Title: Parallel Use of Statistical Packages in Teaching
Description: When teaching statistics, it can often be desirable to
uncouple the content from specific software packages. To ease such
efforts, the Rosetta Stats website (<https://rosettastats.com>) allows
comparing analyses in different packages. This package is the companion
to the Rosetta Stats website, aiming to provide functions that produce
output that is similar to output from other statistical packages, thereby
facilitating 'software-agnostic' teaching of statistics.
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>),
Ron Pat-El [ctb] (<https://orcid.org/0000-0002-4742-0163>),
Peter Verboon [ctb] (<https://orcid.org/0000-0001-8656-0890>),
Melissa Gordon Wolf [ctb] (<https://orcid.org/0000-0001-7677-0659>)
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@behaviorchange.eu>
Diff between rosetta versions 0.3.8 dated 2021-10-30 and 0.3.9 dated 2021-11-13
DESCRIPTION | 15 ++++++++------- MD5 | 8 +++++--- NAMESPACE | 1 + R/descr.R | 6 +++++- R/scatterPlot.R |only man/scatterPlot.Rd |only 6 files changed, 19 insertions(+), 11 deletions(-)
Title: A Collection of Utilities
Description: This is a new version of the 'userfriendlyscience' package,
which has grown a bit unwieldy. Therefore, distinct functionalities
are being 'consciously uncoupled' into different packages. This package
contains the general-purpose tools and utilities (see the
'behaviorchange' package, the 'rosetta' package, and the
soon-to-be-released 'scd' package for other functionality), and
is the most direct 'successor' of the original 'userfriendlyscience' package.
For example, this package contains a number of basic functions to create
higher level plots, such as diamond plots, to easily plot sampling
distributions, to generate confidence intervals, to plan study sample sizes
for confidence intervals, and to do some basic operations such as
(dis)attenuate effect size estimates.
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>),
Stefan Gruijters [ctb] (<https://orcid.org/0000-0003-0141-0071>)
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@behaviorchange.eu>
Diff between ufs versions 0.4.3 dated 2021-02-01 and 0.5.2 dated 2021-11-13
DESCRIPTION | 20 +++++++++--------- MD5 | 51 ++++++++++++++++++++++++++++++++++------------ NAMESPACE | 12 ++++++++++ R/BAC_plot.R |only R/addToLog.R |only R/carelessReport.R | 4 +++ R/checkDataIntegrity.R |only R/checkPkgs.R | 16 +++++++++----- R/descr.R | 4 +-- R/exceptionalScore.R |only R/exceptionalScores.R |only R/exportToHTML.R | 2 - R/fa_failsafe.R | 6 ++++- R/ggPie.R |only R/ggProportionPlot.R | 5 +++- R/insertNumberedCaption.R | 14 ++++++++++-- R/invertItem.R |only R/invertItems.R |only R/pwr.omegasq.R |only R/rbind_df_list.R |only R/rbind_dfs.R |only R/scatterMatrix.R | 4 +++ R/simDataSet.R |only R/wrapVector.R |only README.md | 4 +-- build/partial.rdb |binary inst/CITATION |only man/BAC_plot.Rd |only man/checkDataIntegrity.Rd |only man/checkPkgs.Rd | 4 ++- man/exceptionalScore.Rd |only man/exceptionalScores.Rd |only man/ggPie.Rd |only man/invertingItems.Rd |only man/pwr.omegasq.Rd |only man/rbind_df_list.Rd |only man/rbind_dfs.Rd |only man/simDataSet.Rd |only man/wrapVector.Rd |only 39 files changed, 107 insertions(+), 39 deletions(-)
Title: Analysis of Multiple Time Course Data
Description: Contains general data structures and
functions for longitudinal data with multiple variables,
repeated measurements, and irregularly spaced time points.
Also implements a shrinkage estimator of dynamical correlation
and dynamical covariance.
Author: Rainer Opgen-Rhein and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between longitudinal versions 1.1.12 dated 2015-07-08 and 1.1.13 dated 2021-11-13
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS | 5 +++++ man/dyn.cor.Rd | 9 +++++---- man/dyn.scale.Rd | 5 ++--- man/longitudinal.Rd | 2 +- man/longitudinal.package.Rd | 4 ++-- man/longitudinal.util.Rd | 2 +- 8 files changed, 29 insertions(+), 24 deletions(-)
Title: Estimation of (Local) False Discovery Rates and Higher Criticism
Description: Estimates both tail area-based false
discovery rates (Fdr) as well as local false discovery rates (fdr) for a
variety of null models (p-values, z-scores, correlation coefficients,
t-scores). The proportion of null values and the parameters of the null
distribution are adaptively estimated from the data. In addition, the package
contains functions for non-parametric density estimation (Grenander estimator),
for monotone regression (isotonic regression and antitonic regression with weights),
for computing the greatest convex minorant (GCM) and the least concave majorant (LCM),
for the half-normal and correlation distributions, and for computing
empirical higher criticism (HC) scores and the corresponding decision threshold.
