Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for data management, descriptive statistics, and statistical analysis e.g., reading and writing a SPSS file, frequency table, cross tabulation, multilevel and missing data descriptive statistics, various effect size measures, scale and group scores, centering at the grand mean or within cluster, or coefficient alpha and item statistics.
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.2.0 dated 2020-02-09 and 0.2.1 dated 2020-02-09
misty-0.2.0/misty/R/trim.R |only misty-0.2.0/misty/man/trim.Rd |only misty-0.2.1/misty/DESCRIPTION | 17 - misty-0.2.1/misty/MD5 | 229 ++++++++--------- misty-0.2.1/misty/NAMESPACE | 139 +++++----- misty-0.2.1/misty/R/alpha.coef.R | 177 ++++++------- misty-0.2.1/misty/R/as.na.R | 94 +++---- misty-0.2.1/misty/R/center.R | 39 +-- misty-0.2.1/misty/R/cohens.d.R | 78 +++--- misty-0.2.1/misty/R/cont.coef.R | 91 ++++--- misty-0.2.1/misty/R/cor.matrix.R | 114 +++++--- misty-0.2.1/misty/R/cramers.v.R | 54 ++-- misty-0.2.1/misty/R/crosstab.R | 58 ++-- misty-0.2.1/misty/R/descript.R | 351 ++++++++++++++++----------- misty-0.2.1/misty/R/df.merge.R | 38 +- misty-0.2.1/misty/R/df.rbind.R | 4 misty-0.2.1/misty/R/df.rename.R | 19 - misty-0.2.1/misty/R/df.sort.R | 16 - misty-0.2.1/misty/R/dummy.c.R | 33 +- misty-0.2.1/misty/R/eta.sq.R | 108 ++++++-- misty-0.2.1/misty/R/freq.R | 127 ++++----- misty-0.2.1/misty/R/group.scores.R | 14 - misty-0.2.1/misty/R/kurtosis.R | 26 +- misty-0.2.1/misty/R/multilevel.descript.R | 106 ++++---- misty-0.2.1/misty/R/multilevel.icc.R | 218 +++++++++------- misty-0.2.1/misty/R/na.as.R | 8 misty-0.2.1/misty/R/na.auxiliary.R | 62 ++-- misty-0.2.1/misty/R/na.coverage.R | 27 +- misty-0.2.1/misty/R/na.descript.R | 24 - misty-0.2.1/misty/R/na.indicator.R | 18 - misty-0.2.1/misty/R/na.pattern.R | 80 +++--- misty-0.2.1/misty/R/na.prop.R | 24 - misty-0.2.1/misty/R/phi.coef.R | 115 ++++++-- misty-0.2.1/misty/R/poly.cor.R | 59 ++-- misty-0.2.1/misty/R/print.alpha.coef.R | 6 misty-0.2.1/misty/R/print.cohens.d.R | 16 - misty-0.2.1/misty/R/print.cont.coef.R | 2 misty-0.2.1/misty/R/print.cor.matrix.R | 36 +- misty-0.2.1/misty/R/print.crosstab.R | 8 misty-0.2.1/misty/R/print.descript.R | 217 ++++++---------- misty-0.2.1/misty/R/print.eta.sq.R | 33 +- misty-0.2.1/misty/R/print.freq.R | 22 - misty-0.2.1/misty/R/print.na.pattern.R | 1 misty-0.2.1/misty/R/print.poly.cor.R | 4 misty-0.2.1/misty/R/print.size.R | 91 +++---- misty-0.2.1/misty/R/read.mplus.R | 18 - misty-0.2.1/misty/R/read.sav.R | 6 misty-0.2.1/misty/R/rec.R | 64 ++++ misty-0.2.1/misty/R/reverse.item.R | 15 - misty-0.2.1/misty/R/run.mplus.R | 7 misty-0.2.1/misty/R/rwg.lindell.R | 28 +- misty-0.2.1/misty/R/scores.R | 34 +- misty-0.2.1/misty/R/size.cor.R | 26 +- misty-0.2.1/misty/R/size.mean.R | 14 - misty-0.2.1/misty/R/size.prop.R | 22 - misty-0.2.1/misty/R/skewness.R | 35 +- misty-0.2.1/misty/R/stromit.R | 17 - misty-0.2.1/misty/R/write.mplus.R | 49 ++- misty-0.2.1/misty/R/write.sav.R | 135 +++++----- misty-0.2.1/misty/build |only misty-0.2.1/misty/inst |only misty-0.2.1/misty/man/alpha.coef.Rd | 10 misty-0.2.1/misty/man/as.na.Rd | 26 +- misty-0.2.1/misty/man/center.Rd | 4 misty-0.2.1/misty/man/cohens.d.Rd | 16 - misty-0.2.1/misty/man/cont.coef.Rd | 20 - misty-0.2.1/misty/man/cor.matrix.Rd | 11 misty-0.2.1/misty/man/cramers.v.Rd | 6 misty-0.2.1/misty/man/crosstab.Rd | 9 misty-0.2.1/misty/man/descript.Rd | 44 +-- misty-0.2.1/misty/man/df.merge.Rd | 204 +++++++-------- misty-0.2.1/misty/man/df.rbind.Rd | 126 ++++----- misty-0.2.1/misty/man/df.rename.Rd | 86 +++--- misty-0.2.1/misty/man/df.sort.Rd | 106 ++++---- misty-0.2.1/misty/man/dummy.c.Rd | 176 ++++++------- misty-0.2.1/misty/man/eta.sq.Rd | 3 misty-0.2.1/misty/man/freq.Rd | 6 misty-0.2.1/misty/man/kurtosis.Rd | 92 +++---- misty-0.2.1/misty/man/multilevel.descript.Rd | 20 - misty-0.2.1/misty/man/multilevel.icc.Rd | 12 misty-0.2.1/misty/man/na.as.Rd | 2 misty-0.2.1/misty/man/na.auxiliary.Rd | 5 misty-0.2.1/misty/man/na.coverage.Rd | 5 misty-0.2.1/misty/man/na.descript.Rd | 3 misty-0.2.1/misty/man/na.indicator.Rd | 96 +++---- misty-0.2.1/misty/man/na.pattern.Rd | 3 misty-0.2.1/misty/man/na.prop.Rd | 98 +++---- misty-0.2.1/misty/man/phi.coef.Rd | 20 - misty-0.2.1/misty/man/poly.cor.Rd | 7 misty-0.2.1/misty/man/print.alpha.coef.Rd | 7 misty-0.2.1/misty/man/print.cont.coef.Rd | 87 +++--- misty-0.2.1/misty/man/print.cramers.v.Rd | 87 +++--- misty-0.2.1/misty/man/print.descript.Rd | 6 misty-0.2.1/misty/man/print.eta.sq.Rd | 78 +++--- misty-0.2.1/misty/man/print.freq.Rd | 4 misty-0.2.1/misty/man/print.na.auxiliary.Rd | 4 misty-0.2.1/misty/man/print.na.coverage.Rd | 4 misty-0.2.1/misty/man/print.na.descript.Rd | 4 misty-0.2.1/misty/man/print.na.pattern.Rd | 5 misty-0.2.1/misty/man/print.phi.coef.Rd | 87 +++--- misty-0.2.1/misty/man/print.poly.cor.Rd | 85 +++--- misty-0.2.1/misty/man/print.size.Rd | 118 ++++----- misty-0.2.1/misty/man/read.mplus.Rd | 6 misty-0.2.1/misty/man/read.sav.Rd | 6 misty-0.2.1/misty/man/rec.Rd | 8 misty-0.2.1/misty/man/reverse.item.Rd | 8 misty-0.2.1/misty/man/run.mplus.Rd | 6 misty-0.2.1/misty/man/rwg.lindell.Rd | 12 misty-0.2.1/misty/man/scores.Rd | 11 misty-0.2.1/misty/man/size.cor.Rd | 4 misty-0.2.1/misty/man/size.mean.Rd | 2 misty-0.2.1/misty/man/size.prop.Rd | 2 misty-0.2.1/misty/man/skewness.Rd | 92 +++---- misty-0.2.1/misty/man/stromit.Rd | 3 misty-0.2.1/misty/man/write.mplus.Rd | 10 misty-0.2.1/misty/man/write.sav.Rd | 18 - misty-0.2.1/misty/vignettes |only 117 files changed, 2898 insertions(+), 2555 deletions(-)
Title: A Graphical EDA Tool
Description: An automated graphical exploratory data analysis (EDA) tool that introduces:
a.) wideplot() graphics for exploring the structure of a dataset through a grid of variables
and graphic types.
b.) longplot() graphics, which present the entire catalog of available graphics for representing
a particular variable using a grid of graphic types and variations on these types.
c.) plotup() function, which presents a particular graphic for a specific variable of a dataset.
The plotup() function also makes it possible to obtain the code used to generate the graphic,
meaning that the user can adjust its properties as needed.
Author: Pere Millán-Martínez [aut, cre],
Ramon Oller Piqué [ctb]
Maintainer: Pere Millán-Martínez <info@sciencegraph.org>
Diff between brinton versions 0.1.3 dated 2020-01-07 and 0.1.4 dated 2020-02-09
DESCRIPTION | 15 MD5 | 70 NAMESPACE | 3 R/05_aux_functions.R | 9 R/10_themes.R | 23 R/20_basic_plots.R | 872 +++++--- R/40_outputs.R | 93 R/50_longplot.R | 199 + R/60_wideplot.R | 14 R/70_plotup.R | 3477 +++++++++++++++++++++------------- README.md | 10 inst/doc/brinton.R | 2 inst/doc/brinton.Rmd | 3 inst/doc/brinton.html | 13 inst/doc/specimen.R | 40 inst/doc/specimen.Rmd | 109 - inst/doc/specimen.html | 178 + man/figures/README-plotspane-1.png |binary man/wideplot.Rd | 8 vignettes/brinton.Rmd | 3 vignettes/figures/2numeric_01-1.png |only vignettes/figures/2numeric_02-1.png |only vignettes/figures/2numeric_03-1.png |only vignettes/figures/2numeric_04-1.png |only vignettes/figures/2numeric_05-1.png |only vignettes/figures/2numeric_06-1.png |only vignettes/figures/2numeric_07-1.png |only vignettes/figures/2numeric_08-1.png |only vignettes/figures/2numeric_09-1.png |only vignettes/figures/2numeric_10-1.png |only vignettes/figures/2numeric_11-1.png |only vignettes/figures/2numeric_12-1.png |only vignettes/figures/2numeric_13-1.png |only vignettes/figures/2numeric_14-1.png |only vignettes/figures/2numeric_15-1.png |only vignettes/figures/2numeric_16-1.png |only vignettes/figures/2numeric_17-1.png |only vignettes/figures/2numeric_18-1.png |only vignettes/figures/2numeric_19-1.png |only vignettes/figures/2numeric_20-1.png |only vignettes/figures/2numeric_21-1.png |only vignettes/figures/2numeric_22-1.png |only vignettes/figures/2numeric_23-1.png |only vignettes/figures/2numeric_24-1.png |only vignettes/figures/numeric_01-1.png |binary vignettes/figures/numeric_17-1.png |only vignettes/figures/numeric_18-1.png |only vignettes/figures/numeric_19-1.png |only vignettes/figures/wideplot_esoph.jpeg |only vignettes/specimen.Rmd | 109 - 50 files changed, 3461 insertions(+), 1789 deletions(-)
Title: Black-Litterman and Copula Opinion Pooling Frameworks
Description: An implementation of the Black-Litterman Model and Atilio
Meucci's copula opinion pooling framework.
Author: Francisco Gochez, Richard Chandler-Mant, Suchen Jin, Jinjing Xie
Maintainer: Ava Yang <ayang@mango-solutions.com>
Diff between BLCOP versions 0.3.1 dated 2015-02-04 and 0.3.2 dated 2020-02-09
BLCOP-0.3.1/BLCOP/inst/doc/BlackLitterman.pdf |only BLCOP-0.3.2/BLCOP/DESCRIPTION | 13 ++++++------- BLCOP-0.3.2/BLCOP/MD5 | 23 +++++++++++------------ BLCOP-0.3.2/BLCOP/NAMESPACE | 17 +++++++++++++++-- BLCOP-0.3.2/BLCOP/NEWS | 4 ++++ BLCOP-0.3.2/BLCOP/R/BLbuildViews.r | 2 +- BLCOP-0.3.2/BLCOP/R/utils.R | 2 +- BLCOP-0.3.2/BLCOP/build/vignette.rds |binary BLCOP-0.3.2/BLCOP/inst/doc/BLCOP.R | 8 ++++---- BLCOP-0.3.2/BLCOP/inst/doc/BLCOP.Rnw | 10 +++++----- BLCOP-0.3.2/BLCOP/inst/doc/BLCOP.pdf |binary BLCOP-0.3.2/BLCOP/man/CAPMList.Rd | 1 + BLCOP-0.3.2/BLCOP/vignettes/BLCOP.Rnw | 10 +++++----- 13 files changed, 53 insertions(+), 37 deletions(-)
Title: Music Notation Syntax, Manipulation, Analysis and Transcription
in R
Description: Provides a music notation syntax and a collection of music programming functions for generating, manipulating, organizing and analyzing musical information in R.
The music notation framework facilitates creating and analyzing music data in notation form.
Music data can be viewed, manipulated and analyzed while in different forms of representation based around different data structures: strings and data frames.
Each representation offers advantages over the other for different use cases.
Music syntax can be entered directly and represented in character strings to minimize the formatting overhead of data entry by using simple data structures, for example when wanting to quickly enter and transcribe short pieces of music to sheet music or tablature.
The package contains functions for directly performing various mathematical, logical and organizational operations and musical transformations on special object classes that facilitate working with music data and notation.
