Title: A Consistent Interface to Tokenize Natural Language Text
Description: Convert natural language text into tokens. The tokenizers have a
consistent interface and are compatible with Unicode, thanks to being built
on the 'stringi' package. Includes tokenizers for shingled n-grams, skip
n-grams, words, word stems, sentences, paragraphs, characters, lines, and
regular expressions.
Author: Lincoln Mullen [aut, cre],
Dmitriy Selivanov [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between tokenizers versions 0.1.2 dated 2016-04-14 and 0.1.3 dated 2016-08-18
tokenizers-0.1.2/tokenizers/inst/extdata |only tokenizers-0.1.2/tokenizers/tests/testthat/data-for-tests.R |only tokenizers-0.1.3/tokenizers/DESCRIPTION | 16 ++--- tokenizers-0.1.3/tokenizers/MD5 | 37 ++++++------ tokenizers-0.1.3/tokenizers/NEWS.md | 5 + tokenizers-0.1.3/tokenizers/R/basic-tokenizers.R | 4 - tokenizers-0.1.3/tokenizers/R/ngram-tokenizers.R | 2 tokenizers-0.1.3/tokenizers/R/utils.R | 2 tokenizers-0.1.3/tokenizers/README.md | 12 ++- tokenizers-0.1.3/tokenizers/build |only tokenizers-0.1.3/tokenizers/inst/doc |only tokenizers-0.1.3/tokenizers/man/basic-tokenizers.Rd | 4 - tokenizers-0.1.3/tokenizers/src/shingle_ngrams.cpp | 31 ++++------ tokenizers-0.1.3/tokenizers/tests/testthat/helper-data.R |only tokenizers-0.1.3/tokenizers/tests/testthat/moby-ch1.txt |only tokenizers-0.1.3/tokenizers/tests/testthat/moby-ch2.txt |only tokenizers-0.1.3/tokenizers/tests/testthat/moby-ch3.txt |only tokenizers-0.1.3/tokenizers/tests/testthat/test-basic.R | 2 tokenizers-0.1.3/tokenizers/tests/testthat/test-ngrams.R | 6 + tokenizers-0.1.3/tokenizers/tests/testthat/test-stem.R | 2 tokenizers-0.1.3/tokenizers/tests/testthat/test-utils.R | 2 tokenizers-0.1.3/tokenizers/vignettes |only 22 files changed, 67 insertions(+), 58 deletions(-)
Title: Helpers for Data Analysis and Presentation Focused on Undergrad
Psychology
Description: Contains functions for the easy display of statistical tests as well as
some convenience functions for recoding or data cleanup. It is meant to ease existing workflows
with packages like 'sjPlot', 'dplyr', and 'ggplot2'. The primary components are the functions
prefixed with 'tadaa_', which are built to work in an interactive environment, but also print
tidy markdown tables powered by 'pixiedust' for the creation of 'RMarkdown' reports.
Author: Lukas Burk [aut, cre],
Tobias Anton [aut],
Daniel Lüdecke [ctb]
Maintainer: Lukas Burk <lukas@quantenbrot.de>
Diff between tadaatoolbox versions 0.9.0 dated 2016-02-18 and 0.10.0 dated 2016-08-18
DESCRIPTION | 18 +++++++++------- MD5 | 51 +++++++++++++++++++++++++++------------------- NAMESPACE | 11 +++++++++ NEWS.md | 33 ++++++++++++++++++++++++----- R/aov.R | 33 ++++++++++++++++++----------- R/cleanup_helpers.R | 38 ++++++++++++++++++++++++++++++++++ R/ggplot2_themes.R |only R/heatmap.R |only R/interaction_plots.R | 31 ++++++++++++++++++---------- R/misc_stats.R | 16 ++++++++++++-- R/normtest.R |only R/recode_helpers.R | 14 ++++++------ R/sem.R |only R/t_test.R | 36 ++++++++++++++++++-------------- README.md | 28 ++++++++++++++++++------- build/vignette.rds |binary inst/doc/overview.R | 10 ++++----- inst/doc/overview.Rmd | 17 +++++++++------ inst/doc/overview.html | 52 ++++++++++++++++++++++++----------------------- man/modus.Rd | 11 ++++++++- man/pval_string.Rd |only man/tadaa_aov.Rd | 16 ++++++++------ man/tadaa_heatmap.Rd |only man/tadaa_int.Rd | 15 ++++++++++--- man/tadaa_nom.Rd | 3 +- man/tadaa_normtest.Rd |only man/tadaa_ord.Rd | 3 +- man/tadaa_sem.Rd |only man/tadaa_t.test.Rd | 8 ++++--- man/theme_readthedown.Rd |only vignettes/overview.Rmd | 39 +++++++++++++++++++++++++++++------ 31 files changed, 335 insertions(+), 148 deletions(-)
Title: Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
Description: Algorithms for accelerating the convergence of slow,
monotone sequences from smooth, contraction mapping such as the
EM algorithm. It can be used to accelerate any smooth, linearly
convergent acceleration scheme. A tutorial style introduction
to this package is available in a vignette on the CRAN download
page or, when the package is loaded in an R session, with
vignette("SQUAREM").
Author: Ravi Varadhan
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between SQUAREM versions 2016.8-1 dated 2016-08-12 and 2016.8-2 dated 2016-08-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- NEWS | 1 + build/vignette.rds |binary demo/00Index | 6 +++++- demo/factoranalysis.R |only demo/intcensoring.R |only demo/mmlogistic.R |only demo/poissonmix.R |only 9 files changed, 18 insertions(+), 9 deletions(-)
Title: Semiparametric Copula Regression Models
Description: Routines for fitting several classes of copula regression models, with several types of covariate effects, in the presence of associated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <r.radice@bbk.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between SemiParBIVProbit versions 3.7-1 dated 2016-05-06 and 3.8 dated 2016-08-18
SemiParBIVProbit-3.7-1/SemiParBIVProbit/R/Amat.R |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/R/SemiParTRIVProbit.fit.post.r |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/R/SemiParTRIVProbit.r |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/R/print.SemiParTRIVProbit.r |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/R/print.summary.SemiParTRIVProbit.r |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/R/summary.SemiParTRIVProbit.r |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/R/triprobgHsSS.R |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/Amat.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/BiCDF.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/H.triSS.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/SemiParTRIVProbit.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/SemiParTRIVProbit.fit.post.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/SemiParTRIVProbitObject.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/bcont23.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/bcont3.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/bcont32.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/bprobgHsCont3.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/bprobgHsCont3SS.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/bprobgHsContUniv3.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/bprobgHsPO0.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/copgHs2.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/copgHsAT.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/copgHsCont.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/copulaReg.fit.post.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/copulaSampleSel.fit.post.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/distrHsAT.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/esp.tr.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/g.triSS.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/mm.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/numch.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/print.SemiParTRIVProbit.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/summary.SemiParTRIVProbit.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/teta.tr.Rd |only SemiParBIVProbit-3.7-1/SemiParBIVProbit/man/triprobgHsSS.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/ChangeLog | 4 SemiParBIVProbit-3.8/SemiParBIVProbit/DESCRIPTION | 11 SemiParBIVProbit-3.8/SemiParBIVProbit/MD5 | 293 ++--- SemiParBIVProbit-3.8/SemiParBIVProbit/NAMESPACE | 26 SemiParBIVProbit-3.8/SemiParBIVProbit/R/AT.r | 12 SemiParBIVProbit-3.8/SemiParBIVProbit/R/AT2.r | 1 SemiParBIVProbit-3.8/SemiParBIVProbit/R/BiCDF.r | 7 SemiParBIVProbit-3.8/SemiParBIVProbit/R/H.triSS.r | 285 ++-- SemiParBIVProbit-3.8/SemiParBIVProbit/R/LM.bpm.r | 13 SemiParBIVProbit-3.8/SemiParBIVProbit/R/OR.r | 4 SemiParBIVProbit-3.8/SemiParBIVProbit/R/RR.r | 4 SemiParBIVProbit-3.8/SemiParBIVProbit/R/SemiParBIVProbit.fit.R | 138 +- SemiParBIVProbit-3.8/SemiParBIVProbit/R/SemiParBIVProbit.fit.post.r | 23 SemiParBIVProbit-3.8/SemiParBIVProbit/R/SemiParBIVProbit.r | 270 +++- SemiParBIVProbit-3.8/SemiParBIVProbit/R/SemiParTRIV.fit.post.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/SemiParTRIV.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/TRIapprox.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/adjCov.r | 112 + SemiParBIVProbit-3.8/SemiParBIVProbit/R/adjCovSD.r | 127 +- SemiParBIVProbit-3.8/SemiParBIVProbit/R/bcont.R | 26 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bcont23.R | 23 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bcont3.R | 22 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bcont32.R | 23 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bdiscrcont.R |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bdiscrcont12.R |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bdiscrcont13.R |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bdiscrcont23.R |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bdiscrdiscr.R |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bdiscrdiscr11.R |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bdiscrdiscr12.R |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHs.r | 22 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsCont.r | 23 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsCont3.r | 22 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsCont3SS.r | 22 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsContSS.r | 22 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsContUniv.r | 121 +- SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsContUniv3.r | 94 + SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsDiscr1.