Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-23 1.3.0
2021-04-23 1.2.2
2014-02-12 1.2.1
2014-02-05 1.2
2012-07-24 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-19 0.4.2
2021-10-03 0.4.1
2020-06-18 0.4.0
2020-03-31 0.3.0
2020-03-15 0.2.0
2020-03-07 0.1.1
2020-02-29 0.1.0
Title: Generate Publication Ready Visualizations of Single Cell
Transcriptomics Data
Description: A system that provides a streamlined way of generating publication ready plots for known Single-Cell transcriptomics data in a “publication ready” format. This is, the goal is to automatically generate plots with the highest quality possible, that can be used right away or with minimal modifications for a research article.
Author: Enrique Blanco-Carmona [cre, aut]
Maintainer: Enrique Blanco-Carmona <scpubr@gmail.com>
Diff between SCpubr versions 1.0.2 dated 2022-10-25 and 1.0.3 dated 2022-11-06
DESCRIPTION | 8 MD5 | 58 ++-- NEWS.md | 45 +++ R/do_CopyNumberVariantPlot.R | 32 +- R/do_DimPlot.R | 352 ++++++++++++++++++++++----- R/do_EnrichmentHeatmap.R | 211 +++++++++++++++- R/do_FeaturePlot.R | 236 +++++++++++++++--- R/do_GeyserPlot.R | 139 +++++----- R/do_GroupwiseDEPlot.R | 37 ++ R/do_PathwayActivityPlot.R | 87 +++++- R/do_RidgePlot.R | 4 R/do_TFActivityPlot.R | 74 ++++- R/do_ViolinPlot.R | 14 - R/utils.R | 143 ++++++++-- README.md | 2 man/do_BeeSwarmPlot.Rd | 2 man/do_CellularStatesPlot.Rd | 2 man/do_CopyNumberVariantPlot.Rd | 6 man/do_DimPlot.Rd | 22 + man/do_EnrichmentHeatmap.Rd | 85 ++++++ man/do_FeaturePlot.Rd | 24 + man/do_GeyserPlot.Rd | 15 - man/do_GroupwiseDEPlot.Rd | 6 man/do_PathwayActivityPlot.Rd | 13 man/do_TFActivityPlot.Rd | 15 - man/do_ViolinPlot.Rd | 8 man/doc_function.Rd | 16 + tests/testthat/test-do_GeyserPlot.R | 74 ----- tests/testthat/test-do_PathwayActivityPlot.R | 7 tests/testthat/test-do_TFActivityPlot.R | 7 30 files changed, 1319 insertions(+), 425 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.9.2 dated 2022-10-05 and 0.9.3 dated 2022-11-06
sasLM-0.9.2/sasLM/inst/doc/Report-Different-Simplest2209152151.pdf |only sasLM-0.9.2/sasLM/inst/doc/Report-NOT-OKs2209152151.pdf |only sasLM-0.9.2/sasLM/inst/doc/Validation-Report-GLM-2209152152.pdf |only sasLM-0.9.3/sasLM/DESCRIPTION | 7 sasLM-0.9.3/sasLM/MD5 | 194 +++++----- sasLM-0.9.3/sasLM/R/BasicUtil.R | 171 ++++++++ sasLM-0.9.3/sasLM/R/CV.R | 8 sasLM-0.9.3/sasLM/R/EMS.R | 24 - sasLM-0.9.3/sasLM/R/G2SWEEP.R | 21 - sasLM-0.9.3/sasLM/R/GLM.R | 78 ++-- sasLM-0.9.3/sasLM/R/Kurtosis.R | 12 sasLM-0.9.3/sasLM/R/KurtosisSE.R | 10 sasLM-0.9.3/sasLM/R/LCL.R | 14 sasLM-0.9.3/sasLM/R/Max.R | 12 sasLM-0.9.3/sasLM/R/Mean.R | 12 sasLM-0.9.3/sasLM/R/Median.R | 12 sasLM-0.9.3/sasLM/R/Min.R | 12 sasLM-0.9.3/sasLM/R/ModelMatrix.R | 13 sasLM-0.9.3/sasLM/R/N.R | 10 sasLM-0.9.3/sasLM/R/QuartileRange.R | 8 sasLM-0.9.3/sasLM/R/REG.R | 127 ++++++ sasLM-0.9.3/sasLM/R/Range.R | 12 sasLM-0.9.3/sasLM/R/SD.R | 12 sasLM-0.9.3/sasLM/R/SEM.R | 12 sasLM-0.9.3/sasLM/R/SLICE.R | 15 sasLM-0.9.3/sasLM/R/SS.R | 23 - sasLM-0.9.3/sasLM/R/Skewness.R | 12 sasLM-0.9.3/sasLM/R/SkewnessSE.R | 10 sasLM-0.9.3/sasLM/R/T3MS.R | 20 - sasLM-0.9.3/sasLM/R/T3test.R | 8 sasLM-0.9.3/sasLM/R/UCL.R | 14 sasLM-0.9.3/sasLM/R/UNIV.R | 54 +- sasLM-0.9.3/sasLM/R/WhiteTest.R |only sasLM-0.9.3/sasLM/R/af.R | 2 sasLM-0.9.3/sasLM/R/aov1.R | 39 +- sasLM-0.9.3/sasLM/R/aov2.R | 39 +- sasLM-0.9.3/sasLM/R/aov3.R | 33 + sasLM-0.9.3/sasLM/R/e1.R | 17 sasLM-0.9.3/sasLM/R/e2.R | 92 +++- sasLM-0.9.3/sasLM/R/e3.R | 27 - sasLM-0.9.3/sasLM/R/geoCV.R | 12 sasLM-0.9.3/sasLM/R/geoMean.R | 10 sasLM-0.9.3/sasLM/R/lfit.R | 4 sasLM-0.9.3/sasLM/R/lr.R | 21 - sasLM-0.9.3/sasLM/R/lr0.R | 4 sasLM-0.9.3/sasLM/R/regD.R | 6 sasLM-0.9.3/sasLM/R/trimmedMean.R | 8 sasLM-0.9.3/sasLM/inst/NEWS.Rd | 10 sasLM-0.9.3/sasLM/inst/doc/Report-Different-Simplest2211061531.pdf |only sasLM-0.9.3/sasLM/inst/doc/Report-NOT-OKs2211061532.pdf |only sasLM-0.9.3/sasLM/inst/doc/Validation-Report-GLM-2211061533.pdf |only sasLM-0.9.3/sasLM/inst/doc/sasLM-manual.pdf |binary sasLM-0.9.3/sasLM/man/BY.Rd | 6 sasLM-0.9.3/sasLM/man/BasicUtil.Rd | 2 sasLM-0.9.3/sasLM/man/CIest.Rd | 2 sasLM-0.9.3/sasLM/man/CV.Rd | 6 sasLM-0.9.3/sasLM/man/Coll.Rd | 2 sasLM-0.9.3/sasLM/man/Cor.test.Rd | 2 sasLM-0.9.3/sasLM/man/EMS.Rd | 12 sasLM-0.9.3/sasLM/man/G2SWEEP.Rd | 26 - sasLM-0.9.3/sasLM/man/GLM.Rd | 4 sasLM-0.9.3/sasLM/man/Kurtosis.Rd | 4 sasLM-0.9.3/sasLM/man/KurtosisSE.Rd | 4 sasLM-0.9.3/sasLM/man/LCL.Rd | 4 sasLM-0.9.3/sasLM/man/LSM.Rd | 24 - sasLM-0.9.3/sasLM/man/Max.Rd | 4 sasLM-0.9.3/sasLM/man/Mean.Rd | 4 sasLM-0.9.3/sasLM/man/Median.Rd | 4 sasLM-0.9.3/sasLM/man/Min.Rd | 4 sasLM-0.9.3/sasLM/man/ModelMatrix.Rd | 4 sasLM-0.9.3/sasLM/man/N.Rd | 4 sasLM-0.9.3/sasLM/man/Pcor.test.Rd | 2 sasLM-0.9.3/sasLM/man/QuartileRange.Rd | 4 sasLM-0.9.3/sasLM/man/REG.Rd | 18 sasLM-0.9.3/sasLM/man/Range.Rd | 4 sasLM-0.9.3/sasLM/man/SD.Rd | 4 sasLM-0.9.3/sasLM/man/SEM.Rd | 4 sasLM-0.9.3/sasLM/man/SLICE.Rd | 2 sasLM-0.9.3/sasLM/man/Skewness.Rd | 4 sasLM-0.9.3/sasLM/man/SkewnessSE.Rd | 4 sasLM-0.9.3/sasLM/man/T3MS.Rd | 2 sasLM-0.9.3/sasLM/man/UCL.Rd | 4 sasLM-0.9.3/sasLM/man/UNIV.Rd | 7 sasLM-0.9.3/sasLM/man/WhiteTest.Rd |only sasLM-0.9.3/sasLM/man/aov1.Rd | 3 sasLM-0.9.3/sasLM/man/aov2.Rd | 3 sasLM-0.9.3/sasLM/man/aov3.Rd | 3 sasLM-0.9.3/sasLM/man/e1.Rd | 8 sasLM-0.9.3/sasLM/man/e2.Rd | 11 sasLM-0.9.3/sasLM/man/e3.Rd | 7 sasLM-0.9.3/sasLM/man/geoCV.Rd | 10 sasLM-0.9.3/sasLM/man/geoMean.Rd | 7 sasLM-0.9.3/sasLM/man/lfit.Rd | 10 sasLM-0.9.3/sasLM/man/lr.Rd | 12 sasLM-0.9.3/sasLM/man/lr0.Rd | 8 sasLM-0.9.3/sasLM/man/trimmedMean.Rd | 4 sasLM-0.9.3/sasLM/man/tsum.Rd | 12 sasLM-0.9.3/sasLM/man/tsum0.Rd | 7 sasLM-0.9.3/sasLM/man/tsum1.Rd | 12 sasLM-0.9.3/sasLM/man/tsum2.Rd | 14 sasLM-0.9.3/sasLM/man/tsum3.Rd | 14 sasLM-0.9.3/sasLM/tests/Test.R | 23 - 102 files changed, 1046 insertions(+), 564 deletions(-)
Title: Inference Tools in Time Series Based on Record Statistics
Description: Statistical tools based on the probabilistic properties of the
record occurrence in a sequence of independent and identically distributed
continuous random variables. In particular, tools to prepare a time series
as well as distribution-free trend and change-point tests and graphical
tools to study the record occurrence.
Author: Jorge Castillo-Mateo [aut, cre, cph]
,
Ana C. Cebrian [ths] ,
Jesus Asin [ths]
Maintainer: Jorge Castillo-Mateo <jorgecastillomateo@gmail.com>
Diff between RecordTest versions 2.1.0 dated 2021-08-08 and 2.1.1 dated 2022-11-06
DESCRIPTION | 20 +- MD5 | 80 ++++----- R/N.plot.R | 36 ++-- R/N.test.R | 20 +- R/RecordTest.R | 20 +- R/TX_Zaragoza-data.R | 42 ++-- R/ZaragozaSeries-data.R | 4 R/brown.method.R | 11 - R/change.point.R | 66 ++----- R/foster.plot.R | 24 +- R/foster.test.R | 11 - R/lr.test.R | 7 R/p.plot.R | 36 ++-- R/p.record.R | 5 R/p.regression.test.R | 4 R/score.test.R | 7 R/series_split.R | 7 R/series_uncor.R | 39 ++-- README.md | 28 +++ build/partial.rdb |binary build/vignette.rds |binary data/TX_Zaragoza.rda |binary data/TX_Zaragoza29F.rda |only inst/CITATION |only inst/NEWS.Rd | 21 ++ inst/doc/RecordTest.html | 404 +++++++++++++++++++++++++++++++++++++++++----- man/N.plot.Rd | 27 +-- man/N.test.Rd | 19 +- man/RecordTest-package.Rd | 19 +- man/TX_Zaragoza.Rd | 40 ++-- man/ZaragozaSeries.Rd | 4 man/brown.method.Rd | 11 - man/change.point.Rd | 65 ++----- man/foster.plot.Rd | 19 +- man/foster.test.Rd | 11 - man/lr.test.Rd | 7 man/p.plot.Rd | 19 +- man/p.record.Rd | 5 man/p.regression.test.Rd | 4 man/score.test.Rd | 7 man/series_split.Rd | 7 man/series_uncor.Rd | 31 ++- 42 files changed, 799 insertions(+), 388 deletions(-)
Title: Automatically Position Non-Overlapping Text Labels with
'ggplot2'
Description: Provides text and label geoms for 'ggplot2' that help to avoid
overlapping text labels. Labels repel away from each other and away from the
data points.
Author: Kamil Slowikowski [aut, cre] ,
Alicia Schep [ctb] ,
Sean Hughes [ctb] ,
Trung Kien Dang [ctb] ,
Saulius Lukauskas [ctb],
Jean-Olivier Irisson [ctb] ,
Zhian N Kamvar [ctb] ,
Thompson Ryan [ctb] ,
Dervieux Christophe [ctb] ,
Yutani Hiroaki [ctb],
Pierr [...truncated...]
Maintainer: Kamil Slowikowski <kslowikowski@gmail.com>
Diff between ggrepel versions 0.9.1 dated 2021-01-15 and 0.9.2 dated 2022-11-06
ggrepel-0.9.1/ggrepel/man/figures/ggrepel-allison_horst.jpg |only ggrepel-0.9.1/ggrepel/man/ggrepel-ggproto.Rd |only ggrepel-0.9.2/ggrepel/DESCRIPTION | 13 - ggrepel-0.9.2/ggrepel/MD5 | 33 +- ggrepel-0.9.2/ggrepel/NAMESPACE | 3 ggrepel-0.9.2/ggrepel/NEWS.md | 27 ++ ggrepel-0.9.2/ggrepel/R/geom-label-repel.R | 11 ggrepel-0.9.2/ggrepel/R/geom-text-repel.R | 90 +++++-- ggrepel-0.9.2/ggrepel/R/ggrepel-package.R | 3 ggrepel-0.9.2/ggrepel/R/position-nudge-repel.R | 9 ggrepel-0.9.2/ggrepel/inst/doc/ggrepel.html | 153 +++++++----- ggrepel-0.9.2/ggrepel/man/ggrepel.Rd | 16 - ggrepel-0.9.2/ggrepel/src/RcppExports.cpp | 5 ggrepel-0.9.2/ggrepel/src/repel_boxes.cpp | 20 - ggrepel-0.9.2/ggrepel/tests/testthat.R | 1 ggrepel-0.9.2/ggrepel/tests/testthat/test-grob-order.R | 8 ggrepel-0.9.2/ggrepel/tests/testthat/test-just-with-angle.R |only ggrepel-0.9.2/ggrepel/tests/testthat/test-lots-of-points.R | 3 ggrepel-0.9.2/ggrepel/tests/testthat/test-seed.R | 39 +-- 19 files changed, 279 insertions(+), 155 deletions(-)
Title: Robust Time Series Filters
Description: Implementations for several robust procedures that allow for (online)
extraction of the signal of univariate or multivariate time series by
applying robust regression techniques to a moving time window are provided.
