Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-17 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-21 2.3
2022-10-24 2.2
2022-07-18 2.1
Title: Enhanced 'PAM50' Subtyping of Breast Cancer
Description: Accurate classification of breast cancer tumors based on gene expression data is not a trivial task, and it lacks standard practices.The 'PAM50' classifier, which uses 50 gene centroid correlation distances to classify tumors, faces challenges with balancing estrogen receptor (ER) status and gene centering. The 'PCAPAM50' package leverages principal component analysis and iterative 'PAM50' calls to create a gene expression-based ER-balanced subset for gene centering, avoiding the use of protein expression-based ER data resulting into an enhanced Breast Cancer subtyping.
Author: Praveen-Kumar Raj-Kumar [aut, cre, cph],
Boyi Chen [aut],
Ming-Wen Hu [aut],
Tyler Hohenstein [aut],
Jianfang Liu [aut],
Craig D. Shriver [aut],
Xiaoying Lin [aut, cph],
Hai Hu [aut, cph]
Maintainer: Praveen-Kumar Raj-Kumar <p.rajkumar@wriwindber.org>
Diff between PCAPAM50 versions 1.0.1 dated 2024-07-09 and 1.0.2 dated 2024-11-23
DESCRIPTION | 6 MD5 | 27 +- NEWS.md |only R/functions_PCA-PAM50.R | 115 +++++----- README | 2 inst/CITATION | 70 ++++-- inst/PAM50/bioclassifier_R/subtypePrediction_distributed_PNmodified.R | 7 inst/PAM50/bioclassifier_R/subtypePrediction_functions_PNmodified.R | 17 - inst/doc/PCAPAM50_vignette.Rmd | 30 +- inst/doc/PCAPAM50_vignette.html | 34 +- man/makeCalls.PC1ihc.Rd | 6 man/makeCalls.ihc.Rd | 6 man/makeCalls.v1PAM.Rd | 10 tests/testthat/test-functions_PCA-PAM50.R | 10 vignettes/PCAPAM50_vignette.Rmd | 30 +- 15 files changed, 210 insertions(+), 160 deletions(-)
Title: Database Storage of Genotype Probabilities for QTL Mapping
Description: Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time.
Author: Karl W Broman [aut, cre] ,
Brian S Yandell [aut] ,
Petr Simecek [aut]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2fst versions 0.28 dated 2024-07-16 and 0.30 dated 2024-11-23
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 7 +++++++ R/fst_path.R | 2 +- README.md | 2 +- build/vignette.rds |binary inst/doc/qtl2fst.html | 4 ++-- man/fst_restore.Rd | 4 ++-- man/probs2fst.Rd | 4 ++-- man/replace_path.Rd | 2 +- 10 files changed, 29 insertions(+), 22 deletions(-)
Title: Spatial Prediction Tools
Description: Methods for spatial predictive modeling, especially for spatial distribution models. This includes algorithms for model fitting and prediction, as well as methods for model evaluation.
Author: Robert J. Hijmans [cre, aut] ,
Steven Phillips [ctb],
Marcia Barbosa [ctb],
Chris Brunsdon [ctb],
Barry Rowlingson [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between predicts versions 0.1-16 dated 2024-10-07 and 0.1-17 dated 2024-11-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/divpol.R | 4 ++-- build/partial.rdb |binary man/maxent.Rd | 2 -- 5 files changed, 10 insertions(+), 12 deletions(-)
Title: Differential Evolution Optimization in Pure R
Description: Differential Evolution (DE) stochastic heuristic algorithms for
global optimization of problems with and without general constraints.
The aim is to curate a collection of its variants that
(1) do not sacrifice simplicity of design,
(2) are essentially tuning-free, and
(3) can be efficiently implemented directly in the R language.
Currently, it provides implementations of the algorithms 'jDE' by
Brest et al. (2006) <doi:10.1109/TEVC.2006.872133> for single-objective
optimization and 'NCDE' by Qu et al. (2012) <doi:10.1109/TEVC.2011.2161873>
for multimodal optimization (single-objective problems with
multiple solutions).
