Title: Prepare Questionnaire Data for Analysis
Description: Offers a suite of functions to prepare questionnaire data for analysis (perhaps other types of data as well). By data preparation, I mean data analytic tasks to get your raw data ready for statistical modeling (e.g., regression). There are functions to investigate missing data, reshape data, validate responses, recode variables, score questionnaires, center variables, aggregate by groups, shift scores (i.e., leads or lags), etc. It provides functions for both single level and multilevel (i.e., grouped) data. With a few exceptions (e.g., ncases()), functions without an "s" at the end of their primary word (e.g., center_by()) act on atomic vectors, while functions with an "s" at the end of their primary word (e.g., centers_by()) act on multiple columns of a data.frame.
Author: David Disabato [aut, cre]
Maintainer: David Disabato <ddisab01@gmail.com>
Diff between quest versions 0.1.0 dated 2021-09-10 and 0.2.0 dated 2023-12-04
quest-0.1.0/quest/man/quest.Rd |only quest-0.2.0/quest/DESCRIPTION | 14 ++- quest-0.2.0/quest/MD5 | 85 ++++++++++++++++++-- quest-0.2.0/quest/NAMESPACE | 65 +++++++++++++++ quest-0.2.0/quest/R/describes_functions.R |only quest-0.2.0/quest/R/diary_functions.R |only quest-0.2.0/quest/R/mia_functions.R |only quest-0.2.0/quest/R/psymet_functions.R |only quest-0.2.0/quest/R/quest_functions.R | 122 ++++++++++++++++-------------- quest-0.2.0/quest/man/add_sig.Rd |only quest-0.2.0/quest/man/add_sig_cor.Rd |only quest-0.2.0/quest/man/agg.Rd | 24 +++-- quest-0.2.0/quest/man/agg_dfm.Rd | 14 +-- quest-0.2.0/quest/man/aggs.Rd | 8 - quest-0.2.0/quest/man/amd_bi.Rd |only quest-0.2.0/quest/man/amd_multi.Rd |only quest-0.2.0/quest/man/amd_uni.Rd |only quest-0.2.0/quest/man/auto_by.Rd |only quest-0.2.0/quest/man/boot_ci.Rd |only quest-0.2.0/quest/man/center.Rd | 86 ++++++++++----------- quest-0.2.0/quest/man/composite.Rd |only quest-0.2.0/quest/man/composites.Rd |only quest-0.2.0/quest/man/confint2.Rd |only quest-0.2.0/quest/man/confint2.boot.Rd |only quest-0.2.0/quest/man/confint2.default.Rd |only quest-0.2.0/quest/man/cor_by.Rd |only quest-0.2.0/quest/man/cor_miss.Rd |only quest-0.2.0/quest/man/cor_ml.Rd |only quest-0.2.0/quest/man/corp.Rd |only quest-0.2.0/quest/man/corp_by.Rd |only quest-0.2.0/quest/man/corp_miss.Rd |only quest-0.2.0/quest/man/corp_ml.Rd |only quest-0.2.0/quest/man/covs_test.Rd |only quest-0.2.0/quest/man/cronbach.Rd |only quest-0.2.0/quest/man/cronbachs.Rd |only quest-0.2.0/quest/man/deff.Rd |only quest-0.2.0/quest/man/deffs.Rd |only quest-0.2.0/quest/man/describe_ml.Rd |only quest-0.2.0/quest/man/dot-cronbach.Rd |only quest-0.2.0/quest/man/dot-cronbachs.Rd |only quest-0.2.0/quest/man/dot-gtheory.Rd |only quest-0.2.0/quest/man/dot-gtheorys.Rd |only quest-0.2.0/quest/man/freq.Rd | 3 quest-0.2.0/quest/man/gtheory.Rd |only quest-0.2.0/quest/man/gtheory_ml.Rd |only quest-0.2.0/quest/man/gtheorys.Rd |only quest-0.2.0/quest/man/gtheorys_ml.Rd |only quest-0.2.0/quest/man/icc_11.Rd |only quest-0.2.0/quest/man/icc_all_by.Rd |only quest-0.2.0/quest/man/iccs_11.Rd |only quest-0.2.0/quest/man/length_by.Rd |only quest-0.2.0/quest/man/lengths_by.Rd |only quest-0.2.0/quest/man/make.latent.Rd |only quest-0.2.0/quest/man/mean_change.Rd |only quest-0.2.0/quest/man/mean_compare.Rd |only quest-0.2.0/quest/man/mean_diff.Rd |only quest-0.2.0/quest/man/mean_test.Rd |only quest-0.2.0/quest/man/means_change.Rd |only quest-0.2.0/quest/man/means_compare.Rd |only quest-0.2.0/quest/man/means_diff.Rd |only quest-0.2.0/quest/man/means_test.Rd |only quest-0.2.0/quest/man/n_compare.Rd |only quest-0.2.0/quest/man/ncases_by.Rd |only quest-0.2.0/quest/man/ncases_desc.Rd |only quest-0.2.0/quest/man/ncases_ml.Rd |only quest-0.2.0/quest/man/ngrp.Rd |only quest-0.2.0/quest/man/nhst.Rd |only quest-0.2.0/quest/man/nrow_by.Rd |only quest-0.2.0/quest/man/nrow_ml.Rd |only quest-0.2.0/quest/man/prop_compare.Rd |only quest-0.2.0/quest/man/prop_diff.Rd |only quest-0.2.0/quest/man/prop_test.Rd |only quest-0.2.0/quest/man/props_compare.Rd |only quest-0.2.0/quest/man/props_diff.Rd |only quest-0.2.0/quest/man/props_test.Rd |only quest-0.2.0/quest/man/quest-package.Rd |only quest-0.2.0/quest/man/summary_ucfa.Rd |only quest-0.2.0/quest/man/ucfa.Rd |only 78 files changed, 287 insertions(+), 134 deletions(-)
Title: Sequence ('FASTA'), Annotation ('GFF') and Variants ('VCF') for
17 Samples of 'P. Infestans" and 1 'P. Mirabilis'
Description: Genomic data for the plant pathogen "Phytophthora infestans." It
includes a variant file ('VCF'), a sequence file ('FASTA') and an annotation file
('GFF'). This package is intended to be used as example data for packages that
work with genomic data.
Author: Brian J. Knaus [cre, aut],
Niklaus J. Grunwald [aut]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>
Diff between pinfsc50 versions 1.2.0 dated 2020-06-03 and 1.3.0 dated 2023-12-04
pinfsc50-1.2.0/pinfsc50/man/pinfsc50.Rd |only pinfsc50-1.3.0/pinfsc50/DESCRIPTION | 10 +++++----- pinfsc50-1.3.0/pinfsc50/MD5 | 9 ++++++--- pinfsc50-1.3.0/pinfsc50/NEWS.md |only pinfsc50-1.3.0/pinfsc50/R/pinfsc50-package.R |only pinfsc50-1.3.0/pinfsc50/R/pinfsc50.R | 10 +++++----- pinfsc50-1.3.0/pinfsc50/man/pinfsc50-package.Rd |only pinfsc50-1.3.0/pinfsc50/man/pinfsc50_data.Rd |only 8 files changed, 16 insertions(+), 13 deletions(-)
Title: An R Interface to the Onigmo Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Onigmo library. Offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>
Diff between ore versions 1.7.3.1 dated 2023-01-16 and 1.7.4.1 dated 2023-12-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 9 +++++++++ inst/tinytest/test-10-match.R | 6 ++++++ src/compile.c | 3 ++- src/compile.h | 2 ++ src/match.c | 25 ++++++++++++++++++++++--- 7 files changed, 51 insertions(+), 14 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray,
Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.3.2 dated 2023-01-17 and 1.3.3 dated 2023-12-04
mets-1.3.2/mets/man/easy.survival.twostage.Rd |only mets-1.3.2/mets/man/simRecurrent.Rd |only mets-1.3.2/mets/man/survival.iterative.Rd |only mets-1.3.2/mets/man/survival.twostageCC.Rd |only mets-1.3.2/mets/src/rvpairs2dimrv.cpp |only mets-1.3.3/mets/DESCRIPTION | 14 mets-1.3.3/mets/MD5 | 210 - mets-1.3.3/mets/NAMESPACE | 23 mets-1.3.3/mets/NEWS.md | 5 mets-1.3.3/mets/R/RcppExports.R | 2 mets-1.3.3/mets/R/binomial.regression.R | 289 + mets-1.3.3/mets/R/binomial.twostage.R | 2 mets-1.3.3/mets/R/binregTSR.R |only mets-1.3.3/mets/R/cifreg.R | 105 mets-1.3.3/mets/R/claytonakes.R | 4 mets-1.3.3/mets/R/discrete-survival-haplo.R | 40 mets-1.3.3/mets/R/doubleFGR.R | 3 mets-1.3.3/mets/R/dutils.R | 106 mets-1.3.3/mets/R/efficient-binreg.R | 1 mets-1.3.3/mets/R/gof-phreg.R | 1 mets-1.3.3/mets/R/mets-package.R | 2 mets-1.3.3/mets/R/mutinomialreg.R | 2 mets-1.3.3/mets/R/pch.R | 12 mets-1.3.3/mets/R/phreg.R | 848 +++- mets-1.3.3/mets/R/phreg.par.R | 142 mets-1.3.3/mets/R/recreg.R | 550 ++- mets-1.3.3/mets/R/recurrent.marginal.R | 283 - mets-1.3.3/mets/R/restricted.mean.R | 135 mets-1.3.3/mets/R/sim-pc-hazard.R | 45 mets-1.3.3/mets/R/twostage.R | 1796 ---------- mets-1.3.3/mets/README.md | 2 mets-1.3.3/mets/build/vignette.rds |binary mets-1.3.3/mets/inst/CITATION | 12 mets-1.3.3/mets/inst/doc/basic-dutils.R | 2 mets-1.3.3/mets/inst/doc/basic-dutils.html | 979 ++--- mets-1.3.3/mets/inst/doc/binomial-family.R | 10 mets-1.3.3/mets/inst/doc/binomial-family.Rmd | 8 mets-1.3.3/mets/inst/doc/binomial-family.html | 945 ++--- mets-1.3.3/mets/inst/doc/binomial-twin.R | 4 mets-1.3.3/mets/inst/doc/binomial-twin.Rmd | 2 mets-1.3.3/mets/inst/doc/binomial-twin.html | 933 ++--- mets-1.3.3/mets/inst/doc/binreg-TRS.R |only mets-1.3.3/mets/inst/doc/binreg-TRS.html |only mets-1.3.3/mets/inst/doc/binreg-TRS.rmd |only mets-1.3.3/mets/inst/doc/binreg-ate.R | 6 mets-1.3.3/mets/inst/doc/binreg-ate.Rmd | 20 mets-1.3.3/mets/inst/doc/binreg-ate.html | 544 +-- mets-1.3.3/mets/inst/doc/binreg.R | 2 mets-1.3.3/mets/inst/doc/binreg.Rmd | 4 mets-1.3.3/mets/inst/doc/binreg.html | 362 +- mets-1.3.3/mets/inst/doc/cifreg.R | 2 mets-1.3.3/mets/inst/doc/cifreg.html | 539 +-- mets-1.3.3/mets/inst/doc/glm-utility.R |only mets-1.3.3/mets/inst/doc/glm-utility.Rmd |only mets-1.3.3/mets/inst/doc/glm-utility.html |only mets-1.3.3/mets/inst/doc/haplo-discrete-ttp.R | 2 mets-1.3.3/mets/inst/doc/haplo-discrete-ttp.html | 339 - mets-1.3.3/mets/inst/doc/interval-discrete-survival.R | 4 mets-1.3.3/mets/inst/doc/interval-discrete-survival.Rmd | 2 mets-1.3.3/mets/inst/doc/interval-discrete-survival.html | 395 +- mets-1.3.3/mets/inst/doc/marginal-cox.R | 2 mets-1.3.3/mets/inst/doc/marginal-cox.html | 215 - mets-1.3.3/mets/inst/doc/mediation-survival.R | 32 mets-1.3.3/mets/inst/doc/mediation-survival.Rmd | 95 mets-1.3.3/mets/inst/doc/mediation-survival.html | 804 ++-- mets-1.3.3/mets/inst/doc/quantitative-twin.html | 234 - mets-1.3.3/mets/inst/doc/recurrent-events.R | 69 mets-1.3.3/mets/inst/doc/recurrent-events.Rmd | 125 mets-1.3.3/mets/inst/doc/recurrent-events.html | 1107 +++--- mets-1.3.3/mets/inst/doc/rmst-ate.R | 8 mets-1.3.3/mets/inst/doc/rmst-ate.Rmd | 32 mets-1.3.3/mets/inst/doc/rmst-ate.html | 442 +- mets-1.3.3/mets/inst/doc/survival-ate.R | 23 mets-1.3.3/mets/inst/doc/survival-ate.Rmd | 43 mets-1.3.3/mets/inst/doc/survival-ate.html | 394 +- mets-1.3.3/mets/inst/doc/time-to-event-family-studies-arev.R | 38 mets-1.3.3/mets/inst/doc/time-to-event-family-studies-arev.html | 1769 ++++----- mets-1.3.3/mets/inst/doc/twostage-survival.R | 4 mets-1.3.3/mets/inst/doc/twostage-survival.Rmd | 2 mets-1.3.3/mets/inst/doc/twostage-survival.html | 1719 ++++----- mets-1.3.3/mets/inst/include/mets_RcppExports.h | 105 mets-1.3.3/mets/man/basehazplot.phreg.Rd | 2 mets-1.3.3/mets/man/binreg.Rd | 5 mets-1.3.3/mets/man/binregATE.Rd | 2 mets-1.3.3/mets/man/binregG.Rd |only mets-1.3.3/mets/man/binregTSR.Rd |only mets-1.3.3/mets/man/easy.binomial.twostage.Rd | 2 mets-1.3.3/mets/man/interval.logitsurv.discrete.Rd | 1 mets-1.3.3/mets/man/phreg_IPTW.Rd |only mets-1.3.3/mets/man/phreg_lt.Rd |only mets-1.3.3/mets/man/rchazC.Rd |only mets-1.3.3/mets/man/rcrisk.Rd | 1 mets-1.3.3/mets/man/recreg.Rd | 1 mets-1.3.3/mets/man/recurrentMarginal.Rd | 4 mets-1.3.3/mets/man/resmean.phreg.Rd | 2 mets-1.3.3/mets/man/resmeanIPCW.Rd | 10 mets-1.3.3/mets/man/simMultistate.Rd | 2 mets-1.3.3/mets/man/simRecurrentII.Rd | 23 mets-1.3.3/mets/man/summaryGLM.Rd |only mets-1.3.3/mets/man/survivalG.Rd | 30 mets-1.3.3/mets/man/waldTest.Rd |only mets-1.3.3/mets/src/RcppExports.cpp | 217 + mets-1.3.3/mets/src/fastcox.cpp | 439 +- mets-1.3.3/mets/src/init.c | 18 mets-1.3.3/mets/src/sim-tools.cpp |only mets-1.3.3/mets/vignettes/binomial-family.Rmd | 8 mets-1.3.3/mets/vignettes/binomial-twin.Rmd | 2 mets-1.3.3/mets/vignettes/binreg-TRS.rmd |only mets-1.3.3/mets/vignettes/binreg-ate.Rmd | 20 mets-1.3.3/mets/vignettes/binreg.Rmd | 4 mets-1.3.3/mets/vignettes/glm-utility.Rmd |only mets-1.3.3/mets/vignettes/interval-discrete-survival.Rmd | 2 mets-1.3.3/mets/vignettes/mediation-survival.Rmd | 95 mets-1.3.3/mets/vignettes/recurrent-events.Rmd | 125 mets-1.3.3/mets/vignettes/rmst-ate.Rmd | 32 mets-1.3.3/mets/vignettes/survival-ate.Rmd | 43 mets-1.3.3/mets/vignettes/twostage-survival.Rmd | 2 117 files changed, 9349 insertions(+), 8743 deletions(-)
Title: Event Prediction
Description: Predicts enrollment and events at the design or analysis stage using specified enrollment and time-to-event models through simulations.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between eventPred versions 0.2.1 dated 2023-10-19 and 0.2.2 dated 2023-12-04
DESCRIPTION | 12 MD5 | 38 - NAMESPACE | 13 NEWS.md | 38 + R/eventPred-package.R | 9 R/fitDropout.R | 248 +++---- R/fitEnrollment.R | 14 R/fitEvent.R | 252 ++++--- R/getPrediction.R | 1609 +++++++++++++++++++++++++++++------------------ R/predictEnrollment.R | 4 R/predictEvent.R | 1043 +++++++++++++++++++++++------- R/utilities.R |only man/fitDropout.Rd | 16 man/fitEnrollment.Rd | 4 man/fitEvent.Rd | 13 man/getPrediction.Rd | 20 man/llik_pwexp.Rd |only man/pmodavg.Rd |only man/ppwexp.Rd |only man/predictEnrollment.Rd | 4 man/predictEvent.Rd | 35 - man/pwexpreg.Rd |only man/qpwexp.Rd |only 23 files changed, 2248 insertions(+), 1124 deletions(-)
Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with
audio and video in R. Generates high quality video from images or R graphics with
custom audio. Also offers high performance tools for reading raw audio, creating
'spectrograms', and converting between countless audio / video formats. This package
interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between av versions 0.8.6 dated 2023-10-16 and 0.9.0 dated 2023-12-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ src/avcompat.h | 5 +++++ src/fft.c | 25 ++++++++++++++++++++++++- 5 files changed, 39 insertions(+), 8 deletions(-)
Title: POSIX System Utilities
Description: Bindings to system utilities found in most Unix systems such as
POSIX functions which are not part of the Standard C Library.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between unix versions 1.5.5 dated 2022-10-18 and 1.5.6 dated 2023-12-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ src/fork.c | 2 +- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Visual Documentation for Data Preprocessing
Description: Data practitioners regularly use the 'R' and 'Python' programming languages to
prepare data for analyses. Thus, they encode important data preprocessing decisions in
'R' and 'Python' code. The 'smallsets' package subsequently decodes these decisions into
a Smallset Timeline, a static, compact visualisation of data preprocessing decisions
(Lucchesi et al. (2022) <doi:10.1145/3531146.3533175>). The visualisation consists of
small data snapshots of different preprocessing steps. The 'smallsets' package builds this
visualisation from a user's dataset and preprocessing code located in an 'R', 'R Markdown',
'Python', or 'Jupyter Notebook' file. Users simply add structured comments with snapshot
instructions to the preprocessing code. One optional feature in 'smallsets' requires
installation of the 'Gurobi' optimisation software and 'gurobi' 'R' package, available
from <https://www.gurobi.com>. More information regarding the optional feature and
'gurobi' installation can be found [...truncated...]
Author: Lydia R. Lucchesi [aut, cre] ,
Petra M. Kuhnert [ths],
Jenny L. Davis [ths],
Lexing Xie [ths]
Maintainer: Lydia R. Lucchesi <Lydia.Lucchesi@anu.edu.au>
Diff between smallsets versions 1.0.0 dated 2023-02-03 and 2.0.0 dated 2023-12-04
smallsets-1.0.0/smallsets/man/add_ghost_data.Rd |only smallsets-1.0.0/smallsets/man/build_plot.Rd |only smallsets-1.0.0/smallsets/man/figures/quick-start-example-1.png |only smallsets-1.0.0/smallsets/man/finalise_plot.Rd |only smallsets-1.0.0/smallsets/man/find_data_changes.Rd |only smallsets-1.0.0/smallsets/man/generate_alt_text.Rd |only smallsets-1.0.0/smallsets/man/prepare_colour_sheet.Rd |only smallsets-1.0.0/smallsets/man/prepare_score_sheet.Rd |only smallsets-1.0.0/smallsets/man/retrieve_dimensions.Rd |only smallsets-1.0.0/smallsets/man/retrieve_tables.Rd |only smallsets-1.0.0/smallsets/man/return_scheme.Rd |only smallsets-1.0.0/smallsets/man/run_advanced_gurobi.Rd |only smallsets-1.0.0/smallsets/man/run_simple_gurobi.Rd |only smallsets-1.0.0/smallsets/man/select_smallset.Rd |only smallsets-1.0.0/smallsets/man/write_caption.Rd |only smallsets-1.0.0/smallsets/man/write_cellsEdit.Rd |only smallsets-1.0.0/smallsets/man/write_colourAdd.Rd |only smallsets-1.0.0/smallsets/man/write_colourDelete.Rd |only smallsets-1.0.0/smallsets/man/write_colourEdit.Rd |only smallsets-1.0.0/smallsets/man/write_columnNames.Rd |only smallsets-1.0.0/smallsets/man/write_columnsAdd.Rd |only smallsets-1.0.0/smallsets/man/write_columnsDelete.Rd |only smallsets-1.0.0/smallsets/man/write_dimensions.Rd |only smallsets-1.0.0/smallsets/man/write_rowsAdd.Rd |only smallsets-1.0.0/smallsets/man/write_rowsDelete.Rd |only smallsets-1.0.0/smallsets/man/write_smallset_code.Rd |only smallsets-1.0.0/smallsets/man/write_snapshots.Rd |only smallsets-2.0.0/smallsets/DESCRIPTION | 36 smallsets-2.0.0/smallsets/MD5 | 111 - smallsets-2.0.0/smallsets/NAMESPACE | 4 smallsets-2.0.0/smallsets/NEWS.md | 16 smallsets-2.0.0/smallsets/R/Smallset_Timeline.R | 386 +++- smallsets-2.0.0/smallsets/R/add_ghost_data.R | 7 smallsets-2.0.0/smallsets/R/alt_text_templates.R | 84 - smallsets-2.0.0/smallsets/R/build_plot.R | 119 + smallsets-2.0.0/smallsets/R/finalise_plot.R | 69 smallsets-2.0.0/smallsets/R/find_data_changes.R | 16 smallsets-2.0.0/smallsets/R/generate_alt_text.R | 55 smallsets-2.0.0/smallsets/R/prepare_colour_sheet.R | 23 smallsets-2.0.0/smallsets/R/prepare_score_sheet.R | 6 smallsets-2.0.0/smallsets/R/retrieve_dimensions.R | 2 smallsets-2.0.0/smallsets/R/retrieve_tables.R | 7 smallsets-2.0.0/smallsets/R/return_scheme.R | 34 smallsets-2.0.0/smallsets/R/run_advanced_gurobi.R | 44 smallsets-2.0.0/smallsets/R/run_simple_gurobi.R | 8 smallsets-2.0.0/smallsets/R/select_smallset.R | 21 smallsets-2.0.0/smallsets/R/sets_labelling.R | 21 smallsets-2.0.0/smallsets/R/sets_sizing.R | 24 smallsets-2.0.0/smallsets/R/sets_spacing.R | 28 smallsets-2.0.0/smallsets/R/write_smallset_code.R | 328 ++-- smallsets-2.0.0/smallsets/README.md | 93 - smallsets-2.0.0/smallsets/build/vignette.rds |binary smallsets-2.0.0/smallsets/inst/doc/smallsets.R | 139 + smallsets-2.0.0/smallsets/inst/doc/smallsets.Rmd | 257 ++- smallsets-2.0.0/smallsets/inst/doc/smallsets.html | 783 ++++++---- smallsets-2.0.0/smallsets/inst/s_data_preprocess.R | 12 smallsets-2.0.0/smallsets/inst/s_data_preprocess.Rmd |only smallsets-2.0.0/smallsets/inst/s_data_preprocess.py | 11 smallsets-2.0.0/smallsets/inst/s_data_preprocess_4.R |only smallsets-2.0.0/smallsets/inst/s_data_preprocess_block.R |only smallsets-2.0.0/smallsets/inst/s_data_preprocess_resume.R | 20 smallsets-2.0.0/smallsets/man/Smallset_Timeline.Rd | 47 smallsets-2.0.0/smallsets/man/figures/hex_sticker.png |only smallsets-2.0.0/smallsets/man/figures/quick_start_figure.png |only smallsets-2.0.0/smallsets/man/sets_labelling.Rd | 21 smallsets-2.0.0/smallsets/man/sets_sizing.Rd | 18 smallsets-2.0.0/smallsets/man/sets_spacing.Rd | 21 smallsets-2.0.0/smallsets/tests/testthat/test-changes.R | 46 smallsets-2.0.0/smallsets/tests/testthat/test-enrichment.R |only smallsets-2.0.0/smallsets/tests/testthat/test-output.R | 106 + smallsets-2.0.0/smallsets/tests/testthat/test-selection.R | 99 + smallsets-2.0.0/smallsets/tests/testthat/test-snapshots.R | 51 smallsets-2.0.0/smallsets/vignettes/smallsets.Rmd | 257 ++- 73 files changed, 2205 insertions(+), 1225 deletions(-)
Title: Extract Tables and Sentences from PDFs with User Interface
Description: The PDE (Pdf Data Extractor) allows the extraction of
information and tables optionally based on search words from
PDF (Portable Document Format) files and enables the visualization
of the results, both by providing a convenient user-interface.