Included are univariate filtering procedures based on repeated-median
regression as well as hybrid and trimmed filters derived from it;
see Schettlinger et al. (2006) <doi:10.1515/BMT.2006.010>. The adaptive
online repeated median by Schettlinger et al. (2010) <doi:10.1002/acs.1105>
and the slope comparing adaptive repeated median by Borowski and Fried (2013)
<doi:10.1007/s11222-013-9391-7> choose the width of the moving time
window adaptively. Multivariate versions are also provided; see
Borowski et al. (2009) <doi:10.1080/03610910802514972> for a multivariate
online adaptive repeated median and Borowski (2012) <doi:10.17877/DE290R-14393>
for a multivariate slope comparing adaptive repeated median. Furthermore,
a repeated-median based filter w [...truncated...]
Author: Roland Fried [aut, cre],
Karen Schettlinger [aut],
Matthias Borowski [aut],
Robin Nunkesser [ctb],
Thorsten Bernholt [ctb]
Maintainer: Roland Fried <fried@statistik.tu-dortmund.de>
Diff between robfilter versions 4.1.2 dated 2019-11-21 and 4.1.3 dated 2022-11-06
robfilter-4.1.2/robfilter/inst |only robfilter-4.1.3/robfilter/DESCRIPTION | 9 robfilter-4.1.3/robfilter/MD5 | 22 - robfilter-4.1.3/robfilter/build/partial.rdb |binary robfilter-4.1.3/robfilter/man/dw.filter.Rd | 2 robfilter-4.1.3/robfilter/man/hybrid.filter.Rd | 404 ++++++++++---------- robfilter-4.1.3/robfilter/man/robreg.filter.Rd | 306 +++++++-------- robfilter-4.1.3/robfilter/man/robust.filter.Rd | 486 ++++++++++++------------- robfilter-4.1.3/robfilter/src/Edge.h | 2 robfilter-4.1.3/robfilter/src/Line.h | 2 robfilter-4.1.3/robfilter/src/RMquick.h | 12 robfilter-4.1.3/robfilter/src/segment_tree.h | 10 12 files changed, 627 insertions(+), 628 deletions(-)
Title: Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids
Description: Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids. The genotype
probabilities, posterior mean genotypes, or most probable genotypes can then
be exported for downstream analysis. 'polyRAD' is described by Clark et al.
(2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker
filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>.
A variant calling pipeline for highly duplicated genomes is also included and
is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.
Author: Lindsay V. Clark [aut, cre] ,
U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <Lindsay.Clark@seattlechildrens.org>
Diff between polyRAD versions 1.6 dated 2022-02-15 and 2.0.0 dated 2022-11-06
polyRAD-1.6/polyRAD/NEWS |only polyRAD-1.6/polyRAD/man/AddPriorTimesLikelihood.Rd |only polyRAD-2.0.0/polyRAD/DESCRIPTION | 19 polyRAD-2.0.0/polyRAD/MD5 | 129 polyRAD-2.0.0/polyRAD/NAMESPACE | 18 polyRAD-2.0.0/polyRAD/NEWS.md |only polyRAD-2.0.0/polyRAD/R/RcppExports.R | 16 polyRAD-2.0.0/polyRAD/R/calculations.R | 134 polyRAD-2.0.0/polyRAD/R/classes_methods.R | 1097 ++++--- polyRAD-2.0.0/polyRAD/R/data_export.R | 154 - polyRAD-2.0.0/polyRAD/R/data_import.R | 189 - polyRAD-2.0.0/polyRAD/R/hindhe.R | 27 polyRAD-2.0.0/polyRAD/R/overdispersion.R | 107 polyRAD-2.0.0/polyRAD/R/pipelines.R | 29 polyRAD-2.0.0/polyRAD/R/simulation.R | 49 polyRAD-2.0.0/polyRAD/build/partial.rdb |binary polyRAD-2.0.0/polyRAD/build/vignette.rds |binary polyRAD-2.0.0/polyRAD/data/Msi01genes.RData |binary polyRAD-2.0.0/polyRAD/data/exampleRAD.RData |binary polyRAD-2.0.0/polyRAD/data/exampleRAD_mapping.RData |binary polyRAD-2.0.0/polyRAD/inst/CITATION | 3 polyRAD-2.0.0/polyRAD/inst/doc/isolocus_sorting.Rmd | 7 polyRAD-2.0.0/polyRAD/inst/doc/isolocus_sorting.html | 509 ++- polyRAD-2.0.0/polyRAD/inst/doc/polyRADtutorial.R | 37 polyRAD-2.0.0/polyRAD/inst/doc/polyRADtutorial.Rmd | 140 - polyRAD-2.0.0/polyRAD/inst/doc/polyRADtutorial.html | 1398 ++++++---- polyRAD-2.0.0/polyRAD/inst/extdata/DArTag_BLAST_example2.txt |only polyRAD-2.0.0/polyRAD/inst/extdata/DArTag_example2.csv |only polyRAD-2.0.0/polyRAD/inst/extdata/Msi_ploidies.txt |only polyRAD-2.0.0/polyRAD/inst/extdata/simulate_rad_data.R | 88 polyRAD-2.0.0/polyRAD/inst/extdata/vcfdata.RData |binary polyRAD-2.0.0/polyRAD/man/AddAlleleLinkages.Rd | 2 polyRAD-2.0.0/polyRAD/man/AddGenotypeLikelihood.Rd | 6 polyRAD-2.0.0/polyRAD/man/AddGenotypePosteriorProb.Rd | 25 polyRAD-2.0.0/polyRAD/man/AddGenotypePriorProb_ByTaxa.Rd | 29 polyRAD-2.0.0/polyRAD/man/AddGenotypePriorProb_Even.Rd | 9 polyRAD-2.0.0/polyRAD/man/AddGenotypePriorProb_HWE.Rd | 18 polyRAD-2.0.0/polyRAD/man/AddGenotypePriorProb_Mapping2Parents.Rd | 49 polyRAD-2.0.0/polyRAD/man/AddPloidyChiSq.Rd | 10 polyRAD-2.0.0/polyRAD/man/ExamineGenotype.Rd |only polyRAD-2.0.0/polyRAD/man/ExpectedHindHe.Rd | 23 polyRAD-2.0.0/polyRAD/man/ExportGAPIT.Rd | 32 polyRAD-2.0.0/polyRAD/man/GetLikelyGen.Rd | 2 polyRAD-2.0.0/polyRAD/man/GetTaxa.Rd | 23 polyRAD-2.0.0/polyRAD/man/GetWeightedMeanGenotypes.Rd | 4 polyRAD-2.0.0/polyRAD/man/HindHe.Rd | 5 polyRAD-2.0.0/polyRAD/man/IterateHWE.Rd | 18 polyRAD-2.0.0/polyRAD/man/MergeIdenticalHaplotypes.Rd | 5 polyRAD-2.0.0/polyRAD/man/MergeRareHaplotypes.Rd | 6 polyRAD-2.0.0/polyRAD/man/PipelineMapping2Parents.Rd | 24 polyRAD-2.0.0/polyRAD/man/RADdata.Rd | 29 polyRAD-2.0.0/polyRAD/man/StripDown.Rd | 1 polyRAD-2.0.0/polyRAD/man/SubsetByPloidy.Rd | 10 polyRAD-2.0.0/polyRAD/man/VCF2RADdata.Rd | 6 polyRAD-2.0.0/polyRAD/man/exampleRAD.Rd | 8 polyRAD-2.0.0/polyRAD/man/readDArTag.Rd | 27 polyRAD-2.0.0/polyRAD/man/readHMC.Rd | 6 polyRAD-2.0.0/polyRAD/man/readProcessIsoloci.Rd | 6 polyRAD-2.0.0/polyRAD/man/readProcessSamMulti.Rd | 6 polyRAD-2.0.0/polyRAD/man/readStacks.Rd | 6 polyRAD-2.0.0/polyRAD/man/readTASSELGBSv2.Rd | 10 polyRAD-2.0.0/polyRAD/man/readTagDigger.Rd | 7 polyRAD-2.0.0/polyRAD/src/BestGenos.cpp | 83 polyRAD-2.0.0/polyRAD/src/GiniSimpson.cpp | 4 polyRAD-2.0.0/polyRAD/src/PrepVCFexport.cpp | 59 polyRAD-2.0.0/polyRAD/src/RcppExports.cpp | 43 polyRAD-2.0.0/polyRAD/src/SimulateGenotypes.cpp | 11 polyRAD-2.0.0/polyRAD/vignettes/isolocus_sorting.Rmd | 7 polyRAD-2.0.0/polyRAD/vignettes/polyRADtutorial.Rmd | 140 - 69 files changed, 3174 insertions(+), 1735 deletions(-)
Title: Inferential Statistics
Description: Computation of various confidence intervals (Altman et al. (2000), ISBN:978-0-727-91375-3; Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) including bootstrapped versions (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) as well as Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2), permutation (Janssen (1997), <doi:10.1016/S0167-7152(97)00043-6>), bootstrap (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) and multiple imputation (Barnard and Rubin (1999), <doi:10.1093/biomet/86.4.948>) t-test. Graphical visualization by volcano plots.
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKinfer versions 0.7 dated 2022-09-06 and 0.8 dated 2022-11-06
DESCRIPTION | 15 MD5 | 54 +-- NAMESPACE | 4 NEWS | 9 R/binomCI.R | 10 R/binomDiffCI.R | 10 R/boot.t.test.R | 30 + R/cvCI.R | 4 R/normCI.R | 18 - R/normDiffCI.R | 29 - R/pairwise.ext.t.test.R |only R/pairwise.wilcox.exact.R |only R/perm.t.test.R | 24 + R/quantileCI.R | 79 +---- build/vignette.rds |binary inst/doc/MKinfer.R | 16 - inst/doc/MKinfer.Rmd | 30 + inst/doc/MKinfer.html | 677 +++++++++++++++++++++++++------------------ man/0MKinfer-package.Rd | 6 man/binomCI.Rd | 10 man/binomDiffCI.Rd | 9 man/boot.t.test.Rd | 2 man/cvCI.Rd | 9 man/normCI.Rd | 13 man/normDiffCI.Rd | 12 man/pairwise.ext.t.test.Rd |only man/pairwise.wilcox.exact.Rd |only man/perm.t.test.Rd | 2 man/quantileCI.Rd | 25 - vignettes/MKinfer.Rmd | 30 + 30 files changed, 687 insertions(+), 440 deletions(-)
Title: Mail Sender Using 'Sendgrid' Service
Description: Send email using 'Sendgrid' <https://sendgrid.com/>
mail API(v3) <https://docs.sendgrid.com/api-reference/how-to-use-the-sendgrid-v3-api/authentication>.
Author: Chanyub Park [aut, cre]
Maintainer: Chanyub Park <mrchypark@gmail.com>
Diff between sendgridr versions 0.5.1 dated 2022-08-12 and 0.6.1 dated 2022-11-06
DESCRIPTION | 6 - MD5 | 17 +-- NEWS.md | 9 + R/auth.R | 22 ++-- R/dynamic-templates.R | 218 +++++++++++++++++++++---------------------- R/zzz.R |only README.md | 1 man/auth_set.Rd | 5 man/dynamic_template.Rd | 2 man/dynamic_template_data.Rd | 2 10 files changed, 150 insertions(+), 132 deletions(-)
Title: Bayesian Probit Choice Modeling
Description: Bayes estimation of probit choice models, both in the cross-sectional and
panel setting. The package can analyze binary, multivariate, ordered, and
ranked choices, and places a special focus on modeling heterogeneity of
choice behavior among deciders. The main functionality includes model
fitting via Markov chain Monte Carlo methods, tools for convergence
diagnostic, choice data simulation, in-sample and out-of-sample choice
prediction, and model selection using information criteria and Bayes
factors. The latent class model extension facilitates preference-based
decider classification, where the number of latent classes can be inferred
via the Dirichlet process or a weight-based updating scheme. This allows for
flexible modeling of choice behavior without the need to impose structural
constraints. For a reference on the method see Oelschlaeger and Bauer (2021)
<https://trid.trb.org/view/1759753>.
