Title: Univariate GARCH Models
Description: ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.
Author: Alexios Galanos [aut, cre],
Tobias Kley [ctb]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between rugarch versions 1.4-9 dated 2022-10-26 and 1.5-1 dated 2023-09-19
ChangeLog | 6 DESCRIPTION | 10 - MD5 | 16 +- NAMESPACE | 1 R/rugarch-solvers.R | 144 +++++++++++------------ R/rugarch-tests.R | 2 inst/CITATION | 6 inst/doc/Introduction_to_the_rugarch_package.pdf |binary src/distributions.c | 56 ++++---- 9 files changed, 124 insertions(+), 117 deletions(-)
Title: Repeated Measures with Attrition: Sample Sizes and Power Levels
for 2 Groups
Description: For the calculation of sample size or power in a two-group repeated measures design, accounting for attrition and accommodating a variety of correlation structures for the repeated measures; details of the method can be found in the scientific paper: Donald Hedeker, Robert D. Gibbons, Christine Waternaux (1999) <doi:10.3102/10769986024001070>.
Author: Yiheng Wei [aut] ,
Soumya Sahu [aut, cre],
Donald Hedeker [aut]
Maintainer: Soumya Sahu <ssahu6@uic.edu>
Diff between rmass2 versions 0.0.0.1 dated 2023-08-21 and 0.0.0.2 dated 2023-09-19
DESCRIPTION | 9 +++-- MD5 | 15 ++++++--- NEWS.md | 6 +++ R/functions.R | 55 ++++++++++++++++++++++++--------- R/rmass2.R | 95 +++++++++++++++++++++++++++++++++++----------------------- build |only inst |only man/rmass2.Rd | 40 ++++++++++++++++++------ vignettes |only 9 files changed, 149 insertions(+), 71 deletions(-)
Title: Possible Adverse Events/Reactions from the
Vaccinations/Experimental Gene Therapies
Description: Provides data about the possible adverse events/reactions
resulting from being injected with a vaccine/experimental gene therapy.
Currently, this data set only includes information from six reference
sources. Refer to the CITATION.cff file for the complete citations of
the reference sources. For information about vaccination$/immunization$
hazards, visit <https://www.questionuniverse.com/rethink.html#vaccine>,
<https://www.ecoccs.com/healing.html#vaccines>,
<https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin>,
and <https://www.questionuniverse.com/vaccination.html>.
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>
Diff between jab.adverse.reactions versions 1.0.1 dated 2022-01-13 and 1.0.3 dated 2023-09-19
jab.adverse.reactions-1.0.1/jab.adverse.reactions/LICENSE |only jab.adverse.reactions-1.0.1/jab.adverse.reactions/man/jab.adverse.reactions.Rd |only jab.adverse.reactions-1.0.3/jab.adverse.reactions/DESCRIPTION | 10 +-- jab.adverse.reactions-1.0.3/jab.adverse.reactions/MD5 | 11 +-- jab.adverse.reactions-1.0.3/jab.adverse.reactions/NEWS.md | 13 +++- jab.adverse.reactions-1.0.3/jab.adverse.reactions/R/jab.adverse.reactions.R | 7 +- jab.adverse.reactions-1.0.3/jab.adverse.reactions/README.md | 31 ++++++---- jab.adverse.reactions-1.0.3/jab.adverse.reactions/man/jab.adverse.reactions-package.Rd |only 8 files changed, 46 insertions(+), 26 deletions(-)
More information about jab.adverse.reactions at CRAN
Permanent link
Title: Combine Categories Using Greenacre's Method
Description: Implements a method of iteratively collapsing the rows of a
contingency table, two at a time, by selecting the pair of categories whose
combination yields a new table with the smallest loss of chi-squared, as
described by Greenacre, M.J. (1988) <doi:10.1007/BF01901670>. The result is
compatible with the class of object returned by the 'stats' package's
hclust() function and can be used similarly (plotted as a dendrogram,
cut, etc.). Additional functions are provided for automatic cutting and
diagnostic plotting.
Author: Jeff Jetton [aut, cre]
Maintainer: Jeff Jetton <jeff.jetton@gmail.com>
Diff between greenclust versions 1.1.0 dated 2020-01-10 and 1.1.1 dated 2023-09-19
DESCRIPTION | 9 +++---- LICENSE | 2 - MD5 | 29 ++++++++++++------------- NEWS.md | 6 +++++ R/greenclust.R | 7 +++++- R/greencut.R | 2 - R/greenplot.R | 2 - README.md | 21 ++++++++++-------- build |only man/figures/README-example_clusterplot_1-1.png |binary man/figures/README-example_greenplot-1.png |binary man/greenclust.Rd | 2 - man/greencut.Rd | 2 - man/greenplot.Rd | 2 - tests/testthat/Rplots.pdf |binary tests/testthat/test-greenclust-main.R | 9 ++++++- 16 files changed, 57 insertions(+), 36 deletions(-)
Title: String Interpolation for Documents, Reports and Apps
Description: Extra strength 'glue' for data-driven templates. String
interpolation for 'Shiny' apps or 'R Markdown' and 'knitr'-powered
'Quarto' documents, built on the 'glue' and 'whisker' packages.
Author: Garrick Aden-Buie [aut, cre] ,
Kushagra Gour [ctb] ,
The mustache.js community [ctb]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between epoxy versions 0.1.1 dated 2023-06-11 and 1.0.0 dated 2023-09-19
DESCRIPTION | 14 - MD5 | 112 ++++++---- NAMESPACE | 3 NEWS.md | 84 +++++++ R/engines.R | 137 +++++++++--- R/epoxy.R | 56 ++++- R/epoxy_mustache.R |only R/epoxy_transform_html.R | 5 R/epoxy_transform_inline.R | 107 ++++++---- R/epoxy_use.R |only R/shiny.R | 128 ++++++++---- R/transformers.R | 6 R/utils-knitr.R |only R/utils.R | 5 README.md | 4 build/vignette.rds |binary inst/doc/epoxy-report.R | 2 inst/doc/epoxy-report.Rmd | 71 +++--- inst/doc/epoxy-report.html | 70 +++--- inst/doc/epoxy-script.R | 2 inst/doc/epoxy-shiny.R | 2 inst/doc/inline-reporting.R | 2 inst/doc/inline-reporting.Rmd | 72 +++--- inst/doc/inline-reporting.html | 48 ++-- inst/examples/ui_epoxy_html/app.R | 2 inst/examples/ui_epoxy_mustache/app.R | 6 inst/srcjs/output-epoxy-mustache.js | 139 ++++++++----- inst/srcjs/output-epoxy.js | 222 ++++++++++++++------- man/epoxy.Rd | 83 ++++--- man/epoxy_mustache.Rd |only man/epoxy_transform.Rd | 4 man/epoxy_transform_inline.Rd | 53 ++--- man/epoxy_use.Rd |only man/examples/epoxy.R | 63 ++--- man/examples/epoxy_mustache.R |only man/examples/epoxy_transform.R | 4 man/figures/logo.png |binary man/fragments/setup.Rmd | 2 man/ui_epoxy_html.Rd | 36 ++- man/ui_epoxy_markdown.Rd | 36 ++- man/ui_epoxy_mustache.Rd | 26 ++ man/use_epoxy_knitr_engines.Rd | 13 + tests/testthat/_snaps/transformers.md | 2 tests/testthat/apps |only tests/testthat/helpers.R | 29 ++ tests/testthat/rmds |only tests/testthat/test-engines.R | 60 ++++- tests/testthat/test-epoxy.R | 196 ++++++++++++++++++ tests/testthat/test-epoxy_mustache.R |only tests/testthat/test-epoxy_transform_html.R | 16 + tests/testthat/test-epoxy_transform_inline.R | 34 ++- tests/testthat/test-epoxy_use.R |only tests/testthat/test-shiny.R | 37 ++- tests/testthat/test-shiny_ui_epoxy_html-list.R |only tests/testthat/test-shiny_ui_epoxy_html-no-shiny.R |only tests/testthat/test-shiny_ui_epoxy_mustache.R | 2 tests/testthat/test-utils-knitr.R |only vignettes/epoxy-report.Rmd | 71 +++--- vignettes/inline-reporting.Rmd | 72 +++--- 59 files changed, 1466 insertions(+), 672 deletions(-)
Title: Bayesian Inference on Univariate Normal Mixtures
Description: A program for Bayesian analysis of univariate normal mixtures with an unknown number
of components, following the approach of Richardson and Green (1997) <doi:10.1111/1467-9868.00095>.
This makes use of reversible jump Markov chain Monte Carlo methods that are capable of jumping
between the parameter sub-spaces corresponding to different numbers of components in the mixture.
A sample from the full joint distribution of all unknown variables is thereby generated,
and this can be used as a basis for a thorough presentation of many aspects of the posterior
distribution.
Author: Peter Green [aut, cre]
Maintainer: Peter Green <P.J.Green@bristol.ac.uk>
Diff between Nmix versions 2.0.4 dated 2023-07-19 and 2.0.5 dated 2023-09-19
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/Nmix.R | 7 +++++-- R/plot.nmix.R | 11 +++++++++-- build/partial.rdb |binary man/Nmix.Rd | 1 + src/Nmix-sub3z.f | 41 +++++++++++++++++++++++++++-------------- src/Nmix_init.c | 4 ++-- 8 files changed, 55 insertions(+), 31 deletions(-)
Title: Parameter Estimation of Item Response Theory with Estimation of
Latent Distribution
Description: Item response theory (IRT) parameter estimation using marginal maximum likelihood and expectation-maximization algorithm
(Bock & Aitkin, 1981 <doi:10.1007/BF02293801>).
Within parameter estimation algorithm, several methods for latent distribution estimation are available
(Li, 2022 <http://www.riss.kr/link?id=T16374105>).
Reflecting some features of the true latent distribution, these latent distribution estimation methods can possibly enhance the estimation accuracy and free the normality assumption on the latent distribution.