Author: Bernd Klaus and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between fdrtool versions 1.2.16 dated 2021-01-06 and 1.2.17 dated 2021-11-13
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 6 ++++++ man/dcor0.Rd | 2 +- man/fdrtool.Rd | 2 +- man/gcmlcm.Rd | 2 +- man/grenander.Rd | 2 +- man/hc.score.Rd | 2 +- man/monoreg.Rd | 2 +- man/pval.estimate.eta0.Rd | 2 +- 10 files changed, 27 insertions(+), 21 deletions(-)
Title: Alpha and Beta Proximity to Irreplaceability
Description: Functions to measure Alpha and Beta Proximity to Irreplaceability.
The methods for Alpha and Beta irreplaceability were first described in:
Baisero D., Schuster R. & Plumptre A.J.
Redefining and Mapping Global Irreplaceability.
Conservation Biology 2021;1-11.
<doi:10.1111/cobi.13806>.
Author: Daniele Baisero [aut, cre, cph]
(<https://orcid.org/0000-0002-1266-7174>)
Maintainer: Daniele Baisero <daniele.baisero@gmail.com>
Diff between proxirr versions 0.1 dated 2021-10-20 and 0.2 dated 2021-11-13
DESCRIPTION | 10 +++++----- MD5 | 15 +++++++++++---- NAMESPACE | 6 ++++++ R/marxan.R |only README.md | 11 ++++++++--- build/partial.rdb |binary man/dot-marxan_alpha_parameters.Rd |only man/dot-marxan_data_reader.Rd |only man/dot-marxan_input_parameter.Rd |only man/marxan_alphas.Rd |only man/marxan_betas.Rd |only man/marxan_run.Rd |only 12 files changed, 30 insertions(+), 12 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Description: For one-way layout experiments the one-way ANOVA can
be performed as an omnibus test. All-pairs multiple comparisons
tests (Tukey-Kramer test, Scheffe test, LSD-test)
and many-to-one tests (Dunnett test) for normally distributed
residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test,
Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one
(Tamhane-Dunnett Test) for normally distributed residuals
and heterogeneous variances are provided. Van der Waerden's normal
scores test for omnibus, all-pairs and many-to-one tests is
provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling
omnibus test and all-pairs tests
(Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow-
Fligner test) as well as many-to-one (Nemenyi test, Dunn test,
U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test,
Johnson-Mehrotra test, Spearman test) are included.
In addition, a Friedman-test for one-way ANOVA with repeated
measures on ranks (CRBD) and Skillings-Mack test for unbalanced
CRBD is provided with consequent all-pairs tests (Nemenyi test,
Siegel test, Miller test, Conover test, Exact test)
and many-to-one tests (Nemenyi test, Demsar test, Exact test).
A trend can be tested with Pages's test. Durbin's test
for a two-way balanced incomplete block design (BIBD) is given
in this package as well as Gore's test for CRBD with multiple
observations per cell is given. Outlier tests, Mandel's k- and
h statistic as well as functions for Type I error and Power
analysis as well as generic summary, print and plot methods
are provided.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMRplus versions 1.9.2 dated 2021-10-13 and 1.9.3 dated 2021-11-13
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- R/manyOneUTest.R | 17 ++++++++++++----- R/sysdata.rda |binary build/partial.rdb |binary build/vignette.rds |binary data/Pentosan.rda |binary data/algae.rda |binary data/qPCR.rda |binary data/reviewers.rda |binary data/trout.rda |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/QuickReferenceGuide.html | 4 ++-- man/kwManyOneConoverTest.Rd | 5 +++++ man/kwManyOneDunnTest.Rd | 5 +++++ man/kwManyOneNdwTest.Rd | 5 +++++ man/manyOneUTest.Rd | 31 +++++++++++++++++++++++++++++++ 17 files changed, 88 insertions(+), 27 deletions(-)
Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem.
'memoiR' makes it easy.