Author: Lennart Oelschläger [aut, cre]
,
Dietmar Bauer [aut] ,
Sebastian Buescher [ctb],
Manuel Batram [ctb]
Maintainer: Lennart Oelschläger <oelschlaeger.lennart@gmail.com>
Diff between RprobitB versions 1.1.1 dated 2022-08-11 and 1.1.2 dated 2022-11-06
DESCRIPTION | 10 MD5 | 204 - NAMESPACE | 3 NEWS.md | 5 R/RprobitB_package.R | 140 - R/data_management.R | 4012 +++++++++++++++---------------- R/datasets.R | 120 R/model_evaluation.R | 2 R/model_fitting.R | 36 R/model_selection.R | 83 R/plot.R | 8 R/utils.R | 704 ++--- inst/doc/RprobitB.Rmd | 72 inst/doc/v01_model_definition.Rmd | 228 - inst/doc/v01_model_definition.html | 17 inst/doc/v02_choice_data.Rmd | 534 ++-- inst/doc/v02_choice_data.html | 15 inst/doc/v03_model_fitting.Rmd | 548 ++-- inst/doc/v03_model_fitting.html | 15 inst/doc/v04_modeling_heterogeneity.Rmd | 404 +-- inst/doc/v04_modeling_heterogeneity.html | 15 inst/doc/v05_choice_prediction.Rmd | 242 - inst/doc/v05_choice_prediction.html | 15 inst/doc/v06_model_selection.Rmd | 396 +-- inst/doc/v06_model_selection.html | 27 man/M.Rd | 52 man/R_hat.Rd | 78 man/RprobitB.Rd | 20 man/RprobitB_data.Rd | 242 - man/RprobitB_gibbs_samples_statistics.Rd | 68 man/RprobitB_latent_classes.Rd | 172 - man/RprobitB_parameter.Rd | 186 - man/WAIC.Rd | 4 man/as_cov_names.Rd | 68 man/check_form.Rd | 116 man/check_prior.Rd | 204 - man/choice_probabilities.Rd | 76 man/classification.Rd | 92 man/coef.RprobitB_fit.Rd | 38 man/compute_choice_probabilities.Rd | 60 man/cov_mix.Rd | 42 man/create_labels_Omega.Rd | 62 man/create_labels_Sigma.Rd | 70 man/create_labels_alpha.Rd | 44 man/create_labels_b.Rd | 52 man/create_labels_d.Rd | 58 man/create_labels_s.Rd | 44 man/create_lagged_cov.Rd | 108 man/d_to_gamma.Rd | 58 man/delta.Rd | 64 man/dmvnorm.Rd | 64 man/draw_from_prior.Rd | 52 man/euc_dist.Rd | 42 man/filter_gibbs_samples.Rd | 88 man/gibbs_sampling.Rd | 178 - man/is_covariance_matrix.Rd | 48 man/overview_effects.Rd | 150 - man/parameter_labels.Rd | 88 man/permutations.Rd | 54 man/plot.RprobitB_fit.Rd | 62 man/plot_class_allocation.Rd | 104 man/plot_mixture_contour.Rd | 64 man/plot_mixture_marginal.Rd | 64 man/point_estimates.Rd | 60 man/pprint.Rd | 86 man/predict.RprobitB_fit.Rd | 114 man/rdirichlet.Rd | 44 man/rmvnorm.Rd | 66 man/rtnorm.Rd | 64 man/rttnorm.Rd | 64 man/rwishart.Rd | 68 man/sufficient_statistics.Rd | 104 man/train_test.Rd | 106 man/transform_gibbs_samples.Rd | 74 man/transform_parameter.Rd | 46 man/undiff_Sigma.Rd | 76 man/update_Omega.Rd | 124 man/update_Sigma.Rd | 126 man/update_U.Rd | 100 man/update_U_ranked.Rd | 70 man/update_b.Rd | 126 man/update_classes_dp.Rd | 172 - man/update_classes_wb.Rd | 166 - man/update_d.Rd | 62 man/update_m.Rd | 58 man/update_reg.Rd | 126 man/update_s.Rd | 90 man/update_z.Rd | 100 tests/testthat/_snaps/model_fitting.md | 8 tests/testthat/_snaps/model_selection.md | 2 tests/testthat/test-data_management.R | 530 ++-- tests/testthat/test-model_evaluation.R | 158 - tests/testthat/test-model_fitting.R | 388 +- tests/testthat/test-model_selection.R | 54 tests/testthat/test-utils.R | 88 vignettes/RprobitB.Rmd | 72 vignettes/ref.bib | 874 +++--- vignettes/v01_model_definition.Rmd | 228 - vignettes/v02_choice_data.Rmd | 534 ++-- vignettes/v03_model_fitting.Rmd | 548 ++-- vignettes/v04_modeling_heterogeneity.Rmd | 404 +-- vignettes/v05_choice_prediction.Rmd | 242 - vignettes/v06_model_selection.Rmd | 396 +-- 103 files changed, 8926 insertions(+), 8883 deletions(-)
Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users. Currently the
only such package with read and write support for TIFF files with
floating point (real-numbered) pixels, and the only package that can
correctly import TIFF files that were saved from 'ImageJ' and write
TIFF files than can be correctly read by 'ImageJ'
<https://imagej.nih.gov/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] ,
Kent Johnson [aut],
Simon Urbanek [ctb],
Sergi Padilla-Parra [ths] ,
Jeroen Ooms [rev, ctb] ,
Jon Clayden [rev]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between ijtiff versions 2.2.8 dated 2022-08-31 and 2.2.9 dated 2022-11-06
DESCRIPTION | 10 ++-- MD5 | 22 ++++---- NAMESPACE | 1 R/ijtiff.R | 1 README.md | 10 +--- inst/doc/reading-and-writing-images.html | 25 ++++++---- inst/doc/text-images.html | 4 - inst/doc/the-imagej-problem.html | 17 ++++-- src/common.c | 4 - src/init.c | 4 + src/utils.c | 2 tests/testthat/test-io.R | 76 ++++++++++++++++--------------- 12 files changed, 99 insertions(+), 77 deletions(-)
Title: High Dimensional Data Visualization
Description: It provides materials (i.e. 'serial axes' objects, Andrew's plot, various glyphs for scatter plot) to visualize high dimensional data.
Author: Zehao Xu [aut, cre],
R. Wayne Oldford [aut]
Maintainer: Zehao Xu <z267xu@uwaterloo.ca>
Diff between ggmulti versions 1.0.5 dated 2022-10-08 and 1.0.6 dated 2022-11-06
DESCRIPTION | 8 +- MD5 | 56 +++++++-------- R/add-serialaxes-layers.R | 2 R/coord-serialaxes.R | 2 R/geom-density-.R | 7 - R/geom-quantiles.R | 2 R/geom-serialaxes-quantile.R | 4 - R/geom-serialaxes.R | 2 R/stat-hist-.R | 26 +++++-- R/unexported_ggplot2_functions.R | 4 + inst/doc/glyph.html | 133 ++++++++++++++++++------------------- inst/doc/highDim.R | 2 inst/doc/highDim.Rmd | 2 inst/doc/highDim.html | 137 +++++++++++++++++++-------------------- inst/doc/histogram-density-.html | 12 +-- man/coord_serialaxes.Rd | 2 man/geom_density_.Rd | 14 ++- man/geom_hist_.Rd | 11 +-- man/geom_image_glyph.Rd | 20 +++-- man/geom_polygon_glyph.Rd | 20 +++-- man/geom_quantiles.Rd | 16 ++-- man/geom_serialaxes.Rd | 26 ++++--- man/geom_serialaxes_density.Rd | 24 ++++-- man/geom_serialaxes_glyph.Rd | 20 +++-- man/geom_serialaxes_hist.Rd | 27 ++++--- man/geom_serialaxes_quantile.Rd | 33 +++++---- man/position_dodge_.Rd | 4 - tests/testthat/test_serialaxes.R | 24 +++--- vignettes/highDim.Rmd | 2 29 files changed, 351 insertions(+), 291 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multisession)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers, etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.28.0 dated 2022-09-02 and 1.29.0 dated 2022-11-06
DESCRIPTION | 8 MD5 | 50 - NAMESPACE | 1 NEWS.md | 34 + R/999.DEPRECATED.R | 6 R/expressions.R | 7 R/multiprocess.R | 4 R/utils.R | 2 R/value.R | 1 R/zzz.plan.R | 2 build/vignette.rds |binary inst/doc/future-1-overview.html | 305 +++-------- inst/doc/future-2-output.html | 53 -- inst/doc/future-3-topologies.html | 80 --- inst/doc/future-4-issues.html | 239 ++------- inst/doc/future-4-non-exportable-objects.html | 422 +++++----------- inst/doc/future-4-non-exportable-objects.md.rsp | 18 inst/doc/future-5-startup.html | 33 - inst/doc/future-6-future-api-backend-specification.html | 71 -- inst/doc/future-7-for-package-developers.html | 113 ++-- inst/doc/future-7-for-package-developers.md.rsp | 56 ++ inst/doc/future-8-how-future-is-validated.html | 7 man/pid_exists.Rd | 2 man/value.Rd | 1 vignettes/future-4-non-exportable-objects.md.rsp | 18 vignettes/future-7-for-package-developers.md.rsp | 56 ++ 26 files changed, 613 insertions(+), 976 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-03 0.2.0
2016-04-21 0.1.0
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is
a C++ library for translating between absolute and civil times using the rules
of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License,
is included in this package. See <https://github.com/google/cctz> for more
details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.2.11 dated 2022-08-06 and 0.2.12 dated 2022-11-06
ChangeLog | 14 ++++++ DESCRIPTION | 8 +-- MD5 | 6 +- src/utilities.cpp | 112 ++++++++++++++++++++++++++++-------------------------- 4 files changed, 80 insertions(+), 60 deletions(-)
Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). The package make it easy to
visualize count data and statistical thresholds: rank vs abundance
plots, heatmaps, Ford (1962) and Bertin (1977) diagrams.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Matthew Peeples [ctb] ,
Ben Marwick [ctb] ,
Anne Philippe [ctb] ,
Jean-Baptiste Fourvel [ctb]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 1.8.0 dated 2022-09-08 and 2.0.0 dated 2022-11-06
tabula-1.8.0/tabula/inst/examples/ex-independance.R |only tabula-1.8.0/tabula/inst/examples/ex-plot_bar.R |only tabula-1.8.0/tabula/man/independance.Rd |only tabula-1.8.0/tabula/man/mutator.Rd |only tabula-1.8.0/tabula/man/plot_bar.Rd |only tabula-1.8.0/tabula/man/plot_line.Rd |only tabula-1.8.0/tabula/man/subset.Rd |only tabula-1.8.0/tabula/tests/testthat/_snaps/plots/ford-count-eppm-false.svg |only tabula-1.8.0/tabula/tests/testthat/_snaps/plots/ford-count-eppm-true.svg |only tabula-2.0.0/tabula/DESCRIPTION | 16 tabula-2.0.0/tabula/MD5 | 134 tabula-2.0.0/tabula/NAMESPACE | 15 tabula-2.0.0/tabula/NEWS.md | 12 tabula-2.0.0/tabula/R/AllClasses.R | 6 tabula-2.0.0/tabula/R/AllGenerics.R | 323 tabula-2.0.0/tabula/R/ggplot2.R | 2 tabula-2.0.0/tabula/R/index_diversity.R | 33 tabula-2.0.0/tabula/R/matrigraph.R |only tabula-2.0.0/tabula/R/mutators.R | 2 tabula-2.0.0/tabula/R/plot_bertin.R | 6 tabula-2.0.0/tabula/R/plot_diceleraas.R |only tabula-2.0.0/tabula/R/plot_diversity.R | 4 tabula-2.0.0/tabula/R/plot_ford.R | 88 tabula-2.0.0/tabula/R/plot_heatmap.R | 2 tabula-2.0.0/tabula/R/plot_rank.R | 6 tabula-2.0.0/tabula/R/reexport.R | 20 tabula-2.0.0/tabula/R/seriograph.R |only tabula-2.0.0/tabula/R/statistics.R | 83 tabula-2.0.0/tabula/R/tabula-package.R | 4 tabula-2.0.0/tabula/README.md | 7 tabula-2.0.0/tabula/inst/doc/bibliography.html | 22 tabula-2.0.0/tabula/inst/doc/diversity.html | 25 tabula-2.0.0/tabula/inst/examples/ex-diceleraas.R |only tabula-2.0.0/tabula/inst/examples/ex-matrigraph.R |only tabula-2.0.0/tabula/inst/examples/ex-plot_bertin.R |only tabula-2.0.0/tabula/inst/examples/ex-plot_ford.R |only tabula-2.0.0/tabula/inst/examples/ex-seriograph.R |only tabula-2.0.0/tabula/man/DiversityIndex-class.Rd | 11 tabula-2.0.0/tabula/man/figures/README-bertin-1.png |binary tabula-2.0.0/tabula/man/figures/README-ford-1.png |binary tabula-2.0.0/tabula/man/figures/README-plot-occ-1.png |binary tabula-2.0.0/tabula/man/figures/README-similarity-brainerd-1.png |binary tabula-2.0.0/tabula/man/matrigraph.Rd |only tabula-2.0.0/tabula/man/mutators.Rd |only tabula-2.0.0/tabula/man/plot_bertin.Rd |only tabula-2.0.0/tabula/man/plot_diceleraas.Rd |only tabula-2.0.0/tabula/man/plot_diversity.Rd | 10 tabula-2.0.0/tabula/man/plot_ford.Rd |only tabula-2.0.0/tabula/man/plot_heatmap.Rd | 18 tabula-2.0.0/tabula/man/plot_rank.Rd |only tabula-2.0.0/tabula/man/plot_spot.Rd | 8 tabula-2.0.0/tabula/man/reexports.Rd | 9 tabula-2.0.0/tabula/man/resample.Rd | 8 tabula-2.0.0/tabula/man/seriograph.Rd |only tabula-2.0.0/tabula/man/tabula-package.Rd | 2 tabula-2.0.0/tabula/man/test_diversity.Rd | 4 tabula-2.0.0/tabula/tests/testthat/_snaps/plots/bertin-scale.svg | 546 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/bertin-threshold.svg | 560 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/bertin.svg | 544 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/diceleraas.svg |only tabula-2.0.0/tabula/tests/testthat/_snaps/plots/ford.svg |only tabula-2.0.0/tabula/tests/testthat/_snaps/plots/matrigraph-revese-false.svg |only tabula-2.0.0/tabula/tests/testthat/_snaps/plots/matrigraph-revese-true.svg |only tabula-2.0.0/tabula/tests/testthat/_snaps/plots/mtx-count.svg | 576 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/mtx-freq.svg | 582 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/mtx-incid.svg | 562 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/seriograph-weights-false.svg |only tabula-2.0.0/tabula/tests/testthat/_snaps/plots/seriograph-weights-true.svg |only tabula-2.0.0/tabula/tests/testthat/_snaps/plots/spot-count.svg | 828 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/spot-freq.svg | 828 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/spot-mean-count.svg | 820 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/spot-mean-freq.svg | 814 - tabula-2.0.0/tabula/tests/testthat/_snaps/plots/spot-plain-count.svg | 384 tabula-2.0.0/tabula/tests/testthat/_snaps/plots/spot-plain-freq.svg | 382 tabula-2.0.0/tabula/tests/testthat/_snaps/similarity/mtx-occ.svg | 2118 +-- tabula-2.0.0/tabula/tests/testthat/_snaps/similarity/mtx-sim.svg | 90 tabula-2.0.0/tabula/tests/testthat/_snaps/similarity/spot-occ.svg | 5370 +++++----- tabula-2.0.0/tabula/tests/testthat/_snaps/similarity/spot-plain-sim.svg | 140 tabula-2.0.0/tabula/tests/testthat/_snaps/similarity/spot-ring-sim.svg | 168 tabula-2.0.0/tabula/tests/testthat/test-diversity.R | 2 tabula-2.0.0/tabula/tests/testthat/test-plots.R | 28 tabula-2.0.0/tabula/tests/testthat/test-richness.R | 1 tabula-2.0.0/tabula/vignettes/bibliography.bib | 41 83 files changed, 8150 insertions(+), 8114 deletions(-)
Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10918-6, Nankodo, ISBN: 978-4-524-26158-1, Ohmsha, ISBN: 978-4-274-22632-8), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below. This report has been cited in more than 3,000 scientific articles.