Author: Erik Stricker [aut, cre]
Maintainer: Erik Stricker <erik.stricker@gmx.com>
Diff between PDE versions 1.4.3 dated 2023-02-06 and 1.4.6 dated 2023-12-04
DESCRIPTION | 8 MD5 | 47 NEWS.md | 11 R/PDE.R | 2538 +++++----- README.md | 120 build/vignette.rds |binary inst/doc/PDE.Rmd | 19 inst/doc/PDE.html | 14 inst/examples/tsvs/PDE_parameters_v1.4_all_files+-0.tsv | 1 inst/examples/tsvs/PDE_parameters_v1.4_all_files+-0_table_separation.tsv |only man/PDE-deprecated.Rd | 4 man/PDE.Rd | 5 man/PDE_analyzer.Rd | 2 man/PDE_analyzer_i.Rd | 4 man/PDE_check_Xpdf_install.Rd | 4 man/PDE_extr_data_from_pdfs.Rd | 32 man/PDE_install_Xpdftools4.02.Rd | 4 man/PDE_pdfs2table.Rd | 14 man/PDE_pdfs2table_searchandfilter.Rd | 28 man/PDE_pdfs2txt_searchandfilter.Rd | 18 man/PDE_reader_i.Rd | 4 man/dot-PDE_extr_data_from_pdf.Rd | 34 vignettes/PDE.Rmd | 19 vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.search_words_MTX_example.png |binary vignettes/scrnshots/Screenshot_PDE_analyzer_user_interface.search_words_empty.png |binary 25 files changed, 1674 insertions(+), 1256 deletions(-)
Title: Tools for Clinical Research
Description: Every research team have their own script for data management, statistics and
most importantly hemodynamic indices. The purpose is to standardize scripts
utilized in clinical research. The hemodynamic indices can be used in a long-format dataframe,
and add both periods of interest (trigger-periods), and delete artifacts with deleter-files.
Transfer function analysis (Claassen et al. (2016) <doi:10.1177/0271678X15626425>) and
Mx (Czosnyka et al. (1996) <doi:10.1161/01.str.27.10.1829>) can be calculated using this package.
Author: Markus Harboe Olsen [cre, aut],
Christian Riberholt [ctb],
Ronan Berg [ctb],
Kirsten Moeller [ctb],
Janus Christian Jakobsen [ctb],
Aksel Karl Georg Jensen [ctb]
Maintainer: Markus Harboe Olsen <oel@oelfam.com>
Diff between clintools versions 0.9.9 dated 2023-08-21 and 0.9.10 dated 2023-12-04
DESCRIPTION | 9 +- MD5 | 18 +++-- NAMESPACE | 7 +- NEWS.md | 8 ++ R/cdm.fig.R | 150 ++++++++++++++++++++++++++---------------------- R/comparerel.R |only R/questionaire.R |only R/tbl.R | 161 +++++++++++++++++++++++++++++++++++++++++----------- man/cdm.fig.Rd | 16 +++-- man/comparerel.Rd |only man/questionaire.Rd |only man/tbl.Rd | 20 ++++-- 12 files changed, 266 insertions(+), 123 deletions(-)
Title: Processing Hemispherical Canopy Images
Description: Import and classify canopy fish-eye images, estimate angular gap fraction and derive canopy attributes like leaf area index and openness. Additional information is provided in the study by Chianucci F., Macek M. (2023) <doi:10.1016/j.agrformet.2023.109470>.
Author: Francesco Chianucci [aut, cre]
,
Martin Macek [aut]
Maintainer: Francesco Chianucci <fchianucci@gmail.com>
Diff between hemispheR versions 1.1.1 dated 2023-12-02 and 1.1.2 dated 2023-12-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/import_fisheye.R | 15 +++++++++++++++ 4 files changed, 25 insertions(+), 6 deletions(-)
Title: Clustering of Functional Data Based on Measures of Change
Description: Implements the three-step procedure proposed by Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) calculating a number of measures of change capturing various features of the trajectories; (2) using a Principal Component Analysis based dimension reduction algorithm to select a subset of measures and (3) using the K-means clustering algorithm to identify clusters of trajectories.
Author: Marie-Pierre Sylvestre [aut],
Laurence Boulanger [aut, cre],
Gillis Delmas Tchouangue Dinkou [ctb],
Dan Vatnik [ctb]
Maintainer: Laurence Boulanger <laurence.boulanger@umontreal.ca>
Diff between traj versions 1.3.1 dated 2023-04-12 and 2.0.0 dated 2023-12-04
traj-1.3.1/traj/R/PlotMeanTraj.R |only traj-1.3.1/traj/R/PlotMedTraj.R |only traj-1.3.1/traj/R/check.correlation.R |only traj-1.3.1/traj/R/example.data.R |only traj-1.3.1/traj/R/mcc.R |only traj-1.3.1/traj/R/plot.traj.R |only traj-1.3.1/traj/R/plotBoxplotTraj.R |only traj-1.3.1/traj/R/plotCombTraj.R |only traj-1.3.1/traj/R/predicted.y.R |only traj-1.3.1/traj/R/print.traj.R |only traj-1.3.1/traj/R/reduced.eigen.R |only traj-1.3.1/traj/R/smc.R |only traj-1.3.1/traj/R/step1measures.R |only traj-1.3.1/traj/R/step2factors.R |only traj-1.3.1/traj/R/step3clusters.R |only traj-1.3.1/traj/R/summary.traj.R |only traj-1.3.1/traj/R/wrapperTraj.R |only traj-1.3.1/traj/build |only traj-1.3.1/traj/data/example.data.rda |only traj-1.3.1/traj/inst |only traj-1.3.1/traj/man/example.data.Rd |only traj-1.3.1/traj/man/figures/README-example-1.png |only traj-1.3.1/traj/man/plotBoxplotTraj.Rd |only traj-1.3.1/traj/man/plotCombTraj.Rd |only traj-1.3.1/traj/man/plotMeanTraj.Rd |only traj-1.3.1/traj/man/plotMedTraj.Rd |only traj-1.3.1/traj/man/step1measures.Rd |only traj-1.3.1/traj/man/step2factors.Rd |only traj-1.3.1/traj/man/step3clusters.Rd |only traj-1.3.1/traj/man/wrapperTraj.Rd |only traj-1.3.1/traj/tests |only traj-1.3.1/traj/vignettes |only traj-2.0.0/traj/DESCRIPTION | 49 ++++++---------- traj-2.0.0/traj/LICENSE | 4 - traj-2.0.0/traj/MD5 | 64 +++++++--------------- traj-2.0.0/traj/NAMESPACE | 55 +++++++++++------- traj-2.0.0/traj/NEWS.md | 10 ++- traj-2.0.0/traj/R/CheckCorrelation.R |only traj-2.0.0/traj/R/CubeRoot.R |only traj-2.0.0/traj/R/Der.R |only traj-2.0.0/traj/R/FctMean.R |only traj-2.0.0/traj/R/First.R |only traj-2.0.0/traj/R/Last.R |only traj-2.0.0/traj/R/Step1Measures.R |only traj-2.0.0/traj/R/Step2Selection.R |only traj-2.0.0/traj/R/Step3Clusters.R |only traj-2.0.0/traj/R/plot.trajClusters.R |only traj-2.0.0/traj/README.md | 56 ++----------------- traj-2.0.0/traj/data/trajdata.rda |only traj-2.0.0/traj/man/Step1Measures.Rd |only traj-2.0.0/traj/man/Step2Selection.Rd |only traj-2.0.0/traj/man/Step3Clusters.Rd |only traj-2.0.0/traj/man/figures/README-pressure-1.png |only traj-2.0.0/traj/man/plot.trajClusters.Rd |only traj-2.0.0/traj/man/traj-package.Rd | 18 +++--- traj-2.0.0/traj/man/trajdata.Rd |only 56 files changed, 103 insertions(+), 153 deletions(-)
Title: A Taylor-Russell Function for Multiple Predictors
Description: The Taylor Russell model is a widely used method for assessing test validity in personnel selection tasks. The three functions in this package extend this model in a number of notable ways. TR() estimates test validity for a single selection test via the original Taylor Russell model. It extends this model by allowing users greater flexibility in argument choice. For example, users can specify any three of the four parameters (base rate, selection ratio, criterion validity, and positive predictive value) of the Taylor Russell model and estimate the remaining parameter (see the help file for examples). The TaylorRussell() function generalizes the original Taylor Russell model to allow for multiple selection tests (predictors). To our knowledge, this is the first generalization of the Taylor Russell model to allow for three or more selection tests (it is also the first to correctly handle models with two selection tests). TRDemo() is a 'shiny' program for illustrating the underlying lo [...truncated...]
Author: Niels Waller [aut, cre],
Ziyu Ren [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between TaylorRussell versions 1.2 dated 2023-11-30 and 1.2.1 dated 2023-12-04
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/CITATION | 2 +- inst/TR/server.R | 5 ++++- 4 files changed, 13 insertions(+), 10 deletions(-)
Title: Bindings to AppArmor and Security Related Linux Tools
Description: Bindings to kernel methods for enforcing security restrictions.
AppArmor can apply mandatory access control (MAC) policies on a given task
(process) via security profiles with detailed ACL definitions. In addition
this package implements bindings for setting process resource limits (rlimit),
uid, gid, affinity and priority. The high level R function 'eval.secure'
builds on these methods to perform dynamic sandboxing: it evaluates a single
R expression within a temporary fork which acts as a sandbox by enforcing
fine grained restrictions without affecting the main R process. A portable
version of this function is now available in the 'unix' package.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between RAppArmor versions 3.2.3 dated 2022-10-18 and 3.2.4 dated 2023-12-04
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 3 +++ build/vignette.rds |binary inst/CITATION | 12 +++--------- src/apparmor.c | 2 +- 6 files changed, 17 insertions(+), 20 deletions(-)
Title: Data Version Control for the Targets Package
Description: In computationally demanding data analysis pipelines,
the 'targets' R package (2021, <doi:10.21105/joss.02959>) maintains
an up-to-date set of results while skipping tasks that do not need to rerun.
This process increases speed and increases trust in the final end product.
However, it also overwrites old output with new output, and past
results disappear by default. To preserve historical output, the 'gittargets'
package captures version-controlled snapshots of the data store,
and each snapshot links to the underlying commit of the source code.
That way, when the user rolls back the code to a previous branch or commit,
'gittargets' can recover the data contemporaneous with that commit so that
all targets remain up to date.
Author: William Michael Landau [aut, cre]
,
Saras Windecker [rev],
David Neuzerling [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between gittargets versions 0.0.6 dated 2023-02-09 and 0.0.7 dated 2023-12-04
DESCRIPTION | 10 MD5 | 15 NEWS.md | 4 build/vignette.rds |binary inst/doc/git.R | 20 - inst/doc/git.html | 532 +++++++++++++++++------------- tests/interactive/test-tar_git_snapshot.R | 2 tests/testthat/helper-utils.R |only tests/testthat/test-tar_git_checkout.R | 4 9 files changed, 338 insertions(+), 249 deletions(-)
Title: Run 'shiny' Applications in the Browser
Description: Exporting 'shiny' applications with 'shinylive' allows you to run them entirely in a web browser, without the need for a separate R server. The traditional way of deploying 'shiny' applications involves in a separate server and client: the server runs R and 'shiny', and clients connect via the web browser. When an application is deployed with 'shinylive', R and 'shiny' run in the web browser (via 'webR'): the browser is effectively both the client and server for the application. This allows for your 'shiny' application exported by 'shinylive' to be hosted by a static web server.
Author: Barret Schloerke [aut, cre] ,
Winston Chang [aut] ,
George Stagg [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between shinylive versions 0.1.0 dated 2023-10-11 and 0.1.1 dated 2023-12-04
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/assets.R | 19 ++++++++++++++----- R/export.R | 12 ++++-------- R/version.R | 2 +- README.md | 9 +++------ man/export.Rd | 9 +++------ 8 files changed, 44 insertions(+), 38 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
'Electroencephalography' Data
Description: Implemented fast and memory-efficient 'Notch'-filter,
'Welch-periodogram', discrete wavelet transform algorithm for hours of
high-resolution signals, fast 3D convolution, and image alignment;
providing fundamental toolbox for 'iEEG' pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://openwetware.org/wiki/RAVE>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre, cph],
Beauchamp lab [cph],
Karim Rahim [cph] ,
Prerau Lab [cph] ,
RcppParallel Authors [cph] ,
Marcus Geelnard [cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.1.2 dated 2023-07-16 and 0.1.3 dated 2023-12-04
DESCRIPTION | 11 MD5 | 74 NAMESPACE | 18 NEWS.md | 7 R/RcppExports.R | 452 +++++ R/aaa.R | 6 R/band-pass.R | 41 R/baseline.R | 13 R/class-Matrix4.R |only R/class-Quaternion.R |only R/class-Vector3.R |only R/collapse.R | 2 R/detrend.R | 2 R/fast_cov.R | 2 R/fast_quantile.R | 2 R/fftfilt.R | 2 R/fir1.R | 633 +++++-- R/interpolate.R | 2 R/multitaper.R | 2 R/notch.R | 2 R/pwelch-diagnosis.R | 2 R/pwelch.R | 2 R/shift_array.R | 2 R/wavelet.R | 2 configure | 2407 ++--------------------------- configure.ac | 174 +- inst/include/ravetools_RcppExports.h | 1175 ++++++++++++++ inst/sanity |only man/band_pass.Rd | 41 man/new_matrix4.Rd |only man/new_quaternion.Rd |only man/new_vector3.Rd |only src/Makevars.in | 3 src/Makevars.win | 2 src/RcppExports.cpp | 2890 ++++++++++++++++++++++++++++++++++- src/baseline.cpp | 102 - src/glMatrix4.cpp |only src/glMatrix4.h |only src/glQuaternion.cpp |only src/glQuaternion.h |only src/glVector3.cpp |only src/glVector3.h |only tests/testthat/test-baseline.R |only tests/testthat/test-matrix4.R |only tests/testthat/test-quaternion.R |only tests/testthat/test-vector3.R |only 46 files changed, 5542 insertions(+), 2531 deletions(-)
Title: Archetypes for Targets
Description: Function-oriented Make-like declarative pipelines for
Statistics and data science are supported in the 'targets' R package.