It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>)
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 1.1-2 dated 2021-09-03 and 1.1-3 dated 2021-11-13
DESCRIPTION | 8 +- MD5 | 38 +++++----- NEWS.md | 22 +++++ R/memoiR.R | 8 +- README.md | 3 build/vignette.rds |binary inst/doc/memoiR.Rmd | 6 - inst/doc/memoiR.html | 6 - inst/rmarkdown/templates/beamer_presentation/skeleton/skeleton.Rmd | 1 inst/rmarkdown/templates/memoir/skeleton/81-getting_started.Rmd | 17 +++- inst/rmarkdown/templates/memoir/skeleton/_output.yml | 5 + inst/rmarkdown/templates/memoir/skeleton/index.Rmd | 11 ++ inst/rmarkdown/templates/simple_article/skeleton/latex/template.tex | 4 - inst/rmarkdown/templates/simple_article/skeleton/skeleton.Rmd | 26 ++++++ inst/rmarkdown/templates/stylish_article/skeleton/latex/template.tex | 4 - inst/rmarkdown/templates/stylish_article/skeleton/skeleton.Rmd | 11 ++ man/Knit.Rd | 2 man/add_font.Rd | 38 +++++----- man/add_hyphen.Rd | 38 +++++----- vignettes/memoiR.Rmd | 6 - 20 files changed, 166 insertions(+), 88 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre] (<https://orcid.org/0000-0003-4072-6263>)
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between stevedata versions 0.5.0 dated 2021-09-08 and 0.6.0 dated 2021-11-13
DESCRIPTION | 8 ++++---- MD5 | 27 +++++++++++++++------------ NEWS.md | 12 ++++++++++++ R/rd-clemson_temps.R | 11 ++++------- R/rd-co2emissions.R | 1 - R/rd-usa_migration.R | 4 ++++ R/rd-voteincome.R |only README.md | 4 +++- data/clemson_temps.rda |binary data/turnips.rda |binary data/usa_migration.rda |binary data/voteincome.rda |only man/clemson_temps.Rd | 11 ++++------- man/co2emissions.Rd | 1 - man/usa_migration.Rd | 5 +++++ man/voteincome.Rd |only 16 files changed, 51 insertions(+), 33 deletions(-)
Title: Odds Plot to Visualise a Logistic Regression Model
Description: Uses the outputs of a logistic regression model, from caret <https://CRAN.R-project.org/package=caret>, to build an odds plot.
This allows for the rapid visualisation of odds plot ratios and works best with the outputs of CARET's GLM model class, by returning the final trained model.
Author: Gary Hutson [aut, cre] (<https://orcid.org/0000-0003-3534-6143>)
Maintainer: Gary Hutson <hutsons-hacks@outlook.com>
Diff between OddsPlotty versions 1.0.1 dated 2021-06-22 and 1.0.2 dated 2021-11-13
DESCRIPTION | 11 +-- MD5 | 17 ++--- NEWS.md | 2 R/OddsPlotR.R.R | 12 ++- inst/doc/introduction.R | 36 +++++++++- inst/doc/introduction.Rmd | 55 +++++++++++++++- inst/doc/introduction.html | 129 +++++++++++++++++++++++++++++++++------ man/figures/OddsPlotGraph-01.PNG |only man/odds_plot.Rd | 8 ++ vignettes/introduction.Rmd | 55 +++++++++++++++- 10 files changed, 275 insertions(+), 50 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented wing2015() for
segment_snags()),
Bourdon Jean-François [ctb] (Contributed to Roussel2020() for
track_sensor()),
Gatziolis Demetrios [ctb] (Implemented Gatziolis2019() for
track_sensor()),
Leon Steinmeier [ctb] (Contributed to parallelization management),
Stanislaw Adaszewski [cph] (Author of the C++ concaveman code)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 3.2.2 dated 2021-10-20 and 3.2.3 dated 2021-11-13
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/io_readLAScatalog.R | 2 +- README.md | 2 +- man/find_trees.Rd | 9 +++++---- man/segment_trees.Rd | 9 +++++---- src/RcppFunction.cpp | 22 +++++++++++++--------- tests/testthat/Rplots.pdf |binary tests/testthat/test-find_trees.R | 2 +- 10 files changed, 43 insertions(+), 32 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-28 0.3