Author: Yoshinobu Kanda
Maintainer: Yoshinobu Kanda <ycanda-tky@umin.ac.jp>
Diff between RcmdrPlugin.EZR versions 1.60 dated 2022-10-06 and 1.61 dated 2022-11-06
RcmdrPlugin.EZR-1.60/RcmdrPlugin.EZR/inst/doc/ezr.htm |only RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/DESCRIPTION | 8 ++-- RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/MD5 | 18 +++++----- RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/NEWS | 4 ++ RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/R/EZR.R | 10 +++-- RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/inst/CHANGES | 4 ++ RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/inst/doc/EZR.htm |only RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/inst/doc/ezr.pdf |binary RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.EZR.mo |binary RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/man/EZR.Rd | 4 +- RcmdrPlugin.EZR-1.61/RcmdrPlugin.EZR/po/R-RcmdrPlugin.EZR.po | 6 +-- 11 files changed, 32 insertions(+), 22 deletions(-)
More information about RcmdrPlugin.EZR at CRAN
Permanent link
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 2.6.2 dated 2022-06-14 and 2.7.0 dated 2022-11-06
DESCRIPTION | 6 MD5 | 253 ++--- NEWS | 4 src/bson/bson-atomic.c | 34 src/bson/bson-cmp.h |only src/bson/bson-compat.h | 151 +++ src/bson/bson-decimal128.c | 4 src/bson/bson-iter.c | 4 src/bson/bson-json.c | 190 ++- src/bson/bson-macros.h | 24 src/bson/bson-md5.c | 6 src/bson/bson-memory.c | 167 +++ src/bson/bson-memory.h | 13 src/bson/bson-reader.c | 4 src/bson/bson-timegm-private.h | 22 src/bson/bson-version.h | 10 src/bson/bson-writer.c | 2 src/bson/bson.c | 99 +- src/bson/bson.h | 1 src/client.c | 2 src/common/common-b64-private.h | 45 src/common/common-b64.c | 21 src/common/common-md5-private.h | 15 src/common/common-md5.c | 16 src/common/common-prelude.h | 11 src/common/common-thread-private.h | 19 src/common/common-thread.c | 23 src/jsonsl/jsonsl.c | 16 src/kms/kms_crypto.h | 4 src/kms/kms_crypto_libcrypto.c | 4 src/kms/kms_request_str.c | 4 src/mongoc/mongoc-apm-private.h | 6 src/mongoc/mongoc-apm.c | 69 + src/mongoc/mongoc-apm.h | 9 src/mongoc/mongoc-array-private.h | 7 src/mongoc/mongoc-array.c | 44 src/mongoc/mongoc-async-cmd-private.h | 1 src/mongoc/mongoc-async-cmd.c | 45 src/mongoc/mongoc-async-private.h | 2 src/mongoc/mongoc-async.c | 2 src/mongoc/mongoc-bulk-operation-private.h | 2 src/mongoc/mongoc-bulk-operation.c | 146 ++ src/mongoc/mongoc-bulk-operation.h | 6 src/mongoc/mongoc-change-stream-private.h | 1 src/mongoc/mongoc-change-stream.c | 32 src/mongoc/mongoc-client-private.h | 9 src/mongoc/mongoc-client-session.c | 5 src/mongoc/mongoc-client-side-encryption.c | 1036 ++++++++++++++++++++- src/mongoc/mongoc-client-side-encryption.h | 111 ++ src/mongoc/mongoc-client.c | 27 src/mongoc/mongoc-client.h | 4 src/mongoc/mongoc-cluster-aws.c | 18 src/mongoc/mongoc-cluster-private.h | 5 src/mongoc/mongoc-cluster.c | 118 +- src/mongoc/mongoc-cmd.c | 10 src/mongoc/mongoc-collection.c | 373 +++++-- src/mongoc/mongoc-counters-private.h | 8 src/mongoc/mongoc-crypt-private.h | 42 src/mongoc/mongoc-crypt.c | 392 +++++++ src/mongoc/mongoc-crypto-openssl.c | 11 src/mongoc/mongoc-cursor-array.c | 4 src/mongoc/mongoc-cursor-change-stream.c | 7 src/mongoc/mongoc-cursor-cmd-deprecated.c | 6 src/mongoc/mongoc-cursor-cmd.c | 4 src/mongoc/mongoc-cursor-find-cmd.c | 4 src/mongoc/mongoc-cursor-find-opquery.c | 2 src/mongoc/mongoc-cursor-find.c | 4 src/mongoc/mongoc-cursor-legacy.c | 1 src/mongoc/mongoc-cursor.c | 35 src/mongoc/mongoc-cyrus.c | 22 src/mongoc/mongoc-database-private.h | 31 src/mongoc/mongoc-database.c | 311 ++++++ src/mongoc/mongoc-error-private.h | 3 src/mongoc/mongoc-find-and-modify.c | 2 src/mongoc/mongoc-generation-map-private.h | 2 src/mongoc/mongoc-generation-map.c | 4 src/mongoc/mongoc-gridfs-file.c | 8 src/mongoc/mongoc-handshake-private.h | 3 src/mongoc/mongoc-interrupt.c | 11 src/mongoc/mongoc-log.c | 2 src/mongoc/mongoc-matcher-op.c | 10 src/mongoc/mongoc-matcher.c | 2 src/mongoc/mongoc-ocsp-cache.c | 6 src/mongoc/mongoc-openssl.c | 15 src/mongoc/mongoc-opts-helpers.c | 30 src/mongoc/mongoc-opts-private.h | 10 src/mongoc/mongoc-opts.c | 210 ++++ src/mongoc/mongoc-read-concern.c | 2 src/mongoc/mongoc-read-prefs.c | 39 src/mongoc/mongoc-rpc-private.h | 4 src/mongoc/mongoc-rpc.c | 172 ++- src/mongoc/mongoc-scram.c | 31 src/mongoc/mongoc-secure-channel.c | 10 src/mongoc/mongoc-server-description-private.h | 3 src/mongoc/mongoc-server-description.c | 8 src/mongoc/mongoc-server-monitor.c | 151 ++- src/mongoc/mongoc-server-stream.c | 2 src/mongoc/mongoc-set.c | 3 src/mongoc/mongoc-socket.c | 20 src/mongoc/mongoc-stream-buffered.c | 2 src/mongoc/mongoc-stream-file.c | 81 - src/mongoc/mongoc-stream-gridfs.c | 6 src/mongoc/mongoc-stream-socket.c | 1 src/mongoc/mongoc-stream-tls-openssl-bio-private.h | 2 src/mongoc/mongoc-stream-tls-openssl-bio.c | 13 src/mongoc/mongoc-stream-tls-openssl.c | 61 + src/mongoc/mongoc-stream-tls-secure-channel.c | 16 src/mongoc/mongoc-stream-tls.c | 4 src/mongoc/mongoc-stream.c | 2 src/mongoc/mongoc-timeout-private.h | 2 src/mongoc/mongoc-timeout.c | 2 src/mongoc/mongoc-topology-background-monitoring.c | 6 src/mongoc/mongoc-topology-description-apm.c | 2 src/mongoc/mongoc-topology-description.c | 13 src/mongoc/mongoc-topology-private.h | 19 src/mongoc/mongoc-topology-scanner-private.h | 9 src/mongoc/mongoc-topology-scanner.c | 51 - src/mongoc/mongoc-topology.c | 24 src/mongoc/mongoc-ts-pool-private.h | 17 src/mongoc/mongoc-ts-pool.c | 161 ++- src/mongoc/mongoc-uri.c | 46 src/mongoc/mongoc-util-private.h | 7 src/mongoc/mongoc-util.c | 42 src/mongoc/mongoc-version.h | 10 src/mongoc/mongoc-write-command-legacy.c | 18 src/mongoc/mongoc-write-command-private.h | 2 src/mongoc/mongoc-write-command.c | 8 src/mongoc/mongoc-write-concern.c | 3 128 files changed, 4555 insertions(+), 984 deletions(-)
Title: Classification, Regression and Feature Evaluation
Description: A suite of machine learning algorithms written in C++ with the R
interface contains several learning techniques for classification and regression.
Predictive models include e.g., classification and regression trees with
optional constructive induction and models in the leaves, random forests, kNN,
naive Bayes, and locally weighted regression. All predictions obtained with these
models can be explained and visualized with the 'ExplainPrediction' package.
This package is especially strong in feature evaluation where it contains several variants of
Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini,
information gain, MDL, and DKM. These methods can be used for feature selection
or discretization of numeric attributes.
The OrdEval algorithm and its visualization is used for evaluation
of data sets with ordinal features and class, enabling analysis according to the
Kano model of customer satisfaction.
Several algorithms support parallel multithreaded executi [...truncated...]
Author: Marko Robnik-Sikonja and Petr Savicky
Maintainer: "Marko Robnik-Sikonja" <marko.robnik@fri.uni-lj.si>
Diff between CORElearn versions 1.56.0 dated 2021-03-23 and 1.57.1 dated 2022-11-06
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- man/CORElearn-package.Rd | 2 +- src/Rconvert.cpp | 6 +++--- src/c45read.cpp | 2 +- src/constrct.cpp | 26 +++++++++++++------------- src/constrctReg.cpp | 24 +++++++++++------------- src/dataStore.cpp | 42 +++++++++++++++++++++--------------------- src/expr.cpp | 6 +++--- src/exprReg.cpp | 12 ++++++------ src/frontend.cpp | 44 ++++++++++++++++++++++---------------------- src/options.cpp | 20 ++++++++++---------- src/options.h | 2 +- src/printUtil.cpp | 6 +++--- src/relieff.cpp | 6 +++--- src/rfVisual.cpp | 20 ++++++++++---------- src/rndforest.cpp | 6 +++--- src/rrelieff.cpp | 4 ++-- src/trutil.cpp | 32 ++++++++++++++++---------------- src/trutilReg.cpp | 22 +++++++++++----------- src/utils.cpp | 4 ++-- 22 files changed, 168 insertions(+), 169 deletions(-)
Title: Statistical Modeling of Compound Events
Description: Tools for extracting occurrences, assessing potential driving factors, predicting occurrences, and quantifying impacts of compound events in hydrology and climatology. Please see Hao Zengchao et al. (2019) <doi:10.1088/1748-9326/ab4df5>.
Author: Zengchao Hao
Maintainer: Zengchao Hao <z.hao4univ@gmail.com>
Diff between CompoundEvents versions 0.1.0 dated 2020-02-28 and 0.2.0 dated 2022-11-06
DESCRIPTION | 11 +++++------ MD5 | 14 ++++++++++---- NAMESPACE | 3 +++ R/Empdis1.R |only R/Empdis2.R |only R/GetDH.R | 4 ++-- R/SCEI.R |only man/Empdis1.Rd |only man/Empdis2.Rd |only man/GetDH.Rd | 4 ++-- man/SCEI.Rd |only 11 files changed, 22 insertions(+), 14 deletions(-)
More information about CompoundEvents at CRAN
Permanent link
Title: An Adaptive Lifting Scheme Algorithm
Description: Adaptive wavelet lifting transforms for signal denoising using optimal local neighbourhood regression, from Nunes et al. (2006) <doi:10.1007/s11222-006-6560-y>.
Author: Matt Nunes [aut, cre],
Marina Knight [aut],
Guy Nason [ctb, ths]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between adlift versions 1.4-3 dated 2022-04-06 and 1.4-4 dated 2022-11-06
DESCRIPTION | 8 MD5 | 25 +- R/AdaptNeigh.R | 4 R/AdaptNeighmp.R | 6 R/AdaptPred.R | 2 R/CubicPred.R | 38 ++-- R/LinearPredmp.R | 2 R/PointsUpdate.R | 4 R/PointsUpdatemp.R | 2 R/QuadPred.R | 6 R/QuadPredmp.R | 2 man/as.column.Rd | 8 src/adlift.c | 502 +++++++++-------------------------------------------- src/adlift.h |only 14 files changed, 148 insertions(+), 461 deletions(-)
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax. Can also form bootstrap confidence intervals by doing
bootstrapping only once and reusing the bootstrap estimates in all
subsequent computations. Supports bootstrap confidence intervals for
standardized (partially or completely) indirect effects, conditional
effects, and conditional indirect effects as described in Cheung (2009)
<doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui, and Vong (2022)
<doi:10.1037/hea0001188>. Model fitting can be done by structural equation
modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.1.4.3 dated 2022-09-09 and 0.1.6 dated 2022-11-06
DESCRIPTION | 8 MD5 | 93 - NAMESPACE | 11 NEWS.md | 33 R/all_indirect_paths.R |only R/boot2est_lm.R | 150 ++ R/coef_indirect_list.R |only R/cond_indirect.R | 59 R/confint_indirect_list.R |only R/dat_serial_parallel_latent.R |only R/do_boot.R | 22 R/lm_helpers.R | 2 R/print.paths.R |only R/print_boot_out.R |only R/print_indirect_list.R |only R/total_indirect_effect_list.R |only README.md | 7 build/partial.rdb |binary build/vignette.rds |binary data/data_serial_parallel_latent.rda |only inst/CITATION | 4 inst/doc/do_boot.R | 3 inst/doc/do_boot.Rmd | 10 inst/doc/do_boot.html | 797 +++++----- inst/doc/manymome.html | 1491 +++++++++++--------- inst/doc/med_lav.R | 21 inst/doc/med_lav.Rmd | 84 + inst/doc/med_lav.html | 741 +++++---- inst/doc/med_lm.R | 34 inst/doc/med_lm.Rmd | 118 + inst/doc/med_lm.html | 1064 ++++++++------ inst/doc/mod_levels.html | 754 +++++----- inst/doc/mome_lm.html | 563 ++++--- man/all_indirect_paths.Rd |only man/coef.indirect_list.Rd |only man/cond_indirect.Rd | 42 man/confint.indirect_list.Rd |only man/data_serial_parallel_latent.Rd |only man/do_boot.Rd | 4 man/indirect_effects_from_list.Rd |only man/lm2boot_out.Rd | 53 man/predict.lm_list.Rd | 152 +- man/print.all_paths.Rd |only man/print.boot_out.Rd |only man/print.indirect_list.Rd |only man/total_indirect_effect.Rd |only tests/testthat/test_all_indirect_paths.R |only tests/testthat/test_all_indirect_paths_lv.R |only tests/testthat/test_cond_indirect_effects_lm.R | 13 tests/testthat/test_cond_indirect_lm.R | 13 tests/testthat/test_fit2boot_out_do_boot_parallel.R |only tests/testthat/test_index_mome_complex_models.R | 17 tests/testthat/test_lm2boot_out.R | 3 tests/testthat/test_lm2boot_out_parallel.R |only tests/testthat/test_merge_model_frame.R |only tests/testthat/test_plot_cond_indirect_effects.R | 4 vignettes/do_boot.Rmd | 10 vignettes/med_lav.Rmd | 84 + vignettes/med_lm.Rmd | 118 + 59 files changed, 4120 insertions(+), 2462 deletions(-)
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'PDF', 'Microsoft Word', 'Microsoft PowerPoint'
documents from 'R Markdown' and as 'Grid Graphics' objects. Functions are provided to let users
create tables, modify and format their content. It also extends package 'officer' that does
not contain any feature for customized tabular reporting.
