Title: Lightweight Variable Labels
Description: Assign, extract, or remove variable labels from R vectors.
Lightweight and dependency-free.
Author: Marius Barth [aut, cre] (<https://orcid.org/0000-0002-3421-6665>)
Maintainer: Marius Barth <marius.barth.uni.koeln@gmail.com>
Diff between tinylabels versions 0.2.1 dated 2021-03-27 and 0.2.2 dated 2021-12-06
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 4 ++++ NEWS.md | 6 ++++++ R/methods-base.R | 28 ++++++++++++++++++++++++++++ R/unlabel.R | 9 +++++++-- README.md | 16 ++++++++-------- build/vignette.rds |binary inst/CITATION | 7 ++++--- inst/doc/tinylabels_vignette.Rmd | 4 ++-- inst/doc/tinylabels_vignette.html | 13 +++++++------ tests/testthat/test-methods_base.R | 35 +++++++++++++++++++++++++++++++++++ vignettes/tinylabels_vignette.Rmd | 4 ++-- 13 files changed, 121 insertions(+), 41 deletions(-)
Title: Tools for Working with NHS Number Checksums
Description: Provides functions for working with NHS number checksums.
The UK's National Health Service issues NHS numbers to all users of its
services and this package implements functions for verifying that the
numbers are valid according to the checksum scheme the NHS use.
Numbers can be validated and checksums created.
Author: Mark Sellors [aut, cre, cph]
Maintainer: Mark Sellors <rstats@5vcc.com>
Diff between nhsnumber versions 0.1.1 dated 2020-12-07 and 0.1.2 dated 2021-12-06
DESCRIPTION | 13 ++++++------- MD5 | 20 ++++++++++---------- NEWS.md | 5 +++++ R/get_checksum.R | 19 ++++++++++--------- R/is_number_valid.R | 31 +++++++++++++++++++++---------- R/is_valid.R | 2 +- README.md | 13 +++++++++++-- man/get_checksum.Rd | 5 +++-- tests/testthat/test-get_checksum.R | 1 + tests/testthat/test-is_number_valid.R | 3 +++ tests/testthat/test-is_valid.R | 6 ++++-- 11 files changed, 75 insertions(+), 43 deletions(-)
Title: A Multiple Testing Procedure for High-Dimensional Mediation
Hypotheses
Description: A multiple-testing procedure for high-dimensional mediation hypotheses. Mediation analysis is of rising interest in epidemiology and clinical trials. Among existing methods for mediation analyses, the popular joint significance (JS) test yields an overly conservative type I error rate and therefore low power. In the R package 'HDMT' we implement a multiple-testing procedure that accurately controls the family-wise error rate (FWER) and the false discovery rate (FDR) when using JS for testing high-dimensional mediation hypotheses. The core of our procedure is based on estimating the proportions of three component null hypotheses and deriving the corresponding mixture distribution of null p-values. Results of the data examples include better-behaved quantile-quantile plots and improved detection of novel mediation relationships on the role of DNA methylation in genetic regulation of gene expression. With increasing interest in mediation by molecular intermediaries such as gene expression, the proposed method addresses an unmet methodological challenge. Methods used in the package refer to James Y. Dai, Janet L. Stanford & Michael LeBlanc (2020) <doi:10.1080/01621459.2020.1765785>.
Author: James Dai [aut, cre],
Xiaoyu Wang [aut]
Maintainer: James Dai <jdai@fredhutch.org>
Diff between HDMT versions 1.0.3 dated 2021-02-20 and 1.0.4 dated 2021-12-06
DESCRIPTION | 8 +- MD5 | 26 +++---- NAMESPACE | 6 - R/null_estimation.R | 172 +++++++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/HDMT.R | 4 - inst/doc/HDMT.Rnw | 4 - inst/doc/HDMT.pdf |binary man/adjust_quantile.Rd | 2 man/correct_qqplot.Rd | 2 man/fdr_est.Rd | 2 man/fwer_est.Rd | 2 man/null_estimation.Rd | 135 ++++++++++++++++++-------------------- vignettes/HDMT.Rnw | 4 - 14 files changed, 194 insertions(+), 173 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 2.8.1 dated 2021-09-14 and 2.8.2 dated 2021-12-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 3 +++ R/labkey.provenance.R | 4 +++- man/Rlabkey-package.Rd | 4 ++-- man/labkey.provenance.createProvenanceParams.Rd | 7 ++++--- man/labkey.provenance.stopRecording.Rd | 2 +- 7 files changed, 23 insertions(+), 17 deletions(-)
Title: Morpheme Tokenization
Description: Tokenize text into morphemes. The morphemepiece algorithm uses a
lookup table to determine the morpheme breakdown of words, and falls back on a
modified wordpiece tokenization algorithm for words not found in the lookup
table.
Author: Jonathan Bratt [aut, cre] (<https://orcid.org/0000-0003-2859-0076>),
Jon Harmon [aut] (<https://orcid.org/0000-0003-4781-4346>),
Bedford Freeman & Worth Pub Grp LLC DBA Macmillan Learning [cph]
Maintainer: Jonathan Bratt <jonathan.bratt@macmillan.com>
Diff between morphemepiece versions 1.1.0 dated 2021-10-27 and 1.1.2 dated 2021-12-06
DESCRIPTION | 6 MD5 | 74 +- NAMESPACE | 34 - NEWS.md | 30 R/00package_help.R | 42 - R/imports.R | 64 - R/tokenize.R | 619 +++++++++--------- R/utils.R | 104 +-- R/vocab.R | 536 +++++++-------- README.md | 64 - build/vignette.rds |binary inst/doc/algorithm_test.R | 186 ++--- inst/doc/algorithm_test.Rmd | 254 +++---- inst/doc/algorithm_test.html | 465 ++++++------- inst/doc/generating_vocab.R | 620 +++++++++--------- inst/doc/generating_vocab.Rmd | 832 ++++++++++++------------ inst/doc/generating_vocab.html | 911 +++++++++++++-------------- man/dot-infer_case_from_vocab.Rd | 46 - man/dot-mp_tokenize_single_string.Rd | 58 - man/dot-mp_tokenize_word.Rd | 96 +- man/dot-mp_tokenize_word_bidir.Rd | 74 +- man/dot-mp_tokenize_word_lookup.Rd | 56 - man/dot-new_morphemepiece_vocabulary.Rd | 48 - man/dot-validate_morphemepiece_vocabulary.Rd | 38 - man/load_lookup.Rd | 42 - man/load_or_retrieve_lookup.Rd | 42 - man/load_or_retrieve_vocab.Rd | 56 - man/load_vocab.Rd | 58 - man/morphemepiece_cache_dir.Rd | 52 - man/morphemepiece_tokenize.Rd | 70 +- man/prepare_vocab.Rd | 66 - man/reexports.Rd | 48 - man/set_morphemepiece_cache_dir.Rd | 40 - tests/testthat.R | 8 tests/testthat/test-morphemepiece.R | 210 +++--- vignettes/algorithm_test.Rmd | 254 +++---- vignettes/generating_vocab.Rmd | 832 ++++++++++++------------ vignettes/make_vocab_and_lookup.R | 646 +++++++++---------- 38 files changed, 3824 insertions(+), 3857 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the location
of the species (as a point pattern) is needed together with environmental conditions
(as a categorical raster). To test for significance habitat associations, one of
the two components is randomized. Methods are mainly based on Plotkin et al. (2000)
<doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>)
Maintainer: Maximillian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between shar versions 1.2.1 dated 2021-05-04 and 1.3 dated 2021-12-06
shar-1.2.1/shar/R/RcppExports.R |only shar-1.2.1/shar/R/SHAR.R |only shar-1.2.1/shar/R/onUnload.R |only shar-1.2.1/shar/R/plot_randomized_pattern.R |only shar-1.2.1/shar/R/plot_randomized_raster.R |only shar-1.2.1/shar/man/figures/README-plot-random_pattern-1.png |only shar-1.2.1/shar/man/figures/README-plot-random_pattern-2.png |only shar-1.2.1/shar/man/figures/README-plot_habitat-random-1.png |only shar-1.2.1/shar/man/plot_randomized_pattern.Rd |only shar-1.2.1/shar/man/plot_randomized_raster.Rd |only shar-1.2.1/shar/man/rcpp_sample.Rd |only shar-1.2.1/shar/src |only shar-1.2.1/shar/tests/testthat/test-plot_randomized_pattern.R |only shar-1.2.1/shar/tests/testthat/test-plot_randomized_raster.R |only shar-1.3/shar/DESCRIPTION | 30 shar-1.3/shar/MD5 | 177 +-- shar-1.3/shar/NAMESPACE | 13 shar-1.3/shar/NEWS.md | 19 shar-1.3/shar/R/calculate_energy.R | 98 +- shar-1.3/shar/R/classify_habitats.R | 13 shar-1.3/shar/R/create_neighbourhood.R | 16 shar-1.3/shar/R/data.R | 114 +- shar-1.3/shar/R/estimate_pcf_fast.R | 7 shar-1.3/shar/R/extract_points.R | 15 shar-1.3/shar/R/fit_point_process.R | 94 +- shar-1.3/shar/R/list_to_randomized.R |only shar-1.3/shar/R/plot.rd_mar.R |only shar-1.3/shar/R/plot.rd_pat.R |only shar-1.3/shar/R/plot.rd_ras.R |only shar-1.3/shar/R/plot_energy.R | 46 - shar-1.3/shar/R/print.rd_mar.R | 29 shar-1.3/shar/R/print.rd_pat.R | 35 shar-1.3/shar/R/print.rd_ras.R | 128 +- shar-1.3/shar/R/randomize_raster.R | 459 +++++----- shar-1.3/shar/R/reconstruct_pattern.R |only shar-1.3/shar/R/reconstruct_pattern_cluster.R | 221 ++-- shar-1.3/shar/R/reconstruct_pattern_hetero.R | 179 +-- shar-1.3/shar/R/reconstruct_pattern_homo.R | 181 +-- shar-1.3/shar/R/reconstruct_pattern_marks.R | 97 -- shar-1.3/shar/R/results_habitat_association.R | 87 + shar-1.3/shar/R/shar-package.R |only shar-1.3/shar/R/translate_raster.R | 366 ++++--- shar-1.3/shar/build/vignette.rds |binary shar-1.3/shar/data/gamma_test.rda |binary shar-1.3/shar/data/landscape.rda |binary shar-1.3/shar/data/random_walk.rda |binary shar-1.3/shar/data/reconstruction.rda |binary shar-1.3/shar/data/species_a.rda |binary shar-1.3/shar/data/species_b.rda |binary shar-1.3/shar/data/torus_trans.rda |binary shar-1.3/shar/inst/CITATION |only shar-1.3/shar/inst/doc/get_started.R | 15 shar-1.3/shar/inst/doc/get_started.Rmd | 21 shar-1.3/shar/inst/doc/get_started.html | 58 - shar-1.3/shar/man/calculate_energy.Rd | 20 shar-1.3/shar/man/classify_habitats.Rd | 13 shar-1.3/shar/man/create_neighbourhood.Rd | 7 shar-1.3/shar/man/estimate_pcf_fast.Rd | 7 shar-1.3/shar/man/extract_points.Rd | 10 shar-1.3/shar/man/fit_point_process.Rd | 27 shar-1.3/shar/man/landscape.Rd | 4 shar-1.3/shar/man/list_to_randomized.Rd |only shar-1.3/shar/man/plot.rd_mar.Rd |only shar-1.3/shar/man/plot.rd_pat.Rd |only shar-1.3/shar/man/plot.rd_ras.Rd |only shar-1.3/shar/man/plot_energy.Rd | 20 shar-1.3/shar/man/print.rd_mar.Rd | 14 shar-1.3/shar/man/print.rd_pat.Rd | 20 shar-1.3/shar/man/print.rd_ras.Rd | 13 shar-1.3/shar/man/random_walk.Rd | 2 shar-1.3/shar/man/randomize_raster.Rd | 34 shar-1.3/shar/man/reconstruct_pattern.Rd |only shar-1.3/shar/man/reconstruct_pattern_cluster.Rd | 65 - shar-1.3/shar/man/reconstruct_pattern_hetero.Rd | 71 - shar-1.3/shar/man/reconstruct_pattern_homo.Rd | 74 - shar-1.3/shar/man/reconstruct_pattern_marks.Rd | 48 - shar-1.3/shar/man/results_habitat_association.Rd | 20 shar-1.3/shar/man/shar.Rd | 6 shar-1.3/shar/man/species_a.Rd | 9 shar-1.3/shar/man/species_b.Rd | 9 shar-1.3/shar/man/torus_trans.Rd | 2 shar-1.3/shar/man/translate_raster.Rd | 25 shar-1.3/shar/tests/testthat/Rplots.pdf |binary shar-1.3/shar/tests/testthat/test-calculate_energy.R | 75 - shar-1.3/shar/tests/testthat/test-classify_habitats.R | 25 shar-1.3/shar/tests/testthat/test-create_neighbourhood.R | 8 shar-1.3/shar/tests/testthat/test-estimate_pcf_fast.R | 2 shar-1.3/shar/tests/testthat/test-extract_points.R | 41 shar-1.3/shar/tests/testthat/test-fit-point_process.R | 55 - shar-1.3/shar/tests/testthat/test-list_to_randomized.R |only shar-1.3/shar/tests/testthat/test-plot_energy.R | 65 - shar-1.3/shar/tests/testthat/test-plot_rd_pat.R |only shar-1.3/shar/tests/testthat/test-plot_rd_ras.R |only shar-1.3/shar/tests/testthat/test-print.R | 39 shar-1.3/shar/tests/testthat/test-randomize_raster.R | 159 +-- shar-1.3/shar/tests/testthat/test-reconstruct_pattern.R |only shar-1.3/shar/tests/testthat/test-reconstruct_pattern_cluster.R | 83 - shar-1.3/shar/tests/testthat/test-reconstruct_pattern_hetero.R | 80 - shar-1.3/shar/tests/testthat/test-reconstruct_pattern_homo.R | 95 -- shar-1.3/shar/tests/testthat/test-reconstruct_pattern_marks.R | 134 +- shar-1.3/shar/tests/testthat/test-results_habitat_association.R | 153 +-- shar-1.3/shar/tests/testthat/test-translate_raster.R | 168 +-- shar-1.3/shar/vignettes/get_started.Rmd | 21 103 files changed, 2056 insertions(+), 2185 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2021) <arXiv:2105.04451>.
