Title: Optimally Robust Estimation for Extreme Value Distributions
Description: Optimally robust estimation for extreme value distributions using S4 classes and
methods (based on packages 'distr', 'distrEx', 'distrMod', 'RobAStBase', and
'ROptEst'); the underlying theoretic results can be found in Ruckdeschel and
Horbenko, (2013 and 2012), \doi{10.1080/02331888.2011.628022} and
\doi{10.1007/s00184-011-0366-4}.
Author: Nataliya Horbenko [aut, cph],
Bernhard Spangl [ctb] ,
Sascha Desmettre [ctb] ,
Eugen Massini [ctb] ,
Daria Pupashenko [ctb] ,
Gerald Kroisandt [ctb] ,
Matthias Kohl [aut, cph] ,
Peter Ruckdeschel [cre, aut, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between RobExtremes versions 1.3.1 dated 2024-09-04 and 1.3.2 dated 2025-01-15
RobExtremes-1.3.1/RobExtremes/tests |only RobExtremes-1.3.2/RobExtremes/DESCRIPTION | 18 +++++++------- RobExtremes-1.3.2/RobExtremes/MD5 | 8 ++---- RobExtremes-1.3.2/RobExtremes/inst/NEWS | 7 +++++ RobExtremes-1.3.2/RobExtremes/man/0RobExtremes-package.Rd | 8 +++--- 5 files changed, 23 insertions(+), 18 deletions(-)
Title: Interpolation Grids for Packages of the 'RobASt' - Family of
Packages
Description: Includes 'sysdata.rda' file for packages of the 'RobASt' - family of packages; is
currently used by package 'RobExtremes' only.
Author: Matthias Kohl [aut, cph],
Bernhard Spangl [ctb] ,
Sascha Desmettre [ctb] ,
Eugen Massini [ctb] ,
Mykhailo Pupashenko [ctb] ,
Daria Pupashenko [ctb] ,
Gerald Kroisandt [ctb] ,
Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between RobAStRDA versions 1.2.1 dated 2024-01-29 and 1.2.2 dated 2025-01-15
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- R/sysdata.rda |binary inst/CITATION | 4 ++-- inst/NEWS | 16 ++++++++++++++++ man/0RobRDA-package.Rd | 13 ++++--------- 6 files changed, 35 insertions(+), 24 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between performance versions 0.12.4 dated 2024-10-18 and 0.13.0 dated 2025-01-15
DESCRIPTION | 28 ++-- MD5 | 173 +++++++++++++-------------- NAMESPACE | 7 - NEWS.md | 34 +++++ R/binned_residuals.R | 5 R/check_autocorrelation.R | 2 R/check_clusterstructure.R | 3 R/check_collinearity.R | 52 ++++---- R/check_concurvity.R | 1 R/check_convergence.R | 5 R/check_dag.R | 2 R/check_distribution.R | 9 - R/check_factorstructure.R | 7 - R/check_heterogeneity_bias.R | 11 - R/check_heteroscedasticity.R | 9 - R/check_homogeneity.R | 10 - R/check_htest.R | 1 R/check_itemscale.R | 4 R/check_model.R | 122 +++++++++---------- R/check_model_diagnostics.R | 33 +---- R/check_multimodal.R | 1 R/check_normality.R | 7 - R/check_outliers.R | 155 +++++++++--------------- R/check_overdispersion.R | 5 R/check_predictions.R | 38 ++--- R/check_singularity.R | 6 R/check_sphericity.R | 3 R/compare_performance.R | 2 R/cronbachs_alpha.R | 3 R/icc.R | 3 R/item_difficulty.R | 1 R/looic.R | 1 R/model_performance.R | 1 R/model_performance.bayesian.R | 1 R/model_performance.lavaan.R | 1 R/model_performance.lm.R | 5 R/model_performance.mixed.R | 1 R/model_performance_default.R | 1 R/performance_accuracy.R | 1 R/performance_aicc.R | 77 ++---------- R/performance_hosmer.R | 1 R/performance_logloss.R | 1 R/performance_mae.R | 3 R/performance_mse.R | 3 R/performance_pcp.R | 2 R/performance_roc.R | 39 ++++-- R/performance_score.R | 3 R/print-methods.R | 5 R/r2.R | 47 ++----- R/r2_bayes.R | 3 R/r2_coxsnell.R | 18 +- R/r2_loo.R | 1 R/r2_mcfadden.R | 24 +-- R/r2_nagelkerke.R | 9 - R/r2_nakagawa.R | 2 R/simulate_residuals.R | 7 - R/test_bf.R | 2 R/test_likelihoodratio.R | 2 R/test_performance.R | 7 - R/test_vuong.R | 10 - R/test_wald.R | 1 build/partial.rdb |binary man/binned_residuals.Rd | 7 - man/check_collinearity.Rd | 18 ++ man/check_dag.Rd | 2 man/check_distribution.Rd | 4 man/check_heterogeneity_bias.Rd | 10 - man/check_heteroscedasticity.Rd | 8 - man/check_homogeneity.Rd | 8 - man/check_model.Rd | 22 ++- man/check_normality.Rd | 2 man/check_outliers.Rd | 6 man/check_predictions.Rd | 14 +- man/performance-package.Rd | 12 - man/performance_aicc.Rd | 10 + man/performance_roc.Rd | 19 ++ tests/testthat/_snaps/compare_performance.md |only tests/testthat/_snaps/pkg-ivreg.md | 10 + tests/testthat/test-check_collinearity.R | 23 +++ tests/testthat/test-check_model.R | 4 tests/testthat/test-check_outliers.R | 17 ++ tests/testthat/test-check_overdispersion.R | 2 tests/testthat/test-check_residuals.R | 8 - tests/testthat/test-check_zeroinflation.R | 22 +-- tests/testthat/test-compare_performance.R | 7 + tests/testthat/test-performance_roc.R | 23 +++ tests/testthat/test-pkg-fixest.R | 1 tests/testthat/test-r2_mcfadden.R | 42 ++++++ 88 files changed, 645 insertions(+), 677 deletions(-)
Title: Reading and Writing Open Data Format Files
Description: The Open Data Format (ODF) is a new, non-proprietary, multilingual, metadata enriched, and zip-compressed data format with metadata structured in the Data Documentation Initiative (DDI) Codebook standard. This package allows reading and writing of data files in the Open Data Format (ODF) in R, and displaying metadata in different languages. For further information on the Open Data Format, see <https://opendataformat.github.io/>.
Author: Tom Hartl [aut, cre] ,
Claudia Saalbach [ctb]
Maintainer: Tom Hartl <thartl@diw.de>
Diff between opendataformat versions 2.1.1 dated 2024-12-04 and 2.1.2 dated 2025-01-15
opendataformat-2.1.1/opendataformat/data/data_odf.rda |only opendataformat-2.1.1/opendataformat/man/merge.odf.Rd |only opendataformat-2.1.1/opendataformat/vignettes/opendataformat-tom-D15S-2.html |only opendataformat-2.1.1/opendataformat/vignettes/opendataformat-tom-D15S.html |only opendataformat-2.1.2/opendataformat/DESCRIPTION | 10 opendataformat-2.1.2/opendataformat/MD5 | 43 opendataformat-2.1.2/opendataformat/NAMESPACE | 3 opendataformat-2.1.2/opendataformat/R/as_odf_tbl.R |only opendataformat-2.1.2/opendataformat/R/docu_odf.R | 22 opendataformat-2.1.2/opendataformat/R/merge.R | 37 opendataformat-2.1.2/opendataformat/R/opendataformat-package.R | 9 opendataformat-2.1.2/opendataformat/R/read_odf.R | 29 opendataformat-2.1.2/opendataformat/data/data_odf.RData |only opendataformat-2.1.2/opendataformat/inst/doc/opendataformat.R | 29 opendataformat-2.1.2/opendataformat/inst/doc/opendataformat.Rmd | 40 opendataformat-2.1.2/opendataformat/inst/doc/opendataformat.html | 449 +++++----- opendataformat-2.1.2/opendataformat/man/as_odf_tbl.Rd |only opendataformat-2.1.2/opendataformat/man/merge.odf_tbl.Rd |only opendataformat-2.1.2/opendataformat/man/opendataformat-package.Rd | 13 opendataformat-2.1.2/opendataformat/man/read_odf.Rd | 17 opendataformat-2.1.2/opendataformat/tests/testthat/test-as_odf_tbl.R |only opendataformat-2.1.2/opendataformat/tests/testthat/test-docu_odf.R | 4 opendataformat-2.1.2/opendataformat/tests/testthat/test-read_odf.R | 20 opendataformat-2.1.2/opendataformat/tests/testthat/testdata/data_odf.RData |binary opendataformat-2.1.2/opendataformat/tests/testthat/testdata/data_odf_with_default.RData |binary opendataformat-2.1.2/opendataformat/tests/testthat/testdata/data_odf_with_missings.RData |binary opendataformat-2.1.2/opendataformat/vignettes/opendataformat.Rmd | 40 27 files changed, 485 insertions(+), 280 deletions(-)
More information about opendataformat at CRAN
Permanent link
Title: Nicely Formatted Contingency Tables and Frequency Tables
Description: Nicely formatted frequency tables and contingency tables (1-way, 2-way, 3-way and 4-way tables), that can easily be exported to HTML or 'Office' documents. Designed to work with pipes.
Author: Mans Thulin [aut, cre],
Kajsa Grind [aut],
Stefan Furne [aut]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Diff between ivo.table versions 0.5 dated 2024-08-28 and 0.6 dated 2025-01-15
DESCRIPTION | 10 ++++-- MD5 | 19 ++++++++----- NEWS.md | 3 ++ R/ivo_tables.R | 65 ++++++++++++++++++++++++--------------------- build |only inst/doc |only man/ivo_flextable_theme.Rd | 5 ++- man/ivo_table.Rd | 4 ++ man/ivo_table_add_mask.Rd | 2 - man/ivo_table_masked.Rd | 3 ++ vignettes |only 11 files changed, 68 insertions(+), 43 deletions(-)
Title: Tidy and Geospatial Kernel Smoothing
Description: Extensions of the kernel smoothing functions from the 'ks' package for compatibility with the tidyverse and geospatial ecosystems <doi:10.1007/s00180-024-01543-9>.
Author: Tarn Duong [aut, cre]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between eks versions 1.0.6 dated 2024-11-29 and 1.0.7 dated 2025-01-15
CHANGELOG | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/sf-ks-prelim.R | 27 +++++++++++++++++---------- R/sf-ks.R | 2 ++ R/tidy-ks-prelim.R | 5 +++-- R/tidy-ks.R | 1 + inst/doc/tidysf_kde.html | 4 ++-- 9 files changed, 42 insertions(+), 27 deletions(-)
Title: Utility Functions and Development Tools for the Admiral Package
Family
Description: Utility functions to check data, variables and conditions for
functions used in 'admiral' and 'admiral' extension packages.
Additional utility helper functions to assist developers with
maintaining documentation, testing and general upkeep of 'admiral' and
'admiral' extension packages.
Author: Ben Straub [aut, cre],
Stefan Bundfuss [aut] ,
Jeffrey Dickinson [aut],
Ross Farrugia [aut],
Fanny Gautier [aut],
Edoardo Mancini [aut] ,
Sadchla Mascary [aut],
Gordon Miller [aut],
Daniel Sjoberg [aut] ,
Stefan Thoma [aut] ,
Kangjie Zhang [aut],
Zel [...truncated...]
Maintainer: Ben Straub <ben.x.straub@gsk.com>
Diff between admiraldev versions 1.1.0 dated 2024-06-06 and 1.2.0 dated 2025-01-15
admiraldev-1.1.0/admiraldev/man/assert_function_param.Rd |only admiraldev-1.1.0/admiraldev/man/assert_has_variables.Rd |only admiraldev-1.1.0/admiraldev/man/assert_named_exprs.Rd |only admiraldev-1.2.0/admiraldev/DESCRIPTION | 51 - admiraldev-1.2.0/admiraldev/MD5 | 53 - admiraldev-1.2.0/admiraldev/NAMESPACE | 6 admiraldev-1.2.0/admiraldev/NEWS.md | 49 admiraldev-1.2.0/admiraldev/R/admiraldev-package.R | 4 admiraldev-1.2.0/admiraldev/R/assertions.R | 213 ++-- admiraldev-1.2.0/admiraldev/R/dev_utilities.R | 14 admiraldev-1.2.0/admiraldev/R/get.R | 12 admiraldev-1.2.0/admiraldev/R/lifecycle_admiral.R |only admiraldev-1.2.0/admiraldev/R/quo.R | 12 admiraldev-1.2.0/admiraldev/README.md | 4 admiraldev-1.2.0/admiraldev/inst/WORDLIST | 20 admiraldev-1.2.0/admiraldev/inst/doc/package_extensions.html | 2 admiraldev-1.2.0/admiraldev/inst/doc/rcmd_issues.Rmd | 6 admiraldev-1.2.0/admiraldev/inst/doc/rcmd_issues.html | 8 admiraldev-1.2.0/admiraldev/man/admiraldev-package.Rd | 15 admiraldev-1.2.0/admiraldev/man/assert_list_element.Rd | 41 admiraldev-1.2.0/admiraldev/man/assert_numeric_vector.Rd | 11 admiraldev-1.2.0/admiraldev/man/assert_unit.Rd | 44 admiraldev-1.2.0/admiraldev/man/deprecate_inform.Rd |only admiraldev-1.2.0/admiraldev/man/get_source_vars.Rd | 4 admiraldev-1.2.0/admiraldev/man/replace_values_by_names.Rd | 4 admiraldev-1.2.0/admiraldev/man/vars2chr.Rd | 6 admiraldev-1.2.0/admiraldev/tests/testthat/_snaps/assertions.md | 114 +- admiraldev-1.2.0/admiraldev/tests/testthat/_snaps/lifecycle_admiral.md |only admiraldev-1.2.0/admiraldev/tests/testthat/test-assertions.R | 510 ++++------ admiraldev-1.2.0/admiraldev/tests/testthat/test-lifecycle_admiral.R |only admiraldev-1.2.0/admiraldev/vignettes/rcmd_issues.Rmd | 6 31 files changed, 673 insertions(+), 536 deletions(-)
Title: 'Rcpp' Bindings for the 'fast_float' Header-Only Library for
Number Parsing
Description: Converting ascii text into (floating-point) numeric values is a
very common problem. The 'fast_float' header-only C++ library by Daniel Lemire
does it very well and very fast at up to or over to 1 gigabyte per second as
described in more detail in <doi:10.1002/spe.2984>. 'fast_float' is
licensed under the Apache 2.0 license and provided here for use by other R
packages via a simple 'LinkingTo:' statement.
Author: Dirk Eddelbuettel [aut, cre] ,
Brendan Knapp [aut] ,
Daniel Lemire [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppFastFloat versions 0.0.4 dated 2023-01-20 and 0.0.5 dated 2025-01-15
RcppFastFloat-0.0.4/RcppFastFloat/inst/include/fast_float/simple_decimal_conversion.h |only RcppFastFloat-0.0.5/RcppFastFloat/ChangeLog | 28 RcppFastFloat-0.0.5/RcppFastFloat/DESCRIPTION | 26 RcppFastFloat-0.0.5/RcppFastFloat/MD5 | 28 RcppFastFloat-0.0.5/RcppFastFloat/README.md | 2 RcppFastFloat-0.0.5/RcppFastFloat/inst/NEWS.Rd | 9 RcppFastFloat-0.0.5/RcppFastFloat/inst/include/fast_float/ascii_number.h | 522 +++ RcppFastFloat-0.0.5/RcppFastFloat/inst/include/fast_float/bigint.h | 264 + RcppFastFloat-0.0.5/RcppFastFloat/inst/include/fast_float/constexpr_feature_detect.h |only RcppFastFloat-0.0.5/RcppFastFloat/inst/include/fast_float/decimal_to_binary.h | 141 - RcppFastFloat-0.0.5/RcppFastFloat/inst/include/fast_float/digit_comparison.h | 206 - RcppFastFloat-0.0.5/RcppFastFloat/inst/include/fast_float/fast_float.h | 86 RcppFastFloat-0.0.5/RcppFastFloat/inst/include/fast_float/fast_table.h | 1327 +++++----- RcppFastFloat-0.0.5/RcppFastFloat/inst/include/fast_float/float_common.h | 867 +++++- RcppFastFloat-0.0.5/RcppFastFloat/inst/include/fast_float/parse_number.h | 395 ++ RcppFastFloat-0.0.5/RcppFastFloat/src/Makevars | 4 16 files changed, 2542 insertions(+), 1363 deletions(-)
Title: Fast and Efficient Processing of PAM Data
Description: Processing Chlorophyll Fluorescence & P700 Absorbance data generated by WALZ hardware. Four models are provided for the regression of Pi curves, which can be compared with each other in order to select the most suitable model for the data set. Control plots ensure the successful verification of each regression. Bundled output of alpha, ETRmax, Ik etc. enables fast and reliable further processing of the data.
Author: Julien Boehm [cre, aut] ,
Philipp Schrag [aut]
Maintainer: Julien Boehm <julien.boehm@uni-rostock.de>
Diff between pam versions 1.0.0 dated 2025-01-14 and 1.0.1 dated 2025-01-15
DESCRIPTION | 6 - MD5 | 29 +++--- build/partial.rdb |binary inst/CITATION |only tests/testthat/Rplots.pdf |binary tests/testthat/test-compare_regression_models_etr_I.R | 27 ++++-- tests/testthat/test-compare_regression_models_etr_II.R | 28 ++++-- tests/testthat/test-compare_regression_models_total.R | 71 +++++++++++----- tests/testthat/test-eilers_peeters_etr_I.R | 72 ++++++++++------- tests/testthat/test-eilers_peeters_etr_II.R | 70 ++++++++++------ tests/testthat/test-platt_etr_I.R | 70 ++++++++++------ tests/testthat/test-platt_etr_II.R | 70 ++++++++++------ tests/testthat/test-vollenweider_etr_I.R | 69 +++++++++------- tests/testthat/test-vollenweider_etr_II.R | 70 ++++++++++------ tests/testthat/test-walsby_etr_I.R | 60 ++++++++------ tests/testthat/test-walsby_etr_II.R | 60 ++++++++------ 16 files changed, 434 insertions(+), 268 deletions(-)
Title: Analysis of MHC Data in Non-Model Species
Description: Fifteen tools for bioinformatics processing and analysis of major
histocompatibility complex (MHC) data. The functions are tailored for amplicon data
sets that have been filtered using the dada2 method (for more information on
dada2, visit <https://benjjneb.github.io/dada2/> ), but even other types of data
sets can be analyzed.
The ReplMatch() function matches replicates in data sets in order to evaluate
genotyping success.
The GetReplTable() and GetReplStats() functions perform such an evaluation.
The CreateFas() function creates a fasta file with all the sequences in the data
set.
The CreateSamplesFas() function creates individual fasta files for each sample in
the data set.
The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise
comparisons of all sequences in a data set, and mean distances of all pairwise
comparisons within each sample in a data set. The function additionally outputs five
tables with physico-chemical z-descriptor values (based on S [...truncated...]
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>
Diff between MHCtools versions 1.5.3 dated 2023-07-08 and 1.5.4 dated 2025-01-15
MHCtools-1.5.3/MHCtools/R/BootKmeans_func_20210910.R |only MHCtools-1.5.3/MHCtools/R/ClusterMatch_func_20210910.R |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_10_20210913.RData |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_1_20210913.RData |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_2_20210913.RData |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_3_20210913.RData |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_4_20210913.RData |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_5_20210913.RData |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_6_20210913.RData |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_7_20210913.RData |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_8_20210913.RData |only MHCtools-1.5.3/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_9_20210913.RData |only MHCtools-1.5.4/MHCtools/DESCRIPTION | 10 - MHCtools-1.5.4/MHCtools/LICENSE | 2 MHCtools-1.5.4/MHCtools/MD5 | 92 +++++----- MHCtools-1.5.4/MHCtools/NEWS.md | 13 + MHCtools-1.5.4/MHCtools/R/BootKmeans_func_20250108.R |only MHCtools-1.5.4/MHCtools/R/ClusterMatch_func_20250108.R |only MHCtools-1.5.4/MHCtools/R/CreateFas_func_20230321.R | 9 MHCtools-1.5.4/MHCtools/R/CreateHpltOccTable_func_20221010.R | 9 MHCtools-1.5.4/MHCtools/R/CreateSamplesFas_func_20230321.R | 9 MHCtools-1.5.4/MHCtools/R/DistCalc_func_20230707.R | 20 -- MHCtools-1.5.4/MHCtools/R/GetHpltStats_func_20200915.R | 9 MHCtools-1.5.4/MHCtools/R/GetHpltTable_func_20200915.R | 9 MHCtools-1.5.4/MHCtools/R/GetReplStats_func_20200914.R | 9 MHCtools-1.5.4/MHCtools/R/GetReplTable_func_20200914.R | 9 MHCtools-1.5.4/MHCtools/R/HpltFind_func_20230321.R | 9 MHCtools-1.5.4/MHCtools/R/HpltMatch_func_20230322.R | 9 MHCtools-1.5.4/MHCtools/R/NestTablesXL_func_20221012.R | 9 MHCtools-1.5.4/MHCtools/R/PapaDiv_func_20230630.R | 9 MHCtools-1.5.4/MHCtools/R/ReplMatch_func_20230321.R | 11 - MHCtools-1.5.4/MHCtools/R/zzz.R | 4 MHCtools-1.5.4/MHCtools/README.md | 12 - MHCtools-1.5.4/MHCtools/data/k_summary_table.rda |binary MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_10_20250115.RData |only MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_1_20250115.RData |only MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_2_20250115.RData |only MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_3_20250115.RData |only MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_4_20250115.RData |only MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_5_20250115.RData |only MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_6_20250115.RData |only MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_7_20250115.RData |only MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_8_20250115.RData |only MHCtools-1.5.4/MHCtools/inst/extdata/ClusterMatch/Kclusters_model_9_20250115.RData |only MHCtools-1.5.4/MHCtools/man/BootKmeans.Rd | 22 +- MHCtools-1.5.4/MHCtools/man/ClusterMatch.Rd | 13 - MHCtools-1.5.4/MHCtools/man/CreateFas.Rd | 9 MHCtools-1.5.4/MHCtools/man/CreateHpltOccTable.Rd | 9 MHCtools-1.5.4/MHCtools/man/CreateSamplesFas.Rd | 9 MHCtools-1.5.4/MHCtools/man/DistCalc.Rd | 20 -- MHCtools-1.5.4/MHCtools/man/GetHpltStats.Rd | 9 MHCtools-1.5.4/MHCtools/man/GetHpltTable.Rd | 9 MHCtools-1.5.4/MHCtools/man/GetReplStats.Rd | 9 MHCtools-1.5.4/MHCtools/man/GetReplTable.Rd | 9 MHCtools-1.5.4/MHCtools/man/HpltFind.Rd | 9 MHCtools-1.5.4/MHCtools/man/HpltMatch.Rd | 9 MHCtools-1.5.4/MHCtools/man/NestTablesXL.Rd | 9 MHCtools-1.5.4/MHCtools/man/PapaDiv.Rd | 9 MHCtools-1.5.4/MHCtools/man/ReplMatch.Rd | 9 59 files changed, 206 insertions(+), 220 deletions(-)
Title: Stationary Vine Copula Models
Description: Provides functionality to fit and simulate from stationary vine
copula models for time series, see Nagler et al. (2022)
<doi:10.1016/j.jeconom.2021.11.015>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between svines versions 0.2.3 dated 2024-01-18 and 0.2.4 dated 2025-01-15
DESCRIPTION | 8 +- MD5 | 34 ++++----- NEWS.md | 6 - R/RcppExports.R | 4 - R/svine.R | 6 - R/svinecop.R | 8 +- README.md | 53 +++++++------- build/partial.rdb |binary inst/include/svines/implementation/svine_selector.ipp | 13 +++ man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/svine.Rd | 4 - man/svine_dist.Rd | 2 man/svinecop.Rd | 2 man/svinecop_dist.Rd | 2 src/RcppExports.cpp | 16 ++-- src/wrappers_svine.cpp | 66 ++++++++---------- 18 files changed, 113 insertions(+), 111 deletions(-)
Title: Optimally Robust Estimation
Description: R infrastructure for optimally robust estimation in general smoothly
parameterized models using S4 classes and methods as described Kohl, M.,
Ruckdeschel, P., and Rieder, H. (2010), <doi:10.1007/s10260-010-0133-0>, and in
Rieder, H., Kohl, M., and Ruckdeschel, P. (2008), <doi:10.1007/s10260-007-0047-7>.
Author: Matthias Kohl [cre, cph] ,
Mykhailo Pupashenko [ctb] ,
Gerald Kroisandt [ctb] ,
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between ROptEst versions 1.3.4 dated 2024-09-02 and 1.3.5 dated 2025-01-15
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- build/partial.rdb |binary inst/NEWS | 7 +++++++ man/0ROptEst-package.Rd | 8 ++++---- 5 files changed, 24 insertions(+), 17 deletions(-)
Title: Tree Taper Curves and Sorting Based on 'TapeR'
Description: Providing new german-wide 'TapeR' Models and functions for their
evaluation. Included are the most common tree species in Germany (Norway
spruce, Scots pine, European larch, Douglas fir, Silver fir as well as
European beech, Common/Sessile oak and Red oak). Many other species are mapped
to them so that 36 tree species / groups can be processed. Single trees are
defined by species code, one or multiple diameters in arbitrary measuring
height and tree height. The functions then provide information on diameters
along the stem, bark thickness, height of diameters, volume of the total or
parts of the trunk and total and component above-ground biomass. It is also
possible to calculate assortments from the taper curves. Uncertainty
information is provided for diameter, volume and component biomass estimation.
Author: Christian Vonderach [aut, cre],
Edgar Kublin [aut],
Gerald Kaendler [aut]
Maintainer: Christian Vonderach <christian.vonderach@forst.bwl.de>
Diff between TapeS versions 0.13.0 dated 2024-11-26 and 0.13.1 dated 2025-01-15
TapeS-0.13.0/TapeS/inst/NEWS.rd |only TapeS-0.13.1/TapeS/DESCRIPTION | 10 TapeS-0.13.1/TapeS/MD5 | 13 TapeS-0.13.1/TapeS/NEWS.md | 336 ++++++++--------- TapeS-0.13.1/TapeS/R/tprVolume.r | 641 ++++++++++++++++----------------- TapeS-0.13.1/TapeS/build/partial.rdb |binary TapeS-0.13.1/TapeS/inst/doc/tapes.html | 4 TapeS-0.13.1/TapeS/man/tprVolume.Rd | 4 8 files changed, 506 insertions(+), 502 deletions(-)
Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Tools to help download, process and analyse the UK road collision data collected using the
'STATS19' form. The datasets are provided as 'CSV' files with detailed road safety information about the
circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain
from 1979 to present. Tables are available on 'colissions' with the circumstances (e.g. speed limit
of road), information about 'vehicles' involved (e.g. type of vehicle), and 'casualties' (e.g. age).
The statistics relate only to events on public roads that were reported
to the police, and subsequently recorded, using the 'STATS19' collision reporting form. See
the Department for Transport website
<https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data> for more
information on these datasets.
The package is described in a paper in the Journal of Open Source Software
(Lovelace et al. 2019) <doi:10.21105/joss.01181>.
See
Gilardi et al. (202 [...truncated...]
Author: Robin Lovelace [aut, cre] ,
Malcolm Morgan [aut] ,
Layik Hama [aut] ,
Mark Padgham [aut] ,
David Ranzolin [rev],
Adam Sparks [rev, ctb] ,
Ivo Wengraf [ctb],
RAC Foundation [fnd]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stats19 versions 3.3.0 dated 2025-01-12 and 3.3.1 dated 2025-01-15
DESCRIPTION | 6 MD5 | 23 NEWS.md | 4 R/dl.R | 14 README.md | 289 ++--- inst/doc/blog.html | 659 ++++++----- inst/doc/stats19-training-setup.html | 250 ++-- inst/doc/stats19-training.html | 1260 ++++++++++++++-------- inst/doc/stats19-vehicles.html | 243 ++-- inst/doc/stats19.html | 1764 +++++++++++++++++-------------- man/figures/README-crash-date-plot-1.png |binary man/figures/README-crash-time-plot-1.png |binary man/figures/README-unnamed-chunk-4-1.png |only 13 files changed, 2674 insertions(+), 1838 deletions(-)
Title: Landscape Connectivity, Habitat, and Protected Area Networks
Description: Given a landscape resistance surface, creates minimum planar graph
(Fall et al. (2007) <doi:10.1007/s10021-007-9038-7>) and grains of connectivity
(Galpern et al. (2012) <doi:10.1111/j.1365-294X.2012.05677.x>) models that can be
used to calculate effective distances for landscape connectivity at multiple scales.
Documentation is provided by several vignettes, and a paper
(Chubaty, Galpern & Doctolero (2020) <doi:10.1111/2041-210X.13350>).
Author: Paul Galpern [aut, cph] ,
Sam Doctolero [aut],
Alex M Chubaty [aut, cre]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Diff between grainscape versions 0.4.4 dated 2023-04-20 and 0.5.0 dated 2025-01-15
DESCRIPTION | 23 MD5 | 166 - NEWS.md | 42 R/GOC.R | 32 R/MPG.R | 36 R/RcppExports.R | 14 R/classes.R | 10 R/corridor.R | 41 R/distance.R | 2 R/export.R | 91 R/ggGS.R | 12 R/grainscape-deprecated.R | 6 R/graphdf.R | 41 R/habitatConnectivityEngine.R | 22 R/patchFilter.R | 7 R/plot.R | 13 R/point.R | 18 R/theme_grainscape.R | 4 R/threshold.R | 8 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 22 inst/doc/MPG_algorithm.R | 90 inst/doc/MPG_algorithm.Rmd | 261 +- inst/doc/MPG_algorithm.pdf |binary inst/doc/grainscape_vignette.R | 27 inst/doc/grainscape_vignette.Rmd | 26 inst/doc/grainscape_vignette.pdf |binary inst/examples/example_threshold.R | 2 inst/extdata/issue72_patchID.tif |only inst/extdata/issue72_resistance.tif |only inst/include/DataStruct.h | 223 +- inst/include/Engine.h | 118 - man/MPG.Rd | 10 man/corridor.Rd | 4 man/distance.Rd | 2 man/dot-abbrev.Rd |only man/export.Rd | 8 man/ggGS.Rd | 12 man/goc-class.Rd | 4 man/grainscape-deprecated.Rd | 4 man/grainscape-package.Rd | 2 man/habConnEngine.Rd | 4 man/habConnRcpp.Rd | 12 man/patchFilter.Rd | 7 man/plot.Rd | 5 man/point.Rd | 4 man/show.Rd | 3 man/theme_grainscape.Rd | 4 man/threshold.Rd | 2 src/Engine.cpp | 998 +++++----- src/grainscape_init.c | 1 src/rcpp_HabConnEngine.cpp | 67 tests/test-all.R | 7 tests/testthat/test-MPG.R | 8 tests/testthat/test-corridor-distance-point.R | 22 tests/testthat/test-export.R |only vignettes/MPG_algorithm.Rmd | 261 +- vignettes/MPG_algorithm_files |only vignettes/bibliography.bib | 462 +--- vignettes/grainscape_vignette.Rmd | 26 vignettes/grainscape_vignette_files/figure-latex/figure_03-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_04-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_05-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_06-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_07-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_08-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_09-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_10-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_11-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_12-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_13-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_14-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_15-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_16-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_17-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_18-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_19-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_20-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_21-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_22-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_23-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_24-1.pdf |binary vignettes/grainscape_vignette_files/figure-latex/figure_25-1.pdf |binary 85 files changed, 1708 insertions(+), 1590 deletions(-)
Title: GLCM Textures of Raster Layers
Description: Calculates grey level co-occurrence matrix (GLCM) based texture measures (Hall-Beyer (2017) <https://prism.ucalgary.ca/bitstream/handle/1880/51900/texture%20tutorial%20v%203_0%20180206.pdf>; Haralick et al. (1973) <doi:10.1109/TSMC.1973.4309314>) of raster layers using a sliding rectangular window. It also includes functions to quantize a raster into grey levels as well as tabulate a glcm and calculate glcm texture metrics for a matrix.
Author: Alexander Ilich [aut, cre]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between GLCMTextures versions 0.4.2 dated 2024-08-19 and 0.5 dated 2025-01-15
DESCRIPTION | 13 - MD5 | 40 +-- R/glcm_metrics.R | 93 ++++--- R/glcm_textures.R | 274 +++++++++++----------- R/make_glcm.R | 72 +++--- R/quantize_raster.R | 145 ++++++------ README.md | 47 +-- build/vignette.rds |binary inst/doc/README.R | 12 - inst/doc/README.html | 60 +---- inst/testdata |only man/figures/README-elevation-1.png |binary man/figures/README-textures1-1.png |binary man/figures/README-textures3-1.png |binary man/fragments/README_Frag.Rmd | 444 ++++++++++++++++++------------------- man/glcm_metrics.Rd | 7 man/glcm_textures.Rd | 17 - man/make_glcm.Rd | 2 man/quantize_raster.Rd | 15 - src/glcm_cpp_functions.cpp | 10 tests |only 21 files changed, 639 insertions(+), 612 deletions(-)
Title: Interactively Visualize Structural Equation Modeling Diagrams
Description: It is an R package and web-based application, allowing users to perform interactive and reproducible visualizations of path diagrams for structural equation modeling (SEM) and networks using the 'ggplot2' engine. Its app (built with 'shiny') provides an interface that allows extensive customization, and creates CSV outputs, which can then be used to recreate the figures either using the web app or script-based workflow.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun Min <seung.min@mail.mcgill.ca>
Diff between ggsem versions 0.2.0 dated 2025-01-07 and 0.2.1 dated 2025-01-15
DESCRIPTION | 8 MD5 | 18 NAMESPACE | 1 R/draw_lines.R | 14 R/draw_loops.R | 4 R/draw_points.R | 9 R/launch.R | 1 inst/shiny/app.R | 1783 +++++++++++++++------ inst/shiny/rsconnect/shinyapps.io/smin95/ggsem.dcf | 2 man/draw_loops.Rd | 2 10 files changed, 1335 insertions(+), 507 deletions(-)
Title: 'C++' Standard Template Library Containers
Description: Use 'C++' Standard Template Library containers interactively in R. Includes sets, unordered sets, multisets, unordered multisets, maps,
unordered maps, multimaps, unordered multimaps, stacks, queues, priority queues, vectors, deques, forward lists, and lists.
Author: Christian Dueben [aut, cre]
Maintainer: Christian Dueben <cdueben.ml+cran@proton.me>
Diff between cppcontainers versions 1.0.3 dated 2025-01-09 and 1.0.4 dated 2025-01-15
DESCRIPTION | 6 - MD5 | 106 ++++++++++++++++----------------- NEWS.md | 3 R/map.R | 2 man/cpp_map.Rd | 2 tests/testthat/test-assign.R | 1 tests/testthat/test-at.R | 1 tests/testthat/test-back.R | 1 tests/testthat/test-bucket_count.R | 1 tests/testthat/test-capacity.R | 1 tests/testthat/test-clear.R | 1 tests/testthat/test-contains.R | 1 tests/testthat/test-count.R | 1 tests/testthat/test-emplace.R | 1 tests/testthat/test-emplace_after.R | 1 tests/testthat/test-emplace_back.R | 1 tests/testthat/test-emplace_front.R | 1 tests/testthat/test-empty.R | 1 tests/testthat/test-erase.R | 1 tests/testthat/test-erase_after.R | 1 tests/testthat/test-flip.R | 1 tests/testthat/test-front.R | 1 tests/testthat/test-insert.R | 1 tests/testthat/test-insert_after.R | 1 tests/testthat/test-insert_or_assign.R | 1 tests/testthat/test-load_factor.R | 1 tests/testthat/test-max_bucket_count.R | 1 tests/testthat/test-max_load_factor.R | 1 tests/testthat/test-max_size.R | 1 tests/testthat/test-merge.R | 1 tests/testthat/test-operators.R | 1 tests/testthat/test-pop.R | 1 tests/testthat/test-pop_back.R | 1 tests/testthat/test-pop_front.R | 1 tests/testthat/test-print.R | 1 tests/testthat/test-push.R | 1 tests/testthat/test-push_back.R | 1 tests/testthat/test-push_front.R | 1 tests/testthat/test-rehash.R | 1 tests/testthat/test-remove..R | 1 tests/testthat/test-reserve.R | 1 tests/testthat/test-resize.R | 1 tests/testthat/test-reverse.R | 1 tests/testthat/test-shrink_to_fit.R | 1 tests/testthat/test-size.R | 1 tests/testthat/test-sort.R | 1 tests/testthat/test-sorting.R | 1 tests/testthat/test-splice.R | 1 tests/testthat/test-splice_after.R | 1 tests/testthat/test-to_r.R | 1 tests/testthat/test-top.R | 1 tests/testthat/test-try_emplace.R | 1 tests/testthat/test-type.R | 1 tests/testthat/test-unique.R | 1 54 files changed, 110 insertions(+), 58 deletions(-)
Title: Color Calculations with Emphasis on Spectral Data
Description: Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners.
Build complex systems from simpler parts using a spectral product algebra. For light sources,
compute CCT, CRI, and SSI. For object colors, compute optimal colors and Logvinenko coordinates.
Work with the standard CIE illuminants and color matching functions, and read spectra from
text files, including CGATS files. Estimate a spectrum from its response. A user guide and 9 vignettes are included.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between colorSpec versions 1.5-0 dated 2024-01-28 and 1.6-0 dated 2025-01-15
colorSpec-1.5-0/colorSpec/R/logging-levels.R |only colorSpec-1.6-0/colorSpec/DESCRIPTION | 12 colorSpec-1.6-0/colorSpec/MD5 | 129 - colorSpec-1.6-0/colorSpec/NAMESPACE | 57 colorSpec-1.6-0/colorSpec/NEWS.md | 6 colorSpec-1.6-0/colorSpec/R/CGATS.R | 46 colorSpec-1.6-0/colorSpec/R/atmosphere.R | 12 colorSpec-1.6-0/colorSpec/R/basic.R | 14 colorSpec-1.6-0/colorSpec/R/colorSpec.CCT.R | 4 colorSpec-1.6-0/colorSpec/R/colorSpec.CRI.R | 234 +- colorSpec-1.6-0/colorSpec/R/colorSpec.R | 78 colorSpec-1.6-0/colorSpec/R/colorSpec.SSI.R | 14 colorSpec-1.6-0/colorSpec/R/colorSpec.actinometric.R | 8 colorSpec-1.6-0/colorSpec/R/colorSpec.calibrate.R | 38 colorSpec-1.6-0/colorSpec/R/colorSpec.comp.R | 38 colorSpec-1.6-0/colorSpec/R/colorSpec.emulate.R | 32 colorSpec-1.6-0/colorSpec/R/colorSpec.interpolate.R | 8 colorSpec-1.6-0/colorSpec/R/colorSpec.invert.R | 46 colorSpec-1.6-0/colorSpec/R/colorSpec.metrics.R | 10 colorSpec-1.6-0/colorSpec/R/colorSpec.ops.R | 74 colorSpec-1.6-0/colorSpec/R/colorSpec.optimal.R | 60 colorSpec-1.6-0/colorSpec/R/colorSpec.photometric.R | 2 colorSpec-1.6-0/colorSpec/R/colorSpec.plot.R | 370 +-- colorSpec-1.6-0/colorSpec/R/colorSpec.product.R | 66 colorSpec-1.6-0/colorSpec/R/colorSpec.ptransform.R | 12 colorSpec-1.6-0/colorSpec/R/colorSpec.radiometric.R | 8 colorSpec-1.6-0/colorSpec/R/colorSpec.read.R | 72 colorSpec-1.6-0/colorSpec/R/colorSpec.summary.R | 2 colorSpec-1.6-0/colorSpec/R/events.R | 20 colorSpec-1.6-0/colorSpec/R/interp.R | 18 colorSpec-1.6-0/colorSpec/R/logger.R |only colorSpec-1.6-0/colorSpec/R/logging.R | 166 - colorSpec-1.6-0/colorSpec/R/options.R | 271 +- colorSpec-1.6-0/colorSpec/R/rbind.super.R | 4 colorSpec-1.6-0/colorSpec/R/reparam.R | 14 colorSpec-1.6-0/colorSpec/R/utils.R | 313 +-- colorSpec-1.6-0/colorSpec/R/zonogon.R | 28 colorSpec-1.6-0/colorSpec/R/zonogon3.R | 6 colorSpec-1.6-0/colorSpec/R/zonohedron.R | 66 colorSpec-1.6-0/colorSpec/build/vignette.rds |binary colorSpec-1.6-0/colorSpec/inst/doc/blueflame.pdf |binary colorSpec-1.6-0/colorSpec/inst/doc/colorSpec-guide.R | 2 colorSpec-1.6-0/colorSpec/inst/doc/colorSpec-guide.Rmd | 63 colorSpec-1.6-0/colorSpec/inst/doc/colorSpec-guide.html | 1128 ++++++++--- colorSpec-1.6-0/colorSpec/inst/doc/convexity.pdf |binary colorSpec-1.6-0/colorSpec/inst/doc/emulation.pdf |binary colorSpec-1.6-0/colorSpec/inst/doc/gallery.pdf |binary colorSpec-1.6-0/colorSpec/inst/doc/inversion.pdf |binary colorSpec-1.6-0/colorSpec/inst/doc/lens-aging.pdf |binary colorSpec-1.6-0/colorSpec/inst/doc/optimals.pdf |binary colorSpec-1.6-0/colorSpec/inst/doc/phenolred.R | 16 colorSpec-1.6-0/colorSpec/inst/doc/phenolred.html | 361 +-- colorSpec-1.6-0/colorSpec/inst/doc/photoncounting.R | 10 colorSpec-1.6-0/colorSpec/inst/doc/photoncounting.html | 266 +- colorSpec-1.6-0/colorSpec/inst/extdata/targets/A70.ti3 |only colorSpec-1.6-0/colorSpec/inst/extdata/targets/TCSforCRI.txt | 1 colorSpec-1.6-0/colorSpec/man/computeCCT.Rd | 3 colorSpec-1.6-0/colorSpec/man/computeCRI.Rd | 137 + colorSpec-1.6-0/colorSpec/man/logging.Rd | 32 colorSpec-1.6-0/colorSpec/man/options.Rd | 23 colorSpec-1.6-0/colorSpec/man/plot.Rd | 1 colorSpec-1.6-0/colorSpec/man/readCGATS.Rd | 2 colorSpec-1.6-0/colorSpec/tests/test-CGATS.R | 16 colorSpec-1.6-0/colorSpec/tests/test-read.R | 4 colorSpec-1.6-0/colorSpec/tests/test-sink.R | 9 colorSpec-1.6-0/colorSpec/vignettes/bibliography.bib | 11 colorSpec-1.6-0/colorSpec/vignettes/colorSpec-guide.Rmd | 63 67 files changed, 2679 insertions(+), 1827 deletions(-)
Title: Output Space-Filling Design
Description: Methods to generate a design in the input space that sequentially fills the output space of a black-box function. The output space-filling designs are helpful in inverse design or feature-based modeling problems.
See Wang, Shangkun, Adam P. Generale, Surya R. Kalidindi, and V. Roshan Joseph. (2024), Sequential designs for filling output spaces, Technometrics, 66, 65–76. for details. This work is supported by U.S. National Foundation grant CMMI-1921646.
Author: Shangkun Wang [aut, cre],
Roshan Joseph [aut]
Maintainer: Shangkun Wang <sk_wang@gatech.edu>
Diff between OSFD versions 1.0 dated 2023-06-19 and 2.0 dated 2025-01-14
DESCRIPTION | 14 - MD5 | 22 - NAMESPACE | 20 - R/OSFD.R | 576 ++++++++++++++++++++++++++++---------------- R/RcppExports.R | 8 man/IOSFD.Rd |only man/OSFD-package.Rd | 38 +- man/OSFD.Rd | 18 - man/ball_unif.Rd | 14 - man/mMdist.Rd | 10 man/space_filling_points.Rd |only src/OSFD.cpp | 249 +++++++++++-------- src/RcppExports.cpp | 28 +- 13 files changed, 628 insertions(+), 369 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho [aut, cre]
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.9-7 dated 2024-01-19 and 1.11 dated 2025-01-14
DESCRIPTION | 14 ++-- MD5 | 151 +++++++++++++++++++++++------------------------ R/anm.ExpDesign.r | 24 ++++--- R/anm.LV.r | 5 - R/anm.ci.r | 36 ++++++----- R/anm.coin.r | 23 +++---- R/anm.cont.pdf.r | 36 +++++------ R/anm.die.r | 11 ++- R/anm.loglik.r | 72 +++++++++++----------- R/anm.ls.r | 41 ++++++------ R/anm.ls.reg.r | 48 +++++++------- R/anm.mc.bvn.r | 23 +++---- R/anm.popgrowth.r | 6 + R/anm.samp.design.R | 9 +- R/anm.transM.r | 3 R/dec2bin.R |only R/loglik.exp.plot.r | 89 ++++++++++++++------------- R/loglik.norm.plot.r | 130 ++++++++++++++++++++-------------------- R/plotAncova.r | 5 - R/see.Fcdf.r | 46 +++++++------- R/see.HW.r | 18 +++-- R/see.M.r | 21 +++--- R/see.accPrec.tck.r | 43 ++++++------- R/see.adddel.r | 21 +++--- R/see.ancova.tck.r | 82 ++++++++++++------------- R/see.anova.tck.r | 118 ++++++++++++++++++------------------ R/see.betacdf.r | 65 ++++++++++---------- R/see.bincdf.r | 85 +++++++++++++------------- R/see.chicdf.r | 43 +++++++------ R/see.cor.range.tck.r | 12 ++- R/see.expcdf.r | 57 +++++++++-------- R/see.exppower.r | 24 ++++--- R/see.gamcdf.r | 77 ++++++++++++----------- R/see.geocdf.r | 59 +++++++++--------- R/see.hypercdf.r | 71 +++++++++++----------- R/see.lnormcdf.r | 71 +++++++++++----------- R/see.logiscdf.r | 63 +++++++++---------- R/see.mixedII.r | 28 ++++---- R/see.mnom.tck.r | 26 ++++---- R/see.nbincdf.r | 65 ++++++++++---------- R/see.nlm.r | 59 +++++++++--------- R/see.normcdf.r | 84 +++++++++++++------------- R/see.poiscdf.r | 62 +++++++++---------- R/see.power.r | 83 +++++++++++++------------ R/see.rEffect.tck.r | 16 ++-- R/see.regression.tck.r | 55 ++++++++--------- R/see.roc.tck.r | 89 +++++++++++++-------------- R/see.smooth.tck.r | 65 ++++++++++---------- R/see.tcdf.r | 74 +++++++++++------------ R/see.ttest.tck.r | 98 +++++++++++++++--------------- R/see.unifcdf.r | 65 ++++++++++---------- R/see.weibcdf.r | 67 ++++++++++---------- R/see_discunifcdf.R | 81 +++++++++++++------------ R/selftest.pdfs.r | 111 ++++++++++++++++++++++++++-------- R/selftest.regGLM.R | 2 R/selftest.stats.tck.R | 8 +- build/vignette.rds |binary inst/doc/ranefCov.pdf |binary inst/doc/simpson.pdf |binary inst/doc/typeISS_key.pdf |binary man/anm.LV.rd | 24 +++---- man/anm.ci.rd | 14 ++-- man/anm.coin.Rd | 2 man/anm.cont.pdf.rd | 6 - man/anm.geo.growth.rd | 8 +- man/anm.loglik.rd | 56 ++++++++--------- man/anm.samp.design.Rd | 2 man/bin2dec.rd | 20 +++++- man/bvn.plot.rd | 11 +-- man/plot.pairw.rd | 30 ++++----- man/plotAncova.rd | 6 + man/pseudo.v.Rd | 8 +- man/qq.Plot.Rd | 30 ++++----- man/r.pb.rd | 8 +- man/see.power.rd | 4 - man/see.typeI_II.rd | 4 - man/world.emissions.Rd | 8 +- 77 files changed, 1628 insertions(+), 1453 deletions(-)
Title: Agent Based Model Simulation Framework
Description: A high-performance, flexible and extensible framework to
develop continuous-time agent based models. Its high performance
allows it to simulate millions of agents efficiently. Agents are
defined by their states (arbitrary R lists). The events are handled in
chronological order. This avoids the multi-event interaction problem
in a time step of discrete-time simulations, and gives precise
outcomes. The states are modified by provided or user-defined events.
The framework provides a flexible and customizable implementation of
state transitions (either spontaneous or caused by agent
interactions), making the framework suitable to apply to epidemiology
and ecology, e.g., to model life history stages, competition and
cooperation, and disease and information spread. The agent
interactions are flexible and extensible. The framework provides
random mixing and network interactions, and supports multi-level
mixing patterns. It can be easily extended to other interactions such
as inter- and intra [...truncated...]
Author: Junling Ma [aut, cre]
Maintainer: Junling Ma <junlingm@uvic.ca>
Diff between ABM versions 0.4.1 dated 2024-03-14 and 0.4.2 dated 2025-01-14
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 19 +++++++++++++++++++ inst/include/XP.h | 2 +- src/Agent.cpp | 4 ++-- src/Event.cpp | 4 ++-- src/RNG.cpp | 1 + src/Simulation.cpp | 8 ++++---- src/Transition.cpp | 15 +++++++++------ 9 files changed, 50 insertions(+), 27 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares
or REML by adding the function r() to formulas of lm() and glm(). A collection of
text-book statistics for higher education is also included, e.g. modifications
of the functions lm(), glm() and associated summaries from the package 'stats'.
Author: Kristian Hovde Liland [aut, cre],
Solve Saeboe¸ [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.4.1 dated 2025-01-08 and 1.4.2 dated 2025-01-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 7 +++++++ R/lm.R | 49 +++++-------------------------------------------- 4 files changed, 19 insertions(+), 51 deletions(-)
Title: Interpreting Glucose Data from Continuous Glucose Monitors
Description: Implements a wide range of metrics for measuring glucose control and glucose variability based on continuous glucose monitoring data. The list of implemented metrics is summarized in Rodbard (2009) <doi:10.1089/dia.2009.0015>. Additional visualization tools include time-series plots, lasagna plots and ambulatory glucose profile report.
Author: Elizabeth Chun [aut],
Steve Broll [aut],
David Buchanan [aut],
John Muschelli [aut] ,
Nathaniel Fernandes [aut] ,
Jung Hoon Seo [ctb],
Johnathan Shih [ctb],
Jacek Urbanek [ctb],
John Schwenck [ctb],
Marielle Hicban [ctb],
Mary Martin [ctb],
Pratik Pa [...truncated...]
Maintainer: Irina Gaynanova <irinagn@umich.edu>
Diff between iglu versions 4.2.0 dated 2024-10-15 and 4.2.2 dated 2025-01-14
DESCRIPTION | 6 MD5 | 28 - NEWS.md | 3 R/active_percent.R | 14 R/mage.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/AGP_and_Episodes.html | 2 inst/doc/MAGE.html | 46 - inst/doc/iglu.R | 8 inst/doc/iglu.html | 262 +++++----- inst/shiny_iglu/rsconnect/shinyapps.io/irinagain/shiny_iglu.dcf | 2 man/active_percent.Rd | 4 man/mage.Rd | 1 vignettes/iglu_files/figure-html/unnamed-chunk-27-1.png |binary 15 files changed, 197 insertions(+), 186 deletions(-)
Title: Characterizing Observed and Expected Representation
Description: A system for analyzing descriptive representation, especially for comparing the composition of a political body to the population it represents. Users can compute the expected degree of representation for a body under a random sampling model, the expected degree of representation variability, as well as representation scores from observed political bodies. The package is based on Gerring, Jerzak, and Oncel (2024) <doi:10.1017/S0003055423000680>.
