Title: Decision Analytic Modelling in Health Economics
Description: Classes and functions for modelling health care interventions
using decision trees and semi-Markov models. Mechanisms are provided for
associating an uncertainty distribution with each source variable and for
ensuring transparency of the mathematical relationships between variables.
The package terminology follows Briggs "Decision Modelling for Health
Economic Evaluation" (2006, ISBN:978-0-19-852662-9).
Author: Andrew Sims [aut, cre] (<https://orcid.org/0000-0002-9553-7278>),
Kim Fairbairn [aut] (<https://orcid.org/0000-0001-5108-6279>)
Maintainer: Andrew Sims <andrew.sims@newcastle.ac.uk>
Diff between rdecision versions 1.0.4 dated 2021-05-05 and 1.1.0 dated 2021-09-08
DESCRIPTION | 9 MD5 | 222 +- NAMESPACE | 64 R/Action.R | 281 +- R/Arborescence.R | 1085 ++++----- R/Arrow.R | 88 R/BetaDistribution.R |only R/BetaModVar.R | 133 - R/ChanceNode.R | 17 R/ConstModVar.R | 177 - R/DecisionNode.R | 107 R/DecisionTree.R | 2740 ++++++++++++------------- R/Digraph.R | 881 +++----- R/DiracDistribution.R |only R/DirichletDistribution.R |only R/Distribution.R |only R/Edge.R | 151 - R/ExprModVar.R | 779 +++---- R/GammaDistribution.R |only R/GammaModVar.R | 234 -- R/Graph.R | 811 +++---- R/LeafNode.R | 296 +- R/LogNormDistribution.R |only R/LogNormModVar.R | 278 -- R/MarkovState.R |only R/ModVar.R | 485 ++-- R/Node.R | 99 R/NormModVar.R | 179 - R/NormalDistribution.R |only R/Reaction.R | 284 +- R/SemiMarkovModel.R |only R/Stack.R | 138 - R/Transition.R |only R/data.R |only R/rdecision.R | 39 README.md | 471 +++- build/partial.rdb |binary build/vignette.rds |binary data |only inst/CITATION | 18 inst/NEWS.md | 281 +- inst/REFERENCES.bib | 877 ++++---- inst/WORDLIST | 168 - inst/doc/DT01-Sumatriptan.R | 210 - inst/doc/DT01-Sumatriptan.Rmd | 344 +-- inst/doc/DT01-Sumatriptan.html | 777 +++---- inst/doc/DT02-Tegaderm.R | 490 ++-- inst/doc/DT02-Tegaderm.Rmd | 802 +++---- inst/doc/DT02-Tegaderm.html | 1327 ++++++------ inst/doc/DT03-ShaleGas.R | 160 - inst/doc/DT03-ShaleGas.Rmd | 310 +- inst/doc/DT03-ShaleGas.html | 721 +++--- inst/doc/GT01-NewScientistPuzzle.R | 196 - inst/doc/GT01-NewScientistPuzzle.Rmd | 364 +-- inst/doc/GT01-NewScientistPuzzle.html | 525 ++-- inst/doc/SM01-HIV.R |only inst/doc/SM01-HIV.Rmd |only inst/doc/SM01-HIV.html |only inst/national-institute-of-health-research.csl | 416 +-- man/Action.Rd | 300 +- man/Arborescence.Rd | 483 ++-- man/Arrow.Rd | 210 - man/BetaDistribution.Rd |only man/BetaModVar.Rd | 303 -- man/BriggsEx47.Rd |only man/ChanceNode.Rd | 12 man/ConstModVar.Rd | 313 +- man/DecisionNode.Rd | 7 man/DecisionTree.Rd | 1322 ++++++------ man/Digraph.Rd | 767 +++--- man/DiracDistribution.Rd |only man/DirichletDistribution.Rd |only man/Distribution.Rd |only man/Edge.Rd | 228 +- man/ExprModVar.Rd | 825 +++---- man/GammaDistribution.Rd |only man/GammaModVar.Rd | 343 +-- man/Graph.Rd | 714 +++--- man/LeafNode.Rd | 295 +- man/LogNormDistribution.Rd |only man/LogNormModVar.Rd | 375 +-- man/MarkovState.Rd |only man/ModVar.Rd | 598 ++--- man/Node.Rd | 7 man/NormModVar.Rd | 295 -- man/NormalDistribution.Rd |only man/Reaction.Rd | 299 +- man/SemiMarkovModel.Rd |only man/Stack.Rd | 245 +- man/Transition.Rd |only man/figures/README-sb-1.gv |only man/figures/README-sb-1.png |only man/rdecision.Rd | 14 tests/testthat.R | 8 tests/testthat/setup.R | 156 - tests/testthat/test-Action.R | 84 tests/testthat/test-Arborescence.R | 320 +- tests/testthat/test-Arrow.R | 66 tests/testthat/test-BetaDistribution.R |only tests/testthat/test-BetaModVar.R | 247 +- tests/testthat/test-ChanceNode.R | 20 tests/testthat/test-ConstModVar.R | 102 tests/testthat/test-DecisionNode.R | 18 tests/testthat/test-DecisionTree.R | 1620 +++++++------- tests/testthat/test-Digraph.R | 652 +++-- tests/testthat/test-DiracDistribution.R |only tests/testthat/test-DirichletDistribution.R |only tests/testthat/test-Distribution.R |only tests/testthat/test-Edge.R | 58 tests/testthat/test-ExprModVar.R | 425 ++- tests/testthat/test-GammaDistribution.R |only tests/testthat/test-GammaModVar.R | 170 - tests/testthat/test-Graph.R | 530 ++-- tests/testthat/test-LeafNode.R | 74 tests/testthat/test-LogNormDistribution.R |only tests/testthat/test-LogNormModVar.R | 226 +- tests/testthat/test-MarkovState.R |only tests/testthat/test-ModVar.R | 230 +- tests/testthat/test-Node.R | 26 tests/testthat/test-NormModVar.R | 162 - tests/testthat/test-NormalDistribution.R |only tests/testthat/test-Reaction.R | 86 tests/testthat/test-SemiMarkovModel.R |only tests/testthat/test-Stack.R | 92 tests/testthat/test-Transition.R |only vignettes/DT01-Sumatriptan.Rmd | 344 +-- vignettes/DT02-Tegaderm.Rmd | 802 +++---- vignettes/DT03-ShaleGas.Rmd | 310 +- vignettes/GT01-NewScientistPuzzle.Rmd | 364 +-- vignettes/SM01-HIV.Rmd |only vignettes/mono.gv |only vignettes/mono.png |only 132 files changed, 16670 insertions(+), 16511 deletions(-)
Title: Litter Analysis
Description: Data sets on various litter types like beach litter, riverain
litter, floating litter, and seafloor litter are rapidly growing. This
package offers a simple user interface to analyse these litter data in
a consistent and reproducible way. It also provides functions to
facilitate several kinds of litter analysis, e.g., trend analysis,
power analysis, and baseline analysis. Under the hood, these functions
are also used by the user interface. See Schulz et al. (2019)
<doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are
advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual
for 'RStudio' and 'litteR'.
Author: Dennis Walvoort [aut, cre, cph],
Willem van Loon [aut, cph],
Rijkswaterstaat - The Netherlands [cph, fnd, dtc]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between litteR versions 0.8.2 dated 2020-10-10 and 0.9.0 dated 2021-09-08
litteR-0.8.2/litteR/vignettes/tab/litteR-log-20200602T141829.log |only litteR-0.8.2/litteR/vignettes/tab/litteR-results-20200602T141829.csv |only litteR-0.9.0/litteR/DESCRIPTION | 9 litteR-0.9.0/litteR/MD5 | 83 litteR-0.9.0/litteR/NAMESPACE | 7 litteR-0.9.0/litteR/NEWS.md | 9 litteR-0.9.0/litteR/R/gui.R | 4 litteR-0.9.0/litteR/R/io.R | 131 litteR-0.9.0/litteR/R/onLoad.R | 3 litteR-0.9.0/litteR/R/stats.R | 217 + litteR-0.9.0/litteR/README.md | 34 litteR-0.9.0/litteR/build/partial.rdb |binary litteR-0.9.0/litteR/build/vignette.rds |binary litteR-0.9.0/litteR/inst/app/litter-main.Rmd | 110 litteR-0.9.0/litteR/inst/app/litter-no-regional-analysis.Rmd |only litteR-0.9.0/litteR/inst/app/litter-no-regional-trend-analysis.Rmd |only litteR-0.9.0/litteR/inst/app/litter-outlier.Rmd | 21 litteR-0.9.0/litteR/inst/app/litter-stats-regional.Rmd |only litteR-0.9.0/litteR/inst/app/litter-stats.Rmd | 173 + litteR-0.9.0/litteR/inst/app/litter-trend-plots-regional.Rmd |only litteR-0.9.0/litteR/inst/app/litter-trend-plots.Rmd | 31 litteR-0.9.0/litteR/inst/app/litter-trend-regional.Rmd |only litteR-0.9.0/litteR/inst/app/litter-trend.Rmd | 47 litteR-0.9.0/litteR/inst/app/litter.css | 19 litteR-0.9.0/litteR/inst/doc/litteR-installation.Rmd | 2 litteR-0.9.0/litteR/inst/doc/litteR-installation.html | 221 - litteR-0.9.0/litteR/inst/doc/litteR-manual.R | 112 litteR-0.9.0/litteR/inst/doc/litteR-manual.Rmd | 282 +- litteR-0.9.0/litteR/inst/doc/litteR-manual.html | 1399 ++++++---- litteR-0.9.0/litteR/inst/extdata/beach-litter-nl-2012-2017.csv | 192 - litteR-0.9.0/litteR/inst/extdata/settings.yaml | 16 litteR-0.9.0/litteR/man/kendall_s.Rd |only litteR-0.9.0/litteR/man/kendall_var_s.Rd |only litteR-0.9.0/litteR/man/mann_kendall.Rd | 8 litteR-0.9.0/litteR/man/regional_kendall.Rd |only litteR-0.9.0/litteR/tests/testthat/test-counts.R | 38 litteR-0.9.0/litteR/tests/testthat/test-io.R | 19 litteR-0.9.0/litteR/tests/testthat/test-stats.R | 65 litteR-0.9.0/litteR/vignettes/fig/bar-plot-bergen.png |binary litteR-0.9.0/litteR/vignettes/fig/library-litter.png |binary litteR-0.9.0/litteR/vignettes/fig/outlier.png |binary litteR-0.9.0/litteR/vignettes/fig/regional-trend-sup.png |only litteR-0.9.0/litteR/vignettes/fig/terschelling-bags.png |binary litteR-0.9.0/litteR/vignettes/fig/terschelling-sup.png |binary litteR-0.9.0/litteR/vignettes/fig/terschelling-tc.png |binary litteR-0.9.0/litteR/vignettes/litteR-installation.Rmd | 2 litteR-0.9.0/litteR/vignettes/litteR-manual.Rmd | 282 +- litteR-0.9.0/litteR/vignettes/tab/litteR-log-20210904T221809.log |only litteR-0.9.0/litteR/vignettes/tab/litteR-results-20210904T221809.csv |only 49 files changed, 2421 insertions(+), 1115 deletions(-)
Title: R Library for Spatial Data Analysis
Description: Provides spatial data analysis functionalities including Exploratory Spatial Data Analysis,
Spatial Cluster Detection and Clustering Analysis, Regionalization, etc. based on the C++ source code
of 'GeoDa', which is an open-source software tool that serves as an introduction to spatial data analysis.
The 'GeoDa' software and its documentation are available at <https://geodacenter.github.io>.