The same music data can also be organized in tidy data frames, allowing for a more familiar and powerful approach to the analysis of large amounts of structured music data.
Functions are available for mapping seamlessly between these data structures and their representations of musical information.
The package also provides API wrapper functions for transcribing musical representations in R into guitar tablature ("tabs") and basic sheet music using the 'LilyPond' backend (<http://lilypond.org>).
'LilyPond' is open source music engraving software for generating high quality sheet music based on markup syntax.
The package generates 'LilyPond' files from R code and can pass them to 'LilyPond' to be rendered into sheet music pdf files.
The package offers nominal MIDI file output support in conjunction with rendering sheet music.
The package can read MIDI files and attempts to structure the MIDI data to integrate as best as possible with the data structures and functionality found throughout the package.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>
Diff between tabr versions 0.4.0 dated 2019-12-03 and 0.4.1 dated 2020-02-09
tabr-0.4.0/tabr/inst/doc/tabr-basics.R |only tabr-0.4.0/tabr/inst/doc/tabr-basics.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-basics.html |only tabr-0.4.0/tabr/inst/doc/tabr-chordchart.R |only tabr-0.4.0/tabr/inst/doc/tabr-chordchart.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-chordchart.html |only tabr-0.4.0/tabr/inst/doc/tabr-chords.R |only tabr-0.4.0/tabr/inst/doc/tabr-chords.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-chords.html |only tabr-0.4.0/tabr/inst/doc/tabr-engraving.R |only tabr-0.4.0/tabr/inst/doc/tabr-engraving.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-engraving.html |only tabr-0.4.0/tabr/inst/doc/tabr-fretboard.R |only tabr-0.4.0/tabr/inst/doc/tabr-fretboard.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-fretboard.html |only tabr-0.4.0/tabr/inst/doc/tabr-helpers.R |only tabr-0.4.0/tabr/inst/doc/tabr-helpers.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-helpers.html |only tabr-0.4.0/tabr/inst/doc/tabr-phrases.R |only tabr-0.4.0/tabr/inst/doc/tabr-phrases.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-phrases.html |only tabr-0.4.0/tabr/inst/doc/tabr-prog-converters.R |only tabr-0.4.0/tabr/inst/doc/tabr-prog-converters.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-prog-converters.html |only tabr-0.4.0/tabr/inst/doc/tabr-repeats.R |only tabr-0.4.0/tabr/inst/doc/tabr-repeats.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-repeats.html |only tabr-0.4.0/tabr/inst/doc/tabr-tracks-scores.R |only tabr-0.4.0/tabr/inst/doc/tabr-tracks-scores.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-tracks-scores.html |only tabr-0.4.0/tabr/inst/doc/tabr-tunings.R |only tabr-0.4.0/tabr/inst/doc/tabr-tunings.Rmd |only tabr-0.4.0/tabr/inst/doc/tabr-tunings.html |only tabr-0.4.0/tabr/vignettes/tabr-basics.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-chordchart.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-chords.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-engraving.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-fretboard.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-helpers.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-phrases.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-prog-converters.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-repeats.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-tracks-scores.Rmd |only tabr-0.4.0/tabr/vignettes/tabr-tunings.Rmd |only tabr-0.4.1/tabr/DESCRIPTION | 8 - tabr-0.4.1/tabr/MD5 | 104 ++++++--------------- tabr-0.4.1/tabr/NEWS.md | 14 ++ tabr-0.4.1/tabr/R/class_methods.R | 4 tabr-0.4.1/tabr/R/freq.R | 1 tabr-0.4.1/tabr/R/lilypond.R | 10 +- tabr-0.4.1/tabr/R/lp_render.R | 6 - tabr-0.4.1/tabr/R/music.R | 2 tabr-0.4.1/tabr/R/phrase.R | 29 ++++- tabr-0.4.1/tabr/R/phrase_helpers.R | 4 tabr-0.4.1/tabr/R/scales.R | 1 tabr-0.4.1/tabr/R/sf.R | 6 - tabr-0.4.1/tabr/R/snippet.R | 4 tabr-0.4.1/tabr/README.md | 41 +++++++- tabr-0.4.1/tabr/build/vignette.rds |binary tabr-0.4.1/tabr/inst/doc/tabr-prog-chords.html | 3 tabr-0.4.1/tabr/inst/doc/tabr-prog-music.html | 3 tabr-0.4.1/tabr/inst/doc/tabr-prog-noteinfo.html | 3 tabr-0.4.1/tabr/inst/doc/tabr-prog-notes.html | 3 tabr-0.4.1/tabr/inst/doc/tabr-prog-nw.html | 3 tabr-0.4.1/tabr/inst/doc/tabr-prog-scales.html | 7 - tabr-0.4.1/tabr/man/lilypond.Rd | 4 tabr-0.4.1/tabr/man/note-logic.Rd | 4 tabr-0.4.1/tabr/man/phrase.Rd | 17 ++- tabr-0.4.1/tabr/man/pitch_freq.Rd | 6 - tabr-0.4.1/tabr/man/sf_phrase.Rd | 8 + tabr-0.4.1/tabr/man/tab.Rd | 8 - tabr-0.4.1/tabr/tests/testthat/test-outputs.R | 12 +- tabr-0.4.1/tabr/tests/testthat/test-phrase.R | 8 + tabr-0.4.1/tabr/tests/testthat/test-scales.R | 2 tabr-0.4.1/tabr/tests/testthat/test-sf.R | 6 + 75 files changed, 189 insertions(+), 142 deletions(-)
Title: Simulate Pedigrees Ascertained for a Rare Disease
Description: Routines to simulate and manipulate pedigrees ascertained to
contain multiple family members affected by a rare disease.
Christina Nieuwoudt, Samantha J Jones, Angela Brooks-Wilson,
and Jinko Graham (2018) <doi:10.1101/234153>.
Author: Christina Nieuwoudt [aut, cre],
Jinko Graham [aut]
Maintainer: Christina Nieuwoudt <cnieuwou@sfu.ca>
Diff between SimRVPedigree versions 0.3.0 dated 2018-10-01 and 0.4.4 dated 2020-02-09
SimRVPedigree-0.3.0/SimRVPedigree/tests/testthat/test_new.hazard.R |only SimRVPedigree-0.4.4/SimRVPedigree/DESCRIPTION | 12 SimRVPedigree-0.4.4/SimRVPedigree/MD5 | 116 ++--- SimRVPedigree-0.4.4/SimRVPedigree/NAMESPACE | 3 SimRVPedigree-0.4.4/SimRVPedigree/R/Check_DF_Ped.R | 13 SimRVPedigree-0.4.4/SimRVPedigree/R/Event_Methods.R |only SimRVPedigree-0.4.4/SimRVPedigree/R/Hazard_Methods.R | 130 ++++- SimRVPedigree-0.4.4/SimRVPedigree/R/LifeSim_Functions.R | 225 ++++++---- SimRVPedigree-0.4.4/SimRVPedigree/R/ManipulatePed_Functions.R | 37 + SimRVPedigree-0.4.4/SimRVPedigree/R/Ped2Pedigree_functions.R | 15 SimRVPedigree-0.4.4/SimRVPedigree/R/PedSim_Functions.R | 59 +- SimRVPedigree-0.4.4/SimRVPedigree/R/Ped_Methods.R | 48 +- SimRVPedigree-0.4.4/SimRVPedigree/R/RVPedSim_Functions.R | 154 +++++- SimRVPedigree-0.4.4/SimRVPedigree/R/SimRVPedigree_doc.R | 4 SimRVPedigree-0.4.4/SimRVPedigree/R/SubtypeHazards.R |only SimRVPedigree-0.4.4/SimRVPedigree/R/Utility_Functions.R | 3 SimRVPedigree-0.4.4/SimRVPedigree/R/Validation_Functions.R |only SimRVPedigree-0.4.4/SimRVPedigree/README.md |only SimRVPedigree-0.4.4/SimRVPedigree/build/vignette.rds |binary SimRVPedigree-0.4.4/SimRVPedigree/data/SubtypeHazards.RData |only SimRVPedigree-0.4.4/SimRVPedigree/inst/doc/SimRVPedigree.Rmd | 1 SimRVPedigree-0.4.4/SimRVPedigree/inst/doc/SimRVPedigree.html | 126 ++++- SimRVPedigree-0.4.4/SimRVPedigree/man/SimRVPedigree.Rd | 4 SimRVPedigree-0.4.4/SimRVPedigree/man/SubtypeHazards.Rd |only SimRVPedigree-0.4.4/SimRVPedigree/man/ascertainTrim_ped.Rd | 5 SimRVPedigree-0.4.4/SimRVPedigree/man/ascertain_ped.Rd | 8 SimRVPedigree-0.4.4/SimRVPedigree/man/choose_proband.Rd | 2 SimRVPedigree-0.4.4/SimRVPedigree/man/create_founder.Rd | 2 SimRVPedigree-0.4.4/SimRVPedigree/man/create_mate.Rd | 4 SimRVPedigree-0.4.4/SimRVPedigree/man/create_offspring.Rd | 2 SimRVPedigree-0.4.4/SimRVPedigree/man/disqualify_ped.Rd | 7 SimRVPedigree-0.4.4/SimRVPedigree/man/events.Rd |only SimRVPedigree-0.4.4/SimRVPedigree/man/get_famInfo.Rd | 6 SimRVPedigree-0.4.4/SimRVPedigree/man/get_ind_data.Rd |only SimRVPedigree-0.4.4/SimRVPedigree/man/get_nextEvent.Rd | 2 SimRVPedigree-0.4.4/SimRVPedigree/man/get_onsetHazard.Rd |only SimRVPedigree-0.4.4/SimRVPedigree/man/hazard.Rd | 49 +- SimRVPedigree-0.4.4/SimRVPedigree/man/is.events.Rd |only SimRVPedigree-0.4.4/SimRVPedigree/man/new.ped.Rd | 5 SimRVPedigree-0.4.4/SimRVPedigree/man/reassign_gen.Rd | 2 SimRVPedigree-0.4.4/SimRVPedigree/man/sim_RVped.Rd | 68 ++- SimRVPedigree-0.4.4/SimRVPedigree/man/sim_founderRVstatus.Rd | 2 SimRVPedigree-0.4.4/SimRVPedigree/man/sim_life.Rd | 39 + SimRVPedigree-0.4.4/SimRVPedigree/man/sim_nFam.Rd | 2 SimRVPedigree-0.4.4/SimRVPedigree/man/sim_ped.Rd | 8 SimRVPedigree-0.4.4/SimRVPedigree/man/sim_pop.Rd |only SimRVPedigree-0.4.4/SimRVPedigree/man/summary.ped.Rd | 8 SimRVPedigree-0.4.4/SimRVPedigree/man/trim_ped.Rd | 2 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_ascertain_ped.R | 136 +++++- SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_assign_gen.R | 3 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_censor_ped.R | 5 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_choose_proband.R | 7 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_disqualify_ped.R | 23 - SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_find_mcra.R | 4 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_get_nextEvent.R | 4 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_get_onsetHazard.R |only SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_get_wait_prob.R | 4 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_get_wait_time.R | 4 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_hazard.R |only SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_reassign_gen.R | 4 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_sim_RVped.R | 4 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_sim_founderRVstatus.R | 26 + SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_sim_life.R | 156 ++++++ SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_sim_ped.R | 4 SimRVPedigree-0.4.4/SimRVPedigree/tests/testthat/test_trim_ped.R | 5 SimRVPedigree-0.4.4/SimRVPedigree/vignettes/SimRVPedigree.Rmd | 1 66 files changed, 1190 insertions(+), 373 deletions(-)
Title: An Implementation of Crime Analysis Methods
Description: An implementation of functions for the analysis of crime incident or records
management system data. The package implements analysis algorithms scaled for city
or regional crime analysis units. The package provides functions for kernel density
estimation for crime heat maps, geocoding using the 'Google Maps' API, spatio-temporal
map comparison across time intervals, time series analysis (forecasting and decomposition),
and near repeat analysis (with crime network linkage).