Author: Connor Jerzak [aut, cre] ,
John Gerring [aut] ,
Erzen Oncel [aut]
Maintainer: Connor Jerzak <connor.jerzak@gmail.com>
Diff between DescriptiveRepresentationCalculator versions 1.0.0 dated 2023-10-23 and 1.1.0 dated 2025-01-14
DESCRIPTION | 15 ++++++++------- MD5 | 22 ++++++++++++++-------- R/ExpectedRep.R | 19 ++++++++++++++----- R/ObservedRep.R | 25 ++++++++++++++++--------- R/VarRep.R | 20 +++++++++++++++----- build/partial.rdb |binary build/vignette.rds |only inst |only man/ExpectedRepresentation.Rd | 14 ++++++++++---- man/ObservedRepresentation.Rd | 10 ++++++++-- man/SDRepresentation.Rd | 14 ++++++++++---- vignettes |only 12 files changed, 95 insertions(+), 44 deletions(-)
More information about DescriptiveRepresentationCalculator at CRAN
Permanent link
Title: Analytical Methods for Stream DAGs
Description: Provides indices and tools for directed acyclic graphs (DAGs), particularly DAG representations of intermittent streams. A detailed introduction to the package can be found in the publication: "Non-perennial stream networks as directed acyclic graphs: The R-package streamDAG" (Aho et al., 2023) <doi:10.1016/j.envsoft.2023.105775>, and in the introductory package vignette.
Author: Ken Aho [aut, cre],
Arya Legg [dtc, ctb],
Rob Ramos [dtc],
Maggi Kraft [dtc],
Charles T. Bond [dtc],
Rebecca L. Hale [dtc]
Maintainer: Ken Aho <ahoken@isu.edu>
Diff between streamDAG versions 1.5 dated 2023-10-06 and 1.5-9 dated 2025-01-14
DESCRIPTION | 10 ++-- MD5 | 96 ++++++++++++++++++++++------------------- NAMESPACE | 4 + R/STIC.RFimpute.R |only R/arc_pa_from_nodes.R | 4 - R/delete_nodes_pa.R | 9 +++ R/get.AIMS.data.R |only R/intact_to_sink.R | 35 +++++++++----- R/size_intact_to_arc.R |only R/streamDAGs.R | 28 ++++++++--- R/vector_segments.R |only build/vignette.rds |binary data/AIMS.node.coords.rda |binary data/dc_arc_pres_abs.rda |binary data/dc_lengths.rda |binary data/dc_node_pres_abs.rda |binary data/gj_coords16.rda |binary data/gj_lengths.rda |binary data/gj_lengths_piezo_full.rda |only data/gj_node_pres_abs.rda |binary data/gj_node_pres_abs16.rda |binary data/jd_lengths.rda |binary data/jd_lengths_2023.rda |only data/jd_lengths_full.rda |binary data/jd_node_pres_abs.rda |binary data/kon_coords.rda |binary data/kon_lengths.rda |binary data/mur_arc_pres_abs.rda |binary data/mur_coords.rda |binary data/mur_lengths.rda |binary data/mur_node_pres_abs.rda |binary data/mur_seasons_arc_pa.rda |binary inst/CITATION | 5 -- inst/doc/streamDAG.R | 9 ++- inst/doc/streamDAG.Rmd | 16 +++--- inst/doc/streamDAG.html | 65 ++++++++++++++------------- man/AIMS.node.coords.Rd | 1 man/STIC.RFimpute.Rd |only man/dc_lengths.Rd | 2 man/dc_node_pres_abs.Rd | 13 ++++- man/delete.nodes.pa.Rd | 6 +- man/get.AIMS.data.rd |only man/gj_lengths.Rd | 7 +- man/gj_node_pres_abs.Rd | 15 ++++-- man/intact_to_sink.Rd | 14 +++-- man/isle.Rd | 2 man/jd_lengths.Rd | 5 +- man/jd_node_pres_abs.Rd | 21 ++++++++ man/path.lengths.sink.Rd | 2 man/size.intact.to.arc.Rd |only man/spatial.plot.Rd | 9 ++- man/streamDAGs.Rd | 96 ++++++++++++++++++++++++++++++++--------- man/vector_segments.Rd |only vignettes/streamDAG.Rmd | 16 +++--- 54 files changed, 318 insertions(+), 172 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column and row wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>. c) Chatzipantsiou C., Dimitriadis M., Papadakis M. and Tsagris M. (2020). Extremely Efficient Permutation and Bootstrap Hypothesis Tests Using Hypothesis Tests Using R. Journal of Modern Applied Statistical Methods, 18(2), eP2898. <doi:10.48550/arXiv.1806.10947>. d) Tsagris M., Papadakis M., Alenazi A. and Alzeley O. (2024). Computationally Efficient Outlier Detection for High-Dimensional Data Using the [...truncated...]
Author: Manos Papadakis [aut, cre, cph],
Michail Tsagris [aut],
Marios Dimitriadis [ctb],
Stefanos Fafalios [aut],
Matteo Fasiolo [ctb],
Morgan Jacob [ctb],
Giorgos Borboudakis [ctb],
John Burkardt [ctb],
Changliang Zou [ctb],
Kleanthi Lakiotaki [ctb],
Chris [...truncated...]
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 2.1.3 dated 2024-12-31 and 2.1.4 dated 2025-01-14
Rfast-2.1.3/Rfast/man/dcor.Rd |only Rfast-2.1.3/Rfast/man/spml.regs.Rd |only Rfast-2.1.4/Rfast/DESCRIPTION | 8 - Rfast-2.1.4/Rfast/MD5 | 97 ++++++++--------- Rfast-2.1.4/Rfast/NAMESPACE | 2 Rfast-2.1.4/Rfast/NEWS.md | 20 +++ Rfast-2.1.4/Rfast/R/auc.R | 2 Rfast-2.1.4/Rfast/R/distance_cov_cor.R | 30 ++++- Rfast-2.1.4/Rfast/R/hd.eigen.R | 29 ++--- Rfast-2.1.4/Rfast/R/system_and_package.R | 78 +++++++++----- Rfast-2.1.4/Rfast/build/partial.rdb |binary Rfast-2.1.4/Rfast/inst/include/Rfast/FactorVector.hpp | 10 + Rfast-2.1.4/Rfast/inst/include/Rfast/helpers.hpp | 74 +++++++++++-- Rfast-2.1.4/Rfast/inst/include/Rfast/templates.h | 8 + Rfast-2.1.4/Rfast/man/Lgamma.Rd | 2 Rfast-2.1.4/Rfast/man/acg.mle.Rd | 15 +- Rfast-2.1.4/Rfast/man/beta.mle.Rd | 10 - Rfast-2.1.4/Rfast/man/circlin.cor.Rd | 10 - Rfast-2.1.4/Rfast/man/colvarcomps.mom.Rd | 2 Rfast-2.1.4/Rfast/man/colwatsons.Rd | 4 Rfast-2.1.4/Rfast/man/dcor.ttest.Rd | 4 Rfast-2.1.4/Rfast/man/dcov.Rd | 34 ++++-- Rfast-2.1.4/Rfast/man/dmvnorm.Rd | 4 Rfast-2.1.4/Rfast/man/edist.Rd | 2 Rfast-2.1.4/Rfast/man/fish.kent.Rd | 4 Rfast-2.1.4/Rfast/man/hd.eigen.Rd | 10 - Rfast-2.1.4/Rfast/man/kuiper.Rd | 10 - Rfast-2.1.4/Rfast/man/mahala.Rd | 2 Rfast-2.1.4/Rfast/man/mat.mult.Rd | 2 Rfast-2.1.4/Rfast/man/mediandir.Rd | 4 Rfast-2.1.4/Rfast/man/mvkurtosis.Rd | 2 Rfast-2.1.4/Rfast/man/mvt.mle.Rd | 6 - Rfast-2.1.4/Rfast/man/ompr.Rd | 4 Rfast-2.1.4/Rfast/man/pc.skel.Rd | 2 Rfast-2.1.4/Rfast/man/pdcor.Rd |only Rfast-2.1.4/Rfast/man/permcor.Rd | 3 Rfast-2.1.4/Rfast/man/racg.Rd | 6 - Rfast-2.1.4/Rfast/man/rmdp.Rd | 2 Rfast-2.1.4/Rfast/man/rvmf.Rd | 5 Rfast-2.1.4/Rfast/man/rvonmises.Rd | 4 Rfast-2.1.4/Rfast/man/score.glms.Rd | 14 +- Rfast-2.1.4/Rfast/man/spml.reg.Rd | 31 ++++- Rfast-2.1.4/Rfast/src/col_row_utilities.cpp | 98 ++++++++++++------ Rfast-2.1.4/Rfast/src/dista.cpp | 76 ++++++++++--- Rfast-2.1.4/Rfast/src/dists.cpp | 61 +++++++---- Rfast-2.1.4/Rfast/src/energy.cpp | 4 Rfast-2.1.4/Rfast/src/gaussian_nb.cpp | 4 Rfast-2.1.4/Rfast/src/maha.cpp | 17 +-- Rfast-2.1.4/Rfast/src/maha_ex.cpp | 51 ++++----- Rfast-2.1.4/Rfast/src/rmdp.cpp | 9 + Rfast-2.1.4/Rfast/src/rvmf.cpp | 11 +- 51 files changed, 565 insertions(+), 322 deletions(-)
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability
distributions which are fitted to toxicity concentrations for
different species as described by Posthuma et al.(2001)
<isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to
fit distributions such as the gamma, log-logistic, log-normal and
log-normal log-normal mixture. Multiple distributions can be averaged
using Akaike Information Criteria. Confidence intervals on hazard
concentrations and proportions are produced by bootstrapping.
Author: Joe Thorley [aut, cre] ,
Rebecca Fisher [aut],
David Fox [aut],
Carl Schwarz [aut],
Angeline Tillmanns [ctb],
Seb Dalgarno [ctb] ,
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Doug Spry [ctb],
Rick van Dam [ctb],
Graham Batley [ctb],
Ali Azizishi [...truncated...]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 2.1.0 dated 2024-10-21 and 2.2.0 dated 2025-01-14
ssdtools-2.1.0/ssdtools/inst/doc/additional-technical-details.R |only ssdtools-2.1.0/ssdtools/inst/doc/additional-technical-details.Rmd |only ssdtools-2.1.0/ssdtools/inst/doc/additional-technical-details.html |only ssdtools-2.1.0/ssdtools/inst/doc/customising-plots.R |only ssdtools-2.1.0/ssdtools/inst/doc/customising-plots.Rmd |only ssdtools-2.1.0/ssdtools/inst/doc/customising-plots.html |only ssdtools-2.1.0/ssdtools/inst/doc/distributions.R |only ssdtools-2.1.0/ssdtools/inst/doc/distributions.Rmd |only ssdtools-2.1.0/ssdtools/inst/doc/distributions.html |only ssdtools-2.1.0/ssdtools/inst/doc/model-averaging.R |only ssdtools-2.1.0/ssdtools/inst/doc/model-averaging.Rmd |only ssdtools-2.1.0/ssdtools/inst/doc/model-averaging.html |only ssdtools-2.1.0/ssdtools/inst/doc/small-sample-bias.pdf |only ssdtools-2.1.0/ssdtools/inst/doc/small-sample-bias.pdf.asis |only ssdtools-2.1.0/ssdtools/src/gompertz.cpp |only ssdtools-2.1.0/ssdtools/src/gumbel.cpp |only ssdtools-2.1.0/ssdtools/vignettes/additional-technical-details.Rmd |only ssdtools-2.1.0/ssdtools/vignettes/customising-plots.Rmd |only ssdtools-2.1.0/ssdtools/vignettes/distributions.Rmd |only ssdtools-2.1.0/ssdtools/vignettes/images |only ssdtools-2.1.0/ssdtools/vignettes/model-averaging.Rmd |only ssdtools-2.1.0/ssdtools/vignettes/small-sample-bias.pdf.asis |only ssdtools-2.2.0/ssdtools/DESCRIPTION | 34 - ssdtools-2.2.0/ssdtools/MD5 | 225 ++++------ ssdtools-2.2.0/ssdtools/NAMESPACE | 2 ssdtools-2.2.0/ssdtools/NEWS.md | 25 - ssdtools-2.2.0/ssdtools/R/RcppExports.R | 8 ssdtools-2.2.0/ssdtools/R/censor.R | 14 ssdtools-2.2.0/ssdtools/R/censored.R | 2 ssdtools-2.2.0/ssdtools/R/d.R | 30 - ssdtools-2.2.0/ssdtools/R/devtools-helpers.R | 2 ssdtools-2.2.0/ssdtools/R/dists.R | 15 ssdtools-2.2.0/ssdtools/R/ggplot.R | 35 - ssdtools-2.2.0/ssdtools/R/gof.R | 2 ssdtools-2.2.0/ssdtools/R/gompertz.R | 22 ssdtools-2.2.0/ssdtools/R/hc-burrlioz.R | 18 ssdtools-2.2.0/ssdtools/R/lgumbel.R | 17 ssdtools-2.2.0/ssdtools/R/params.R | 16 ssdtools-2.2.0/ssdtools/R/plot-cf.R | 13 ssdtools-2.2.0/ssdtools/R/plot.R | 2 ssdtools-2.2.0/ssdtools/R/scales.R | 28 + ssdtools-2.2.0/ssdtools/R/ssd-plot.R | 98 +++- ssdtools-2.2.0/ssdtools/R/utils.R | 3 ssdtools-2.2.0/ssdtools/R/wqg.R | 43 - ssdtools-2.2.0/ssdtools/README.md | 74 +-- ssdtools-2.2.0/ssdtools/build/vignette.rds |binary ssdtools-2.2.0/ssdtools/data/boron_pred.rda |binary ssdtools-2.2.0/ssdtools/data/dist_data.rda |binary ssdtools-2.2.0/ssdtools/inst/WORDLIST | 13 ssdtools-2.2.0/ssdtools/inst/doc/faqs.R |only ssdtools-2.2.0/ssdtools/inst/doc/faqs.Rmd |only ssdtools-2.2.0/ssdtools/inst/doc/faqs.html |only ssdtools-2.2.0/ssdtools/inst/doc/ssdtools.R | 8 ssdtools-2.2.0/ssdtools/inst/doc/ssdtools.html | 15 ssdtools-2.2.0/ssdtools/man/comma_signif.Rd | 5 ssdtools-2.2.0/ssdtools/man/dist_data.Rd | 3 ssdtools-2.2.0/ssdtools/man/figures/README-unnamed-chunk-4-1.png |binary ssdtools-2.2.0/ssdtools/man/figures/README-unnamed-chunk-8-1.png |binary ssdtools-2.2.0/ssdtools/man/geom_hcintersect.Rd | 2 ssdtools-2.2.0/ssdtools/man/geom_ssd.Rd | 8 ssdtools-2.2.0/ssdtools/man/params.Rd | 23 - ssdtools-2.2.0/ssdtools/man/pgompertz.Rd | 3 ssdtools-2.2.0/ssdtools/man/plgumbel.Rd | 3 ssdtools-2.2.0/ssdtools/man/predict.fitburrlioz.Rd | 2 ssdtools-2.2.0/ssdtools/man/predict.fitdists.Rd | 2 ssdtools-2.2.0/ssdtools/man/qgompertz.Rd | 3 ssdtools-2.2.0/ssdtools/man/qlgumbel.Rd | 3 ssdtools-2.2.0/ssdtools/man/rgompertz.Rd | 3 ssdtools-2.2.0/ssdtools/man/rlgumbel.Rd | 7 ssdtools-2.2.0/ssdtools/man/scale_colour_ssd.Rd | 10 ssdtools-2.2.0/ssdtools/man/ssd_censor_data.Rd | 3 ssdtools-2.2.0/ssdtools/man/ssd_dists.Rd | 3 ssdtools-2.2.0/ssdtools/man/ssd_dists_all.Rd | 3 ssdtools-2.2.0/ssdtools/man/ssd_dists_shiny.Rd |only ssdtools-2.2.0/ssdtools/man/ssd_gof.Rd | 2 ssdtools-2.2.0/ssdtools/man/ssd_hc.Rd | 2 ssdtools-2.2.0/ssdtools/man/ssd_hc_burrlioz.Rd | 2 ssdtools-2.2.0/ssdtools/man/ssd_label_comma_hc.Rd |only ssdtools-2.2.0/ssdtools/man/ssd_plot.Rd | 25 - ssdtools-2.2.0/ssdtools/man/ssd_plot_cf.Rd | 2 ssdtools-2.2.0/ssdtools/man/ssd_plot_data.Rd | 4 ssdtools-2.2.0/ssdtools/man/ssd_wqg_bc.Rd | 18 ssdtools-2.2.0/ssdtools/man/ssd_wqg_burrlioz.Rd | 17 ssdtools-2.2.0/ssdtools/man/ssdtools-package.Rd | 5 ssdtools-2.2.0/ssdtools/man/stat_ssd.Rd | 6 ssdtools-2.2.0/ssdtools/src/RcppExports.cpp | 26 - ssdtools-2.2.0/ssdtools/src/fun.cpp |only ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/autoplot/autoplot.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/autoplot/autoplot_bigmark.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/autoplot/autoplot_new.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/autoplot/autoplot_rescale.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/autoplot/suffix.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/match-moments/cdf.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-cdf/fits.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-cdf/fits_average.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-cdf/fits_average_na.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-cdf/fits_bigmark.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-cdf/fits_delta.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-cdf/fits_rescale.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-cdf/list.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-cdf/suffix.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-data/big_mark_comma.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-data/big_mark_space.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-data/ccme_boron.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-data/ccme_boron2.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/plot-data/suffix.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_bigmark.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_breaks.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_color.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_hcdup.png |only ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_labelsize.png |only ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_limits.png |only ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_nohc.png |only ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_pred.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_pred_label.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_pred_shift_x.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_shape.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_textsize.png |only ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/boron_themeclassic.png |only ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/missing_order.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/no_ribbon.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/ribbon.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/_snaps/ssd-plot/suffix.png |binary ssdtools-2.2.0/ssdtools/tests/testthat/test-dists.R | 10 ssdtools-2.2.0/ssdtools/tests/testthat/test-ssd-plot.R | 24 + ssdtools-2.2.0/ssdtools/vignettes/faqs.Rmd |only 126 files changed, 512 insertions(+), 481 deletions(-)
Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from
eBird (<http://ebird.org>), an online tool for recording bird
observations. Public access to the full eBird database is via the
eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download>
for access), a downloadable text file. This package is an interface to
AWK for extracting data from the EBD based on taxonomic, spatial, or
temporal filters, to produce a manageable file size that can be
imported into R.
Author: Matthew Strimas-Mackey [aut, cre]
,
Eliot Miller [aut],
Wesley Hochachka [aut],
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between auk versions 0.7.0 dated 2023-11-14 and 0.8.0 dated 2025-01-14
DESCRIPTION | 8 +-- MD5 | 37 ++++++++-------- NAMESPACE | 1 NEWS.md | 5 ++ R/auk-country.R | 2 R/auk-filter.R | 1 R/auk-version.R | 6 +- R/process_barcharts.R |only build/vignette.rds |binary data/ebird_taxonomy.rda |binary inst/doc/auk.R | 88 +++++++++++++++++++-------------------- inst/doc/auk.html | 16 +++---- inst/doc/development.R | 52 +++++++++++------------ inst/doc/development.html | 4 - inst/extdata/barchart-sample.txt |only man/auk_country.Rd | 2 man/auk_ebd_version.Rd | 3 - man/auk_version.Rd | 3 - man/ebird_species.Rd | 3 - man/get_ebird_taxonomy.Rd | 3 - man/process_barcharts.Rd |only 21 files changed, 124 insertions(+), 110 deletions(-)
Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our 'JSS'
paper (2016, <doi:10.18637/jss.v071.i02>. A sufficiently recent version of
'Protocol Buffers' library is required; currently version 3.3.0 from 2017
is the stated minimum.
Author: Romain Francois [aut] ,
Dirk Eddelbuettel [aut, cre] ,
Murray Stokely [aut] ,
Jeroen Ooms [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.22 dated 2024-01-21 and 0.4.23 dated 2025-01-14
ChangeLog | 77 +++ DESCRIPTION | 23 MD5 | 62 +- R/00classes.R | 4 R/extensions.R | 10 R/field_count.R | 2 R/wrapper_ServiceDescriptor.R | 4 README.md | 2 build/vignette.rds |binary configure | 851 +++++++++++++++++++----------------- configure.ac | 10 inst/NEWS.Rd | 25 - inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-paper.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary inst/tinytest/test_addressbook.R | 4 src/DescriptorPoolLookup.cpp | 6 src/DescriptorPoolLookup.h | 8 src/RWarningErrorCollector.cpp | 16 src/RWarningErrorCollector.h | 6 src/init.c | 8 src/mutators.cpp | 22 src/rprotobuf.cpp | 6 src/rprotobuf.h | 3 src/wrapper_Descriptor.cpp | 14 src/wrapper_EnumDescriptor.cpp | 6 src/wrapper_EnumValueDescriptor.cpp | 2 src/wrapper_FieldDescriptor.cpp | 2 src/wrapper_FileDescriptor.cpp | 18 src/wrapper_Message.cpp | 8 src/wrapper_MethodDescriptor.cpp | 2 src/wrapper_ServiceDescriptor.cpp | 6 32 files changed, 706 insertions(+), 501 deletions(-)
Title: Robust Asymptotic Statistics
Description: Base S4-classes and functions for robust asymptotic statistics.
Author: Matthias Kohl [cre, cph, aut],
Peter Ruckdeschel [aut, cph],
Mykhailo Pupashenko [ctb] ,
Gerald Kroisandt [ctb] ,
R Core Team [ctb, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RobAStBase versions 1.2.6 dated 2024-09-02 and 1.2.7 dated 2025-01-14
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- inst/CITATION | 3 ++- inst/NEWS | 10 ++++++++++ man/0RobAStBase-package.Rd | 8 ++++---- 5 files changed, 29 insertions(+), 18 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.0.9 dated 2025-01-07 and 2.1.0 dated 2025-01-14
DESCRIPTION | 14 - MD5 | 36 +-- R/GeoCompositeLik2.R | 16 - R/GeoCorrFct.r | 18 - R/GeoCorrFct_Cop.R | 30 +- R/GeoCovmatrix.r | 104 +++++--- R/GeoKrig.r | 65 +++-- R/GeoLik.r | 304 ++----------------------- R/GeoSim.r | 4 R/GeoSimapprox.r | 2 R/GeoVariogram.r | 96 +++++--- R/TB.R | 40 ++- R/Utility.r | 104 ++++---- src/CompositeLikelihood2_ani.c | 78 +++--- src/CompositeLikelihoodCond2_ani.c | 70 ++--- src/CorrelationFunction.c | 9 src/Distributions.c | 13 - src/GeoModels_init.c | 444 +++++++++++++++++++------------------ src/Utility.c | 26 -- 19 files changed, 653 insertions(+), 820 deletions(-)
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Lucas Mation [aut]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between enderecobr versions 0.3.0 dated 2024-12-12 and 0.4.0 dated 2025-01-14
DESCRIPTION | 6 MD5 | 29 - NEWS.md | 19 + R/padronizar_enderecos.R | 15 R/padronizar_numeros.R | 68 +++- README.md | 2 inst/doc/enderecobr.R | 37 ++ inst/doc/enderecobr.Rmd | 80 ++++ inst/doc/enderecobr.html | 430 +++++++++++++++----------- man/padronizar_enderecos.Rd | 6 man/padronizar_numeros.Rd | 6 tests/testthat/_snaps/padronizar_enderecos.md | 12 tests/testthat/_snaps/padronizar_numeros.md |only tests/testthat/test-padronizar_enderecos.R | 41 ++ tests/testthat/test-padronizar_numeros.R | 90 +++++ vignettes/enderecobr.Rmd | 80 ++++ 16 files changed, 689 insertions(+), 232 deletions(-)
Title: At-Risk
Description: The at-Risk (aR) approach is based on a two-step parametric estimation procedure that allows to forecast the full conditional distribution of an economic variable at a given horizon, as a function of a set of factors. These density forecasts are then be used to produce coherent forecasts for any downside risk measure, e.g., value-at-risk, expected shortfall, downside entropy. Initially introduced by Adrian et al. (2019) <doi:10.1257/aer.20161923> to reveal the vulnerability of economic growth to financial conditions, the aR approach is currently extensively used by international financial institutions to provide Value-at-Risk (VaR) type forecasts for GDP growth (Growth-at-Risk) or inflation (Inflation-at-Risk). This package provides methods for estimating these models. Datasets for the US and the Eurozone are available to allow testing of the Adrian et al. (2019) model. This package constitutes a useful toolbox (data and functions) for private practitioners, scholars as well as p [...truncated...]
Author: Quentin Lajaunie [aut, cre],
Guillaume Flament [aut, ctb],
Christophe Hurlin [aut],
Souzan Kazemi [rev]
Maintainer: Quentin Lajaunie <quentin_lajaunie@hotmail.fr>
Diff between atRisk versions 0.1.0 dated 2023-08-08 and 0.2.0 dated 2025-01-14
atRisk-0.1.0/atRisk/R/f_param_histo.R |only atRisk-0.1.0/atRisk/data/data_param_histo.rda |only atRisk-0.1.0/atRisk/man/data_param_histo.Rd |only atRisk-0.1.0/atRisk/man/f_param_histo.Rd |only atRisk-0.2.0/atRisk/DESCRIPTION | 9 atRisk-0.2.0/atRisk/MD5 | 46 +- atRisk-0.2.0/atRisk/NAMESPACE | 6 atRisk-0.2.0/atRisk/R/f_ES.R | 82 ++--- atRisk-0.2.0/atRisk/R/f_VaR.R | 92 +++-- atRisk-0.2.0/atRisk/R/f_compile_quantile.R | 179 +++++------ atRisk-0.2.0/atRisk/R/f_distrib.R | 291 ++++++++++-------- atRisk-0.2.0/atRisk/R/f_histo_RM.R | 52 +-- atRisk-0.2.0/atRisk/R/f_nadaraya_watson_quantile.R |only atRisk-0.2.0/atRisk/R/f_plot_distrib_2D.R | 73 ++-- atRisk-0.2.0/atRisk/R/f_plot_distrib_3D.R | 75 ++-- atRisk-0.2.0/atRisk/data/data_US.rda |binary atRisk-0.2.0/atRisk/data/data_param_histo_US.rda |only atRisk-0.2.0/atRisk/man/data_US.Rd | 8 atRisk-0.2.0/atRisk/man/data_euro.Rd | 2 atRisk-0.2.0/atRisk/man/data_param_histo_US.Rd |only atRisk-0.2.0/atRisk/man/f_ES.Rd | 6 atRisk-0.2.0/atRisk/man/f_VaR.Rd | 2 atRisk-0.2.0/atRisk/man/f_compile_quantile.Rd | 13 atRisk-0.2.0/atRisk/man/f_distrib.Rd | 28 - atRisk-0.2.0/atRisk/man/f_histo_RM.Rd | 29 - atRisk-0.2.0/atRisk/man/f_nadaraya_watson_quantile.Rd |only atRisk-0.2.0/atRisk/man/f_plot_distrib_2D.Rd | 29 + atRisk-0.2.0/atRisk/man/f_plot_distrib_3D.Rd | 28 - 28 files changed, 579 insertions(+), 471 deletions(-)
Title: FDR Power
Description: Computing Average and TPX Power under various BHFDR type sequential
procedures. All of these procedures involve control of some summary of the
distribution of the FDP, e.g. the proportion of discoveries which are false
in a given experiment. The most widely known of these, the BH-FDR procedure,
controls the FDR which is the mean of the FDP. A lesser known procedure, due
to Lehmann and Romano, controls the FDX, or probability that the FDP exceeds
a user provided threshold. This is less conservative than FWE control
procedures but much more conservative than the BH-FDR proceudre. This
package and the references supporting it introduce a new procedure for
controlling the FDX which we call the BH-FDX procedure. This procedure
iteratively identifies, given alpha and lower threshold delta, an alpha*
less than alpha at which BH-FDR guarantees FDX control. This uses
asymptotic approximation and is only slightly more conservative than the
BH-FDR procedure. Likewise, we can think of the power i [...truncated...]
Author: Grant Izmirlian [aut, cre]
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Diff between pwrFDR versions 3.2.2 dated 2024-12-18 and 3.2.4 dated 2025-01-14
DESCRIPTION | 6 MD5 | 14 - R/pwrFDR.R | 354 ++++++++++++++++++++------------- inst/doc/pwrFDR-vignette.R | 171 +++++++++++++--- inst/doc/pwrFDR-vignette.Rnw | 438 +++++++++++++++++++++++++++++------------- inst/doc/pwrFDR-vignette.pdf |binary man/Ch01-pwrFDR.Rd | 2 vignettes/pwrFDR-vignette.Rnw | 438 +++++++++++++++++++++++++++++------------- 8 files changed, 988 insertions(+), 435 deletions(-)
Title: Curved Text in 'ggplot2'
Description: A 'ggplot2' extension that allows text to follow curved paths.
Curved text makes it easier to directly label paths or neatly annotate in
polar co-ordinates.
Author: Allan Cameron [aut, cre],
Teun van den Brand [aut]
Maintainer: Allan Cameron <Allan.Cameron@nhs.scot>
Diff between geomtextpath versions 0.1.4 dated 2024-06-13 and 0.1.5 dated 2025-01-14
DESCRIPTION | 8 +- MD5 | 58 ++++++++++---------- NEWS.md | 97 +++++++++++++++++++---------------- R/geom_labelpath.R | 2 R/geom_textabline.R | 1 R/geom_textpath.R | 2 R/geom_textsf.R | 37 +++++++++---- R/grob_labelpath.R | 9 ++- R/grob_textpath.R | 11 +++ R/path_handling.R | 25 ++++++++- R/sf_helpers.R | 41 +++++++++----- R/text_helpers.R | 17 +++++- R/text_placement.R | 4 - README.md | 3 - build/vignette.rds |binary inst/doc/aesthetics.R | 2 inst/doc/aesthetics.Rmd | 2 inst/doc/aesthetics.html | 46 ++++++++-------- inst/doc/curved_polar.R | 2 inst/doc/curved_polar.Rmd | 2 inst/doc/curved_polar.html | 20 +++---- inst/doc/geomtextpath.R | 2 inst/doc/geomtextpath.Rmd | 2 inst/doc/geomtextpath.html | 14 ++--- man/figures/README-geom_textsf-1.png |binary man/geom_textsf.Rd | 45 ++++++++-------- tests/testthat/Rplots.pdf |binary vignettes/aesthetics.Rmd | 2 vignettes/curved_polar.Rmd | 2 vignettes/geomtextpath.Rmd | 2 30 files changed, 273 insertions(+), 185 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging
(Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>,
Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.17 dated 2024-02-20 and 0.2.18 dated 2025-01-14
DESCRIPTION | 8 MD5 | 64 ++-- NAMESPACE | 6 NEWS.md | 10 R/JAGS-diagnostics.R | 24 + R/JAGS-fit.R | 457 ++++++++++++++++++++++++++--- R/JAGS-formula.R | 55 +-- R/JAGS-marglik.R | 136 ++++---- R/interpret.R | 52 +++ R/marginal-distributions.R | 634 +++++++++++++++++++++++++++++++++++++++-- R/model-averaging-plots.R | 57 +++ R/model-averaging.R | 484 ++++++++++++++++++++++++++++++- R/priors-plot.R | 50 ++- R/priors-print.R | 46 ++ R/priors-tools.R | 88 +++++ R/priors.R | 334 +++++++++++++++++---- R/summary-tables.R | 623 ++++++++++++++++++++++++++++------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/ComparisonR.html | 21 - inst/doc/SpikeAndSlab.html | 30 - man/BayesTools.Rd | 1 man/BayesTools_model_tables.Rd | 9 man/JAGS_check_convergence.Rd | 9 man/as_marginal_inference.Rd |only man/as_mixed_posteriors.Rd |only man/interpret.Rd | 3 man/is.prior.Rd | 3 man/marginal_inference.Rd | 5 man/marginal_posterior.Rd | 2 man/mix_posteriors.Rd | 2 man/prior_mixture.Rd |only man/prior_weightfunction.Rd | 8 man/update.BayesTools_table.Rd |only man/weightfunctions_mapping.Rd | 4 35 files changed, 2708 insertions(+), 517 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.24.0 dated 2024-11-27 and 0.24.1 dated 2025-01-14
DESCRIPTION | 30 +- MD5 | 221 +++++++-------- NAMESPACE | 1 NEWS.md | 22 + R/1_model_parameters.R | 198 ++++++------- R/4_standard_error.R | 6 R/5_simulate_model.R | 5 R/bootstrap_model.R | 4 R/ci_kenward.R | 1 R/ci_profile_boot.R | 3 R/cluster_analysis.R | 3 R/cluster_discrimination.R | 1 R/cluster_meta.R | 4 R/convert_efa_to_cfa.R | 5 R/display.R | 14 R/dof_kenward.R | 2 R/dof_ml1.R | 8 R/dominance_analysis.R | 76 ++--- R/equivalence_test.R | 18 - R/extract_parameters.R | 14 R/extract_parameters_anova.R | 4 R/extract_random_parameters.R | 1 R/extract_random_variances.R | 13 R/factor_analysis.R | 16 - R/format.R | 14 R/format_p_adjust.R | 5 R/format_parameters.R | 3 R/methods_BayesFM.R | 49 +-- R/methods_BayesFactor.R | 2 R/methods_aov.R | 7 R/methods_base.R | 4 R/methods_brglm2.R | 4 R/methods_cplm.R | 4 R/methods_emmeans.R | 2 R/methods_fixest.R | 57 +-- R/methods_gam.R | 2 R/methods_glmmTMB.R | 6 R/methods_glmx.R | 1 R/methods_hclust.R | 1 R/methods_htest.R | 26 - R/methods_kmeans.R | 8 R/methods_lavaan.R | 9 R/methods_lm.R | 2 R/methods_lme4.R | 1 R/methods_lqmm.R | 2 R/methods_lrm.R | 4 R/methods_mass.R | 3 R/methods_metaplus.R | 9 R/methods_mfx.R | 4 R/methods_mhurdle.R | 1 R/methods_mice.R | 11 R/methods_mmrm.R | 53 +-- R/methods_model_fit.R | 4 R/methods_nlme.R | 2 R/methods_ordinal.R | 5 R/methods_other.R | 2 R/methods_panelr.R | 5 R/methods_plm.R | 2 R/methods_posterior.R | 3 R/methods_pscl.R | 5 R/methods_quantreg.R | 7 R/methods_survey.R | 6 R/methods_survival.R | 58 +++ R/methods_varest.R | 5 R/methods_vgam.R | 5 R/n_clusters.R | 6 R/n_clusters_easystats.R | 13 R/n_factors.R | 4 R/p_function.R | 44 +- R/p_significance.R | 1 R/p_value_kenward.R | 4 R/parameters_type.R | 6 R/pool_parameters.R | 3 R/principal_components.R | 6 R/print.parameters_model.R | 11 R/print_html.R | 1 R/print_md.R | 14 R/random_parameters.R | 2 R/reduce_parameters.R | 18 - R/reshape_loadings.R | 4 R/select_parameters.R | 1 R/standardize_info.R | 12 R/standardize_parameters.R | 5 R/utils.R | 2 R/utils_cleaners.R | 2 R/utils_format.R | 14 R/utils_model_parameters.R | 9 R/utils_pca_efa.R | 31 -- man/p_function.Rd | 41 +- tests/testthat/_snaps/brms.md | 8 tests/testthat/_snaps/model_parameters.fixest.md | 25 + tests/testthat/_snaps/model_parameters_ordinal.md | 28 - tests/testthat/_snaps/printing-stan.md | 74 ++++- tests/testthat/_snaps/printing.md | 21 + tests/testthat/_snaps/windows/model_parameters.logitr.md |only tests/testthat/test-GLMMadaptive.R | 1 tests/testthat/test-dominance_analysis.R | 1 tests/testthat/test-geeglm.R | 15 - tests/testthat/test-glmer.R | 1 tests/testthat/test-glmmTMB.R | 2 tests/testthat/test-model_parameters.anova.R | 1 tests/testthat/test-model_parameters.fixest.R | 14 tests/testthat/test-model_parameters.logitr.R |only tests/testthat/test-model_parameters_df.R | 1 tests/testthat/test-p_value.R | 1 tests/testthat/test-polr.R |only tests/testthat/test-pool_parameters.R | 4 tests/testthat/test-printing-stan.R | 13 tests/testthat/test-printing.R | 10 tests/testthat/test-quantreg.R | 1 tests/testthat/test-random_effects_ci.R | 10 tests/testthat/test-robust.R | 6 tests/testthat/test-standardize_parameters.R | 3 113 files changed, 662 insertions(+), 905 deletions(-)
Title: Easily Install and Load the 'mlr3' Package Family
Description: The 'mlr3' package family is a set of packages for
machine-learning purposes built in a modular fashion. This wrapper
package is aimed to simplify the installation and loading of the core
'mlr3' packages. Get more information about the 'mlr3' project at
<https://mlr3book.mlr-org.com/>.
Author: Michel Lang [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3verse versions 0.3.0 dated 2024-06-30 and 0.3.1 dated 2025-01-14
DESCRIPTION | 25 +++++++++++++++---------- MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/mlr3verse_info.R | 24 ++++++++++++++++-------- R/zzz.R | 19 +------------------ README.md | 28 ++++++++++++++++++++++------ man/mlr3verse-package.Rd | 26 -------------------------- man/mlr3verse_info.Rd | 3 ++- 9 files changed, 70 insertions(+), 77 deletions(-)
Title: Control of the Median of the FDP
Description: Methods for controlling the median of the false discovery proportion (mFDP).
Depending on the method, simultaneous or non-simultaneous inference is provided.
The methods take a vector of p-values or test statistics as input.
Author: Jesse Hemerik [aut, cre]
Maintainer: Jesse Hemerik <hemerik@ese.eur.nl>
Diff between mFDP versions 0.1.0 dated 2022-08-22 and 0.2.0 dated 2025-01-14
DESCRIPTION | 21 ++++++++++----------- MD5 | 6 +++++- R/mFDP.direc.R |only R/mFDP.equiv.R |only man/mFDP.direc.Rd |only man/mFDP.equiv.Rd |only 6 files changed, 15 insertions(+), 12 deletions(-)
Title: Linear Mixed Model Solver
Description: An efficient and flexible system to solve sparse mixed model
equations. Important applications are the use of splines to model spatial or temporal
trends as described in Boer (2023). (<doi:10.1177/1471082X231178591>).
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between LMMsolver versions 1.0.8 dated 2024-08-26 and 1.0.9 dated 2025-01-14
DESCRIPTION | 13 MD5 | 111 ++- NAMESPACE | 1 NEWS.md | 11 R/DifferentiationCholesky.R | 2 R/LMMsolve-class.R | 150 ++-- R/LMMsolve.R | 506 +++------------- R/RcppExports.R | 2 R/chkInputLMMsolve.R |only R/chkResponse.R |only R/chkSplinesFormula.R |only R/constructFixed.R |only R/constructGinv.R |only R/constructRandom.R |only R/diagnosticsMME.R |only R/displayMME.R |only R/fitLMM.R |only R/getWeights.R |only R/multinomial.R |only R/obtainSmoothTrend.R | 6 R/predictFunctions.R | 21 R/spl1D.R | 2 R/splinesFunctions.R | 4 R/utils.R | 67 +- README.md | 15 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Solving_Linear_Mixed_Models.R | 156 ++++- inst/doc/Solving_Linear_Mixed_Models.Rmd | 260 ++++++-- inst/doc/Solving_Linear_Mixed_Models.html | 929 +++++++++++++++++------------- inst/tinytest/GLMMFull |binary inst/tinytest/LMMsolve0 |binary inst/tinytest/LMMsolve1 |binary inst/tinytest/LMMsolve2 |binary inst/tinytest/LMMsolve3 |binary inst/tinytest/LMMsolve4 |binary inst/tinytest/LMMsolve5 |binary inst/tinytest/binomial1 |only inst/tinytest/binomial2 |only inst/tinytest/binomial3 |only inst/tinytest/cfFull |binary inst/tinytest/effDims |binary inst/tinytest/gam1DFull |binary inst/tinytest/modCoefs |binary inst/tinytest/modCoefsSe |binary inst/tinytest/modFit |binary inst/tinytest/modResid |binary inst/tinytest/multinomial1 |only inst/tinytest/smooth3D1 |binary inst/tinytest/smooth3D2 |binary inst/tinytest/spl1DFull |binary inst/tinytest/spl2DFull |binary inst/tinytest/spl3DFull |binary inst/tinytest/test_binomial.R |only inst/tinytest/test_multinomial.R |only inst/tinytest/test_offset.R |only man/LMMsolve.Rd | 14 man/LMMsolveObject.Rd | 1 man/constructRinv.Rd | 24 man/diagnosticsMME.Rd | 2 man/displayMME.Rd | 2 man/multinomial.Rd |only man/predict.LMMsolve.Rd | 20 src/ADcholesky.cpp | 2 vignettes/Solving_Linear_Mixed_Models.Rmd | 260 ++++++-- vignettes/bibliography.bib | 17 66 files changed, 1515 insertions(+), 1083 deletions(-)
Title: Methods for Closed Testing with Simes Inequality, in Particular
Hommel's Method
Description: Provides methods for closed testing using Simes local tests. In particular, calculates adjusted p-values for Hommel's multiple testing method, and provides lower confidence bounds for true discovery proportions. A robust but more conservative variant of the closed testing procedure that does not require the assumption of Simes inequality is also implemented. The methods have been described in detail in Goeman et al (Biometrika 106, 841-856, 2019).
Author: Jelle Goeman [aut, cre],
Rosa Meijer [aut],
Thijmen Krebs [aut]
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between hommel versions 1.6 dated 2021-12-17 and 1.8 dated 2025-01-14
ChangeLog | 9 +++ DESCRIPTION | 24 ++++++-- MD5 | 22 +++---- R/concentration-function.R | 8 ++ R/discoveries-function.R | 4 - man/concentration-function.Rd | 7 +- man/fdp-function.Rd | 118 +++++++++++++++++++++--------------------- man/hommel-class.Rd | 4 - man/hommel-function.Rd | 2 man/hommel-package.Rd | 60 +++++++++++---------- man/localtest-function.Rd | 2 src/hommel.cpp | 5 + 12 files changed, 148 insertions(+), 117 deletions(-)
Title: Build a Package from Rmarkdown Files
Description: Use Rmarkdown First method to build your package. Start your
package with documentation, functions, examples and tests in the same
unique file. Everything can be set from the Rmarkdown template file
provided in your project, then inflated as a package. Inflating the
template copies the relevant chunks and sections in the appropriate
files required for package development.
Author: Sebastien Rochette [aut] ,
Vincent Guyader [aut, cre] ,
Yohann Mansiaux [aut],
ThinkR [cph]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between fusen versions 0.6.0 dated 2024-05-14 and 0.7.0 dated 2025-01-14
DESCRIPTION | 32 MD5 | 167 +- NAMESPACE | 5 NEWS.md | 147 +- R/add_flat_template.R | 112 + R/build_fusen_chunks.R | 32 R/create_fusen_rsproject.R | 31 R/deprecate_flat_file.R | 18 R/fill_description.R | 10 R/get_all_created_funs.R | 5 R/get_package_structure.R | 36 R/globals.R | 5 R/inflate-utils.R | 116 + R/inflate.R | 124 + R/inflate_all.R | 44 R/inflate_all_utils.R | 2 R/init_share_on_github.R | 5 R/load_flat_functions.R | 3 R/pre_inflate_all_diagnosis_eval.R | 10 R/register_config_file.R | 113 + R/rename_flat_file.R | 27 R/sepuku.R |only R/sepuku_utils.R |only README.md | 197 +- build/vignette.rds |binary inst/doc/How-to-use-fusen.html | 308 ++-- inst/doc/Maintain-packages-with-fusen.html | 353 +++-- inst/doc/deal-with-a-fusen-flat-file.R | 8 inst/doc/deal-with-a-fusen-flat-file.Rmd | 10 inst/doc/deal-with-a-fusen-flat-file.html | 226 +-- inst/doc/draw-a-tree-of-your-package-files-and-functions.R | 6 inst/doc/draw-a-tree-of-your-package-files-and-functions.Rmd | 6 inst/doc/draw-a-tree-of-your-package-files-and-functions.html | 354 ++--- inst/doc/inflate-all-your-flat-files.R | 6 inst/doc/inflate-all-your-flat-files.Rmd | 10 inst/doc/inflate-all-your-flat-files.html | 313 ++-- inst/doc/register-files-in-config.R | 12 inst/doc/register-files-in-config.Rmd | 12 inst/doc/register-files-in-config.html | 459 +++--- inst/doc/share-on-a-github-website.html | 231 +-- inst/doc/switch-from-a-package-developed-with-fusen-to-a-classical-package.R |only inst/doc/switch-from-a-package-developed-with-fusen-to-a-classical-package.Rmd |only inst/doc/switch-from-a-package-developed-with-fusen-to-a-classical-package.html |only inst/doc/tips-and-tricks.Rmd | 8 inst/doc/tips-and-tricks.html | 659 +++++----- inst/flat-template-additional.Rmd | 4 inst/flat-template-full.Rmd | 18 inst/flat-template-minimal_package.Rmd | 4 inst/flat-template-teaching.Rmd | 7 inst/rmarkdown/templates/additional/skeleton/skeleton.Rmd | 4 inst/the-dev-history.Rmd | 8 man/check_not_registered_files.Rd | 6 man/deprecate_flat_file.Rd | 4 man/fill_description.Rd | 7 man/fusen-package.Rd | 8 man/get_package_structure.Rd | 6 man/inflate.Rd | 10 man/inflate_all.Rd | 11 man/register_all_to_config.Rd | 6 man/rename_flat_file.Rd | 4 man/sepuku.Rd |only man/sepuku_utils.Rd |only tests/testthat/config_fusen_register.yaml | 78 - tests/testthat/test-add_flat_template.R | 126 + tests/testthat/test-build_fusen_chunks.R | 66 - tests/testthat/test-deprecate_flat_file.R | 18 tests/testthat/test-fill_description.R | 36 tests/testthat/test-get_all_created_funs.R | 2 tests/testthat/test-get_package_structure.R | 8 tests/testthat/test-inflate-part1.R | 176 +- tests/testthat/test-inflate-part2.R | 220 ++- tests/testthat/test-inflate-part3.R |only tests/testthat/test-inflate_all.R | 257 +++ tests/testthat/test-inflate_all_utils.R | 77 - tests/testthat/test-inflate_qmd.R | 6 tests/testthat/test-inflate_utils.R | 43 tests/testthat/test-init_share_on_github.R | 2 tests/testthat/test-pre_inflate_all_diagnosis_eval.R | 11 tests/testthat/test-register_config_file.R | 287 ++-- tests/testthat/test-rename_flat_file.R | 23 tests/testthat/test-sepuku.R |only tests/testthat/test-sepuku_utils.R |only tests/testthat/test-skeleton.R | 3 tests/testthat/test-user-story.R | 12 vignettes/deal-with-a-fusen-flat-file.Rmd | 10 vignettes/draw-a-tree-of-your-package-files-and-functions.Rmd | 6 vignettes/inflate-all-your-flat-files.Rmd | 10 vignettes/register-files-in-config.Rmd | 12 vignettes/switch-from-a-package-developed-with-fusen-to-a-classical-package.Rmd |only vignettes/tips-and-tricks.Rmd | 8 90 files changed, 3512 insertions(+), 2314 deletions(-)
Title: Joint Clustering and Alignment of Functional Data
Description: Implementations of the k-means, hierarchical agglomerative and
DBSCAN clustering methods for functional data which allows for jointly
aligning and clustering curves. It supports functional data defined on
one-dimensional domains but possibly evaluating in multivariate codomains.
It supports functional data defined in arrays but also via the 'fd' and
'funData' classes for functional data defined in the 'fda' and 'funData'
packages respectively. It currently supports shift, dilation and affine
warping functions for functional data defined on the real line and uses the
SRVF framework to handle boundary-preserving warping for functional data
defined on a specific interval. Main reference for the k-means algorithm:
Sangalli L.M., Secchi P., Vantini S., Vitelli V. (2010) "k-mean alignment
for curve clustering" <doi:10.1016/j.csda.2009.12.008>. Main reference for
the SRVF framework: Tucker, J. D., Wu, W., & Srivastava, A. (2013)
"Generative models for functional data using phase and [...truncated...]
Author: Aymeric Stamm [aut, cre] ,
Laura Sangalli [ctb],
Piercesare Secchi [ctb],
Simone Vantini [ctb],
Valeria Vitelli [ctb],
Alessandro Zito [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between fdacluster versions 0.4.0 dated 2025-01-12 and 0.4.1 dated 2025-01-14
DESCRIPTION | 10 +++++----- MD5 | 32 +++++++++++++++++--------------- NEWS.md | 7 +++++++ R/compare-caps.R | 4 ++-- R/fdadbscan.R | 2 +- R/fdadist.R | 6 +++--- R/fdahclust.R | 2 +- R/fdakmeans.R | 34 +++++++++++++++++----------------- R/utils.R | 11 ++++++----- man/compare_caps.Rd | 8 ++++---- man/fdacluster-package.Rd | 2 +- man/fdadbscan.Rd | 20 ++++++++++---------- man/fdadist.Rd | 6 +++--- man/fdahclust.Rd | 20 ++++++++++---------- man/fdakmeans.Rd | 20 ++++++++++---------- src/kumaraswamyWarpingClass.cpp |only src/kumaraswamyWarpingClass.h |only tests/testthat/test-fdakmeans.R | 2 +- 18 files changed, 98 insertions(+), 88 deletions(-)
Title: Create and Maintain a Relational Database of Data from
PubMed/MEDLINE
Description: Provides a simple interface for extracting various elements from
the publicly available PubMed XML files, incorporating PubMed's regular
updates, and combining the data with the NIH Open Citation Collection. See
Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut],
Elliot Outland [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between pmparser versions 1.0.20 dated 2024-01-13 and 1.0.21 dated 2025-01-14
pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/baseline/pubmed24n1219.xml.gz |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/baseline/pubmed24n1219.xml.gz.md5 |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/pubmed24n1219.rds |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/pubmed24n1220.rds |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed24n1220.xml.gz |only pmparser-1.0.20/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed24n1220.xml.gz.md5 |only pmparser-1.0.21/pmparser/DESCRIPTION | 8 pmparser-1.0.21/pmparser/MD5 | 38 pmparser-1.0.21/pmparser/NEWS.md | 3 pmparser-1.0.21/pmparser/build/vignette.rds |binary pmparser-1.0.21/pmparser/tests/testthat/parsing_tables/create_parsing_tables_no_suffix.db |binary pmparser-1.0.21/pmparser/tests/testthat/parsing_tables/create_parsing_tables_with_suffix.db |binary pmparser-1.0.21/pmparser/tests/testthat/parsing_tables/get_parsing_tables_no_suffix.rds |binary pmparser-1.0.21/pmparser/tests/testthat/parsing_tables/get_parsing_tables_with_suffix.rds |binary pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/baseline/pubmed25n1274.xml.gz |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/baseline/pubmed25n1274.xml.gz.md5 |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/file_info_postdown.csv | 8 pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/file_info_predown_all.csv | 2536 +++++----- pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/file_info_predown_baseline.csv | 2493 +++++---- pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/open_citation_collection.zip |binary pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/pmdb_sample_create.db |binary pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/pmdb_sample_update.db |binary pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/pubmed25n1274.rds |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/pubmed25n1275.rds |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed25n1275.xml.gz |only pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/updatefiles/pubmed25n1275.xml.gz.md5 |only 26 files changed, 2583 insertions(+), 2503 deletions(-)
Title: Co-Data Learning for Bayesian Additive Regression Trees
Description: Estimate prior variable weights for Bayesian Additive Regression
Trees (BART). These weights correspond to the probabilities of the variables
being selected in the splitting rules of the sum-of-trees.