Author: Xun Li [aut, cre],
Luc Anselin [aut]
Maintainer: Xun Li <lixun910@gmail.com>
Diff between rgeoda versions 0.0.8-4 dated 2021-08-05 and 0.0.8-6 dated 2021-09-08
DESCRIPTION | 8 MD5 | 46 +++-- NAMESPACE | 4 R/RcppExports.R | 16 + R/clustering.R | 95 +++++++++++ R/lisa.R | 54 ++++++ man/join_count_ratio.Rd |only man/local_bimoran.Rd |only man/make_spatial.Rd |only man/spatial_validation.Rd |only src/Makevars | 8 src/Makevars.win | 8 src/RcppExports.cpp | 59 +++++++ src/libgeoda/SpatialIndAlgs.cpp | 23 ++ src/libgeoda/clustering/joincount_ratio.cpp |only src/libgeoda/clustering/joincount_ratio.h |only src/libgeoda/clustering/make_spatial.cpp |only src/libgeoda/clustering/make_spatial.h |only src/libgeoda/clustering/schc_wrapper.cpp | 2 src/libgeoda/clustering/spatial_validation.cpp |only src/libgeoda/clustering/spatial_validation.h |only src/libgeoda/gda_clustering.cpp | 79 +++++++++ src/libgeoda/gda_clustering.h | 111 +++++++++++++ src/libgeoda/gda_sa.cpp | 23 ++ src/libgeoda/gda_sa.h | 23 ++ src/libgeoda/geofeature.h | 2 src/libgeoda/sa/BiLocalMoran.cpp |only src/libgeoda/sa/BiLocalMoran.h |only src/rcpp_clustering.cpp | 209 +++++++++++++++++++++++++ src/rcpp_lisa.cpp | 23 ++ 30 files changed, 765 insertions(+), 28 deletions(-)
Title: Fast, Flexible, and User-Friendly Record Linkage Methods
Description: Provides a flexible set of tools for matching two un-linked data sets.
'fedmatch' allows for three ways to match data: exact matches, fuzzy matches, and multi-variable matches.
It also allows an easy combination of these three matches via the tier matching function.
Author: Melanie Friedrichs [aut],
Chris Webster [aut, cre],
Blake Marsh [aut],
Jacob Dice [aut],
Seung Lee [aut]
Maintainer: Chris Webster <chris0webster@gmail.com>
Diff between fedmatch versions 2.0.2 dated 2021-08-03 and 2.0.3 dated 2021-09-08
DESCRIPTION | 6 +- MD5 | 54 ++++++++++---------- NEWS.md | 7 ++ R/build_tier.R | 4 - R/clean_strings.R | 2 R/data_documentation.R | 2 R/merge_plus.R | 8 +-- R/multivar_match.R | 22 ++++---- R/multivar_match_helpers.R | 18 +++--- README.md | 35 +++++++++---- build/vignette.rds |binary data/State_FIPS.rda |binary inst/doc/Fuzzy-matching.Rmd | 2 inst/doc/Fuzzy-matching.html | 2 inst/doc/Intro-to-fedmatch.Rmd | 2 inst/doc/Intro-to-fedmatch.html | 46 ++++++++--------- inst/doc/Multivar_matching.R | 2 inst/doc/Multivar_matching.Rmd | 14 ++--- inst/doc/Multivar_matching.html | 100 +++++++++++++++++++------------------- inst/doc/Using-clean-strings.html | 2 inst/doc/Using-tier-match.html | 14 ++--- man/State_FIPS.Rd | 4 - man/build_tier.Rd | 4 - man/multivar_match.Rd | 10 +-- src/wgt_jaccard.cpp | 2 vignettes/Fuzzy-matching.Rmd | 2 vignettes/Intro-to-fedmatch.Rmd | 2 vignettes/Multivar_matching.Rmd | 14 ++--- 28 files changed, 202 insertions(+), 178 deletions(-)
Title: Zigzag Expanded Navigation Plots
Description: Graphical tools for visualizing high-dimensional data along a path
of alternating one- and two-dimensional plots. Note that this
includes interactive graphics plots based on 'loon' in turn based on 'tcltk'
(included as part of the standard R distribution). It also requires 'graph' from Bioconductor.
For more detail on use and algorithms, see <doi:10.18637/jss.v095.i04>.
Author: Marius Hofert [aut],
Wayne Oldford [aut, cre]
Maintainer: Wayne Oldford <rwoldford@uwaterloo.ca>
Diff between zenplots versions 1.0.3 dated 2020-11-28 and 1.0.4 dated 2021-09-08
zenplots-1.0.3/zenplots/tests/basics.R |only zenplots-1.0.4/zenplots/DESCRIPTION | 12 zenplots-1.0.4/zenplots/MD5 | 74 - zenplots-1.0.4/zenplots/NAMESPACE | 2 zenplots-1.0.4/zenplots/NEWS.md |only zenplots-1.0.4/zenplots/R/plot1dgraphics.R | 3 zenplots-1.0.4/zenplots/R/plot1dgrid.R | 5 zenplots-1.0.4/zenplots/R/plot1dloon.R | 3 zenplots-1.0.4/zenplots/R/plot2dgraphics.R | 5 zenplots-1.0.4/zenplots/R/plot2dgrid.R | 3 zenplots-1.0.4/zenplots/R/plot2dloon.R | 3 zenplots-1.0.4/zenplots/R/tools.R | 121 +-- zenplots-1.0.4/zenplots/R/zenpath.R | 131 +-- zenplots-1.0.4/zenplots/R/zenplot.R | 298 +++---- zenplots-1.0.4/zenplots/R/zenplots.R | 22 zenplots-1.0.4/zenplots/build/vignette.rds |binary zenplots-1.0.4/zenplots/data/olive.rda |binary zenplots-1.0.4/zenplots/inst/doc/intro.html | 626 +++++----------- zenplots-1.0.4/zenplots/inst/doc/selected_features.R | 14 zenplots-1.0.4/zenplots/inst/doc/selected_features.Rmd | 18 zenplots-1.0.4/zenplots/inst/doc/selected_features.html | 513 ++++--------- zenplots-1.0.4/zenplots/man/burst.Rd | 40 - zenplots-1.0.4/zenplots/man/connect_pairs.Rd | 12 zenplots-1.0.4/zenplots/man/convert_occupancy.Rd | 2 zenplots-1.0.4/zenplots/man/extract_1d.Rd | 12 zenplots-1.0.4/zenplots/man/extract_2d.Rd | 16 zenplots-1.0.4/zenplots/man/extract_pairs.Rd | 2 zenplots-1.0.4/zenplots/man/graph_pairs.Rd | 19 zenplots-1.0.4/zenplots/man/groupData.Rd | 6 zenplots-1.0.4/zenplots/man/indexData.Rd | 10 zenplots-1.0.4/zenplots/man/olive.Rd | 4 zenplots-1.0.4/zenplots/man/plot_region.Rd | 4 zenplots-1.0.4/zenplots/man/unfold.Rd | 30 zenplots-1.0.4/zenplots/man/vport.Rd | 4 zenplots-1.0.4/zenplots/man/zenpath.Rd | 15 zenplots-1.0.4/zenplots/man/zenplot.Rd | 163 ++-- zenplots-1.0.4/zenplots/man/zenplots.Rd | 4 zenplots-1.0.4/zenplots/tests/testthat |only zenplots-1.0.4/zenplots/tests/testthat.R |only zenplots-1.0.4/zenplots/vignettes/selected_features.Rmd | 18 40 files changed, 956 insertions(+), 1258 deletions(-)
Title: Analysis and Simulation of Environmental DNA Experiments
Description: Provides a modeling framework for the design and analysis of experiments collecting environmental DNA.
Author: Matt Espe [aut, cre],
Myfanwy Johnston [aut]
Maintainer: Matt Espe <mespe@ucdavis.edu>
Diff between artemis versions 1.1.0 dated 2021-08-19 and 1.1.1 dated 2021-09-08
DESCRIPTION | 6 MD5 | 32 +-- R/utils.R | 24 +- inst/doc/artemis-overview.Rmd | 2 inst/doc/artemis-overview.html | 306 +++++++++++++++++++++++++----- inst/doc/modeling.html | 315 +++++++++++++++++++++++++------ inst/doc/simulation.html | 395 +++++++++++++++++++++++++++++---------- inst/stan/eDNA_lm.stan | 16 - inst/stan/eDNA_lmer.stan | 22 +- man/cq_to_lnconc.Rd | 4 man/eDNA_lmer.Rd | 8 man/lnconc_to_cq.Rd | 14 - src/stanExports_eDNA_lm.h | 90 +++++--- src/stanExports_eDNA_lmer.h | 128 ++++++------ tests/testthat/test_model_funs.R | 15 + tests/testthat/test_utils.R | 6 vignettes/artemis-overview.Rmd | 2 17 files changed, 1038 insertions(+), 347 deletions(-)
Title: Interpreting Glucose Data from Continuous Glucose Monitors
Description: Implements a wide range of metrics for measuring glucose control and glucose variability based on continuous glucose monitoring data. The list of implemented metrics is summarized in Rodbard (2009) <doi:10.1089/dia.2009.0015>. Additional visualization tools include time-series plots, lasagna plots and ambulatory glucose profile report.
Author: Steve Broll [aut],
David Buchanan [aut],
Elizabeth Chun [aut],
John Muschelli [aut] (<https://orcid.org/0000-0001-6469-1750>),
Nathaniel Fernandes [aut],
Jung Hoon Seo [aut],
Johnathan Shih [aut],
Jacek Urbanek [aut],
John Schwenck [aut],
Marielle Hicban [ctb],
Mary Martin [ctb],
Pratik Patel [ctb],
Meyappan Ashok [ctb],
Nhan Nguyen [ctb],
Irina Gaynanova [aut, cre] (<https://orcid.org/0000-0002-4116-0268>)
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>
Diff between iglu versions 3.0.0 dated 2021-07-23 and 3.1.0 dated 2021-09-08
DESCRIPTION | 6 MD5 | 25 - NEWS.md | 4 R/calculate_sleep_wake.r | 13 R/mag.R | 14 R/read_raw_data.r | 7 R/roc.R | 7 README.md | 55 +- build/partial.rdb |binary inst/shiny_iglu/rsconnect/shinyapps.io/irinagain |only inst/shiny_iglu/server.R | 549 ++++++++--------------- inst/shiny_iglu/ui.R | 41 - man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary 14 files changed, 316 insertions(+), 405 deletions(-)
Title: Simulating Triad Genomewide Genotypes
Description: Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.