Author: Seewoo Li [aut, cre, cph]
Maintainer: Seewoo Li <cu@yonsei.ac.kr>
Diff between IRTest versions 1.7.0 dated 2023-08-17 and 1.11.0 dated 2023-09-19
DESCRIPTION | 8 MD5 | 87 +- NAMESPACE | 6 NEWS.md | 40 R/DataGeneration.R | 32 R/IRTest_Dich.R | 73 - R/IRTest_Mix.R | 109 +- R/IRTest_Poly.R | 95 +- R/category_collapsing.R |only R/dist2.R | 6 R/information.R |only R/item_fit.R | 26 R/latent_distribution.R |only R/non_exporting_functions.R | 275 +++++- R/original_par_2GM.R | 2 R/plot.irtest.R | 71 - R/plot_item.R | 12 R/print.irtest.R | 35 R/reliability.R | 124 ++- R/summary.irtest.R | 28 README.md | 268 +++--- inst/CITATION | 8 inst/doc/vignette_for_IRTest.R | 326 ++++++-- inst/doc/vignette_for_IRTest.Rmd | 481 +++++++++-- inst/doc/vignette_for_IRTest.html | 1243 ++++++++++++++++++++----------- man/DataGeneration.Rd | 4 man/IRTest_Dich.Rd | 36 man/IRTest_Mix.Rd | 40 man/IRTest_Poly.Rd | 46 - man/cat_clps.Rd |only man/figures/README-plotLD-1.png |binary man/figures/README-results-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-6-1.png |only man/inform_f_item.Rd |only man/inform_f_test.Rd |only man/item_fit.Rd | 2 man/latent_distribution.Rd |only man/original_par_2GM.Rd | 2 man/plot.irtest.Rd | 35 man/print.irtest.Rd | 33 man/recategorize.Rd |only man/reliability.Rd | 38 man/summary.irtest.Rd | 9 tests/testthat/test-IRTest_Mix.R | 8 tests/testthat/test-IRTest_Poly.R | 10 tests/testthat/test-summary_n_print.R | 18 vignettes/vignette_for_IRTest.Rmd | 481 +++++++++-- 49 files changed, 2845 insertions(+), 1272 deletions(-)
Title: Affinity Propagation Clustering
Description: Implements Affinity Propagation clustering introduced by Frey and
Dueck (2007) <DOI:10.1126/science.1136800>. The algorithms are largely
analogous to the 'Matlab' code published by Frey and Dueck.
The package further provides leveraged affinity propagation and an
algorithm for exemplar-based agglomerative clustering that can also be
used to join clusters obtained from affinity propagation. Various
plotting functions are available for analyzing clustering results.
Author: Ulrich Bodenhofer [aut, cre],
Johannes Palme [ctb],
Chrats Melkonian [ctb],
Andreas Kothmeier [aut],
Nikola Kostic [ctb]
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Diff between apcluster versions 1.4.10 dated 2022-05-31 and 1.4.11 dated 2023-09-19
DESCRIPTION | 15 +++++++++------ MD5 | 18 +++++++++--------- R/AllClasses.R | 8 +++++++- R/apcluster-methods.R | 2 +- R/apclusterK-methods.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 14 +++++++------- inst/NEWS | 5 +++++ inst/doc/apcluster.pdf |binary 10 files changed, 39 insertions(+), 25 deletions(-)
Title: Connect to Your 'Skilljar' Data
Description: Functions that simplify calls to the 'Skilljar' API. See
<https://api.skilljar.com/docs/> for documentation on the 'Skilljar' API.
This package is not supported by 'Skilljar'.
Author: Chris Umphlett [aut, cre]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>
Diff between skilljaR versions 0.1.1 dated 2023-06-09 and 0.1.2 dated 2023-09-19
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- NAMESPACE | 1 + R/get_user_domain.R |only man/get_user_domain.Rd |only 5 files changed, 8 insertions(+), 5 deletions(-)
Title: Spatial Entropy Measures
Description: The heterogeneity of spatial data presenting a finite number of categories can be measured via computation of spatial entropy. Functions are available for the computation of the main entropy and spatial entropy measures in the literature. They include the traditional version of Shannon's entropy (Shannon, 1948 <doi:10.1002/j.1538-7305.1948.tb01338.x>), Batty's spatial entropy (Batty, 1974 <doi:10.1111/j.1538-4632.1974.tb01014.x>), O'Neill's entropy (O'Neill et al., 1998 <doi:10.1007/BF00162741>), Li and Reynolds' contagion index (Li and Reynolds, 1993 <doi:10.1007/BF00125347>), Karlstrom and Ceccato's entropy (Karlstrom and Ceccato, 2002 <urn:nbn:se:kth:diva-61351>), Leibovici's entropy (Leibovici, 2009 <doi:10.1007/978-3-642-03832-7_24>), Parresol and Edwards' entropy (Parresol and Edwards, 2014 <doi:10.3390/e16041842>) and Altieri's entropy (Altieri et al., 2018, <doi:10.1007/s10651-017-0383-1>). Full references for all measures can be [...truncated...]
Author: L. Altieri, D. Cocchi, G. Roli
Maintainer: Altieri Linda <linda.altieri@unibo.it>
Diff between SpatEntropy versions 2.2-0 dated 2022-11-22 and 2.2-1 dated 2023-09-19
DESCRIPTION | 10 - MD5 | 56 +++--- NAMESPACE | 1 R/SpatEntropy.R | 1 R/altieri_entropy.R | 67 +++++-- R/batty_karlstrom_entropy.R | 379 ++++++++++++++++++++++++++++++------------- R/data.R | 271 ++++++++++++++++++++++++++++-- R/oneill_leibovici_entropy.R | 161 +++++++++++++----- R/shannon.R | 47 +++-- data/bologna.RData |only data/bolognaTess.RData |only data/bolognaW.RData |only data/raintrees2.RData |only man/SpatEntropy.Rd | 1 man/altieri.Rd | 11 - man/areapart.Rd | 22 +- man/batty.Rd | 46 ++--- man/bologna.Rd |only man/bolognaTess.Rd |only man/bolognaW.Rd |only man/contagion.Rd | 14 + man/karlstrom.Rd | 52 ++++- man/leibovici.Rd | 32 ++- man/oneill.Rd | 19 +- man/parredw.Rd | 18 +- man/raintrees.Rd | 12 - man/raintrees2.Rd |only man/raintreesCOV.Rd | 7 man/shannon.Rd | 9 - man/shannonZ.Rd | 8 man/turin.Rd | 6 man/turinTess.Rd | 8 man/turinW.Rd | 2 33 files changed, 912 insertions(+), 348 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Description: Formatting of population and case data, calculation of Standardized
Incidence Ratios, and fitting the BYM model using 'INLA'. For details see Brown (2015) <doi:10.18637/jss.v063.i12>.
Author: Patrick Brown [aut, cre, cph],
Lutong Zhou [aut]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between diseasemapping versions 2.0.1 dated 2023-09-17 and 2.0.2 dated 2023-09-19
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- build/diseasemapping.pdf |binary build/stage23.rdb |binary inst/doc/bym.R | 14 +++++++++----- inst/doc/bym.Rnw | 15 ++++++++++----- inst/doc/bym.pdf |binary man/bym.Rd | 11 ++++++++--- man/diseasemapping-package.Rd | 2 +- tests/bym.R | 26 ++++++++++++++------------ vignettes/bym.Rnw | 15 ++++++++++----- 11 files changed, 66 insertions(+), 45 deletions(-)
More information about diseasemapping at CRAN
Permanent link
Title: 'Rcpp'-Based Helper Functions to Pass 'Int64' and 'nanotime'
Values Between 'R' and 'C++'
Description: 'Int64' values can be created and accessed via the 'bit64' package and its 'integer64'
class which package the 'int64' representation cleverly into a 'double'. The 'nanotime' packages
builds on this to support nanosecond-resolution timestamps. This packages helps conversions between
'R' and 'C++' via several helper functions provided via a single header file. A complete example
client package is included as an illustration.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppInt64 versions 0.0.2 dated 2023-09-12 and 0.0.3 dated 2023-09-19
ChangeLog | 32 +++++++++++ DESCRIPTION | 21 ++++--- MD5 | 26 +++++---- R/RcppExports.R | 22 +++++++- README.md | 61 +++++++++++++++++++++- build/partial.rdb |binary inst/NEWS.Rd | 14 ++++- inst/include/rcppint64_bits/as_wrap.h | 8 +- inst/include/rcppint64_bits/functions.h | 86 +++++++++++++++++++++++++++++++- inst/tinytest/cpp/nanotime_tests.cpp |only inst/tinytest/test-nanotime.R |only man/Int64toInt64.Rd | 2 man/NanotimeToNanotime.Rd |only src/RcppExports.cpp | 12 ++++ src/int64.cpp | 2 src/nanotime.cpp |only 16 files changed, 252 insertions(+), 34 deletions(-)
Title: Datasets from the Survival TV Series Alone
Description: A collection of datasets on the Alone survival TV series in tidy format.
Included in the package are 4 datasets detailing the survivors, their loadouts,
episode details and season information.
Author: Daniel Oehm [aut, cre]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between alone versions 0.2 dated 2023-05-29 and 0.3 dated 2023-09-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ data/episodes.rda |binary data/loadouts.rda |binary data/seasons.rda |binary data/survivalists.rda |binary 7 files changed, 14 insertions(+), 9 deletions(-)
Title: Fast Best Subset Selection
Description: Extremely efficient toolkit for solving the best subset selection problem <https://www.jmlr.org/papers/v23/21-1060.html>. This package is its R interface. The package implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times for linear model. It also supports best subset selection for logistic regression, Poisson regression, Cox proportional hazard model, Gamma regression, multiple-response regression, multinomial logistic regression, ordinal regression, (sequential) principal component analysis, and robust principal component analysis. The other valuable features such as the best subset of group selection <doi:10.1287/ijoc.2022.1241> and sure independence screening <doi:10.1111/j.1467-9868.2008.00674.x> are also provided.