Weights are estimated using empirical Bayes and external information on
the explanatory variables (co-data).
BART models are fitted using the 'dbarts' 'R' package.
See Goedhart and others (2023) <doi:10.48550/arXiv.2311.09997> for details.
Author: Jeroen M. Goedhart [aut, cre, cph]
,
Thomas Klausch [aut],
Mark A. van de Wiel [aut],
Vincent Dorie [ctb] ,
Hanarth Fonds [fnd]
Maintainer: Jeroen M. Goedhart <jeroengoed@gmail.com>
Diff between EBcoBART versions 1.1.0 dated 2024-09-26 and 1.1.1 dated 2025-01-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/EBcoBART_Functions.R | 30 +++++++++++++++--------------- R/data.R | 6 +++--- man/Bloodplatelet.Rd | 2 +- man/Dat_EBcoBART.Rd | 20 ++++++++++---------- man/EBcoBART.Rd | 4 ++-- man/Lymphoma.Rd | 4 ++-- 9 files changed, 49 insertions(+), 44 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.1.2 dated 2024-11-12 and 2.2.0 dated 2025-01-14
GitStats-2.1.2/GitStats/inst/roche_get_commits_workflow.R |only GitStats-2.1.2/GitStats/inst/roche_get_files_workflow.R |only GitStats-2.1.2/GitStats/inst/roche_get_release_logs_workflow.R |only GitStats-2.1.2/GitStats/man/get_files_content.Rd |only GitStats-2.1.2/GitStats/man/get_files_structure.Rd |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_commits-GitHub.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_commits-GitStats.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_content-GitHub.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_content-GitLab.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_structure-GitHub.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_structure-GitLab.md |only GitStats-2.1.2/GitStats/tests/testthat/_snaps/get_files_structure-GitStats.md |only GitStats-2.1.2/GitStats/tests/testthat/test-get_commits-GitHub.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_commits-GitLab.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_commits-GitStats.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_content-GitHub.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_content-GitLab.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_content-GitStats.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_structure-GitHub.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_structure-GitLab.R |only GitStats-2.1.2/GitStats/tests/testthat/test-get_files_structure-GitStats.R |only GitStats-2.2.0/GitStats/DESCRIPTION | 6 GitStats-2.2.0/GitStats/MD5 | 194 - GitStats-2.2.0/GitStats/NAMESPACE | 4 GitStats-2.2.0/GitStats/NEWS.md | 23 GitStats-2.2.0/GitStats/R/EngineGraphQL.R | 14 GitStats-2.2.0/GitStats/R/EngineGraphQLGitHub.R | 169 + GitStats-2.2.0/GitStats/R/EngineGraphQLGitLab.R | 130 - GitStats-2.2.0/GitStats/R/EngineRestGitHub.R | 166 + GitStats-2.2.0/GitStats/R/EngineRestGitLab.R | 185 + GitStats-2.2.0/GitStats/R/GQLQueryGitHub.R | 22 GitStats-2.2.0/GitStats/R/GQLQueryGitLab.R | 6 GitStats-2.2.0/GitStats/R/GitHost.R | 1027 +++++++--- GitStats-2.2.0/GitStats/R/GitHostGitHub.R | 173 - GitStats-2.2.0/GitStats/R/GitHostGitLab.R | 323 +-- GitStats-2.2.0/GitStats/R/GitStats-package.R | 1 GitStats-2.2.0/GitStats/R/GitStats.R | 425 ---- GitStats-2.2.0/GitStats/R/get_commits.R |only GitStats-2.2.0/GitStats/R/get_files.R |only GitStats-2.2.0/GitStats/R/get_repos.R |only GitStats-2.2.0/GitStats/R/gitstats_functions.R | 456 ---- GitStats-2.2.0/GitStats/R/global.R | 7 GitStats-2.2.0/GitStats/R/message_handler.R | 16 GitStats-2.2.0/GitStats/R/set_host.R |only GitStats-2.2.0/GitStats/R/test_helpers.R | 47 GitStats-2.2.0/GitStats/R/utils.R | 20 GitStats-2.2.0/GitStats/README.md | 172 + GitStats-2.2.0/GitStats/inst/cache_workflow.R | 12 GitStats-2.2.0/GitStats/inst/doc/get_repos_with_code.R | 8 GitStats-2.2.0/GitStats/inst/doc/get_repos_with_code.Rmd | 8 GitStats-2.2.0/GitStats/inst/doc/get_repos_with_code.html | 8 GitStats-2.2.0/GitStats/inst/doc/set_hosts.R | 24 GitStats-2.2.0/GitStats/inst/doc/set_hosts.Rmd | 51 GitStats-2.2.0/GitStats/inst/doc/set_hosts.html | 91 GitStats-2.2.0/GitStats/inst/example_workflow.R | 50 GitStats-2.2.0/GitStats/inst/get_commits_workflow.R | 25 GitStats-2.2.0/GitStats/inst/get_files_workflow.R | 44 GitStats-2.2.0/GitStats/inst/get_storage_workflow.R | 6 GitStats-2.2.0/GitStats/inst/package_usage_workflow.R | 25 GitStats-2.2.0/GitStats/inst/roche |only GitStats-2.2.0/GitStats/inst/set_hosts.R |only GitStats-2.2.0/GitStats/inst/set_many_repos.R |only GitStats-2.2.0/GitStats/man/get_R_package_usage.Rd | 8 GitStats-2.2.0/GitStats/man/get_commits.Rd | 8 GitStats-2.2.0/GitStats/man/get_commits_stats.Rd | 24 GitStats-2.2.0/GitStats/man/get_files.Rd |only GitStats-2.2.0/GitStats/man/get_release_logs.Rd | 6 GitStats-2.2.0/GitStats/man/get_repos.Rd | 8 GitStats-2.2.0/GitStats/man/get_repos_urls.Rd | 8 GitStats-2.2.0/GitStats/man/get_storage.Rd | 6 GitStats-2.2.0/GitStats/man/get_users.Rd | 9 GitStats-2.2.0/GitStats/man/is_verbose.Rd | 4 GitStats-2.2.0/GitStats/man/set_github_host.Rd | 12 GitStats-2.2.0/GitStats/man/set_gitlab_host.Rd | 12 GitStats-2.2.0/GitStats/man/show_orgs.Rd | 4 GitStats-2.2.0/GitStats/man/verbose_off.Rd | 4 GitStats-2.2.0/GitStats/man/verbose_on.Rd | 4 GitStats-2.2.0/GitStats/tests/testthat/_snaps/01-get_repos-GitHub.md | 72 GitStats-2.2.0/GitStats/tests/testthat/_snaps/01-get_repos-GitLab.md | 26 GitStats-2.2.0/GitStats/tests/testthat/_snaps/02-get_commits-GitHub.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/02-get_commits-GitLab.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/02-get_commits-GitStats.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/03-get_files_structure-GitHub.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/03-get_files_structure-GitLab.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/04-get_files_content-GitHub.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/04-get_files_content-GitLab.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/05-get_files.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/get_commits_stats.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/get_release-GitHub.md | 8 GitStats-2.2.0/GitStats/tests/testthat/_snaps/get_release-GitLab.md | 16 GitStats-2.2.0/GitStats/tests/testthat/_snaps/get_urls_repos-GitHub.md |only GitStats-2.2.0/GitStats/tests/testthat/_snaps/helpers.md | 16 GitStats-2.2.0/GitStats/tests/testthat/_snaps/set_host.md | 70 GitStats-2.2.0/GitStats/tests/testthat/helper-expect-responses.R | 12 GitStats-2.2.0/GitStats/tests/testthat/helper-fixtures.R | 160 - GitStats-2.2.0/GitStats/tests/testthat/setup.R | 22 GitStats-2.2.0/GitStats/tests/testthat/test-01-get_repos-GitHub.R | 313 ++- GitStats-2.2.0/GitStats/tests/testthat/test-01-get_repos-GitLab.R | 139 + GitStats-2.2.0/GitStats/tests/testthat/test-01-get_repos-GitStats.R | 24 GitStats-2.2.0/GitStats/tests/testthat/test-02-get_commits-GitHub.R |only GitStats-2.2.0/GitStats/tests/testthat/test-02-get_commits-GitLab.R |only GitStats-2.2.0/GitStats/tests/testthat/test-02-get_commits-GitStats.R |only GitStats-2.2.0/GitStats/tests/testthat/test-03-get_files_structure-GitHub.R |only GitStats-2.2.0/GitStats/tests/testthat/test-03-get_files_structure-GitLab.R |only GitStats-2.2.0/GitStats/tests/testthat/test-04-get_files_content-GitHub.R |only GitStats-2.2.0/GitStats/tests/testthat/test-04-get_files_content-GitLab.R |only GitStats-2.2.0/GitStats/tests/testthat/test-05-get_files.R |only GitStats-2.2.0/GitStats/tests/testthat/test-GitHost-helpers.R | 12 GitStats-2.2.0/GitStats/tests/testthat/test-get_commits_stats.R |only GitStats-2.2.0/GitStats/tests/testthat/test-get_release-GitHub.R | 93 GitStats-2.2.0/GitStats/tests/testthat/test-get_release-GitLab.R | 117 + GitStats-2.2.0/GitStats/tests/testthat/test-get_storage.R | 12 GitStats-2.2.0/GitStats/tests/testthat/test-get_urls_repos-GitHub.R | 211 +- GitStats-2.2.0/GitStats/tests/testthat/test-get_urls_repos-GitLab.R | 119 - GitStats-2.2.0/GitStats/tests/testthat/test-get_urls_repos-GitStats.R | 30 GitStats-2.2.0/GitStats/tests/testthat/test-get_usage_R_package.R | 2 GitStats-2.2.0/GitStats/tests/testthat/test-helpers.R | 24 GitStats-2.2.0/GitStats/tests/testthat/test-set_host.R | 34 GitStats-2.2.0/GitStats/vignettes/get_repos_with_code.Rmd | 8 GitStats-2.2.0/GitStats/vignettes/set_hosts.Rmd | 51 120 files changed, 3470 insertions(+), 2176 deletions(-)
Title: Object Oriented Implementation of Probability Models
Description: Implements S4 classes for probability models based on packages 'distr' and
'distrEx'.
Author: Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
R Core Team [ctb, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrMod versions 2.9.6 dated 2024-10-23 and 2.9.7 dated 2025-01-14
DESCRIPTION | 10 +-- MD5 | 12 +-- inst/CITATION | 4 - inst/NEWS | 11 +++ inst/doc/distrMod.pdf |binary man/0distrMod-package.Rd | 8 +- tests/Examples/distrMod-Ex.Rout.save | 116 ++++++++++++----------------------- 7 files changed, 68 insertions(+), 93 deletions(-)
Title: Bootstrap p-Values
Description: Computation of bootstrap p-values through inversion of confidence intervals, including convenience functions for regression models.
Author: Mans Thulin [aut, cre]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Diff between boot.pval versions 0.5 dated 2023-09-28 and 0.6 dated 2025-01-14
DESCRIPTION | 12 ++++++++---- MD5 | 32 +++++++++++++++++++------------- NEWS.md | 3 +++ R/boot.pval.R | 6 +++--- R/boot_summary.R | 22 +++++++++++++--------- R/censboot_summary.R | 7 ++++--- R/summary_to_gt.R | 4 ---- README.md | 29 ++++++++++++++++++++++++++--- build/partial.rdb |binary build/vignette.rds |only inst/REFERENCES.bib | 8 ++++---- inst/doc |only man/boot.pval.Rd | 4 ++-- man/boot_summary.Rd | 6 +++--- man/censboot_summary.Rd | 2 +- man/figures |only man/summary_to_gt.Rd | 9 +-------- vignettes |only 18 files changed, 87 insertions(+), 57 deletions(-)
Title: Likelihood-Free Parameter Estimation using Neural Networks
Description: An 'R' interface to the 'Julia' package 'NeuralEstimators.jl'. The package facilitates the user-friendly development of neural point estimators, which are neural networks that map data to a point summary of the posterior distribution. These estimators are likelihood-free and amortised, in the sense that, after an initial setup cost, inference from observed data can be made in a fraction of the time required by conventional approaches; see Sainsbury-Dale, Zammit-Mangion, and Huser (2024) <doi:10.1080/00031305.2023.2249522> for further details and an accessible introduction. The package also enables the construction of neural networks that approximate the likelihood-to-evidence ratio in an amortised manner, allowing one to perform inference based on the likelihood function or the entire posterior distribution; see Zammit-Mangion, Sainsbury-Dale, and Huser (2024, Sec. 5.2) <doi:10.48550/arXiv.2404.12484>, and the references therein. The package accommodates any model for which [...truncated...]
Author: Matthew Sainsbury-Dale [aut, cre]
Maintainer: Matthew Sainsbury-Dale <msainsburydale@gmail.com>
Diff between NeuralEstimators versions 0.1.2 dated 2024-12-19 and 0.1.3 dated 2025-01-14
DESCRIPTION | 8 MD5 | 18 NAMESPACE | 2 R/core.R | 10 R/missingdata.R | 203 +++++++++++ README.md | 76 ++-- inst/doc/NeuralEstimators.html | 698 ++++++++++++++++++++++++++------------ man/spatialgraph.Rd |only man/spatialgraphlist.Rd |only tests/testthat/test-core.R | 1 tests/testthat/test-missingdata.R | 62 +++ 11 files changed, 802 insertions(+), 276 deletions(-)
More information about NeuralEstimators at CRAN
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Title: Documentation for 'distr' Family of R Packages
Description: Provides documentation in form of a common vignette to packages 'distr',
'distrEx', 'distrMod', 'distrSim', 'distrTEst', 'distrTeach', and 'distrEllipse'.
Author: Florian Camphausen [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrDoc versions 2.8.4 dated 2024-10-24 and 2.8.5 dated 2025-01-14
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- inst/CITATION | 8 ++++---- inst/NEWS | 10 ++++++++++ inst/doc/distr.pdf |binary man/0distrDoc-package.Rd | 8 ++++---- 6 files changed, 32 insertions(+), 22 deletions(-)
Title: Sourcing Archaeological Materials by Chemical Composition
Description: Exploration and analysis of compositional data in the
framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package
provides tools for chemical fingerprinting and source tracking of
ancient materials.
Author: Nicolas Frerebeau [aut, cre] ,
Anne Philippe [aut] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between nexus versions 0.3.0 dated 2024-09-03 and 0.4.0 dated 2025-01-14
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Title: Utility-Based Optimal Phase II/III Drug Development Planning
Description: Plan optimal sample size allocation and go/no-go decision rules
for phase II/III drug development programs with time-to-event, binary or
normally distributed endpoints when assuming fixed treatment effects or a
prior distribution for the treatment effect, using methods from Kirchner et al.
(2016) <doi:10.1002/sim.6624> and Preussler (2020). Optimal is in the sense of
maximal expected utility, where the utility is a function taking into account
the expected cost and benefit of the program. It is possible to extend to more
complex settings with bias correction (Preussler S et al. (2020)
<doi:10.1186/s12874-020-01093-w>), multiple phase III trials (Preussler et
al. (2019) <doi:10.1002/bimj.201700241>), multi-arm trials (Preussler et al.
(2019) <doi:10.1080/19466315.2019.1702092>), and multiple endpoints
(Kieser et al. (2018) <doi:10.1002/pst.1861>).
Author: Stella Erdmann [aut],
Johannes Cepicka [aut],
Marietta Kirchner [aut],
Meinhard Kieser [aut],
Lukas D. Sauer [aut, cre]
Maintainer: Lukas D. Sauer <sauer@imbi.uni-heidelberg.de>
Diff between drugdevelopR versions 1.0.1 dated 2024-01-10 and 1.0.2 dated 2025-01-14
DESCRIPTION | 8 MD5 | 191 +++---- NAMESPACE | 288 +++++----- NEWS.md | 14 R/drugdevelopR-package.R |only R/optimal_bias.R | 44 - R/optimal_bias_binary.R | 539 ++++++++++++++------ R/optimal_bias_generic.R | 50 - R/optimal_bias_normal.R | 43 - R/optimal_binary.R | 12 R/optimal_generic.R | 46 - R/optimal_multiarm.R | 17 R/optimal_multiarm_binary.R | 17 R/optimal_multiarm_generic.R | 40 - R/optimal_multiarm_normal.R | 21 R/optimal_multiple_normal.R | 17 R/optimal_multiple_tte.R | 15 R/optimal_multitrial.R | 586 ++++++++++++++++------ R/optimal_multitrial_binary.R | 37 + R/optimal_multitrial_normal.R | 31 + R/optimal_normal.R | 14 R/optimal_return_doc.R | 6 R/optimal_tte.R | 14 R/print.drugdevelopResult.R | 547 ++++++++++---------- README.md | 262 ++++----- build/partial.rdb |only build/vignette.rds |binary inst/doc/Bias_adjustment.R | 28 - inst/doc/Bias_adjustment.Rmd | 248 ++++----- inst/doc/Bias_adjustment.html | 6 inst/doc/Binary_outcomes.R | 26 inst/doc/Binary_outcomes.html | 4 inst/doc/Fixed_and_prior_distributions.R | 24 inst/doc/Fixed_and_prior_distributions.html | 4 inst/doc/Interpreting_Output.R | 24 inst/doc/Interpreting_Output.html | 4 inst/doc/Introduction-to-drugdevelopR.R | 24 inst/doc/Introduction-to-drugdevelopR.Rmd | 238 ++++---- inst/doc/Introduction-to-drugdevelopR.html | 4 inst/doc/More_Parameters.R | 140 ++--- inst/doc/More_Parameters.html | 14 inst/doc/Multiarm_Trials.R | 16 inst/doc/Multiarm_Trials.html | 2 inst/doc/Multiple_Endpoints.R | 52 - inst/doc/Multiple_Endpoints.html | 8 inst/doc/Multitrial.R | 22 inst/doc/Multitrial.html | 8 inst/doc/Package_validation.R | 4 inst/doc/Package_validation.Rmd | 98 +-- inst/doc/Package_validation.html | 6 inst/doc/Time-to-event_outcomes.R | 26 inst/doc/Time-to-event_outcomes.html | 4 man/drugdevelopR-package.Rd |only man/drugdevelopResult.Rd | 38 - man/get_sample_multiple_normal.Rd | 52 - man/get_sample_multiple_tte.Rd | 52 - man/optimal_bias.Rd | 6 man/optimal_bias_binary.Rd | 4 man/optimal_bias_normal.Rd | 4 man/optimal_binary.Rd | 6 man/optimal_generic.Rd | 70 +- man/optimal_multiarm.Rd | 4 man/optimal_multiarm_binary.Rd | 4 man/optimal_multiarm_normal.Rd | 4 man/optimal_multiple_generic.Rd | 56 +- man/optimal_multiple_normal.Rd | 4 man/optimal_multiple_tte.Rd | 4 man/optimal_multitrial.Rd | 6 man/optimal_multitrial_binary.Rd | 4 man/optimal_multitrial_generic.Rd | 54 +- man/optimal_multitrial_normal.Rd | 4 man/optimal_normal.Rd | 5 man/optimal_return_doc.Rd | 46 - man/optimal_tte.Rd | 6 man/print.drugdevelopResult.Rd | 88 +-- man/print_drugdevelopResult_helper.Rd | 40 - tests/testthat/test-function_bias_binary.R | 272 +++++----- tests/testthat/test-function_bias_normal.R | 304 +++++------ tests/testthat/test-functions_bias.R | 134 ++--- tests/testthat/test-functions_binary.R | 82 +-- tests/testthat/test-functions_multiple_normal.R | 72 +- tests/testthat/test-functions_multiple_tte.R | 134 ++--- tests/testthat/test-functions_multitrial.R | 412 +++++++-------- tests/testthat/test-functions_multitrial_binary.R | 356 ++++++------- tests/testthat/test-functions_multitrial_normal.R | 350 ++++++------- tests/testthat/test-optimal_bias.R | 168 +++--- tests/testthat/test-optimal_bias_binary.R | 92 +-- tests/testthat/test-optimal_bias_normal.R | 92 +-- tests/testthat/test-optimal_multiarm.R | 26 tests/testthat/test-optimal_multiarm_binary.R | 24 tests/testthat/test-optimal_multiarm_normal.R | 26 tests/testthat/test-optimal_multitrial_binary.R | 2 tests/testthat/test-optimal_multitrial_normal.R | 26 tests/testthat/test-optimal_return_doc.R | 46 - tests/testthat/test-print.drugdevelopResult.R | 2 vignettes/Bias_adjustment.Rmd | 248 ++++----- vignettes/Introduction-to-drugdevelopR.Rmd | 238 ++++---- vignettes/Package_validation.Rmd | 98 +-- 98 files changed, 4140 insertions(+), 3518 deletions(-)
Title: The Analysis of Dark Adaptation Data
Description: The recovery of visual sensitivity in a dark environment is known
as dark adaptation. In a clinical or research setting the recovery is typically
measured after a dazzling flash of light and can be described by the Mahroo,
Lamb and Pugh (MLP) model of dark adaptation. The functions in this package take
dark adaptation data and use nonlinear regression to find the parameters of the
model that 'best' describe the data. They do this by firstly, generating rapid
initial objective estimates of data adaptation parameters, then a multi-start
algorithm is used to reduce the possibility of a local minimum. There is also a
bootstrap method to calculate parameter confidence intervals. The functions rely
upon a 'dark' list or object. This object is created as the first step in the
workflow and parts of the object are updated as it is processed.
Author: Jeremiah MF Kelly [aut, cre, cph]
Maintainer: Jeremiah MF Kelly <emkayoh@mac.com>
Diff between Dark versions 0.9.8 dated 2016-06-02 and 0.9.9 dated 2025-01-14
DESCRIPTION | 24 + MD5 | 53 ++-- NEWS.md |only R/BestFit.R | 4 R/Declutter.R | 2 README.md | 14 - build/vignette.rds |binary inst/WORDLIST |only inst/doc/Workflow.R | 22 - inst/doc/Workflow.html | 548 +++++++++++++++++++++++++++++++++----------- inst/doc/parameter_exp.R | 6 inst/doc/parameter_exp.html | 310 ++++++++++++++++++++++-- man/AICc.Rd | 10 man/BestFit.Rd | 9 man/BootDark.Rd | 11 man/Dark-package.Rd | 6 man/Declutter.Rd | 9 man/GetData.Rd | 7 man/H.Rd | 15 - man/ModelSelect.Rd | 8 man/MultiStart.Rd | 6 man/P3.Rd | 9 man/P5c.Rd | 9 man/P6c.Rd | 9 man/P7c.Rd | 9 man/Start.Rd | 6 man/TestData.Rd | 6 man/dark.Rd | 4 tests/spelling.R |only 29 files changed, 838 insertions(+), 278 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a sample of suitable variables of
cost and effectiveness / utility for two or more interventions,
e.g. from a Bayesian model in the form of MCMC simulations.
This package computes the most cost-effective alternative and
produces graphical summaries and probabilistic sensitivity analysis,
see Baio et al (2017) <doi:10.1007/978-3-319-55718-2>.
Author: Gianluca Baio [aut, cre, cph] ,
Andrea Berardi [aut] ,
Anna Heath [aut] ,
Nathan Green [aut]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between BCEA versions 2.4.6 dated 2024-02-16 and 2.4.7 dated 2025-01-14
DESCRIPTION | 17 MD5 | 150 ++-- NAMESPACE | 318 ++++----- NEWS.md | 20 R/CEriskav.R | 47 - R/CEriskav_plot_graph.R | 4 R/bcea.R | 69 - R/ceac_plot_graph.R | 8 R/ceaf.plot.R | 10 R/ceef_plot_graph.R | 5 R/ceplane.plot.R | 56 - R/ceplane_base_params.R | 2 R/ceplane_base_params_xxx.R | 8 R/ceplane_geom_params.R | 4 R/ceplane_ggplot_params.R | 19 R/ceplane_plot_graph.R | 12 R/compute_eib_cri.R | 4 R/contour_graph.R | 2 R/diag.evppi.R | 1 R/eib.plot.R | 27 R/eib_params_ggplot.R | 8 R/eib_plot_graph.R | 9 R/evi.plot.R | 5 R/evi.plot.mixedAn.R | 2 R/evi_plot_graph.R | 16 R/evppi.R | 46 - R/evppi.default.R | 6 R/evppi_plot_ggplot.R | 3 R/helper_ggplot_params.R | 17 R/ib.plot.R | 2 R/info_rank_graph.R | 17 R/inforank_params.R | 8 R/make_legend_ggplot.R | 29 R/mce.plot.R | 34 R/misc_helpers.R | 7 R/plot.bcea.R | 19 R/plot.evppi.R | 5 R/prep_ceplane_params.R | 34 R/prep_contour_params.R | 10 R/prep_eib_params.R | 8 R/prepare_ceac_params.R | 3 R/select_plot_type.R | 5 R/themes_ggplot.R | 2 README.md | 6 build/partial.rdb |binary inst/doc/CEriskav.R | 6 inst/doc/CEriskav.html | 60 - inst/doc/Set_bcea_parameters.R | 14 inst/doc/bcea.html | 18 inst/doc/ceac.R | 10 inst/doc/ceac.Rmd | 17 inst/doc/ceac.html | 170 ++-- inst/doc/ceef.R | 16 inst/doc/ceef.html | 88 +- inst/doc/ceplane.R | 67 + inst/doc/ceplane.Rmd | 155 ++++ inst/doc/ceplane.html | 149 +++- inst/doc/contour.html | 62 - inst/doc/eib.html | 44 - inst/doc/paired_vs_multiple_comps.html | 8 man/BCEA-package.Rd | 1 man/CEriskav_assign.Rd | 45 - man/bcea.Rd | 70 -- man/ceplane.plot.Rd | 51 - man/ceplane_ggplot_params.Rd | 4 man/ceplane_plot_graph.Rd | 2 man/eib.plot.Rd | 2 man/evppi.Rd | 49 - man/get_fitted_.Rd | 30 man/is.rel.Rd |only man/plot.bcea.Rd | 11 man/plot.evppi.Rd | 4 man/prep_ceplane_params.Rd | 4 man/prep_contour_params.Rd |only tests/testthat/test-evppi.R | 1150 ++++++++++++++++----------------- vignettes/ceac.Rmd | 17 vignettes/ceplane.Rmd | 155 ++++ 77 files changed, 2088 insertions(+), 1475 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>;
Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>;
Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank mo [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Waldir Leoncio [aut],
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 2.2.2 dated 2024-08-17 and 2.2.3 dated 2025-01-14
DESCRIPTION | 6 +- MD5 | 52 +++++++++---------- NEWS.md | 5 + R/tidy_mcmc.R | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/BayesMallows.html | 36 ++++++------- inst/doc/SMC-Mallows.html | 38 ++++++------- inst/doc/parallel_chains.html | 22 ++++---- inst/examples/compute_mallows_sequentially_example.R | 2 inst/examples/estimate_partition_function_example.R | 2 inst/examples/sample_prior_example.R | 2 man/compute_mallows_sequentially.Rd | 2 man/estimate_partition_function.Rd | 2 man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/sample_prior.Rd | 2 tests/testthat.R | 6 ++ tests/testthat/test-acceptance_ratio.R | 1 tests/testthat/test-assign_cluster.R | 25 +++++++++ tests/testthat/test-compute_mallows.R | 1 tests/testthat/test-estimate_partition_function.R | 1 tests/testthat/test-plot_top_k.R | 1 tests/testthat/test-setup_rank_data.R | 1 tests/testthat/test-smc_pairwise.R | 1 tests/testthat/test-smc_update_correctness.R | 1 27 files changed, 134 insertions(+), 79 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <r.puggaard@phonetik.uni-muenchen.de>
Diff between praatpicture versions 1.3.0 dated 2024-10-14 and 1.4.0 dated 2025-01-14
praatpicture-1.3.0/praatpicture/LICENSE |only praatpicture-1.4.0/praatpicture/DESCRIPTION | 8 praatpicture-1.4.0/praatpicture/MD5 | 44 praatpicture-1.4.0/praatpicture/NEWS.md | 230 - praatpicture-1.4.0/praatpicture/R/emupicture.R | 193 - praatpicture-1.4.0/praatpicture/R/formantplot.R | 371 +- praatpicture-1.4.0/praatpicture/R/intensityplot.R | 196 - praatpicture-1.4.0/praatpicture/R/pitchplot.R | 310 + praatpicture-1.4.0/praatpicture/R/praatanimation.R | 559 +-- praatpicture-1.4.0/praatpicture/R/praatpicture.R | 1611 +++++----- praatpicture-1.4.0/praatpicture/R/specplot.R | 890 +++-- praatpicture-1.4.0/praatpicture/R/tgplot.R | 220 - praatpicture-1.4.0/praatpicture/R/waveplot.R | 254 - praatpicture-1.4.0/praatpicture/inst/CITATION | 18 praatpicture-1.4.0/praatpicture/inst/shiny/shiny_praatpicture/rsconnect |only praatpicture-1.4.0/praatpicture/inst/shiny/shiny_praatpicture/server.R | 1413 ++++---- praatpicture-1.4.0/praatpicture/inst/shiny/shiny_praatpicture/ui.R | 700 ++-- praatpicture-1.4.0/praatpicture/man/formantplot.Rd | 10 praatpicture-1.4.0/praatpicture/man/intensityplot.Rd | 10 praatpicture-1.4.0/praatpicture/man/pitchplot.Rd | 10 praatpicture-1.4.0/praatpicture/man/praatpicture.Rd | 66 praatpicture-1.4.0/praatpicture/man/specplot.Rd | 39 praatpicture-1.4.0/praatpicture/man/tgplot.Rd | 9 praatpicture-1.4.0/praatpicture/man/waveplot.Rd | 11 24 files changed, 3987 insertions(+), 3185 deletions(-)
Title: Secure in-Browser and Database Storage for 'shiny' Inputs,
Outputs, Views and User Likes
Description: Store persistent and synchronized data from 'shiny' inputs within the browser. Refresh 'shiny' applications and preserve user-inputs over multiple sessions. A database-like storage format is implemented using 'Dexie.js' <https://dexie.org>, a minimal wrapper for 'IndexedDB'. Transfer browser link parameters to 'shiny' input or output values. Store app visitor views, likes and followers.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between shinyStorePlus versions 1.3 dated 2024-12-06 and 1.4 dated 2025-01-14
DESCRIPTION | 6 +- MD5 | 38 ++++++++-------- NAMESPACE | 2 NEWS.md | 6 -- R/includes.R | 4 - R/persistentObserveEvent.R |only R/setup.R | 2 build/vignette.rds |binary inst/doc/introduction_to_shinystoreplus.html | 4 - inst/doc/shinystoreplus_v08.html | 4 - inst/doc/shinystoreplus_v12.html | 4 - inst/doc/store_shiny_visitor_views_likes_followers.Rmd | 4 - inst/doc/store_shiny_visitor_views_likes_followers.html | 10 ++-- inst/doc/using_shinystoreplus.html | 4 - inst/example/shinyObserveOnce |only inst/scripts/misc.js |only inst/scripts/rpkg.js | 9 +++ inst/scripts/shinystoreplus.js | 15 +++++- man/initStore.Rd | 6 +- man/observeonce.Rd |only man/setupStorage.Rd | 2 vignettes/store_shiny_visitor_views_likes_followers.Rmd | 4 - 22 files changed, 74 insertions(+), 50 deletions(-)
More information about shinyStorePlus at CRAN
Permanent link
Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic
and Atmospheric Administration (NOAA) Integrated Surface Database
(ISD, see
<https://www.ncei.noaa.gov/products/land-based-station/integrated-surface-database>).
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.9.8 dated 2023-06-05 and 0.9.9 dated 2025-01-14
worldmet-0.9.8/worldmet/build |only worldmet-0.9.8/worldmet/inst |only worldmet-0.9.8/worldmet/man/figures/README-map.png |only worldmet-0.9.8/worldmet/man/figures/README-windRose-1.png |only worldmet-0.9.8/worldmet/vignettes |only worldmet-0.9.9/worldmet/DESCRIPTION | 46 ++-- worldmet-0.9.9/worldmet/LICENSE |only worldmet-0.9.9/worldmet/MD5 | 31 +- worldmet-0.9.9/worldmet/NEWS.md |only worldmet-0.9.9/worldmet/R/getMeta.R | 14 - worldmet-0.9.9/worldmet/R/metNOAA.R | 19 + worldmet-0.9.9/worldmet/R/weatherCodes.R | 12 - worldmet-0.9.9/worldmet/R/worldmet-package.R | 6 worldmet-0.9.9/worldmet/README.md | 157 +++++--------- worldmet-0.9.9/worldmet/data/weatherCodes.rda |binary worldmet-0.9.9/worldmet/man/figures/feature-banner.png |only worldmet-0.9.9/worldmet/man/figures/logo.png |only worldmet-0.9.9/worldmet/man/importNOAA.Rd | 9 worldmet-0.9.9/worldmet/man/weatherCodes.Rd | 15 + worldmet-0.9.9/worldmet/man/worldmet-package.Rd | 12 - 20 files changed, 153 insertions(+), 168 deletions(-)
Title: Spatial Empirical Dynamic Modeling
Description: Integrates empirical dynamic modeling (EDM) with geospatial cross-sectional data to analyze causality via geographical convergent cross mapping (GCCM) described in Gao et al. (2023) <doi:10.1038/s41467-023-41619-6>.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between spEDM versions 1.1 dated 2024-12-19 and 1.2 dated 2025-01-14
DESCRIPTION | 10 - MD5 | 53 +++---- NAMESPACE | 6 NEWS.md | 12 + R/RcppExports.R | 8 - R/ccm_formatoutput.R |only R/gccm.R | 126 ++++++++--------- R/globals.R | 2 R/spEDM-package.R | 8 - R/variable_check.R |only R/xmapdf.R |only R/zzz.R | 2 inst/doc/GCCM.Rmd | 299 +++++++++------------------------------- inst/doc/GCCM.html | 325 +++++++++++--------------------------------- man/figures/gccm/fig1-1.png |binary man/figures/gccm/fig2-1.png |binary man/figures/gccm/fig3-1.png |binary man/gccm.Rd | 47 +++++- src/CppGridUtils.cpp | 1 src/CppGridUtils.h | 2 src/GCCM4Grid.cpp | 45 +++--- src/GCCM4Grid.h | 16 +- src/GCCM4Lattice.cpp | 44 +++-- src/GCCM4Lattice.h | 15 +- src/GridExp.cpp | 10 + src/LatticeExp.cpp | 17 +- src/RcppExports.cpp | 22 +- vignettes/GCCM.Rmd | 299 +++++++++------------------------------- vignettes/GCCM.Rmd.orig | 87 ++--------- 29 files changed, 512 insertions(+), 944 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre] ,
Hugh Benjamin Zachariae [aut],
Indrajeet Patil [ctb] ,
Daniel Luedecke [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 1.6.2 dated 2024-07-31 and 1.6.3 dated 2025-01-14
DESCRIPTION | 22 - MD5 | 48 ++-- NEWS.md | 4 R/get_nested_model_coefficients.R | 12 - build/stage23.rdb |binary inst/doc/Creating_a_confusion_matrix.html | 26 +- inst/doc/available_metrics.html | 4 inst/doc/cross_validating_custom_functions.R | 24 +- inst/doc/cross_validating_custom_functions.html | 12 - inst/doc/evaluate_by_id.html | 8 inst/doc/picking_the_number_of_folds_for_cross-validation.R | 48 ++-- inst/doc/picking_the_number_of_folds_for_cross-validation.html | 14 - tests/testthat/test_validate_fn.R | 119 +++++----- vignettes/man/figures/vignette_conf_mat-unnamed-chunk-12-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-13-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-14-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-15-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-2.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-17-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-18-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-5-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-6-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-9-1.png |binary vignettes/man/figures/vignette_cv_custom_fn-unnamed-chunk-35-1.png |binary 25 files changed, 184 insertions(+), 157 deletions(-)
Title: Hardware-Accelerated Rerandomization for Improved Balance
Description: Provides hardware-accelerated tools for performing rerandomization
and randomization testing in experimental research. Using a 'JAX' backend, the
package enables exact rerandomization inference even for large experiments
with hundreds of billions of possible randomizations. Key functionalities
include generating pools of acceptable rerandomizations based on covariate
balance, conducting exact randomization tests, and performing pre-analysis
evaluations to determine optimal rerandomization acceptance thresholds. The
package supports various hardware acceleration frameworks including 'CPU',
'CUDA', and 'METAL', making it versatile across accelerated computing environments. This
allows researchers to efficiently implement stringent rerandomization designs and
conduct valid inference even with large sample sizes. The package is partly based on Jerzak and Goldstein (2023) <doi:10.48550/arXiv.2310.00861>.
Author: Fucheng Warren Zhu [aut] ,
Aniket Sachin Kamat [aut] ,
Connor Jerzak [aut, cre] ,
Rebecca Goldstein [aut]
Maintainer: Connor Jerzak <connor.jerzak@gmail.com>
Diff between fastrerandomize versions 0.1 dated 2025-01-13 and 0.2 dated 2025-01-14
DESCRIPTION | 6 MD5 | 24 +-- R/FRR_BuildBackend.R | 6 R/FRR_GenerateRandomizations.R | 16 -- R/FRR_GenerateRandomizations_Exact.R | 32 +++- R/FRR_GenerateRandomizations_MonteCarlo.R | 41 +++-- R/FRR_InitializeJAX.R | 64 +++++--- R/FRR_RandomizationTest.R | 15 + inst/doc/MainVignette.html | 236 ++++++++++++++++++++++++------ man/generate_randomizations.Rd | 11 - man/generate_randomizations_exact.Rd | 5 man/generate_randomizations_mc.Rd | 4 man/randomization_test.Rd | 3 13 files changed, 327 insertions(+), 136 deletions(-)
More information about fastrerandomize at CRAN
Permanent link
Title: Non-Interactive Spatial Tools for Raster Processing and
Visualization
Description: S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.
Author: Nikita Platonov [aut] ,
Nikita G. Platonov [cre]
Maintainer: Nikita G. Platonov <platonov@sev-in.ru>
Diff between ursa versions 3.11.1 dated 2024-09-26 and 3.11.2 dated 2025-01-14
DESCRIPTION | 6 +-- MD5 | 86 +++++++++++++++++++++++++------------------------- NEWS.md | 6 ++- R/allocate.R | 7 ++-- R/classCRS.R | 13 +++++-- R/classGrid.R | 18 ++++++++-- R/classRaster_close.R | 8 ++++ R/classStack.R | 22 ++++++++++-- R/colorize.R | 40 ++++++++++++++++++----- R/compose_panel.R | 2 - R/conn.open_envi.R | 12 ++++++ R/conn.write_gdal.R | 4 +- R/cubehelix.R | 23 +++++++++---- R/glance.R | 2 - R/identify.R | 13 +++++++ R/legend_mtext.R | 13 ++++--- R/package_vapour.R | 4 +- R/panel_annotation.R | 8 ++-- R/panel_coastline.R | 4 +- R/panel_graticule.R | 2 - R/panel_new.R | 3 + R/panel_raster.R | 13 ++++--- R/session.R | 33 ++++++++++++------- R/spatial_engine.R | 11 ++++++ R/trackline.R | 37 ++++++++++++++++++--- R/ursa_info.R | 4 +- R/whiteboxing.R | 2 - R/xxx.browse.R | 5 ++ R/xxx.gdalwarp.R | 4 +- R/xxx.geomap.R | 9 ++++- R/xxx.ncdf.R | 11 ++++-- R/xxx.panel_WMS.R | 25 +++++++++++++- R/xxx.panel_cluster.R | 4 +- R/xxx.panel_legend.R | 4 ++ R/xxx.polarmap.R | 30 +++++++++-------- R/xxx.spatialize.R | 72 +++++++++++++++++++++++++++++------------ R/yyy.cache.R | 13 +++++-- R/yyy.plot.R | 41 ++++++++++++++++++++--- R/yyy.project.R | 1 R/yyy.tile.R | 10 ++++- R/yyy.util.R | 5 ++ man/allocate.Rd | 7 ++-- man/colorize.Rd | 8 ++-- src/ursa.c | 37 +++++++++++++++++++-- 44 files changed, 495 insertions(+), 187 deletions(-)
Title: Implementation of Random Variables
Description: Implements random variables by means of S4 classes and methods.
Author: Matthias Kohl [cre, cph, aut] ,
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RandVar versions 1.2.4 dated 2024-09-02 and 1.2.5 dated 2025-01-14
DESCRIPTION | 27 ++--- MD5 | 14 +- build/vignette.rds |binary inst/CITATION | 5 inst/NEWS | 16 +++ inst/doc/RandVar.pdf |binary man/0RandVar-package.Rd | 92 ++++++++--------- tests/tests.Rout.save | 255 ++++++++++++++++++++++-------------------------- 8 files changed, 203 insertions(+), 206 deletions(-)
Title: Quantitative Text Kit
Description: Support package for the textbook "An Introduction to
Quantitative Text Analysis for Linguists: Reproducible Research Using
R" (Francom, 2024) <doi:10.4324/9781003393764>. Includes functions to
acquire, clean, and analyze text data as well as functions to document
and share the results of text analysis. The package is designed to be
used in conjunction with the book, but can also be used as a standalone
package for text analysis.
Author: Jerid Francom [aut, cre, cph]
Maintainer: Jerid Francom <francojc@wfu.edu>
Diff between qtkit versions 1.1.0 dated 2024-12-07 and 1.1.1 dated 2025-01-14
DESCRIPTION | 6 - MD5 | 18 ++--- NEWS.md | 17 ++++- R/calc_assoc_metrics.R | 102 ++++++++++++++++--------------- R/calc_type_metrics.R | 72 ++++++++------------- R/create_data_dictionary.R | 65 ++++++++++++------- man/calculate_bigram_probabilities.Rd | 7 +- man/calculate_metrics.Rd | 13 ++- man/validate_inputs_cam.Rd | 6 - tests/testthat/test-calc_assoc_metrics.R | 4 - 10 files changed, 168 insertions(+), 142 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predicti [...truncated...]
Author: John Wambaugh [aut, cre] ,
Sarah Davidson-Fritz [aut] ,
Robert Pearce [aut] ,
Caroline Ring [aut] ,
Greg Honda [aut] ,
Mark Sfeir [aut],
Matt Linakis [aut] ,
Dustin Kapraun [aut] ,
Nathan Pollesch [ctb] ,
Miyuki Breen [ctb] ,
Shannon Bell [ctb] ,
Xia [...truncated...]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 2.4.0 dated 2024-09-05 and 2.5.0 dated 2025-01-14
httk-2.4.0/httk/R/onAtttach.R |only httk-2.5.0/httk/DESCRIPTION | 18 httk-2.5.0/httk/MD5 | 175 ++-- httk-2.5.0/httk/NAMESPACE | 5 httk-2.5.0/httk/NEWS.md | 52 + httk-2.5.0/httk/R/armitage.R | 6 httk-2.5.0/httk/R/calc_analytic_css_1comp.R | 23 httk-2.5.0/httk/R/calc_analytic_css_3comp2.R |only httk-2.5.0/httk/R/calc_analytic_css_sumclearances.R |only httk-2.5.0/httk/R/calc_css.R | 215 +++--- httk-2.5.0/httk/R/calc_elimination_rate.R | 89 -- httk-2.5.0/httk/R/calc_half_life.R | 46 + httk-2.5.0/httk/R/calc_hep_bioavailability.R | 2 httk-2.5.0/httk/R/calc_kair.R | 114 ++- httk-2.5.0/httk/R/calc_oral_bioavailability.R | 2 httk-2.5.0/httk/R/calc_total_clearance.R | 89 +- httk-2.5.0/httk/R/calc_volume_of_distribution.R | 15 httk-2.5.0/httk/R/check_model.R | 21 httk-2.5.0/httk/R/create_mc_samples.R | 7 httk-2.5.0/httk/R/data.R | 67 + httk-2.5.0/httk/R/get_cheminfo.R | 12 httk-2.5.0/httk/R/get_weight_class.R | 6 httk-2.5.0/httk/R/modelinfo_1comp.R | 3 httk-2.5.0/httk/R/modelinfo_3comp2.R |only httk-2.5.0/httk/R/modelinfo_gas_pbtk.R | 1 httk-2.5.0/httk/R/modelinfo_sumclearances.R |only httk-2.5.0/httk/R/onAttach.R |only httk-2.5.0/httk/R/parameterize_1comp.R | 34 httk-2.5.0/httk/R/parameterize_3comp.R | 8 httk-2.5.0/httk/R/parameterize_3comp2.R |only httk-2.5.0/httk/R/parameterize_gas_pbtk.R | 15 httk-2.5.0/httk/R/parameterize_pbtk.R | 14 httk-2.5.0/httk/R/parameterize_schmitt.R | 14 httk-2.5.0/httk/R/parameterize_steadystate.R | 5 httk-2.5.0/httk/R/parameterize_sumclearances.R |only httk-2.5.0/httk/R/predict_partitioning_schmitt.R | 6 httk-2.5.0/httk/R/propagate_invitrouv_1comp.R | 43 - httk-2.5.0/httk/R/scale_dosing.R | 2 httk-2.5.0/httk/R/solve_3comp2.R |only httk-2.5.0/httk/R/solve_gas_pbtk.R | 4 httk-2.5.0/httk/R/solve_model.R | 42 - httk-2.5.0/httk/R/sysdata.rda |binary httk-2.5.0/httk/README.md | 8 httk-2.5.0/httk/build/partial.rdb |binary httk-2.5.0/httk/inst/doc/V1_IntroToHTTK.html | 22 httk-2.5.0/httk/inst/doc/Va_Pearce2017.html | 97 +- httk-2.5.0/httk/inst/doc/Vb_Ring2017.html | 4 httk-2.5.0/httk/inst/doc/Ve_Wambaugh2018.html | 4 httk-2.5.0/httk/inst/doc/Vg_Wambaugh2019.html | 4 httk-2.5.0/httk/inst/doc/Vi_Kapraun2022.html | 4 httk-2.5.0/httk/man/armitage_eval.Rd | 2 httk-2.5.0/httk/man/calc_analytic_css_3comp2.Rd |only httk-2.5.0/httk/man/calc_analytic_css_sumclearances.Rd |only httk-2.5.0/httk/man/calc_css.Rd | 66 + httk-2.5.0/httk/man/calc_elimination_rate.Rd | 12 httk-2.5.0/httk/man/calc_half_life.Rd | 9 httk-2.5.0/httk/man/calc_hep_bioavailability.Rd | 1 httk-2.5.0/httk/man/calc_kair.Rd | 14 httk-2.5.0/httk/man/calc_total_clearance.Rd | 16 httk-2.5.0/httk/man/calc_vdist.Rd | 14 httk-2.5.0/httk/man/check_model.Rd | 5 httk-2.5.0/httk/man/get_cheminfo.Rd | 10 httk-2.5.0/httk/man/get_weight_class.Rd | 6 httk-2.5.0/httk/man/httk-package.Rd | 1 httk-2.5.0/httk/man/parameterize_1comp.Rd | 9 httk-2.5.0/httk/man/parameterize_3comp.Rd | 5 httk-2.5.0/httk/man/parameterize_3comp2.Rd |only httk-2.5.0/httk/man/parameterize_gas_pbtk.Rd | 4 httk-2.5.0/httk/man/parameterize_pbtk.Rd | 10 httk-2.5.0/httk/man/parameterize_schmitt.Rd | 24 httk-2.5.0/httk/man/parameterize_sumclearances.Rd |only httk-2.5.0/httk/man/physiology.data.Rd | 33 httk-2.5.0/httk/man/predict_partitioning_schmitt.Rd | 23 httk-2.5.0/httk/man/solve_3comp2.Rd |only httk-2.5.0/httk/man/solve_gas_pbtk.Rd | 4 httk-2.5.0/httk/man/solve_model.Rd | 8 httk-2.5.0/httk/man/tissue.data.Rd | 31 httk-2.5.0/httk/man/wfl.Rd | 4 httk-2.5.0/httk/src/init.c | 35 httk-2.5.0/httk/src/model3comp2.c |only httk-2.5.0/httk/src/model_gas_pbtk.c | 2 httk-2.5.0/httk/src/modelpbtk.c | 2 httk-2.5.0/httk/tests/1comp_test.Rout.save | 296 ++++---- httk-2.5.0/httk/tests/3comp_test.Rout.save | 606 ++++++++--------- httk-2.5.0/httk/tests/caco2_test.Rout.save | 24 httk-2.5.0/httk/tests/cheminfo_test.Rout.save | 8 httk-2.5.0/httk/tests/fetal_pbtk_testing.Rout.save | 270 +++---- httk-2.5.0/httk/tests/montecarlo_tests.R | 2 httk-2.5.0/httk/tests/montecarlo_tests.Rout.save | 22 httk-2.5.0/httk/tests/other_tests.Rout.save | 392 +++++----- httk-2.5.0/httk/tests/pbtk_test.Rout.save | 36 - httk-2.5.0/httk/tests/solve_gas_test.R | 16 httk-2.5.0/httk/tests/solve_gas_test.Rout.save | 114 +-- httk-2.5.0/httk/tests/testthat |only httk-2.5.0/httk/tests/testthat.R |only httk-2.5.0/httk/tests/unit_test.R | 4 httk-2.5.0/httk/tests/unit_test.Rout.save | 41 - 97 files changed, 1986 insertions(+), 1493 deletions(-)
Title: ExifTool Functionality from R
Description: Reads, writes, and edits EXIF and other file metadata using
ExifTool <https://exiftool.org/>, returning read results as a data
frame. ExifTool supports many different metadata formats including EXIF,
GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP
and ID3, Lyrics3, as well as the maker notes of many digital cameras by
Canon, Casio, DJI, FLIR, FujiFilm, GE, GoPro, HP, JVC/Victor, Kodak, Leaf,
Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson,
Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung, Sanyo,
Sigma/Foveon and Sony.
Author: Joshua O'Brien [aut, cre]
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>
Diff between exiftoolr versions 0.2.6 dated 2024-07-19 and 0.2.7 dated 2025-01-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 12 ++++++++++++ R/install.R | 3 ++- R/utils.R | 12 ++++++++---- 5 files changed, 30 insertions(+), 13 deletions(-)
Title: Quick and Essential 'R' Tricks for Better Scripts
Description: The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.