Author: David B. Dahl [aut, cre] (<https://orcid.org/0000-0002-8173-1547>),
Devin J. Johnson [aut] (<https://orcid.org/0000-0003-2619-6649>),
Peter Müller [aut]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.2.23 dated 2021-08-13 and 0.3.0 dated 2021-12-06
DESCRIPTION | 8 - MD5 | 63 ++++++------ NAMESPACE | 1 NEWS | 10 + R/bell.R | 4 R/dlso.R | 13 +- R/internal.R | 2 R/iris.clusterings-data.R | 2 R/minimize.by.enumeration.R | 2 R/partition.loss.R | 186 ++++++++++++++++++------------------ R/plot.salso.summary.R | 1 R/psm.R | 2 R/salso.R | 21 ++-- R/summary.salso.estimate.R | 12 +- man/bell.Rd | 4 man/dlso.Rd | 21 +--- man/partition.loss.Rd | 116 ++++++++++------------ man/plot.salso.summary.Rd | 1 man/psm.Rd | 2 man/salso.Rd | 5 man/summary.salso.estimate.Rd | 1 src/rustlib/Cargo.lock | 56 +++------- src/rustlib/Cargo.toml | 4 src/rustlib/roxido/Cargo.lock | 8 - src/rustlib/roxido/Cargo.toml | 7 - src/rustlib/roxido/README.md |only src/rustlib/roxido/src/lib.rs | 20 +++ src/rustlib/roxido/src/r.rs | 14 ++ src/rustlib/roxido_macro/Cargo.lock | 10 - src/rustlib/roxido_macro/Cargo.toml | 8 - src/rustlib/roxido_macro/src/lib.rs | 20 +++ tools/cargo.R | 29 ++--- tools/staticlib.R | 11 +- 33 files changed, 370 insertions(+), 294 deletions(-)
Title: Tools to Accompany the 'psych' Package for Psychological
Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as one vignette. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psychTools versions 2.1.8 dated 2021-09-20 and 2.1.12 dated 2021-12-06
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- build/partial.rdb |binary data/eminence.rda |only inst/NEWS.Rd | 26 +++++++++++++++++++------- inst/doc/factor.pdf |binary inst/doc/mediation.pdf |binary inst/doc/omega.pdf |binary inst/doc/overview.pdf |binary man/ability.Rd | 12 ++++++++++++ man/eminence.Rd |only man/epi.Rd | 5 +++-- 12 files changed, 49 insertions(+), 22 deletions(-)
Title: General-Purpose Phase-Type Functions
Description: General implementation of core function from phase-type
theory. 'PhaseTypeR' can be used to model continuous and discrete
phase-type distributions, both univariate and multivariate. The
package includes functions for outputting the mean and (co)variance of
phase-type distributions; their density, probability and quantile
functions; functions for random draws; functions for
reward-transformation; and functions for plotting the distributions as
networks. For more information on these functions please refer to
Bladt and Nielsen (2017, ISBN: 978-1-4939-8377-3) and Campillo Navarro
(2019)
<https://orbit.dtu.dk/en/publications/order-statistics-and-multivariate-discrete-phase-type-distributio>.
Author: Iker Rivas-González [aut, cre]
(<https://orcid.org/0000-0002-0515-0628>),
Colin Guetemme [aut],
Asger Hobolth [aut],
Lars Nørvang Andersen [aut]
Maintainer: Iker Rivas-González <ikerrivas96@gmail.com>
Diff between PhaseTypeR versions 1.0.0 dated 2021-11-30 and 1.0.1 dated 2021-12-06
DESCRIPTION | 6 - MD5 | 30 ++--- NEWS.md | 4 R/DPH.R | 7 - R/MDPH.R | 6 - R/MPH.R | 3 R/PH.R | 2 R/check_phase_type.R | 8 - R/reward_phase_type.R | 7 - inst/doc/a3_phasetypeR_SFS.R | 15 ++ inst/doc/a3_phasetypeR_SFS.Rmd | 15 ++ inst/doc/a3_phasetypeR_SFS.html | 165 +++++++++++++++++--------------- tests/testthat/_snaps/DPH_functions.md | 6 - tests/testthat/_snaps/MDPH_functions.md | 6 - tests/testthat/_snaps/MPH_functions.md | 6 - vignettes/a3_phasetypeR_SFS.Rmd | 15 ++ 16 files changed, 179 insertions(+), 122 deletions(-)
Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Ashley Tarasiewicz [aut],
Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>),
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 0.4.2 dated 2021-10-15 and 0.4.3 dated 2021-12-06
Tplyr-0.4.2/Tplyr/vignettes/validation |only Tplyr-0.4.3/Tplyr/DESCRIPTION | 8 - Tplyr-0.4.3/Tplyr/MD5 | 24 ++--- Tplyr-0.4.3/Tplyr/NEWS.md | 6 + Tplyr-0.4.3/Tplyr/R/count.R | 3 Tplyr-0.4.3/Tplyr/inst/doc/Tplyr.html | 12 +- Tplyr-0.4.3/Tplyr/inst/doc/denom.html | 108 +++++++++++++------------- Tplyr-0.4.3/Tplyr/inst/doc/options.R | 21 +++++ Tplyr-0.4.3/Tplyr/inst/doc/options.Rmd | 29 ++++++ Tplyr-0.4.3/Tplyr/inst/doc/options.html | 35 ++++++++ Tplyr-0.4.3/Tplyr/tests/testthat/test-count.R | 19 ++++ Tplyr-0.4.3/Tplyr/vignettes/options.Rmd | 29 ++++++ 12 files changed, 215 insertions(+), 79 deletions(-)
Title: Bayesian Additive Regression Trees with Stan-Sampled Parametric
Extensions
Description: Fits semiparametric linear and multilevel models with non-parametric additive Bayesian additive regression tree (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) components and Stan (Stan Development Team (2021) <https://mc-stan.org/>) sampled parametric ones. Multilevel models can be expressed using 'lme4' syntax (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] (<https://orcid.org/0000-0002-9576-3064>),
Ben Goodrich [ctb] (rstanarm_functions.R, StanHeaders),
Jonah Gabry [ctb] (rstanarm_functions.R, StanHeaders),
Imad Ali [ctb] (rstanarm_functions.R),
Sam Brilleman [ctb] (rstanarm_functions.R),
Paul-Christian Burkner [ctb] (rstanarm_functions.R,
<https://orcid.org/0000-0001-5765-8995>),
Joshua Pritikin [ctb] (StanHeaders,
<https://orcid.org/0000-0002-9862-5484>),
Andrew Gelman [ctb] (StanHeaders,
<https://orcid.org/0000-0002-6975-2601>),
Bob Carpenter [ctb] (StanHeaders),
Matt Hoffman [ctb] (StanHeaders),
Daniel Lee [ctb] (StanHeaders),
Michael Betancourt [ctb] (StanHeaders,
<https://orcid.org/0000-0002-2900-0931>),
Marcus Brubaker [ctb] (StanHeaders,
<https://orcid.org/0000-0002-7892-9026>),
Jiqiang Guo [ctb] (StanHeaders),
Peter Li [ctb] (StanHeaders),
Allen Riddell [ctb] (StanHeaders),
Marco Inacio [ctb] (StanHeaders,
<https://orcid.org/0000-0002-6865-5404>),
Mitzi Morris [ctb] (StanHeaders),
Jeffrey Arnold [ctb] (StanHeaders,
<https://orcid.org/0000-0001-9953-3904>),
Rob Goedman [ctb] (StanHeaders),
Brian Lau [ctb] (StanHeaders),
Rob Trangucci [ctb] (StanHeaders),
Alp Kucukelbir [ctb] (StanHeaders),
Robert Grant [ctb] (StanHeaders),
Dustin Tran [ctb] (StanHeaders),
Michael Malecki [ctb] (StanHeaders),
Yuanjun Gao [ctb] (StanHeaders),
Trustees of Columbia University [cph] (rstanarm_functions.R,
StanHeaders),
Lawrence Livermore National Security [cph] (CVODES),
The Regents of the University of California [cph] (CVODES),
Southern Methodist University [cph] (CVODES),
Douglas Bates [ctb] (lme4_functions.R,
<https://orcid.org/0000-0001-8316-9503>),
Martin Maechler [ctb] (lme4_functions.R,
<https://orcid.org/0000-0002-8685-9910>),
Ben Bolker [ctb] (lme4_functions.R,
<https://orcid.org/0000-0002-2127-0443>),
Steve Walker [ctb] (lme4_functions.R,
<https://orcid.org/0000-0002-4394-9078>),
Armon Dadgar [ctb] (adaptive radix tree),
Bothner Per [ctb] (config.guess),
Elliston Ben [ctb] (config.guess),
Free Software Foundation [cph] (config.sub),
Guido U Draheim [ctb] (ax_check_compile_flag.m4),
Maarten Bosmans [ctb] (ax_check_compile_flag.m4),
Christophe Tournayre [ctb] (ax_ext.m4),
Michael Petch [ctb] (ax_ext.m4, ax_gcc_x86_avx_xgetbv.m4,
ax_gcc_x86_cpuid.m4),
Rafael de Lucena Valle [ctb] (ax_ext.m4),
Steven G. Johnson [ctb] (ax_gcc_x86_cpuid.m4,
<https://orcid.org/0000-0001-7327-4967>),
Matteo Frigo [ctb] (ax_gcc_x86_cpuid.m4),
Scott Pakin [ctb] (ax_func_posix_memalign.m4,
<https://orcid.org/0000-0002-5220-1985>)
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between stan4bart versions 0.0-1 dated 2021-11-22 and 0.0-2 dated 2021-12-06
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ configure | 26 +++++++++----------------- configure.ac | 2 +- src/Makevars.in | 2 +- src/config.h.in | 2 -- src/config.h.win | 4 ++-- src/init.cpp | 25 +++++++++++++++---------- src/interruptable_sampler.hpp | 12 ++++++++---- src/stan_files/continuous.hpp | 2 +- src/stan_sampler.cpp | 15 +++++++++------ src/stan_sampler_includes.hpp | 12 ++++++++---- tests/testthat/test-02-binary.R | 5 ++++- 13 files changed, 74 insertions(+), 65 deletions(-)
Title: Online Prediction by Expert Aggregation
Description: Misc methods to form online predictions, for regression-oriented
time-series, by combining a finite set of forecasts provided by the user. See
Cesa-Bianchi and Lugosi (2006) <doi:10.1017/CBO9780511546921> for an overview.