Author: Min Shi [aut, cre]
Maintainer: Min Shi <shi2@niehs.nih.gov>
Diff between TriadSim versions 0.2.0 dated 2020-07-12 and 0.3.0 dated 2021-09-08
DESCRIPTION | 6 ++-- MD5 | 8 ++--- NEWS.md | 3 +- R/TriadSim_functions.R | 2 - inst/doc/TriadSim.html | 72 +++++++++++++++++++++++++++---------------------- 5 files changed, 51 insertions(+), 40 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] (<https://orcid.org/0000-0003-3716-0668>)
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.2.2 dated 2021-04-30 and 0.3.0 dated 2021-09-08
naijR-0.2.2/naijR/R/numbers.R |only naijR-0.2.2/naijR/R/regions.R |only naijR-0.2.2/naijR/tests/testthat/test-numbers.R |only naijR-0.2.2/naijR/tests/testthat/test-regions.R |only naijR-0.3.0/naijR/DESCRIPTION | 10 naijR-0.3.0/naijR/MD5 | 51 ++-- naijR-0.3.0/naijR/NAMESPACE | 9 naijR-0.3.0/naijR/NEWS.md | 24 +- naijR-0.3.0/naijR/R/class-regions.R |only naijR-0.3.0/naijR/R/helps.R |only naijR-0.3.0/naijR/R/isregion.R |only naijR-0.3.0/naijR/R/lgas_nigeria.R |only naijR-0.3.0/naijR/R/map_nigeria.R | 28 +- naijR-0.3.0/naijR/R/methods-fix_region.R |only naijR-0.3.0/naijR/R/mobile.R |only naijR-0.3.0/naijR/R/sysdata.rda |binary naijR-0.3.0/naijR/README.md | 144 ++++++++----- naijR-0.3.0/naijR/build/vignette.rds |binary naijR-0.3.0/naijR/data/lgas_nigeria.rda |binary naijR-0.3.0/naijR/inst/doc/nigeria-maps.html | 38 ++- naijR-0.3.0/naijR/man/coercion.Rd |only naijR-0.3.0/naijR/man/fix_mobile.Rd | 2 naijR-0.3.0/naijR/man/fix_region.Rd | 6 naijR-0.3.0/naijR/man/is_lga.Rd | 2 naijR-0.3.0/naijR/man/is_state.Rd | 2 naijR-0.3.0/naijR/man/lgas.Rd | 7 naijR-0.3.0/naijR/man/lgas_nigeria.Rd | 2 naijR-0.3.0/naijR/man/map_ng.Rd | 5 naijR-0.3.0/naijR/man/states.Rd | 28 ++ naijR-0.3.0/naijR/tests/testthat/test-class-regions.R |only naijR-0.3.0/naijR/tests/testthat/test-isregion.R |only naijR-0.3.0/naijR/tests/testthat/test-map_nigeria.R | 2 naijR-0.3.0/naijR/tests/testthat/test-methods-fix_region.R |only naijR-0.3.0/naijR/tests/testthat/test-mobile.R |only 34 files changed, 234 insertions(+), 126 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, and PDF 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
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between reporter versions 1.1.3 dated 2021-08-06 and 1.1.6 dated 2021-09-08
DESCRIPTION | 8 MD5 | 244 NAMESPACE | 1 NEWS.md | 16 R/page_template.R | 20 R/page_template_rtf.R |only R/plot_spec.R | 200 R/report_spec.r | 157 R/table_spec.r | 3 R/text_spec.R | 131 R/utilities.R | 34 R/write_report_pdf.R | 308 R/write_report_rtf.R | 2 R/write_report_rtf2.R |only README.md | 3 inst/doc/reporter-figure.R | 5 inst/doc/reporter-figure.Rmd | 5 inst/doc/reporter-figure.html | 11 man/options_fixed.Rd | 440 tests/testthat/output/reg.txt |only tests/testthat/output/test10.out | 6 tests/testthat/output/test11.out | 6 tests/testthat/output/test16.out | 4 tests/testthat/output/test17.out | 2 tests/testthat/output/test3.out | 6 tests/testthat/output/test36.txt | 6 tests/testthat/output/test37.out | 24 tests/testthat/output/test4.out | 12 tests/testthat/output/test44.out | 24 tests/testthat/output/test45.out | 24 tests/testthat/output/test47.out | 2 tests/testthat/output/test48.out | 4 tests/testthat/output/test49.out | 4 tests/testthat/output/test5.out | 6 tests/testthat/output/test50.out | 2 tests/testthat/output/test6.out | 8 tests/testthat/output/test63.out | 2 tests/testthat/output/test66.out | 40 tests/testthat/output/test67.out | 20 tests/testthat/output/test68.out | 2 tests/testthat/output/test69.out | 2 tests/testthat/output/test7.out | 2 tests/testthat/output/test8.out | 2 tests/testthat/output/test9.out | 4 tests/testthat/pdf/test1.pdf | 148 tests/testthat/pdf/test10.pdf | 1819 +- tests/testthat/pdf/test11.pdf | 1823 +- tests/testthat/pdf/test12.pdf | 314 tests/testthat/pdf/test14.pdf | 178 tests/testthat/pdf/test15.pdf | 148 tests/testthat/pdf/test16.pdf | 466 tests/testthat/pdf/test17.pdf | 502 tests/testthat/pdf/test18.pdf | 5523 ++++++-- tests/testthat/pdf/test19.pdf | 5523 ++++++-- tests/testthat/pdf/test2.pdf | 148 tests/testthat/pdf/test21.pdf | 554 tests/testthat/pdf/test22.pdf | 554 tests/testthat/pdf/test23.pdf | 1819 +- tests/testthat/pdf/test24.pdf | 1819 +- tests/testthat/pdf/test25.pdf | 194 tests/testthat/pdf/test3.pdf | 148 tests/testthat/pdf/test4.pdf | 466 tests/testthat/pdf/test5.pdf | 148 tests/testthat/pdf/test6.pdf | 148 tests/testthat/pdf/test7.pdf | 136 tests/testthat/pdf/test8.pdf | 230 tests/testthat/pdf/test9.pdf | 1819 +- tests/testthat/rtf/test10.rtf | 8367 +++--------- tests/testthat/rtf/test11.rtf | 8363 +++--------- tests/testthat/rtf/test12.rtf | 4 tests/testthat/rtf/test14.rtf | 4 tests/testthat/rtf/test15.rtf | 4 tests/testthat/rtf/test18.rtf |22675 +++++++++------------------------ tests/testthat/rtf/test19.rtf |22639 +++++++++----------------------- tests/testthat/rtf/test20.rtf | 9121 +++---------- tests/testthat/rtf/test21.rtf | 6 tests/testthat/rtf/test23.rtf | 8367 +++--------- tests/testthat/rtf/test24.rtf | 8375 +++--------- tests/testthat/rtf/test25.rtf | 16 tests/testthat/rtf/test26.rtf | 24 tests/testthat/rtf/test6.rtf | 2 tests/testthat/rtf/test9.rtf | 8363 +++--------- tests/testthat/rtf2 |only tests/testthat/test-plot_spec.R | 11 tests/testthat/test-print_utilities.R |only tests/testthat/test-report_spec.R | 30 tests/testthat/test-rtf.R | 15 tests/testthat/test-rtf2.R |only tests/testthat/test-sizing_functions.R | 14 tests/testthat/test-user.R | 124 tests/testthat/text/text3.out | 8 tests/testthat/text/text5.out | 4 tests/testthat/text/text6.out |only tests/testthat/text/text7.out | 6 tests/testthat/text/text8.out | 4 tests/testthat/titles/ttfn1.out | 2 tests/testthat/titles/ttfn12.out | 4 tests/testthat/titles/ttfn13.out | 4 tests/testthat/titles/ttfn14.out | 2 tests/testthat/titles/ttfn15.out | 2 tests/testthat/titles/ttfn2.out | 2 tests/testthat/titles/ttfn22.out | 2 tests/testthat/titles/ttfn23.out | 2 tests/testthat/titles/ttfn3.out | 2 tests/testthat/titles/ttfn4.out | 2 tests/testthat/user/user1.out | 40 tests/testthat/user/user1.pdf | 142 tests/testthat/user/user1.rtf | 50 tests/testthat/user/user12.rtf | 6 tests/testthat/user/user13.rtf |only tests/testthat/user/user13.txt |only tests/testthat/user/user14.rtf |only tests/testthat/user/user2.out | 2 tests/testthat/user/user2.rtf | 4 tests/testthat/user/user3.out | 24 tests/testthat/user/user3.pdf | 1338 - tests/testthat/user/user3.rtf | 24 tests/testthat/user/user4.out | 48 tests/testthat/user/user4.pdf | 1338 - tests/testthat/user/user4.rtf | 24 tests/testthat/user/user6.pdf | 1662 +- tests/testthat/user/user6.rtf | 30 tests/testthat/user/user6.txt | 54 tests/testthat/user/user7.rtf | 72 tests/testthat/user/user7.txt | 72 vignettes/reporter-figure.Rmd | 5 126 files changed, 48972 insertions(+), 78962 deletions(-)
Title: Bayesian Power Prior Design
Description: Bayesian power/type I error calculation and model fitting using
the power prior and the normalized power prior for generalized linear models.
The Bayesian clinical trial design methodology is described in Chen et al. (2011)
<doi:10.1111/j.1541-0420.2011.01561.x>, and Psioda and Ibrahim (2019)
<doi:10.1093/biostatistics/kxy009>. The normalized power prior is described in Duan et al. (2006)
<doi:10.1002/env.752> and Ibrahim et al. (2015) <doi:10.1002/sim.6728>.
Author: Yueqi Shen [aut, cre],
Matthew A. Psioda [aut],
Joseph G. Ibrahim [aut]
Maintainer: Yueqi Shen <ys137@live.unc.edu>
Diff between BayesPPD versions 1.0.2 dated 2021-07-20 and 1.0.3 dated 2021-09-08
DESCRIPTION | 6 +- MD5 | 8 +- R/BayesPPD-package.R | 146 +++++++++++++++++++++++++------------------------- src/NI_fixed_glm.cpp | 6 -- src/NI_random_glm.cpp | 2 5 files changed, 83 insertions(+), 85 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 0.4.0 dated 2021-04-21 and 0.5.0 dated 2021-09-08
DESCRIPTION | 6 ++--- MD5 | 52 +++++++++++++++++++++++++-------------------- NEWS.md | 17 ++++++++++++++ R/rd-ODGI.R | 2 - R/rd-clemson_temps.R | 3 -- R/rd-coffee_imports.R | 2 - R/rd-coffee_price.R | 2 - R/rd-so2concentrations.R | 12 +++++----- R/rd-sugar_price.R | 2 - R/rd-wvs_usa_educat.R |only R/rd-wvs_usa_regions.R |only README.md | 22 +++++++++++-------- data/af_crime93.rda |binary data/aluminum_premiums.rda |binary data/clemson_temps.rda |binary data/coffee_imports.rda |binary data/coffee_price.rda |binary data/so2concentrations.rda |binary data/sugar_price.rda |binary data/turnips.rda |binary data/wvs_usa_educat.rda |only data/wvs_usa_regions.rda |only man/ODGI.Rd | 2 - man/clemson_temps.Rd | 3 -- man/coffee_imports.Rd | 2 - man/coffee_price.Rd | 2 - man/so2concentrations.Rd | 12 +++++----- man/sugar_price.Rd | 2 - man/wvs_usa_educat.Rd |only man/wvs_usa_regions.Rd |only 30 files changed, 84 insertions(+), 59 deletions(-)
Title: Two Event Mark-Recapture Experiment
Description: Tools are provided for estimating, testing, and simulating
abundance in a two-event (Petersen) mark-recapture experiment. Functions are
given to calculate the Petersen, Chapman, and Bailey estimators and associated
variances. However, the principal utility is a set of functions to simulate
random draws from these estimators, and use these to conduct hypothesis
tests and power calculations. Additionally, a set of functions are provided
for generating confidence intervals via bootstrapping. Functions are also
provided to test abundance estimator consistency under complete or partial
stratification, and to calculate stratified or partially stratified estimators.
Functions are also provided to calculate recommended sample sizes.
Referenced methods can be found in Arnason et al. (1996) <ISSN:0706-6457>,
Bailey (1951) <DOI:10.2307/2332575>,
Bailey (1952) <DOI:10.2307/1913>,
Chapman (1951) NAID:20001644490,
Cohen (1988) ISBN:0-12-179060-6,
Darroch (1961) <DOI:10.2307/2332748>, and
Robson and Regier (1964) <ISSN:1548-8659>.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matttyersstat@gmail.com>
Diff between recapr versions 0.4.3 dated 2020-07-03 and 0.4.4 dated 2021-09-08
DESCRIPTION | 13 - MD5 | 8 - build/vignette.rds |binary inst/doc/recapr_vignette1.html | 308 +++++++++-------------------------------- man/recapr-package.Rd | 4 5 files changed, 86 insertions(+), 247 deletions(-)
Title: Dose Finding in Drug Combination Phase I Trials Using PO-CRM
Description: Provides functions to implement and simulate the partial order continual reassessment method (PO-CRM) of Wages, Conaway and O'Quigley (2011) <doi:10.1177/1740774511408748> for use in Phase I trials of combinations of agents. Provides a function for generating a set of initial guesses (skeleton) for the toxicity probabilities at each combination that correspond to the set of possible orderings of the toxicity probabilities specified by the user.
Author: Nolan A. Wages
Maintainer: "Brewer, Ben (arb5mt)" <arb5mt@virginia.edu>
Diff between pocrm versions 0.12 dated 2019-03-15 and 0.13 dated 2021-09-08
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Statistical Methods for Modelling Operational Risk
Description: Functions for computing the value-at-risk in compound Poisson models.
The implementation comprises functions for modeling loss frequencies and loss severities with plain, mixed (Frigessi et al. (2012) <doi:10.1023/A:1024072610684>) or spliced distributions using Maximum Likelihood estimation and Bayesian approaches (Ergashev et al. (2013) <doi:10.21314/JOP.2013.131>).
In particular, the parametrization of tail distributions includes the fitting of Tukey-type distributions (Kuo and Headrick (2014) <doi:10.1155/2014/645823>). Furthermore, the package contains the modeling of bivariate dependencies between loss severities and frequencies, Monte Carlo simulation for total loss estimation as well as a closed-form approximation based on Degen (2010) <doi:10.21314/JOP.2010.084> to determine the value-at-risk.
