Title: Mean Partition, Uncertainty Assessment, Cluster Validation and
Visualization Selection for Cluster Analysis
Description: Providing mean partition for ensemble clustering by optimal transport alignment(OTA), uncertainty measures for both partition-wise and cluster-wise assessment and multiple visualization functions to show uncertainty, for instance, membership heat map and plot of covering point set. A partition refers to an overall clustering result.
Author: Lixiang Zhang [aut, cre],
Beomseok Seo [aut],
Lin Lin [aut],
Jia Li [aut]
Maintainer: Lixiang Zhang <lzz46@psu.edu>
Diff between OTclust versions 1.0.3 dated 2020-10-19 and 1.0.4 dated 2020-12-17
OTclust-1.0.3/OTclust/vignettes/OTclust_cache/html/unnamed-chunk-13_7f3f088d7d9d8ba5b03976ebdbb24983.RData |only OTclust-1.0.3/OTclust/vignettes/OTclust_cache/html/unnamed-chunk-13_7f3f088d7d9d8ba5b03976ebdbb24983.rdb |only OTclust-1.0.3/OTclust/vignettes/OTclust_cache/html/unnamed-chunk-13_7f3f088d7d9d8ba5b03976ebdbb24983.rdx |only OTclust-1.0.4/OTclust/DESCRIPTION | 6 - OTclust-1.0.4/OTclust/MD5 | 43 +++++----- OTclust-1.0.4/OTclust/NAMESPACE | 1 OTclust-1.0.4/OTclust/R/CPS.R | 5 - OTclust-1.0.4/OTclust/R/clustCPS.R | 5 - OTclust-1.0.4/OTclust/R/perturb.R | 13 ++- OTclust-1.0.4/OTclust/R/pplot.R |only OTclust-1.0.4/OTclust/R/visCPS.R | 5 - OTclust-1.0.4/OTclust/inst/doc/OTclust.R | 13 +++ OTclust-1.0.4/OTclust/inst/doc/OTclust.Rmd | 6 + OTclust-1.0.4/OTclust/inst/doc/OTclust.html | 43 +++++----- OTclust-1.0.4/OTclust/man/CPS.Rd | 2 OTclust-1.0.4/OTclust/man/clustCPS.Rd | 2 OTclust-1.0.4/OTclust/man/perturb.Rd | 6 - OTclust-1.0.4/OTclust/man/pplot.Rd |only OTclust-1.0.4/OTclust/man/visCPS.Rd | 2 OTclust-1.0.4/OTclust/src/huge.cpp | 21 +++- OTclust-1.0.4/OTclust/vignettes/OTclust.Rmd | 6 + OTclust-1.0.4/OTclust/vignettes/OTclust_cache/html/unnamed-chunk-13_e236f832cd371fb91ca3a7c0e79dcf5f.RData |only OTclust-1.0.4/OTclust/vignettes/OTclust_cache/html/unnamed-chunk-13_e236f832cd371fb91ca3a7c0e79dcf5f.rdb |only OTclust-1.0.4/OTclust/vignettes/OTclust_cache/html/unnamed-chunk-13_e236f832cd371fb91ca3a7c0e79dcf5f.rdx |only OTclust-1.0.4/OTclust/vignettes/OTclust_files/figure-html/unnamed-chunk-13-1.png |binary OTclust-1.0.4/OTclust/vignettes/OTclust_files/figure-html/unnamed-chunk-13-2.png |binary OTclust-1.0.4/OTclust/vignettes/OTclust_files/figure-html/unnamed-chunk-13-3.png |only 27 files changed, 114 insertions(+), 65 deletions(-)
Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse
set of pipelining operators ('PipeOps') that can be composed into graphs.
Operations exist for data preprocessing, model fitting, and ensemble
learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can
therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre],
Florian Pfisterer [aut] (<https://orcid.org/0000-0001-8867-762X>),
Lennart Schneider [aut] (<https://orcid.org/0000-0003-4152-5308>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Susanne Dandl [aut]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr3pipelines versions 0.3.1 dated 2020-11-16 and 0.3.2 dated 2020-12-17
mlr3pipelines-0.3.1/mlr3pipelines/tests/testthat/test_graphlearner.R |only mlr3pipelines-0.3.2/mlr3pipelines/DESCRIPTION | 6 mlr3pipelines-0.3.2/mlr3pipelines/MD5 | 44 ++--- mlr3pipelines-0.3.2/mlr3pipelines/NEWS.md | 5 mlr3pipelines-0.3.2/mlr3pipelines/R/GraphLearner.R | 8 mlr3pipelines-0.3.2/mlr3pipelines/R/LearnerAvg.R | 2 mlr3pipelines-0.3.2/mlr3pipelines/R/PipeOp.R | 1 mlr3pipelines-0.3.2/mlr3pipelines/R/PipeOpColApply.R | 71 +++----- mlr3pipelines-0.3.2/mlr3pipelines/R/PipeOpCopy.R | 2 mlr3pipelines-0.3.2/mlr3pipelines/R/PipeOpImputeOOR.R | 2 mlr3pipelines-0.3.2/mlr3pipelines/R/PipeOpSmote.R | 2 mlr3pipelines-0.3.2/mlr3pipelines/R/PipeOpTaskPreproc.R | 15 - mlr3pipelines-0.3.2/mlr3pipelines/R/bibentries.R | 5 mlr3pipelines-0.3.2/mlr3pipelines/R/mlr_pipeops.R | 8 mlr3pipelines-0.3.2/mlr3pipelines/R/typecheck.R | 19 +- mlr3pipelines-0.3.2/mlr3pipelines/build/partial.rdb |binary mlr3pipelines-0.3.2/mlr3pipelines/man/PipeOpTaskPreproc.Rd | 3 mlr3pipelines-0.3.2/mlr3pipelines/man/mlr_pipeops_colapply.Rd | 52 +++--- mlr3pipelines-0.3.2/mlr3pipelines/man/mlr_pipeops_copy.Rd | 2 mlr3pipelines-0.3.2/mlr3pipelines/tests/testthat/helper_compat.R | 2 mlr3pipelines-0.3.2/mlr3pipelines/tests/testthat/test_GraphLearner.R |only mlr3pipelines-0.3.2/mlr3pipelines/tests/testthat/test_PipeOp.R | 1 mlr3pipelines-0.3.2/mlr3pipelines/tests/testthat/test_mlr_graphs_robustify.R | 10 + mlr3pipelines-0.3.2/mlr3pipelines/tests/testthat/test_pipeop_colapply.R | 81 ++++++++++ 24 files changed, 220 insertions(+), 121 deletions(-)
Title: Tools to Evaluate Disclosure Risk
Description: Tools for calculating disclosure risk measures for microdata,
including record-level and file-level measures. The record-level disclosure
risk is estimated primarily using exhaustive tabulation. The file-level
disclosure risk is estimated by fitting loglinear models on the observed
sample counts in cells formed by key variables and their interactions.
Funded by the National Center for Education Statistics. See Skinner and
Shlomo (2008) <doi:10.1198/016214507000001328> for a description of the
file-level risk measures and the loglinear model approach.
Author: John Riddles [aut, cre],
Westat [cph]
Maintainer: John Riddles <JohnRiddles@westat.com>
Diff between SDCNway versions 1.0.0 dated 2020-09-22 and 1.0.1 dated 2020-12-17
DESCRIPTION | 25 +++++++++++++++---------- MD5 | 8 ++++++-- build/partial.rdb |binary build/vignette.rds |only inst/doc |only vignettes |only 6 files changed, 21 insertions(+), 12 deletions(-)
Title: Reproducible Reports in Psychology
Description: Helper functions for producing reports in Psychology (Reproducible Research). Provides required formatted strings (APA style) for use in 'Knitr'/'Latex' integration within *.Rnw files.
Author: Ian G Mackenzie
Maintainer: Ian G Mackenzie <ian.mackenzie@uni-tuebingen.de>
Diff between psychReport versions 1.1.1 dated 2020-09-18 and 2.0.0 dated 2020-12-17
DESCRIPTION | 6 - MD5 | 40 ++++---- NAMESPACE | 2 R/anova.R | 112 ++++++++++++++-------- R/psychReportData.R | 2 R/ttest.R | 1 R/utils.R | 174 ++++++++++++++++++----------------- man/addDataDF.Rd | 1 man/aovEffectSize.Rd | 1 man/aovRoundDigits.Rd | 8 - man/aovSphericityAdjustment.Rd | 4 man/aovTable.Rd | 11 -- man/aovTidyTable.Rd | 5 - man/ciStrT.Rd | 1 man/pValueString.Rd | 10 -- man/printTable.Rd | 7 + tests/testthat/test-aovRoundDigits.R | 17 +-- tests/testthat/test-aovTable.R | 2 tests/testthat/test-pValueString.R | 4 tests/testthat/test-statStrAov.R | 25 ++--- tests/testthat/test-statStrT.R | 2 21 files changed, 235 insertions(+), 200 deletions(-)
Title: Board Game Graphics
Description: Functions to make board game graphics. By default makes game diagrams, animations, and "Print & Play" layouts for the 'piecepack' <https://www.ludism.org/ppwiki> but can be configured to make graphics for other board game systems.
Author: Trevor L Davis [aut, cre],
Delapouite <https://delapouite.com/> [dtc] (Meeple shape extracted from
"Meeple icon" <https://game-icons.net/1x1/delapouite/meeple.html> /
"CC BY 3.0" <https://creativecommons.org/licenses/by/3.0/>)
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between piecepackr versions 1.6.2 dated 2020-12-17 and 1.6.3 dated 2020-12-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 2 +- R/basicPieceGrobs.R | 2 +- tests/testthat/test-draw_component.R | 5 ++++- 5 files changed, 13 insertions(+), 10 deletions(-)
Title: A Causal Mediation Method with Methylated Region (MR) as the
Mediator
Description: A causal mediation approach under the counterfactual framework
to test the significance of total, direct and indirect effects. In this approach,
a group of methylated sites from a predefined region are utilized as the mediator,
and the functional transformation is used to reduce the possible high dimension
in the region-based methylated sites and account for their location information.
Author: Qi Yan
Maintainer: Qi Yan <qy2253@cumc.columbia.edu>
Diff between MRmediation versions 1.0.0 dated 2020-07-07 and 1.0.1 dated 2020-12-17
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- NAMESPACE | 1 + R/mediation_single.R |only man/mediation_single.Rd |only 5 files changed, 10 insertions(+), 7 deletions(-)
Title: Multi-Trait Dissimilarity with more Uniform Contributions
Description: R function gawdis() produces multi-trait dissimilarity with more uniform contributions of different traits. de Bello et al. (2021) <doi:10.1111/2041-210X.13537> presented the approach based on minimizing the differences in the correlation between the dissimilarity of each trait, or groups of traits, and the multi-trait dissimilarity. This is done using either an analytic or a numerical solution, both available in the function.
Author: Francesco de Bello [aut],
Zoltan Botta-Dukat [aut],
Jan Leps [aut],
Pavel Fibich [aut, cre]
Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>
Diff between gawdis versions 0.1.0 dated 2020-11-05 and 0.1.2 dated 2020-12-17
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/GAgawdis.R | 8 ++++---- R/gawdis.R | 34 +++++++++++++++++----------------- README.md | 16 ++++++++-------- inst/CITATION | 4 ++-- inst/doc/gawdis.R | 2 +- inst/doc/gawdis.Rmd | 18 +++++++++--------- inst/doc/gawdis.html | 49 ++++++++++++++++++++++++------------------------- man/GAgawdis.Rd | 4 ++-- man/gawdis.Rd | 16 ++++++++-------- vignettes/gawdis.Rmd | 18 +++++++++--------- 12 files changed, 99 insertions(+), 100 deletions(-)
Title: Data Only: The Correlates of State Policy Project Dataset
Description: Contains the Correlates of State Policy Project dataset (+ codebook) assembled by Marty P. Jordan and Matt Grossmann (2020) <http://ippsr.msu.edu/public-policy/correlates-state-policy> used by the 'cspp' package. The Correlates data contains over 2000 variables across more than 100 years that pertain to state politics and policy in the United States.
Author: Caleb Lucas (https://caleblucas.com/) and Joshua McCrain (http://joshuamccrain.com/)
Maintainer: Josh McCrain <josh.mccrain@gmail.com>
Diff between csppData versions 0.1.0 dated 2020-12-17 and 0.1.1 dated 2020-12-17
DESCRIPTION | 7 +++---- MD5 | 10 +++++----- README.md | 19 ++++++++++--------- data/codebook.rda |binary data/correlates.rda |binary man/codebook.Rd | 2 +- 6 files changed, 19 insertions(+), 19 deletions(-)
Title: Flexible Polyline Encoding
Description: Binding to the C++ implementation of the flexible polyline
encoding by HERE <https://github.com/heremaps/flexible-polyline>. The
flexible polyline encoding is a lossy compressed representation of a list of
coordinate pairs or coordinate triples. The encoding is achieved by:
(1) Reducing the decimal digits of each value;
(2) encoding only the offset from the previous point;
(3) using variable length for each coordinate delta; and
(4) using 64 URL-safe characters to display the result.
Author: Merlin Unterfinger [aut, cre] (<https://orcid.org/0000-0003-2020-2366>),
HERE Europe B.V. [aut, cph] (Flexible polyline encoding C++
implementation)
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between flexpolyline versions 0.1.1 dated 2020-08-07 and 0.2.0 dated 2020-12-17
DESCRIPTION | 12 - MD5 | 54 ++-- NAMESPACE | 2 NEWS.md | 15 + R/RcppExports.R | 75 +++++- R/decode_sf.R | 22 + R/encode_sf.R | 66 ++--- README.md | 8 build/vignette.rds |binary inst/doc/cpp-binding.Rmd | 7 inst/doc/cpp-binding.html | 293 ++++-------------------- inst/doc/flexpolyline.html | 305 +++++-------------------- inst/doc/sf-support.Rmd | 4 inst/doc/sf-support.html | 449 +++++++++++--------------------------- inst/include/hf/flexpolyline.h | 9 man/decode.Rd | 7 man/decode_sf.Rd | 8 man/encode.Rd | 12 - man/encode_sf.Rd | 40 +-- man/flexpolyline-package.Rd | 6 man/get_third_dimension.Rd |only man/set_third_dimension.Rd |only src/RcppExports.cpp | 27 ++ src/flexpolyline.cpp | 267 +++++++++++++++------- tests/testthat/test-cpp_binding.R | 20 + tests/testthat/test-decode_sf.R | 28 +- tests/testthat/test-encode_sf.R | 72 ++---- vignettes/cpp-binding.Rmd | 7 vignettes/sf-support.Rmd | 4 29 files changed, 732 insertions(+), 1087 deletions(-)
Title: 'Coroutines' for R
Description: Provides 'coroutines' for R, a family of functions that
can be suspended and resumed later on. This includes 'async'
functions (which await) and generators (which yield). 'Async'
functions are based on the concurrency framework of the 'promises'
package. Generators are based on a dependency free iteration
protocol defined in 'coro' and are compatible with iterators from
the 'reticulate' package.
Author: Lionel Henry [aut, cre],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between coro versions 1.0.0 dated 2020-12-09 and 1.0.1 dated 2020-12-17
DESCRIPTION | 6 MD5 | 12 NEWS.md | 4 R/utils-vector.R | 3 README.md | 4 inst/doc/generator.html | 500 +++++++++++--------------------------- tests/testthat/test-step-reduce.R | 29 ++ 7 files changed, 192 insertions(+), 366 deletions(-)
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Seqinr includes
utilities for sequence data management under the ACNUC system
described in Gouy, M. et al. (1984) Nucleic Acids Res.
12:121-127 <doi:10.1093/nar/12.1Part1.121>.
Author: Delphine Charif [aut],
Olivier Clerc [ctb],
Carolin Frank [ctb],
Jean R. Lobry [aut, cph],
Anamaria Necşulea [ctb],
Leonor Palmeira [ctb],
Simon Penel [cre],
Guy Perrière [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>
Diff between seqinr versions 4.2-4 dated 2020-10-10 and 4.2-5 dated 2020-12-17
DESCRIPTION | 14 +++++----- MD5 | 66 ++++++++++++++++++++++++------------------------ R/GC.R | 27 +++++++++++-------- R/read.alignment.R | 22 ++++++++++++---- data/AnoukResult.RData |binary data/ECH.RData |binary data/EXP.RData |binary data/JLO.RData |binary data/SEQINR.UTIL.RData |binary data/aacost.RData |binary data/aaindex.RData |binary data/caitab.RData |binary data/chargaff.RData |binary data/clustal.RData |binary data/dinucl.RData |binary data/ec999.RData |binary data/fasta.RData |binary data/gcO2.rda |binary data/gcT.rda |binary data/gs500liz.RData |binary data/identifiler.RData |binary data/kaksTorture.RData |binary data/m16j.RData |binary data/mase.RData |binary data/msf.RData |binary data/pK.RData |binary data/phylip.RData |binary data/prochlo.RData |binary data/revaligntest.RData |binary data/sysdata.rda |binary data/toyaa.RData |binary data/toycodon.RData |binary data/waterabs.RData |binary man/GC.Rd | 29 +++++++++++---------- 34 files changed, 89 insertions(+), 69 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.5.4 dated 2020-11-06 and 2.5.5 dated 2020-12-17
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 1 + NEWS | 3 +++ man/Rlabkey-package.Rd | 4 ++-- man/labkey.getRequestOptions.Rd |only 6 files changed, 15 insertions(+), 10 deletions(-)
Title: Correct Bias in DNA Methylation Analyses
Description: Implementation of the algorithms (with minor
modifications) to correct bias in quantitative DNA methylation
analyses as described by Moskalev et al. (2011)
<doi:10.1093/nar/gkr213>.