2017-06-02 0.2
2017-02-27 0.1
Title: Distributions for Generalized Additive Models for Location Scale
and Shape
Description: A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a ''log'' or a ''logit' transformation respectively.
Author: Mikis Stasinopoulos [aut, cre, cph],
Robert Rigby [aut],
Calliope Akantziliotou [ctb],
Vlasios Voudouris [ctb],
Gillian Heller [ctb],
Fernanda De Bastiani [ctb],
Raydonal Ospina [ctb],
Nicoletta Motpan [ctb],
Fiona McElduff [ctb],
Majid Djennad [ctb],
Marco Enea [ctb],
Alexios Ghalanos [ctb],
Christos Argyropoulos [ctb],
Almond Stocker [ctb],
Jens Lichter [ctb],
Stanislaus Stadlmann [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.dist versions 5.3-2 dated 2021-03-09 and 6.0-1 dated 2021-11-13
DESCRIPTION | 8 MD5 | 256 +++++++++++----------- R/BB.R | 2 R/BEINF.R | 468 ++++++++++++++++++++--------------------- R/BI.R | 2 R/BNB.R | 2 R/DELAPORT.R | 2 R/DoubleBinomial.R | 2 R/DoublePoisson-30-12-14.R | 2 R/Functions_for_SK_in_gamlss.R | 43 +-- R/GEOM.R | 2 R/GEOMo.R | 2 R/LG.R | 2 R/MN3.R | 218 +++++++++---------- R/MN4.R | 262 +++++++++++----------- R/MN5.R | 346 +++++++++++++++--------------- R/NBF.R | 2 R/NBI.R | 2 R/NBII.R | 2 R/PIG2.R | 2 R/SI.R | 2 R/SICHEL-10-09-12.R | 2 R/WARING_BOB.r | 4 R/YULE.R | 2 R/ZABB.R | 2 R/ZABI.R | 2 R/ZABNB.R | 2 R/ZALG.R | 2 R/ZANBI.R | 2 R/ZAP.R | 2 R/ZAPIG.R | 2 R/ZASICHEL.R | 2 R/ZAZIPF.R | 2 R/ZIBB.R | 2 R/ZIBI.R | 2 R/ZIBNB.R | 2 R/ZINBF.R | 2 R/ZINBI.R | 2 R/ZIP.R | 2 R/ZIP2.R | 2 R/ZIPF.R | 2 R/ZIPIG.R | 2 R/ZISICHEL.R | 2 R/discBURR12.R | 2 R/po.r | 2 build/partial.rdb |binary man/BB.Rd | 8 man/BCCG.Rd | 12 - man/BCPE.Rd | 9 man/BCt.Rd | 14 - man/BE.Rd | 9 man/BEINF.Rd | 8 man/BEOI.Rd | 9 man/BEZI.Rd | 9 man/BI.Rd | 8 man/BNB.Rd | 9 man/DBI.Rd | 10 man/DBURR12.Rd | 11 man/DEL.Rd | 8 man/DPO.Rd | 10 man/EGB2.Rd | 8 man/EXP.Rd | 8 man/GA.Rd | 7 man/GAF.Rd | 9 man/GB1.Rd | 9 man/GB2.Rd | 6 man/GEOM.Rd | 10 man/GG.Rd | 7 man/GIG.Rd | 8 man/GPO.Rd | 8 man/GT.Rd | 7 man/GU.rd | 7 man/IG.Rd | 8 man/IGAMMA.Rd | 8 man/JSU.Rd | 9 man/JSUoriginal.Rd | 7 man/LG.Rd | 9 man/LNO.Rd | 9 man/LOGISTIC.Rd | 7 man/LOGITNO.Rd | 7 man/LQNO.Rd | 3 man/Multinomial.Rd | 10 man/NBF.Rd | 13 - man/NBI.Rd | 8 man/NBII.Rd | 12 - man/NET.Rd | 14 - man/NO.Rd | 9 man/NO2.Rd | 7 man/NOF.Rd | 13 - man/PARETO2.Rd | 9 man/PE.Rd | 8 man/PIG.Rd | 12 - man/PO.Rd | 15 - man/RG.Rd | 8 man/RGE.Rd | 7 man/SEP.Rd | 9 man/SEP1.Rd | 7 man/SHASH.Rd | 7 man/SI.Rd | 10 man/SICHEL.Rd | 17 - man/SIMPLEX.Rd | 10 man/SN1.Rd | 7 man/SN2.Rd | 8 man/ST1.Rd | 11 man/TF.Rd | 3 man/WARING.Rd | 8 man/WEI.Rd | 9 man/WEI2.Rd | 9 man/WEI3.Rd | 9 man/YULE.Rd | 10 man/ZABB.Rd | 7 man/ZABI.Rd | 9 man/ZAGA.Rd | 10 man/ZAIG.Rd | 13 - man/ZANBI.Rd | 10 man/ZAP.Rd | 9 man/ZIP.Rd | 9 man/ZIP2.Rd | 9 man/ZIPF.Rd | 10 man/checklink.Rd | 7 man/count_1_31.Rd | 8 man/exGAUS.Rd | 7 man/flexDist.Rd | 10 man/gamlss.dist-package.Rd | 13 - man/gamlss.family.Rd | 14 - man/gen.Family.Rd | 8 man/hazardFun.Rd | 6 man/make.link.gamlss.Rd | 7 man/momentSK.Rd | 15 - 129 files changed, 1309 insertions(+), 1125 deletions(-)
Title: Doubly Robust Difference-in-Differences Estimators
Description: Implements the locally efficient doubly robust difference-in-differences (DiD)
estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020)
<doi:10.1016/j.jeconom.2020.06.003>. The estimator combines inverse probability weighting and outcome
regression estimators (also implemented in the package) to form estimators with
more attractive statistical properties. Two different estimation methods can be used
to estimate the nuisance functions.