Author: Jamie Spaulding and Keith Morris
Maintainer: Jamie Spaulding <jspauldi@mix.wvu.edu>
Diff between rcrimeanalysis versions 0.1.0 dated 2019-12-01 and 0.2.0 dated 2020-02-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/kde_map.R | 14 +++++++++++++- man/kde_map.Rd | 5 ++++- 4 files changed, 23 insertions(+), 8 deletions(-)
More information about rcrimeanalysis at CRAN
Permanent link
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.9.800.4.0 dated 2020-01-24 and 0.9.850.1.0 dated 2020-02-09
ChangeLog | 22 DESCRIPTION | 8 MD5 | 104 ++-- R/SciPy2R.R | 13 inst/NEWS.Rd | 18 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo | 7 inst/include/armadillo_bits/BaseCube_bones.hpp | 2 inst/include/armadillo_bits/BaseCube_meat.hpp | 53 ++ inst/include/armadillo_bits/Base_bones.hpp | 2 inst/include/armadillo_bits/Base_meat.hpp | 53 ++ inst/include/armadillo_bits/Mat_bones.hpp | 4 inst/include/armadillo_bits/Mat_meat.hpp | 194 +++++++ inst/include/armadillo_bits/SpBase_bones.hpp | 2 inst/include/armadillo_bits/SpBase_meat.hpp | 58 ++ inst/include/armadillo_bits/SpMat_bones.hpp | 4 inst/include/armadillo_bits/SpMat_meat.hpp | 168 ++++++ inst/include/armadillo_bits/arma_forward.hpp | 87 --- inst/include/armadillo_bits/arma_ostream_bones.hpp | 12 inst/include/armadillo_bits/arma_ostream_meat.hpp | 129 ++--- inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/arrayops_bones.hpp | 10 inst/include/armadillo_bits/arrayops_meat.hpp | 66 ++ inst/include/armadillo_bits/compiler_setup.hpp | 36 - inst/include/armadillo_bits/constants.hpp | 46 - inst/include/armadillo_bits/csv_name.hpp |only inst/include/armadillo_bits/diskio_bones.hpp | 10 inst/include/armadillo_bits/diskio_meat.hpp | 512 +++++++++++--------- inst/include/armadillo_bits/fn_cross.hpp | 11 inst/include/armadillo_bits/fn_log_normpdf.hpp |only inst/include/armadillo_bits/fn_norm.hpp | 4 inst/include/armadillo_bits/fn_normcdf.hpp | 16 inst/include/armadillo_bits/fn_normpdf.hpp | 8 inst/include/armadillo_bits/fn_quantile.hpp |only inst/include/armadillo_bits/glue_cross_bones.hpp | 2 inst/include/armadillo_bits/glue_cross_meat.hpp | 9 inst/include/armadillo_bits/glue_quantile_bones.hpp |only inst/include/armadillo_bits/glue_quantile_meat.hpp |only inst/include/armadillo_bits/glue_times_meat.hpp | 4 inst/include/armadillo_bits/hdf5_name.hpp |only inst/include/armadillo_bits/op_all_bones.hpp | 10 inst/include/armadillo_bits/op_all_meat.hpp | 10 inst/include/armadillo_bits/op_any_bones.hpp | 10 inst/include/armadillo_bits/op_any_meat.hpp | 10 inst/include/armadillo_bits/op_diagmat_bones.hpp | 6 inst/include/armadillo_bits/op_diagmat_meat.hpp | 190 +++++++ inst/include/armadillo_bits/op_find_bones.hpp | 20 inst/include/armadillo_bits/op_find_meat.hpp | 20 inst/include/armadillo_bits/spdiagview_meat.hpp | 2 inst/include/armadillo_bits/subview_bones.hpp | 1 inst/include/armadillo_bits/subview_cube_bones.hpp | 1 inst/include/armadillo_bits/subview_cube_meat.hpp | 35 + inst/include/armadillo_bits/subview_meat.hpp | 21 inst/include/armadillo_bits/wall_clock_bones.hpp | 4 inst/tinytest/test_scipy2r.R | 16 56 files changed, 1486 insertions(+), 550 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp'
objects. 'OSM' data are extracted from the 'Overpass' web server and
processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre],
Bob Rudis [aut],
Robin Lovelace [aut],
Maëlle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Andrea Gilardi [ctb],
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Finkelstein Noam [ctb, cph] (Author of included stub.R code),
Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmdata versions 0.1.2 dated 2019-12-14 and 0.1.3 dated 2020-02-09
osmdata-0.1.2/osmdata/man/osmdata_pbf.Rd |only osmdata-0.1.3/osmdata/DESCRIPTION | 8 osmdata-0.1.3/osmdata/MD5 | 49 ++-- osmdata-0.1.3/osmdata/NAMESPACE | 2 osmdata-0.1.3/osmdata/NEWS.md | 16 + osmdata-0.1.3/osmdata/R/get-osmdata.R | 30 --- osmdata-0.1.3/osmdata/R/getbb.R | 167 +++++++++-------- osmdata-0.1.3/osmdata/R/opq.R | 12 - osmdata-0.1.3/osmdata/R/osmdata-class.R | 1 osmdata-0.1.3/osmdata/R/osmdata-methods.R | 3 osmdata-0.1.3/osmdata/R/overpass-query.R | 11 - osmdata-0.1.3/osmdata/build/vignette.rds |binary osmdata-0.1.3/osmdata/inst/doc/osm-sf-translation.html | 4 osmdata-0.1.3/osmdata/inst/doc/osmdata-sc.Rmd | 19 - osmdata-0.1.3/osmdata/inst/doc/osmdata-sc.html | 8 osmdata-0.1.3/osmdata/inst/doc/osmdata.R | 31 +-- osmdata-0.1.3/osmdata/inst/doc/osmdata.Rmd | 39 ++- osmdata-0.1.3/osmdata/inst/doc/osmdata.html | 50 ++--- osmdata-0.1.3/osmdata/man/add_osm_feature.Rd | 13 - osmdata-0.1.3/osmdata/man/bbox_to_string.Rd | 14 - osmdata-0.1.3/osmdata/man/getbb.Rd | 41 ++-- osmdata-0.1.3/osmdata/man/osmdata.Rd | 2 osmdata-0.1.3/osmdata/src/convert-osm-rcpp.cpp | 11 - osmdata-0.1.3/osmdata/tests/testthat/test-getbb.R | 2 osmdata-0.1.3/osmdata/vignettes/osmdata-sc.Rmd | 19 - osmdata-0.1.3/osmdata/vignettes/osmdata.Rmd | 39 ++- 26 files changed, 278 insertions(+), 313 deletions(-)
Title: Provides Foreach Looping Construct
Description: Support for the foreach looping construct. Foreach is an
idiom that allows for iterating over elements in a collection,
without the use of an explicit loop counter. This package in
particular is intended to be used for its return value, rather
than for its side effects. In that sense, it is similar to the
standard lapply function, but doesn't require the evaluation
of a function. Using foreach without side effects also
facilitates executing the loop in parallel.
Author: Hong Ooi [cre],
Microsoft [aut, cph],
Steve Weston [aut]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between foreach versions 1.4.7 dated 2019-07-27 and 1.4.8 dated 2020-02-09
foreach-1.4.7/foreach/NEWS |only foreach-1.4.7/foreach/R/acc.R |only foreach-1.4.7/foreach/inst/doc/foreach.Rnw |only foreach-1.4.7/foreach/inst/doc/foreach.pdf |only foreach-1.4.7/foreach/inst/doc/nested.Rnw |only foreach-1.4.7/foreach/inst/doc/nested.pdf |only foreach-1.4.7/foreach/inst/unitTests |only foreach-1.4.7/foreach/tests/doRUnit.R |only foreach-1.4.7/foreach/vignettes/foreach.Rnw |only foreach-1.4.7/foreach/vignettes/nested.Rnw |only foreach-1.4.8/foreach/DESCRIPTION | 21 foreach-1.4.8/foreach/MD5 | 138 - foreach-1.4.8/foreach/NAMESPACE | 72 foreach-1.4.8/foreach/NEWS.md |only foreach-1.4.8/foreach/R/callCombine.R |only foreach-1.4.8/foreach/R/do.R | 379 +-- foreach-1.4.8/foreach/R/foreach-ext.R |only foreach-1.4.8/foreach/R/foreach-pkg.R |only foreach-1.4.8/foreach/R/foreach.R | 945 ++------ foreach-1.4.8/foreach/R/getDoPar.R |only foreach-1.4.8/foreach/R/getDoSeq.R |only foreach-1.4.8/foreach/R/getsyms.R | 192 - foreach-1.4.8/foreach/R/iter.R |only foreach-1.4.8/foreach/R/nextElem.R |only foreach-1.4.8/foreach/R/onLoad.R |only foreach-1.4.8/foreach/R/setDoPar.R |only foreach-1.4.8/foreach/R/setDoSeq.R |only foreach-1.4.8/foreach/R/times.R | 48 foreach-1.4.8/foreach/R/utils.R |only foreach-1.4.8/foreach/build/vignette.rds |binary foreach-1.4.8/foreach/demo/00Index | 2 foreach-1.4.8/foreach/demo/sincSEQ.R | 72 foreach-1.4.8/foreach/inst/doc/foreach.R | 137 - foreach-1.4.8/foreach/inst/doc/foreach.Rmd |only foreach-1.4.8/foreach/inst/doc/foreach.html |only foreach-1.4.8/foreach/inst/doc/nested.R | 57 foreach-1.4.8/foreach/inst/doc/nested.Rmd |only foreach-1.4.8/foreach/inst/doc/nested.html |only foreach-1.4.8/foreach/inst/examples/apply.R | 276 +- foreach-1.4.8/foreach/inst/examples/bigmax.R | 86 foreach-1.4.8/foreach/inst/examples/bigmean.R | 102 foreach-1.4.8/foreach/inst/examples/bigmean2.R | 60 foreach-1.4.8/foreach/inst/examples/bootpar.R | 40 foreach-1.4.8/foreach/inst/examples/bootpar2.R | 46 foreach-1.4.8/foreach/inst/examples/bootseq.R | 40 foreach-1.4.8/foreach/inst/examples/colMeans.R | 40 foreach-1.4.8/foreach/inst/examples/comprehensions.R | 82 foreach-1.4.8/foreach/inst/examples/cross.R | 52 foreach-1.4.8/foreach/inst/examples/feapply.R | 58 foreach-1.4.8/foreach/inst/examples/for.R | 312 +- foreach-1.4.8/foreach/inst/examples/germandata.txt | 2000 +++++++++---------- foreach-1.4.8/foreach/inst/examples/isplit.R | 62 foreach-1.4.8/foreach/inst/examples/matmul.R | 32 foreach-1.4.8/foreach/inst/examples/matmul2.R | 76 foreach-1.4.8/foreach/inst/examples/output.R | 54 foreach-1.4.8/foreach/inst/examples/pi.R | 24 foreach-1.4.8/foreach/inst/examples/qsort.R | 36 foreach-1.4.8/foreach/inst/examples/rf.R | 50 foreach-1.4.8/foreach/inst/examples/sinc.R | 46 foreach-1.4.8/foreach/inst/examples/sinc2.R | 72 foreach-1.4.8/foreach/inst/examples/sqlite.R | 84 foreach-1.4.8/foreach/inst/examples/tuneRF.R | 86 foreach-1.4.8/foreach/man/foreach-ext.Rd | 97 foreach-1.4.8/foreach/man/foreach-package.Rd | 36 foreach-1.4.8/foreach/man/foreach.Rd | 232 +- foreach-1.4.8/foreach/man/getDoParWorkers.Rd | 22 foreach-1.4.8/foreach/man/getDoSeqWorkers.Rd | 22 foreach-1.4.8/foreach/man/registerDoSEQ.Rd | 18 foreach-1.4.8/foreach/man/setDoPar.Rd | 23 foreach-1.4.8/foreach/man/setDoSeq.Rd | 23 foreach-1.4.8/foreach/tests/testthat |only foreach-1.4.8/foreach/tests/testthat.R |only foreach-1.4.8/foreach/vignettes/foreach.Rmd |only foreach-1.4.8/foreach/vignettes/nested.Rmd |only 74 files changed, 2986 insertions(+), 3366 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code or use an easy to remember set of tidy functions for exploratory data analysis. Introduces three main verbs. explore() to graphically explore a variable or table, describe() to describe a variable or table and report() to create an automated report.
