Title: Computation and Visualization of Package Download Counts and
Percentile Ranks
Description: Compute and visualize package download counts and percentile ranks
from Posit/RStudio's CRAN mirror.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>
Diff between packageRank versions 0.9.6 dated 2025-05-01 and 0.9.7 dated 2025-10-14
packageRank-0.9.6/packageRank/R/annualDownloads.R |only packageRank-0.9.7/packageRank/DESCRIPTION | 16 packageRank-0.9.7/packageRank/MD5 | 85 - packageRank-0.9.7/packageRank/NAMESPACE | 16 packageRank-0.9.7/packageRank/NEWS.md | 42 packageRank-0.9.7/packageRank/R/annualPlot.R |only packageRank-0.9.7/packageRank/R/bioconductorDownloads.R | 12 packageRank-0.9.7/packageRank/R/countryDistribution.R | 25 packageRank-0.9.7/packageRank/R/countryPackage.R | 42 packageRank-0.9.7/packageRank/R/cranDownloads.R | 40 packageRank-0.9.7/packageRank/R/cranDownloadsA.R | 16 packageRank-0.9.7/packageRank/R/cranDownloadsB.R | 16 packageRank-0.9.7/packageRank/R/cranDownloadsPlotFunctions.R | 774 ++++++---- packageRank-0.9.7/packageRank/R/cranDownloadsPlotSmoother.R | 146 - packageRank-0.9.7/packageRank/R/data.R | 7 packageRank-0.9.7/packageRank/R/fetchLog.R | 10 packageRank-0.9.7/packageRank/R/filteredDownloads.R | 24 packageRank-0.9.7/packageRank/R/gg_axis.annotation_polygon.R |only packageRank-0.9.7/packageRank/R/importFrom.R | 7 packageRank-0.9.7/packageRank/R/ipPackage.R | 42 packageRank-0.9.7/packageRank/R/logInfo.R | 33 packageRank-0.9.7/packageRank/R/missingDatesPolygons.R |only packageRank-0.9.7/packageRank/R/packageCountry.R | 15 packageRank-0.9.7/packageRank/R/packageDistribution.R | 4 packageRank-0.9.7/packageRank/R/packageHistory.R | 8 packageRank-0.9.7/packageRank/R/packageLog.R | 42 packageRank-0.9.7/packageRank/R/packageRank-package.R | 1 packageRank-0.9.7/packageRank/R/packageRank.R | 4 packageRank-0.9.7/packageRank/R/packageVersionPercent.R | 8 packageRank-0.9.7/packageRank/R/populationPlot.R | 2 packageRank-0.9.7/packageRank/R/topCountry.R | 11 packageRank-0.9.7/packageRank/R/versionFilter.R |only packageRank-0.9.7/packageRank/R/versionPlot.R | 12 packageRank-0.9.7/packageRank/R/weeklyDownloads.R | 18 packageRank-0.9.7/packageRank/README.md | 57 packageRank-0.9.7/packageRank/data/missing.dates.rda |only packageRank-0.9.7/packageRank/man/annualPlot.Rd |only packageRank-0.9.7/packageRank/man/countryDistribution.Rd | 13 packageRank-0.9.7/packageRank/man/countryPackage.Rd | 17 packageRank-0.9.7/packageRank/man/figures/README-missing-1.png |only packageRank-0.9.7/packageRank/man/filteredDownloads.Rd | 14 packageRank-0.9.7/packageRank/man/ipPackage.Rd | 13 packageRank-0.9.7/packageRank/man/logInfo.Rd | 5 packageRank-0.9.7/packageRank/man/missing.dates.Rd |only packageRank-0.9.7/packageRank/man/packageCountry.Rd | 13 packageRank-0.9.7/packageRank/man/packageLog.Rd | 6 packageRank-0.9.7/packageRank/man/packageRank-package.Rd | 1 packageRank-0.9.7/packageRank/man/plot.cranDownloads.Rd | 2 48 files changed, 922 insertions(+), 697 deletions(-)
Title: Exponential-Family Random Network Models
Description: Estimation of fully and partially observed Exponential-Family Random Network Models (ERNM). Exponential-family Random Graph Models (ERGM) and Gibbs Fields are special cases of ERNMs and can also be estimated with the package. Please cite Fellows and Handcock (2012), "Exponential-family Random Network Models" available at <doi:10.48550/arXiv.1208.0121>.
Author: Ian Fellows [aut],
Duncan Clark [aut, cre]
Maintainer: Duncan Clark <dac6@williams.edu>
Diff between ernm versions 1.0.3 dated 2025-10-06 and 1.0.4 dated 2025-10-14
ernm-1.0.3/ernm/R/00-classes.R |only ernm-1.0.4/ernm/DESCRIPTION | 8 +-- ernm-1.0.4/ernm/MD5 | 23 ++++---- ernm-1.0.4/ernm/R/ernm-gof.R | 9 ++- ernm-1.0.4/ernm/R/ernm.R | 2 ernm-1.0.4/ernm/R/zzz.R | 2 ernm-1.0.4/ernm/inst/include/Model.h | 60 ++++++++++++++++++++--- ernm-1.0.4/ernm/man/createCppSampler.Rd | 1 ernm-1.0.4/ernm/man/ernm.Rd | 3 - ernm-1.0.4/ernm/man/ernm_gof.Rd | 5 + ernm-1.0.4/ernm/src/RcppModule.cpp | 2 ernm-1.0.4/ernm/tests/testthat/test-model.R | 69 ++++++++++++++++++++++++++ ernm-1.0.4/ernm/tests/testthat/test-stats.R | 73 ++++++++++++++++++++++++++-- 13 files changed, 221 insertions(+), 36 deletions(-)
Title: Multi-Modal Immune Repertoire Analytics for Immunotherapy and
Vaccine Design in R
Description: A comprehensive analytics framework for building reproducible pipelines on T-cell and B-cell immune receptor repertoire data.
Delivers multi-modal immune profiling (bulk, single-cell, CITE-seq/AbSeq, spatial, immunogenicity data),
feature engineering (ML-ready feature tables and matrices), and biomarker discovery workflows
(cohort comparisons, longitudinal tracking, repertoire similarity, enrichment).
Provides a user-friendly interface to widely used AIRR methods —
clonality/diversity, V(D)J usage, similarity, annotation, tracking, and many more.
Think Scanpy or Seurat, but for AIRR data, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq, RepSeq, or
VDJ sequencing data. A successor to our previously published "tcR" R package (Nazarov 2015).
Author: Vadim I. Nazarov [aut, cre] ,
Vasily O. Tsvetkov [aut],
Aleksandr A. Popov [aut],
Ivan Balashov [aut]
Maintainer: Vadim I. Nazarov <support@immunomind.com>
Diff between immunarch versions 0.9.1 dated 2024-03-18 and 0.10.3 dated 2025-10-14
immunarch-0.10.3/immunarch/DESCRIPTION | 91 +- immunarch-0.10.3/immunarch/MD5 | 323 +++++----- immunarch-0.10.3/immunarch/NAMESPACE | 132 ++-- immunarch-0.10.3/immunarch/R/aaa-registry.R |only immunarch-0.10.3/immunarch/R/globals.R |only immunarch-0.10.3/immunarch/R/immunarch-package.R | 64 + immunarch-0.10.3/immunarch/R/import-standalone-purrr.R |only immunarch-0.10.3/immunarch/R/v0_align_lineage.R |only immunarch-0.10.3/immunarch/R/v0_annotation.R |only immunarch-0.10.3/immunarch/R/v0_clonality.R |only immunarch-0.10.3/immunarch/R/v0_clustering.R |only immunarch-0.10.3/immunarch/R/v0_data_docs.R |only immunarch-0.10.3/immunarch/R/v0_dimensions.R |only immunarch-0.10.3/immunarch/R/v0_distance.R |only immunarch-0.10.3/immunarch/R/v0_diversity.R |only immunarch-0.10.3/immunarch/R/v0_dynamics.R |only immunarch-0.10.3/immunarch/R/v0_explore.R |only immunarch-0.10.3/immunarch/R/v0_filters.R |only immunarch-0.10.3/immunarch/R/v0_gene_usage.R |only immunarch-0.10.3/immunarch/R/v0_gene_usage_analysis.R |only immunarch-0.10.3/immunarch/R/v0_germline.R |only immunarch-0.10.3/immunarch/R/v0_immunr_data_format.R |only immunarch-0.10.3/immunarch/R/v0_info_theory.R |only immunarch-0.10.3/immunarch/R/v0_io.R |only immunarch-0.10.3/immunarch/R/v0_io_parsers.R |only immunarch-0.10.3/immunarch/R/v0_io_savers.R |only immunarch-0.10.3/immunarch/R/v0_io_utility.R |only immunarch-0.10.3/immunarch/R/v0_kmers.R |only immunarch-0.10.3/immunarch/R/v0_overlap.R |only immunarch-0.10.3/immunarch/R/v0_overlap_analysis.R |only immunarch-0.10.3/immunarch/R/v0_phylip.R |only immunarch-0.10.3/immunarch/R/v0_preprocessing.R |only immunarch-0.10.3/immunarch/R/v0_public.R |only immunarch-0.10.3/immunarch/R/v0_sampling.R |only immunarch-0.10.3/immunarch/R/v0_seqCluster.R |only immunarch-0.10.3/immunarch/R/v0_shiny.R |only immunarch-0.10.3/immunarch/R/v0_singlecell.R |only immunarch-0.10.3/immunarch/R/v0_somatic_hypermutation.R |only immunarch-0.10.3/immunarch/R/v0_spectratyping.R |only immunarch-0.10.3/immunarch/R/v0_tools.R |only immunarch-0.10.3/immunarch/R/v0_vis.R |only immunarch-0.10.3/immunarch/R/v1_aaa_commons_vis.R |only immunarch-0.10.3/immunarch/R/v1_aaa_registry_utils.R |only immunarch-0.10.3/immunarch/R/v1_clonality_airr.R |only immunarch-0.10.3/immunarch/R/v1_clonality_annotate.R |only immunarch-0.10.3/immunarch/R/v1_clonality_base.R |only immunarch-0.10.3/immunarch/R/v1_diversity_airr.R |only immunarch-0.10.3/immunarch/R/v1_diversity_vis.R |only immunarch-0.10.3/immunarch/R/v1_migration_updates.R |only immunarch-0.10.3/immunarch/R/v1_migration_utils.R |only immunarch-0.10.3/immunarch/R/v1_package.R |only immunarch-0.10.3/immunarch/R/v1_public_airr.R |only immunarch-0.10.3/immunarch/R/v1_public_vis.R |only immunarch-0.10.3/immunarch/R/v1_stats_airr.R |only immunarch-0.10.3/immunarch/R/v1_stats_vis.R |only immunarch-0.10.3/immunarch/R/wip-v1-planning.R |only immunarch-0.10.3/immunarch/R/zzz.R |only immunarch-0.10.3/immunarch/README.md | 307 +++++---- immunarch-0.10.3/immunarch/build/vignette.rds |binary immunarch-0.10.3/immunarch/inst/doc/immunarch.Rmd |only immunarch-0.10.3/immunarch/inst/doc/immunarch.html |only immunarch-0.10.3/immunarch/inst/doc/immunarch_threads.R |only immunarch-0.10.3/immunarch/inst/doc/immunarch_threads.Rmd |only immunarch-0.10.3/immunarch/inst/doc/immunarch_threads.html |only immunarch-0.10.3/immunarch/man/aa_properties.Rd | 2 immunarch-0.10.3/immunarch/man/aa_table.Rd | 2 immunarch-0.10.3/immunarch/man/add_class.Rd | 2 immunarch-0.10.3/immunarch/man/airr_clonality.Rd |only immunarch-0.10.3/immunarch/man/airr_diversity.Rd |only immunarch-0.10.3/immunarch/man/airr_public.Rd |only immunarch-0.10.3/immunarch/man/airr_stats.Rd |only immunarch-0.10.3/immunarch/man/annotate_clonality.Rd |only immunarch-0.10.3/immunarch/man/apply_symm.Rd | 4 immunarch-0.10.3/immunarch/man/bcrdata.Rd | 8 immunarch-0.10.3/immunarch/man/bunch_translate.Rd | 2 immunarch-0.10.3/immunarch/man/check_distribution.Rd | 2 immunarch-0.10.3/immunarch/man/coding.Rd | 14 immunarch-0.10.3/immunarch/man/dbAnnotate.Rd | 20 immunarch-0.10.3/immunarch/man/dbLoad.Rd | 6 immunarch-0.10.3/immunarch/man/dot-quant_column_choice.Rd | 2 immunarch-0.10.3/immunarch/man/entropy.Rd | 4 immunarch-0.10.3/immunarch/man/figures |only immunarch-0.10.3/immunarch/man/fixVis.Rd | 4 immunarch-0.10.3/immunarch/man/geneUsage.Rd | 18 immunarch-0.10.3/immunarch/man/geneUsageAnalysis.Rd | 18 immunarch-0.10.3/immunarch/man/gene_segments.Rd | 2 immunarch-0.10.3/immunarch/man/gene_stats.Rd | 4 immunarch-0.10.3/immunarch/man/getKmers.Rd | 8 immunarch-0.10.3/immunarch/man/get_immunarch_news.Rd |only immunarch-0.10.3/immunarch/man/group_from_metadata.Rd | 2 immunarch-0.10.3/immunarch/man/has_class.Rd | 2 immunarch-0.10.3/immunarch/man/im_common_args.Rd |only immunarch-0.10.3/immunarch/man/immdata.Rd | 8 immunarch-0.10.3/immunarch/man/immunarch_v1_updates.Rd |only immunarch-0.10.3/immunarch/man/immunr_data_format.Rd | 48 - immunarch-0.10.3/immunarch/man/immunr_hclust.Rd | 35 - immunarch-0.10.3/immunarch/man/immunr_pca.Rd | 25 immunarch-0.10.3/immunarch/man/inc_overlap.Rd | 10 immunarch-0.10.3/immunarch/man/list_immunarch_news.Rd |only immunarch-0.10.3/immunarch/man/matrixdiagcopy.Rd | 4 immunarch-0.10.3/immunarch/man/pubRep.Rd | 19 immunarch-0.10.3/immunarch/man/pubRepApply.Rd | 6 immunarch-0.10.3/immunarch/man/pubRepFilter.Rd | 4 immunarch-0.10.3/immunarch/man/pubRepStatistics.Rd | 4 immunarch-0.10.3/immunarch/man/public_matrix.Rd | 4 immunarch-0.10.3/immunarch/man/register_immunarch_method.Rd |only immunarch-0.10.3/immunarch/man/repAlignLineage.Rd | 28 immunarch-0.10.3/immunarch/man/repClonalFamily.Rd | 32 immunarch-0.10.3/immunarch/man/repClonality.Rd | 8 immunarch-0.10.3/immunarch/man/repDiversity.Rd | 38 - immunarch-0.10.3/immunarch/man/repExplore.Rd | 8 immunarch-0.10.3/immunarch/man/repFilter.Rd | 58 - immunarch-0.10.3/immunarch/man/repGermline.Rd | 16 immunarch-0.10.3/immunarch/man/repLoad.Rd | 68 -- immunarch-0.10.3/immunarch/man/repOverlap.Rd | 8 immunarch-0.10.3/immunarch/man/repOverlapAnalysis.Rd | 20 immunarch-0.10.3/immunarch/man/repSample.Rd | 8 immunarch-0.10.3/immunarch/man/repSave.Rd | 8 immunarch-0.10.3/immunarch/man/repSomaticHypermutation.Rd | 22 immunarch-0.10.3/immunarch/man/select_barcodes.Rd | 8 immunarch-0.10.3/immunarch/man/select_clusters.Rd | 4 immunarch-0.10.3/immunarch/man/seqCluster.Rd | 9 immunarch-0.10.3/immunarch/man/seqDist.Rd | 14 immunarch-0.10.3/immunarch/man/set_pb.Rd | 2 immunarch-0.10.3/immunarch/man/spectratype.Rd | 8 immunarch-0.10.3/immunarch/man/split_to_kmers.Rd | 4 immunarch-0.10.3/immunarch/man/switch_type.Rd | 2 immunarch-0.10.3/immunarch/man/top.Rd | 6 immunarch-0.10.3/immunarch/man/trackClonotypes.Rd | 19 immunarch-0.10.3/immunarch/man/vis.Rd | 75 +- immunarch-0.10.3/immunarch/man/vis.clonal_family.Rd | 8 immunarch-0.10.3/immunarch/man/vis.clonal_family_tree.Rd | 8 immunarch-0.10.3/immunarch/man/vis.immunr_chao1.Rd | 16 immunarch-0.10.3/immunarch/man/vis.immunr_clonal_prop.Rd | 16 immunarch-0.10.3/immunarch/man/vis.immunr_dynamics.Rd | 6 immunarch-0.10.3/immunarch/man/vis.immunr_exp_vol.Rd | 16 immunarch-0.10.3/immunarch/man/vis.immunr_gene_usage.Rd | 37 - immunarch-0.10.3/immunarch/man/vis.immunr_hclust.Rd | 8 immunarch-0.10.3/immunarch/man/vis.immunr_inc_overlap.Rd | 6 immunarch-0.10.3/immunarch/man/vis.immunr_kmeans.Rd | 16 immunarch-0.10.3/immunarch/man/vis.immunr_kmer_table.Rd | 6 immunarch-0.10.3/immunarch/man/vis.immunr_mds.Rd | 17 immunarch-0.10.3/immunarch/man/vis.immunr_ov_matrix.Rd | 28 immunarch-0.10.3/immunarch/man/vis.immunr_public_repertoire.Rd | 16 immunarch-0.10.3/immunarch/man/vis.immunr_public_statistics.Rd | 8 immunarch-0.10.3/immunarch/man/vis.step_failure_ignored.Rd | 5 immunarch-0.10.3/immunarch/man/vis_bar.Rd | 6 immunarch-0.10.3/immunarch/man/vis_box.Rd | 8 immunarch-0.10.3/immunarch/man/vis_circos.Rd | 10 immunarch-0.10.3/immunarch/man/vis_heatmap.Rd | 6 immunarch-0.10.3/immunarch/man/vis_heatmap2.Rd | 14 immunarch-0.10.3/immunarch/man/vis_hist.Rd | 14 immunarch-0.10.3/immunarch/man/vis_immunr_kmer_profile_main.Rd | 14 immunarch-0.10.3/immunarch/man/vis_public_clonotypes.Rd | 6 immunarch-0.10.3/immunarch/man/vis_public_frequencies.Rd | 6 immunarch-0.10.3/immunarch/man/vis_textlogo.Rd | 12 immunarch-0.10.3/immunarch/vignettes/immunarch.Rmd |only immunarch-0.10.3/immunarch/vignettes/immunarch_threads.Rmd |only immunarch-0.10.3/immunarch/vignettes/web_only_v0 |only immunarch-0.9.1/immunarch/R/align_lineage.R |only immunarch-0.9.1/immunarch/R/annotation.R |only immunarch-0.9.1/immunarch/R/clonality.R |only immunarch-0.9.1/immunarch/R/clustering.R |only immunarch-0.9.1/immunarch/R/data_docs.R |only immunarch-0.9.1/immunarch/R/dimensions.R |only immunarch-0.9.1/immunarch/R/distance.R |only immunarch-0.9.1/immunarch/R/diversity.R |only immunarch-0.9.1/immunarch/R/dynamics.R |only immunarch-0.9.1/immunarch/R/explore.R |only immunarch-0.9.1/immunarch/R/filters.R |only immunarch-0.9.1/immunarch/R/gene_usage.R |only immunarch-0.9.1/immunarch/R/gene_usage_analysis.R |only immunarch-0.9.1/immunarch/R/germline.R |only immunarch-0.9.1/immunarch/R/immunarch-remaster.R |only immunarch-0.9.1/immunarch/R/immunr_data_format.R |only immunarch-0.9.1/immunarch/R/info_theory.R |only immunarch-0.9.1/immunarch/R/io-parsers.R |only immunarch-0.9.1/immunarch/R/io-savers.R |only immunarch-0.9.1/immunarch/R/io-utility.R |only immunarch-0.9.1/immunarch/R/io.R |only immunarch-0.9.1/immunarch/R/kmers.R |only immunarch-0.9.1/immunarch/R/overlap.R |only immunarch-0.9.1/immunarch/R/overlap_analysis.R |only immunarch-0.9.1/immunarch/R/phylip.R |only immunarch-0.9.1/immunarch/R/preprocessing.R |only immunarch-0.9.1/immunarch/R/public.R |only immunarch-0.9.1/immunarch/R/sampling.R |only immunarch-0.9.1/immunarch/R/seqCluster.R |only immunarch-0.9.1/immunarch/R/shiny.R |only immunarch-0.9.1/immunarch/R/singlecell.R |only immunarch-0.9.1/immunarch/R/somatic_hypermutation.R |only immunarch-0.9.1/immunarch/R/spectratyping.R |only immunarch-0.9.1/immunarch/R/tools.R |only immunarch-0.9.1/immunarch/R/vis.R |only immunarch-0.9.1/immunarch/data/scdata.rda |only immunarch-0.9.1/immunarch/inst/doc/v1_introduction.Rmd |only immunarch-0.9.1/immunarch/inst/doc/v1_introduction.html |only immunarch-0.9.1/immunarch/inst/doc/v2_data.R |only immunarch-0.9.1/immunarch/inst/doc/v2_data.Rmd |only immunarch-0.9.1/immunarch/inst/doc/v2_data.html |only immunarch-0.9.1/immunarch/man/scdata.Rd |only immunarch-0.9.1/immunarch/vignettes/v1_introduction.Rmd |only immunarch-0.9.1/immunarch/vignettes/v2_data.Rmd |only immunarch-0.9.1/immunarch/vignettes/web_only |only 204 files changed, 1117 insertions(+), 879 deletions(-)
Title: Information Analysis for Test and Rating Scale Data
Description: Develop, evaluate, and score multiple choice examinations,
psychological scales, questionnaires, and similar types of data involving
sequences of choices among one or more sets of answers.
This version of the package should be considered as brand new. Almost all
of the functions have been changed, including their argument list.
See the file NEWS.Rd in the Inst folder for more information.
Using the package does not require any formal statistical knowledge
beyond what would be provided by a first course in statistics in a
social science department. There the user would encounter the concept
of probability and how it is used to model data and make decisions,
and would become familiar with basic mathematical and statistical notation.
Most of the output is in graphical form.
Author: James Ramsay [aut, cre],
Juan Li [ctb],
Marie Wiberg [ctb],
Joakim Wallmark [ctb],
Spencer Graves [ctb]
Maintainer: James Ramsay <james.ramsay@mcgill.ca>
Diff between TestGardener versions 3.3.5 dated 2024-09-18 and 3.3.6 dated 2025-10-14
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 1 - R/Ffuns_plot.R | 2 +- 4 files changed, 9 insertions(+), 10 deletions(-)
Title: Execute R in a 'Docker' Context
Description: The goal of 'jetty' is to execute R functions and code
snippets in an isolated R subprocess within a 'Docker' container
and return the evaluated results to the local R session. 'jetty'
can install necessary packages at runtime and seamlessly propagates
errors and outputs from the 'Docker' subprocess back to the main
session. 'jetty' is primarily designed for sandboxed testing and
quick execution of example code.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between jetty versions 0.2.1 dated 2025-04-14 and 0.2.2 dated 2025-10-14
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/run.R | 13 ++++++++++--- R/script.R | 4 ++-- README.md | 12 ++++++------ man/run.Rd | 4 ++-- man/run_script.Rd | 4 ++-- tests/testthat/test-docker.R | 28 ++++++++++++---------------- 9 files changed, 51 insertions(+), 43 deletions(-)
Title: B Cell Receptor Phylogenetics Toolkit
Description: Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
Author: Kenneth Hoehn [aut, cre],
Cole Jensen [aut],
Jessie Fielding [aut],
Hunter Melton [aut],
Susanna Marquez [ctb],
Jason Vander Heiden [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Kenneth Hoehn <kenneth.b.hoehn@dartmouth.edu>
Diff between dowser versions 2.3 dated 2024-10-22 and 2.4.0 dated 2025-10-14
DESCRIPTION | 42 +- MD5 | 154 +++++--- NAMESPACE | 10 NEWS.md | 10 R/Classes.R | 2 R/Clones.R | 376 ++++++++++++++++----- R/Data.R | 28 + R/Dowser.R | 1 R/Germlines.R | 15 R/Plotting.R | 122 +++++-- R/Statistics.R | 13 R/TimeTreesFunctions.R |only R/TreeFunctions.R | 394 +++++++++++++++++++--- README.md | 25 + build/partial.rdb |binary build/vignette.rds |binary data/ExampleAirrTyCHE.rda |only inst/doc/Building-Time-Trees-Vignette.R |only inst/doc/Building-Time-Trees-Vignette.Rmd |only inst/doc/Building-Time-Trees-Vignette.pdf |only inst/doc/Building-Trees-Vignette.R | 172 +++++----- inst/doc/Building-Trees-Vignette.Rmd | 2 inst/doc/Building-Trees-Vignette.pdf |binary inst/doc/Discrete-Trait-Vignette.R | 446 +++++++++++++------------- inst/doc/Discrete-Trait-Vignette.Rmd | 6 inst/doc/Discrete-Trait-Vignette.pdf |binary inst/doc/Germlines-Vignette.R | 38 +- inst/doc/Germlines-Vignette.Rmd | 2 inst/doc/Germlines-Vignette.pdf |binary inst/doc/Measurable-Evolution.R | 126 +++---- inst/doc/Measurable-Evolution.pdf |binary inst/doc/NonB-Cell-Data.R |only inst/doc/NonB-Cell-Data.Rmd |only inst/doc/NonB-Cell-Data.html |only inst/doc/Plotting-Trees-Vignette.R | 10 inst/doc/Plotting-Trees-Vignette.pdf |binary inst/doc/Quickstart-Vignette.pdf |binary inst/doc/Resolve-Light-Chains-Vignette.R | 52 +-- inst/doc/Resolve-Light-Chains-Vignette.Rmd | 6 inst/doc/Resolve-Light-Chains-Vignette.pdf |binary inst/doc/Sequences-Vignette.R | 8 inst/doc/Sequences-Vignette.pdf |binary man/ExampleAirrTyCHE.Rd |only man/airrClone-class.Rd | 2 man/bootstrapTrees.Rd | 8 man/buildBeast.Rd |only man/buildIgphyml.Rd | 6 man/buildPML.Rd | 16 man/buildPhylo.Rd | 2 man/buildPratchet.Rd | 2 man/buildRAxML.Rd | 10 man/checkDivergence.Rd |only man/createGermlines.Rd | 2 man/create_MRCA_prior_germline.Rd |only man/create_MRCA_prior_observed.Rd |only man/create_alignment.Rd |only man/create_height_prior.Rd |only man/create_max_height_prior.Rd |only man/create_root_freqs.Rd |only man/create_starting_tree.Rd |only man/create_traitset.Rd |only man/dowser-package.Rd | 6 man/exportTrees.Rd | 2 man/findSwitches.Rd | 8 man/formatClones.Rd | 6 man/getBootstraps.Rd | 2 man/getSkylines.Rd |only man/getTimeTrees.Rd |only man/getTimeTreesIterate.Rd |only man/getTrees.Rd | 9 man/makeAirrClone.Rd | 2 man/makeSkyline.Rd |only man/plotSkylines.Rd |only man/plotTrees.Rd | 11 man/readBEAST.Rd |only man/readIMGT.Rd | 4 man/readModelFile.Rd | 2 man/sampleCloneMultiGroup.Rd |only man/sampleClones.Rd |only man/stitchRegions.Rd | 4 man/stopCodonCheck.Rd |only man/testPS.Rd | 2 man/testSC.Rd | 2 man/testSP.Rd | 2 man/writeLineageFile.Rd | 5 man/write_clone_to_xml.Rd |only man/write_clones_to_xmls.Rd |only vignettes/Building-Time-Trees-Vignette.Rmd |only vignettes/Building-Time-Trees-gc-trees.png |only vignettes/Building-Time-Trees-mixed-trees.png |only vignettes/Building-Trees-Vignette.Rmd | 2 vignettes/Discrete-Trait-Vignette.Rmd | 6 vignettes/Germlines-Vignette.Rmd | 2 vignettes/NonB-Cell-Data.Rmd |only vignettes/Resolve-Light-Chains-Vignette.Rmd | 6 95 files changed, 1429 insertions(+), 762 deletions(-)
Title: Datasets and Functions to Accompany Analisis De Datos Con R
Description: Datasets and functions to accompany the book 'Analisis de datos con el programa
estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109).
The package helps carry out data management, exploratory analyses, and model fitting.
Author: Christian Salas-Eljatib [aut, cre] ,
Nicolas Campos [ctb] ,
Joaquin Riquelme [ctb] ,
Nicolas Pino [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Diff between datana versions 1.1.4 dated 2025-09-23 and 1.1.5 dated 2025-10-14
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- R/descstat.r | 36 ++++++++++++++++++++++++------- R/valesta.r | 65 +++++++++++++++++++++++++++++++++++++------------------- inst/CITATION | 4 +-- man/descstat.Rd | 12 +++++++++- man/valesta.Rd | 15 ++++++++++++ 7 files changed, 108 insertions(+), 42 deletions(-)
Title: 'shiny' Application for Biological Dosimetry
Description: A tool to perform all different statistical tests and calculations
needed by Biological dosimetry Laboratories. Detailed documentation is
available in <https://biodosetools-team.github.io/documentation/>.
Author: Alfredo Hernandez [aut] ,
Anna Frances-Abellan [aut, cre] ,
David Endesfelder [aut],
Pere Puig [aut]
Maintainer: Anna Frances-Abellan <anna.frances@uab.cat>
Diff between biodosetools versions 3.6.2 dated 2025-10-10 and 3.7 dated 2025-10-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/app_ui.R | 9 ++++++--- inst/doc/interlab.html | 12 ++++++------ 4 files changed, 18 insertions(+), 15 deletions(-)
Title: Fast C++ Primitives for the 'NeuroAnatomy Toolbox'
Description: Fast functions implemented in C++ via 'Rcpp' to support the
'NeuroAnatomy Toolbox' ('nat') ecosystem. These functions provide large
speed-ups for basic manipulation of neuronal skeletons over pure R
functions found in the 'nat' package. The expectation is that end
users will not use this package directly, but instead the 'nat'
package will automatically use routines from this package when it is
available to enable large performance gains.
Author: Gregory Jefferis [aut, cre]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between natcpp versions 0.1.0 dated 2021-07-13 and 0.2 dated 2025-10-14
DESCRIPTION | 13 ++++---- MD5 | 24 +++++++++----- NAMESPACE | 4 ++ NEWS.md | 14 ++++++++ R/RcppExports.R | 61 ++++++++++++++++++++++++++++++++++++++ README.md | 20 +++++++----- inst/WORDLIST | 1 man/c_ListofMatrixRows.Rd |only man/c_coords21dindex.Rd |only man/c_ijkpos.Rd |only man/c_sub2ind.Rd |only man/natcpp-package.Rd | 9 +---- src/RcppExports.cpp | 57 +++++++++++++++++++++++++++++++++++ src/coordinates.cpp |only src/matrix.cpp |only tests/testthat/test-coordinates.R |only tests/testthat/test-matrix.R |only 17 files changed, 174 insertions(+), 29 deletions(-)
Title: Simulation Tools for Small Area Estimation
Description: Tools for the simulation of data in the context of small area
estimation. Combine all steps of your simulation - from data generation
over drawing samples to model fitting - in one object. This enables easy
modification and combination of different scenarios. You can store your
results in a folder or start the simulation in parallel.