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsDiscr1SS.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsDiscr2.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsDiscr2SS.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsFixTheta.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsPO.r | 50 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsPO0.r | 23 SemiParBIVProbit-3.8/SemiParBIVProbit/R/bprobgHsSS.r | 47 SemiParBIVProbit-3.8/SemiParBIVProbit/R/copgHs.r | 48 SemiParBIVProbit-3.8/SemiParBIVProbit/R/copgHsCont.r | 32 SemiParBIVProbit-3.8/SemiParBIVProbit/R/copulaReg.fit.post.r | 11 SemiParBIVProbit-3.8/SemiParBIVProbit/R/copulaReg.r | 578 ++++++++-- SemiParBIVProbit-3.8/SemiParBIVProbit/R/copulaSampleSel.fit.post.r | 32 SemiParBIVProbit-3.8/SemiParBIVProbit/R/copulaSampleSel.r | 235 +++- SemiParBIVProbit-3.8/SemiParBIVProbit/R/distrHs.r | 31 SemiParBIVProbit-3.8/SemiParBIVProbit/R/distrHsATDiscr.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/distrHsDiscr.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/enu.tr.R |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/esp.tr.R | 6 SemiParBIVProbit-3.8/SemiParBIVProbit/R/eta.tr.R | 11 SemiParBIVProbit-3.8/SemiParBIVProbit/R/g.triSS.r | 86 - SemiParBIVProbit-3.8/SemiParBIVProbit/R/jc.probs.r | 20 SemiParBIVProbit-3.8/SemiParBIVProbit/R/numch.r | 20 SemiParBIVProbit-3.8/SemiParBIVProbit/R/numgh.r | 27 SemiParBIVProbit-3.8/SemiParBIVProbit/R/pen.r | 166 +- SemiParBIVProbit-3.8/SemiParBIVProbit/R/post.check.R | 141 ++ SemiParBIVProbit-3.8/SemiParBIVProbit/R/prev.r | 6 SemiParBIVProbit-3.8/SemiParBIVProbit/R/print.SemiParBIVProbit.r | 44 SemiParBIVProbit-3.8/SemiParBIVProbit/R/print.SemiParTRIV.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/print.copulaReg.r | 93 + SemiParBIVProbit-3.8/SemiParBIVProbit/R/print.copulaSampleSel.r | 14 SemiParBIVProbit-3.8/SemiParBIVProbit/R/print.summary.SemiParBIVProbit.r | 43 SemiParBIVProbit-3.8/SemiParBIVProbit/R/print.summary.SemiParTRIV.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/print.summary.copulaReg.r | 198 ++- SemiParBIVProbit-3.8/SemiParBIVProbit/R/print.summary.copulaSampleSel.r | 20 SemiParBIVProbit-3.8/SemiParBIVProbit/R/probm.R | 68 - SemiParBIVProbit-3.8/SemiParBIVProbit/R/resp.check.R | 181 ++- SemiParBIVProbit-3.8/SemiParBIVProbit/R/summary.SemiParBIVProbit.r | 173 ++ SemiParBIVProbit-3.8/SemiParBIVProbit/R/summary.SemiParTRIV.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/summary.copulaReg.r | 164 ++ SemiParBIVProbit-3.8/SemiParBIVProbit/R/summary.copulaSampleSel.r | 129 +- SemiParBIVProbit-3.8/SemiParBIVProbit/R/triprobgHs.R | 63 - SemiParBIVProbit-3.8/SemiParBIVProbit/R/triprobgHsSS.r |only SemiParBIVProbit-3.8/SemiParBIVProbit/R/working.comp.r | 4 SemiParBIVProbit-3.8/SemiParBIVProbit/man/AT.Rd | 26 SemiParBIVProbit-3.8/SemiParBIVProbit/man/AT2.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/BCDF.Rd | 3 SemiParBIVProbit-3.8/SemiParBIVProbit/man/H.tri.Rd | 3 SemiParBIVProbit-3.8/SemiParBIVProbit/man/LM.bpm.Rd | 5 SemiParBIVProbit-3.8/SemiParBIVProbit/man/OR.Rd | 22 SemiParBIVProbit-3.8/SemiParBIVProbit/man/RR.Rd | 21 SemiParBIVProbit-3.8/SemiParBIVProbit/man/SemiParBIVProbit-package.Rd | 78 - SemiParBIVProbit-3.8/SemiParBIVProbit/man/SemiParBIVProbit.Rd | 209 --- SemiParBIVProbit-3.8/SemiParBIVProbit/man/SemiParBIVProbit.fit.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/SemiParBIVProbit.fit.post.Rd | 5 SemiParBIVProbit-3.8/SemiParBIVProbit/man/SemiParTRIV.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/man/SemiParTRIVObject.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/man/TRIapprox.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/man/VuongClarke.Rd | 7 SemiParBIVProbit-3.8/SemiParBIVProbit/man/adjCov.Rd | 15 SemiParBIVProbit-3.8/SemiParBIVProbit/man/adjCovSD.Rd | 22 SemiParBIVProbit-3.8/SemiParBIVProbit/man/bcont.Rd | 7 SemiParBIVProbit-3.8/SemiParBIVProbit/man/bdiscrcont.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/man/bdiscrdiscr.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/man/bprobgHs.Rd | 8 SemiParBIVProbit-3.8/SemiParBIVProbit/man/bprobgHsCont.Rd | 8 SemiParBIVProbit-3.8/SemiParBIVProbit/man/bprobgHsContSS.Rd | 8 SemiParBIVProbit-3.8/SemiParBIVProbit/man/bprobgHsContUniv.Rd | 3 SemiParBIVProbit-3.8/SemiParBIVProbit/man/bprobgHsDiscr1.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/man/bprobgHsDiscr1SS.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/man/bprobgHsPO.Rd | 5 SemiParBIVProbit-3.8/SemiParBIVProbit/man/bprobgHsSS.Rd | 7 SemiParBIVProbit-3.8/SemiParBIVProbit/man/conv.check.Rd | 9 SemiParBIVProbit-3.8/SemiParBIVProbit/man/copgHs.Rd | 10 SemiParBIVProbit-3.8/SemiParBIVProbit/man/copulaReg.Rd | 161 ++ SemiParBIVProbit-3.8/SemiParBIVProbit/man/copulaSampleSel.Rd | 63 - SemiParBIVProbit-3.8/SemiParBIVProbit/man/distrHs.Rd | 6 SemiParBIVProbit-3.8/SemiParBIVProbit/man/eta.tr.Rd | 5 SemiParBIVProbit-3.8/SemiParBIVProbit/man/g.tri.Rd | 5 SemiParBIVProbit-3.8/SemiParBIVProbit/man/gt.bpm.Rd | 3 SemiParBIVProbit-3.8/SemiParBIVProbit/man/hiv.Rd | 10 SemiParBIVProbit-3.8/SemiParBIVProbit/man/jc.probs.Rd | 9 SemiParBIVProbit-3.8/SemiParBIVProbit/man/logLik.SemiParBIVProbit.Rd | 10 SemiParBIVProbit-3.8/SemiParBIVProbit/man/meps.Rd | 14 SemiParBIVProbit-3.8/SemiParBIVProbit/man/numgh.Rd | 5 SemiParBIVProbit-3.8/SemiParBIVProbit/man/pen.Rd | 1 SemiParBIVProbit-3.8/SemiParBIVProbit/man/plot.SemiParBIVProbit.Rd | 10 SemiParBIVProbit-3.8/SemiParBIVProbit/man/polys.map.Rd | 1 SemiParBIVProbit-3.8/SemiParBIVProbit/man/polys.setup.Rd | 4 SemiParBIVProbit-3.8/SemiParBIVProbit/man/post.check.Rd | 23 SemiParBIVProbit-3.8/SemiParBIVProbit/man/predict.SemiParBIVProbit.Rd | 9 SemiParBIVProbit-3.8/SemiParBIVProbit/man/prev.Rd | 18 SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.AT.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.AT2.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.OR.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.RR.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.SemiParBIVProbit.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.SemiParTRIV.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.copulaReg.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.copulaSampleSel.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.mb.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/print.prev.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/regH.Rd | 3 SemiParBIVProbit-3.8/SemiParBIVProbit/man/resp.check.Rd | 25 SemiParBIVProbit-3.8/SemiParBIVProbit/man/summary.SemiParBIVProbit.Rd | 3 SemiParBIVProbit-3.8/SemiParBIVProbit/man/summary.SemiParTRIV.Rd |only SemiParBIVProbit-3.8/SemiParBIVProbit/man/summary.copulaReg.Rd | 5 SemiParBIVProbit-3.8/SemiParBIVProbit/man/summary.copulaSampleSel.Rd | 2 SemiParBIVProbit-3.8/SemiParBIVProbit/man/triprobgHs.Rd | 3 180 files changed, 3699 insertions(+), 1716 deletions(-)
More information about SemiParBIVProbit at CRAN
Permanent link
Title: Search and Install Missing Packages
Description: Search R files for not installed packages and run install.packages.
Author: Calli Gross
Maintainer: Calli Gross <calli@calligross.de>
Diff between reinstallr versions 0.1.2 dated 2016-08-13 and 0.1.3 dated 2016-08-18
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- R/reinstallr.R | 2 +- tests/testthat/test_01_show_package_stats.R | 6 +++--- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modelling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete variable
models are supported.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.18 dated 2016-06-24 and 1.19 dated 2016-08-18
DESCRIPTION | 14 - MD5 | 108 ++++---- NAMESPACE | 1 NEWS.md | 42 +++ R/02-item_methods.R | 129 ++++++++++ R/03-estimation.R | 60 ++-- R/Discrete-methods.R | 12 R/EMstep.group.R | 54 +++- R/EMstep.utils.R | 46 ++- R/LoadPars.R | 66 ++++- R/M2.R | 433 ++++++++++++++++++------------------ R/MHRM.group.R | 17 + R/PLCI.mirt.R | 1 R/PrepData.R | 24 + R/SE.methods.R | 33 +- R/SingleGroup-methods.R | 24 + R/bfactor.R | 68 ++++- R/extract.mirt.R | 1 R/fscores.R | 29 ++ R/fscores.internal.R | 64 +++-- R/imputeMissing.R | 16 - R/itemfit.R | 84 +++--- R/mdirt.R | 146 +++++++++++- R/mirt-package.R | 19 - R/mirt.R | 39 ++- R/mirt.model.R | 1 R/mixedmirt.R | 3 R/model.elements.R | 4 R/multipleGroup.R | 27 ++ R/simdata.R | 63 ++++- R/utils.R | 121 +++++++--- R/wald.R | 2 build/vignette.rds |binary man/M2.Rd | 6 man/bfactor.Rd | 65 +++-- man/fscores.Rd | 14 - man/imputeMissing.Rd | 4 man/itemfit.Rd | 13 - man/mdirt.Rd | 148 +++++++++++- man/mirt-package.Rd | 17 - man/mirt.Rd | 37 ++- man/multipleGroup.Rd | 27 ++ man/residuals-method.Rd | 4 man/simdata.Rd | 41 ++- src/Estep.cpp | 53 ++-- src/Estep.h | 6 src/dpars.cpp | 248 +++++++++++++------- src/traceLinePts.cpp | 2 tests/tests/test-01-mirtOne.R | 17 + tests/tests/test-03-bfactor.R | 2 tests/tests/test-04-multipleGroup.R | 33 ++ tests/tests/test-09-mirt.model.R | 2 tests/tests/test-10-extras.R | 2 tests/tests/test-11-discrete.R | 36 ++ tests/tests/test-12-gpcm_mats.R | 6 55 files changed, 1799 insertions(+), 735 deletions(-)
Title: Evaluate Differentially Private Algorithms for Publishing
Cumulative Distribution Functions
Description: Designed by and for the community of differential privacy algorithm developers. It can be used to empirically evaluate and visualize Cumulative Distribution Functions incorporating noise that satisfies differential privacy, with numerous options made to streamline collection of utility measurements across variations of key parameters, such as epsilon, domain size, sample size, data shape, etc. Developed by researchers at Harvard PSI.