Author: David Gohel [aut, cre],
Clementine Jager [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] ,
Titouan Robert [ctb],
Michael Barrowman [ctb] ,
Atsushi Yasumoto [ctb] ,
Paul Julian [ctb] ,
Sean Browning [ctb] ,
Remi Theriaul [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.8.2 dated 2022-09-26 and 0.8.3 dated 2022-11-06
flextable-0.8.2/flextable/inst/web_1.1.0 |only flextable-0.8.2/flextable/man/figures/fig_add_footer_row_1.png |only flextable-0.8.2/flextable/man/figures/fig_add_header_row_1.png |only flextable-0.8.2/flextable/tests/testthat/_snaps |only flextable-0.8.3/flextable/DESCRIPTION | 6 flextable-0.8.3/flextable/MD5 | 219 ++---- flextable-0.8.3/flextable/NAMESPACE | 7 flextable-0.8.3/flextable/NEWS.md | 42 + flextable-0.8.3/flextable/R/00_utils.R | 11 flextable-0.8.3/flextable/R/05_content.R | 29 flextable-0.8.3/flextable/R/append_chunk.R | 28 flextable-0.8.3/flextable/R/as_flextable.R | 108 +- flextable-0.8.3/flextable/R/as_flextable_tabulator.R | 81 +- flextable-0.8.3/flextable/R/augment_rows.R | 364 +++++++--- flextable-0.8.3/flextable/R/body_add_flextable.R | 54 - flextable-0.8.3/flextable/R/border_fix.R | 4 flextable-0.8.3/flextable/R/borders.R | 74 +- flextable-0.8.3/flextable/R/captions.R | 55 - flextable-0.8.3/flextable/R/chunk_images.R | 120 ++- flextable-0.8.3/flextable/R/compose.R | 8 flextable-0.8.3/flextable/R/defaults.R | 104 ++ flextable-0.8.3/flextable/R/docx_str.R | 15 flextable-0.8.3/flextable/R/empty.R | 4 flextable-0.8.3/flextable/R/flextable.R | 236 +++++- flextable-0.8.3/flextable/R/flextable_sizes.R | 4 flextable-0.8.3/flextable/R/footnote.R | 9 flextable-0.8.3/flextable/R/formatters.R | 6 flextable-0.8.3/flextable/R/grid_funs.R | 4 flextable-0.8.3/flextable/R/html_str.R | 86 +- flextable-0.8.3/flextable/R/latex_chunks.R | 4 flextable-0.8.3/flextable/R/latex_str.R | 17 flextable-0.8.3/flextable/R/merge_flextable.R | 20 flextable-0.8.3/flextable/R/nrowcol.R | 8 flextable-0.8.3/flextable/R/printers.R | 186 ++--- flextable-0.8.3/flextable/R/proc_freq.R | 2 flextable-0.8.3/flextable/R/read_structure.R | 2 flextable-0.8.3/flextable/R/styles.R | 63 + flextable-0.8.3/flextable/R/summarizor.R | 232 +++++- flextable-0.8.3/flextable/R/tabpart_tools.R | 173 ++-- flextable-0.8.3/flextable/R/themes.R | 18 flextable-0.8.3/flextable/R/utils.R | 31 flextable-0.8.3/flextable/R/xtable_to_flextable.R | 5 flextable-0.8.3/flextable/inst/web_1.1.2 |only flextable-0.8.3/flextable/man/add_body.Rd | 9 flextable-0.8.3/flextable/man/add_body_row.Rd | 57 + flextable-0.8.3/flextable/man/add_footer.Rd | 12 flextable-0.8.3/flextable/man/add_footer_lines.Rd | 15 flextable-0.8.3/flextable/man/add_footer_row.Rd | 58 + flextable-0.8.3/flextable/man/add_header.Rd | 12 flextable-0.8.3/flextable/man/add_header_lines.Rd | 34 flextable-0.8.3/flextable/man/add_header_row.Rd | 50 - flextable-0.8.3/flextable/man/as_b.Rd | 1 flextable-0.8.3/flextable/man/as_bracket.Rd | 1 flextable-0.8.3/flextable/man/as_chunk.Rd | 1 flextable-0.8.3/flextable/man/as_equation.Rd | 1 flextable-0.8.3/flextable/man/as_flextable.Rd | 1 flextable-0.8.3/flextable/man/as_flextable.gam.Rd | 1 flextable-0.8.3/flextable/man/as_flextable.glm.Rd | 1 flextable-0.8.3/flextable/man/as_flextable.grouped_data.Rd | 1 flextable-0.8.3/flextable/man/as_flextable.htest.Rd | 1 flextable-0.8.3/flextable/man/as_flextable.lm.Rd | 1 flextable-0.8.3/flextable/man/as_flextable.summarizor.Rd |only flextable-0.8.3/flextable/man/as_flextable.tabulator.Rd | 1 flextable-0.8.3/flextable/man/as_flextable.xtable.Rd | 16 flextable-0.8.3/flextable/man/as_grouped_data.Rd | 7 flextable-0.8.3/flextable/man/as_highlight.Rd | 1 flextable-0.8.3/flextable/man/as_i.Rd | 1 flextable-0.8.3/flextable/man/as_image.Rd | 9 flextable-0.8.3/flextable/man/as_paragraph.Rd | 12 flextable-0.8.3/flextable/man/as_sub.Rd | 1 flextable-0.8.3/flextable/man/as_sup.Rd | 1 flextable-0.8.3/flextable/man/as_word_field.Rd | 1 flextable-0.8.3/flextable/man/body_add_flextable.Rd | 11 flextable-0.8.3/flextable/man/border.Rd | 9 flextable-0.8.3/flextable/man/colorize.Rd | 1 flextable-0.8.3/flextable/man/figures/fig_summarizor_1.png |binary flextable-0.8.3/flextable/man/figures/fig_summarizor_2.png |binary flextable-0.8.3/flextable/man/flextable_html_dependency.Rd | 6 flextable-0.8.3/flextable/man/flextable_to_rmd.Rd | 10 flextable-0.8.3/flextable/man/fmt_2stats.Rd | 52 + flextable-0.8.3/flextable/man/fmt_avg_dev.Rd |only flextable-0.8.3/flextable/man/fmt_header_n.Rd |only flextable-0.8.3/flextable/man/fmt_n_percent.Rd |only flextable-0.8.3/flextable/man/gg_chunk.Rd | 20 flextable-0.8.3/flextable/man/grid_chunk.Rd |only flextable-0.8.3/flextable/man/htmltools_value.Rd | 5 flextable-0.8.3/flextable/man/hyperlink_text.Rd | 1 flextable-0.8.3/flextable/man/knit_print.flextable.Rd | 3 flextable-0.8.3/flextable/man/line_spacing.Rd | 4 flextable-0.8.3/flextable/man/linerange.Rd | 9 flextable-0.8.3/flextable/man/lollipop.Rd | 9 flextable-0.8.3/flextable/man/minibar.Rd | 9 flextable-0.8.3/flextable/man/plot_chunk.Rd | 9 flextable-0.8.3/flextable/man/prepend_chunks.Rd | 3 flextable-0.8.3/flextable/man/proc_freq.Rd | 2 flextable-0.8.3/flextable/man/separate_header.Rd | 7 flextable-0.8.3/flextable/man/set_caption.Rd | 78 +- flextable-0.8.3/flextable/man/set_flextable_defaults.Rd | 38 + flextable-0.8.3/flextable/man/set_header_footer_df.Rd | 7 flextable-0.8.3/flextable/man/set_header_labels.Rd | 7 flextable-0.8.3/flextable/man/set_table_properties.Rd | 84 ++ flextable-0.8.3/flextable/man/summarizor.Rd | 51 - flextable-0.8.3/flextable/tests/testthat.R | 1 flextable-0.8.3/flextable/tests/testthat/rmd/keep-next.Rmd |only flextable-0.8.3/flextable/tests/testthat/test-as_flextable.R |only flextable-0.8.3/flextable/tests/testthat/test-cell-content.R | 23 flextable-0.8.3/flextable/tests/testthat/test-dimensions.R | 12 flextable-0.8.3/flextable/tests/testthat/test-errors.R | 37 - flextable-0.8.3/flextable/tests/testthat/test-keep-next.R |only flextable-0.8.3/flextable/tests/testthat/test-md-captions.R | 7 flextable-0.8.3/flextable/tests/testthat/test-text.R | 7 flextable-0.8.3/flextable/tests/testthat/to-img.R | 16 112 files changed, 2300 insertions(+), 984 deletions(-)
Title: Drug Target Set Enrichment Analysis
Description: It is a novel tool used to identify the candidate drugs against a particular disease based on the drug target set enrichment analysis. It assumes the most effective drugs are those with a closer affinity in the protein-protein interaction network to the specified disease. (See Gómez-Carballa et al. (2022) <doi: 10.1016/j.envres.2022.112890> and Feng et al. (2022) <doi: 10.7150/ijms.67815> for disease expression profiles; see Wishart et al. (2018) <doi: 10.1093/nar/gkx1037> and Gaulton et al. (2017) <doi: 10.1093/nar/gkw1074> for drug target information; see Kanehisa et al. (2021) <doi: 10.1093/nar/gkaa970> for the details of KEGG database.)
Author: Junwei Han [aut, cre, cph],
Yinchun Su [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between DTSEA versions 0.0.2 dated 2022-10-18 and 0.0.3 dated 2022-11-06
DESCRIPTION | 11 MD5 | 56 +- NAMESPACE | 95 ++-- NEWS.md | 11 R/DTSEA-package.R | 39 + R/DTSEA.R | 54 ++ R/calculate_p0.R | 7 R/cronbach.alpha.R | 6 R/data.R | 13 R/get_data.R |only R/kendall.w.R | 3 R/random.walk.R | 24 - R/separation.R | 2 README.md | 51 +- build/vignette.rds |binary inst/doc/DTSEA.R | 38 + inst/doc/DTSEA.Rmd | 98 ++++ inst/doc/DTSEA.html | 789 ++++++---------------------------------- man/DTSEA-package.Rd | 36 + man/DTSEA.Rd | 49 ++ man/calculate_between.Rd | 1 man/calculate_p0.Rd | 11 man/calculate_within.Rd | 1 man/example_drug_target_list.Rd | 8 man/example_ppi.Rd | 7 man/figures/manual.pdf |binary man/get_data.Rd |only man/kendall.w.Rd | 4 man/random.walk.Rd | 36 + vignettes/DTSEA.Rmd | 98 ++++ 30 files changed, 702 insertions(+), 846 deletions(-)
Title: Utility Functions, Datasets and Extended Examples for Survival
Analysis
Description: Utility functions, datasets and extended examples for survival analysis. This extends a range of other packages, some simple wrappers for time-to-event analyses, datasets, and extensive examples in HTML with R scripts. The package also supports the course Biostatistics III entitled "Survival analysis for epidemiologists in R".
Author: Annika Tillander [ctb],
Andreas Karlsson [aut],
Johan Zetterqvist [ctb],
Peter Strom [ctb],
Benedicte Delcoigne [ctb],
Mark Clements [aut, cre]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between biostat3 versions 0.1.6 dated 2021-11-03 and 0.1.8 dated 2022-11-06
DESCRIPTION | 10 MD5 | 110 ++++----- NAMESPACE | 2 R/eform.R | 1 R/lincom.R | 3 R/survPHplot.R | 2 build/partial.rdb |binary inst/doc/labs/q10.Rmd | 16 + inst/doc/labs/q10.html | 114 +++------ inst/doc/labs/q11.Rmd | 2 inst/doc/labs/q11.html | 1 inst/doc/labs/q13.html | 2 inst/doc/labs/q14.html | 12 - inst/doc/labs/q2.Rmd | 1 inst/doc/labs/q2.html | 1 inst/doc/labs/q22.html | 16 - inst/doc/labs/q23.Rmd | 175 +++++++++----- inst/doc/labs/q23.html | 212 +++++++++-------- inst/doc/labs/q28.html | 149 ++++++------ inst/doc/labs/q6.Rmd | 4 inst/doc/labs/q6.html | 12 - inst/doc/labs/q7.Rmd | 2 inst/doc/labs/q7.html | 33 +- inst/doc/labs/q8.html | 10 inst/doc/labs/q9.Rmd | 4 inst/doc/labs/q9.html | 10 inst/doc/q10.R | 43 ++- inst/doc/q13.R | 2 inst/doc/q22.R | 16 - inst/doc/q23.R | 205 ++++++++++------- inst/doc/q28.R | 4 inst/doc/q3.R | 4 inst/doc/q6.R | 10 inst/doc/q7.R | 32 +- inst/doc/q8.R | 12 - inst/doc/q9.R | 6 inst/doc/solutions/q10.Rmd | 107 ++++++-- inst/doc/solutions/q10.html | 324 ++++++++++++++++----------- inst/doc/solutions/q11.Rmd | 32 +- inst/doc/solutions/q11.html | 11 inst/doc/solutions/q13.html | 2 inst/doc/solutions/q14.html | 12 - inst/doc/solutions/q22.html | 18 - inst/doc/solutions/q23.Rmd | 52 +++- inst/doc/solutions/q23.html | 527 +++++++++++++++++++++++++++++--------------- inst/doc/solutions/q28.html | 297 ++++++++++++------------ inst/doc/solutions/q3.html | 14 - inst/doc/solutions/q4.Rmd | 7 inst/doc/solutions/q4.html | 6 inst/doc/solutions/q6.Rmd | 52 +++- inst/doc/solutions/q6.html | 28 +- inst/doc/solutions/q7.Rmd | 151 +++++++----- inst/doc/solutions/q7.html | 258 ++++++--------------- inst/doc/solutions/q8.html | 10 inst/doc/solutions/q9.Rmd | 41 ++- inst/doc/solutions/q9.html | 98 ++++---- 56 files changed, 1889 insertions(+), 1396 deletions(-)
Title: Read Human Mortality Database and Human Fertility Database Data
from the Web
Description: Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<https://www.fertilitydata.org>), The Japanese Mortality Database (<https://www.ipss.go.jp/p-toukei/JMD/index-en.html>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Author: Tim Riffe [aut, cre],
Carl Boe [aut],
Jason Hilton [aut],
Josh Goldstein [ctb],
Stephen Holzman [ctb]
Maintainer: Tim Riffe <tim.riffe@gmail.com>
Diff between HMDHFDplus versions 1.9.18 dated 2022-06-18 and 1.9.19 dated 2022-11-06
HMDHFDplus-1.9.18/HMDHFDplus/man/extract_HFD_items.Rd |only HMDHFDplus-1.9.19/HMDHFDplus/DESCRIPTION | 15 - HMDHFDplus-1.9.19/HMDHFDplus/MD5 | 17 - HMDHFDplus-1.9.19/HMDHFDplus/NAMESPACE | 34 ++ HMDHFDplus-1.9.19/HMDHFDplus/NEWS.md | 14 + HMDHFDplus-1.9.19/HMDHFDplus/R/HFDutils.R | 247 +++++++++++------- HMDHFDplus-1.9.19/HMDHFDplus/R/readHFD.R | 116 +++++--- HMDHFDplus-1.9.19/HMDHFDplus/man/getHFDcountries.Rd | 4 HMDHFDplus-1.9.19/HMDHFDplus/man/getHFDitemavail.Rd | 4 HMDHFDplus-1.9.19/HMDHFDplus/man/readHFDweb.Rd | 2 10 files changed, 307 insertions(+), 146 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-23 1.0.0
2021-01-13 0.7.1
2020-09-24 0.5.0
2020-02-03 0.2.0
2019-05-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-09 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-16 0.1.0.2
2021-06-17 0.1.0.1
2020-09-29 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-16 0.1.4
2020-03-31 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-17 1.1.1
2017-10-24 1.1.0
2017-08-20 1.0.0
2017-03-20 0.2.1
2017-03-16 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-20 1.0.0
Title: Handling Heteroskedasticity in the Linear Regression Model
Description: Implements numerous methods for testing for, modelling, and
correcting for heteroskedasticity in the classical linear regression
model. The most novel contribution of the
package is found in the functions that implement the as-yet-unpublished
auxiliary linear variance models and auxiliary nonlinear variance
models that are designed to estimate error variances in a heteroskedastic
linear regression model. These models follow principles of statistical
learning described in Hastie (2009) <doi:10.1007/978-0-387-21606-5>.