Author: Jin Zhu [aut, cre] ,
Zezhi Wang [aut],
Liyuan Hu [aut],
Junhao Huang [aut],
Kangkang Jiang [aut],
Yanhang Zhang [aut],
Borui Tang [aut],
Shiyun Lin [aut],
Junxian Zhu [aut],
Canhong Wen [aut],
Heping Zhang [aut] ,
Xueqin Wang [aut] ,
spectra contribu [...truncated...]
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between abess versions 0.4.7 dated 2023-02-19 and 0.4.8 dated 2023-09-19
DESCRIPTION | 10 LICENSE | 744 ++++++------ MD5 | 154 +- NAMESPACE | 100 - NEWS.md | 109 - R/RcppExports.R | 30 R/abess-package.R | 112 - R/abess.R | 1272 ++++++++++---------- R/abesspca.R | 801 ++++++------- R/abessrpca.R | 411 +++--- R/coef.abess.R | 144 +- R/coef.abesspca.R | 138 +- R/coef.abessrpca.R | 94 - R/deviance.abess.R | 98 - R/extract.abess.R | 198 +-- R/generate.data.R | 822 ++++++------- R/generate.matrix.R | 280 ++-- R/generate.spc.matrix.R | 162 +- R/initialization.R | 2463 ++++++++++++++++++++-------------------- R/plot.abess.R | 338 ++--- R/plot.abesspca.R | 368 ++--- R/plot.abessrpca.R | 144 +- R/predict.abess.R | 232 +-- R/print.abess.R | 76 - R/print.abesspca.R | 88 - R/print.abessrpca.R | 80 - R/utility.R | 248 ++-- README.md | 208 +-- build/partial.rdb |binary build/vignette.rds |binary configure.win | 22 inst/CITATION | 92 - inst/COPYRIGHTS | 758 ++++++------ inst/doc/v01-abess-guide.R | 277 ++-- inst/doc/v01-abess-guide.Rmd | 503 ++++---- inst/doc/v01-abess-guide.html | 1459 +++++++++++------------ man/abess-package.Rd | 90 - man/abess.Rd | 780 ++++++------ man/abesspca.Rd | 439 +++---- man/abessrpca.Rd | 333 ++--- man/coef.abess.Rd | 76 - man/coef.abesspca.Rd | 84 - man/coef.abessrpca.Rd | 60 man/deviance.abess.Rd | 66 - man/extract.abess.Rd | 94 - man/generate.data.Rd | 302 ++-- man/generate.matrix.Rd | 180 +- man/generate.spc.matrix.Rd | 104 - man/plot.abess.Rd | 114 - man/plot.abesspca.Rd | 94 - man/plot.abessrpca.Rd | 76 - man/predict.abess.Rd | 82 - man/print.abess.Rd | 70 - man/print.abesspca.Rd | 64 - man/print.abessrpca.Rd | 54 man/trim32.Rd | 52 src/Algorithm.h | 13 src/AlgorithmGLM.h | 184 +- src/RcppExports.cpp | 11 src/api.cpp | 46 src/api.h | 3 src/normalize.cpp | 14 src/utilities.h | 41 src/workflow.h | 5 tests/testthat/Rplots.pdf |binary tests/testthat/test-exception.R | 392 +++--- tests/testthat/test-generic.R | 514 ++++---- tests/testthat/test-glm-group.R | 588 ++++----- tests/testthat/test-glm.R | 1338 ++++++++++----------- tests/testthat/test-rpca.R | 50 tests/testthat/test-screening.R | 386 +++--- tests/testthat/test-sparse.R | 260 ++-- tests/testthat/test-spca.R | 578 ++++----- tests/testthat/utility.R | 1224 +++++++++---------- vignettes/Hitters.csv | 646 +++++----- vignettes/lung.csv | 458 +++---- vignettes/train.csv | 1784 ++++++++++++++-------------- vignettes/v01-abess-guide.Rmd | 503 ++++---- 78 files changed, 12725 insertions(+), 12562 deletions(-)
Title: Analysis of Selection Index in Plant Breeding
Description: The aim of most plant breeding programmes is simultaneous improvement of several characters. An objective method involving simultaneous selection for several attributes then becomes necessary. It has been recognised that most rapid improvements in the economic value is expected from selection applied simultaneously to all the characters which determine the economic value of a plant, and appropriate assigned weights to each character according to their economic importance, heritability and correlations between characters. So the selection for economic value is a complex matter. If the component characters are combined together into an index in such a way that when selection is applied to the index, as if index is the character to be improved, most rapid improvement of economic value is expected. Such an index was first proposed by Smith (1937 <doi:10.1111/j.1469-1809.1936.tb02143.x>) based on the Fisher's (1936 <doi:10.1111/j.1469-1809.1936.tb02137.x>) "discriminant function [...truncated...]
Author: Zankrut Goyani [aut, cre, cph]
Maintainer: Zankrut Goyani <zankrut20@gmail.com>
Diff between selection.index versions 1.1.4 dated 2022-06-13 and 1.2.0 dated 2023-09-19
DESCRIPTION | 17 MD5 | 63 +- NAMESPACE | 23 NEWS.md | 44 - R/comb.indices.R | 98 +-- R/gen.advance.R | 42 - R/gen.varcov.R | 120 ++-- R/meanPerformance.R |only R/phen.varcov.R | 122 ++-- R/rcomb.indices.R | 126 ++-- R/seldata.R | 42 - R/weight.R | 28 - R/weight.mat.R | 28 - README.md | 296 +++++------ build/vignette.rds |binary inst/doc/Examples.R | 64 +- inst/doc/Examples.Rmd | 128 ++-- inst/doc/Examples.html | 906 +++++++++++++++++----------------- man/comb.indices.Rd | 68 +- man/gen.advance.Rd | 52 - man/gen.varcov.Rd | 48 - man/meanPerformance.Rd |only man/phen.varcov.Rd | 48 - man/rcomb.indices.Rd | 72 +- man/seldata.Rd | 58 +- man/weight.Rd | 44 - man/weight.mat.Rd | 40 - tests/testthat.R | 8 tests/testthat/test-comb.indices.R | 12 tests/testthat/test-gen.advance.R | 18 tests/testthat/test-genphen.R | 14 tests/testthat/test-meanPerformance.R |only tests/testthat/test-rcomb.indices.R | 12 vignettes/Examples.Rmd | 128 ++-- 34 files changed, 1390 insertions(+), 1379 deletions(-)
More information about selection.index at CRAN
Permanent link
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data structure from the file extension, reasonable defaults are used for
data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is
natively supported (including from SSL/HTTPS), compressed files can be read
directly without explicit decompression, and fast import packages are used where
appropriate. An additional convenience function, 'convert()', provides a simple
method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.0.0 dated 2023-09-14 and 1.0.1 dated 2023-09-19
rio-1.0.0/rio/tests/testthat/iris.html |only rio-1.0.1/rio/DESCRIPTION | 12 ++-- rio-1.0.1/rio/MD5 | 41 ++++++++-------- rio-1.0.1/rio/NEWS.md | 4 + rio-1.0.1/rio/R/import.R | 5 +- rio-1.0.1/rio/R/import_methods.R | 2 rio-1.0.1/rio/R/set_class.R | 2 rio-1.0.1/rio/R/sysdata.rda |binary rio-1.0.1/rio/README.md | 4 - rio-1.0.1/rio/inst/doc/extension.R | 2 rio-1.0.1/rio/inst/doc/labelled.R | 2 rio-1.0.1/rio/inst/doc/labelled.html | 4 - rio-1.0.1/rio/inst/doc/remap.R | 4 - rio-1.0.1/rio/inst/doc/rio.R | 10 ++-- rio-1.0.1/rio/inst/doc/rio.html | 52 ++++++++++----------- rio-1.0.1/rio/man/import.Rd | 2 rio-1.0.1/rio/man/import_list.Rd | 2 rio-1.0.1/rio/tests/testthat/test_format_feather.R | 3 + rio-1.0.1/rio/tests/testthat/test_format_parquet.R | 1 rio-1.0.1/rio/tests/testthat/test_identical.R | 1 rio-1.0.1/rio/tests/testthat/test_import_list.R | 2 rio-1.0.1/rio/tests/testthat/test_set_class.R | 12 ++++ 22 files changed, 98 insertions(+), 69 deletions(-)
Title: Methods for Multivariate Quadrature
Description: Provides methods to construct multivariate grids, which can be used
for multivariate quadrature. This grids can be based on different quadrature
rules like Newton-Cotes formulas (trapezoidal-, Simpson's- rule, ...) or Gauss
quadrature (Gauss-Hermite, Gauss-Legendre, ...). For the construction of the
multidimensional grid the product-rule or the combination- technique can be
applied.
Author: Constantin Weiser
Maintainer: Constantin Weiser <constantin.weiser@gmail.com>
Diff between mvQuad versions 1.0-6 dated 2016-07-19 and 1.0-8 dated 2023-09-19
DESCRIPTION | 12 MD5 | 17 - R/mvQuad.R | 14 README.md |only build/vignette.rds |binary inst/CITATION | 13 inst/NEWS | 7 inst/doc/mvQuad_intro.R | 18 - inst/doc/mvQuad_intro.html | 756 +++++++++++++++++++++++++++++++++++---------- man/mvQuad-package.Rd | 8 10 files changed, 633 insertions(+), 212 deletions(-)
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.