As an extension to 'targets', the 'tarchetypes' package provides
convenient user-side functions to make 'targets' easier to use.
By establishing reusable archetypes for common kinds of
targets and pipelines, these functions help express complicated
reproducible pipelines concisely and compactly.
The methods in this package were influenced by the 'drake' R package
by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre]
,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between tarchetypes versions 0.7.9 dated 2023-10-04 and 0.7.10 dated 2023-12-04
DESCRIPTION | 8 +++--- MD5 | 39 +++++++++++++++++----------------- NAMESPACE | 1 NEWS.md | 5 ++++ R/tar_map2_raw.R | 10 +------- R/tar_package.R | 8 +++--- R/tar_quarto_rep_raw.R | 10 +------- R/tar_render_rep_raw.R | 10 +------- R/tar_rep2_raw.R | 10 +------- R/tar_rep_raw.R | 21 +++--------------- R/utils_seed.R |only man/tar_download.Rd | 8 +++--- man/tar_download_run.Rd | 8 +++--- tests/testthat/helper-utils.R | 23 ++++++++++++++++++++ tests/testthat/test-tar_files.R | 4 +-- tests/testthat/test-tar_files_input.R | 4 +-- tests/testthat/test-tar_hook_before.R | 2 - tests/testthat/test-tar_hook_inner.R | 2 - tests/testthat/test-tar_hook_outer.R | 2 - tests/testthat/test-tar_quarto_rep.R | 2 - tests/testthat/test-tar_render_rep.R | 2 - 21 files changed, 85 insertions(+), 94 deletions(-)
Title: 'Stata' Markdown
Description: Settings and functions to extend the 'knitr' 'Stata' engine.
Author: Doug Hemken [aut, cre] ,
Tom Palmer [ctb] ,
Philipp Lepert [ctb]
Maintainer: Doug Hemken <dehemken@wisc.edu>
Diff between Statamarkdown versions 0.8.0 dated 2023-06-01 and 0.9.2 dated 2023-12-04
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NAMESPACE | 2 + R/engine_output.R | 26 +++++++++++------- R/find_stata.r | 8 ++--- R/misc.r | 2 - R/stata_collectcode.r | 53 ++++++++++++++++++++++-------------- R/stata_engine_output.r | 69 +++++++++++++++++++++++++----------------------- 8 files changed, 104 insertions(+), 78 deletions(-)
Title: Uniformity Tests on the Circle, Sphere, and Hypersphere
Description: Implementation of uniformity tests on the circle and
(hyper)sphere. The main function of the package is unif_test(), which
conveniently collects more than 30 tests for assessing uniformity on
S^{p-1}={x in R^p : ||x||=1}, p >= 2. The test statistics are implemented
in the unif_stat() function, which allows computing several statistics to
several samples within a single call, thus facilitating Monte Carlo
experiments. Furthermore, the unif_stat_MC() function allows
parallelizing them in a simple way. The asymptotic null distributions of
the statistics are available through the function unif_stat_distr(). The
core of 'sphunif' is coded in C++ by relying on the 'Rcpp' package.
The package also provides several novel datasets and gives the
replicability for the data application in García-Portugués,
Navarro-Esteban and Cuesta-Albertos (2023) <arXiv:2008.09897>.
Author: Eduardo Garcia-Portugues [aut, cre]
,
Thomas Verdebout [aut] ,
Paula Navarro [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between sphunif versions 1.1.0 dated 2023-08-21 and 1.3.0 dated 2023-12-04
sphunif-1.1.0/sphunif/src/cir_stat_distr.cpp |only sphunif-1.1.0/sphunif/tests/testthat/test-harmonics.R |only sphunif-1.3.0/sphunif/DESCRIPTION | 10 sphunif-1.3.0/sphunif/MD5 | 102 - sphunif-1.3.0/sphunif/NAMESPACE | 34 sphunif-1.3.0/sphunif/NEWS.md | 9 sphunif-1.3.0/sphunif/R/Pn.R | 2 sphunif-1.3.0/sphunif/R/RcppExports.R | 467 ++--- sphunif-1.3.0/sphunif/R/Sobolev.R | 270 ++ sphunif-1.3.0/sphunif/R/cir_distr.R | 23 sphunif-1.3.0/sphunif/R/cir_stat.R | 10 sphunif-1.3.0/sphunif/R/data.R | 6 sphunif-1.3.0/sphunif/R/int_sph_MC.R | 10 sphunif-1.3.0/sphunif/R/sph_distr.R | 123 + sphunif-1.3.0/sphunif/R/sphunif-package.R | 6 sphunif-1.3.0/sphunif/R/unif-alts.R | 139 + sphunif-1.3.0/sphunif/R/unif_stat.R | 469 ++++- sphunif-1.3.0/sphunif/R/unif_stat_MC.R | 24 sphunif-1.3.0/sphunif/R/unif_stat_distr.R | 157 + sphunif-1.3.0/sphunif/R/unif_test.R | 238 ++ sphunif-1.3.0/sphunif/R/wschisq.R | 6 sphunif-1.3.0/sphunif/inst/WORDLIST |only sphunif-1.3.0/sphunif/inst/doc/sphunif.R | 26 sphunif-1.3.0/sphunif/inst/doc/sphunif.html | 382 ++-- sphunif-1.3.0/sphunif/man/Sobolev.Rd | 27 sphunif-1.3.0/sphunif/man/Sobolev_coefs.Rd | 7 sphunif-1.3.0/sphunif/man/avail_tests.Rd | 4 sphunif-1.3.0/sphunif/man/cir_stat.Rd | 24 sphunif-1.3.0/sphunif/man/cir_stat_distr.Rd | 14 sphunif-1.3.0/sphunif/man/comets.Rd | 6 sphunif-1.3.0/sphunif/man/r_alt.Rd | 2 sphunif-1.3.0/sphunif/man/sph_stat.Rd | 26 sphunif-1.3.0/sphunif/man/sph_stat_Sobolev.Rd |only sphunif-1.3.0/sphunif/man/sph_stat_distr.Rd | 20 sphunif-1.3.0/sphunif/man/unif_stat.Rd | 19 sphunif-1.3.0/sphunif/man/unif_stat_MC.Rd | 22 sphunif-1.3.0/sphunif/man/unif_stat_distr.Rd | 58 sphunif-1.3.0/sphunif/man/unif_test.Rd | 24 sphunif-1.3.0/sphunif/src/RcppExports.cpp | 1116 ++++++------ sphunif-1.3.0/sphunif/src/cir_distr.cpp |only sphunif-1.3.0/sphunif/src/cir_stat.cpp | 75 sphunif-1.3.0/sphunif/src/sph_distr.cpp | 67 sphunif-1.3.0/sphunif/src/sph_stat.cpp | 306 ++- sphunif-1.3.0/sphunif/tests/testthat/Rplots.pdf |binary sphunif-1.3.0/sphunif/tests/testthat/test_A_theta_x.R | 3 sphunif-1.3.0/sphunif/tests/testthat/test_Pn_vs_Sobolev.R | 8 sphunif-1.3.0/sphunif/tests/testthat/test_Sobolev.R | 290 ++- sphunif-1.3.0/sphunif/tests/testthat/test_harmonics.R |only sphunif-1.3.0/sphunif/tests/testthat/test_int_sph_MC.R | 6 sphunif-1.3.0/sphunif/tests/testthat/test_sph_stat.R | 257 +- sphunif-1.3.0/sphunif/tests/testthat/test_unif-alts.R | 59 sphunif-1.3.0/sphunif/tests/testthat/test_unif_stat.R | 173 + sphunif-1.3.0/sphunif/tests/testthat/test_unif_stat_MC.R | 97 - sphunif-1.3.0/sphunif/tests/testthat/test_unif_stat_distr.R | 22 sphunif-1.3.0/sphunif/tests/testthat/test_unif_test.R | 114 + 55 files changed, 3844 insertions(+), 1515 deletions(-)
Title: Optimal Binning of Data
Description: Defines thresholds for breaking data into a number of
discrete levels, minimizing the (mean) squared error within all bins.
Author: Greg Kreider
Maintainer: Greg Kreider <support@primachvis.com>
Diff between optbin versions 1.2 dated 2022-09-19 and 1.3 dated 2023-12-04
optbin-1.2/optbin/tests/bist_optbin.R.orig |only optbin-1.3/optbin/ChangeLog | 3 ++- optbin-1.3/optbin/DESCRIPTION | 8 ++++---- optbin-1.3/optbin/MD5 | 7 +++---- optbin-1.3/optbin/src/optbin.c | 5 ++++- 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between mongolite versions 2.7.2 dated 2023-03-31 and 2.7.3 dated 2023-12-04
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS | 3 +++ R/mongo.R | 4 ++-- R/stream.R | 2 +- man/mongo.Rd | 4 ++-- src/Makevars.win | 5 +---- src/client.c | 5 +++-- src/collection.c | 2 +- src/gridfs.c | 4 ++-- src/mongolite.h | 3 ++- src/reader.c | 2 +- 12 files changed, 33 insertions(+), 31 deletions(-)
Title: R Bindings for 'ZeroMQ'
Description: Interface to the 'ZeroMQ' lightweight messaging kernel (see <https://zeromq.org/> for more information).
Author: Whit Armstrong [aut],
Michael Schubert [ctb],
Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between rzmq versions 0.9.11 dated 2023-10-16 and 0.9.12 dated 2023-12-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/interface.cpp | 2 +- 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] ,
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] ,
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] ,
Timothy Waterhouse [ctb] ,
Kyle Meyer [ctb],
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 1.1.1 dated 2023-08-16 and 1.3.0 dated 2023-12-04
DESCRIPTION | 6 +- MD5 | 27 +++++----- NEWS.md |only R/handle_spec_block.R | 2 R/mread.R | 4 - R/package.R | 10 --- inst/WORDLIST | 4 + inst/base/mrgsolv.h | 2 inst/include/datarecord.h | 34 +++++++------ man/mrgsolve_package.Rd | 30 +++++++++++ src/LSODA.cpp | 52 +++++++++++--------- src/datarecord.cpp | 40 ++++++++------- src/devtran.cpp | 106 ++++++++++++++++++++++++++++++------------ src/housemodel-mread-header.h | 6 +- src/odeproblem.cpp | 5 + 15 files changed, 209 insertions(+), 119 deletions(-)
Title: Text Processing for Small or Big Data Files
Description: It offers functions for splitting, parsing, tokenizing and creating a vocabulary for big text data files. Moreover, it includes functions for building a document-term matrix and extracting information from those (term-associations, most frequent terms). It also embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. Lastly, it includes functions for Word Vector Representations (i.e. 'GloVe', 'fasttext') and incorporates functions for the calculation of (pairwise) text document dissimilarities. The source code is based on 'C++11' and exported in R through the 'Rcpp', 'RcppArmadillo' and 'BH' packages.