Author: Pierre Gaillard [cre, aut],
Yannig Goude [aut],
Laurent Plagne [ctb],
Thibaut Dubois [ctb],
Benoit Thieurmel [ctb]
Maintainer: Pierre Gaillard <pierre@gaillard.me>
Diff between opera versions 1.1.1 dated 2021-06-15 and 1.2.0 dated 2021-12-06
opera-1.1.1/opera/R/lossPred.R |only opera-1.1.1/opera/inst/img |only opera-1.1.1/opera/man/mixture.Rd |only opera-1.2.0/opera/DESCRIPTION | 23 opera-1.2.0/opera/MD5 | 164 +- opera-1.2.0/opera/NAMESPACE | 21 opera-1.2.0/opera/NEWS | 9 opera-1.2.0/opera/R/BOA.R | 93 - opera-1.2.0/opera/R/FTRL.R |only opera-1.2.0/opera/R/MLewa.R | 152 +- opera-1.2.0/opera/R/MLpol.R | 82 - opera-1.2.0/opera/R/MLprod.R | 75 - opera-1.2.0/opera/R/OGD.R | 141 +- opera-1.2.0/opera/R/RcppExports.R |only opera-1.2.0/opera/R/bestConvex.R | 156 +- opera-1.2.0/opera/R/bestLinear.R | 125 - opera-1.2.0/opera/R/bestShifts.R | 119 - opera-1.2.0/opera/R/blockToSeries.R | 24 opera-1.2.0/opera/R/check_loss.R |only opera-1.2.0/opera/R/check_matrix.R |only opera-1.2.0/opera/R/electric_load-data.R | 55 opera-1.2.0/opera/R/ewa.R | 51 opera-1.2.0/opera/R/ewaCalib.R | 128 + opera-1.2.0/opera/R/fixedshare.R | 129 + opera-1.2.0/opera/R/fixedshareCalib.R | 329 ++-- opera-1.2.0/opera/R/loss.R | 159 +- opera-1.2.0/opera/R/lossConv.R | 42 opera-1.2.0/opera/R/methods-oracle.R | 236 +-- opera-1.2.0/opera/R/mixture.R | 449 +++--- opera-1.2.0/opera/R/opera-package.R | 8 opera-1.2.0/opera/R/oracle.R | 432 +++--- opera-1.2.0/opera/R/plot-mixture.R | 1315 ++++++++++++++----- opera-1.2.0/opera/R/plot-oracle.R | 319 +++- opera-1.2.0/opera/R/predict-mixture.R | 202 +- opera-1.2.0/opera/R/predictReal-mixture.R | 517 +++---- opera-1.2.0/opera/R/print-mixture.R | 43 opera-1.2.0/opera/R/progress.R |only opera-1.2.0/opera/R/regional_load-data.R |only opera-1.2.0/opera/R/ridge.R | 37 opera-1.2.0/opera/R/ridgeCalib.R | 112 - opera-1.2.0/opera/R/seriesToBlock.R | 103 - opera-1.2.0/opera/R/simplexProj.R | 46 opera-1.2.0/opera/R/summary-mixture.R | 95 - opera-1.2.0/opera/R/truncate1.R | 30 opera-1.2.0/opera/R/zzz.R |only opera-1.2.0/opera/README.md | 108 - opera-1.2.0/opera/build/partial.rdb |only opera-1.2.0/opera/build/vignette.rds |binary opera-1.2.0/opera/inst/REFERENCES.bib |only opera-1.2.0/opera/inst/doc/opera-vignette.R | 55 opera-1.2.0/opera/inst/doc/opera-vignette.Rmd | 29 opera-1.2.0/opera/inst/doc/opera-vignette.html | 501 ++++--- opera-1.2.0/opera/inst/doc/regional_forecasting.R |only opera-1.2.0/opera/inst/doc/regional_forecasting.Rmd |only opera-1.2.0/opera/inst/doc/regional_forecasting.html |only opera-1.2.0/opera/inst/extdata |only opera-1.2.0/opera/inst/rmd/example.Rmd | 66 opera-1.2.0/opera/man/FTRL.Rd |only opera-1.2.0/opera/man/check_loss.Rd |only opera-1.2.0/opera/man/check_matrix.Rd |only opera-1.2.0/opera/man/figures |only opera-1.2.0/opera/man/loss.Rd | 39 opera-1.2.0/opera/man/mixture-opera.Rd |only opera-1.2.0/opera/man/opera-package.Rd | 64 opera-1.2.0/opera/man/oracle.Rd | 26 opera-1.2.0/opera/man/plot-opera-rAmCharts.Rd |only opera-1.2.0/opera/man/plot.mixture.Rd | 26 opera-1.2.0/opera/man/plot.oracle.Rd |only opera-1.2.0/opera/man/plt_oracle_convex.Rd |only opera-1.2.0/opera/man/predict.mixture.Rd | 7 opera-1.2.0/opera/src |only opera-1.2.0/opera/tests/testthat/test-custom_loss.R |only opera-1.2.0/opera/tests/testthat/test-mixture.R | 559 ++++---- opera-1.2.0/opera/tests/testthat/test-oracle.R | 27 opera-1.2.0/opera/vignettes/opera-vignette.Rmd | 29 opera-1.2.0/opera/vignettes/regional_forecasting.Rmd |only 76 files changed, 4574 insertions(+), 2983 deletions(-)
Title: Binary Classification Using Extensions of Discriminant Analysis
Description: Implements methods for sample size
reduction within Linear and Quadratic Discriminant Analysis in Lapanowski and Gaynanova (2020) <arXiv:2005.03858>.
Also includes methods for non-linear discriminant analysis with simultaneous sparse feature selection in Lapanowski and Gaynanova (2019) PMLR 89:1704-1713.
Author: Alexander F. Lapanowski [aut, cre],
Irina Gaynanova [aut]
Maintainer: Alexander F. Lapanowski <aflapan@gmail.com>
Diff between biClassify versions 1.2 dated 2021-07-29 and 1.3 dated 2021-12-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/SparseKOS_functions.R | 6 +++--- R/Wrappers.R | 4 +--- inst/doc/biClassify.Rmd | 2 +- inst/doc/biClassify.pdf |binary man/KOS.Rd | 6 ++---- vignettes/biClassify.Rmd | 2 +- 8 files changed, 19 insertions(+), 23 deletions(-)
Title: Interface to the arXiv API
Description: An interface to the API for 'arXiv',
a repository of electronic preprints for
computer science, mathematics, physics, quantitative biology,
quantitative finance, and statistics.
Author: Karthik Ram [aut] (<https://orcid.org/0000-0002-0233-1757>),
Karl Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)
Maintainer: Karl Broman <broman@wisc.edu>
Diff between aRxiv versions 0.5.19 dated 2019-08-08 and 0.6 dated 2021-12-06
DESCRIPTION | 19 +- MD5 | 34 ++-- NEWS | 23 +++ R/arxiv_cats-data.R | 2 R/arxiv_count.R | 4 R/arxiv_search.R | 7 R/query_terms-data.R | 2 README.md | 14 - build/vignette.rds |binary data/arxiv_cats.RData |binary data/query_terms.RData |binary inst/doc/aRxiv.R | 48 +++--- inst/doc/aRxiv.Rmd | 4 inst/doc/aRxiv.html | 348 ++++++++++++------------------------------------- man/arxiv_cats.Rd | 8 - man/arxiv_search.Rd | 16 +- man/query_terms.Rd | 8 - vignettes/aRxiv.Rmd | 4 18 files changed, 208 insertions(+), 333 deletions(-)
Title: Twitter Topic Modeling and Visualization for R
Description: Tailored for topic modeling with tweets and fit for visualization tasks in R.
Collect, pre-process and analyze the contents of tweets using
LDA and structural topic models (STM). Comes with visualizing capabilities like tweet and hashtag maps
and built-in support for 'LDAvis'.
Author: Andreas Buchmueller [aut, cre] (github.com/abuchmueller),
Gillian Kant [aut, ths] (<https://orcid.org/0000-0003-2346-2841>),
Christoph Weisser [aut, ths] (<https://orcid.org/0000-0003-0616-1027>),
Benjamin Saefken [aut, ths] (<https://orcid.org/0000-0003-4702-3333>),
Thomas Kneib [rev, ths, dgs] (<https://orcid.org/0000-0003-3390-0972>),
Krisztina Kis-Katos [rev] (<https://orcid.org/0000-0003-2459-1274>)
Maintainer: Andreas Buchmueller <a.buchmueller@stud.uni-goettingen.de>
Diff between Twitmo versions 0.1.1 dated 2021-10-28 and 0.1.2 dated 2021-12-06
DESCRIPTION | 38 +++++-- MD5 | 11 +- NEWS.md |only R/fit_stm.R | 35 +++++-- README.md | 183 +++++++++++++++++++------------------- man/figures/README-ldatuner-1.png |binary man/fit_stm.Rd | 2 7 files changed, 152 insertions(+), 117 deletions(-)
Title: Graphic Devices Based on AGG
Description: Anti-Grain Geometry (AGG) is a high-quality and high-performance
2D drawing library. The 'ragg' package provides a set of graphic devices
based on AGG to use as alternative to the raster devices provided through
the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
Maxim Shemanarev [aut, cph] (Author of AGG),
Tony Juricic [ctb, cph] (Contributor to AGG),
Milan Marusinec [ctb, cph] (Contributor to AGG),
Spencer Garrett [ctb] (Contributor to AGG),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between ragg versions 1.2.0 dated 2021-10-30 and 1.2.1 dated 2021-12-06
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ README.md | 2 +- cleanup | 1 + man/figures/README-unnamed-chunk-3-1.png |binary src/AggDeviceTiff.h | 3 ++- 7 files changed, 18 insertions(+), 11 deletions(-)
Title: Quadratic Programming Solver using the 'OSQP' Library
Description: Provides bindings to the 'OSQP' solver. The 'OSQP' solver is a numerical optimization package or solving convex quadratic programs written in 'C' and based on the alternating direction method of multipliers. See <arXiv:1711.08013> for details.
Author: Bartolomeo Stellato [aut, ctb, cph],
Goran Banjac [aut, ctb, cph],
Paul Goulart [aut, ctb, cph],
Stephen Boyd [aut, ctb, cph],
Eric Anderson [ctb],
Vineet Bansal [cre]
Maintainer: Vineet Bansal <vineetb@princeton.edu>
Diff between osqp versions 0.6.0.3 dated 2019-10-28 and 0.6.0.4 dated 2021-12-06
osqp-0.6.0.3/osqp/src/osqp_sources/lin_sys/direct/qdldl/qdldl_sources/include/qdldl_types.h |only osqp-0.6.0.4/osqp/DESCRIPTION | 20 +++++----- osqp-0.6.0.4/osqp/MD5 | 5 +- osqp-0.6.0.4/osqp/src/osqp_sources/configure/cmake/FindR.cmake | 7 +++ 4 files changed, 19 insertions(+), 13 deletions(-)
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a unified
interface for model fitting, prediction, performance assessment, and
presentation of results. Approaches for model fitting and prediction of
numerical, categorical, or censored time-to-event outcomes include
traditional regression models, regularization methods, tree-based methods,
support vector machines, neural networks, ensembles, data preprocessing,
filtering, and model tuning and selection. Performance metrics are provided
for model assessment and can be estimated with independent test sets, split
sampling, cross-validation, or bootstrap resampling. Resample estimation
can be executed in parallel for faster processing and nested in cases of
model tuning and selection. Modeling results can be summarized with
descriptive statistics; calibration curves; variable importance; partial
dependence plots; confusion matrices; and ROC, lift, and other performance
curves.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 3.1.0 dated 2021-10-01 and 3.2.0 dated 2021-12-06
