012-06-25 0.8
2011-05-03 0.7
2011-03-31 0.6.1
2011-03-24 0.6
2010-09-22 0.5.4
2010-08-16 0.5.1
2010-06-24 0.5
2010-05-19 0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-14 0.1-3
2012-01-16 0.1-2
2005-06-22 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-19 1.0