Author: Roland Krasser
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 0.5.3 dated 2020-01-17 and 0.5.4 dated 2020-02-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/explore.R | 4 ++-- inst/doc/explore.html | 4 ++-- inst/doc/explore_mtcars.html | 4 ++-- man/explore.Rd | 2 +- man/explore_bar.Rd | 2 +- 8 files changed, 26 insertions(+), 18 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see support list of insight; Lüdecke,
Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), this package
implements features like bootstrapping or simulating of parameters and
models, feature reduction (feature extraction and variable selection)
as well as functions to describe data and variable characteristics
(e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>),
Søren Højsgaard [aut],
Zen J. Lau [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between parameters versions 0.4.1 dated 2020-01-17 and 0.5.0 dated 2020-02-09
DESCRIPTION | 33 - MD5 | 290 +++++++---- NAMESPACE | 38 + NEWS.md | 47 + R/bootstrap_model.R | 2 R/ci.R | 148 ++++-- R/ci_betwithin.R |only R/ci_kenward.R |only R/ci_ml1.R |only R/ci_profile_boot.R | 2 R/ci_satterthwaite.R |only R/ci_wald.R | 18 R/cluster_analysis.R | 2 R/convert_efa_to_cfa.R | 20 R/data_partition.R | 6 R/describe_distribution.R | 78 +++ R/dof.R | 57 +- R/dof_betwithin.R |only R/dof_kenward.R | 389 +++++++++++++++ R/dof_ml1.R | 5 R/dof_satterthwaite.R | 21 R/extract_parameters.R | 219 +++++--- R/factor_analysis.R | 5 R/fish.R |only R/format_p.R | 2 R/format_parameters.R | 40 + R/get_scores.R |only R/model_parameters.Mclust.R | 2 R/model_parameters.R | 12 R/model_parameters.aov.R | 7 R/model_parameters.bayesian.R | 14 R/model_parameters.gam.R | 12 R/model_parameters.lavaan.R | 66 +- R/model_parameters.multinom.R |only R/model_parameters.psych.R | 4 R/model_parameters.rma.R |only R/model_parameters.wbm.R | 9 R/model_parameters.zeroinfl.R | 12 R/model_parameters_default.R | 128 ----- R/model_parameters_mixed.R | 138 ++++- R/n_clusters.R | 39 + R/n_factors.R | 2 R/p_value.R | 142 ++++- R/p_value_betwithin.R |only R/p_value_kenward.R | 40 - R/p_value_ml1.R | 60 +- R/p_value_satterthwaite.R | 44 - R/p_value_wald.R | 12 R/parameters_table.R | 12 R/parameters_type.R | 17 R/plot.R | 9 R/principal_components.R | 40 + R/print.parameters_model.R | 129 ++++- R/random_parameters.R |only R/rescale_weights.R | 45 - R/robust_estimation.R | 88 ++- R/se_betwithin.R |only R/se_kenward.R | 9 R/se_ml1.R | 2 R/se_satterthwaite.R | 26 - R/select_parameters.R | 25 - R/select_parameters.stanreg.R |only R/simulate_model.R | 153 ++---- R/simulate_parameters.R | 2 R/skewness_kurtosis.R | 193 ++++++- R/standard_error.R | 136 +++-- R/utils.R | 30 + R/utils_model_parameters.R | 2 README.md | 72 +- build/partial.rdb |binary build/vignette.rds |only data |only inst/WORDLIST | 11 inst/doc |only man/bootstrap_parameters.Rd | 5 man/ci.merMod.Rd | 77 +-- man/cluster_analysis.Rd | 5 man/convert_efa_to_cfa.Rd | 20 man/data_partition.Rd | 6 man/degrees_of_freedom.Rd | 26 - man/describe_distribution.Rd | 18 man/fish.Rd |only man/get_scores.Rd |only man/model_parameters.BFBayesFactor.Rd | 5 man/model_parameters.Mclust.Rd | 2 man/model_parameters.Rd | 12 man/model_parameters.aov.Rd | 7 man/model_parameters.befa.Rd | 5 man/model_parameters.default.Rd | 9 man/model_parameters.gam.Rd | 9 man/model_parameters.lavaan.Rd | 66 +- man/model_parameters.merMod.Rd | 83 ++- man/model_parameters.mlm.Rd |only man/model_parameters.rma.Rd |only man/model_parameters.stanreg.Rd | 23 man/model_parameters.zeroinfl.Rd | 18 man/n_clusters.Rd | 9 man/n_factors.Rd | 3 man/p_value.Rd | 43 - man/p_value_betwithin.Rd |only man/p_value_kenward.Rd | 28 - man/p_value_ml1.Rd | 50 +- man/p_value_satterthwaite.Rd | 27 - man/p_value_wald.Rd | 14 man/parameters_table.Rd | 9 man/principal_components.Rd | 11 man/print.Rd | 27 - man/random_parameters.Rd |only man/rescale_weights.Rd | 45 - man/select_parameters.Rd | 33 - man/simulate_parameters.Rd | 8 man/skewness.Rd | 34 + man/standard_error.Rd | 68 -- man/standard_error_robust.Rd |only tests/testthat/test-GLMMadaptive.R | 77 +-- tests/testthat/test-backticks.R | 2 tests/testthat/test-betareg.R | 4 tests/testthat/test-bracl.R |only tests/testthat/test-checks.R | 22 tests/testthat/test-ci.R | 49 - tests/testthat/test-coxph.R | 21 tests/testthat/test-describe_distribution.R | 12 tests/testthat/test-distributions.R | 18 tests/testthat/test-equivalence_test.R | 16 tests/testthat/test-format_parameters.R | 419 +++++++++-------- tests/testthat/test-geeglm.R | 4 tests/testthat/test-glmer.R |only tests/testthat/test-glmmTMB.R | 78 +-- tests/testthat/test-lme.R | 26 + tests/testthat/test-model_parameters.aov.R | 138 ++--- tests/testthat/test-model_parameters.efa_cfa.R | 104 ++-- tests/testthat/test-model_parameters.glm.R | 77 +-- tests/testthat/test-model_parameters.htest.R | 32 - tests/testthat/test-model_parameters.hurdle.R |only tests/testthat/test-model_parameters.metafor.R |only tests/testthat/test-model_parameters.mixed.R | 53 +- tests/testthat/test-model_parameters.truncreg.R |only tests/testthat/test-model_parameters_df_method.R |only tests/testthat/test-model_parameters_labels.R | 176 +++---- tests/testthat/test-model_parameters_mixed_coeforder.R | 33 - tests/testthat/test-model_parameters_robust.R |only tests/testthat/test-model_parameters_std.R | 4 tests/testthat/test-model_parameters_std_mixed.R |only tests/testthat/test-n_factors.R | 17 tests/testthat/test-p_value.R | 137 ++--- tests/testthat/test-panelr.R | 112 ++-- tests/testthat/test-parameters_selection.R | 30 - tests/testthat/test-pca.R | 93 +-- tests/testthat/test-skewness.R |only tests/testthat/test-zeroinfl.R | 17 vignettes |only 151 files changed, 3633 insertions(+), 2109 deletions(-)
Title: Pedigree and Genetic Groups
Description: Calculates additive and dominance genetic relationship matrices and their inverses, in matrix and tabular-sparse formats. It includes functions for checking and processing pedigree, as well as functions to calculate the matrix of genetic group contributions (Q), and adding those contributions to the genetic merit of animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>). Calculation of Q is computationally extensive. There are computationally optimized functions to calculate Q.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between ggroups versions 1.2.1 dated 2019-05-10 and 1.3.0 dated 2020-02-09
ggroups-1.2.1/ggroups/R/qmat.R |only ggroups-1.2.1/ggroups/man/qmat.Rd |only ggroups-1.3.0/ggroups/DESCRIPTION | 10 +++++----- ggroups-1.3.0/ggroups/MD5 | 28 +++++++++++++--------------- ggroups-1.3.0/ggroups/NAMESPACE | 1 - ggroups-1.3.0/ggroups/NEWS.md | 6 ++++++ ggroups-1.3.0/ggroups/R/Qgpu.R | 4 ++-- ggroups-1.3.0/ggroups/R/peddown.R | 15 +++++++++++++-- ggroups-1.3.0/ggroups/R/pedup.R | 22 ++++++++++++++++++++-- ggroups-1.3.0/ggroups/R/pruneped.R | 3 +-- ggroups-1.3.0/ggroups/R/qmatL.R | 5 ----- ggroups-1.3.0/ggroups/R/tabD.R | 10 ++++------ ggroups-1.3.0/ggroups/man/Qgpu.Rd | 4 ++-- ggroups-1.3.0/ggroups/man/peddown.Rd | 5 ++++- ggroups-1.3.0/ggroups/man/pedup.Rd | 5 ++++- ggroups-1.3.0/ggroups/man/qmatL.Rd | 5 ----- 16 files changed, 74 insertions(+), 49 deletions(-)
Title: A Grammar of Animated Graphics
Description: The grammar of graphics as implemented in the 'ggplot2' package has
been successful in providing a powerful API for creating static
visualisation. In order to extend the API for animated graphics this package
provides a completely new set of grammar, fully compatible with 'ggplot2'
for specifying transitions and animations in a flexible and extensible way.
Author: Thomas Lin Pedersen [aut, cre]
(<https://orcid.org/0000-0002-5147-4711>),
David Robinson [aut],
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between gganimate versions 1.0.4 dated 2019-11-18 and 1.0.5 dated 2020-02-09
DESCRIPTION | 10 +++---- MD5 | 58 +++++++++++++++++++++---------------------- NEWS.md | 5 +++ R/aaa.R | 12 ++++++++ R/renderers.R | 6 ---- R/zzz.R | 11 ++++++++ inst/doc/gganimate.html | 19 ++++++-------- man/anim_save.Rd | 4 -- man/animate.Rd | 18 +++++++++++-- man/enter_exit.Rd | 2 - man/gganimate-package.Rd | 4 +- man/gif_file.Rd | 2 - man/renderers.Rd | 15 +++++------ man/shadow_mark.Rd | 6 ++-- man/shadow_null.Rd | 6 ++-- man/shadow_trail.Rd | 9 +++--- man/shadow_wake.Rd | 20 +++++++++++--- man/transition_components.Rd | 26 +++++++++++-------- man/transition_events.Rd | 26 +++++++++++-------- man/transition_filter.Rd | 26 +++++++++++-------- man/transition_layers.Rd | 28 ++++++++++++-------- man/transition_manual.Rd | 17 ++++++------ man/transition_null.Rd | 17 ++++++------ man/transition_reveal.Rd | 17 ++++++------ man/transition_states.Rd | 20 +++++++------- man/transition_time.Rd | 17 ++++++------ man/view_follow.Rd | 14 +++++++--- man/view_static.Rd | 6 ++-- man/view_step.Rd | 50 +++++++++++++++++++++++++++---------- man/view_zoom.Rd | 52 ++++++++++++++++++++++++++++---------- 30 files changed, 328 insertions(+), 195 deletions(-)
Title: SHAP Plots for 'XGBoost'
Description: The aim of 'SHAPforxgboost' is to aid in visual data investigations
using SHAP (SHapley Additive exPlanation) visualization plots for 'XGBoost'.
It provides summary plot, dependence plot, interaction plot, and force plot.
It relies on the 'dmlc/xgboost' package to produce SHAP values.
Please refer to 'slundberg/shap' for the original implementation of SHAP in 'Python'.
Author: Yang Liu [aut, cre] (<https://orcid.org/0000-0001-6557-6439>),
Allan Just [aut, ctb] (<https://orcid.org/0000-0003-4312-5957>)
Maintainer: Yang Liu <lyhello@gmail.com>
Diff between SHAPforxgboost versions 0.0.2 dated 2019-08-28 and 0.0.3 dated 2020-02-09
DESCRIPTION | 12 - MD5 | 59 +++--- NAMESPACE | 2 NEWS.md | 8 R/SHAP_funcs.R | 343 ++++++++++++++++++++++-------------- R/example/example_categorical.R |only R/example/example_fit_summary.R | 5 R/simple_plots.R | 18 - README.md | 19 + data/shap_long_iris.rda |binary man/dataXY_df.Rd | 32 +-- man/label.feature.Rd | 37 +-- man/labels_within_package.Rd | 82 ++++---- man/new_labels.Rd | 26 +- man/plot.label.Rd | 36 +-- man/scatter.plot.diagonal.Rd | 92 +++++---- man/scatter.plot.simple.Rd | 84 ++++---- man/shap.plot.dependence.Rd | 212 +++++++++++----------- man/shap.plot.force_plot.Rd | 86 ++++----- man/shap.plot.force_plot_bygroup.Rd | 59 +++--- man/shap.plot.summary.Rd | 146 ++++++++------- man/shap.plot.summary.wrap1.Rd | 112 +++++------ man/shap.plot.summary.wrap2.Rd | 116 +++++------- man/shap.prep.Rd | 147 +++++++++------ man/shap.prep.interaction.Rd | 80 ++++---- man/shap.prep.stack.data.Rd | 89 +++++---- man/shap.values.Rd | 107 +++++------ man/shap_int_iris.Rd | 26 +- man/shap_long_iris.Rd | 26 +- man/shap_score.Rd | 32 +-- man/shap_values_iris.Rd | 26 +- 31 files changed, 1154 insertions(+), 965 deletions(-)
More information about SHAPforxgboost at CRAN
Permanent link
Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source
or Commercial Software
Description: An interface to the 'mclust' package to easily
carry out latent profile analysis ("LPA"). Provides functionality to
estimate commonly-specified models. Follows a tidy approach, in that
output is in the form of a data frame that can subsequently be
computed on. Also has functions to interface to the commercial 'MPlus'
software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre],
Caspar van Lissa [aut],
Jennifer A Schmidt [ctb],
Patrick N Beymer [ctb],
Daniel Anderson [ctb],
Matthew J. Schell [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Diff between tidyLPA versions 1.0.4 dated 2019-08-19 and 1.0.5 dated 2020-02-09
tidyLPA-1.0.4/tidyLPA/R/deprecated_functions.R |only tidyLPA-1.0.4/tidyLPA/R/tidyLPA-deprecated.r |only tidyLPA-1.0.4/tidyLPA/inst/doc/introduction-to-major-changes.R |only tidyLPA-1.0.4/tidyLPA/inst/doc/introduction-to-major-changes.Rmd |only tidyLPA-1.0.4/tidyLPA/inst/doc/introduction-to-major-changes.html |only tidyLPA-1.0.4/tidyLPA/man/bootstrap_lrt-deprecated.Rd |only tidyLPA-1.0.4/tidyLPA/man/compare_solutions_mplus-deprecated.Rd |only tidyLPA-1.0.4/tidyLPA/man/estimate_profiles_mplus-deprecated.Rd |only tidyLPA-1.0.4/tidyLPA/man/plot_profiles_mplus-deprecated.Rd |only tidyLPA-1.0.4/tidyLPA/tests/testthat/test-estimate-profiles-mplus.R |only tidyLPA-1.0.4/tidyLPA/tests/testthat/test-plot-profiles-mplus.R |only tidyLPA-1.0.4/tidyLPA/vignettes/introduction-to-major-changes.Rmd |only tidyLPA-1.0.5/tidyLPA/DESCRIPTION | 15 tidyLPA-1.0.5/tidyLPA/MD5 | 85 +- tidyLPA-1.0.5/tidyLPA/NAMESPACE | 15 tidyLPA-1.0.5/tidyLPA/NEWS.md | 10 tidyLPA-1.0.5/tidyLPA/R/as.tidyLPA.r | 11 tidyLPA-1.0.5/tidyLPA/R/calc_functions.R | 83 +- tidyLPA-1.0.5/tidyLPA/R/data-mac.R |only tidyLPA-1.0.5/tidyLPA/R/estimate-profiles-mplus.R | 126 +-- tidyLPA-1.0.5/tidyLPA/R/estimate-profiles.R | 13 tidyLPA-1.0.5/tidyLPA/R/helpers.R | 2 tidyLPA-1.0.5/tidyLPA/R/plot-corplot.R |only tidyLPA-1.0.5/tidyLPA/R/plot-mixture_densities.R | 217 +++-- tidyLPA-1.0.5/tidyLPA/R/plot-profiles.R | 76 + tidyLPA-1.0.5/tidyLPA/README.md | 211 ----- tidyLPA-1.0.5/tidyLPA/build/vignette.rds |binary tidyLPA-1.0.5/tidyLPA/data/curry_mac.csv |only tidyLPA-1.0.5/tidyLPA/inst/CITATION | 1 tidyLPA-1.0.5/tidyLPA/inst/doc/Introduction_to_tidyLPA.R | 45 - tidyLPA-1.0.5/tidyLPA/inst/doc/Introduction_to_tidyLPA.Rmd | 37 tidyLPA-1.0.5/tidyLPA/inst/doc/Introduction_to_tidyLPA.html | 248 +++--- tidyLPA-1.0.5/tidyLPA/inst/doc/benchmarking-mclust-and-mplus.R | 10 tidyLPA-1.0.5/tidyLPA/inst/doc/benchmarking-mclust-and-mplus.html | 7 tidyLPA-1.0.5/tidyLPA/man/AHP.Rd | 7 tidyLPA-1.0.5/tidyLPA/man/calc_lrt.Rd |only tidyLPA-1.0.5/tidyLPA/man/curry_mac.Rd |only tidyLPA-1.0.5/tidyLPA/man/estimate_profiles.Rd | 15 tidyLPA-1.0.5/tidyLPA/man/estimate_profiles_mplus2.Rd | 10 tidyLPA-1.0.5/tidyLPA/man/figures/README-unnamed-chunk-6-1.png |binary tidyLPA-1.0.5/tidyLPA/man/plot_bivariate.Rd |only tidyLPA-1.0.5/tidyLPA/man/plot_density.Rd | 12 tidyLPA-1.0.5/tidyLPA/man/plot_profiles.Rd | 45 - tidyLPA-1.0.5/tidyLPA/man/print.tidyLPA.Rd | 10 tidyLPA-1.0.5/tidyLPA/man/tidyLPA-deprecated.Rd | 35 tidyLPA-1.0.5/tidyLPA/man/tidyLPA.Rd | 1 tidyLPA-1.0.5/tidyLPA/tests/testthat.R | 13 tidyLPA-1.0.5/tidyLPA/tests/testthat/test-compare-fit-stats.R | 405 ++++++---- tidyLPA-1.0.5/tidyLPA/tests/testthat/test-local-estimate-profiles-mplus.R |only tidyLPA-1.0.5/tidyLPA/tests/testthat/test-local-estimate_profiles_mplus2-arguments.R |only tidyLPA-1.0.5/tidyLPA/tests/testthat/test-local-plot-profiles-mplus.R |only tidyLPA-1.0.5/tidyLPA/tests/testthat/test-plot-mixtures.R | 8 tidyLPA-1.0.5/tidyLPA/tests/testthat/test-plot-profiles.R | 2 tidyLPA-1.0.5/tidyLPA/vignettes/Introduction_to_tidyLPA.Rmd | 37 54 files changed, 1050 insertions(+), 762 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990's.