Author: Eduardo L. T. Conceicao [aut, cre],
Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Diff between DEoptimR versions 1.1-3 dated 2023-10-07 and 1.1-3-1 dated 2024-11-23
DESCRIPTION | 13 +++++++------ MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Download Forestry Data
Description: Functions for downloading forestry and land use data for use in spatial analysis. This packages offers a user-friendly solution to quickly obtain datasets such as forest height, forest types, tree species under various climate change scenarios, or land use data among others.
Author: Adrian Cidre Gonzalez [aut, cre]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between forestdata versions 0.1.0 dated 2024-09-10 and 0.2.0 dated 2024-11-23
forestdata-0.1.0/forestdata/R/canopy_height.R |only forestdata-0.1.0/forestdata/R/chorological_maps.R |only forestdata-0.1.0/forestdata/R/forest_country.R |only forestdata-0.1.0/forestdata/R/forest_inventory.R |only forestdata-0.1.0/forestdata/R/global_land_cover.R |only forestdata-0.1.0/forestdata/R/land_cover_explorer.R |only forestdata-0.1.0/forestdata/R/utils_notExported.R |only forestdata-0.2.0/forestdata/DESCRIPTION | 18 forestdata-0.2.0/forestdata/MD5 | 120 ++-- forestdata-0.2.0/forestdata/NAMESPACE | 42 - forestdata-0.2.0/forestdata/NEWS.md | 60 +- forestdata-0.2.0/forestdata/R/GLAD.R | 295 ++++++++-- forestdata-0.2.0/forestdata/R/allometry.R |only forestdata-0.2.0/forestdata/R/canopy-height.R |only forestdata-0.2.0/forestdata/R/chorological-maps.R |only forestdata-0.2.0/forestdata/R/eutrees4f.R | 34 - forestdata-0.2.0/forestdata/R/forest-country.R |only forestdata-0.2.0/forestdata/R/forest-inventory.R |only forestdata-0.2.0/forestdata/R/forestdata-package.R |only forestdata-0.2.0/forestdata/R/globals.R | 4 forestdata-0.2.0/forestdata/R/land-cover.R |only forestdata-0.2.0/forestdata/R/pathogens.R | 35 - forestdata-0.2.0/forestdata/R/sysdata.rda |binary forestdata-0.2.0/forestdata/R/utils-not-exported.R |only forestdata-0.2.0/forestdata/README.md | 18 forestdata-0.2.0/forestdata/build |only forestdata-0.2.0/forestdata/data/metadata_forestdata.rda |binary forestdata-0.2.0/forestdata/man/create_mfe50_table.Rd | 38 - forestdata-0.2.0/forestdata/man/fd_allometry_tallo.Rd |only forestdata-0.2.0/forestdata/man/fd_canopy_height.Rd | 129 ++-- forestdata-0.2.0/forestdata/man/fd_canopy_height_eth.Rd |only forestdata-0.2.0/forestdata/man/fd_canopy_height_meta.Rd |only forestdata-0.2.0/forestdata/man/fd_forest_chorological.Rd | 109 +-- forestdata-0.2.0/forestdata/man/fd_forest_eutrees4f.Rd | 244 ++++---- forestdata-0.2.0/forestdata/man/fd_forest_extent_glad.Rd | 125 ++-- forestdata-0.2.0/forestdata/man/fd_forest_france.Rd | 166 ++--- forestdata-0.2.0/forestdata/man/fd_forest_glad.Rd |only forestdata-0.2.0/forestdata/man/fd_forest_spain_mfe50.Rd | 87 +- forestdata-0.2.0/forestdata/man/fd_inventory_spain.Rd | 105 +-- forestdata-0.2.0/forestdata/man/fd_landcover_copernicus.Rd | 182 ++---- forestdata-0.2.0/forestdata/man/fd_landcover_esri.Rd | 72 +- forestdata-0.2.0/forestdata/man/fd_pathogens_defid2.Rd | 150 ++--- forestdata-0.2.0/forestdata/man/fdi_download_7zip.Rd | 70 +- forestdata-0.2.0/forestdata/man/fdi_download_raster.Rd | 40 - forestdata-0.2.0/forestdata/man/fdi_download_unzip.Rd | 70 +- forestdata-0.2.0/forestdata/man/fdi_fix_names.Rd | 38 - forestdata-0.2.0/forestdata/man/figures/functions_gt.png |binary forestdata-0.2.0/forestdata/man/figures/lifecycle-deprecated.svg |only forestdata-0.2.0/forestdata/man/figures/lifecycle-experimental.svg |only forestdata-0.2.0/forestdata/man/figures/lifecycle-stable.svg |only forestdata-0.2.0/forestdata/man/figures/lifecycle-superseded.svg |only forestdata-0.2.0/forestdata/man/forestdata-package.Rd |only forestdata-0.2.0/forestdata/man/get_bdforet_tbl.Rd | 32 - forestdata-0.2.0/forestdata/man/get_chorological_tbl.Rd | 34 - forestdata-0.2.0/forestdata/man/get_combined_raster.Rd | 34 - forestdata-0.2.0/forestdata/man/get_combined_raster_2l.Rd | 34 - forestdata-0.2.0/forestdata/man/get_eutrees4f_tbl.Rd | 34 - forestdata-0.2.0/forestdata/man/get_forest_extent_tbl.Rd | 38 - forestdata-0.2.0/forestdata/man/get_gch_tbl.Rd | 41 - forestdata-0.2.0/forestdata/man/get_glad_tiles.Rd |only forestdata-0.2.0/forestdata/man/get_glc_tbl.Rd | 44 - forestdata-0.2.0/forestdata/man/get_landcoverexplorer_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/get_meta_tiles.Rd |only forestdata-0.2.0/forestdata/man/get_mfe50_ccaa_tbl.Rd | 32 - forestdata-0.2.0/forestdata/man/get_mfe50_provinces_tbl.Rd | 32 - forestdata-0.2.0/forestdata/man/get_spain_ifn2_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/get_spain_ifn3_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/get_spain_ifn4_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/get_spain_ifn_metadata_tbl.Rd | 30 - forestdata-0.2.0/forestdata/man/metadata_forestdata.Rd | 48 - forestdata-0.2.0/forestdata/tests/testthat/test-GLAD.R |only forestdata-0.2.0/forestdata/tests/testthat/test-allometry.R |only forestdata-0.2.0/forestdata/tests/testthat/test-canopy-height.R |only forestdata-0.2.0/forestdata/tests/testthat/test-chorological-maps.R |only forestdata-0.2.0/forestdata/tests/testthat/test-eutrees4f.R |only forestdata-0.2.0/forestdata/tests/testthat/test-forest-country.R |only forestdata-0.2.0/forestdata/tests/testthat/test-forest-inventory.R |only forestdata-0.2.0/forestdata/tests/testthat/test-land-cover.R |only forestdata-0.2.0/forestdata/tests/testthat/test-pathogens.R |only 79 files changed, 1565 insertions(+), 1239 deletions(-)
Title: Phase Portraits of Functions in the Complex Number Plane
Description: Functionality for creating phase portraits of functions in the
complex number plane. Works with R base graphics, whose full
functionality is available. Parallel processing is used for optimum
performance.
Author: Peter Biber [aut, cre]
Maintainer: Peter Biber <castor.fiber@gmx.de>
Diff between viscomplexr versions 1.1.1 dated 2021-09-18 and 1.1.2 dated 2024-11-23
DESCRIPTION | 14 MD5 | 18 NEWS.md | 24 R/VisComplex.R | 2 README.md | 10 build/partial.rdb |binary build/vignette.rds |binary inst/doc/viscomplexr-vignette.R | 792 +++++++------- inst/doc/viscomplexr-vignette.html | 2073 ++++++++++++++++++++++++++----------- man/phasePortrait.Rd | 2 10 files changed, 1938 insertions(+), 997 deletions(-)
Title: Creating and Significance Testing Language Features for
Visualisation
Description: Implements differential language analysis with statistical tests and offers various language visualization techniques for n-grams and topics. It also supports the 'text' package. For more information, visit <https://r-topics.org/> and <https://www.r-text.org/>.