Author: Lorenz A. Kapsner [cre, aut, cph]
(<https://orcid.org/0000-0003-1866-860X>),
Evgeny A. Moskalev [aut]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between rBiasCorrection versions 0.2.4 dated 2020-11-16 and 0.2.5 dated 2020-12-17
DESCRIPTION | 9 MD5 | 28 + R/helper-table_prep.R |only inst/doc/rBiasCorrection_benchmarking.html | 4 inst/doc/rBiasCorrection_howto.html | 8 tests/testthat.R | 2 tests/testthat/_snaps |only tests/testthat/test-algorithm_minmax_FALSE.R | 406 +++++++-------------- tests/testthat/test-algorithm_minmax_FALSE_re.R |only tests/testthat/test-algorithm_minmax_TRUE.R | 446 +++++++----------------- tests/testthat/test-algorithm_minmax_TRUE_re.R |only tests/testthat/test-clean_dt.R | 246 +++++++------ tests/testthat/test-create_aggregated.R | 61 +-- tests/testthat/test-hyperbolic.R | 14 14 files changed, 496 insertions(+), 728 deletions(-)
More information about rBiasCorrection at CRAN
Permanent link
Title: Horizontal 'ggplot2' Components
Description: A 'ggplot2' extension that provides flipped components:
horizontal versions of 'Stats' and 'Geoms', and vertical versions
of 'Positions'. This package is now superseded by 'ggplot2' itself
which now has full native support for horizontal layouts. It
remains available for backward compatibility.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
Winston Chang [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between ggstance versions 0.3.4 dated 2020-04-02 and 0.3.5 dated 2020-12-17
DESCRIPTION | 16 ++++++++++------ MD5 | 26 +++++++++++++------------- NEWS.md | 2 ++ R/geom-barh.R | 10 ---------- R/stat-summaryh.R | 12 +++++++----- README.md | 6 ++++-- man/geom_barh.Rd | 5 ----- man/hmisc_h.Rd | 12 +++++++----- man/stat_binh.Rd | 12 ++++++------ man/stat_xdensity.Rd | 2 +- tests/testthat/helper-utils.R | 7 ++++++- tests/testthat/test-geom-errorbarh.R | 2 +- tests/testthat/test-positions.R | 4 ++-- tests/testthat/test-stats.R | 2 ++ 14 files changed, 61 insertions(+), 57 deletions(-)
Title: Bayesian Additive Regression Trees
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner and Justin Bleich (R package)
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between bartMachine versions 1.2.5.1 dated 2020-08-13 and 1.2.6 dated 2020-12-17
CHANGELOG | 12 ++ DESCRIPTION | 8 - MD5 | 21 ++--- NAMESPACE | 2 R/bart_node_related_methods.R | 88 ++++++++++++++++++++- R/bart_package_builders.R | 5 + R/bart_package_cross_validation.R | 11 +- R/bart_package_plots.R | 2 inst/doc/bartMachine.pdf |binary inst/java/bart_java.jar |binary java/bartMachine/bartMachine_f_gibbs_internal.java | 4 man/extract_raw_node_data.Rd |only 12 files changed, 130 insertions(+), 23 deletions(-)
Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0,
both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (submitted, 2020).
Author: Peter Bourke [aut, cre],
Geert van Geest [aut],
Roeland Voorrips [ctb],
Yanlin Liao [ctb]
Maintainer: Peter Bourke <pbourkey@gmail.com>
Diff between polymapR versions 1.1.0 dated 2020-07-15 and 1.1.1 dated 2020-12-17
DESCRIPTION | 11 +- MD5 | 26 ++--- R/aiding_functions.R | 31 +++++- R/exported_functions.R | 124 +++++++++++++++++--------- inst/doc/Vignette_genotype_probabilities.R | 2 inst/doc/Vignette_genotype_probabilities.Rmd | 9 - inst/doc/Vignette_genotype_probabilities.html | 16 +-- inst/doc/Vignette_polymapR.R | 2 inst/doc/Vignette_polymapR.Rmd | 6 - inst/doc/Vignette_polymapR.html | 42 ++++---- vignettes/Vignette_genotype_probabilities.Rmd | 9 - vignettes/Vignette_polymapR.Rmd | 6 - vignettes/figures/LG1_check_map_plotA.png |binary vignettes/figures/LG1_check_map_plotB.png |binary 14 files changed, 176 insertions(+), 108 deletions(-)
Title: Board Game Graphics
Description: Functions to make board game graphics. By default makes game diagrams, animations, and "Print & Play" layouts for the 'piecepack' <https://www.ludism.org/ppwiki> but can be configured to make graphics for other board game systems.
Author: Trevor L Davis [aut, cre],
Delapouite <https://delapouite.com/> [dtc] (Meeple shape extracted from
"Meeple icon" <https://game-icons.net/1x1/delapouite/meeple.html> /
"CC BY 3.0" <https://creativecommons.org/licenses/by/3.0/>)
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between piecepackr versions 1.5.1 dated 2020-08-10 and 1.6.2 dated 2020-12-17
DESCRIPTION | 16 MD5 | 117 +- NAMESPACE | 4 NEWS.md | 60 + R/basicPieceGrobs.R | 10 R/boards.R | 14 R/game_systems.R | 232 ++++- R/geometry.R | 8 R/hooks.R |only R/make_images.R | 8 R/op_grobs_fns.R | 41 R/op_transform.R | 10 R/piece_opt.R | 18 R/piecepackr-deprecated.R | 1 R/pips.R | 126 +++ R/pmap_piece.R | 12 R/pnp.R | 88 +- R/pp_cfg.R | 27 R/pp_shape.R | 2 R/sysdata.rda |binary R/token.R | 28 R/utils.R | 6 R/write_obj.R | 231 +++++ README.md | 411 ++++------ man/figures/README-breakthrough-1.png |binary man/figures/README-cards-1.png |only man/figures/README-config-1.png |binary man/figures/README-diagram-1.png |binary man/figures/README-dominoes-1.png |binary man/figures/README-go.png |only man/figures/README-intro1-1.png |binary man/figures/README-pmap-1.png |binary man/figures/README-proj-1.png |binary man/figures/README-rayrender-1.png |binary man/figures/README-rgl_snapshot.png |binary man/game_systems.Rd | 47 - man/obj_fns.Rd |only man/piecepackr-deprecated.Rd | 1 man/pmap_piece.Rd | 2 tests/figs/deps.txt | 2 tests/figs/no-regressions-in-figures/black-joker-no-star.svg |only tests/figs/no-regressions-in-figures/checkers.svg | 78 - tests/figs/no-regressions-in-figures/coin-face-r4oval.svg | 10 tests/figs/no-regressions-in-figures/go.svg |only tests/figs/no-regressions-in-figures/king-of-stars.svg | 7 tests/figs/no-regressions-in-figures/knight-of-diamonds.svg |only tests/figs/no-regressions-in-figures/pyramid-face-op.svg | 20 tests/figs/no-regressions-in-figures/pyramid-top-op.svg | 4 tests/figs/no-regressions-in-figures/pyramid-top-s4-r3.svg | 24 tests/figs/no-regressions-in-figures/red-joker.svg | 5 tests/figs/oblique-projection-works/coin-face-op.svg | 6 tests/figs/oblique-projection-works/diagram-op.svg | 18 tests/figs/oblique-projection-works/meeple.svg | 6 tests/figs/oblique-projection-works/pawn-face-op.svg | 20 tests/figs/pp-shape-works-as-expected/polyclip-circle.svg | 2 tests/figs/save-piece-images-works-as-expected/diagram-op-ppgf.svg | 70 - tests/testthat/test-deprecated.R | 4 tests/testthat/test-draw_component.R | 6 tests/testthat/test-game_systems.R | 50 + tests/testthat/test-obj.R | 9 tests/testthat/test-op_transform.R | 3 tests/testthat/test-options.R | 4 tests/testthat/test-pp_shape.R | 13 63 files changed, 1265 insertions(+), 616 deletions(-)
Title: Scans R Projects for Vulnerable Third Party Dependencies
Description: Collects a list of your third party R packages, and
scans them with the 'OSS' Index provided by 'Sonatype', reporting back
on any vulnerabilities that are found in the third party packages you
use.
Author: Jeffry Hesse [aut],
Brittany Belle [aut],
Colin Gillespie [aut, cre] (<https://orcid.org/0000-0003-1787-0275>),
Dan Rollo [aut],
Josiah Parry [ctb],
Sonatype [cph]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between oysteR versions 0.0.3 dated 2020-07-02 and 0.1.0 dated 2020-12-17
oysteR-0.0.3/oysteR/R/api_call.R |only oysteR-0.0.3/oysteR/R/audit_deps.R |only oysteR-0.0.3/oysteR/R/zzz.R |only oysteR-0.0.3/oysteR/tests/testthat/ossindex.sonatype.org |only oysteR-0.0.3/oysteR/tests/testthat/test-api_call.R |only oysteR-0.0.3/oysteR/tests/testthat/test-audit_deps.R |only oysteR-0.0.3/oysteR/tests/testthat/test-get_purls.R |only oysteR-0.1.0/oysteR/DESCRIPTION | 18 ++- oysteR-0.1.0/oysteR/MD5 | 58 ++++++---- oysteR-0.1.0/oysteR/NAMESPACE | 14 ++ oysteR-0.1.0/oysteR/NEWS.md | 16 ++ oysteR-0.1.0/oysteR/R/audit.R |only oysteR-0.1.0/oysteR/R/cache.R |only oysteR-0.1.0/oysteR/R/call_os_index.R |only oysteR-0.1.0/oysteR/R/deprecated.R |only oysteR-0.1.0/oysteR/R/expect_secure.R |only oysteR-0.1.0/oysteR/R/file_audits.R |only oysteR-0.1.0/oysteR/R/get_vulnerabilities.R |only oysteR-0.1.0/oysteR/R/print.R | 9 - oysteR-0.1.0/oysteR/R/utils.R |only oysteR-0.1.0/oysteR/inst |only oysteR-0.1.0/oysteR/man/audit.Rd |only oysteR-0.1.0/oysteR/man/audit_deps.Rd | 23 --- oysteR-0.1.0/oysteR/man/audit_description.Rd |only oysteR-0.1.0/oysteR/man/audit_installed_r_pkgs.Rd |only oysteR-0.1.0/oysteR/man/audit_renv_lock.Rd |only oysteR-0.1.0/oysteR/man/audit_req_txt.Rd |only oysteR-0.1.0/oysteR/man/expect_secure.Rd |only oysteR-0.1.0/oysteR/man/figures |only oysteR-0.1.0/oysteR/man/generate_purls.Rd |only oysteR-0.1.0/oysteR/man/get_r_pkgs.Rd |only oysteR-0.1.0/oysteR/man/get_vulnerabilities.Rd | 13 -- oysteR-0.1.0/oysteR/man/remove_cache.Rd |only oysteR-0.1.0/oysteR/tests/testthat/DESCRIPTION |only oysteR-0.1.0/oysteR/tests/testthat/renv.lock |only oysteR-0.1.0/oysteR/tests/testthat/requirements.txt |only oysteR-0.1.0/oysteR/tests/testthat/test-audit.R |only oysteR-0.1.0/oysteR/tests/testthat/test-audit_pkg.R |only oysteR-0.1.0/oysteR/tests/testthat/test-cache.R |only oysteR-0.1.0/oysteR/tests/testthat/test-check_installed_pkgs.R |only oysteR-0.1.0/oysteR/tests/testthat/test-get_vulnerabilities.R |only oysteR-0.1.0/oysteR/tests/testthat/test-renv.R |only oysteR-0.1.0/oysteR/tests/testthat/test-requirements.R |only oysteR-0.1.0/oysteR/tests/testthat/test-secure.R |only 44 files changed, 89 insertions(+), 62 deletions(-)
Title: Quantify the Robustness of Causal Inferences
Description: Statistical methods that quantify the conditions necessary to alter
inferences, also known as sensitivity analysis, are becoming increasingly
important to a variety of quantitative sciences. A series of recent works,
including Frank (2000) <doi:10.1177/0049124100029002001> and Frank et al.
(2013) <doi:10.3102/0162373713493129> extend previous sensitivity analyses
by considering the characteristics of omitted variables or unobserved cases
that would change an inference if such variables or cases were observed. These
analyses generate statements such as "an omitted variable would have to be
correlated at xx with the predictor of interest (e.g., treatment) and outcome
to invalidate an inference of a treatment effect". Or "one would have to replace
pp percent of the observed data with null hypothesis cases to invalidate the
inference". We implement these recent developments of sensitivity analysis and
provide modules to calculate these two robustness indices and generate such
statements in R. In particular, the functions konfound(), pkonfound() and
mkonfound() allow users to calculate the robustness of inferences for a user's
own model, a single published study and multiple studies respectively.
Author: Joshua M Rosenberg [aut, cre],
Ran Xu [ctb],
Qinyun Lin [ctb],
Spiro Maroulis [ctb],
Kenneth A Frank [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Diff between konfound versions 0.2.2 dated 2020-08-18 and 0.3.0 dated 2020-12-17
konfound-0.2.2/konfound/R/test.R |only konfound-0.2.2/konfound/R/tkonfound_fig.R |only konfound-0.2.2/konfound/man/getswitch_chisq.Rd |only konfound-0.2.2/konfound/man/tkonfound.Rd |only konfound-0.2.2/konfound/man/tkonfound_fig.Rd |only konfound-0.3.0/konfound/DESCRIPTION | 31 konfound-0.3.0/konfound/MD5 | 61 konfound-0.3.0/konfound/NAMESPACE | 4 konfound-0.3.0/konfound/NEWS.md | 4 konfound-0.3.0/konfound/R/binary_dummy_data.R |only konfound-0.3.0/konfound/R/concord1.R |only konfound-0.3.0/konfound/R/helper_output_dataframe.R | 4 konfound-0.3.0/konfound/R/helper_output_print.R | 77 - konfound-0.3.0/konfound/R/helper_plot_threshold.R | 4 konfound-0.3.0/konfound/R/konfound-glm-dichotomous.R |only konfound-0.3.0/konfound/R/konfound-glm.R | 11 konfound-0.3.0/konfound/R/konfound-lm.R | 11 konfound-0.3.0/konfound/R/konfound-lmer.R | 7 konfound-0.3.0/konfound/R/konfound.R | 67 - konfound-0.3.0/konfound/R/nonlinear_auxiliary.R | 636 ++++++++-- konfound-0.3.0/konfound/R/pkonfound.R | 133 +- konfound-0.3.0/konfound/R/test_sensitivity.R | 5 konfound-0.3.0/konfound/R/test_sensitivity_ln.R | 197 ++- konfound-0.3.0/konfound/R/tkonfound.R | 353 +++-- konfound-0.3.0/konfound/README.md | 136 -- konfound-0.3.0/konfound/build/vignette.rds |binary konfound-0.3.0/konfound/data |only konfound-0.3.0/konfound/inst/doc/introduction-to-konfound.R | 16 konfound-0.3.0/konfound/inst/doc/introduction-to-konfound.Rmd | 53 konfound-0.3.0/konfound/inst/doc/introduction-to-konfound.html | 555 +++++--- konfound-0.3.0/konfound/man/binary_dummy_data.Rd |only konfound-0.3.0/konfound/man/concord1.Rd |only konfound-0.3.0/konfound/man/konfound.Rd | 21 konfound-0.3.0/konfound/man/pkonfound.Rd | 45 konfound-0.3.0/konfound/tests/testthat/test-konfound.R |only konfound-0.3.0/konfound/tests/testthat/test-pkonfound.R | 5 konfound-0.3.0/konfound/vignettes/introduction-to-konfound.Rmd | 53 37 files changed, 1710 insertions(+), 779 deletions(-)
Title: R Interface to the ClassyFire RESTful API
Description: Access to the ClassyFire RESTful API <http://classyfire.wishartlab.com>. Retrieve existing entity classifications and submit new entities for classification.