Author: Christina Zou [aut,cre],
Marius Pfeuffer [aut],
Matthias Fischer [aut],
Nina Buoni [ctb], Kristina Dehler [ctb], Nicole Derfuss [ctb], Benedikt Graswald [ctb], Linda Moestel [ctb], Jixuan Wang [ctb], Leonie Wicht [ctb]
Maintainer: Christina Zou <christina.zou@maths.ox.ac.uk>
Diff between OpVaR versions 1.1.1 dated 2020-07-02 and 1.2 dated 2021-09-08
OpVaR-1.1.1/OpVaR/vignettes/OpVaR_vignette_files |only OpVaR-1.2/OpVaR/DESCRIPTION | 10 ++++----- OpVaR-1.2/OpVaR/MD5 | 25 +++++++++++------------ OpVaR-1.2/OpVaR/NAMESPACE | 4 +-- OpVaR-1.2/OpVaR/R/buildSevdist.R | 6 ++--- OpVaR-1.2/OpVaR/R/dpqrmixing.R | 2 - OpVaR-1.2/OpVaR/R/dpqrspliced.R | 2 - OpVaR-1.2/OpVaR/R/qqplot.sevdist.R |only OpVaR-1.2/OpVaR/build/partial.rdb |binary OpVaR-1.2/OpVaR/build/vignette.rds |binary OpVaR-1.2/OpVaR/inst/doc/OpVaR_vignette.Rmd | 2 - OpVaR-1.2/OpVaR/inst/doc/OpVaR_vignette.html | 12 +++++------ OpVaR-1.2/OpVaR/man/dsevdist.Rd | 4 --- OpVaR-1.2/OpVaR/man/plot.sevdist.Rd |only OpVaR-1.2/OpVaR/vignettes/OpVaR_vignette.Rmd | 2 - 15 files changed, 33 insertions(+), 36 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with this
package as described in Ostoic (2020) <DOI:10.18637/jss.v092.i11>. Among other things, it
makes it possible to create and manipulate multiplex, multimode, and multilevel network data
with different formats. There are effective ways available to treat multiple networks with
routines that combine algebraic systems like the partially ordered semigroup or the semiring
structure with the relational bundles occurring in different types of multivariate network
data sets. It also provides an algebraic approach for affiliation networks through Galois
derivations between families of the pairs of subsets in the two domains.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 2.9.4 dated 2020-02-28 and 2.9.6 dated 2021-09-08
multiplex-2.9.4/multiplex/data/incA.RData |only multiplex-2.9.4/multiplex/data/incB.RData |only multiplex-2.9.4/multiplex/data/incC.RData |only multiplex-2.9.4/multiplex/data/incD.RData |only multiplex-2.9.4/multiplex/data/incubA.RData |only multiplex-2.9.4/multiplex/data/incubB.RData |only multiplex-2.9.4/multiplex/data/incubC.RData |only multiplex-2.9.4/multiplex/data/incubD.RData |only multiplex-2.9.4/multiplex/data/incubs.RData |only multiplex-2.9.6/multiplex/DESCRIPTION | 10 - multiplex-2.9.6/multiplex/MD5 | 36 ++--- multiplex-2.9.6/multiplex/R/fltr.R | 4 multiplex-2.9.6/multiplex/R/mlvl.R | 110 ++++++++--------- multiplex-2.9.6/multiplex/R/partial.order.R | 5 multiplex-2.9.6/multiplex/R/transl.R | 22 +-- multiplex-2.9.6/multiplex/data/incA.rda |only multiplex-2.9.6/multiplex/data/incB.rda |only multiplex-2.9.6/multiplex/data/incC.rda |only multiplex-2.9.6/multiplex/data/incD.rda |only multiplex-2.9.6/multiplex/data/incubA.rda |only multiplex-2.9.6/multiplex/data/incubB.rda |only multiplex-2.9.6/multiplex/data/incubC.rda |only multiplex-2.9.6/multiplex/data/incubD.rda |only multiplex-2.9.6/multiplex/data/incubs.rda |only multiplex-2.9.6/multiplex/inst/CHANGELOG | 10 + multiplex-2.9.6/multiplex/inst/doc/TwoModeNetworks.pdf |binary multiplex-2.9.6/multiplex/man/incubs.Rd | 16 +- multiplex-2.9.6/multiplex/man/multiplex-package.Rd | 6 28 files changed, 112 insertions(+), 107 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>),
Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>),
John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>),
Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>),
David Wilson [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 1.0.3 dated 2021-07-29 and 1.0.4 dated 2021-09-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ inst/doc/intro.html | 6 +++--- inst/doc/traits.pdf |binary src/RcppExports.cpp | 5 +++++ src/meiosis.cpp | 24 +++++++++++++++++++----- 7 files changed, 42 insertions(+), 18 deletions(-)
Title: Truncated Multivariate Normal and Student Distributions
Description: A collection of functions to deal with the truncated univariate and multivariate normal and Student distributions, described in Botev (2017) <doi:10.1111/rssb.12162> and Botev and L'Ecuyer (2015) <doi:10.1109/WSC.2015.7408180>.
Author: Zdravko Botev [aut] (<https://orcid.org/0000-0001-9054-3452>),
Leo Belzile [aut, cre] (<https://orcid.org/0000-0002-9135-014X>)
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between TruncatedNormal versions 2.2 dated 2020-05-17 and 2.2.2 dated 2021-09-08
DESCRIPTION | 12 MD5 | 28 - NEWS.md | 6 R/ntail.R | 45 +-- R/tmvnorm.R | 8 R/tmvt.R | 10 R/tn.R | 46 +-- R/trandn.R | 18 - build/vignette.rds |binary inst/doc/TruncatedNormal_vignette.html | 486 +++++++++++---------------------- man/pmvnorm.Rd | 12 man/pmvt.Rd | 15 - man/tmvt.Rd | 2 src/RcppExports.cpp | 5 tests/testthat/test-wrappers.R | 6 15 files changed, 276 insertions(+), 423 deletions(-)
More information about TruncatedNormal at CRAN
Permanent link
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI <http://vcg.isti.cnr.it>,
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk
<https://github.com/cnr-isti-vclab/vcglib> and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager [aut, cre, cph],
Girinon Francois [ctb],
Tim Schaefer [ctb]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.20 dated 2021-09-02 and 0.20.2 dated 2021-09-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/Rvcg-package.R | 8 ++++---- data/humface.rda |binary inst/NEWS.Rd | 10 ++++++++++ man/Rvcg-package.Rd | 4 ++-- man/humface.Rd | 3 ++- src/Rdijkstra.cpp | 8 ++++---- 8 files changed, 33 insertions(+), 22 deletions(-)
More information about NonpModelCheck at CRAN
Permanent link
Title: Molecular Acquisition, Cleaning, and Evaluation in R 'MACER'
Description: To assist biological researchers in assembling taxonomically and marker focused molecular sequence data sets. 'MACER' accepts a list of genera as a user input and uses NCBI-GenBank and BOLD as resources to download and assemble molecular sequence datasets. These datasets are then assembled by marker, aligned, trimmed, and cleaned. The use of this package allows the publication of specific parameters to ensure reproducibility. The 'MACER' package has four core functions and an example run through using all of these functions can be found in the associated repository <https://github.com/rgyoung6/MACER_example>.
Author: Robert G Young [aut, cre, cph]
(<https://orcid.org/0000-0002-6731-2506>),
Rekkab Gill [aut],
Daniel Gillis [aut],
Robert H Hanner [aut, cph]
Maintainer: Robert G Young <rgyoung6@gmail.com>
Diff between MACER versions 0.1.0 dated 2021-07-05 and 0.1.1 dated 2021-09-08
DESCRIPTION | 10 - MD5 | 36 ++--- R/BOLD_download.R | 2 R/MSA_data_matrix.R | 2 R/NCBI_download.R | 2 R/align_to_ref.R | 68 +++++++-- R/auto_seq_download.R | 56 +++++--- R/barcode_clean.R | 322 +++++++++++++++++++++++++---------------------- R/create_fastas.R | 82 ++++++++--- R/data_clean.R | 15 -- R/fasta_to_table.R | 2 R/forward_reverse_trim.R | 2 R/readpath.R | 2 R/remove_internal_gaps.R | 2 README.md | 90 ++++++++----- man/align_to_ref.Rd | 23 ++- man/auto_seq_download.Rd | 28 ++-- man/barcode_clean.Rd | 28 +--- man/create_fastas.Rd | 40 +++-- 19 files changed, 481 insertions(+), 331 deletions(-)
Title: HTML Widgets for R
Description: A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents, and 'Shiny'
web applications.
Author: Ramnath Vaidyanathan [aut, cph],
Yihui Xie [aut],
JJ Allaire [aut],
Joe Cheng [aut],
Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Kenton Russell [aut, cph],
Ellis Hughes [ctb],
RStudio [cph]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between htmlwidgets versions 1.5.3 dated 2020-12-10 and 1.5.4 dated 2021-09-08
DESCRIPTION | 6 MD5 | 18 NEWS.md | 6 R/utils.R | 24 - build/vignette.rds |binary inst/doc/develop_advanced.R | 2 inst/doc/develop_advanced.html | 657 +++++++++++++++++-------------- inst/doc/develop_intro.html | 844 +++++++++++++++++++++-------------------- inst/doc/develop_sizing.html | 666 ++++++++++++++++++-------------- inst/www/htmlwidgets.js | 2 10 files changed, 1229 insertions(+), 996 deletions(-)
Title: Access Clean External Data Easily
Description: This Fidap <https://app.fidap.com> client connect to our big data warehouses and gives you seamless access to external data.
Author: Ashish Singal [aut, cre, cph] (<https://orcid.org/0000-0002-6409-4304>)
Maintainer: Ashish Singal <arslan@fidap.com>
Diff between fidap versions 0.0.2 dated 2021-08-16 and 0.0.3 dated 2021-09-08
fidap-0.0.2/fidap/man/fidap_cleint.Rd |only fidap-0.0.3/fidap/DESCRIPTION | 6 +++--- fidap-0.0.3/fidap/MD5 | 16 ++++++++-------- fidap-0.0.3/fidap/NAMESPACE | 2 +- fidap-0.0.3/fidap/R/fidap.R | 6 +++++- fidap-0.0.3/fidap/inst/doc/my-vignette.R | 3 +++ fidap-0.0.3/fidap/inst/doc/my-vignette.Rmd | 10 ++++++++++ fidap-0.0.3/fidap/inst/doc/my-vignette.html | 9 ++++++++- fidap-0.0.3/fidap/man/fidap_client.Rd |only fidap-0.0.3/fidap/vignettes/my-vignette.Rmd | 10 ++++++++++ 10 files changed, 48 insertions(+), 14 deletions(-)
Title: Tool for Secure Shipment of Content
Description: Convenient tools for exchanging files securely from within R. By
encrypting the content safe passage of files (shipment) can be provided by
common but insecure carriers such as ftp and email. Based on asymmetric
cryptography no management of shared secrets is needed to make a secure
shipment as long as authentic public keys are available. Public keys used
for secure shipments may also be obtained from external providers as part of
the overall process. Transportation of files will require that relevant
services such as ftp and email servers are available.
Author: Are Edvardsen [aut, cre] (<https://orcid.org/0000-0002-5210-3656>)
Maintainer: Are Edvardsen <biorakel@gmail.com>
Diff between sship versions 0.7.0 dated 2021-09-07 and 0.7.1 dated 2021-09-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/enc.R | 2 +- README.md | 13 +++++++++++-- 5 files changed, 23 insertions(+), 10 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions
used in 'mlr3' and its companion packages. Comes with helper functions
for functional programming, for printing, to work with 'data.table',
as well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.9.3 dated 2021-07-14 and 0.9.4 dated 2021-09-08
DESCRIPTION | 8 ++++---- MD5 | 30 ++++++++++++++++++------------ NAMESPACE | 3 +++ NEWS.md | 7 +++++++ R/capitalize.R |only R/load_dataset.R | 1 + R/named_vector.R | 4 +++- R/register_namespace_callback.R | 18 +++++++++++------- R/to_decimal.R |only R/topo_sort.R | 1 - R/unnest.R | 2 +- R/which_max.R | 4 ++-- man/capitalize.Rd |only man/to_decimal.Rd |only man/unnest.Rd | 2 +- man/which_min.Rd | 4 ++-- src/init.c | 2 ++ src/to_decimal.c |only tests/testthat/test_to_decimal.R |only 19 files changed, 55 insertions(+), 31 deletions(-)
Title: Heteroskedasticity Robust Testing
Description: Functions for testing affine hypotheses on the regression coefficient vector in regression models with heteroskedastic errors: (i) a function for computing various test statistics (in particular using HC0-HC4 covariance estimators based on unrestricted or restricted residuals); (ii) a function for numerically approximating the size of a test based on such test statistics and a user-supplied critical value; and, most importantly, (iii) a function for determining size-controlling critical values for such test statistics and a user-supplied significance level (also incorporating a check of conditions under which such a size-controlling critical value exists). The three functions are based on results in Poetscher and Preinerstorfer (2021) "Valid Heteroskedasticity Robust Testing" <arXiv:2104.12597>.