Author: Lampros Mouselimis [aut, cre]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between textTinyR versions 1.1.7 dated 2021-10-26 and 1.1.8 dated 2023-12-04
DESCRIPTION | 10 MD5 | 61 NAMESPACE | 1 NEWS.md | 10 R/utils.R | 246 +- README.md | 4 build/vignette.rds |binary inst/doc/functionality_of_textTinyR_package.R | 138 - inst/doc/functionality_of_textTinyR_package.html | 2599 +++++++++++++---------- inst/doc/word_vectors_doc2vec.R | 30 inst/doc/word_vectors_doc2vec.html | 976 +++++--- man/Doc2Vec.Rd | 24 man/batch_compute.Rd |only man/big_tokenize_transform.Rd | 91 man/bytes_converter.Rd | 6 man/load_sparse_binary.Rd | 6 man/read_characters.Rd | 6 man/read_rows.Rd | 6 man/sparse_term_matrix.Rd | 78 man/text_file_parser.Rd | 43 man/text_intersect.Rd | 24 man/token_stats.Rd | 72 man/vocabulary_parser.Rd | 14 src/Makevars | 1 src/Makevars.win | 3 src/export_all_funcs.cpp | 1 src/init.c | 128 - src/rcpp_similarities.cpp | 1 src/term_matrix.h | 4 src/token_big_files.h | 2 src/word_vecs_pointer_embedding.cpp | 5 tests/testthat/helper-function_for_tests.R | 1 32 files changed, 2640 insertions(+), 1951 deletions(-)
Title: Client to Access and Operate on the 'Open Source Vulnerability'
API
Description: Connect, query, and operate on information available from the
'Open Source Vulnerability' database <https://osv.dev/>. Although 'CRAN'
has vulnerabilities listed, these are few compared to projects such as
'PyPI'. With tighter integration between 'R' and 'Python', having an
'R' specific package to access details about vulnerabilities from
various sources is a worthwhile enterprise.
Author: Allen OBrien [aut, cre, cph]
Maintainer: Allen OBrien <allen.g.obrien@gmail.com>
Diff between rosv versions 0.5.0 dated 2023-11-23 and 0.5.1 dated 2023-12-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/RosvQuery1.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Bifurcation Analysis of Ordinary Differential Equation Systems
Description: Shiny application that performs bifurcation and phaseplane analysis of systems of ordinary
differential equations. The package allows for computation of equilibrium curves as a function of
a single free parameter, detection of transcritical, saddle-node and hopf bifurcation points along
these curves, and computation of curves representing these transcritical, saddle-node and hopf
bifurcation points as a function of two free parameters. The shiny-based GUI allows visualization
of the results in both 2D- and 3D-plots. The implemented methods for solution localisation and curve
continuation are based on the book "Elements of applied bifurcation theory" (Kuznetsov, Y. A., 1995;
ISBN: 0-387-94418-4).
Author: Andre M. de Roos [aut, cre]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>
Diff between deBif versions 0.1.7 dated 2023-01-18 and 0.1.8 dated 2023-12-04
DESCRIPTION | 10 +-- MD5 | 26 ++++---- NAMESPACE | 1 NEWS.md | 12 +++ R/LCfuncs.R | 48 +++++++++++++++ R/bif1parplot.R | 127 +++++++++++++++++++++++++++++++++++------- R/bifComputeCurves.R | 46 ++++++++++++++- R/bifurcation.R | 4 - R/deBifReset.R |only R/setup.R | 6 + build/vignette.rds |binary inst/shiny-examples/budworm.R | 2 man/deBifReset.Rd |only src/curve.c | 13 +++- src/deBif-LC.c | 4 - 15 files changed, 251 insertions(+), 48 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre] ,
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Siddharth Agrawal [cph] ),
Brendan Frey [cph] ),
Delbert Dueck [cph] ,
Vitalie Spinu [ctb]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.3.1 dated 2023-04-29 and 1.3.2 dated 2023-12-04
DESCRIPTION | 8 MD5 | 24 NEWS.md | 9 README.md | 3 build/vignette.rds |binary inst/CITATION | 2 inst/doc/the_clusterR_package.R | 32 - inst/doc/the_clusterR_package.Rmd | 2 inst/doc/the_clusterR_package.html | 998 +++++++++++++++++++++++++----------- inst/include/affinity_propagation.h | 4 src/Makevars.win | 2 src/init.c | 48 - vignettes/the_clusterR_package.Rmd | 2 13 files changed, 772 insertions(+), 362 deletions(-)
Title: Parse XML
Description: Work with XML files using a simple, consistent interface.
Built on top of the 'libxml2' C library.
Author: Hadley Wickham [aut, cre],
Jim Hester [aut],
Jeroen Ooms [aut],
Posit Software, PBC [cph, fnd],
R Foundation [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between xml2 versions 1.3.5 dated 2023-07-06 and 1.3.6 dated 2023-12-04
xml2-1.3.5/xml2/tests/testthat/output |only xml2-1.3.5/xml2/tests/testthat/test-cdata.R |only xml2-1.3.5/xml2/tests/testthat/test-comment.R |only xml2-1.3.5/xml2/tests/testthat/test-dtd.R |only xml2-1.3.5/xml2/tests/testthat/test-modify-xml.R |only xml2-1.3.5/xml2/tests/testthat/test-namespaces.R |only xml2-1.3.5/xml2/tests/testthat/test-print.R |only xml2-1.3.5/xml2/tests/testthat/test-read-xml.R |only xml2-1.3.5/xml2/tests/testthat/test-url.R |only xml2-1.3.5/xml2/tests/testthat/test-write_xml.R |only xml2-1.3.5/xml2/tests/testthat/test-xml_attrs.R |only xml2-1.3.6/xml2/DESCRIPTION | 30 - xml2-1.3.6/xml2/LICENSE | 2 xml2-1.3.6/xml2/MD5 | 173 +++--- xml2-1.3.6/xml2/NAMESPACE | 32 - xml2-1.3.6/xml2/NEWS.md | 21 xml2-1.3.6/xml2/R/as_list.R | 6 xml2-1.3.6/xml2/R/as_xml_document.R | 19 xml2-1.3.6/xml2/R/classes.R | 253 --------- xml2-1.3.6/xml2/R/format.R |only xml2-1.3.6/xml2/R/import-standalone-obj-type.R |only xml2-1.3.6/xml2/R/import-standalone-purrr.R |only xml2-1.3.6/xml2/R/import-standalone-types-check.R |only xml2-1.3.6/xml2/R/init.R | 2 xml2-1.3.6/xml2/R/nodeset_apply.R |only xml2-1.3.6/xml2/R/paths.R | 22 xml2-1.3.6/xml2/R/utils.R | 24 xml2-1.3.6/xml2/R/xml2-package.R |only xml2-1.3.6/xml2/R/xml_attr.R | 47 - xml2-1.3.6/xml2/R/xml_children.R | 24 xml2-1.3.6/xml2/R/xml_document.R |only xml2-1.3.6/xml2/R/xml_find.R | 73 +- xml2-1.3.6/xml2/R/xml_missing.R |only xml2-1.3.6/xml2/R/xml_modify.R | 30 - xml2-1.3.6/xml2/R/xml_name.R | 21 xml2-1.3.6/xml2/R/xml_namespaces.R | 2 xml2-1.3.6/xml2/R/xml_node.R |only xml2-1.3.6/xml2/R/xml_nodeset.R |only xml2-1.3.6/xml2/R/xml_parse.R | 97 ++- xml2-1.3.6/xml2/R/xml_path.R | 17 xml2-1.3.6/xml2/R/xml_serialize.R | 12 xml2-1.3.6/xml2/R/xml_structure.R | 15 xml2-1.3.6/xml2/R/xml_text.R | 56 -- xml2-1.3.6/xml2/R/xml_type.R | 17 xml2-1.3.6/xml2/R/xml_write.R | 24 xml2-1.3.6/xml2/README.md | 56 +- xml2-1.3.6/xml2/build/stage23.rdb |only xml2-1.3.6/xml2/build/vignette.rds |binary xml2-1.3.6/xml2/build/xml2.pdf |binary xml2-1.3.6/xml2/inst/doc/modification.R | 20 xml2-1.3.6/xml2/inst/doc/modification.Rmd | 18 xml2-1.3.6/xml2/inst/doc/modification.html | 50 - xml2-1.3.6/xml2/inst/include/xml2_types.h | 4 xml2-1.3.6/xml2/man/as_xml_document.Rd | 5 xml2-1.3.6/xml2/man/figures |only xml2-1.3.6/xml2/man/xml2-package.Rd |only xml2-1.3.6/xml2/man/xml_dtd.Rd | 12 xml2-1.3.6/xml2/man/xml_find_all.Rd | 3 xml2-1.3.6/xml2/man/xml_missing.Rd | 2 xml2-1.3.6/xml2/man/xml_ns_strip.Rd | 5 xml2-1.3.6/xml2/man/xml_structure.Rd | 2 xml2-1.3.6/xml2/src/init.c | 1 xml2-1.3.6/xml2/src/xml2_init.cpp | 13 xml2-1.3.6/xml2/src/xml2_node.cpp | 501 ++++++++++++++---- xml2-1.3.6/xml2/src/xml2_output.cpp | 2 xml2-1.3.6/xml2/src/xml2_schema.cpp | 13 xml2-1.3.6/xml2/src/xml2_utils.h | 42 + xml2-1.3.6/xml2/tests/testthat.R | 8 xml2-1.3.6/xml2/tests/testthat/_snaps |only xml2-1.3.6/xml2/tests/testthat/setup.R | 1 xml2-1.3.6/xml2/tests/testthat/test-as_list.R | 20 xml2-1.3.6/xml2/tests/testthat/test-as_xml_document.R | 2 xml2-1.3.6/xml2/tests/testthat/test-classes.R |only xml2-1.3.6/xml2/tests/testthat/test-format.R | 3 xml2-1.3.6/xml2/tests/testthat/test-null.R | 5 xml2-1.3.6/xml2/tests/testthat/test-xml_attr.R |only xml2-1.3.6/xml2/tests/testthat/test-xml_children.R | 13 xml2-1.3.6/xml2/tests/testthat/test-xml_document.R |only xml2-1.3.6/xml2/tests/testthat/test-xml_find.R | 71 +- xml2-1.3.6/xml2/tests/testthat/test-xml_missing.R | 15 xml2-1.3.6/xml2/tests/testthat/test-xml_modify.R |only xml2-1.3.6/xml2/tests/testthat/test-xml_name.R | 27 xml2-1.3.6/xml2/tests/testthat/test-xml_namespaces.R |only xml2-1.3.6/xml2/tests/testthat/test-xml_node.R |only xml2-1.3.6/xml2/tests/testthat/test-xml_nodeset.R | 27 xml2-1.3.6/xml2/tests/testthat/test-xml_parse.R | 105 +++ xml2-1.3.6/xml2/tests/testthat/test-xml_schema.R | 4 xml2-1.3.6/xml2/tests/testthat/test-xml_serialize.R | 17 xml2-1.3.6/xml2/tests/testthat/test-xml_structure.R | 27 xml2-1.3.6/xml2/tests/testthat/test-xml_text.R | 55 + xml2-1.3.6/xml2/tests/testthat/test-xml_type.R |only xml2-1.3.6/xml2/tests/testthat/test-xml_url.R |only xml2-1.3.6/xml2/tests/testthat/test-xml_write.R |only xml2-1.3.6/xml2/tests/testthat/xml |only xml2-1.3.6/xml2/vignettes/modification.Rmd | 18 95 files changed, 1253 insertions(+), 933 deletions(-)
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets. Use all of your data at once, with few limits. Memory mapped data can be shared between multiple R processes. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface or a fast network file system. The data is memory mapped into R and then accessed using usual R list and array subscription operators. Convenience functions are provided for merging, grouping and indexing large vectors and data.frames. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as a standalone C library. libMVL has simple C API making it easy to interchange datasets with outside programs. Large MVL datasets are distributed via Academic Torrents <https://academictorrents.com/collection/mvl-datasets>.
Author: Vladimir Dergachev [aut, cre]
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 0.0.4.9 dated 2023-10-30 and 1.0.0.1 dated 2023-12-04
DESCRIPTION | 11 +++++++---- MD5 | 4 ++-- src/RlibMVL.c | 6 +++--- 3 files changed, 12 insertions(+), 9 deletions(-)
Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used,
but may require higher performance that what can be obtained from base R.