Author: Daniel Muise [aut,cre],
Kobbi Nissim [aut],
Georgios Kellaris [aut]
Maintainer: Daniel Muise <dmuise@stanford.edu>
Diff between CDF.PSIdekick versions 1.0 dated 2016-08-12 and 1.1 dated 2016-08-18
DESCRIPTION | 6 MD5 | 6 src/cdf.cpp | 452 +++++++++++++++++++++++++++++---------------------------- src/smooth.cpp | 28 +-- 4 files changed, 256 insertions(+), 236 deletions(-)
Title: Bayesian Structural Time Series
Description: Time series regression using dynamic linear models fit using MCMC.
Author: Steven L. Scott <stevescott@google.com>
Maintainer: Steven L. Scott <stevescott@google.com>
Diff between bsts versions 0.6.4 dated 2016-08-03 and 0.6.5 dated 2016-08-18
DESCRIPTION | 8 +++---- MD5 | 30 ++++++++++++++--------------- R/bsts.R | 2 - R/date.functions.R | 2 - R/mixed.frequency.R | 2 - R/predict.bsts.R | 2 - src/aggregate_time_series.cc | 3 -- src/bsts.cc | 11 +++------- src/mixed_frequency.cc | 5 ---- src/model_manager.h | 6 ++--- src/state_space_gaussian_model_manager.h | 6 ++--- src/state_space_logit_model_manager.h | 6 ++--- src/state_space_poisson_model_manager.h | 6 ++--- src/state_space_regression_model_manager.h | 6 ++--- src/state_space_student_model_manager.h | 6 ++--- src/utils.h | 6 ++--- 16 files changed, 50 insertions(+), 57 deletions(-)
Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scattered points by 3rd dimension,
enhance date- and log-axis plots, zoom in X11 graphics,
use the unit hydrograph in a linear storage cascade, convert lists to data.frames,
fit multiple functions by regression (power, reciprocal, exponential, logarithmic,
polynomial, rational).
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between berryFunctions versions 1.10.0 dated 2016-04-30 and 1.11.0 dated 2016-08-18
berryFunctions-1.10.0/berryFunctions/R/rcor.R |only berryFunctions-1.10.0/berryFunctions/R/require2.R |only berryFunctions-1.10.0/berryFunctions/man/rcor.Rd |only berryFunctions-1.10.0/berryFunctions/man/require2.Rd |only berryFunctions-1.11.0/berryFunctions/DESCRIPTION | 18 berryFunctions-1.11.0/berryFunctions/MD5 | 249 +++++----- berryFunctions-1.11.0/berryFunctions/NAMESPACE | 16 berryFunctions-1.11.0/berryFunctions/NEWS | 26 - berryFunctions-1.11.0/berryFunctions/R/addAlpha.R | 3 berryFunctions-1.11.0/berryFunctions/R/addFade.R | 3 berryFunctions-1.11.0/berryFunctions/R/anhang.R |only berryFunctions-1.11.0/berryFunctions/R/approx2.R | 32 - berryFunctions-1.11.0/berryFunctions/R/berryFunctions-package.R | 4 berryFunctions-1.11.0/berryFunctions/R/betaPlot.R | 3 berryFunctions-1.11.0/berryFunctions/R/betaPlotComp.R | 2 berryFunctions-1.11.0/berryFunctions/R/checkFile.R |only berryFunctions-1.11.0/berryFunctions/R/ci.R | 1 berryFunctions-1.11.0/berryFunctions/R/ciBand.R | 1 berryFunctions-1.11.0/berryFunctions/R/cie.R | 2 berryFunctions-1.11.0/berryFunctions/R/circle.R | 2 berryFunctions-1.11.0/berryFunctions/R/classify.R | 9 berryFunctions-1.11.0/berryFunctions/R/climateGraph.R | 7 berryFunctions-1.11.0/berryFunctions/R/cls.R | 2 berryFunctions-1.11.0/berryFunctions/R/colPoints.R | 157 ++++-- berryFunctions-1.11.0/berryFunctions/R/colPointsHist.R | 1 berryFunctions-1.11.0/berryFunctions/R/colPointsLegend.R | 52 +- berryFunctions-1.11.0/berryFunctions/R/combineFiles.R | 3 berryFunctions-1.11.0/berryFunctions/R/compareFiles.R | 2 berryFunctions-1.11.0/berryFunctions/R/createFun.R | 3 berryFunctions-1.11.0/berryFunctions/R/dataDWD.R |only berryFunctions-1.11.0/berryFunctions/R/dataStr.R | 1 berryFunctions-1.11.0/berryFunctions/R/distance.R | 40 + berryFunctions-1.11.0/berryFunctions/R/divPal.R | 1 berryFunctions-1.11.0/berryFunctions/R/dupes.R | 1 berryFunctions-1.11.0/berryFunctions/R/exTime.R |only berryFunctions-1.11.0/berryFunctions/R/exp4p.R | 2 berryFunctions-1.11.0/berryFunctions/R/expReg.R | 3 berryFunctions-1.11.0/berryFunctions/R/funSource.R | 1 berryFunctions-1.11.0/berryFunctions/R/funTinn.R | 2 berryFunctions-1.11.0/berryFunctions/R/funnelPlot.R | 2 berryFunctions-1.11.0/berryFunctions/R/googleLink2pdf.R | 1 berryFunctions-1.11.0/berryFunctions/R/groupHist.R | 13 berryFunctions-1.11.0/berryFunctions/R/headtail.R | 28 - berryFunctions-1.11.0/berryFunctions/R/horizHist.R | 1 berryFunctions-1.11.0/berryFunctions/R/insertRows.R | 25 - berryFunctions-1.11.0/berryFunctions/R/instGit.R | 1 berryFunctions-1.11.0/berryFunctions/R/is.error.R |only berryFunctions-1.11.0/berryFunctions/R/l2df.R | 9 berryFunctions-1.11.0/berryFunctions/R/library2.R |only berryFunctions-1.11.0/berryFunctions/R/linLogHist.R | 1 berryFunctions-1.11.0/berryFunctions/R/linLogTrans.R | 1 berryFunctions-1.11.0/berryFunctions/R/linReg.R | 2 berryFunctions-1.11.0/berryFunctions/R/locArrow.R |only berryFunctions-1.11.0/berryFunctions/R/locLine.R | 3 berryFunctions-1.11.0/berryFunctions/R/logAxis.R | 8 berryFunctions-1.11.0/berryFunctions/R/logHist.R | 23 berryFunctions-1.11.0/berryFunctions/R/logSpaced.R | 2 berryFunctions-1.11.0/berryFunctions/R/lsMem.R | 1 berryFunctions-1.11.0/berryFunctions/R/lsc.R | 4 berryFunctions-1.11.0/berryFunctions/R/mReg.R | 9 berryFunctions-1.11.0/berryFunctions/R/monthAxis.R | 89 ++- berryFunctions-1.11.0/berryFunctions/R/movAv.R | 3 berryFunctions-1.11.0/berryFunctions/R/movAvLines.R | 1 berryFunctions-1.11.0/berryFunctions/R/na9.R | 27 - berryFunctions-1.11.0/berryFunctions/R/nameSample.R | 1 berryFunctions-1.11.0/berryFunctions/R/normPlot.R | 3 berryFunctions-1.11.0/berryFunctions/R/nse.R | 2 berryFunctions-1.11.0/berryFunctions/R/panelDim.R | 1 berryFunctions-1.11.0/berryFunctions/R/pastec.R | 5 berryFunctions-1.11.0/berryFunctions/R/pointZoom.R | 5 berryFunctions-1.11.0/berryFunctions/R/pretty2.R | 1 berryFunctions-1.11.0/berryFunctions/R/quantileBands.R | 4 berryFunctions-1.11.0/berryFunctions/R/quantileMean.R | 1 berryFunctions-1.11.0/berryFunctions/R/rainbow2.R | 1 berryFunctions-1.11.0/berryFunctions/R/randomPoints.R | 5 berryFunctions-1.11.0/berryFunctions/R/readDWD.R |only berryFunctions-1.11.0/berryFunctions/R/removeSpace.R | 6 berryFunctions-1.11.0/berryFunctions/R/rmse.R | 2 berryFunctions-1.11.0/berryFunctions/R/rsquare.R | 3 berryFunctions-1.11.0/berryFunctions/R/runAxis.R |only berryFunctions-1.11.0/berryFunctions/R/seasonality.R |only berryFunctions-1.11.0/berryFunctions/R/seqPal.R | 4 berryFunctions-1.11.0/berryFunctions/R/seqR.R | 2 berryFunctions-1.11.0/berryFunctions/R/showPal.R | 12 berryFunctions-1.11.0/berryFunctions/R/smallPlot.R | 87 ++- berryFunctions-1.11.0/berryFunctions/R/smoothLines.R | 1 berryFunctions-1.11.0/berryFunctions/R/spiralDate.R |only berryFunctions-1.11.0/berryFunctions/R/spiralDateAnim.R |only berryFunctions-1.11.0/berryFunctions/R/tableColVal.R | 2 berryFunctions-1.11.0/berryFunctions/R/textField.R | 9 berryFunctions-1.11.0/berryFunctions/R/timer.R | 1 berryFunctions-1.11.0/berryFunctions/R/toupper1.R |only berryFunctions-1.11.0/berryFunctions/R/triangleArea.R | 1 berryFunctions-1.11.0/berryFunctions/R/unitHydrograph.R | 11 berryFunctions-1.11.0/berryFunctions/build/vignette.rds |binary berryFunctions-1.11.0/berryFunctions/inst/doc/berryFunctions.R | 6 berryFunctions-1.11.0/berryFunctions/inst/doc/berryFunctions.Rmd | 20 