Author: Pedro H. C. Sant'Anna [aut, cre],
Jun Zhao [aut]
Maintainer: Pedro H. C. Sant'Anna <pedro.h.santanna@vanderbilt.edu>
Diff between DRDID versions 1.0.1 dated 2021-01-07 and 1.0.3 dated 2021-11-13
DESCRIPTION | 12 MD5 | 80 +++--- NEWS.md | 38 +- R/drdid.R | 4 R/drdid_imp_panel.R | 4 R/drdid_panel.R | 4 R/ipw_did_panel.R | 4 R/ipwdid.R | 4 R/ordid.R | 5 R/pre_process_drdid.R | 484 ++++++++++++++++++++----------------- R/reg_did_panel.R | 4 R/std_ipw_did_panel.R | 4 R/twfe_did_panel.R | 4 README.md | 119 ++++----- build/partial.rdb |binary data/nsw.rda |binary data/nsw_long.rda |binary data/sim_rc.rda |binary inst/WORDLIST | 1 man/DRDID-package.Rd | 44 +-- man/drdid.Rd | 310 ++++++++++++------------ man/drdid_imp_panel.Rd | 204 ++++++++-------- man/drdid_imp_rc.Rd | 190 +++++++------- man/drdid_imp_rc1.Rd | 192 +++++++-------- man/drdid_panel.Rd | 178 +++++++------ man/drdid_rc.Rd | 166 ++++++------- man/drdid_rc1.Rd | 170 ++++++------- man/ipw_did_panel.Rd | 160 ++++++------ man/ipw_did_rc.Rd | 146 +++++------ man/ipwdid.Rd | 232 +++++++++--------- man/nsw.Rd | 104 ++++---- man/nsw_long.Rd | 104 ++++---- man/ordid.Rd | 229 +++++++++-------- man/reg_did_panel.Rd | 178 +++++++------ man/reg_did_rc.Rd | 164 ++++++------ man/sim_rc.Rd | 82 +++--- man/std_ipw_did_panel.Rd | 162 ++++++------ man/std_ipw_did_rc.Rd | 148 +++++------ man/twfe_did_panel.Rd | 136 +++++----- man/twfe_did_rc.Rd | 124 ++++----- tests/testthat/test_errors.R | 548 +++++++++++++++++++++---------------------- 41 files changed, 2425 insertions(+), 2317 deletions(-)
Title: Methods and Data for Spatial Epidemiology
Description: Methods and data for cluster detection and disease mapping.
Author: Cici Chen [ctb],
Albert Y. Kim [aut, cre] (<https://orcid.org/0000-0001-7824-306X>),
Michelle Ross [ctb],
Jon Wakefield [aut],
Mikael Moise [aut] (<https://orcid.org/0000-0002-3608-1178>)
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between SpatialEpi versions 1.2.5 dated 2021-08-02 and 1.2.6 dated 2021-11-13
DESCRIPTION | 6 +- MD5 | 24 +++++----- NEWS.md | 5 ++ R/grid2latlong.R | 2 R/latlong2grid.R | 4 - R/polygon2spatial_polygon.R | 6 +- data/scotland.rda |binary inst/doc/install_geo_libraries.html | 4 - man/polygon2spatial_polygon.Rd | 4 - vignettes/Manuscript/Manuscript.Rmd | 80 ++++++++++++++++++---------------- vignettes/Manuscript/bibliography.bib |only vignettes/Manuscript/ieee.csl |only vignettes/Manuscript/wlpeerj.cls | 7 +- vignettes/Old_Vignette/SpatialEpi.Rnw | 3 - 14 files changed, 80 insertions(+), 65 deletions(-)
Title: Creates Statistical Reports
Description: Contains functions to create regulatory-style statistical reports.
Originally designed to create tables, listings, and figures for the
pharmaceutical, biotechnology, and medical device industries, these
reports are generalized enough that they could be used in any industry.
Generates text, rich-text, PDF and HTML file formats. The package specializes
in printing wide and long tables with automatic page wrapping and splitting.
Reports can be produced with a minimum of function calls, and without
relying on other table packages. The package supports titles, footnotes,
page header, page footers, spanning headers, page by variables,
and automatic page numbering.
Author: David Bosak [aut, cre],
Kevin Kramer [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between reporter versions 1.2.0 dated 2021-10-10 and 1.2.6 dated 2021-11-13
DESCRIPTION | 8 MD5 | 201 +++++++++++------ NEWS.md | 18 + R/create_table_html.R |only R/create_table_rtf.R | 72 +++++- R/graphics_utilities.R | 38 +++ R/page_template_html.R |only R/page_template_rtf.R | 34 ++- R/plot_spec.R | 210 +++++++++++++++++- R/report_spec.r | 103 ++++++--- R/reporter.R | 25 +- R/table_spec.r | 11 R/text_spec.R | 145 ++++++++++++ R/utilities.R | 145 ++++++++++-- R/write_pdf.R | 2 R/write_report_html.R |only R/write_report_rtf.R | 8 R/write_report_rtf2.R | 70 ++++-- README.md | 2 build/vignette.rds |binary inst/doc/reporter-figure.Rmd | 7 inst/doc/reporter-figure.html | 6 inst/doc/reporter-fonts.R |only inst/doc/reporter-fonts.Rmd |only inst/doc/reporter-fonts.html |only inst/doc/reporter-rtf.Rmd | 