The nonlinear version of the model is estimated using quasi-likelihood
methods as described in Seber and Wild (2003, ISBN: 0-471-47135-6).
Bootstrap methods for approximate confidence intervals for error variances
are implemented as described in Efron and Tibshirani
(1993, ISBN: 978-1-4899-4541-9), including also the expansion technique
described in Hesterberg (2014) <doi:10.1080/00031305.2015.1089789>. The
wild bootstrap employed here follows the description i [...truncated...]
Author: Thomas Farrar [aut, cre] ,
University of the Western Cape [cph]
Maintainer: Thomas Farrar <tjfarrar@alumni.uwaterloo.ca>
Diff between skedastic versions 1.0.4 dated 2022-02-21 and 2.0.1 dated 2022-11-06
skedastic-1.0.4/skedastic/R/white_lm.R |only skedastic-1.0.4/skedastic/man/white_lm.Rd |only skedastic-1.0.4/skedastic/tests/testthat/test-whitelm.R |only skedastic-2.0.1/skedastic/DESCRIPTION | 66 skedastic-2.0.1/skedastic/MD5 | 156 - skedastic-2.0.1/skedastic/NAMESPACE | 12 skedastic-2.0.1/skedastic/R/GSS.R |only skedastic-2.0.1/skedastic/R/alvm.fit.R |only skedastic-2.0.1/skedastic/R/anlvm.fit.R |only skedastic-2.0.1/skedastic/R/anscombe.R | 8 skedastic-2.0.1/skedastic/R/avm.ci.R |only skedastic-2.0.1/skedastic/R/avm.fwls.R |only skedastic-2.0.1/skedastic/R/avm.vcov.R |only skedastic-2.0.1/skedastic/R/avmutils.R |only skedastic-2.0.1/skedastic/R/bamset.R | 47 skedastic-2.0.1/skedastic/R/bickel.R | 2 skedastic-2.0.1/skedastic/R/blus.R | 20 skedastic-2.0.1/skedastic/R/bootlm.R |only skedastic-2.0.1/skedastic/R/breusch_pagan.R | 11 skedastic-2.0.1/skedastic/R/carapeto_holt.R | 10 skedastic-2.0.1/skedastic/R/cook_weisberg.R | 21 skedastic-2.0.1/skedastic/R/data.R | 20 skedastic-2.0.1/skedastic/R/diblasi_bowman.R | 25 skedastic-2.0.1/skedastic/R/dufour_etal.R | 8 skedastic-2.0.1/skedastic/R/evans_king.R | 4 skedastic-2.0.1/skedastic/R/glejser.R | 4 skedastic-2.0.1/skedastic/R/godfrey_orme.R | 4 skedastic-2.0.1/skedastic/R/goldfeld_quandt.R | 23 skedastic-2.0.1/skedastic/R/harrison_mccabe.R | 18 skedastic-2.0.1/skedastic/R/harvey.R | 2 skedastic-2.0.1/skedastic/R/hccme.R |only skedastic-2.0.1/skedastic/R/hetplot.R | 91 skedastic-2.0.1/skedastic/R/honda.R | 15 skedastic-2.0.1/skedastic/R/horn.R | 6 skedastic-2.0.1/skedastic/R/li_yao.R | 14 skedastic-2.0.1/skedastic/R/myutils.R | 89 skedastic-2.0.1/skedastic/R/pRQF.R | 4 skedastic-2.0.1/skedastic/R/peaks.R | 14 skedastic-2.0.1/skedastic/R/rackauskas_zuokas.R | 11 skedastic-2.0.1/skedastic/R/simonoff_tsai.R | 93 skedastic-2.0.1/skedastic/R/szroeter.R | 4 skedastic-2.0.1/skedastic/R/trend.R | 46 skedastic-2.0.1/skedastic/R/twosidedpval.R | 56 skedastic-2.0.1/skedastic/R/verbyla.R | 24 skedastic-2.0.1/skedastic/R/white.R |only skedastic-2.0.1/skedastic/R/wilcox_keselman.R | 6 skedastic-2.0.1/skedastic/R/yuce.R | 13 skedastic-2.0.1/skedastic/R/zhou_etal.R | 8 skedastic-2.0.1/skedastic/README.md | 57 skedastic-2.0.1/skedastic/build/partial.rdb |binary skedastic-2.0.1/skedastic/inst/REFERENCES.bib | 1220 +++++++++- skedastic-2.0.1/skedastic/man/GSS.Rd |only skedastic-2.0.1/skedastic/man/alvm.fit.Rd |only skedastic-2.0.1/skedastic/man/anlvm.fit.Rd |only skedastic-2.0.1/skedastic/man/anscombe.Rd | 6 skedastic-2.0.1/skedastic/man/avm.ci.Rd |only skedastic-2.0.1/skedastic/man/avm.fwls.Rd |only skedastic-2.0.1/skedastic/man/avm.vcov.Rd |only skedastic-2.0.1/skedastic/man/bamset.Rd | 24 skedastic-2.0.1/skedastic/man/blus.Rd | 20 skedastic-2.0.1/skedastic/man/bootlm.Rd |only skedastic-2.0.1/skedastic/man/breusch_pagan.Rd | 10 skedastic-2.0.1/skedastic/man/cook_weisberg.Rd | 20 skedastic-2.0.1/skedastic/man/dDtrend.Rd | 27 skedastic-2.0.1/skedastic/man/diblasi_bowman.Rd | 6 skedastic-2.0.1/skedastic/man/dpeakdat.Rd | 21 skedastic-2.0.1/skedastic/man/dufour_etal.Rd | 6 skedastic-2.0.1/skedastic/man/glejser.Rd | 2 skedastic-2.0.1/skedastic/man/goldfeld_quandt.Rd | 14 skedastic-2.0.1/skedastic/man/harrison_mccabe.Rd | 14 skedastic-2.0.1/skedastic/man/hccme.Rd |only skedastic-2.0.1/skedastic/man/hetplot.Rd | 20 skedastic-2.0.1/skedastic/man/honda.Rd | 11 skedastic-2.0.1/skedastic/man/li_yao.Rd | 14 skedastic-2.0.1/skedastic/man/pDtrend.Rd | 13 skedastic-2.0.1/skedastic/man/pRQF.Rd | 8 skedastic-2.0.1/skedastic/man/rackauskas_zuokas.Rd | 11 skedastic-2.0.1/skedastic/man/simonoff_tsai.Rd | 80 skedastic-2.0.1/skedastic/man/twosidedpval.Rd | 29 skedastic-2.0.1/skedastic/man/verbyla.Rd | 20 skedastic-2.0.1/skedastic/man/white.Rd |only skedastic-2.0.1/skedastic/man/yuce.Rd | 12 skedastic-2.0.1/skedastic/man/zhou_etal.Rd | 5 skedastic-2.0.1/skedastic/tests/testthat.R | 1 skedastic-2.0.1/skedastic/tests/testthat/test-alvm.fit.R |only skedastic-2.0.1/skedastic/tests/testthat/test-anlvm.fit.R |only skedastic-2.0.1/skedastic/tests/testthat/test-avm.ci.R |only skedastic-2.0.1/skedastic/tests/testthat/test-dufour_etal.R | 2 skedastic-2.0.1/skedastic/tests/testthat/test-godfrey_orme.R | 2 skedastic-2.0.1/skedastic/tests/testthat/test-hypothesis_tests_default_args.R | 2 skedastic-2.0.1/skedastic/tests/testthat/test-pRQF.R | 42 skedastic-2.0.1/skedastic/tests/testthat/test-white.R |only 92 files changed, 2028 insertions(+), 646 deletions(-)
Title: Make Dealing with Dates a Little Easier
Description: Functions to work with date-times and time-spans: fast and
user friendly parsing of date-time data, extraction and updating of
components of a date-time (years, months, days, hours, minutes, and
seconds), algebraic manipulation on date-time and time-span objects.
The 'lubridate' package has a consistent and memorable syntax that
makes working with dates easy and fun.
Author: Vitalie Spinu [aut, cre],
Garrett Grolemund [aut],
Hadley Wickham [aut],
Davis Vaughan [ctb],
Ian Lyttle [ctb],
Imanuel Costigan [ctb],
Jason Law [ctb],
Doug Mitarotonda [ctb],
Joseph Larmarange [ctb],
Jonathan Boiser [ctb],
Chel Hee Lee [ctb]
Maintainer: Vitalie Spinu <spinuvit@gmail.com>
Diff between lubridate versions 1.8.0 dated 2021-10-07 and 1.9.0 dated 2022-11-06
lubridate-1.8.0/lubridate/R/cpp11-wrappers.R |only lubridate-1.8.0/lubridate/R/cpp11.R |only lubridate-1.8.0/lubridate/po |only lubridate-1.8.0/lubridate/src/Makevars |only lubridate-1.8.0/lubridate/src/Makevars.win |only lubridate-1.8.0/lubridate/src/cctz |only lubridate-1.8.0/lubridate/src/cpp11.cpp |only lubridate-1.8.0/lubridate/src/update.cpp |only lubridate-1.8.0/lubridate/tests/testthat/output |only lubridate-1.9.0/lubridate/DESCRIPTION | 100 - lubridate-1.9.0/lubridate/MD5 | 252 +- lubridate-1.9.0/lubridate/NAMESPACE | 15 lubridate-1.9.0/lubridate/NEWS.md | 44 lubridate-1.9.0/lubridate/R/Dates.r | 20 lubridate-1.9.0/lubridate/R/POSIXt.r | 23 lubridate-1.9.0/lubridate/R/accessors-date.R | 14 lubridate-1.9.0/lubridate/R/accessors-day.r | 117 - lubridate-1.9.0/lubridate/R/accessors-dst.r | 6 lubridate-1.9.0/lubridate/R/accessors-hour.r | 45 lubridate-1.9.0/lubridate/R/accessors-minute.r | 40 lubridate-1.9.0/lubridate/R/accessors-month.r | 64 lubridate-1.9.0/lubridate/R/accessors-quarter.r | 20 lubridate-1.9.0/lubridate/R/accessors-second.r | 41 lubridate-1.9.0/lubridate/R/accessors-tz.r | 4 lubridate-1.9.0/lubridate/R/accessors-week.r | 6 lubridate-1.9.0/lubridate/R/accessors-year.r | 43 lubridate-1.9.0/lubridate/R/coercion.r | 383 ++-- lubridate-1.9.0/lubridate/R/constants.r | 122 - lubridate-1.9.0/lubridate/R/cyclic_encoding.r | 14 lubridate-1.9.0/lubridate/R/decimal-dates.r | 18 lubridate-1.9.0/lubridate/R/deprecated.r | 40 lubridate-1.9.0/lubridate/R/difftimes.r | 14 lubridate-1.9.0/lubridate/R/durations.r | 225 +- lubridate-1.9.0/lubridate/R/format_ISO8601.r | 239 +- lubridate-1.9.0/lubridate/R/guess.r | 320 ++- lubridate-1.9.0/lubridate/R/instants.r | 28 lubridate-1.9.0/lubridate/R/intervals.r | 222 +- lubridate-1.9.0/lubridate/R/ops-addition.r | 156 + lubridate-1.9.0/lubridate/R/ops-compare.r | 27 lubridate-1.9.0/lubridate/R/ops-division.r | 127 - lubridate-1.9.0/lubridate/R/ops-m+.r | 66 lubridate-1.9.0/lubridate/R/ops-modulo.r | 48 lubridate-1.9.0/lubridate/R/ops-multiplication.r | 20 lubridate-1.9.0/lubridate/R/ops-subtraction.r | 63 lubridate-1.9.0/lubridate/R/package.r | 1 lubridate-1.9.0/lubridate/R/parse.r | 270 +-- lubridate-1.9.0/lubridate/R/periods.r | 354 ++- lubridate-1.9.0/lubridate/R/pretty.r | 52 lubridate-1.9.0/lubridate/R/round.r | 340 +-- lubridate-1.9.0/lubridate/R/stamp.r | 103 - lubridate-1.9.0/lubridate/R/time-zones.r | 80 lubridate-1.9.0/lubridate/R/timespans.r | 11 lubridate-1.9.0/lubridate/R/update.r | 223 +- lubridate-1.9.0/lubridate/R/util.r | 62 lubridate-1.9.0/lubridate/R/vctrs.R | 130 - lubridate-1.9.0/lubridate/R/zzz.R | 8 lubridate-1.9.0/lubridate/README.md | 18 lubridate-1.9.0/lubridate/build/vignette.rds |binary lubridate-1.9.0/lubridate/inst/doc/lubridate.html | 534 ++++-- lubridate-1.9.0/lubridate/man/DateTimeUpdate.Rd | 42 lubridate-1.9.0/lubridate/man/as.duration.Rd | 3 lubridate-1.9.0/lubridate/man/as.interval.Rd | 8 lubridate-1.9.0/lubridate/man/as.period.Rd | 9 lubridate-1.9.0/lubridate/man/as_date.Rd | 27 lubridate-1.9.0/lubridate/man/cyclic_encoding.Rd | 5 lubridate-1.9.0/lubridate/man/date_decimal.Rd | 2 lubridate-1.9.0/lubridate/man/day.Rd | 16 lubridate-1.9.0/lubridate/man/decimal_date.Rd | 2 lubridate-1.9.0/lubridate/man/fit_to_timeline.Rd | 31 lubridate-1.9.0/lubridate/man/force_tz.Rd | 51 lubridate-1.9.0/lubridate/man/format_ISO8601.Rd | 21 lubridate-1.9.0/lubridate/man/format_ISO8601_precision_check.Rd | 15 lubridate-1.9.0/lubridate/man/hidden_aliases.Rd | 51 lubridate-1.9.0/lubridate/man/interval.Rd | 2 lubridate-1.9.0/lubridate/man/lubridate-package.Rd | 1 lubridate-1.9.0/lubridate/man/parse_date_time.Rd | 16 lubridate-1.9.0/lubridate/man/period.Rd | 6 lubridate-1.9.0/lubridate/man/reexports.Rd | 5 lubridate-1.9.0/lubridate/man/round_date.Rd | 69 lubridate-1.9.0/lubridate/man/stamp.Rd | 6 lubridate-1.9.0/lubridate/man/timespan.Rd | 2 lubridate-1.9.0/lubridate/man/with_tz.Rd | 7 lubridate-1.9.0/lubridate/man/within-interval.Rd | 22 lubridate-1.9.0/lubridate/man/year.Rd | 2 lubridate-1.9.0/lubridate/src/init.c |only lubridate-1.9.0/lubridate/src/period.c | 54 lubridate-1.9.0/lubridate/src/tparse.c | 16 lubridate-1.9.0/lubridate/src/utils.h | 1 lubridate-1.9.0/lubridate/tests/testthat.R | 8 lubridate-1.9.0/lubridate/tests/testthat/_snaps |only lubridate-1.9.0/lubridate/tests/testthat/test-Dates.R | 33 lubridate-1.9.0/lubridate/tests/testthat/test-POSIXt.R | 74 lubridate-1.9.0/lubridate/tests/testthat/test-accessors.R | 449 +++-- lubridate-1.9.0/lubridate/tests/testthat/test-am-pm.R | 2 lubridate-1.9.0/lubridate/tests/testthat/test-daylight-savings.R | 87 lubridate-1.9.0/lubridate/tests/testthat/test-decimal-date.R | 6 lubridate-1.9.0/lubridate/tests/testthat/test-difftimes.R | 3 lubridate-1.9.0/lubridate/tests/testthat/test-durations.R | 233 +- lubridate-1.9.0/lubridate/tests/testthat/test-format_ISO8601.R | 267 +-- lubridate-1.9.0/lubridate/tests/testthat/test-guess.R | 27 lubridate-1.9.0/lubridate/tests/testthat/test-instants.R | 36 lubridate-1.9.0/lubridate/tests/testthat/test-intervals.R | 626 ++++--- lubridate-1.9.0/lubridate/tests/testthat/test-namespace.R | 29 lubridate-1.9.0/lubridate/tests/testthat/test-ops-addition.R | 239 +- lubridate-1.9.0/lubridate/tests/testthat/test-ops-compare.R | 26 lubridate-1.9.0/lubridate/tests/testthat/test-ops-division.R | 100 - lubridate-1.9.0/lubridate/tests/testthat/test-ops-integer-division.R | 5 lubridate-1.9.0/lubridate/tests/testthat/test-ops-modulo.R | 112 - lubridate-1.9.0/lubridate/tests/testthat/test-ops-multiplication.R | 34 lubridate-1.9.0/lubridate/tests/testthat/test-ops-subtraction.R | 28 lubridate-1.9.0/lubridate/tests/testthat/test-parsers.R | 886 ++++++---- lubridate-1.9.0/lubridate/tests/testthat/test-periods.R | 104 - lubridate-1.9.0/lubridate/tests/testthat/test-pretty.R | 31 lubridate-1.9.0/lubridate/tests/testthat/test-rollback.R | 76 lubridate-1.9.0/lubridate/tests/testthat/test-round.R | 665 +++++-- lubridate-1.9.0/lubridate/tests/testthat/test-settors.R | 419 +++- lubridate-1.9.0/lubridate/tests/testthat/test-stamp.R | 91 - lubridate-1.9.0/lubridate/tests/testthat/test-time-zones.R | 205 +- lubridate-1.9.0/lubridate/tests/testthat/test-timespans.R | 90 - lubridate-1.9.0/lubridate/tests/testthat/test-update.R | 251 +- lubridate-1.9.0/lubridate/tests/testthat/test-utilities.R | 2 lubridate-1.9.0/lubridate/tests/testthat/test-vctrs.R | 57 122 files changed, 6891 insertions(+), 4074 deletions(-)
Title: Global Optimization by Differential Evolution
Description: Implements the Differential Evolution algorithm for global
optimization of a real-valued function of a real-valued parameter
vector as described in Mullen et al. (2011) <doi:10.18637/jss.v040.i06>.