berryFunctions-1.11.0/berryFunctions/inst/doc/berryFunctions.html | 70 +- berryFunctions-1.11.0/berryFunctions/inst/extdata/discharge39072.csv |only berryFunctions-1.11.0/berryFunctions/inst/extdata/solitaire.txt | 13 berryFunctions-1.11.0/berryFunctions/man/anhang.Rd |only berryFunctions-1.11.0/berryFunctions/man/approx2.Rd | 16 berryFunctions-1.11.0/berryFunctions/man/checkFile.Rd |only berryFunctions-1.11.0/berryFunctions/man/climateGraph.Rd | 6 berryFunctions-1.11.0/berryFunctions/man/colPoints.Rd | 88 ++- berryFunctions-1.11.0/berryFunctions/man/colPointsLegend.Rd | 23 berryFunctions-1.11.0/berryFunctions/man/combineFiles.Rd | 2 berryFunctions-1.11.0/berryFunctions/man/dataDWD.Rd |only berryFunctions-1.11.0/berryFunctions/man/distance.Rd | 12 berryFunctions-1.11.0/berryFunctions/man/exTime.Rd |only berryFunctions-1.11.0/berryFunctions/man/funTinn.Rd | 2 berryFunctions-1.11.0/berryFunctions/man/groupHist.Rd | 4 berryFunctions-1.11.0/berryFunctions/man/headtail.Rd | 27 - berryFunctions-1.11.0/berryFunctions/man/insertRows.Rd | 11 berryFunctions-1.11.0/berryFunctions/man/is.error.Rd |only berryFunctions-1.11.0/berryFunctions/man/l2df.Rd | 6 berryFunctions-1.11.0/berryFunctions/man/library2.Rd |only berryFunctions-1.11.0/berryFunctions/man/locArrow.Rd |only berryFunctions-1.11.0/berryFunctions/man/locLine.Rd | 2 berryFunctions-1.11.0/berryFunctions/man/logAxis.Rd | 8 berryFunctions-1.11.0/berryFunctions/man/logHist.Rd | 14 berryFunctions-1.11.0/berryFunctions/man/lsc.Rd | 2 berryFunctions-1.11.0/berryFunctions/man/mReg.Rd | 4 berryFunctions-1.11.0/berryFunctions/man/monthAxis.Rd | 36 + berryFunctions-1.11.0/berryFunctions/man/na9.Rd | 15 berryFunctions-1.11.0/berryFunctions/man/pastec.Rd | 4 berryFunctions-1.11.0/berryFunctions/man/pointZoom.Rd | 2 berryFunctions-1.11.0/berryFunctions/man/randomPoints.Rd | 2 berryFunctions-1.11.0/berryFunctions/man/readDWD.Rd |only berryFunctions-1.11.0/berryFunctions/man/removeSpace.Rd | 6 berryFunctions-1.11.0/berryFunctions/man/runAxis.Rd |only berryFunctions-1.11.0/berryFunctions/man/seasonality.Rd |only berryFunctions-1.11.0/berryFunctions/man/seqPal.Rd | 4 berryFunctions-1.11.0/berryFunctions/man/showPal.Rd | 4 berryFunctions-1.11.0/berryFunctions/man/smallPlot.Rd | 79 ++- berryFunctions-1.11.0/berryFunctions/man/spiralDate.Rd |only berryFunctions-1.11.0/berryFunctions/man/spiralDateAnim.Rd |only berryFunctions-1.11.0/berryFunctions/man/textField.Rd | 8 berryFunctions-1.11.0/berryFunctions/man/toupper1.Rd |only berryFunctions-1.11.0/berryFunctions/man/unitHydrograph.Rd | 4 berryFunctions-1.11.0/berryFunctions/vignettes/berryFunctions.Rmd | 20 141 files changed, 1026 insertions(+), 567 deletions(-)
More information about berryFunctions at CRAN
Permanent link
Title: Capture the Spirit of Your 'ggplot2' Calls
Description: Creates a reproducible 'ggplot2' object by storing the data and calls.
Author: Jonathan Carroll [aut, cre]
Maintainer: Jonathan Carroll <rpkg@jcarroll.com.au>
Diff between ggghost versions 0.1.0 dated 2016-08-07 and 0.2.0 dated 2016-08-18
ggghost-0.1.0/ggghost/inst |only ggghost-0.2.0/ggghost/DESCRIPTION | 7 - ggghost-0.2.0/ggghost/MD5 | 44 +++---- ggghost-0.2.0/ggghost/NAMESPACE | 2 ggghost-0.2.0/ggghost/NEWS.md |only ggghost-0.2.0/ggghost/R/ghost.R | 127 +++++++++++++++++++---- ggghost-0.2.0/ggghost/README.md | 107 +++++++++++-------- ggghost-0.2.0/ggghost/man/identify_data.Rd | 2 ggghost-0.2.0/ggghost/man/is.ggghost.Rd | 4 ggghost-0.2.0/ggghost/man/minus-ggghost.Rd | 2 ggghost-0.2.0/ggghost/man/print.ggghost.Rd | 4 ggghost-0.2.0/ggghost/man/reanimate.Rd | 2 ggghost-0.2.0/ggghost/man/recover_data.Rd | 22 ++- ggghost-0.2.0/ggghost/man/subset.ggghost.Rd | 2 ggghost-0.2.0/ggghost/man/summary.ggghost.Rd | 2 ggghost-0.2.0/ggghost/man/supp_data-set.Rd |only ggghost-0.2.0/ggghost/man/supp_data.Rd |only ggghost-0.2.0/ggghost/tests/testthat/Rplots.pdf |binary ggghost-0.2.0/ggghost/tests/testthat/test_data.R | 46 ++++++++ 19 files changed, 269 insertions(+), 104 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre],
David Meyer [aut],
Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between slam versions 0.1-37 dated 2016-08-05 and 0.1-38 dated 2016-08-18
DESCRIPTION | 8 +++--- MD5 | 22 ++++++++++-------- NAMESPACE | 3 ++ R/array.R | 19 ++++++++++----- R/matrix.R | 55 +++++++++++++++++++++++++++++++--------------- R/misc.R |only R/subassign.R | 28 +++++++++-------------- man/array.Rd | 5 +++- man/options.Rd |only tests/extract.R | 11 +++++++++ tests/extract.Rout.save | 26 +++++++++++++++++---- tests/subassign.R | 6 +++++ tests/subassign.Rout.save | 15 ++++++++++-- 13 files changed, 134 insertions(+), 64 deletions(-)
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized ML estimators for the
precision matrix as well as supporting functions to employ these estimators
in a graphical modeling setting.
Author: Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]
Maintainer: Carel F.W. Peeters <cf.peeters@vumc.nl>
Diff between rags2ridges versions 2.1 dated 2016-08-12 and 2.1.1 dated 2016-08-18
DESCRIPTION | 6 ++--- MD5 | 16 ++++++------- R/rags2ridges.R | 49 ++++++++++++++++++++++++++++++---------- README.md | 17 +++++++------- inst/CITATION | 54 +++++++++++++++++++++++++++++---------------- inst/NEWS.Rd | 15 ++++++++++++ man/CNplot.Rd | 2 - man/rags2ridges-package.Rd | 3 +- man/sparsify.Rd | 35 +++++++++++++++-------------- 9 files changed, 128 insertions(+), 69 deletions(-)
Title: Exponentiation Operations
Description: Computation of matrix and scalar exponentiation.
Author: Albert Dorador
Maintainer: Albert Dorador <albert.dorador@estudiant.upc.edu>
Diff between powerplus versions 2.0 dated 2016-07-14 and 3.0 dated 2016-08-18
powerplus-2.0/powerplus/R/MatpowV2.R |only powerplus-2.0/powerplus/man/MatpowV2.Rd |only powerplus-2.0/powerplus/man/explusV2.Rd |only powerplus-3.0/powerplus/DESCRIPTION | 13 ++-- powerplus-3.0/powerplus/MD5 | 12 ++-- powerplus-3.0/powerplus/NAMESPACE | 12 ++-- powerplus-3.0/powerplus/R/MatpowV3.R |only powerplus-3.0/powerplus/R/explusV2.R | 96 +++++++++++++++++++++++++------- powerplus-3.0/powerplus/man/Matpow.Rd |only powerplus-3.0/powerplus/man/explus.Rd |only 10 files changed, 96 insertions(+), 37 deletions(-)
Title: Hyper-Ensemble Smote Undersampled Random Forests
Description: Machine learning supervised method to learn rare genomic features in imbalanced genetic data sets. This method can be also applied to classify or rank examples characterized by a high imbalance between the minority and majority class. hyperSMURF adopts a hyper-ensemble (ensemble of ensembles) approach, undersampling of the majority class and oversampling of the minority class to learn highly imbalanced data. Both single-core and parallel multi-core version of hyperSMURF are implemented.
Author: Giorgio Valentini [aut, cre] - AnacletoLab, Dipartimento di Informatica, Universita' degli Studi di Milano;
Max Schubach [ctb] - Charite, Universitatsmedizin Berlin;
Matteo Re [ctb] - AnacletoLab, Dipartimento di Informatica, Universita' degli Studi di Milano;
Peter N Robinson [ctb] - The Jackson Laboratory for Genomic Medicine, Farmington CT, USA.