Author: Obinna Obianom [aut, cre],
Brice Richard [aut]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between quickcode versions 1.0.3 dated 2024-12-01 and 1.0.4 dated 2025-01-14
quickcode-1.0.3/quickcode/man/clean.Rd |only quickcode-1.0.4/quickcode/DESCRIPTION | 6 - quickcode-1.0.4/quickcode/MD5 | 24 ++-- quickcode-1.0.4/quickcode/NAMESPACE | 2 quickcode-1.0.4/quickcode/NEWS.md | 4 quickcode-1.0.4/quickcode/R/clean.R | 24 +++- quickcode-1.0.4/quickcode/R/func_chain.R | 60 ++++++++++ quickcode-1.0.4/quickcode/R/track.R | 1 quickcode-1.0.4/quickcode/inst/doc/add_today_date_to_filenames_quickcode.html | 54 ++++----- quickcode-1.0.4/quickcode/inst/doc/nullish_coalescing_operator_r.html | 4 quickcode-1.0.4/quickcode/inst/doc/quickcode_r_introduction.html | 4 quickcode-1.0.4/quickcode/inst/doc/track_function_usage_r.html | 4 quickcode-1.0.4/quickcode/man/clearenvironment.Rd |only quickcode-1.0.4/quickcode/man/lastwd.Rd |only quickcode-1.0.4/quickcode/man/simplechaining2.Rd |only 15 files changed, 138 insertions(+), 49 deletions(-)
Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE)
Solvers
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
Author: Satyaprakash Nayak [aut, cre, cph]
,
Lawrence Livermore National Security [cph],
Southern Methodist University [cph]
Maintainer: Satyaprakash Nayak <satyaprakash.nayak@gmail.com>
Diff between sundialr versions 0.1.6.1 dated 2024-12-18 and 0.1.6.2 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS | 4 ++++ cleanup | 2 +- configure.ac | 8 ++++---- inst/doc/my-vignette.html | 8 ++++---- inst/include/sundials/sundials_config.h | 10 +++++----- src/scripts/sundials_download.sh | 19 ++++++++++++++----- src/sundials-mod-7.2.1.tar.gz |only tools/cmake_call.sh | 2 +- 10 files changed, 45 insertions(+), 31 deletions(-)
Title: Table Monster
Description: Provides a user friendly interface to
generation of booktab style tables using 'xtable'.
Author: Grant Izmirlian [aut, cre]
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Diff between TableMonster versions 1.7.5 dated 2024-12-18 and 1.7.6 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/TableMonster.R | 7 +++++-- 3 files changed, 10 insertions(+), 7 deletions(-)
Title: Read and Write PNG Files with Configurable Decoder/Encoder
Options
Description: Read and write PNG images with arrays, rasters, native
rasters, numeric arrays, integer arrays, raw vectors and indexed
values. This PNG encoder exposes configurable internal options
enabling the user to select a speed-size tradeoff. For example,
disabling compression can speed up writing PNG by a factor of 50.
Multiple image formats are supported including raster, native rasters,
and integer and numeric arrays at color depths of 1, 2, 3 or 4. 16-bit
images are also supported. This implementation uses the 'libspng' 'C'
library which is available from
<https://github.com/randy408/libspng/>.
Author: Mike Cheng [aut, cre, cph],
Randy408 [aut, cph] ,
The PNG Reference Library Authors [aut, cph],
Cosmin Truta [cph] ,
Glenn Randers-Pehrson [cph] ,
Andreas Dilger [cph],
Guy Eric Schalnat [cph],
Mike Klein [ctb] ,
Matt Sarett [ctb] ,
James Yu [ctb] ,
[...truncated...]
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Diff between fastpng versions 0.1.5 dated 2024-09-04 and 0.1.7 dated 2025-01-13
fastpng-0.1.5/fastpng/src/hash-color.c |only fastpng-0.1.5/fastpng/src/hash-color.h |only fastpng-0.1.7/fastpng/DESCRIPTION | 8 fastpng-0.1.7/fastpng/LICENSE | 2 fastpng-0.1.7/fastpng/MD5 | 24 - fastpng-0.1.7/fastpng/NAMESPACE | 1 fastpng-0.1.7/fastpng/NEWS.md | 9 fastpng-0.1.7/fastpng/R/write-png.R | 1 fastpng-0.1.7/fastpng/inst/doc/Overview.R | 4 fastpng-0.1.7/fastpng/inst/doc/Overview.html | 27 - fastpng-0.1.7/fastpng/src/R-get-png-info.c | 47 +- fastpng-0.1.7/fastpng/src/R-read-png.c | 173 ++++----- fastpng-0.1.7/fastpng/src/R-write-png.c | 366 ++++++-------------- fastpng-0.1.7/fastpng/vignettes/image/benchmark.png |binary 14 files changed, 272 insertions(+), 390 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Michael Chirico [ctb],
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb],
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-5 dated 2024-12-12 and 1.8-10 dated 2025-01-13
DESCRIPTION | 26 MD5 | 324 +++--- NAMESPACE | 7 NEWS.md | 2281 +++++++++++++++++++++---------------------- R/Aclasses.R | 56 - R/Agenerics.R | 6 R/Arith_generics.R | 114 +- R/RGB.R | 24 R/RcppExports.R | 28 R/SpatRasterDataset.R | 78 - R/SpatVectorCollection.R | 34 R/Zdeprecated.R | 21 R/aggregate.R | 36 R/animate.R | 3 R/app.R | 4 R/autocor.R | 6 R/cells.R | 8 R/click.R | 17 R/coerce.R | 33 R/colors.R | 16 R/crs.R | 54 - R/dimensions.R | 34 R/distance.R | 101 + R/divide.R |only R/draw.R | 3 R/expand.R | 2 R/extent.R | 58 - R/extract.R | 51 R/extract_single.R | 4 R/focal.R | 22 R/focalMat.R | 2 R/gdal.R | 48 R/generics.R | 219 ++-- R/geom.R | 242 ++-- R/graticule.R | 24 R/init.R | 15 R/layerCor.R | 2 R/levels.R | 69 - R/lines.R | 6 R/match.R | 2 R/math.R | 30 R/merge.R | 30 R/messages.R | 15 R/names.R | 68 - R/ncdf.R | 53 R/options.R | 22 R/panel.R | 69 - R/plot.R | 29 R/plot_let.R | 1280 ++++++++++++------------ R/plot_raster.R | 48 R/plot_vector.R | 29 R/rapp.R | 6 R/rast.R | 28 R/rasterize.R | 18 R/rasterizeWin.R | 14 R/read.R | 16 R/relate.R | 90 + R/replace.R | 12 R/replace_values.R | 16 R/roll.R | 2 R/sample.R | 41 R/show.R | 32 R/spatvec.R | 528 +++++---- R/subset.R | 25 R/tags.R | 93 + R/tapp.R | 4 R/tiles.R | 39 R/time.R | 97 + R/update.R | 5 R/values.R | 86 - R/vect.R | 64 - R/watershed.R | 10 R/window.R | 6 R/wrap.R | 12 R/write.R | 21 R/xyRowColCell.R | 32 R/zonal.R | 42 R/zzz.R | 2 configure | 19 configure.ac | 19 inst/tinytest/test_extract.R | 6 inst/tinytest/test_plot.R |only man/aggregate.Rd | 6 man/as.lines.Rd | 6 man/as.points.Rd | 6 man/as.polygons.Rd | 6 man/click.Rd | 2 man/convhull.Rd | 39 man/cover.Rd | 7 man/datatype.Rd | 32 man/deprecated.Rd | 2 man/describe.Rd | 5 man/direction.Rd | 7 man/distance.Rd | 282 ++--- man/divide.Rd |only man/draw.Rd | 2 man/elongate.Rd | 86 - man/expanse.Rd | 4 man/ext.Rd | 1 man/extend.Rd | 132 +- man/extract.Rd | 3 man/factors.Rd | 8 man/gdal.Rd | 12 man/geometry.Rd | 2 man/init.Rd | 5 man/lines.Rd | 2 man/merge.Rd | 21 man/metags.Rd | 14 man/nearby.Rd | 7 man/not.na.Rd | 88 - man/nseg.Rd |only man/panel.Rd | 5 man/perim.Rd | 2 man/plot.Rd | 12 man/predict.Rd | 2 man/project.Rd | 1 man/rast.Rd | 2 man/relate.Rd | 292 ++--- man/sample.Rd | 206 +-- man/scale.Rd | 4 man/scale_linear.Rd |only man/select.Rd | 2 man/shade.Rd | 20 man/surfArea.Rd | 2 man/terra-package.Rd | 4 man/terraOptions.Rd | 124 +- man/text.Rd | 8 man/update.Rd | 6 man/viewshed.Rd | 13 man/voronoi.Rd | 3 man/vrt.Rd | 5 man/writeCDF.Rd | 2 src/RcppExports.cpp | 109 -- src/RcppFunctions.cpp | 19 src/RcppModule.cpp | 156 +- src/crs.cpp | 35 src/distRaster.cpp | 1586 +++++------------------------ src/distVector.cpp |only src/distance.cpp | 454 ++++++-- src/distance.h | 20 src/extract.cpp | 613 ++++++++--- src/gdal_algs.cpp | 43 src/gdalio.cpp | 68 - src/gdalio.h | 1 src/geos_methods.cpp | 267 ++++- src/geos_spat.h | 19 src/geosphere.cpp | 371 ++---- src/geosphere.h |only src/nearest.cpp |only src/patches.cpp | 95 + src/raster_methods.cpp | 522 ++++++++- src/rasterize.cpp | 7 src/read.cpp | 9 src/read_gdal.cpp | 317 +++++ src/read_ogr.cpp | 2 src/sample.cpp | 64 - src/spatBase.cpp | 4 src/spatBase.h | 8 src/spatRaster.cpp | 9 src/spatRaster.h | 66 - src/spatRasterMultiple.cpp | 136 ++ src/spatRasterMultiple.h | 46 src/spatVector.cpp | 17 src/spatVector.h | 37 src/vector_methods.cpp | 33 src/write_gdal.cpp | 17 src/write_ogr.cpp | 26 167 files changed, 7426 insertions(+), 6390 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.3.1 dated 2024-07-25 and 3.3.2 dated 2025-01-13
DESCRIPTION | 13 - MD5 | 36 +-- R/generic.predict.rfsrc.R | 2 R/rfsrc.R | 4 configure | 551 ++++++++++++++++++++++++---------------------- configure.ac | 2 data/breast.rda |binary data/follic.rda |binary data/hd.rda |binary data/housing.rda |binary data/nutrigenomic.rda |binary data/pbc.rda |binary data/peakVO2.rda |binary data/vdv.rda |binary data/veteran.rda |binary data/wihs.rda |binary data/wine.rda |binary inst/NEWS | 4 src/randomForestSRC.c | 29 ++ 19 files changed, 354 insertions(+), 287 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
David Collins [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
L [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.1.0 dated 2024-05-10 and 5.2.0 dated 2025-01-13
DESCRIPTION | 40 +- MD5 | 143 +++++----- NAMESPACE | 6 NEWS.md | 20 + R/clustering.R | 184 +++++++------ R/convenience.R | 107 ++++++- R/differential_expression.R | 22 + R/dimensional_reduction.R | 81 ++++- R/generics.R | 18 - R/integration.R | 43 +-- R/integration5.R | 2 R/objects.R | 40 +- R/preprocessing.R | 357 +++++++++++++++++++++----- R/sketching.R | 79 ++++- R/visualization.R | 48 ++- README.md | 1 build/Seurat.pdf |binary build/stage23.rdb |binary man/CCAIntegration.Rd | 4 man/CalculateBarcodeInflections.Rd | 2 man/ColorDimSplit.Rd | 3 man/DimPlot.Rd | 5 man/DotPlot.Rd | 2 man/FastRPCAIntegration.Rd | 2 man/FeaturePlot.Rd | 4 man/FeatureScatter.Rd | 2 man/FindAllMarkers.Rd | 4 man/FindClusters.Rd | 15 - man/FindMarkers.Rd | 2 man/FindNeighbors.Rd | 14 - man/FindSubCluster.Rd | 2 man/FindTransferAnchors.Rd | 6 man/FindVariableFeatures.Rd | 4 man/GetImage.Rd | 3 man/ISpatialDimPlot.Rd | 2 man/ISpatialFeaturePlot.Rd | 2 man/ImageDimPlot.Rd | 2 man/ImageFeaturePlot.Rd | 2 man/IntegrateData.Rd | 10 man/IntegrateEmbeddings.Rd | 4 man/JackStraw.Rd | 2 man/JointPCAIntegration.Rd | 4 man/LeverageScore.Rd | 5 man/LinkedPlots.Rd | 2 man/Load10X_Spatial.Rd | 2 man/MULTIseqDemux.Rd | 2 man/PredictAssay.Rd | 2 man/PrepSCTIntegration.Rd | 8 man/PrepareBridgeReference.Rd | 2 man/ProjectDim.Rd | 2 man/RPCAIntegration.Rd | 4 man/Radius.Rd | 2 man/Read10X_Image.Rd | 5 man/ReadXenium.Rd | 37 ++ man/RunCCA.Rd | 2 man/RunLeiden.Rd |only man/RunSLSI.Rd | 20 + man/RunSPCA.Rd | 2 man/RunUMAP.Rd | 6 man/SCTAssay-class.Rd | 6 man/SingleDimPlot.Rd | 3 man/SingleSpatialPlot.Rd | 4 man/SketchData.Rd | 8 man/SpatialPlot.Rd | 4 man/TopNeighbors.Rd | 2 man/TransferData.Rd | 4 man/VisiumV2-class.Rd | 4 man/VlnPlot.Rd | 2 man/fortify-Spatial.Rd | 6 tests/testthat/test_differential_expression.R | 17 - tests/testthat/test_find_clusters.R |only tests/testthat/test_integration5.R | 112 ++++++++ tests/testthat/test_load_10X.R | 25 + tests/testthat/test_sketching.R |only 74 files changed, 1142 insertions(+), 451 deletions(-)
Title: Causal Inference with Tree-Based Machine Learning Algorithms
Description: Estimating heterogeneous treatment effects with tree-based machine
learning algorithms and visualizing estimated results in flexible and
presentation-ready ways. For more information, see Brand, Xu, Koch,
and Geraldo (2021) <doi:10.1177/0081175021993503>. Our current package
first started as a fork of the 'causalTree' package on 'GitHub' and we
greatly appreciate the authors for their extremely useful and free package.
Author: Jiahui Xu [cre, aut],
Tanvi Shinkre [aut],
Jennie Brand [aut]
Maintainer: Jiahui Xu <jiahuixu@ucla.edu>
Diff between htetree versions 0.1.19 dated 2024-10-13 and 0.1.20 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/causalForest.R | 17 ----------------- R/causalTree.R | 15 --------------- R/honest.causalTree.R | 31 ------------------------------- R/matchinleaves.R | 2 +- man/causalForest.Rd | 17 ----------------- man/causalTree.Rd | 15 --------------- man/honest.causalTree.Rd | 31 ------------------------------- 9 files changed, 12 insertions(+), 138 deletions(-)
Title: Thematic Map Tools
Description: Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmaptools versions 3.1-1 dated 2021-01-19 and 3.2 dated 2025-01-13
tmaptools-3.1-1/tmaptools/NEWS |only tmaptools-3.1-1/tmaptools/R/pkg.R |only tmaptools-3.2/tmaptools/DESCRIPTION | 18 ++++++------ tmaptools-3.2/tmaptools/MD5 | 32 +++++++++++------------ tmaptools-3.2/tmaptools/NEWS.md |only tmaptools-3.2/tmaptools/R/bb.R | 4 +- tmaptools-3.2/tmaptools/R/calc_densities.R | 4 +- tmaptools-3.2/tmaptools/R/get_brewer_pal.R | 7 +++-- tmaptools-3.2/tmaptools/R/palette_explorer.R | 6 +++- tmaptools-3.2/tmaptools/R/tmaptools-package.R |only tmaptools-3.2/tmaptools/man/approx_areas.Rd | 5 ++- tmaptools-3.2/tmaptools/man/bb.Rd | 7 ++--- tmaptools-3.2/tmaptools/man/calc_densities.Rd | 28 +++++++++++--------- tmaptools-3.2/tmaptools/man/crop_shape.Rd | 6 ++-- tmaptools-3.2/tmaptools/man/get_brewer_pal.Rd | 4 +- tmaptools-3.2/tmaptools/man/map_coloring.Rd | 13 +++++---- tmaptools-3.2/tmaptools/man/palette_explorer.Rd | 5 ++- tmaptools-3.2/tmaptools/man/pipe.Rd | 2 - tmaptools-3.2/tmaptools/man/tmaptools-package.Rd | 16 +++++++++-- 19 files changed, 93 insertions(+), 64 deletions(-)
Title: Spatial Modeling of Infectious Disease with Reinfection
Description: Geographically Dependent Individual Level Models (GDILMs) within the Susceptible-Exposed-Infectious-Recovered-Susceptible (SEIRS) framework are applied to model infectious disease transmission, incorporating reinfection dynamics. This package employs a likelihood based Monte Carlo Expectation Conditional Maximization (MCECM) algorithm for estimating model parameters. It also provides tools for GDILM fitting, parameter estimation, AIC calculation on real pandemic data, and simulation studies customized to user-defined model settings.
Author: Amin Abed [aut, cre, cph] ,
Mahmoud Torabi [ths],
Zeinab Mashreghi [ths]
Maintainer: Amin Abed <abeda@myumanitoba.ca>
Diff between GDILM.SEIRS versions 0.0.2 dated 2024-12-07 and 0.0.3 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/GDILM_SEIRS_Sim_Par_Est.R | 8 ++++---- man/GDILM_SEIRS_Sim_Par_Est.Rd | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Fit Dynamic Structural Equation Models
Description: Applies dynamic structural equation models to time-series data
with generic and simplified specification for simultaneous and lagged
effects. Methods are described in Thorson et al. (2024)
"Dynamic structural equation models synthesize ecosystem dynamics
constrained by ecological mechanisms."
Author: James Thorson [aut, cre]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Diff between dsem versions 1.3.0 dated 2024-07-22 and 1.4.0 dated 2025-01-13
DESCRIPTION | 13 MD5 | 61 +- NAMESPACE | 38 + NEWS.md | 13 R/cAIC.R |only R/compute_nll.R |only R/convert_equations.R |only R/data.R | 2 R/dsem.R | 139 ++++ R/dsemRTMB.R |only R/make_dsem_ram.R | 56 + R/make_matrices.R |only R/read_model.R |only R/rgmrf.R |only R/stepwise_selection.R |only R/utility.R |only build/partial.rdb |only inst/CITATION | 5 inst/doc/dynamic_factor_analysis.R | 31 - inst/doc/dynamic_factor_analysis.Rmd | 31 - inst/doc/dynamic_factor_analysis.html | 133 ++-- inst/doc/vignette.R | 93 ++- inst/doc/vignette.Rmd | 102 +++ inst/doc/vignette.html | 969 ++++++++++++++++++---------------- man/cAIC.Rd |only man/convert_equations.Rd |only man/dsem.Rd | 16 man/dsemRTMB.Rd |only man/dsem_control.Rd | 12 man/isle_royale.Rd | 2 man/logLik.dsem.Rd | 2 man/loo_residuals.Rd |only man/plot.dsem.Rd | 15 man/read_model.Rd |only man/stepwise_selection.Rd |only src/dsem.cpp | 2 tests/testthat/test-platform.R | 130 ++-- tests/testthat/test-priors.R |only vignettes/dynamic_factor_analysis.Rmd | 31 - vignettes/vignette.Rmd | 102 +++ 40 files changed, 1336 insertions(+), 662 deletions(-)
Title: Manipulate Matrix Row and Column Labels with Ease
Description: Functions to assist manipulation of matrix
row and column labels for all types of matrix mathematics
where row and column labels are to be respected.
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between RCLabels versions 0.1.10 dated 2024-01-29 and 0.1.11 dated 2025-01-13
DESCRIPTION | 10 ++--- LICENSE | 2 - MD5 | 24 ++++++------- NEWS.md | 46 +++++++++++++++++--------- R/extractors.R | 25 ++++++++++++++ R/utilities.R | 39 +++++++++++++++------- build/vignette.rds |binary inst/CITATION | 8 ++-- inst/doc/RCLabels.html | 8 ++-- man/get_prepositions.Rd | 26 ++++++++++++++ man/regex_funcs.Rd | 34 ++++++++++++++----- tests/testthat/test-extractors.R | 69 ++++++++++++++++++++++++++++++++++++++- tests/testthat/test-utilities.R | 24 +++++++++++++ 13 files changed, 253 insertions(+), 62 deletions(-)
Title: Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'
Description: Provides an interface to the 'Mapbox GL JS' (<https://docs.mapbox.com/mapbox-gl-js/guides>)
and the 'MapLibre GL JS' (<https://maplibre.org/maplibre-gl-js/docs/>) interactive mapping libraries to help users
create custom interactive maps in R. Users can create interactive globe visualizations; layer 'sf' objects to create
filled maps, circle maps, 'heatmaps', and three-dimensional graphics; and customize map styles and views. The package
also includes utilities to use 'Mapbox' and 'MapLibre' maps in 'Shiny' web applications.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapgl versions 0.1.4 dated 2024-11-01 and 0.2.0 dated 2025-01-13
DESCRIPTION | 15 MD5 | 45 +- NAMESPACE | 8 NEWS.md | 5 R/layers.R | 8 R/legends.R | 23 - R/plugins.R | 4 R/shiny.R | 49 +++ R/storymaps.R |only R/style_helpers.R | 22 + README.md | 2 inst/htmlwidgets/lib/maplibre-gl/maplibre-gl.css | 2 inst/htmlwidgets/lib/maplibre-gl/maplibre-gl.js | 8 inst/htmlwidgets/lib/pmtiles |only inst/htmlwidgets/mapboxgl.js | 332 +++++++++++++++++++--- inst/htmlwidgets/mapboxgl.yaml | 4 inst/htmlwidgets/maplibregl.js | 347 ++++++++++++++++++++--- inst/htmlwidgets/maplibregl.yaml | 7 inst/htmlwidgets/styles/filter-control.css |only man/add_symbol_layer.Rd | 6 man/mapgl-package.Rd | 1 man/on_section.Rd |only man/set_projection.Rd |only man/set_source.Rd |only man/set_tooltip.Rd |only man/story_leaflet.Rd |only man/story_map.Rd |only man/story_maplibre.Rd |only man/story_section.Rd |only 29 files changed, 763 insertions(+), 125 deletions(-)
Title: Helper Functions for Bayesian Analyses
Description: Functions to 'numericise' 'R' objects (coerce to numeric
objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and
calculate deviance residuals as well as 'R' translations of some
'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs
Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.
Author: Nicole Hill [aut, cre] ,
Joe Thorley [aut] ,
Kirill Mueller [ctb] ,
Nadine Hussein [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Nicole Hill <nicole@poissonconsulting.ca>
Diff between extras versions 0.7.3 dated 2024-08-27 and 0.8.0 dated 2025-01-13
extras-0.7.3/extras/tests/testthat/test-translations.R |only extras-0.8.0/extras/DESCRIPTION | 15 - extras-0.8.0/extras/MD5 | 92 +++---- extras-0.8.0/extras/NAMESPACE | 1 extras-0.8.0/extras/NEWS.md | 16 + extras-0.8.0/extras/R/dev.R | 123 +++++++--- extras-0.8.0/extras/R/extras-package.R | 1 extras-0.8.0/extras/R/ilog.R |only extras-0.8.0/extras/R/log-lik.R | 84 +++++- extras-0.8.0/extras/R/log.R | 51 ---- extras-0.8.0/extras/R/numericise.R | 7 extras-0.8.0/extras/R/ran.R | 2 extras-0.8.0/extras/R/res.R | 2 extras-0.8.0/extras/R/sens.R | 2 extras-0.8.0/extras/R/skewnorm.R | 2 extras-0.8.0/extras/R/zzz.R |only extras-0.8.0/extras/README.md | 55 +++- extras-0.8.0/extras/build/partial.rdb |binary extras-0.8.0/extras/build/vignette.rds |binary extras-0.8.0/extras/inst/WORDLIST | 4 extras-0.8.0/extras/inst/doc/beta-binomial-deviance-residuals.R | 8 extras-0.8.0/extras/inst/doc/beta-binomial-deviance-residuals.Rmd | 10 extras-0.8.0/extras/inst/doc/beta-binomial-deviance-residuals.html | 6 extras-0.8.0/extras/inst/doc/deviance-residuals.html | 2 extras-0.8.0/extras/man/dev_skewnorm.Rd | 2 extras-0.8.0/extras/man/figures/lifecycle-deprecated.svg | 22 + extras-0.8.0/extras/man/figures/lifecycle-experimental.svg | 22 + extras-0.8.0/extras/man/figures/lifecycle-stable.svg | 30 ++ extras-0.8.0/extras/man/figures/lifecycle-superseded.svg | 22 + extras-0.8.0/extras/man/figures/logo.png |binary extras-0.8.0/extras/man/ilog.Rd | 2 extras-0.8.0/extras/man/ilog10.Rd | 2 extras-0.8.0/extras/man/ilog2.Rd | 2 extras-0.8.0/extras/man/log_lik_beta_binom.Rd | 4 extras-0.8.0/extras/man/log_lik_skewnorm.Rd | 2 extras-0.8.0/extras/man/numericise.Rd | 2 extras-0.8.0/extras/man/ran_skewnorm.Rd | 2 extras-0.8.0/extras/man/res_skewnorm.Rd | 2 extras-0.8.0/extras/man/sens_skewnorm.Rd | 2 extras-0.8.0/extras/man/skewnorm.Rd | 2 extras-0.8.0/extras/tests/testthat.R | 8 extras-0.8.0/extras/tests/testthat/_snaps/dev.md |only extras-0.8.0/extras/tests/testthat/test-dev.R | 41 ++- extras-0.8.0/extras/tests/testthat/test-ilogit.R |only extras-0.8.0/extras/tests/testthat/test-log-lik.R | 40 +++ extras-0.8.0/extras/tests/testthat/test-log.R | 8 extras-0.8.0/extras/tests/testthat/test-logit.R |only extras-0.8.0/extras/tests/testthat/test-phi.R |only extras-0.8.0/extras/tests/testthat/test-pow.R |only extras-0.8.0/extras/tests/testthat/test-res.R | 6 extras-0.8.0/extras/vignettes/beta-binomial-deviance-residuals.Rmd | 10 51 files changed, 503 insertions(+), 213 deletions(-)
Title: Modeling Animal Movement with Continuous-Time Discrete-Space
Markov Chains
Description: Software to facilitates taking movement data in xyt format and pairing it with raster covariates within a continuous time Markov chain (CTMC) framework. As described in Hanks et al. (2015) <DOI:10.1214/14-AOAS803> , this allows flexible modeling of movement in response to covariates (or covariate gradients) with model fitting possible within a Poisson GLM framework.
Author: Ephraim Hanks [aut, cre]
Maintainer: Ephraim Hanks <hanks@psu.edu>
Diff between ctmcmove versions 1.2.9 dated 2018-04-20 and 1.2.10 dated 2025-01-13
DESCRIPTION | 16 +- MD5 | 26 ++-- R/ctmc2glm.R | 40 +++---- R/get.rate.matrix.R | 32 ++--- R/path2ctmc.R | 14 +- R/rast.grad.R | 12 +- man/Pctmc.Rd | 112 ++++++++++---------- man/ctmc.sim.Rd | 136 ++++++++++++------------- man/ctmc2glm.Rd | 212 +++++++++++++++++++-------------------- man/get.UD.Rd | 144 +++++++++++++------------- man/get.rate.matrix.Rd | 184 +++++++++++++++++----------------- man/mcmc.fmove.Rd | 262 ++++++++++++++++++++++++------------------------- man/path2ctmc.Rd | 216 ++++++++++++++++++++-------------------- man/rast.grad.Rd | 144 +++++++++++++------------- 14 files changed, 777 insertions(+), 773 deletions(-)
Title: Clustering via Quadratic Scoring
Description: Performs tuning of clustering models, methods and algorithms including the problem of determining an appropriate number of clusters. Validation of cluster analysis results is performed via quadratic scoring using resampling methods, as in Coraggio, L. and Coretto, P. (2023) <doi:10.1016/j.jmva.2023.105181>.
Author: Luca Coraggio [cre, aut] ,
Pietro Coretto [aut]
Maintainer: Luca Coraggio <luca.coraggio@unina.it>
Diff between qcluster versions 1.2 dated 2024-12-06 and 1.2.1 dated 2025-01-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 6 +++++- build/partial.rdb |binary inst/CITATION | 4 ++-- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metR versions 0.16.0 dated 2024-10-14 and 0.17.0 dated 2025-01-13
DESCRIPTION | 6 +- MD5 | 32 +++++++-------- NEWS.md | 11 ++++- R/geom_streamline.R | 2 R/scale_longitude.R | 3 - README.md | 7 --- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Visualization-tools.html | 77 ++++++++++++++++---------------------- inst/doc/Working-with-data.html | 18 ++++---- man/discretised_scale.Rd | 6 +- man/figures/field-1.png |binary man/figures/timeseries-1.png |binary man/label_scales.Rd | 6 +- man/metR.Rd | 3 - man/scale_divergent.Rd | 6 +- man/scale_longitude.Rd | 6 -- 17 files changed, 86 insertions(+), 97 deletions(-)
Title: A GeoJson Processing Toolkit
Description: Includes functions for processing GeoJson objects <https://en.wikipedia.org/wiki/GeoJSON> relying on 'RFC 7946' <https://datatracker.ietf.org/doc/html/rfc7946>. The geojson encoding is based on 'json11', a tiny JSON library for 'C++11' <https://github.com/dropbox/json11>. Furthermore, the source code is exported in R through the 'Rcpp' and 'RcppArmadillo' packages.
Author: Lampros Mouselimis [aut, cre] ,
Dropbox Inc [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between geojsonR versions 1.1.1 dated 2023-01-12 and 1.1.2 dated 2025-01-13
DESCRIPTION | 12 MD5 | 26 NEWS.md | 8 README.md | 4 build/vignette.rds |binary inst/doc/the_geojsonR_package.R | 654 +++++++++++------------ inst/doc/the_geojsonR_package.Rmd | 6 inst/doc/the_geojsonR_package.html | 1016 +++++++++++++++++++++++-------------- src/FROM_geojson.cpp | 2 src/Makevars | 1 src/Makevars.win | 3 src/TO_geojson.cpp | 2 src/json11.cpp | 1 vignettes/the_geojsonR_package.Rmd | 6 14 files changed, 1015 insertions(+), 726 deletions(-)
Title: Estimation and Testing Classes Based on Package 'distr'
Description: Evaluation (S4-)classes based on package distr for evaluating procedures
(estimators/tests) at data/simulation in a unified way.
Author: Florian Camphausen [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrTEst versions 2.8.2 dated 2024-01-31 and 2.8.3 dated 2025-01-13
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 14 ++++++++++++++ man/0distrTEst-package.Rd | 8 ++++---- 5 files changed, 34 insertions(+), 19 deletions(-)
Title: Extensions of Package 'distr' for Teaching
Stochastics/Statistics in Secondary School
Description: Provides flexible examples of LLN and CLT for teaching purposes in secondary
school.
Author: Eleonora Feist [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Anja Hueller [ctb]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrTeach versions 2.9.1 dated 2024-01-31 and 2.9.2 dated 2025-01-13
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 13 +++++++++++++ man/0distrTeach-package.Rd | 8 ++++---- 5 files changed, 29 insertions(+), 16 deletions(-)
Title: Bayesian Power Prior Design
Description: Bayesian power/type I error calculation and model fitting using
the power prior and the normalized power prior for generalized linear models.
Detailed examples of applying the package are available at <doi:10.32614/RJ-2023-016>.
Models for time-to-event outcomes are implemented in the R package 'BayesPPDSurv'.
The Bayesian clinical trial design methodology is described in Chen et al. (2011)
<doi:10.1111/j.1541-0420.2011.01561.x>, and Psioda and Ibrahim (2019)
<doi:10.1093/biostatistics/kxy009>. The normalized power prior is described in Duan et al. (2006)
<doi:10.1002/env.752> and Ibrahim et al. (2015) <doi:10.1002/sim.6728>.
Author: Yueqi Shen [aut, cre],
Matthew A. Psioda [aut],
Joseph G. Ibrahim [aut]
Maintainer: Yueqi Shen <angieshen6@gmail.com>
Diff between BayesPPD versions 1.1.2 dated 2023-11-25 and 1.1.3 dated 2025-01-13
DESCRIPTION | 15 - MD5 | 15 - NEWS.md | 10 + R/glm_fixed.R | 1 R/glm_random.R | 2 inst/CITATION |only inst/doc/bayesppd-vignette.R | 60 +++--- inst/doc/bayesppd-vignette.html | 362 ++++++++++++++++++++-------------------- src/PP_random.cpp | 83 ++++----- 9 files changed, 283 insertions(+), 265 deletions(-)
Title: File IO for Intracranial Electroencephalography
Description: Integrated toolbox supporting common file formats used for intracranial
Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ieegio versions 0.0.2 dated 2024-10-31 and 0.0.3 dated 2025-01-13
DESCRIPTION | 15 MD5 | 76 ++-- NAMESPACE | 19 + NEWS.md | 19 + R/aaa-generics-surface.R | 136 ++++--- R/aaa-generics-volume.R | 709 ++++++++++++++++++++++++++++++++-------- R/aaa.R | 39 ++ R/as_ieegio_surface.R |only R/bci2000-cache.R | 2 R/brainvis-cache.R | 2 R/edf-cache.R | 25 - R/edf.R | 360 +++++++++++++++++--- R/hdf5-class.R | 20 - R/hdf5.R | 2 R/mat.R | 6 R/math-volume.R |only R/math.R | 14 R/mgz.R | 2 R/nifti.R | 598 ++++++++++++++++++++++++++++----- R/nsx-cache.R | 2 R/py-setup.R | 40 +- R/r3js.R |only R/rgl.R | 2 R/zzz.R | 1 inst/WORDLIST | 1 inst/doc/read-ephys.R | 43 +- inst/doc/read-ephys.Rmd | 1 inst/doc/read-imaging-data.R | 124 +++--- inst/sample_data_registry.txt | 3 man/LazyH5.Rd | 4 man/as_ieegio_surface.Rd |only man/as_ieegio_volume.Rd |only man/burn_volume.Rd |only man/imaging-surface.Rd | 3 man/imaging-volume.Rd | 30 + man/plot.ieegio_surface.Rd | 10 man/plot.ieegio_volume.Rd | 45 +- man/resample_volume.Rd |only tests/testthat.R | 2 tests/testthat/test-hdf5.R | 3 tests/testthat/test-rgbaNifti.R |only tests/testthat/test-volume.R | 10 vignettes/read-ephys.Rmd | 1 43 files changed, 1843 insertions(+), 526 deletions(-)
Title: Simulation Classes Based on Package 'distr'
Description: S4-classes for setting up a coherent framework for simulation within the distr
family of packages.
Author: Florian Camphausen [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrSim versions 2.8.3 dated 2024-08-29 and 2.8.5 dated 2025-01-13
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 18 ++++++++++++++++++ man/0distrSim-package.Rd | 6 +++--- 5 files changed, 37 insertions(+), 18 deletions(-)
Title: Distribution Classes for Distributions from Rmetrics
Description: S4-distribution classes based on package distr for distributions from packages
'fBasics' and 'fGarch'.
Author: Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrRmetrics versions 2.8.2 dated 2024-01-30 and 2.8.3 dated 2025-01-13
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 11 +++++++++++ man/0distrRmetrics-package.Rd | 6 +++--- 5 files changed, 26 insertions(+), 15 deletions(-)
Title: S4 Classes for Elliptically Contoured Distributions
Description: Distribution (S4-)classes for elliptically contoured distributions (based on
package 'distr').
Author: Peter Ruckdeschel [aut, cre, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrEllipse versions 2.8.3 dated 2024-08-29 and 2.8.4 dated 2025-01-13
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 11 +++++++++++ man/0distrEllipse-package.Rd | 8 ++++---- 5 files changed, 30 insertions(+), 19 deletions(-)
Title: Split a Dataframe, Tibble, or Data.table into Training and Test
Sets
Description: Split a dataframe, tibble, or data.table into training and test sets. Return either a list, an index, or directly assign training and test sets into memory.
Author: Zhaochen He [aut, cre]
Maintainer: Zhaochen He <eastnileuc@gmail.com>
Diff between trainsplit versions 1.1 dated 2024-04-04 and 1.2 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/trainsplit.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Fit Models Derived from Point Processes to Species Distributions
using 'inlabru'
Description: Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models.
Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking.
We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them.
There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions.
An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Author: Philip Mostert [aut, cre],
Bob O'hara [aut]
Maintainer: Philip Mostert <philip.s.mostert@ntnu.no>
Diff between PointedSDMs versions 2.1.2 dated 2024-08-21 and 2.1.3 dated 2025-01-13
DESCRIPTION | 18 - MD5 | 127 ++++++------- NAMESPACE | 2 R/blockedCV.R | 68 ++++++- R/bruSDM_predict.R | 14 - R/data.BBSColinusVirginianus.R | 2 R/data.SetophagaData.rda.R | 2 R/dataOrganize.R | 17 + R/datasetOut.R | 14 - R/fitISDM.R | 9 R/intModel.R | 22 -- R/makeLhoods.R | 21 +- R/modISDM_predict.R | 10 - R/modMarks_predict.R | 12 - R/modSpecies_predict.R | 22 +- R/nearestValue.R |only R/specifyISDM.R | 54 +++-- R/specifyMarks.R | 21 +- R/specifySpecies.R | 242 ++++++++++++++++--------- R/startISDM.R | 6 R/startMarks.R | 8 R/startSpecies.R | 8 README.md | 116 +++++------- build/vignette.rds |binary inst/doc/Marked_Point_Process.R | 17 + inst/doc/Marked_Point_Process.Rmd | 25 ++ inst/doc/Marked_Point_Process.html | 201 ++++++++++++--------- inst/doc/Setophaga.R | 141 +++++++------- inst/doc/Setophaga.Rmd | 180 +++++++++---------- inst/doc/Setophaga.html | 283 +++++++++++++++--------------- inst/doc/Solitary_tinamou.R | 59 +++--- inst/doc/Solitary_tinamou.Rmd | 71 ++++--- inst/doc/Solitary_tinamou.html | 88 +++++---- inst/doc/Spatiotemporal_example.R | 52 ++++- inst/doc/Spatiotemporal_example.Rmd | 58 ++++-- inst/doc/Spatiotemporal_example.html | 93 ++++++--- man/BBS.Rd | 2 man/BBSColinusVirginianus.Rd | 2 man/figures/README-predict_and_plot-1.png |binary man/intModel.Rd | 4 man/makeLhoods.Rd | 2 man/nearestValue.Rd |only man/predict.Rd | 2 man/specifyISDM.Rd | 106 +++++++++++ man/specifyMarks.Rd | 108 +++++++++++ man/specifySpecies.Rd | 108 +++++++++++ man/startISDM.Rd | 4 man/startMarks.Rd | 4 man/startSpecies.Rd | 4 tests/testthat/setup.R |only tests/testthat/testthat_blockedCV.R | 6 tests/testthat/testthat_dataOrganize.R | 6 tests/testthat/testthat_datasetOut.R | 7 tests/testthat/testthat_fitISDM.R | 6 tests/testthat/testthat_intModel.R | 6 tests/testthat/testthat_makeLhoods.R | 9 tests/testthat/testthat_specifyISDM.R | 8 tests/testthat/testthat_specifyMarks.R | 17 - tests/testthat/testthat_specifySpecies.R | 9 tests/testthat/testthat_startISDM.R | 13 - tests/testthat/testthat_startMarks.R | 11 - tests/testthat/testthat_startSpecies.R | 16 - vignettes/Marked_Point_Process.Rmd | 25 ++ vignettes/Setophaga.Rmd | 180 +++++++++---------- vignettes/Solitary_tinamou.Rmd | 71 ++++--- vignettes/Spatiotemporal_example.Rmd | 58 ++++-- 66 files changed, 1798 insertions(+), 1079 deletions(-)
Title: IMAGing engINEs, Tools for Application of Image Filters to Data
Matrices
Description: Provides fast application of image filters to data matrices,
using R and C++ algorithms.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between imagine versions 2.1.1 dated 2024-09-23 and 2.1.2 dated 2025-01-13
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- NEWS.md | 5 +++ R/imagine-main.R | 5 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/imagine-intro.R | 64 +++++++++++++++++++-------------------- inst/doc/imagine-intro.html | 8 ++-- man/contextualMF.Rd | 5 +-- src/contextual-median-filter.cpp | 5 +-- 10 files changed, 60 insertions(+), 58 deletions(-)
Title: Animation of Multiple Trajectories with Uncertainty
Description: Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Author: Henry Scharf [aut, cre],
Kristine Dinh [aut],
Rosales Hugo [aut],
Rivera Angelica [aut]
Maintainer: Henry Scharf <hscharf@arizona.edu>
Diff between anipaths versions 0.10.3 dated 2024-02-02 and 0.10.4 dated 2025-01-13
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS | 5 +++++ R/animate_paths.R | 8 ++++---- R/animation_expression.R | 1 + R/check_overwrite.R | 2 +- build/vignette.rds |binary inst/doc/anipaths.R | 4 ++-- inst/doc/anipaths.html | 4 ++-- inst/doc/anipaths_crawl.html | 4 ++-- inst/doc/anipaths_gam.R | 8 ++++---- man/check_overwrite.Rd | 2 +- 12 files changed, 38 insertions(+), 32 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut, cre]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.7-3.1 dated 2025-01-13 and 0.7-3.3 dated 2025-01-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- configure | 9 +++++---- configure.ac | 9 +++++---- 4 files changed, 17 insertions(+), 15 deletions(-)
Title: Interface for Multiple Data Providers 'EDDS' and 'FRED'
Description: Interface for multiple data sources, such as the
`EDDS` API <https://evds2.tcmb.gov.tr/index.php?/evds/userDocs> of the
Central Bank of the Republic of Türkiye and the
`FRED` API <https://fred.stlouisfed.org/docs/api/fred/> of the Federal Reserve Bank.
Both data providers require API keys for access, which users can easily obtain
by creating accounts on their respective websites.
The package provides caching ability with the selection of periods to increase the
speed and efficiency of requests.
It combines datasets requested from different sources,
helping users when the data has common frequencies.
While combining data frames whenever possible, it also keeps all requested data
available as separate data frames to increase efficiency.
Author: Sermet Pekin [aut, cre, cph]
Maintainer: Sermet Pekin <sermet.pekin@gmail.com>
Diff between Rapi versions 1.0.5 dated 2024-04-06 and 1.0.6 dated 2025-01-13
Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/0edfb96425ca0841082054975994159b_2024_14_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/0edfb96425ca0841082054975994159b_2024_8_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/0edfb96425ca0841082054975994159b_2024_9_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/28e64743469b182c516544244dbf7bed_2024_14_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/28e64743469b182c516544244dbf7bed_2024_8_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/28e64743469b182c516544244dbf7bed_2024_9_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/3d4dc283b1b4c53f5aba5057bf787a63_2024_14_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/3d4dc283b1b4c53f5aba5057bf787a63_2024_8_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/3d4dc283b1b4c53f5aba5057bf787a63_2024_9_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/56cf7bda13139d113fde8412f5baa875_2024_14_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/56cf7bda13139d113fde8412f5baa875_2024_8_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/56cf7bda13139d113fde8412f5baa875_2024_9_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rsearch |only Rapi-1.0.5/Rapi/tests/testthat/caches_vyos |only Rapi-1.0.6/Rapi/DESCRIPTION | 18 +- Rapi-1.0.6/Rapi/MD5 | 68 +++------- Rapi-1.0.6/Rapi/NEWS.md | 8 + Rapi-1.0.6/Rapi/R/api_keys.R | 14 +- Rapi-1.0.6/Rapi/R/excel.R | 4 Rapi-1.0.6/Rapi/R/generics.R | 1 Rapi-1.0.6/Rapi/R/get_series_export.R | 4 Rapi-1.0.6/Rapi/R/internal_evds.R | 14 +- Rapi-1.0.6/Rapi/R/lag_df.R | 6 Rapi-1.0.6/Rapi/R/post_process_data.R | 2 Rapi-1.0.6/Rapi/R/request_funcs.R | 26 ++- Rapi-1.0.6/Rapi/R/sp_df_utils.R | 17 +- Rapi-1.0.6/Rapi/README.md | 19 +- Rapi-1.0.6/Rapi/man/excel.Rd | 4 Rapi-1.0.6/Rapi/man/get_series.Rd | 4 Rapi-1.0.6/Rapi/man/lag_df.Rd | 4 Rapi-1.0.6/Rapi/man/lag_df2.Rd | 2 Rapi-1.0.6/Rapi/man/remove_na_safe.Rd | 12 - Rapi-1.0.6/Rapi/man/set_api_key.Rd | 14 +- Rapi-1.0.6/Rapi/tests/testthat/caches_Rapi/3d4dc283b1b4c53f5aba5057bf787a63_2025_3_CACHE.RData |only Rapi-1.0.6/Rapi/tests/testthat/caches_Rapi/4fcf0e6cfe19b2219df6c66baeb0e31f_2025_3_CACHE.RData |only Rapi-1.0.6/Rapi/tests/testthat/caches_Rapi/7d9973e792dc706aa56d9dad7c226ea2_2025_3_CACHE.RData |only Rapi-1.0.6/Rapi/tests/testthat/caches_Rapi/e9343e9f8aa0c7553e699bb6a4034301_2025_3_CACHE.RData |only 37 files changed, 112 insertions(+), 129 deletions(-)
Title: Interface with Live Bikeshare Data
Description: Supplies a set of functions to interface with bikeshare data
following the General Bikeshare Feed Specification, allowing users to query
and accumulate tidy datasets for specified cities/bikeshare programs.
Author: Simon P. Couch [aut, cre],
Kaelyn Rosenberg [aut],
Mark Padgham [ctb]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>
Diff between gbfs versions 1.3.9 dated 2024-01-25 and 1.3.10 dated 2025-01-13
DESCRIPTION | 6 - MD5 | 8 - NEWS.md | 180 ++++++++++++++++++++++---------------------- R/utils.R | 2 tests/testthat/test-utils.R | 33 +++----- 5 files changed, 114 insertions(+), 115 deletions(-)
Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform
reproducible parallel foreach loops, using independent
random streams as generated by L'Ecuyer's combined
multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>].
It enables to easily convert standard '%dopar%' loops into
fully reproducible loops, independently of the number
of workers, the task scheduling strategy, or the chosen
parallel environment and associated foreach backend.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between doRNG versions 1.8.6 dated 2023-01-16 and 1.8.6.1 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/doRNG.Rnw | 2 +- inst/doc/doRNG.pdf |binary vignettes/doRNG.Rnw | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.151 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 7.2 dated 2024-12-04 and 7.3 dated 2025-01-13
DESCRIPTION | 11 +++-- MD5 | 80 ++++++++++++++++++++++--------------------- NAMESPACE | 2 - R/acor.R | 65 ++++++++++++++++++---------------- R/acor.tune.R | 4 -- R/aeqdist.etest.R | 45 ++++++++++++++++++------ R/eqdist.etest.R |only R/hotel2T2.R | 5 +- R/james.R | 7 +-- R/scls.betest.R | 3 + R/scls2.R | 3 + man/Compositional-package.Rd | 5 +- man/acor.Rd | 5 ++ man/acor.tune.Rd | 11 +++-- man/aeqdist.etest.Rd | 13 +++++- man/alfa.pca.Rd | 2 - man/ascls.Rd | 4 +- man/atflr.Rd | 4 +- man/comp.den.Rd | 8 ++-- man/comp.test.Rd | 14 +++---- man/cv.ascls.Rd | 4 +- man/cv.atflr.Rd | 4 +- man/cv.scls.Rd | 4 +- man/cv.scrq.Rd | 16 ++------ man/cv.tflr.Rd | 4 +- man/eqdist.etest.Rd |only man/hd.meantest2.Rd | 2 - man/rcompsn.Rd | 2 - man/scls.Rd | 4 +- man/scls.betest.Rd | 4 +- man/scls.indeptest.Rd | 4 +- man/scls2.Rd | 4 +- man/scrq.Rd | 4 +- man/skewnorm.contour.Rd | 2 - man/ternary.Rd | 2 - man/ternary.coef.Rd | 2 - man/ternary.coefcr.Rd | 4 +- man/ternary.mcr.Rd | 2 - man/tflr.Rd | 4 +- man/tflr.betest.Rd | 4 +- man/tflr.indeptest.Rd | 7 ++- man/tflr2.Rd | 4 +- 42 files changed, 206 insertions(+), 172 deletions(-)
Title: Spatial Data Science Complementary Features
Description: Wrapping and supplementing commonly used functions in the R ecosystem related to spatial data science,
while serving as a basis for other packages maintained by Wenbo Lv.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between sdsfun versions 0.6.0 dated 2024-12-11 and 0.7.0 dated 2025-01-13
DESCRIPTION | 6 MD5 | 36 +-- NEWS.md | 4 R/fuzzyoverlay.R | 12 - R/linear_regression.R | 14 + R/sf_helpers.R | 422 ++++++++++++++++++++++---------------------- R/spdep_helpers.R | 430 ++++++++++++++++++++++----------------------- R/ssh_test.R | 100 +++++----- R/stratification.R | 7 R/utils.R | 1 R/vector_toolkits.R | 130 ++++++------- man/check_tbl_na.Rd | 50 ++--- man/fuzzyoverlay.Rd | 1 man/generate_subsets.Rd | 60 +++--- man/geodetector_q.Rd | 46 ++-- man/hclustgeo_disc.Rd | 4 man/sf_gk_proj_cgcs2000.Rd | 54 ++--- man/tbl_all2int.Rd | 50 ++--- src/Tbl2Mat.cpp | 10 - 19 files changed, 727 insertions(+), 710 deletions(-)
Title: Read and Write ODS Files
Description: Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.
Author: Gerrit-Jan Schutten [aut],
Chung-hong Chan [aut, cre] ,
Peter Brohan [aut],
Detlef Steuer [aut] ,
Thomas J. Leeper [aut] ,
John Foster [ctb],
Sergio Oller [ctb],
Jim Hester [ctb] ,
Stephen Watts [ctb],
Arthur Katossky [ctb],
Stas Malavin [ctb],
Dunca [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between readODS versions 2.3.1 dated 2024-11-05 and 2.3.2 dated 2025-01-13
readODS-2.3.1/readODS/tests/testdata/issue81.ods |only readODS-2.3.1/readODS/tests/testdata/layout_test.xls |only readODS-2.3.1/readODS/tests/testdata/layout_test.xlsx |only readODS-2.3.2/readODS/DESCRIPTION | 12 +-- readODS-2.3.2/readODS/MD5 | 20 ++--- readODS-2.3.2/readODS/NEWS.md | 6 + readODS-2.3.2/readODS/R/read_ods.R | 36 +++------- readODS-2.3.2/readODS/README.md | 4 - readODS-2.3.2/readODS/build/vignette.rds |binary readODS-2.3.2/readODS/inst/doc/overview.R | 2 readODS-2.3.2/readODS/tests/testdata/test_may_make_read_ods_crash_v2.ods |only readODS-2.3.2/readODS/tests/testthat/test_issue81.R | 4 - readODS-2.3.2/readODS/tests/testthat/test_read_ods.R | 4 + 13 files changed, 45 insertions(+), 43 deletions(-)
Title: Search Data Frames for Personally Identifiable Information
Description: Check a data frame for personal information, including names, location, disability status, and geo-coordinates.
Author: Jacob Patterson-Stein [aut, cre]
Maintainer: Jacob Patterson-Stein <jacobpstein@gmail.com>
Diff between pii versions 1.1.0 dated 2025-01-08 and 1.3.0 dated 2025-01-13
DESCRIPTION | 6 - MD5 | 8 +- NAMESPACE | 1 NEWS.md | 4 + R/check_PII.R | 196 ++++++++++++++++++++-------------------------------------- 5 files changed, 80 insertions(+), 135 deletions(-)
Title: Creates Safety Results Summary in XML to Upload to EudraCT, or
ClinicalTrials.gov
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by Eudr [...truncated...]