MachineShop-3.1.0/MachineShop/R/ML_NullModel.R |only MachineShop-3.1.0/MachineShop/R/RcppExports.R |only MachineShop-3.1.0/MachineShop/inst/doc/UsersGuide.R |only MachineShop-3.1.0/MachineShop/inst/doc/UsersGuide.Rmd |only MachineShop-3.1.0/MachineShop/inst/doc/UsersGuide.html |only MachineShop-3.1.0/MachineShop/man/Grid.Rd |only MachineShop-3.1.0/MachineShop/src/RcppExports.cpp |only MachineShop-3.1.0/MachineShop/src/hazfit_efron.cpp |only MachineShop-3.1.0/MachineShop/vignettes/UsersGuide.Rmd |only MachineShop-3.2.0/MachineShop/DESCRIPTION | 48 MachineShop-3.2.0/MachineShop/MD5 | 453 +- MachineShop-3.2.0/MachineShop/NAMESPACE | 73 MachineShop-3.2.0/MachineShop/NEWS.md | 66 MachineShop-3.2.0/MachineShop/R/MLControl.R | 152 MachineShop-3.2.0/MachineShop/R/MLModel.R | 80 MachineShop-3.2.0/MachineShop/R/ML_AdaBagModel.R | 22 MachineShop-3.2.0/MachineShop/R/ML_AdaBoostModel.R | 24 MachineShop-3.2.0/MachineShop/R/ML_BARTMachineModel.R | 26 MachineShop-3.2.0/MachineShop/R/ML_BARTModel.R | 26 MachineShop-3.2.0/MachineShop/R/ML_BlackBoostModel.R | 43 MachineShop-3.2.0/MachineShop/R/ML_C50Model.R | 37 MachineShop-3.2.0/MachineShop/R/ML_CForestModel.R | 15 MachineShop-3.2.0/MachineShop/R/ML_CoxModel.R | 40 MachineShop-3.2.0/MachineShop/R/ML_EarthModel.R | 39 MachineShop-3.2.0/MachineShop/R/ML_FDAModel.R | 23 MachineShop-3.2.0/MachineShop/R/ML_GAMBoostModel.R | 32 MachineShop-3.2.0/MachineShop/R/ML_GBMModel.R | 46 MachineShop-3.2.0/MachineShop/R/ML_GLMBoostModel.R | 39 MachineShop-3.2.0/MachineShop/R/ML_GLMModel.R | 55 MachineShop-3.2.0/MachineShop/R/ML_GLMNetModel.R | 30 MachineShop-3.2.0/MachineShop/R/ML_KNNModel.R | 9 MachineShop-3.2.0/MachineShop/R/ML_LARSModel.R | 15 MachineShop-3.2.0/MachineShop/R/ML_LDAModel.R | 19 MachineShop-3.2.0/MachineShop/R/ML_LMModel.R | 7 MachineShop-3.2.0/MachineShop/R/ML_MDAModel.R | 19 MachineShop-3.2.0/MachineShop/R/ML_NNetModel.R | 22 MachineShop-3.2.0/MachineShop/R/ML_NaiveBayesModel.R | 15 MachineShop-3.2.0/MachineShop/R/ML_Null.R |only MachineShop-3.2.0/MachineShop/R/ML_PLSModel.R | 15 MachineShop-3.2.0/MachineShop/R/ML_POLRModel.R | 7 MachineShop-3.2.0/MachineShop/R/ML_ParsnipModel.R |only MachineShop-3.2.0/MachineShop/R/ML_QDAModel.R | 12 MachineShop-3.2.0/MachineShop/R/ML_RFSRCModel.R | 38 MachineShop-3.2.0/MachineShop/R/ML_RPartModel.R | 14 MachineShop-3.2.0/MachineShop/R/ML_RandomForestModel.R | 26 MachineShop-3.2.0/MachineShop/R/ML_RangerModel.R | 31 MachineShop-3.2.0/MachineShop/R/ML_SVMModel.R | 77 MachineShop-3.2.0/MachineShop/R/ML_StackedModel.R | 72 MachineShop-3.2.0/MachineShop/R/ML_SuperModel.R | 68 MachineShop-3.2.0/MachineShop/R/ML_SurvRegModel.R | 55 MachineShop-3.2.0/MachineShop/R/ML_TreeModel.R | 15 MachineShop-3.2.0/MachineShop/R/ML_XGBModel.R | 249 - MachineShop-3.2.0/MachineShop/R/MachineShop-package.R | 1 MachineShop-3.2.0/MachineShop/R/ModelFrame.R | 174 MachineShop-3.2.0/MachineShop/R/ModelRecipe.R | 35 MachineShop-3.2.0/MachineShop/R/ModeledInput.R | 99 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MachineShop-3.2.0/MachineShop/R/modelinfo.R | 10 MachineShop-3.2.0/MachineShop/R/models.R | 1 MachineShop-3.2.0/MachineShop/R/performance.R | 30 MachineShop-3.2.0/MachineShop/R/performance_curve.R | 31 MachineShop-3.2.0/MachineShop/R/plot.R | 57 MachineShop-3.2.0/MachineShop/R/predict.R | 27 MachineShop-3.2.0/MachineShop/R/predictors.R | 7 MachineShop-3.2.0/MachineShop/R/print.R | 834 ++- MachineShop-3.2.0/MachineShop/R/recipe_roles.R | 27 MachineShop-3.2.0/MachineShop/R/resample.R | 351 - MachineShop-3.2.0/MachineShop/R/response.R | 36 MachineShop-3.2.0/MachineShop/R/rfe.R |only MachineShop-3.2.0/MachineShop/R/settings.R | 70 MachineShop-3.2.0/MachineShop/R/step_kmeans.R | 2 MachineShop-3.2.0/MachineShop/R/step_kmedoids.R | 8 MachineShop-3.2.0/MachineShop/R/step_lincomp.R | 18 MachineShop-3.2.0/MachineShop/R/step_sbf.R | 17 MachineShop-3.2.0/MachineShop/R/step_spca.R | 12 MachineShop-3.2.0/MachineShop/R/summary.R | 26 MachineShop-3.2.0/MachineShop/R/survival.R | 56 MachineShop-3.2.0/MachineShop/R/utils.R | 341 - MachineShop-3.2.0/MachineShop/R/varimp.R | 173 MachineShop-3.2.0/MachineShop/README.md | 12 MachineShop-3.2.0/MachineShop/build/vignette.rds |binary MachineShop-3.2.0/MachineShop/inst/doc/MLModels.Rmd | 2 MachineShop-3.2.0/MachineShop/inst/doc/MLModels.html | 2 MachineShop-3.2.0/MachineShop/inst/doc/UserGuide.R |only MachineShop-3.2.0/MachineShop/inst/doc/UserGuide.Rmd |only MachineShop-3.2.0/MachineShop/inst/doc/UserGuide.html |only MachineShop-3.2.0/MachineShop/man/AdaBagModel.Rd | 4 MachineShop-3.2.0/MachineShop/man/AdaBoostModel.Rd | 4 MachineShop-3.2.0/MachineShop/man/BARTMachineModel.Rd | 7 MachineShop-3.2.0/MachineShop/man/BARTModel.Rd | 22 MachineShop-3.2.0/MachineShop/man/BlackBoostModel.Rd | 8 MachineShop-3.2.0/MachineShop/man/C50Model.Rd | 6 MachineShop-3.2.0/MachineShop/man/CForestModel.Rd | 4 MachineShop-3.2.0/MachineShop/man/CoxModel.Rd | 8 MachineShop-3.2.0/MachineShop/man/EarthModel.Rd | 12 MachineShop-3.2.0/MachineShop/man/FDAModel.Rd | 14 MachineShop-3.2.0/MachineShop/man/GAMBoostModel.Rd | 8 MachineShop-3.2.0/MachineShop/man/GBMModel.Rd | 10 MachineShop-3.2.0/MachineShop/man/GLMBoostModel.Rd | 8 MachineShop-3.2.0/MachineShop/man/GLMModel.Rd | 10 MachineShop-3.2.0/MachineShop/man/GLMNetModel.Rd | 10 MachineShop-3.2.0/MachineShop/man/KNNModel.Rd | 4 MachineShop-3.2.0/MachineShop/man/LARSModel.Rd | 10 MachineShop-3.2.0/MachineShop/man/LDAModel.Rd | 12 MachineShop-3.2.0/MachineShop/man/LMModel.Rd | 2 MachineShop-3.2.0/MachineShop/man/MDAModel.Rd | 12 MachineShop-3.2.0/MachineShop/man/MLControl.Rd | 22 MachineShop-3.2.0/MachineShop/man/MLModel.Rd | 22 MachineShop-3.2.0/MachineShop/man/MachineShop-package.Rd | 1 MachineShop-3.2.0/MachineShop/man/ModelFrame-methods.Rd | 52 MachineShop-3.2.0/MachineShop/man/ModeledInput-methods.Rd | 38 MachineShop-3.2.0/MachineShop/man/NNetModel.Rd | 14 MachineShop-3.2.0/MachineShop/man/NaiveBayesModel.Rd | 2 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MachineShop-3.2.0/MachineShop/man/TunedModel.Rd | 31 MachineShop-3.2.0/MachineShop/man/TuningGrid.Rd |only MachineShop-3.2.0/MachineShop/man/XGBModel.Rd | 123 MachineShop-3.2.0/MachineShop/man/as.MLModel.Rd | 15 MachineShop-3.2.0/MachineShop/man/calibration.Rd | 2 MachineShop-3.2.0/MachineShop/man/combine-methods.Rd | 4 MachineShop-3.2.0/MachineShop/man/confusion.Rd | 2 MachineShop-3.2.0/MachineShop/man/dependence.Rd | 4 MachineShop-3.2.0/MachineShop/man/deprecated.Rd |only MachineShop-3.2.0/MachineShop/man/diff-methods.Rd | 4 MachineShop-3.2.0/MachineShop/man/expand_model.Rd | 7 MachineShop-3.2.0/MachineShop/man/expand_modelgrid-methods.Rd | 33 MachineShop-3.2.0/MachineShop/man/extract-methods.Rd | 23 MachineShop-3.2.0/MachineShop/man/fit-methods.Rd | 41 MachineShop-3.2.0/MachineShop/man/metrics.Rd | 6 MachineShop-3.2.0/MachineShop/man/models.Rd | 1 MachineShop-3.2.0/MachineShop/man/performance.Rd | 6 MachineShop-3.2.0/MachineShop/man/performance_curve.Rd | 4 MachineShop-3.2.0/MachineShop/man/plot-methods.Rd | 21 MachineShop-3.2.0/MachineShop/man/predict.Rd | 6 MachineShop-3.2.0/MachineShop/man/print-methods.Rd | 44 MachineShop-3.2.0/MachineShop/man/recipe_roles.Rd | 6 MachineShop-3.2.0/MachineShop/man/resample-methods.Rd | 44 MachineShop-3.2.0/MachineShop/man/rfe-methods.Rd |only MachineShop-3.2.0/MachineShop/man/set_monitor.Rd | 6 MachineShop-3.2.0/MachineShop/man/set_predict.Rd | 11 MachineShop-3.2.0/MachineShop/man/set_strata.Rd | 6 MachineShop-3.2.0/MachineShop/man/settings.Rd | 18 MachineShop-3.2.0/MachineShop/man/step_spca.Rd | 2 MachineShop-3.2.0/MachineShop/man/summary-methods.Rd | 10 MachineShop-3.2.0/MachineShop/man/varimp.Rd | 38 MachineShop-3.2.0/MachineShop/src/hazfit_efron.c |only MachineShop-3.2.0/MachineShop/src/init.c |only MachineShop-3.2.0/MachineShop/tests/testthat/Rplots.pdf |binary MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_AdaBagModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_AdaBoostModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_BARTMachineModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_BARTModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_BlackBoostModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_C50Model.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_CForestModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_CoxModel.R | 17 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_EarthModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_FDAModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_GAMBoostModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_GBMModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_GLMBoostModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_GLMModel.R | 6 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_GLMNetModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_KNNModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_LARSModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_LDAModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_LMModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_MDAModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_NNetModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_NaiveBayesModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_PLSModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_POLRModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_QDAModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_RFSRCModel.R | 17 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_RPartModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_RandomForestModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_RangerModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_SVMModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_StackedModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_SuperModel.R | 4 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_SurvRegModel.R | 17 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_TreeModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ML_XGBModel.R | 5 MachineShop-3.2.0/MachineShop/tests/testthat/test-ModeledInputs.R | 25 MachineShop-3.2.0/MachineShop/tests/testthat/test-TrainedInputs.R | 146 MachineShop-3.2.0/MachineShop/tests/testthat/test-TrainedModels.R | 122 MachineShop-3.2.0/MachineShop/tests/testthat/test-combine.R | 7 MachineShop-3.2.0/MachineShop/tests/testthat/test-controls.R | 96 MachineShop-3.2.0/MachineShop/tests/testthat/test-discrete-vars.R | 110 MachineShop-3.2.0/MachineShop/tests/testthat/test-grids.R | 43 MachineShop-3.2.0/MachineShop/tests/testthat/test-info.R | 34 MachineShop-3.2.0/MachineShop/tests/testthat/test-model-comparisons.R | 89 MachineShop-3.2.0/MachineShop/tests/testthat/test-offsets.R | 79 MachineShop-3.2.0/MachineShop/tests/testthat/test-rfe.R |only MachineShop-3.2.0/MachineShop/tests/testthat/test-settings.R | 26 MachineShop-3.2.0/MachineShop/tests/testthat/test-survival.R | 123 MachineShop-3.2.0/MachineShop/tests/testthat/test-survival.txt | 2185 +++++----- MachineShop-3.2.0/MachineShop/tests/testthat/test-varimp.R | 95 MachineShop-3.2.0/MachineShop/tests/testthat/test-weights.R | 49 MachineShop-3.2.0/MachineShop/vignettes/MLModels.Rmd | 2 MachineShop-3.2.0/MachineShop/vignettes/UserGuide.Rmd |only MachineShop-3.2.0/MachineShop/vignettes/img/FigModelDAG.png |binary MachineShop-3.2.0/MachineShop/vignettes/img/using_strategies_tune_plot-1.png |binary 239 files changed, 6012 insertions(+), 4840 deletions(-)
Title: Compute Risk Scores for Cardiovascular Diseases
Description: Calculate various cardiovascular disease risk scores from the
Framingham Heart Study (FHS), the American College of Cardiology (ACC),
and the American Heart Association (AHA) as described in D’agostino, et al
(2008) <doi:10.1161/circulationaha.107.699579>, Goff, et al (2013)
<doi:10.1161/01.cir.0000437741.48606.98>, and Mclelland, et al (2015)
<doi:10.1016/j.jacc.2015.08.035>.