Author: Sebastian Warnholz [aut, cre],
Timo Schmid [aut]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between saeSim versions 0.11.0 dated 2022-02-07 and 0.12.0 dated 2025-10-14
DESCRIPTION | 8 - MD5 | 30 +++---- NEWS | 163 +++++++++++++++++++++++----------------- R/01-sim.R | 56 +++++++------ R/01-sim_setup.R | 9 -- R/03-sim_base.R | 45 ++++++----- build/vignette.rds |binary inst/doc/Introduction.R | 42 +++++----- inst/doc/Introduction.html | 117 +++++++++++++++++----------- man/sim.Rd | 22 ++--- man/sim_base.Rd | 4 man/sim_resp.Rd | 2 man/sim_setup_preconfigured.Rd | 18 +++- tests/testthat/test-sim.R | 2 tests/testthat/test-sim_comp.R | 2 tests/testthat/test-sim_setup.R | 4 16 files changed, 299 insertions(+), 225 deletions(-)
Title: Randomization Inference for Randomized Experiments
Description: Randomization inference procedures for simple and complex randomized designs, including multi-armed trials, as described in Gerber and Green (2012, ISBN: 978-0393979954). Users formally describe their randomization procedure and test statistic. The randomization distribution of the test statistic under some null hypothesis is efficiently simulated.
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between ri2 versions 0.4.0 dated 2022-05-26 and 0.4.1 dated 2025-10-14
ri2-0.4.0/ri2/man/ri2.Rd |only ri2-0.4.1/ri2/DESCRIPTION | 8 ri2-0.4.1/ri2/MD5 | 16 ri2-0.4.1/ri2/NEWS.md | 5 ri2-0.4.1/ri2/R/conduct_ri.R | 4 ri2-0.4.1/ri2/R/ri2.R | 10 ri2-0.4.1/ri2/build/vignette.rds |binary ri2-0.4.1/ri2/inst/doc/ri2_vignette.html | 834 ++++++++++++++++++++----------- ri2-0.4.1/ri2/man/conduct_ri.Rd | 4 ri2-0.4.1/ri2/man/ri2-package.Rd |only 10 files changed, 589 insertions(+), 292 deletions(-)
Title: Raven Hydrological Modelling Framework R Support and Analysis
Description: Utilities for processing input and output files associated with the Raven Hydrological Modelling Framework. Includes various plotting functions, model diagnostics, reading output files into extensible time series format, and support for writing Raven input files.
The 'RavenR' package is also archived at Chlumsky et al. (2020) <doi:10.5281/zenodo.4248183>.
The Raven Hydrologic Modelling Framework method can be referenced with Craig et al. (2020) <doi:10.1016/j.envsoft.2020.104728>.
Author: Robert Chlumsky [cre, aut] ,
James Craig [ctb, aut] ,
Leland Scantlebury [ctb, aut],
Simon Lin [ctb, aut],
Sarah Grass [ctb, aut],
Genevieve Brown [ctb, aut],
Rezgar Arabzadeh [ctb, aut]
Maintainer: Robert Chlumsky <rchlumsk@uwaterloo.ca>
Diff between RavenR versions 2.2.3 dated 2025-07-25 and 2.2.4 dated 2025-10-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/rvn_rvi_write_template.R | 5 +++-- inst/doc/Introduction_to_RavenR.html | 31 +++++++++++++++++++------------ 4 files changed, 29 insertions(+), 21 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut, cre],
Mu Sigma, Inc. [cph]
Maintainer: Zubin Dowlaty <zubin.dowlaty@mu-sigma.com>
Diff between HVT versions 25.2.5 dated 2025-07-04 and 25.2.6 dated 2025-10-14
HVT-25.2.5/HVT/R/msm_plots.R |only HVT-25.2.5/HVT/man/VQ_codebookSplit.Rd |only HVT-25.2.5/HVT/vignettes/pngs/ref.png |only HVT-25.2.5/HVT/vignettes/pngs/ref1.png |only HVT-25.2.5/HVT/vignettes/pngs/ref2.png |only HVT-25.2.5/HVT/vignettes/pngs/ref3.png |only HVT-25.2.6/HVT/DESCRIPTION | 40 HVT-25.2.6/HVT/MD5 | 85 +- HVT-25.2.6/HVT/NAMESPACE | 7 HVT-25.2.6/HVT/NEWS.md | 7 HVT-25.2.6/HVT/R/Add_boundary_points.R | 1 HVT-25.2.6/HVT/R/Corrected_Tessellations.R | 2 HVT-25.2.6/HVT/R/DelaunayInfo.R | 1 HVT-25.2.6/HVT/R/Delete_Outpoints.R | 2 HVT-25.2.6/HVT/R/HVTMSM_support.R |only HVT-25.2.6/HVT/R/HVTMSMoptimization.R |only HVT-25.2.6/HVT/R/ScaleMat.R | 1 HVT-25.2.6/HVT/R/Transform_Coordinates.R | 2 HVT-25.2.6/HVT/R/VQ_codebookSplit.R | 42 - HVT-25.2.6/HVT/R/clustHVT.R | 61 - HVT-25.2.6/HVT/R/clusterPlot.R | 464 ++++++----- HVT-25.2.6/HVT/R/create_highlighted_results_table.R |only HVT-25.2.6/HVT/R/diagSuggestion.R | 1 HVT-25.2.6/HVT/R/getCellId.R | 2 HVT-25.2.6/HVT/R/getCentroids.R | 1 HVT-25.2.6/HVT/R/getCentroids_for_opti.R | 1 HVT-25.2.6/HVT/R/global.R | 7 HVT-25.2.6/HVT/R/hvq.R | 9 HVT-25.2.6/HVT/R/madPlot.R | 1 HVT-25.2.6/HVT/R/mcmc_plots.R |only HVT-25.2.6/HVT/R/msm.R | 835 ++++++++++---------- HVT-25.2.6/HVT/R/plotAnimatedFlowmap.R | 376 ++++----- HVT-25.2.6/HVT/R/plotHVT.R | 40 HVT-25.2.6/HVT/R/plotModelDiagnostics.R | 2 HVT-25.2.6/HVT/R/plotMsmKN.R |only HVT-25.2.6/HVT/R/scoreHVT.R | 84 +- HVT-25.2.6/HVT/R/scoreLayeredHVT.R | 10 HVT-25.2.6/HVT/README.md | 92 +- HVT-25.2.6/HVT/build/vignette.rds |binary HVT-25.2.6/HVT/inst/doc/HVT.R | 34 HVT-25.2.6/HVT/inst/doc/HVT.Rmd | 83 + HVT-25.2.6/HVT/inst/doc/HVT.html | 187 ++-- HVT-25.2.6/HVT/man/HVTMSMoptimization.Rd |only HVT-25.2.6/HVT/man/clustHVT.Rd | 6 HVT-25.2.6/HVT/man/mcmc_plots.Rd |only HVT-25.2.6/HVT/man/msm.Rd | 31 HVT-25.2.6/HVT/man/plotAnimatedFlowmap.Rd | 30 HVT-25.2.6/HVT/man/plotModelDiagnostics.Rd | 2 HVT-25.2.6/HVT/man/scoreLayeredHVT.Rd | 10 HVT-25.2.6/HVT/vignettes/HVT.Rmd | 83 + 50 files changed, 1448 insertions(+), 1194 deletions(-)
Title: Graph of Daily and Cumulative Downloads of your Packages
Description: Plot the daily and cumulative number of downloads of your packages.
It is designed to be slightly more convenient than the several similar programs. If you want to run this each morning,
you do not need to keep typing in the names of your packages. Also, this combines the daily and cumulative counts in one
run, you do not need to run separate programs to get both types of information.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between myCRAN versions 1.2 dated 2025-03-21 and 1.3 dated 2025-10-14
DESCRIPTION | 13 +-- MD5 | 22 +++-- NAMESPACE | 3 R/myCRAN.R | 219 ++++++++++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/myCRAN.Rmd | 30 ++++++ inst/doc/myCRAN.html | 55 ++++++++++++ man/myCRAN.Rd | 10 +- vignettes/Fig0.jpg |only vignettes/Fig1.jpg |only vignettes/Fig2.jpg |only vignettes/Fig3.jpg |only vignettes/Fig4.jpg |only vignettes/Fig6.jpg |only vignettes/myCRAN.Rmd | 30 ++++++ 15 files changed, 275 insertions(+), 107 deletions(-)
Title: Explore Flora e Funga do Brasil Database
Description: A collection of functions designed to retrieve, filter and spatialize data from the Flora e Funga do Brasil dataset. For more information about the dataset, please visit <https://floradobrasil.jbrj.gov.br/consulta/>.
Author: Weverton Trindade [aut, cre]
Maintainer: Weverton Trindade <wevertonf1993@gmail.com>
Diff between florabr versions 1.3.0 dated 2024-09-09 and 1.3.1 dated 2025-10-14
DESCRIPTION | 11 MD5 | 28 - NEWS.md | 8 R/check_names.R | 9 R/filter_florabr.R | 20 - README.md | 6 build/vignette.rds |binary inst/doc/Spatialize_florabr.R | 324 +++++++++--------- inst/doc/Spatialize_florabr.html | 20 - inst/doc/getting_pam.R | 124 +++---- inst/doc/getting_pam.html | 6 inst/doc/getting_started.R | 218 ++++++------ inst/doc/getting_started.html | 4 inst/doc/selecting_species.R | 686 +++++++++++++++++++-------------------- inst/doc/selecting_species.html | 4 15 files changed, 746 insertions(+), 722 deletions(-)
Title: 'Gephi' Network Visualization
Description: Implements key features of 'Gephi' for network visualization, including 'ForceAtlas2' (with LinLog mode), network scaling, and network rotations. It also includes easy network visualization tools such as edge and node color assignment for recreating 'Gephi'-style graphs in R. The package references layout algorithms developed by Jacomy, M., Venturini T., Heymann S., and Bastian M. (2014) <doi:10.1371/journal.pone.0098679> and Noack, A. (2009) <doi:10.48550/arXiv.0807.4052>.
Author: Julia Manso [aut, cre]
Maintainer: Julia Manso <gephiforr@gmail.com>
Diff between GephiForR versions 0.1.0 dated 2024-08-27 and 0.1.1 dated 2025-10-14
DESCRIPTION | 8 - MD5 | 29 +++---- NEWS |only R/ForceAtlas2.R | 15 ++- R/assign_edge_colors.R | 104 ++++++++++++------------- R/assign_node_colors.R | 182 ++++++++++++++++++++++---------------------- R/easyplot.R | 2 R/rotate.R | 126 +++++++++++++++++------------- R/scaling.R | 116 ++++++++++++++-------------- build/partial.rdb |binary man/assign_edge_colors.Rd | 2 man/assign_node_colors.Rd | 2 man/easyplot.Rd | 2 man/layout.forceatlas2.Rd | 10 +- man/rotate_layout.Rd | 28 +++++- man/scale_node_positions.Rd | 2 16 files changed, 339 insertions(+), 289 deletions(-)
Title: Pac-Man Visualization Package
Description: Provides a broad-view perspective on data via
linear mapping of data onto a radial coordinate system. The package
contains functions to visualize the residual values of linear
regression and Cartesian data in the defined radial scheme. See the
'pacviz' documentation page for more information:
<https://pacviz.sriley.dev/>.
Author: Sarah Riley [aut, cre]
Maintainer: Sarah Riley <academic@sriley.dev>
This is a re-admission after prior archival of version 1.0.3 dated 2023-03-12
Diff between pacviz versions 1.0.3 dated 2023-03-12 and 1.0.4 dated 2025-10-14
DESCRIPTION | 16 ++-- LICENSE | 2 MD5 | 16 ++-- R/plot.r | 2 build/vignette.rds |binary inst/doc/pacviz.Rmd | 2 inst/doc/pacviz.html | 170 ++++++++++++++++++++++++++------------------------- man/pac.plot.Rd | 2 vignettes/pacviz.Rmd | 2 9 files changed, 108 insertions(+), 104 deletions(-)
Title: Implements Generic Composite Similarity Measure
Description: Provides implementation of the generic composite similarity measure
(GCSM) described in Liu et al. (2020) <doi:10.1016/j.ecoinf.2020.101169>. The
implementation is in C++ and uses 'RcppArmadillo'. Additionally, implementations
of the structural similarity (SSIM) and the composite similarity measure based
on means, standard deviations, and correlation coefficient (CMSC), are included.
Author: Yadong Liu [aut, cre]
Maintainer: Yadong Liu <liuyadong828@gmail.com>
Diff between GCSM versions 0.1.1 dated 2021-03-27 and 0.2.0 dated 2025-10-14
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 4 ++++ README.md | 19 ++++++++++--------- src/Makevars | 2 +- src/Makevars.win | 2 +- src/RcppExports.cpp | 5 +++++ 7 files changed, 32 insertions(+), 22 deletions(-)
Title: The R Interface to 'SyncroSim'
Description: 'SyncroSim' is a generalized framework for managing scenario-based
datasets (<https://syncrosim.com/>). 'rsyncrosim' provides an interface to
'SyncroSim'. Simulation models can be added to 'SyncroSim' in order to
transform these datasets, taking advantage of general features such as
defining scenarios of model inputs, running Monte Carlo simulations, and
summarizing model outputs. 'rsyncrosim' requires 'SyncroSim' 2.3.5 or higher
(API documentation: <https://docs.syncrosim.com/>).