Author: David Hodge [aut, cre, cph] ,
Nik Mitchell [ctb]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 5.0.0 dated 2023-09-12 and 5.1.0 dated 2023-09-19
DESCRIPTION | 15 +- MD5 | 98 +++++++++--------- NAMESPACE | 2 NEWS.md | 7 + R/dark_mode.R | 18 +-- R/gg_area.R | 2 R/gg_bar.R | 2 R/gg_bin_2d.R | 2 R/gg_blank.R | 2 R/gg_boxplot.R | 2 R/gg_col.R | 2 R/gg_contour.R | 2 R/gg_contour_filled.R | 2 R/gg_crossbar.R | 2 R/gg_density.R | 2 R/gg_density_2d.R | 2 R/gg_density_2d_filled.R | 2 R/gg_errorbar.R | 2 R/gg_freqpoly.R | 2 R/gg_hex.R | 2 R/gg_histogram.R | 2 R/gg_jitter.R | 2 R/gg_label.R | 3 R/gg_line.R | 2 R/gg_linerange.R | 2 R/gg_path.R | 2 R/gg_point.R | 2 R/gg_pointrange.R | 2 R/gg_polygon.R | 2 R/gg_qq.R | 2 R/gg_raster.R | 2 R/gg_rect.R | 2 R/gg_ribbon.R | 2 R/gg_segment.R | 2 R/gg_smooth.R | 2 R/gg_step.R | 2 R/gg_text.R | 3 R/gg_tile.R | 2 R/gg_violin.R | 2 R/light_mode.R | 16 +-- R/pal.R | 46 ++++++-- inst/doc/ggblanket.R | 143 ++++++++++++--------------- inst/doc/ggblanket.Rmd | 151 +++++++++++++--------------- inst/doc/ggblanket.html | 245 ++++++++++++++++++++++------------------------- man/dark_mode.Rd | 8 - man/gg_label.Rd | 1 man/gg_text.Rd | 1 man/light_mode.Rd | 8 - man/pal_dark_mode.Rd |only man/pal_light_mode.Rd |only vignettes/ggblanket.Rmd | 151 +++++++++++++--------------- 51 files changed, 481 insertions(+), 499 deletions(-)
Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'.
Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>.
Some more specific algorithms allow the user to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between graphlayouts versions 1.0.0 dated 2023-05-01 and 1.0.1 dated 2023-09-19
DESCRIPTION | 10 MD5 | 56 ++-- NEWS.md | 4 R/annotate_functions.R | 98 ++++---- R/graph_manipulate.R | 25 +- R/layout_backbone.R | 148 +++++------- R/layout_dynamic.R | 98 ++++---- R/layout_manipulate.R | 41 +-- R/layout_multilevel.R | 323 +++++++++++++------------- R/layout_spectral.R | 40 +-- R/layout_stress.R | 536 +++++++++++++++++++++----------------------- R/layout_umap.R | 18 - R/layouts.R | 80 +++--- build/vignette.rds |binary inst/doc/graphlayouts.html | 209 ++++++++--------- man/annotate_circle.Rd | 16 - man/figures/dynamic_ex.png |binary man/graph_manipulate.Rd | 2 man/graphlayouts-package.Rd | 2 man/layout_backbone.Rd | 17 - man/layout_centrality.Rd | 12 man/layout_dynamic.Rd | 8 man/layout_focus.Rd | 4 man/layout_focus_group.Rd | 6 man/layout_manipulate.Rd | 8 man/layout_multilevel.Rd | 14 - man/layout_spectral.Rd | 10 man/layout_stress.Rd | 10 man/layout_umap.Rd | 4 29 files changed, 897 insertions(+), 902 deletions(-)
Title: 'DT' Extension for CRUD (Create, Read, Update, Delete)
Applications in 'shiny'
Description: The core of this package is a function eDT() which enhances DT::datatable() such that it can be used to interactively modify data in 'shiny'. By the use of generic 'dplyr' methods it supports many types of data storage, with relational databases ('dbplyr') being the main use case.
Author: Jasper Schelfhout [aut, cre],
Maxim Nazarov [rev],
Daan Seynaeve [rev]
Maintainer: Jasper Schelfhout <jasper.schelfhout@openanalytics.eu>
Diff between editbl versions 0.9.5 dated 2023-09-05 and 0.9.6 dated 2023-09-19
DESCRIPTION | 20 +++++++++++++------- MD5 | 21 +++++++++++---------- R/demoApp.R | 25 ++++++++++++++++--------- R/eDT.R | 7 ++++++- R/tbl_dbi.R | 36 ++++++++++++++++++++++++++++++------ README.md |only man/eDT.Rd | 7 ++++++- man/eDTOutput.Rd | 7 ++++++- man/rows_delete.tbl_dbi.Rd | 12 ++++++++++-- man/rows_insert.tbl_dbi.Rd | 11 ++++++++++- man/rows_update.tbl_dbi.Rd | 12 ++++++++++-- man/runDemoApp.Rd | 25 ++++++++++++++++--------- 12 files changed, 134 insertions(+), 49 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/web/main/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX) Web Services
(<https://wikis.ec.europa.eu/pages/viewpage.action?pageId=44165555>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Matyas Meszaros [aut, cre],
Sebastian Weinand [ctb]
Maintainer: Matyas Meszaros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.21.2 dated 2023-08-08 and 0.22.1 dated 2023-09-19
DESCRIPTION | 8 MD5 | 28 - NEWS.md | 15 R/extract_data.R | 3 R/get_compressed_sdmx.R | 16 R/get_eurostat_bulk.R | 2 R/get_eurostat_codelist.R | 8 R/get_eurostat_data.R | 46 +- R/get_eurostat_dsd.R | 21 - R/get_eurostat_raw.R | 14 R/get_eurostat_toc.R | 8 inst/tinytest/test_restatapi.R | 792 +++++++++++++++++------------------------ man/get_eurostat_bulk.Rd | 2 man/get_eurostat_data.Rd | 2 man/get_eurostat_raw.Rd | 6 15 files changed, 459 insertions(+), 512 deletions(-)
Title: Latent Dirichlet Allocation Coupled with Time Series Analyses
Description: Combines Latent Dirichlet Allocation (LDA) and Bayesian multinomial time series methods in a two-stage analysis to quantify dynamics in high-dimensional temporal data. LDA decomposes multivariate data into lower-dimension latent groupings, whose relative proportions are modeled using generalized Bayesian time series models that include abrupt changepoints and smooth dynamics. The methods are described in Blei et al. (2003) <doi:10.1162/jmlr.2003.3.4-5.993>, Western and Kleykamp (2004) <doi:10.1093/pan/mph023>, Venables and Ripley (2002, ISBN-13:978-0387954578), and Christensen et al. (2018) <doi:10.1002/ecy.2373>.
Author: Juniper L. Simonis [aut, cre] ,
Erica M. Christensen [aut] ,
David J. Harris [aut] ,
Renata M. Diaz [aut] ,
Hao Ye [aut] ,
Ethan P. White [aut] ,
S.K. Morgan Ernest [aut] ,
Weecology [cph]
Maintainer: Juniper L. Simonis <juniper.simonis@weecology.org>
Diff between LDATS versions 0.2.7 dated 2020-03-19 and 0.3.0 dated 2023-09-19
DESCRIPTION | 24 MD5 | 113 +-- NEWS.md | 21 R/LDA.R | 6 R/LDATS.R | 14 R/LDA_TS.R | 6 R/TS.R | 10 R/data.R | 8 R/ptMCMC.R | 10 README.md | 26 build/vignette.rds |binary inst/WORDLIST | 84 +- inst/doc/LDATS_codebase.R | 6 inst/doc/LDATS_codebase.Rmd | 4 inst/doc/LDATS_codebase.html | 191 +++-- inst/doc/paper-comparison.R | 490 -------------- inst/doc/paper-comparison.Rmd | 281 ++++---- inst/doc/paper-comparison.html | 1153 +++++++++++++++++++--------------- inst/doc/rodents-example.R | 38 - inst/doc/rodents-example.Rmd | 4 inst/doc/rodents-example.html | 481 ++++++++------ man/LDATS.Rd | 15 man/LDA_TS.Rd | 32 man/LDA_TS_control.Rd | 28 man/LDA_set.Rd | 5 man/LDA_set_control.Rd | 3 man/TS.Rd | 30 man/TS_control.Rd | 23 man/TS_on_LDA.Rd | 24 man/TS_summary_plot.Rd | 32 man/check_document_covariate_table.Rd | 7 man/count_trips.Rd | 2 man/diagnose_ptMCMC.Rd | 2 man/est_changepoints.Rd | 10 man/est_regressors.Rd | 5 man/jornada.Rd | 10 man/logLik.LDA_VEM.Rd | 4 man/multinom_TS.Rd | 21 man/multinom_TS_chunk.Rd | 10 man/plot.LDA_TS.Rd | 11 man/plot.LDA_VEM.Rd | 34 - man/plot.TS_fit.Rd | 16 man/prep_cpts.Rd | 3 man/prep_ptMCMC_inputs.Rd | 10 man/rodents.Rd | 10 man/set_LDA_TS_plot_cols.Rd | 11 man/set_TS_summary_plot_cols.Rd | 11 man/step_chains.Rd | 2 man/swap_chains.Rd | 4 man/verify_changepoint_locations.Rd | 3 vignettes/LDATS_codebase.Rmd | 4 vignettes/output |only vignettes/paper-comparison.Rmd | 281 ++++---- vignettes/rodents-example.Rmd | 4 54 files changed, 1879 insertions(+), 1758 deletions(-)
Title: Volume Approximation and Sampling of Convex Polytopes
Description: Provides an R interface for 'volesti' C++ package. 'volesti' computes estimations of volume
of polytopes given by (i) a set of points, (ii) linear inequalities or (iii) Minkowski sum of segments
(a.k.a. zonotopes). There are three algorithms for volume estimation as well as algorithms
for sampling, rounding and rotating polytopes. Moreover, 'volesti' provides algorithms for
estimating copulas useful in computational finance. Methods implemented in 'volesti' are described
in A. Chalkis and V. Fisikopoulos (2022) <doi:10.32614/RJ-2021-077> and references therein.
Author: Vissarion Fisikopoulos <vissarion.fisikopoulos@gmail.com> [aut, cph, cre],
Apostolos Chalkis <tolis.chal@gmail.com> [cph, aut],
contributors in file inst/AUTHORS
Maintainer: Vissarion Fisikopoulos <vissarion.fisikopoulos@gmail.com>
Diff between volesti versions 1.1.2-6 dated 2023-04-11 and 1.1.2-7 dated 2023-09-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ src/external/lpsolve/build/lp_solve/lusol.c | 11 +++++++++++ 4 files changed, 22 insertions(+), 7 deletions(-)
Title: Seeding the Default RNG with a Numeric Vector
Description: A function setVectorSeed() is provided. Its argument
is a numeric vector of an arbitrary nonzero length, whose
components have integer values from [0, 2^32-1]. The input
vector is transformed using AES (Advanced Encryption Standard)
algorithm into an initial state of Mersenne-Twister random
number generator. The function provides a better alternative
to the R base function set.seed(), if the input vector is
a single integer. Initializing a stream of random numbers
with a vector is a convenient way to obtain several streams,
each of which is identified by several integer indices.