Author: Leon Ackermann [aut] ,
Zhuojun Gu [aut] ,
Oscar Kjell [aut, cre]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between topics versions 0.20.0 dated 2024-11-22 and 0.21.0 dated 2024-11-23
DESCRIPTION | 10 +- MD5 | 25 ++--- NAMESPACE | 5 - R/0_globals.R | 5 - R/main.R | 169 +++++++++++++++++++++++++++++++++- R/utils.R | 16 ++- R/wordclouds.R | 25 +++++ README.md | 9 - man/topicsDtmEval.Rd |only tests/testthat/test_1_1_topicsGrams.R | 4 tests/testthat/test_1_2_topicsDtm.R | 1 tests/testthat/test_1_4_topicsPreds.R | 4 tests/testthat/test_1_5_topicsTest.R | 4 tests/testthat/test_1_6_topicsPlot.R | 6 - 14 files changed, 234 insertions(+), 49 deletions(-)
Title: Computing f-Statistics and Building Admixture Graphs Based on
Allele Count or Pool-Seq Read Count Data
Description: Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, Patterson's F2, F3, F3*, F4 and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in TreeMix, BayPass and SelEstim format).
Author: Mathieu Gautier [aut, cre]
Maintainer: Mathieu Gautier <mathieu.gautier@inrae.fr>
Diff between poolfstat versions 2.2.0 dated 2023-09-06 and 3.0.0 dated 2024-11-23
poolfstat-2.2.0/poolfstat/man/compute_Ddenom.Rd |only poolfstat-2.2.0/poolfstat/man/compute_Ddenom_bjmeans.Rd |only poolfstat-2.2.0/poolfstat/man/compute_F2_bjmeans.Rd |only poolfstat-2.2.0/poolfstat/man/compute_Q_bjmeans.Rd |only poolfstat-2.2.0/poolfstat/src/fast_block_averages.cpp |only poolfstat-3.0.0/poolfstat/ChangeLog | 15 poolfstat-3.0.0/poolfstat/DESCRIPTION | 19 poolfstat-3.0.0/poolfstat/MD5 | 76 + poolfstat-3.0.0/poolfstat/NAMESPACE | 21 poolfstat-3.0.0/poolfstat/R/RcppExports.R | 357 +++++++- poolfstat-3.0.0/poolfstat/R/add.leaf.R | 2 poolfstat-3.0.0/poolfstat/R/compute.F4ratio.R | 16 poolfstat-3.0.0/poolfstat/R/compute.pairwiseFST.R | 222 ++--- poolfstat-3.0.0/poolfstat/R/computeFST.R | 400 +++++----- poolfstat-3.0.0/poolfstat/R/countdata2genobaypass.R |only poolfstat-3.0.0/poolfstat/R/generate.graph.params.R | 2 poolfstat-3.0.0/poolfstat/R/graph.params2qpGraphFiles.R | 2 poolfstat-3.0.0/poolfstat/R/is.fitted.graph.R | 3 poolfstat-3.0.0/poolfstat/R/poolfstat-package.R | 8 poolfstat-3.0.0/poolfstat/R/sim.readcounts.R |only poolfstat-3.0.0/poolfstat/R/sliding.windows.fstat.R |only poolfstat-3.0.0/poolfstat/build/vignette.rds |binary poolfstat-3.0.0/poolfstat/inst/CITATION | 8 poolfstat-3.0.0/poolfstat/inst/doc/vignette.pdf |binary poolfstat-3.0.0/poolfstat/man/add.leaf.Rd | 2 poolfstat-3.0.0/poolfstat/man/block_sum.Rd |only poolfstat-3.0.0/poolfstat/man/block_sum2.Rd |only poolfstat-3.0.0/poolfstat/man/compute.f4ratio.Rd | 6 poolfstat-3.0.0/poolfstat/man/compute.pairwiseFST.Rd | 2 poolfstat-3.0.0/poolfstat/man/computeFST.Rd | 27 poolfstat-3.0.0/poolfstat/man/compute_snpFstAov.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpHierFstAov.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ1.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ1onepop.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ1rw.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ2.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ2onepair.Rd |only poolfstat-3.0.0/poolfstat/man/compute_snpQ2w.Rd |only poolfstat-3.0.0/poolfstat/man/countdata2genobaypass.Rd |only poolfstat-3.0.0/poolfstat/man/fitted.graph-class.Rd | 1 poolfstat-3.0.0/poolfstat/man/generate.graph.params.Rd | 2 poolfstat-3.0.0/poolfstat/man/graph.params2qpGraphFiles.Rd | 2 poolfstat-3.0.0/poolfstat/man/poolfstat.Rd | 7 poolfstat-3.0.0/poolfstat/man/sim.readcounts.Rd |only poolfstat-3.0.0/poolfstat/man/simureads_mono.Rd |only poolfstat-3.0.0/poolfstat/man/simureads_poly.Rd |only poolfstat-3.0.0/poolfstat/man/sliding.windows.fstat.Rd |only poolfstat-3.0.0/poolfstat/src/RcppExports.cpp | 190 +++- poolfstat-3.0.0/poolfstat/src/fst_utils.cpp |only poolfstat-3.0.0/poolfstat/src/fstats_utils.cpp |only poolfstat-3.0.0/poolfstat/src/simulate.readcounts.utils.cpp |only poolfstat-3.0.0/poolfstat/vignettes/poolfstat_vignette_6pops.pdf |binary 52 files changed, 911 insertions(+), 479 deletions(-)
Title: Estimate Bayesian Multilevel Models for Compositional Data
Description: Implement Bayesian Multilevel Modelling for compositional data
in a multilevel framework. Compute multilevel compositional data and
Isometric log ratio (ILR) at between and within-person levels,
fit Bayesian multilevel models for compositional predictors and outcomes,
and run post-hoc analyses such as isotemporal substitution models.