Author: Colin Daniel [aut],
Josie Hughes [aut],
Valentin Lucet [aut],
Alex Embrey [aut],
Katie Birchard [aut, cre],
Leonardo Frid [aut],
Tabitha Kennedy [aut],
Shreeram Senthivasan [aut],
ApexRMS [cph]
Maintainer: Katie Birchard <katie.birchard@apexrms.com>
Diff between rsyncrosim versions 2.1.2 dated 2025-05-06 and 2.1.9 dated 2025-10-14
rsyncrosim-2.1.2/rsyncrosim/man/figures |only rsyncrosim-2.1.9/rsyncrosim/DESCRIPTION | 10 rsyncrosim-2.1.9/rsyncrosim/MD5 | 261 ++++----- rsyncrosim-2.1.9/rsyncrosim/NAMESPACE | 8 rsyncrosim-2.1.9/rsyncrosim/NEWS.md | 28 - rsyncrosim-2.1.9/rsyncrosim/R/AAAClassDefinitions.R | 52 + rsyncrosim-2.1.9/rsyncrosim/R/addPackage.R | 4 rsyncrosim-2.1.9/rsyncrosim/R/backup.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/chart.R | 7 rsyncrosim-2.1.9/rsyncrosim/R/chartCriteria.R | 4 rsyncrosim-2.1.9/rsyncrosim/R/chartData.R | 12 rsyncrosim-2.1.9/rsyncrosim/R/chartDisagg.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/chartErrorBar.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/chartId.R | 4 rsyncrosim-2.1.9/rsyncrosim/R/chartInclude.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/chartOptionsFont.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/chartOptionsFormat.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/chartOptionsLegend.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/chartOptionsXAxis.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/chartOptionsYAxis.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/command.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/compact.R |only rsyncrosim-2.1.9/rsyncrosim/R/condaFilepath.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/createCondaEnv.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/datasheet.R | 22 rsyncrosim-2.1.9/rsyncrosim/R/datasheetSpatRaster.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/dateModified.R | 8 rsyncrosim-2.1.9/rsyncrosim/R/delete.R | 14 rsyncrosim-2.1.9/rsyncrosim/R/dependency.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/description.R | 8 rsyncrosim-2.1.9/rsyncrosim/R/filepath.R | 18 rsyncrosim-2.1.9/rsyncrosim/R/folder.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/folderId.R | 12 rsyncrosim-2.1.9/rsyncrosim/R/ignoreDependencies.R | 4 rsyncrosim-2.1.9/rsyncrosim/R/info.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/installConda.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/installPackage.R | 5 rsyncrosim-2.1.9/rsyncrosim/R/mergeDependencies.R | 4 rsyncrosim-2.1.9/rsyncrosim/R/name.R | 8 rsyncrosim-2.1.9/rsyncrosim/R/owner.R | 8 rsyncrosim-2.1.9/rsyncrosim/R/packages.R | 10 rsyncrosim-2.1.9/rsyncrosim/R/parentId.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/printCmd.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/project.R | 14 rsyncrosim-2.1.9/rsyncrosim/R/projectId.R | 8 rsyncrosim-2.1.9/rsyncrosim/R/readOnly.R | 10 rsyncrosim-2.1.9/rsyncrosim/R/removePackage.R | 4 rsyncrosim-2.1.9/rsyncrosim/R/restore.R |only rsyncrosim-2.1.9/rsyncrosim/R/run.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/runLog.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/saveDatasheet.R | 470 +++++------------ rsyncrosim-2.1.9/rsyncrosim/R/scenario.R | 12 rsyncrosim-2.1.9/rsyncrosim/R/scenarioId.R | 4 rsyncrosim-2.1.9/rsyncrosim/R/session.R | 22 rsyncrosim-2.1.9/rsyncrosim/R/signin.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/signout.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/silent.R | 4 rsyncrosim-2.1.9/rsyncrosim/R/ssimEnvironment.R | 3 rsyncrosim-2.1.9/rsyncrosim/R/ssimLibrary.R | 12 rsyncrosim-2.1.9/rsyncrosim/R/uninstallPackage.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/useConda.R | 6 rsyncrosim-2.1.9/rsyncrosim/R/version.R | 2 rsyncrosim-2.1.9/rsyncrosim/R/viewProfile.R | 2 rsyncrosim-2.1.9/rsyncrosim/man/Chart-class.Rd | 5 rsyncrosim-2.1.9/rsyncrosim/man/Folder-class.Rd | 63 +- rsyncrosim-2.1.9/rsyncrosim/man/Project-class.Rd | 59 +- rsyncrosim-2.1.9/rsyncrosim/man/Scenario-class.Rd | 75 +- rsyncrosim-2.1.9/rsyncrosim/man/Session-class.Rd | 57 +- rsyncrosim-2.1.9/rsyncrosim/man/SsimLibrary-class.Rd | 53 - rsyncrosim-2.1.9/rsyncrosim/man/addPackage.Rd | 4 rsyncrosim-2.1.9/rsyncrosim/man/backup.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chart.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chartCriteria.Rd | 4 rsyncrosim-2.1.9/rsyncrosim/man/chartData.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chartDisagg.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chartErrorBar.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chartId.Rd | 4 rsyncrosim-2.1.9/rsyncrosim/man/chartInclude.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chartOptionsFont.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chartOptionsFormat.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chartOptionsLegend.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chartOptionsXAxis.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/chartOptionsYAxis.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/command.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/compact.Rd |only rsyncrosim-2.1.9/rsyncrosim/man/condaFilepath.Rd | 100 +-- rsyncrosim-2.1.9/rsyncrosim/man/createCondaEnv.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/datasheet.Rd | 18 rsyncrosim-2.1.9/rsyncrosim/man/datasheetSpatRaster.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/dateModified.Rd | 8 rsyncrosim-2.1.9/rsyncrosim/man/delete.Rd | 14 rsyncrosim-2.1.9/rsyncrosim/man/deleteLibrary.Rd | 150 ++--- rsyncrosim-2.1.9/rsyncrosim/man/dependency.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/description.Rd | 8 rsyncrosim-2.1.9/rsyncrosim/man/filepath.Rd | 10 rsyncrosim-2.1.9/rsyncrosim/man/folder.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/folderId.Rd | 12 rsyncrosim-2.1.9/rsyncrosim/man/ignoreDependencies.Rd | 4 rsyncrosim-2.1.9/rsyncrosim/man/info.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/installConda.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/installPackage.Rd | 4 rsyncrosim-2.1.9/rsyncrosim/man/mergeDependencies.Rd | 4 rsyncrosim-2.1.9/rsyncrosim/man/name.Rd | 8 rsyncrosim-2.1.9/rsyncrosim/man/owner.Rd | 8 rsyncrosim-2.1.9/rsyncrosim/man/packages.Rd | 8 rsyncrosim-2.1.9/rsyncrosim/man/parentId.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/printCmd.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/project.Rd | 14 rsyncrosim-2.1.9/rsyncrosim/man/projectId.Rd | 8 rsyncrosim-2.1.9/rsyncrosim/man/readOnly.Rd | 10 rsyncrosim-2.1.9/rsyncrosim/man/removePackage.Rd | 4 rsyncrosim-2.1.9/rsyncrosim/man/restore.Rd |only rsyncrosim-2.1.9/rsyncrosim/man/rsyncrosim.Rd | 94 +-- rsyncrosim-2.1.9/rsyncrosim/man/run.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/runLog.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/runtimeDataFolder.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/saveDatasheet.Rd | 124 ---- rsyncrosim-2.1.9/rsyncrosim/man/scenario.Rd | 12 rsyncrosim-2.1.9/rsyncrosim/man/scenarioId.Rd | 4 rsyncrosim-2.1.9/rsyncrosim/man/session.Rd | 8 rsyncrosim-2.1.9/rsyncrosim/man/signIn.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/signOut.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/silent.Rd | 4 rsyncrosim-2.1.9/rsyncrosim/man/ssimLibrary.Rd | 12 rsyncrosim-2.1.9/rsyncrosim/man/tempfilepath.Rd | 8 rsyncrosim-2.1.9/rsyncrosim/man/uninstallPackage.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/updateRunLog.Rd | 68 +- rsyncrosim-2.1.9/rsyncrosim/man/useConda.Rd | 6 rsyncrosim-2.1.9/rsyncrosim/man/version.Rd | 2 rsyncrosim-2.1.9/rsyncrosim/man/viewProfile.Rd | 2 130 files changed, 1046 insertions(+), 1306 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr [aut, cre]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between rms versions 8.0-0 dated 2025-04-04 and 8.1-0 dated 2025-10-14
DESCRIPTION | 20 +++++----- MD5 | 65 ++++++++++++++++++----------------- NAMESPACE | 2 - NEWS | 12 ++++++ R/Gls.s | 7 ++- R/Olinks.r | 5 +- R/adapt_orm.r |only R/calibrate.cph.s | 43 ++++++++++++++--------- R/calibrate.default.s | 38 +++++++++++++------- R/calibrate.orm.r | 15 +++++--- R/calibrate.s | 34 +++++++++++------- R/ggplot.npsurv.r | 3 + R/intCalibration.r | 35 +++++++++---------- R/lrm.fit.r | 2 - R/plotIntercepts.r | 6 ++- R/predab.resample.s | 68 ++++++++++++++++++++++++++++++++----- R/quickRefit.r | 8 ++-- R/residuals.lrm.s | 2 - R/rmsMisc.s | 47 ++++++++++--------------- R/val.surv.s | 2 + R/validate.lrm.s | 48 ++++++++++++++------------ R/validate.ols.s | 25 +++++++------ inst/tests/anova-glm.qmd |only inst/tests/orm-censor-likelihood.r | 7 ++- man/Olinks.Rd | 9 ++++ man/adapt_orm.Rd |only man/calibrate.Rd | 6 ++- man/intCalibration.Rd | 9 ++-- man/predab.resample.Rd | 18 +++++++-- man/rmsMisc.Rd | 3 + man/validate.Rd | 2 + man/validate.Rq.Rd | 4 +- man/validate.cph.Rd | 2 + man/validate.lrm.Rd | 4 ++ man/validate.ols.Rd | 3 - 35 files changed, 349 insertions(+), 205 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions II
Description: A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions. References: Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.
Author: Manos Papadakis [aut, cre, cph],
Michail Tsagris [aut],
Stefanos Fafalios [aut],
Marios Dimitriadis [aut],
Manos Lasithiotakis [aut],
Nikolaos Kontemeniotis [ctb]
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast2 versions 0.1.5.4 dated 2025-05-02 and 0.1.5.5 dated 2025-10-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 13 ++++++++++++- build/partial.rdb |binary src/cts.cpp | 6 +++--- src/kernel.cpp | 6 +++--- src/mmp_c.cpp | 4 ++-- src/skel_helper.cpp | 2 +- 8 files changed, 32 insertions(+), 21 deletions(-)
Title: Block Assignment Files
Description: Download and read US Census Bureau data relationship files. Provides
support for cleaning and using block assignment files since 2010, as described in
<https://www.census.gov/geographies/reference-files/time-series/geo/block-assignment-files.html>.
Also includes support for working with block equivalency files, used for years
outside of decennial census years.
Author: Christopher T. Kenny [aut, cre] ,
Cory McCartan [ctb]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between baf versions 0.0.3 dated 2025-08-31 and 0.0.4 dated 2025-10-14
DESCRIPTION | 6 LICENSE | 4 MD5 | 26 +-- NEWS.md | 4 R/baf.R | 318 ++++++++++++++++++++++---------------------- R/baf_download.R | 104 +++++++------- R/clean.R | 174 ++++++++++++------------ R/data.R | 52 +++---- R/links.R | 140 +++++++++---------- man/baf_download.Rd | 56 +++---- man/baf_download_path.Rd | 34 ++-- man/example_baf.Rd | 36 ++-- tests/testthat/test-baf.R | 24 +-- tests/testthat/test-clean.R | 24 +-- 14 files changed, 503 insertions(+), 499 deletions(-)
Title: Differential Analysis of Intercellular Communication from
scRNA-Seq Data
Description: Analysis tools to investigate changes in intercellular
communication from scRNA-seq data. Using a Seurat object as input,
the package infers which cell-cell interactions are present in the dataset
and how these interactions change between two conditions of interest
(e.g. young vs old). It relies on an internal database of ligand-receptor
interactions (available for human, mouse and rat) that have been gathered
from several published studies. Detection and differential analyses
rely on permutation tests. The package also contains several tools
to perform over-representation analysis and visualize the results. See
Lagger, C. et al. (2023) <doi:10.1038/s43587-023-00514-x> for a full
description of the methodology.
Author: Cyril Lagger [aut, cre] ,
Eugen Ursu [aut],
Anais Equey [ctb]
Maintainer: Cyril Lagger <lagger.cyril@gmail.com>
Diff between scDiffCom versions 1.0.0 dated 2023-11-03 and 1.2.0 dated 2025-10-14
DESCRIPTION | 22 LICENSE | 4 MD5 | 88 NAMESPACE | 51 NEWS.md | 141 - R/data.R | 350 +-- R/interaction_analysis.R | 658 +++-- R/objects.R | 2621 +++++++++++----------- R/sysdata.rda |binary R/utils_LRI.R | 4470 +++++++++++++++++++-------------------- R/utils_cci.R | 1606 +++++++------- R/utils_filtering.R | 1341 +++++------ R/utils_interactiveNetworks.R | 3384 ++++++++++++++--------------- R/utils_ora.R | 2105 +++++++++--------- R/utils_permutation.R | 1206 +++++----- R/utils_preprocessing.R | 968 ++++---- R/utils_shiny.R | 372 +-- R/utils_validation.R | 618 ++--- README.md | 128 - inst/WORDLIST | 123 - inst/appdir/app.R | 8 inst/appdir/server.R | 3446 +++++++++++++++--------------- inst/appdir/ui.R | 354 +-- man/BuildNetwork.Rd | 86 man/BuildShiny.Rd | 54 man/EraseRawCCI.Rd | 48 man/FilterCCI.Rd | 162 - man/GetDistributions.Rd | 42 man/GetParameters.Rd | 44 man/GetTableCCI.Rd | 56 man/GetTableORA.Rd | 56 man/LRI_human.Rd | 92 man/LRI_mouse.Rd | 92 man/LRI_rat.Rd | 92 man/PlotORA.Rd | 124 - man/ReduceGO.Rd | 76 man/RunORA.Rd | 122 - man/gene_ontology_level.Rd | 46 man/run_interaction_analysis.Rd | 406 +-- man/scDiffCom-class.Rd | 72 man/seurat_sample_tms_liver.Rd | 50 man/show-scDiffCom-method.Rd | 34 tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/test-everything.R | 2295 ++++++++++---------- 45 files changed, 14187 insertions(+), 13940 deletions(-)
Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2016. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods 19(1), 10-52) <doi:10.1177/1094428115584005>.
NCA identifies necessary (but not sufficient) conditions in datasets, where x causes (e.g. precedes) y. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations.
(Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates which level of x (e.g. an effort or [...truncated...]
Author: Jan Dul [aut],
Govert Buijs [cre]
Maintainer: Govert Buijs <buijs@rsm.nl>
Diff between NCA versions 4.0.2 dated 2024-11-09 and 4.0.3 dated 2025-10-14
DESCRIPTION | 11 +- MD5 | 66 ++++++------- NEWS.md | 7 + R/nca.R | 5 - R/nca_bottleneck.R | 4 R/nca_outliers.R | 20 ++-- R/nca_plotly.R | 15 +-- R/nca_plots.R | 2 R/nca_power.R | 88 ++++++++++-------- R/nca_random.R | 4 R/nca_summary.R | 8 - R/p_ceiling.R | 22 ++-- R/p_constants.R | 3 R/p_graphics.R | 6 - R/p_ineffs.R | 2 R/p_nca_c_lp.R | 9 + R/p_nca_ce_fdhi.R | 5 - R/p_nca_ce_lfdh.R | 2 R/p_nca_ce_vrs.R | 2 R/p_nca_cols.R | 7 + R/p_nca_cr_cm.R | 11 +- R/p_nca_cr_fdh.R | 7 - R/p_nca_cr_fdhi.R | 10 +- R/p_nca_cr_vrs.R | 7 - R/p_nca_ct_fdh.R | 8 + R/p_nca_lh.R | 9 + R/p_nca_qr.R | 7 + R/p_peers.R | 252 +++++++++++++++++++--------------------------------- R/p_utils.R | 13 ++ R/p_validate.R | 8 - build/partial.rdb |binary man/NCA-package.Rd | 4 man/nca_analysis.Rd | 5 - man/point.type.Rd | 2 34 files changed, 309 insertions(+), 322 deletions(-)
Title: Generates Incidence Matrices and Bipartite Graphs
Description: Functions to generate incidence matrices and bipartite graphs that have (1) a fixed fill rate, (2) given marginal sums, (3) marginal sums that follow given distributions, or (4) represent bill sponsorships in the US Congress <doi:10.31219/osf.io/ectms>. It can also generate an incidence matrix from an adjacency matrix, or bipartite graph from a unipartite graph, via a social process mirroring team, group, or organization formation <doi:10.48550/arXiv.2204.13670>, or examine the space of binary matrices with fixed marginals.