Incidentally provides support for 'reverse geocoding', such as matching a point
with its nearest neighbour in another array. Used as a complement to package
'hutils' by sacrificing compilation or installation time for higher running
speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre],
Simon Urbanek [ctb]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between hutilscpp versions 0.10.2 dated 2023-10-11 and 0.10.4 dated 2023-12-04
DESCRIPTION | 6 MD5 | 26 NEWS.md | 22 R/fmatchp.R | 252 R/is_constant.R | 1 R/logical3s.R | 632 inst/tinytest/test-and3s.R | 596 inst/tinytest/test-fmatch.R | 2 inst/tinytest/test-or3s.R |61835 ++++++++++++++++++++++---------------------- man/is_constant.Rd | 1 src/C_character2integer.c | 2 src/Cand3s.c | 278 src/Cor3s.c | 4 src/Cwhich_first.c | 2 14 files changed, 31964 insertions(+), 31695 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code
ported from S-PLUS. A modern 'MySQL' client written in 'C++' is available
from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] ,
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between RMySQL versions 0.10.26 dated 2023-09-26 and 0.10.27 dated 2023-12-04
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/result.R | 2 +- man/query.Rd | 2 +- src/db-apply.c | 4 ++-- 6 files changed, 17 insertions(+), 13 deletions(-)
Title: R MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for
arbitrary precision floating point numbers, including transcendental
("special") functions. To this end, the package interfaces to
the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library
which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Author: Martin Maechler [aut, cre] ,
Richard M. Heiberger [ctb] , *Bin, *Dec),
John C. Nash [ctb] , origin of unirootR),
Hans W. Borchers [ctb] ; origin of
hjkMpfr)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between Rmpfr versions 0.9-3 dated 2023-08-08 and 0.9-4 dated 2023-12-04
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/AllClasses.R | 27 ++++++++++++++++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 15 ++++++++++----- inst/doc/Maechler_useR_2011-abstr.pdf |binary inst/doc/Rmpfr-pkg.pdf |binary inst/doc/log1mexp-note.pdf |binary src/convert.c | 2 +- src/utils.c | 8 ++++---- tests/arith-ex.R | 2 ++ 12 files changed, 55 insertions(+), 31 deletions(-)
Title: Partially Ordered Sets in R
Description: Provides a set of basic tools for generating, analyzing, summarizing and visualizing finite partially ordered sets. In particular, it implements flexible and very efficient algorithms for the extraction of linear extensions and for the computation of mutual ranking probabilities and other user-defined functionals, over them. The package is meant as a computationally efficient "engine", for the implementation of data analysis procedures, on systems of multidimensional ordinal indicators and partially ordered data, in the spirit of Fattore, M. (2016) "Partially ordered sets and the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-015-1059-6>, and Fattore M. and Arcagni, A. (2018) "A reduced posetic approach to the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-016-1501-4>.
Author: Alberto Arcagni [aut, cre],
Alessandro Avellone [aut],
Marco Fattore [aut]
Maintainer: Alberto Arcagni <alberto.arcagni@uniroma1.it>
Diff between POSetR versions 1.1.1 dated 2023-01-17 and 1.1.4 dated 2023-12-04
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 1 + R/POSetR-package.R | 1 + build/partial.rdb |binary src/RMod.cpp | 11 ++++------- 6 files changed, 16 insertions(+), 17 deletions(-)
Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical
data and the web. Offers simple, flexible tools for working with JSON in R, and
is particularly powerful for building pipelines and interacting with a web API.
The implementation is based on the mapping described in the vignette (Ooms, 2014).
In addition to converting JSON data from/to R objects, 'jsonlite' contains
functions to stream, validate, and prettify JSON data. The unit tests included
with the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] ,
Duncan Temple Lang [ctb],
Lloyd Hilaiel [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between jsonlite versions 1.8.7 dated 2023-06-29 and 1.8.8 dated 2023-12-04
DESCRIPTION | 6 - MD5 | 82 +++++++++++++------------- NEWS | 4 + R/stream.R | 4 - build/vignette.rds |binary inst/doc/json-aaquickstart.html | 2 inst/doc/json-mapping.pdf |binary man/stream_in.Rd | 4 - src/parse.c | 2 src/push_parser.c | 2 src/yajl/yajl_buf.c | 12 +++ src/yajl/yajl_encode.c | 4 - src/yajl/yajl_tree.c | 8 ++ tests/testthat/flatten.R | 6 - tests/testthat/test-fromJSON-NA-values.R | 12 +-- tests/testthat/test-fromJSON-array.R | 30 ++++----- tests/testthat/test-fromJSON-dataframe.R | 24 +++---- tests/testthat/test-fromJSON-datasets.R | 12 +-- tests/testthat/test-fromJSON-date.R | 20 +++--- tests/testthat/test-fromJSON-matrix.R | 22 +++--- tests/testthat/test-libjson-escaping.R | 8 +- tests/testthat/test-libjson-large.R | 10 +-- tests/testthat/test-libjson-utf8.R | 16 ++--- tests/testthat/test-libjson-validator.R | 2 tests/testthat/test-network-Github.R | 54 ++++++++--------- tests/testthat/test-serializeJSON-S4.R | 2 tests/testthat/test-serializeJSON-datasets.R | 8 +- tests/testthat/test-serializeJSON-functions.R | 4 - tests/testthat/test-serializeJSON-types.R | 6 - tests/testthat/test-toJSON-AsIs.R | 18 ++--- tests/testthat/test-toJSON-Date.R | 26 ++++---- tests/testthat/test-toJSON-NA-values.R | 6 - tests/testthat/test-toJSON-NULL-values.R | 20 +++--- tests/testthat/test-toJSON-POSIXt.R | 60 +++++++++---------- tests/testthat/test-toJSON-complex.R | 28 ++++---- tests/testthat/test-toJSON-dataframe.R | 10 +-- tests/testthat/test-toJSON-factor.R | 8 +- tests/testthat/test-toJSON-logical.R | 30 ++++----- tests/testthat/test-toJSON-matrix.R | 12 +-- tests/testthat/test-toJSON-numeric.R | 42 ++++++------- tests/testthat/test-toJSON-raw.R | 6 - tests/testthat/test-toJSON-zerovec.R | 40 ++++++------ 42 files changed, 347 insertions(+), 325 deletions(-)
Title: Download Flight and Airport Data from Brazil
Description: Download flight and airport data from Brazil’s Civil Aviation Agency
(ANAC) <https://www.gov.br/anac>. The data includes detailed
information on all aircrafts, aerodromes, airports, and airport
movements registered in ANAC, on airfares and on every international
flight to and from Brazil, as well as domestic flights within the country.
Author: Rafael H. M. Pereira [aut, cre]
,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between flightsbr versions 0.3.0 dated 2023-06-29 and 0.4.0 dated 2023-12-04
DESCRIPTION | 6 MD5 | 65 ++++--- NAMESPACE | 3 NEWS.md | 14 + R/flightsbr.R | 10 - R/read_aircrafts.R | 128 +++++++++----- R/read_airfares.R | 17 + R/read_airport_movements.R | 26 ++- R/read_airports.R | 18 +- R/read_flights.R | 25 +- R/utils.R | 234 +++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/airports.R | 8 inst/doc/airports.html | 34 +-- inst/doc/flights.R | 10 - inst/doc/flights.html | 94 +++++----- inst/doc/intro_flightsbr.R | 16 - inst/doc/intro_flightsbr.html | 42 ++-- man/download_aircrafts_data.Rd |only man/download_airfares_data.Rd | 8 man/download_airport_movement_data.Rd | 10 - man/download_flights_data.Rd | 11 + man/download_flightsbr_file.Rd | 15 + man/get_aircrafts_dates_available.Rd |only man/get_aircrafts_url.Rd |only man/read_aircrafts.Rd | 6 man/read_airfares.Rd | 6 man/read_airport_movements.Rd | 6 man/read_flights.Rd | 13 + man/roxygen |only tests/testthat/test_read_aircrafts.R | 13 + tests/testthat/test_read_airport_movements.R | 13 + tests/testthat/test_read_flights.R | 18 +- 33 files changed, 613 insertions(+), 256 deletions(-)
Title: Chi-Square and G-Square Test of Independence, Residual Analysis,
and Measures of Categorical Association
Description: Provides the facility to perform the chi-square and G-square test of independence, calculates permutation-based p value, and provides measures of association such as Phi, odds ratio with 95 percent CI and p value, adjusted contingency coefficient, Cramer's V and 95 percent CI, bias-corrected Cramer's V, Cohen's w, Goodman-Kruskal's lambda, gamma and its p value, and tau, Cohen's k and its 95 percent CI. It also calculates standardized, moment-corrected standardized, and adjusted standardized residuals, and their significance. Different outputs are returned in nicely formatted tables.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between chisquare versions 0.7 dated 2023-11-03 and 0.8 dated 2023-12-04
DESCRIPTION | 6 MD5 | 14 - NAMESPACE | 3 NEWS.md | 31 +- R/chisquare.r | 416 ++++++++++++++++++++++++++------------ R/suggest_chi_squared_meth.R |only README.md | 20 + man/chisquare.Rd | 222 +++++++++++++------- man/suggest_chi_squared_method.Rd |only 9 files changed, 484 insertions(+), 228 deletions(-)
Title: Bayesian Inference for Log-Normal Data
Description: Bayesian inference under log-normality assumption must be performed very carefully. In fact, under the common priors for the variance, useful quantities in the original data scale (like mean and quantiles) do not have posterior moments that are finite (Fabrizi et al. 2012 <doi:10.1214/12-BA733>). This package allows to easily carry out a proper Bayesian inferential procedure by fixing a suitable distribution (the generalized inverse Gaussian) as prior for the variance. Functions to estimate several kind of means (unconditional, conditional and conditional under a mixed model) and quantiles (unconditional and conditional) are provided.
Author: Aldo Gardini [aut, cre] ,
Enrico Fabrizi [aut] ,
Carlo Trivisano [aut]
Maintainer: Aldo Gardini <aldo.gardini2@unibo.it>
Diff between BayesLN versions 0.2.8 dated 2022-10-26 and 0.2.10 dated 2023-12-04
DESCRIPTION | 10 MD5 | 16 - R/RcppExports.R | 2 build/vignette.rds |binary inst/doc/BayesLogNormal.html | 458 +++++++++++++++++++++---------------------- src/Makevars | 3 src/Makevars.win | 3 src/RcppExports.cpp | 6 src/gibbs.cpp | 2 9 files changed, 248 insertions(+), 252 deletions(-)
More information about diseasemapping at CRAN
Permanent link
Title: Construction and Evaluation of Metamodels
Description: Estimation, validation and prediction of models of different types : linear models, additive models, MARS,PolyMARS and Kriging.
Author: D. Dupuy and C. Helbert
Maintainer: C. Helbert <Celine.Helbert@ec-lyon.fr>
Diff between DiceEval versions 1.5.1 dated 2022-07-04 and 1.6.1 dated 2023-12-04
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/crossValidation.R | 2 +- R/modelComparison.R | 18 +++++++++--------- inst/CITATION | 4 ++-- man/dataIRSN5D.Rd | 2 +- man/testIRSN5D.Rd | 2 +- 7 files changed, 25 insertions(+), 25 deletions(-)
Title: Nested Data Summary and Adverse Events
Description: Miscellaneous code snippets and functions with pipes and
multiple package dependencies used for summarizing nested data and
adverse events.
Author: Lisa Avery [aut] ,
Zeynep Baskurt [aut],
Osvaldo Espin-Garcia [aut],
Katrina Hueniken [aut],
Katherine Lajkosz [aut] ,
Xuan Li [aut],
Tyler Pittman [cre, aut] ,
Anna Santiago [aut] ,
Jessica Weiss [aut],
Wei Xu [aut]
Maintainer: Tyler Pittman <tyler.pittman@uhn.ca>
Diff between BiostatsUHNplus versions 0.0.8 dated 2023-11-28 and 0.0.9 dated 2023-12-04
DESCRIPTION | 27 MD5 | 84 - NAMESPACE | 7 NEWS.md | 24 R/ae_timeline_plot.R | 2 R/caterpillar_plot.R |only R/covsum_nested.R | 108 +- R/data.R | 16 R/dsmb_ccru.R | 4 R/globals.R | 3 R/nice_mcmcglmm.R | 55 - R/nice_mcmcglmm_icc.R |only README.md | 497 +++++++--- man/ae.Rd | 8 man/caterpillar_plot.Rd |only man/covsum_nested.Rd | 25 man/demography.Rd | 6 man/drug1_admin.Rd | 8 man/drug2_admin.Rd | 8 man/dsmb_ccru.Rd | 4 man/figures/ana10-1.png |binary man/figures/caterpillar_plot_Cows_Model.png |binary man/figures/caterpillar_plot_Yards_Model.png |binary man/figures/caterpillar_plot_ae_category.png |only man/figures/caterpillar_plot_subject.png |only man/figures/variance_pie_plot.png |binary man/ineligibility.Rd | 6 man/nice_mcmcglmm.Rd | 22 man/nice_mcmcglmm_icc.Rd |only man/rm_covsum_nested.Rd | 36 man/tables/ae_detail_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY__30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY__30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY__30OCT2020.xlsx |binary man/tables/output_tab.html |only man/tables/output_tab.tex |only 47 files changed, 668 insertions(+), 282 deletions(-)
More information about BiostatsUHNplus at CRAN
Permanent link
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript
and WebAssembly engine. This package can be compiled either with V8 version 6
and up or NodeJS when built as a shared library.