Author: Simon Bond [cre],
Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>
Diff between eudract versions 1.0.2 dated 2024-11-28 and 1.0.3 dated 2025-01-13
DESCRIPTION | 8 MD5 | 160 NEWS.md | 96 R/clintrials_gov_convert.R | 140 R/clintrials_gov_upload.R | 186 R/eudract_convert.R | 72 R/incidence_table.R | 100 R/safety.R | 54 R/safety_summary.R | 572 R/simple_safety_xml.R | 120 R/soc_code.R | 28 build/vignette.rds |binary inst/doc/eudract.Rmd | 286 inst/doc/eudract.html | 15 inst/doc/standard_reporting.Rmd | 182 inst/doc/standard_reporting.html | 51 inst/extdata/1234.xml | 454 inst/extdata/ProtocolRecordSchema.xsd | 1452 +- inst/extdata/RRSUploadSchema.xsd | 1368 +- inst/extdata/adverseEvents.xsd | 570 inst/extdata/ct_safety_upload.xml | 2904 ++-- inst/extdata/find_replace.xslt | 48 inst/extdata/safety__upload.xml | 3676 ++--- inst/extdata/simple.xsd | 394 inst/extdata/simpleToCtGov.xslt | 248 inst/extdata/simpleToEudraCT.xslt | 288 inst/extdata/soc.xml | 276 man/append_xml.Rd | 24 man/clintrials_gov_convert.Rd | 134 man/clintrials_gov_upload.Rd | 170 man/create.safety_summary.Rd | 42 man/df_to_char.Rd | 30 man/dot_plot.Rd | 124 man/eudract_convert.Rd | 116 man/incidence_table.Rd | 66 man/plot.dot_plot.Rd | 32 man/print.dot_plot.Rd | 32 man/print.safety_summary.Rd | 34 man/relative_risk.Rd | 156 man/safety.Rd | 66 man/safety_summary.Rd | 134 man/simple_safety_xml.Rd | 104 man/soc_code.Rd | 48 tests/testthat.R | 10 tests/testthat/1234.xml | 454 tests/testthat/GROUP.csv | 8 tests/testthat/NONSERIOUS.csv | 164 tests/testthat/Rplots.pdf |binary tests/testthat/SERIOUS.csv | 164 tests/testthat/_snaps/dotplot/dotplot-1group.svg | 208 tests/testthat/_snaps/dotplot/dotplot-3groups.svg | 772 - tests/testthat/_snaps/dotplot/dotplot-ref-rr.svg | 488 tests/testthat/_snaps/dotplot/dotplot-ref.svg | 472 tests/testthat/_snaps/dotplot/dotplot.svg | 472 tests/testthat/bak_study_file.xml | 4030 +++--- tests/testthat/ct.xml | 3316 ++--- tests/testthat/data/all_soc.csv | 54 tests/testthat/data/all_soc_v2.csv | 56 tests/testthat/data/events.csv | 3278 ++--- tests/testthat/data/fix_ucl.R | 52 tests/testthat/data/multiple_soc.csv | 6 tests/testthat/data/no_aes.csv | 4 tests/testthat/data/no_saes.csv | 4 tests/testthat/data/output_from_ucl.xml |14114 +++++++++++----------- tests/testthat/data/repeat_occurrences.csv | 8 tests/testthat/data/socless.xml | 9846 +++++++-------- tests/testthat/data/sparse.csv | 6 tests/testthat/events.csv | 3328 ++--- tests/testthat/reference/simple.xml | 2904 ++-- tests/testthat/reference/table_ct.xml | 4016 +++--- tests/testthat/reference/table_eudract.xml | 4972 +++---- tests/testthat/simple.xml | 2904 ++-- tests/testthat/study_file.xml | 4030 +++--- tests/testthat/table_ct.xml | 4016 +++--- tests/testthat/table_eudract.xml | 3894 +++--- tests/testthat/test_append_xml.R | 36 tests/testthat/test_basic.R | 808 - tests/testthat/test_bea.R | 74 tests/testthat/test_errors.R | 566 vignettes/eudract.Rmd | 286 vignettes/standard_reporting.Rmd | 182 81 files changed, 42533 insertions(+), 42529 deletions(-)
Title: Produce Charts Following UK Government Analysis Function
Guidance
Description: Colour palettes and a 'ggplot2' theme to follow the UK Government
Analysis Function best practice guidance for producing data visualisations,
available at
<https://analysisfunction.civilservice.gov.uk/policy-store/data-visualisation-charts/>.
Includes continuous and discrete colour and fill scales, as well as a
'ggplot2' theme.
Author: Crown Copyright [cph],
Government Analysis Function [fnd],
Alice Hannah [aut],
Olivia Box Power [cre, ctb]
Maintainer: Olivia Box Power <Olivia.BoxPower@dhsc.gov.uk>
Diff between afcharts versions 0.4.0 dated 2024-11-06 and 0.4.1 dated 2025-01-13
DESCRIPTION | 10 MD5 | 75 +- NEWS.md | 8 R/af_palette.R | 6 R/afcharts-package.R | 2 R/scale_colour_continuous_af.R | 2 R/scale_colour_discrete_af.R | 1 R/scale_fill_continuous_af.R | 2 R/scale_fill_discrete_af.R | 1 R/use_afcharts.R | 16 R/utils.R | 2 README.md | 82 +- build/vignette.rds |binary inst/doc/colours.R | 17 inst/doc/colours.Rmd | 1 inst/doc/colours.html | 608 ++++++++-------- inst/doc/cookbook.R | 433 +++++++----- inst/doc/cookbook.Rmd | 1 inst/doc/cookbook.html | 1145 +++++++++++++++++--------------- inst/doc/saving.R | 11 inst/doc/saving.Rmd | 14 inst/doc/saving.html | 67 - man/figures/README-ex1-1.svg | 1077 +++++++++++++++--------------- man/figures/README-ex2-1.svg | 858 ++++++++++++----------- man/figures/README-ex3-1.svg |only man/use_afcharts.Rd | 2 tests/testthat.R | 1 tests/testthat/_snaps |only tests/testthat/helper.R |only tests/testthat/test-af_palette.R | 7 tests/testthat/test-chart-output.R |only vignettes/colours.Rmd | 1 vignettes/cookbook.Rmd | 1 vignettes/cookbook/_annotations.Rmd | 110 ++- vignettes/cookbook/_chart-types.Rmd | 170 +++- vignettes/cookbook/_colour-palettes.Rmd | 24 vignettes/cookbook/_customisations.Rmd | 143 ++- vignettes/saving.Rmd | 14 38 files changed, 2713 insertions(+), 2199 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.9.1 dated 2024-12-04 and 1.10.0 dated 2025-01-13
DESCRIPTION | 6 MD5 | 260 ++++++++++++++-------------- NAMESPACE | 6 NEWS.md | 37 +++ R/class_active.R | 57 +++--- R/class_auto.R | 27 ++ R/class_branch.R | 7 R/class_builder.R | 104 ++++++----- R/class_counter.R | 55 ++++- R/class_cue.R | 109 +++++------ R/class_database.R | 152 +++++++++++----- R/class_database_aws.R | 2 R/class_database_gcp.R | 2 R/class_database_local.R | 6 R/class_external.R | 10 - R/class_file.R | 61 ++++-- R/class_forecast.R | 11 - R/class_frames.R | 3 R/class_graph.R | 77 +++++--- R/class_junction.R | 4 R/class_lookup.R | 18 + R/class_meta.R | 62 +++--- R/class_metrics.R | 2 R/class_outdated.R | 30 +-- R/class_parallel.R | 7 R/class_pattern.R | 3 R/class_pipeline.R | 12 - R/class_progress.R | 17 + R/class_queue.R | 1 R/class_record.R | 12 - R/class_reporter.R | 16 + R/class_runtime.R | 16 - R/class_scheduler.R | 14 - R/class_sequential.R | 22 +- R/class_silent.R | 3 R/class_sitrep.R | 18 + R/class_store.R | 55 +++-- R/class_store_format_custom.R | 7 R/class_store_format_custom_methods.R | 18 + R/class_store_repository_cas.R | 2 R/class_store_repository_cas_methods.R | 43 +++- R/class_summary.R | 10 - R/class_target.R | 5 R/class_timestamp.R | 14 - R/class_vector.R | 17 + R/class_verbose.R | 17 - R/tar_built.R | 2 R/tar_config_get.R | 8 R/tar_config_set.R | 43 +++- R/tar_deduplicate.R | 4 R/tar_engine_knitr.R | 2 R/tar_format.R | 23 +- R/tar_make.R | 20 +- R/tar_make_clustermq.R | 2 R/tar_make_future.R | 2 R/tar_mermaid.R | 3 R/tar_network.R | 3 R/tar_outdated.R | 19 +- R/tar_repository_cas.R | 6 R/tar_resources_crew.R | 6 R/tar_script.R | 6 R/tar_seed.R | 4 R/tar_sitrep.R | 27 +- R/tar_started.R | 2 R/tar_target.R | 12 + R/tar_visnetwork.R | 3 R/use_targets.R | 4 R/utils_assert.R | 29 ++- R/utils_callr.R | 2 R/utils_cli.R | 7 R/utils_data.R | 15 - R/utils_files.R | 81 +++++++- R/utils_language.R | 2 inst/WORDLIST | 2 man/callr_args_default.Rd | 2 man/tar_built.Rd | 2 man/tar_config_set.Rd | 30 ++- man/tar_deduplicate.Rd | 2 man/tar_format.Rd | 10 - man/tar_make.Rd | 22 +- man/tar_make_clustermq.Rd | 22 +- man/tar_make_future.Rd | 22 +- man/tar_mermaid.Rd | 22 +- man/tar_network.Rd | 22 +- man/tar_option_set.Rd | 2 man/tar_outdated.Rd | 25 +- man/tar_resources_crew.Rd | 4 man/tar_script.Rd | 6 man/tar_seed.Rd | 2 man/tar_sitrep.Rd | 39 ++-- man/tar_started.Rd | 2 man/tar_target.Rd | 12 + man/tar_visnetwork.Rd | 22 +- man/use_targets.Rd | 4 tests/aws/test-aws_bad_args.R | 2 tests/aws/test-delete.R | 2 tests/aws/test-utils_aws.R | 68 ++++--- tests/gcp/test-class_gcp_qs.R | 10 - tests/interactive/test-class_url.R | 11 - tests/interactive/test-tar_repository_cas.R | 4 tests/testthat/test-class_auto.R | 24 ++ tests/testthat/test-class_aws.R | 12 - tests/testthat/test-class_aws_file.R | 12 - tests/testthat/test-class_counter.R | 8 tests/testthat/test-class_cue.R | 4 tests/testthat/test-class_database.R | 17 + tests/testthat/test-class_feather.R | 12 - tests/testthat/test-class_file.R | 15 + tests/testthat/test-class_fst.R | 12 - tests/testthat/test-class_fst_dt.R | 12 - tests/testthat/test-class_fst_tbl.R | 12 - tests/testthat/test-class_gcp.R | 12 - tests/testthat/test-class_gcp_file.R | 12 - tests/testthat/test-class_graph.R | 50 ++--- tests/testthat/test-class_keras.R | 12 - tests/testthat/test-class_parquet.R | 12 - tests/testthat/test-class_qs.R | 12 - tests/testthat/test-class_rds.R | 12 - tests/testthat/test-class_runtime.R | 18 - tests/testthat/test-class_sequential.R | 42 ++++ tests/testthat/test-class_store_file.R | 25 ++ tests/testthat/test-class_torch.R | 12 - tests/testthat/test-class_vector.R | 9 tests/testthat/test-tar_config_set.R | 23 ++ tests/testthat/test-tar_repository_cas.R | 13 - tests/testthat/test-tar_sitrep.R | 18 - tests/testthat/test-utils_assert.R | 8 tests/testthat/test-utils_callr.R | 21 -- tests/testthat/test-utils_data.R | 6 tests/testthat/test-utils_files.R | 113 ++++++------ tests/testthat/test-utils_oop.R | 4 131 files changed, 1769 insertions(+), 952 deletions(-)
Title: Simple Blinding Index for Randomized Controlled Trials
Description: Computes a simple blinding index for randomized controlled trials introduced in Petroff, Bacak, Dagres, Dilk, Wachter: A simple blinding index for randomized controlled trials. Contemp Clin Trials Commun. 2024 Nov 26;42:101393. <doi:10.1016/j.conctc.2024.101393>. PMID: 39686958.
Author: David Petroff [aut, cre, cph],
Miroslav Bacak [aut, cph]
Maintainer: David Petroff <david.petroff@zks.uni-leipzig.de>
Diff between SBI versions 0.1.1 dated 2024-09-11 and 0.1.2 dated 2025-01-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/sbi.R | 10 ++++------ man/BlindingIndex.Rd | 6 ++---- 4 files changed, 13 insertions(+), 17 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate and play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR versions 0.4.3 dated 2024-02-15 and 0.4.4 dated 2025-01-13
ProTrackR-0.4.3/ProTrackR/R/10ModArchiveHelpers.r |only ProTrackR-0.4.3/ProTrackR/R/11MODPlugHelpers.r |only ProTrackR-0.4.3/ProTrackR/R/12ModLandHelpers.r |only ProTrackR-0.4.3/ProTrackR/man/modArchive.Rd |only ProTrackR-0.4.3/ProTrackR/man/modLand.Rd |only ProTrackR-0.4.4/ProTrackR/DESCRIPTION | 10 ProTrackR-0.4.4/ProTrackR/MD5 | 76 ProTrackR-0.4.4/ProTrackR/NEWS.md | 472 +- ProTrackR-0.4.4/ProTrackR/R/01supporting_functions.r | 1158 +++--- ProTrackR-0.4.4/ProTrackR/R/02PTCell.r | 1490 ++++---- ProTrackR-0.4.4/ProTrackR/R/03PTTrack.r | 298 - ProTrackR-0.4.4/ProTrackR/R/04PTPattern.r | 346 - ProTrackR-0.4.4/ProTrackR/R/05PTSample.r | 2147 +++++------ ProTrackR-0.4.4/ProTrackR/R/06PTModule.r | 2682 +++++++------- ProTrackR-0.4.4/ProTrackR/R/07PTBlock.r | 314 - ProTrackR-0.4.4/ProTrackR/R/08coercion.r | 1092 ++--- ProTrackR-0.4.4/ProTrackR/R/09playing_routines.r | 3459 +++++++++---------- ProTrackR-0.4.4/ProTrackR/R/10MODPlugHelpers.r |only ProTrackR-0.4.4/ProTrackR/R/ProTrackR-package.r | 332 - ProTrackR-0.4.4/ProTrackR/R/deprecated.R |only ProTrackR-0.4.4/ProTrackR/README.md | 38 ProTrackR-0.4.4/ProTrackR/man/MODPlugToPTPattern.Rd | 4 ProTrackR-0.4.4/ProTrackR/man/PTModule-class.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/PTPatternToMODPlug.Rd | 16 ProTrackR-0.4.4/ProTrackR/man/PTSample-method.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/PTTrack-class.Rd | 6 ProTrackR-0.4.4/ProTrackR/man/ProTrackR-package.Rd | 8 ProTrackR-0.4.4/ProTrackR/man/fix.PTModule.Rd | 12 ProTrackR-0.4.4/ProTrackR/man/modToWave.Rd | 6 ProTrackR-0.4.4/ProTrackR/man/note.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/nybble.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/openmpt-deprecated.Rd |only ProTrackR-0.4.4/ProTrackR/man/patternOrder.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/playMod.Rd | 10 ProTrackR-0.4.4/ProTrackR/man/playSample.Rd | 35 ProTrackR-0.4.4/ProTrackR/man/playWave.Rd | 18 ProTrackR-0.4.4/ProTrackR/man/playingtable.Rd | 6 ProTrackR-0.4.4/ProTrackR/man/plot.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/rawToPTModule.Rd | 4 ProTrackR-0.4.4/ProTrackR/man/read.module.Rd | 19 ProTrackR-0.4.4/ProTrackR/man/read.sample.Rd | 7 ProTrackR-0.4.4/ProTrackR/man/write.module.Rd | 7 ProTrackR-0.4.4/ProTrackR/man/write.sample.Rd | 9 43 files changed, 6999 insertions(+), 7094 deletions(-)
Title: Reproducible Integrated Species Distribution Models Across
Norway using 'INLA'
Description: Integration of disparate datasets is needed in order to make efficient use of all available data and thereby address the issues currently threatening biodiversity.
Data integration is a powerful modeling framework which allows us to combine these datasets together into a single model, yet retain the strengths of each individual dataset.
We therefore introduce the package, 'intSDM': an R package designed to help ecologists develop a reproducible workflow of integrated species distribution models, using data both provided from the user as well as data obtained freely online.
An introduction to data integration methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Author: Philip Mostert [aut, cre],
Angeline Bruls [aut],
Ragnhild {Bjoerkas} [aut],
Wouter Koch [aut],
Ellen Martin [aut]
Maintainer: Philip Mostert <philip.s.mostert@ntnu.no>
Diff between intSDM versions 2.1.0 dated 2024-08-21 and 2.1.1 dated 2025-01-13
DESCRIPTION | 16 +- MD5 | 56 +++++----- NAMESPACE | 2 R/obtainCovariate.R | 15 ++ R/obtainGBIF.R | 32 ++++- R/obtainRichness.R |only R/sdmWorkflow.R | 119 ++++----------------- R/species_model.R | 107 ++++++++++++++----- R/startWorkflow.R | 2 build/vignette.rds |binary inst/doc/PennsylvaniaWarbler.R | 6 - inst/doc/PennsylvaniaWarbler.Rmd | 8 - inst/doc/PennsylvaniaWarbler.html | 29 ++--- inst/doc/RedList.R | 79 ++++++++------ inst/doc/RedList.Rmd | 135 +++++++++++++----------- inst/doc/RedList.html | 180 +++++++++++++++++---------------- inst/doc/Richness.html | 6 - man/obtainCovariate.Rd | 6 - man/obtainGBIF.Rd | 4 man/obtainRichness.Rd |only man/species_model.Rd | 18 +-- tests/testthat/setup.R |only tests/testthat/test-generateAbsences.R | 48 +++++++- tests/testthat/test-initValues.R | 6 - tests/testthat/test-obtainCovariate.R | 20 +++ tests/testthat/test-obtainGBIF.R | 22 +++- tests/testthat/test-obtainRichness.R |only tests/testthat/test-sdmWorkflow.R | 4 tests/testthat/test-species_model.R | 6 - vignettes/PennsylvaniaWarbler.Rmd | 8 - vignettes/RedList.Rmd | 135 +++++++++++++----------- 31 files changed, 598 insertions(+), 471 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data and some useful functions for
tabulation and plotting, as well as a number of epidemiological data
sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.58 dated 2024-11-25 and 2.59 dated 2025-01-13
CHANGES | 6 DESCRIPTION | 8 - MD5 | 55 ++++---- NAMESPACE | 2 R/AaJ.Lexis.R | 2 R/ci.eta.R | 4 R/paths.Lexis.R |only inst/doc/aaflup.R | 2 inst/doc/aaflup.pdf |binary inst/doc/aaflup.rnw | 1 inst/doc/addLexis.R | 6 inst/doc/addLexis.pdf |binary inst/doc/addLexis.rnw | 6 inst/doc/crisk.R | 210 ++++++++++++++++----------------- inst/doc/crisk.pdf |binary inst/doc/crisk.rnw | 310 +++++++++++++++++++++++++------------------------ inst/doc/simLexis.R | 94 +++++++++----- inst/doc/simLexis.pdf |binary inst/doc/simLexis.rnw | 43 +++++- inst/doc/yll.R | 61 ++++++--- inst/doc/yll.pdf |binary inst/doc/yll.rnw | 47 +++++-- man/B.dk.Rd | 53 ++++---- man/paths.Lexis.Rd |only vignettes/aaflup.rnw | 1 vignettes/addLexis.rnw | 6 vignettes/crisk.rnw | 310 +++++++++++++++++++++++++------------------------ vignettes/rtall.bat |only vignettes/simLexis.rnw | 43 +++++- vignettes/yll.rnw | 47 +++++-- 30 files changed, 731 insertions(+), 586 deletions(-)
Title: Optimal Adaptive Allocation Using Deep Reinforcement Learning
Description: An implementation to compute an optimal adaptive allocation rule
using deep reinforcement learning in a dose-response study
(Matsuura et al. (2022) <doi:10.1002/sim.9247>).
The adaptive allocation rule can directly optimize a performance metric,
such as power, accuracy of the estimated target dose, or mean absolute error
over the estimated dose-response curve.
Author: Kentaro Matsuura [aut, cre, cph]
,
Koji Makiyama [aut, ctb]
Maintainer: Kentaro Matsuura <matsuurakentaro55@gmail.com>
Diff between RLoptimal versions 1.2.0 dated 2024-12-20 and 1.2.1 dated 2025-01-13
RLoptimal-1.2.0/RLoptimal/tests/testthat/test-generate_setup_code.R |only RLoptimal-1.2.1/RLoptimal/DESCRIPTION | 6 ++-- RLoptimal-1.2.1/RLoptimal/MD5 | 13 ++++------ RLoptimal-1.2.1/RLoptimal/R/rl_dnn_config.R | 1 RLoptimal-1.2.1/RLoptimal/R/simulate_one_trial.R | 2 - RLoptimal-1.2.1/RLoptimal/inst/doc/RLoptimal.html | 4 +-- RLoptimal-1.2.1/RLoptimal/man/rl_dnn_config.Rd | 1 RLoptimal-1.2.1/RLoptimal/man/simulate_one_trial.Rd | 2 - 8 files changed, 13 insertions(+), 16 deletions(-)
Title: Relationship Inference for DNA Mixtures
Description: Analysis of DNA mixtures involving relatives by computation of likelihood ratios that account for dropout and drop-in, mutations, silent alleles and population
substructure. This is useful in kinship cases, like non-invasive prenatal paternity testing, where deductions about individuals' relationships rely on DNA mixtures,
and in criminal cases where the contributors to a mixed DNA stain may be related. Relationships are represented
by pedigrees and can include kinship between more than two individuals. The main function is relMix() and its graphical user interface relMixGUI().
The implementation and method is described in Dorum et al. (2017) <doi:10.1007/s00414-016-1526-x>, Hernandis et al. (2019)
<doi:10.1016/j.fsigss.2019.09.085> and Kaur et al. (2016) <doi:10.1007/s00414-015-1276-1>.
Author: Guro Dorum [aut, cre],
Elias Hernandis [aut],
Navreet Kaur [ctb],
Thore Egeland [ctb],
Magnus Dehli Vigeland [ctb]
Maintainer: Guro Dorum <guro.dorum@gmail.com>
Diff between relMix versions 1.4 dated 2024-04-23 and 1.4.1 dated 2025-01-13
DESCRIPTION | 27 +++++++++++---------- MD5 | 32 ++++++++++++------------- NAMESPACE | 1 NEWS.md | 7 ++++- R/checkFrequenciesFile.R | 2 - R/createDatamatrix.R | 4 +-- R/relMix.R | 13 ++++++---- R/relMixGUI.R | 8 ++++-- README.md | 7 ++++- build/vignette.rds |binary inst/doc/relMix.R | 56 +++++++++++++++++++++---------------------- inst/doc/relMix.Rmd | 60 +++++++++++++++++++++++++---------------------- inst/doc/relMix.html | 42 ++++++++++++++++---------------- man/createDatamatrix.Rd | 4 +-- man/relMix.Rd | 10 ++++--- man/relMixGUI.Rd | 2 - vignettes/relMix.Rmd | 60 +++++++++++++++++++++++++---------------------- 17 files changed, 182 insertions(+), 153 deletions(-)
Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre, cph]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.0.6 dated 2024-08-23 and 0.0.7 dated 2025-01-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/expect_snapshot_print.R | 28 +++++++++++++++++++++++----- README.md | 20 ++++++++++++++++++++ build/partial.rdb |binary man/expect_snapshot_print.Rd | 3 +++ 7 files changed, 60 insertions(+), 15 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.11.0 dated 2024-07-11 and 2.12.0 dated 2025-01-13
DESCRIPTION | 6 MD5 | 26 +-- NEWS.md | 3 R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rfacebookstat-authorization.R | 26 +-- inst/doc/rfacebookstat-authorization.html | 8 - inst/doc/rfacebookstat-cost-data.R | 48 +++--- inst/doc/rfacebookstat-cost-data.html | 18 +- inst/doc/rfacebookstat-get-statistics.R | 232 ++++++++++++++--------------- inst/doc/rfacebookstat-get-statistics.Rmd | 2 inst/doc/rfacebookstat-get-statistics.html | 6 vignettes/rfacebookstat-get-statistics.Rmd | 2 14 files changed, 191 insertions(+), 188 deletions(-)
Title: Bayesian partial least squares regression
Description: Fits the Bayesian partial least squares regression model
introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable
for univariate and multivariate regression with high-dimensional data.
Author: Szymon Urbas [aut, cre],
Pierre Lovera [ctb],
Robert Daly [ctb],
Alan O'Riordan [ctb],
Donagh Berry [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Szymon Urbas <szymon.urbas@mu.ie>
Diff between bplsr versions 1.0.1 dated 2024-12-02 and 1.0.2 dated 2025-01-13
bplsr-1.0.1/bplsr/man/figures/README-pressure-1.png |only bplsr-1.0.2/bplsr/DESCRIPTION | 6 ++--- bplsr-1.0.2/bplsr/MD5 | 7 ++--- bplsr-1.0.2/bplsr/R/BPLSR.R | 24 +++----------------- bplsr-1.0.2/bplsr/man/bplsr.Rd | 2 - 5 files changed, 11 insertions(+), 28 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing
framework for R that is easy to learn and use, and integrates with
your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb] )
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between testthat versions 3.2.2 dated 2024-12-10 and 3.2.3 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/expect-no-condition.R | 7 ++++++- R/snapshot-reporter.R | 4 +++- tests/testthat/test-expect-no-condition.R | 10 ++++++---- 6 files changed, 30 insertions(+), 14 deletions(-)
Title: Extensions of Package 'distr'
Description: Extends package 'distr' by functionals, distances, and conditional distributions.
Author: Matthias Kohl [cre, cph],
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between distrEx versions 2.9.5 dated 2024-09-02 and 2.9.6 dated 2025-01-13
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- R/sysdata.rda |binary inst/NEWS | 10 ++++++++++ man/0distrEx-package.Rd | 8 ++++---- 5 files changed, 28 insertions(+), 17 deletions(-)
Title: Fast Conversion of R Colors to Color Component Values and Native
Packed Integer Format
Description: Color values in R are often represented as strings of hexadecimal
colors or named colors. This package offers fast conversion of
these color representations to either an array of red/green/blue/alpha values
or to the packed integer format used in native raster objects. Functions
for conversion are also exported at the 'C' level for use in other packages.
This fast conversion
of colors is implemented using an order-preserving minimal perfect hash
derived from Majewski et al (1996) "A Family of Perfect Hashing Methods"
<doi:10.1093/comjnl/39.6.547>.
Author: Mike Cheng [aut, cre, cph]
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Diff between colorfast versions 1.0.0 dated 2024-12-16 and 1.0.1 dated 2025-01-13
colorfast-1.0.0/colorfast/src/col_to_packed_int.c |only colorfast-1.0.1/colorfast/DESCRIPTION | 17 + colorfast-1.0.1/colorfast/LICENSE | 2 colorfast-1.0.1/colorfast/MD5 | 30 +- colorfast-1.0.1/colorfast/NAMESPACE | 2 colorfast-1.0.1/colorfast/NEWS.md | 9 colorfast-1.0.1/colorfast/R/col_to_rgb.R | 46 ++++ colorfast-1.0.1/colorfast/build |only colorfast-1.0.1/colorfast/inst |only colorfast-1.0.1/colorfast/man/col_to_int.Rd | 2 colorfast-1.0.1/colorfast/man/int_to_col.Rd |only colorfast-1.0.1/colorfast/man/set_alpha.Rd |only colorfast-1.0.1/colorfast/src/alpha.c |only colorfast-1.0.1/colorfast/src/col_to_int.c |only colorfast-1.0.1/colorfast/src/col_to_rgb.c | 110 +++++----- colorfast-1.0.1/colorfast/src/init.c | 24 +- colorfast-1.0.1/colorfast/src/int_to_col.c |only colorfast-1.0.1/colorfast/tests/testthat/test-named-colours.R | 23 +- colorfast-1.0.1/colorfast/vignettes |only 19 files changed, 194 insertions(+), 71 deletions(-)
Title: The R WINS Package
Description: Calculate the win statistics (win ratio, net benefit and win odds) for prioritized multiple endpoints, plot the win statistics and win proportions over study time if at least one time-to-event endpoint is analyzed, and simulate datasets with dependent endpoints. The package can handle any type of outcomes (continuous, ordinal, binary, time-to-event) and allow users to perform stratified analysis, inverse probability of censoring weighting (IPCW) and inverse probability of treatment weighting (IPTW) analysis.
Author: Ying Cui [aut, cre],
Bo Huang [aut]
Maintainer: Ying Cui <cuiyingbeicheng@gmail.com>
Diff between WINS versions 1.4.2 dated 2024-04-29 and 1.4.3 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++++---- R/iptw_covipcw.adjusted.KL.R |only R/iptw_covipcw.win.stat.R |only R/iptw_ipcw.adjusted.KL.R |only R/iptw_ipcw.win.stat.R |only R/win.stat.R | 15 +++++++++++++-- inst/doc/vignette.pdf |binary man/win.stat.Rd | 6 +++++- 9 files changed, 29 insertions(+), 10 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut, cre]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.7-2.1 dated 2024-09-23 and 0.7-3.1 dated 2025-01-13
DESCRIPTION | 14 MD5 | 6 configure | 2741 +++++++++++++++++++++++++++++++---------------------------- configure.ac | 15 4 files changed, 1476 insertions(+), 1300 deletions(-)
Title: JavaScript Charts Tool
Description: Provides an R interface for using 'AmCharts' Library. Based on
'htmlwidgets', it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced but
can easily be added in the constructors. Complex properties (e.g. 'JavaScript'
object) can be passed as named list. See examples at
<https://datastorm-open.github.io/introduction_ramcharts/>
and <https://www.amcharts.com/> for
more information about the library. The package includes the free version
of 'AmCharts' Library. Its only limitation is a small link to the web site
displayed on your charts. If you enjoy this library, do not hesitate to refer
to this page <https://www.amcharts.com/online-store/> to purchase a licence,
and thus support its creators and get a period of Priority Support. See also
<https://www.amcharts.com/about/> for more information about 'AmChart [...truncated...]
Author: Benoit Thieurmel [aut, cre],
Antanas Marcelionis [aut, cph]
Maintainer: Benoit Thieurmel <bthieurmel@gmail.com>
Diff between rAmCharts versions 2.1.15 dated 2022-09-30 and 2.1.16 dated 2025-01-13
DESCRIPTION | 8 MD5 | 74 +- NAMESPACE | 1 R/chart_amBarplot.R | 5 R/chart_amFloatingBar.R | 5 R/chart_amGauge.R | 5 R/chart_amRadar.R | 7 R/chart_amTimeSeries.R | 8 R/class_AmChart.R | 3 R/class_AmGraph.R | 2 R/class_AmObject.R | 20 R/class_AmStockChart.R | 3 R/class_DataSet.R | 2 R/shiny_modules_export.R | 10 R/shiny_modules_timeSeries.R | 20 R/union_AmCharts.R | 1 R/utils_amOptions.R | 2 inst/htmlwidgets/lib/plugins/export/README.md | 6 man/AmGraph.Rd | 2 man/DataSet-class.Rd | 2 man/amBarplot.Rd | 5 man/amFloatingBar.Rd | 5 man/amOptions.Rd | 2 man/amPlot.Rd | 8 man/amRadar.Rd | 5 man/amSolidGauge.Rd | 5 man/amTimeSeries.Rd | 18 man/getCurrentStockData.Rd | 4 man/getTransformTS.Rd | 4 man/initialize-AmChart.Rd | 3 man/listProperties-AmObject.Rd | 4 man/methods-AmObject.Rd | 14 man/rAmCharts-shinymodules-ts.Rd | 26 man/rAmCharts-shinymodules.Rd | 10 tests/testthat/test_AmStockChart_setters.R | 66 +- tests/testthat/test_amBoxplot.R | 112 ++-- tests/testthat/test_amchart_setters.R | 330 ++++++------ tests/testthat/test_getAggregateTS.R | 714 +++++++++++++------------- 38 files changed, 731 insertions(+), 790 deletions(-)
Title: Get Data from the French National Database on Water 'Hub'Eau'
Description: Collection of functions to help retrieving data from
'Hub'Eau' the free and public French National APIs on water
<https://hubeau.eaufrance.fr/>.
Author: David Dorchies [aut, cre] ,
Pascal Irz [ctb] ,
Sebastien Grall [ctb],
Philippe Amiotte Suchet [ctb]
Maintainer: David Dorchies <david.dorchies@inrae.fr>
Diff between hubeau versions 0.5.0 dated 2024-03-04 and 0.5.1 dated 2025-01-13
DESCRIPTION | 9 LICENSE | 4 MD5 | 84 +-- NEWS.md | 7 R/get_ecoulement.R | 170 +++---- R/get_hydrobio.R | 138 ++--- R/get_hydrometrie.R | 301 ++++++------ R/get_indicateurs_services.R | 200 ++++---- R/get_niveaux_nappes.R | 132 ++--- R/get_prelevements.R | 106 ++-- R/get_qualite_eau_potable.R | 122 ++--- R/get_qualite_nappes.R | 100 ++-- R/get_temperature.R | 100 ++-- R/list_apis.R | 64 +- R/list_endpoints.R | 10 R/list_params.R | 24 - README.md | 424 +++++++++--------- build/vignette.rds |binary inst/CITATION | 46 - inst/WORDLIST | 244 +++++----- inst/doc/data_extraction_naiades.R | 70 +- inst/doc/data_extraction_naiades.html | 6 inst/doc/example_ecoulement_api.R | 28 - inst/doc/example_ecoulement_api.html | 48 +- inst/doc/example_niveaux_nappes_api.R | 60 +- inst/doc/example_niveaux_nappes_api.html | 45 + man/convert_list_to_tibble.Rd | 82 +-- man/doApiQuery.Rd | 120 ++--- man/get_ecoulement.Rd | 130 ++--- man/get_hydrobio.Rd | 110 ++-- man/get_hydrometrie.Rd | 138 ++--- man/get_indicateurs_services.Rd | 144 +++--- man/get_niveaux_nappes.Rd | 110 ++-- man/get_prelevements.Rd | 90 +-- man/get_qualite_eau_potable.Rd | 114 ++-- man/get_temperature.Rd | 94 +-- man/lists.Rd | 90 +-- tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/test-convert_ellipsis_to_params.R | 10 tests/testthat/test-doApiQuery.R | 19 tests/testthat/test-get_hydrometrie_observations_tr.R | 46 - tests/testthat/test-run_all_examples.R | 56 +- 43 files changed, 1976 insertions(+), 1933 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous (and discrete) time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE) or difference equation, measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling.
See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. Priors may be used. For the conceptual overview of the hierarchical Bayesian
linear SDE approach,
see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Mod [...truncated...]
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsem versions 3.10.1 dated 2024-08-19 and 3.10.2 dated 2025-01-13
DESCRIPTION | 10 MD5 | 51 - NEWS.md | 4 R/ctACF.R | 9 R/ctCheckFit.R | 233 ++++-- R/ctDataHelp.R | 2 R/ctDiscretePars.R | 2 R/ctLOO.R | 228 +++--- R/ctStanFit.R | 5 R/ctSummarise.R | 60 + R/ctTIpredAuto.R | 99 +- R/sgd.R | 24 R/stanoptimis.R | 437 +++++------- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 2 inst/doc/hierarchicalmanual.pdf |binary inst/doc/hierarchicalmanual.rnw | 76 -- man/AnomAuth.Rd | 2 man/ctFitCovCheck.Rd |only man/ctLOO.Rd | 10 man/stanoptimis.Rd | 13 tests/testthat/test-bootstrapScoreHessian.R |only tests/testthat/test-ctLOO.R | 61 + tests/testthat/test-stantipred.R | 2 tests/testthat/test-timevarying.R | 15 vignettes/hierarchicalmanual.rnw | 76 -- vignettes/hierarchicalrefs.bib | 1004 +++++++++++++++++++--------- 28 files changed, 1502 insertions(+), 923 deletions(-)
Title: Data Only Package to 'healthyR'
Description: Provides data for functions typically used in the 'healthyR' package.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.data versions 1.1.1 dated 2024-07-04 and 1.2.0 dated 2025-01-12
DESCRIPTION | 6 ++-- MD5 | 8 ++--- NEWS.md | 13 ++++++++- R/utils-valid-url.R | 74 ++++++++++++++++++++++++++-------------------------- README.md | 3 -- 5 files changed, 57 insertions(+), 47 deletions(-)
Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 2.1.25 dated 2024-07-24 and 3.1.10 dated 2025-01-12
growthPheno-2.1.25/growthPheno/R/dataLongi_v9.r |only growthPheno-2.1.25/growthPheno/R/softDeprec.r |only growthPheno-2.1.25/growthPheno/man/fitSpline.Rd |only growthPheno-2.1.25/growthPheno/man/intervalGRaverage.Rd |only growthPheno-2.1.25/growthPheno/man/intervalGRdiff.Rd |only growthPheno-2.1.25/growthPheno/man/intervalValueCalculate.Rd |only growthPheno-2.1.25/growthPheno/man/intervalWUI.Rd |only growthPheno-2.1.25/growthPheno/man/longitudinalPrime.Rd |only growthPheno-2.1.25/growthPheno/man/plotLongitudinal.Rd |only growthPheno-2.1.25/growthPheno/man/plotMedianDeviations.Rd |only growthPheno-2.1.25/growthPheno/man/probeSmoothing.Rd |only growthPheno-2.1.25/growthPheno/man/splitContGRdiff.Rd |only growthPheno-2.1.25/growthPheno/man/splitSplines.Rd |only growthPheno-2.1.25/growthPheno/man/splitValueCalculate.Rd |only growthPheno-2.1.25/growthPheno/tests/testthat/testProbeSmoothing.r |only growthPheno-2.1.25/growthPheno/tests/testthat/testSplines.r |only growthPheno-3.1.10/growthPheno/DESCRIPTION | 8 growthPheno-3.1.10/growthPheno/MD5 | 73 ++---- growthPheno-3.1.10/growthPheno/NAMESPACE | 2 growthPheno-3.1.10/growthPheno/R/PVA.v3.r | 55 +++-- growthPheno-3.1.10/growthPheno/R/S3methodsDeprecations.r | 71 ++++++ growthPheno-3.1.10/growthPheno/R/dataLongi_v10.r |only growthPheno-3.1.10/growthPheno/build/partial.rdb |binary growthPheno-3.1.10/growthPheno/build/vignette.rds |binary growthPheno-3.1.10/growthPheno/inst/News.Rd | 15 + growthPheno-3.1.10/growthPheno/inst/doc/Rice.pdf |binary growthPheno-3.1.10/growthPheno/inst/doc/Tomato.pdf |binary growthPheno-3.1.10/growthPheno/inst/doc/growthPheno-manual.pdf |binary growthPheno-3.1.10/growthPheno/man/byIndv4Intvl_GRsAvg.Rd | 4 growthPheno-3.1.10/growthPheno/man/byIndv4Intvl_GRsDiff.Rd | 2 growthPheno-3.1.10/growthPheno/man/byIndv4Intvl_ValueCalc.Rd | 2 growthPheno-3.1.10/growthPheno/man/byIndv4Intvl_WaterUse.Rd | 8 growthPheno-3.1.10/growthPheno/man/byIndv4Times_SplinesGRs.Rd | 4 growthPheno-3.1.10/growthPheno/man/growthPheno-deprecated.Rd | 36 +++ growthPheno-3.1.10/growthPheno/man/growthPheno-pkg.Rd | 3 growthPheno-3.1.10/growthPheno/man/plotAnom.Rd | 2 growthPheno-3.1.10/growthPheno/man/plotCorrmatrix.Rd | 36 +-- growthPheno-3.1.10/growthPheno/man/plotDeviationsBoxes.Rd | 2 growthPheno-3.1.10/growthPheno/man/smoothSpline.Rd | 2 growthPheno-3.1.10/growthPheno/man/traitExtractFeatures.Rd | 3 growthPheno-3.1.10/growthPheno/tests/testthat/testContGRdiff.r | 5 growthPheno-3.1.10/growthPheno/tests/testthat/testCorrPlot.r | 52 ++++ growthPheno-3.1.10/growthPheno/tests/testthat/testbyIndv4Times.r | 108 +++++----- growthPheno-3.1.10/growthPheno/tests/testthat/testexampleData.r | 9 growthPheno-3.1.10/growthPheno/tests/testthat/testprepImageData.r |only growthPheno-3.1.10/growthPheno/tests/testthat/testsmoothSpline.R | 2 growthPheno-3.1.10/growthPheno/tests/testthat/testthat-problems.rds |only 47 files changed, 337 insertions(+), 167 deletions(-)
Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Tools to help download, process and analyse the UK road collision data collected using the
'STATS19' form. The datasets are provided as 'CSV' files with detailed road safety information about the
circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain
from 1979 to present. Tables are available on 'colissions' with the circumstances (e.g. speed limit
of road), information about 'vehicles' involved (e.g. type of vehicle), and 'casualties' (e.g. age).
The statistics relate only to events on public roads that were reported
to the police, and subsequently recorded, using the 'STATS19' collision reporting form. See
the Department for Transport website
<https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data> for more
information on these datasets.
The package is described in a paper in the Journal of Open Source Software
(Lovelace et al. 2019) <doi:10.21105/joss.01181>.
See
Gilardi et al. (202 [...truncated...]
Author: Robin Lovelace [aut, cre] ,
Malcolm Morgan [aut] ,
Layik Hama [aut] ,
Mark Padgham [aut] ,
David Ranzolin [rev],
Adam Sparks [rev, ctb] ,
Ivo Wengraf [ctb],
RAC Foundation [fnd]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stats19 versions 3.2.0 dated 2024-10-24 and 3.3.0 dated 2025-01-12
DESCRIPTION | 14 MD5 | 66 - NEWS.md | 5 R/dl.R | 2 R/format.R | 28 README.md | 7 build/vignette.rds |binary data/accidents_sample.rda |binary data/accidents_sample_raw.rda |binary data/casualties_sample.rda |binary data/file_names.rda |binary data/file_names_old.rda |binary data/stats19_schema.rda |binary data/stats19_variables.rda |binary data/vehicles_sample.rda |binary inst/doc/blog.R | 292 +++--- inst/doc/blog.Rmd | 4 inst/doc/blog.html | 659 +++++-------- inst/doc/stats19-training-setup.R | 44 inst/doc/stats19-training-setup.Rmd | 3 inst/doc/stats19-training-setup.html | 250 ++--- inst/doc/stats19-training.R | 534 +++++------ inst/doc/stats19-training.html | 1266 +++++++++----------------- inst/doc/stats19-vehicles.R | 230 ++-- inst/doc/stats19-vehicles.html | 243 ++--- inst/doc/stats19.R | 59 - inst/doc/stats19.Rmd | 27 inst/doc/stats19.html | 1648 ++++++++++++++++------------------- man/dl_stats19.Rd | 4 man/format_collisions.Rd | 14 man/get_stats19.Rd | 10 vignettes/blog.Rmd | 4 vignettes/stats19-training-setup.Rmd | 3 vignettes/stats19.Rmd | 27 34 files changed, 2400 insertions(+), 3043 deletions(-)
Title: Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by transparently
mapping only a section (pagesize) in main memory - the effective
virtual memory consumption per ff object. ff supports R's standard
atomic data types 'double', 'logical', 'raw' and 'integer' and
non-standard atomic types boolean (1 bit), quad (2 bit unsigned),
nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte
unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned),
single (4 byte float with NAs). For example 'quad' allows efficient
storage of genomic data as an 'A','T','G','C' factor. The unsigned
types support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and
custom close-to-atomic types.
ff not only has native C-support for vectors, matrices and arrays
with flexible dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf cla [...truncated...]
Author: Daniel Adler [aut],
Christian Glaeser [ctb],
Oleg Nenadic [ctb],
Jens Oehlschlaegel [aut, cre],
Martijn Schuemie [ctb],
Walter Zucchini [ctb]
Maintainer: Jens Oehlschlaegel <Jens.Oehlschlaegel@truecluster.com>
Diff between ff versions 4.5.0 dated 2024-09-20 and 4.5.2 dated 2025-01-12
DESCRIPTION | 10 ++--- MD5 | 14 +++---- NEWS | 19 +++++++++ R/ff.R | 1 R/hi.R | 92 ++++++++++++++++++++++++++---------------------- R/zzz.R | 4 +- src/MMapFileMapping.cpp | 2 - src/r_ff_addgetset.h | 13 +++++- 8 files changed, 94 insertions(+), 61 deletions(-)
Title: Object Oriented Implementation of Distributions
Description: S4-classes and methods for distributions.
Author: Florian Camphausen [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] ,
R Core Team [ctb, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distr versions 2.9.5 dated 2024-08-29 and 2.9.7 dated 2025-01-12
DESCRIPTION | 18 ++++----- MD5 | 18 ++++----- R/makedots.R | 2 - R/plot-methods.R | 9 ++-- inst/NEWS | 12 ++++++ inst/doc/newDistributions-knitr.Rnw | 5 +- inst/doc/newDistributions-knitr.pdf |binary man/0distr-package.Rd | 8 ++-- tests/Examples/distr-Ex.Rout.save | 65 ++++++++++++++++------------------- vignettes/newDistributions-knitr.Rnw | 5 +- 10 files changed, 77 insertions(+), 65 deletions(-)
Title: Access Data from the Atlas do Estado Brasileiro
Description: Facilitates access to the data from the Atlas do Estado Brasileiro
(<https://www.ipea.gov.br/atlasestado/>), maintained by the Instituto de
Pesquisa Econômica Aplicada (Ipea). It allows users to search for specific
series, list series or themes, and download data when available.
Author: Hugo Macedo [aut, cre, cph]
Maintainer: Hugo Macedo <aebdata@hhmace.do>
Diff between aebdata versions 0.1.2 dated 2024-11-08 and 0.1.3 dated 2025-01-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 2 ++ inst/doc/exploring-data.html | 22 +++++++++++----------- tests/testthat/_data/search.rds |binary 5 files changed, 20 insertions(+), 18 deletions(-)
Title: Libraries, Data Dictionaries, and a Data Step for R
Description: Contains a set of functions to create data libraries,
generate data dictionaries, and simulate a data step.
The libname() function will load a directory of data into
a library in one line of code. The dictionary() function
will generate data dictionaries for individual
data frames or an entire library. And the datestep() function
will perform row-by-row data processing.
Author: David Bosak [aut, cre],
Brian Varney [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between libr versions 1.3.8 dated 2024-12-13 and 1.3.9 dated 2025-01-12
libr-1.3.8/libr/tests/testthat/data/CRF/lab.sas7bdat |only libr-1.3.8/libr/tests/testthat/data/SDTM/DS_IHOR.csv |only libr-1.3.8/libr/tests/testthat/data/SDTM/QS.csv |only libr-1.3.8/libr/tests/testthat/data/SDTM/ds_ihor.sas7bdat |only libr-1.3.8/libr/tests/testthat/data/SDTM/qs.sas7bdat |only libr-1.3.9/libr/DESCRIPTION | 6 ++-- libr-1.3.9/libr/MD5 | 17 ++++---------- libr-1.3.9/libr/NEWS.md | 3 ++ libr-1.3.9/libr/R/utilities.R | 2 - libr-1.3.9/libr/tests/testthat/test-libname.R | 2 - libr-1.3.9/libr/tests/testthat/test-manipulation.R | 4 +-- libr-1.3.9/libr/tests/testthat/test-specs.R | 5 ++-- 12 files changed, 19 insertions(+), 20 deletions(-)
Title: Board Game Graphics
Description: Functions to make board game graphics with the 'ggplot2', 'grid', 'rayrender', 'rayvertex', and 'rgl' packages. Specializes in game diagrams, animations, and "Print & Play" layouts for the 'piecepack' <https://www.ludism.org/ppwiki> but can make graphics for other board game systems. Includes configurations for several public domain game systems such as checkers, (double-18) dominoes, go, 'piecepack', playing cards, etc.
Author: Trevor L. Davis [aut, cre] ,
Linux Foundation [dtc] ,
Delapouite <https://delapouite.com/> [ill] ,
Creative Commons [ill] ` uses "license badges"
from Creative Commons to describe the generated print-and-play
file's license)
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between piecepackr versions 1.13.11 dated 2024-08-16 and 1.14.1 dated 2025-01-12
piecepackr-1.13.11/piecepackr/tests/testthat/_snaps/op_transform/simple-points.svg |only piecepackr-1.13.11/piecepackr/tests/testthat/_snaps/op_transform/simple-square.svg |only piecepackr-1.13.11/piecepackr/tests/testthat/test-affine.R |only piecepackr-1.14.1/piecepackr/DESCRIPTION | 10 piecepackr-1.14.1/piecepackr/MD5 | 109 +- piecepackr-1.14.1/piecepackr/NAMESPACE | 27 piecepackr-1.14.1/piecepackr/NEWS.md | 81 + piecepackr-1.14.1/piecepackr/R/aabb_piece.R | 17 piecepackr-1.14.1/piecepackr/R/cropmarkGrob.R | 227 +++-- piecepackr-1.14.1/piecepackr/R/crosshairGrob.R |only piecepackr-1.14.1/piecepackr/R/game_systems.R | 66 - piecepackr-1.14.1/piecepackr/R/install_ppverse.R |only piecepackr-1.14.1/piecepackr/R/op_transform.R | 18 piecepackr-1.14.1/piecepackr/R/piece-rayrender.R | 17 piecepackr-1.14.1/piecepackr/R/piece3d-rgl.R | 39 piecepackr-1.14.1/piecepackr/R/pieceGrob-grid.R | 38 piecepackr-1.14.1/piecepackr/R/piece_mesh-rayvertex.R | 33 piecepackr-1.14.1/piecepackr/R/pp_cfg.R | 2 piecepackr-1.14.1/piecepackr/R/pp_shape.R | 2 piecepackr-1.14.1/piecepackr/R/save_piece_obj.R | 122 ++ piecepackr-1.14.1/piecepackr/R/sysdata.rda |binary piecepackr-1.14.1/piecepackr/R/utils-composite.R | 97 -- piecepackr-1.14.1/piecepackr/R/utils-d10.R | 78 + piecepackr-1.14.1/piecepackr/R/utils-d12.R | 22 piecepackr-1.14.1/piecepackr/R/utils-d20.R | 27 piecepackr-1.14.1/piecepackr/R/utils-d4.R | 41 piecepackr-1.14.1/piecepackr/R/utils-d6.R | 21 piecepackr-1.14.1/piecepackr/R/utils-d8.R | 31 piecepackr-1.14.1/piecepackr/R/utils-font.R | 41 piecepackr-1.14.1/piecepackr/R/utils-geometry.R | 450 +--------- piecepackr-1.14.1/piecepackr/R/utils-mat-grobs.R | 2 piecepackr-1.14.1/piecepackr/R/utils-misc.R | 3 piecepackr-1.14.1/piecepackr/R/utils-op-grobs.R | 76 - piecepackr-1.14.1/piecepackr/R/utils-pips.R | 29 piecepackr-1.14.1/piecepackr/R/utils-token.R | 142 +-- piecepackr-1.14.1/piecepackr/R/utils-transformation.R | 241 ----- piecepackr-1.14.1/piecepackr/R/utils-xyz.R | 34 piecepackr-1.14.1/piecepackr/R/zzz.R | 5 piecepackr-1.14.1/piecepackr/README.md | 60 + piecepackr-1.14.1/piecepackr/data/spdx_license_list.rda |binary piecepackr-1.14.1/piecepackr/man/geometry_utils.Rd | 4 piecepackr-1.14.1/piecepackr/man/grid.cropmark.Rd | 10 piecepackr-1.14.1/piecepackr/man/grid.crosshair.Rd |only piecepackr-1.14.1/piecepackr/man/install_ppverse.Rd |only piecepackr-1.14.1/piecepackr/man/obj_fns.Rd | 2 piecepackr-1.14.1/piecepackr/man/piecepackr-package.Rd | 2 piecepackr-1.14.1/piecepackr/man/save_piece_obj.Rd | 9 piecepackr-1.14.1/piecepackr/tests/testthat/_snaps/crosshairs |only piecepackr-1.14.1/piecepackr/tests/testthat/_snaps/draw_component/tile-face-op.svg | 2 piecepackr-1.14.1/piecepackr/tests/testthat/_snaps/game_systems/go.svg | 300 +++--- piecepackr-1.14.1/piecepackr/tests/testthat/_snaps/game_systems/joystick-op.svg | 8 piecepackr-1.14.1/piecepackr/tests/testthat/_snaps/op_transform/oblique-pyramids.svg | 28 piecepackr-1.14.1/piecepackr/tests/testthat/_snaps/op_transform/op-transform-225.svg | 12 piecepackr-1.14.1/piecepackr/tests/testthat/_snaps/op_transform/pyramid-tops-larger-on-top.svg | 6 piecepackr-1.14.1/piecepackr/tests/testthat/_snaps/op_transform/pyramid-tops-smaller-on-top.svg | 6 piecepackr-1.14.1/piecepackr/tests/testthat/_snaps/op_transform/rotated-tile-faces.svg | 2 piecepackr-1.14.1/piecepackr/tests/testthat/test-crosshairs.R |only piecepackr-1.14.1/piecepackr/tests/testthat/test-draw_component.R | 12 piecepackr-1.14.1/piecepackr/tests/testthat/test-op_transform.R | 15 piecepackr-1.14.1/piecepackr/tests/testthat/test-ppverse.R |only 60 files changed, 1170 insertions(+), 1456 deletions(-)
Title: Joint Clustering and Alignment of Functional Data
Description: Implementations of the k-means, hierarchical agglomerative and
DBSCAN clustering methods for functional data which allows for jointly
aligning and clustering curves. It supports functional data defined on
one-dimensional domains but possibly evaluating in multivariate codomains.