Author: Zachary Neal [aut, cre]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between incidentally versions 1.0.3 dated 2025-07-28 and 1.0.4 dated 2025-10-14
DESCRIPTION | 8 - MD5 | 12 +- NEWS.md | 4 R/incidence.from.adjacency.R | 2 R/incidence.from.congress.R | 2 inst/doc/congress.html | 184 ++++++++++++++++++++++--------------------- inst/doc/incidentally.html | 22 ++--- 7 files changed, 124 insertions(+), 110 deletions(-)
Title: Continuous Norming
Description: A comprehensive toolkit for generating continuous test norms in
psychometrics and biometrics, and analyzing model fit. The package offers
both distribution-free modeling using Taylor polynomials and parametric
modeling using the beta-binomial and the 'Sinh-Arcsinh' distribution.
Originally developed for achievement tests, it is applicable to a wide
range of mental, physical, or other test scores dependent on continuous or
discrete explanatory variables. The package provides several advantages:
It minimizes deviations from representativeness in subsamples, interpolates
between discrete levels of explanatory variables, and significantly reduces
the required sample size compared to conventional norming per age group.
cNORM enables graphical and analytical evaluation of model fit,
accommodates a wide range of scales including those with negative and
descending values, and even supports conventional norming. It generates
norm tables including confidence intervals. It also includes methods f [...truncated...]
Author: Alexandra Lenhard [aut] ,
Wolfgang Lenhard [cre, aut] ,
Sebastian Gary [aut],
WPS Publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 3.5.0 dated 2025-09-27 and 3.5.1 dated 2025-10-14
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Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 1.1.1 dated 2025-08-23 and 1.1.2 dated 2025-10-14
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aifeducation-1.1.2/aifeducation/tests/testthat/test-03_01_LargeDataSetForTexts.R | 10 aifeducation-1.1.2/aifeducation/tests/testthat/test-03_02_LargeDataSetForTextEmbeddings.R | 14 aifeducation-1.1.2/aifeducation/tests/testthat/test-03_03_EmbeddedText.R | 11 aifeducation-1.1.2/aifeducation/tests/testthat/test-03_04_DataManager.R | 13 aifeducation-1.1.2/aifeducation/tests/testthat/test-03_05_FeatureExtractor.R | 128 aifeducation-1.1.2/aifeducation/tests/testthat/test-03_06_TextEmbeddingModels.R | 1049 ++---- aifeducation-1.1.2/aifeducation/tests/testthat/test-03_08_TEClassifiers_core.R | 335 + aifeducation-1.1.2/aifeducation/tests/testthat/test-03_09_TEClassifiersProtoNet_old.R | 23 aifeducation-1.1.2/aifeducation/tests/testthat/test-03_09_TEClassifiersPrototype.R | 70 aifeducation-1.1.2/aifeducation/tests/testthat/test-04_01_LoadOldModels.R |only aifeducation-1.1.2/aifeducation/vignettes/aifeducation.Rmd | 22 229 files changed, 7067 insertions(+), 7762 deletions(-)
Title: Generating Multi-Omics Datasets for Testing and Benchmarking
Description: Provides tools to simulate multi-omics datasets with predefined signal structures. The generated data can be used for testing, validating, and benchmarking integrative analysis methods such as factor models and clustering approaches. This version includes enhanced signal customization, visualization tools (scatter, histogram, 3D), MOFA-based analysis pipelines, PowerPoint export, and statistical profiling of datasets. Designed for both method development and teaching, SUMO supports real and synthetic data pipelines with interpretable outputs. Tini, Giulia, et al (2019) <doi:10.1093/bib/bbx167>.
Author: Bernard Isekah Osang'ir [aut, cre] ,
Ziv Shkedy [ctb],
Surya Gupta [ctb],
Juergen Claesen [ctb]
Maintainer: Bernard Isekah Osang'ir <Bernard.Osangir@sckcen.be>
Diff between SUMO versions 1.2.1 dated 2025-09-02 and 1.2.2 dated 2025-10-14
DESCRIPTION | 19 - MD5 | 36 +- NAMESPACE | 11 NEWS.md | 58 ++- R/convert_legacy_to_current_std.R |only R/demo_multiomics_analysis.R | 601 ++++++++++++++++++++++++---------- R/plot_simData.R | 228 +++++++----- R/plot_weights.R | 187 +++++++--- R/pretrained.R |only R/simulateMultiOmics.R | 187 ++++++---- R/sumo_py.R |only inst |only man/as_multiomics.Rd |only man/demo_multiomics_analysis.Rd | 83 ++++ man/plot_simData.Rd | 80 +++- man/plot_weights.Rd | 52 +- man/sumo_config_path.Rd |only man/sumo_load_pretrained_mofa.Rd |only man/sumo_mofa_backend.Rd |only man/sumo_pretrained_mofa_available.Rd |only man/sumo_pretrained_mofa_path.Rd |only man/sumo_setup_mofa.Rd |only tests/testthat/test-plot_simData.R | 3 tests/testthat/test-plot_weights.R | 3 24 files changed, 1039 insertions(+), 509 deletions(-)
Title: Build Reproducible Analytical Pipelines with 'Nix'
Description: Streamlines the creation of reproducible analytical pipelines using
'default.nix' expressions generated via the 'rix' package for reproducibility. Define
derivations in 'R', 'Python' or 'Julia', chain them into a composition of pure
functions and build the resulting pipeline using 'Nix' as the underlying
end-to-end build tool. Functions to plot the pipeline as a directed acyclic
graph are included, as well as functions to load and inspect intermediary results
for interactive analysis. User experience heavily inspired by the 'targets' package.
Author: Bruno Rodrigues [aut, cre] ,
William Michael Landau [rev]
for rOpenSci, see
<https://github.com/ropensci/software-review/issues/706>),
Anthony Martinez [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>)
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rixpress versions 0.10.0 dated 2025-10-07 and 0.10.1 dated 2025-10-14
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS.md | 7 +- R/derivs.R | 126 ++++++--------------------------------- R/rxp_init.R | 2 R/rxp_io.R | 7 -- inst/doc/importing-data.html | 4 - tests/testthat/test-derive_r.R | 38 ++++------- tests/testthat/test-parse-pkgs.R | 2 9 files changed, 59 insertions(+), 149 deletions(-)
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.2.2 dated 2025-09-29 and 0.2.3 dated 2025-10-14
DESCRIPTION | 6 MD5 | 84 ++++++------ NEWS.md | 7 + R/get_pvol.R | 30 ++-- R/get_pvol_cz.R | 9 + R/get_pvol_de.R | 211 +++++++++++++++++++++---------- R/get_pvol_dk.R | 4 R/get_pvol_ee.R | 105 ++++++++++----- R/get_pvol_fi.R | 12 + R/get_pvol_nl.R | 41 ++++-- R/get_pvol_se.R | 25 ++- R/get_pvol_sk.R | 17 +- R/get_pvol_us.R | 79 ++++++++--- R/get_vpts.R | 76 +++++++---- R/get_vpts_aloft.R | 19 +- R/get_vpts_coverage.R | 9 - R/get_vpts_coverage_aloft.R | 7 - R/get_vpts_coverage_rmi.R | 49 ++++--- R/get_vpts_rmi.R | 31 ++-- R/get_weather_radars.R | 109 +++++++++++----- R/secrets.R | 24 ++- R/utils.R | 138 ++++++++++++-------- R/utils_pvol.R | 31 ++-- R/utils_vpts_aloft.R | 75 +++++------ R/utils_vpts_rmi.R | 3 R/zzz.R | 18 +- inst/doc/supported_sources.html | 4 tests/testthat/test-get_pvol.R | 35 +++-- tests/testthat/test-get_pvol_cz.R | 24 ++- tests/testthat/test-get_pvol_de.R | 21 ++- tests/testthat/test-get_pvol_dk.R | 8 - tests/testthat/test-get_pvol_ee.R | 14 +- tests/testthat/test-get_pvol_nl.R | 26 ++- tests/testthat/test-get_pvol_ro.R | 16 +- tests/testthat/test-get_pvol_se.R | 30 +++- tests/testthat/test-get_pvol_sk.R | 21 +-- tests/testthat/test-get_pvol_us.R | 12 + tests/testthat/test-get_vpts.R | 5 tests/testthat/test-get_vpts_coverage.R | 14 +- tests/testthat/test-get_vpts_rmi.R | 3 tests/testthat/test-get_weather_radars.R | 31 +++- tests/testthat/test-secrets.R | 57 ++++++-- tests/testthat/test-utils.R | 46 ++++++ 43 files changed, 1062 insertions(+), 524 deletions(-)
Title: Fundamentos de estadística descriptiva e inferencial
Description: Este paquete pretende apoyar el proceso enseñanza-aprendizaje de estadística descriptiva e inferencial. Las funciones contenidas en el paquete 'estadistica' cubren los conceptos básicos estudiados en un curso introductorio. Muchos conceptos son ilustrados con gráficos dinámicos o web apps para facilitar su comprensión. This package aims to help the teaching-learning process of descriptive and inferential statistics. The functions contained in the package 'estadistica' cover the basic concepts studied in a statistics introductory course. Many concepts are illustrated with dynamic graphs or web apps to make the understanding easier. See: Esteban et al. (2005, ISBN: 9788497323741), Newbold et al.(2019, ISBN:9781292315034 ), Murgui et al. (2002, ISBN:9788484424673) .
Author: Vicente Coll-Serrano [aut, cre],
Rosario Martinez Verdu [aut]
Maintainer: Vicente Coll-Serrano <estadistic@uv.es>
Diff between estadistica versions 0.2.3 dated 2023-05-15 and 1.0 dated 2025-10-14
estadistica-0.2.3/estadistica/R/cuantiles.int.R |only estadistica-0.2.3/estadistica/R/mediana.int.R |only estadistica-0.2.3/estadistica/R/momento.central.R |only estadistica-0.2.3/estadistica/inst/examples/probabilidad/www/e_R_logoB_web.jpg |only estadistica-0.2.3/estadistica/man/momento.central.Rd |only estadistica-1.0/estadistica/DESCRIPTION | 24 estadistica-1.0/estadistica/MD5 | 155 +++--- estadistica-1.0/estadistica/NAMESPACE | 18 estadistica-1.0/estadistica/R/calculo.probabilidad.R |only estadistica-1.0/estadistica/R/coeficiente.variacion.R | 169 ++---- estadistica-1.0/estadistica/R/contraste.correlacion.R | 6 estadistica-1.0/estadistica/R/contraste.diferencia.medias.R | 9 estadistica-1.0/estadistica/R/contraste.diferencia.proporciones.R | 8 estadistica-1.0/estadistica/R/contraste.media.R | 8 estadistica-1.0/estadistica/R/contraste.proporcion.R | 8 estadistica-1.0/estadistica/R/contraste.razon.varianzas.R | 8 estadistica-1.0/estadistica/R/contraste_bondad.R |only estadistica-1.0/estadistica/R/contraste_bondad_cat.R |only estadistica-1.0/estadistica/R/contraste_homogeneidad.R |only estadistica-1.0/estadistica/R/contraste_independencia.R |only estadistica-1.0/estadistica/R/correlacion.R | 165 ++---- estadistica-1.0/estadistica/R/covarianza.R | 209 ++------ estadistica-1.0/estadistica/R/cuantiles.R | 187 +++---- estadistica-1.0/estadistica/R/data.sets.R | 2 estadistica-1.0/estadistica/R/descriptivos.R | 243 +++------- estadistica-1.0/estadistica/R/desviacion.R | 180 ++----- estadistica-1.0/estadistica/R/globals.R | 6 estadistica-1.0/estadistica/R/ic.correlacion.R | 5 estadistica-1.0/estadistica/R/ic.diferencia.medias.R | 8 estadistica-1.0/estadistica/R/ic.diferencia.proporciones.R | 6 estadistica-1.0/estadistica/R/ic.media.R | 14 estadistica-1.0/estadistica/R/ic.proporcion.R | 7 estadistica-1.0/estadistica/R/ic.razon.varianzas.R | 12 estadistica-1.0/estadistica/R/ic.varianza.R | 12 estadistica-1.0/estadistica/R/matriz.correlacion.R | 30 - estadistica-1.0/estadistica/R/matriz.covarianzas.R | 106 +--- estadistica-1.0/estadistica/R/media.R | 149 ++---- estadistica-1.0/estadistica/R/mediana.R | 150 +----- estadistica-1.0/estadistica/R/medidas.forma.R | 137 +++-- estadistica-1.0/estadistica/R/moda.R | 4 estadistica-1.0/estadistica/R/muestra.R | 5 estadistica-1.0/estadistica/R/nivel.confianza.R | 8 estadistica-1.0/estadistica/R/print.resumen.R |only estadistica-1.0/estadistica/R/regresion.simple.R | 112 ++-- estadistica-1.0/estadistica/R/series.temporales.R | 130 +++-- estadistica-1.0/estadistica/R/tabla.bidimensional.R | 36 - estadistica-1.0/estadistica/R/tabla.frecuencias.R | 5 estadistica-1.0/estadistica/R/utils.R |only estadistica-1.0/estadistica/R/varianza.R | 193 ++----- estadistica-1.0/estadistica/R/zzz.R | 54 +- estadistica-1.0/estadistica/inst/examples/calculo |only estadistica-1.0/estadistica/man/calculo.probabilidad.Rd |only estadistica-1.0/estadistica/man/coeficiente.variacion.Rd | 10 estadistica-1.0/estadistica/man/contraste.correlacion.Rd | 14 estadistica-1.0/estadistica/man/contraste.diferencia.medias.Rd | 20 estadistica-1.0/estadistica/man/contraste.diferencia.proporciones.Rd | 16 estadistica-1.0/estadistica/man/contraste.media.Rd | 18 estadistica-1.0/estadistica/man/contraste.proporcion.Rd | 16 estadistica-1.0/estadistica/man/contraste.razon.varianzas.Rd | 16 estadistica-1.0/estadistica/man/contraste_bondad.Rd |only estadistica-1.0/estadistica/man/contraste_bondad_cat.Rd |only estadistica-1.0/estadistica/man/contraste_homogeneidad.Rd |only estadistica-1.0/estadistica/man/contraste_independencia.Rd |only estadistica-1.0/estadistica/man/correlacion.Rd | 2 estadistica-1.0/estadistica/man/covarianza.Rd | 5 estadistica-1.0/estadistica/man/cuantiles.Rd | 12 estadistica-1.0/estadistica/man/desviacion.Rd | 5 estadistica-1.0/estadistica/man/ic.correlacion.Rd | 5 estadistica-1.0/estadistica/man/ic.diferencia.medias.Rd | 16 estadistica-1.0/estadistica/man/ic.diferencia.proporciones.Rd | 12 estadistica-1.0/estadistica/man/ic.media.Rd | 16 estadistica-1.0/estadistica/man/ic.proporcion.Rd | 14 estadistica-1.0/estadistica/man/ic.razon.varianzas.Rd | 14 estadistica-1.0/estadistica/man/ic.varianza.Rd | 14 estadistica-1.0/estadistica/man/matriz.covar.Rd | 10 estadistica-1.0/estadistica/man/medidas.forma.Rd | 14 estadistica-1.0/estadistica/man/muestra.Rd | 10 estadistica-1.0/estadistica/man/nivel.confianza.Rd | 18 estadistica-1.0/estadistica/man/print.resumen.Rd |only estadistica-1.0/estadistica/man/regresion.simple.Rd | 32 - estadistica-1.0/estadistica/man/resumen.descriptivos.Rd | 5 estadistica-1.0/estadistica/man/salarios2018.Rd | 2 estadistica-1.0/estadistica/man/series.temporales.Rd | 34 - estadistica-1.0/estadistica/man/tabla.bidimensional.Rd | 14 estadistica-1.0/estadistica/man/tabla.frecuencias.Rd | 5 estadistica-1.0/estadistica/man/varianza.Rd | 5 86 files changed, 1247 insertions(+), 1715 deletions(-)
Title: Determining the Number of Factors in Exploratory Factor Analysis
Description: Provides a collection of standard factor retention methods in Exploratory Factor
Analysis (EFA), making it easier to determine the number of factors. Traditional
methods such as the scree plot by Cattell (1966) <doi:10.1207/s15327906mbr0102_10>,
Kaiser-Guttman Criterion (KGC) by Guttman (1954) <doi:10.1007/BF02289162> and
Kaiser (1960) <doi:10.1177/001316446002000116>, and flexible Parallel Analysis
(PA) by Horn (1965) <doi:10.1007/BF02289447> based on eigenvalues form PCA or EFA
are readily available. This package also implements several newer methods, such as
the Empirical Kaiser Criterion (EKC) by Braeken and van Assen (2017)
<doi:10.1037/met0000074>, Comparison Data (CD) by Ruscio and Roche (2012)
<doi:10.1037/a0025697>, and Hull method by Lorenzo-Seva et al. (2011)
<doi:10.1080/00273171.2011.564527>, as well as some AI-based methods like
Comparison Data Forest (CDF) by Goretzko and Ruscio (2024)
<doi:10.3758/s13428-023-02122-4> and F [...truncated...]