Maintainer: Giorgio Valentini <valentini@di.unimi.it>
Diff between hyperSMURF versions 1.0 dated 2016-08-11 and 1.1.2 dated 2016-08-18
hyperSMURF-1.0/hyperSMURF/R/hyperSMURF1.0.R |only hyperSMURF-1.1.2/hyperSMURF/DESCRIPTION | 12 ++-- hyperSMURF-1.1.2/hyperSMURF/MD5 | 30 +++++----- hyperSMURF-1.1.2/hyperSMURF/NAMESPACE | 2 hyperSMURF-1.1.2/hyperSMURF/R/hyperSMURF1.1.R |only hyperSMURF-1.1.2/hyperSMURF/build/partial.rdb |binary hyperSMURF-1.1.2/hyperSMURF/inst/doc/hyperSMURF-manual.pdf |binary hyperSMURF-1.1.2/hyperSMURF/man/do.stratified.cv.data.Rd | 2 hyperSMURF-1.1.2/hyperSMURF/man/hyperSMURF.corr.cv.parallel.Rd | 15 ++--- hyperSMURF-1.1.2/hyperSMURF/man/hyperSMURF.cv.Rd | 6 +- hyperSMURF-1.1.2/hyperSMURF/man/hyperSMURF.cv.parallel.Rd | 14 ++-- hyperSMURF-1.1.2/hyperSMURF/man/hyperSMURF.test.Rd | 2 hyperSMURF-1.1.2/hyperSMURF/man/hyperSMURF.test.parallel.Rd | 18 ++---- hyperSMURF-1.1.2/hyperSMURF/man/hyperSMURF.test.thresh.Rd | 14 ++-- hyperSMURF-1.1.2/hyperSMURF/man/hyperSMURF.train.Rd | 6 +- hyperSMURF-1.1.2/hyperSMURF/man/hyperSMURF.train.parallel.Rd | 13 ++-- hyperSMURF-1.1.2/hyperSMURF/man/imbalanced.data.generator.Rd | 6 +- 17 files changed, 68 insertions(+), 72 deletions(-)
Title: Lightweight GitHub Package Installer
Description: A lightweight, vectorized drop-in replacement for
'devtools::install_github()' that uses native git and R methods to clone and
install a package from GitHub.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between ghit versions 0.2.10 dated 2016-07-26 and 0.2.12 dated 2016-08-18
ghit-0.2.10/ghit/man/install.Rd |only ghit-0.2.12/ghit/DESCRIPTION | 17 ++++---- ghit-0.2.12/ghit/MD5 | 19 ++++---- ghit-0.2.12/ghit/NAMESPACE | 17 ++++++-- ghit-0.2.12/ghit/NEWS | 6 ++ ghit-0.2.12/ghit/R/build_and_insert.R | 14 ++++++ ghit-0.2.12/ghit/R/checkout_github.R | 2 ghit-0.2.12/ghit/R/ghit-packages.R |only ghit-0.2.12/ghit/R/install.R | 53 ++++++++++++++++++++++--- ghit-0.2.12/ghit/man/ghit.Rd | 7 ++- ghit-0.2.12/ghit/man/install_github.Rd |only ghit-0.2.12/ghit/tests/testthat/test_install.R | 21 +++------ 12 files changed, 114 insertions(+), 42 deletions(-)
Title: Structural Equation Modelling in R with 'OpenMx'
Description: Create, run, and report structural equation and twin models quickly.
If you're just starting out, try typing '?umx'.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.2.7 dated 2016-05-06 and 1.3.0 dated 2016-08-18
umx-1.2.7/umx/man/umx_RAM_ordinal_objective.Rd |only umx-1.2.7/umx/man/umx_sql_from_excel.Rd |only umx-1.3.0/umx/DESCRIPTION | 10 umx-1.3.0/umx/MD5 | 231 +- umx-1.3.0/umx/NAMESPACE | 13 umx-1.3.0/umx/NEWS | 48 umx-1.3.0/umx/R/build_run_modify.r | 1578 ++++++++-------- umx-1.3.0/umx/R/fit_and_reporting.r | 294 +- umx-1.3.0/umx/R/misc_and_utility.r | 737 +++++-- umx-1.3.0/umx/R/model_builders.r | 4 umx-1.3.0/umx/R/mxSE.R |only umx-1.3.0/umx/R/xmu.r | 137 + umx-1.3.0/umx/inst/extdata |only umx-1.3.0/umx/man/dl_from_dropbox.Rd | 6 umx-1.3.0/umx/man/figures/ACE.png |binary umx-1.3.0/umx/man/figures/ACEcov.png |binary umx-1.3.0/umx/man/figures/Bivariate_GxE.png |only umx-1.3.0/umx/man/figures/CP.png |binary umx-1.3.0/umx/man/figures/GxE.png |binary umx-1.3.0/umx/man/figures/IP.png |binary umx-1.3.0/umx/man/figures/umx_help_figures.graffle |binary umx-1.3.0/umx/man/getOpenMx.Rd | 3 umx-1.3.0/umx/man/loadings.MxModel.Rd | 9 umx-1.3.0/umx/man/mxSE.Rd |only umx-1.3.0/umx/man/plot.MxModel.Rd | 7 umx-1.3.0/umx/man/umx-deprecated.Rd | 4 umx-1.3.0/umx/man/umx.Rd | 18 umx-1.3.0/umx/man/umxACE.Rd | 43 umx-1.3.0/umx/man/umxACEcov.Rd | 22 umx-1.3.0/umx/man/umxAPA.Rd | 26 umx-1.3.0/umx/man/umxCP.Rd | 2 umx-1.3.0/umx/man/umxDiagnose.Rd | 5 umx-1.3.0/umx/man/umxEFA.Rd | 1 umx-1.3.0/umx/man/umxFactor.Rd | 41 umx-1.3.0/umx/man/umxGxE_window.Rd | 7 umx-1.3.0/umx/man/umxIP.Rd | 3 umx-1.3.0/umx/man/umxJiggle.Rd | 3 umx-1.3.0/umx/man/umxLabel.Rd | 5 umx-1.3.0/umx/man/umxLatent.Rd | 5 umx-1.3.0/umx/man/umxModify.Rd | 5 umx-1.3.0/umx/man/umxPath.Rd | 31 umx-1.3.0/umx/man/umxPlotACE.Rd | 8 umx-1.3.0/umx/man/umxPlotACEcov.Rd | 10 umx-1.3.0/umx/man/umxPlotCP.Rd | 8 umx-1.3.0/umx/man/umxPlotIP.Rd | 8 umx-1.3.0/umx/man/umxRAM.Rd | 15 umx-1.3.0/umx/man/umxRAM2Ordinal.Rd |only umx-1.3.0/umx/man/umxRun.Rd | 3 umx-1.3.0/umx/man/umxSummary.MxModel.Rd | 16 umx-1.3.0/umx/man/umxSummaryACE.Rd | 8 umx-1.3.0/umx/man/umxSummaryACEcov.Rd | 16 umx-1.3.0/umx/man/umxSummaryCP.Rd | 18 umx-1.3.0/umx/man/umxSummaryGxE.Rd | 4 umx-1.3.0/umx/man/umxSummaryIP.Rd | 7 umx-1.3.0/umx/man/umxThresholdMatrix.Rd | 96 umx-1.3.0/umx/man/umxValues.Rd | 4 umx-1.3.0/umx/man/umx_APA_pval.Rd | 7 umx-1.3.0/umx/man/umx_aggregate.Rd | 9 umx-1.3.0/umx/man/umx_apply.Rd | 6 umx-1.3.0/umx/man/umx_check.Rd | 1 umx-1.3.0/umx/man/umx_check_OS.Rd | 1 umx-1.3.0/umx/man/umx_check_model.Rd | 1 umx-1.3.0/umx/man/umx_check_names.Rd | 8 umx-1.3.0/umx/man/umx_check_parallel.Rd | 10 umx-1.3.0/umx/man/umx_explode_twin_names.Rd |only umx-1.3.0/umx/man/umx_fix_first_loadings.Rd | 4 umx-1.3.0/umx/man/umx_fix_latents.Rd | 4 umx-1.3.0/umx/man/umx_get_checkpoint.Rd | 4 umx-1.3.0/umx/man/umx_get_cores.Rd | 12 umx-1.3.0/umx/man/umx_get_optimizer.Rd | 12 umx-1.3.0/umx/man/umx_get_options.Rd |only umx-1.3.0/umx/man/umx_grep.Rd | 2 umx-1.3.0/umx/man/umx_has_CIs.Rd | 1 umx-1.3.0/umx/man/umx_has_been_run.Rd | 1 umx-1.3.0/umx/man/umx_has_means.Rd | 1 umx-1.3.0/umx/man/umx_has_square_brackets.Rd | 2 umx-1.3.0/umx/man/umx_is_MxData.Rd |only umx-1.3.0/umx/man/umx_is_MxMatrix.Rd | 1 umx-1.3.0/umx/man/umx_is_MxModel.Rd | 10 umx-1.3.0/umx/man/umx_is_RAM.Rd | 1 umx-1.3.0/umx/man/umx_is_cov.Rd | 1 umx-1.3.0/umx/man/umx_is_endogenous.Rd | 1 umx-1.3.0/umx/man/umx_is_exogenous.Rd | 1 umx-1.3.0/umx/man/umx_is_ordered.Rd | 1 umx-1.3.0/umx/man/umx_make_sql_from_excel.Rd |only umx-1.3.0/umx/man/umx_move_file.Rd | 3 umx-1.3.0/umx/man/umx_msg.Rd | 2 umx-1.3.0/umx/man/umx_names.Rd | 3 umx-1.3.0/umx/man/umx_open.Rd | 4 umx-1.3.0/umx/man/umx_pad.Rd |only umx-1.3.0/umx/man/umx_paste_names.Rd | 7 umx-1.3.0/umx/man/umx_print.Rd | 7 umx-1.3.0/umx/man/umx_rename_file.Rd | 3 umx-1.3.0/umx/man/umx_scale.Rd | 2 umx-1.3.0/umx/man/umx_set_auto_plot.Rd | 2 umx-1.3.0/umx/man/umx_set_auto_run.Rd | 2 umx-1.3.0/umx/man/umx_set_checkpoint.Rd | 2 umx-1.3.0/umx/man/umx_set_condensed_slots.Rd | 2 umx-1.3.0/umx/man/umx_set_cores.Rd | 2 umx-1.3.0/umx/man/umx_set_optimizer.Rd | 2 umx-1.3.0/umx/man/umx_set_plot_format.Rd | 2 umx-1.3.0/umx/man/umx_set_table_format.Rd | 3 umx-1.3.0/umx/man/umx_show.Rd | 9 umx-1.3.0/umx/man/umx_standardize_ACE.Rd | 3 umx-1.3.0/umx/man/umx_standardize_ACEcov.Rd | 5 umx-1.3.0/umx/man/umx_standardize_CP.Rd | 3 umx-1.3.0/umx/man/umx_standardize_IP.Rd | 3 umx-1.3.0/umx/man/umx_time.Rd | 11 umx-1.3.0/umx/man/xmuHasSquareBrackets.Rd | 4 umx-1.3.0/umx/man/xmuLabel_MATRIX_Model.Rd | 4 umx-1.3.0/umx/man/xmuLabel_Matrix.Rd | 4 umx-1.3.0/umx/man/xmuLabel_RAM_Model.Rd | 4 umx-1.3.0/umx/man/xmuMI.Rd | 4 umx-1.3.0/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 4 umx-1.3.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 4 umx-1.3.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 4 umx-1.3.0/umx/man/xmuMaxLevels.Rd | 13 umx-1.3.0/umx/man/xmuMinLevels.Rd | 13 umx-1.3.0/umx/man/xmuPropagateLabels.Rd | 4 umx-1.3.0/umx/man/xmu_check_levels_identical.Rd |only umx-1.3.0/umx/man/xmu_dot_make_paths.Rd | 4 umx-1.3.0/umx/man/xmu_dot_make_residuals.Rd | 4 umx-1.3.0/umx/man/xmu_start_value_list.Rd | 4 123 files changed, 2331 insertions(+), 1446 deletions(-)
Title: Meta-Analysis using Structural Equation Modeling
Description: A collection of functions for conducting meta-analysis using a
structural equation modeling (SEM) approach via the 'OpenMx' package.