14 - inst/doc/reporter-rtf.html | 12 - inst/doc/reporter-title_header.Rmd | 2 inst/doc/reporter-title_header.html | 2 inst/doc/reporter.Rmd | 18 - inst/doc/reporter.html | 12 - man/add_content.Rd | 230 ++++++++++---------- man/create_report.Rd | 15 - man/create_table.Rd | 7 man/images/fonts.png |only man/options_fixed.Rd | 7 man/reporter.Rd | 25 +- man/titles.Rd | 15 + man/write_report.Rd | 255 +++++++++++----------- tests/testthat/html |only tests/testthat/pdf/test1.pdf | 4 tests/testthat/pdf/test10.pdf | 4 tests/testthat/pdf/test11.pdf | 4 tests/testthat/pdf/test12.pdf | 4 tests/testthat/pdf/test13.pdf |only tests/testthat/pdf/test14.pdf | 4 tests/testthat/pdf/test15.pdf | 4 tests/testthat/pdf/test16.pdf | 4 tests/testthat/pdf/test17.pdf | 4 tests/testthat/pdf/test18.pdf | 4 tests/testthat/pdf/test19.pdf | 4 tests/testthat/pdf/test2.pdf | 4 tests/testthat/pdf/test21.pdf | 4 tests/testthat/pdf/test22.pdf | 4 tests/testthat/pdf/test23.pdf | 4 tests/testthat/pdf/test24.pdf | 4 tests/testthat/pdf/test25.pdf | 4 tests/testthat/pdf/test26.pdf | 4 tests/testthat/pdf/test27.pdf | 4 tests/testthat/pdf/test28.pdf | 4 tests/testthat/pdf/test29.pdf |only tests/testthat/pdf/test3.pdf | 4 tests/testthat/pdf/test30.pdf |only tests/testthat/pdf/test31.pdf |only tests/testthat/pdf/test32.pdf |only tests/testthat/pdf/test4.pdf | 4 tests/testthat/pdf/test5.pdf | 4 tests/testthat/pdf/test6.pdf | 4 tests/testthat/pdf/test7.pdf | 4 tests/testthat/pdf/test8.pdf | 4 tests/testthat/pdf/test9.pdf | 4 tests/testthat/rtf/test34.rtf |only tests/testthat/rtf/test35.rtf |only tests/testthat/rtf/test36.rtf |only tests/testthat/rtf/test37.rtf |only tests/testthat/rtf2/test1.rtf | 4 tests/testthat/rtf2/test15.rtf | 350 +++++++++++++++---------------- tests/testthat/rtf2/test45.rtf |only tests/testthat/rtf2/test46.rtf |only tests/testthat/rtf2/test47.rtf |only tests/testthat/rtf2/test48.rtf |only tests/testthat/rtf2/test49.rtf |only tests/testthat/rtf2/test50.rtf |only tests/testthat/rtf2/test6.rtf | 36 +-- tests/testthat/test-create_table_html.R |only tests/testthat/test-html.R |only tests/testthat/test-page_template_html.R |only tests/testthat/test-page_template_rtf.R | 7 tests/testthat/test-pdf.R | 87 +++++++ tests/testthat/test-report_spec.R | 15 + tests/testthat/test-rtf.R | 87 +++++++ tests/testthat/test-rtf2.R | 174 ++++++++++++++- tests/testthat/test-system_text.R | 5 tests/testthat/test-text_spec.R | 10 tests/testthat/test-utilities.R | 33 ++ tests/testthat/test-write_report_text.R | 25 ++ vignettes/reporter-figure.Rmd | 7 vignettes/reporter-fonts.Rmd |only vignettes/reporter-rtf.Rmd | 14 - vignettes/reporter-title_header.Rmd | 2 vignettes/reporter.Rmd | 18 - 101 files changed, 1906 insertions(+), 791 deletions(-)
Title: Penalized Cox Proportional Hazard Model for Time-Dependent
Covariates
Description: Fits penalized models for both time-independent and time-dependent survival data. It fully implements elastic net and uses proximal gradient descent to solve the optimization problem. The package is an implementation of Steve Cygu and Benjamin M. Bolker. (2021) <arXiv:2102.02297>.
Author: Bicko Cygu [aut, cre] (<https://orcid.org/0000-0002-9284-8863>),
Ben Bolker [aut] (<https://orcid.org/0000-0002-2127-0443>),
Trevor Hastie [cph] (getmin function implementation copied from package
glmnet)
Maintainer: Bicko Cygu <cygubicko@gmail.com>
Diff between pcoxtime versions 1.0.2 dated 2021-07-06 and 1.0.3 dated 2021-11-13
DESCRIPTION | 28 +++--- MD5 | 23 +++-- NAMESPACE | 6 + R/methodfuns.R | 9 + R/pcoxtime.R | 2 R/pcoxtimecv.R | 16 ++- R/pcoxtimeplots.R | 76 ++++++++++++++++ R/posthocfuns.R | 215 +++++++++++++++++++++++++++++++++++++++++++++++ build |only man/coefvimp.pcoxtime.Rd |only man/pcoxtimecv.Rd | 2 man/plot.varimp.Rd |only man/pvimp.pcoxtime.Rd |only man/varimp.pcoxtime.Rd |only src/RcppExports.cpp | 5 + 15 files changed, 356 insertions(+), 26 deletions(-)
Title: Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging
Description: Bayesian Model Averaging to create probabilistic forecasts
from ensemble forecasts and weather observations
<https://stat.uw.edu/sites/default/files/files/reports/2007/tr516.pdf>.