References:
Le, Stanford, Dumuid, and Wiley (2024) <doi:10.48550/arXiv.2405.03985>,
Le, Dumuid, Stanford, and Wiley (2024) <doi:10.48550/arXiv.2411.12407>.
Author: Flora Le [aut, cre] ,
Joshua F. Wiley [aut]
Maintainer: Flora Le <floralebui@gmail.com>
Diff between multilevelcoda versions 1.3.0.2 dated 2024-07-09 and 1.3.1 dated 2024-11-23
multilevelcoda-1.3.0.2/multilevelcoda/R/basesub.R |only multilevelcoda-1.3.0.2/multilevelcoda/man/basesub.Rd |only multilevelcoda-1.3.1/multilevelcoda/DESCRIPTION | 19 multilevelcoda-1.3.1/multilevelcoda/MD5 | 99 - multilevelcoda-1.3.1/multilevelcoda/NAMESPACE | 12 multilevelcoda-1.3.1/multilevelcoda/NEWS.md | 44 multilevelcoda-1.3.1/multilevelcoda/R/brmcoda.R | 6 multilevelcoda-1.3.1/multilevelcoda/R/build.R |only multilevelcoda-1.3.1/multilevelcoda/R/coef.R |only multilevelcoda-1.3.1/multilevelcoda/R/complr-methods.R | 12 multilevelcoda-1.3.1/multilevelcoda/R/complr.R | 15 multilevelcoda-1.3.1/multilevelcoda/R/internal.R | 17 multilevelcoda-1.3.1/multilevelcoda/R/pivot-coord.R |only multilevelcoda-1.3.1/multilevelcoda/R/substitution-bsub.R | 7 multilevelcoda-1.3.1/multilevelcoda/R/substitution-bsubmargins.R | 3 multilevelcoda-1.3.1/multilevelcoda/R/substitution-helpers.R | 593 +++++----- multilevelcoda-1.3.1/multilevelcoda/R/substitution-sub-margins.R | 10 multilevelcoda-1.3.1/multilevelcoda/R/substitution-wsub.R | 7 multilevelcoda-1.3.1/multilevelcoda/R/substitution-wsubmargins.R | 3 multilevelcoda-1.3.1/multilevelcoda/R/substitution.R | 167 +- multilevelcoda-1.3.1/multilevelcoda/R/summary.R | 100 + multilevelcoda-1.3.1/multilevelcoda/R/update.R | 44 multilevelcoda-1.3.1/multilevelcoda/README.md | 29 multilevelcoda-1.3.1/multilevelcoda/build/vignette.rds |binary multilevelcoda-1.3.1/multilevelcoda/inst/doc/A-introduction.html | 8 multilevelcoda-1.3.1/multilevelcoda/inst/doc/B-composition-MLM.html | 2 multilevelcoda-1.3.1/multilevelcoda/inst/doc/C-composition-MMLM.html | 2 multilevelcoda-1.3.1/multilevelcoda/inst/doc/D-substitution.html | 8 multilevelcoda-1.3.1/multilevelcoda/inst/doc/E-simmodel-diag.Rmd | 2 multilevelcoda-1.3.1/multilevelcoda/inst/doc/E-simmodel-diag.html | 13 multilevelcoda-1.3.1/multilevelcoda/man/bsub.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/bsubmargins.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/build.basesub.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/build.sbp.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/complr.Rd | 2 multilevelcoda-1.3.1/multilevelcoda/man/pivot_coord.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/pivot_coord_refit.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/pivot_coord_rotate.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/sub.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/submargins.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/substitution.Rd | 24 multilevelcoda-1.3.1/multilevelcoda/man/summary.complr.Rd | 3 multilevelcoda-1.3.1/multilevelcoda/man/summary.pivot_coord.Rd |only multilevelcoda-1.3.1/multilevelcoda/man/var.complr.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/wsub.