Author: Petr Savicky
Maintainer: Petr Savicky <savicky@cs.cas.cz>
Diff between rngSetSeed versions 0.3-2 dated 2014-12-03 and 0.3-3 dated 2023-09-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/generateInitialization.Rd | 6 +++--- man/rngSetSeed-package.Rd | 1 + 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.0.2 dated 2023-08-15 and 1.0.3 dated 2023-09-19
renv-1.0.2/renv/inst/repos/src/contrib/renv_1.0.2.tar.gz |only renv-1.0.3/renv/DESCRIPTION | 6 renv-1.0.3/renv/MD5 | 132 +++++++-------- renv-1.0.3/renv/NEWS.md | 26 ++ renv-1.0.3/renv/R/aaa.R | 5 renv-1.0.3/renv/R/autoload.R | 3 renv-1.0.3/renv/R/bootstrap.R | 13 - renv-1.0.3/renv/R/cache.R | 31 --- renv-1.0.3/renv/R/clean.R | 1 renv-1.0.3/renv/R/cleanse.R |only renv-1.0.3/renv/R/dynamic.R | 5 renv-1.0.3/renv/R/graph.R | 4 renv-1.0.3/renv/R/init.R | 11 + renv-1.0.3/renv/R/install.R | 13 + renv-1.0.3/renv/R/load.R | 24 +- renv-1.0.3/renv/R/lockfile-diff.R | 14 + renv-1.0.3/renv/R/lockfile.R | 18 +- renv-1.0.3/renv/R/manifest-convert.R | 2 renv-1.0.3/renv/R/methods.R | 5 renv-1.0.3/renv/R/pak.R | 11 + renv-1.0.3/renv/R/paths.R | 49 +---- renv-1.0.3/renv/R/rehash.R | 1 renv-1.0.3/renv/R/restore.R | 5 renv-1.0.3/renv/R/sandbox.R | 17 + renv-1.0.3/renv/R/snapshot.R | 11 + renv-1.0.3/renv/R/status.R | 9 - renv-1.0.3/renv/R/utils.R | 28 +-- renv-1.0.3/renv/R/watchdog.R | 19 +- renv-1.0.3/renv/R/zzz.R | 19 ++ renv-1.0.3/renv/inst/doc/ci.R | 2 renv-1.0.3/renv/inst/doc/ci.Rmd | 2 renv-1.0.3/renv/inst/doc/ci.html | 6 renv-1.0.3/renv/inst/doc/docker.R | 2 renv-1.0.3/renv/inst/doc/faq.html | 2 renv-1.0.3/renv/inst/doc/package-install.R | 10 - renv-1.0.3/renv/inst/doc/package-install.html | 2 renv-1.0.3/renv/inst/doc/package-sources.R | 8 renv-1.0.3/renv/inst/doc/package-sources.html | 2 renv-1.0.3/renv/inst/doc/packages.R | 2 renv-1.0.3/renv/inst/doc/packages.Rmd | 56 +----- renv-1.0.3/renv/inst/doc/packages.html | 52 ++--- renv-1.0.3/renv/inst/doc/packrat.R | 2 renv-1.0.3/renv/inst/doc/packrat.html | 2 renv-1.0.3/renv/inst/doc/profiles.R | 2 renv-1.0.3/renv/inst/doc/profiles.html | 2 renv-1.0.3/renv/inst/doc/python.R | 2 renv-1.0.3/renv/inst/doc/renv.R | 2 renv-1.0.3/renv/inst/doc/renv.Rmd | 12 - renv-1.0.3/renv/inst/doc/renv.html | 54 +++--- renv-1.0.3/renv/inst/doc/rsconnect.R | 2 renv-1.0.3/renv/inst/repos/src/contrib/PACKAGES | 4 renv-1.0.3/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.0.3/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.0.3/renv/inst/repos/src/contrib/renv_1.0.3.tar.gz |only renv-1.0.3/renv/inst/resources/activate.R | 25 -- renv-1.0.3/renv/man/graph.Rd | 4 renv-1.0.3/renv/man/init.Rd | 4 renv-1.0.3/renv/man/install.Rd | 5 renv-1.0.3/renv/man/lockfiles.Rd | 2 renv-1.0.3/renv/man/snapshot.Rd | 15 + renv-1.0.3/renv/man/status.Rd | 13 + renv-1.0.3/renv/tests/testthat/test-autoload.R | 4 renv-1.0.3/renv/tests/testthat/test-cleanse.R |only renv-1.0.3/renv/tests/testthat/test-lockfile.R | 2 renv-1.0.3/renv/tests/testthat/test-migrate.R | 8 renv-1.0.3/renv/tests/testthat/test-restore.R | 9 + renv-1.0.3/renv/vignettes/ci.Rmd | 2 renv-1.0.3/renv/vignettes/packages.Rmd | 56 +----- renv-1.0.3/renv/vignettes/renv.Rmd | 12 - 69 files changed, 441 insertions(+), 432 deletions(-)
Title: Simulating Forest Growth using the 3-PG Model
Description: Provides a flexible and easy-to-use interface for the Physiological Processes Predicting Growth (3-PG) model written in Fortran. The r3PG serves as a flexible and easy-to-use interface for the 3-PGpjs (monospecific, evenaged and evergreen forests) described in Landsberg & Waring (1997) <doi:10.1016/S0378-1127(97)00026-1> and the 3-PGmix (deciduous, uneven-aged or mixed-species forests) described in Forrester & Tang (2016) <doi:10.1016/j.ecolmodel.2015.07.010>.
Author: Volodymyr Trotsiuk [aut, cre] ,
Florian Hartig [aut] ,
David Forrester [aut],
Ramiro Silveyra Gonzalez [aut]
Maintainer: Volodymyr Trotsiuk <volodymyr.trotsiuk@wsl.ch>
Diff between r3PG versions 0.1.5 dated 2023-07-04 and 0.1.6 dated 2023-09-19
DESCRIPTION | 8 MD5 | 12 - R/r3PG.R | 1 man/r3PG.Rd | 1 src/i_decl_var.h | 412 +++++++++++++++++++++++++------------------------- src/md_3PG.f95 | 268 ++++++++++++++++---------------- src/md_decl_const.f95 | 20 +- 7 files changed, 362 insertions(+), 360 deletions(-)
Title: Meta-Analysis Methods Correcting for Publication Bias
Description: Provides meta-analysis methods that correct for
publication bias and outcome reporting bias. Four methods and a visual tool
are currently included in the package. The p-uniform method as described in
van Assen, van Aert, and Wicherts (2015) <doi:10.1037/met0000025>
can be used for estimating the average effect size, testing the null hypothesis
of no effect, and testing for publication bias using only the statistically
significant effect sizes of primary studies. The second method in the package
is the p-uniform* method as described in van Aert and van Assen (2023)
<doi:10.31222/osf.io/zqjr9>. This method is an extension of the p-uniform
method that allows for estimation of the average effect size and the
between-study variance in a meta-analysis, and uses both the statistically
significant and nonsignificant effect sizes. The third method in the package
is the hybrid method as described in van Aert and van Assen (2018)
<doi:10.3758/s13428-017-0967-6>. The hybrid metho [...truncated...]
Author: Robbie C.M. van Aert
Maintainer: Robbie C.M. van Aert <R.C.M.vanAert@tilburguniversity.edu>
Diff between puniform versions 0.2.6 dated 2023-07-17 and 0.2.7 dated 2023-09-19
DESCRIPTION | 51 +-- MD5 | 35 +- NEWS.md | 12 R/get_profile_ci.R |only R/hy.R | 418 +++++++++++++++++++++++++---- R/hy0.R | 15 - R/hybrid.R | 697 +++++++++++++++++++++++++------------------------ R/meta_plot.R | 19 + R/ml_hy.R |only R/pdist_hy.R | 6 R/print.hybridoutput.R | 181 ++++++++---- R/puni_star.R | 11 R/puniform.R | 11 R/repl.R | 6 R/report.R |only R/zzz.R | 2 man/hybrid.Rd | 411 +++++++++++++--------------- man/meta_plot.Rd | 22 + man/puni_star.Rd | 11 man/puniform.Rd | 11 20 files changed, 1180 insertions(+), 739 deletions(-)
Title: Spatial Designs for Ecological and Environmental Surveys
Description: Provides spatially survey balanced designs using the quasi-random number method described Robinson et al. (2013) <doi:10.1111/biom.12059> and adjusted in Robinson et al. (2017) <doi:10.1016/j.spl.2017.05.004>. Designs using MBHdesign can: 1) accommodate, without substantial detrimental effects on spatial balance, legacy sites (Foster et al., 2017 <doi:10.1111/2041-210X.12782>); 2) be based on points or transects (foster et al. 2020 <doi:10.1111/2041-210X.13321> and produce clustered samples (Foster et al. (in press). Additional information about the package use itself is given in Foster (2021) <doi:10.1111/2041-210X.13535>.