Author: David Preinerstorfer
Maintainer: David Preinerstorfer <david.preinerstorfer@ulb.be>
Diff between hrt versions 1.0.0 dated 2021-04-28 and 1.0.1 dated 2021-09-08
DESCRIPTION | 8 - MD5 | 14 - NEWS | 4 R/RcppExports.R | 30 +-- R/expl.start.R | 398 ++++++++++++++++++++++++++-------------------------- R/zzz.R | 70 ++++----- build/partial.rdb |binary src/RcppExports.cpp | 5 8 files changed, 269 insertions(+), 260 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle, Darshan Baral,
Ulrike Groemping, Bill Venables
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.8-1 dated 2021-01-21 and 3.8-2 dated 2021-09-08
DESCRIPTION | 8 ++-- MD5 | 26 ++++++++-------- NEWS | 6 +++ R/gap.boxplot.R | 4 +- R/radial.grid.R | 4 +- R/radial.plot.R | 79 ++++++++++++++++++++++++++++++------------------- R/sizetree.R | 4 +- data/soils.rda |binary man/clock24.plot.Rd | 6 +++ man/gap.boxplot.Rd | 5 +-- man/multivari.Rd | 2 - man/plotrix-package.Rd | 6 +-- man/polar.plot.Rd | 6 +++ man/radial.plot.Rd | 56 ++++++++++++++++++++++++---------- 14 files changed, 135 insertions(+), 77 deletions(-)
Title: Identification of Parental Lines via Genomic Prediction
Description: Combining genomic prediction with Monte Carlo simulation, three different
strategies are implemented to select parental lines for multiple traits in plant
breeding. The selection strategies include (i) GEBV-O considers only genomic
estimated breeding values (GEBVs) of the candidate individuals; (ii) GD-O
considers only genomic diversity (GD) of the candidate individuals; and (iii)
GEBV-GD considers both GEBV and GD. The above method can be seen in Chung PY,
Liao CT (2020) <doi:10.1371/journal.pone.0243159>. Multi-trait genomic best
linear unbiased prediction (MT-GBLUP) model is used to simultaneously estimate
GEBVs of the target traits, and then a selection index is adopted to evaluate
the composite performance of an individual.
Author: Ping-Yuan Chung [cre],
Chen-Tuo Liao [aut]
Maintainer: Ping-Yuan Chung <r06621204@ntu.edu.tw>
Diff between IPLGP versions 1.2.0 dated 2021-04-23 and 1.3.0 dated 2021-09-08
DESCRIPTION | 6 +-- MD5 | 26 ++++++++-------- R/GBLUP.fit.R | 22 +++++++------- R/output.best.R | 18 ++++++----- R/output.gain.R | 18 ++++++----- R/simu.GDO.R | 82 ++++++++++++++++++++++++++++++++--------------------- R/simu.GEBVGD.R | 82 ++++++++++++++++++++++++++++++++--------------------- R/simu.GEBVO.R | 82 ++++++++++++++++++++++++++++++++--------------------- man/GBLUP.fit.Rd | 15 ++++++--- man/output.best.Rd | 18 ++++++----- man/output.gain.Rd | 18 ++++++----- man/simu.GDO.Rd | 74 +++++++++++++++++++++++++++++------------------ man/simu.GEBVGD.Rd | 74 +++++++++++++++++++++++++++++------------------ man/simu.GEBVO.Rd | 74 +++++++++++++++++++++++++++++------------------ 14 files changed, 363 insertions(+), 246 deletions(-)
Title: R Interface to API 'vk.com'
Description: Load data from vk.com api about your communiti users and views,
ads performance, post on user wall and etc. For more information
see API Documentation <https://vk.com/dev/first_guide>.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rvkstat versions 3.0.1 dated 2021-04-07 and 3.1.0 dated 2021-09-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- NEWS.md | 10 ++++++++++ R/vkGetAdsLayout.R | 3 ++- R/zzz.R | 2 +- build/partial.rdb |binary 7 files changed, 24 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-12 0.4.0
2020-04-07 0.3.2
2020-02-10 0.3.0
2016-03-07 0.1.1
2016-03-04 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-01 0.3.9
2020-07-01 0.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-25 0.5.2
2021-08-10 0.5.1
Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file,
and collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'Roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph]
(<https://orcid.org/0000-0003-4757-117X>),
Peter Danenberg [aut, cph],
Gábor Csárdi [aut],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 7.1.1 dated 2020-06-27 and 7.1.2 dated 2021-09-08
roxygen2-7.1.1/roxygen2/R/RcppExports.R |only roxygen2-7.1.1/roxygen2/src/RcppExports.cpp |only roxygen2-7.1.1/roxygen2/tests/testthat/test-rd-includermd.R |only roxygen2-7.1.2/roxygen2/DESCRIPTION | 19 roxygen2-7.1.2/roxygen2/LICENSE |only roxygen2-7.1.2/roxygen2/MD5 | 86 - roxygen2-7.1.2/roxygen2/NAMESPACE | 3 roxygen2-7.1.2/roxygen2/NEWS.md | 20 roxygen2-7.1.2/roxygen2/R/block.R | 7 roxygen2-7.1.2/roxygen2/R/cpp11.R |only roxygen2-7.1.2/roxygen2/R/load.R | 2 roxygen2-7.1.2/roxygen2/R/markdown.R | 7 roxygen2-7.1.2/roxygen2/R/object-rc.R | 2 roxygen2-7.1.2/roxygen2/R/parse.R | 1 roxygen2-7.1.2/roxygen2/R/rd-examples.R | 29 roxygen2-7.1.2/roxygen2/R/rd-usage.R | 2 roxygen2-7.1.2/roxygen2/R/roxygen.R | 1 roxygen2-7.1.2/roxygen2/R/tag-parser.R | 19 roxygen2-7.1.2/roxygen2/README.md | 2 roxygen2-7.1.2/roxygen2/build/vignette.rds |binary roxygen2-7.1.2/roxygen2/inst/doc/extending.html | 616 +++----- roxygen2-7.1.2/roxygen2/inst/doc/namespace.html | 222 --- roxygen2-7.1.2/roxygen2/inst/doc/rd-formatting.Rmd | 23 roxygen2-7.1.2/roxygen2/inst/doc/rd-formatting.html | 546 ++----- roxygen2-7.1.2/roxygen2/inst/doc/rd.R | 22 roxygen2-7.1.2/roxygen2/inst/doc/rd.Rmd | 49 roxygen2-7.1.2/roxygen2/inst/doc/rd.html | 686 +++------- roxygen2-7.1.2/roxygen2/inst/doc/roxygen2.html | 320 ---- roxygen2-7.1.2/roxygen2/man/figures/test-figure-1.png |binary roxygen2-7.1.2/roxygen2/man/load.Rd | 2 roxygen2-7.1.2/roxygen2/man/markdown_pass1.Rd | 9 roxygen2-7.1.2/roxygen2/src/cpp11.cpp |only roxygen2-7.1.2/roxygen2/src/escapeExamples.cpp | 6 roxygen2-7.1.2/roxygen2/src/isComplete.cpp | 12 roxygen2-7.1.2/roxygen2/src/leadingSpaces.cpp | 13 roxygen2-7.1.2/roxygen2/src/parser2.cpp | 50 roxygen2-7.1.2/roxygen2/src/wrapUsage.cpp | 9 roxygen2-7.1.2/roxygen2/tests/testthat/test-markdown-link.R | 16 roxygen2-7.1.2/roxygen2/tests/testthat/test-markdown.R | 2 roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-examples.R | 15 roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-examplesIf.txt |only roxygen2-7.1.2/roxygen2/tests/testthat/test-rd-include-rmd.R |only roxygen2-7.1.2/roxygen2/tests/testthat/test-tag.R | 42 roxygen2-7.1.2/roxygen2/tests/testthat/test-tokenize.R | 24 roxygen2-7.1.2/roxygen2/tests/testthat/test-utils-io.R | 8 roxygen2-7.1.2/roxygen2/tests/testthat/testNamespace/DESCRIPTION | 2 roxygen2-7.1.2/roxygen2/vignettes/rd-formatting.Rmd | 23 roxygen2-7.1.2/roxygen2/vignettes/rd.Rmd | 49 48 files changed, 1087 insertions(+), 1879 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>;
artificial extinction (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.4.5 dated 2021-06-23 and 1.5.0 dated 2021-09-08
TreeTools-1.4.5/TreeTools/man/as.Splits.Rd |only TreeTools-1.4.5/TreeTools/tests/testthat/Rplots.pdf |only TreeTools-1.5.0/TreeTools/DESCRIPTION | 26 TreeTools-1.5.0/TreeTools/MD5 | 225 +++-- TreeTools-1.5.0/TreeTools/NAMESPACE | 11 TreeTools-1.5.0/TreeTools/NEWS.md | 52 + TreeTools-1.5.0/TreeTools/R/ArtificialExtinction.R | 8 TreeTools-1.5.0/TreeTools/R/Consensus.R |only TreeTools-1.5.0/TreeTools/R/ImposeConstraint.R |only TreeTools-1.5.0/TreeTools/R/Information.R | 3 TreeTools-1.5.0/TreeTools/R/RcppExports-manual.R | 4 TreeTools-1.5.0/TreeTools/R/RcppExports.R | 12 TreeTools-1.5.0/TreeTools/R/Splits.R | 76 + TreeTools-1.5.0/TreeTools/R/Support.R | 27 TreeTools-1.5.0/TreeTools/R/TotalCopheneticIndex.R | 8 TreeTools-1.5.0/TreeTools/R/TreeNumber.R | 2 TreeTools-1.5.0/TreeTools/R/as.multiPhylo.R | 7 TreeTools-1.5.0/TreeTools/R/parse_files.R | 232 +++-- TreeTools-1.5.0/TreeTools/R/phylo.R | 6 TreeTools-1.5.0/TreeTools/R/tree_display.R | 73 - TreeTools-1.5.0/TreeTools/R/tree_generation.R | 46 + TreeTools-1.5.0/TreeTools/R/tree_numbering.R | 57 + TreeTools-1.5.0/TreeTools/R/tree_properties.R | 11 TreeTools-1.5.0/TreeTools/R/tree_rearrangement.R | 159 ++-- TreeTools-1.5.0/TreeTools/R/tree_shape.R | 4 TreeTools-1.5.0/TreeTools/R/tree_write.R | 6 TreeTools-1.5.0/TreeTools/R/zzz.R | 3 TreeTools-1.5.0/TreeTools/build/partial.rdb |binary TreeTools-1.5.0/TreeTools/build/vignette.rds |binary TreeTools-1.5.0/TreeTools/inst/REFERENCES.bib | 131 +-- TreeTools-1.5.0/TreeTools/inst/WORDLIST | 4 TreeTools-1.5.0/TreeTools/inst/doc/filesystem-navigation.html | 4 TreeTools-1.5.0/TreeTools/inst/doc/load-data.html | 4 TreeTools-1.5.0/TreeTools/inst/doc/load-trees.html | 10 TreeTools-1.5.0/TreeTools/inst/extdata/input/dataset.nex | 10 TreeTools-1.5.0/TreeTools/inst/extdata/input/notes.nex |only TreeTools-1.5.0/TreeTools/inst/include/TreeTools.h | 3 TreeTools-1.5.0/TreeTools/inst/include/TreeTools/ClusterTable.h |only TreeTools-1.5.0/TreeTools/inst/include/TreeTools/SplitList.h |only TreeTools-1.5.0/TreeTools/inst/include/TreeTools/renumber_tree.h | 393 ++++++---- TreeTools-1.5.0/TreeTools/inst/include/TreeTools/root_tree.h | 41 - TreeTools-1.5.0/TreeTools/inst/include/TreeTools/types.h | 1 TreeTools-1.5.0/TreeTools/man/AddTip.Rd | 1 TreeTools-1.5.0/TreeTools/man/ArtificialExtinction.Rd | 5 TreeTools-1.5.0/TreeTools/man/CladisticInfo.Rd | 1 TreeTools-1.5.0/TreeTools/man/CollapseNode.Rd | 1 TreeTools-1.5.0/TreeTools/man/Consensus.Rd |only TreeTools-1.5.0/TreeTools/man/ConsensusWithout.Rd | 9 TreeTools-1.5.0/TreeTools/man/ConstrainedNJ.Rd |only TreeTools-1.5.0/TreeTools/man/DropTip.Rd | 25 TreeTools-1.5.0/TreeTools/man/EndSentence.Rd | 62 - TreeTools-1.5.0/TreeTools/man/EnforceOutgroup.Rd | 1 TreeTools-1.5.0/TreeTools/man/GenerateTree.Rd | 1 TreeTools-1.5.0/TreeTools/man/ImposeConstraint.Rd |only TreeTools-1.5.0/TreeTools/man/LabelSplits.Rd | 3 TreeTools-1.5.0/TreeTools/man/LeafLabelInterchange.Rd | 1 TreeTools-1.5.0/TreeTools/man/MakeTreeBinary.Rd | 1 TreeTools-1.5.0/TreeTools/man/MorphoBankDecode.Rd | 56 - TreeTools-1.5.0/TreeTools/man/NJTree.Rd | 1 TreeTools-1.5.0/TreeTools/man/NSplits.Rd | 3 TreeTools-1.5.0/TreeTools/man/NTip.Rd | 3 TreeTools-1.5.0/TreeTools/man/PairwiseDistances.Rd | 80 +- TreeTools-1.5.0/TreeTools/man/PolarizeSplits.Rd |only TreeTools-1.5.0/TreeTools/man/ReadCharacters.Rd | 50 - TreeTools-1.5.0/TreeTools/man/Renumber.Rd | 1 TreeTools-1.5.0/TreeTools/man/RenumberTips.Rd | 1 TreeTools-1.5.0/TreeTools/man/Reorder.Rd | 31 TreeTools-1.5.0/TreeTools/man/RootTree.Rd | 1 TreeTools-1.5.0/TreeTools/man/SingleTaxonTree.Rd | 2 TreeTools-1.5.0/TreeTools/man/SortTree.Rd | 1 TreeTools-1.5.0/TreeTools/man/SplitFrequency.Rd | 3 TreeTools-1.5.0/TreeTools/man/Splits.Rd |only TreeTools-1.5.0/TreeTools/man/SplitsInBinaryTree.Rd | 7 TreeTools-1.5.0/TreeTools/man/Stemwardness.Rd | 1 TreeTools-1.5.0/TreeTools/man/Subtree.Rd | 1 TreeTools-1.5.0/TreeTools/man/TipLabels.Rd | 3 TreeTools-1.5.0/TreeTools/man/TipsInSplits.Rd | 3 TreeTools-1.5.0/TreeTools/man/TotalCopheneticIndex.Rd | 1 TreeTools-1.5.0/TreeTools/man/TreeNumber.Rd | 1 TreeTools-1.5.0/TreeTools/man/Unquote.Rd | 62 - TreeTools-1.5.0/TreeTools/man/figures/Stemwardness.png |binary TreeTools-1.5.0/TreeTools/man/match.Rd | 5 TreeTools-1.5.0/TreeTools/src/RcppExports-manual.cpp | 5 TreeTools-1.5.0/TreeTools/src/RcppExports.cpp | 41 + TreeTools-1.5.0/TreeTools/src/TreeTools-init.c | 10 TreeTools-1.5.0/TreeTools/src/consensus.cpp |only TreeTools-1.5.0/TreeTools/src/drop_tip.cpp |only TreeTools-1.5.0/TreeTools/src/splits.cpp | 12 TreeTools-1.5.0/TreeTools/src/splits_to_tree.cpp |only TreeTools-1.5.0/TreeTools/tests/benchmark |only TreeTools-1.5.0/TreeTools/tests/testthat/_snaps/Support/labelsplits-names.svg |only TreeTools-1.5.0/TreeTools/tests/testthat/_snaps/Support/labelsplits.svg | 20 TreeTools-1.5.0/TreeTools/tests/testthat/test-ArtificialExtinction.R | 30 TreeTools-1.5.0/TreeTools/tests/testthat/test-ImposeConstraint.R |only TreeTools-1.5.0/TreeTools/tests/testthat/test-SplitFunctions.R | 33 TreeTools-1.5.0/TreeTools/tests/testthat/test-Splits.R | 66 + TreeTools-1.5.0/TreeTools/tests/testthat/test-Stemwardness.R | 2 TreeTools-1.5.0/TreeTools/tests/testthat/test-Support.R | 25 TreeTools-1.5.0/TreeTools/tests/testthat/test-TotalCopheneticIndex.R | 2 TreeTools-1.5.0/TreeTools/tests/testthat/test-TreeNumber.R | 10 TreeTools-1.5.0/TreeTools/tests/testthat/test-as.multiPhylo.R | 4 TreeTools-1.5.0/TreeTools/tests/testthat/test-combinatorics.R | 2 TreeTools-1.5.0/TreeTools/tests/testthat/test-consensus.R |only TreeTools-1.5.0/TreeTools/tests/testthat/test-drop_tip.cpp.R |only TreeTools-1.5.0/TreeTools/tests/testthat/test-helper_functions.R | 16 TreeTools-1.5.0/TreeTools/tests/testthat/test-information.R | 2 TreeTools-1.5.0/TreeTools/tests/testthat/test-int_to_tree.cpp.R | 9 TreeTools-1.5.0/TreeTools/tests/testthat/test-mst.R | 4 TreeTools-1.5.0/TreeTools/tests/testthat/test-parsers.R | 74 + TreeTools-1.5.0/TreeTools/tests/testthat/test-phylo.R | 31 TreeTools-1.5.0/TreeTools/tests/testthat/test-root_tree.h.R | 5 TreeTools-1.5.0/TreeTools/tests/testthat/test-split_analysis.R | 1 TreeTools-1.5.0/TreeTools/tests/testthat/test-splits.cpp.R | 2 TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_comparison.R | 2 TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_display.R | 26 TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_generation-random.R | 2 TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_generation.R | 37 TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_information.R | 2 TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_numbering.R | 36 TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_properties.R | 16 TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_rearrange.R | 153 ++- TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_shape.R | 39 TreeTools-1.5.0/TreeTools/tests/testthat/test-tree_write.R | 11 123 files changed, 1713 insertions(+), 1104 deletions(-)
Title: Load Data from 'MyTarget API v2 and v3'
Description: Allows work with 'MyTarget API v2'
<https://target.my.com/doc/api/> and 'MyTarget API v3'
<https://target.my.com/adv/api-marketing/doc/stat-v2#statisticsv3>
load data by ads, campaigns, agency clients and statistic from
your ads account.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>),
Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rmytarget versions 2.1.8 dated 2019-08-19 and 2.3.1 dated 2021-09-08
rmytarget-2.1.8/rmytarget/inst/logo/desktop.ini |only rmytarget-2.3.1/rmytarget/DESCRIPTION | 30 - rmytarget-2.3.1/rmytarget/LICENSE |only rmytarget-2.3.1/rmytarget/MD5 | 57 + rmytarget-2.3.1/rmytarget/NAMESPACE | 9 rmytarget-2.3.1/rmytarget/NEWS.md | 20 rmytarget-2.3.1/rmytarget/R/myTarCheckLimits.R |only rmytarget-2.3.1/rmytarget/R/myTarGetAdList.R | 2 rmytarget-2.3.1/rmytarget/R/myTarGetCampaignList.R | 2 rmytarget-2.3.1/rmytarget/R/myTarGetClientList.R | 3 rmytarget-2.3.1/rmytarget/R/myTarGetGoalList.R |only rmytarget-2.3.1/rmytarget/R/myTarGetGoalsStats.R |only rmytarget-2.3.1/rmytarget/R/myTarGetStats.R | 461 +++++++++++----- rmytarget-2.3.1/rmytarget/R/zzz.R | 19 rmytarget-2.3.1/rmytarget/README.md | 14 rmytarget-2.3.1/rmytarget/build/partial.rdb |binary rmytarget-2.3.1/rmytarget/build/vignette.rds |binary rmytarget-2.3.1/rmytarget/inst/doc/rmytarget-auth.R | 8 rmytarget-2.3.1/rmytarget/inst/doc/rmytarget-auth.Rmd | 8 rmytarget-2.3.1/rmytarget/inst/doc/rmytarget-auth.html | 289 ++-------- rmytarget-2.3.1/rmytarget/inst/doc/rmytarget-intro.R | 8 rmytarget-2.3.1/rmytarget/inst/doc/rmytarget-intro.Rmd | 2 rmytarget-2.3.1/rmytarget/inst/doc/rmytarget-intro.html | 425 ++++---------- rmytarget-2.3.1/rmytarget/man/myTarAuth.Rd | 6 rmytarget-2.3.1/rmytarget/man/myTarGetAdList.Rd | 2 rmytarget-2.3.1/rmytarget/man/myTarGetCampaignList.Rd | 2 rmytarget-2.3.1/rmytarget/man/myTarGetGoalList.Rd |only rmytarget-2.3.1/rmytarget/man/myTarGetGoalsStats.Rd |only rmytarget-2.3.1/rmytarget/man/myTarGetStats.Rd | 39 - rmytarget-2.3.1/rmytarget/man/myTarRefreshToken.Rd | 2 rmytarget-2.3.1/rmytarget/man/rmytarget-package.Rd | 4 rmytarget-2.3.1/rmytarget/vignettes/rmytarget-auth.Rmd | 8 rmytarget-2.3.1/rmytarget/vignettes/rmytarget-intro.Rmd | 2 33 files changed, 687 insertions(+), 735 deletions(-)
Title: Data Visualization for QTL Experiments
Description: Functions to plot QTL (quantitative trait loci) analysis
results and related diagnostics.
Part of 'qtl2', an upgrade of the 'qtl'
package to better handle high-dimensional data and complex cross
designs.
Author: Brian S Yandell [aut, cre],
Karl W Broman [aut]
Maintainer: Brian S Yandell <brian.yandell@wisc.edu>
Diff between qtl2ggplot versions 1.0.6 dated 2021-05-26 and 1.1.0 dated 2021-09-08
qtl2ggplot-1.0.6/qtl2ggplot/vignettes/DOex.zip |only qtl2ggplot-1.0.6/qtl2ggplot/vignettes/c2_snpinfo.rds |only qtl2ggplot-1.1.0/qtl2ggplot/DESCRIPTION | 15 qtl2ggplot-1.1.0/qtl2ggplot/MD5 | 61 - qtl2ggplot-1.1.0/qtl2ggplot/NAMESPACE | 25 qtl2ggplot-1.1.0/qtl2ggplot/R/color_patterns.R | 15 qtl2ggplot-1.1.0/qtl2ggplot/R/ggplot_coef.R | 49 - qtl2ggplot-1.1.0/qtl2ggplot/R/ggplot_genes.R | 22 qtl2ggplot-1.1.0/qtl2ggplot/R/ggplot_genes_internal.R | 8 qtl2ggplot-1.1.0/qtl2ggplot/R/ggplot_listof_scan1coef.R |only qtl2ggplot-1.1.0/qtl2ggplot/R/ggplot_onegeno.R | 8 qtl2ggplot-1.1.0/qtl2ggplot/R/ggplot_scan1.R | 20 qtl2ggplot-1.1.0/qtl2ggplot/R/ggplot_scan1_internal.R | 29 qtl2ggplot-1.1.0/qtl2ggplot/R/ggplot_snpasso.R | 130 --- qtl2ggplot-1.1.0/qtl2ggplot/R/listof_scan1coef.R |only qtl2ggplot-1.1.0/qtl2ggplot/R/map2.R |only qtl2ggplot-1.1.0/qtl2ggplot/R/sdp_to_pattern.R |only qtl2ggplot-1.1.0/qtl2ggplot/R/snpinfo_to_haplos.R |only qtl2ggplot-1.1.0/qtl2ggplot/R/snpinfo_to_map.R |only qtl2ggplot-1.1.0/qtl2ggplot/R/summary_scan1.R |only qtl2ggplot-1.1.0/qtl2ggplot/build/vignette.rds |binary qtl2ggplot-1.1.0/qtl2ggplot/inst/License.md | 2 qtl2ggplot-1.1.0/qtl2ggplot/inst/ReadMe.md | 39 - qtl2ggplot-1.1.0/qtl2ggplot/inst/doc/qtl2ggplot.R | 184 +++-- qtl2ggplot-1.1.0/qtl2ggplot/inst/doc/qtl2ggplot.Rmd | 311 ++++++-- qtl2ggplot-1.1.0/qtl2ggplot/inst/doc/qtl2ggplot.html | 477 ++++++++----- qtl2ggplot-1.1.0/qtl2ggplot/man/ggplot_coef.Rd | 15 qtl2ggplot-1.1.0/qtl2ggplot/man/ggplot_genes.Rd | 20 qtl2ggplot-1.1.0/qtl2ggplot/man/ggplot_listof_scan1coef.Rd |only qtl2ggplot-1.1.0/qtl2ggplot/man/ggplot_onegeno.Rd | 6 qtl2ggplot-1.1.0/qtl2ggplot/man/ggplot_scan1.Rd | 14 qtl2ggplot-1.1.0/qtl2ggplot/man/ggplot_snpasso.Rd | 63 - qtl2ggplot-1.1.0/qtl2ggplot/man/listof_scan1coef.Rd |only qtl2ggplot-1.1.0/qtl2ggplot/man/sdp_to_pattern.Rd |only qtl2ggplot-1.1.0/qtl2ggplot/man/summary_scan1.Rd |only qtl2ggplot-1.1.0/qtl2ggplot/src/RcppExports.cpp | 5 qtl2ggplot-1.1.0/qtl2ggplot/src/arrange_genes.cpp | 6 qtl2ggplot-1.1.0/qtl2ggplot/vignettes/qtl2ggplot.Rmd | 311 ++++++-- 38 files changed, 1137 insertions(+), 698 deletions(-)
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>),
Bradley Jones [ctb],
Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidytree versions 0.3.4 dated 2021-05-22 and 0.3.5 dated 2021-09-08
DESCRIPTION | 12 ++-- MD5 | 36 +++++++----- NAMESPACE | 16 +++++ NEWS.md | 6 ++ R/AllClasses.R | 11 ++- R/as-tibble.R | 4 + R/filter.R | 12 ++++ R/get-fields.R | 20 ++++--- R/left-join.R |only R/methods-tidyr.R |only R/mutate.R | 16 +++++ R/pull.R |only R/reexports.R | 17 +++++- R/rename.R |only R/select.R | 12 ++++ R/show.R | 101 +++++++++++++++++++++++++++--------- R/tidy_utilities.R |only build/vignette.rds |binary inst/doc/tidytree.html | 4 - man/get.fields-methods.Rd | 3 - man/reexports.Rd | 7 ++ tests/testthat/test-dplyr-methods.R |only 22 files changed, 217 insertions(+), 60 deletions(-)
Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the
'simdjson' library written by Daniel Lemire (and many contributors) provides
a high-performance parser for these files which by relying on parallel 'SIMD'
instruction manages to parse these files as faster than disk speed. See the
<arXiv:1902.08318> paper for more details about 'simdjson'. This package
parses 'JSON' from string, file, or remote URLs under a variety of settings.