Author: Victor Castro [aut, cre] (<https://orcid.org/0000-0001-7390-6354>)
Maintainer: Victor Castro <vcastro@mgh.harvard.edu>
Diff between CVrisk versions 1.0.0 dated 2020-10-27 and 1.1.0 dated 2021-12-06
DESCRIPTION | 8 ++--- MD5 | 38 +++++++++++++++----------- NAMESPACE | 2 + NEWS.md | 14 +++++++++ R/CVrisk.R | 2 - R/ascvd_10y_accaha.R | 39 ++++++++++++++++---------- R/ascvd_10y_frs.R | 43 ++++++++++++++++++++++++----- R/ascvd_10y_frs_simple.R | 35 +++++++++++++++++++----- R/chd_10y_mesa.R |only R/chd_10y_mesa_cac.R |only R/compute_CVrisk.R | 20 +++++++++---- R/data.R | 3 ++ README.md | 28 ++++++++++++------- data/sample_data.rda |binary man/ascvd_10y_accaha.Rd | 2 - man/chd_10y_mesa.Rd |only man/chd_10y_mesa_cac.Rd |only man/compute_CVrisk.Rd | 17 +++++++++-- man/sample_data.Rd | 3 ++ tests/testthat/test-ascvd_10y_accaha.R | 48 +++++++++++++++++++++++++++++++++ tests/testthat/test-chd_10y_mesa.R |only tests/testthat/test-chd_10y_mesa_cac.R |only tests/testthat/test-compute_CVrisk.R | 11 ++++--- 23 files changed, 238 insertions(+), 75 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-24 1.6
2017-03-23 1.5.1
Title: Tidy C++ Header-Only Definitions for Parts of the C API of R
Description: Core parts of the C API of R are wrapped in a C++ namespace via a set
of inline functions giving a tidier representation of the underlying data structures
and functionality using a header-only implementation without additional dependencies.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tidyCpp versions 0.0.5 dated 2021-09-17 and 0.0.6 dated 2021-12-06
tidyCpp-0.0.5/tidyCpp/inst/doc/motivation.Rmd |only tidyCpp-0.0.5/tidyCpp/vignettes/motivation.Rmd |only tidyCpp-0.0.6/tidyCpp/ChangeLog | 20 tidyCpp-0.0.6/tidyCpp/DESCRIPTION | 12 tidyCpp-0.0.6/tidyCpp/MD5 | 20 tidyCpp-0.0.6/tidyCpp/build/partial.rdb |binary tidyCpp-0.0.6/tidyCpp/build/vignette.rds |binary tidyCpp-0.0.6/tidyCpp/inst/NEWS.Rd | 15 tidyCpp-0.0.6/tidyCpp/inst/doc/motivation.html | 1046 +++++++++++----------- tidyCpp-0.0.6/tidyCpp/inst/doc/motivation.md |only tidyCpp-0.0.6/tidyCpp/inst/include/tidy/protect.h | 6 tidyCpp-0.0.6/tidyCpp/tests |only tidyCpp-0.0.6/tidyCpp/vignettes/motivation.md |only tidyCpp-0.0.6/tidyCpp/vignettes/water.css |only 14 files changed, 585 insertions(+), 534 deletions(-)
Title: Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
Description: Fast and memory efficient methods for truncated singular value
decomposition and principal components analysis of large sparse and dense
matrices.
Author: Jim Baglama [aut, cph],
Lothar Reichel [aut, cph],
B. W. Lewis [aut, cre, cph]
Maintainer: B. W. Lewis <blewis@illposed.net>
Diff between irlba versions 2.3.4 dated 2021-12-03 and 2.3.5 dated 2021-12-06
irlba-2.3.4/irlba/README |only irlba-2.3.5/irlba/DESCRIPTION | 8 +++--- irlba-2.3.5/irlba/MD5 | 9 +++--- irlba-2.3.5/irlba/inst/doc/irlba.pdf |binary irlba-2.3.5/irlba/src/irlb.c | 46 +++++++++++++++++------------------ irlba-2.3.5/irlba/src/utility.c | 12 ++++++--- 6 files changed, 39 insertions(+), 36 deletions(-)
Title: Interface to 'Interpretable AI' Modules
Description: An interface to the algorithms of 'Interpretable AI'
<https://www.interpretable.ai> from the R programming language.
'Interpretable AI' provides various modules, including 'Optimal Trees' for
classification, regression, prescription and survival analysis, 'Optimal
Imputation' for missing data imputation and outlier detection, and 'Optimal
Feature Selection' for exact sparse regression. The 'iai' package is an
open-source project. The 'Interpretable AI' software modules are proprietary
products, but free academic and evaluation licenses are available.
Author: Jack Dunn [aut, cre],
Ying Zhuo [aut],
Interpretable AI LLC [cph]
Maintainer: Jack Dunn <jack@interpretable.ai>
Diff between iai versions 1.6.0 dated 2021-06-09 and 1.7.0 dated 2021-12-06
DESCRIPTION | 8 MD5 | 351 ++++++++++----------- NAMESPACE | 14 NEWS.md | 12 R/JuliaCall_aaa.R |only R/JuliaCall_zzz.R |only R/heuristics.R | 65 +++ R/iaibase.R | 146 +++++--- R/iaitrees.R | 140 ++++---- R/install.R | 227 ++++++++++--- R/interface.R | 33 + R/optimalfeatureselection.R | 12 R/optimaltrees.R | 79 ++++ R/optimpute.R | 90 ++++- R/rewardestimation.R | 98 ++++- R/utils.R | 14 inst/julia/convert.jl | 29 + man/all_treatment_combinations.Rd | 2 man/apply.Rd | 2 man/apply_nodes.Rd | 2 man/as.mixeddata.Rd | 4 man/autoplot.grid_search.Rd | 2 man/categorical_classification_reward_estimator.Rd | 2 man/categorical_regression_reward_estimator.Rd | 2 man/categorical_reward_estimator.Rd | 5 man/categorical_survival_reward_estimator.Rd | 2 man/cleanup_installation.Rd |only man/clone.Rd | 2 man/convert_treatments_to_numeric.Rd | 2 man/copy_splits_and_refit_leaves.Rd |only man/decision_path.Rd | 2 man/delete_rich_output_param.Rd | 2 man/equal_propensity_estimator.Rd | 2 man/fit.Rd | 4 man/fit_and_expand.Rd |only man/fit_cv.Rd | 4 man/fit_predict.Rd | 2 man/fit_transform.Rd | 8 man/fit_transform_cv.Rd | 4 man/get_best_params.Rd | 2 man/get_classification_label.Rd | 2 man/get_classification_proba.Rd | 2 man/get_cluster_assignments.Rd | 2 man/get_cluster_details.Rd | 2 man/get_cluster_distances.Rd | 2 man/get_depth.Rd | 2 man/get_estimation_densities.Rd | 8 man/get_features_used.Rd | 2 man/get_grid_result_details.Rd | 2 man/get_grid_result_summary.Rd | 2 man/get_grid_results.Rd | 2 man/get_learner.Rd | 2 man/get_lower_child.Rd | 2 man/get_machine_id.Rd |only man/get_num_fits.Rd | 2 man/get_num_nodes.Rd | 2 man/get_num_samples.Rd | 2 man/get_params.Rd | 2 man/get_parent.Rd | 2 man/get_policy_treatment_outcome.Rd | 2 man/get_policy_treatment_rank.Rd | 2 man/get_prediction_constant.Rd | 2 man/get_prediction_weights.Rd | 2 man/get_prescription_treatment_rank.Rd | 2 man/get_regression_constant.Rd | 4 man/get_regression_weights.Rd | 4 man/get_rich_output_params.Rd | 2 man/get_roc_curve_data.Rd | 4 man/get_split_categories.Rd | 2 man/get_split_feature.Rd | 2 man/get_split_threshold.Rd | 2 man/get_split_weights.Rd | 2 man/get_stability_results.Rd | 2 man/get_survival_curve.Rd | 2 man/get_survival_curve_data.Rd | 6 man/get_survival_expected_time.Rd | 2 man/get_survival_hazard.Rd | 2 man/get_train_errors.Rd | 2 man/get_tree.Rd | 2 man/get_upper_child.Rd | 2 man/glmnetcv_classifier.Rd |only man/glmnetcv_regressor.Rd | 5 man/glmnetcv_survival_learner.Rd |only man/grid_search.Rd | 4 man/iai_setup.Rd | 2 man/imputation_learner.Rd | 2 man/impute.Rd | 8 man/impute_cv.Rd | 8 man/install_julia.Rd | 8 man/install_system_image.Rd | 2 man/is_categoric_split.Rd | 2 man/is_hyperplane_split.Rd | 2 man/is_leaf.Rd | 2 man/is_mixed_ordinal_split.Rd | 2 man/is_mixed_parallel_split.Rd | 2 man/is_ordinal_split.Rd | 2 man/is_parallel_split.Rd | 2 man/mean_imputation_learner.Rd | 2 man/missing_goes_lower.Rd | 2 man/multi_questionnaire.Rd | 2 man/multi_questionnaire.default.Rd | 6 man/multi_questionnaire.grid_search.Rd | 2 man/multi_tree_plot.Rd | 2 man/multi_tree_plot.default.Rd | 6 man/multi_tree_plot.grid_search.Rd | 2 man/numeric_classification_reward_estimator.Rd | 2 man/numeric_regression_reward_estimator.Rd | 2 man/numeric_reward_estimator.Rd | 5 man/numeric_survival_reward_estimator.Rd | 2 man/opt_knn_imputation_learner.Rd | 2 man/opt_svm_imputation_learner.Rd | 2 man/opt_tree_imputation_learner.Rd | 2 man/optimal_feature_selection_classifier.Rd | 2 man/optimal_feature_selection_regressor.Rd | 2 man/optimal_tree_classifier.Rd | 2 man/optimal_tree_policy_maximizer.Rd | 2 man/optimal_tree_policy_minimizer.Rd | 2 man/optimal_tree_prescription_maximizer.Rd | 2 man/optimal_tree_prescription_minimizer.Rd | 2 man/optimal_tree_regressor.Rd | 2 man/optimal_tree_survival_learner.Rd | 2 man/plot.grid_search.Rd | 2 man/predict.Rd | 2 man/predict_expected_survival_time.Rd | 6 man/predict_hazard.Rd | 6 man/predict_outcomes.Rd | 2 man/predict_proba.Rd | 2 man/predict_reward.Rd |only man/predict_shap.Rd | 2 man/predict_treatment_outcome.Rd | 2 man/predict_treatment_rank.Rd | 2 man/print_path.Rd | 2 man/prune_trees.Rd |only man/questionnaire.Rd | 4 man/rand_imputation_learner.Rd | 2 man/random_forest_classifier.Rd | 2 man/random_forest_regressor.Rd | 2 man/random_forest_survival_learner.Rd | 2 man/read_json.Rd | 2 man/refit_leaves.Rd |only man/reset_display_label.Rd | 2 man/reward_estimator.Rd | 8 man/roc_curve.Rd | 2 man/roc_curve.default.Rd | 2 man/roc_curve.learner.Rd | 2 man/score.Rd | 18 - man/score.default.Rd |only man/score.learner.Rd |only man/set_display_label.Rd | 2 man/set_params.Rd | 2 man/set_reward_kernel_bandwidth.Rd | 8 man/set_rich_output_param.Rd | 2 man/set_threshold.Rd | 2 man/show_in_browser.Rd | 2 man/show_questionnaire.Rd | 2 man/similarity_comparison.Rd | 4 man/single_knn_imputation_learner.Rd | 2 man/split_data.Rd | 4 man/stability_analysis.Rd | 4 man/transform.Rd | 2 man/transform_and_expand.Rd |only man/tree_plot.Rd | 4 man/tune_reward_kernel_bandwidth.Rd | 8 man/variable_importance.Rd | 8 man/variable_importance_similarity.Rd | 2 man/write_booster.Rd | 2 man/write_dot.Rd | 2 man/write_html.Rd | 2 man/write_json.Rd | 2 man/write_pdf.Rd | 2 man/write_png.Rd | 2 man/write_questionnaire.Rd | 2 man/write_svg.Rd | 2 man/xgboost_classifier.Rd | 2 man/xgboost_regressor.Rd | 2 man/xgboost_survival_learner.Rd | 2 man/zero_imputation_learner.Rd |only tests/testthat/helper.R | 7 tests/testthat/test_heuristics.R | 81 ++++ tests/testthat/test_iaibase.R | 50 ++ tests/testthat/test_iaitrees.R | 10 tests/testthat/test_optimaltrees.R | 87 +++++ tests/testthat/test_optimpute.R | 53 +++ tests/testthat/test_rewardestimation.R | 80 ++++ 184 files changed, 1482 insertions(+), 623 deletions(-)
Title: Tools for Reading and Writing ISO/OGC Geographic Metadata
Description: Provides facilities to handle reading and writing of geographic metadata
defined with OGC/ISO 19115, 11119 and 19110 geographic information metadata standards,
and encoded using the ISO 19139 (XML) standard. It includes also a facility to check
the validity of ISO 19139 XML encoded metadata.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geometa versions 0.6-4 dated 2021-09-16 and 0.6-5 dated 2021-12-06
geometa-0.6-4/geometa/inst/extdata/schemas/smil |only geometa-0.6-4/geometa/inst/extdata/schemas/xlink |only geometa-0.6-5/geometa/DESCRIPTION | 8 +- geometa-0.6-5/geometa/MD5 | 21 +++---- geometa-0.6-5/geometa/R/INSPIREMetadataValidator.R | 29 ++++++++-- geometa-0.6-5/geometa/R/ISOAbstractObject.R | 16 +---- geometa-0.6-5/geometa/R/ISOOnlineResource.R | 1 geometa-0.6-5/geometa/R/geometa.R | 4 - geometa-0.6-5/geometa/README.md | 2 geometa-0.6-5/geometa/man/geometa.Rd | 4 - geometa-0.6-5/geometa/tests/testthat/test_INSPIREMetadataValidator.R | 8 ++ geometa-0.6-5/geometa/tests/testthat/test_ISOOnlineResource.R | 19 ++++++ 12 files changed, 72 insertions(+), 40 deletions(-)
Title: Bayes Factors for Informative Hypotheses
Description: Computes approximated adjusted fractional Bayes factors for
equality, inequality, and about equality constrained hypotheses.