Author: Tom Wilson [aut, cre] (<https://orcid.org/0000-0003-3112-4682>),
Jasen Finch [aut],
Gordon Getzinger [ctb]
Maintainer: Tom Wilson <tpw2@aber.ac.uk>
Diff between classyfireR versions 0.3.3 dated 2020-02-18 and 0.3.6 dated 2020-12-17
DESCRIPTION | 24 +++++++------ MD5 | 47 +++++++++++++++----------- NAMESPACE | 3 + NEWS.md | 15 ++++++++ R/accessor-methods.R | 79 ++++++++++++++++++++++++++++++++++++++++++++ R/allClasses.R | 35 ++++++++++++++++++- R/get_classification.R | 8 +++- R/internals.R | 25 ++++++------- R/query.R |only R/show-method.R | 78 +++++++++++++++++++++++++++++++------------ R/zzz.R | 20 ++++++++++- build |only inst/classyfireR-manual.pdf |binary inst/doc |only man/ClassyFire-class.Rd | 2 - man/Query-class.Rd |only man/alternative_parents.Rd | 7 +++ man/chebi.Rd | 7 +++ man/classification.Rd | 7 +++ man/description.Rd | 7 +++ man/descriptors.Rd | 7 +++ man/direct_parent.Rd | 7 +++ man/get_query.Rd |only man/meta.Rd | 7 +++ man/show.Rd | 7 +++ man/submit_query.Rd |only vignettes |only 27 files changed, 316 insertions(+), 76 deletions(-)
Title: TERN AusPlots Analysis Package
Description: Extraction, preparation, visualisation and analysis of TERN AusPlots ecosystem monitoring data. Direct access to plot-based data on vegetation and soils across Australia, including physical sample barcode numbers. Simple function calls extract the data and merge them into species occurrence matrices for downstream analysis, or calculate things like basal area and fractional cover. TERN AusPlots is a national field plot-based ecosystem surveillance monitoring method and dataset for Australia. The data have been collected across a national network of plots and transects by the Terrestrial Ecosystem Research Network (TERN - <https://www.tern.org.au>), an Australian Government NCRIS-enabled project, and its Ecosystem Surveillance platform (<https://www.tern.org.au/tern-observatory/tern-ecosystem-surveillance/>).
Author: Greg Guerin [aut, cre],
Tom Saleeba [aut],
Samantha Munroe [aut],
Bernardo Blanco-Martin [aut],
Irene Martín-Forés [aut],
Andrew Tokmakoff [aut]
Maintainer: Greg Guerin <ggueri01@gmail.com>
Diff between ausplotsR versions 1.2 dated 2020-11-04 and 1.2.1 dated 2020-12-17
DESCRIPTION | 8 +- MD5 | 10 +-- R/ausplots_visual.R | 2 R/fraction_pie.R | 2 inst/doc/start_guide.html | 127 +++++++++++++++++++++------------------------- man/ausplotsR-package.Rd | 4 - 6 files changed, 73 insertions(+), 80 deletions(-)
Title: Goodness-of-Fit Tests Based on Kullback-Leibler Divergence
Description: An implementation of Vasicek and Song goodness-of-fit tests. Several functions are provided to estimate differential Shannon entropy, i.e., estimate Shannon entropy of real random variables with density, and test the goodness-of-fit of some family of distributions, including uniform, Gaussian, log-normal, exponential, gamma, Weibull, Pareto, Fisher, Laplace and beta distributions; see Lequesne and Regnault (2020) <doi:10.18637/jss.v096.c01>.
Author: Justine Lequesne [aut], Philippe Regnault [aut, cre]
Maintainer: Philippe Regnault <philipperegnault@hotmail.com>
Diff between vsgoftest versions 0.3-2 dated 2018-06-24 and 1.0-1 dated 2020-12-17
DESCRIPTION | 10 MD5 | 24 - R/external.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 25 - inst/doc/vsgoftest_performances.R | 8 inst/doc/vsgoftest_tutorial.R | 54 +- inst/doc/vsgoftest_tutorial.Rnw | 862 +++++++++++++++++++------------------- inst/doc/vsgoftest_tutorial.pdf |binary man/vs.test.Rd | 2 man/vsgoftest-package.Rd | 2 vignettes/vsgoftest_tutorial.Rnw | 862 +++++++++++++++++++------------------- 13 files changed, 930 insertions(+), 923 deletions(-)
Title: Variable Importance Plots
Description: A general framework for constructing variable importance plots from
various types of machine learning models in R. Aside from some standard model-
specific variable importance measures, this package also provides model-
agnostic approaches that can be applied to any supervised learning algorithm.
These include 1) an efficient permutation-based variable importance measure,
2) variable importance based on Shapley values (Strumbelj and Kononenko,
2014) <doi:10.1007/s10115-013-0679-x>, and 3) the variance-based
approach described in Greenwell et al. (2018) <arXiv:1805.04755>. A
variance-based method for quantifying the relative strength of interaction
effects is also included (see the previous reference for details).
Author: Brandon Greenwell [aut, cre] (<https://orcid.org/0000-0002-8120-0084>),
Brad Boehmke [aut] (<https://orcid.org/0000-0002-3611-8516>),
Bernie Gray [aut] (<https://orcid.org/0000-0001-9190-6032>)
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between vip versions 0.2.2 dated 2020-04-06 and 0.3.2 dated 2020-12-17
vip-0.2.2/vip/man/pipe.Rd |only vip-0.2.2/vip/tools |only vip-0.3.2/vip/DESCRIPTION | 9 vip-0.3.2/vip/MD5 | 38 vip-0.3.2/vip/NEWS.md | 370 +-- vip-0.3.2/vip/R/utils.R | 142 - vip-0.3.2/vip/R/vi_model.R | 2680 +++++++++++++------------- vip-0.3.2/vip/R/vi_permute.R | 2 vip-0.3.2/vip/R/vint.R | 2 vip-0.3.2/vip/R/vip.R | 559 ++--- vip-0.3.2/vip/README.md | 178 - vip-0.3.2/vip/build |only vip-0.3.2/vip/inst/CITATION |only vip-0.3.2/vip/inst/doc |only vip-0.3.2/vip/inst/tinytest/test_pkg_glmnet.R | 182 - vip-0.3.2/vip/man/grid.arrange.Rd | 2 vip-0.3.2/vip/man/reexports.Rd |only vip-0.3.2/vip/man/vi_model.Rd | 38 vip-0.3.2/vip/man/vi_permute.Rd | 2 vip-0.3.2/vip/man/vip.Rd | 49 vip-0.3.2/vip/vignettes |only 21 files changed, 2086 insertions(+), 2167 deletions(-)
Title: Estimate Univariate Gaussian or Student's t Mixture
Autoregressive Model
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2018) <arXiv:1805.04010>,
Savi Virolainen (2020) <arXiv:2003.05221>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.2.5 dated 2020-04-04 and 3.2.6 dated 2020-12-17
DESCRIPTION | 8 +- MD5 | 74 +++++++++++---------- NAMESPACE | 4 + NEWS.md | 8 ++ R/GSMARconstructor.R | 5 - R/MAINest.R | 9 +- R/WaldAndLR.R |only R/argumentChecks.R | 5 - R/diagnosticPlot.R | 2 R/loglikelihood.R | 97 +++++++++++++++++++++------- R/morePlots.R | 7 -- R/predictMethod.R | 2 R/printMethods.R | 37 ++++++++++ R/quantileResidualTests.R | 2 R/simulateGSMAR.R | 37 ++++------ R/uGMAR.R | 2 README.md | 18 ++++- build/vignette.rds |binary inst/doc/intro-to-uGMAR.Rmd | 4 + inst/doc/intro-to-uGMAR.html | 26 ++++++- man/GSMAR.Rd | 2 man/LR_test.Rd |only man/T10Y1Y.Rd | 4 - man/Wald_test.Rd |only man/check_gsmar.Rd | 4 - man/condmomentPlot.Rd | 7 -- man/diagnosticPlot.Rd | 2 man/fitGSMAR.Rd | 3 man/get_alpha_mt.Rd |only man/predict.gsmar.Rd | 2 man/quantileResidualTests.Rd | 2 man/simudata.Rd | 4 - man/simulateGSMAR.Rd | 22 +++--- man/uGMAR.Rd | 2 tests/testthat/test_GAfunctions.R | 10 ++ tests/testthat/test_MAINest.R | 22 ++++-- tests/testthat/test_gsmarConstructor.R |only tests/testthat/test_loglikelihood.R | 13 +++ tests/testthat/test_quantileResidualTests.R | 4 - tests/testthat/test_waldAndLR.R |only vignettes/intro-to-uGMAR.Rmd | 4 + 41 files changed, 320 insertions(+), 134 deletions(-)
Title: Lightweight and Feature Complete Unit Testing Framework
Description: Provides a lightweight (zero-dependency) and easy to use
unit testing framework. Main features: install tests with
the package. Test results are treated as data that can be stored and
manipulated. Test files are R scripts interspersed with test commands, that
can be programmed over. Fully automated build-install-test sequence for
packages. Skip tests when not run locally (e.g. on CRAN). Flexible and
configurable output printing. Compare computed output with output stored
with the package. Run tests in parallel. Extensible by other packages.
Report side effects.
Author: Mark van der Loo [aut, cre] (<https://orcid.org/0000-0002-9807-4686>)
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between tinytest versions 1.2.3 dated 2020-10-07 and 1.2.4 dated 2020-12-17
DESCRIPTION | 6 - MD5 | 40 +++++------ NAMESPACE | 1 NEWS | 19 +++++ R/expectations.R | 44 +++++++++--- R/methods.R | 18 +++-- R/tinytest.R | 147 ++++++++++++++++++++++++++++++----------- README.md | 5 - build/vignette.rds |binary inst/doc/tinytest_examples.pdf |binary inst/doc/using_tinytest.R | 80 +++++++++++----------- inst/doc/using_tinytest.Rnw | 3 inst/doc/using_tinytest.pdf |binary inst/tinytest/test_call_wd.R | 1 inst/tinytest/test_file.R | 4 - inst/tinytest/test_tiny.R | 4 + inst/tinytest/test_utils.R | 6 + man/build_install_test.Rd | 2 man/expect_equal.Rd | 11 ++- man/test_package.Rd | 28 ++++++- vignettes/using_tinytest.Rnw | 3 21 files changed, 288 insertions(+), 134 deletions(-)
Title: R Interface to Use 'MiniZinc'
Description: Constraint optimization, or constraint programming, is the name given to identifying
feasible solutions out of a very large set of candidates, where the problem can be modeled in terms
of arbitrary constraints. 'MiniZinc' is a free and open-source constraint modeling language.
Constraint satisfaction and discrete optimization problems can be formulated in a high-level
modeling language. Models are compiled into an intermediate representation that is understood by a
wide range of solvers. 'MiniZinc' itself provides several solvers, for instance 'GeCode'. R users
can use the package to solve constraint programming problems without using 'MiniZinc' directly,
modify existing 'MiniZinc' models and also create their own models.
Author: Akshit Achara, Lars Kotthoff, Hans W. Borchers, Guido Tack
Maintainer: Akshit Achara <acharaakshit@gmail.com>
Diff between rminizinc versions 0.0.1 dated 2020-12-14 and 0.0.2 dated 2020-12-17
DESCRIPTION | 23 + MD5 | 31 +- NEWS.md |only cleanup | 2 cleanup.win | 2 configure | 69 ++-- configure.ac | 32 +- configure.win | 673 +++++++++++++++++++++++------------------------ data/config.RData |binary data/proot.RData |binary inst/doc/R_MiniZinc.R | 8 inst/doc/R_MiniZinc.Rmd | 24 - inst/doc/R_MiniZinc.html | 402 ++++++++++++++-------------- man/rminizinc-package.Rd | 8 src/Makevars.win.in | 2 src/config.h.in | 21 - vignettes/R_MiniZinc.Rmd | 24 - 17 files changed, 683 insertions(+), 638 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices, vectors,
numerical solvers and related algorithms. It supports dense and sparse
matrices on integer, floating point and complex numbers, decompositions of
such matrices, and solutions of linear systems. Its performance on many
algorithms is comparable with some of the best implementations based on
'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header
files from the 'Eigen' C++ template library (currently version 3.3.4). Thus
users do not need to install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.3.7.0 dated 2019-11-16 and 0.3.3.9.1 dated 2020-12-17
ChangeLog | 42 DESCRIPTION | 9 MD5 | 184 +- README.md | 74 - build/vignette.rds |binary inst/CITATION | 4 inst/NEWS.Rd | 7 inst/doc/RcppEigen-Introduction.pdf |binary inst/include/Eigen/Core | 7 inst/include/Eigen/Eigenvalues | 4 inst/include/Eigen/Geometry | 4 inst/include/Eigen/QR | 4 inst/include/Eigen/SparseQR | 1 inst/include/Eigen/src/Core/ArrayBase.h | 4 inst/include/Eigen/src/Core/CwiseUnaryView.h | 2 inst/include/Eigen/src/Core/DenseBase.h | 7 inst/include/Eigen/src/Core/DenseStorage.h | 6 inst/include/Eigen/src/Core/GenericPacketMath.h | 9 inst/include/Eigen/src/Core/MapBase.h | 5 inst/include/Eigen/src/Core/MathFunctions.h | 16 inst/include/Eigen/src/Core/MatrixBase.h | 3 inst/include/Eigen/src/Core/PermutationMatrix.h | 28 inst/include/Eigen/src/Core/PlainObjectBase.h | 12 inst/include/Eigen/src/Core/ProductEvaluators.h | 28 inst/include/Eigen/src/Core/Ref.h | 5 inst/include/Eigen/src/Core/SolveTriangular.h | 6 inst/include/Eigen/src/Core/Transpose.h | 2 inst/include/Eigen/src/Core/Transpositions.h | 39 inst/include/Eigen/src/Core/TriangularMatrix.h | 8 inst/include/Eigen/src/Core/arch/AVX512/MathFunctions.h | 74 - inst/include/Eigen/src/Core/arch/AVX512/PacketMath.h | 717 ++++------ inst/include/Eigen/src/Core/arch/CUDA/Half.h | 5 inst/include/Eigen/src/Core/arch/CUDA/PacketMathHalf.h | 4 inst/include/Eigen/src/Core/functors/UnaryFunctors.h | 2 inst/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h | 7 inst/include/Eigen/src/Core/products/GeneralMatrixMatrix.h | 37 inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h | 68 inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h | 10 inst/include/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h | 6 inst/include/Eigen/src/Core/products/Parallelizer.h | 9 inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix.h | 54 inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h | 24 inst/include/Eigen/src/Core/products/SelfadjointProduct.h | 4 inst/include/Eigen/src/Core/products/TriangularMatrixMatrix.h | 54 inst/include/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h | 26 inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h | 62 inst/include/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h | 12 inst/include/Eigen/src/Core/util/BlasUtil.h | 115 + inst/include/Eigen/src/Core/util/DisableStupidWarnings.h | 13 inst/include/Eigen/src/Core/util/ForwardDeclarations.h | 6 inst/include/Eigen/src/Core/util/Macros.h | 58 inst/include/Eigen/src/Core/util/Meta.h | 34 inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h | 6 inst/include/Eigen/src/Core/util/XprHelper.h | 17 inst/include/Eigen/src/Eigenvalues/ComplexSchur.h | 9 inst/include/Eigen/src/Eigenvalues/RealSchur.h | 15 inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h | 7 inst/include/Eigen/src/Geometry/Quaternion.h | 22 inst/include/Eigen/src/Geometry/Scaling.h | 2 inst/include/Eigen/src/Geometry/Transform.h | 4 inst/include/Eigen/src/Geometry/Translation.h | 6 inst/include/Eigen/src/Geometry/Umeyama.h | 2 inst/include/Eigen/src/LU/PartialPivLU.h | 5 inst/include/Eigen/src/LU/arch/Inverse_SSE.h | 4 inst/include/Eigen/src/PardisoSupport/PardisoSupport.h | 3 inst/include/Eigen/src/SVD/BDCSVD.h | 61 inst/include/Eigen/src/SVD/SVDBase.h | 2 inst/include/Eigen/src/SparseCholesky/SimplicialCholesky.h | 2 inst/include/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h | 2 inst/include/Eigen/src/SparseCore/AmbiVector.h | 5 inst/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h | 2 inst/include/Eigen/src/SparseCore/SparseMatrix.h | 3 inst/include/Eigen/src/SparseCore/SparseSelfAdjointView.h | 4 inst/include/Eigen/src/SparseCore/SparseView.h | 1 inst/include/Eigen/src/SparseLU/SparseLU.h | 4 inst/include/Eigen/src/StlSupport/StdDeque.h | 6 inst/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h | 2 inst/include/unsupported/Eigen/ArpackSupport | 4 inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h | 2 inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h | 2 inst/include/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h | 2 inst/include/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h | 2 inst/include/unsupported/Eigen/Polynomials | 4 inst/include/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h | 28 inst/include/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h | 21 inst/include/unsupported/Eigen/src/FFT/ei_fftw_impl.h | 2 inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h | 2 inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h | 18 inst/include/unsupported/Eigen/src/Polynomials/Companion.h | 57 inst/include/unsupported/Eigen/src/Polynomials/PolynomialSolver.h | 46 inst/include/unsupported/Eigen/src/Splines/Spline.h | 2 man/RcppEigen-package.Rd | 2 man/fastLm.Rd | 12 93 files changed, 1366 insertions(+), 957 deletions(-)
Title: Data Preparation, Estimation and Prediction in Multi-State
Models
Description: Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.