For graphics, have pretty (Log-scale) axes, an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Werner Stahel [ctb] (Functions: compresid2way(), f.robftest(), last(),
p.scales(), p.dnorm()),
Andreas Ruckstuhl [ctb] (Functions: p.arrows(), p.profileTraces(),
p.res.2x()),
Christian Keller [ctb] (Functions: histBxp(), p.tachoPlot()),
Kjetil Halvorsen [ctb] (Functions: KSd(), ecdf.ksCI()),
Alain Hauser [ctb] (Functions: cairoSwd(), is.whole(),
toLatex.numeric()*),
Christoph Buser [ctb] (to function Duplicated()),
Lorenz Gygax [ctb] (to function p.res.2fact()),
Bill Venables [ctb] (Functions: empty.dimnames(), primes()),
Tony Plate [ctb] (to inv.seq()),
Isabelle Fl<fc>ckiger [ctb],
Marcel Wolbers [ctb],
Markus Keller [ctb],
Sandrine Dudoit [ctb],
Jane Fridlyand [ctb],
Greg Snow [ctb] (to loessDemo()),
Henrik Aa. Nielsen [ctb] (to loessDemo()),
Vincent Carey [ctb],
Ben Bolker [ctb],
Philippe Grosjean [ctb],
Fr<e9>d<e9>ric Ibanez [ctb],
Caterina Savi [ctb],
Charles Geyer [ctb],
Jens Oehlschl<e4>gel [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-4 dated 2019-05-11 and 1.1-5 dated 2020-02-09
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- NAMESPACE | 2 ++ R/p.ts.R | 6 ++---- R/ps.goodies.R | 4 ++-- R/unix/package-props.R | 14 ++++++++++---- TODO | 3 ++- inst/NEWS.Rd | 25 ++++++++++++++++++++++++- man/mat2tex.Rd | 7 ++++--- man/ps.end.Rd | 8 +++++--- man/unix/pkgLibs.Rd |only tests/posdef.R | 20 ++++++++++++-------- tests/posdef.Rout.save | 44 ++++++++++++++++++++++++-------------------- 13 files changed, 103 insertions(+), 61 deletions(-)
Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of
Extension Program Evaluation in R" and "An R
Companion for the Handbook of Biological Statistics".
Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
(<https://orcid.org/0000-0003-4668-6821>)
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 2.3.21 dated 2020-01-09 and 2.3.25 dated 2020-02-09
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 3 +++ R/groupwisePercentile.r | 2 +- R/quantileCI.r |only man/groupwisePercentile.Rd | 2 +- man/quantileCI.Rd |only 7 files changed, 15 insertions(+), 10 deletions(-)
Title: Piece-Wise Exponential Additive Mixed Modeling Tools for
Survival Analysis
Description: The Piece-wise exponential (Additive Mixed) Model
(PAMM; Bender and Scheipl (2018) <doi: 10.1177/1471082X17748083>) is a
powerful model class for the analysis of survival (or time-to-event) data,
based on Generalized Additive (Mixed) Models (GA(M)Ms). It offers intuitive specification and robust estimation of complex survival models with stratified baseline hazards, random effects, time-varying effects, time-dependent covariates and cumulative effects (Bender and others (2018) <doi: 10.1093/biostatistics/kxy003>.
pammtools provides tidy workflow for survival analysis with PAMMs,
including data simulation, transformation and other functions for data
preprocessing and model post-processing as well as visualization.
Author: Andreas Bender [aut, cre] (<https://orcid.org/0000-0001-5628-8611>),
Fabian Scheipl [aut]
Maintainer: Andreas Bender <andreas.bender@stat.uni-muenchen.de>
Diff between pammtools versions 0.1.14 dated 2019-09-08 and 0.2.1 dated 2020-02-09
pammtools-0.1.14/pammtools/man/get_cumu_coef_baseline.Rd |only pammtools-0.2.1/pammtools/DESCRIPTION | 19 - pammtools-0.2.1/pammtools/MD5 | 118 +++++----- pammtools-0.2.1/pammtools/NAMESPACE | 14 + pammtools-0.2.1/pammtools/NEWS.md | 15 + pammtools-0.2.1/pammtools/R/add-functions.R | 40 +-- pammtools-0.2.1/pammtools/R/as-ped.R | 77 +++++- pammtools-0.2.1/pammtools/R/convenience-plots.R | 4 pammtools-0.2.1/pammtools/R/cumulative-coefficient.R | 5 pammtools-0.2.1/pammtools/R/data.R | 1 pammtools-0.2.1/pammtools/R/formula-specials.R | 30 -- pammtools-0.2.1/pammtools/R/formula-utils.R | 58 +++- pammtools-0.2.1/pammtools/R/interval-information.R | 14 - pammtools-0.2.1/pammtools/R/lag-lead-utils.R | 4 pammtools-0.2.1/pammtools/R/make-newdata.R | 5 pammtools-0.2.1/pammtools/R/model-evaluation.R |only pammtools-0.2.1/pammtools/R/nest-utils.R | 35 +- pammtools-0.2.1/pammtools/R/pammfit.R |only pammtools-0.2.1/pammtools/R/predict.R |only pammtools-0.2.1/pammtools/R/rpexp.R |only pammtools-0.2.1/pammtools/R/sim-pexp.R | 25 +- pammtools-0.2.1/pammtools/R/split-data.R | 8 pammtools-0.2.1/pammtools/R/tidiers.R | 2 pammtools-0.2.1/pammtools/R/zzz.R | 8 pammtools-0.2.1/pammtools/README.md | 2 pammtools-0.2.1/pammtools/inst/CITATION | 4 pammtools-0.2.1/pammtools/man/add_hazard.Rd | 39 ++- pammtools-0.2.1/pammtools/man/add_surv_prob.Rd | 13 - pammtools-0.2.1/pammtools/man/add_term.Rd | 3 pammtools-0.2.1/pammtools/man/as.data.frame.crps.Rd |only pammtools-0.2.1/pammtools/man/as_ped.Rd | 32 ++ pammtools-0.2.1/pammtools/man/combine_cut.Rd | 3 pammtools-0.2.1/pammtools/man/cumulative_coefficient.Rd | 6 pammtools-0.2.1/pammtools/man/dplyr_verbs.Rd | 74 +++--- pammtools-0.2.1/pammtools/man/geom_hazard.Rd | 56 +++- pammtools-0.2.1/pammtools/man/geom_stepribbon.Rd | 25 +- pammtools-0.2.1/pammtools/man/get_cumu_hazard.Rd | 17 + pammtools-0.2.1/pammtools/man/get_cut.Rd | 3 pammtools-0.2.1/pammtools/man/get_hazard.Rd | 17 + pammtools-0.2.1/pammtools/man/get_intervals.Rd | 4 pammtools-0.2.1/pammtools/man/get_ped_form.Rd | 6 pammtools-0.2.1/pammtools/man/get_surv_prob.Rd | 14 - pammtools-0.2.1/pammtools/man/get_tdc_form.Rd | 7 pammtools-0.2.1/pammtools/man/get_tdc_vars.Rd | 2 pammtools-0.2.1/pammtools/man/gg_laglead.Rd | 9 pammtools-0.2.1/pammtools/man/gg_partial.Rd | 22 + pammtools-0.2.1/pammtools/man/gg_smooth.Rd | 2 pammtools-0.2.1/pammtools/man/pamm.Rd |only pammtools-0.2.1/pammtools/man/pammtools.Rd | 1 pammtools-0.2.1/pammtools/man/predictSurvProb.pamm.Rd |only pammtools-0.2.1/pammtools/man/rpexp.Rd |only pammtools-0.2.1/pammtools/man/specials.Rd | 3 pammtools-0.2.1/pammtools/man/tidiers.Rd | 3 pammtools-0.2.1/pammtools/man/tidy_smooth2d.Rd | 8 pammtools-0.2.1/pammtools/man/tidyr_verbs.Rd | 11 pammtools-0.2.1/pammtools/tests/testthat/test-add-functions.R | 13 + pammtools-0.2.1/pammtools/tests/testthat/test-as-ped.R | 4 pammtools-0.2.1/pammtools/tests/testthat/test-cumulative-coefficients.R | 16 - pammtools-0.2.1/pammtools/tests/testthat/test-cumulative-effect.R | 16 - pammtools-0.2.1/pammtools/tests/testthat/test-formula-utils.R | 6 pammtools-0.2.1/pammtools/tests/testthat/test-model-evaluation.R |only pammtools-0.2.1/pammtools/tests/testthat/test-newdata.R | 2 pammtools-0.2.1/pammtools/tests/testthat/test-pamm-fit.R |only pammtools-0.2.1/pammtools/tests/testthat/test-predict-functions.R |only pammtools-0.2.1/pammtools/tests/testthat/test-specials.R | 18 - pammtools-0.2.1/pammtools/tests/testthat/test-tdc-transform.R | 12 - 66 files changed, 589 insertions(+), 366 deletions(-)
Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula
in 'Tidy Eval' code that calculates the predictions.
It works with several databases back-ends because it leverages 'dplyr'
and 'dbplyr' for the final 'SQL' translation of the algorithm. It currently
supports lm(), glm(), randomForest(), ranger(), earth(), xgb.Booster.complete(),
cubist(), and ctree() models.
Author: Edgar Ruiz [aut, cre]
Maintainer: Edgar Ruiz <edgararuiz@gmail.com>
Diff between tidypredict versions 0.4.3 dated 2019-09-03 and 0.4.4 dated 2020-02-09
DESCRIPTION | 12 ++++---- MD5 | 58 +++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/cubist.R | 16 +++++------ inst/doc/cubist.html | 33 +++++++++++------------- inst/doc/glm.R | 14 +++++----- inst/doc/glm.html | 3 -- inst/doc/lm.R | 24 ++++++++--------- inst/doc/lm.html | 3 -- inst/doc/mars.R | 22 ++++++++-------- inst/doc/mars.html | 17 +++++------- inst/doc/non-r.R | 14 +++++----- inst/doc/non-r.html | 3 -- inst/doc/ranger.R | 10 +++---- inst/doc/ranger.html | 3 -- inst/doc/regression.R | 4 +- inst/doc/regression.html | 3 -- inst/doc/rf.R | 10 +++---- inst/doc/rf.html | 3 -- inst/doc/save.R | 22 ++++++++-------- inst/doc/save.html | 3 -- inst/doc/sql.R | 32 +++++++++++------------ inst/doc/sql.html | 7 ++--- inst/doc/tree.R | 4 +- inst/doc/tree.html | 3 -- inst/doc/xgboost.R | 18 ++++++------- inst/doc/xgboost.html | 27 +++++++++----------- man/tidypredict-package.Rd | 4 +- man/tidypredict_test.Rd | 10 +++++-- man/tidypredict_to_column.Rd | 9 +++++- 30 files changed, 195 insertions(+), 196 deletions(-)
Title: Single Objective Optimization Benchmark Functions
Description: Collection of different single objective test functions
useful for benchmarks and algorithm development.