It supports functional data defined in arrays but also via the 'fd' and
'funData' classes for functional data defined in the 'fda' and 'funData'
packages respectively. It currently supports shift, dilation and affine
warping functions for functional data defined on the real line and uses the
SRSF framework to handle boundary-preserving warping for functional data
defined on a specific interval. Main reference for the k-means algorithm:
Sangalli L.M., Secchi P., Vantini S., Vitelli V. (2010) "k-mean alignment
for curve clustering" <doi:10.1016/j.csda.2009.12.008>. Main reference for
the SRSF framework: Tucker, J. D., Wu, W., & Srivastava, A. (2013)
"Generative models for functional data using phase and [...truncated...]
Author: Aymeric Stamm [aut, cre] ,
Laura Sangalli [ctb],
Piercesare Secchi [ctb],
Simone Vantini [ctb],
Valeria Vitelli [ctb],
Alessandro Zito [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between fdacluster versions 0.3.0 dated 2023-07-04 and 0.4.0 dated 2025-01-12
fdacluster-0.3.0/fdacluster/src/kumaraswamyWarpingClass.cpp |only fdacluster-0.3.0/fdacluster/src/kumaraswamyWarpingClass.h |only fdacluster-0.4.0/fdacluster/DESCRIPTION | 16 fdacluster-0.4.0/fdacluster/MD5 | 84 +-- fdacluster-0.4.0/fdacluster/NAMESPACE | 2 fdacluster-0.4.0/fdacluster/NEWS.md | 35 + fdacluster-0.4.0/fdacluster/R/caps-diagnostic.R | 34 - fdacluster-0.4.0/fdacluster/R/caps-plot.R | 57 +- fdacluster-0.4.0/fdacluster/R/compare-caps.R | 160 +++--- fdacluster-0.4.0/fdacluster/R/fdacluster-package.R | 2 fdacluster-0.4.0/fdacluster/R/fdadbscan.R | 61 +- fdacluster-0.4.0/fdacluster/R/fdadist.R | 49 + fdacluster-0.4.0/fdacluster/R/fdahclust.R | 62 +- fdacluster-0.4.0/fdacluster/R/fdakmeans.R | 251 ++++++---- fdacluster-0.4.0/fdacluster/R/sysdata.rda |binary fdacluster-0.4.0/fdacluster/R/utils.R | 144 +++++ fdacluster-0.4.0/fdacluster/README.md | 93 --- fdacluster-0.4.0/fdacluster/build/partial.rdb |binary fdacluster-0.4.0/fdacluster/build/vignette.rds |binary fdacluster-0.4.0/fdacluster/inst/doc/berkeley-growth.R | 167 ++++-- fdacluster-0.4.0/fdacluster/inst/doc/berkeley-growth.Rmd | 102 +++- fdacluster-0.4.0/fdacluster/inst/doc/berkeley-growth.html | 249 +++++---- fdacluster-0.4.0/fdacluster/inst/doc/kmeans-initialisation.R | 156 +++--- fdacluster-0.4.0/fdacluster/inst/doc/kmeans-initialisation.Rmd | 20 fdacluster-0.4.0/fdacluster/inst/doc/kmeans-initialisation.html | 31 - fdacluster-0.4.0/fdacluster/man/compare_caps.Rd | 23 fdacluster-0.4.0/fdacluster/man/fdacluster-package.Rd | 2 fdacluster-0.4.0/fdacluster/man/fdadbscan.Rd | 38 + fdacluster-0.4.0/fdacluster/man/fdadist.Rd | 31 - fdacluster-0.4.0/fdacluster/man/fdahclust.Rd | 48 + fdacluster-0.4.0/fdacluster/man/fdakmeans.Rd | 38 + fdacluster-0.4.0/fdacluster/man/figures/README-kmeans-amplitude-viz-1.png |binary fdacluster-0.4.0/fdacluster/man/figures/README-kmeans-amplitude-viz-2.png |binary fdacluster-0.4.0/fdacluster/man/figures/README-kmeans-phase-viz-1.png |binary fdacluster-0.4.0/fdacluster/man/figures/README-kmeans-phase-viz-2.png |binary fdacluster-0.4.0/fdacluster/src/kmaModelClass.cpp | 7 fdacluster-0.4.0/fdacluster/src/l2DissimilarityClass.cpp | 19 fdacluster-0.4.0/fdacluster/src/normalizedL2DissimilarityClass.cpp |only fdacluster-0.4.0/fdacluster/src/normalizedL2DissimilarityClass.h |only fdacluster-0.4.0/fdacluster/src/pearsonDissimilarityClass.cpp | 4 fdacluster-0.4.0/fdacluster/tests/testthat/test-fdadbscan.R | 2 fdacluster-0.4.0/fdacluster/tests/testthat/test-fdahclust.R | 2 fdacluster-0.4.0/fdacluster/tests/testthat/test-fdakmeans.R | 12 fdacluster-0.4.0/fdacluster/vignettes/berkeley-growth.Rmd | 102 +++- fdacluster-0.4.0/fdacluster/vignettes/kmeans-initialisation.Rmd | 20 45 files changed, 1306 insertions(+), 817 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98), other curves (e.g., NOTCal04 [van der Plicht et al. 2004], Arnold & Libby 1951) and postbomb curves. Also provided are functions to copy the curves into memory, and to read, query and plot the data underlying the IntCal20 curves.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rintcal versions 1.1.1 dated 2024-12-19 and 1.1.2 dated 2025-01-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 3 +++ R/data.R | 20 +++++++++++++++----- R/rintcal.R | 2 -- inst/doc/rintcal.html | 4 ++-- 6 files changed, 28 insertions(+), 17 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
JJ Allaire [aut] ,
Kevin Ushey [aut] ,
Qiang Kou [aut] ,
Nathan Russell [aut],
Inaki Ucar [aut] ,
Doug Bates [aut] ,
John Chambers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.0.13-1 dated 2024-11-02 and 1.0.14 dated 2025-01-12
ChangeLog | 142 +++++++++++++++++++- DESCRIPTION | 8 - MD5 | 106 +++++++------- R/Rcpp.package.skeleton.R | 23 ++- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 45 ++++++ inst/bib/Rcpp.bib | 4 inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-jss-2011.pdf |binary inst/doc/Rcpp-libraries.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/include/Rcpp/Benchmark/Timer.h | 8 - inst/include/Rcpp/DataFrame.h | 2 inst/include/Rcpp/DottedPair.h | 2 inst/include/Rcpp/Environment.h | 15 -- inst/include/Rcpp/Function.h | 2 inst/include/Rcpp/InternalFunctionWithStdFunction.h | 2 inst/include/Rcpp/Language.h | 8 - inst/include/Rcpp/Module.h | 11 - inst/include/Rcpp/Pairlist.h | 8 - inst/include/Rcpp/config.h | 10 - inst/include/Rcpp/exceptions_impl.h | 19 +- inst/include/Rcpp/grow.h | 2 inst/include/Rcpp/internal/call.h | 6 inst/include/Rcpp/module/class.h | 4 inst/include/Rcpp/platform/compiler.h | 6 inst/include/Rcpp/r_cast.h | 11 - inst/include/Rcpp/traits/index_sequence.h | 2 inst/include/Rcpp/traits/named_object.h | 2 inst/include/Rcpp/vector/Vector.h | 6 inst/tinytest/test_date.R | 2 inst/tinytest/test_module.R | 25 +++ inst/tinytest/test_rcpp_package_skeleton.R | 8 - inst/tinytest/test_sugar.R | 2 src/api.cpp | 2 src/attributes.cpp | 2 tests/tinytest.R | 12 - vignettes/pdf/Rcpp-FAQ.pdf |binary vignettes/pdf/Rcpp-attributes.pdf |binary vignettes/pdf/Rcpp-extending.pdf |binary vignettes/pdf/Rcpp-introduction.pdf |binary vignettes/pdf/Rcpp-jss-2011.pdf |binary vignettes/pdf/Rcpp-libraries.pdf |binary vignettes/pdf/Rcpp-modules.pdf |binary vignettes/pdf/Rcpp-package.pdf |binary vignettes/pdf/Rcpp-quickref.pdf |binary vignettes/pdf/Rcpp-sugar.pdf |binary 54 files changed, 349 insertions(+), 158 deletions(-)
Title: Plant Photobiology Related Functions and Data
Description: Provides functions for quantifying visible (VIS) and ultraviolet
(UV) radiation in relation to the photoreceptors Phytochromes,
Cryptochromes, and UVR8 which are present in plants. It also includes data
sets on the optical properties of plants. Part of the 'r4photobiology'
suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyPlants versions 0.5.0 dated 2024-04-02 and 0.6.0 dated 2025-01-12
DESCRIPTION | 13 - MD5 | 72 ++++--- NAMESPACE | 12 + NEWS.md | 8 R/leaf-fluo-mspct.r |only R/water.et.r |only R/water.vapour.R |only README.md | 29 ++ build/partial.rdb |binary build/vignette.rds |binary data/CRYs.mspct.rda |binary data/McCree.rda |binary data/PHOTs.mspct.rda |binary data/UVR8s.mspct.rda |binary data/ZTLs.mspct.rda |binary data/carotenoids-mspct.rda |binary data/chlorophylls-fluorescence-mspct.rda |binary data/chlorophylls-mspct.rda |binary data/leaf-fluorescence-mspct.rda |only data/leaves.spct.rda |binary data/phytochrome.spct.rda |binary inst/doc/r4p-introduction.html | 6 inst/doc/user-guide.R | 74 +++++++ inst/doc/user-guide.Rmd | 117 +++++++++++ inst/doc/user-guide.html | 313 +++++++++++++++++-------------- man/ET_ref.Rd |only man/figures/README-unnamed-chunk-4-1.png |binary man/leaf_fluorescence.mspct.Rd |only man/net_irradiance.Rd |only man/water_vp_sat.Rd |only tests |only vignettes/user-guide.Rmd | 117 +++++++++++ 32 files changed, 575 insertions(+), 186 deletions(-)
More information about photobiologyPlants at CRAN
Permanent link
Title: Less Code, More Results
Description: Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis (facet) graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.3.9 dated 2024-12-08 and 4.4.0 dated 2025-01-12
lessR-4.3.9/lessR/R/Sort.R |only lessR-4.4.0/lessR/DESCRIPTION | 10 lessR-4.4.0/lessR/MD5 | 103 +-- lessR-4.4.0/lessR/NAMESPACE | 13 lessR-4.4.0/lessR/NEWS.md | 39 + lessR-4.4.0/lessR/R/ANOVA.R | 38 - lessR-4.4.0/lessR/R/BarChart.R | 2 lessR-4.4.0/lessR/R/Logit.R | 80 +- lessR-4.4.0/lessR/R/PieChart.R | 50 - lessR-4.4.0/lessR/R/Plot.R | 231 +++++--- lessR-4.4.0/lessR/R/Read.R | 18 lessR-4.4.0/lessR/R/Regression.R | 108 +-- lessR-4.4.0/lessR/R/STL.R | 89 ++- lessR-4.4.0/lessR/R/bar.lattice.R | 56 +- lessR-4.4.0/lessR/R/bc.ParamValid.R | 4 lessR-4.4.0/lessR/R/bc.main.R | 14 lessR-4.4.0/lessR/R/hst.stats.R | 13 lessR-4.4.0/lessR/R/order_by.R |only lessR-4.4.0/lessR/R/param.VBS.R | 50 - lessR-4.4.0/lessR/R/pc.main.R | 48 - lessR-4.4.0/lessR/R/pivot.R | 2 lessR-4.4.0/lessR/R/plt.colors.R | 12 lessR-4.4.0/lessR/R/plt.fill.R | 2 lessR-4.4.0/lessR/R/plt.forecast.R | 373 +++++++++---- lessR-4.4.0/lessR/R/plt.funnel.R | 4 lessR-4.4.0/lessR/R/plt.lattice.R | 96 +-- lessR-4.4.0/lessR/R/plt.legend.R | 7 lessR-4.4.0/lessR/R/plt.main.R | 125 ++-- lessR-4.4.0/lessR/R/plt.marg.R | 2 lessR-4.4.0/lessR/R/plt.panel.R | 72 +- lessR-4.4.0/lessR/R/plt.shapes.R | 2 lessR-4.4.0/lessR/R/plt.time.R | 101 ++- lessR-4.4.0/lessR/R/plt.txt.R | 557 +++++++++++++------ lessR-4.4.0/lessR/R/print.outall.R | 2 lessR-4.4.0/lessR/R/reg.1fitBasic.R | 12 lessR-4.4.0/lessR/R/rename.R | 4 lessR-4.4.0/lessR/R/sort_by.R | 107 --- lessR-4.4.0/lessR/R/ss.numeric.R | 16 lessR-4.4.0/lessR/R/style.R | 116 ++-- lessR-4.4.0/lessR/R/tsExtract.R | 64 +- lessR-4.4.0/lessR/R/tsMake.R | 32 - lessR-4.4.0/lessR/R/ttest.R | 82 +- lessR-4.4.0/lessR/R/zzz.R | 54 + lessR-4.4.0/lessR/build/vignette.rds |binary lessR-4.4.0/lessR/inst/doc/intro.R | 62 ++ lessR-4.4.0/lessR/inst/doc/intro.Rmd | 173 ++++++ lessR-4.4.0/lessR/inst/doc/intro.html | 948 ++++++++++++++++++++++++++++------ lessR-4.4.0/lessR/man/BarChart.Rd | 3 lessR-4.4.0/lessR/man/Histogram.Rd | 4 lessR-4.4.0/lessR/man/Plot.Rd | 299 +++++----- lessR-4.4.0/lessR/man/STL.Rd | 37 + lessR-4.4.0/lessR/man/order_by.Rd |only lessR-4.4.0/lessR/man/sort_by.Rd | 68 -- lessR-4.4.0/lessR/vignettes/intro.Rmd | 173 ++++++ 54 files changed, 3048 insertions(+), 1529 deletions(-)
Title: Extra Functionality for 'leaflet' Package
Description: Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Author: Gatscha Sebastian [aut, cre],
Ricardo Rodrigo Basa [ctb],
Jeffrey O Hanson [ctb]
Maintainer: Gatscha Sebastian <sebastian_gatscha@gmx.at>
Diff between leaflet.extras2 versions 1.2.2 dated 2023-08-21 and 1.3.0 dated 2025-01-12
leaflet.extras2-1.2.2/leaflet.extras2/man/leaflet.extras2.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/DESCRIPTION | 14 leaflet.extras2-1.3.0/leaflet.extras2/MD5 | 230 ++-- leaflet.extras2-1.3.0/leaflet.extras2/NAMESPACE | 12 leaflet.extras2-1.3.0/leaflet.extras2/NEWS.md | 12 leaflet.extras2-1.3.0/leaflet.extras2/R/antpath.R | 63 - leaflet.extras2-1.3.0/leaflet.extras2/R/arrowhead.R | 74 - leaflet.extras2-1.3.0/leaflet.extras2/R/buildings.R |only leaflet.extras2-1.3.0/leaflet.extras2/R/clusterCharts.R |only leaflet.extras2-1.3.0/leaflet.extras2/R/contextmenu.R | 80 - leaflet.extras2-1.3.0/leaflet.extras2/R/divicon.R |only leaflet.extras2-1.3.0/leaflet.extras2/R/easyprint.R | 86 - leaflet.extras2-1.3.0/leaflet.extras2/R/gibs.R | 59 - leaflet.extras2-1.3.0/leaflet.extras2/R/heightgraph.R | 99 +- leaflet.extras2-1.3.0/leaflet.extras2/R/hexbin.R | 81 - leaflet.extras2-1.3.0/leaflet.extras2/R/history.R | 41 leaflet.extras2-1.3.0/leaflet.extras2/R/labelgun.R | 26 leaflet.extras2-1.3.0/leaflet.extras2/R/layergroupcollision.R |only leaflet.extras2-1.3.0/leaflet.extras2/R/layergroupconditional.R |only leaflet.extras2-1.3.0/leaflet.extras2/R/leaflet.extras2-package.R | 14 leaflet.extras2-1.3.0/leaflet.extras2/R/leafletsync.R | 34 leaflet.extras2-1.3.0/leaflet.extras2/R/mapkeyIcon.R | 172 +-- leaflet.extras2-1.3.0/leaflet.extras2/R/movingmarker.R | 97 + leaflet.extras2-1.3.0/leaflet.extras2/R/openweather.R | 99 +- leaflet.extras2-1.3.0/leaflet.extras2/R/playback.R | 177 ++- leaflet.extras2-1.3.0/leaflet.extras2/R/reachability.R | 28 leaflet.extras2-1.3.0/leaflet.extras2/R/sidebar.R | 67 - leaflet.extras2-1.3.0/leaflet.extras2/R/sidebyside.R | 59 - leaflet.extras2-1.3.0/leaflet.extras2/R/spin.R | 17 leaflet.extras2-1.3.0/leaflet.extras2/R/tangram.R | 37 leaflet.extras2-1.3.0/leaflet.extras2/R/timeslider.R | 116 +- leaflet.extras2-1.3.0/leaflet.extras2/R/velocity.R | 30 leaflet.extras2-1.3.0/leaflet.extras2/R/wms.R | 38 leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/Buildings_mini.geojson |only leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/antpath_app.R | 15 leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/arrowhead_app.R | 45 leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/buildings_app.R |only leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/clusterCharts_app.R |only leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/clustercharts_sum.R |only leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/conditional_app.R |only leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/contextmenu_app.R | 73 - leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/divicons_app.R |only leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/divicons_html_app.R |only leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/layergroupcollision_app.R |only leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/leafletsync/sync_basic.R | 2 leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/sidebar_app.R | 7 leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/timeslider_app.R | 1 leaflet.extras2-1.3.0/leaflet.extras2/inst/examples/www |only leaflet.extras2-1.3.0/leaflet.extras2/inst/htmlwidgets/lfx-antpath/lfx-ant-path.js | 2 leaflet.extras2-1.3.0/leaflet.extras2/inst/htmlwidgets/lfx-building |only leaflet.extras2-1.3.0/leaflet.extras2/inst/htmlwidgets/lfx-clustercharts |only leaflet.extras2-1.3.0/leaflet.extras2/inst/htmlwidgets/lfx-conditional |only leaflet.extras2-1.3.0/leaflet.extras2/inst/htmlwidgets/lfx-divicon |only leaflet.extras2-1.3.0/leaflet.extras2/inst/htmlwidgets/lfx-layergroupcollision |only leaflet.extras2-1.3.0/leaflet.extras2/inst/htmlwidgets/lfx-sidebar/leaflet-sidebar-binding.js | 32 leaflet.extras2-1.3.0/leaflet.extras2/inst/htmlwidgets/lfx-sidebar/leaflet-sidebar.css | 4 leaflet.extras2-1.3.0/leaflet.extras2/man/LayerGroupCollision.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/addBuildings.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/addClusterCharts.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/addContextmenu.Rd | 44 leaflet.extras2-1.3.0/leaflet.extras2/man/addDivicon.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/addEasyprint.Rd | 9 leaflet.extras2-1.3.0/leaflet.extras2/man/addGIBS.Rd | 10 leaflet.extras2-1.3.0/leaflet.extras2/man/addHeightgraph.Rd | 19 leaflet.extras2-1.3.0/leaflet.extras2/man/addHexbin.Rd | 20 leaflet.extras2-1.3.0/leaflet.extras2/man/addHistory.Rd | 2 leaflet.extras2-1.3.0/leaflet.extras2/man/addLabelgun.Rd | 14 leaflet.extras2-1.3.0/leaflet.extras2/man/addLayerGroupConditional.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/addMapkeyMarkers.Rd | 20 leaflet.extras2-1.3.0/leaflet.extras2/man/addMovingMarker.Rd | 26 leaflet.extras2-1.3.0/leaflet.extras2/man/addOpenweatherCurrent.Rd | 13 leaflet.extras2-1.3.0/leaflet.extras2/man/addOpenweatherTiles.Rd | 10 leaflet.extras2-1.3.0/leaflet.extras2/man/addPlayback.Rd | 83 - leaflet.extras2-1.3.0/leaflet.extras2/man/addReachability.Rd | 2 leaflet.extras2-1.3.0/leaflet.extras2/man/addSidebar.Rd | 12 leaflet.extras2-1.3.0/leaflet.extras2/man/addSidebyside.Rd | 36 leaflet.extras2-1.3.0/leaflet.extras2/man/addSpinner.Rd | 2 leaflet.extras2-1.3.0/leaflet.extras2/man/addTangram.Rd | 17 leaflet.extras2-1.3.0/leaflet.extras2/man/addTimeslider.Rd | 23 leaflet.extras2-1.3.0/leaflet.extras2/man/addVelocity.Rd | 4 leaflet.extras2-1.3.0/leaflet.extras2/man/addWMS.Rd | 22 leaflet.extras2-1.3.0/leaflet.extras2/man/antpathOptions.Rd | 5 leaflet.extras2-1.3.0/leaflet.extras2/man/clearConditionalLayers.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/clusterchartOptions.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/disableContextmenu.Rd | 72 - leaflet.extras2-1.3.0/leaflet.extras2/man/easyprintMap.Rd | 48 leaflet.extras2-1.3.0/leaflet.extras2/man/enableContextmenu.Rd | 72 - leaflet.extras2-1.3.0/leaflet.extras2/man/historyOptions.Rd | 9 leaflet.extras2-1.3.0/leaflet.extras2/man/isSynced.Rd | 2 leaflet.extras2-1.3.0/leaflet.extras2/man/leaflet.extras2-package.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/leafletsyncOptions.Rd | 2 leaflet.extras2-1.3.0/leaflet.extras2/man/makeMapkeyIcon.Rd | 12 leaflet.extras2-1.3.0/leaflet.extras2/man/mapkeyIconList.Rd | 2 leaflet.extras2-1.3.0/leaflet.extras2/man/mapkeyIcons.Rd | 15 leaflet.extras2-1.3.0/leaflet.extras2/man/playbackOptions.Rd | 2 leaflet.extras2-1.3.0/leaflet.extras2/man/removeConditionalLayer.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/setBuildingData.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/setBuildingStyle.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/sidebar_tabs.Rd | 12 leaflet.extras2-1.3.0/leaflet.extras2/man/startMoving.Rd | 14 leaflet.extras2-1.3.0/leaflet.extras2/man/unsync.Rd | 2 leaflet.extras2-1.3.0/leaflet.extras2/man/updateBuildingTime.Rd |only leaflet.extras2-1.3.0/leaflet.extras2/man/velocityOptions.Rd | 3 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-antpath.R | 14 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-arrowhead.R | 10 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-clustercharts.R |only leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-contextmenu.R | 198 ++-- leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-divicon.R |only leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-easyprint.R | 32 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-gibs.R | 62 - leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-heightgraph.R | 80 - leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-hexbin.R | 84 + leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-history.R | 27 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-labelgun.R | 10 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-layergroupcollision.R |only leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-leafletsync.R | 39 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-mapkeyicon.R | 235 ++-- leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-movingmarker.R | 166 +-- leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-openweathermap.R | 93 + leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-osmbuildings.R |only leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-playback.R | 492 +++++----- leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-reachability.R | 22 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-sidebar.R | 74 - leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-sidebyside.R | 55 - leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-spin.R | 5 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-tangram.R | 22 leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-timeslider.R | 86 + leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-velocity.R | 54 - leaflet.extras2-1.3.0/leaflet.extras2/tests/testthat/test-wms.R | 22 129 files changed, 2676 insertions(+), 1909 deletions(-)
More information about leaflet.extras2 at CRAN
Permanent link
Title: Concise, Lazy and Reliable Wrapper for 'chromote' and 'selenium'
Description: A user-friendly wrapper for web automation, using either
'chromote' or 'selenium'. Provides a simple and consistent API to make
web scraping and testing scripts easy to write and understand.
Elements are lazy, and automatically wait for the website to be valid,
resulting in reliable and reproducible code, with no visible impact on
the experience of the programmer.
Author: Ashby Thorpe [aut, cre, cph]
Maintainer: Ashby Thorpe <ashbythorpe@gmail.com>
Diff between selenider versions 0.4.0 dated 2024-04-20 and 0.4.1 dated 2025-01-12
selenider-0.4.0/selenider/R/find_browser_and_version.R |only selenider-0.4.0/selenider/inst/scripts |only selenider-0.4.0/selenider/tests/testthat/test-find_browser_and_version.R |only selenider-0.4.1/selenider/DESCRIPTION | 12 - selenider-0.4.1/selenider/MD5 | 86 +++---- selenider-0.4.1/selenider/NAMESPACE | 2 selenider-0.4.1/selenider/NEWS.md | 9 selenider-0.4.1/selenider/R/aaa_env.R | 5 selenider-0.4.1/selenider/R/actions.R | 3 selenider-0.4.1/selenider/R/api.R | 7 selenider-0.4.1/selenider/R/cache.R | 4 selenider-0.4.1/selenider/R/elem_filter.R | 2 selenider-0.4.1/selenider/R/find_browser.R |only selenider-0.4.1/selenider/R/find_elements.R | 9 selenider-0.4.1/selenider/R/get_actual_element.R | 2 selenider-0.4.1/selenider/R/global_actions.R | 108 ++++++++- selenider-0.4.1/selenider/R/session-options.R | 117 +++++----- selenider-0.4.1/selenider/R/session.R | 101 +++----- selenider-0.4.1/selenider/R/utils.R | 28 +- selenider-0.4.1/selenider/README.md | 2 selenider-0.4.1/selenider/build/vignette.rds |binary selenider-0.4.1/selenider/inst/doc/advanced-usage.R |only selenider-0.4.1/selenider/inst/doc/advanced-usage.Rmd |only selenider-0.4.1/selenider/inst/doc/advanced-usage.html |only selenider-0.4.1/selenider/inst/doc/selenider.R | 14 - selenider-0.4.1/selenider/inst/doc/selenider.Rmd | 14 - selenider-0.4.1/selenider/inst/doc/selenider.html | 9 selenider-0.4.1/selenider/inst/doc/unit-testing.html | 30 +- selenider-0.4.1/selenider/inst/doc/with-rvest.html | 8 selenider-0.4.1/selenider/man/back.Rd | 9 selenider-0.4.1/selenider/man/chromote_options.Rd | 48 ---- selenider-0.4.1/selenider/man/current_url.Rd | 1 selenider-0.4.1/selenider/man/elem_cache.Rd | 4 selenider-0.4.1/selenider/man/elem_filter.Rd | 2 selenider-0.4.1/selenider/man/execute_js_fn.Rd | 1 selenider-0.4.1/selenider/man/find_elements.Rd | 9 selenider-0.4.1/selenider/man/get_page_source.Rd | 1 selenider-0.4.1/selenider/man/open_url.Rd | 7 selenider-0.4.1/selenider/man/reload.Rd | 9 selenider-0.4.1/selenider/man/s.Rd | 7 selenider-0.4.1/selenider/man/scroll_to.Rd |only selenider-0.4.1/selenider/man/selenider_available.Rd | 9 selenider-0.4.1/selenider/man/selenider_session.Rd | 28 +- selenider-0.4.1/selenider/man/take_screenshot.Rd | 3 selenider-0.4.1/selenider/man/wdman_server_options.Rd |only selenider-0.4.1/selenider/tests/testthat/test-find_browser.R |only selenider-0.4.1/selenider/tests/testthat/test-global_actions.R | 49 ++++ selenider-0.4.1/selenider/vignettes/advanced-usage.Rmd |only selenider-0.4.1/selenider/vignettes/selenider.Rmd | 14 - 49 files changed, 481 insertions(+), 292 deletions(-)
Title: Produce Forest Plots to Visualize Covariate Effects
Description: Produce forest plots to visualize covariate effects using either
the command line or an interactive 'Shiny' application.
Author: Samer Mouksassi [aut, cre] ,
Benjamin Rich [aut],
Dean Attali [ctb]
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Diff between coveffectsplot versions 1.0.5 dated 2024-01-18 and 1.0.6 dated 2025-01-12
DESCRIPTION | 8 MD5 | 45 - NAMESPACE | 2 NEWS.md | 4 R/deltamethod.R |only R/forest_plot.R | 10 build/vignette.rds |binary inst/doc/Exposure_Response_Example.R | 35 inst/doc/Exposure_Response_Example.Rmd | 36 inst/doc/Exposure_Response_Example.html | 1015 +++++++++++++-------------- inst/doc/PKPD_Example.html | 18 inst/doc/PK_Example.R | 11 inst/doc/PK_Example.Rmd | 11 inst/doc/PK_Example.html | 119 +-- inst/doc/PK_Example_full.html | 124 +-- inst/doc/Pediatric_Cov_Sim.html | 18 inst/doc/app.html | 2 inst/doc/introduction_to_coveffectsplot.R | 119 +-- inst/doc/introduction_to_coveffectsplot.Rmd | 1 inst/doc/introduction_to_coveffectsplot.html | 71 - man/deltamethod.Rd |only vignettes/Exposure_Response_Example.Rmd | 36 vignettes/Figure_8_4.png |only vignettes/PK_Example.Rmd | 11 vignettes/introduction_to_coveffectsplot.Rmd | 1 25 files changed, 858 insertions(+), 839 deletions(-)
More information about coveffectsplot at CRAN
Permanent link
Title: Utilities for Start-Up Messages
Description: Provides utilities to create or suppress start-up messages.
Author: Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between startupmsg versions 0.9.7 dated 2024-08-29 and 1.0.0 dated 2025-01-12
DESCRIPTION | 17 ++++---- MD5 | 16 ++++---- NAMESPACE | 1 R/00.r | 1 R/illustration.R | 57 +++++++++++++++++++++++----- R/startUpMessage.R | 14 +++---- inst/NEWS | 27 +++++++++++++ man/StartupUtilities.Rd | 9 +++- man/myStartupUtilities.Rd | 92 +++++++++++++++++++++++++++++++++------------- 9 files changed, 170 insertions(+), 64 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to 'FishBase', re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to 'SeaLifeBase' data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut] ,
Scott Chamberlain [aut] ,
Duncan Temple Lang [aut],
Peter Wainwright [aut],
Kevin Cazelles [ctb] ,
Guohuan Su [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfishbase versions 5.0.0 dated 2024-09-02 and 5.0.1 dated 2025-01-12
DESCRIPTION | 17 ++++++++++------- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/fb_tbl.R | 26 ++++++++++++++++++++++++++ README.md | 2 +- inst/WORDLIST | 8 ++++++-- 6 files changed, 53 insertions(+), 15 deletions(-)
Title: Nonparametric Preprocessing for Parametric Causal Inference
Description: Selects matched samples of the original treated and
control groups with similar covariate distributions -- can be
used to match exactly on covariates, to match on propensity
scores, or perform a variety of other matching procedures. The
package also implements a series of recommendations offered in
Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>. (The
'gurobi' package, which is not on CRAN, is optional and comes with
an installation of the Gurobi Optimizer, available at
<https://www.gurobi.com>.)
Author: Daniel Ho [aut] ,
Kosuke Imai [aut] ,
Gary King [aut] ,
Elizabeth Stuart [aut] ,
Alex Whitworth [ctb],
Noah Greifer [cre, aut]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between MatchIt versions 4.6.0 dated 2024-11-13 and 4.7.0 dated 2025-01-12
MatchIt-4.6.0/MatchIt/R/match.data.R |only MatchIt-4.6.0/MatchIt/man/match.data.Rd |only MatchIt-4.7.0/MatchIt/DESCRIPTION | 12 MatchIt-4.7.0/MatchIt/MD5 | 143 +-- MatchIt-4.7.0/MatchIt/NAMESPACE | 1 MatchIt-4.7.0/MatchIt/NEWS.md | 14 MatchIt-4.7.0/MatchIt/R/RcppExports.R | 4 MatchIt-4.7.0/MatchIt/R/add_s.weights.R | 7 MatchIt-4.7.0/MatchIt/R/aux_functions.R | 47 - MatchIt-4.7.0/MatchIt/R/dist_functions.R | 35 MatchIt-4.7.0/MatchIt/R/distance2_methods.R | 101 +- MatchIt-4.7.0/MatchIt/R/get_weights_from_mm.R | 6 MatchIt-4.7.0/MatchIt/R/get_weights_from_subclass.R | 32 MatchIt-4.7.0/MatchIt/R/input_processing.R | 61 + MatchIt-4.7.0/MatchIt/R/match.qoi.R | 28 MatchIt-4.7.0/MatchIt/R/match_data.R |only MatchIt-4.7.0/MatchIt/R/matchit.R | 65 - MatchIt-4.7.0/MatchIt/R/matchit2cardinality.R | 138 +-- MatchIt-4.7.0/MatchIt/R/matchit2cem.R | 31 MatchIt-4.7.0/MatchIt/R/matchit2exact.R | 4 MatchIt-4.7.0/MatchIt/R/matchit2full.R | 34 MatchIt-4.7.0/MatchIt/R/matchit2genetic.R | 180 ++-- MatchIt-4.7.0/MatchIt/R/matchit2nearest.R | 70 + MatchIt-4.7.0/MatchIt/R/matchit2optimal.R | 78 +- MatchIt-4.7.0/MatchIt/R/matchit2quick.R | 16 MatchIt-4.7.0/MatchIt/R/matchit2subclass.R | 17 MatchIt-4.7.0/MatchIt/R/plot.matchit.R | 56 - MatchIt-4.7.0/MatchIt/R/plot.summary.matchit.R | 27 MatchIt-4.7.0/MatchIt/R/rbind.matchdata.R | 27 MatchIt-4.7.0/MatchIt/R/summary.matchit.R | 139 ++- MatchIt-4.7.0/MatchIt/R/utils.R | 78 +- MatchIt-4.7.0/MatchIt/build/stage23.rdb |binary MatchIt-4.7.0/MatchIt/build/vignette.rds |binary MatchIt-4.7.0/MatchIt/inst/doc/MatchIt.Rmd | 53 - MatchIt-4.7.0/MatchIt/inst/doc/MatchIt.html | 75 +- MatchIt-4.7.0/MatchIt/inst/doc/assessing-balance.Rmd | 3 MatchIt-4.7.0/MatchIt/inst/doc/assessing-balance.html | 32 MatchIt-4.7.0/MatchIt/inst/doc/estimating-effects.Rmd | 105 +- MatchIt-4.7.0/MatchIt/inst/doc/estimating-effects.html | 631 ++++++++--------- MatchIt-4.7.0/MatchIt/inst/doc/matching-methods.Rmd | 6 MatchIt-4.7.0/MatchIt/inst/doc/matching-methods.html | 29 MatchIt-4.7.0/MatchIt/inst/doc/sampling-weights.Rmd | 9 MatchIt-4.7.0/MatchIt/inst/doc/sampling-weights.html | 21 MatchIt-4.7.0/MatchIt/man/add_s.weights.Rd | 7 MatchIt-4.7.0/MatchIt/man/distance.Rd | 46 - MatchIt-4.7.0/MatchIt/man/match_data.Rd |only MatchIt-4.7.0/MatchIt/man/matchit.Rd | 51 - MatchIt-4.7.0/MatchIt/man/method_cardinality.Rd | 61 - MatchIt-4.7.0/MatchIt/man/method_cem.Rd | 26 MatchIt-4.7.0/MatchIt/man/method_exact.Rd | 4 MatchIt-4.7.0/MatchIt/man/method_full.Rd | 23 MatchIt-4.7.0/MatchIt/man/method_genetic.Rd | 17 MatchIt-4.7.0/MatchIt/man/method_nearest.Rd | 39 - MatchIt-4.7.0/MatchIt/man/method_optimal.Rd | 26 MatchIt-4.7.0/MatchIt/man/method_quick.Rd | 11 MatchIt-4.7.0/MatchIt/man/method_subclass.Rd | 15 MatchIt-4.7.0/MatchIt/man/plot.matchit.Rd | 15 MatchIt-4.7.0/MatchIt/man/plot.summary.matchit.Rd | 9 MatchIt-4.7.0/MatchIt/man/rbind.matchdata.Rd | 12 MatchIt-4.7.0/MatchIt/man/summary.matchit.Rd | 12 MatchIt-4.7.0/MatchIt/src/RcppExports.cpp | 13 MatchIt-4.7.0/MatchIt/src/all_equal_to.cpp | 2 MatchIt-4.7.0/MatchIt/src/internal.cpp | 94 +- MatchIt-4.7.0/MatchIt/src/nn_matchC_distmat.cpp | 22 MatchIt-4.7.0/MatchIt/src/nn_matchC_mahcovs.cpp | 22 MatchIt-4.7.0/MatchIt/src/nn_matchC_vec.cpp | 22 MatchIt-4.7.0/MatchIt/src/pairdistC.cpp | 21 MatchIt-4.7.0/MatchIt/src/preprocess_matchC.cpp |only MatchIt-4.7.0/MatchIt/src/subclass2mm.cpp | 22 MatchIt-4.7.0/MatchIt/vignettes/MatchIt.Rmd | 53 - MatchIt-4.7.0/MatchIt/vignettes/assessing-balance.Rmd | 3 MatchIt-4.7.0/MatchIt/vignettes/estimating-effects.Rmd | 105 +- MatchIt-4.7.0/MatchIt/vignettes/matching-methods.Rmd | 6 MatchIt-4.7.0/MatchIt/vignettes/references.bib | 2 MatchIt-4.7.0/MatchIt/vignettes/sampling-weights.Rmd | 9 75 files changed, 1841 insertions(+), 1344 deletions(-)
Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata',
'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of
'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka',
and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre] ,
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Swetlana Herbrandt [ctb],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Michael [...truncated...]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-87 dated 2024-06-26 and 0.8-88 dated 2025-01-12
ChangeLog | 3 +++ DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- R/octave.R | 4 ++-- R/writeForeignCode.R | 3 ++- tests/keep/codefile.sps | 2 +- 6 files changed, 21 insertions(+), 16 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, principal component analysis, correspondence analysis, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov, Kuiper, Wasserstein-2 or Sircombe-Hazelton L2 distances. Categorical provenance proxies such as chemical compositions are compared with the Aitchison and Bray-Curtis distances,and count data with the chi-square distance. Varietal data can either be converted to one or more distributional datasets, or directly compared using the multivariate Wasserstein distance. Also included are tools to plot compositional and count data on ternary diagrams and point-counting data on radial plots, [...truncated...]
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 4.3 dated 2024-05-04 and 4.4 dated 2025-01-12
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/gui.R | 9 ++++++--- R/io.R | 12 ++++++------ README.md | 2 +- man/read.distributional.Rd | 12 ++++++------ 6 files changed, 29 insertions(+), 26 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.8.0 dated 2024-03-05 and 1.8.1 dated 2025-01-12
DESCRIPTION | 10 - MD5 | 58 +++++----- NAMESPACE | 9 + NEWS.md | 8 + R/IC.R | 85 +++++++++------ R/diagtest.R | 20 ++- R/estimate.default.R | 223 +++++++++++++++++++++++----------------- R/ksmooth.R | 5 R/lava-package.R | 5 R/matrices.R | 19 ++- R/parsedesign.R | 35 +++--- R/sim.default.R | 207 +++++++++++++++++++++---------------- R/utils.R | 10 + build/partial.rdb |only build/vignette.rds |binary inst/doc/correlation.html | 95 ++++++++--------- inst/doc/influencefunction.R | 44 +++---- inst/doc/influencefunction.Rmd | 51 +++++---- inst/doc/influencefunction.html | 209 +++++++++++++++++-------------------- inst/doc/nonlinear.R | 42 +++---- inst/doc/nonlinear.html | 65 +++++------ man/IC.Rd | 3 man/estimate.array.Rd | 3 man/estimate.default.Rd | 49 +++++--- man/internal.Rd | 1 man/ksmooth2.Rd | 5 man/lava-package.Rd | 22 +++ man/sim.default.Rd | 12 +- tests/testthat/test-influence.R | 31 +++-- tests/testthat/test-simdef.R |only vignettes/influencefunction.Rmd | 51 +++++---- 31 files changed, 780 insertions(+), 597 deletions(-)
Title: Implementation of the Bayesian Discount Prior Approach for
Clinical Trials
Description: Functions for data augmentation using the Bayesian discount prior
method for single arm and two-arm clinical trials, as described in Haddad
et al. (2017) <doi:10.1080/10543406.2017.1300907>. The discount power prior
methodology was developed in collaboration with the The Medical Device
Innovation Consortium (MDIC) Computer Modeling & Simulation Working Group.
Author: Shawn Balcome [aut],
Donnie Musgrove [aut],
Tarek Haddad [aut],
Graeme L. Hickey [cre, aut] ,
Christopher Jackson [ctb]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>
Diff between bayesDP versions 1.3.6 dated 2022-01-30 and 1.3.7 dated 2025-01-12
DESCRIPTION | 8 MD5 | 38 - NAMESPACE | 1 NEWS.md | 12 R/bdpbinomial.R | 143 +++--- R/bdpnormal.R | 191 ++++----- R/bdpsurvival.R | 185 ++++----- README.md | 7 build/vignette.rds |binary inst/doc/bdpbinomial-vignette.R | 6 inst/doc/bdpbinomial-vignette.html | 592 +++++++++++++++++++--------- inst/doc/bdplm-vignette.R | 6 inst/doc/bdplm-vignette.html | 511 ++++++++++++++++-------- inst/doc/bdpnormal-vignette.R | 6 inst/doc/bdpnormal-vignette.html | 595 +++++++++++++++++++---------- inst/doc/bdpsurvival-vignette.R | 8 inst/doc/bdpsurvival-vignette.html | 757 +++++++++++++++++++++++++------------ man/bdpbinomial.Rd | 140 +++--- man/bdpnormal.Rd | 176 ++++---- man/bdpsurvival.Rd | 178 ++++---- 20 files changed, 2247 insertions(+), 1313 deletions(-)
Title: Analysis of Archaeological Mortality Data
Description: A collection of functions for the analysis of archaeological mortality
data (on the topic see e.g. Chamberlain 2006
<https://books.google.de/books?id=nG5FoO_becAC&lpg=PA27&ots=LG0b_xrx6O&dq=life%20table%20archaeology&pg=PA27#v=onepage&q&f=false>).
It takes demographic data in different formats and displays the result in a standard life table
as well as plots the relevant indices (percentage of deaths, survivorship, probability of death,
life expectancy, percentage of population). It also checks for possible biases in the age
structure and applies corrections to life tables.
Author: Nils Mueller-Scheessel [aut, cre, cph],
Martin Hinz [aut],
Clemens Schmid [aut],
Christoph Rinne [aut],
Daniel Knitter [aut],
Wolfgang Hamer [aut],
Dirk Seidensticker [aut],
Franziska Faupel [aut],
Carolin Tietze [aut],
Nicole Grunert [aut]
Maintainer: Nils Mueller-Scheessel <nils.mueller-scheessel@ufg.uni-kiel.de>
Diff between mortAAR versions 1.1.6 dated 2024-03-05 and 1.1.7 dated 2025-01-12
DESCRIPTION | 15 +-- MD5 | 64 +++++++----- NAMESPACE | 4 NEWS.md | 6 + R/halley_band.R |only R/input_functions.R | 2 R/lifetable_indices.R | 29 +++++ R/plot_functions.R | 3 R/population_simulation.R |only R/random_categories.R |only R/representativity.R | 34 +++++- R/reproduction_indices.R | 26 +++-- README.md | 6 - build/partial.rdb |binary inst/REFERENCES.bib | 64 ++++++++++++ inst/doc/mortAAR_vignette-1.html | 10 +- inst/doc/mortAAR_vignette_extended.Rmd | 2 inst/doc/mortAAR_vignette_extended.html | 8 - inst/doc/mortAAR_vignette_lt_correction.R | 3 inst/doc/mortAAR_vignette_lt_correction.Rmd | 14 ++ inst/doc/mortAAR_vignette_lt_correction.html | 63 ++++++++++-- inst/doc/mortAAR_vignette_reproduction.R | 3 inst/doc/mortAAR_vignette_reproduction.Rmd | 12 ++ inst/doc/mortAAR_vignette_reproduction.html | 82 ++++++++++------ man/halley.band.Rd |only man/lt.indices.Rd | 4 man/lt.representativity.Rd | 19 +++ man/lt.reproduction.Rd | 19 ++- man/pop.sim.gomp.Rd |only man/random.cat.apply.Rd |only tests/testthat/_snaps/indices.md | 33 +++++- tests/testthat/_snaps/representativity.md | 133 +-------------------------- tests/testthat/test_representativity.R | 8 - vignettes/mortAAR_vignette_extended.Rmd | 2 vignettes/mortAAR_vignette_lt_correction.Rmd | 14 ++ vignettes/mortAAR_vignette_reproduction.Rmd | 12 ++ 36 files changed, 427 insertions(+), 267 deletions(-)
Title: Modified Poisson and Least-Squares Regressions for Binary
Outcome and Their Generalizations
Description: Modified Poisson and least-squares regression analyses for binary outcomes of Zou (2004) <doi:10.1093/aje/kwh090> and Cheung (2007) <doi:10.1093/aje/kwm223> have been standard multivariate analysis methods to estimate risk ratio and risk difference in clinical and epidemiological studies. This R package involves an easy-to-handle function to implement these analyses by simple commands. Missing data analysis tools (multiple imputation) are also involved. In addition, recent studies have shown the ordinary robust variance estimator possibly has serious bias under small or moderate sample size situations for these methods. This package also provides computational tools to calculate alternative accurate confidence intervals (Noma and Gosho (2024) <Forthcoming>).
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between rqlm versions 2.1-1 dated 2024-05-23 and 2.3-1 dated 2025-01-12
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++++---- NAMESPACE | 2 ++ NEWS.md | 8 ++++++++ R/mi_glm.r |only data/mch.RData |only man/mch.Rd |only man/mi_glm.Rd |only man/rqlm-package.Rd | 2 +- 9 files changed, 25 insertions(+), 11 deletions(-)
Title: OLS, Moderated, Logistic, and Count Regressions Made Simple
Description: Provides SPSS- and SAS-like output for least squares multiple regression,
logistic regression, and count variable regressions. Detailed output is also provided for
OLS moderated regression, interaction plots, and Johnson-Neyman
regions of significance. The output includes standardized
coefficients, partial and semi-partial correlations, collinearity diagnostics,
plots of residuals, and detailed information about simple slopes for interactions.
The output for some functions includes Bayes Factors and, if requested,
regression coefficients from Bayesian Markov Chain Monte Carlo analyses.
There are numerous options for model plots.
The REGIONS_OF_SIGNIFICANCE function also provides
Johnson-Neyman regions of significance and plots of interactions for both lm
and lme models.
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between SIMPLE.REGRESSION versions 0.1.9 dated 2024-07-14 and 0.2.1 dated 2025-01-11
DESCRIPTION | 35 ++- MD5 | 28 +-- NAMESPACE | 9 R/COUNT_REGRESSION.R | 359 +++++++++++++++++++++++++++++++-------- R/LOGISTIC_REGRESSION.R | 40 ++++ R/MODERATED_REGRESSION.R | 158 +++++++++++++++-- R/OLS_REGRESSION.R | 211 ++++++++++++++++++++-- R/PLOT_MODEL.R | 63 ++++-- R/utilities_boc.R | 144 ++++++++++++++- man/COUNT_REGRESSION.Rd | 63 ++++++ man/LOGISTIC_REGRESSION.Rd | 28 ++- man/MODERATED_REGRESSION.Rd | 33 +++ man/OLS_REGRESSION.Rd | 49 ++++- man/PLOT_MODEL.Rd | 11 - man/SIMPLE.REGRESSION-package.Rd | 6 15 files changed, 1043 insertions(+), 194 deletions(-)
More information about SIMPLE.REGRESSION at CRAN
Permanent link
Title: Estimate Orientation of an Inertial Measurement Unit
Description: Estimate the orientation of an inertial measurement unit
(IMU) with a 3-axis accelerometer and a 3-axis gyroscope using a
complementary filter. 'imuf' takes an IMU's accelerometer and gyroscope
readings, time duration, its initial orientation, and a gain factor as
inputs, and returns an estimate of the IMU's final orientation.
Author: Felix Chan [aut, cre, cph],
Ricardo Cabello [cph]
Maintainer: Felix Chan <chanfelix@gmail.com>
Diff between imuf versions 0.4.0 dated 2024-12-08 and 0.5.0 dated 2025-01-11
DESCRIPTION | 21 ++++++++++++--------- LICENSE |only LICENSE.note |only MD5 | 29 +++++++++++++++++++++-------- NAMESPACE | 4 ++++ NEWS.md | 2 ++ R/animate_imu.R |only build/vignette.rds |binary inst/doc/animate_imu.R |only inst/doc/animate_imu.Rmd |only inst/doc/animate_imu.html |only inst/doc/imuf.Rmd | 2 +- inst/doc/imuf.html | 4 ++-- inst/htmlwidgets |only man/animate_imu-shiny.Rd |only man/animate_imu.Rd |only man/imuf-package.Rd | 5 +++++ tests/testthat/test-animate_imu.R |only vignettes/animate_imu.Rmd |only vignettes/imuf.Rmd | 2 +- 20 files changed, 48 insertions(+), 21 deletions(-)
Title: Effect Plots
Description: High-performance implementation of various effect plots
useful for regression and probabilistic classification tasks. The
package includes partial dependence plots (Friedman, 2021,
<doi:10.1214/aos/1013203451>), accumulated local effect plots and
M-plots (both from Apley and Zhu, 2016, <doi:10.1111/rssb.12377>), as
well as plots that describe the statistical associations between model
response and features. It supports visualizations with either
'ggplot2' or 'plotly', and is compatible with most models, including
'Tidymodels', models wrapped in 'DALEX' explainers, or models with
case weights.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between effectplots versions 0.2.0 dated 2024-12-11 and 0.2.1 dated 2025-01-11
DESCRIPTION | 9 ++-- MD5 | 14 +++--- NEWS.md | 11 +++++ R/feature_effects.R | 4 + R/plot.R | 40 ++++++++++++++++-- R/utils.R | 61 ++++++++++++++++++++++++++++ README.md | 2 tests/testthat/test-feature_effects.R | 72 ++++++++++++++++++++++++++++++++++ 8 files changed, 194 insertions(+), 19 deletions(-)
Title: Chinese Numerals Processing
Description: Chinese numerals processing in R, such as conversion between
Chinese numerals and Arabic numerals as well as detection and extraction of
Chinese numerals in character objects and string. This package supports
the casual scale naming system and the respective SI prefix systems used
in mainland China and Taiwan:
"The State Council's Order on the Unified Implementation of Legal Measurement Units in Our Country"
The State Council of the People's Republic of China (1984)
"Names, Definitions and Symbols of the Legal Units of Measurement and the Decimal Multiples and Submultiples"
Ministry of Economic Affairs (2019) <https://gazette.nat.gov.tw/egFront/detail.do?metaid=108965>.