Author: Hein Putter [aut, cre],
Liesbeth C. de Wreede [aut],
Marta Fiocco [aut],
Ronald B. Geskus [ctb],
Edouard F. Bonneville [ctb],
Damjan Manevski [ctb]
Maintainer: Hein Putter <H.Putter@lumc.nl>
Diff between mstate versions 0.2.12 dated 2019-12-11 and 0.3.1 dated 2020-12-17
mstate-0.2.12/mstate/man/crprep.Rd |only mstate-0.2.12/mstate/man/cuminc.Rd |only mstate-0.2.12/mstate/man/ebmt1.Rd |only mstate-0.2.12/mstate/man/ebmt2.Rd |only mstate-0.2.12/mstate/man/ebmt3.Rd |only mstate-0.2.12/mstate/man/ebmt4.Rd |only mstate-0.2.12/mstate/man/prothr.Rd |only mstate-0.2.12/mstate/man/trans.Rd |only mstate-0.3.1/mstate/ChangeLog | 11 mstate-0.3.1/mstate/DESCRIPTION | 58 +++ mstate-0.3.1/mstate/MD5 | 159 ++++++---- mstate-0.3.1/mstate/NAMESPACE | 105 +++++- mstate-0.3.1/mstate/R/ELOS.R | 57 +++ mstate-0.3.1/mstate/R/LMAJ.R | 54 +++ mstate-0.3.1/mstate/R/MarkovTest.R |only mstate-0.3.1/mstate/R/crprep.R | 156 +++++++++- mstate-0.3.1/mstate/R/cuminc.R | 93 +++++ mstate-0.3.1/mstate/R/cutLMms.R | 36 ++ mstate-0.3.1/mstate/R/datasets.R |only mstate-0.3.1/mstate/R/etm2msdata.R |only mstate-0.3.1/mstate/R/events.R | 33 ++ mstate-0.3.1/mstate/R/expand.covs.R | 124 +++++++ mstate-0.3.1/mstate/R/ggplot.Cuminc.R |only mstate-0.3.1/mstate/R/ggplot.helpers.R |only mstate-0.3.1/mstate/R/ggplot.msfit.R |only mstate-0.3.1/mstate/R/ggplot.probtrans.R |only mstate-0.3.1/mstate/R/imports.R |only mstate-0.3.1/mstate/R/misc.R | 26 - mstate-0.3.1/mstate/R/msboot.R | 46 ++ mstate-0.3.1/mstate/R/msfit.R | 86 +++++ mstate-0.3.1/mstate/R/msprep.R | 116 +++++++ mstate-0.3.1/mstate/R/mssample.R | 103 ++++++ mstate-0.3.1/mstate/R/paths.R | 33 ++ mstate-0.3.1/mstate/R/plot.Cuminc.R | 105 ++++++ mstate-0.3.1/mstate/R/plot.MarkovTest.R |only mstate-0.3.1/mstate/R/plot.msfit.R | 125 +++++++- mstate-0.3.1/mstate/R/plot.probtrans.R | 173 ++++++++++- mstate-0.3.1/mstate/R/print.Cuminc.R | 1 mstate-0.3.1/mstate/R/print.MarkovTest.R |only mstate-0.3.1/mstate/R/print.msdata.R | 35 ++ mstate-0.3.1/mstate/R/probtrans.R | 88 +++++ mstate-0.3.1/mstate/R/redrank.R | 95 ++++++ mstate-0.3.1/mstate/R/summary.Cuminc.R | 7 mstate-0.3.1/mstate/R/summary.msfit.R | 239 ++++++++++++--- mstate-0.3.1/mstate/R/summary.probtrans.R | 264 +++++++++++++++-- mstate-0.3.1/mstate/R/trans.R | 3 mstate-0.3.1/mstate/R/transMat.R | 39 ++ mstate-0.3.1/mstate/R/transhelp.R |only mstate-0.3.1/mstate/R/vis.mirror.pt.R |only mstate-0.3.1/mstate/R/vis.multiple.pt.R |only mstate-0.3.1/mstate/R/xsect.R | 32 ++ mstate-0.3.1/mstate/README.md |only mstate-0.3.1/mstate/build/vignette.rds |binary mstate-0.3.1/mstate/inst/CITATION | 6 mstate-0.3.1/mstate/inst/doc/Tutorial.R | 1 mstate-0.3.1/mstate/inst/doc/Tutorial.pdf |binary mstate-0.3.1/mstate/inst/doc/visuals_demo.R |only mstate-0.3.1/mstate/inst/doc/visuals_demo.Rmd |only mstate-0.3.1/mstate/inst/doc/visuals_demo.html |only mstate-0.3.1/mstate/man/Cuminc.Rd |only mstate-0.3.1/mstate/man/EBMT-cause-of-death-data.Rd |only mstate-0.3.1/mstate/man/EBMT-data.Rd |only mstate-0.3.1/mstate/man/EBMT-platelet-recovery-data.Rd |only mstate-0.3.1/mstate/man/EBMT-year-of-relapse-data.Rd |only mstate-0.3.1/mstate/man/ELOS.Rd | 54 +-- mstate-0.3.1/mstate/man/LMAJ.Rd | 53 ++- mstate-0.3.1/mstate/man/Liver-cirrhosis-data.Rd |only mstate-0.3.1/mstate/man/MarkovTest.Rd |only mstate-0.3.1/mstate/man/aidssi.Rd | 129 +++----- mstate-0.3.1/mstate/man/bmt.Rd | 124 ++----- mstate-0.3.1/mstate/man/crprep.default.Rd |only mstate-0.3.1/mstate/man/cutLMms.Rd | 59 ++- mstate-0.3.1/mstate/man/etm2msdata.Rd |only mstate-0.3.1/mstate/man/events.Rd | 52 +-- mstate-0.3.1/mstate/man/expand.covs.Rd | 100 +++--- mstate-0.3.1/mstate/man/expand.covs.msdata.Rd | 106 +++--- mstate-0.3.1/mstate/man/msboot.Rd | 65 ++-- mstate-0.3.1/mstate/man/msdata2etm.Rd |only mstate-0.3.1/mstate/man/msfit.Rd | 139 +++++--- mstate-0.3.1/mstate/man/msprep.Rd | 195 ++++++------ mstate-0.3.1/mstate/man/mssample.Rd | 174 ++++++----- mstate-0.3.1/mstate/man/mstate-package.Rd | 49 +-- mstate-0.3.1/mstate/man/paths.Rd | 45 +- mstate-0.3.1/mstate/man/plot.Cuminc.Rd |only mstate-0.3.1/mstate/man/plot.MarkovTest.Rd |only mstate-0.3.1/mstate/man/plot.msfit.Rd | 118 +++++-- mstate-0.3.1/mstate/man/plot.probtrans.Rd | 172 +++++++---- mstate-0.3.1/mstate/man/print.MarkovTest.Rd |only mstate-0.3.1/mstate/man/print.msdata.Rd | 36 +- mstate-0.3.1/mstate/man/print.summary.msfit.Rd |only mstate-0.3.1/mstate/man/print.summary.probtrans.Rd |only mstate-0.3.1/mstate/man/probtrans.Rd | 134 ++++---- mstate-0.3.1/mstate/man/redrank.Rd | 134 +++++--- mstate-0.3.1/mstate/man/summary.Cuminc.Rd |only mstate-0.3.1/mstate/man/summary.msfit.Rd | 121 +++++-- mstate-0.3.1/mstate/man/summary.probtrans.Rd | 137 +++++--- mstate-0.3.1/mstate/man/trans2tra.Rd |only mstate-0.3.1/mstate/man/transMat.Rd |only mstate-0.3.1/mstate/man/transhelp.Rd |only mstate-0.3.1/mstate/man/vis.mirror.pt.Rd |only mstate-0.3.1/mstate/man/vis.multiple.pt.Rd |only mstate-0.3.1/mstate/man/xsect.Rd | 47 +-- mstate-0.3.1/mstate/vignettes/Tutorial.bib | 9 mstate-0.3.1/mstate/vignettes/visuals_demo.Rmd |only 104 files changed, 3590 insertions(+), 1171 deletions(-)
Title: Multiples Comparisons Procedures
Description: Performs the execution of the main procedures of multiple
comparisons in the literature, Scott-Knott (1974) <http://www.jstor.org/stable/2529204>,
Batista (2016) <http://repositorio.ufla.br/jspui/handle/1/11466>, including graphic representations
and export to different extensions of its results. An additional
part of the package is the presence of the performance evaluation
of the tests (Type I error per experiment and the power). This will
assist the user in making the decision for the chosen test.
Author: Ben Deivide [aut, cre],
Daniel Furtado [aut],
Diego Arthur [aut],
Matheus Fernando [ctb]
Maintainer: Ben Deivide <ben.deivide@ufsj.edu.br>
Diff between MCPtests versions 1.0 dated 2020-10-14 and 1.0.1 dated 2020-12-17
DESCRIPTION | 10 MD5 | 8 NAMESPACE | 1 NEWS | 5 R/guiMCP.R | 2815 ++++++++++++++++++++++++++++++------------------------------ 5 files changed, 1424 insertions(+), 1415 deletions(-)
Title: Model for Semisupervised Text Analysis Based on Word Embeddings
Description: A word embeddings-based semisupervised model for document scaling Watanabe (2020) <doi:10.1080/19312458.2020.1832976>.
LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
It can generate word vectors on a users-provided corpus or incorporate a pre-trained word vectors.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between LSX versions 0.9.5 dated 2020-11-20 and 0.9.6 dated 2020-12-17
LSX-0.9.5/LSX/man/reexports.Rd |only LSX-0.9.6/LSX/DESCRIPTION | 17 ++++++---- LSX-0.9.6/LSX/MD5 | 29 ++++++++---------- LSX-0.9.6/LSX/NAMESPACE | 23 +++++++++++++- LSX-0.9.6/LSX/NEWS.md | 5 +++ LSX-0.9.6/LSX/R/as.textmodel.R | 14 +++++++- LSX-0.9.6/LSX/R/data.R | 1 LSX-0.9.6/LSX/R/textmodel.R | 18 ++++++----- LSX-0.9.6/LSX/R/textplot.R | 6 +-- LSX-0.9.6/LSX/R/textstat.R | 7 ++-- LSX-0.9.6/LSX/R/utils.R | 10 +++--- LSX-0.9.6/LSX/man/as.seedwords.Rd | 4 +- LSX-0.9.6/LSX/man/seedwords.Rd | 4 +- LSX-0.9.6/LSX/man/textmodel_lss.Rd | 6 +-- LSX-0.9.6/LSX/man/textstat_context.Rd | 2 - LSX-0.9.6/LSX/tests/testthat/test-as.textmodel.R | 37 +++++++++++++++++++++-- 16 files changed, 125 insertions(+), 58 deletions(-)
Title: Obtain 'jQuery' as an HTML Dependency Object
Description: Obtain any major version of 'jQuery' (<https://code.jquery.com/>) and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown').
Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.
Author: Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Joe Cheng [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/lib/jquery-AUTHORS.txt)
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between jquerylib versions 0.1.1 dated 2020-04-30 and 0.1.3 dated 2020-12-17
jquerylib-0.1.1/jquerylib/inst/lib/jquery-3.5.0.js |only jquerylib-0.1.1/jquerylib/inst/lib/jquery-3.5.0.min.js |only jquerylib-0.1.3/jquerylib/DESCRIPTION | 6 ++-- jquerylib-0.1.3/jquerylib/MD5 | 19 ++++++++------- jquerylib-0.1.3/jquerylib/NEWS.md | 8 ++++++ jquerylib-0.1.3/jquerylib/R/jquery.R | 12 ++------- jquerylib-0.1.3/jquerylib/inst/lib/LICENSE.txt | 2 - jquerylib-0.1.3/jquerylib/inst/lib/jquery-1.12.4.min.map |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-2.2.4.min.map |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-3.5.1.js |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-3.5.1.min.js |only jquerylib-0.1.3/jquerylib/inst/lib/jquery-3.5.1.min.map |only jquerylib-0.1.3/jquerylib/tests/testthat/test-jquery.R | 2 - jquerylib-0.1.3/jquerylib/tools/download.R | 17 +++++-------- 14 files changed, 34 insertions(+), 32 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 3.5 dated 2020-11-10 and 3.6 dated 2020-12-17
DESCRIPTION | 8 ++--- MD5 | 12 ++++---- R/discfilter.R | 25 ++++++++---------- R/kde.R | 74 ++++++++++++++++++++++++++---------------------------- R/ludwig.R | 2 - data/examples.rda |binary man/kde.Rd | 31 ++++++++++------------ 7 files changed, 74 insertions(+), 78 deletions(-)
Title: Web Interface to 'IsoplotR'
Description: Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Author: Pieter Vermeesch [aut, cre],
Tim Band [ctb]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotRgui versions 3.5 dated 2020-11-04 and 3.6 dated 2020-12-17
DESCRIPTION | 8 - MD5 | 58 ++++++------ R/IsoplotR.R | 92 +++++++++---------- R/server.R | 4 build/CRAN.md | 114 ++++++++++++----------- build/CentOS.md |only build/deploy.sh | 2 build/docker.md | 95 ++++--------------- build/docker.sh | 2 build/git.md | 125 +++++++------------------- build/podman.md |only build/start-gui.R | 1 inst/www/css/IsoplotR.css | 2 inst/www/home/map.html | 45 +-------- inst/www/home/news.html | 2 inst/www/home/offline.html | 12 +- inst/www/home/world.svg | 44 +-------- inst/www/js/IsoplotR.js | 8 - inst/www/js/js2R.js | 18 +-- inst/www/js/settings.json | 4 inst/www/locales/en/contextual_help.json | 3 inst/www/locales/en/dictionary_id.json | 1 inst/www/locales/en/home_id.json | 9 + inst/www/locales/es/home_id.json | 7 - inst/www/locales/zh_Hans/contextual_help.json | 2 inst/www/locales/zh_Hans/home_id.json | 7 - inst/www/options/KDE.html | 12 -- inst/www/version.txt | 2 man/IsoplotR.Rd | 2 man/daemon.Rd | 2 man/stopIsoplotR.Rd | 6 - 31 files changed, 269 insertions(+), 420 deletions(-)
Title: Interface for the 'Julia' 'TKTD' Simulator 'TKTDsimulations.jl'
Description: Tools for 'ecotoxicology' dedicated to the simulation of
'toxicokinetic-toxicodynamic' models. See 'Baudrot' and 'Charles'
(2019) <doi:10.1038/s41598-019-47698-0>.
Author: Virgile Baudrot [aut, cre] (<https://orcid.org/0000-0003-1327-9728>)
Maintainer: Virgile Baudrot <virgile.baudrot@posteo.net>
Diff between tktdjl2r versions 0.1.0 dated 2020-11-11 and 0.2.0 dated 2020-12-17
DESCRIPTION | 7 ++- MD5 | 35 ++++++++++++------- NAMESPACE | 5 ++ R/MultiplicationFactor.R |only R/TKTDsimulations.R | 79 ++++++++++++++++++++++++++++++++++++++++++-- R/data.R |only R/tktdjl2r.R | 6 ++- data |only inst/doc/Tutorial.R | 28 +++------------ inst/doc/Tutorial.Rmd | 28 +++------------ inst/doc/Tutorial.html | 28 +++------------ man/list_paramIT_PRZcst.Rd |only man/list_paramSD_PRZcst.Rd |only man/runIT_MCMC.Rd |only man/runMFx.Rd |only man/runSD_MCMC.Rd |only man/runTK_MCMC.Rd |only man/tktdjl2r_setup.Rd | 4 +- tests/testthat/test-runIT.R | 38 +++++++++++++++++---- tests/testthat/test-runMF.R |only tests/testthat/test-runSD.R | 38 +++++++++++++++++---- tests/testthat/test-runTK.R | 24 ++++++++++--- vignettes/Tutorial.Rmd | 28 +++------------ 23 files changed, 223 insertions(+), 125 deletions(-)
Title: 'sf'-Compatible Interface to 'Google Maps' APIs
Description: Interface to the 'Google Maps' APIs: (1) routing directions based on the 'Directions' API, returned as 'sf' objects, either as single feature per alternative route, or a single feature per segment per alternative route; (2) travel distance or time matrices based on the 'Distance Matrix' API; (3) geocoded locations based on the 'Geocode' API, returned as 'sf' objects, either points or bounds; (4) map images using the 'Maps Static' API, returned as 'stars' objects.
Author: Michael Dorman [aut, cre],
Tom Buckley [ctb],
Alex Dannenberg [ctb],
Mihir Bhaskar [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between mapsapi versions 0.4.7 dated 2020-09-19 and 0.4.8 dated 2020-12-17
DESCRIPTION | 13 ++++--- MD5 | 24 +++++++------- NEWS.md | 9 ++++- R/mp_geocode.R | 3 - R/mp_get_bounds.R | 57 +++++++++++++++++++++++++++------- R/mp_get_points.R | 2 - build/vignette.rds |binary inst/doc/intro.R | 8 +++- inst/doc/intro.Rmd | 7 +++- inst/doc/intro.html | 84 ++++++++++++++++++++++++++++++++++++++++----------- man/mp_geocode.Rd | 3 - man/mp_get_bounds.Rd | 13 ++++++- vignettes/intro.Rmd | 7 +++- 13 files changed, 170 insertions(+), 60 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-20 0.2.1
2020-11-19 0.2.0
Title: Animal Trajectory Analysis
Description: A toolbox to assist with statistical analysis of 2-dimensional animal trajectories.
It provides simple access to algorithms for calculating and assessing a variety of
characteristics such as speed and acceleration, as well as multiple measures of
straightness or tortuosity. McLean & Skowron Volponi (2018) <doi:10.1111/eth.12739>.