Author: Haijiang Qin [aut, cre, cph] ,
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between EFAfactors versions 1.2.3 dated 2025-06-14 and 1.2.4 dated 2025-10-14
EFAfactors-1.2.3/EFAfactors/R/DNN_predictor.R |only EFAfactors-1.2.3/EFAfactors/R/data.datasets.R |only EFAfactors-1.2.3/EFAfactors/R/data.scaler.R |only EFAfactors-1.2.3/EFAfactors/R/extractor.feature.DNN.R |only EFAfactors-1.2.3/EFAfactors/data/data.datasets.rda |only EFAfactors-1.2.3/EFAfactors/data/data.scaler.rda |only EFAfactors-1.2.3/EFAfactors/man/DNN_predictor.Rd |only EFAfactors-1.2.3/EFAfactors/man/data.datasets.Rd |only EFAfactors-1.2.3/EFAfactors/man/data.scaler.Rd |only EFAfactors-1.2.3/EFAfactors/man/extractor.feature.DNN.Rd |only EFAfactors-1.2.3/EFAfactors/man/load_DNN.Rd |only EFAfactors-1.2.3/EFAfactors/man/load_scaler.Rd |only EFAfactors-1.2.3/EFAfactors/man/load_xgb.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.CD.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.CDF.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.DNN_predictor.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.EFAhclust.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.EFAkmeans.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.EFAscreet.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.EFAvote.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.EKC.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.FF.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.Hull.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.KGC.Rd |only EFAfactors-1.2.3/EFAfactors/man/plot.PA.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.CD.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.CDF.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.DNN_predictor.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.EFAdata.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.EFAhclust.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.EFAkmeans.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.EFAscreet.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.EFAvote.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.EKC.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.FF.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.Hull.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.KGC.Rd |only EFAfactors-1.2.3/EFAfactors/man/print.PA.Rd |only EFAfactors-1.2.4/EFAfactors/DESCRIPTION | 38 EFAfactors-1.2.4/EFAfactors/MD5 | 166 +--- EFAfactors-1.2.4/EFAfactors/NAMESPACE | 22 EFAfactors-1.2.4/EFAfactors/NEWS.md | 14 EFAfactors-1.2.4/EFAfactors/R/CD.R | 58 - EFAfactors-1.2.4/EFAfactors/R/CDF.R | 48 - EFAfactors-1.2.4/EFAfactors/R/EFAhclust.R | 40 EFAfactors-1.2.4/EFAfactors/R/EFAindex.R | 15 EFAfactors-1.2.4/EFAfactors/R/EFAscreet.R | 17 EFAfactors-1.2.4/EFAfactors/R/EFAsim.data.R | 2 EFAfactors-1.2.4/EFAfactors/R/EFAvote.R | 2 EFAfactors-1.2.4/EFAfactors/R/EKC.R | 19 EFAfactors-1.2.4/EFAfactors/R/FF.R | 21 EFAfactors-1.2.4/EFAfactors/R/GenData.R | 19 EFAfactors-1.2.4/EFAfactors/R/Hull.R | 34 EFAfactors-1.2.4/EFAfactors/R/KGC.R | 19 EFAfactors-1.2.4/EFAfactors/R/MAP.R |only EFAfactors-1.2.4/EFAfactors/R/NN.R |only EFAfactors-1.2.4/EFAfactors/R/PA.R | 29 EFAfactors-1.2.4/EFAfactors/R/STOC.R |only EFAfactors-1.2.4/EFAfactors/R/af.softmax.R | 6 EFAfactors-1.2.4/EFAfactors/R/check_python_libraries.R | 4 EFAfactors-1.2.4/EFAfactors/R/data.DAPCS.R |only EFAfactors-1.2.4/EFAfactors/R/data.datasets.DNN.R |only EFAfactors-1.2.4/EFAfactors/R/data.datasets.LSTM.R |only EFAfactors-1.2.4/EFAfactors/R/data.scaler.DNN.R |only EFAfactors-1.2.4/EFAfactors/R/data.scaler.LSTM.R |only EFAfactors-1.2.4/EFAfactors/R/extractor.feature.FF.R | 11 EFAfactors-1.2.4/EFAfactors/R/extractor.feature.NN.R |only EFAfactors-1.2.4/EFAfactors/R/factor.analysis.R | 11 EFAfactors-1.2.4/EFAfactors/R/load.R | 62 - EFAfactors-1.2.4/EFAfactors/R/model.xgb.R | 4 EFAfactors-1.2.4/EFAfactors/R/normalizor.R | 26 EFAfactors-1.2.4/EFAfactors/R/plot.R | 487 ++---------- EFAfactors-1.2.4/EFAfactors/R/print.R | 208 +---- EFAfactors-1.2.4/EFAfactors/data/data.DAPCS.rda |only EFAfactors-1.2.4/EFAfactors/data/data.datasets.DNN.rda |only EFAfactors-1.2.4/EFAfactors/data/data.datasets.LSTM.rda |only EFAfactors-1.2.4/EFAfactors/data/data.scaler.DNN.rda |only EFAfactors-1.2.4/EFAfactors/data/data.scaler.LSTM.rda |only EFAfactors-1.2.4/EFAfactors/data/datalist |only EFAfactors-1.2.4/EFAfactors/inst/extdata/LSTM.onnx |only EFAfactors-1.2.4/EFAfactors/man/CD.Rd | 57 - EFAfactors-1.2.4/EFAfactors/man/CDF.Rd | 49 - EFAfactors-1.2.4/EFAfactors/man/EFAhclust.Rd | 38 EFAfactors-1.2.4/EFAfactors/man/EFAindex.Rd | 15 EFAfactors-1.2.4/EFAfactors/man/EFAscreet.Rd | 19 EFAfactors-1.2.4/EFAfactors/man/EFAsim.data.Rd | 2 EFAfactors-1.2.4/EFAfactors/man/EFAvote.Rd | 2 EFAfactors-1.2.4/EFAfactors/man/EKC.Rd | 19 EFAfactors-1.2.4/EFAfactors/man/FF.Rd | 19 EFAfactors-1.2.4/EFAfactors/man/GenData.Rd | 19 EFAfactors-1.2.4/EFAfactors/man/Hull.Rd | 29 EFAfactors-1.2.4/EFAfactors/man/KGC.Rd | 19 EFAfactors-1.2.4/EFAfactors/man/MAP.Rd |only EFAfactors-1.2.4/EFAfactors/man/NN.Rd |only EFAfactors-1.2.4/EFAfactors/man/PA.Rd | 31 EFAfactors-1.2.4/EFAfactors/man/STOC.Rd |only EFAfactors-1.2.4/EFAfactors/man/af.softmax.Rd | 6 EFAfactors-1.2.4/EFAfactors/man/check_python_libraries.Rd | 4 EFAfactors-1.2.4/EFAfactors/man/data.DAPCS.Rd |only EFAfactors-1.2.4/EFAfactors/man/data.datasets.DNN.Rd |only EFAfactors-1.2.4/EFAfactors/man/data.datasets.LSTM.Rd |only EFAfactors-1.2.4/EFAfactors/man/data.scaler.DNN.Rd |only EFAfactors-1.2.4/EFAfactors/man/data.scaler.LSTM.Rd |only EFAfactors-1.2.4/EFAfactors/man/extractor.feature.FF.Rd | 11 EFAfactors-1.2.4/EFAfactors/man/extractor.feature.NN.Rd |only EFAfactors-1.2.4/EFAfactors/man/factor.analysis.Rd | 11 EFAfactors-1.2.4/EFAfactors/man/load.NN.Rd |only EFAfactors-1.2.4/EFAfactors/man/load.scaler.Rd |only EFAfactors-1.2.4/EFAfactors/man/load.xgb.Rd |only EFAfactors-1.2.4/EFAfactors/man/model.xgb.Rd | 4 EFAfactors-1.2.4/EFAfactors/man/normalizor.Rd | 20 EFAfactors-1.2.4/EFAfactors/man/plot.Rd |only EFAfactors-1.2.4/EFAfactors/man/print.Rd |only EFAfactors-1.2.4/EFAfactors/src/calculateRMSE.cpp | 3 EFAfactors-1.2.4/EFAfactors/tests/building.R | 8 EFAfactors-1.2.4/EFAfactors/tests/testthat/demo_realdata.R | 20 EFAfactors-1.2.4/EFAfactors/tests/testthat/demo_simulate.R | 212 ++--- EFAfactors-1.2.4/EFAfactors/tests/testthat/demo_simulate2.R | 341 ++++---- 118 files changed, 1065 insertions(+), 1275 deletions(-)
Title: Date and Time Functions for Public Health Purposes
Description: Provides easy and consistent time conversion for public health purposes. The time conversion functions provided here are between date, ISO week, ISO yearweek, ISO year, calendar month/year, season, season week.
Author: Chi Zhang [aut] ,
Richard Aubrey White [aut, cre] ,
CSIDS [cph]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between cstime versions 2023.5.3 dated 2023-05-15 and 2025.10.13 dated 2025-10-14
DESCRIPTION | 23 ++- LICENSE | 2 MD5 | 55 +++++---- NAMESPACE | 24 ++++ NEWS.md | 12 ++ R/conversion_date_isoweek_isoyear.R | 197 ++++++++++++++++++++++++++++++++- R/conversion_season.R | 10 - R/sysdata.rda |binary README.md | 31 ++--- build/vignette.rds |binary data/dates_by_isoyearweek.rda |binary data/nor_workdays_by_date.rda |binary data/nor_workdays_by_isoyearweek.rda |binary inst/doc/cstime.R | 2 inst/doc/cstime.html | 32 ++--- inst/doc/date_conversion.html | 127 +++++++++++---------- inst/doc/season.R | 2 inst/doc/season.Rmd | 2 inst/doc/season.html | 44 +++---- man/date_to_isoquarter_c.Rd |only man/date_to_isoquarter_n.Rd |only man/date_to_isoyearquarter_c.Rd |only man/figures/logo.png |binary man/isoweek_to_seasonweek_n.Rd | 6 - man/isoyearweek_to_isoquarter_c.Rd |only man/isoyearweek_to_isoquarter_n.Rd |only man/isoyearweek_to_isoyearquarter_c.Rd |only man/isoyearweek_to_seasonweek_n.Rd | 4 man/season_to_last_date.Rd |only man/seasonweek_to_isoweek_c.Rd | 4 man/seasonweek_to_isoweek_n.Rd | 4 vignettes/season.Rmd | 2 32 files changed, 413 insertions(+), 170 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-11 0.5.0
2020-11-12 0.4.0
Title: Mapping Brain Folding Patterns
Description: Visualizes sulcal morphometry data derived from 'BrainVisa' <https://brainvisa.info/> including width, depth, surface area, and length. The package enables mapping of statistical group results or subject-level values onto cortical surface maps, with options to focus on all sulci or only selected regions of interest. Users can display all four measures simultaneously or restrict plots to chosen measures, creating composite, publication-quality brain visualizations in R to support the analysis and interpretation of sulcal morphology.