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann
Gneiting, University of Washington.
Maintainer: Chris Fraley <fraley@u.washington.edu>
Diff between ensembleBMA versions 5.1.6 dated 2021-10-02 and 5.1.7 dated 2021-11-13
ensembleBMA-5.1.6/ensembleBMA/R/matchEnsembleMembers.default.R |only ensembleBMA-5.1.6/ensembleBMA/R/matchEnsembleMembers.ensembleBMAgamma.R |only ensembleBMA-5.1.6/ensembleBMA/R/matchEnsembleMembers.ensembleBMAgamma0.R |only ensembleBMA-5.1.6/ensembleBMA/R/matchEnsembleMembers.ensembleBMAnormal.R |only ensembleBMA-5.1.6/ensembleBMA/R/matchEnsembleMembers.fitBMAgamma.R |only ensembleBMA-5.1.6/ensembleBMA/R/matchEnsembleMembers.fitBMAgamma0.R |only ensembleBMA-5.1.6/ensembleBMA/R/matchEnsembleMembers.fitBMAnormal.R |only ensembleBMA-5.1.6/ensembleBMA/R/matchITandFH.default.R |only ensembleBMA-5.1.7/ensembleBMA/CHANGELOG | 4 ensembleBMA-5.1.7/ensembleBMA/DESCRIPTION | 11 ensembleBMA-5.1.7/ensembleBMA/MD5 | 46 ensembleBMA-5.1.7/ensembleBMA/R/dataNA.ensembleData.R | 1 ensembleBMA-5.1.7/ensembleBMA/R/ensembleBMAgamma.R | 5 ensembleBMA-5.1.7/ensembleBMA/R/ensembleBMAgamma0.R | 5 ensembleBMA-5.1.7/ensembleBMA/R/ensembleBMAnormal.R | 4 ensembleBMA-5.1.7/ensembleBMA/R/ensembleForecasts.ensembleData.R | 2 ensembleBMA-5.1.7/ensembleBMA/R/fitBMAgamma.R | 462 ++++------ ensembleBMA-5.1.7/ensembleBMA/R/fitBMAgamma0.R | 56 - ensembleBMA-5.1.7/ensembleBMA/R/fitBMAnormal.R | 14 ensembleBMA-5.1.7/ensembleBMA/R/matchEnsembleMembers.R | 268 +++++ ensembleBMA-5.1.7/ensembleBMA/R/matchITandFH.R | 38 ensembleBMA-5.1.7/ensembleBMA/R/quantileForecast.fitBMAnormal.R | 91 - ensembleBMA-5.1.7/ensembleBMA/R/subset.ensembleBMAnormal.R | 32 ensembleBMA-5.1.7/ensembleBMA/man/ensembleBMA.Rd | 17 ensembleBMA-5.1.7/ensembleBMA/man/ensembleBMAnormal.Rd | 1 ensembleBMA-5.1.7/ensembleBMA/man/ensembleData.Rd | 2 ensembleBMA-5.1.7/ensembleBMA/man/fitBMA.Rd | 10 ensembleBMA-5.1.7/ensembleBMA/man/fitBMAnormal.Rd | 6 28 files changed, 645 insertions(+), 430 deletions(-)
Title: Bayesian Generalized Linear Regression
Description: Bayesian Generalized Linear Regression.
Author: Gustavo de los Campos, Paulino Perez Rodriguez
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Diff between BGLR versions 1.0.8 dated 2018-11-11 and 1.0.9 dated 2021-11-13
BGLR-1.0.8/BGLR/build |only BGLR-1.0.8/BGLR/inst/doc/BGLR-extdoc.Rnw |only BGLR-1.0.8/BGLR/man/figures |only BGLR-1.0.9/BGLR/CHANGELOG | 40 +++++- BGLR-1.0.9/BGLR/DESCRIPTION | 12 -- BGLR-1.0.9/BGLR/MD5 | 71 ++++++++---- BGLR-1.0.9/BGLR/NAMESPACE | 27 +++- BGLR-1.0.9/BGLR/R/BGLR.R | 134 ++++++++++++++--------- BGLR-1.0.9/BGLR/R/BLRCross.R |only BGLR-1.0.9/BGLR/R/Multitrait.R |only BGLR-1.0.9/BGLR/R/utils.R | 51 +++++++- BGLR-1.0.9/BGLR/data/datalist | 5 BGLR-1.0.9/BGLR/data/simulated3t.RData |only BGLR-1.0.9/BGLR/demo/Bernoulli.R | 4 BGLR-1.0.9/BGLR/inst/doc/BGLR-extdoc.pdf |binary BGLR-1.0.9/BGLR/inst/md/BRR_UN_RKHS_UN.md |only BGLR-1.0.9/BGLR/inst/md/BRR_UN_UN.md |only BGLR-1.0.9/BGLR/inst/md/GBLUP.md | 82 +++++++++++++- BGLR-1.0.9/BGLR/inst/md/GxE_usingInteractions.md | 43 +++++++ BGLR-1.0.9/BGLR/inst/md/MULTITRAIT.md |only BGLR-1.0.9/BGLR/inst/md/RKHS_FA_DIAG.md |only