Author: Elgar Teo [aut, cre]
Maintainer: Elgar Teo <elgarteo@connect.hku.hk>
Diff between cnum versions 0.1.4 dated 2025-01-11 and 0.1.5 dated 2025-01-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/num2c-utils.R | 2 +- R/num2c.R | 6 +++--- man/conversion.Rd | 6 +++--- 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Distance and Travel Time Between Two Points from Google Maps
Description: Get distance and travel time between two points from Google Maps.
Four possible modes of transportation (bicycling, walking, driving and
public transportation).
Author: Rodrigo Azuero Melo [aut],
David Zarruk [aut],
Jindra Lacko [cre]
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between gmapsdistance versions 4.0.4 dated 2023-08-10 and 4.0.5 dated 2025-01-11
DESCRIPTION | 29 +- MD5 | 24 +- NEWS.md | 4 README.md | 16 + build/vignette.rds |binary inst/doc/vignette.Rmd | 312 ++++++++++++++++------------- inst/doc/vignette.html | 364 ++++++++++++++++++---------------- tests/testthat/test-1-sanity.R | 18 - tests/testthat/test-3-matrix.R | 4 tests/testthat/test-5-vignette.R | 8 tests/testthat/test-6-graceful-fail.R | 2 tests/testthat/test-7-arrival-time.R | 9 vignettes/vignette.Rmd | 312 ++++++++++++++++------------- 13 files changed, 618 insertions(+), 484 deletions(-)
Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with
parametric or nonparametric pair-copulas. See
Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
Schallhorn et al. (2017) <doi:10.48550/arXiv.1705.08310>.
Author: Thomas Nagler [aut, cre],
Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between vinereg versions 0.10.0 dated 2024-02-09 and 0.11.0 dated 2025-01-11
DESCRIPTION | 12 +++---- MD5 | 42 +++++++++++++-------------- NEWS.md | 13 +++++++- R/RcppExports.R | 4 +- R/cpit.R | 12 +++---- R/generics.R | 4 +- R/predict.vinereg.R | 14 ++------- R/tools.R | 25 +++++++++++----- R/vinereg.R | 16 +++++----- README.md | 26 ++++++++-------- build/vignette.rds |binary inst/doc/abalone-example.html | 45 +++++++++++++++-------------- inst/doc/bike-rental.html | 48 +++++++++++++++---------------- man/cll.Rd | 4 +- man/cpdf.Rd | 4 +- man/cpit.Rd | 4 +- man/figures/README-unnamed-chunk-1-1.png |binary man/plot_effects.Rd | 4 +- man/predict.vinereg.Rd | 14 ++------- man/vinereg.Rd | 4 +- src/RcppExports.cpp | 10 +++--- src/vinereg.cpp | 26 +++++++--------- 22 files changed, 171 insertions(+), 160 deletions(-)
Title: Replacements for Base String Functions Powered by 'stringi'
Description: English is the native language for only 5% of the World population.
Also, only 17% of us can understand this text. Moreover, the Latin alphabet
is the main one for merely 36% of the total.
The early computer era, now a very long time ago, was dominated by the US.
Due to the proliferation of the internet, smartphones, social media, and
other technologies and communication platforms, this is no longer the case.
This package replaces base R string functions (such as grep(),
tolower(), sprintf(), and strptime()) with ones that fully
support the Unicode standards related to natural language and
date-time processing. It also fixes some long-standing inconsistencies,
and introduces some new, useful features.
Thanks to 'ICU' (International Components for Unicode) and 'stringi',
they are fast, reliable, and portable across different platforms.
Author: Marek Gagolewski [aut, cre, cph]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringx versions 0.2.8 dated 2024-04-09 and 0.2.9 dated 2025-01-11
DESCRIPTION | 10 +++--- MD5 | 60 ++++++++++++++++++++-------------------- NEWS | 9 ++++++ R/ISOdatetime.R | 2 - R/about_stringx.R | 4 +- R/chartr.R | 2 - R/common.R | 2 - R/constants.R | 2 - R/gregexpr.R | 2 - R/gregextr.R | 2 - R/grepl.R | 2 - R/gsub.R | 2 - R/nchar.R | 2 - R/paste.R | 2 - R/sort.R | 2 - R/sprintf.R | 2 - R/startswith.R | 2 - R/strcoll.R | 2 - R/strptime.R | 14 ++++++--- R/strrep.R | 2 - R/strsplit.R | 2 - R/strtrim.R | 2 - R/strwrap.R | 2 - R/substr.R | 2 - R/trimws.R | 2 - inst/realtest/ISOdatetime-all.R | 3 +- inst/realtest/strptime-all.R | 12 ++++++-- man/about_stringx.Rd | 3 +- man/chartr.Rd | 1 man/constants.Rd | 1 tests/realtest.R | 2 - 31 files changed, 92 insertions(+), 67 deletions(-)
Title: Genome Interval Arithmetic
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R, enabling
interactive analysis and visualization of genome-scale data. Riemondy
et al. (2017) <doi:10.12688/f1000research.11997.1>.
Author: Jay Hesselberth [aut] ,
Kent Riemondy [aut, cre] ,
RNA Bioscience Initiative [fnd, cph]
Maintainer: Kent Riemondy <kent.riemondy@gmail.com>
Diff between valr versions 0.8.2 dated 2024-08-30 and 0.8.3 dated 2025-01-11
DESCRIPTION | 12 ++--- MD5 | 24 ++++++----- NAMESPACE | 2 NEWS.md | 47 +++++++++++++--------- R/read_bed.r | 69 ++++++++++++++------------------- R/valr-package.r | 1 README.md | 2 inst/doc/valr.html | 4 - man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/read_bigwig.Rd | 25 ++++------- man/read_gtf.Rd | 4 + tests/testthat/test_read_bed.r | 7 +-- 15 files changed, 101 insertions(+), 96 deletions(-)
Title: Read/Write, Analyze, and Visualize 'BIOM' Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files.
Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and
beta diversity (including 'UniFrac'). Summarize counts by taxonomic level.
Subset based on metadata. Generate visualizations and statistical analyses.
CPU intensive operations are coded in C++ for speed.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between rbiom versions 1.0.3 dated 2021-11-05 and 2.0.7 dated 2025-01-11
rbiom-1.0.3/rbiom/NEWS.md |only rbiom-1.0.3/rbiom/R/accessors.r |only rbiom-1.0.3/rbiom/R/alpha.div.r |only rbiom-1.0.3/rbiom/R/beta.div.r |only rbiom-1.0.3/rbiom/R/imports.r |only rbiom-1.0.3/rbiom/R/print.r |only rbiom-1.0.3/rbiom/R/rbiom.r |only rbiom-1.0.3/rbiom/R/read.biom.r |only rbiom-1.0.3/rbiom/R/read.fasta.r |only rbiom-1.0.3/rbiom/R/read.tree.r |only rbiom-1.0.3/rbiom/R/select.r |only rbiom-1.0.3/rbiom/R/subset.r |only rbiom-1.0.3/rbiom/R/subtree.r |only rbiom-1.0.3/rbiom/R/taxa.rollup.r |only rbiom-1.0.3/rbiom/R/tips.r |only rbiom-1.0.3/rbiom/R/unifrac.r |only rbiom-1.0.3/rbiom/R/write.biom.r |only rbiom-1.0.3/rbiom/R/write.fasta.r |only rbiom-1.0.3/rbiom/R/write.tree.r |only rbiom-1.0.3/rbiom/R/write.xlsx.r |only rbiom-1.0.3/rbiom/man/alpha.div.Rd |only rbiom-1.0.3/rbiom/man/beta.div.Rd |only rbiom-1.0.3/rbiom/man/counts.Rd |only rbiom-1.0.3/rbiom/man/info.Rd |only rbiom-1.0.3/rbiom/man/metadata.Rd |only rbiom-1.0.3/rbiom/man/nsamples.Rd |only 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rbiom-1.0.3/rbiom/src/par_unifrac.cpp |only rbiom-1.0.3/rbiom/tests/testthat.R |only rbiom-1.0.3/rbiom/tests/testthat/outputs/alpha.div.rds |only rbiom-1.0.3/rbiom/tests/testthat/outputs/beta.div.rds |only rbiom-1.0.3/rbiom/tests/testthat/outputs/taxa.rollup.rds |only rbiom-1.0.3/rbiom/tests/testthat/test_accessors.r |only rbiom-1.0.3/rbiom/tests/testthat/test_calculations.r |only rbiom-1.0.3/rbiom/tests/testthat/test_distance.r |only rbiom-1.0.3/rbiom/tests/testthat/test_file_io.r |only rbiom-1.0.3/rbiom/tests/testthat/test_subsetting.r |only rbiom-1.0.3/rbiom/tests/testthat/test_tree.r |only rbiom-2.0.7/rbiom/DESCRIPTION | 63 +- rbiom-2.0.7/rbiom/LICENSE |only rbiom-2.0.7/rbiom/MD5 | 279 +++++++++---- rbiom-2.0.7/rbiom/NAMESPACE | 245 +++++++++-- rbiom-2.0.7/rbiom/R/RcppExports.R | 38 + rbiom-2.0.7/rbiom/R/adiv_table.r |only rbiom-2.0.7/rbiom/R/apcoa.r |only rbiom-2.0.7/rbiom/R/as_rbiom.r |only rbiom-2.0.7/rbiom/R/bdiv_heatmap.r |only rbiom-2.0.7/rbiom/R/bdiv_ord_plot.r |only rbiom-2.0.7/rbiom/R/bdiv_ord_table.r |only rbiom-2.0.7/rbiom/R/bdiv_table.r |only rbiom-2.0.7/rbiom/R/biom_merge.r |only rbiom-2.0.7/rbiom/R/biom_ply.r |only rbiom-2.0.7/rbiom/R/boxplot.r |only rbiom-2.0.7/rbiom/R/boxplot_build.r |only rbiom-2.0.7/rbiom/R/boxplot_stats.r |only rbiom-2.0.7/rbiom/R/cache.r |only rbiom-2.0.7/rbiom/R/clustering.r |only rbiom-2.0.7/rbiom/R/convert.r |only rbiom-2.0.7/rbiom/R/corrplot.r |only rbiom-2.0.7/rbiom/R/corrplot_build.r |only rbiom-2.0.7/rbiom/R/corrplot_stats.r |only rbiom-2.0.7/rbiom/R/data.r |only rbiom-2.0.7/rbiom/R/distmat_ord_table.r |only rbiom-2.0.7/rbiom/R/distmat_stats.r |only rbiom-2.0.7/rbiom/R/documentation.r |only rbiom-2.0.7/rbiom/R/embed.r |only rbiom-2.0.7/rbiom/R/geom_dendro.r |only rbiom-2.0.7/rbiom/R/import_table.r |only rbiom-2.0.7/rbiom/R/plot_build.r |only rbiom-2.0.7/rbiom/R/plot_facets.r |only rbiom-2.0.7/rbiom/R/plot_heatmap.r |only rbiom-2.0.7/rbiom/R/plot_layers.r |only rbiom-2.0.7/rbiom/R/plot_palettes.r |only rbiom-2.0.7/rbiom/R/provenance.r |only rbiom-2.0.7/rbiom/R/rare_multiplot.r |only rbiom-2.0.7/rbiom/R/rare_stacked.r |only rbiom-2.0.7/rbiom/R/rarefy.r | 299 +++++++++----- rbiom-2.0.7/rbiom/R/rbiom-deprecated.r |only rbiom-2.0.7/rbiom/R/rbiom-package.R |only rbiom-2.0.7/rbiom/R/rbiom_objects.r |only rbiom-2.0.7/rbiom/R/read_biom.r |only rbiom-2.0.7/rbiom/R/read_fasta.r |only rbiom-2.0.7/rbiom/R/read_tree.r |only rbiom-2.0.7/rbiom/R/reexport.r |only rbiom-2.0.7/rbiom/R/s3_methods.r |only rbiom-2.0.7/rbiom/R/speed_ups.r |only rbiom-2.0.7/rbiom/R/stats_common.r |only rbiom-2.0.7/rbiom/R/stats_emmeans.r |only rbiom-2.0.7/rbiom/R/stats_table.r |only rbiom-2.0.7/rbiom/R/stats_wilcox.r |only rbiom-2.0.7/rbiom/R/taxa_heatmap.r |only rbiom-2.0.7/rbiom/R/taxa_map.r |only rbiom-2.0.7/rbiom/R/taxa_stacked.r |only rbiom-2.0.7/rbiom/R/taxa_table.r |only rbiom-2.0.7/rbiom/R/tree_plot.r |only rbiom-2.0.7/rbiom/R/utils.r |only rbiom-2.0.7/rbiom/R/validate.r |only rbiom-2.0.7/rbiom/R/write_biom.r |only rbiom-2.0.7/rbiom/R/write_xlsx.r |only rbiom-2.0.7/rbiom/R/zzz.r |only rbiom-2.0.7/rbiom/README.md | 105 +++- rbiom-2.0.7/rbiom/build |only rbiom-2.0.7/rbiom/data |only rbiom-2.0.7/rbiom/exec |only rbiom-2.0.7/rbiom/inst/extdata/babies.bz2 |only rbiom-2.0.7/rbiom/inst/extdata/gems.bz2 |only rbiom-2.0.7/rbiom/inst/extdata/hmp50.bz2 |binary rbiom-2.0.7/rbiom/man/adiv_boxplot.Rd |only rbiom-2.0.7/rbiom/man/adiv_corrplot.Rd |only rbiom-2.0.7/rbiom/man/adiv_matrix.Rd |only rbiom-2.0.7/rbiom/man/adiv_stats.Rd |only rbiom-2.0.7/rbiom/man/adiv_table.Rd |only rbiom-2.0.7/rbiom/man/as.list.rbiom.Rd |only rbiom-2.0.7/rbiom/man/as.matrix.rbiom.Rd |only rbiom-2.0.7/rbiom/man/as_rbiom.Rd |only rbiom-2.0.7/rbiom/man/babies.Rd |only rbiom-2.0.7/rbiom/man/bdiv_boxplot.Rd |only rbiom-2.0.7/rbiom/man/bdiv_clusters.Rd |only rbiom-2.0.7/rbiom/man/bdiv_corrplot.Rd |only rbiom-2.0.7/rbiom/man/bdiv_heatmap.Rd |only rbiom-2.0.7/rbiom/man/bdiv_ord_plot.Rd |only rbiom-2.0.7/rbiom/man/bdiv_ord_table.Rd |only 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rbiom-2.0.7/rbiom/man/taxa_boxplot.Rd |only rbiom-2.0.7/rbiom/man/taxa_clusters.Rd |only rbiom-2.0.7/rbiom/man/taxa_corrplot.Rd |only rbiom-2.0.7/rbiom/man/taxa_heatmap.Rd |only rbiom-2.0.7/rbiom/man/taxa_map.Rd |only rbiom-2.0.7/rbiom/man/taxa_matrix.Rd |only rbiom-2.0.7/rbiom/man/taxa_stacked.Rd |only rbiom-2.0.7/rbiom/man/taxa_stats.Rd |only rbiom-2.0.7/rbiom/man/taxa_sums.Rd |only rbiom-2.0.7/rbiom/man/tree_subset.Rd |only rbiom-2.0.7/rbiom/man/with.Rd |only rbiom-2.0.7/rbiom/man/write_biom.Rd |only rbiom-2.0.7/rbiom/src/Makevars |only rbiom-2.0.7/rbiom/src/RcppExports.cpp | 145 ++++++ rbiom-2.0.7/rbiom/src/parallel_beta_div.cpp |only rbiom-2.0.7/rbiom/src/parallel_unifrac.cpp |only rbiom-2.0.7/rbiom/src/rcpp_alpha_div.cpp | 7 rbiom-2.0.7/rbiom/src/rcpp_rarefy.cpp | 12 rbiom-2.0.7/rbiom/src/rcpp_treeIO.cpp | 5 rbiom-2.0.7/rbiom/tests/testthat.r |only rbiom-2.0.7/rbiom/tests/testthat/_test-accessors.r |only rbiom-2.0.7/rbiom/tests/testthat/_test-adiv_boxplot.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_calculations.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_distance.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_file_io.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_subsetting.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_tree.r |only rbiom-2.0.7/rbiom/tests/testthat/helper.r |only rbiom-2.0.7/rbiom/tests/testthat/outputs/adiv_table.rds |only rbiom-2.0.7/rbiom/tests/testthat/outputs/bdiv_dist.rds |only rbiom-2.0.7/rbiom/tests/testthat/outputs/subset_ex2.rds |binary rbiom-2.0.7/rbiom/tests/testthat/outputs/taxa_rollup.rds |only rbiom-2.0.7/rbiom/tests/testthat/test-adiv_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-as_rbiom.r |only rbiom-2.0.7/rbiom/tests/testthat/test-bdiv_heatmap.r |only rbiom-2.0.7/rbiom/tests/testthat/test-bdiv_ord_plot.r |only rbiom-2.0.7/rbiom/tests/testthat/test-bdiv_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-biom_merge.r |only rbiom-2.0.7/rbiom/tests/testthat/test-biom_ply.r |only rbiom-2.0.7/rbiom/tests/testthat/test-boxplot.r |only rbiom-2.0.7/rbiom/tests/testthat/test-boxplot_build.r |only rbiom-2.0.7/rbiom/tests/testthat/test-cache.r |only rbiom-2.0.7/rbiom/tests/testthat/test-clustering.r |only rbiom-2.0.7/rbiom/tests/testthat/test-convert.r |only rbiom-2.0.7/rbiom/tests/testthat/test-corrplot.r |only rbiom-2.0.7/rbiom/tests/testthat/test-distmat_ord_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-distmat_stats.r |only rbiom-2.0.7/rbiom/tests/testthat/test-embed.r |only rbiom-2.0.7/rbiom/tests/testthat/test-import_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-plot_heatmap.r |only rbiom-2.0.7/rbiom/tests/testthat/test-plot_palettes.r |only rbiom-2.0.7/rbiom/tests/testthat/test-provenance.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rare_multiplot.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rare_stacked.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rarefy.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rbiom-deprecated.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rbiom_objects.r |only rbiom-2.0.7/rbiom/tests/testthat/test-read_biom.r |only rbiom-2.0.7/rbiom/tests/testthat/test-read_fasta.r |only rbiom-2.0.7/rbiom/tests/testthat/test-read_tree.r |only rbiom-2.0.7/rbiom/tests/testthat/test-s3_methods.r |only rbiom-2.0.7/rbiom/tests/testthat/test-stats_emmeans.r |only rbiom-2.0.7/rbiom/tests/testthat/test-stats_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-stats_wilcox.r |only rbiom-2.0.7/rbiom/tests/testthat/test-taxa_heatmap.r |only rbiom-2.0.7/rbiom/tests/testthat/test-taxa_map.r |only rbiom-2.0.7/rbiom/tests/testthat/test-taxa_stacked.r |only rbiom-2.0.7/rbiom/tests/testthat/test-taxa_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-utils.r |only rbiom-2.0.7/rbiom/tests/testthat/test-validate.r |only rbiom-2.0.7/rbiom/tests/testthat/test-write_biom.r |only rbiom-2.0.7/rbiom/tests/testthat/test-write_xlsx.r |only 260 files changed, 1050 insertions(+), 382 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb]
,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-35.5 dated 2024-07-03 and 1.1-36 dated 2025-01-11
DESCRIPTION | 9 MD5 | 47 ++--- NAMESPACE | 17 + R/lmer.R | 40 ++++ R/predict.R | 36 +-- R/utilities.R | 263 ---------------------------- inst/NEWS.Rd | 29 ++- inst/doc/PLSvGLS.pdf |binary inst/doc/Theory.pdf |binary inst/doc/lmer.R | 124 ++++++------- inst/doc/lmer.pdf |binary inst/doc/lmerperf.R | 4 inst/doc/lmerperf.html | 4 man/lmer.Rd | 3 man/merMod-class.Rd | 36 --- man/vcov.merMod.Rd |only tests/simulate.R | 12 - tests/testthat/test-glmFamily.R | 17 + tests/testthat/test-glmer.R | 5 tests/testthat/test-glmernbref.R | 3 tests/testthat/test-glmmFail.R | 3 tests/testthat/test-lmer.R | 16 + tests/testthat/test-methods.R | 25 +- tests/testthat/test-resids.R | 8 tests/testthat/test-summary_testlevel_1.rda |binary 25 files changed, 251 insertions(+), 450 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg]
,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.9.1 dated 2024-09-07 and 2.9.2 dated 2025-01-11
DESCRIPTION | 8 MD5 | 46 NEWS.md | 505 ++--- R/cluster_stats.R | 548 +++--- R/tree_distance_utilities.R | 2 build/partial.rdb |binary inst/apa-old-doi-prefix.csl | 2306 +++++++++++++++++--------- inst/doc/Generalized-RF.html | 34 inst/doc/Robinson-Foulds.html | 32 inst/doc/Using-TreeDist.html | 12 inst/doc/compare-treesets.html | 14 inst/doc/different-leaves.html | 8 inst/doc/information.html | 8 inst/doc/landscapes.html | 1955 +++++++++++++++++++++- inst/doc/treespace.html | 20 inst/doc/using-distances.html | 22 src/ints.h | 2 src/nni_distance.cpp | 151 - src/spr.cpp | 33 src/tree_distances.cpp | 48 tests/testthat/test-tree_distance.R | 1 tests/testthat/test-tree_distance_nni.R | 366 ++-- tests/testthat/test-tree_distance_spr.R | 331 +-- tests/testthat/test-tree_distance_utilities.R | 26 24 files changed, 4682 insertions(+), 1796 deletions(-)
Title: Classical Age-Depth Modelling of Cores from Deposits
Description: Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010) <doi:10.1016/j.quageo.2010.01.002>.
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [ctb] ,
Judith Esquivel Vazquez [ctb],
Simon Goring [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between clam versions 2.6.1 dated 2024-09-25 and 2.6.2 dated 2025-01-11
clam-2.6.1/clam/man/calib.t.Rd |only clam-2.6.1/clam/vignettes/clam_runs |only clam-2.6.2/clam/DESCRIPTION | 11 ++- clam-2.6.2/clam/MD5 | 55 ++++++------------ clam-2.6.2/clam/NAMESPACE | 3 - clam-2.6.2/clam/NEWS.md | 5 + clam-2.6.2/clam/R/calibrate.R | 104 ----------------------------------- clam-2.6.2/clam/R/clam-package.R | 2 clam-2.6.2/clam/R/clam.R | 15 +++-- clam-2.6.2/clam/R/plots.R | 5 + clam-2.6.2/clam/R/postanalysis.R | 21 +++++-- clam-2.6.2/clam/R/readwrite.R | 68 +++++++++++++--------- clam-2.6.2/clam/build/partial.rdb |binary clam-2.6.2/clam/build/vignette.rds |binary clam-2.6.2/clam/inst/doc/clam.R | 14 +++- clam-2.6.2/clam/inst/doc/clam.Rmd | 10 ++- clam-2.6.2/clam/inst/doc/clam.html | 29 +++++---- clam-2.6.2/clam/man/add.dates.Rd | 5 + clam-2.6.2/clam/man/clam.Rd | 7 +- clam-2.6.2/clam/man/deptime.age.Rd | 5 + clam-2.6.2/clam/man/deptime.depth.Rd | 5 + clam-2.6.2/clam/man/plot_proxies.Rd | 9 ++- clam-2.6.2/clam/vignettes/clam.Rmd | 10 ++- 23 files changed, 164 insertions(+), 219 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray,
Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.3.4 dated 2024-02-16 and 1.3.5 dated 2025-01-11
mets-1.3.4/mets/inst/doc/binreg-TRS.rmd |only mets-1.3.4/mets/src/init.c |only mets-1.3.4/mets/vignettes/binreg-TRS.rmd |only mets-1.3.5/mets/DESCRIPTION | 14 mets-1.3.5/mets/MD5 | 232 + mets-1.3.5/mets/NAMESPACE | 36 mets-1.3.5/mets/NEWS.md | 11 mets-1.3.5/mets/R/Event.Split.R | 127 mets-1.3.5/mets/R/RcppExports.R | 16 mets-1.3.5/mets/R/WA-estimands.R |only mets-1.3.5/mets/R/binomial.regression.R | 1282 ++++++---- mets-1.3.5/mets/R/binregTSR.R | 91 mets-1.3.5/mets/R/casewise.R | 3 mets-1.3.5/mets/R/cifreg.R | 141 - mets-1.3.5/mets/R/claytonakes.R | 17 mets-1.3.5/mets/R/clusterindex-reshape.R | 6 mets-1.3.5/mets/R/daggregate.R | 2 mets-1.3.5/mets/R/event.r | 90 mets-1.3.5/mets/R/fastapprox.R | 13 mets-1.3.5/mets/R/gof-phreg.R | 40 mets-1.3.5/mets/R/ipw.R | 44 mets-1.3.5/mets/R/kmplot.R |only mets-1.3.5/mets/R/mets-package.R | 48 mets-1.3.5/mets/R/normal0.R | 42 mets-1.3.5/mets/R/phreg.R | 1133 ++------ mets-1.3.5/mets/R/phreg_rct.R |only mets-1.3.5/mets/R/pmvn.R | 42 mets-1.3.5/mets/R/recreg.R | 411 ++- mets-1.3.5/mets/R/recurrent.marginal.R | 473 +++ mets-1.3.5/mets/R/restricted.mean.R | 193 - mets-1.3.5/mets/R/riskRegression.R |only mets-1.3.5/mets/R/sim-pc-hazard.R | 659 +++-- mets-1.3.5/mets/R/wild-phreg.R | 10 mets-1.3.5/mets/build/partial.rdb |only mets-1.3.5/mets/build/vignette.rds |binary mets-1.3.5/mets/data/ACTG175.rda |only mets-1.3.5/mets/data/calgb8923.rda |only mets-1.3.5/mets/data/hfaction_cpx12.rda |only mets-1.3.5/mets/inst/doc/basic-dutils.html | 42 mets-1.3.5/mets/inst/doc/binomial-family.html | 42 mets-1.3.5/mets/inst/doc/binomial-twin.html | 118 mets-1.3.5/mets/inst/doc/binreg-TRS.R | 15 mets-1.3.5/mets/inst/doc/binreg-TRS.Rmd |only mets-1.3.5/mets/inst/doc/binreg-TRS.html | 592 ++-- mets-1.3.5/mets/inst/doc/binreg-ate.R | 4 mets-1.3.5/mets/inst/doc/binreg-ate.Rmd | 4 mets-1.3.5/mets/inst/doc/binreg-ate.html | 191 - mets-1.3.5/mets/inst/doc/binreg.Rmd | 7 mets-1.3.5/mets/inst/doc/binreg.html | 94 mets-1.3.5/mets/inst/doc/cifreg.R | 3 mets-1.3.5/mets/inst/doc/cifreg.Rmd | 8 mets-1.3.5/mets/inst/doc/cifreg.html | 472 +-- mets-1.3.5/mets/inst/doc/cooking-survival-data.R |only mets-1.3.5/mets/inst/doc/cooking-survival-data.Rmd |only mets-1.3.5/mets/inst/doc/cooking-survival-data.html |only mets-1.3.5/mets/inst/doc/glm-utility.html | 45 mets-1.3.5/mets/inst/doc/haplo-discrete-ttp.html | 43 mets-1.3.5/mets/inst/doc/interval-discrete-survival.R | 25 mets-1.3.5/mets/inst/doc/interval-discrete-survival.Rmd | 25 mets-1.3.5/mets/inst/doc/interval-discrete-survival.html | 152 - mets-1.3.5/mets/inst/doc/marginal-cox.html | 49 mets-1.3.5/mets/inst/doc/mediation-survival.R | 20 mets-1.3.5/mets/inst/doc/mediation-survival.html | 135 - mets-1.3.5/mets/inst/doc/phreg_rct.R |only mets-1.3.5/mets/inst/doc/phreg_rct.Rmd |only mets-1.3.5/mets/inst/doc/phreg_rct.html |only mets-1.3.5/mets/inst/doc/quantitative-twin.R | 8 mets-1.3.5/mets/inst/doc/quantitative-twin.html | 11 mets-1.3.5/mets/inst/doc/recurrent-events.R | 172 - mets-1.3.5/mets/inst/doc/recurrent-events.Rmd | 46 mets-1.3.5/mets/inst/doc/recurrent-events.html | 991 ++++--- mets-1.3.5/mets/inst/doc/rmst-ate.R | 12 mets-1.3.5/mets/inst/doc/rmst-ate.Rmd | 12 mets-1.3.5/mets/inst/doc/rmst-ate.html | 396 +-- mets-1.3.5/mets/inst/doc/survival-ate.R | 10 mets-1.3.5/mets/inst/doc/survival-ate.Rmd | 15 mets-1.3.5/mets/inst/doc/survival-ate.html | 400 +-- mets-1.3.5/mets/inst/doc/time-to-event-family-studies-arev.R | 277 +- mets-1.3.5/mets/inst/doc/time-to-event-family-studies-arev.Rmd | 13 mets-1.3.5/mets/inst/doc/time-to-event-family-studies-arev.html | 283 -- mets-1.3.5/mets/inst/doc/twostage-survival.html | 58 mets-1.3.5/mets/inst/doc/while-alive.R |only mets-1.3.5/mets/inst/doc/while-alive.Rmd |only mets-1.3.5/mets/inst/doc/while-alive.html |only mets-1.3.5/mets/inst/include/mets_RcppExports.h | 29 mets-1.3.5/mets/man/ACTG175.Rd |only mets-1.3.5/mets/man/ClaytonOakes.Rd | 16 mets-1.3.5/mets/man/Event.Rd |only mets-1.3.5/mets/man/WA_recurrent.Rd |only mets-1.3.5/mets/man/aalenMets.Rd | 4 mets-1.3.5/mets/man/basehazplot.phreg.Rd | 2 mets-1.3.5/mets/man/binreg.Rd | 29 mets-1.3.5/mets/man/binregATE.Rd | 19 mets-1.3.5/mets/man/binregTSR.Rd | 3 mets-1.3.5/mets/man/calgb8923.Rd |only mets-1.3.5/mets/man/cifreg.Rd | 4 mets-1.3.5/mets/man/daggregate.Rd | 2 mets-1.3.5/mets/man/evalTerminal.Rd |only mets-1.3.5/mets/man/event.split.Rd |only mets-1.3.5/mets/man/hfaction_cpx12.Rd |only mets-1.3.5/mets/man/ipw2.Rd | 44 mets-1.3.5/mets/man/mets-package.Rd | 23 mets-1.3.5/mets/man/phreg_IPTW.Rd | 9 mets-1.3.5/mets/man/phreg_rct.Rd | 18 mets-1.3.5/mets/man/predictRisk.phreg.Rd |only mets-1.3.5/mets/man/rchaz.Rd | 7 mets-1.3.5/mets/man/rcrisk.Rd | 18 mets-1.3.5/mets/man/recreg.Rd | 13 mets-1.3.5/mets/man/resmean.phreg.Rd | 1 mets-1.3.5/mets/man/resmeanATE.Rd | 18 mets-1.3.5/mets/man/resmeanIPCW.Rd | 80 mets-1.3.5/mets/man/sim.cause.cox.Rd | 30 mets-1.3.5/mets/man/sim.cox.Rd | 39 mets-1.3.5/mets/man/simRecurrentII.Rd | 14 mets-1.3.5/mets/man/survivalG.Rd | 4 mets-1.3.5/mets/src/RcppExports.cpp | 216 + mets-1.3.5/mets/src/fastcox.cpp | 15 mets-1.3.5/mets/src/mvn.cpp | 309 -- mets-1.3.5/mets/src/sim-tools.cpp | 13 mets-1.3.5/mets/tests/testthat/test_binreg.R |only mets-1.3.5/mets/tests/testthat/test_iid.R | 2 mets-1.3.5/mets/tests/testthat/test_mvn.R |only mets-1.3.5/mets/tests/testthat/test_rmst.R |only mets-1.3.5/mets/vignettes/binreg-TRS.Rmd |only mets-1.3.5/mets/vignettes/binreg-ate.Rmd | 4 mets-1.3.5/mets/vignettes/binreg.Rmd | 7 mets-1.3.5/mets/vignettes/cifreg.Rmd | 8 mets-1.3.5/mets/vignettes/cooking-survival-data.Rmd |only mets-1.3.5/mets/vignettes/interval-discrete-survival.Rmd | 25 mets-1.3.5/mets/vignettes/phreg_rct.Rmd |only mets-1.3.5/mets/vignettes/recurrent-events.Rmd | 46 mets-1.3.5/mets/vignettes/rmst-ate.Rmd | 12 mets-1.3.5/mets/vignettes/survival-ate.Rmd | 15 mets-1.3.5/mets/vignettes/time-to-event-family-studies-arev.Rmd | 13 mets-1.3.5/mets/vignettes/while-alive.Rmd |only 135 files changed, 6257 insertions(+), 4820 deletions(-)
Title: Fake Web Apps for HTTP Testing
Description: Create a web app that makes it easier to test web clients
without using the internet. It includes a web app framework with path
matching, parameters and templates. Can parse various 'HTTP' request
bodies. Can send 'JSON' data or files from the disk. Includes a web
app that implements the 'httpbin.org' web service.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd],
Civetweb contributors [ctb] ,
Redoc contributors [ctb] ,
L. Peter Deutsch [ctb] ,
Martin Purschke [ctb] ,
Aladdin Enterprises [cph] ,
Maelle Salmon [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between webfakes versions 1.3.1 dated 2024-04-25 and 1.3.2 dated 2025-01-11
DESCRIPTION | 8 MD5 | 41 NEWS.md | 5 R/app-process.R | 5 R/mw-cgi.R | 4 R/server.R | 10 README.md | 6 man/mw_cgi.Rd | 4 man/server_opts.Rd | 8 src/Makevars | 1 src/Makevars.win | 1 src/civetweb.c | 9092 ++++++++++++++++++++--------------- src/civetweb.h | 540 +- src/handle_form.h | 74 src/http2.h |only src/match.h |only src/md5.h | 19 src/mod_mbedtls.h |only src/response.h |only src/sha1.h |only src/sort.h |only src/timer.h |only tests/testthat.R | 2 tests/testthat/_snaps/app-process.md |only tests/testthat/test-app-process.R | 19 tests/testthat/test-decode-url.R |only 26 files changed, 5952 insertions(+), 3887 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] ,
David Bard [ctb] ,
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb] ,
Benjamin Nutter [ctb],
Andrew Peters [ctb] ,
Hao Zhu [ctb] ,
Janosch Linkersdoerfer [ctb] ,
Jonathan Mang [ctb] ,
Felix Torres [ctb],
Philip [...truncated...]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 1.3.0 dated 2024-10-23 and 1.4.0 dated 2025-01-11
REDCapR-1.3.0/REDCapR/inst/test-data/projects/super-wide-3/generate-dictionary.R |only REDCapR-1.4.0/REDCapR/DESCRIPTION | 11 REDCapR-1.4.0/REDCapR/MD5 | 121 REDCapR-1.4.0/REDCapR/NAMESPACE | 1 REDCapR-1.4.0/REDCapR/NEWS.md | 794 ++-- REDCapR-1.4.0/REDCapR/R/REDCapR-package.R | 4 REDCapR-1.4.0/REDCapR/R/helpers-testing.R | 32 REDCapR-1.4.0/REDCapR/R/redcap-file-repo-list.R |only REDCapR-1.4.0/REDCapR/R/sanitize-token.R | 3 REDCapR-1.4.0/REDCapR/R/skippers.R | 12 REDCapR-1.4.0/REDCapR/README.md | 6 REDCapR-1.4.0/REDCapR/build/vignette.rds |binary REDCapR-1.4.0/REDCapR/inst/doc/BasicREDCapROperations.R | 126 REDCapR-1.4.0/REDCapR/inst/doc/BasicREDCapROperations.Rmd | 10 REDCapR-1.4.0/REDCapR/inst/doc/BasicREDCapROperations.html | 257 - REDCapR-1.4.0/REDCapR/inst/doc/SecurityDatabase.Rmd | 1 REDCapR-1.4.0/REDCapR/inst/doc/SecurityDatabase.html | 2 REDCapR-1.4.0/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd | 8 REDCapR-1.4.0/REDCapR/inst/doc/TroubleshootingApiCalls.html | 10 REDCapR-1.4.0/REDCapR/inst/doc/advanced-redcapr-operations.R | 220 - REDCapR-1.4.0/REDCapR/inst/doc/advanced-redcapr-operations.Rmd | 7 REDCapR-1.4.0/REDCapR/inst/doc/advanced-redcapr-operations.html | 377 -- REDCapR-1.4.0/REDCapR/inst/doc/longitudinal-and-repeating.R | 169 - REDCapR-1.4.0/REDCapR/inst/doc/longitudinal-and-repeating.Rmd | 1 REDCapR-1.4.0/REDCapR/inst/doc/longitudinal-and-repeating.html | 1297 -------- REDCapR-1.4.0/REDCapR/inst/doc/workflow-read.R | 161 REDCapR-1.4.0/REDCapR/inst/doc/workflow-read.Rmd | 3 REDCapR-1.4.0/REDCapR/inst/doc/workflow-read.html | 1615 ---------- REDCapR-1.4.0/REDCapR/inst/doc/workflow-write.Rmd | 15 REDCapR-1.4.0/REDCapR/inst/doc/workflow-write.html | 53 REDCapR-1.4.0/REDCapR/inst/misc/coph.credentials |only REDCapR-1.4.0/REDCapR/inst/misc/dev-2.credentials | 1 REDCapR-1.4.0/REDCapR/inst/misc/example.credentials | 1 REDCapR-1.4.0/REDCapR/inst/misc/plugin-redirection.yml | 8 REDCapR-1.4.0/REDCapR/inst/misc/project-redirection.yml | 36 REDCapR-1.4.0/REDCapR/inst/test-data/projects/README.md | 11 REDCapR-1.4.0/REDCapR/inst/test-data/projects/arm-multiple-delete/README.md |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/arm-single-delete/README.md |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/blank-for-gray-status/README.md |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/dag-write/README.md | 7 REDCapR-1.4.0/REDCapR/inst/test-data/projects/dag/README.md | 7 REDCapR-1.4.0/REDCapR/inst/test-data/projects/file-repo |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/simple/README.md |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/simple/project-old.xml |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/super-wide-3/README.md | 15 REDCapR-1.4.0/REDCapR/inst/test-data/projects/super-wide-3/generate-project.R |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/survey/README.md | 2 REDCapR-1.4.0/REDCapR/inst/test-data/specific-redcapr/file-repo-list-oneshot |only REDCapR-1.4.0/REDCapR/inst/test-data/specific-redcapr/project-info-read/all-test-projects.R | 117 REDCapR-1.4.0/REDCapR/man/REDCapR-package.Rd | 4 REDCapR-1.4.0/REDCapR/man/redcap_file_repo_list_oneshot.Rd |only REDCapR-1.4.0/REDCapR/man/sanitize_token.Rd | 3 REDCapR-1.4.0/REDCapR/tests/test-all.R | 7 REDCapR-1.4.0/REDCapR/tests/testthat/test-event-instruments.R | 12 REDCapR-1.4.0/REDCapR/tests/testthat/test-file-repo-list-oneshot.R |only REDCapR-1.4.0/REDCapR/tests/testthat/test-instruments-metadata.R | 11 REDCapR-1.4.0/REDCapR/tests/testthat/test-instruments.R | 6 REDCapR-1.4.0/REDCapR/tests/testthat/test-read-batch-longitudinal.R | 4 REDCapR-1.4.0/REDCapR/tests/testthat/test-read-batch-plumbing.R | 8 REDCapR-1.4.0/REDCapR/vignettes/BasicREDCapROperations.Rmd | 10 REDCapR-1.4.0/REDCapR/vignettes/SecurityDatabase.Rmd | 1 REDCapR-1.4.0/REDCapR/vignettes/TroubleshootingApiCalls.Rmd | 8 REDCapR-1.4.0/REDCapR/vignettes/advanced-redcapr-operations.Rmd | 7 REDCapR-1.4.0/REDCapR/vignettes/longitudinal-and-repeating.Rmd | 1 REDCapR-1.4.0/REDCapR/vignettes/workflow-read.Rmd | 3 REDCapR-1.4.0/REDCapR/vignettes/workflow-write.Rmd | 15 66 files changed, 1319 insertions(+), 4302 deletions(-)
Title: The Iterated Score Regression-Based Estimation
Description: We use the ISR to handle with PCA-based missing data with high correlation, and the DISR to handle with distributed PCA-based missing data. The philosophy of the package is described in Guo G. (2024) <doi:10.1080/03610918.2022.2091779>.
Author: Guangbao Guo [aut, cre] ,
Haoyue Song [aut],
Lixing Zhu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between ISR versions 2022.4.22 dated 2022-04-22 and 2025-01-10 dated 2025-01-11
DESCRIPTION | 27 +++++++++++---------- LICENSE | 2 - MD5 | 34 +++++++++++++-------------- NAMESPACE | 23 +++++++++--------- R/DISR.R | 40 ++++++++++++++++++-------------- R/ISR.R | 31 +++++++++++++++---------- R/MMLPCA.R | 29 +++++++++++++---------- R/MNIPALS.R | 27 +++++++++++++-------- R/MRPCA.R | 28 +++++++++++++--------- R/Mean.R | 26 +++++++++++++-------- R/SR.R | 27 +++++++++++++-------- man/DISR.Rd | 70 +++++++++++++++++++++++++++++++-------------------------- man/ISR.Rd | 68 ++++++++++++++++++++++++++++++------------------------- man/MMLPCA.Rd | 67 ++++++++++++++++++++++++++++++------------------------ man/MNIPALS.Rd | 67 ++++++++++++++++++++++++++++++------------------------ man/MRPCA.Rd | 68 ++++++++++++++++++++++++++++++------------------------- man/Mean.Rd | 67 ++++++++++++++++++++++++++++++------------------------ man/SR.Rd | 66 +++++++++++++++++++++++++++++------------------------ 18 files changed, 430 insertions(+), 337 deletions(-)
Title: Datetimes with Optional UTC Offsets and/or Heterogeneous Time
Zones
Description: Supports import/export for a number of datetime string standards
and R datetime classes often including
lossless re-export of
any original reduced precision including 'ISO 8601' <https://en.wikipedia.org/wiki/ISO_8601> and
'pdfmark' <https://opensource.adobe.com/dc-acrobat-sdk-docs/library/pdfmark/> datetime strings.
Supports local/global datetimes with optional UTC offsets and/or (possibly heterogeneous) time zones
with up to nanosecond precision.
Author: Trevor L. Davis [aut, cre]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between datetimeoffset versions 0.3.1 dated 2023-05-11 and 0.4.1 dated 2025-01-11
DESCRIPTION | 22 - LICENSE | 4 MD5 | 44 +-- NAMESPACE | 17 + NEWS.md | 19 + R/as_datetimeoffset.r | 4 R/format.r | 52 ++- R/from-datetimeoffset.r | 48 +-- R/getset.r | 8 R/hooks.r | 8 R/precision.r | 5 R/timezone.r | 2 README.md | 3 build/vignette.rds |binary inst/doc/datetimeoffset.html | 434 ++++++++++++++++++++++-------- man/format.Rd | 7 man/from_datetimeoffset.Rd | 30 ++ man/getters.Rd | 3 tests/testthat/test-as_datetimeoffset.r | 21 + tests/testthat/test-format.r | 50 +++ tests/testthat/test-from-datetimeoffset.r | 4 tests/testthat/test-getset-clock.r | 2 tests/testthat/test-leap-seconds.r | 2 23 files changed, 577 insertions(+), 212 deletions(-)
More information about datetimeoffset at CRAN
Permanent link
Title: 'CDsampling': Constraint Sampling in Paid Research Studies
Description: In the context of paid research studies and clinical trials, budget considerations and patient sampling from available populations are subject to inherent constraints. We introduce the 'CDsampling' package, which integrates optimal design theories within the framework of constrained sampling. This package offers the possibility to find both D-optimal approximate and exact allocations for samplings with or without constraints. Additionally, it provides functions to find constrained uniform sampling as a robust sampling strategy with limited model information. Our package offers functions for the computation of the Fisher information matrix under generalized linear models (including regular linear regression model) and multinomial logistic models.To demonstrate the applications, we also provide a simulated dataset and a real dataset embedded in the package. Yifei Huang, Liping Tong, and Jie Yang (2025)<doi:10.5705/ss.202022.0414>.
Author: Yifei Huang [aut, cre],
Liping Tong [aut],
Jie Yang [aut]
Maintainer: Yifei Huang <yhuan39@uic.edu>
Diff between CDsampling versions 0.1.3 dated 2025-01-07 and 0.1.4 dated 2025-01-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/Intro_to_CDsampling.R | 2 +- inst/doc/Intro_to_CDsampling.Rmd | 2 +- inst/doc/Intro_to_CDsampling.html | 36 ++++++++++++++++++------------------ vignettes/Intro_to_CDsampling.Rmd | 2 +- 6 files changed, 29 insertions(+), 29 deletions(-)
Title: Visualizing the Elements Within Bio-Sequences
Description: Visualizing the types and distribution of elements within
bio-sequences. At the same time, We have developed a geom layer,
geom_rrect(), that can generate rounded rectangles. No external references
are used in the development of this package.
Author: Shiqi Zhao [aut, cre, cph]
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Diff between BioVizSeq versions 1.0.0 dated 2024-12-22 and 1.0.1 dated 2025-01-11
BioVizSeq-1.0.0/BioVizSeq/man/get_motif_location.Rd |only BioVizSeq-1.0.0/BioVizSeq/man/motif_seq.Rd |only BioVizSeq-1.0.1/BioVizSeq/DESCRIPTION | 8 +- BioVizSeq-1.0.1/BioVizSeq/MD5 | 35 +++++----- BioVizSeq-1.0.1/BioVizSeq/NAMESPACE | 5 - BioVizSeq-1.0.1/BioVizSeq/NEWS.md | 5 + BioVizSeq-1.0.1/BioVizSeq/R/combi_plot.R | 29 ++++++-- BioVizSeq-1.0.1/BioVizSeq/R/meme_plot.R | 18 ++--- BioVizSeq-1.0.1/BioVizSeq/README.md | 3 BioVizSeq-1.0.1/BioVizSeq/inst/extdata/ID_rename.csv |only BioVizSeq-1.0.1/BioVizSeq/inst/extdata/idpro2.gff3 |only BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/app.R | 2 BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/global.R | 1 BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/script/aboutpage.R |only BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/script/mod_advplot.R | 38 +++++++++-- BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/script/mod_gff.R | 13 +++ BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/script/mod_meme.R | 2 BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/www/css/custom.css | 2 BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/www/html/README.html | 4 - BioVizSeq-1.0.1/BioVizSeq/man/combi_p.Rd | 6 + BioVizSeq-1.0.1/BioVizSeq/man/meme_seq.Rd |only BioVizSeq-1.0.1/BioVizSeq/man/meme_to_loc.Rd |only 22 files changed, 123 insertions(+), 48 deletions(-)
Title: Species Distribution Modelling
Description: An extensible framework for developing species distribution
models using individual and community-based approaches, generate ensembles of
models, evaluate the models, and predict species potential distributions in
space and time. For more information, please check the following paper:
Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
Author: Babak Naimi [aut, cre] ,
Miguel B. Araujo [aut]
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between sdm versions 1.2-46 dated 2024-07-17 and 1.2-55 dated 2025-01-11
DESCRIPTION | 21 +++- MD5 | 32 ++++--- NAMESPACE | 2 R/aoa.R |only R/ensemble.R | 9 +- R/evaluates.R | 140 ++++++++++++++++++++++++++++++- R/nicheSimilarity.R | 207 +++++++++++++++++++++++++++++++++++++++------- R/pa.R | 32 +++++-- R/predict.R | 10 +- R/sdmData.R | 8 + R/show.R | 35 +++++++ R/threshold.R |only build/vignette.rds |binary inst/methods/sdm/maxNet.R | 4 man/aoa.Rd |only man/evaluates.Rd | 4 man/nicheSimilarity.Rd | 7 + man/pa.Rd | 1 man/threshold.Rd |only 19 files changed, 434 insertions(+), 78 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival, Including Copula-Based Analyses for
Dependent Censoring
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Estimation of survival functions via copula-graphic (CG) estimators is also implemented, which is useful for
sensitivity analyses under dependent censoring (Yeh et al 2023 Biomedicines) <DOI:10.3390/biomedicines11030797> and
factorial survival analyses (Emura et al 2024 Stat Methods Med Res) <DOI:10.1177/09622802231215805>.
Author: Takeshi Emura [aut, cre],
Hsuan-Yu Chen [aut],
Shigeyuki Matsui [aut],
Yi-Hau Chen [aut]
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.31 dated 2024-10-05 and 3.32 dated 2025-01-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/surv.factorial.R | 4 ++-- man/CG.Clayton.Rd | 4 ++-- man/CG.Frank.Rd | 4 ++-- man/CG.Gumbel.Rd | 4 ++-- man/compound.Cox-package.Rd | 4 ++-- 7 files changed, 20 insertions(+), 20 deletions(-)
Title: Chinese Numerals Processing
Description: Chinese numerals processing in R, such as conversion between
Chinese numerals and Arabic numerals as well as detection and extraction of
Chinese numerals in character objects and string. This package supports
the casual scale naming system and the respective SI prefix systems used
in mainland China and Taiwan:
"The State Council's Order on the Unified Implementation of Legal Measurement Units in Our Country"
The State Council of the People's Republic of China (1984)
"Names, Definitions and Symbols of the Legal Units of Measurement and the Decimal Multiples and Submultiples"
Ministry of Economic Affairs (2019) <https://gazette.nat.gov.tw/egFront/detail.do?metaid=108965>.
Author: Elgar Teo [aut, cre]
Maintainer: Elgar Teo <elgarteo@connect.hku.hk>
Diff between cnum versions 0.1.3 dated 2021-01-11 and 0.1.4 dated 2025-01-11
DESCRIPTION | 14 ++++++-------- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/cnum-tools.R | 7 +++---- R/conversion.R | 27 +++++++++++++-------------- R/data-utils.R | 5 +++-- R/num2c-utils.R | 2 +- R/num2c.R | 4 ++-- man/conversion.Rd | 37 ++++++++++++++++++------------------- man/tools.Rd | 35 +++++++++++++++++------------------ src/RcppExports.cpp | 5 +++++ 11 files changed, 82 insertions(+), 78 deletions(-)
Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging and variable selection for linear models,
generalized linear models and survival models (cox
regression).
Author: Adrian Raftery [aut],
Jennifer Hoeting [aut],
Chris Volinsky [aut],
Ian Painter [aut],
Ka Yee Yeung [aut],
Hana Sevcikova [cre]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between BMA versions 3.18.19 dated 2024-10-18 and 3.18.20 dated 2025-01-11
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/iBMA.glm.R | 5 +++-- R/iBMA.surv.R | 5 +++-- 5 files changed, 17 insertions(+), 12 deletions(-)
Title: Minimal R/Shiny Interface to JavaScript Library 'ECharts'
Description: Deliver the full functionality of 'ECharts' with minimal overhead. 'echarty' users build R lists for 'ECharts' API. Lean set of powerful commands.