Author: Olaf Mersmann <olafm@p-value.net>, Bernd Bischl
<bernd_bischl@gmx.net>, Jakob Bossek
<jakob.bossek@tu-dortmund.de> and Leonard Judt <judt@gmx.net>
Maintainer: Eric Kalosa-Kenyon <eric@opsani.com>
Diff between soobench versions 1.9.12 dated 2020-01-27 and 1.9.18 dated 2020-02-09
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/plot_soo_function.R | 3 ++- man/bbob2009_function.Rd | 5 +++-- man/is_soo_function_generator.Rd | 2 +- man/plot_2d_soo_function.Rd | 3 ++- man/recorded_values.Rd | 4 ++-- man/recording_function.Rd | 2 +- man/rotate_parameter_space.Rd | 2 +- man/with_fixed_budget.Rd | 4 ++-- src/benchmarksnoisy.h | 4 ++-- 12 files changed, 34 insertions(+), 27 deletions(-)
Title: Execute and Control System Processes
Description: Tools to run system processes in the background.
It can check if a background process is running; wait on a background
process to finish; get the exit status of finished processes; kill
background processes. It can read the standard output and error of
the processes, using non-blocking connections. 'processx' can poll
a process for standard output or error, with a timeout. It can also
poll several processes at once.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between processx versions 3.4.1 dated 2019-07-18 and 3.4.2 dated 2020-02-09
DESCRIPTION | 8 - MD5 | 73 +++++----- NAMESPACE | 4 NEWS.md | 25 +++ R/cleancall.R |only R/errors.R | 208 ++++++++++++++++++++++++++--- R/on-load.R | 2 R/poll.R | 6 R/process.R | 29 ++-- R/run.R | 115 ++++++++++------ R/utils.R | 17 ++ README.md | 45 +++++- man/poll.Rd | 6 man/process.Rd | 108 +++++++-------- man/process_initialize.Rd | 27 +++ man/processx_connections.Rd | 3 man/run.Rd | 63 +++++--- src/Makevars | 2 src/Makevars.win | 2 src/cleancall.c |only src/cleancall.h |only src/client.c | 8 - src/errors.c | 19 +- src/errors.h | 17 +- src/init.c | 15 +- src/processx-connection.c | 32 +++- src/processx-vector.c | 4 src/processx.h | 12 - src/unix/processx-unix.h | 2 src/unix/processx.c | 103 ++++++++++---- src/unix/sigchld.c | 26 +++ src/win/processx-win.h | 9 - src/win/processx.c | 90 +++++++----- src/win/stdio.c | 35 ++-- tests/testthat/test-err.R | 72 ++++++++++ tests/testthat/test-errors.R | 37 +++-- tests/testthat/test-kill-tree.R | 2 tests/testthat/test-sigchld.R | 283 ++++++++++++++++++++++++++++++---------- tests/testthat/test-wait.R | 31 ++++ 39 files changed, 1113 insertions(+), 427 deletions(-)
Title: Permanent Random Number Sampling
Description: Survey sampling using permanent random numbers (PRN's). A solution to the
problem of unknown overlap between survey samples, which leads to a low
precision in estimates when the survey is repeated or combined with other
surveys. The PRN solution is to supply the U(0, 1) random numbers to the
sampling procedure, instead of having the sampling procedure generate them.
In Lindblom (2014) <doi:10.2478/jos-2014-0047>, and therein cited articles,
it is shown how this is carried out and how it improves the estimates. This
package supports two common fixed-size sampling procedures (simple random
sampling and probability-proportional-to-size sampling) and includes a
function for transforming the PRN's in order to control the sample overlap.
Author: Kira Coder Gylling
Maintainer: Kira Coder Gylling <kira.gylling@gmail.com>
Diff between prnsamplr versions 0.1.0 dated 2019-03-02 and 0.1.1 dated 2020-02-09
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 8 ++++++-- R/pps.R | 6 +++--- R/samp.R | 1 + R/srs.R | 5 +++-- R/transf.R | 1 + README.md | 6 +++++- data/ExampleData.RData |binary man/ExampleData.Rd | 8 ++++---- man/pps.Rd | 6 +++++- man/samp.Rd | 14 ++++++++++++-- man/srs.Rd | 5 ++++- man/transformprn.Rd | 2 +- 15 files changed, 65 insertions(+), 37 deletions(-)
Title: Person-Centered Analysis
Description: Provides an easy-to-use yet adaptable set of tools to conduct person-center analysis using a two-step clustering procedure. As described in Bergman and El-Khouri (1999) <DOI:10.1002/(SICI)1521-4036(199910)41:6%3C753::AID-BIMJ753%3E3.0.CO;2-K>, hierarchical clustering is performed to determine the initial partition for the subsequent k-means clustering procedure.
Author: Joshua M Rosenberg [aut, cre],
Jennifer A Schmidt [aut],
Patrick N Beymer [aut],
Rebecca R Steingut [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Diff between prcr versions 0.1.5 dated 2017-08-25 and 0.2.1 dated 2020-02-09
prcr-0.1.5/prcr/R/functions.R |only prcr-0.1.5/prcr/R/helpers.R |only prcr-0.1.5/prcr/man/create_profiles.Rd |only prcr-0.1.5/prcr/man/cross_validate.Rd |only prcr-0.1.5/prcr/man/plot.prcr.Rd |only prcr-0.1.5/prcr/man/plot_r_squared.Rd |only prcr-0.2.1/prcr/DESCRIPTION | 14 prcr-0.2.1/prcr/MD5 | 39 + prcr-0.2.1/prcr/NAMESPACE | 11 prcr-0.2.1/prcr/R/create_profiles_cluster.R |only prcr-0.2.1/prcr/R/cross_validate.R |only prcr-0.2.1/prcr/R/estimate_r_squared.R |only prcr-0.2.1/prcr/R/explore_models.R |only prcr-0.2.1/prcr/R/helpers_clusters.R |only prcr-0.2.1/prcr/R/tidymixmod.R |only prcr-0.2.1/prcr/README.md | 60 ++ prcr-0.2.1/prcr/build/vignette.rds |binary prcr-0.2.1/prcr/data |only prcr-0.2.1/prcr/inst/doc/introduction_to_prcr.R | 45 -- prcr-0.2.1/prcr/inst/doc/introduction_to_prcr.Rmd | 70 --- prcr-0.2.1/prcr/inst/doc/introduction_to_prcr.html | 444 ++++++++++++++------- prcr-0.2.1/prcr/man/create_profiles_cluster.Rd |only prcr-0.2.1/prcr/man/detect_outliers.Rd | 4 prcr-0.2.1/prcr/man/estimate_r_squared.Rd |only prcr-0.2.1/prcr/man/pisaUSA15.Rd |only prcr-0.2.1/prcr/man/plot_profiles.Rd |only prcr-0.2.1/prcr/man/print.prcr.Rd | 2 prcr-0.2.1/prcr/man/summary.prcr.Rd | 2 prcr-0.2.1/prcr/vignettes/introduction_to_prcr.Rmd | 70 --- 29 files changed, 426 insertions(+), 335 deletions(-)
Title: Penalized Elastic Net S/MM-Estimator of Regression
Description: Robust penalized elastic net S and MM estimator for linear
regression. The method is described in detail in
Cohen Freue, G. V., Kepplinger, D., Salibian-Barrera, M., and Smucler, E.
(2017) <https://gcohenfr.github.io/pdfs/PENSE_manuscript.pdf>.
Author: David Kepplinger [aut, cre],
Matias Salibian-Barrera [aut],
Gabriela Cohen Freue [aut],
Derek Cho [ctb]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between pense versions 1.2.5 dated 2019-06-08 and 1.2.9 dated 2020-02-09
DESCRIPTION | 10 ++++----- MD5 | 52 ++++++++++++++++++++++++------------------------ NEWS.md | 4 +++ cleanup | 2 - configure | 22 ++++++++++---------- configure.ac | 6 ++--- man/coef.elnetfit.Rd | 3 -- man/coef.pense.Rd | 3 -- man/elnet.Rd | 16 ++++++++++++-- man/elnet_cv.Rd | 19 ++++++++++++++--- man/en_options.Rd | 18 ++++++++++++---- man/enpy.Rd | 12 +++++++++-- man/initest_options.Rd | 24 +++++++++++++++------- man/mscale.Rd | 10 +++++++-- man/mstep_options.Rd | 17 +++++++++++---- man/pense.Rd | 23 ++++++++++++++++----- man/pense_options.Rd | 20 ++++++++++++------ man/pensem.Rd | 50 ++++++++++++++++++++++++++++++++++++---------- man/predict.elnetfit.Rd | 3 -- man/predict.pense.Rd | 3 -- man/prinsens.Rd | 11 ++++++++-- man/residuals.pense.Rd | 3 -- src/BLAS.h | 36 ++++++++++++++++++--------------- src/Makevars.in | 2 - src/Makevars.win | 2 - src/autoconfig.win.h | 4 +-- src/config.h | 8 +++++-- 27 files changed, 254 insertions(+), 129 deletions(-)
Title: Multivariate Methods Based on the Oja Median and Related
Concepts
Description: Functions to calculate the Oja median, Oja signs and ranks and methods based upon them.
Author: Daniel Fischer, Karl Mosler, Jyrki Möttönen, Klaus Nordhausen, Oleksii Pokotylo, Daniel Vogel
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between OjaNP versions 0.9-12 dated 2018-11-20 and 0.9-13 dated 2020-02-09
DESCRIPTION | 8 +-- MD5 | 24 +++++----- R/OjaMedian.R | 21 +++++++-- R/ojaGradient.hyperplane.R | 11 ++-- R/ojaMedian.control.R | 16 +++--- inst/ChangeLog | 6 ++ man/OjaNP-package.Rd | 4 - man/ojaMedianControl.Rd | 105 ++++++++++++++++++++++----------------------- src/algorithms.cpp | 10 ++-- src/bounded_search.cpp | 16 +++--- src/global.cpp | 4 - src/global.h | 13 ++++- src/interface.cpp | 8 +-- 13 files changed, 135 insertions(+), 111 deletions(-)
Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre],
Julian Flowers [aut, ctb],
Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>),
Duncan Gormansway [ctb],
Carl Ganz [ctb],
David Whiting [ctb],
Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipsR versions 1.0.1 dated 2020-01-28 and 1.0.2 dated 2020-02-09
DESCRIPTION | 6 - MD5 | 30 +++---- NEWS.md | 6 + R/area_types.R | 6 + R/deprivation_decile.R | 10 -- R/fingertips_data.R | 10 +- R/indicators.R | 3 R/profiles.R | 4 - README.md | 32 +------- inst/doc/lifeExpectancy.html | 120 +++++++++++++++---------------- inst/doc/selectIndicatorsRedRed.html | 2 man/indicator_areatypes.Rd | 101 +++++++++++++------------- man/indicators_unique.Rd | 101 +++++++++++++------------- man/nearest_neighbours.Rd | 133 +++++++++++++++++------------------ man/profiles.Rd | 112 ++++++++++++++--------------- tests/testthat/test-deprivation.R | 5 - 16 files changed, 330 insertions(+), 351 deletions(-)
Title: Computational Graphs
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various operations including basic arithmetic, trigonometry operations, and linear algebra operations. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>
Diff between cgraph versions 6.0.0 dated 2020-02-04 and 6.0.1 dated 2020-02-09
DESCRIPTION | 6 - MD5 | 53 ++++++------ NAMESPACE | 2 NEWS.md | 14 ++- R/array.R | 62 ++++++++++++++ R/subset.R | 4 man/cg_colmeans.Rd |only man/cg_rowmeans.Rd |only man/cg_subset1.Rd | 2 man/cg_subset2.Rd | 2 src/class.c | 50 ++--------- src/class.h | 30 ------ src/function.c | 53 +----------- src/function.h | 57 +++++++++++- src/graph.c | 172 ++++++++++++++++++--------------------- src/graph.h | 46 ++++++++-- src/init.c | 32 +++++-- src/internal.c | 2 src/internal.h | 2 src/node.c | 193 ++++++++------------------------------------ src/node.h | 165 +++++++++++++++++++++++++++++++++---- src/session.c | 56 +----------- src/session.h | 17 +-- src/stack.c | 61 +++---------- src/stack.h | 62 +++++++++++--- src/symbols.h |only src/vector.c | 2 src/vector.h | 2 tests/testthat/test_array.R | 24 +++++ 29 files changed, 619 insertions(+), 552 deletions(-)
Title: Parse Eye-Tracking Data into Fixations
Description: Eye-tracking data must be transformed into fixations and saccades before it can be analyzed. This package provides a non-parametric speed-based approach to do this on a trial basis. The method is especially useful when there are large differences in data quality, as the thresholds are adjusted accordingly. The same pre-processing procedure can be applied to all participants, while accounting for individual differences in data quality.
Author: Daan van Renswoude & Ingmar Visser
Maintainer: Daan van Renswoude <D.R.vanRenswoude@uva.nl>
Diff between gazepath versions 1.2 dated 2017-03-13 and 1.3 dated 2020-02-09
DESCRIPTION | 14 ++--- MD5 | 21 ++++--- NAMESPACE | 2 R/Interpolate.R | 6 +- R/comhull.R | 42 ++++++++------- R/gazepath-internal.R | 127 ------------------------------------------------ R/pnt.in.poly.R |only data/eye_dat.RData |binary data/screen.RData |binary man/eye_dat.Rd | 2 man/gazepath-package.Rd | 4 - man/screen.Rd | 2 12 files changed, 49 insertions(+), 171 deletions(-)
Title: Subgroup Discovery and Bump Hunting
Description: Developed to assist in discovering interesting subgroups in high-dimensional data.
The PRIM implementation is based on the 1998 paper "Bump hunting in high-dimensional data" by Jerome H. Friedman and Nicholas I. Fisher <doi:10.1023/A:1008894516817>.
PRIM involves finding a set of "rules" which combined imply unusually large values of some other target variable.
Specifically one tries to find a set of sub regions in which the target variable is substantially larger than overall mean.