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/man/wsubmargins.Rd | 8 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-brmcoda.R | 2 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-bsub.R | 24 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-bsubmargins.R | 24 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-submargins.R | 20 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-substitution.R | 12 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-update.R | 76 - multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-wsub.R | 24 multilevelcoda-1.3.1/multilevelcoda/tests/testthat/test-wsubmargins.R | 24 multilevelcoda-1.3.1/multilevelcoda/vignettes/E-simmodel-diag.Rmd | 2 multilevelcoda-1.3.1/multilevelcoda/vignettes/E-simmodel-diag.Rmd.orig | 2 56 files changed, 885 insertions(+), 632 deletions(-)
More information about multilevelcoda at CRAN
Permanent link
Title: Junction Tree Inference
Description: Minimal and memory efficient implementation of the junction tree
algorithm using the Lauritzen-Spiegelhalter scheme;
S. L. Lauritzen and D. J. Spiegelhalter (1988)
<https://www.jstor.org/stable/2345762?seq=1>. The jti package is
part of the paper <doi:10.18637/jss.v111.i02>.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <madslindskou@gmail.com>
Diff between jti versions 0.8.4 dated 2022-04-12 and 1.0.0 dated 2024-11-23
DESCRIPTION | 14 MD5 | 53 +- NAMESPACE | 15 NEWS.md | 9 R/api_compile.R | 7 R/api_jt.R | 18 R/helper_elimination_game.R | 6 R/helper_jt.R | 4 README.md | 30 - build/vignette.rds |binary inst/CITATION |only inst/doc/using_jti.R | 16 inst/doc/using_jti.Rmd | 8 inst/doc/using_jti.html | 653 ++++++++++++++++-------------- man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-22-1.png |binary man/figures/README-unnamed-chunk-23-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/jt.Rd | 8 man/jti-package.Rd | 2 man/par_lvs.Rd | 18 man/send_messages.Rd | 4 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 vignettes/using_jti.Rmd | 8 28 files changed, 489 insertions(+), 393 deletions(-)
Title: Computing a New Informative Distribution Set of Asset Returns
Description: Estimation of the most-left informative set of gross returns
(i.e., the informative set).
The procedure to compute the informative set adjusts the method
proposed by
Mariani et al. (2022a) <doi:10.1007/s11205-020-02440-6>
and
Mariani et al. (2022b) <doi:10.1007/s10287-022-00422-2>
to gross returns of financial assets.
This is accomplished through an adaptive algorithm
that identifies sub-groups of gross returns in
each iteration by approximating their distribution with a
sequence of two-component log-normal mixtures.
These sub-groups emerge when a significant change
in the distribution occurs below the median of the
financial returns, with their boundary termed as
the “change point" of the mixture.
The process concludes when no further change points are detected.
The outcome encompasses parameters of the leftmost mixture
distributions and change points of the
analyzed financial time series.
The functionalities of the INFOSET package include: (i) modelling asset distribution [...truncated...]