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@data61.csiro.au>
Diff between MBHdesign versions 2.2.2 dated 2022-01-24 and 2.3.14 dated 2023-09-19
MBHdesign-2.2.2/MBHdesign/inst/doc/MBHdesign.Rnw |only MBHdesign-2.2.2/MBHdesign/vignettes/MBHdesign.Rnw |only MBHdesign-2.2.2/MBHdesign/vignettes/MB_Hub_MED.jpg |only MBHdesign-2.3.14/MBHdesign/DESCRIPTION | 13 MBHdesign-2.3.14/MBHdesign/INDEX |only MBHdesign-2.3.14/MBHdesign/MD5 | 45 ++- MBHdesign-2.3.14/MBHdesign/NAMESPACE | 15 - MBHdesign-2.3.14/MBHdesign/NEWS | 7 MBHdesign-2.3.14/MBHdesign/R/FunsForTransect8.R | 2 MBHdesign-2.3.14/MBHdesign/R/MBHdesign4.R | 205 +++++++-------- MBHdesign-2.3.14/MBHdesign/R/alterInclProbs.cluster.R |only MBHdesign-2.3.14/MBHdesign/R/quasiSamp.cluster.R |only MBHdesign-2.3.14/MBHdesign/build/vignette.rds |binary MBHdesign-2.3.14/MBHdesign/inst/CITATION | 42 +-- MBHdesign-2.3.14/MBHdesign/inst/doc/MBHdesign.R | 132 ++++++++- MBHdesign-2.3.14/MBHdesign/inst/doc/MBHdesign.pdf |binary MBHdesign-2.3.14/MBHdesign/inst/doc/MBHdesign.rnw |only MBHdesign-2.3.14/MBHdesign/inst/extdata |only MBHdesign-2.3.14/MBHdesign/man/alterInclProbs.Rd | 2 MBHdesign-2.3.14/MBHdesign/man/alterInclProbs.cluster.Rd |only MBHdesign-2.3.14/MBHdesign/man/modEsti.Rd | 2 MBHdesign-2.3.14/MBHdesign/man/quasiSamp.Rd | 47 ++- MBHdesign-2.3.14/MBHdesign/man/transectSamp.Rd | 2 MBHdesign-2.3.14/MBHdesign/vignettes/MBHdesign.bib | 105 ++++++- MBHdesign-2.3.14/MBHdesign/vignettes/MBHdesign.rnw |only 25 files changed, 424 insertions(+), 195 deletions(-)
Title: Hydro-Meteorology Time-Series
Description: Functions for the management and treatment of hydrology and
meteorology time-series stored in a 'Sqlite' data base.
Author: Pierre Chevallier [aut, cre]
Maintainer: Pierre Chevallier <pierre.chevallier@mailo.com>
Diff between htsr versions 2.1.0 dated 2023-08-29 and 2.1.1 dated 2023-09-19
htsr-2.1.0/htsr/inst/extdata/app_exphts |only htsr-2.1.0/htsr/inst/extdata/app_invent |only htsr-2.1.0/htsr/inst/extdata/app_plothts |only htsr-2.1.0/htsr/inst/extdata/app_sensor |only htsr-2.1.0/htsr/inst/extdata/app_station |only htsr-2.1.0/htsr/inst/extdata/app_tstep |only htsr-2.1.1/htsr/DESCRIPTION | 18 +- htsr-2.1.1/htsr/MD5 | 96 +++++----- htsr-2.1.1/htsr/NAMESPACE | 8 htsr-2.1.1/htsr/R/d_convert_hydraccess.R | 2 htsr-2.1.1/htsr/R/d_convert_weewx.R | 78 ++++++-- htsr-2.1.1/htsr/R/d_exp_discalib.R |only htsr-2.1.1/htsr/R/d_wind.R | 12 - htsr-2.1.1/htsr/R/ds_exp_hts.R | 149 +++++++++++++++-- htsr-2.1.1/htsr/R/ds_inventory.R | 101 ++++++++++- htsr-2.1.1/htsr/R/ds_sensor.R | 205 ++++++++++++++++++++++- htsr-2.1.1/htsr/R/ds_station.R | 245 +++++++++++++++++++++++++++- htsr-2.1.1/htsr/R/h_etp.R |only htsr-2.1.1/htsr/R/h_month.R | 38 ++-- htsr-2.1.1/htsr/R/hs_tstep.R | 157 ++++++++++++++++- htsr-2.1.1/htsr/R/p_bar.R | 45 ++--- htsr-2.1.1/htsr/R/p_gaps.R | 6 htsr-2.1.1/htsr/R/p_hypso.R | 1 htsr-2.1.1/htsr/R/p_line.R | 42 ++-- htsr-2.1.1/htsr/R/p_wind.R | 4 htsr-2.1.1/htsr/R/ps_plothts.R | 214 ++++++++++++++++++++++++ htsr-2.1.1/htsr/R/z_set.R | 36 +--- htsr-2.1.1/htsr/inst/doc/htsr-package.R | 2 htsr-2.1.1/htsr/inst/doc/htsr-package.Rmd | 2 htsr-2.1.1/htsr/inst/doc/htsr-package.html | 2 htsr-2.1.1/htsr/inst/extdata/conf.RData |only htsr-2.1.1/htsr/inst/extdata/fil.RData |only htsr-2.1.1/htsr/inst/extdata/settings.RData |only htsr-2.1.1/htsr/inst/extdata/tab.RData |only htsr-2.1.1/htsr/man/d_convert_weewx.Rd | 16 + htsr-2.1.1/htsr/man/d_exp_discalib.Rd |only htsr-2.1.1/htsr/man/d_wind.Rd | 2 htsr-2.1.1/htsr/man/ds_exp_hts.Rd | 8 htsr-2.1.1/htsr/man/ds_inventory.Rd | 5 htsr-2.1.1/htsr/man/ds_sensor.Rd | 7 htsr-2.1.1/htsr/man/ds_station.Rd | 5 htsr-2.1.1/htsr/man/h_etp.Rd |only htsr-2.1.1/htsr/man/h_month.Rd | 2 htsr-2.1.1/htsr/man/hs_tstep.Rd | 11 - htsr-2.1.1/htsr/man/htsr-package.Rd | 8 htsr-2.1.1/htsr/man/p_bar.Rd | 2 htsr-2.1.1/htsr/man/p_gaps.Rd | 2 htsr-2.1.1/htsr/man/p_line.Rd | 2 htsr-2.1.1/htsr/man/p_wind.Rd | 2 htsr-2.1.1/htsr/man/ps_plothts.Rd | 2 htsr-2.1.1/htsr/vignettes/htsr-package.Rmd | 2 51 files changed, 1288 insertions(+), 251 deletions(-)
Title: Visualization the Effects of Collinearity in Distributed Lag
Models and Other Linear Models
Description: Tool to assessing whether the results of a study could be influenced by
collinearity. Simulations under a given hypothesized truth regarding effects of an
exposure on the outcome are used and the resulting curves of lagged effects are
visualized. A user's manual is provided, which includes detailed examples (e.g. a
cohort study looking for windows of vulnerability to air pollution, a time series
study examining the linear association of air pollution with hospital admissions,
and a time series study examining the non-linear association between temperature and
mortality). The methods are described in Basagana and Barrera-Gomez (2021) <doi:10.1093/ije/dyab179>.
Author: Jose Barrera-Gomez [aut, cre] ,
Xavier Basagana [aut]
Maintainer: Jose Barrera-Gomez <jose.barrera@isglobal.org>
Diff between collin versions 0.0.3 dated 2023-09-18 and 0.0.4 dated 2023-09-19
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 10 ++++++++-- README.md |only build/partial.rdb |binary inst/doc/collin.pdf |binary 6 files changed, 16 insertions(+), 9 deletions(-)
Title: Trait Evolution on Phylogenies Using the Cauchy Process
Description: The Cauchy Process can model pulsed continuous trait evolution
on phylogenies. The likelihood is tractable, and is used for parameter
inference and ancestral trait reconstruction.
See Bastide and Didier (2023) <doi:10.1093/sysbio/syad053>.
Author: Gilles Didier [aut, cph],
Paul Bastide [aut, cre]
Maintainer: Paul Bastide <paul.bastide@cnrs.fr>
Diff between cauphy versions 1.0.0 dated 2023-09-12 and 1.0.1 dated 2023-09-19
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/densities.R | 2 +- R/fitCauchy.R | 2 +- README.md | 4 ++-- inst/WORDLIST | 1 + inst/doc/lizards.html | 4 ++-- man/fitCauchy.Rd | 2 +- man/logDensityTipsCauchy.Rd | 2 +- src/init.c | 2 +- 11 files changed, 27 insertions(+), 22 deletions(-)
Title: Comprehensive Statistical Analysis of Plant Breeding Experiments
Description: Performs statistical data analysis of various Plant Breeding experiments. Contains functions for Line by Tester analysis as per Arunachalam, V.(1974) <http://repository.ias.ac.in/89299/> and Diallel analysis as per Griffing, B. (1956) <https://www.publish.csiro.au/bi/pdf/BI9560463>.
Author: Nandan Patil [cre, aut] ,
Lakshmi R. Gangavati [aut, ctb]
Maintainer: Nandan Patil <tryanother609@gmail.com>
Diff between gpbStat versions 0.4.0 dated 2023-01-09 and 0.4.1 dated 2023-09-19
DESCRIPTION | 11 MD5 | 36 NAMESPACE | 9 R/datdti.R |only R/datrdti.R |only R/dti.R |only R/utils-pipe.R |only build/vignette.rds |binary data/datdti.rda |only data/datrdti.rda |only inst/CITATION | 53 inst/doc/dm2.html | 540 +++---- inst/doc/ltc.html | 412 ++--- inst/doc/ltcchk.html | 420 ++--- inst/doc/ltcmt.html | 720 +++++----- inst/doc/ltcs.html | 298 ++-- man/datdti.Rd |only man/datrdti.Rd |only man/dti.Rd |only man/pipe.Rd |only tests/testthat.R | 8 tests/testthat/test-on-attach.R | 6 vignettes/rsconnect/documents/dm2.Rmd/rpubs.com/rpubs/Document.dcf | 22 vignettes/rsconnect/documents/ltcmt.Rmd/rpubs.com/rpubs/Document.dcf | 22 24 files changed, 1270 insertions(+), 1287 deletions(-)
Title: R2 Statistic
Description: R2 statistic for significance test. Variance and covariance of R2 values used to assess the 95% CI and p-value of the R2 difference.