Author: Jim McLean [aut, cre]
Maintainer: Jim McLean <jim_mclean@optusnet.com.au>
Diff between trajr versions 1.3.0 dated 2019-06-10 and 1.4.0 dated 2020-12-17
DESCRIPTION | 13 MD5 | 90 +- NAMESPACE | 6 NEWS.md | 11 R/dirn_autocorr.R | 6 R/simulate.R |only R/smooth/app.R | 1 R/speed.R | 255 ++++++- R/straightness.R | 15 R/trajectory.R | 22 README.md | 78 +- build/vignette.rds |binary inst/doc/simulations.R |only inst/doc/simulations.Rmd |only inst/doc/simulations.html |only inst/doc/stop-start.R |only inst/doc/stop-start.Rmd |only inst/doc/stop-start.html |only inst/doc/trajr-vignette.R | 30 inst/doc/trajr-vignette.Rmd | 18 inst/doc/trajr-vignette.html | 998 ++++++++++++++++++------------ man/TrajAcceleration.Rd |only man/TrajDAMinMax.Rd | 4 man/TrajDerivatives.Rd | 29 man/TrajExpectedSquareDisplacement.Rd | 8 man/TrajFromCoords.Rd | 13 man/TrajGenerate.Rd | 14 man/TrajInPolygon.Rd |only man/TrajMerge.Rd |only man/TrajSinuosity2.Rd | 15 man/TrajSmoothSG.Rd | 8 man/TrajSpeedIntervals.Rd | 38 - man/TrajSplit.Rd |only man/TrajSplitAtFirstCrossing.Rd |only man/TrajVelocity.Rd |only man/TrajsBuild.Rd | 20 man/TrajsMergeStats.Rd | 8 man/TrajsStatsReplaceNAs.Rd | 8 man/lines.Trajectory.Rd | 12 man/plot.TrajDirectionAutocorrelations.Rd | 11 man/plot.TrajSpeedIntervals.Rd | 14 man/plot.Trajectory.Rd | 20 man/points.Trajectory.Rd | 3 man/trajr.Rd | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test_basic.R | 48 + tests/testthat/test_sim.R |only tests/testthat/test_vel.R |only vignettes/examples_cache |only vignettes/simulations.Rmd |only vignettes/stop-start.Rmd |only vignettes/trajr-vignette.Rmd | 18 52 files changed, 1209 insertions(+), 626 deletions(-)
Title: Robust Bootstrap Forecast Densities for GARCH Models
Description: Bootstrap forecast densities for GARCH (Generalized Autoregressive Conditional Heteroskedastic) returns and volatilities using the robust residual-based bootstrap procedure of Trucios, Hotta and Ruiz (2017) <DOI:10.1080/00949655.2017.1359601>.
Author: Carlos Trucios
Maintainer: Carlos Trucios <ctrucios@gmail.com>
Diff between RobGARCHBoot versions 1.1.1 dated 2020-12-08 and 1.2.0 dated 2020-12-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ROBUSTGARCH.R | 2 +- R/RcppExports.R | 2 +- man/RobGARCHBoot-package.Rd | 2 +- src/ROBUSTGARCH.cpp | 4 +++- 6 files changed, 15 insertions(+), 13 deletions(-)
Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut, cre],
Davis Vaughan [aut],
data.table team [cph] (Radix sort based on data.table's forder() and
their contribution to R's order()),
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vctrs versions 0.3.5 dated 2020-11-17 and 0.3.6 dated 2020-12-17
vctrs-0.3.5/vctrs/build/vctrs.pdf |only vctrs-0.3.6/vctrs/DESCRIPTION | 6 vctrs-0.3.6/vctrs/MD5 | 76 vctrs-0.3.6/vctrs/NEWS.md | 10 vctrs-0.3.6/vctrs/R/bind.R | 2 vctrs-0.3.6/vctrs/R/conditions.R | 2 vctrs-0.3.6/vctrs/R/fill.R | 2 vctrs-0.3.6/vctrs/R/group.R | 2 vctrs-0.3.6/vctrs/R/order-radix.R | 2 vctrs-0.3.6/vctrs/R/order.R | 2 vctrs-0.3.6/vctrs/R/proxy.R | 6 vctrs-0.3.6/vctrs/R/subscript.R | 2 vctrs-0.3.6/vctrs/R/type-vctr.R | 2 vctrs-0.3.6/vctrs/R/vctrs-deprecated.R | 12 vctrs-0.3.6/vctrs/R/vctrs-package.R | 2 vctrs-0.3.6/vctrs/inst/doc/pillar.html | 641 ++----- vctrs-0.3.6/vctrs/inst/doc/s3-vector.html | 1485 +++++++---------- vctrs-0.3.6/vctrs/inst/doc/stability.html | 653 ++----- vctrs-0.3.6/vctrs/inst/doc/type-size.html | 771 ++------ vctrs-0.3.6/vctrs/man/figures/lifecycle-superseded.svg |only vctrs-0.3.6/vctrs/man/maybe_lossy_cast.Rd | 2 vctrs-0.3.6/vctrs/man/new_vctr.Rd | 2 vctrs-0.3.6/vctrs/man/reference-faq-compatibility.Rd | 14 vctrs-0.3.6/vctrs/man/theory-faq-coercion.Rd | 4 vctrs-0.3.6/vctrs/man/vctrs-package.Rd | 2 vctrs-0.3.6/vctrs/man/vec_as_index.Rd | 4 vctrs-0.3.6/vctrs/man/vec_as_subscript.Rd | 2 vctrs-0.3.6/vctrs/man/vec_cbind_frame_ptype.Rd | 2 vctrs-0.3.6/vctrs/man/vec_data.Rd | 2 vctrs-0.3.6/vctrs/man/vec_empty.Rd | 2 vctrs-0.3.6/vctrs/man/vec_fill_missing.Rd | 2 vctrs-0.3.6/vctrs/man/vec_group.Rd | 2 vctrs-0.3.6/vctrs/man/vec_proxy.Rd | 4 vctrs-0.3.6/vctrs/man/vec_repeat.Rd | 4 vctrs-0.3.6/vctrs/man/vec_type.Rd | 2 vctrs-0.3.6/vctrs/src/proxy.c | 77 vctrs-0.3.6/vctrs/src/runs.c | 11 vctrs-0.3.6/vctrs/src/version.c | 2 vctrs-0.3.6/vctrs/tests/testthat/test-order.R | 17 vctrs-0.3.6/vctrs/tests/testthat/test-translate.R | 14 40 files changed, 1450 insertions(+), 2399 deletions(-)
Title: Measuring Information Flow Between Time Series with Shannon and
Renyi Transfer Entropy
Description: Measuring information flow between time series with Shannon and Rényi transfer entropy. See also Dimpfl and Peter (2013) <doi:10.1515/snde-2012-0044> and Dimpfl and Peter (2014) <doi:10.1016/j.intfin.2014.03.004> for theory and applications to financial time series. Additional references can be found in the theory part of the vignette.
Author: David Zimmermann [aut, cre],
Simon Behrendt [aut],
Thomas Dimpfl [aut],
Franziska Peter [aut]
Maintainer: David Zimmermann <david_j_zimmermann@hotmail.com>
Diff between RTransferEntropy versions 0.2.12 dated 2019-08-19 and 0.2.13 dated 2020-12-17
DESCRIPTION | 18 MD5 | 38 NAMESPACE | 38 R/RcppExports.R | 30 README.md | 705 ++++++----- build/vignette.rds |binary inst/doc/transfer-entropy.R | 668 +++++----- inst/doc/transfer-entropy.html | 1848 +++++++++++++++-------------- man/calc_ete.Rd | 214 +-- man/calc_te.Rd | 210 +-- man/coef.transfer_entropy.Rd | 72 - man/figures/README-contemp_plot-1.png |binary man/is.transfer_entropy.Rd | 40 man/print.transfer_entropy.Rd | 160 +- man/set_quiet.Rd | 40 man/stocks.Rd | 50 man/summary.transfer_entropy.Rd | 87 - man/transfer_entropy.Rd | 268 ++-- src/calculate_transition_probabilities.cpp | 5 tests/testthat/test.transfer_entropy.R | 400 +++--- 20 files changed, 2610 insertions(+), 2281 deletions(-)
More information about RTransferEntropy at CRAN
Permanent link
Title: Reads, Annotates, and Normalizes Reverse Phase Protein Array
Data
Description: Reads in sample description and slide description files and
annotates the expression values taken from GenePix results files
(text file format used by many microarray scanner and software providers).
After normalization data can be visualized as boxplot, heatmap or dotplot.
Author: Heiko Mannsperger with contributions of Stephan Gade
Maintainer: Torsten Schoeps <torsten.schoeps@bioinf.med.uni-goettingen.de>
Diff between RPPanalyzer versions 1.4.6 dated 2020-07-15 and 1.4.7 dated 2020-12-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/read.sampledescription.R | 3 ++- inst/doc/RPPanalyzer.pdf |binary 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Project Future Case Incidence
Description: Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>. The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.
Author: Thibaut Jombart [aut, cre],
Pierre Nouvellet [aut],
Sangeeta Bhatia [ctb],
Zhian N. Kamvar [ctb],
Tim Taylor [ctb],
Stephane Ghozzi [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between projections versions 0.5.1 dated 2020-06-30 and 0.5.2 dated 2020-12-17
projections-0.5.1/projections/tests/figs |only projections-0.5.1/projections/tests/testthat/rds |only projections-0.5.2/projections/DESCRIPTION | 47 ++- projections-0.5.2/projections/MD5 | 77 ++--- projections-0.5.2/projections/NEWS.md | 7 projections-0.5.2/projections/tests/testthat.R | 1 projections-0.5.2/projections/tests/testthat/_snaps |only projections-0.5.2/projections/tests/testthat/test-accessors.R | 2 projections-0.5.2/projections/tests/testthat/test-build_projections.R | 2 projections-0.5.2/projections/tests/testthat/test-conversion.R | 2 projections-0.5.2/projections/tests/testthat/test-cumulate.R | 2 projections-0.5.2/projections/tests/testthat/test-internals.R | 2 projections-0.5.2/projections/tests/testthat/test-merge_add_projections.R | 2 projections-0.5.2/projections/tests/testthat/test-merge_projections.R | 2 projections-0.5.2/projections/tests/testthat/test-plots.R | 146 ++++------ projections-0.5.2/projections/tests/testthat/test-print.R | 2 projections-0.5.2/projections/tests/testthat/test-project.R | 20 - projections-0.5.2/projections/tests/testthat/test-subset.R | 2 projections-0.5.2/projections/tests/testthat/test-summary.R | 2 19 files changed, 138 insertions(+), 180 deletions(-)
Title: Dyadic Network Analysis
Description: Contains functions for the MCMC simulation of dyadic network models j2 (Zijlstra, 2017, <doi:10.1080/0022250X.2017.1387858>) and p2 (Van Duijn, Snijders & Zijlstra, 2004, <doi: 10.1046/j.0039-0402.2003.00258.x>), and the bidirectional (multilevel) counterpart of the the multilevel p2 model as described in Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>, the (multilevel) b2 model.
Author: Bonne J.H. Zijlstra <B.J.H.Zijlstra@uva.nl>
Maintainer: Bonne J.H. Zijlstra <B.J.H.Zijlstra@uva.nl>
Diff between dyads versions 1.1.2 dated 2019-03-28 and 1.1.3 dated 2020-12-17
DESCRIPTION | 14 - MD5 | 16 - NAMESPACE | 37 +- R/b2ML.R |only R/internalFunctionsDyads.R | 214 +++++++++++++---- R/j2.R | 562 ++++++++++++++++++++++----------------------- R/p2.R | 548 +++++++++++++++++++++---------------------- build/partial.rdb |binary man/b2ML.Rd |only man/dyads-package.Rd | 139 +++++------ 10 files changed, 829 insertions(+), 701 deletions(-)
Title: Manage Environment Specific Configuration Values
Description: Manage configuration values across multiple environments (e.g.
development, test, production). Read values using a function that determines
the current environment and returns the appropriate value.
Author: JJ Allaire [aut],
Andrie de Vries [cre],
RStudio [cph, fnd]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between config versions 0.3 dated 2018-03-27 and 0.3.1 dated 2020-12-17
config-0.3.1/config/DESCRIPTION | 26 config-0.3.1/config/MD5 | 63 - config-0.3.1/config/NAMESPACE | 12 config-0.3.1/config/NEWS.md |only config-0.3.1/config/R/active.R | 50 config-0.3.1/config/R/get.R | 213 +-- config-0.3.1/config/R/merge.R | 91 - config-0.3.1/config/R/package.R | 30 config-0.3.1/config/build/vignette.rds |binary config-0.3.1/config/inst/WORDLIST |only config-0.3.1/config/inst/doc/introduction.R | 70 - config-0.3.1/config/inst/doc/introduction.Rmd | 161 -- config-0.3.1/config/inst/doc/introduction.html | 840 +++++++------- config-0.3.1/config/man/config.Rd | 33 config-0.3.1/config/man/figures |only config-0.3.1/config/man/fragments |only config-0.3.1/config/man/get.Rd | 81 - config-0.3.1/config/man/is_active.Rd | 59 config-0.3.1/config/man/merge.Rd | 43 config-0.3.1/config/tests/spelling.R |only config-0.3.1/config/tests/testthat.R | 8 config-0.3.1/config/tests/testthat/config-inheritself.yml | 22 config-0.3.1/config/tests/testthat/config-multiple.yml | 34 config-0.3.1/config/tests/testthat/config.yml | 41 config-0.3.1/config/tests/testthat/config/conf.yml | 28 config-0.3.1/config/tests/testthat/config/config.yml | 28 config-0.3.1/config/tests/testthat/errors/nodefault.yml | 22 config-0.3.1/config/tests/testthat/parent/config.yaml | 28 config-0.3.1/config/tests/testthat/test-active.R | 8 config-0.3.1/config/tests/testthat/test-errors.R | 12 config-0.3.1/config/tests/testthat/test-inherit.R | 50 config-0.3.1/config/tests/testthat/test-parent.R | 52 config-0.3.1/config/tests/testthat/test-read.R | 102 - config-0.3.1/config/vignettes/introduction.Rmd | 161 -- config-0.3/config/inst/NEWS |only 35 files changed, 1131 insertions(+), 1237 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxonomic, phylogenetic and functional). It allows
performing a number of analyses based on species identities/abundances, phylogenetic/functional trees, convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Author: Pedro Cardoso, Stefano Mammola, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.4.0 dated 2020-11-24 and 2.4.1 dated 2020-12-17
DESCRIPTION | 14 ++++++-------- MD5 | 4 ++-- R/BAT.R | 10 +++++----- 3 files changed, 13 insertions(+), 15 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because
it is frustrating and boring, many of us avoid it. 'testthat' is a
testing framework for R that is easy to learn and use, and integrates
with your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd],
R Core team [ctb] (Implementation of utils::recover())
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 3.0.0 dated 2020-10-31 and 3.0.1 dated 2020-12-17