Author: David Ardia [aut] ,
Katharine Mullen [aut, cre],
Brian Peterson [aut],
Joshua Ulrich [aut],
Kris Boudt [ctb]
Maintainer: Katharine Mullen <mullenkate@gmail.com>
Diff between DEoptim versions 2.2-6 dated 2021-05-05 and 2.2-7 dated 2022-11-06
DESCRIPTION | 12 ++-- MD5 | 23 ++++----- NAMESPACE | 6 +- NEWS | 33 ++++++++++++ R/DEoptim.R | 125 +++++++++++++++++++++++++++++++++++-------------- README.md | 26 ++++++++-- THANKS | 3 - build/partial.rdb |binary man/DEoptim.Rd | 3 - man/DEoptim.control.Rd | 31 +++++------- src/de4_0.c | 44 ++++++++--------- src/evaluate.c | 28 ++-------- tests |only 13 files changed, 212 insertions(+), 122 deletions(-)
Title: Modeling Multivariate Origins Determinants - Evolutionary
Lineages in Ecology
Description: Perform multivariate modeling of evolved traits, with special attention to
understanding the interplay of the multi-factorial determinants of their origins
in complex ecological settings (Stephens, 2007 <doi:10.1016/j.tree.2006.12.003>).
This software primarily concentrates on phylogenetic regression analysis, enabling
implementation of tree transformation averaging and visualization functionality.
Functions additionally support information theoretic approaches
(Grueber, 2011 <doi:10.1111/j.1420-9101.2010.02210.x>;
Garamszegi, 2011 <doi:10.1007/s00265-010-1028-7>)
such as model averaging and selection of phylogenetic models.
There are other numerous functions for visualizing confounded variables,
plotting phylogenetic trees, as well as reporting and exporting modeling results.
Lastly, as challenges to ecology are inherently multifarious, and therefore often
multi-dataset, this package features several functions to support the identification,
interpolation, merging, an [...truncated...]
Author: David M Schruth
Maintainer: David M Schruth <dschruth@anthropoidea.org>
Diff between mmodely versions 0.2.0 dated 2022-11-04 and 0.2.2 dated 2022-11-06
mmodely-0.2.0/mmodely/man/calculate.weighted.means.Rd |only mmodely-0.2.0/mmodely/man/get.best.model.Rd |only mmodely-0.2.0/mmodely/man/modsel.distro.dots.Rd |only mmodely-0.2.2/mmodely/DESCRIPTION | 6 mmodely-0.2.2/mmodely/MD5 | 38 +-- mmodely-0.2.2/mmodely/NAMESPACE | 2 mmodely-0.2.2/mmodely/R/pgls.R | 47 ++- mmodely-0.2.2/mmodely/R/plotting.R | 11 mmodely-0.2.2/mmodely/build/vignette.rds |binary mmodely-0.2.2/mmodely/inst/doc/Schruth-mmodely-vignette-Vision.R | 71 ++++- mmodely-0.2.2/mmodely/inst/doc/Schruth-mmodely-vignette-Vision.Rnw | 110 +++++---- mmodely-0.2.2/mmodely/inst/doc/Schruth-mmodely-vignette-Vision.pdf |binary mmodely-0.2.2/mmodely/inst/doc/Schruth-mmodely-vignette-Vocal.R | 68 +++-- mmodely-0.2.2/mmodely/inst/doc/Schruth-mmodely-vignette-Vocal.Rnw | 119 ++++++---- mmodely-0.2.2/mmodely/inst/doc/Schruth-mmodely-vignette-Vocal.pdf |binary mmodely-0.2.2/mmodely/man/average.fit.models.Rd |only mmodely-0.2.2/mmodely/man/distro.dots.modsel.Rd |only mmodely-0.2.2/mmodely/man/get.pgls.coefs.Rd | 2 mmodely-0.2.2/mmodely/man/plot.pgls.R2AIC.Rd | 5 mmodely-0.2.2/mmodely/man/plot.pgls.iters.Rd | 4 mmodely-0.2.2/mmodely/man/select.best.models.Rd |only mmodely-0.2.2/mmodely/vignettes/Schruth-mmodely-vignette-Vision.Rnw | 110 +++++---- mmodely-0.2.2/mmodely/vignettes/Schruth-mmodely-vignette-Vocal.Rnw | 119 ++++++---- 23 files changed, 451 insertions(+), 261 deletions(-)
Title: Wrap Vectors in Markdown Formatting
Description: Ease the transition between R vectors and markdown
text. With 'gluedown' and 'rmarkdown', users can create traditional
vectors in R, glue those strings together with the markdown syntax,
and print those formatted vectors directly to the document. This
package primarily uses GitHub Flavored Markdown (GFM), an offshoot of
the unambiguous CommonMark specification by John MacFarlane (2019)
<https://spec.commonmark.org/>.
Author: Kiernan Nicholls [aut, cre]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Diff between gluedown versions 1.0.5 dated 2022-11-04 and 1.0.6 dated 2022-11-06
DESCRIPTION | 6 - MD5 | 10 - NEWS.md | 2 README.md | 2 inst/doc/github-spec.html | 203 +++++++++++++++++++------------------- inst/doc/literal-programming.html | 2 6 files changed, 115 insertions(+), 110 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous (and discrete) time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE) or difference equation, measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling.
See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. Priors may be used. For the conceptual overview of the hierarchical Bayesian
linear SDE approach,
see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Mod [...truncated...]
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver@ibe.uzh.ch>
Diff between ctsem versions 3.7.1 dated 2022-08-08 and 3.7.2 dated 2022-11-06
ctsem-3.7.1/ctsem/R/JKalman.R |only ctsem-3.7.1/ctsem/R/ctGuessPriors.R |only ctsem-3.7.1/ctsem/R/llsurface.R |only ctsem-3.7.1/ctsem/tests/testthat/test-bivariatetrait_hmc.R |only ctsem-3.7.1/ctsem/tests/testthat/test-bootHessian.R |only ctsem-3.7.1/ctsem/tests/testthat/test-tdeffectvariation_covtest.R |only ctsem-3.7.2/ctsem/DESCRIPTION | 8 ctsem-3.7.2/ctsem/MD5 | 176 +- ctsem-3.7.2/ctsem/R/ctDiscretePars.R | 2 ctsem-3.7.2/ctsem/R/ctLOO.R | 2 ctsem-3.7.2/ctsem/R/ctModelLatex.R | 4 ctsem-3.7.2/ctsem/R/ctStanData.R | 6 ctsem-3.7.2/ctsem/R/ctStanGenerate.R | 35 ctsem-3.7.2/ctsem/R/ctStanGenerateFromFit.R | 16 ctsem-3.7.2/ctsem/R/ctStanModelWriter.R | 8 ctsem-3.7.2/ctsem/R/ctStanPostPredict.R | 11 ctsem-3.7.2/ctsem/R/sdpcor2cov.R | 4 ctsem-3.7.2/ctsem/R/sgd.R | 9 ctsem-3.7.2/ctsem/R/stanoptimis.R | 113 - ctsem-3.7.2/ctsem/build/vignette.rds |binary ctsem-3.7.2/ctsem/data/ctstantestdat.rda |binary ctsem-3.7.2/ctsem/data/ctstantestfit.rda |binary ctsem-3.7.2/ctsem/inst/doc/hierarchicalmanual.pdf |binary ctsem-3.7.2/ctsem/man/AnomAuth.Rd | 30 ctsem-3.7.2/ctsem/man/Oscillating.Rd | 30 ctsem-3.7.2/ctsem/man/ctAddSamples.Rd | 52 ctsem-3.7.2/ctsem/man/ctCheckFit.Rd | 214 +- ctsem-3.7.2/ctsem/man/ctChisqTest.Rd | 68 ctsem-3.7.2/ctsem/man/ctCollapse.Rd | 56 ctsem-3.7.2/ctsem/man/ctDeintervalise.Rd | 40 ctsem-3.7.2/ctsem/man/ctDensity.Rd | 64 ctsem-3.7.2/ctsem/man/ctDiscretiseData.Rd | 82 - ctsem-3.7.2/ctsem/man/ctDocs.Rd | 34 ctsem-3.7.2/ctsem/man/ctExample1.Rd | 24 ctsem-3.7.2/ctsem/man/ctExample1TIpred.Rd | 26 ctsem-3.7.2/ctsem/man/ctExample2.Rd | 28 ctsem-3.7.2/ctsem/man/ctExample2level.Rd | 28 ctsem-3.7.2/ctsem/man/ctExample3.Rd | 24 ctsem-3.7.2/ctsem/man/ctExample4.Rd | 24 ctsem-3.7.2/ctsem/man/ctExtract.Rd | 58 ctsem-3.7.2/ctsem/man/ctFit.Rd | 50 ctsem-3.7.2/ctsem/man/ctFitMultiModel.Rd | 136 - ctsem-3.7.2/ctsem/man/ctGenerate.Rd | 116 - ctsem-3.7.2/ctsem/man/ctIndplot.Rd | 144 - ctsem-3.7.2/ctsem/man/ctIntervalise.Rd | 170 +- ctsem-3.7.2/ctsem/man/ctLOO.Rd | 82 - ctsem-3.7.2/ctsem/man/ctLongToWide.Rd | 108 - ctsem-3.7.2/ctsem/man/ctModel.Rd | 444 +++--- ctsem-3.7.2/ctsem/man/ctModelHigherOrder.Rd | 88 - ctsem-3.7.2/ctsem/man/ctModelLatex.Rd | 152 +- ctsem-3.7.2/ctsem/man/ctPlotArray.Rd | 130 - ctsem-3.7.2/ctsem/man/ctPoly.Rd | 70 ctsem-3.7.2/ctsem/man/ctStanContinuousPars.Rd | 70 ctsem-3.7.2/ctsem/man/ctStanDiscretePars.Rd | 136 - ctsem-3.7.2/ctsem/man/ctStanFit.Rd | 740 +++++----- ctsem-3.7.2/ctsem/man/ctStanFitUpdate.Rd | 64 ctsem-3.7.2/ctsem/man/ctStanGenerate.Rd | 90 - ctsem-3.7.2/ctsem/man/ctStanGenerateFromFit.Rd | 76 - ctsem-3.7.2/ctsem/man/ctStanKalman.Rd | 106 - ctsem-3.7.2/ctsem/man/ctStanModel.Rd | 84 - ctsem-3.7.2/ctsem/man/ctStanParnames.Rd | 98 - ctsem-3.7.2/ctsem/man/ctStanPlotPost.Rd | 102 - ctsem-3.7.2/ctsem/man/ctStanPostPredict.Rd | 113 - ctsem-3.7.2/ctsem/man/ctStanSubjectPars.Rd | 66 ctsem-3.7.2/ctsem/man/ctStanTIpredeffects.Rd | 170 +- ctsem-3.7.2/ctsem/man/ctStanUpdModel.Rd | 40 ctsem-3.7.2/ctsem/man/ctWideNames.Rd | 74 - ctsem-3.7.2/ctsem/man/ctWideToLong.Rd | 130 - ctsem-3.7.2/ctsem/man/ctsem.Rd | 56 ctsem-3.7.2/ctsem/man/ctstantestdat.Rd | 22 ctsem-3.7.2/ctsem/man/ctstantestfit.Rd | 22 ctsem-3.7.2/ctsem/man/datastructure.Rd | 30 ctsem-3.7.2/ctsem/man/inv_logit.Rd | 34 ctsem-3.7.2/ctsem/man/isdiag.Rd | 90 - ctsem-3.7.2/ctsem/man/log1p_exp.Rd | 34 ctsem-3.7.2/ctsem/man/longexample.Rd | 28 ctsem-3.7.2/ctsem/man/plot.ctKalmanDF.Rd | 154 +- ctsem-3.7.2/ctsem/man/plot.ctStanFit.Rd | 90 - ctsem-3.7.2/ctsem/man/plot.ctStanModel.Rd | 132 - ctsem-3.7.2/ctsem/man/sdpcor2cov.Rd | 52 ctsem-3.7.2/ctsem/man/stanWplot.Rd | 82 - ctsem-3.7.2/ctsem/man/stan_checkdivergences.Rd | 96 - ctsem-3.7.2/ctsem/man/stan_postcalc.Rd | 68 ctsem-3.7.2/ctsem/man/stan_reinitsf.Rd | 54 ctsem-3.7.2/ctsem/man/stan_unconstrainsamples.Rd | 92 - ctsem-3.7.2/ctsem/man/standatact_specificsubjects.Rd | 54 ctsem-3.7.2/ctsem/man/stanoptimis.Rd | 2 ctsem-3.7.2/ctsem/man/summary.ctStanFit.Rd | 90 - ctsem-3.7.2/ctsem/man/w32chk.Rd | 34 ctsem-3.7.2/ctsem/src/stan_files/ctsm.stan | 4 ctsem-3.7.2/ctsem/src/stan_files/ctsmgen.stan | 8 ctsem-3.7.2/ctsem/tests/testthat/test-timevarying.R | 4 92 files changed, 3230 insertions(+), 3227 deletions(-)
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on Markov
chain Monte Carlo. Although boom contains a few R utilities (mainly plotting
functions), its primary purpose is to install the BOOM C++ library on your
system so that other packages can link against it.