It also implements the two-stage SEM approach to conduct meta-analytic
structural equation modeling on correlation and covariance matrices.
Author: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Maintainer: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Diff between metaSEM versions 0.9.8 dated 2016-04-19 and 0.9.10 dated 2016-08-18
DESCRIPTION | 13 +++--- MD5 | 84 ++++++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS | 15 +++++++ R/impliedSigma.R |only R/is.pd.R | 65 +++++++++++++++++----------------- R/lavaan2RAM.R | 6 +-- R/summary.R | 15 +++++++ R/tssem.R | 26 ++++++++++--- README.md |only build |only data/Aloe14.rda |binary data/BCG.rda |binary data/Becker09.rda |binary data/Becker83.rda |binary data/Becker92.rda |binary data/Becker94.rda |binary data/Berkey98.rda |binary data/Bornmann07.rda |binary data/Cheung00.rda |binary data/Cheung09.rda |binary data/Cooper03.rda |binary data/Digman97.rda |binary data/HedgesOlkin85.rda |binary data/Hox02.rda |binary data/Hunter83.rda |binary data/Jaramillo05.rda |binary data/Mak09.rda |binary data/Norton13.rda |binary data/Roorda11.rda |binary data/issp05.rda |binary data/issp89.rda |binary data/wvs94a.rda |binary data/wvs94b.rda |binary inst/doc/Examples.html |only inst/doc/Examples.html.asis |only inst/doc/metaSEM.pdf |binary inst/doc/metaSEM.pdf.asis |only man/Cheung00.Rd | 4 +- man/VarCorr.Rd |only man/impliedSigma.Rd |only man/is.pd.Rd | 6 +-- man/metaSEM-package.Rd | 9 ++-- man/print.Rd | 14 ++++--- man/wls.Rd | 6 +-- man/wvs94b.Rd | 4 +- vignettes |only 47 files changed, 162 insertions(+), 106 deletions(-)
Title: Correspondence Analysis Variants
Description: Provides six variants of two-way correspondence analysis (ca):
simple ca, singly ordered ca, doubly ordered ca, non-symmetrical ca,
singly ordered non symmetrical ca, and doubly ordered non symmetrical
ca.
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo <rosaria.lombardo@unina2.it>
Diff between CAvariants versions 3.1 dated 2016-02-11 and 3.2 dated 2016-08-18
DESCRIPTION | 9 - MD5 | 84 +++++----- NAMESPACE | 2 R/CAvariants.R | 171 +++++++++++++------- R/cabasic.R | 6 R/caellipse.R | 28 +-- R/compsonetable.exe.R | 33 ++-- R/compstable.exe.R | 62 +++---- R/docabasic.R | 7 R/donscabasic.R | 6 R/nscabasic.R | 4 R/nscaellipse.R | 21 +- R/plot.CAvariants.R | 83 +++++----- R/plotone.R | 18 -- R/print.CAvariants.R | 90 +++++----- R/socabasic.R | 6 R/sonscabasic.R | 5 R/summary.CAvariants.R | 53 +++--- data/asbestos.rda |binary data/shopdataM.rda |binary man/CAvariants.Rd | 362 +++++++++++--------------------------------- man/angle.Rd | 5 man/asbestos.Rd | 4 man/cabasic.Rd | 66 -------- man/cabasicresults-class.Rd | 77 +-------- man/caellipse.Rd | 51 ++---- man/compsonetable.exe.Rd | 50 ------ man/compstable.exe.Rd | 64 ------- man/docabasic.Rd | 73 -------- man/donscabasic.Rd | 73 -------- man/ellipse.Rd | 18 -- man/emerson.poly.Rd | 54 ------ man/nscabasic.Rd | 62 ------- man/nscaellipse.Rd | 64 +++---- man/plot.CAvariants.Rd | 108 +++++-------- man/plotone.Rd | 47 +---- man/print.CAvariants.Rd | 132 +++++++--------- man/printwithaxes.Rd | 29 --- man/shopdataM.Rd | 2 man/socabasic.Rd | 68 -------- man/sonscabasic.Rd | 77 +-------- man/summary.CAvariants.Rd | 47 ++--- man/trendplot.Rd | 54 ------ 43 files changed, 743 insertions(+), 1532 deletions(-)
Title: Extract Statistics from Articles and Recompute p Values
Description: Extract statistics from articles and recompute p values.
Author: Sacha Epskamp <mail@sachaepskamp.com> & Michele B. Nuijten
<m.b.nuijten@uvt.nl>
Maintainer: Michele B. Nuijten <m.b.nuijten@uvt.nl>
Diff between statcheck versions 1.0.1 dated 2015-02-04 and 1.2.2 dated 2016-08-18
DESCRIPTION | 13 +- MD5 | 36 ++++---- NAMESPACE | 8 + R/PDFimport.R | 2 R/checkdir.R | 50 +++++++---- R/htmlImport.R | 13 ++ R/identify.statcheck.R | 2 R/plot.statcheck.R | 203 +++++++++++++++++++++++++++++++++------------- R/statcheck.R | 77 ++++++++--------- README | 2 man/checkHTML.Rd | 3 man/checkHTMLdir.Rd | 133 ++++++++++++++++++++---------- man/checkPDF.Rd | 3 man/checkPDFdir.Rd | 3 man/checkdir.Rd | 3 man/identify.statcheck.Rd | 3 man/plot.statcheck.Rd | 65 ++++++++++---- man/statcheck.Rd | 34 +++---- man/summary.statcheck.Rd | 3 19 files changed, 427 insertions(+), 229 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>
Diff between NNS versions 0.1.9.4 dated 2016-07-30 and 0.2.0 dated 2016-08-18
NNS-0.1.9.4/NNS/R/ARMA_Regression.R |only NNS-0.1.9.4/NNS/man/VN.ARMA.reg.Rd |only NNS-0.2.0/NNS/DESCRIPTION | 8 NNS-0.2.0/NNS/MD5 | 55 +-- NNS-0.2.0/NNS/NAMESPACE | 7 NNS-0.2.0/NNS/R/ANOVA.R | 26 + NNS-0.2.0/NNS/R/ARMA.R | 8 NNS-0.2.0/NNS/R/Binary_ANOVA.R | 26 - NNS-0.2.0/NNS/R/Causation.R | 8 NNS-0.2.0/NNS/R/Classifier.R | 377 +++------------------- NNS-0.2.0/NNS/R/Correlation.R | 56 +-- NNS-0.2.0/NNS/R/Dependence.R | 70 +--- NNS-0.2.0/NNS/R/Feature_probability.R | 2 NNS-0.2.0/NNS/R/Nonlinear_FWL.R |only NNS-0.2.0/NNS/R/Normalization.R | 9 NNS-0.2.0/NNS/R/Numerical_Differentiation.R |only NNS-0.2.0/NNS/R/Partial_Moments.R | 2 NNS-0.2.0/NNS/R/Partition_Map.R | 66 +++ NNS-0.2.0/NNS/R/Regression.R | 463 ++++++++-------------------- NNS-0.2.0/NNS/R/dy_dx.R |only NNS-0.2.0/NNS/man/Feature.probability.Rd | 2 NNS-0.2.0/NNS/man/Finite.step.Rd |only NNS-0.2.0/NNS/man/NNS.FWL.Rd |only NNS-0.2.0/NNS/man/NNS.diff.Rd |only NNS-0.2.0/NNS/man/VN.ANOVA.Rd | 7 NNS-0.2.0/NNS/man/VN.ANOVA.bin.Rd | 4 NNS-0.2.0/NNS/man/VN.ARMA.Rd | 2 NNS-0.2.0/NNS/man/VN.class.Rd | 4 NNS-0.2.0/NNS/man/VN.dep.Rd | 9 NNS-0.2.0/NNS/man/VN.norm.Rd | 4 NNS-0.2.0/NNS/man/VN.reg.Rd | 19 - NNS-0.2.0/NNS/man/dy.dx.Rd |only NNS-0.2.0/NNS/man/partition.map.Rd | 6 33 files changed, 420 insertions(+), 820 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh
(2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller
(2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al.
(2008, <doi:10.1214/07-AOS517>); Jiang et al.