Author: Jeroen Ooms [aut, cre] ,
Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between V8 versions 4.4.0 dated 2023-10-09 and 4.4.1 dated 2023-12-04
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 3 +++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/npm.html | 4 ++-- inst/doc/v8_intro.html | 6 +++--- src/bindings.cpp | 2 +- 8 files changed, 19 insertions(+), 16 deletions(-)
Title: Client for 'jq', a 'JSON' Processor
Description: Client for 'jq', a 'JSON' processor (<https://jqlang.github.io/jq/>),
written in C. 'jq' allows the following with 'JSON' data: index into, parse,
do calculations, cut up and filter, change key names and values, perform
conditionals and comparisons, and more.
Author: Rich FitzJohn [aut],
Jeroen Ooms [aut, cre],
Scott Chamberlain [aut],
Stefan Milton Bache [aut]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between jqr versions 1.3.2 dated 2023-11-20 and 1.3.3 dated 2023-12-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ src/jqr.c | 2 +- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gert versions 2.0.0 dated 2023-09-26 and 2.0.1 dated 2023-12-04
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 3 +++ build/vignette.rds |binary cleanup | 1 - configure | 2 +- inst/doc/gert.html | 23 ++++++++++++----------- src/clone.c | 2 +- 8 files changed, 27 insertions(+), 24 deletions(-)
Title: Generate Simulated Sawn Timber Strength Grading Data
Description: Tools for generating simulated sawn timber
strength grading data with a main focus on statistical simulation based on
covariance matrices. Simulation data
for Norway spruce sawn timber from Austria and reference values of means and
standard deviations of grade determining properties from literature
for a number of European countries are provided, as well.
Author: Andreas Weidenhiller [cre, aut]
,
Anton Wegscheider [aut]
Maintainer: Andreas Weidenhiller <a.weidenhiller@holzforschung.at>
Diff between WoodSimulatR versions 0.6.0 dated 2022-06-20 and 0.6.1 dated 2023-12-04
DESCRIPTION | 10 MD5 | 54 - NEWS.md | 85 +-- R/stat_sim_dataset.r | 948 ++++++++++++++++----------------- R/statistical_simulation.r | 36 - R/subsample_data.r | 11 build/vignette.rds |binary data/gdp_data.rda |binary data/ws_be.rda |binary data/ws_be_logf.rda |binary data/ws_be_te.rda |binary data/ws_be_te_logf.rda |binary data/ws_be_tr.rda |binary data/ws_be_tr_logf.rda |binary data/ws_t.rda |binary data/ws_t_logf.rda |binary data/ws_t_te.rda |binary data/ws_t_te_logf.rda |binary data/ws_t_tr.rda |binary data/ws_t_tr_logf.rda |binary inst/doc/woodsimulatr_basics.R | 2 inst/doc/woodsimulatr_basics.Rmd | 1070 +++++++++++++++++++------------------- inst/doc/woodsimulatr_basics.html | 747 +++++++++++++------------- man/get_transform_names.Rd | 7 man/simbase_covar.Rd | 3 man/simbase_labeler.Rd | 6 tests/testthat.R | 8 vignettes/woodsimulatr_basics.Rmd | 1070 +++++++++++++++++++------------------- 28 files changed, 2051 insertions(+), 2006 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity
in all their dimensions (taxonomic, phylogenetic and functional).
It allows performing a number of analyses based on species
identities/abundances, phylogenetic/functional distances, trees,
convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Author: Pedro Cardoso [aut, cre],
Stefano Mammola [aut],
Francois Rigal [aut],
Jose Carvalho [aut]
Maintainer: Pedro Cardoso <pmcardoso@fc.ul.pt>
Diff between BAT versions 2.9.4 dated 2023-10-10 and 2.9.5 dated 2023-12-04
DESCRIPTION | 8 MD5 | 26 +- R/BAT.R | 497 ++++++++++++++++++++++++++++------------------- man/hull.build.Rd | 8 man/hyper.build.Rd | 12 - man/hyper.quality.Rd | 4 man/kernel.build.Rd | 8 man/mixture.Rd | 4 man/optim.alpha.Rd | 19 + man/optim.alpha.stats.Rd | 15 - man/optim.beta.Rd | 31 ++ man/optim.beta.stats.Rd | 17 - man/ses.Rd | 2 man/tree.build.Rd | 10 14 files changed, 403 insertions(+), 258 deletions(-)
Title: Regression Models for Ordinal Data
Description: Implementation of cumulative link (mixed) models also known
as ordered regression models, proportional odds models, proportional
hazards models for grouped survival times and ordered logit/probit/...
models. Estimation is via maximum likelihood and mixed models are fitted
with the Laplace approximation and adaptive Gauss-Hermite quadrature.
Multiple random effect terms are allowed and they may be nested, crossed or
partially nested/crossed. Restrictions of symmetry and equidistance can be
imposed on the thresholds (cut-points/intercepts). Standard model
methods are available (summary, anova, drop-methods, step,
confint, predict etc.) in addition to profile methods and slice
methods for visualizing the likelihood function and checking
convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>
Diff between ordinal versions 2022.11-16 dated 2022-11-16 and 2023.12-4 dated 2023-12-04
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS | 6 +++++- R/clm.R | 4 ++-- R/clm.Thetamat.R | 2 +- R/clm.fit.R | 6 +++--- R/clm.fitter.R | 8 ++++---- R/clm.profile.R | 4 ++-- R/clm.simple.R | 4 ++-- R/clm.start.R | 19 +++++++++++-------- R/clmm.ssr.R | 4 ++-- R/convergence.R | 2 +- R/utils.R | 6 +++--- inst/CITATION | 25 +++++++++++-------------- inst/doc/clm_article.pdf |binary inst/doc/clmm2_tutorial.pdf |binary 16 files changed, 66 insertions(+), 62 deletions(-)
Title: Nested Cross-Validation with 'glmnet' and 'caret'
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.
Author: Myles Lewis [aut, cre] ,
Athina Spiliopoulou [aut] ,
Katriona Goldmann [aut]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between nestedcv versions 0.7.0 dated 2023-10-26 and 0.7.3 dated 2023-12-04
nestedcv-0.7.0/nestedcv/man/boxplot_model.Rd |only nestedcv-0.7.3/nestedcv/DESCRIPTION | 9 nestedcv-0.7.3/nestedcv/MD5 | 51 +-- nestedcv-0.7.3/nestedcv/NAMESPACE | 15 - nestedcv-0.7.3/nestedcv/NEWS.md | 18 + nestedcv-0.7.3/nestedcv/R/cva.glmnet.R | 9 nestedcv-0.7.3/nestedcv/R/nest_filter_balance.R | 41 ++ nestedcv-0.7.3/nestedcv/R/nestcv.train.R | 53 +++ nestedcv-0.7.3/nestedcv/R/nestcv_SuperLearner.R | 176 ++++++++++-- nestedcv-0.7.3/nestedcv/R/nestedcv.R | 53 +++ nestedcv-0.7.3/nestedcv/R/outercv.R | 41 ++ nestedcv-0.7.3/nestedcv/R/plots.R | 4 nestedcv-0.7.3/nestedcv/R/repeatcv.R |only nestedcv-0.7.3/nestedcv/R/shap.R | 5 nestedcv-0.7.3/nestedcv/R/txtProgressBar2.R |only nestedcv-0.7.3/nestedcv/inst/doc/nestedcv.R | 76 +++++ nestedcv-0.7.3/nestedcv/inst/doc/nestedcv.Rmd | 163 ++++++++++- nestedcv-0.7.3/nestedcv/inst/doc/nestedcv.html | 273 ++++++++++++++----- nestedcv-0.7.3/nestedcv/inst/doc/nestedcv_shap.html | 2 nestedcv-0.7.3/nestedcv/man/boxplot_expression.Rd |only nestedcv-0.7.3/nestedcv/man/nestcv.SuperLearner.Rd | 30 ++ nestedcv-0.7.3/nestedcv/man/nestcv.glmnet.Rd | 24 + nestedcv-0.7.3/nestedcv/man/nestcv.train.Rd | 19 + nestedcv-0.7.3/nestedcv/man/outercv.Rd | 19 + nestedcv-0.7.3/nestedcv/man/pred_nestcv_glmnet.Rd | 3 nestedcv-0.7.3/nestedcv/man/predict.nestcv.glmnet.Rd | 5 nestedcv-0.7.3/nestedcv/man/repeatcv.Rd |only nestedcv-0.7.3/nestedcv/man/repeatfolds.Rd |only nestedcv-0.7.3/nestedcv/man/txtProgressBar2.Rd |only nestedcv-0.7.3/nestedcv/vignettes/nestedcv.Rmd | 163 ++++++++++- 30 files changed, 1069 insertions(+), 183 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.12.6.6.0 dated 2023-10-31 and 0.12.6.6.1 dated 2023-12-04
ChangeLog | 12 +++++++ DESCRIPTION | 8 ++-- MD5 | 20 ++++++------ build/partial.rdb |binary build/vignette.rds |binary configure | 18 +++++----- configure.ac | 2 - inst/NEWS.Rd | 9 +++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/RcppArmadillo/interface/RcppArmadilloForward.h | 14 ++++---- 11 files changed, 52 insertions(+), 31 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library implementing 'Scalability Protocols', a reliable,
high-performance standard for common communications patterns including
publish/subscribe, request/reply and service discovery, over in-process,
IPC, TCP, WebSocket and secure TLS transports. As its own threaded
concurrency framework, provides a toolkit for asynchronous programming and
distributed computing, with intuitive 'aio' objects which resolve
automatically upon completion of asynchronous operations, and
synchronisation primitives allowing R to wait upon events signalled by
concurrent threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 0.10.4 dated 2023-11-03 and 0.11.0 dated 2023-12-04
nanonext-0.10.4/nanonext/man/nextmode.Rd |only nanonext-0.10.4/nanonext/man/weakref.Rd |only nanonext-0.10.4/nanonext/src/mbedtls-1ec6906.tar.xz |only nanonext-0.10.4/nanonext/src/nng-a54820f.tar.xz |only nanonext-0.11.0/nanonext/DESCRIPTION | 6 nanonext-0.11.0/nanonext/LICENSE.note | 220 --------- nanonext-0.11.0/nanonext/MD5 | 81 +-- nanonext-0.11.0/nanonext/NAMESPACE | 9 nanonext-0.11.0/nanonext/NEWS.md | 24 + nanonext-0.11.0/nanonext/R/aio.R | 18 nanonext-0.11.0/nanonext/R/docs.R | 30 - nanonext-0.11.0/nanonext/R/messenger.R | 2 nanonext-0.11.0/nanonext/R/nano.R | 10 nanonext-0.11.0/nanonext/R/sendrecv.R | 8 nanonext-0.11.0/nanonext/R/socket.R | 10 nanonext-0.11.0/nanonext/R/sync.R | 76 ++- nanonext-0.11.0/nanonext/R/utils.R | 110 ---- nanonext-0.11.0/nanonext/README.md | 55 +- nanonext-0.11.0/nanonext/configure | 4 nanonext-0.11.0/nanonext/configure.ucrt | 4 nanonext-0.11.0/nanonext/man/call_aio.Rd | 14 nanonext-0.11.0/nanonext/man/cv.Rd | 21 nanonext-0.11.0/nanonext/man/dot-until.Rd |only nanonext-0.11.0/nanonext/man/grapes-twiddle-greater-than-grapes.Rd |only nanonext-0.11.0/nanonext/man/next_config.Rd |only nanonext-0.11.0/nanonext/man/pipe_notify.Rd | 8 nanonext-0.11.0/nanonext/man/protocols.Rd | 20 nanonext-0.11.0/nanonext/man/reap.Rd | 10 nanonext-0.11.0/nanonext/man/reply.Rd | 8 nanonext-0.11.0/nanonext/man/request.Rd | 8 nanonext-0.11.0/nanonext/man/send.Rd | 8 nanonext-0.11.0/nanonext/man/send_aio.Rd | 8 nanonext-0.11.0/nanonext/man/stop_aio.Rd | 2 nanonext-0.11.0/nanonext/man/transports.Rd | 10 nanonext-0.11.0/nanonext/src/Makevars.win | 6 nanonext-0.11.0/nanonext/src/aio.c | 136 ++++- nanonext-0.11.0/nanonext/src/core.c | 202 ++++---- nanonext-0.11.0/nanonext/src/init.c | 38 - nanonext-0.11.0/nanonext/src/keycert.c | 18 nanonext-0.11.0/nanonext/src/mbedtls-edb8fec.tar.xz |only nanonext-0.11.0/nanonext/src/nanonext.h | 226 ++++----- nanonext-0.11.0/nanonext/src/nng-a6de76c.tar.xz |only nanonext-0.11.0/nanonext/src/protocol.c | 13 nanonext-0.11.0/nanonext/src/thread.c | 237 +++++++++- nanonext-0.11.0/nanonext/src/utils.c | 26 - nanonext-0.11.0/nanonext/tests/tests.R | 49 +- 46 files changed, 928 insertions(+), 807 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [ctb],
Denes Toth [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 2.3.0 dated 2023-10-25 and 2.3.1 dated 2023-12-04
DESCRIPTION | 6 +-- MD5 | 12 +++--- NEWS.md | 3 + build/vignette.rds |binary inst/doc/checkmate.html | 96 ++++++++++++++++++++++++------------------------ inst/doc/tinytest.html | 4 +- src/helper.c | 2 - 7 files changed, 63 insertions(+), 60 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-15 0.1.2
Title: Estimates and Plots Single-Level and Multilevel Latent Class
Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al (2023) <arXiv:2305.07276>.