BGLR-1.0.9/BGLR/inst/md/RKHS_FIXED_UN_UN.md |only BGLR-1.0.9/BGLR/inst/md/RKHS_REC_DIAG.md |only BGLR-1.0.9/BGLR/inst/md/RKHS_UN_DIAG.md |only BGLR-1.0.9/BGLR/inst/md/RKHS_UN_UN.md |only BGLR-1.0.9/BGLR/inst/md/SS_UN_UN.md |only BGLR-1.0.9/BGLR/inst/md/heritability.md | 22 ++- BGLR-1.0.9/BGLR/inst/md/setMethods.md |only BGLR-1.0.9/BGLR/inst/md/tesingEffects.md |only BGLR-1.0.9/BGLR/inst/md/variancePartition.md |only BGLR-1.0.9/BGLR/man/BFDR.Rd |only BGLR-1.0.9/BGLR/man/BGLR.Rd | 26 ++-- BGLR-1.0.9/BGLR/man/BLRCross.Rd |only BGLR-1.0.9/BGLR/man/BLRXy.Rd |only BGLR-1.0.9/BGLR/man/Multitrait.Rd |only BGLR-1.0.9/BGLR/man/getGCovar.Rd |only BGLR-1.0.9/BGLR/man/mice.Rd | 1 BGLR-1.0.9/BGLR/man/readBinMat.Rd | 3 BGLR-1.0.9/BGLR/man/readBinMatMultitrait.Rd |only BGLR-1.0.9/BGLR/man/simulated3t.Rd |only BGLR-1.0.9/BGLR/man/simulated3t.X.Rd |only BGLR-1.0.9/BGLR/man/simulated3t.pheno.Rd |only BGLR-1.0.9/BGLR/man/vech.Rd |only BGLR-1.0.9/BGLR/man/wheat.A.Rd | 2 BGLR-1.0.9/BGLR/man/wheat.Rd | 2 BGLR-1.0.9/BGLR/man/xpnd.Rd |only BGLR-1.0.9/BGLR/src/Makevars | 4 BGLR-1.0.9/BGLR/src/Makevars.win | 4 BGLR-1.0.9/BGLR/src/init.c | 25 +++- BGLR-1.0.9/BGLR/src/sampler_multitrait.c |only BGLR-1.0.9/BGLR/src/util_sample_cross.c |only BGLR-1.0.9/BGLR/vignettes/BGLR-extdoc.Rnw | 4 52 files changed, 417 insertions(+), 145 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides
C implementations of the association mining algorithms Apriori and Eclat.
Hahsler, Gruen and Hornik (2005) <doi:10.18637/jss.v014.i15>.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Ian Johnson [ctb, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.6-8 dated 2021-05-17 and 1.7-0 dated 2021-11-13
DESCRIPTION | 10 MD5 | 110 - NAMESPACE | 81 NEWS.md | 35 R/AAADefs.R | 3 R/AllClasses.R | 1 R/AllGenerics.R | 13 R/aggregate.R | 61 R/apriori.R | 7 R/check_installed.R |only R/confint.R |only R/crossTable.R | 34 R/discretize.R | 2 R/dissimilarity.R | 18 R/eclat.R | 13 R/inspect.R | 8 R/interestMeasures.R | 998 +++++----- R/is.closed.R | 2 R/is.generator.R |only R/is.maximal.R | 2 R/is.redundant.R | 49 R/is.significant.R | 2 R/itemMatrix.R | 17 R/itemsets.R | 9 R/pmml.R | 4 R/read_write.R | 19 R/rules.R | 22 R/sets.R | 108 - R/transactions.R | 24 README.md | 344 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/arules.pdf |binary man/aggregate.Rd | 42 man/apriori.Rd | 4 man/confint.Rd |only man/crossTable.Rd | 11 man/dissimilarity.Rd | 4 man/eclat.Rd | 3 man/interestMeasure.Rd | 445 ++-- man/is.closed.Rd | 9 man/is.generator.Rd |only man/is.maximal.Rd | 20 man/is.redundant.Rd | 79 man/itemCoding.Rd | 31 man/itemMatrix-class.Rd | 3 man/itemsets-class.Rd | 26 man/rules-class.Rd | 37 man/sets.Rd | 41 man/transactions-class.Rd | 62 man/weclat.Rd | 6 src/rapriori.c | 4 tests/testthat/test-apriori.R | 147 + tests/testthat/test-associations.R | 337 +-- tests/testthat/test-concise.R |only tests/testthat/test-confint.R |only tests/testthat/test-crossTable.R |only tests/testthat/test-interestMeasures.R | 3174 +++++++++++++++++++++++++++++---- tests/testthat/test-sets.R | 4 tests/testthat/test-transactions.R | 15 60 files changed, 4800 insertions(+), 1700 deletions(-)