(2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre],
Samuel Mueller [aut],
Alan Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between mplot versions 0.7.8 dated 2016-08-16 and 0.7.9 dated 2016-08-18
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/vis.R | 12 ++++++------ 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 2.4 dated 2016-07-10 and 2.5 dated 2016-08-18
DESCRIPTION | 8 - MD5 | 62 +++++------ NAMESPACE | 1 NEWS | 15 ++ R/DJL-internal.R | 251 +++++++++++++++++++++++----------------------- R/dm.ddf.R | 123 ++++++++++++---------- R/dm.dea.R | 129 +++++++++++++---------- R/dm.hdf.R |only R/dm.mahalanobis.R | 89 ++++++++-------- R/dm.sbm.R | 213 ++++++++++++++++++++++----------------- R/dm.sf.R | 118 ++++++++++++--------- R/map.corr.R | 130 +++++++++++++++-------- R/map.soa.ddf.R | 99 +++++++++--------- R/map.soa.sf.R | 98 +++++++++-------- R/roc.sf.R | 136 ++++++++++++++---------- R/target.arrival.sf.R | 112 +++++++++++--------- man/dm.ddf.Rd | 19 +-- man/dm.dea.Rd | 19 +-- man/dm.hdf.Rd |only man/dm.mahalanobis.Rd | 8 - man/dm.sbm.Rd | 26 ++-- man/dm.sf.Rd | 22 ++-- man/ma.aps.reg.Rd | 8 - man/map.corr.Rd | 4 man/map.soa.ddf.Rd | 19 +-- man/map.soa.dea.Rd | 12 +- man/map.soa.sbm.Rd | 12 +- man/map.soa.sf.Rd | 21 ++- man/roc.dea.Rd | 28 ++--- man/roc.sf.Rd | 21 ++- man/target.arrival.dea.Rd | 10 - man/target.arrival.sf.Rd | 17 +-- man/target.spec.dea.Rd | 26 ++-- 33 files changed, 1032 insertions(+), 824 deletions(-)
Title: Data Sets and Functions, for Demonstrations with Expression
Arrays and Gene Sequences
Description: Data sets and functions, for the display of gene expression array (microarray) data, and for demonstrations with such data.
Author: John Maindonald
Maintainer: John Maindonald <john.maindonald@anu.edu.au>
Diff between DAAGbio versions 0.62 dated 2013-10-05 and 0.63-1 dated 2016-08-18
DAAGbio-0.62/DAAGbio/build |only DAAGbio-0.62/DAAGbio/data/coralRG.RData |only DAAGbio-0.62/DAAGbio/inst/doc/marray-notes.R |only DAAGbio-0.62/DAAGbio/inst/doc/marray-notes.Rnw |only DAAGbio-0.63-1/DAAGbio/DESCRIPTION | 18 - DAAGbio-0.63-1/DAAGbio/MD5 | 26 +- DAAGbio-0.63-1/DAAGbio/NAMESPACE | 5 DAAGbio-0.63-1/DAAGbio/NEWS |only DAAGbio-0.63-1/DAAGbio/R/imgplot.R | 2 DAAGbio-0.63-1/DAAGbio/R/xplot.R | 2 DAAGbio-0.63-1/DAAGbio/data/coralRG.rda |only DAAGbio-0.63-1/DAAGbio/data/plantStressCounts.rda |only DAAGbio-0.63-1/DAAGbio/man/imgplot.Rd | 4 DAAGbio-0.63-1/DAAGbio/man/plantStressCounts.Rd |only DAAGbio-0.63-1/DAAGbio/man/xplot.Rd | 4 DAAGbio-0.63-1/DAAGbio/vignettes/marray-notes-concordance.tex |only DAAGbio-0.63-1/DAAGbio/vignettes/marray-notes.Rnw | 118 ++++------ DAAGbio-0.63-1/DAAGbio/vignettes/marray-notes.pdf |only DAAGbio-0.63-1/DAAGbio/vignettes/marray-notes.synctex.gz |only DAAGbio-0.63-1/DAAGbio/vignettes/marray-notes.tex |only 20 files changed, 91 insertions(+), 88 deletions(-)
Title: MCMC for Spike and Slab Regression
Description: Spike and slab regression a la McCulloch and George (1997).
Author: Steven L. Scott <stevescott@google.com>
Maintainer: Steven L. Scott <stevescott@google.com>
Diff between BoomSpikeSlab versions 0.6.0 dated 2016-05-21 and 0.7.0 dated 2016-08-18
DESCRIPTION | 10 +++++----- MD5 | 31 +++++++++++++++++-------------- NAMESPACE | 33 +++++++++++++++++++++++---------- R/lm.spike.R | 2 +- R/mlm.spike.R | 2 +- R/poisson.spike.R | 2 +- R/probit.spike.R |only man/plot.logit.spike.Rd | 7 +++++++ man/plot.logit.spike.fit.summary.Rd | 23 +++++++++++++++++------ man/plot.logit.spike.residuals.Rd | 6 +++++- man/predict.lm.spike.Rd | 8 +++++++- man/probit.spike.Rd |only man/summary.logit.spike.Rd | 13 ++++++++++++- src/logit_spike_slab_wrapper.cc | 5 ----- src/mlm_spike_slab_wrapper.cc | 7 +------ src/poisson_spike_slab_wrapper.cc | 7 +------ src/probit_spike_slab_wrapper.cc |only src/spike_slab_wrapper.cc | 7 +------ 18 files changed, 99 insertions(+), 64 deletions(-)
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on
Markov chain Monte Carlo. Although boom contains a few R utilities
(mainly plotting functions), its primary purpose is to install the
BOOM C++ library on your system so that other packages can link
against it.
Author: Steven L. Scott is the sole author and creator of the BOOM
project. Some code in the BOOM libraries has been modified from
other open source projects. These include Cephes (obtained from
Netlib, written by Stephen L. Moshier), NEWUOA (M.J.D Powell,
obtained from Powell's web site), and a modified version of the R
math libraries (R core development team). Original copyright
notices have been maintained in all source files. In these cases,
copyright claimed by Steven L. Scott is limited to modifications
made to the original code.
Maintainer: Steve Scott <stevescott@google.com>
Diff between Boom versions 0.4 dated 2016-05-21 and 0.5 dated 2016-08-18
Boom-0.4/Boom/inst/include/LinAlg/Types.hpp |only Boom-0.4/Boom/inst/include/r_interface/check_interrupt.h |only Boom-0.4/Boom/inst/include/r_interface/error.h |only Boom-0.4/Boom/src/check_interrupt.cpp |only Boom-0.4/Boom/src/error.cpp |only Boom-0.5/Boom/DESCRIPTION | 8 Boom-0.5/Boom/MD5 | 335 +++++----- Boom-0.5/Boom/R/prior_specification.R | 39 + Boom-0.5/Boom/inst/include/BOOM.hpp | 3 Boom-0.5/Boom/inst/include/LinAlg/Array.hpp | 3 Boom-0.5/Boom/inst/include/LinAlg/Array3.hpp | 7 Boom-0.5/Boom/inst/include/LinAlg/ArrayIterator.hpp | 109 ++- Boom-0.5/Boom/inst/include/LinAlg/LinAlgExceptions.hpp | 2 Boom-0.5/Boom/inst/include/LinAlg/Matrix.hpp | 141 ++-- Boom-0.5/Boom/inst/include/LinAlg/SWEEP.hpp | 78 +- Boom-0.5/Boom/inst/include/LinAlg/Selector.hpp | 9 Boom-0.5/Boom/inst/include/LinAlg/SpdMatrix.hpp | 59 + Boom-0.5/Boom/inst/include/Models/BetaBinomialModel.hpp | 7 Boom-0.5/Boom/inst/include/Models/CompositeVectorModel.hpp |only Boom-0.5/Boom/inst/include/Models/DataTypes.hpp | 2 Boom-0.5/Boom/inst/include/Models/Glm/BinomialProbitModel.hpp |only Boom-0.5/Boom/inst/include/Models/Glm/GlmMvnPriorBase.hpp | 2 Boom-0.5/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.hpp |only Boom-0.5/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.hpp |only Boom-0.5/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.hpp |only Boom-0.5/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.hpp |only Boom-0.5/Boom/inst/include/Models/Glm/WeightedRegressionModel.hpp | 3 Boom-0.5/Boom/inst/include/Models/Glm/ZeroInflatedLognormalRegression.hpp | 4 Boom-0.5/Boom/inst/include/Models/Glm/ZeroInflatedPoissonRegression.hpp | 16 Boom-0.5/Boom/inst/include/Models/HMM/HmmFilter.hpp | 2 Boom-0.5/Boom/inst/include/Models/HMM/hmm_tools.hpp | 8 Boom-0.5/Boom/inst/include/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.hpp | 7 Boom-0.5/Boom/inst/include/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.hpp | 6 Boom-0.5/Boom/inst/include/Models/IRT/IRT.hpp | 12 Boom-0.5/Boom/inst/include/Models/IRT/IrtModel.hpp | 2 Boom-0.5/Boom/inst/include/Models/MarginallyUniformCorrelationModel.hpp | 4 Boom-0.5/Boom/inst/include/Models/MarkovModel.hpp | 2 Boom-0.5/Boom/inst/include/Models/MvnModel.hpp | 2 Boom-0.5/Boom/inst/include/Models/MvtModel.hpp | 2 Boom-0.5/Boom/inst/include/Models/Policies/IID_DataPolicy.hpp | 63 - Boom-0.5/Boom/inst/include/Models/PosteriorSamplers/CorrelationSampler.hpp | 2 Boom-0.5/Boom/inst/include/Models/PosteriorSamplers/PosteriorSampler.hpp | 2 Boom-0.5/Boom/inst/include/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.hpp | 27 Boom-0.5/Boom/inst/include/Models/StateSpace/Filters/KalmanTools.hpp | 2 Boom-0.5/Boom/inst/include/Models/StateSpace/Filters/SparseKalmanTools.hpp | 2 Boom-0.5/Boom/inst/include/Models/StateSpace/Filters/SparseMatrix.hpp | 7 Boom-0.5/Boom/inst/include/Models/StateSpace/Filters/SparseVector.hpp | 2 Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/ArStateModel.hpp | 35 - Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/DynamicRegressionStateModel.hpp | 45 - Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/LocalLevelStateModel.hpp | 19 Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/LocalLinearTrend.hpp | 27 Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.hpp | 61 + Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.hpp | 35 - Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/RegressionStateModel.hpp | 37 - Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/SeasonalStateModel.hpp | 34 - Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/StateModel.hpp | 42 + Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/StudentLocalLinearTrend.hpp | 80 +- Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/TrigStateModel.hpp | 14 Boom-0.5/Boom/inst/include/Models/StateSpace/StateSpaceModel.hpp | 38 - Boom-0.5/Boom/inst/include/Models/StateSpace/StateSpaceModelBase.hpp | 2 Boom-0.5/Boom/inst/include/Models/Sufstat.hpp | 9 Boom-0.5/Boom/inst/include/Models/TimeSeries/ArModel.hpp | 22 Boom-0.5/Boom/inst/include/Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.hpp |only Boom-0.5/Boom/inst/include/Models/UniformCorrelationModel.hpp | 6 Boom-0.5/Boom/inst/include/Models/WeightedMvnModel.hpp | 8 Boom-0.5/Boom/inst/include/Models/ZeroInflatedPoissonModel.hpp | 9 Boom-0.5/Boom/inst/include/Models/ZeroMeanGaussianModel.hpp | 1 Boom-0.5/Boom/inst/include/Samplers/ARMS.hpp | 2 Boom-0.5/Boom/inst/include/Samplers/MH_Proposals.hpp | 113 +-- Boom-0.5/Boom/inst/include/Samplers/Sampler.hpp | 7 Boom-0.5/Boom/inst/include/Samplers/SliceSampler.hpp | 43 + Boom-0.5/Boom/inst/include/Samplers/TIM.hpp | 4 Boom-0.5/Boom/inst/include/TargetFun/TargetFun.hpp | 8 Boom-0.5/Boom/inst/include/cpputil/ParamHolder.hpp | 2 Boom-0.5/Boom/inst/include/cpputil/lse.hpp | 3 Boom-0.5/Boom/inst/include/cpputil/math_utils.hpp | 2 Boom-0.5/Boom/inst/include/cpputil/rep.hpp | 2 Boom-0.5/Boom/inst/include/cpputil/report_error.hpp | 17 Boom-0.5/Boom/inst/include/distributions.hpp | 7 Boom-0.5/Boom/inst/include/distributions/Markov.hpp | 12 Boom-0.5/Boom/inst/include/numopt.hpp | 2 Boom-0.5/Boom/inst/include/r_interface/boom_r_tools.hpp | 35 + Boom-0.5/Boom/inst/include/r_interface/list_io.hpp | 28 Boom-0.5/Boom/inst/include/r_interface/prior_specification.hpp | 3 Boom-0.5/Boom/inst/include/stats/ChiSquareTest.hpp | 2 Boom-0.5/Boom/inst/include/stats/NaturalSpline.hpp | 7 Boom-0.5/Boom/inst/include/stats/Resampler.hpp | 2 Boom-0.5/Boom/inst/include/stats/Spline.hpp | 2 Boom-0.5/Boom/inst/include/stats/diff.hpp | 2 Boom-0.5/Boom/inst/include/stats/moments.hpp | 4 Boom-0.5/Boom/inst/include/stats/regression.hpp | 2 Boom-0.5/Boom/man/normal.prior.Rd | 8 Boom-0.5/Boom/src/LinAlg/Array.cpp | 309 ++++----- Boom-0.5/Boom/src/LinAlg/ArrayIterator.cpp | 147 +++- Boom-0.5/Boom/src/LinAlg/Cholesky.cpp | 3 Boom-0.5/Boom/src/LinAlg/CorrelationMatrix.cpp | 49 - Boom-0.5/Boom/src/LinAlg/LU.cpp | 16 Boom-0.5/Boom/src/LinAlg/SVD.cpp | 6 Boom-0.5/Boom/src/LinAlg/SWEEP.cpp | 205 ++---- Boom-0.5/Boom/src/LinAlg/Selector.cpp | 2 Boom-0.5/Boom/src/LinAlg/SpdMatrix.cpp | 235 ++++--- Boom-0.5/Boom/src/LinAlg/VectorView.cpp | 17 Boom-0.5/Boom/src/Models/BetaBinomialModel.cpp | 8 Boom-0.5/Boom/src/Models/CompositeVectorModel.cpp |only Boom-0.5/Boom/src/Models/DirichletModel.cpp | 2 Boom-0.5/Boom/src/Models/GammaModel.cpp | 26 Boom-0.5/Boom/src/Models/Glm/BinomialLogitModel.cpp | 7 Boom-0.5/Boom/src/Models/Glm/BinomialProbitModel.cpp |only Boom-0.5/Boom/src/Models/Glm/Glm.cpp | 2 Boom-0.5/Boom/src/Models/Glm/OrdinalCutpointModel.cpp | 2 Boom-0.5/Boom/src/Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.cpp |only Boom-0.5/Boom/src/Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.cpp |only Boom-0.5/Boom/src/Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.cpp |only Boom-0.5/Boom/src/Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.cpp |only Boom-0.5/Boom/src/Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.cpp | 2 Boom-0.5/Boom/src/Models/Glm/RegressionModel.cpp | 3 Boom-0.5/Boom/src/Models/Glm/TRegression.cpp | 2 Boom-0.5/Boom/src/Models/Glm/WeightedRegressionModel.cpp | 11 Boom-0.5/Boom/src/Models/Glm/ZeroInflatedLognormalRegression.cpp | 17 Boom-0.5/Boom/src/Models/Glm/ZeroInflatedPoissonRegression.cpp | 15 Boom-0.5/Boom/src/Models/HMM/HMM2.cpp | 2 Boom-0.5/Boom/src/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.cpp | 17 Boom-0.5/Boom/src/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.cpp | 11 Boom-0.5/Boom/src/Models/MarginallyUniformCorrelationModel.cpp | 4 Boom-0.5/Boom/src/Models/MvnModel.cpp | 2 Boom-0.5/Boom/src/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.cpp | 3 Boom-0.5/Boom/src/Models/PosteriorSamplers/BetaBinomialSampler.cpp | 23 Boom-0.5/Boom/src/Models/PosteriorSamplers/BetaPosteriorSampler.cpp | 2 Boom-0.5/Boom/src/Models/PosteriorSamplers/DirichletPosteriorSampler.cpp | 3 Boom-0.5/Boom/src/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.cpp | 47 + Boom-0.5/Boom/src/Models/StateSpace/Filters/SparseKalmanTools.cpp | 35 - Boom-0.5/Boom/src/Models/StateSpace/Filters/SparseMatrix.cpp | 10 Boom-0.5/Boom/src/Models/StateSpace/Filters/SparseVector.cpp | 4 Boom-0.5/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.cpp | 3 Boom-0.5/Boom/src/Models/StateSpace/StateModels/ArStateModel.cpp | 43 + Boom-0.5/Boom/src/Models/StateSpace/StateModels/DynamicRegressionStateModel.cpp | 78 +- Boom-0.5/Boom/src/Models/StateSpace/StateModels/LocalLevelStateModel.cpp | 72 +- Boom-0.5/Boom/src/Models/StateSpace/StateModels/LocalLinearTrend.cpp | 23 Boom-0.5/Boom/src/Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.cpp | 46 - Boom-0.5/Boom/src/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.cpp | 26 Boom-0.5/Boom/src/Models/StateSpace/StateModels/RegressionStateModel.cpp | 51 + Boom-0.5/Boom/src/Models/StateSpace/StateModels/SeasonalStateModel.cpp | 42 + Boom-0.5/Boom/src/Models/StateSpace/StateModels/StateModel.cpp | 9 Boom-0.5/Boom/src/Models/StateSpace/StateModels/StudentLocalLinearTrend.cpp | 132 ++- Boom-0.5/Boom/src/Models/StateSpace/StateModels/TrigStateModel.cpp | 13 Boom-0.5/Boom/src/Models/StateSpace/StateSpaceModel.cpp | 100 +- Boom-0.5/Boom/src/Models/StateSpace/StateSpacePoissonModel.cpp | 7 Boom-0.5/Boom/src/Models/Sufstat.cpp | 1 Boom-0.5/Boom/src/Models/TimeSeries/ArModel.cpp | 13 Boom-0.5/Boom/src/Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.cpp |only Boom-0.5/Boom/src/Models/UniformShrinkagePriorModel.cpp | 2 Boom-0.5/Boom/src/Models/WeightedMvnModel.cpp | 2 Boom-0.5/Boom/src/Models/ZeroInflatedPoissonModel.cpp | 8 Boom-0.5/Boom/src/Models/ZeroMeanGaussianModel.cpp | 21 Boom-0.5/Boom/src/Samplers/MH_Proposals.cpp | 39 - Boom-0.5/Boom/src/Samplers/MetropolisHastings.cpp | 4 Boom-0.5/Boom/src/Samplers/SliceSampler.cpp | 168 +++-- Boom-0.5/Boom/src/Samplers/TIM.cpp | 37 - Boom-0.5/Boom/src/TargetFun/TargetFun.cpp | 5 Boom-0.5/Boom/src/boom_r_tools.cpp | 32 Boom-0.5/Boom/src/cpputil/lse.cpp | 2 Boom-0.5/Boom/src/create_state_model.cpp | 38 + Boom-0.5/Boom/src/distributions/Wishart.cpp | 2 Boom-0.5/Boom/src/distributions/dirichlet.cpp | 26 Boom-0.5/Boom/src/distributions/matrix_normal.cpp | 16 Boom-0.5/Boom/src/distributions/mvn.cpp | 6 Boom-0.5/Boom/src/distributions/mvt.cpp | 18 Boom-0.5/Boom/src/distributions/rmulti.cpp | 30 Boom-0.5/Boom/src/distributions/trun_norm.cpp | 67 +- Boom-0.5/Boom/src/list_io.cpp | 96 ++ Boom-0.5/Boom/src/numopt/bfgs.cpp | 9 Boom-0.5/Boom/src/numopt/conj_grad.cpp | 146 ++-- Boom-0.5/Boom/src/numopt/max_nd.cpp | 2 Boom-0.5/Boom/src/numopt/nelder_mead.cpp | 286 ++++---- Boom-0.5/Boom/src/numopt/newton.cpp | 2 Boom-0.5/Boom/src/numopt/simulated_annealing.cpp | 44 - Boom-0.5/Boom/src/prior_specification.cpp | 9 Boom-0.5/Boom/src/stats/moments.cpp | 1 178 files changed, 3055 insertions(+), 1795 deletions(-)