The objective of bump hunting in general is to find regions in the input (attribute/feature) space with relatively high values for the target variable.
The regions are described by simple rules of the type if: condition-1 and ... and condition-n then: estimated target value. Given the data (or a subset of the data),
the goal is to produce a box B within which the target mean is as large as possible.
Author: Jurian Baas [aut, cre, cph],
Ad Feelders [ctb]
Maintainer: Jurian Baas <j.baas@uu.nl>
Diff between subgroup.discovery versions 0.3.0 dated 2020-02-03 and 0.3.1 dated 2020-02-09
DESCRIPTION | 8 MD5 | 34 - NAMESPACE | 44 - NEWS.md | 31 - R/RcppExports.R | 38 - R/data.R | 370 ++++++++-------- R/prim.R | 1020 +++++++++++++++++++++++----------------------- R/subgroup.discovery.R | 16 README.md | 90 ++-- man/plot.prim.peel.Rd | 2 src/mapreduce.cpp | 181 ++++---- src/mapreduce.h | 92 ++-- src/prim.cpp | 95 ++-- src/prim.h | 14 src/quantile.cpp | 13 src/quantile.h | 9 tests/testthat.R | 8 tests/testthat/testPrim.R | 102 ++-- 18 files changed, 1102 insertions(+), 1065 deletions(-)
More information about subgroup.discovery at CRAN
Permanent link
Title: An Alternative to the Hodrick-Prescott Filter
Description: In the working paper titled "Why You Should Never Use the Hodrick-Prescott
Filter", James D. Hamilton proposes a new alternative to economic time series
filtering. The neverhpfilter package provides functions and data for reproducing his work. Hamilton (2017) <doi:10.3386/w23429>.
Author: Justin M. Shea [aut, cre]
Maintainer: Justin M. Shea <jshea@roosevelt.edu>
Diff between neverhpfilter versions 0.2-0 dated 2018-01-24 and 0.3-1 dated 2020-02-09
neverhpfilter-0.2-0/neverhpfilter/tests/testthat |only neverhpfilter-0.2-0/neverhpfilter/tests/testthat.R |only neverhpfilter-0.3-1/neverhpfilter/DESCRIPTION | 20 neverhpfilter-0.3-1/neverhpfilter/MD5 | 121 neverhpfilter-0.3-1/neverhpfilter/NAMESPACE | 15 neverhpfilter-0.3-1/neverhpfilter/NEWS.md | 98 neverhpfilter-0.3-1/neverhpfilter/R/EXPGSC1.R | 60 neverhpfilter-0.3-1/neverhpfilter/R/FEDFUNDS.R | 153 - neverhpfilter-0.3-1/neverhpfilter/R/GCEC1.R | 60 neverhpfilter-0.3-1/neverhpfilter/R/GDPC1.R | 82 neverhpfilter-0.3-1/neverhpfilter/R/GDPDEF.R | 60 neverhpfilter-0.3-1/neverhpfilter/R/GPDIC1.R | 64 neverhpfilter-0.3-1/neverhpfilter/R/GS10.R | 67 neverhpfilter-0.3-1/neverhpfilter/R/Hamilton_table_2.R | 54 neverhpfilter-0.3-1/neverhpfilter/R/IMPGSC1.R | 60 neverhpfilter-0.3-1/neverhpfilter/R/PAYEMS.R | 146 - neverhpfilter-0.3-1/neverhpfilter/R/PCECC96.R | 60 neverhpfilter-0.3-1/neverhpfilter/R/SP500.R | 132 - neverhpfilter-0.3-1/neverhpfilter/R/UNRATENSA.R | 78 neverhpfilter-0.3-1/neverhpfilter/R/USREC.R | 173 - neverhpfilter-0.3-1/neverhpfilter/R/yth_filter.R | 301 +- neverhpfilter-0.3-1/neverhpfilter/R/yth_glm.R | 168 - neverhpfilter-0.3-1/neverhpfilter/README.md | 118 neverhpfilter-0.3-1/neverhpfilter/build/vignette.rds |binary neverhpfilter-0.3-1/neverhpfilter/data/EXPGSC1.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/FEDFUNDS.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/GCEC1.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/GDPC1.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/GDPDEF.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/GPDIC1.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/GS10.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/Hamilton_table_2.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/IMPGSC1.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/PAYEMS.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/PCECC96.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/SP500.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/UNRATENSA.RData |binary neverhpfilter-0.3-1/neverhpfilter/data/USREC.RData |binary neverhpfilter-0.3-1/neverhpfilter/inst/doc/Getting-started.R |only neverhpfilter-0.3-1/neverhpfilter/inst/doc/Getting-started.Rmd |only neverhpfilter-0.3-1/neverhpfilter/inst/doc/Getting-started.html |only neverhpfilter-0.3-1/neverhpfilter/inst/doc/Reproducing-Hamilton.R | 176 - neverhpfilter-0.3-1/neverhpfilter/inst/doc/Reproducing-Hamilton.Rmd | 448 +-- neverhpfilter-0.3-1/neverhpfilter/inst/doc/Reproducing-Hamilton.html | 1294 ++++------ neverhpfilter-0.3-1/neverhpfilter/inst/tinytest |only neverhpfilter-0.3-1/neverhpfilter/man/EXPGSC1.Rd | 76 neverhpfilter-0.3-1/neverhpfilter/man/FEDFUNDS.Rd | 165 - neverhpfilter-0.3-1/neverhpfilter/man/GCEC1.Rd | 76 neverhpfilter-0.3-1/neverhpfilter/man/GDPC1.Rd | 90 neverhpfilter-0.3-1/neverhpfilter/man/GDPDEF.Rd | 76 neverhpfilter-0.3-1/neverhpfilter/man/GPDIC1.Rd | 80 neverhpfilter-0.3-1/neverhpfilter/man/GS10.Rd | 79 neverhpfilter-0.3-1/neverhpfilter/man/Hamilton_table_2.Rd | 70 neverhpfilter-0.3-1/neverhpfilter/man/IMPGSC1.Rd | 76 neverhpfilter-0.3-1/neverhpfilter/man/PAYEMS.Rd | 160 - neverhpfilter-0.3-1/neverhpfilter/man/PCECC96.Rd | 76 neverhpfilter-0.3-1/neverhpfilter/man/SP500.Rd | 148 - neverhpfilter-0.3-1/neverhpfilter/man/UNRATENSA.Rd | 92 neverhpfilter-0.3-1/neverhpfilter/man/USREC.Rd | 187 - neverhpfilter-0.3-1/neverhpfilter/man/yth_filter.Rd | 193 - neverhpfilter-0.3-1/neverhpfilter/man/yth_glm.Rd | 124 neverhpfilter-0.3-1/neverhpfilter/tests/tinytest.R |only neverhpfilter-0.3-1/neverhpfilter/vignettes/Getting-started.Rmd |only neverhpfilter-0.3-1/neverhpfilter/vignettes/Reproducing-Hamilton.Rmd | 448 +-- 64 files changed, 3133 insertions(+), 3091 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-05 2.1.0
2017-12-14 2.0.2
Title: Miscellaneous Pedometric Tools
Description: An R implementation of some useful tools employed in the field of pedometrics.
Author: Alessandro Samuel-Rosa [aut, cre]
(<https://orcid.org/0000-0003-0877-1320>),
Lucia Helena Cunha dos Anjos [ths]
(<https://orcid.org/0000-0003-0063-3521>),
Gustavo Vasques [ths] (<https://orcid.org/0000-0001-9463-1898>),
Gerard B M Heuvelink [ths] (<https://orcid.org/0000-0003-0959-9358>),
Tony Olsen [ctb],
Tom Kincaid [ctb],
Juan Carlos Ruiz Cuetos [ctb],
Maria Eugenia Polo Garcia [ctb],
Pablo Garcia Rodriguez [ctb],
Joshua French [ctb],
Ken Kleinman [ctb],
Dick Brus [ctb] (<https://orcid.org/0000-0003-2194-4783>),
Frank Harrell Jr [ctb],
Ruo Xu [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between pedometrics versions 0.6-6 dated 2015-12-03 and 0.7.0 dated 2020-02-09
DESCRIPTION | 82 +++++++--------- MD5 | 103 +++++++++++---------- NAMESPACE | 1 NEWS.md |only R/AAAA.R | 3 R/RcppExports.R | 4 R/adjR2.R | 3 R/bbox2sp.R | 18 ++- R/cdfPlot.R | 6 + R/cdfStats.R | 12 +- R/cdfTable.R | 10 +- R/checkGMU.R | 8 - R/cont2cat.R | 111 ++++++++++++---------- R/coordenadas.R | 41 ++++---- R/cramer.R | 2 R/gcpDiff.R | 6 - R/gcpVector.R | 13 +- R/pedometrics.R | 16 --- R/plotCor.R |only R/plotESDA.R | 34 +++---- R/plotHD.R | 48 ++++----- R/plotMS.R | 10 +- R/stepVIF.R | 96 ++++++++----------- R/vgmICP.R | 218 +++++++++++++++++++++++---------------------- R/vgmLags.R | 2 R/vgmSCV.R | 2 inst |only man/adjR2.Rd | 14 +- man/bbox2sp.Rd | 21 ++-- man/buildMS.Rd | 71 ++++++++------ man/cdfPlot.Rd | 40 +++++--- man/cdfStats.Rd | 11 +- man/cdfTable.Rd | 13 +- man/checkGMU.Rd | 138 ++++++++++++++-------------- man/cont2cat.Rd | 42 +++----- man/coordenadas.Rd | 39 +++----- man/cramer.Rd | 13 +- man/gcpDiff.Rd | 11 +- man/gcpVector.Rd | 21 +--- man/numint.Rd | 23 ++-- man/optimRandomForest.Rd | 56 ++++++----- man/pedometrics-package.Rd | 32 ++---- man/plotCor.Rd |only man/plotESDA.Rd | 56 ++++++----- man/plotHD.Rd | 66 +++++++------ man/plotMS.Rd | 143 ++++++++++++++++------------- man/rowMinCpp.Rd | 7 - man/statsMS.Rd | 80 ++++++++-------- man/stepVIF.Rd | 100 ++++++++------------ man/trend.Rd | 9 - man/vgmICP.Rd | 152 +++++++++++++++---------------- man/vgmLags.Rd | 42 ++++---- man/vgmSCV.Rd | 15 +-- src/RcppExports.cpp | 22 +++- 54 files changed, 1067 insertions(+), 1019 deletions(-)
Title: Plastome Assembly Coverage Visualization
Description: Visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes. For more information, please see Gruenstaeudl and Jenke (2019) <doi:10.1101/697821>.
Author: Michael Gruenstaeudl [aut, cre],
Nils Jenke [ctb]
Maintainer: Michael Gruenstaeudl <m.gruenstaeudl@fu-berlin.de>
Diff between PACVr versions 0.8.2 dated 2019-09-13 and 0.9.1 dated 2020-02-09
PACVr-0.8.2/PACVr/R/calcCoverage.R |only PACVr-0.8.2/PACVr/R/generateHistogramData.R |only PACVr-0.8.2/PACVr/R/generateIRGeneData.R |only PACVr-0.8.2/PACVr/R/histogramPlotter.R |only PACVr-0.8.2/PACVr/R/parseGenes.R |only PACVr-0.8.2/PACVr/R/parseRegions.R |only PACVr-0.9.1/PACVr/DESCRIPTION | 11 PACVr-0.9.1/PACVr/MD5 | 36 PACVr-0.9.1/PACVr/NAMESPACE | 2 PACVr-0.9.1/PACVr/R/PACVr.R | 272 - PACVr-0.9.1/PACVr/R/customizedRCircos.R |only PACVr-0.9.1/PACVr/R/generatePlotData.R |only PACVr-0.9.1/PACVr/R/helpers.R | 109 PACVr-0.9.1/PACVr/R/parseData.R |only PACVr-0.9.1/PACVr/R/visualizeWithRCircos.R | 217 - PACVr-0.9.1/PACVr/build/vignette.rds |binary PACVr-0.9.1/PACVr/inst/doc/PACVr_Vignette.Rnw | 24 PACVr-0.9.1/PACVr/inst/doc/PACVr_Vignette.pdf |binary PACVr-0.9.1/PACVr/inst/extdata/MH161174/MH161174.gb | 1750 ++++++++-- PACVr-0.9.1/PACVr/inst/extdata/MH161174/MH161174.gb.new |only PACVr-0.9.1/PACVr/man/PACVr-complete.Rd | 14 PACVr-0.9.1/PACVr/man/PACVr-package.Rd | 2 PACVr-0.9.1/PACVr/vignettes/MH161174_AssemblyCoverage_viz.pdf |binary PACVr-0.9.1/PACVr/vignettes/PACVr_Vignette.Rnw | 24 24 files changed, 1786 insertions(+), 675 deletions(-)
Title: Miscellaneous Functions for Data Cleaning and Analysis
Description: Provides functions needed for data cleaning and
formatting and forms data cleaning and wrangling backend for the
following packages: 'ggstatsplot', 'groupedstats',
'pairwiseComparisons', and 'statsExpressions'.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ipmisc versions 1.0.0 dated 2020-02-06 and 1.1.0 dated 2020-02-09
DESCRIPTION | 13 +++--- MD5 | 29 +++++++++---- NAMESPACE | 11 +++++ NEWS.md | 9 +++- R/easystats_to_tidy_names.R |only R/reexports.R | 22 ++++++++++ R/sort_xy.R |only README.md | 12 ++--- build |only inst/WORDLIST | 10 ++++ inst/doc |only man/easystats_to_tidy_names.Rd |only man/reexports.Rd | 9 +++- man/sort_xy.Rd |only tests/README.md | 56 ++++++++++++++------------ tests/testthat/test-easystats_to_tidy_names.R |only tests/testthat/test-outlier_df.R | 4 - tests/testthat/test-sort_xy.R |only vignettes |only 19 files changed, 122 insertions(+), 53 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>),
George Athanasopoulos [aut],
Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>),
Gabriel Caceres [aut],
Leanne Chhay [aut],
Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>),
Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>),
Slava Razbash [aut],
Earo Wang [aut],
Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>),
R Core Team [ctb, cph],
Ross Ihaka [ctb, cph],
Daniel Reid [ctb],
David Shaub [ctb],
Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>),
Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.10 dated 2019-12-05 and 8.11 dated 2020-02-09
DESCRIPTION | 8 ++-- MD5 | 30 +++++++-------- NAMESPACE | 4 +- NEWS.md | 3 + R/arfima.R | 7 ++- R/ggplot.R | 21 ++++++---- R/mstl.R | 89 +++++++++++++++++++++++----------------------- R/residuals.R | 4 +- build/vignette.rds |binary inst/doc/JSS2008.pdf |binary man/accuracy.Rd | 4 +- man/fitted.Arima.Rd | 6 +-- man/forecast.stl.Rd | 10 ++--- man/gghistogram.Rd | 2 - man/mstl.Rd | 2 - man/residuals.forecast.Rd | 6 +-- 16 files changed, 101 insertions(+), 95 deletions(-)
Title: Extremely Fast Implementation of a Naive Bayes Classifier
Description: This is an extremely fast implementation of a Naive Bayes classifier. This
package is currently the only package that supports a Bernoulli distribution, a Multinomial
distribution, and a Gaussian distribution, making it suitable for both binary features,
frequency counts, and numerical features. Another feature is the support of a mix of
different event models. Only numerical variables are allowed, however, categorical variables
can be transformed into dummies and used with the Bernoulli distribution.