Author: Mahan Shafie [aut, cre]
Maintainer: Mahan Shafie <mahan.shafie@unito.it>
Diff between sulcimap versions 1.0.4 dated 2025-10-06 and 1.0.5 dated 2025-10-14
sulcimap-1.0.4/sulcimap/man/dot-ensure_sulcimap_assets.Rd |only sulcimap-1.0.5/sulcimap/DESCRIPTION | 6 - sulcimap-1.0.5/sulcimap/MD5 | 12 +- sulcimap-1.0.5/sulcimap/NEWS.md |only sulcimap-1.0.5/sulcimap/R/assets.R | 65 ++++++++++---- sulcimap-1.0.5/sulcimap/R/plot_sulci.R | 4 sulcimap-1.0.5/sulcimap/man/get_sulcimap_assets_dir.Rd | 3 sulcimap-1.0.5/sulcimap/man/get_sulcus_image.Rd | 2 8 files changed, 65 insertions(+), 27 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Author: Craig Gower-Page [aut, cre],
Isaac Gravestock [aut],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Daniel Sabanes Bove [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Craig Gower-Page <craig.gower-page@novartis.com>
Diff between rbmi versions 1.4.1 dated 2025-03-03 and 1.5.1 dated 2025-10-14
DESCRIPTION | 23 - MD5 | 182 ++++++---- NAMESPACE | 7 NEWS.md | 24 + R/analyse.R | 77 +++- R/ancova.R | 11 R/as_ascii_table.R | 22 - R/bootstrap.R | 2 R/controls.R | 133 +++++-- R/dataclasses.R | 49 -- R/delta.R | 14 R/draws.R | 80 +++- R/expand.R | 30 - R/impute.R | 153 +++++--- R/longData.R | 110 +++--- R/lsmeans.R | 23 - R/mcmc.R | 137 ++++++- R/methods.R | 95 +++++ R/mmrm.R | 205 ++++++++--- R/parallel.R | 17 R/pool.R | 220 ++++++++++-- R/rbmi.R | 1 R/scaling.R | 14 R/simulate.R | 33 + R/simulate_data.R | 86 +++- R/stack.R | 3 R/strategies.R | 21 - R/utilities.R | 322 +++++++++++++++--- R/validate.R | 1 R/validate_datalong.R | 18 - R/zzz.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/CondMean_Inference.html | 7 inst/doc/advanced.html | 5 inst/doc/quickstart.html | 66 +-- inst/doc/stat_specs.html | 147 ++++++-- inst/stan/MMRM.stan | 24 - inst/stan/covariance_priors |only man/STAN_BLOCKS.Rd |only man/adjust_dimensions.Rd |only man/as_mmrm_df.Rd | 3 man/as_stan_fragments.Rd |only man/clear_model_cache.Rd |only man/complete_control_bayes.Rd |only man/draws.Rd | 3 man/eval_mmrm.Rd | 8 man/extract_params.Rd | 4 man/find_stan_file.Rd |only man/fit_mmrm.Rd | 3 man/get_stan_model.Rd | 13 man/is_valid_covariance_prior.Rd |only man/mcse_internal.Rd |only man/method.Rd | 16 man/pool.Rd | 24 + man/prepare_init_vals.Rd |only man/prepare_prior_params.Rd |only man/rbmi-package.Rd | 4 man/theta_to_cor.Rd |only man/theta_to_cs_cor.Rd |only tests/testthat.R | 10 tests/testthat/_snaps/impute.md |only tests/testthat/_snaps/mmrm.md |only tests/testthat/_snaps/pool.md |only tests/testthat/_snaps/print.md | 2 tests/testthat/_snaps/utilities.md |only tests/testthat/helper-misc.R | 91 ++++- tests/testthat/setup.R |only tests/testthat/test-analyse.R | 33 - tests/testthat/test-ancova.R | 37 +- tests/testthat/test-controls.R | 69 +++ tests/testthat/test-delta.R | 88 +++-- tests/testthat/test-draws.R | 163 +++++---- tests/testthat/test-expand.R | 158 ++++----- tests/testthat/test-fullusage.R | 305 +++++++++++++---- tests/testthat/test-impute.R | 254 +++++++------- tests/testthat/test-longData.R | 517 +++++++++++++++++++---------- tests/testthat/test-lsmeans.R | 28 - tests/testthat/test-mcmc.R | 557 +++++++++++++++++++++++++++----- tests/testthat/test-methods.R | 5 tests/testthat/test-misc.R | 25 - tests/testthat/test-mmrm.R | 226 +++++++++--- tests/testthat/test-parallel.R | 58 ++- tests/testthat/test-pool.R | 322 +++++++++--------- tests/testthat/test-print.R | 37 -- tests/testthat/test-reproducibility.R | 42 +- tests/testthat/test-scaling.R | 9 tests/testthat/test-simulate.R | 10 tests/testthat/test-simulate_data.R | 149 +++++--- tests/testthat/test-strategies.R | 33 - tests/testthat/test-utilities.R | 107 ++++-- tests/testthat/test-validate-longdata.R | 70 +--- vignettes/FAQ.html | 3 vignettes/build.R | 2 vignettes/references.bib | 33 + vignettes/retrieved_dropout.html | 15 vignettes/stat_specs.Rmd | 70 +++- 97 files changed, 4050 insertions(+), 1920 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel [aut, cre] ,
QuantLib Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.16 dated 2025-07-23 and 0.0.17 dated 2025-10-14
ChangeLog | 14 + DESCRIPTION | 8 MD5 | 248 +++++++++++++++--------------- README.md | 2 build/partial.rdb |binary src/ql/errors.cpp | 2 src/ql/errors.hpp | 2 src/ql/optional.hpp | 2 src/ql/patterns/observable.cpp | 2 src/ql/patterns/observable.hpp | 2 src/ql/patterns/singleton.hpp | 2 src/ql/qldefines.hpp | 2 src/ql/settings.cpp | 2 src/ql/settings.hpp | 2 src/ql/shared_ptr.hpp | 2 src/ql/time/businessdayconvention.cpp | 2 src/ql/time/businessdayconvention.hpp | 2 src/ql/time/calendar.cpp | 2 src/ql/time/calendar.hpp | 2 src/ql/time/calendars/argentina.cpp | 2 src/ql/time/calendars/argentina.hpp | 2 src/ql/time/calendars/australia.cpp | 2 src/ql/time/calendars/australia.hpp | 2 src/ql/time/calendars/austria.cpp | 2 src/ql/time/calendars/austria.hpp | 2 src/ql/time/calendars/bespokecalendar.cpp | 2 src/ql/time/calendars/bespokecalendar.hpp | 2 src/ql/time/calendars/botswana.cpp | 2 src/ql/time/calendars/botswana.hpp | 2 src/ql/time/calendars/brazil.cpp | 2 src/ql/time/calendars/brazil.hpp | 2 src/ql/time/calendars/canada.cpp | 2 src/ql/time/calendars/canada.hpp | 2 src/ql/time/calendars/chile.cpp | 2 src/ql/time/calendars/chile.hpp | 2 src/ql/time/calendars/china.cpp | 2 src/ql/time/calendars/china.hpp | 2 src/ql/time/calendars/czechrepublic.cpp | 2 src/ql/time/calendars/czechrepublic.hpp | 2 src/ql/time/calendars/denmark.cpp | 2 src/ql/time/calendars/denmark.hpp | 2 src/ql/time/calendars/finland.cpp | 2 src/ql/time/calendars/finland.hpp | 2 src/ql/time/calendars/france.cpp | 2 src/ql/time/calendars/france.hpp | 2 src/ql/time/calendars/germany.cpp | 2 src/ql/time/calendars/germany.hpp | 2 src/ql/time/calendars/hongkong.cpp | 2 src/ql/time/calendars/hongkong.hpp | 2 src/ql/time/calendars/hungary.cpp | 2 src/ql/time/calendars/hungary.hpp | 2 src/ql/time/calendars/iceland.cpp | 2 src/ql/time/calendars/iceland.hpp | 2 src/ql/time/calendars/india.cpp | 2 src/ql/time/calendars/india.hpp | 2 src/ql/time/calendars/indonesia.cpp | 2 src/ql/time/calendars/indonesia.hpp | 2 src/ql/time/calendars/israel.cpp | 2 src/ql/time/calendars/israel.hpp | 2 src/ql/time/calendars/italy.cpp | 2 src/ql/time/calendars/italy.hpp | 2 src/ql/time/calendars/japan.cpp | 2 src/ql/time/calendars/japan.hpp | 2 src/ql/time/calendars/jointcalendar.cpp | 2 src/ql/time/calendars/jointcalendar.hpp | 2 src/ql/time/calendars/mexico.cpp | 2 src/ql/time/calendars/mexico.hpp | 2 src/ql/time/calendars/newzealand.cpp | 2 src/ql/time/calendars/newzealand.hpp | 2 src/ql/time/calendars/norway.cpp | 2 src/ql/time/calendars/norway.hpp | 2 src/ql/time/calendars/nullcalendar.hpp | 2 src/ql/time/calendars/poland.cpp | 2 src/ql/time/calendars/poland.hpp | 2 src/ql/time/calendars/romania.cpp | 2 src/ql/time/calendars/romania.hpp | 2 src/ql/time/calendars/russia.cpp | 2 src/ql/time/calendars/russia.hpp | 2 src/ql/time/calendars/saudiarabia.cpp | 2 src/ql/time/calendars/saudiarabia.hpp | 2 src/ql/time/calendars/singapore.cpp | 16 + src/ql/time/calendars/singapore.hpp | 2 src/ql/time/calendars/slovakia.cpp | 2 src/ql/time/calendars/slovakia.hpp | 2 src/ql/time/calendars/southafrica.cpp | 2 src/ql/time/calendars/southafrica.hpp | 2 src/ql/time/calendars/southkorea.cpp | 2 src/ql/time/calendars/southkorea.hpp | 2 src/ql/time/calendars/sweden.cpp | 2 src/ql/time/calendars/sweden.hpp | 2 src/ql/time/calendars/switzerland.cpp | 2 src/ql/time/calendars/switzerland.hpp | 2 src/ql/time/calendars/taiwan.cpp | 2 src/ql/time/calendars/taiwan.hpp | 2 src/ql/time/calendars/target.cpp | 2 src/ql/time/calendars/target.hpp | 2 src/ql/time/calendars/thailand.cpp | 2 src/ql/time/calendars/thailand.hpp | 2 src/ql/time/calendars/turkey.cpp | 2 src/ql/time/calendars/turkey.hpp | 2 src/ql/time/calendars/ukraine.cpp | 2 src/ql/time/calendars/ukraine.hpp | 2 src/ql/time/calendars/unitedkingdom.cpp | 2 src/ql/time/calendars/unitedkingdom.hpp | 2 src/ql/time/calendars/unitedstates.cpp | 2 src/ql/time/calendars/unitedstates.hpp | 2 src/ql/time/calendars/weekendsonly.cpp | 2 src/ql/time/calendars/weekendsonly.hpp | 2 src/ql/time/date.cpp | 2 src/ql/time/date.hpp | 2 src/ql/time/frequency.cpp | 2 src/ql/time/frequency.hpp | 2 src/ql/time/period.cpp | 8 src/ql/time/period.hpp | 2 src/ql/time/timeunit.cpp | 2 src/ql/time/timeunit.hpp | 2 src/ql/time/weekday.cpp | 2 src/ql/time/weekday.hpp | 2 src/ql/types.hpp | 2 src/ql/utilities/dataformatters.cpp | 2 src/ql/utilities/dataformatters.hpp | 2 src/ql/utilities/dataparsers.cpp | 2 src/ql/utilities/dataparsers.hpp | 2 src/ql/utilities/null.hpp | 2 src/ql/utilities/observablevalue.hpp | 2 125 files changed, 283 insertions(+), 249 deletions(-)
Title: Additional Predictor with Maximum Effect Size
Description: Methods of selecting one from many numeric predictors
for a regression model, to ensure that the additional
predictor has the maximum effect size.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [aut]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between maxEff versions 0.1.1 dated 2025-04-02 and 0.2.0 dated 2025-10-14
maxEff-0.1.1/maxEff/R/add_num.R |only maxEff-0.1.1/maxEff/R/splitd.R |only maxEff-0.1.1/maxEff/inst/doc/intro.Rmd |only maxEff-0.1.1/maxEff/man/S3_add_.Rd |only maxEff-0.1.1/maxEff/man/S3_add_dummy.Rd |only maxEff-0.1.1/maxEff/man/add_num.Rd |only maxEff-0.1.1/maxEff/man/predict.add_num.Rd |only maxEff-0.1.1/maxEff/vignettes/intro.Rmd |only maxEff-0.2.0/maxEff/DESCRIPTION | 24 maxEff-0.2.0/maxEff/MD5 | 54 + maxEff-0.2.0/maxEff/NAMESPACE | 30 - maxEff-0.2.0/maxEff/R/0PACKAGE.R | 4 maxEff-0.2.0/maxEff/R/add_S3.R | 27 maxEff-0.2.0/maxEff/R/add_dummy.R | 295 ++++++---- maxEff-0.2.0/maxEff/R/add_dummy_partition.R |only maxEff-0.2.0/maxEff/R/add_numeric.R |only maxEff-0.2.0/maxEff/R/node1.R | 246 ++++---- maxEff-0.2.0/maxEff/R/onLoad_parallel.R |only maxEff-0.2.0/maxEff/R/prepare_add.R | 13 maxEff-0.2.0/maxEff/build/vignette.rds |binary maxEff-0.2.0/maxEff/inst/doc/intro.R | 123 ---- maxEff-0.2.0/maxEff/inst/doc/intro.html | 733 ++++--------------------- maxEff-0.2.0/maxEff/inst/doc/intro.qmd |only maxEff-0.2.0/maxEff/man/add_dummy.Rd | 41 - maxEff-0.2.0/maxEff/man/add_dummy_partition.Rd |only maxEff-0.2.0/maxEff/man/add_numeric.Rd |only maxEff-0.2.0/maxEff/man/labels.add_dummy.Rd |only maxEff-0.2.0/maxEff/man/labels.add_numeric.Rd |only maxEff-0.2.0/maxEff/man/maxEff-package.Rd | 7 maxEff-0.2.0/maxEff/man/node1.Rd | 61 -- maxEff-0.2.0/maxEff/man/predict.node1.Rd | 15 maxEff-0.2.0/maxEff/man/predict_add_dummy.Rd |only maxEff-0.2.0/maxEff/man/predict_add_numeric.Rd |only maxEff-0.2.0/maxEff/man/print.add_dummy.Rd |only maxEff-0.2.0/maxEff/man/print.add_numeric.Rd |only maxEff-0.2.0/maxEff/man/sort_by.add_.Rd |only maxEff-0.2.0/maxEff/man/splitd.Rd | 8 maxEff-0.2.0/maxEff/man/subset.add_dummy.Rd |only maxEff-0.2.0/maxEff/vignettes/intro.qmd |only maxEff-0.2.0/maxEff/vignettes/maxEff.bib |only 40 files changed, 572 insertions(+), 1109 deletions(-)
Title: Simulated Grouped Hyper Data Frame
Description: An intuitive interface to simulate (1) superimposed (marked) point patterns with vectorized parameterization of random point pattern and distribution of marks; and (2) grouped hyper data frame based on population parameters and subject-specific random effects.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [aut]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe.random versions 0.1.0 dated 2025-04-07 and 0.2.0 dated 2025-10-14
groupedHyperframe.random-0.1.0/groupedHyperframe.random/R/append_marks_ppp.R |only groupedHyperframe.random-0.1.0/groupedHyperframe.random/R/rmarks_ppp.R |only groupedHyperframe.random-0.1.0/groupedHyperframe.random/R/rmvnorm_.R |only groupedHyperframe.random-0.1.0/groupedHyperframe.random/inst/doc/intro.R |only groupedHyperframe.random-0.1.0/groupedHyperframe.random/inst/doc/intro.Rmd |only groupedHyperframe.random-0.1.0/groupedHyperframe.random/inst/doc/intro.html |only groupedHyperframe.random-0.1.0/groupedHyperframe.random/man/append_marks.ppp-set.Rd |only groupedHyperframe.random-0.1.0/groupedHyperframe.random/man/rmarks_ppp.Rd |only groupedHyperframe.random-0.1.0/groupedHyperframe.random/man/rmvnorm_.Rd |only groupedHyperframe.random-0.1.0/groupedHyperframe.random/vignettes/intro.Rmd |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/DESCRIPTION | 23 +++--- groupedHyperframe.random-0.2.0/groupedHyperframe.random/MD5 | 36 ++++------ groupedHyperframe.random-0.2.0/groupedHyperframe.random/NAMESPACE | 7 - groupedHyperframe.random-0.2.0/groupedHyperframe.random/R/0PACKAGE.R | 2 groupedHyperframe.random-0.2.0/groupedHyperframe.random/R/grouped_rppp.R | 6 - groupedHyperframe.random-0.2.0/groupedHyperframe.random/R/mvrnorm2.R |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/R/onLoad.R |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/R/rfactor.R |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/R/rppp.R | 35 ++++++--- groupedHyperframe.random-0.2.0/groupedHyperframe.random/build/vignette.rds |binary groupedHyperframe.random-0.2.0/groupedHyperframe.random/inst/doc/groupedHyperframe.random.R |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/inst/doc/groupedHyperframe.random.html |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/inst/doc/groupedHyperframe.random.qmd |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/man/groupedHyperframe.random-package.Rd | 7 + groupedHyperframe.random-0.2.0/groupedHyperframe.random/man/mvrnorm2.Rd | 29 ++++---- groupedHyperframe.random-0.2.0/groupedHyperframe.random/man/rfactor.Rd | 12 ++- groupedHyperframe.random-0.2.0/groupedHyperframe.random/vignettes/groupedHyperframe.random.bib |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/vignettes/groupedHyperframe.random.qmd |only 28 files changed, 91 insertions(+), 66 deletions(-)
More information about groupedHyperframe.random at CRAN
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Title: Grouped Hyper Data Frame: An Extension of Hyper Data Frame
Description: An S3 class 'groupedHyperframe' that
inherits from hyper data frame. Batch
processes on point-pattern hyper column.