testthat-3.0.0/testthat/man/RstudioReporter.Rd |only testthat-3.0.1/testthat/DESCRIPTION | 16 testthat-3.0.1/testthat/MD5 | 191 ++--- testthat-3.0.1/testthat/NAMESPACE | 2 testthat-3.0.1/testthat/NEWS.md | 55 + testthat-3.0.1/testthat/R/auto-test.R | 6 testthat-3.0.1/testthat/R/expect-condition.R | 13 testthat-3.0.1/testthat/R/expect-known.R | 35 - testthat-3.0.1/testthat/R/local.R | 52 - testthat-3.0.1/testthat/R/parallel.R | 2 testthat-3.0.1/testthat/R/reporter-check.R | 80 +- testthat-3.0.1/testthat/R/reporter-progress.R | 26 testthat-3.0.1/testthat/R/reporter-rstudio.R | 2 testthat-3.0.1/testthat/R/reporter.R | 3 testthat-3.0.1/testthat/R/skip.R | 68 -- testthat-3.0.1/testthat/R/snapshot-file.R | 24 testthat-3.0.1/testthat/R/snapshot-reporter.R | 18 testthat-3.0.1/testthat/R/snapshot.R | 65 + testthat-3.0.1/testthat/R/test-compiled-code.R | 15 testthat-3.0.1/testthat/R/test-files.R | 23 testthat-3.0.1/testthat/R/test-package.R | 2 testthat-3.0.1/testthat/R/test-that.R | 10 testthat-3.0.1/testthat/R/utils.R | 26 testthat-3.0.1/testthat/README.md | 6 testthat-3.0.1/testthat/build/vignette.rds |binary testthat-3.0.1/testthat/inst/doc/custom-expectation.html | 295 -------- testthat-3.0.1/testthat/inst/doc/parallel.html | 293 -------- testthat-3.0.1/testthat/inst/doc/skipping.R | 25 testthat-3.0.1/testthat/inst/doc/skipping.Rmd | 74 +- testthat-3.0.1/testthat/inst/doc/skipping.html | 336 ---------- testthat-3.0.1/testthat/inst/doc/snapshotting.Rmd | 12 testthat-3.0.1/testthat/inst/doc/snapshotting.html | 310 --------- testthat-3.0.1/testthat/inst/doc/test-fixtures.R | 4 testthat-3.0.1/testthat/inst/doc/test-fixtures.Rmd | 8 testthat-3.0.1/testthat/inst/doc/test-fixtures.html | 301 -------- testthat-3.0.1/testthat/inst/doc/third-edition.Rmd | 2 testthat-3.0.1/testthat/inst/doc/third-edition.html | 295 -------- testthat-3.0.1/testthat/inst/include/testthat/vendor/catch.h | 9 testthat-3.0.1/testthat/man/CheckReporter.Rd | 2 testthat-3.0.1/testthat/man/DebugReporter.Rd | 2 testthat-3.0.1/testthat/man/FailReporter.Rd | 2 testthat-3.0.1/testthat/man/ListReporter.Rd | 2 testthat-3.0.1/testthat/man/LocationReporter.Rd | 2 testthat-3.0.1/testthat/man/MinimalReporter.Rd | 2 testthat-3.0.1/testthat/man/MultiReporter.Rd | 2 testthat-3.0.1/testthat/man/ProgressReporter.Rd | 2 testthat-3.0.1/testthat/man/RStudioReporter.Rd |only testthat-3.0.1/testthat/man/Reporter.Rd | 2 testthat-3.0.1/testthat/man/SilentReporter.Rd | 2 testthat-3.0.1/testthat/man/StopReporter.Rd | 2 testthat-3.0.1/testthat/man/SummaryReporter.Rd | 2 testthat-3.0.1/testthat/man/TapReporter.Rd | 2 testthat-3.0.1/testthat/man/TeamcityReporter.Rd | 2 testthat-3.0.1/testthat/man/expect_error.Rd | 9 testthat-3.0.1/testthat/man/expect_known_output.Rd | 1 testthat-3.0.1/testthat/man/expect_output_file.Rd |only testthat-3.0.1/testthat/man/expect_snapshot.Rd | 20 testthat-3.0.1/testthat/man/expect_snapshot_file.Rd | 7 testthat-3.0.1/testthat/man/local_test_context.Rd | 14 testthat-3.0.1/testthat/man/skip.Rd | 70 -- testthat-3.0.1/testthat/man/teardown_env.Rd | 6 testthat-3.0.1/testthat/man/test_dir.Rd | 11 testthat-3.0.1/testthat/man/test_file.Rd | 3 testthat-3.0.1/testthat/man/test_package.Rd | 2 testthat-3.0.1/testthat/man/test_that.Rd | 3 testthat-3.0.1/testthat/man/use_catch.Rd | 7 testthat-3.0.1/testthat/tests/testthat/_snaps/reporter-check.md | 60 - testthat-3.0.1/testthat/tests/testthat/_snaps/reporter-progress.md | 44 - testthat-3.0.1/testthat/tests/testthat/_snaps/reporter-stop.md | 12 testthat-3.0.1/testthat/tests/testthat/_snaps/reporter-summary.md | 20 testthat-3.0.1/testthat/tests/testthat/_snaps/snapshot-file.md |only testthat-3.0.1/testthat/tests/testthat/_snaps/snapshot.md | 4 testthat-3.0.1/testthat/tests/testthat/reporters/long-test.R |only testthat-3.0.1/testthat/tests/testthat/test-deprec-condition.R | 2 testthat-3.0.1/testthat/tests/testthat/test-edition.R | 4 testthat-3.0.1/testthat/tests/testthat/test-examples.R | 2 testthat-3.0.1/testthat/tests/testthat/test-expect-equality.R | 4 testthat-3.0.1/testthat/tests/testthat/test-local.R | 1 testthat-3.0.1/testthat/tests/testthat/test-parallel-crash.R | 2 testthat-3.0.1/testthat/tests/testthat/test-parallel-outside.R | 2 testthat-3.0.1/testthat/tests/testthat/test-parallel-setup.R | 2 testthat-3.0.1/testthat/tests/testthat/test-parallel-startup.R | 2 testthat-3.0.1/testthat/tests/testthat/test-parallel-teardown.R | 2 testthat-3.0.1/testthat/tests/testthat/test-parallel.R | 14 testthat-3.0.1/testthat/tests/testthat/test-reporter-check.R | 14 testthat-3.0.1/testthat/tests/testthat/test-reporter-debug.R | 6 testthat-3.0.1/testthat/tests/testthat/test-reporter-progress.R | 2 testthat-3.0.1/testthat/tests/testthat/test-reporter-rstudio.R | 2 testthat-3.0.1/testthat/tests/testthat/test-reporter.R | 2 testthat-3.0.1/testthat/tests/testthat/test-snapshot-file.R | 6 testthat-3.0.1/testthat/tests/testthat/test-snapshot-reporter.R | 2 testthat-3.0.1/testthat/tests/testthat/test-snapshot.R | 23 testthat-3.0.1/testthat/tests/testthat/test-test-files.R | 10 testthat-3.0.1/testthat/tests/testthat/test-test-path.R | 4 testthat-3.0.1/testthat/tests/testthat/test-test-that.R | 41 - testthat-3.0.1/testthat/vignettes/skipping.Rmd | 74 +- testthat-3.0.1/testthat/vignettes/snapshotting.Rmd | 12 testthat-3.0.1/testthat/vignettes/test-fixtures.Rmd | 8 testthat-3.0.1/testthat/vignettes/third-edition.Rmd | 2 99 files changed, 938 insertions(+), 2332 deletions(-)
Title: The Composer of Plots
Description: The 'ggplot2' package provides a strong API for sequentially
building up a plot, but does not concern itself with composition of multiple
plots. 'patchwork' is a package that expands the API to allow for
arbitrarily complex composition of plots by, among others, providing
mathematical operators for combining multiple plots. Other packages that try
to address this need (but with a different approach) are 'gridExtra' and
'cowplot'.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>)
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between patchwork versions 1.1.0 dated 2020-11-09 and 1.1.1 dated 2020-12-17
DESCRIPTION | 6 MD5 | 23 +- NAMESPACE | 3 NEWS.md | 8 R/add_plot.R | 7 R/arithmetic.R | 6 R/plot_patchwork.R | 28 ++- README.md | 12 - build/vignette.rds |binary inst/doc/patchwork.html | 284 ++++--------------------------- man/figures/README-example-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary tests/testthat/helper-vdiffr.R |only 13 files changed, 106 insertions(+), 271 deletions(-)
Title: Improved Text Rendering Support for 'ggplot2'
Description: A 'ggplot2' extension that enables the rendering of
complex formatted plot labels (titles, subtitles, facet labels,
axis labels, etc.). Text boxes with automatic word wrap are also
supported.
Author: Claus O. Wilke [aut, cre] (<https://orcid.org/0000-0002-7470-9261>)
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between ggtext versions 0.1.0 dated 2020-06-04 and 0.1.1 dated 2020-12-17
DESCRIPTION | 10 MD5 | 49 +-- NEWS.md | 4 README.md | 372 ++++++++++++++--------------- build/vignette.rds |binary inst/doc/plotting_text.Rmd | 2 inst/doc/plotting_text.html | 333 +++++++++++++------------- inst/doc/theme_elements.Rmd | 2 inst/doc/theme_elements.html | 379 +++++++++++++++--------------- man/element_markdown.Rd | 4 man/element_textbox.Rd | 4 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/geom_richtext.Rd | 4 tests/testthat/helper-vdiffr.R |only tests/testthat/test-element-markdown.R | 2 tests/testthat/test-element-textbox.R | 8 tests/testthat/test-geom-richtext.R | 2 tests/testthat/test-geom-textbox.R | 2 vignettes/plotting_text.Rmd | 2 vignettes/theme_elements.Rmd | 2 26 files changed, 596 insertions(+), 585 deletions(-)
Title: Comparison of Variance - Covariance Patterns
Description: Comparison of variance - covariance patterns using relative principal component analysis (relative eigenanalysis), as described in Le Maitre and Mitteroecker (2019) <doi:10.1111/2041-210X.13253>. Also provides functions to compute group covariance matrices, distance matrices, and perform proportionality tests. A worked sample on the body shape of cichlid fishes is included, based on the dataset from Kerschbaumer et al. (2013) <doi:10.5061/dryad.fc02f>.
Author: Anne Le Maitre [aut, cre] (<https://orcid.org/0000-0003-2690-7367>),
Philipp Mitteroecker [aut]
Maintainer: Anne Le Maitre <anne.le.maitre@univie.ac.at>
Diff between vcvComp versions 1.0.1 dated 2019-06-28 and 1.0.2 dated 2020-12-17
vcvComp-1.0.1/vcvComp/R/vcvComp-datasets.R |only vcvComp-1.0.2/vcvComp/DESCRIPTION | 18 - vcvComp-1.0.2/vcvComp/MD5 | 70 +++---- vcvComp-1.0.2/vcvComp/NEWS |only vcvComp-1.0.2/vcvComp/R/Tropheus-IK-coord-dataset.R |only vcvComp-1.0.2/vcvComp/R/Tropheus-dataset.R |only vcvComp-1.0.2/vcvComp/R/cov.B.R | 19 -- vcvComp-1.0.2/vcvComp/R/cov.W.R | 37 ++- vcvComp-1.0.2/vcvComp/R/cov.group.R | 18 - vcvComp-1.0.2/vcvComp/R/eigen.test.R | 21 -- vcvComp-1.0.2/vcvComp/R/euclidean.dist.R | 13 - vcvComp-1.0.2/vcvComp/R/mat.sq.dist.R | 13 - vcvComp-1.0.2/vcvComp/R/minv.R | 13 - vcvComp-1.0.2/vcvComp/R/pr.coord.R | 13 - vcvComp-1.0.2/vcvComp/R/prop.vcv.test.R | 15 - vcvComp-1.0.2/vcvComp/R/relGV.multi.R | 13 - vcvComp-1.0.2/vcvComp/R/relative.eigen.R | 13 - vcvComp-1.0.2/vcvComp/R/scaling.BW.R | 15 - vcvComp-1.0.2/vcvComp/build/vignette.rds |binary vcvComp-1.0.2/vcvComp/data/Tropheus.IK.coord.rda |only vcvComp-1.0.2/vcvComp/inst/CITATION | 8 vcvComp-1.0.2/vcvComp/inst/doc/vcvComp-worked-example.R | 30 +-- vcvComp-1.0.2/vcvComp/inst/doc/vcvComp-worked-example.Rmd | 8 vcvComp-1.0.2/vcvComp/inst/doc/vcvComp-worked-example.html | 95 +++++----- vcvComp-1.0.2/vcvComp/man/Tropheus.IK.coord.Rd |only vcvComp-1.0.2/vcvComp/man/Tropheus.Rd | 8 vcvComp-1.0.2/vcvComp/man/cov.B.Rd | 17 - vcvComp-1.0.2/vcvComp/man/cov.W.Rd | 25 +- vcvComp-1.0.2/vcvComp/man/cov.group.Rd | 18 - vcvComp-1.0.2/vcvComp/man/eigen.test.Rd | 19 -- vcvComp-1.0.2/vcvComp/man/euclidean.dist.Rd | 93 ++++----- vcvComp-1.0.2/vcvComp/man/mat.sq.dist.Rd | 101 +++++----- vcvComp-1.0.2/vcvComp/man/minv.Rd | 97 ++++------ vcvComp-1.0.2/vcvComp/man/pr.coord.Rd | 115 +++++------- vcvComp-1.0.2/vcvComp/man/prop.vcv.test.Rd | 115 +++++------- vcvComp-1.0.2/vcvComp/man/relGV.multi.Rd | 87 ++++----- vcvComp-1.0.2/vcvComp/man/relative.eigen.Rd | 121 ++++++------- vcvComp-1.0.2/vcvComp/man/scaling.BW.Rd | 99 +++++----- vcvComp-1.0.2/vcvComp/vignettes/vcvComp-worked-example.Rmd | 8 39 files changed, 640 insertions(+), 715 deletions(-)
Title: Downloading Supplementary Data from Published Manuscripts
Description: Downloads data supplementary materials from manuscripts,
using papers' DOIs as references. Facilitates open, reproducible
research workflows: scientists re-analyzing published datasets can
work with them as easily as if they were stored on their own
computer, and others can track their analysis workflow
painlessly. The main function suppdata() returns a (temporary)
location on the user's computer where the file is stored, making
it simple to use suppdata() with standard functions like
read.csv().
Author: William D. Pearse [aut, cre] (<https://orcid.org/0000-0002-6241-3164>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Daniel Nuest [aut] (<https://orcid.org/0000-0002-0024-5046>),
Ross Mounce [rev] (Ross Mounce reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/195),
Sarah Supp [rev] (Sarah Supp reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/195)
Maintainer: William D. Pearse <will.pearse@gmail.com>
Diff between suppdata versions 1.1-5 dated 2020-10-31 and 1.1-6 dated 2020-12-17
DESCRIPTION | 6 - MD5 | 34 +++---- inst/doc/suppdata-intro.pdf |binary tests/test-all.R | 5 - tests/testthat/test-biorxiv.R | 23 ++-- tests/testthat/test-copernicus.R | 121 ++++++++++++------------- tests/testthat/test-dryad.R | 43 ++++---- tests/testthat/test-epmc.R | 25 ++--- tests/testthat/test-figshare.R | 15 +-- tests/testthat/test-fulltext.R | 78 ++++++++-------- tests/testthat/test-inputs.R | 187 +++++++++++++++++++-------------------- tests/testthat/test-jstatsoft.R | 109 +++++++++++----------- tests/testthat/test-mdpi.R | 71 +++++++------- tests/testthat/test-peerj.R | 95 ++++++++++--------- tests/testthat/test-plos.R | 39 ++++---- tests/testthat/test-rsbp.R | 25 ++--- tests/testthat/test-science.R | 25 ++--- tests/testthat/test-wiley.R | 57 ++++++----- 18 files changed, 485 insertions(+), 473 deletions(-)
Title: Seeded-LDA for Topic Modeling
Description: Implements the seeded-LDA model (Lu, Ott, Cardie & Tsou 2010) <doi:10.1109/ICDMW.2011.125> using the quanteda package and the GibbsLDA++ library for semisupervised topic modeling.
Seeded-LDA allows users to pre-define topics with keywords to perform theory-driven analysis of textual data in social sciences and humanities (Watanabe & Zhou 2020) <doi:10.1177/0894439320907027>.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph] (GibbsLDA++)
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 0.5 dated 2020-09-10 and 0.5.1 dated 2020-12-17
DESCRIPTION | 8 +- MD5 | 16 ++--- NEWS.md | 7 ++ R/lda.R | 4 - R/seededlda.R | 11 ++- man/textmodel_seededlda.Rd | 2 src/lda.cpp | 15 +++-- src/lda.h | 86 +++++++++++++++--------------- tests/testthat/test-textmodel_seededlda.R | 43 ++++++++++++++- 9 files changed, 126 insertions(+), 66 deletions(-)
Title: Advanced Plotting of Ordinal Regression Models
Description: An extension to the Regression Modeling Strategies package that
facilitates plotting ordinal regression model predictions together with
confidence intervals for each dependent variable level.
It also adds a functionality to plot the model summary as a modifiable
object.