The implementation is largely based on the paper
"A comparison of event models for Naive Bayes anti-spam e-mail filtering"
written by K.M. Schneider (2003) <doi:10.3115/1067807.1067848>. Any issues can be
submitted to: <https://github.com/mskogholt/fastNaiveBayes/issues>.
Author: Martin Skogholt
Maintainer: Martin Skogholt <m.skogholt@gmail.com>
Diff between fastNaiveBayes versions 2.1.0 dated 2019-08-28 and 2.1.1 dated 2020-02-09
fastNaiveBayes-2.1.0/fastNaiveBayes/R/predict.fastNaiveBayes.R |only fastNaiveBayes-2.1.0/fastNaiveBayes/R/predict.fnb.bernoulli.R |only fastNaiveBayes-2.1.0/fastNaiveBayes/R/predict.fnb.gaussian.R |only fastNaiveBayes-2.1.0/fastNaiveBayes/R/predict.fnb.multinomial.R |only fastNaiveBayes-2.1.0/fastNaiveBayes/tests/testthat/test-fastnaivebayes_mixed.R |only fastNaiveBayes-2.1.1/fastNaiveBayes/DESCRIPTION | 8 fastNaiveBayes-2.1.1/fastNaiveBayes/MD5 | 51 - fastNaiveBayes-2.1.1/fastNaiveBayes/NAMESPACE | 4 fastNaiveBayes-2.1.1/fastNaiveBayes/NEWS.md | 8 fastNaiveBayes-2.1.1/fastNaiveBayes/R/fastNaiveBayes.R | 86 --- fastNaiveBayes-2.1.1/fastNaiveBayes/R/fnb.bernoulli.R | 225 ++++++- fastNaiveBayes-2.1.1/fastNaiveBayes/R/fnb.check.args.R | 157 ----- fastNaiveBayes-2.1.1/fastNaiveBayes/R/fnb.detect_distribution.R | 1 fastNaiveBayes-2.1.1/fastNaiveBayes/R/fnb.gaussian.R | 179 ++++++ fastNaiveBayes-2.1.1/fastNaiveBayes/R/fnb.io.R |only fastNaiveBayes-2.1.1/fastNaiveBayes/R/fnb.multinomial.R | 199 ++++++- fastNaiveBayes-2.1.1/fastNaiveBayes/R/fnb.train.R | 282 +++++++++- fastNaiveBayes-2.1.1/fastNaiveBayes/README.md | 14 fastNaiveBayes-2.1.1/fastNaiveBayes/inst/doc/fastnaivebayes.html | 4 fastNaiveBayes-2.1.1/fastNaiveBayes/man/fastNaiveBayesF.Rd | 24 fastNaiveBayes-2.1.1/fastNaiveBayes/man/fnb.detect_distribution.Rd | 2 fastNaiveBayes-2.1.1/fastNaiveBayes/man/fnb.io.Rd |only fastNaiveBayes-2.1.1/fastNaiveBayes/man/predict.fastNaiveBayes.Rd | 70 -- fastNaiveBayes-2.1.1/fastNaiveBayes/tests/testthat/test-fastnaivebayes_bernoulli.R | 253 ++++++-- fastNaiveBayes-2.1.1/fastNaiveBayes/tests/testthat/test-fastnaivebayes_checkargs.R | 93 ++- fastNaiveBayes-2.1.1/fastNaiveBayes/tests/testthat/test-fastnaivebayes_detect_distribution.R | 2 fastNaiveBayes-2.1.1/fastNaiveBayes/tests/testthat/test-fastnaivebayes_fastNaiveBayes.R | 44 - fastNaiveBayes-2.1.1/fastNaiveBayes/tests/testthat/test-fastnaivebayes_gaussian.R | 186 ++++-- fastNaiveBayes-2.1.1/fastNaiveBayes/tests/testthat/test-fastnaivebayes_io.R |only fastNaiveBayes-2.1.1/fastNaiveBayes/tests/testthat/test-fastnaivebayes_multinomial.R | 276 +++++++-- fastNaiveBayes-2.1.1/fastNaiveBayes/tests/testthat/test-fastnaivebayes_train.R |only 31 files changed, 1507 insertions(+), 661 deletions(-)
More information about fastNaiveBayes at CRAN
Permanent link
Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data (Markos, Iodice D'Enza and van de Velden 2019; <DOI:10.18637/jss.v091.i10>). For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between clustrd versions 1.3.6-2 dated 2019-10-28 and 1.3.7 dated 2020-02-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/clusCA.R | 6 +++--- man/global_bootclus.Rd | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Encode Categorical Features
Description: Functions for aggregate encoding, dummy encoding,
frequency encoding, label encoding, leave-one-out encoding,
mean encoding, median encoding, and one-hot encoding.
Author: Bernie Gray [aut, cre] (<https://orcid.org/0000-0001-9190-6032>),
Mark Roepke [ctb]
Maintainer: Bernie Gray <bfgray3@gmail.com>
Diff between cattonum versions 0.0.3 dated 2019-12-17 and 0.0.4 dated 2020-02-09
DESCRIPTION | 18 +++++++++--------- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/aggregate.R | 10 ++++++++-- R/utils.R | 7 ++++++- README.md | 6 ++---- build/vignette.rds |binary inst/doc/introduction.html | 37 +++++++++++++++++++++++-------------- man/catto_aggregate.Rd | 10 ++++++++-- man/catto_median.Rd | 3 +-- man/cattonum.Rd | 1 - tests/testthat/test-conditions.R | 6 ++++-- 13 files changed, 78 insertions(+), 49 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Jeroen Ooms [aut],
Neal Richardson [aut, cre],
Javier Luraschi [ctb],
Jeffrey Wong [ctb],
Apache Arrow [aut, cph]
Maintainer: Neal Richardson <neal@ursalabs.org>
Diff between arrow versions 0.15.1.1 dated 2019-11-05 and 0.16.0 dated 2020-02-09
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Title: Probabilistic and Possibilistic Cluster Analysis
Description: Partitioning clustering divides the objects in a data set into non-overlapping subsets or clusters by using the prototype-based probabilistic and possibilistic clustering algorithms. This package covers a set of the functions for Fuzzy C-Means (Bezdek, 1974) <doi:10.1080/01969727308546047>, Possibilistic C-Means (Krishnapuram & Keller, 1993) <doi:10.1109/91.227387>, Possibilistic Fuzzy C-Means (Pal et al, 2005) <doi:10.1109/TFUZZ.2004.840099>, Possibilistic Clustering Algorithm (Yang et al, 2006) <doi:10.1016/j.patcog.2005.07.005>, Possibilistic C-Means with Repulsion (Wachs et al, 2006) <doi:10.1007/3-540-31662-0_6> and the other variants of hard and soft clustering algorithms. The cluster prototypes and membership matrices required by these partitioning algorithms are initialized with different initialization techniques that are available in the package 'inaparc'. As the distance metrics, not only the Euclidean distance but also a set of the commonly used distance metrics are available to use with some of the algorithms in the package.
Author: Zeynel Cebeci [aut, cre],
Figen Yildiz [aut],
Alper Tuna Kavlak [aut],
Cagatay Cebeci [aut],
Hasan Onder [aut]
Maintainer: Zeynel Cebeci <zcebeci@cukurova.edu.tr>
Diff between ppclust versions 0.1.3 dated 2019-07-23 and 1.1.0 dated 2020-02-09
ppclust-0.1.3/ppclust/inst/doc/pcm.R |only ppclust-0.1.3/ppclust/inst/doc/pcm.Rmd |only ppclust-0.1.3/ppclust/inst/doc/pcm.html |only ppclust-0.1.3/ppclust/vignettes/pcm.Rmd |only ppclust-1.1.0/ppclust/DESCRIPTION | 12 - ppclust-1.1.0/ppclust/MD5 | 56 +++----- ppclust-1.1.0/ppclust/NAMESPACE | 1 ppclust-1.1.0/ppclust/R/fcm.R | 4 ppclust-1.1.0/ppclust/R/fcm2.R | 4 ppclust-1.1.0/ppclust/R/fpcm.R | 4 ppclust-1.1.0/ppclust/R/fpppcm.R | 4 ppclust-1.1.0/ppclust/R/gg.R | 6 ppclust-1.1.0/ppclust/R/gk.R | 6 ppclust-1.1.0/ppclust/R/gkpfcm.R | 4 ppclust-1.1.0/ppclust/R/mfpcm.R | 4 ppclust-1.1.0/ppclust/R/pca.R | 4 ppclust-1.1.0/ppclust/R/pcm.R | 4 ppclust-1.1.0/ppclust/R/pcmr.R | 4 ppclust-1.1.0/ppclust/R/pfcm.R | 4 ppclust-1.1.0/ppclust/R/tools.R | 8 - ppclust-1.1.0/ppclust/R/upfc.R | 4 ppclust-1.1.0/ppclust/build/vignette.rds |binary ppclust-1.1.0/ppclust/inst/CITATION | 29 ++-- ppclust-1.1.0/ppclust/inst/NEWS.Rd | 11 + ppclust-1.1.0/ppclust/inst/doc/fcm.Rmd | 6 ppclust-1.1.0/ppclust/inst/doc/fcm.html | 188 ++++++++++++++------------- ppclust-1.1.0/ppclust/inst/doc/upfc.Rmd | 2 ppclust-1.1.0/ppclust/inst/doc/upfc.html | 187 ++++++++++++++------------ ppclust-1.1.0/ppclust/man/ppclust-package.Rd | 29 ++-- ppclust-1.1.0/ppclust/vignettes/fcm.Rmd | 6 ppclust-1.1.0/ppclust/vignettes/upfc.Rmd | 2 31 files changed, 311 insertions(+), 282 deletions(-)
Title: Pattern-Based Zoneless Method for Analysis and Visualization of
Racial Topography
Description: Implements a computational framework for a pattern-based,
zoneless analysis, and visualization of (ethno)racial topography. It is a reimagined
approach for analyzing residential segregation and racial diversity based on
the concept of 'landscape’ used in the domain of landscape ecology.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Anna Dmowska [aut],
Tomasz Stepinski [aut]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between raceland versions 1.0.3 dated 2019-10-13 and 1.0.4 dated 2020-02-09
DESCRIPTION | 8 MD5 | 32 - README.md | 40 +- build/vignette.rds |binary inst/doc/raceland-intro1.R | 44 +- inst/doc/raceland-intro1.html | 188 ++++----- inst/doc/raceland-intro2.R | 44 +- inst/doc/raceland-intro2.html | 345 ++++++++--------- inst/doc/raceland-intro3.R | 8 inst/doc/raceland-intro3.html | 609 +++++++++++++++---------------- inst/results/grid_sf.rda |binary man/calculate_metrics.Rd | 15 man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/raceland-package.Rd | 2 tests/testthat/test-results.R | 2 17 files changed, 671 insertions(+), 666 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-31 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-08 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-13 0.11.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-09 0.1.18
2018-10-14 0.1.14
Title: A Mixture Model-Based Approach to the Clustering of Microarray
Expression Data
Description: Provides unsupervised selection and clustering of microarray data
using mixture models. Following the methods described in McLachlan, Bean and
Peel (2002) <doi:10.1093/bioinformatics/18.3.413> a subset of genes are selected
based one the likelihood ratio statistic for the test of one versus two
components when fitting mixtures of t-distributions to the expression data
for each gene. The dimensionality of this gene subset is further reduced through
the use of mixtures of factor analyzers, allowing the tissue samples to be
clustered by fitting mixtures of normal distributions.
Author: Andrew Thomas Jones
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>
Diff between EMMIXgene versions 0.1.1 dated 2019-01-04 and 0.1.2 dated 2020-02-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/EMMIXgene.pdf.asis | 2 -- man/plot_single_gene.Rd | 6 +++--- man/select_genes.Rd | 4 ++-- src/emmix.cpp | 15 +++------------ vignettes/EMMIXgene.pdf.asis | 2 -- 9 files changed, 24 insertions(+), 33 deletions(-)