Author: Steven L. Scott is the sole author and creator of the BOOM project.
Some code in the BOOM libraries has been modified from other open source
projects. These include Cephes , NEWUOA , and a
modified version of the R math libraries . Original
copyrig [...truncated...]
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between Boom versions 0.9.9 dated 2022-05-27 and 0.9.11 dated 2022-11-06
Boom-0.9.11/Boom/DESCRIPTION | 11 Boom-0.9.11/Boom/MD5 | 184 +++--- Boom-0.9.11/Boom/inst/include/LinAlg/ArrayIterator.hpp | 41 - Boom-0.9.11/Boom/inst/include/LinAlg/Eigen.hpp | 14 Boom-0.9.11/Boom/inst/include/LinAlg/Matrix.hpp | 26 Boom-0.9.11/Boom/inst/include/LinAlg/Selector.hpp | 20 Boom-0.9.11/Boom/inst/include/LinAlg/SpdMatrix.hpp | 2 Boom-0.9.11/Boom/inst/include/LinAlg/VectorViewIterator.hpp | 34 - Boom-0.9.11/Boom/inst/include/Models/BetaBinomialModel.hpp | 51 + Boom-0.9.11/Boom/inst/include/Models/ConstrainedVectorParams.hpp | 80 ++ Boom-0.9.11/Boom/inst/include/Models/DataTypes.hpp | 3 Boom-0.9.11/Boom/inst/include/Models/Glm/Glm.hpp | 2 Boom-0.9.11/Boom/inst/include/Models/Glm/GlmCoefs.hpp | 4 Boom-0.9.11/Boom/inst/include/Models/Glm/PosteriorSamplers/RegressionConjSampler.hpp | 3 Boom-0.9.11/Boom/inst/include/Models/Glm/RegressionModel.hpp | 6 Boom-0.9.11/Boom/inst/include/Models/IRT/PartialCreditModel.hpp | 6 Boom-0.9.11/Boom/inst/include/Models/Mixtures/BetaBinomialMixture.hpp |only Boom-0.9.11/Boom/inst/include/Models/Mixtures/PosteriorSamplers/BetaBinomialMixturePosteriorSampler.hpp |only Boom-0.9.11/Boom/inst/include/Models/MultinomialModel.hpp | 4 Boom-0.9.11/Boom/inst/include/Models/ParamTypes.hpp | 8 Boom-0.9.11/Boom/inst/include/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.hpp | 84 +- Boom-0.9.11/Boom/inst/include/Models/PosteriorSamplers/DirichletPosteriorSampler.hpp | 81 -- Boom-0.9.11/Boom/inst/include/Models/PosteriorSamplers/GenericStudentSampler.hpp | 2 Boom-0.9.11/Boom/inst/include/Models/StateSpace/Filters/ConditionalIidKalmanFilter.hpp | 8 Boom-0.9.11/Boom/inst/include/Models/StateSpace/Filters/ConditionallyIndependentKalmanFilter.hpp | 10 Boom-0.9.11/Boom/inst/include/Models/StateSpace/Filters/KalmanFilterBase.hpp | 9 Boom-0.9.11/Boom/inst/include/Models/StateSpace/Filters/MultivariateKalmanFilterBase.hpp | 92 +-- Boom-0.9.11/Boom/inst/include/Models/StateSpace/Filters/ScalarKalmanFilter.hpp | 2 Boom-0.9.11/Boom/inst/include/Models/StateSpace/Filters/SparseKalmanTools.hpp | 30 - Boom-0.9.11/Boom/inst/include/Models/StateSpace/Filters/SparseMatrix.hpp | 128 +++- Boom-0.9.11/Boom/inst/include/Models/StateSpace/Multivariate/MultivariateStateSpaceModelBase.hpp | 40 + Boom-0.9.11/Boom/inst/include/Models/StateSpace/Multivariate/MultivariateStateSpaceRegressionModel.hpp | 7 Boom-0.9.11/Boom/inst/include/Models/StateSpace/Multivariate/PosteriorSamplers/SADSampler.hpp |only Boom-0.9.11/Boom/inst/include/Models/StateSpace/Multivariate/StateModels/ScalarStateModelAdapter.hpp | 183 ++++-- Boom-0.9.11/Boom/inst/include/Models/StateSpace/Multivariate/tests/mv_framework.hpp | 20 Boom-0.9.11/Boom/inst/include/Models/StateSpace/StateModels/ArStateModel.hpp | 2 Boom-0.9.11/Boom/inst/include/Models/StateSpace/StateModels/GeneralSeasonalStateModel.hpp | 2 Boom-0.9.11/Boom/inst/include/Models/StateSpace/StateModels/LocalLinearTrend.hpp | 2 Boom-0.9.11/Boom/inst/include/Models/StateSpace/StateModels/StateModel.hpp | 2 Boom-0.9.11/Boom/inst/include/TargetFun/JacobianChecker.hpp | 5 Boom-0.9.11/Boom/inst/include/TargetFun/LogTransform.hpp |only Boom-0.9.11/Boom/inst/include/TargetFun/LogitTransform.hpp |only Boom-0.9.11/Boom/inst/include/TargetFun/MultinomialLogitTransform.hpp |only Boom-0.9.11/Boom/inst/include/TargetFun/Transformation.hpp | 48 - Boom-0.9.11/Boom/inst/include/distributions.hpp | 3 Boom-0.9.11/Boom/inst/include/distributions/Markov.hpp | 31 - Boom-0.9.11/Boom/inst/include/stats/ChiSquareTest.hpp | 23 Boom-0.9.11/Boom/inst/include/stats/FreqDist.hpp | 11 Boom-0.9.11/Boom/inst/include/stats/logit.hpp | 6 Boom-0.9.11/Boom/src/LinAlg/Eigen.cpp | 33 + Boom-0.9.11/Boom/src/LinAlg/Givens.cpp | 1 Boom-0.9.11/Boom/src/LinAlg/LU.cpp | 4 Boom-0.9.11/Boom/src/LinAlg/Matrix.cpp | 51 + Boom-0.9.11/Boom/src/LinAlg/Selector.cpp | 24 Boom-0.9.11/Boom/src/LinAlg/SpdMatrix.cpp | 22 Boom-0.9.11/Boom/src/Models/BetaBinomialModel.cpp | 203 +++++- Boom-0.9.11/Boom/src/Models/ConstrainedVectorParams.cpp | 116 ++- Boom-0.9.11/Boom/src/Models/DataTypes.cpp | 1 Boom-0.9.11/Boom/src/Models/Glm/GlmCoefs.cpp | 24 Boom-0.9.11/Boom/src/Models/IRT/PartialCreditModel.cpp | 22 Boom-0.9.11/Boom/src/Models/MarkovModel.cpp | 1 Boom-0.9.11/Boom/src/Models/Mixtures/BetaBinomialMixture.cpp |only Boom-0.9.11/Boom/src/Models/Mixtures/PosteriorSamplers/BetaBinomialMixturePosteriorSampler.cpp |only Boom-0.9.11/Boom/src/Models/ModelTypes.cpp | 4 Boom-0.9.11/Boom/src/Models/MultinomialModel.cpp | 17 Boom-0.9.11/Boom/src/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.cpp | 160 +---- Boom-0.9.11/Boom/src/Models/PosteriorSamplers/DirichletPosteriorSampler.cpp | 153 ----- Boom-0.9.11/Boom/src/Models/PosteriorSamplers/GenericStudentSampler.cpp | 2 Boom-0.9.11/Boom/src/Models/SpdData.cpp | 20 Boom-0.9.11/Boom/src/Models/StateSpace/Filters/ConditionalIidKalmanFilter.cpp | 103 +++ Boom-0.9.11/Boom/src/Models/StateSpace/Filters/ConditionallyIndependentKalmanFilter.cpp | 125 +++- Boom-0.9.11/Boom/src/Models/StateSpace/Filters/MultivariateKalmanFilterBase.cpp | 294 ++++++++-- Boom-0.9.11/Boom/src/Models/StateSpace/Filters/SparseMatrix.cpp | 254 +++++++- Boom-0.9.11/Boom/src/Models/StateSpace/Filters/SparseVector.cpp | 1 Boom-0.9.11/Boom/src/Models/StateSpace/Multivariate/MultivariateStateSpaceModelBase.cpp | 81 ++ Boom-0.9.11/Boom/src/Models/StateSpace/Multivariate/MultivariateStateSpaceRegressionModel.cpp | 73 -- Boom-0.9.11/Boom/src/Models/StateSpace/Multivariate/PosteriorSamplers/SADSampler.cpp |only Boom-0.9.11/Boom/src/Models/StateSpace/Multivariate/StateModels/ScalarStateModelAdapter.cpp | 192 ++---- Boom-0.9.11/Boom/src/Models/StateSpace/StateModels/StateModel.cpp | 15 Boom-0.9.11/Boom/src/Models/StateSpace/StateModels/test_utils/ArStateModelTestModule.cpp | 4 Boom-0.9.11/Boom/src/Models/ZeroMeanGaussianModel.cpp | 4 Boom-0.9.11/Boom/src/Samplers/Gilks/arms.cpp | 57 - Boom-0.9.11/Boom/src/TargetFun/JacobianChecker.cpp | 60 +- Boom-0.9.11/Boom/src/TargetFun/LogTransform.cpp |only Boom-0.9.11/Boom/src/TargetFun/LogitTransform.cpp |only Boom-0.9.11/Boom/src/TargetFun/MultinomialLogitTransform.cpp |only Boom-0.9.11/Boom/src/TargetFun/Transformation.cpp | 52 - Boom-0.9.11/Boom/src/cpputil/LongString.cpp | 16 Boom-0.9.11/Boom/src/cpputil/report_error.cpp | 4 Boom-0.9.11/Boom/src/distributions/Markov.cpp | 19 Boom-0.9.11/Boom/src/math/cephes/planck.cpp | 2 Boom-0.9.11/Boom/src/numopt/NelderMead.cpp | 1 Boom-0.9.11/Boom/src/numopt/bfgs.cpp | 1 Boom-0.9.11/Boom/src/numopt/max_nd.cpp | 1 Boom-0.9.11/Boom/src/numopt/newton.cpp | 1 Boom-0.9.11/Boom/src/stats/ChiSquareTest.cpp | 38 + Boom-0.9.11/Boom/src/stats/DataTable.cpp | 1 Boom-0.9.11/Boom/src/stats/FreqDist.cpp | 12 Boom-0.9.9/Boom/inst/include/cpputil/date_utils.hpp |only Boom-0.9.9/Boom/src/cpputil/get_date.cpp |only 100 files changed, 2287 insertions(+), 1312 deletions(-)
Title: Fast Best Subset Selection
Description: Extremely efficient toolkit for solving the best subset selection problem <https://www.jmlr.org/papers/v23/21-1060.html>. This package is its R interface. The package implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times for linear model. It also supports best subset selection for logistic regression, Poisson regression, Cox proportional hazard model, Gamma regression, multiple-response regression, multinomial logistic regression, ordinal regression, (sequential) principal component analysis, and robust principal component analysis. The other valuable features such as the best subset of group selection <arXiv:2104.12576> and sure independence screening <doi:10.1111/j.1467-9868.2008.00674.x> are also provided.
Author: Jin Zhu [aut, cre] ,
Liyuan Hu [aut],
Junhao Huang [aut],
Kangkang Jiang [aut],
Yanhang Zhang [aut],
Zezhi Wang [aut],
Borui Tang [aut],
Shiyun Lin [aut],
Junxian Zhu [aut],
Canhong Wen [aut],
Heping Zhang [aut] ,
Xueqin Wang [aut] ,
spectra contribu [...truncated...]
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between abess versions 0.4.5 dated 2022-03-22 and 0.4.6 dated 2022-11-06
abess-0.4.5/abess/R/tmp |only abess-0.4.5/abess/tests/testthat/Rplots.pdf |only abess-0.4.6/abess/DESCRIPTION | 10 - abess-0.4.6/abess/MD5 | 24 +- abess-0.4.6/abess/NEWS.md | 7 abess-0.4.6/abess/R/abess.R | 6 abess-0.4.6/abess/README.md | 15 - abess-0.4.6/abess/build/partial.rdb |binary abess-0.4.6/abess/inst/CITATION | 16 + abess-0.4.6/abess/inst/doc/v01-abess-guide.html | 209 +++++++++++++++++++----- abess-0.4.6/abess/man/abess-package.Rd | 2 abess-0.4.6/abess/man/abess.Rd | 4 abess-0.4.6/abess/src/AlgorithmGLM.h | 4 abess-0.4.6/abess/src/Metric.h | 4 14 files changed, 217 insertions(+), 84 deletions(-)