Author: Richard Meitern [aut, cre] (<https://orcid.org/0000-0002-2600-3002>)
Maintainer: Richard Meitern <richard.meitern@ut.ee>
Diff between ormPlot versions 0.3.2 dated 2019-06-21 and 0.3.4 dated 2020-12-17
ormPlot-0.3.2/ormPlot/tests/figs/forestplot-full.svg |only ormPlot-0.3.2/ormPlot/tests/figs/forestplot-left.svg |only ormPlot-0.3.2/ormPlot/tests/figs/forestplot-right.svg |only ormPlot-0.3.2/ormPlot/tests/figs/orm-forestplot |only ormPlot-0.3.2/ormPlot/tests/figs/plot-oddstable |only ormPlot-0.3.2/ormPlot/tests/figs/plot-orm-graph |only ormPlot-0.3.2/ormPlot/tests/figs/plot-orm-predictwithci |only ormPlot-0.3.4/ormPlot/DESCRIPTION | 17 ormPlot-0.3.4/ormPlot/LICENSE | 2 ormPlot-0.3.4/ormPlot/MD5 | 89 - ormPlot-0.3.4/ormPlot/NEWS.md | 8 ormPlot-0.3.4/ormPlot/README.md | 7 ormPlot-0.3.4/ormPlot/build/vignette.rds |binary ormPlot-0.3.4/ormPlot/inst/CITATION | 14 ormPlot-0.3.4/ormPlot/inst/doc/ormPlot.R | 30 ormPlot-0.3.4/ormPlot/inst/doc/ormPlot.html | 836 ++++++---- ormPlot-0.3.4/ormPlot/man/educ_data.Rd | 6 ormPlot-0.3.4/ormPlot/man/forestplot.Rd | 17 ormPlot-0.3.4/ormPlot/man/join_ggplots.Rd | 8 ormPlot-0.3.4/ormPlot/man/oddstable_graph.Rd | 9 ormPlot-0.3.4/ormPlot/man/ormPlot.Rd | 1 ormPlot-0.3.4/ormPlot/man/orm_graph.Rd | 12 ormPlot-0.3.4/ormPlot/man/plot.orm.Rd | 32 ormPlot-0.3.4/ormPlot/man/predict_with_ci.Rd | 23 ormPlot-0.3.4/ormPlot/tests/figs/deps.txt | 2 ormPlot-0.3.4/ormPlot/tests/figs/ggplot-breaks-orm-graph.svg | 2 ormPlot-0.3.4/ormPlot/tests/figs/ggplot-letters-orm-graph.svg | 4 ormPlot-0.3.4/ormPlot/tests/figs/ggplot-limits-orm-graph.svg | 8 ormPlot-0.3.4/ormPlot/tests/figs/ggplot-nr-graph.svg | 2 ormPlot-0.3.4/ormPlot/tests/figs/ggplot-reduced-graph.svg | 2 ormPlot-0.3.4/ormPlot/tests/figs/ggplot-shape-orm-graph.svg | 4 ormPlot-0.3.4/ormPlot/tests/figs/ggplot-vertical-graph-light.svg | 2 ormPlot-0.3.4/ormPlot/tests/figs/ggplot-vertical-graph-minimal.svg | 2 ormPlot-0.3.4/ormPlot/tests/figs/ggplot-vertical-graph.svg | 3 ormPlot-0.3.4/ormPlot/tests/figs/orm-graph-4.svg | 4 ormPlot-0.3.4/ormPlot/tests/figs/prediction-ggplot-article-edited.svg | 72 ormPlot-0.3.4/ormPlot/tests/figs/prediction-ggplot-article.svg | 72 ormPlot-0.3.4/ormPlot/tests/figs/prediction-ggplot-simplest.svg | 6 ormPlot-0.3.4/ormPlot/tests/testthat/Rplots.pdf |binary ormPlot-0.3.4/ormPlot/tests/testthat/test-orm_forestplot.R | 16 ormPlot-0.3.4/ormPlot/tests/testthat/test-plot_oddstable.R | 17 ormPlot-0.3.4/ormPlot/tests/testthat/test-plot_orm_graph.R | 17 ormPlot-0.3.4/ormPlot/tests/testthat/test-plot_orm_predictWithCI.R | 17 43 files changed, 818 insertions(+), 545 deletions(-)
Title: Systems Insights from Generation of Hydroclimatic Timeseries
Description: A tool to create hydroclimate scenarios, stress test systems and visualize system performance in scenario-neutral climate change impact assessments. Scenario-neutral approaches 'stress-test' the performance of a modelled system by applying a wide range of plausible hydroclimate conditions (see Brown & Wilby (2012) <doi:10.1029/2012EO410001> and Prudhomme et al. (2010) <doi:10.1016/j.jhydrol.2010.06.043>). These approaches allow the identification of hydroclimatic variables that affect the vulnerability of a system to hydroclimate variation and change. This tool enables the generation of perturbed time series using a range of approaches including simple scaling of observed time series (e.g. Culley et al. (2016) <doi:10.1002/2015WR018253>) and stochastic simulation of perturbed time series via an inverse approach (see Guo et al. (2018) <doi:10.1016/j.jhydrol.2016.03.025>). It incorporates 'Richardson-type' weather generator model configurations documented in Richardson (1981) <doi:10.1029/WR017i001p00182>, Richardson and Wright (1984), as well as latent variable type model configurations documented in Bennett et al. (2018) <doi:10.1016/j.jhydrol.2016.12.043>, Rasmussen (2013) <doi:10.1002/wrcr.20164>, Bennett et al. (2019) <doi:10.5194/hess-23-4783-2019> to generate hydroclimate variables on a daily basis (e.g. precipitation, temperature, potential evapotranspiration) and allows a variety of different hydroclimate variable properties, herein called attributes, to be perturbed. Options are included for the easy integration of existing system models both internally in R and externally for seamless 'stress-testing'. A suite of visualization options for the results of a scenario-neutral analysis (e.g. plotting performance spaces and overlaying climate projection information) are also included. As further developments in scenario-neutral approaches occur the tool will be updated to incorporate these advances.
Author: Bree Bennett [aut, cre] (<https://orcid.org/0000-0002-2131-088X>),
Sam Culley [aut] (<https://orcid.org/0000-0003-4798-8522>),
Anjana Devanand [aut] (<https://orcid.org/0000-0001-9422-3894>),
Seth Westra [aut] (<https://orcid.org/0000-0003-4023-6061>),
Danlu Guo [ctb] (<https://orcid.org/0000-0003-1083-1214>),
Holger Maier [ths] (<https://orcid.org/0000-0002-0277-6887>)
Maintainer: Bree Bennett <bree.bennett@adelaide.edu.au>
Diff between foreSIGHT versions 0.9.81 dated 2019-12-04 and 1.0.0 dated 2020-12-17
foreSIGHT-0.9.81/foreSIGHT/NEWS |only foreSIGHT-0.9.81/foreSIGHT/R/TEMP_performanceSpaces.R |only foreSIGHT-0.9.81/foreSIGHT/R/devScenarioClean.R |only foreSIGHT-0.9.81/foreSIGHT/R/exSpArgsVisual.R |only foreSIGHT-0.9.81/foreSIGHT/R/performanceSpace.R |only foreSIGHT-0.9.81/foreSIGHT/R/plotLayers.R |only foreSIGHT-0.9.81/foreSIGHT/R/quickSpace.R |only foreSIGHT-0.9.81/foreSIGHT/R/visualizeSpaces.R |only foreSIGHT-0.9.81/foreSIGHT/data/climdata2030.RData |only foreSIGHT-0.9.81/foreSIGHT/data/datalist |only foreSIGHT-0.9.81/foreSIGHT/data/oatScenarios.RData |only foreSIGHT-0.9.81/foreSIGHT/data/tankPlot.RData |only foreSIGHT-0.9.81/foreSIGHT/data/tankSimpleScale.RData |only foreSIGHT-0.9.81/foreSIGHT/inst/doc/Vignette.Rmd |only foreSIGHT-0.9.81/foreSIGHT/inst/doc/Vignette.html |only foreSIGHT-0.9.81/foreSIGHT/man/attributeCalculator.Rd |only foreSIGHT-0.9.81/foreSIGHT/man/devScenarioClean.Rd |only foreSIGHT-0.9.81/foreSIGHT/man/exSpArgsVisual.Rd |only foreSIGHT-0.9.81/foreSIGHT/man/oat_out.Rd |only foreSIGHT-0.9.81/foreSIGHT/man/performanceSpaces.Rd |only foreSIGHT-0.9.81/foreSIGHT/man/plotLayers.Rd |only foreSIGHT-0.9.81/foreSIGHT/man/quickSpace.Rd |only foreSIGHT-0.9.81/foreSIGHT/man/scenarioGenerator.Rd |only foreSIGHT-0.9.81/foreSIGHT/man/tank_simpleScale_plot.Rd |only foreSIGHT-0.9.81/foreSIGHT/man/tank_simple_scenarios.Rd |only foreSIGHT-0.9.81/foreSIGHT/vignettes/SimpleScale.png |only foreSIGHT-0.9.81/foreSIGHT/vignettes/Stochastic.png |only foreSIGHT-0.9.81/foreSIGHT/vignettes/Vignette.Rmd |only foreSIGHT-0.9.81/foreSIGHT/vignettes/attSel.png |only foreSIGHT-0.9.81/foreSIGHT/vignettes/diog1.png |only foreSIGHT-0.9.81/foreSIGHT/vignettes/diog2.png |only foreSIGHT-0.9.81/foreSIGHT/vignettes/exSpArgs.png |only foreSIGHT-0.9.81/foreSIGHT/vignettes/framework.png |only foreSIGHT-0.9.81/foreSIGHT/vignettes/process.png |only foreSIGHT-0.9.81/foreSIGHT/vignettes/processFlow.png |only foreSIGHT-0.9.81/foreSIGHT/vignettes/quickSpace.png |only foreSIGHT-1.0.0/foreSIGHT/DESCRIPTION | 59 foreSIGHT-1.0.0/foreSIGHT/MD5 | 191 - foreSIGHT-1.0.0/foreSIGHT/NAMESPACE | 106 foreSIGHT-1.0.0/foreSIGHT/NEWS.md |only foreSIGHT-1.0.0/foreSIGHT/R/LogfileEntry.R | 130 foreSIGHT-1.0.0/foreSIGHT/R/RcppExports.R |only foreSIGHT-1.0.0/foreSIGHT/R/WGEN_lib.R | 854 ++--- foreSIGHT-1.0.0/foreSIGHT/R/analyzeSpaces.R | 18 foreSIGHT-1.0.0/foreSIGHT/R/argumentInputChecker.R | 635 ++- foreSIGHT-1.0.0/foreSIGHT/R/argumentLogicChecker.R | 281 - foreSIGHT-1.0.0/foreSIGHT/R/attributeCalculator.R | 153 foreSIGHT-1.0.0/foreSIGHT/R/attributeManager.R | 999 +++--- foreSIGHT-1.0.0/foreSIGHT/R/calc.stat.lib.R | 1221 +++---- foreSIGHT-1.0.0/foreSIGHT/R/calibrationArgCheck.R | 162 - foreSIGHT-1.0.0/foreSIGHT/R/calibrationNation.R | 831 ++--- foreSIGHT-1.0.0/foreSIGHT/R/collate.stats.R | 408 +- foreSIGHT-1.0.0/foreSIGHT/R/control.R | 1505 +++++---- foreSIGHT-1.0.0/foreSIGHT/R/controlFileFunctions.R |only foreSIGHT-1.0.0/foreSIGHT/R/control_utilityFuncs.R |only foreSIGHT-1.0.0/foreSIGHT/R/createExpSpace.R |only foreSIGHT-1.0.0/foreSIGHT/R/dataInputChecker.R | 162 - foreSIGHT-1.0.0/foreSIGHT/R/dateManager.R | 451 +- foreSIGHT-1.0.0/foreSIGHT/R/defaultParams_diagAndPlotting.R |only foreSIGHT-1.0.0/foreSIGHT/R/default_parameters.R |only foreSIGHT-1.0.0/foreSIGHT/R/demoTankModel.R | 515 +-- foreSIGHT-1.0.0/foreSIGHT/R/diagnosticPlotLib.R | 1603 ++++++---- foreSIGHT-1.0.0/foreSIGHT/R/exposureSpaceSampler.R | 679 ++-- foreSIGHT-1.0.0/foreSIGHT/R/foreSIGHT.R |only foreSIGHT-1.0.0/foreSIGHT/R/getArguments.R | 126 foreSIGHT-1.0.0/foreSIGHT/R/harmonicFit.R | 429 +- foreSIGHT-1.0.0/foreSIGHT/R/modEvaluate.R |only foreSIGHT-1.0.0/foreSIGHT/R/modEvaluate_masterLists_v2.R |only foreSIGHT-1.0.0/foreSIGHT/R/modEvaluate_v2.R |only foreSIGHT-1.0.0/foreSIGHT/R/modelInputEnvironments.R |only foreSIGHT-1.0.0/foreSIGHT/R/modelSequencer.R | 380 +- foreSIGHT-1.0.0/foreSIGHT/R/objFuncTown.R | 206 - foreSIGHT-1.0.0/foreSIGHT/R/optimManagement.R | 462 +- foreSIGHT-1.0.0/foreSIGHT/R/outputManager.R | 464 +- foreSIGHT-1.0.0/foreSIGHT/R/plotExpSpace.R |only foreSIGHT-1.0.0/foreSIGHT/R/plotOptions.R |only foreSIGHT-1.0.0/foreSIGHT/R/plotPerformanceOAT.R |only foreSIGHT-1.0.0/foreSIGHT/R/plotPerformanceSpace.R |only foreSIGHT-1.0.0/foreSIGHT/R/plotPerformanceSpaceMulti.R |only foreSIGHT-1.0.0/foreSIGHT/R/simCity.R | 328 +- foreSIGHT-1.0.0/foreSIGHT/R/simPerformance.R | 89 foreSIGHT-1.0.0/foreSIGHT/R/simplyScale_lib.R | 76 foreSIGHT-1.0.0/foreSIGHT/R/stochParManager.R | 1309 +++----- foreSIGHT-1.0.0/foreSIGHT/R/summariseSimulatedSeries.R | 1245 +++++-- foreSIGHT-1.0.0/foreSIGHT/R/sysdata.rda |only foreSIGHT-1.0.0/foreSIGHT/R/targetFinder.R | 143 foreSIGHT-1.0.0/foreSIGHT/R/zzz.R | 42 foreSIGHT-1.0.0/foreSIGHT/build/vignette.rds |binary foreSIGHT-1.0.0/foreSIGHT/data/egClimData.rda |only foreSIGHT-1.0.0/foreSIGHT/data/egScalPerformance.rda |only foreSIGHT-1.0.0/foreSIGHT/data/egScalSummary.rda |only foreSIGHT-1.0.0/foreSIGHT/data/egSimOATPerformance.rda |only foreSIGHT-1.0.0/foreSIGHT/data/egSimOATSummary.rda |only foreSIGHT-1.0.0/foreSIGHT/data/egSimPerformance.rda |only foreSIGHT-1.0.0/foreSIGHT/data/egSimPerformance_systemB.rda |only foreSIGHT-1.0.0/foreSIGHT/data/egSimSummary.rda |only foreSIGHT-1.0.0/foreSIGHT/data/tankDat.RData |binary foreSIGHT-1.0.0/foreSIGHT/inst/doc/Vignette_QuickStart_simpleScal.Rmd |only foreSIGHT-1.0.0/foreSIGHT/inst/doc/Vignette_QuickStart_simpleScal.html |only foreSIGHT-1.0.0/foreSIGHT/inst/doc/Vignette_Tutorial.Rmd |only foreSIGHT-1.0.0/foreSIGHT/inst/doc/Vignette_Tutorial.html |only foreSIGHT-1.0.0/foreSIGHT/man/calculateAttributes.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/climdata2030.Rd | 60 foreSIGHT-1.0.0/foreSIGHT/man/createExpSpace.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/egClimData.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/egScalPerformance.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/egScalSummary.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/egSimOATPerformance.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/egSimOATSummary.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/egSimPerformance.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/egSimPerformance_systemB.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/egSimSummary.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/generateScenario.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/generateScenarios.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/getSimSummary.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/modCalibrator.Rd | 142 foreSIGHT-1.0.0/foreSIGHT/man/modSimulator.Rd | 180 - foreSIGHT-1.0.0/foreSIGHT/man/plotExpSpace.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/plotOptions.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/plotPerformanceOAT.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/plotPerformanceSpace.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/plotPerformanceSpaceMulti.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/plotScenarios.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/runSystemModel.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/tankPerformance.Rd | 74 foreSIGHT-1.0.0/foreSIGHT/man/tankWrapper.Rd | 86 foreSIGHT-1.0.0/foreSIGHT/man/tank_obs.Rd | 50 foreSIGHT-1.0.0/foreSIGHT/man/viewAttributeDef.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/viewAttributes.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/viewDefaultOptimArgs.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/viewModelParameters.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/viewModels.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/viewTankMetrics.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/viewVariables.Rd |only foreSIGHT-1.0.0/foreSIGHT/man/writeControlFile.Rd |only foreSIGHT-1.0.0/foreSIGHT/src |only foreSIGHT-1.0.0/foreSIGHT/tests |only foreSIGHT-1.0.0/foreSIGHT/vignettes/Vignette_QuickStart_simpleScal.Rmd |only foreSIGHT-1.0.0/foreSIGHT/vignettes/Vignette_Tutorial.Rmd |only foreSIGHT-1.0.0/foreSIGHT/vignettes/diag_usecaseB2.png |only foreSIGHT-1.0.0/foreSIGHT/vignettes/plotScenarios_usecaseB2.png |only foreSIGHT-1.0.0/foreSIGHT/vignettes/stepsOfCRAFT.png |only foreSIGHT-1.0.0/foreSIGHT/vignettes/usecaseB3_sim1.png |only foreSIGHT-1.0.0/foreSIGHT/vignettes/usecaseB3_sim2.png |only foreSIGHT-1.0.0/foreSIGHT/vignettes/usecaseB3_sim3.png |only 145 files changed, 9152 insertions(+), 7702 deletions(-)
Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results and where your package stands in the
CRAN submission queue in your R terminal.