For a tutorial on this method, see Hoijtink, Mulder, van Lissa, & Gu,
(2019) <doi:10.31234/osf.io/v3shc>. For applications in structural equation
modeling, see: Van Lissa, Gu, Mulder, Rosseel, Van Zundert, &
Hoijtink, (2021) <doi:10.1080/10705511.2020.1745644>. For the statistical
underpinnings, see Gu, Mulder, and Hoijtink (2018) <doi:10.1111/bmsp.12110>;
Hoijtink, Gu, & Mulder, J. (2019) <doi:10.1111/bmsp.12145>; Hoijtink, Gu,
Mulder, & Rosseel, (2019) <doi:10.31234/osf.io/q6h5w>.
Author: Xin Gu [aut],
Herbert Hoijtink [aut],
Joris Mulder [aut],
Caspar J van Lissa [aut, cre],
Van Zundert Camiel [ctb],
Jeff Jones [ctb],
Niels Waller [ctb]
Maintainer: Caspar J van Lissa <c.j.vanlissa@uu.nl>
Diff between bain versions 0.2.7 dated 2021-11-26 and 0.2.8 dated 2021-12-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/bain_methods.R | 23 ++++++++++++++--------- R/complement2.R | 15 ++++++++++----- README.md | 4 ++-- build/partial.rdb |binary inst/doc/Introduction_to_bain.html | 4 ++-- tests/testthat/test-complement.R | 10 +++++----- 8 files changed, 44 insertions(+), 34 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web services for chemical information. Sources include: Alan
Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,
ChEBI, Chemical Translation Service, ChemIDplus, ChemSpider, ETOX,
Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,
SRS, Wikidata.
Author: Eduard Szöcs [aut],
Robert Allaway [ctb],
Daniel Muench [ctb],
Johannes Ranke [ctb],
Andreas Scharmüller [ctb],
Eric R Scott [ctb],
Jan Stanstrup [ctb],
João Vitor F Cavalcante [ctb],
Gordon Getzinger [ctb],
Tamás Stirling [ctb, cre]
Maintainer: Tamás Stirling <stirling.tamas@gmail.com>
Diff between webchem versions 1.1.1 dated 2021-02-07 and 1.1.2 dated 2021-12-06
webchem-1.1.1/webchem/R/alanwood.R |only webchem-1.1.1/webchem/man/aw_query.Rd |only webchem-1.1.1/webchem/tests/testthat/test-alanwood.R |only webchem-1.1.2/webchem/DESCRIPTION | 16 webchem-1.1.2/webchem/MD5 | 168 +++--- webchem-1.1.2/webchem/NAMESPACE | 8 webchem-1.1.2/webchem/NEWS.md | 51 +- webchem-1.1.2/webchem/R/bcpc.R |only webchem-1.1.2/webchem/R/chebi.R | 6 webchem-1.1.2/webchem/R/chemid.R | 149 +----- webchem-1.1.2/webchem/R/chemspider.R | 28 - webchem-1.1.2/webchem/R/cir.R | 6 webchem-1.1.2/webchem/R/cts.R | 63 +- webchem-1.1.2/webchem/R/etox.R | 12 webchem-1.1.2/webchem/R/extractors.R | 6 webchem-1.1.2/webchem/R/flavornet.R | 3 webchem-1.1.2/webchem/R/integration.R | 6 webchem-1.1.2/webchem/R/nist.R | 2 webchem-1.1.2/webchem/R/opsin.R | 2 webchem-1.1.2/webchem/R/ping.R | 18 webchem-1.1.2/webchem/R/pubchem.R | 24 webchem-1.1.2/webchem/R/srs.R | 2 webchem-1.1.2/webchem/R/utils.R | 61 ++ webchem-1.1.2/webchem/R/webchem-deprecated.R | 15 webchem-1.1.2/webchem/R/webchem-package.R | 4 webchem-1.1.2/webchem/R/wikidata.R | 4 webchem-1.1.2/webchem/build/partial.rdb |binary webchem-1.1.2/webchem/build/vignette.rds |binary webchem-1.1.2/webchem/inst/doc/webchem.html | 388 ++++------------ webchem-1.1.2/webchem/man/bcpc_query.Rd |only webchem-1.1.2/webchem/man/chebi_comp_entity.Rd | 2 webchem-1.1.2/webchem/man/ci_query.Rd | 46 - webchem-1.1.2/webchem/man/cir_img.Rd | 4 webchem-1.1.2/webchem/man/cir_query.Rd | 2 webchem-1.1.2/webchem/man/cs_compinfo.Rd | 4 webchem-1.1.2/webchem/man/cs_control.Rd | 2 webchem-1.1.2/webchem/man/cs_convert.Rd | 4 webchem-1.1.2/webchem/man/cs_datasources.Rd | 4 webchem-1.1.2/webchem/man/cs_extcompinfo.Rd | 2 webchem-1.1.2/webchem/man/cs_img.Rd | 10 webchem-1.1.2/webchem/man/cts_compinfo.Rd | 15 webchem-1.1.2/webchem/man/cts_convert.Rd | 31 - webchem-1.1.2/webchem/man/cts_from.Rd | 7 webchem-1.1.2/webchem/man/cts_to.Rd | 7 webchem-1.1.2/webchem/man/etox_basic.Rd | 2 webchem-1.1.2/webchem/man/etox_targets.Rd | 2 webchem-1.1.2/webchem/man/etox_tests.Rd | 2 webchem-1.1.2/webchem/man/find_db.Rd | 2 webchem-1.1.2/webchem/man/fn_percept.Rd | 2 webchem-1.1.2/webchem/man/get_chebiid.Rd | 2 webchem-1.1.2/webchem/man/get_cid.Rd | 2 webchem-1.1.2/webchem/man/get_csid.Rd | 4 webchem-1.1.2/webchem/man/get_etoxid.Rd | 2 webchem-1.1.2/webchem/man/get_wdid.Rd | 2 webchem-1.1.2/webchem/man/is.cas.Rd | 2 webchem-1.1.2/webchem/man/is.inchikey.Rd | 6 webchem-1.1.2/webchem/man/is.inchikey_cs.Rd | 2 webchem-1.1.2/webchem/man/is.inchikey_format.Rd | 2 webchem-1.1.2/webchem/man/is.smiles.Rd | 2 webchem-1.1.2/webchem/man/lc50.Rd | 4 webchem-1.1.2/webchem/man/nist_ri.Rd | 2 webchem-1.1.2/webchem/man/opsin_query.Rd | 2 webchem-1.1.2/webchem/man/pc_prop.Rd | 2 webchem-1.1.2/webchem/man/pc_sect.Rd | 4 webchem-1.1.2/webchem/man/pc_synonyms.Rd | 2 webchem-1.1.2/webchem/man/ping_service.Rd | 4 webchem-1.1.2/webchem/man/srs_query.Rd | 2 webchem-1.1.2/webchem/man/wd_ident.Rd | 2 webchem-1.1.2/webchem/man/webchem-deprecated.Rd | 6 webchem-1.1.2/webchem/man/with_cts.Rd | 2 webchem-1.1.2/webchem/man/write_mol.Rd |only webchem-1.1.2/webchem/tests/fixtures |only webchem-1.1.2/webchem/tests/testthat/setup-webchem.R |only webchem-1.1.2/webchem/tests/testthat/test-bcpc.R |only webchem-1.1.2/webchem/tests/testthat/test-chebi.R | 10 webchem-1.1.2/webchem/tests/testthat/test-chemid.R | 28 - webchem-1.1.2/webchem/tests/testthat/test-chemspider.R | 321 +++++-------- webchem-1.1.2/webchem/tests/testthat/test-cir.R | 17 webchem-1.1.2/webchem/tests/testthat/test-cts.R | 27 - webchem-1.1.2/webchem/tests/testthat/test-etox.R | 29 - webchem-1.1.2/webchem/tests/testthat/test-extractors.R | 76 +-- webchem-1.1.2/webchem/tests/testthat/test-integration.R | 4 webchem-1.1.2/webchem/tests/testthat/test-nist.R | 5 webchem-1.1.2/webchem/tests/testthat/test-pubchem.R | 53 -- webchem-1.1.2/webchem/tests/testthat/test-srs.R | 4 webchem-1.1.2/webchem/tests/testthat/test-utils.R | 63 ++ webchem-1.1.2/webchem/tests/testthat/test-wikidata.R | 17 87 files changed, 852 insertions(+), 1052 deletions(-)
Title: Hierarchical Latent Space Network Model
Description: Implements Hierarchical Latent Space Network Model (HLSM) for ensemble of networks as described in Sweet, Thomas & Junker (2013). <DOI:10.3102/1076998612458702>.
Author: Samrachana Adhikari, Brian Junker, Tracy Sweet, Andrew C. Thomas
Maintainer: Tracy Sweet <tsweet@umd.edu>
Diff between HLSM versions 0.8.2 dated 2020-03-01 and 0.9.0 dated 2021-12-06
HLSM-0.8.2/HLSM/R/MainDiagnosticFunctions.R |only HLSM-0.8.2/HLSM/R/PlottingHLSMFitsfromHLSMPackage.R |only HLSM-0.8.2/HLSM/R/adjust.my.tune.R |only HLSM-0.8.2/HLSM/R/diagnosticBoxplots.R |only HLSM-0.8.2/HLSM/R/plotDiagnostic.R |only HLSM-0.8.2/HLSM/R/runningmeans.R |only HLSM-0.8.2/HLSM/R/which.suck.R |only HLSM-0.8.2/HLSM/man/HLSM-data.Rd |only HLSM-0.8.2/HLSM/man/HLSM_diag.Rd |only HLSM-0.9.0/HLSM/DESCRIPTION | 10 HLSM-0.9.0/HLSM/MD5 | 54 +-- HLSM-0.9.0/HLSM/NAMESPACE | 19 - HLSM-0.9.0/HLSM/R/HLSM_C.R | 53 +-- HLSM-0.9.0/HLSM/R/HLSM_C_fixedEf.R | 60 ++- HLSM-0.9.0/HLSM/R/HLSM_run.R | 65 ---- HLSM-0.9.0/HLSM/R/HLSM_run_fixedEF.R | 69 +--- HLSM-0.9.0/HLSM/R/LSM_C.R |only HLSM-0.9.0/HLSM/R/LSM_run.R |only HLSM-0.9.0/HLSM/R/MCMCTuning.R |only HLSM-0.9.0/HLSM/R/PlottingHLSMFits.R |only HLSM-0.9.0/HLSM/R/RemoveNextInterationplotDiagnostic.R |only HLSM-0.9.0/HLSM/R/RemoveNextIterationDiagnosticFunctions.R |only HLSM-0.9.0/HLSM/R/RemoveNextIterationrunningmeans.R |only HLSM-0.9.0/HLSM/R/covFunction.R | 30 - HLSM-0.9.0/HLSM/R/helper.R | 13 HLSM-0.9.0/HLSM/R/modular_diags.R | 100 +++--- HLSM-0.9.0/HLSM/R/plotLikelihood.R | 2 HLSM-0.9.0/HLSM/R/print.summary.HLSM.R | 7 HLSM-0.9.0/HLSM/R/summary.HLSM.R | 15 HLSM-0.9.0/HLSM/data/schoolsAdviceData.RData |binary HLSM-0.9.0/HLSM/demo/HLSM.school.advice.R | 32 -- HLSM-0.9.0/HLSM/man/HLSM_data.Rd |only HLSM-0.9.0/HLSM/man/HLSM_run.Rd | 74 ++-- HLSM-0.9.0/HLSM/man/HLSMdiag.Rd |only HLSM-0.9.0/HLSM/man/plots.Rd | 52 +-- HLSM-0.9.0/HLSM/src/HLSM.cpp | 200 +++++++++---- HLSM-0.9.0/HLSM/src/init.c | 10 37 files changed, 414 insertions(+), 451 deletions(-)
Title: R Session Information
Description: Query and print information about the current R
session. It is similar to 'utils::sessionInfo()', but includes more
information about packages, and where they were installed from.