Author: Hong Lee [aut, cph],
Moksedul Momin [aut, cre, cph]
Maintainer: Moksedul Momin <cvasu.momin@gmail.com>
Diff between r2redux versions 1.0.15 dated 2023-09-01 and 1.0.16 dated 2023-09-19
DESCRIPTION | 6 MD5 | 8 R/r2_diff2.r | 452 ++++++++++++++++++++++++++++-------------- man/r2_diff.Rd | 182 +++++++++++++++- tests/testthat/test-r2redux.R | 6 5 files changed, 484 insertions(+), 170 deletions(-)
Title: R Functions for Generalized Simulated Annealing
Description: Performs search for global minimum of a very complex non-linear
objective function with a very large number of optima.
Author: Sylvain Gubian, Yang Xiang, Brian Suomela, Julia Hoeng, PMP SA.
Maintainer: Sylvain Gubian <DL.RSupport@pmi.com>
Diff between GenSA versions 1.1.10 dated 2023-09-14 and 1.1.10.1 dated 2023-09-19
GenSA-1.1.10.1/GenSA/DESCRIPTION | 6 +++--- GenSA-1.1.10.1/GenSA/MD5 | 7 +++---- GenSA-1.1.10.1/GenSA/src/Utils.cpp | 1 - GenSA-1.1.10.1/GenSA/src/Utils.h | 3 ++- GenSA-1.1.10/GenSA/src/Linpack.h |only 5 files changed, 8 insertions(+), 9 deletions(-)
Title: Utilities for Fude Polygon
Description: Provides utilities to facilitate handling of Fude Polygon data
downloadable from the Ministry of Agriculture, Forestry and Fisheries
website <https://open.fude.maff.go.jp>.
Author: Takeshi Nishimura [aut, cph, cre]
Maintainer: Takeshi Nishimura <takenishi@gmail.com>
Diff between fude versions 0.3.3 dated 2023-08-18 and 0.3.4 dated 2023-09-19
fude-0.3.3/fude/man/figures/README-ja-nishiuwa-1.png |only fude-0.3.4/fude/DESCRIPTION | 6 - fude-0.3.4/fude/MD5 | 14 +- fude-0.3.4/fude/NEWS.md | 4 fude-0.3.4/fude/R/combine_fude.R | 28 +++++ fude-0.3.4/fude/README.md | 49 ++++++---- fude-0.3.4/fude/man/figures/README-gogoshima-1.png |binary fude-0.3.4/fude/man/figures/README-gogoshima_with_minimap-1.png |binary fude-0.3.4/fude/man/figures/README-nosplit_gogoshima-1.png |only 9 files changed, 75 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-15 0.1.6
2020-07-15 0.1.5
2020-05-31 0.1.4
2020-04-03 0.1.3
2019-11-21 0.1.2
2019-03-23 0.1.1
2019-03-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-13 1.1.0
2019-04-24 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-31 0.1.1
2022-10-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-18 0.2.6
2023-03-23 0.2.5
2022-07-01 0.2.4
2022-06-22 0.2.3
2022-04-28 0.2.2
2021-10-19 0.2.1
2021-07-28 0.2.0
2019-11-28 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-25 6.1
2020-06-24 6.0
2019-11-24 5.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-15 0.4
2012-11-05 0.3
2008-07-30 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-26 0.7-15
2018-06-27 0.7-14
2018-03-19 0.7-13
2014-08-30 0.7-12
2013-12-16 0.7-11
2013-02-13 0.7-10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-07-07 0.3-1.2
2009-02-23 0.2-1.1
2007-05-29 0.2-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-26 1.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-03 0.7-11
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. The central algorithm is
Fisher scoring and iterative reweighted least squares.
At the heart of this package are the vector generalized linear
and additive model (VGLM/VGAM) classes. VGLMs can be loosely
thought of as multivariate GLMs. VGAMs are data-driven
VGLMs that use smoothing. The book "Vector Generalized
Linear and Additive Models: With an Implementation in R"
(Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of
the statistical framework and the package. Currently only
fixed-effects models are implemented. Many (100+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE. The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CA [...truncated...]
Author: Thomas Yee [aut, cre] ,
Cleve Moler [ctb]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 1.1-8 dated 2023-03-09 and 1.1-9 dated 2023-09-19
VGAM-1.1-8/VGAM/man/bigamma.mckay.Rd |only VGAM-1.1-8/VGAM/man/gaitzetaUC.Rd |only VGAM-1.1-9/VGAM/DESCRIPTION | 8 VGAM-1.1-9/VGAM/MD5 | 241 +++--- VGAM-1.1-9/VGAM/NAMESPACE | 11 VGAM-1.1-9/VGAM/NEWS | 43 + VGAM-1.1-9/VGAM/R/aamethods.q | 68 - VGAM-1.1-9/VGAM/R/cqo.fit.q | 4 VGAM-1.1-9/VGAM/R/family.bivariate.R | 861 ++++++++++++---------- VGAM-1.1-9/VGAM/R/family.categorical.R | 848 ++++++++++++++------- VGAM-1.1-9/VGAM/R/family.extremes.R | 1041 +++++++++++++++++---------- VGAM-1.1-9/VGAM/R/family.gaitd.R | 111 ++ VGAM-1.1-9/VGAM/R/family.positive.R | 230 +++-- VGAM-1.1-9/VGAM/R/family.univariate.R | 14 VGAM-1.1-9/VGAM/R/family.zeroinf.R | 700 ++++++++++-------- VGAM-1.1-9/VGAM/R/hdeff.R | 161 +++- VGAM-1.1-9/VGAM/R/links.q | 306 ++++--- VGAM-1.1-9/VGAM/R/mux.q | 267 ++++-- VGAM-1.1-9/VGAM/R/rrvglm.fit.q | 16 VGAM-1.1-9/VGAM/R/vgam.fit.q | 11 VGAM-1.1-9/VGAM/R/vglm.fit.q | 15 VGAM-1.1-9/VGAM/R/wald0.R | 5 VGAM-1.1-9/VGAM/build/partial.rdb |binary VGAM-1.1-9/VGAM/data/Huggins89.t1.rda |binary VGAM-1.1-9/VGAM/data/Huggins89table1.rda |binary VGAM-1.1-9/VGAM/data/alclevels.rda |binary VGAM-1.1-9/VGAM/data/alcoff.rda |binary VGAM-1.1-9/VGAM/data/auuc.rda |binary VGAM-1.1-9/VGAM/data/backPain.rda |binary VGAM-1.1-9/VGAM/data/backPain2.rda |binary VGAM-1.1-9/VGAM/data/beggs.rda |binary VGAM-1.1-9/VGAM/data/budworm.rda |binary VGAM-1.1-9/VGAM/data/car.all.rda |binary VGAM-1.1-9/VGAM/data/cfibrosis.rda |binary VGAM-1.1-9/VGAM/data/corbet.rda |binary VGAM-1.1-9/VGAM/data/crashbc.rda |binary VGAM-1.1-9/VGAM/data/crashf.rda |binary VGAM-1.1-9/VGAM/data/crashi.rda |binary VGAM-1.1-9/VGAM/data/crashmc.rda |binary VGAM-1.1-9/VGAM/data/crashp.rda |binary VGAM-1.1-9/VGAM/data/crashtr.rda |binary VGAM-1.1-9/VGAM/data/deermice.rda |binary VGAM-1.1-9/VGAM/data/ducklings.rda |binary VGAM-1.1-9/VGAM/data/finney44.rda |binary VGAM-1.1-9/VGAM/data/flourbeetle.rda |binary VGAM-1.1-9/VGAM/data/hspider.rda |binary VGAM-1.1-9/VGAM/data/lakeO.rda |binary VGAM-1.1-9/VGAM/data/leukemia.rda |binary VGAM-1.1-9/VGAM/data/lpossums.rda |binary VGAM-1.1-9/VGAM/data/marital.nz.rda |binary VGAM-1.1-9/VGAM/data/melbmaxtemp.rda |binary VGAM-1.1-9/VGAM/data/pneumo.rda |binary VGAM-1.1-9/VGAM/data/prinia.rda |binary VGAM-1.1-9/VGAM/data/ruge.rda |binary VGAM-1.1-9/VGAM/data/toxop.rda |binary VGAM-1.1-9/VGAM/data/venice.rda |binary VGAM-1.1-9/VGAM/data/venice90.rda |binary VGAM-1.1-9/VGAM/data/wine.rda |binary VGAM-1.1-9/VGAM/man/CommonVGAMffArguments.Rd | 45 + VGAM-1.1-9/VGAM/man/Huggins89.t1.Rd | 57 - VGAM-1.1-9/VGAM/man/Influence.Rd | 19 VGAM-1.1-9/VGAM/man/Trunc.Rd | 13 VGAM-1.1-9/VGAM/man/VGAM-package.Rd | 27 VGAM-1.1-9/VGAM/man/acat.Rd | 6 VGAM-1.1-9/VGAM/man/alteredvglm.Rd | 23 VGAM-1.1-9/VGAM/man/betaII.Rd | 2 VGAM-1.1-9/VGAM/man/cao.Rd | 228 +++-- VGAM-1.1-9/VGAM/man/cao.control.Rd | 137 +-- VGAM-1.1-9/VGAM/man/cardUC.Rd | 16 VGAM-1.1-9/VGAM/man/cardioid.Rd | 25 VGAM-1.1-9/VGAM/man/cauchitlink.Rd | 36 VGAM-1.1-9/VGAM/man/cauchy.Rd | 36 VGAM-1.1-9/VGAM/man/cdf.lmscreg.Rd | 29 VGAM-1.1-9/VGAM/man/cens.gumbel.Rd | 80 +- VGAM-1.1-9/VGAM/man/confintvglm.Rd | 13 VGAM-1.1-9/VGAM/man/cops.Rd |only VGAM-1.1-9/VGAM/man/cratio.Rd | 6 VGAM-1.1-9/VGAM/man/cumulative.Rd | 65 + VGAM-1.1-9/VGAM/man/dagum.Rd | 3 VGAM-1.1-9/VGAM/man/gaitdbinomUC.Rd | 28 