Author: Roberto Di Mari [aut, cre],
Johan Lyrvall [aut],
Zsuzsa Bakk [ctb],
Jennifer Oser [ctb],
Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>
Diff between multilevLCA versions 1.3 dated 2023-10-23 and 1.4 dated 2023-12-04
DESCRIPTION | 8 - MD5 | 16 +- R/MLCAfunctions.R | 372 +++++++++++++++++++++++++++++++++++++------------- build/partial.rdb |binary man/multiLCA.Rd | 8 - man/plot.multiLCA.Rd | 100 ++++++------- src/LCAfit.cpp | 128 +++++++++++++---- src/Utils.cpp | 39 ++++- src/multilevLC_EM.cpp | 149 ++++++++++---------- 9 files changed, 557 insertions(+), 263 deletions(-)
Title: Bayesian Meta-Analysis of Pleiotropic Effects Using Group
Structure
Description: Run a Gibbs sampler for a multivariate Bayesian sparse group selection model with Dirac, continuous and hierarchical spike prior for detecting pleiotropy on the traits. This package is designed for summary statistics containing estimated regression coefficients and its estimated covariance matrix. The methodology is available from: Baghfalaki, T., Sugier, P. E., Truong, T., Pettitt, A. N., Mengersen, K., & Liquet, B. (2021) <doi:10.1002/sim.8855>.
Author: Taban Baghfalaki
Maintainer: Taban Baghfalaki <t.baghfalaki@gmail.com>
Diff between GCPBayes versions 4.0.0 dated 2022-11-02 and 4.1.0 dated 2023-12-04
DESCRIPTION | 12 +++++++----- MD5 | 15 ++++++++++----- NAMESPACE | 52 +++++++++++++++++++++++++++------------------------- NEWS.md | 21 ++++++++------------- R/DS.R | 14 +++++++------- R/HS.R | 24 ++++++++++++------------ R/RcppExports.R |only src |only 8 files changed, 71 insertions(+), 67 deletions(-)
Title: Statistical Tools for Immune Correlates Analysis of Vaccine
Clinical Trial Data
Description: Various semiparametric and nonparametric statistical tools for
immune correlates analysis of vaccine clinical trial data. This includes
calculation of summary statistics and estimation of risk, vaccine efficacy,
controlled effects (controlled risk and controlled vaccine efficacy), and
mediation effects (natural direct effect, natural indirect effect,
proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022)
<doi:10.1093/biostatistics/kxac024> and Fay MP and Follmann DA (2023)
<doi:10.48550/arXiv.2208.06465>.
Author: Avi Kenny [aut, cre, cph]
Maintainer: Avi Kenny <avi.kenny@gmail.com>
Diff between vaccine versions 1.0.0 dated 2023-10-20 and 1.1.0 dated 2023-12-04
DESCRIPTION | 13 + MD5 | 34 ++-- NEWS.md | 10 + R/est_ce.R | 19 +- R/est_cox.R | 20 ++ R/est_np.R | 205 ++++++++++++++++++++++++++++-- R/influence_functions.R | 53 +++++++ R/load_data.R | 48 +++++-- R/nuisance_estimators.R | 84 ++++++++++++ R/one_step_estimators.R | 56 ++++++++ README.md | 7 - inst/doc/basic.Rmd | 2 inst/doc/basic.html | 2 man/est_ce.Rd | 7 - man/vaccine-package.Rd | 2 tests/testthat/test-test-core-functions.R | 34 ++++ vignettes/basic.Rmd | 2 vignettes/basic.Rmd.orig | 2 18 files changed, 538 insertions(+), 62 deletions(-)
Title: Simplified Fetching and Processing of Microarray and RNA-Seq
Data
Description: Wrapper around various existing tools and command-line interfaces,
providing a standard interface, simple parallelization, and detailed logging.
For microarray data, maps probe sets to standard gene IDs, building on
'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>,
'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>,
Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>,
and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>.
For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology
Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and
quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>,
performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>,
quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197& [...truncated...]
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between seeker versions 1.1.3 dated 2023-05-23 and 1.1.4 dated 2023-12-04
DESCRIPTION | 8 - MD5 | 34 ++-- R/array_utils.R | 6 R/tximport.R | 2 build/vignette.rds |binary inst/doc/introduction.R | 8 - inst/doc/introduction.html | 136 +++++++++---------- inst/doc/reproducibility.R | 16 +- inst/doc/reproducibility.html | 208 +++++++++++++++--------------- inst/extdata/platform_cdf.csv | 1 tests/testthat/data/GPL6887.qs |binary tests/testthat/data/GPL7202.qs |binary tests/testthat/data/GSE147674_eset.qs |binary tests/testthat/data/GSE167458_eset.qs |binary tests/testthat/data/GSE50143_eset.qs |binary tests/testthat/data/map_pkg_ver.qs |binary tests/testthat/data/multiqc_output.qs |binary tests/testthat/data/seeker_output_full.qs |binary 18 files changed, 210 insertions(+), 209 deletions(-)
Title: R Commander Plug-in for Case 2 Best-Worst Scaling
Description: Adds menu items for Case 2 (profile case) best-worst scaling (BWS2) to the R Commander. BWS2 is a question-based survey method that constructs profiles (combinations of attribute levels) using an orthogonal array, asks respondents to select the best and worst levels in each profile, and measures preferences for attribute levels by analyzing the responses. For details, see Aizaki and Fogarty (2019) <doi:10.1016/j.jocm.2019.100171>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between RcmdrPlugin.BWS2 versions 0.1-0 dated 2022-06-07 and 0.2-0 dated 2023-12-04
DESCRIPTION | 8 MD5 | 11 - NEWS |only R/RcmdrPlugin.BWS2.R | 324 +++++++++++++++++++++++++++++----------- inst/CITATION | 24 +- inst/etc/menus.txt | 8 man/RcmdrPlugin.BWS2-package.Rd | 13 + 7 files changed, 272 insertions(+), 116 deletions(-)
More information about RcmdrPlugin.BWS2 at CRAN
Permanent link
Title: Processing and Analyzing of Diagnostics Trials
Description: Provides methods and functions to analyze the quantitative or
qualitative performance for diagnostic assays, and outliers detection,
reader precision and reference range are discussed. Most of the methods
and algorithms refer to CLSI (Clinical & Laboratory Standards Institute)
recommendations and NMPA (National Medical Products Administration)
guidelines. In additional, relevant plots are constructed by 'ggplot2'.
Author: Kai Gu [aut, cre, cph]
Maintainer: Kai Gu <gukai1212@163.com>
Diff between mcradds versions 1.0.1 dated 2023-10-11 and 1.1.0 dated 2023-12-04
mcradds-1.0.1/mcradds/man/MCR-class.Rd |only mcradds-1.1.0/mcradds/DESCRIPTION | 19 mcradds-1.1.0/mcradds/MD5 | 71 mcradds-1.1.0/mcradds/NAMESPACE | 14 mcradds-1.1.0/mcradds/NEWS.md | 17 mcradds-1.1.0/mcradds/R/autoplot.R | 312 +- mcradds-1.1.0/mcradds/R/data.R | 16 mcradds-1.1.0/mcradds/R/desc.R |only mcradds-1.1.0/mcradds/R/mcr.R | 46 mcradds-1.1.0/mcradds/R/package.R | 33 mcradds-1.1.0/mcradds/R/pkg_class.R | 55 mcradds-1.1.0/mcradds/R/pkg_methods.R | 48 mcradds-1.1.0/mcradds/R/qual_stat.R | 12 mcradds-1.1.0/mcradds/R/utils.R | 44 mcradds-1.1.0/mcradds/README.md | 4 mcradds-1.1.0/mcradds/data/adsl_sub.rda |only mcradds-1.1.0/mcradds/inst/WORDLIST | 22 mcradds-1.1.0/mcradds/inst/doc/mcradds.R | 106 mcradds-1.1.0/mcradds/inst/doc/mcradds.Rmd | 83 mcradds-1.1.0/mcradds/inst/doc/mcradds.html | 1096 +++++----- mcradds-1.1.0/mcradds/man/Desc-class.Rd |only mcradds-1.1.0/mcradds/man/adsl_sub.Rd |only mcradds-1.1.0/mcradds/man/autoplot.Rd | 56 mcradds-1.1.0/mcradds/man/calcBias.Rd |only mcradds-1.1.0/mcradds/man/calcium.Rd | 3 mcradds-1.1.0/mcradds/man/descfreq.Rd |only mcradds-1.1.0/mcradds/man/descvar.Rd |only mcradds-1.1.0/mcradds/man/diagTab.Rd | 2 mcradds-1.1.0/mcradds/man/getAccuracy.Rd | 3 mcradds-1.1.0/mcradds/man/getCoefficients.Rd |only mcradds-1.1.0/mcradds/man/h_fmt_count_perc.Rd |only mcradds-1.1.0/mcradds/man/mcreg.Rd |only mcradds-1.1.0/mcradds/man/platelet.Rd | 2 mcradds-1.1.0/mcradds/man/printSummary.Rd |only mcradds-1.1.0/mcradds/man/show.Rd | 24 mcradds-1.1.0/mcradds/tests/spelling.R | 9 mcradds-1.1.0/mcradds/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-default-arguments.svg |only mcradds-1.1.0/mcradds/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-multiple-arguments.svg |only mcradds-1.1.0/mcradds/tests/testthat/test-autoplot.R | 58 mcradds-1.1.0/mcradds/tests/testthat/test-desc.R |only mcradds-1.1.0/mcradds/tests/testthat/test-mcr.R | 122 - mcradds-1.1.0/mcradds/tests/testthat/test-pkg_methods.R | 35 mcradds-1.1.0/mcradds/tests/testthat/test-qual_stat.R | 7 mcradds-1.1.0/mcradds/vignettes/mcradds.Rmd | 83 44 files changed, 1506 insertions(+), 896 deletions(-)
Title: Inferring Cell-Specific Gene Regulatory Network
Description: A method for inferring cell-specific gene regulatory network from single-cell sequencing data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 0.99.7 dated 2023-10-30 and 0.99.8 dated 2023-12-04
DESCRIPTION | 8 LICENSE | 4 MD5 | 70 NAMESPACE | 68 R/RcppExports.R | 198 +- R/auc.calculate.R | 256 +-- R/compute.gene.rank.R | 58 R/data.R | 30 R/inferCSN-package.R | 24 R/inferCSN.R | 459 ++--- R/network.visualization.R | 438 ++--- R/sparse.regression.R | 826 +++++----- R/utils.R | 662 ++++---- README.md | 86 - man/acc.calculate.Rd | 34 man/auc.calculate.Rd | 80 man/check.parameters.Rd | 122 - man/coef.inferCSN.Rd | 60 man/compute.gene.rank.Rd | 54 man/contrast.networks.Rd | 72 man/dynamic.networks.Rd | 58 man/exampleGroundTruth.Rd | 18 man/exampleMatrix.Rd | 18 man/figures/inferCSN.svg | 3377 ----------------------------------------- man/inferCSN-package.Rd | 30 man/inferCSN.Rd | 202 +- man/inferCSN.fit.Rd | 212 +- man/is.scalar.Rd | 34 man/net.format.Rd | 38 man/network.heatmap.Rd | 136 - man/predict.inferCSN.Rd | 74 man/print.inferCSN.Rd | 48 man/sparse.regression.Rd | 110 - man/sub.inferCSN.Rd | 116 - tests/testthat.R | 18 tests/testthat/test-inferCSN.R | 8 36 files changed, 2356 insertions(+), 5750 deletions(-)
Title: Fetch Data from Various Data Sources
Description: Contains functions to fetch data from various data sources.
The user first creates a catalog of objects from a data source,
then fetches data from the catalog. The package provides an easy
way to access data from many different types of sources.
Author: David Bosak [aut, cre],
Kevin Kramer [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between fetch versions 0.1.3 dated 2023-09-09 and 0.1.4 dated 2023-12-04
DESCRIPTION | 8 +++----- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 9 insertions(+), 7 deletions(-)