Author: Gábor Csárdi [cre],
Hadley Wickham [aut],
Winston Chang [aut],
Robert Flight [aut],
Kirill Müller [aut],
Jim Hester [aut],
R Core team [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between sessioninfo versions 1.2.1 dated 2021-11-02 and 1.2.2 dated 2021-12-06
sessioninfo-1.2.1/sessioninfo/R/hash.R |only sessioninfo-1.2.1/sessioninfo/man/figures/session-info.svg |only sessioninfo-1.2.1/sessioninfo/tests/testthat/test-skip.R |only sessioninfo-1.2.2/sessioninfo/DESCRIPTION | 8 +-- sessioninfo-1.2.2/sessioninfo/MD5 | 22 ++++------ sessioninfo-1.2.2/sessioninfo/NEWS.md | 15 ++++++ sessioninfo-1.2.2/sessioninfo/R/package-info.R | 12 ++++- sessioninfo-1.2.2/sessioninfo/R/session-info.R | 20 --------- sessioninfo-1.2.2/sessioninfo/R/utils.R | 9 ++++ sessioninfo-1.2.2/sessioninfo/README.md | 16 +------ sessioninfo-1.2.2/sessioninfo/man/figures/session-info2.svg |only sessioninfo-1.2.2/sessioninfo/tests/testthat/fixtures/devtools-info-unix.rda |binary sessioninfo-1.2.2/sessioninfo/tests/testthat/fixtures/devtools-info-windows.rda |binary sessioninfo-1.2.2/sessioninfo/tests/testthat/test-package-info.R | 2 14 files changed, 54 insertions(+), 50 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] (<https://orcid.org/0000-0003-3716-0668>)
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.3.3 dated 2021-11-05 and 0.3.4 dated 2021-12-06
DESCRIPTION | 8 ++--- MD5 | 26 +++++++++---------- NAMESPACE | 1 R/class-regions.R | 41 +++++++++++++++++++++++++++--- R/isregion.R | 25 ------------------ R/map_nigeria.R | 39 ++++++++++++++++++++++++---- R/sysdata.rda |binary build/vignette.rds |binary data/lgas_nigeria.rda |binary inst/doc/nigeria-maps.html | 20 +++++++------- tests/testthat/data/pvc2015.rds |binary tests/testthat/data/pvc2015_badcolumn.rds |binary tests/testthat/test-class-regions.R | 16 ----------- tests/testthat/test-map_nigeria.R | 7 +++++ 14 files changed, 108 insertions(+), 75 deletions(-)
Title: Hierarchical and Variation Partitioning for Canonical Analysis
Description: This function conducts variation partitioning and hierarchical partitioning to calculate the unique, shared (referred as to "common") and individual contributions of each predictor (or matrix) towards explained variation (R-square and adjusted R-square) on canonical analysis (RDA,CCA and db-RDA), applying the algorithm of Chevan, A. and Sutherland, M. 1991 Hierarchical Partitioning.The American Statistician, 90-96 <doi:10.1080/00031305.1991.10475776>.
Author: Jiangshan Lai,Pedro Peres-Neto,Kim Nimon
Maintainer: Jiangshan Lai <lai@ibcas.ac.cn>
Diff between rdacca.hp versions 1.0-3 dated 2021-09-14 and 1.0-4 dated 2021-12-06
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/rdacca.hp.r | 32 ++++++++++++++++---------------- man/rdacca.hp.Rd | 25 +++++++++++++------------ 4 files changed, 37 insertions(+), 36 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological
analyses. Specializes on the construction of historical matrices,
which are 2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices. Methodology based on Ehrlen
(2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2> and
deVries and Caswell (2018) <doi:10.1007/s12080-017-0353-0>.
Author: Richard P. Shefferson [aut, cre]
(<https://orcid.org/0000-0002-5234-3131>),
Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 4.0.1 dated 2021-11-16 and 4.1.0 dated 2021-12-06
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Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V. (2019) The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression. <doi:10.1177/0962280219842890>, and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019) The R package islasso: estimation and hypothesis testing in lasso regression. <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre],
Giovanna Cilluffo [aut, ctb],
Vito MR Muggeo [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between islasso versions 1.4.1 dated 2021-11-16 and 1.4.2 dated 2021-12-06
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Title: GNU Privacy Guard for R
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods.
Includes utilities for public key encryption, creating and verifying digital signatures,
and managing your local keyring. Note that some functionality depends on the version of
GnuPG that is installed on the system. On Windows this package can be used together with
'GPG4Win' which provides a GUI for managing keys and entering passphrases.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gpg versions 1.2.4 dated 2021-11-17 and 1.2.5 dated 2021-12-06
DESCRIPTION | 6 - MD5 | 18 ++-- NEWS | 3 cleanup | 1 inst/doc/intro.R | 4 - inst/doc/intro.Rmd | 4 - inst/doc/intro.html | 192 +++++++++++++++++++++------------------------------- src/keys.c | 3 tests |only vignettes/intro.Rmd | 4 - 10 files changed, 106 insertions(+), 129 deletions(-)
Title: Fast Approximate Shapley Values
Description: Computes fast (relative to other implementations) approximate
Shapley values for any supervised learning model. Shapley values help to
explain the predictions from any black box model using ideas from game
theory; see Strumbel and Kononenko (2014) <doi:10.1007/s10115-013-0679-x>
for details.
Author: Brandon Greenwell [aut, cre] (<https://orcid.org/0000-0002-8120-0084>)
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between fastshap versions 0.0.6 dated 2021-12-03 and 0.0.7 dated 2021-12-06
DESCRIPTION | 6 +- MD5 | 6 +- NEWS.md | 4 + inst/tinytest/test_fastshap_exact.R | 97 ++++++++++++++++++------------------ 4 files changed, 60 insertions(+), 53 deletions(-)
Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation.
Data diagnostics provides information and visualization of missing values and outliers and
unique and negative values to help you understand the distribution and quality of your data.
Data exploration provides information and visualization of the descriptive statistics of
univariate variables, normality tests and outliers, correlation of two variables, and
relationship between target variable and predictor. Data transformation supports binning
for categorizing continuous variables, imputates missing values and outliers, resolving skewness.
And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
Diff between dlookr versions 0.5.3 dated 2021-11-29 and 0.5.4 dated 2021-12-06
DESCRIPTION | 10 +++---- MD5 | 18 ++++++------- NEWS | 52 +++++++++++++++++++++++++++++++++------ R/compare.R | 2 + R/graphics.R | 12 +++++++-- R/zzz.R | 56 ++++++++++++++++++++++++++++--------------- inst/doc/EDA.html | 4 +-- inst/doc/diagonosis.html | 4 +-- inst/doc/introduce.html | 4 +-- inst/doc/transformation.html | 4 +-- 10 files changed, 115 insertions(+), 51 deletions(-)
Title: A Framework for Dimensionality Reduction
Description: A collection of dimensionality reduction
techniques from R packages and a common
interface for calling the methods.
Author: Guido Kraemer [aut, cre]
Maintainer: Guido Kraemer <guido.kraemer@uni-leipzig.de>
Diff between dimRed versions 0.2.3 dated 2019-05-08 and 0.2.4 dated 2021-12-06
DESCRIPTION | 16 +- MD5 | 138 +++++++++++----------- R/autoencoder.R | 59 ++++----- R/diffmap.R | 18 +- R/drr.R | 15 -- R/fastica.R | 12 - R/get_info.R | 3 R/graph_embed.R | 32 ----- R/hlle.R | 10 - R/isomap.R | 8 - R/kpca.R | 9 - R/l1pca.R | 12 - R/leim.R | 32 ++--- R/lle.R | 10 - R/mds.R | 14 +- R/nmds.R | 12 - R/nnmf.R | 14 -- R/pca.R | 10 - R/quality.R | 8 - R/tsne.R | 10 - R/umap.R | 50 +++++-- build/vignette.rds |binary inst/doc/dimensionality-reduction.R | 16 +- inst/doc/dimensionality-reduction.pdf |binary man/AUC_lnK_R_NX-dimRedResult-method.Rd | 28 ++-- man/AutoEncoder-class.Rd | 50 ++++--- man/DRR-class.Rd | 47 +++---- man/DiffusionMaps-class.Rd | 50 ++++--- man/DrL-class.Rd | 47 +++---- man/FastICA-class.Rd | 45 +++---- man/FruchtermanReingold-class.Rd | 43 +++--- man/HLLE-class.Rd | 43 +++--- man/Isomap-class.Rd | 41 +++--- man/KamadaKawai-class.Rd | 39 +++--- man/LCMC-dimRedResult-method.Rd | 28 ++-- man/LLE-class.Rd | 42 +++--- man/LaplacianEigenmaps-class.Rd | 6 man/MDS-class.Rd | 46 ++++--- man/NNMF-class.Rd | 46 +++---- man/PCA-class.Rd | 42 +++--- man/PCA_L1-class.Rd | 42 +++--- man/Q_NX-dimRedResult-method.Rd | 28 ++-- man/Q_global-dimRedResult-method.Rd | 28 ++-- man/Q_local-dimRedResult-method.Rd | 28 ++-- man/R_NX-dimRedResult-method.Rd | 28 ++-- man/UMAP-class.Rd | 47 ++++--- man/as.dimRedData.Rd | 4 man/cophenetic_correlation-dimRedResult-method.Rd | 31 ++-- man/dimRed-package.Rd | 5 man/dimRedData-class.Rd | 9 - man/dimRedMethod-class.Rd | 32 +++-- man/dimRedMethodList.Rd | 33 +++-- man/dimRedResult-class.Rd | 8 - man/distance_correlation-dimRedResult-method.Rd | 28 ++-- man/embed.Rd | 29 +++- man/kPCA-class.Rd | 42 +++--- man/maximize_correlation-dimRedResult-method.Rd | 8 - man/mean_R_NX-dimRedResult-method.Rd | 28 ++-- man/mixColorRamps.Rd | 13 +- man/nMDS-class.Rd | 45 +++---- man/plot.Rd | 21 ++- man/plot_R_NX.Rd | 27 ++-- man/quality.Rd | 35 ++--- man/reconstruction_error-dimRedResult-method.Rd | 31 ++-- man/reconstruction_rmse-dimRedResult-method.Rd | 28 ++-- man/tSNE-class.Rd | 43 +++--- man/total_correlation-dimRedResult-method.Rd | 36 +++-- tests/testthat/test_autoencoder.R | 11 + tests/testthat/test_quality.R | 8 - tests/testthat/test_umap.R | 66 ++++++++-- 70 files changed, 1002 insertions(+), 971 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Also used to display, in tables and graphs, predictions
obtained using any model fitting function and to explore differences between predictions.
The content falls into the following natural groupings: (i) Data, (ii) Object
manipulation functions, (iii) Model modification functions, (iv) Model testing functions,
(v) Model diagnostics functions, (vi) Prediction production and presentation functions,
(vii) Response transformation functions, and (viii) Miscellaneous functions (for further
details see 'asremlPlus-package' in help). A history of
the fitting of a sequence of models is kept in a data frame. Procedures are available for
choosing models that conform to the hierarchy or marginality principle and for displaying
predictions for significant terms in tables and graphs. The 'asreml' package provides a
computationally efficient algorithm for fitting mixed models using Residual Maximum
Likelihood. It is a commercial package that can be purchased from
'VSNi' <https://www.vsni.co.uk/> as 'asreml-R', who will supply a zip file for local
installation/updating (see <https://asreml.kb.vsni.co.uk/>). It is not needed for functions that are
methods for 'alldiffs' and 'data.frame' objects. The package 'asremPlus' can also be
installed from <http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre] (<https://orcid.org/0000-0003-0581-1817>)
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.3-21 dated 2021-09-23 and 4.3-31 dated 2021-12-06
DESCRIPTION | 10 MD5 | 107 ++-- NAMESPACE | 3 R/LSDutilities.R | 94 +++ R/REMLRTIC.v3.r | 9 R/S3methodsDeprecations.r | 1 R/alldiffs.v2.r | 156 +++++- R/asremlPlusUtilities.r | 24 + R/choose.r | 73 ++- R/plotPvalues.r | 16 R/reml4.v8.r | 615 +++++++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 47 + inst/doc/Ladybird.asreml.pdf |binary inst/doc/Ladybird.lm.pdf |binary inst/doc/Wheat.analysis.pdf |binary inst/doc/Wheat.infoCriteria.pdf |binary inst/doc/asremlPlus-manual.pdf |binary man/allDifferences.data.frame.Rd | 17 man/as.asrtests.Rd | 2 man/changeModelOnIC.asrtests.Rd | 29 - man/changeTerms.asrtests.Rd | 25 - man/chooseModel.asrtests.Rd | 17 man/exploreLSDs.alldiffs.Rd | 84 ++- man/linTransform.alldiffs.Rd | 24 - man/newfit.asreml.Rd | 25 - man/pairdiffsTransform.alldiffs.Rd | 23 man/plotPvalues.alldiffs.Rd | 24 - man/plotPvalues.data.frame.Rd | 14 man/predictPlus.asreml.Rd | 20 man/predictPresent.asreml.Rd | 20 man/recalcLSD.alldiffs.Rd | 17 man/redoErrorIntervals.alldiffs.Rd | 17 man/reparamSigDevn.asrtests.Rd | 19 man/rmboundary.asrtests.Rd | 2 man/testranfix.asrtests.Rd | 19 man/testresidual.asrtests.Rd | 15 man/testswapran.asrtests.Rd | 25 - tests/testthat/data/Exp355.Control.dat.rda |binary tests/testthat/data/MET.rda |binary tests/testthat/data/PSA.27.dat.rda |only tests/testthat/data/Ricecart.dat.rda |binary tests/testthat/data/Smarthouse.dat.rda |binary tests/testthat/data/cart.dat.rda |binary tests/testthat/data/chkpeadat.rda |binary tests/testthat/data/gw.dat.rda |binary tests/testthat/data/local851.rda |binary tests/testthat/data/longit.dat.rda |binary tests/testthat/data/orange.rda |binary tests/testthat/data/wheat94.dat.rda |binary tests/testthat/test4PredictionsPresentation.r | 9 tests/testthat/test4Selection.r | 192 +++++++- tests/testthat/test4alldiffs.r | 117 ++++ tests/testthat/test4alldiffslme.r | 17 55 files changed, 1363 insertions(+), 565 deletions(-)
Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 1.6 dated 2020-03-02 and 1.7 dated 2021-12-06
DESCRIPTION | 8 +++---- MD5 | 15 +++++++------ NEWS | 7 ++++++ R/boot.overlap.R | 57 ++++++++++++---------------------------------------- R/final.plot.R | 13 +++-------- R/overlap.R | 12 +++++++++- build |only man/boot.overlap.Rd | 7 +++--- man/overlap.Rd | 11 +++++----- 9 files changed, 57 insertions(+), 73 deletions(-)
Title: Analysis of Physiologically Structured Population Models
Description: Performs demographic, bifurcation and evolutionary analysis of physiologically structured population models, which is a class of models that consistently translates continuous-time models of individual life history to the population level.