Author: Dirk Eddelbuettel, Brendan Knapp, Daniel Lemire
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSimdJson versions 0.1.5 dated 2021-02-24 and 0.1.6 dated 2021-09-08
ChangeLog | 27 DESCRIPTION | 11 MD5 | 34 R/utils.R | 4 README.md | 2 build/partial.rdb |binary inst/NEWS.Rd | 10 inst/include/RcppSimdJson/deserialize.hpp | 63 inst/include/RcppSimdJson/deserialize/Type_Doctor.hpp | 6 inst/include/RcppSimdJson/deserialize/dataframe.hpp | 52 inst/include/RcppSimdJson/deserialize/matrix.hpp | 29 inst/include/RcppSimdJson/deserialize/scalar.hpp | 26 inst/include/RcppSimdJson/deserialize/simplify.hpp | 25 inst/include/RcppSimdJson/deserialize/vector.hpp | 8 inst/include/simdjson.cpp | 2790 + inst/include/simdjson.h |25893 ++++++------------ src/exported-utils.cpp | 18 src/simdjson_example.cpp | 3 18 files changed, 11720 insertions(+), 17281 deletions(-)
Title: Latin Hypercube Samples
Description: Provides a number of methods for creating and augmenting Latin Hypercube Samples and Orthogonal Array Latin Hypercube Samples.
Author: Rob Carnell [aut, cre]
Maintainer: Rob Carnell <bertcarnell@gmail.com>
Diff between lhs versions 1.1.2 dated 2021-09-07 and 1.1.3 dated 2021-09-08
ChangeLog | 8 +++++++- DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- inst/doc/augment_lhs.html | 4 ++-- inst/doc/lhs_basics.html | 4 ++-- inst/doc/lhs_faq.html | 4 ++-- src/Makevars | 10 ---------- src/Makevars.win | 2 +- 8 files changed, 24 insertions(+), 28 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological
analyses. Specializes on the construction of historical matrices,
which are 2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices. Methodology based on Ehrlen
(2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2> and
deVries and Caswell (2018) <doi:10.1007/s12080-017-0353-0>.
Author: Richard P. Shefferson [aut, cre]
(<https://orcid.org/0000-0002-5234-3131>),
Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 3.7.0 dated 2021-08-18 and 3.8.0 dated 2021-09-08
lefko3-3.7.0/lefko3/vignettes/Ch9.11-1.png |only lefko3-3.7.0/lefko3/vignettes/Ch9.12-1.png |only lefko3-3.7.0/lefko3/vignettes/Ch9.7-1.png |only lefko3-3.7.0/lefko3/vignettes/Chapter9.Rmd.orig |only lefko3-3.8.0/lefko3/DESCRIPTION | 8 lefko3-3.8.0/lefko3/MD5 | 111 - lefko3-3.8.0/lefko3/NAMESPACE | 4 lefko3-3.8.0/lefko3/NEWS | 33 lefko3-3.8.0/lefko3/R/RcppExports.R | 80 + lefko3-3.8.0/lefko3/R/datamanag.R | 1473 ++++++++++++++++++++--- lefko3-3.8.0/lefko3/R/matrixcreation.R | 18 lefko3-3.8.0/lefko3/R/modelselection.R | 7 lefko3-3.8.0/lefko3/R/popchar.R | 4 lefko3-3.8.0/lefko3/R/popdyn.R | 484 ++++++- lefko3-3.8.0/lefko3/build/vignette.rds |binary lefko3-3.8.0/lefko3/inst/doc/Chapter1.Rmd | 154 +- lefko3-3.8.0/lefko3/inst/doc/Chapter1.html | 164 +- lefko3-3.8.0/lefko3/inst/doc/Chapter2.Rmd | 12 lefko3-3.8.0/lefko3/inst/doc/Chapter2.html | 23 lefko3-3.8.0/lefko3/inst/doc/Chapter5.Rmd | 17 lefko3-3.8.0/lefko3/inst/doc/Chapter5.html | 8 lefko3-3.8.0/lefko3/inst/doc/Chapter6.Rmd | 7 lefko3-3.8.0/lefko3/inst/doc/Chapter6.html | 16 lefko3-3.8.0/lefko3/inst/doc/Chapter8.Rmd | 35 lefko3-3.8.0/lefko3/inst/doc/Chapter8.html | 43 lefko3-3.8.0/lefko3/inst/doc/Chapter9.R |only lefko3-3.8.0/lefko3/inst/doc/Chapter9.Rmd | 355 ++--- lefko3-3.8.0/lefko3/inst/doc/Chapter9.html | 928 +++++++++----- lefko3-3.8.0/lefko3/man/add_lM.Rd |only lefko3-3.8.0/lefko3/man/aflefko2.Rd | 7 lefko3-3.8.0/lefko3/man/create_lM.Rd | 132 +- lefko3-3.8.0/lefko3/man/delete_lM.Rd |only lefko3-3.8.0/lefko3/man/historicalize3.Rd | 34 lefko3-3.8.0/lefko3/man/lambda3.lefkoMat.Rd | 6 lefko3-3.8.0/lefko3/man/lambda3.matrix.Rd | 4 lefko3-3.8.0/lefko3/man/modelsearch.Rd | 2 lefko3-3.8.0/lefko3/man/projection3.Rd | 44 lefko3-3.8.0/lefko3/man/repvalue3.Rd | 4 lefko3-3.8.0/lefko3/man/repvalue3.lefkoMat.Rd | 55 lefko3-3.8.0/lefko3/man/sf_distrib.Rd | 2 lefko3-3.8.0/lefko3/man/stablestage3.Rd | 4 lefko3-3.8.0/lefko3/man/stablestage3.lefkoMat.Rd | 53 lefko3-3.8.0/lefko3/man/subset_lM.Rd |only lefko3-3.8.0/lefko3/man/summary.lefkoMat.Rd | 3 lefko3-3.8.0/lefko3/man/summary.lefkoProj.Rd |only lefko3-3.8.0/lefko3/man/supplemental.Rd | 2 lefko3-3.8.0/lefko3/man/verticalize3.Rd | 58 lefko3-3.8.0/lefko3/src/DataManagement.cpp | 88 + lefko3-3.8.0/lefko3/src/RcppExports.cpp | 25 lefko3-3.8.0/lefko3/src/popdynamics.cpp | 149 +- lefko3-3.8.0/lefko3/vignettes/Chapter1.Rmd | 154 +- lefko3-3.8.0/lefko3/vignettes/Chapter2.Rmd | 12 lefko3-3.8.0/lefko3/vignettes/Chapter2.Rmd.orig | 10 lefko3-3.8.0/lefko3/vignettes/Chapter5.Rmd | 17 lefko3-3.8.0/lefko3/vignettes/Chapter5.Rmd.orig | 5 lefko3-3.8.0/lefko3/vignettes/Chapter6.Rmd | 7 lefko3-3.8.0/lefko3/vignettes/Chapter6.Rmd.orig | 5 lefko3-3.8.0/lefko3/vignettes/Chapter8.Rmd | 35 lefko3-3.8.0/lefko3/vignettes/Chapter8.Rmd.orig | 3 lefko3-3.8.0/lefko3/vignettes/Chapter9.Rmd | 355 ++--- lefko3-3.8.0/lefko3/vignettes/Lefko3Tutorial.bib | 2 61 files changed, 3838 insertions(+), 1423 deletions(-)
Title: Audio Interface for R
Description: Interfaces to audio devices (mainly sample-based) from R to allow recording and playback of audio. Built-in devices include Windows MM, Mac OS X AudioUnits and PortAudio (the last one is very experimental).
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between audio versions 0.1-7 dated 2020-03-09 and 0.1-8 dated 2021-09-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/driver.h | 1 - src/file.c | 5 ++--- 4 files changed, 8 insertions(+), 10 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired by the end of 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Daniel Baston [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.5-23 dated 2021-02-03 and 1.5-25 dated 2021-09-08
rgdal-1.5-23/rgdal/inst/vectors/airports.gfs |only rgdal-1.5-25/rgdal/ChangeLog | 2271 ++++------ rgdal-1.5-25/rgdal/DESCRIPTION | 10 rgdal-1.5-25/rgdal/MD5 | 46 rgdal-1.5-25/rgdal/NEWS.md | 16 rgdal-1.5-25/rgdal/R/AAA.R | 8 rgdal-1.5-25/rgdal/R/make_EPSG.R | 27 rgdal-1.5-25/rgdal/R/ogr.R | 16 rgdal-1.5-25/rgdal/R/ogr_sp.R | 55 rgdal-1.5-25/rgdal/build/vignette.rds |binary rgdal-1.5-25/rgdal/configure | 44 rgdal-1.5-25/rgdal/configure.ac | 13 rgdal-1.5-25/rgdal/inst/ChangeLog | 2271 ++++------ rgdal-1.5-25/rgdal/inst/SVN_VERSION | 2 rgdal-1.5-25/rgdal/inst/doc/CRS_projections_transformations.Rmd | 4 rgdal-1.5-25/rgdal/inst/doc/CRS_projections_transformations.html | 342 - rgdal-1.5-25/rgdal/inst/doc/OGR_shape_encoding.pdf |binary rgdal-1.5-25/rgdal/inst/doc/PROJ6_GDAL3.Rmd | 2 rgdal-1.5-25/rgdal/inst/doc/PROJ6_GDAL3.html | 459 +- rgdal-1.5-25/rgdal/man/readOGR.Rd | 7 rgdal-1.5-25/rgdal/man/spTransform-methods.Rd | 20 rgdal-1.5-25/rgdal/src/Makevars.ucrt |only rgdal-1.5-25/rgdal/src/Makevars.win | 2 rgdal-1.5-25/rgdal/vignettes/CRS_projections_transformations.Rmd | 4 rgdal-1.5-25/rgdal/vignettes/PROJ6_GDAL3.Rmd | 2 25 files changed, 2971 insertions(+), 2650 deletions(-)
Title: Polynomial Regression
Description: Automate formation and evaluation of polynomial regression models. The motivation for this package is described in 'Polynomial Regression As an Alternative to Neural Nets' by Xi Cheng, Bohdan Khomtchouk, Norman Matloff, and Pete Mohanty (<arXiv:1806.06850>).