Author: Gloria Polinesi [aut, cre],
Francesca Mariani [aut],
Maria Cristina Recchioni [aut]
Maintainer: Gloria Polinesi <g.polinesi@staff.univpm.it>
Diff between INFOSET versions 4.0.6 dated 2024-09-06 and 4.1 dated 2024-11-23
DESCRIPTION | 14 MD5 | 25 - NAMESPACE | 11 R/my_functions.R | 898 ++++++++++++++++++++++--------------- build |only inst |only man/LR_cp.Rd |only man/create_overlapping_windows.Rd |only man/infoset.Rd | 335 ------------- man/plot_LR_cp.Rd |only man/plot_ptf.Rd |only man/ptf_construction.Rd |only man/summary_ptf.Rd |only man/tail_mixture.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-my_functions.R | 8 vignettes |only 17 files changed, 607 insertions(+), 688 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic, robust and
programmer friendly. Core functionality includes a rich set of S3 generic grouped
and weighted statistical functions for vectors, matrices and data frames, which
provide efficient low-level vectorizations, OpenMP multithreading, and skip missing
values by default. These are integrated with fast grouping and ordering algorithms
(also callable from C), and efficient data manipulation functions. The package also
provides a flexible and rigorous approach to time series and panel data in R.
It further includes fast functions for common statistical procedures, detailed
(grouped, weighted) summary statistics, powerful tools to work with nested data,
fast data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data.
It is well integrated with base R classes, 'dplyr'/' [...truncated...]
Author: Sebastian Krantz [aut, cre] ,
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 2.0.17 dated 2024-11-03 and 2.0.18 dated 2024-11-23
DESCRIPTION | 8 +++---- MD5 | 28 ++++++++++++------------- NEWS.md | 8 +++++++ R/GRP.R | 5 ++-- R/pivot.R | 2 + inst/doc/collapse_and_sf.html | 4 +-- inst/doc/collapse_documentation.html | 4 +-- inst/doc/collapse_for_tidyverse_users.html | 6 ++--- inst/doc/collapse_object_handling.html | 6 ++--- src/data.table_subset.c | 4 ++- src/data.table_utils.c | 15 +++---------- src/kit.h | 2 - src/kit_dup.c | 32 ++++++++++++++--------------- src/pivot.c | 2 - tests/testthat/test-miscellaneous-issues.R | 4 +++ 15 files changed, 70 insertions(+), 60 deletions(-)
Title: Allelic Series Test
Description: Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1016/j.ajhg.2023.07.001>.
Author: Zachary McCaw [aut, cre] ,
Christoph Klein [ctb] ,
Thomas Soare [ctb] ,
Jianhui Gao [ctb] ,
insitro [cph]
Maintainer: Zachary McCaw <zmccaw@insitro.com>
Diff between AllelicSeries versions 0.1.1.1 dated 2024-11-21 and 0.1.1.2 dated 2024-11-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test-data_generation.R | 5 +++-- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Hierarchical Partitioning of R2 for Phylogenetic Linear
Regression
Description: Conducts hierarchical partitioning to calculate individual contributions of phylogenetic tree and predictors (groups) towards total R2 for phylogenetic linear regression models.
Author: Jiangshan Lai [aut, cre] ,
Gang Wang [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between phylolm.hp versions 0.0-1 dated 2024-11-13 and 0.0-2 dated 2024-11-23
phylolm.hp-0.0-1/phylolm.hp/R/phylolmhp.r |only phylolm.hp-0.0-1/phylolm.hp/man/phylolm.hp.Rd |only phylolm.hp-0.0-2/phylolm.hp/DESCRIPTION | 10 - phylolm.hp-0.0-2/phylolm.hp/MD5 | 10 - phylolm.hp-0.0-2/phylolm.hp/NAMESPACE | 1 phylolm.hp-0.0-2/phylolm.hp/R/phyloglmhp.r | 155 +++++++++++++++++++------ phylolm.hp-0.0-2/phylolm.hp/man/phyloglm.hp.Rd | 30 +++- 7 files changed, 152 insertions(+), 54 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with
interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3learners versions 0.8.0 dated 2024-10-25 and 0.9.0 dated 2024-11-23
DESCRIPTION | 6 +- MD5 | 68 ++++++++++++------------- NEWS.md | 6 ++ R/LearnerClassifLogReg.R | 8 -- R/LearnerClassifMultinom.R | 8 -- R/LearnerClassifRanger.R | 19 +++++- R/LearnerRegrLM.R | 8 -- R/LearnerRegrRanger.R | 6 +- R/helpers.R | 10 --- build/partial.rdb |binary inst/paramtest/test_paramtest_classif.ranger.R | 1 man/mlr_learners_classif.cv_glmnet.Rd | 1 man/mlr_learners_classif.glmnet.Rd | 1 man/mlr_learners_classif.kknn.Rd | 1 man/mlr_learners_classif.lda.Rd | 1 man/mlr_learners_classif.log_reg.Rd | 12 ---- man/mlr_learners_classif.multinom.Rd | 12 ---- man/mlr_learners_classif.naive_bayes.Rd | 1 man/mlr_learners_classif.nnet.Rd | 3 - man/mlr_learners_classif.qda.Rd | 1 man/mlr_learners_classif.ranger.Rd | 17 +++--- man/mlr_learners_classif.svm.Rd | 1 man/mlr_learners_classif.xgboost.Rd | 2 man/mlr_learners_regr.cv_glmnet.Rd | 1 man/mlr_learners_regr.glmnet.Rd | 1 man/mlr_learners_regr.kknn.Rd | 1 man/mlr_learners_regr.km.Rd | 1 man/mlr_learners_regr.lm.Rd | 12 ---- man/mlr_learners_regr.nnet.Rd | 3 - man/mlr_learners_regr.ranger.Rd | 15 +++-- man/mlr_learners_regr.svm.Rd | 1 man/mlr_learners_regr.xgboost.Rd | 2 tests/testthat/test_regr_lm.R | 2 tests/testthat/test_regr_ranger.R | 2 tests/testthat/test_regr_xgboost.R | 2 35 files changed, 110 insertions(+), 126 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-22 0.3.0
2024-09-19 0.2.0
2024-09-05 0.1.0
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 3.0.1 dated 2024-10-22 and 3.0.2 dated 2024-11-23
nlmixr2est-3.0.1/nlmixr2est/R/preProcessModel.R |only nlmixr2est-3.0.2/nlmixr2est/DESCRIPTION | 6 - nlmixr2est-3.0.2/nlmixr2est/MD5 | 46 ++++++---- nlmixr2est-3.0.2/nlmixr2est/NAMESPACE | 6 + nlmixr2est-3.0.2/nlmixr2est/NEWS.md | 12 ++ nlmixr2est-3.0.2/nlmixr2est/R/bobyqa.R | 4 nlmixr2est-3.0.2/nlmixr2est/R/hook.R |only nlmixr2est-3.0.2/nlmixr2est/R/lbfgsb3c.R | 3 nlmixr2est-3.0.2/nlmixr2est/R/n1qn1.R | 3 nlmixr2est-3.0.2/nlmixr2est/R/newuoa.R | 3 nlmixr2est-3.0.2/nlmixr2est/R/nlm.R | 3 nlmixr2est-3.0.2/nlmixr2est/R/nlminb.R | 4 nlmixr2est-3.0.2/nlmixr2est/R/nlmixr2.R | 9 + nlmixr2est-3.0.2/nlmixr2est/R/nlmixr2_md5.R | 2 nlmixr2est-3.0.2/nlmixr2est/R/nls.R | 2 nlmixr2est-3.0.2/nlmixr2est/R/optim.R | 4 nlmixr2est-3.0.2/nlmixr2est/R/preProcessDataUi.R |only nlmixr2est-3.0.2/nlmixr2est/R/preProcessLiteralFix.R |only nlmixr2est-3.0.2/nlmixr2est/R/preProcessZeroOmega.R |only nlmixr2est-3.0.2/nlmixr2est/R/uobyqa.R | 3 nlmixr2est-3.0.2/nlmixr2est/inst/tools/workaround.R | 22 +++- nlmixr2est-3.0.2/nlmixr2est/man/dot-nlmixrPreprocessLiteralFix.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/dot-preProcessDataUi.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/dot-preProcessZeroOmega.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/figures/README-example-1.png |binary nlmixr2est-3.0.2/nlmixr2est/man/preProcessHooks.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/preProcessHooksAdd.Rd |only nlmixr2est-3.0.2/nlmixr2est/man/preProcessHooksRm.Rd |only nlmixr2est-3.0.2/nlmixr2est/src/inner.cpp | 8 + nlmixr2est-3.0.2/nlmixr2est/tests/testthat/test-omega-boundary.R |only 30 files changed, 96 insertions(+), 44 deletions(-)