VGAM-1.1-9/VGAM/man/gaitdlog.Rd | 74 + VGAM-1.1-9/VGAM/man/gaitdlogUC.Rd | 55 - VGAM-1.1-9/VGAM/man/gaitdnbinomUC.Rd | 27 VGAM-1.1-9/VGAM/man/gaitdnbinomial.Rd | 13 VGAM-1.1-9/VGAM/man/gaitdpoisUC.Rd | 97 ++ VGAM-1.1-9/VGAM/man/gaitdpoisson.Rd | 187 ++-- VGAM-1.1-9/VGAM/man/gaitdzeta.Rd | 75 + VGAM-1.1-9/VGAM/man/gaitdzetaUC.Rd |only VGAM-1.1-9/VGAM/man/gamma1.Rd | 3 VGAM-1.1-9/VGAM/man/gamma2.Rd | 4 VGAM-1.1-9/VGAM/man/gammaR.Rd | 4 VGAM-1.1-9/VGAM/man/gammaff.mm.Rd |only VGAM-1.1-9/VGAM/man/gompertz.Rd | 9 VGAM-1.1-9/VGAM/man/hdeff.Rd | 20 VGAM-1.1-9/VGAM/man/hdeffsev.Rd | 17 VGAM-1.1-9/VGAM/man/hurea.Rd |only VGAM-1.1-9/VGAM/man/hureaUC.Rd |only VGAM-1.1-9/VGAM/man/multinomial.Rd | 76 - VGAM-1.1-9/VGAM/man/nakagami.Rd | 6 VGAM-1.1-9/VGAM/man/nbcanlink.Rd | 157 ++-- VGAM-1.1-9/VGAM/man/negbinomial.Rd | 58 - VGAM-1.1-9/VGAM/man/notdocumentedyet.Rd | 6 VGAM-1.1-9/VGAM/man/posnegbinomial.Rd | 9 VGAM-1.1-9/VGAM/man/profilevglm.Rd | 27 VGAM-1.1-9/VGAM/man/propodds.Rd | 11 VGAM-1.1-9/VGAM/man/specialsvglm.Rd | 10 VGAM-1.1-9/VGAM/man/sratio.Rd | 6 VGAM-1.1-9/VGAM/man/triangle.Rd | 4 VGAM-1.1-9/VGAM/man/trinormal.Rd | 34 VGAM-1.1-9/VGAM/man/trinormalUC.Rd | 6 VGAM-1.1-9/VGAM/man/vcovvlm.Rd | 3 VGAM-1.1-9/VGAM/man/vglm.Rd | 1 VGAM-1.1-9/VGAM/man/vglmff-class.Rd | 11 VGAM-1.1-9/VGAM/man/vonmises.Rd | 9 VGAM-1.1-9/VGAM/man/vplot.profile.Rd | 13 VGAM-1.1-9/VGAM/src/VGAM_init.c | 2 VGAM-1.1-9/VGAM/src/lms.f | 7 VGAM-1.1-9/VGAM/src/muxr3.c | 166 ++-- VGAM-1.1-9/VGAM/src/rgam.f | 34 VGAM-1.1-9/VGAM/src/tyeepolygamma.f | 3 VGAM-1.1-9/VGAM/src/vgam.f | 252 +++--- VGAM-1.1-9/VGAM/src/vlinpack1.f | 7 VGAM-1.1-9/VGAM/src/vlinpack2.f | 120 --- VGAM-1.1-9/VGAM/src/vlinpack3.f | 229 ----- VGAM-1.1-9/VGAM/src/vmux.f | 76 + 125 files changed, 4672 insertions(+), 3111 deletions(-)
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija (2019)
<doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9>
for more details.
Author: Christoph Hafemeister [aut] ,
Saket Choudhary [aut, cre] ,
Rahul Satija [ctb]
Maintainer: Saket Choudhary <schoudhary@nygenome.org>
Diff between sctransform versions 0.3.5 dated 2022-09-21 and 0.4.0 dated 2023-09-19
sctransform-0.3.5/sctransform/man/get_nz_median.Rd |only sctransform-0.4.0/sctransform/DESCRIPTION | 14 - sctransform-0.4.0/sctransform/MD5 | 29 +--- sctransform-0.4.0/sctransform/NEWS.md | 15 ++ sctransform-0.4.0/sctransform/R/denoise.R | 12 + sctransform-0.4.0/sctransform/R/fit.R | 101 ++++++++++++-- sctransform-0.4.0/sctransform/R/utils.R | 42 ++--- sctransform-0.4.0/sctransform/R/vst.R | 58 ++++++-- sctransform-0.4.0/sctransform/README.md | 3 sctransform-0.4.0/sctransform/build/partial.rdb |binary sctransform-0.4.0/sctransform/inst/CITATION | 14 + sctransform-0.4.0/sctransform/man/get_nz_median2.Rd | 5 sctransform-0.4.0/sctransform/src/Makevars | 2 sctransform-0.4.0/sctransform/src/Makevars.win | 2 sctransform-0.4.0/sctransform/src/utils.cpp | 11 - sctransform-0.4.0/sctransform/tests/testthat/test_utils.R | 33 ++++ 16 files changed, 250 insertions(+), 91 deletions(-)
Title: R Interface to 'Quarto' Markdown Publishing System
Description: Convert R Markdown documents and 'Jupyter' notebooks to a variety of
output formats using 'Quarto'.
Author: JJ Allaire [aut, cre]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between quarto versions 1.2 dated 2022-07-06 and 1.3 dated 2023-09-19
quarto-1.2/quarto/man/quarto_run.Rd |only quarto-1.2/quarto/tests/testthat/project/project.html |only quarto-1.2/quarto/tests/testthat/project/project_files |only quarto-1.2/quarto/tests/testthat/test.html |only quarto-1.3/quarto/DESCRIPTION | 11 quarto-1.3/quarto/MD5 | 49 +--- quarto-1.3/quarto/NAMESPACE | 2 quarto-1.3/quarto/R/preview.R | 2 quarto-1.3/quarto/R/publish.R | 15 - quarto-1.3/quarto/R/quarto.R | 4 quarto-1.3/quarto/R/render.R | 4 quarto-1.3/quarto/R/run.R | 18 - quarto-1.3/quarto/README.md | 2 quarto-1.3/quarto/build/vignette.rds |binary quarto-1.3/quarto/inst/doc/publishing.Rmd | 16 - quarto-1.3/quarto/inst/doc/publishing.html | 190 ++++++++--------- quarto-1.3/quarto/man/quarto_preview.Rd | 2 quarto-1.3/quarto/man/quarto_publish_doc.Rd | 12 - quarto-1.3/quarto/man/quarto_render.Rd | 2 quarto-1.3/quarto/man/quarto_serve.Rd |only quarto-1.3/quarto/tests/testthat/test-render.R | 2 quarto-1.3/quarto/vignettes/publishing.Rmd | 16 - 22 files changed, 170 insertions(+), 177 deletions(-)
Title: Phylogenetic Structural Equation Model
Description: Applies phylogenetic comparative methods (PCM) and phylogenetic trait imputation using
structural equation models (SEM), extending methods from Thorson et al. (2023) <doi:10.1111/2041-210X.14076>.
This implementation includes a minimal set of features, to
allow users to easily read all of the documentation and source code. PCM using SEM
includes phylogenetic linear models and structural equation models as nested submodels,
but also allows imputation of missing values. Features and comparison with other packages
are described in Thorson and van der Bijl (In revisions).
Author: James Thorson [aut, cre] ,
Wouter van der Bijl [ctb]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Diff between phylosem versions 1.0.0 dated 2023-08-25 and 1.0.1 dated 2023-09-19
phylosem-1.0.0/phylosem/inst/doc/comparison.html |only phylosem-1.0.0/phylosem/inst/doc/demonstration.html |only phylosem-1.0.0/phylosem/inst/doc/phylopath.html |only phylosem-1.0.1/phylosem/DESCRIPTION | 13 +++++---- phylosem-1.0.1/phylosem/MD5 | 26 ++++++++++--------- phylosem-1.0.1/phylosem/R/phylosem.R | 23 ++++------------ phylosem-1.0.1/phylosem/README.md | 2 + phylosem-1.0.1/phylosem/build/vignette.rds |binary phylosem-1.0.1/phylosem/inst/CITATION |only phylosem-1.0.1/phylosem/inst/doc/comparison.R | 22 ++++++++-------- phylosem-1.0.1/phylosem/inst/doc/comparison.pdf |only phylosem-1.0.1/phylosem/inst/doc/demonstration.R | 8 ++--- phylosem-1.0.1/phylosem/inst/doc/demonstration.pdf |only phylosem-1.0.1/phylosem/inst/doc/phylopath.R | 8 ++--- phylosem-1.0.1/phylosem/inst/doc/phylopath.pdf |only phylosem-1.0.1/phylosem/man/phylosem.Rd | 23 ++++------------ phylosem-1.0.1/phylosem/vignettes/comparison.html |only phylosem-1.0.1/phylosem/vignettes/demonstration.html |only phylosem-1.0.1/phylosem/vignettes/phylopath.html |only 19 files changed, 55 insertions(+), 70 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-31 1.1.4
2020-10-09 1.1.2.1
2020-10-08 1.1.2
2020-05-25 1.1.1
2020-05-21 1.1.0
2020-03-28 1.0.4
2020-03-26 1.0.3
2019-09-26 1.0.2
2019-06-11 1.0.1
2019-03-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-08 0.1.0
2022-06-30 0.0.14
2022-04-20 0.0.12
2021-06-04 0.0.11
2020-03-13 0.0.10
2019-06-17 0.0.9
2019-06-13 0.0.8
2019-05-05 0.0.6
2019-03-28 0.0.5
2019-03-15 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-26 0.0.4-0
2022-05-10 0.0.3-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-21 2.1.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-04 4.1.10
2022-11-30 4.1.9
2022-03-27 4.1.8
2022-03-21 4.1.6
2022-03-17 4.1.5
2021-07-27 4.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-29 0.0.4
2021-12-10 0.0.3