Author: Norm Matloff [aut, cre] (<https://orcid.org/0000-0001-9179-6785>),
Xi Cheng [aut],
Pete Mohanty [aut] (<https://orcid.org/0000-0001-8531-3345>),
Bohdan Khomtchouk [aut],
Matthew Kotila [aut],
Robin Yancey [aut],
Robert Tucker [aut],
Allan Zhao [aut],
Tiffany Jiang [aut]
Maintainer: Norm Matloff <matloff@cs.ucdavis.edu>
Diff between polyreg versions 0.6.7 dated 2020-04-04 and 0.6.9 dated 2021-09-08
DESCRIPTION | 12 MD5 | 26 - NAMESPACE | 38 - R/FSR.R | 627 +++++++++++++++--------------- R/S3methods.R | 571 ++++++++++++++-------------- R/getPoly.R | 456 +++++++++++----------- R/helper_functions.R | 1035 ++++++++++++++++++++++++++------------------------- R/onAttach.R | 12 R/polyFit.R | 383 +++++++++--------- man/FSR.Rd | 138 +++--- man/getPoly.Rd | 221 +++++----- man/misc.Rd | 52 +- man/polyFit.Rd | 199 ++++----- man/predict.FSR.Rd | 64 +-- 14 files changed, 1959 insertions(+), 1875 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with Rscript to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L Davis [aut, cre],
Allen Day [ctb] (Some documentation and examples ported from the getopt
package.),
Python Software Foundation [ctb] (Some documentation from the optparse
Python module.),
Paul Newell [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 2.0.4 dated 2021-08-06 and 2.1.1 dated 2021-09-08
DESCRIPTION | 6 +-- MD5 | 18 +++++----- NEWS.md | 16 +++++++-- R/argparse.R | 69 ++++++++++++++++++++++------------------- README.md | 13 ++----- inst/doc/argparse.Rmd | 2 - inst/doc/argparse.html | 54 ++++++++++++++++---------------- man/ArgumentParser.Rd | 5 -- tests/testthat/test-argparse.R | 11 ++++++ vignettes/argparse.Rmd | 2 - 10 files changed, 106 insertions(+), 90 deletions(-)
Title: Tidy Verbs for Fast Data Manipulation
Description: A toolkit of tidy data manipulation verbs with 'data.table' as the backend.
Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table',
'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain.
This package is an extension of 'data.table'. While enjoying a tidy syntax,
it also wraps combinations of efficient functions to facilitate frequently-used data operations.
Author: Tian-Yuan Huang [aut, cre] (<https://orcid.org/0000-0002-3591-4203>)
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between tidyfst versions 0.9.9 dated 2020-09-01 and 1.0.0 dated 2021-09-08
tidyfst-0.9.9/tidyfst/tests/testthat/test-dummy.R |only tidyfst-1.0.0/tidyfst/DESCRIPTION | 9 tidyfst-1.0.0/tidyfst/MD5 | 63 tidyfst-1.0.0/tidyfst/NAMESPACE | 3 tidyfst-1.0.0/tidyfst/R/col_max.R |only tidyfst-1.0.0/tidyfst/R/distinct_dt.R | 10 tidyfst-1.0.0/tidyfst/R/dummy_dt.R | 43 tidyfst-1.0.0/tidyfst/R/mutate_dt.R | 1 tidyfst-1.0.0/tidyfst/build/vignette.rds |binary tidyfst-1.0.0/tidyfst/inst/doc/benchmark.html | 674 +--- tidyfst-1.0.0/tidyfst/inst/doc/chinese_tutorial.html | 1185 +++----- tidyfst-1.0.0/tidyfst/inst/doc/english_tutorial.html | 2658 ++++++++----------- tidyfst-1.0.0/tidyfst/inst/doc/example1_intro.Rmd | 2 tidyfst-1.0.0/tidyfst/inst/doc/example1_intro.html | 620 +--- tidyfst-1.0.0/tidyfst/inst/doc/example2_join.Rmd | 2 tidyfst-1.0.0/tidyfst/inst/doc/example2_join.html | 816 ++--- tidyfst-1.0.0/tidyfst/inst/doc/example3_reshape.Rmd | 2 tidyfst-1.0.0/tidyfst/inst/doc/example3_reshape.html | 754 ++--- tidyfst-1.0.0/tidyfst/inst/doc/example4_nest.Rmd | 2 tidyfst-1.0.0/tidyfst/inst/doc/example4_nest.html | 384 -- tidyfst-1.0.0/tidyfst/inst/doc/example5_fst.Rmd | 2 tidyfst-1.0.0/tidyfst/inst/doc/example5_fst.html | 304 -- tidyfst-1.0.0/tidyfst/inst/doc/example6_dt.Rmd | 2 tidyfst-1.0.0/tidyfst/inst/doc/example6_dt.html | 264 - tidyfst-1.0.0/tidyfst/man/col_max.Rd |only tidyfst-1.0.0/tidyfst/man/distinct_dt.Rd | 7 tidyfst-1.0.0/tidyfst/man/dummy_dt.Rd | 3 tidyfst-1.0.0/tidyfst/man/reexports.Rd | 5 tidyfst-1.0.0/tidyfst/vignettes/example1_intro.Rmd | 2 tidyfst-1.0.0/tidyfst/vignettes/example2_join.Rmd | 2 tidyfst-1.0.0/tidyfst/vignettes/example3_reshape.Rmd | 2 tidyfst-1.0.0/tidyfst/vignettes/example4_nest.Rmd | 2 tidyfst-1.0.0/tidyfst/vignettes/example5_fst.Rmd | 2 tidyfst-1.0.0/tidyfst/vignettes/example6_dt.Rmd | 2 34 files changed, 3119 insertions(+), 4708 deletions(-)
Title: Legislative Speeches
Description: Converts the floor speeches of Uruguayan legislators, extracted from the
parliamentary minutes, to tidy data.frame where each observation is the intervention of a single legislator.
Author: Nicolas Schmidt [aut, cre] (<https://orcid.org/0000-0001-5083-5792>),
Diego Lujan [aut],
Juan Andres Moraes [aut],
Elina Gomez [ctb]
Maintainer: Nicolas Schmidt <nschmidt@cienciassociales.edu.uy>
Diff between speech versions 0.1.0 dated 2019-12-22 and 0.1.3 dated 2021-09-08
speech-0.1.0/speech/man/reexports.Rd |only speech-0.1.3/speech/DESCRIPTION | 24 speech-0.1.3/speech/MD5 | 41 speech-0.1.3/speech/NAMESPACE | 8 speech-0.1.3/speech/NEWS.md |only speech-0.1.3/speech/R/speech_build.R | 38 speech-0.1.3/speech/R/speech_check.R | 23 speech-0.1.3/speech/R/speech_legis_replace.R | 24 speech-0.1.3/speech/R/speech_recompiler.R | 22 speech-0.1.3/speech/R/speech_uncompiler.R |only speech-0.1.3/speech/R/speech_url.R |only speech-0.1.3/speech/R/speech_view.R | 20 speech-0.1.3/speech/R/speech_word_count.R | 46 speech-0.1.3/speech/R/sysdata.rda |only speech-0.1.3/speech/R/utils.R | 615 +++++++++-- speech-0.1.3/speech/README.md | 139 +- speech-0.1.3/speech/man/figures/README-unnamed-chunk-2-1.png |binary speech-0.1.3/speech/man/speech_build.Rd | 21 speech-0.1.3/speech/man/speech_check.Rd | 8 speech-0.1.3/speech/man/speech_legis_replace.Rd | 8 speech-0.1.3/speech/man/speech_recompiler.Rd | 15 speech-0.1.3/speech/man/speech_uncompiler.Rd |only speech-0.1.3/speech/man/speech_url.Rd |only speech-0.1.3/speech/man/speech_view.Rd | 6 speech-0.1.3/speech/man/speech_word_count.Rd | 13 25 files changed, 780 insertions(+), 291 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>)
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between inti versions 0.4.2 dated 2021-08-15 and 0.4.3 dated 2021-09-08
DESCRIPTION | 8 LICENSE | 4 MD5 | 229 NAMESPACE | 210 NEWS.md | 409 R/H2cal.R | 930 R/colortext.R | 158 R/footnotes.R | 268 R/include_figure.R | 108 R/include_table.R | 128 R/jc_tombola.R | 152 R/mean_comparison.R | 290 R/met.R | 68 R/metamorfosis.R | 346 R/outliers_remove.R | 190 R/plot_diag.R | 104 R/plot_raw.R | 500 R/plot_smr.R | 608 R/potato.R | 62 R/tarpuy.R | 98 R/tarpuy_design.R | 900 R/tarpuy_plex.R | 538 R/tarpuy_plotdesign.R | 210 R/tarpuy_varlist.R | 274 R/utils.R | 12 R/web_table.R | 166 R/yupana.R | 96 R/yupana_analysis.R | 308 R/yupana_export_smr.R | 392 R/yupana_import_smr.R | 272 R/yupana_mvr.R | 292 R/yupana_reshape.R | 132 README.md | 132 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 54 inst/doc/apps.R | 6 inst/doc/apps.Rmd | 252 inst/doc/apps.html | 326 inst/doc/heritability.R | 98 inst/doc/heritability.Rmd | 306 inst/doc/heritability.html | 1394 inst/doc/policy.Rmd | 126 inst/doc/policy.html | 226 inst/doc/rticles.R | 52 inst/doc/rticles.Rmd | 336 inst/doc/rticles.html | 602 inst/doc/tarpuy.R | 18 inst/doc/tarpuy.Rmd | 104 inst/doc/tarpuy.html | 252 inst/doc/yupana.R | 86 inst/doc/yupana.Rmd | 240 inst/doc/yupana.html | 562 inst/rmarkdown/templates/books/skeleton/_bookdown.yml | 54 inst/rmarkdown/templates/books/skeleton/_output.yml | 52 inst/rmarkdown/templates/books/skeleton/files/book.bib | 138 inst/rmarkdown/templates/books/skeleton/files/style_rbooks.css | 94 inst/rmarkdown/templates/books/skeleton/index.Rmd | 820 inst/rmarkdown/templates/books/skeleton/skeleton.Rmd | 412 inst/rmarkdown/templates/books/template.yaml | 8 inst/rmarkdown/templates/rticles/skeleton/files/book.bib | 138 inst/rmarkdown/templates/rticles/skeleton/skeleton.Rmd | 852 inst/rmarkdown/templates/rticles/template.yaml | 8 inst/rstudio/addins.dcf | 20 inst/tarpuy/msgs.R | 98 inst/tarpuy/pkgs.R | 44 inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 26 inst/tarpuy/server.R | 1358 inst/tarpuy/ui.R | 1606 inst/tarpuy/www/analytics.html | 18 inst/tarpuy/www/bootstrap_sandstone.css |21904 +++++----- inst/tarpuy/www/custom.css | 12 inst/yupana/msgs.R | 100 inst/yupana/pkgs.R | 50 inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf |only inst/yupana/rsconnect/shinyapps.io/flavjack/yupanapro.dcf | 26 inst/yupana/server.R | 3216 - inst/yupana/ui.R | 1670 inst/yupana/www/analytics.html | 18 inst/yupana/www/bootstrap_sandstone.css |21902 ++++----- inst/yupana/www/custom.css | 12 man/H2cal.Rd | 264 man/colortext.Rd | 68 man/footnotes.Rd | 58 man/include_figure.Rd | 66 man/include_table.Rd | 90 man/jc_tombola.Rd | 96 man/mean_comparison.Rd | 120 man/met.Rd | 68 man/metamorphosis.Rd | 74 man/outliers_remove.Rd | 88 man/plot_diag.Rd | 34 man/plot_raw.Rd | 192 man/plot_smr.Rd | 226 man/potato.Rd | 76 man/reexports.Rd | 32 man/tarpuy.Rd | 58 man/tarpuy_design.Rd | 136 man/tarpuy_plex.Rd | 194 man/tarpuy_plotdesign.Rd | 84 man/tarpuy_varlist.Rd | 54 man/web_table.Rd | 98 man/yupana.Rd | 58 man/yupana_analysis.Rd | 134 man/yupana_export_smr.Rd | 202 man/yupana_import_smr.Rd | 92 man/yupana_mvr.Rd | 116 man/yupana_reshape.Rd | 88 vignettes/apps.Rmd | 252 vignettes/files/book.bib | 3118 - vignettes/files/pkgs.bib | 738 vignettes/heritability.Rmd | 306 vignettes/policy.Rmd | 126 vignettes/rticles.Rmd | 336 vignettes/tarpuy.Rmd | 104 vignettes/yupana.Rmd | 240 116 files changed, 38176 insertions(+), 38200 deletions(-)