A model of individual life history has to be implemented specifying the individual-level functions that determine the life history, such as development and mortality rates and fecundity.
M.A. Kirkilionis, O. Diekmann, B. Lisser, M. Nool, B. Sommeijer & A.M. de Roos (2001) <doi:10.1142/S0218202501001264>.
O.Diekmann, M.Gyllenberg & J.A.J.Metz (2003) <doi:10.1016/S0040-5809(02)00058-8>.
A.M. de Roos (2008) <doi:10.1111/j.1461-0248.2007.01121.x>.
Author: Andre M. de Roos [aut, cre],
Ernst Hairer [ctb],
Gerhard Wanner [ctb]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>
Diff between PSPManalysis versions 0.3.4 dated 2020-10-13 and 0.3.7 dated 2021-12-06
DESCRIPTION | 9 +-- MD5 | 44 ++++++++-------- NEWS.md | 14 +++++ R/PSPMdemo.R | 44 +++++++++------- R/PSPMecodyn.R | 54 ++++++++++---------- R/PSPMequi.R | 96 ++++++++++++++++++++++-------------- R/buildSO.R | 2 R/setup.R | 2 build/vignette.rds |binary demo/deRoosPersson.R | 8 +-- demo/deRoosPersson5.R | 8 +-- inst/C/PSPMRinterface.h | 28 ++++++---- inst/C/PSPMdemo.c | 4 - inst/C/PSPMecodyn.c | 10 ++- inst/C/PSPMequi.c | 60 ++++++++++++++++++++-- inst/C/PSPMevodyn.c | 4 - inst/C/PSPMind.c | 4 - inst/C/dopri5.h | 10 ++- inst/C/lifehistory.h | 14 +++-- inst/doc/PSPManalysis.pdf |binary inst/manual/PSPManalysis-manual.zip |binary man/PSPMequi.Rd | 19 ++++++- tests/testthat/test.02-PNAS2002.R | 6 +- 23 files changed, 285 insertions(+), 155 deletions(-)
More information about PracticalEquiDesign at CRAN
Permanent link
More information about crossvalidationCP at CRAN
Permanent link
Title: Categorical Functional Data Analysis
Description: Package for the analysis of categorical functional data.
The main purpose is to compute an encoding (real functional variable) for each state <doi:10.1080/00031305.2017.1375990>.
It also provides functions to perform basic statistical analysis on categorical functional data.
Author: Cristian Preda [aut],
Quentin Grimonprez [aut, cre],
Vincent Vandewalle [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between cfda versions 0.9.9 dated 2021-02-12 and 0.9.10 dated 2021-12-06
cfda-0.9.10/cfda/DESCRIPTION | 17 cfda-0.9.10/cfda/MD5 | 109 - cfda-0.9.10/cfda/R/bootstrap.R | 161 +- cfda-0.9.10/cfda/R/cfd.R |only cfda-0.9.10/cfda/R/cfda-package.R | 59 - cfda-0.9.10/cfda/R/check.R | 70 - cfda-0.9.10/cfda/R/dataPlot.R | 248 ++-- cfda-0.9.10/cfda/R/datasets.R | 66 - cfda-0.9.10/cfda/R/encoding.R | 350 +++--- cfda-0.9.10/cfda/R/estimation.R | 134 +- cfda-0.9.10/cfda/R/fmca.print.R | 2 cfda-0.9.10/cfda/R/generateData.R | 123 +- cfda-0.9.10/cfda/R/plotEncoding.R | 337 +++--- cfda-0.9.10/cfda/R/predict.R | 61 - cfda-0.9.10/cfda/R/pretreatment.R | 119 -- cfda-0.9.10/cfda/R/stat.R | 556 ++++------ cfda-0.9.10/cfda/build/vignette.rds |binary cfda-0.9.10/cfda/inst/CITATION |only cfda-0.9.10/cfda/inst/doc/cfda.Rmd | 5 cfda-0.9.10/cfda/inst/doc/cfda.html | 33 cfda-0.9.10/cfda/man/biofam2.Rd | 13 cfda-0.9.10/cfda/man/boxplot.timeSpent.Rd | 11 cfda-0.9.10/cfda/man/care.Rd | 9 cfda-0.9.10/cfda/man/cfda-package.Rd | 19 cfda-0.9.10/cfda/man/compute_duration.Rd | 5 cfda-0.9.10/cfda/man/compute_number_jumps.Rd | 8 cfda-0.9.10/cfda/man/compute_optimal_encoding.Rd | 15 cfda-0.9.10/cfda/man/compute_time_spent.Rd | 5 cfda-0.9.10/cfda/man/cut_data.Rd | 7 cfda-0.9.10/cfda/man/estimate_Markov.Rd | 7 cfda-0.9.10/cfda/man/estimate_pt.Rd | 5 cfda-0.9.10/cfda/man/generate_Markov.Rd | 14 cfda-0.9.10/cfda/man/get_encoding.Rd | 5 cfda-0.9.10/cfda/man/get_state.Rd | 5 cfda-0.9.10/cfda/man/hist.duration.Rd | 9 cfda-0.9.10/cfda/man/hist.njump.Rd | 7 cfda-0.9.10/cfda/man/plot.Markov.Rd | 9 cfda-0.9.10/cfda/man/plot.fmca.Rd | 11 cfda-0.9.10/cfda/man/plot.pt.Rd | 5 cfda-0.9.10/cfda/man/plotComponent.Rd | 7 cfda-0.9.10/cfda/man/plotData.Rd | 17 cfda-0.9.10/cfda/man/plotEigenvalues.Rd | 9 cfda-0.9.10/cfda/man/predict.fmca.Rd | 21 cfda-0.9.10/cfda/man/remove_duplicated_states.Rd | 9 cfda-0.9.10/cfda/man/statetable.Rd | 8 cfda-0.9.10/cfda/man/summary_cfd.Rd | 3 cfda-0.9.10/cfda/tests/testthat/test.bootstrap.R | 138 +- cfda-0.9.10/cfda/tests/testthat/test.check.R | 18 cfda-0.9.10/cfda/tests/testthat/test.encoding.R | 184 +-- cfda-0.9.10/cfda/tests/testthat/test.encoding0columnManagement.R | 227 ++-- cfda-0.9.10/cfda/tests/testthat/test.estimation.R | 86 - cfda-0.9.10/cfda/tests/testthat/test.generate.R | 92 - cfda-0.9.10/cfda/tests/testthat/test.predict.R | 15 cfda-0.9.10/cfda/tests/testthat/test.pretreatment.R | 100 - cfda-0.9.10/cfda/tests/testthat/test.stat.R | 294 ++--- cfda-0.9.10/cfda/vignettes/cfda.Rmd | 5 cfda-0.9.9/cfda/R/oldBootstrap.R |only 57 files changed, 1956 insertions(+), 1896 deletions(-)
Title: Quiver Plots for 'ggplot2'
Description: An extension of 'ggplot2' to provide quiver plots to visualise vector fields.
This functionality is implemented using a geom to produce a new graphical layer, which
allows aesthetic options. This layer can be overlaid on a map to improve visualisation
of mapped data.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between ggquiver versions 0.3.1 dated 2021-11-25 and 0.3.2 dated 2021-12-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/geom-quiver.r | 13 +++++++++++-- R/stat-quiver.r | 3 ++- man/figures/README-windplot-1.png |binary 6 files changed, 25 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-22 0.6.0
Title: Simplified Statistics for PA 606
Description: Simplifies functions assess normality for bivariate and multivariate statistical techniques, including hst(), box(), and qq(). Plots designed to replicate those that would result from similar calls in 'SPSS'. Also includes simplified formulae, such as mode(), scatter(), and ow.anova().
Author: Burrel Vann Jr [aut, cre]
Maintainer: Burrel Vann Jr <bvannjr@sdsu.edu>
Diff between vannstats versions 1.0.7.15 dated 2021-06-16 and 1.0.12.5 dated 2021-12-06
DESCRIPTION | 6 +++--- MD5 | 8 +++++++- R/US_Counties.R |only R/US_States.R |only data/US_Counties.RData |only data/US_States.RData |only man/US_Counties.Rd |only man/US_States.Rd |only 8 files changed, 10 insertions(+), 4 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and
provides an interface compliant with the DBI package. The source for
the SQLite engine is included.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
SQLite Authors [ctb] (for the included SQLite sources),
Liam Healy [ctb] (for the included SQLite sources),
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RSQLite versions 2.2.8 dated 2021-08-21 and 2.2.9 dated 2021-12-06
.aspell |only DESCRIPTION | 18 MD5 | 34 NAMESPACE | 1 NEWS.md | 29 R/transactions.R | 9 build/vignette.rds |binary man/sqliteSetBusyHandler.Rd | 2 src/DbResult.cpp | 5 src/DbResult.h | 2 src/Makevars | 1 src/SqliteResultImpl.cpp | 5 src/SqliteResultImpl.h | 3 src/vendor/sqlite3/regexp.c | 4 src/vendor/sqlite3/sqlite3.c |14692 ++++++++++++++++++++----------------- src/vendor/sqlite3/sqlite3.h | 167 src/vendor/sqlite3/sqlite3ext.h | 12 tests/testthat/helper-DBItest.R | 10 tests/testthat/test-transactions.R | 29 19 files changed, 8572 insertions(+), 6451 deletions(-)
Title: Curriculum Vitae for R Markdown
Description: Provides templates and functions to simplify the production and maintenance of curriculum vitae.
Author: Mitchell O'Hara-Wild [aut, cre]
(<https://orcid.org/0000-0001-6729-7695>),
Rob Hyndman [aut] (<https://orcid.org/0000-0002-2140-5352>),
Yihui Xie [ctb] (<https://orcid.org/0000-0003-0645-5666>),
Albert Krewinkel [cph] (Multiple bibliographies lua filter),
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>)
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between vitae versions 0.4.2 dated 2021-02-17 and 0.5.1 dated 2021-12-06
DESCRIPTION | 11 - MD5 | 57 ++--- NEWS.md | 12 + R/awesomecv.R | 8 R/bibliography.R | 22 +- R/brief.R | 5 R/csl_date.R | 1 R/csl_name.R | 1 R/cv_document.R | 1 R/detailed.R | 5 README.md | 61 +++-- inst/doc/data.html | 9 inst/doc/extending.html | 9 inst/doc/vitae.Rmd | 13 + inst/doc/vitae.html | 103 +++++++++- inst/rmarkdown/templates/awesomecv/resources/awesome-cv.tex | 12 - inst/rmarkdown/templates/awesomecv/skeleton/skeleton.Rmd | 4 inst/rmarkdown/templates/hyndman/resources/hyndmantemplate.tex | 20 - inst/rmarkdown/templates/latexcv/resources/classic/main.tex | 4 inst/rmarkdown/templates/moderncv/resources/moderncv.tex | 4 inst/rmarkdown/templates/moderncv/skeleton/moderncv.cls | 11 - inst/rmarkdown/templates/twentyseconds/resources/twentysecondstemplate.tex | 2 man/awesomecv.Rd | 6 man/bibliography_entries.Rd | 6 man/csl_date.Rd | 1 man/csl_name.Rd | 1 man/cv_document.Rd | 1 man/figures/freecodecamp.jpg |only man/moderncv.Rd | 2 vignettes/vitae.Rmd | 13 + 30 files changed, 309 insertions(+), 96 deletions(-)
Title: Standard and User-Defined RGB Color Spaces, with Conversion
Between RGB and CIE XYZ
Description: Standard RGB spaces included are sRGB, 'Adobe' RGB, 'ProPhoto' RGB, BT.709, and others. User-defined RGB spaces are also possible. There is partial support for ACES Color workflows.
Author: Glenn Davis [aut,cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesRGB versions 1.3-0 dated 2019-12-11 and 1.4-0 dated 2021-12-06
DESCRIPTION | 9 ++-- MD5 | 14 +++---- NEWS.md | 5 ++ build/vignette.rds |binary inst/doc/spacesRGB-guide.html | 78 +++++++++++++++++++++++++----------------- man/basicTF.Rd | 4 +- man/primaries.Rd | 2 - vignettes/bibliography.bib | 6 +-- 8 files changed, 69 insertions(+), 49 deletions(-)