Author: Francois Michonneau [aut, cre],
Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between foghorn versions 1.3.1 dated 2020-09-08 and 1.3.2 dated 2020-12-17
DESCRIPTION | 6 +-- MD5 | 10 +++--- NEWS.md | 7 ++++ R/winbuilder_queue.R | 4 +- build/vignette.rds |binary inst/doc/foghorn.html | 80 +++++++++++++++++++++++++++++++++++++++++--------- 6 files changed, 83 insertions(+), 24 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: LUOMUS - Finnish Museum of Natural History [cph],
William Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William Morris <willi@mmorris.email>
Diff between finbif versions 0.3.1 dated 2020-11-24 and 0.4.0 dated 2020-12-17
finbif-0.3.1/finbif/inst/vign/cache/habitat-type-head_fa1e3055877ea9be31e403fab184b2a8.RData |only finbif-0.3.1/finbif/inst/vign/cache/habitat-type-head_fa1e3055877ea9be31e403fab184b2a8.rdb |only finbif-0.3.1/finbif/inst/vign/cache/habitat-type-head_fa1e3055877ea9be31e403fab184b2a8.rdx |only finbif-0.3.1/finbif/inst/vign/cache/habitat-type-specific-meta_6443171006db81511095b655fe72c149.RData |only finbif-0.3.1/finbif/inst/vign/cache/habitat-type-specific-meta_6443171006db81511095b655fe72c149.rdb |only finbif-0.3.1/finbif/inst/vign/cache/habitat-type-specific-meta_6443171006db81511095b655fe72c149.rdx |only finbif-0.4.0/finbif/DESCRIPTION | 9 finbif-0.4.0/finbif/MD5 | 91 finbif-0.4.0/finbif/NEWS.md | 35 finbif-0.4.0/finbif/R/finbif_metadata.R | 48 finbif-0.4.0/finbif/R/finbif_occurrence.R | 131 finbif-0.4.0/finbif/R/finbif_records.R | 235 - finbif-0.4.0/finbif/R/methods.R | 59 finbif-0.4.0/finbif/R/sysdata.rda |binary finbif-0.4.0/finbif/R/utils.R | 18 finbif-0.4.0/finbif/inst/NEWS.Rd | 32 finbif-0.4.0/finbif/inst/doc/v02_occurrence_data.Rmd | 49 finbif-0.4.0/finbif/inst/doc/v02_occurrence_data.html | 142 finbif-0.4.0/finbif/inst/doc/v05_filtering.Rmd | 8 finbif-0.4.0/finbif/inst/doc/v05_filtering.html | 8 finbif-0.4.0/finbif/inst/vign/cache/aggregate_2dab671d1523f27bfa252131c41b88f2.RData |only finbif-0.4.0/finbif/inst/vign/cache/aggregate_2dab671d1523f27bfa252131c41b88f2.rdb |only finbif-0.4.0/finbif/inst/vign/cache/aggregate_2dab671d1523f27bfa252131c41b88f2.rdx |only finbif-0.4.0/finbif/inst/vign/cache/habitat-type-head_271f014e702c28643a756e3230b2e6f1.RData |only finbif-0.4.0/finbif/inst/vign/cache/habitat-type-head_271f014e702c28643a756e3230b2e6f1.rdb |only finbif-0.4.0/finbif/inst/vign/cache/habitat-type-head_271f014e702c28643a756e3230b2e6f1.rdx |only finbif-0.4.0/finbif/inst/vign/cache/habitat-type-specific-meta_dd826d7a286a1e6639610e10626658e3.RData |only finbif-0.4.0/finbif/inst/vign/cache/habitat-type-specific-meta_dd826d7a286a1e6639610e10626658e3.rdb |only finbif-0.4.0/finbif/inst/vign/cache/habitat-type-specific-meta_dd826d7a286a1e6639610e10626658e3.rdx |only finbif-0.4.0/finbif/inst/vign/v02_occurrence_data.Rmd | 22 finbif-0.4.0/finbif/inst/vign/v02_occurrence_data.md | 49 finbif-0.4.0/finbif/inst/vign/v05_filtering.Rmd | 8 finbif-0.4.0/finbif/inst/vign/v05_filtering.md | 8 finbif-0.4.0/finbif/man/finbif_occurrence.Rd | 5 finbif-0.4.0/finbif/man/finbif_records.Rd | 5 finbif-0.4.0/finbif/tests/api-dev-cassettes/finbif_occurrence.yml | 599 ++ finbif-0.4.0/finbif/tests/api-dev-cassettes/finbif_records.yml | 107 finbif-0.4.0/finbif/tests/cassettes/finbif_occurrence.yml | 679 ++ finbif-0.4.0/finbif/tests/cassettes/finbif_records.yml | 171 finbif-0.4.0/finbif/tests/figs/deps.txt | 2 finbif-0.4.0/finbif/tests/figs/querying-finbif-occurrence-data/occurrence-plot-dev.svg | 2259 ++++----- finbif-0.4.0/finbif/tests/figs/querying-finbif-occurrence-data/occurrence-plot.svg | 2269 ++++------ finbif-0.4.0/finbif/tests/testthat/helper-finbif.R | 41 finbif-0.4.0/finbif/tests/testthat/test-finbif_api_get.R | 2 finbif-0.4.0/finbif/tests/testthat/test-finbif_check_taxa.R | 2 finbif-0.4.0/finbif/tests/testthat/test-finbif_collections.R | 2 finbif-0.4.0/finbif/tests/testthat/test-finbif_dates.R | 2 finbif-0.4.0/finbif/tests/testthat/test-finbif_occurrence.R | 27 finbif-0.4.0/finbif/tests/testthat/test-finbif_records.R | 11 finbif-0.4.0/finbif/tests/testthat/test-finbif_taxa.R | 2 finbif-0.4.0/finbif/tests/testthat/test-metadata.R | 26 finbif-0.4.0/finbif/tests/testthat/test-zzz-finbif.R | 2 finbif-0.4.0/finbif/vignettes/v02_occurrence_data.Rmd | 49 finbif-0.4.0/finbif/vignettes/v05_filtering.Rmd | 8 54 files changed, 4193 insertions(+), 3029 deletions(-)
Title: Plot Maps from Switzerland by Swiss Federal Statistical Office
Description: At the Swiss Federal Statistical Office (SFSO), spatial maps of Switzerland are available free of charge as 'Cartographic bases for small-scale thematic mapping'. This package contains convenience functions to import ESRI (Environmental Systems Research Institute) shape files using the package 'rgdal' and to plot them easily and quickly without having to worry too much about the technical details.
It contains utilities to combine multiple areas to one single polygon and to find neighbours for single regions. For any point on a map, a special locator can be used to determine to which municipality, district or canton it belongs.
Author: Andri Signorell [aut, cre],
Juerg Guggenbuehl [ctb],
Jeffery S. Evans [ctb]
Maintainer: Andri Signorell <andri@signorell.net>
Diff between bfsMaps versions 0.9.5 dated 2020-12-09 and 0.9.6 dated 2020-12-17
DESCRIPTION | 17 ++++--- MD5 | 16 +++---- NEWS | 11 ++++ R/bfsMaps.R | 93 ++++++++++++------------------------------ R/utils.R | 19 ++++---- data/d.bfsrg.rda |binary inst/doc/bfsMapsCompanion.pdf |binary man/CombinePolygons.Rd | 2 man/SwissLocator.Rd | 3 - 9 files changed, 69 insertions(+), 92 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut],
Trustees of Columbia University [cph],
Lawrence Livermore National Security [cph] (CVODES),
The Regents of the University of California [cph] (CVODES),
Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.21.0-6 dated 2020-08-16 and 2.21.0-7 dated 2020-12-17
DESCRIPTION | 8 +- MD5 | 12 +-- R/Flags.R | 2 R/stanFunction.R | 18 ++++ inst/doc/stanmath.html | 68 ++++++++++++++++- inst/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp | 20 ++++- man/stanFunction.Rd | 4 + 7 files changed, 116 insertions(+), 16 deletions(-)
Title: Get Executing Script's Path, from 'RStudio', 'RGui', 'Rterm' and
'Rscript' (Command-Line / / Terminal), and when using 'source'
Description: Determine the full path of the executing script. Works when running
a line or selection from an open R script in 'RStudio' and 'RGui', when using
'source' and 'sys.source' and 'debugSource' ('RStudio' exclusive), and when
running R (including 'Rscript') from the command-line / / terminal.
Author: Andrew Simmons
Maintainer: Andrew Simmons <akwsimmo@gmail.com>
Diff between this.path versions 0.2.0 dated 2020-12-03 and 0.2.1 dated 2020-12-17
DESCRIPTION | 12 +++--- MD5 | 8 ++-- R/this.path.R | 95 ++++++++++++++++++++++++++++++++++++++++++++++++------ build/partial.rdb |binary man/this.path.Rd | 12 ++++-- 5 files changed, 103 insertions(+), 24 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>
Diff between Sequential versions 3.2 dated 2020-11-29 and 3.2.1 dated 2020-12-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/Analyze.Poisson.R | 17 ++++++++--------- R/AnalyzeSetUp.Binomial.R | 4 ++-- R/Optimal.Binomial.R | 6 ++++-- man/AnalyzeSetUp.Binomial.Rd | 7 +++++-- man/Optimal.Binomial.Rd | 4 ++-- man/Sequential-package.Rd | 8 ++++++-- 8 files changed, 38 insertions(+), 30 deletions(-)
Title: Interface to the 'Request Tracker' API
Description: Provides a programmatic interface to the 'Request Tracker' (RT)
HTTP API <https://rt-wiki.bestpractical.com/wiki/REST>. 'RT' is a popular
ticket tracking system.
Author: Bryce Mecum [aut, cre] (<https://orcid.org/0000-0002-0381-3766>),
Irene Steves [ctb],
National Center for Ecological Analysis and Synthesis [cph]
Maintainer: Bryce Mecum <mecum@nceas.ucsb.edu>
Diff between rt versions 1.0.0 dated 2020-04-27 and 1.0.1 dated 2020-12-17
DESCRIPTION | 16 - MD5 | 20 - NEWS.md | 8 R/rt_login.R | 5 README.md | 2 build/vignette.rds |binary inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 493 ++++++++++++++------------------------ inst/doc/searching.html | 513 +++++++++++++++------------------------ inst/doc/workflows.html | 578 ++++++++++++++++++--------------------------- vignettes/introduction.Rmd | 2 11 files changed, 665 insertions(+), 974 deletions(-)
Title: R Commander Plug-in for Case 1 (Object Case) Best-Worst Scaling
Description: Adds menu items to the R Commander for implementing case 1 (object case) best-worst scaling (BWS1) from designing choice sets to measuring preferences for items. BWS1 is a question-based survey method that constructs various combinations of items (choice sets) using the experimental designs, asks respondents to select the best and worst items in each choice set, and then measures preferences for the items by analyzing the responses. For details on BWS1, refer to Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between RcmdrPlugin.BWS1 versions 0.1-3 dated 2020-09-07 and 0.1-4 dated 2020-12-17
DESCRIPTION | 8 MD5 | 12 NEWS | 3 R/RcmdrPlugin.BWS1.R | 582 ++++++++++++++++++++++++++++------------ R/globals.R | 2 inst/etc/menus.txt | 44 +-- man/RcmdrPlugin.BWS1-package.Rd | 14 7 files changed, 456 insertions(+), 209 deletions(-)
More information about RcmdrPlugin.BWS1 at CRAN
Permanent link
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut] (<https://orcid.org/0000-0002-7672-0712>)
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.12-2 dated 2020-11-19 and 2.12-3 dated 2020-12-17
DESCRIPTION | 26 MD5 | 75 +- NAMESPACE | 5 R/BiodiversityRGUI.R | 3 R/sites.long.R | 34 + inst/ChangeLog | 21 inst/etc/BiodiversityGUI.R | 28 inst/etc/Rcmdr-hex.pdf |only inst/etc/Rcmdr-menus.txt | 1059 +++++++++++++++++----------------- inst/etc/Rcmdr-model-capabilities.txt | 100 +-- inst/etc/model-classes.txt | 18 man/BiodiversityR-package.Rd | 2 man/BiodiversityRGUI.Rd | 4 man/CAPdiscrim.Rd | 2 man/NMSrandom.Rd | 2 man/PCAsignificance.Rd | 2 man/accumresult.Rd | 6 man/add.spec.scores.Rd | 2 man/balanced.specaccum.Rd | 2 man/crosstabanalysis.Rd | 2 man/deviancepercentage.Rd | 2 man/dist.eval.Rd | 2 man/dist.zeroes.Rd | 2 man/distdisplayed.Rd | 2 man/disttransform.Rd | 2 man/diversityresult.Rd | 2 man/ensemble.bioclim.Rd | 2 man/ensemble.evaluate.Rd | 2 man/faramea.Rd | 6 man/makecommunitydataset.Rd | 2 man/ordicoeno.Rd | 2 man/ordisymbol.Rd | 2 man/radfitresult.Rd | 2 man/rankabundance.Rd | 2 man/removeNAcomm.Rd | 2 man/renyiresult.Rd | 3 man/residualssurface.Rd | 2 man/sites.long.Rd | 43 + man/spatialsample.Rd | 2 39 files changed, 800 insertions(+), 677 deletions(-)
Title: Applied Statistical Time Series Analysis
Description: Data sets and scripts to accompany Time Series Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2017, <DOI:10.1007/978-3-319-52452-8>, and Time Series: A Data Analysis Approach Using R. Chapman-Hall, 2019, <ISBN: 978-0367221096>.
Author: David Stoffer
Maintainer: David Stoffer <stoffer@pitt.edu>
Diff between astsa versions 1.11 dated 2020-12-05 and 1.12 dated 2020-12-17
DESCRIPTION | 8 +- MD5 | 170 +++++++++++++++++++++++++-------------------------- R/sarima.sim.R | 24 +++---- man/ARMAtoAR.Rd | 2 man/EM0.Rd | 2 man/EM1.Rd | 2 man/EQ5.Rd | 2 man/EQcount.Rd | 2 man/EXP6.Rd | 2 man/Grid.Rd | 2 man/HCT.Rd | 2 man/Hare.Rd | 4 - man/Kfilter0.Rd | 4 - man/Kfilter1.Rd | 4 - man/Kfilter2.Rd | 4 - man/Ksmooth0.Rd | 4 - man/Ksmooth1.Rd | 4 - man/Ksmooth2.Rd | 4 - man/LagReg.Rd | 2 man/Lynx.Rd | 4 - man/PLT.Rd | 2 man/SVfilter.Rd | 2 man/SigExtract.Rd | 2 man/UnempRate.Rd | 2 man/WBC.Rd | 2 man/acf1.Rd | 4 - man/acf2.Rd | 2 man/ar1miss.Rd | 2 man/arf.Rd | 2 man/arma.spec.Rd | 2 man/astsa-package.Rd | 7 +- man/beamd.Rd | 2 man/birth.Rd | 2 man/blood.Rd | 2 man/bnrf1ebv.Rd | 2 man/cardox.Rd | 2 man/ccf2.Rd | 2 man/chicken.Rd | 2 man/climhyd.Rd | 2 man/cmort.Rd | 2 man/cpg.Rd | 2 man/djia.Rd | 4 - man/econ5.Rd | 2 man/eqexp.Rd | 2 man/flu.Rd | 2 man/fmri.Rd | 2 man/fmri1.Rd | 2 man/gas.Rd | 5 - man/gdp.Rd | 2 man/globtemp.Rd | 2 man/globtempl.Rd | 2 man/gnp.Rd | 10 --- man/gtemp.Rd | 8 -- man/gtemp2.Rd | 7 -- man/gtemp_land.Rd | 8 -- man/gtemp_ocean.Rd | 10 --- man/hor.Rd | 4 - man/jj.Rd | 2 man/lag1.plot.Rd | 2 man/lag2.plot.Rd | 2 man/lap.Rd | 2 man/mvspec.Rd | 16 ++-- man/oil.Rd | 13 --- man/part.Rd | 17 ----- man/prodn.Rd | 2 man/qinfl.Rd | 2 man/qintr.Rd | 2 man/rec.Rd | 7 -- man/salmon.Rd | 3 man/salt.Rd | 2 man/saltemp.Rd | 2 man/sarima.Rd | 9 +- man/sarima.for.Rd | 4 - man/sarima.sim.Rd | 2 man/soi.Rd | 2 man/soiltemp.Rd | 2 man/sp500w.Rd | 2 man/spec.ic.Rd | 4 - man/speech.Rd | 2 man/ssm.Rd | 2 man/star.Rd | 2 man/stoch.reg.Rd | 2 man/sunspotz.Rd | 2 man/tsplot.Rd | 2 man/unemp.Rd | 2 man/varve.Rd | 2 86 files changed, 214 insertions(+), 274 deletions(-)
Title: Pipe-Friendly Vector Replacement with Case Statements
Description: Offers a pipe-friendly alternative to the 'dplyr'
functions case_when() and if_else(). These functions accept a vector
as an optional first argument, allowing conditional statements to be
built using the 'magrittr' dot operator. The functions also coerce
all possible outputs to the same type, meaning you no longer have to
worry about using specific typed variants of NA or explicitly
declaring integer outputs.
Author: Alexander Rossell Hayes [aut, cre, cph]
(<https://orcid.org/0000-0001-9412-0457>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between incase versions 0.1.0 dated 2020-09-15 and 0.2.0 dated 2020-12-17
DESCRIPTION | 10 - MD5 | 31 +++-- NAMESPACE | 19 +-- NEWS.md |only R/fn_case.R |only R/glubort.R | 8 + R/grep_case.R |only R/in_case.R | 25 ++-- R/switch_case.R | 77 ++++++++++--- README.md | 60 +++++++--- man/fn_case.Rd |only man/grep_case.Rd |only man/in_case.Rd | 220 +++++++++++++++++++------------------- man/incase-package.Rd | 3 man/switch_case.Rd | 212 ++++++++++++++++++++---------------- tests/testthat/test-fn_case.R |only tests/testthat/test-formatting.R | 7 + tests/testthat/test-grep_case.R |only tests/testthat/test-in_case.R | 2 tests/testthat/test-switch_case.R | 24 +++- 20 files changed, 425 insertions(+), 273 deletions(-)