Author: Larry Helgason [aut, cre]
Maintainer: Larry Helgason <larry@helgasoft.com>
Diff between echarty versions 1.6.4 dated 2024-06-04 and 1.6.5 dated 2025-01-10
echarty-1.6.4/echarty/R/examples.R |only echarty-1.6.4/echarty/man/ec.examples.Rd |only echarty-1.6.5/echarty/DESCRIPTION | 20 echarty-1.6.5/echarty/MD5 | 61 +- echarty-1.6.5/echarty/NAMESPACE | 1 echarty-1.6.5/echarty/NEWS.md | 428 +++++++++--------- echarty-1.6.5/echarty/R/echarty.R | 300 ++++++------ echarty-1.6.5/echarty/R/util.R | 285 +++++++---- echarty-1.6.5/echarty/build/vignette.rds |binary echarty-1.6.5/echarty/demo/00Index | 1 echarty-1.6.5/echarty/demo/examples.R |only echarty-1.6.5/echarty/inst/doc/echarty.R | 2 echarty-1.6.5/echarty/inst/doc/echarty.Rmd | 120 +++-- echarty-1.6.5/echarty/inst/doc/echarty.html | 158 +++++- echarty-1.6.5/echarty/inst/htmlwidgets/echarty.js | 6 echarty-1.6.5/echarty/inst/js/echarts.min.js | 4 echarty-1.6.5/echarty/man/Introduction.Rd | 59 +- echarty-1.6.5/echarty/man/ec.clmn.Rd | 22 echarty-1.6.5/echarty/man/ec.data.Rd | 8 echarty-1.6.5/echarty/man/ec.fromJson.Rd | 9 echarty-1.6.5/echarty/man/ec.init.Rd | 50 +- echarty-1.6.5/echarty/man/ec.inspect.Rd | 6 echarty-1.6.5/echarty/man/ec.plugjs.Rd | 18 echarty-1.6.5/echarty/man/ec.upd.Rd | 2 echarty-1.6.5/echarty/man/ec.util.Rd | 270 ++++++----- echarty-1.6.5/echarty/man/ecr.ebars.Rd | 43 + echarty-1.6.5/echarty/man/ecs.exec.Rd | 4 echarty-1.6.5/echarty/tests/testthat/test-ec.clmn.R | 11 echarty-1.6.5/echarty/tests/testthat/test-ec.util.R | 119 +++-- echarty-1.6.5/echarty/tests/testthat/test-other.R | 82 ++- echarty-1.6.5/echarty/tests/testthat/test-presets.R | 60 +- echarty-1.6.5/echarty/tests/testthat/test-renderers.R | 20 echarty-1.6.5/echarty/vignettes/echarty.Rmd | 120 +++-- 33 files changed, 1350 insertions(+), 939 deletions(-)
Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). It allows to easily visualize
count data and statistical thresholds: rank vs abundance plots,
heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Matthew Peeples [ctb] ,
Ben Marwick [ctb] ,
Anne Philippe [ctb] ,
Jean-Baptiste Fourvel [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 3.1.1 dated 2024-09-05 and 3.2.0 dated 2025-01-10
DESCRIPTION | 33 - MD5 | 137 ++--- NAMESPACE | 1 NEWS.md | 17 R/AllGenerics.R | 76 +- R/diversity_alpha.R | 84 +-- R/occurrence.R | 83 ++- R/plot_diceleraas.R | 3 R/plot_diversity.R | 30 - R/plot_matrix.R | 18 R/plot_rank.R | 8 R/rarefaction.R | 6 R/similarity.R | 104 +-- R/statistics.R | 8 R/tabula-deprecated.R | 56 -- R/tabula-internal.R | 5 R/tabula-package.R | 9 R/validate.R | 4 R/zzz.R | 4 README.md | 22 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/alpha.R | 2 inst/doc/alpha.html | 12 inst/doc/beta.R | 4 inst/doc/beta.Rmd | 11 inst/doc/beta.html | 36 - inst/examples/ex-occurrence.R | 11 inst/examples/ex-similarity.R | 11 inst/po |only inst/tinytest/_tinysnapshot/plot_dice_leraas.svg | 2 inst/tinytest/_tinysnapshot/plot_mtx_count.svg | 526 +++++++++---------- inst/tinytest/_tinysnapshot/plot_mtx_notfixed.svg | 496 +++++++++--------- inst/tinytest/_tinysnapshot/plot_mtx_occ.svg | 20 inst/tinytest/_tinysnapshot/plot_mtx_prop1.svg | 532 ++++++++++---------- inst/tinytest/_tinysnapshot/plot_mtx_prop2.svg | 532 ++++++++++---------- inst/tinytest/_tinysnapshot/plot_mtx_sim.svg | 14 inst/tinytest/_tinysnapshot/plot_spot_occ.svg | 20 inst/tinytest/_tinysnapshot/plot_spot_plain.svg | 18 inst/tinytest/_tinysnapshot/plot_spot_prop1.svg | 16 inst/tinytest/_tinysnapshot/plot_spot_prop2.svg | 14 inst/tinytest/_tinysnapshot/plot_spot_ring.svg | 18 inst/tinytest/_tinysnapshot/plot_spot_sim_plain.svg | 14 inst/tinytest/_tinysnapshot/plot_spot_sim_ring.svg | 14 inst/tinytest/test_diversity.R | 2 inst/tinytest/test_index.R | 7 inst/tinytest/test_occurrence.R | 7 inst/tinytest/test_plots.R | 2 inst/tinytest/test_rarefaction.R | 2 inst/tinytest/test_richness.R | 2 inst/tinytest/test_similarity.R | 4 inst/tinytest/test_statistics.R | 3 man/figures/README-ford-1.png |binary man/figures/README-occurrence-1.png |binary man/figures/README-sample-size-1.png |binary man/figures/README-sample-size-2.png |binary man/index_binomial.Rd | 4 man/occurrence.Rd | 29 - man/plot_diversity.Rd | 4 man/plot_rank.Rd | 6 man/plot_rarefaction.Rd | 4 man/plot_spot.Rd | 2 man/profiles.Rd | 6 man/she.Rd | 6 man/similarity.Rd | 21 man/tabula-deprecated.Rd | 11 man/tabula-package.Rd | 13 po |only vignettes/beta.Rmd | 11 70 files changed, 1599 insertions(+), 1580 deletions(-)
Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with
nanosecond granularity is provided, with easy transition to and from
the standard 'POSIXct' type. Three additional classes offer interval,
period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel [aut, cre] ,
Leonardo Silvestri [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.3.10 dated 2024-09-16 and 0.3.11 dated 2025-01-10
ChangeLog | 20 ++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/nanotime.R | 7 ++++++- build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++++ inst/doc/nanotime-introduction.pdf |binary src/period.cpp | 27 +++++++++++++++++++-------- 8 files changed, 65 insertions(+), 20 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, simulation, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX and html code,
recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.
Author: Frank E Harrell Jr [aut, cre] ,
Charles Dupont [ctb]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between Hmisc versions 5.2-1 dated 2024-12-02 and 5.2-2 dated 2025-01-10
DESCRIPTION | 8 +-- MD5 | 30 +++++++------ NAMESPACE | 2 NEWS | 6 ++ R/cut2.s | 99 +++++++++++++++++++++++++++++++++++++++++++++- R/num.intercepts.s | 5 ++ R/ordGroupBoot.r |only R/plsmo.s | 4 - R/popower.s | 8 ++- R/xy.group.s | 29 +++++++------ inst/tests/ordGroupBoot.r |only man/cut2.Rd | 23 +++++++++- man/num.intercepts.Rd | 2 man/ordGroupBoot.Rd |only man/plsmo.Rd | 6 +- man/xy.group.Rd | 10 ++-- src/cutgn.f90 |only src/init.c | 2 18 files changed, 187 insertions(+), 47 deletions(-)
Title: Retrieve and Plot Google n-Gram Data
Description: Retrieve and plot word frequencies through time from the "Google
Ngram Viewer" <https://books.google.com/ngrams>.
Author: Sean Carmody [aut, cre, cph]
Maintainer: Sean Carmody <seancarmody@gmail.com>
Diff between ngramr versions 1.9.3 dated 2023-01-16 and 1.10.0 dated 2025-01-10
ngramr-1.10.0/ngramr/DESCRIPTION | 10 ++++---- ngramr-1.10.0/ngramr/MD5 | 25 ++++++++++------------ ngramr-1.10.0/ngramr/NEWS.md | 7 ++++++ ngramr-1.10.0/ngramr/R/data.R | 2 - ngramr-1.10.0/ngramr/R/ggram.R | 7 ------ ngramr-1.10.0/ngramr/R/ngram.R | 25 ++++++---------------- ngramr-1.10.0/ngramr/R/ngramr-package.R | 9 ++++--- ngramr-1.10.0/ngramr/R/sysdata.rda |binary ngramr-1.10.0/ngramr/man/corpuses.Rd | 2 - ngramr-1.10.0/ngramr/man/ggram.Rd | 4 --- ngramr-1.10.0/ngramr/man/ngram.Rd | 10 +------- ngramr-1.10.0/ngramr/man/ngramr.Rd | 10 ++++---- ngramr-1.10.0/ngramr/tests/testthat/test-ngramr.R | 6 ++--- ngramr-1.9.3/ngramr/R/add_count.R |only 14 files changed, 49 insertions(+), 68 deletions(-)
Title: Simulation of Inter-Related Genomic Datasets
Description: Generates three inter-related genomic datasets: methylation, gene expression and protein expression having user specified cluster patterns. The simulation utilizes the realistic inter- and intra- relationships from real DNA methylation, mRNA expression and protein expression data from the TCGA ovarian cancer study, Chalise (2016) <doi:10.1016/j.cmpb.2016.02.011>.
Author: Prabhakar Chalise [aut, cre],
Rama Raghavan [aut],
Brooke Fridley [aut]
Maintainer: Prabhakar Chalise <pchalise@kumc.edu>
Diff between InterSIM versions 2.2.0 dated 2018-07-16 and 2.3.0 dated 2025-01-10
DESCRIPTION | 24 ++++++++++++++++++------ MD5 | 8 ++++---- R/InterSIM.R | 4 ++-- man/InterSIM-package.Rd | 7 ++++--- man/InterSIM.Rd | 6 ++++-- 5 files changed, 32 insertions(+), 17 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate
the command line behaviour of R.
Author: Hadley Wickham [aut, cre],
Yihui Xie [aut] ,
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Jeroen Ooms [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb],
Hiroaki Yutani [ctb],
Michel Lang [ctb],
Karolis Koncevicius [ctb],
Posit Software, PBC [cph, [...truncated...]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between evaluate versions 1.0.1 dated 2024-10-10 and 1.0.3 dated 2025-01-10
DESCRIPTION | 10 ++--- MD5 | 32 ++++++++++++---- NEWS.md | 8 +++- R/conditions.R | 3 + R/evaluate.R | 8 +++- tests/testthat/_snaps/conditions |only tests/testthat/_snaps/conditions.md | 4 +- tests/testthat/helper.R | 17 ++++++++ tests/testthat/ressources |only tests/testthat/test-conditions.R | 71 ++++++++++++++++++++++++++++++++++-- 10 files changed, 133 insertions(+), 20 deletions(-)
Title: Read, Plot and Analyse Output from the DEPONS Model
Description: Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.
Author: Jacob Nabe-Nielsen [aut, cre],
Caitlin K. Frankish [aut],
Axelle Cordier [aut],
Florian G. Weller [aut]
Maintainer: Jacob Nabe-Nielsen <jnn@ecos.au.dk>
Diff between DEPONS2R versions 1.2.4 dated 2024-11-20 and 1.2.5 dated 2025-01-10
DESCRIPTION | 18 MD5 | 49 - NAMESPACE | 4 R/a-misc.R | 218 +++-- R/calibrate_methods.R |only R/dyn-methods.R | 23 R/parameter-methods.R | 2 R/raster-methods.R | 2 R/ships_methods.R | 1300 ++++++++++++++++++++------------ R/track-methods.R | 35 R/z-accessors.R | 6 data/shipdata.RData |binary man/ais.to.DeponsShips.Rd | 3 man/as.data.frame-DeponsTrack-method.Rd | 2 man/calib_01.Rd |only man/check.DeponsShips.Rd |only man/get.simtime.Rd | 2 man/interpolate.ais.data.Rd | 5 man/make.DeponsDyn.Rd | 4 man/make.stationary.ships.Rd |only man/plot-DeponsDyn-missing-method.Rd | 2 man/read.DeponsDyn.Rd | 7 man/read.DeponsDynBatch.Rd |only man/read.DeponsShips.Rd | 3 man/read.DeponsTrack.Rd | 2 man/read.DeponsTrackBatch.Rd |only man/shipdata.Rd | 6 man/tick.to.time.Rd | 11 man/time.to.tick.Rd |only 29 files changed, 1081 insertions(+), 623 deletions(-)
Title: Access and Manipulate Amiga Disk Files
Description: Amiga Disk Files (ADF) are virtual
representations of 3.5 inch floppy disks for the
Commodore Amiga. Most disk drives from other systems
(including modern drives) are not able to read these
disks. The 'adfExplorer' package enables you to
establish R connections to files on such
virtual DOS-formatted disks, which can be use to
read from and write to those files.
Author: Pepijn de Vries [aut, cre] ,
Laurent Clevy [aut, cph]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between adfExplorer versions 2.0.0 dated 2024-12-23 and 2.0.3 dated 2025-01-10
DESCRIPTION | 13 MD5 | 110 +++---- NAMESPACE | 2 NEWS.md | 180 ++++++----- R/adfExplorer-package.R | 28 - R/blocks.R | 170 ++++++----- R/compress.R | 93 +++--- R/connect_adf.R | 257 +++++++++------- R/cpp11.R | 18 - R/demo.R |only R/device_create.R | 201 ++++++------- R/device_info.R | 417 +++++++++++++-------------- R/directory.R | 458 ++++++++++++++--------------- R/entry_info.R | 497 +++++++++++++++----------------- R/helpers.R | 8 R/move.R | 597 +++++++++++++++++++-------------------- R/remove.R | 172 +++++------ R/s3_conn.R | 304 +++++++++---------- R/s3_methods.R | 336 +++++++++++---------- R/virtual_path.R | 72 ++-- README.md | 3 configure.win | 30 - inst/doc/version2.Rmd | 284 +++++++++--------- inst/doc/version2.html | 2 man/adf_block.Rd | 19 + man/adf_directory.Rd | 9 man/close_all_devices.Rd |only man/demo_adf.Rd |only man/device_info.Rd | 9 man/entry_info.Rd | 3 man/exists.Rd | 3 man/list_adf_entries.Rd | 9 man/name.Rd | 9 man/remove_adf_entry.Rd | 10 man/s3_methods.Rd | 19 + man/virtual_path.Rd | 4 src/adf_file_info.cpp | 20 - src/adf_file_operators.cpp | 349 +++++----------------- src/adflib/adf_bitm.c | 2 src/adflib/adf_dev.c | 1 src/adflib/adf_dev_flop.c | 1 src/adflib/adf_file.c | 2 src/adflib/adf_util.h | 6 src/block_adf.cpp | 14 src/cpp11.cpp | 38 +- src/dev_format.cpp | 16 - src/dev_info.cpp | 18 - src/open_adf.cpp | 42 ++ src/open_adf.h | 3 src/open_adf_file.cpp | 153 ++++++--- src/open_adf_file.h | 7 tests/testthat.R | 9 tests/testthat/test_deprecated.R |only tests/testthat/test_directory.R |only tests/testthat/test_entryinfo.R |only tests/testthat/test_examples.R | 6 tests/testthat/test_exceptions.R |only tests/testthat/test_move.R |only tests/testthat/test_remove.R |only tests/testthat/test_s3.R |only vignettes/version2.Rmd | 284 +++++++++--------- 61 files changed, 2670 insertions(+), 2647 deletions(-)
Title: Helper Functions for Simulation Studies
Description: Calculates performance criteria measures and associated Monte Carlo standard errors for simulation results. Includes functions to help run simulation studies, following a general simulation workflow that closely aligns with the approach described by Morris, White, and Crowther (2019) <DOI:10.1002/sim.8086>. Also includes functions for calculating bootstrap confidence intervals (including normal, basic, studentized, percentile, bias-corrected, and bias-corrected-and-accelerated) with tidy output, as well as for extrapolating confidence interval coverage rates and hypothesis test rejection rates following techniques suggested by Boos and Zhang (2000) <DOI:10.1080/01621459.2000.10474226>.
Author: Megha Joshi [aut, cre] ,
James Pustejovsky [aut]
Maintainer: Megha Joshi <megha.j456@gmail.com>
Diff between simhelpers versions 0.3.0 dated 2024-09-04 and 0.3.1 dated 2025-01-10
DESCRIPTION | 8 - MD5 | 26 ++-- NEWS.md | 5 R/bootstrap-projection.R | 69 ++++++++-- R/bundle_sim.R | 2 build/partial.rdb |binary inst/REFERENCES.bib | 13 -- inst/doc/MCSE.html | 4 inst/doc/simulation_workflow.html | 6 inst/doc/visualization.html | 4 man/bootstrap_CIs.Rd | 23 ++- man/bundle_sim.Rd | 2 tests/testthat/test_bootstrap_CI_construction.R | 146 ++++++++++++++--------- tests/testthat/test_bootstrap_CI_extrapolation.R | 4 14 files changed, 198 insertions(+), 114 deletions(-)
Title: Confidence Intervals for Comparisons of Binomial or Poisson
Rates
Description: Computes confidence intervals for the rate (or risk)
difference ('RD') or rate ratio (or relative risk, 'RR') for
binomial proportions or Poisson rates, or for odds ratio
('OR', binomial only). Also confidence intervals for a single
binomial or Poisson rate, and intervals for matched pairs.
Includes skewness-corrected asymptotic score ('SCAS') methods,
which have been developed in Laud (2017) <doi:10.1002/pst.1813>
from Miettinen & Nurminen (1985) <doi:10.1002/sim.4780040211> and
Gart & Nam (1988) <doi:10.2307/2531848>. The same score produces
hypothesis tests analogous to the test for binomial RD and RR by
Farrington & Manning (1990) <doi:10.1002/sim.4780091208>, or the
McNemar test for paired data.
The package also includes MOVER methods
(Method Of Variance Estimates Recovery) for all contrasts, derived
from the Newcombe method but with options to use equal-tailed
intervals in place of the Wilson score method,
and generalised for Bayesian applicati [...truncated...]
Author: Pete Laud [aut, cre]
Maintainer: Pete Laud <p.j.laud@sheffield.ac.uk>
Diff between ratesci versions 0.4-0 dated 2021-12-05 and 0.5.0 dated 2025-01-10
DESCRIPTION | 30 + MD5 | 45 +- NAMESPACE | 1 NEWS.md | 47 +++ R/moverci.R | 83 +++-- R/pairbinci.R | 754 +++++++++++++++++++++++++++++++++++++++++++------ R/rateci.R | 160 +++++++--- R/ratesci-package.R | 30 - R/scoreci.R | 394 ++++++++++++++++--------- build |only man/jeffreysci.Rd | 6 man/moverbci.Rd | 6 man/moverci.Rd | 37 +- man/pairbinci.Rd | 169 ++++++++-- man/rateci.Rd | 9 man/ratesci-package.Rd | 53 +-- man/scasci.Rd | 56 ++- man/scaspci.Rd | 13 man/scoreci.Rd | 130 ++++---- man/tdasci.Rd | 56 ++- tests/testthat/test1.R | 95 +++++- tests/testthat/test2.R | 23 - tests/testthat/test3.R | 166 ++++++++++ tests/testthat/test4.R | 10 24 files changed, 1806 insertions(+), 567 deletions(-)
Title: Access the 'Quickbase' JSON API
Description: Programmatically access the 'Quickbase' JSON API <https://developer.quickbase.com>.
You supply parameters for an API call, 'qbr' delivers an http request to the
API endpoint and returns its response. Outputs follow 'tidyverse' philosophy.
Author: John Erdmann [aut, cre],
Keene State College [cph, fnd]
Maintainer: John Erdmann <john.erdmann@keene.edu>
Diff between qbr versions 1.2.4 dated 2024-09-26 and 1.3.0 dated 2025-01-10
DESCRIPTION | 8 ++--- MD5 | 13 ++++---- NAMESPACE | 1 NEWS.md | 3 + R/glob_vars.R | 1 R/qb_fields.R | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 59 +++++++++++++++++++-------------------- man/delete_fields.Rd |only 8 files changed, 123 insertions(+), 39 deletions(-)
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton [aut, cre],
D.L. Parkhurst [aut],
C.A.J. Appelo [aut],
with contributions from D. Gillespie for Chipmunk BASIC [aut],
S.D. Cohen [aut],
A.C. Hindmarsh [aut],
R. Serban [aut],
D. Shumaker [aut],
A.G. Taylor for CVODE/SUNDIALS [aut]
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 3.8.5 dated 2024-12-04 and 3.8.6 dated 2025-01-10
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- R/phreeqc.R | 4 ++-- data/databases.rda |binary data/examples.rda |binary man/phreeqc-package.Rd | 4 ++-- src/CSelectedOutput.cpp | 8 ++++---- src/IPhreeqc.cpp | 14 +++++++------- src/IPhreeqc.h | 12 ++++++------ src/IPhreeqchpp.h | 4 ++-- src/Version.h | 8 ++++---- src/phreeqcpp/mainsubs.cpp | 12 +++++++++--- src/phreeqcpp/tidy.cpp | 9 +++++++++ src/phreeqcpp/transport.cpp | 18 +++++++++++------- 14 files changed, 72 insertions(+), 53 deletions(-)
Title: Query 'nycflights13'-Like Air Travel Data for Given Years and
Airports
Description: Supplies a set of functions to query air travel data for user-
specified years and airports. Datasets include on-time flights, airlines,
airports, planes, and weather.
Author: Simon P. Couch [aut, cre],
Hadley Wickham [ctb],
Jay Lee [ctb],
Dennis Irorere [ctb]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>
Diff between anyflights versions 0.3.4 dated 2023-09-11 and 0.3.5 dated 2025-01-10
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- NEWS.md | 31 +++++++++++++++---------------- R/get_airports.R | 2 +- R/utils.R | 11 ++++++++++- README.md | 36 +++++++++++++++++------------------- man/anyflights_description.Rd | 2 +- man/get_airports.Rd | 2 +- 8 files changed, 59 insertions(+), 52 deletions(-)
Title: Data Processing of SMN Hi-Res Weather Forecast from 'AWS'
Description: Exploration of Weather Research & Forecasting ('WRF') Model data
of Servicio Meteorologico Nacional (SMN) from Amazon Web Services
(<https://registry.opendata.aws/smn-ar-wrf-dataset/>) cloud. The package
provides the possibility of data downloading, processing and correction
methods. It also has map management and series exploration of available
meteorological variables of 'WRF' forecast.
Author: Gonzalo Diaz [cre, aut]
Maintainer: Gonzalo Diaz <gonzalomartindiaz22@gmail.com>
Diff between aws.wrfsmn versions 0.0.3 dated 2024-03-08 and 0.0.4 dated 2025-01-10
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NAMESPACE | 3 +++ NEWS.md | 6 ++++++ R/ith.R |only R/load_by_variable.R | 4 ++-- build/vignette.rds |binary inst/doc/Multiple-Linear-Regression-Correction.html | 4 ++-- inst/doc/Package-Introduction.html | 2 +- man/ith.Rd |only man/load.by.variable.Rd | 4 ++-- 11 files changed, 30 insertions(+), 19 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.12.0 dated 2024-07-25 and 1.13.0 dated 2025-01-10
DESCRIPTION | 8 MD5 | 147 +- NAMESPACE | 5 NEWS.md | 10 R/AddTip.R | 468 +++--- R/ClusterTable.R | 2 R/Decompose.R |only R/ReadTntTree.R | 4 R/SplitFunctions.R | 898 ++++++------ R/Splits.R | 1305 ++++++++---------- R/as.multiPhylo.R | 1 R/helper_functions.R | 8 R/in.R |only R/match.R |only R/mst.R | 1 R/parse_files.R | 10 R/phylo.R | 628 ++++---- R/sort.R | 1 R/tree_generation.R | 1061 +++++++-------- R/tree_shape.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/REFERENCES.bib | 45 inst/WORDLIST | 2 inst/apa-old-doi-prefix.csl | 2306 ++++++++++++++++++++++----------- inst/doc/filesystem-navigation.Rmd | 3 inst/doc/filesystem-navigation.html | 8 inst/doc/load-data.html | 10 inst/doc/load-trees.html | 12 inst/include/TreeTools/ClusterTable.h | 18 inst/include/TreeTools/SplitList.h | 36 inst/include/TreeTools/assert.h | 6 inst/include/TreeTools/keep_tip.h | 4 inst/include/TreeTools/renumber_tree.h | 13 man/AddTip.Rd | 272 +-- man/AncestorEdge.Rd | 106 - man/ClusterTable-methods.Rd | 14 man/ClusterTable.Rd | 13 man/Decompose.Rd |only man/DescendantEdges.Rd | 178 +- man/EdgeAncestry.Rd | 124 - man/Hamming.Rd | 13 man/LabelSplits.Rd | 2 man/ListAncestors.Rd | 218 +-- man/MSTEdges.Rd | 13 man/MatrixToPhyDat.Rd | 1 man/NSplits.Rd | 2 man/NTip.Rd | 2 man/Neworder.Rd | 128 - man/PhyToString.Rd | 1 man/PolarizeSplits.Rd | 2 man/ReadCharacters.Rd | 277 ++- man/Reorder.Rd | 558 +++---- man/SampleOne.Rd | 17 man/SplitFrequency.Rd | 2 man/Splits.Rd | 2 man/SplitsInBinaryTree.Rd | 2 man/Subtree.Rd | 124 - man/TipLabels.Rd | 244 +-- man/TipTimedTree.Rd | 12 man/TipsInSplits.Rd | 2 man/TreeShape.Rd | 322 ++-- man/UnshiftTree.Rd | 13 man/as.multiPhylo.Rd | 14 man/match.Splits.Rd | 129 - man/match.multiPhylo.Rd |only man/sapply64.Rd | 151 +- man/sort.multiPhylo.Rd | 14 man/xor.Rd | 2 src/RcppExports.cpp | 4 src/splits.cpp | 76 - src/splits_to_tree.cpp | 9 src/tips_in_splits.cpp | 3 src/tree_shape.cpp | 4 tests/testthat/test-Decompose.R |only tests/testthat/test-match.R |only vignettes/filesystem-navigation.Rmd | 3 78 files changed, 5583 insertions(+), 4516 deletions(-)
Title: Base Tools for Semi-Automatic Reporting of Ordinary Surveys
Description: Scaffold an entire web-based report using template chunks, based on a small chapter overview and a dataset.
Highly adaptable with prefixes, suffixes, translations, etc. Also contains tools for password-protecting,
e.g. for each organization's report on a website. Developed for the common case of a survey across multiple organizations/sites
where each organization wants to obtain results for their organization compared with everyone else.
See 'saros' (<https://CRAN.R-project.org/package=saros>) for tools used for authors in the drafted reports.
Author: Stephan Daus [aut, cre, cph] ,
Nordic Institute for The Studies of Innovation, Research and Education
[fnd],
Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
Diff between saros.base versions 0.2.1 dated 2024-09-18 and 1.0.0 dated 2025-01-10
DESCRIPTION | 16 MD5 | 143 ++- NAMESPACE | 3 NEWS.md | 18 R/add_chapter_foldername_to_chapter_structure.R | 38 R/add_max_chars_labels_to_chapter_structure.R |only R/add_n_cats_to_chapter_structure.R | 34 R/add_n_range_to_chapter_structure.R | 18 R/add_n_to_chapter_structure.R | 45 - R/add_n_vars_to_chapter_structure.R | 15 R/add_obj_name_to_chapter_structure.R | 53 - R/add_parsed_vars_to_chapter_structure.R | 32 R/append_main_password_file.R | 31 R/arrange2.R | 115 +- R/attach_chapter_dataset.R | 53 - R/check_chapter_structure_for_duplicates.R |only R/collapse_chapter_structure_to_chr.R | 14 R/download_zip_to_folder.R | 9 R/draft_report.R | 38 R/eval_cols.R | 46 - R/filename_sanitizer.R | 101 +- R/find_stat_test.R | 438 ++++------ R/gen_qmd_chapters.R | 138 +-- R/gen_qmd_file.R | 124 +- R/gen_qmd_structure.R | 86 + R/get_organize_by_opts.R |only R/insert_chunk.R | 35 R/log_unused_variables.R | 16 R/look_for_extended.R | 298 +++--- R/process_yaml.R | 55 - R/refine_chapter_overview.R | 396 +++++---- R/remove_entry_from_sidebar.R |only R/remove_from_chapter_structure_if_n_below.R | 15 R/remove_from_chapter_structure_if_no_overlap.R |only R/remove_from_chapter_structure_if_no_type_match.R | 38 R/remove_from_chapter_structure_if_non_significant.R | 149 +-- R/replace_label_groups_with_name_groups.R | 4 R/setup_mesos.R |only R/split_chapter_structure_groups_if_single_y_bivariates.R | 42 R/validate_chapter_structure.R | 128 +- R/validate_draft_report_args.R | 40 R/validate_refine_chapter_overview_args.R | 73 - R/zzz.R | 98 +- build |only inst/WORDLIST | 35 inst/doc |only man/draft_report.Rd | 30 man/gen_qmd_chapters.Rd | 15 man/gen_qmd_file.Rd | 5 man/get_organize_by_opts.Rd |only man/refine_chapter_overview.Rd | 25 man/remove_entry_from_sidebar.Rd |only man/setup_mesos.Rd |only tests/testthat/test-add_chapter_foldername_to_chapter_structure.R | 9 tests/testthat/test-add_max_chars_labels_to_chapter_structure.R |only tests/testthat/test-add_n_cats_to_chapter_structure.R | 15 tests/testthat/test-arrange2.R | 7 tests/testthat/test-check_chapter_structure_for_duplicates.R |only tests/testthat/test-draft_report.R | 72 - tests/testthat/test-filename_sanitizer.R | 14 tests/testthat/test-find_stat_test.R |only tests/testthat/test-gen_qmd_file.R | 6 tests/testthat/test-refine_chapter_overview.R | 94 +- tests/testthat/test-remove_from_chapter_structure_if_no_overlap.R |only tests/testthat/test-setup_mesos.R |only vignettes |only 66 files changed, 1892 insertions(+), 1430 deletions(-)
Title: 'KorAP' Web Service Client Package
Description: A client package that makes the 'KorAP' web service API accessible from R.
The corpus analysis platform 'KorAP' has been developed as a scientific tool to make
potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo'
or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify
hypotheses and to find interesting patterns in real language use.
The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code,
as a programmatic alternative to the 'KorAP' web user-interface.
You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Author: Marc Kupietz [aut, cre],
Nils Diewald [ctb],
Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Diff between RKorAPClient versions 0.8.1 dated 2024-05-02 and 0.9.0 dated 2025-01-10
DESCRIPTION | 8 - MD5 | 41 +++--- NAMESPACE | 15 ++ NEWS.md | 13 + R/KorAPConnection.R | 2 R/KorAPCorpusStats.R | 8 - R/KorAPQuery.R | 135 ++++++++++++-------- R/collocationAnalysis.R | 1 R/collocationScoreQuery.R | 44 ++++++ R/hc_freq_by_year_ci.R | 2 R/textMetadata.R | 35 +++-- demo/00Index | 1 demo/relativeTextpositionBoxplot.R |only inst/CITATION |only man/KorAPConnection-class.Rd | 2 man/KorAPQuery-class.Rd | 9 - man/collocationAnalysis-KorAPConnection-method.Rd | 2 man/collocationScoreQuery-KorAPConnection-method.Rd | 2 man/hc_freq_by_year_ci.Rd | 2 man/mergeDuplicateCollocates.Rd |only tests/testthat/test-collocations.R | 2 tests/testthat/test-corpusQuery.R | 93 +++++++++++++ tests/testthat/test-textMetadata.R | 6 23 files changed, 322 insertions(+), 101 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 10.9.6 dated 2024-12-17 and 11.0 dated 2025-01-10
DESCRIPTION | 8 - MD5 | 34 ++--- R/ARMA.R | 203 +++++++++++++++++++-------------- R/ARMA_optim.R | 95 +++++++++++++-- R/Internal_Functions.R | 81 +++++++++++-- R/Multivariate_Regression.R | 206 ++++++++++++++++++++++++---------- R/NNS_VAR.R | 1 R/NNS_meboot.R | 119 +++++++++---------- R/RcppExports.R | 4 R/Regression.R | 4 README.md | 4 inst/doc/NNSvignette_Forecasting.Rmd | 2 inst/doc/NNSvignette_Forecasting.html | 2 man/NNS.ARMA.optim.Rd | 4 man/PM.matrix.Rd | 4 src/Makevars | 1 src/partial_moments_rcpp.cpp | 4 vignettes/NNSvignette_Forecasting.Rmd | 2 18 files changed, 510 insertions(+), 268 deletions(-)
Title: Collection of Data Sets for Teaching Purposes
Description: Collection (syllogi in greek) of real and fictitious data sets for teaching purposes.
The datasets were manually entered by the author from the respective references as listed in the individual dataset documentation.
The fictions datasets are the creation of the author, that he has found useful for teaching statistics.
Author: Jared Studyvin [aut, cre]
Maintainer: Jared Studyvin <studyvinstat@gmail.com>
Diff between syllogi versions 1.0.3 dated 2024-07-08 and 1.0.4 dated 2025-01-10
DESCRIPTION | 8 +++--- MD5 | 50 +++++++++++++++++++++++++---------------- R/beer.R |only R/golf.R |only R/shipDamage.R |only R/ski.R |only data/alligatorDiet.RData |binary data/alligatorLength.RData |binary data/annualSales.RData |binary data/beer.RData |only data/bighornSheep.RData |binary data/bladderCancer.RData |binary data/butterflyPlot.RData |binary data/depression.RData |binary data/dogFood.RData |binary data/federalistPapers.RData |binary data/genericData.RData |binary data/golf.RData |only data/nutritionCancer.RData |binary data/osteosarcoma.RData |binary data/patientSatisfaction.RData |binary data/politicalIdeology.RData |binary data/schoolProgram.RData |binary data/shipDamage.RData |only data/shipGold.RData |binary data/ski.RData |only data/weightLoss.RData |binary data/wheat.RData |binary man/beer.Rd |only man/golf.Rd |only man/shipDamage.Rd |only man/ski.Rd |only 32 files changed, 35 insertions(+), 23 deletions(-)
Title: Semi-Automatic Reporting of Ordinary Surveys
Description: Offers a systematic way for conditional reporting of figures and tables for many
(and bivariate combinations of) variables, typically from survey data.
Contains interactive 'ggiraph'-based
(<https://CRAN.R-project.org/package=ggiraph>) plotting functions and
data frame-based summary tables (bivariate significance tests,
frequencies/proportions, unique open ended responses, etc) with
many arguments for customization, and extensions possible. Uses a global
options() system for neatly reducing redundant code.
Also contains tools for immediate saving of objects and returning a hashed link to the object,
useful for creating download links to high resolution images upon rendering in 'Quarto'.
Suitable for highly customized reports, primarily intended for survey
research.
Author: Stephan Daus [aut, cre, cph] ,
Julia Silge [ctb] ,
David Robinson [ctb] ,
Nordic Institute for The Studies of Innovation, Research and Education
[fnd],
Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
Diff between saros versions 1.2.0 dated 2024-09-03 and 1.5.0 dated 2025-01-10
saros-1.2.0/saros/tests/testthat/_snaps |only saros-1.2.0/saros/tests/testthat/test-cat_plot_docx.R |only saros-1.2.0/saros/tests/testthat/test-cat_table_docx.R |only saros-1.2.0/saros/tests/testthat/test-summarize_data.R |only saros-1.5.0/saros/DESCRIPTION | 18 saros-1.5.0/saros/MD5 | 104 + saros-1.5.0/saros/NAMESPACE | 5 saros-1.5.0/saros/NEWS.md | 20 saros-1.5.0/saros/R/check_no_duplicated_label_suffix.R |only saros-1.5.0/saros/R/check_sort_by.R | 43 saros-1.5.0/saros/R/crosstable.R | 336 +----- saros-1.5.0/saros/R/crosstable.data.frame.R |only saros-1.5.0/saros/R/crosstable.survey.R |only saros-1.5.0/saros/R/fig_height_h_barchart.R | 548 +++++----- saros-1.5.0/saros/R/get_main_question.R | 45 saros-1.5.0/saros/R/ggsaver.R | 4 saros-1.5.0/saros/R/girafe.R |only saros-1.5.0/saros/R/keep_subitem.R | 25 saros-1.5.0/saros/R/make_content.R | 4 saros-1.5.0/saros/R/make_content.cat_freq_plot_docx.R | 98 + saros-1.5.0/saros/R/make_content.cat_plot_html.R | 160 +- saros-1.5.0/saros/R/make_content.cat_table_html.R | 111 +- saros-1.5.0/saros/R/make_content.chr_table_html.R | 17 saros-1.5.0/saros/R/make_content.sigtest_table_html.R | 56 - saros-1.5.0/saros/R/make_link.R | 144 ++ saros-1.5.0/saros/R/makeme.R | 363 +++--- saros-1.5.0/saros/R/makeme_helpers.R |only saros-1.5.0/saros/R/n_rng.R | 161 +- saros-1.5.0/saros/R/scale_x_reordered.R | 19 saros-1.5.0/saros/R/simple_desciptives.R | 92 + saros-1.5.0/saros/R/summarize_cat_cat_data.R | 374 ++++-- saros-1.5.0/saros/R/summarize_int_cat_data.R | 37 saros-1.5.0/saros/R/validate_makeme_options.R | 64 - saros-1.5.0/saros/R/zzz.R | 77 - saros-1.5.0/saros/build |only saros-1.5.0/saros/inst/WORDLIST | 9 saros-1.5.0/saros/inst/doc |only saros-1.5.0/saros/man/fig_height_h_barchart.Rd | 104 + saros-1.5.0/saros/man/fig_height_h_barchart2.Rd | 37 saros-1.5.0/saros/man/girafe.Rd |only saros-1.5.0/saros/man/make_link.Rd | 142 +- saros-1.5.0/saros/man/make_link.default.Rd |only saros-1.5.0/saros/man/make_link.list.Rd |only saros-1.5.0/saros/man/makeme.Rd | 107 + saros-1.5.0/saros/man/n_range.Rd | 2 saros-1.5.0/saros/man/summarize_cat_cat_data.Rd | 31 saros-1.5.0/saros/tests/testthat/test-add_n_to_label.R |only saros-1.5.0/saros/tests/testthat/test-crosstable.R | 75 - saros-1.5.0/saros/tests/testthat/test-fig_height_h_barchart.R | 226 +--- saros-1.5.0/saros/tests/testthat/test-make_content.cat_plot_docx.R |only saros-1.5.0/saros/tests/testthat/test-make_content.cat_table_docx.R |only saros-1.5.0/saros/tests/testthat/test-make_content.cat_table_html.R | 58 - saros-1.5.0/saros/tests/testthat/test-make_link.R | 15 saros-1.5.0/saros/tests/testthat/test-simple_desciptives.R | 12 saros-1.5.0/saros/tests/testthat/test-summarize_cat_cat_data.R |only saros-1.5.0/saros/vignettes |only 56 files changed, 2133 insertions(+), 1610 deletions(-)
Title: Loading Data from 'Google Ads API'
Description: Interface for loading data from 'Google Ads API',
see <https://developers.google.com/google-ads/api/docs/start>.
Package provide function for authorization and loading reports.
Author: Alexey Seleznev [aut, cre] ,
Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rgoogleads versions 0.11.0 dated 2024-05-14 and 0.12.0 dated 2025-01-10
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS.md | 3 R/zzz.R | 2 build/vignette.rds |binary inst/doc/migrate_from_radrowds_us.R | 84 ++++++++++----------- inst/doc/migrate_from_radrowds_us.html | 127 ++++++++++++++++++++++----------- inst/doc/migrate_from_radwords_ru.R | 84 ++++++++++----------- inst/doc/migrate_from_radwords_ru.html | 124 +++++++++++++++++++++----------- 9 files changed, 268 insertions(+), 178 deletions(-)
Title: Construction of Genetic Maps in Experimental Crosses
Description: Analysis of molecular marker data from model (backcrosses,
F2 and recombinant inbred lines) and non-model systems (i. e.
outcrossing species). For the later, it allows statistical
analysis by simultaneously estimating linkage and linkage
phases (genetic map construction) according to Wu et al. (2002)
<doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint
approaches using hidden Markov models.
Author: Gabriel Margarido [aut],
Marcelo Mollinari [aut],
Cristiane Taniguti [ctb, cre],
Getulio Ferreira [ctb],
Rodrigo Amadeu [ctb],
Jeekin Lau [ctb],
Karl Broman [ctb],
Katharine Preedy [ctb, cph] ,
Bastian Schiffthaler [ctb, cph] ,
Augusto Garcia [aut, c [...truncated...]
Maintainer: Cristiane Taniguti <cht47@cornell.edu>
Diff between onemap versions 3.0.0 dated 2022-11-25 and 3.2.0 dated 2025-01-10
DESCRIPTION | 25 MD5 | 123 NAMESPACE | 9 R/codif_data.R | 354 - R/cpp_utils.R | 360 - R/create_dataset_bins.R | 297 - R/export_functions.R |only R/filters.R | 324 - R/find_bins.R | 30 R/make_seq.R | 10 R/map.R | 5 R/onemap_read_vcfR.R | 107 R/plot_genome_vs_cm.R |only R/read_mapmaker.R | 658 +- R/return_geno.R | 53 R/rf_graph_table.R | 680 +- R/summary_maps.R |only R/utils.R | 1280 ++-- R/write_haplotypes.R | 1036 +-- R/zzz.R | 32 build/partial.rdb |binary build/vignette.rds |binary data/onemap_example_f2.RData |binary data/simu_example_bc.RData |only data/simu_example_f2.RData |only data/simu_example_out.RData |only inst/doc/Inbred_Based_Populations.R | 1385 ++--- inst/doc/Inbred_Based_Populations.Rmd | 3705 +++++++------ inst/doc/Inbred_Based_Populations.html | 5853 ++++++++++------------ inst/doc/Introduction_R.R | 202 inst/doc/Introduction_R.Rmd | 794 +- inst/doc/Introduction_R.html | 1346 ++--- inst/doc/Outcrossing_Populations.R | 1661 +++--- inst/doc/Outcrossing_Populations.Rmd | 3908 +++++++------- inst/doc/Outcrossing_Populations.html | 7685 ++++++++++++++--------------- inst/doc/Overview.R | 28 inst/doc/Overview.Rmd | 32 inst/doc/Overview.html | 875 +-- inst/extdata/simParall_f2.raw |only inst/extdata/simParall_out.raw |only inst/extdata/simu_cod_f2.vcf.gz |only inst/extdata/simu_cod_out.vcf.gz |only inst/extdata/simu_example_bc.raw |only inst/extdata/simu_example_f2.raw |only inst/extdata/simu_example_out.raw |only inst/extdata/vcf_example_bc.raw |only inst/extdata/vcf_example_bc.vcf.gz |only inst/extdata/vcf_example_bc.vcf.gz.tbi |only inst/extdata/vcf_example_riself.raw |only inst/extdata/vcf_example_riself.vcf.gz |only inst/extdata/vcf_example_riself.vcf.gz.tbi |only man/edit_order_onemap.Rd |only man/export_mappoly_genoprob.Rd |only man/export_viewpoly.Rd |only man/load_onemap_sequences.Rd |only man/onemap_read_vcfR.Rd | 2 man/ord_by_geno.Rd |only man/parents_haplotypes.Rd | 11 man/plot_genome_vs_cm.Rd |only man/remove_inds.Rd | 25 man/save_onemap_sequences.Rd |only man/simu_example_bc.Rd |only man/simu_example_f2.Rd |only man/simu_example_out.Rd |only man/summary_maps_onemap.Rd |only src/Makevars.win | 1 src/twopts_bc.cpp | 4 src/twopts_out.cpp | 4 vignettes/Inbred_Based_Populations.Rmd | 3705 +++++++------ vignettes/Introduction_R.Rmd | 794 +- vignettes/Outcrossing_Populations.Rmd | 3908 +++++++------- vignettes/Overview.Rmd | 32 vignettes/f2_img/map.jpg |binary vignettes/f2_img/mds.jpg |binary vignettes/f2_img/plot.simParallel.jpg |only vignettes/f2_img/rcd.jpg |binary vignettes/f2_img/record.jpg |binary vignettes/f2_img/ug.jpg |binary 78 files changed, 21139 insertions(+), 20204 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates,
and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae
parameterised by Cholesky factors of covariance or precision matrices are implemented
for interval-censored and exact data, or a mix thereof. Score functions for these
log-likelihoods are available. A class representing multiple lower triangular matrices
and corresponding methods are part of this package.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] ,
Martin Maechler [ctb] ,
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.3-2 dated 2024-11-04 and 1.3-3 dated 2025-01-10
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/partial.rdb |binary inst/NEWS.Rd | 13 +++++++++++++ inst/doc/MVT_Rnews.pdf |binary inst/doc/lmvnorm_src.pdf |binary src/miwa.h | 8 +++++++- 7 files changed, 30 insertions(+), 11 deletions(-)
Title: Ratios of Coefficients in the General Linear Model
Description: Performs (simultaneous) inferences for ratios of linear combinations of coefficients in the general linear model, linear mixed model, and for quantiles in a one-way layout. Multiple comparisons and simultaneous confidence interval estimations can be performed for ratios of treatment means in the normal one-way layout with homogeneous and heterogeneous treatment variances, according to Dilba et al. (2007) <https://cran.r-project.org/doc/Rnews/Rnews_2007-1.pdf> and Hasler and Hothorn (2008) <doi:10.1002/bimj.200710466>. Confidence interval estimations for ratios of linear combinations of linear model parameters like in (multiple) slope ratio and parallel line assays can be carried out. Moreover, it is possible to calculate the sample sizes required in comparisons with a control based on relative margins. For the simple two-sample problem, functions for a t-test for ratio-formatted hypotheses and the corresponding confidence interval are provided assuming homogeneous or hetero [...truncated...]
Author: Gemechis Djira [aut],
Mario Hasler [aut],
Daniel Gerhard [aut],
Lawrence Segbehoe [aut],
Frank Schaarschmidt [aut, cre]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>
Diff between mratios versions 1.4.2 dated 2020-06-19 and 1.4.4 dated 2025-01-10
DESCRIPTION | 9 ++++--- MD5 | 22 +++++++++--------- R/ttestratio.R | 8 +++--- data/ASAT.rda |binary data/BW.rda |binary data/Mutagenicity.rda |binary data/SRAssay.rda |binary data/angina.rda |binary data/rat.weight.rda |binary man/mcpqrci.Rd | 8 ++++-- man/sci.ratioVH.Rd | 29 +++--------------------- man/simtest.ratioVH.Rd | 57 ++++++++++++++++++------------------------------- 12 files changed, 51 insertions(+), 82 deletions(-)
Title: Colour Schemes for Scientific Data Visualization
Description: Color schemes ready for each type of data (qualitative,
diverging or sequential), with colors that are distinct for all
people, including color-blind readers. This package provides an
implementation of Paul Tol (2018) and Fabio Crameri (2018)
<doi:10.5194/gmd-11-2541-2018> color schemes for use with 'graphics'
or 'ggplot2'. It provides tools to simulate color-blindness and to
test how well the colors of any palette are identifiable. Several
scientific thematic schemes (geologic timescale, land cover, FAO
soils, etc.) are also implemented.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Vincent Arel-Bundock [ctb] ,
Ulrik Stervbo [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between khroma versions 1.14.0 dated 2024-08-26 and 1.15.0 dated 2025-01-10
khroma-1.14.0/khroma/man/palette_size_range.Rd |only khroma-1.15.0/khroma/DESCRIPTION | 26 +++---- khroma-1.15.0/khroma/MD5 | 44 ++++++------- khroma-1.15.0/khroma/NAMESPACE | 2 khroma-1.15.0/khroma/NEWS.md | 7 ++ khroma-1.15.0/khroma/R/khroma-deprecated.R | 13 +++ khroma-1.15.0/khroma/R/khroma-package.R | 2 khroma-1.15.0/khroma/R/palettes.R | 30 +++++++- khroma-1.15.0/khroma/README.md | 4 - khroma-1.15.0/khroma/build/partial.rdb |binary khroma-1.15.0/khroma/build/vignette.rds |binary khroma-1.15.0/khroma/inst/CITATION | 2 khroma-1.15.0/khroma/inst/doc/crameri.html | 2 khroma-1.15.0/khroma/inst/doc/tol.html | 2 khroma-1.15.0/khroma/inst/examples/ex-palette-continuous.R | 21 ++++++ khroma-1.15.0/khroma/inst/examples/ex-palette-discrete.R | 1 khroma-1.15.0/khroma/inst/tinytest/test_palettes.R | 16 ++-- khroma-1.15.0/khroma/man/khroma-deprecated.Rd | 3 khroma-1.15.0/khroma/man/khroma-package.Rd | 2 khroma-1.15.0/khroma/man/palette_color_continuous.Rd | 23 ++++++ khroma-1.15.0/khroma/man/palette_color_discrete.Rd | 3 khroma-1.15.0/khroma/man/palette_color_picker.Rd | 2 khroma-1.15.0/khroma/man/palette_shape.Rd | 3 khroma-1.15.0/khroma/man/palette_size.Rd |only 24 files changed, 150 insertions(+), 58 deletions(-)
Title: Interactive Forest Plot
Description: Interactive forest plot for clinical trial safety analysis
using 'metalite', 'reactable', 'plotly', and Analysis Data Model (ADaM)
datasets. Includes functionality for adverse event filtering,
incidence-based group filtering, hover-over reveals, and search and sort
operations. The workflow allows for metadata construction, data preparation,
output formatting, and interactive plot generation.
Author: Yilong Zhang [aut],
Benjamin Wang [aut, cre],
Yujie Zhao [aut],
Nan Xiao [ctb],
Hiroaki Fukuda [ctb],
Yulia Sidi [ctb],
Xuan Deng [ctb],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Benjamin Wang <benjamin.wang@merck.com>
Diff between forestly versions 0.1.1 dated 2024-07-08 and 0.1.2 dated 2025-01-10
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 19 ++++++++++++------- R/ae_forestly.R | 16 ++++++++++++---- R/reactable2.R | 2 +- README.md | 7 +++++-- inst/doc/forest-plot-static.html | 8 ++++---- inst/doc/forestly-cran.R | 1 + inst/doc/forestly-cran.Rmd | 1 + inst/doc/forestly-cran.html | 13 +++++++------ man/ae_forestly.Rd | 3 +++ vignettes/forestly-cran.Rmd | 1 + 12 files changed, 62 insertions(+), 39 deletions(-)
Title: DSM and LiDAR downloader
Description: A collection of functions to search and donwload
DSM (Digital Surface Model) and LiDAR (Light Detection and Ranging) data via APIs,
including 'OpenTopography' <https://portal.opentopography.org/apidocs/> and
'TNMAccess' <https://apps.nationalmap.gov/tnmaccess/#/>.
Author: Xiaohao Yang [aut, cre, cph],
Nathan Fox [aut],
Derek Van Berkel [aut],
Mark Lindquist [aut]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>
Diff between dsmSearch versions 1.1.0 dated 2024-12-19 and 1.1.1 dated 2025-01-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/get_lidar.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)