Aggregation of function-value-table hyper
column(s) and numeric hyper column(s) over a
nested grouping structure.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [aut]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.2.4 dated 2025-06-27 and 0.3.0 dated 2025-10-14
groupedHyperframe-0.2.4/groupedHyperframe/R/aggregate_fv.R |only groupedHyperframe-0.2.4/groupedHyperframe/R/aggregate_num.R |only groupedHyperframe-0.2.4/groupedHyperframe/R/key1.R |only groupedHyperframe-0.2.4/groupedHyperframe/R/mark_names.R |only groupedHyperframe-0.2.4/groupedHyperframe/R/slice.R |only groupedHyperframe-0.2.4/groupedHyperframe/man/aggregate_by_.Rd |only groupedHyperframe-0.2.4/groupedHyperframe/man/aggregate_fv.Rd |only groupedHyperframe-0.2.4/groupedHyperframe/man/aggregate_num.Rd |only groupedHyperframe-0.2.4/groupedHyperframe/man/check_fvlist.Rd |only groupedHyperframe-0.2.4/groupedHyperframe/man/dot-slice.Rd |only groupedHyperframe-0.2.4/groupedHyperframe/man/key1.Rd |only groupedHyperframe-0.2.4/groupedHyperframe/man/mark_names.Rd |only groupedHyperframe-0.2.4/groupedHyperframe/man/na.omit.ppp.Rd |only groupedHyperframe-0.2.4/groupedHyperframe/man/op_ppp.Rd |only groupedHyperframe-0.2.4/groupedHyperframe/man/user_hyperframe.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/DESCRIPTION | 18 groupedHyperframe-0.3.0/groupedHyperframe/MD5 | 146 - groupedHyperframe-0.3.0/groupedHyperframe/NAMESPACE | 266 + groupedHyperframe-0.3.0/groupedHyperframe/R/0PACKAGE.R | 15 groupedHyperframe-0.3.0/groupedHyperframe/R/Defunct.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/aggregate.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/aggregate_marks.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/append_marks.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/cbind.groupedHyperframe.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/cor_spatial.R | 12 groupedHyperframe-0.3.0/groupedHyperframe/R/data_doc.R | 8 groupedHyperframe-0.3.0/groupedHyperframe/R/density_marks.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/fvlist.R | 353 ++ groupedHyperframe-0.3.0/groupedHyperframe/R/groupedHyperframe.R | 30 groupedHyperframe-0.3.0/groupedHyperframe/R/grouped_ppp.R | 129 groupedHyperframe-0.3.0/groupedHyperframe/R/hyperframe_S3.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/interpolation.fv.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/kerndens.R | 106 groupedHyperframe-0.3.0/groupedHyperframe/R/key1val.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/kmeans.R | 36 groupedHyperframe-0.3.0/groupedHyperframe/R/lastLegal.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/mc_identical_by.R | 144 - groupedHyperframe-0.3.0/groupedHyperframe/R/nncross.R | 11 groupedHyperframe-0.3.0/groupedHyperframe/R/onLoad_parallel.R | 58 groupedHyperframe-0.3.0/groupedHyperframe/R/op_hyperframe.R | 676 +++- groupedHyperframe-0.3.0/groupedHyperframe/R/op_ppp.R | 179 - groupedHyperframe-0.3.0/groupedHyperframe/R/op_ppplist.R | 185 - groupedHyperframe-0.3.0/groupedHyperframe/R/pmean.R | 16 groupedHyperframe-0.3.0/groupedHyperframe/R/ppp_S3.R | 140 groupedHyperframe-0.3.0/groupedHyperframe/R/quantile.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/randLabel_test.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/rmax.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/split_kmeans.R | 3 groupedHyperframe-0.3.0/groupedHyperframe/R/subset_ppp_tzh.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/summary_fv.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/superimpose.hyperframe.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/trapz.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/vectorlist.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/vignette.R |only groupedHyperframe-0.3.0/groupedHyperframe/R/vtrapz.R |only groupedHyperframe-0.3.0/groupedHyperframe/data/Ki67.rda |binary groupedHyperframe-0.3.0/groupedHyperframe/data/wrobel_lung.rda |binary groupedHyperframe-0.3.0/groupedHyperframe/inst/doc/groupedHyperframe.R | 239 - groupedHyperframe-0.3.0/groupedHyperframe/inst/doc/groupedHyperframe.html | 1413 ++-------- groupedHyperframe-0.3.0/groupedHyperframe/inst/doc/groupedHyperframe.qmd | 764 +---- groupedHyperframe-0.3.0/groupedHyperframe/man/Ki67.Rd | 9 groupedHyperframe-0.3.0/groupedHyperframe/man/aggregate.groupedHyperframe.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/aggregate.vectorlist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/aggregate_marks.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/append_marks_set.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/as.fvlist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/as.vectorlist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/batch.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/cbind.groupedHyperframe.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/cli_defunct_.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/defunct.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/density_marks.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/dot-nncross.Rd | 12 groupedHyperframe-0.3.0/groupedHyperframe/man/foobar.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/fv2theo.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/get_nested.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/groupedHyperframe-package.Rd | 9 groupedHyperframe-0.3.0/groupedHyperframe/man/interpolation_fv.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/is.fvlist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/is.numeric.ppp.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/is.vectorlist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/kerndens.Rd | 26 groupedHyperframe-0.3.0/groupedHyperframe/man/keyval.fv.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/lastLegal.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/length.hyperframe.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/log_ppp.Rd | 18 groupedHyperframe-0.3.0/groupedHyperframe/man/mc_identical_by.Rd | 6 groupedHyperframe-0.3.0/groupedHyperframe/man/na_fail_ppp.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/op_hyperframe.Rd | 19 groupedHyperframe-0.3.0/groupedHyperframe/man/op_ppplist.Rd | 42 groupedHyperframe-0.3.0/groupedHyperframe/man/pairwise_cor_spatial.Rd | 5 groupedHyperframe-0.3.0/groupedHyperframe/man/pmean.Rd | 2 groupedHyperframe-0.3.0/groupedHyperframe/man/ppp2..Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/print.fvlist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/quantile.anylist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/quantile.hyperframe.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/quantile.ppp.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/quantile.ppplist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/rmax.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/sub-.ppp_tzh.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/summary.fvlist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/summary_fv.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/superimpose.groupedHyperframe.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/superimpose.hyperframe.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/t.vectorlist.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/trapz_fv.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/vignette_methods.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/visualize_vtrapz.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/man/vtrapz.Rd |only groupedHyperframe-0.3.0/groupedHyperframe/vignettes/groupedHyperframe.bib | 184 - groupedHyperframe-0.3.0/groupedHyperframe/vignettes/groupedHyperframe.qmd | 764 +---- 111 files changed, 2588 insertions(+), 3455 deletions(-)
More information about groupedHyperframe at CRAN
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Title: Dice Plot Visualization for 'ggplot2'
Description: Provides 'ggplot2' extensions for creating dice-based visualizations
where each dot position represents a specific categorical variable. The package
includes geom_dice() for displaying presence/absence of categorical variables
using traditional dice patterns. Each dice position (1-6) represents a different
category, with dots shown only when that category is present. This allows
intuitive visualization of up to 6 categorical variables simultaneously.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between ggdiceplot versions 0.1.0 dated 2025-08-21 and 0.1.1 dated 2025-10-14
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- R/geom-dice-ggprotto.R |only R/utils.R | 24 ++++++++++++++++++++---- README.md | 8 ++++++++ 5 files changed, 35 insertions(+), 10 deletions(-)
Title: Load Configuration Values
Description: A simple approach to configuring R projects with different
parameter values. Configurations are specified using a reduced subset of base
R and parsed accordingly.
Author: Tim Taylor [aut, cre, cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ronfig versions 0.0.4 dated 2025-10-06 and 0.0.5 dated 2025-10-14
ronfig-0.0.4/ronfig/inst/doc/ronfig.Rmd |only ronfig-0.0.4/ronfig/vignettes/ronfig.Rmd |only ronfig-0.0.5/ronfig/DESCRIPTION | 10 ronfig-0.0.5/ronfig/MD5 | 14 ronfig-0.0.5/ronfig/NEWS.md | 11 ronfig-0.0.5/ronfig/build/vignette.rds |binary ronfig-0.0.5/ronfig/inst/doc/ronfig.R | 9 ronfig-0.0.5/ronfig/inst/doc/ronfig.html | 473 ++++++++++++++++++++----------- ronfig-0.0.5/ronfig/inst/doc/ronfig.qmd |only ronfig-0.0.5/ronfig/vignettes/ronfig.qmd |only 10 files changed, 342 insertions(+), 175 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous and continuous response data using latent factor by both 1PL LSIRM and 2PL LSIRM as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>. It includes original 1PL LSIRM and 2PL LSIRM provided for binary response data and its extension for continuous response data. Bayesian model selection with spike-and-slab prior and method for dealing data with missing value under missing at random, missing completely at random are also supported. Various diagnostic plots are available to inspect the latent space and summary of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 1.3.7 dated 2025-08-21 and 1.3.8 dated 2025-10-14
DESCRIPTION | 8 - MD5 | 146 ++++++++++++++++---------------- R/lsirm1pl_fixed_gamma.R | 4 R/lsirm1pl_fixed_gamma_mar.R | 4 R/lsirm1pl_fixed_gamma_mcar.R | 4 R/lsirm1pl_mar.R | 4 R/lsirm1pl_mar_ss.R | 4 R/lsirm1pl_mcar.R | 4 R/lsirm1pl_mcar_ss.R | 4 R/lsirm1pl_normal_fixed_gamma.R | 4 R/lsirm1pl_normal_fixed_gamma_mar.R | 4 R/lsirm1pl_normal_fixed_gamma_mcar.R | 4 R/lsirm1pl_normal_mar.R | 4 R/lsirm1pl_normal_mar_ss.R | 4 R/lsirm1pl_normal_mcar.R | 4 R/lsirm1pl_normal_mcar_ss.R | 4 R/lsirm1pl_normal_o.R | 4 R/lsirm1pl_normal_ss.R | 4 R/lsirm1pl_o.R | 4 R/lsirm1pl_ss.R | 4 R/lsirm2pl_fixed_gamma.R | 4 R/lsirm2pl_fixed_gamma_mar.R | 4 R/lsirm2pl_fixed_gamma_mcar.R | 4 R/lsirm2pl_mar.R | 4 R/lsirm2pl_mar_ss.R | 4 R/lsirm2pl_mcar.R | 4 R/lsirm2pl_mcar_ss.R | 4 R/lsirm2pl_normal_fixed_gamma.R | 4 R/lsirm2pl_normal_fixed_gamma_mar.R | 4 R/lsirm2pl_normal_fixed_gamma_mcar.R | 4 R/lsirm2pl_normal_mar.R | 4 R/lsirm2pl_normal_mar_ss.R | 4 R/lsirm2pl_normal_mcar.R | 4 R/lsirm2pl_normal_mcar_ss.R | 4 R/lsirm2pl_normal_o.R | 4 R/lsirm2pl_normal_ss.R | 4 R/lsirm2pl_o.R | 4 R/lsirm2pl_ss.R | 4 man/lsirm1pl_fixed_gamma.Rd | 2 man/lsirm1pl_fixed_gamma_mar.Rd | 2 man/lsirm1pl_fixed_gamma_mcar.Rd | 2 man/lsirm1pl_mar.Rd | 2 man/lsirm1pl_mar_ss.Rd | 2 man/lsirm1pl_mcar.Rd | 2 man/lsirm1pl_mcar_ss.Rd | 2 man/lsirm1pl_normal_fixed_gamma.Rd | 2 man/lsirm1pl_normal_fixed_gamma_mar.Rd | 2 man/lsirm1pl_normal_fixed_gamma_mcar.Rd | 2 man/lsirm1pl_normal_mar.Rd | 2 man/lsirm1pl_normal_mar_ss.Rd | 2 man/lsirm1pl_normal_mcar.Rd | 2 man/lsirm1pl_normal_mcar_ss.Rd | 2 man/lsirm1pl_normal_o.Rd | 2 man/lsirm1pl_normal_ss.Rd | 2 man/lsirm1pl_o.Rd | 2 man/lsirm1pl_ss.Rd | 2 man/lsirm2pl_fixed_gamma.Rd | 2 man/lsirm2pl_fixed_gamma_mar.Rd | 2 man/lsirm2pl_fixed_gamma_mcar.Rd | 2 man/lsirm2pl_mar.Rd | 2 man/lsirm2pl_mar_ss.Rd | 2 man/lsirm2pl_mcar.Rd | 2 man/lsirm2pl_mcar_ss.Rd | 2 man/lsirm2pl_normal_fixed_gamma.Rd | 2 man/lsirm2pl_normal_fixed_gamma_mar.Rd | 2 man/lsirm2pl_normal_fixed_gamma_mcar.Rd | 2 man/lsirm2pl_normal_mar.Rd | 2 man/lsirm2pl_normal_mar_ss.Rd | 2 man/lsirm2pl_normal_mcar.Rd | 2 man/lsirm2pl_normal_mcar_ss.Rd | 2 man/lsirm2pl_normal_o.Rd | 2 man/lsirm2pl_normal_ss.Rd | 2 man/lsirm2pl_o.Rd | 2 man/lsirm2pl_ss.Rd | 2 74 files changed, 293 insertions(+), 77 deletions(-)
Title: Conventional and Fuzzy Data Envelopment Analysis
Description: Set of functions for Data Envelopment Analysis, including classical, fuzzy, cross-efficiency, bootstrapping, and Malmquist models. See: Banker, R.; Charnes, A.; Cooper, W.W. (1984). <doi:10.1287/mnsc.30.9.1078>, Charnes, A.; Cooper, W.W.; Rhodes, E. (1978). <doi:10.1016/0377-2217(78)90138-8> and Charnes, A.; Cooper, W.W.; Rhodes, E. (1981). <doi:10.1287/mnsc.27.6.668>.
Author: Vicente Bolos [aut, cre],
Vicente Coll-Serrano [aut],
Rafael Benitez Suarez [aut]
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between deaR versions 1.5.1 dated 2025-10-07 and 1.5.2 dated 2025-10-14
DESCRIPTION | 8 - MD5 | 11 - R/model_lgo.R | 59 +++---- R/model_qgo.R | 435 ++++++++++++++++++++++++++++++++++--------------------- inst |only man/model_lgo.Rd | 9 - man/model_qgo.Rd | 21 +- 7 files changed, 328 insertions(+), 215 deletions(-)
Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya [aut, cre]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-19 dated 2025-05-26 and 1.2-20 dated 2025-10-14
ChangeLog | 10 + DESCRIPTION | 8 - MD5 | 28 ++-- NAMESPACE | 1 R/plot.r | 11 + R/predict.scam.R | 212 ++++++++++++++++++------------- R/residuals.scam.R | 126 ++++++++++++++++++ R/scam.check.R | 34 +++- R/scam.r | 2 R/uni.smooth.const-lscop.r | 85 ++++++------ build/partial.rdb |binary man/anova.scam.Rd | 2 man/residuals.scam.Rd | 62 +++++++-- man/scam.check.Rd | 63 ++++++--- man/smooth.construct.lmpi.smooth.spec.Rd | 4 15 files changed, 450 insertions(+), 198 deletions(-)
Title: Automate the Delineation of Urban River Spaces
Description: Provides tools to automate the morphological delineation of
riverside urban areas based on a method introduced in Forgaci (2018)
<doi:10.7480/abe.2018.31>. Delineation entails the identification of
corridor boundaries, segmentation of the corridor, and delineation of
the river space using two-dimensional spatial information from street
network data and digital elevation data in a projected CRS. The
resulting delineation can be used to characterise spatial phenomena
that can be related to the river as a central element.
Author: Claudiu Forgaci [aut, cre, cph] ,
Francesco Nattino [aut] ,
Fakhereh Alidoost [ctb] ,
Meiert Willem Grootes [ctb] ,
Netherlands eScience Center [fnd]
Maintainer: Claudiu Forgaci <c.forgaci@tudelft.nl>
Diff between rcrisp versions 0.2.0 dated 2025-08-21 and 0.3.0 dated 2025-10-14
rcrisp-0.2.0/rcrisp/man/get_osm_river.Rd |only rcrisp-0.3.0/rcrisp/DESCRIPTION | 6 rcrisp-0.3.0/rcrisp/MD5 | 48 ++- rcrisp-0.3.0/rcrisp/NAMESPACE | 3 rcrisp-0.3.0/rcrisp/NEWS.md | 24 + rcrisp-0.3.0/rcrisp/R/corridor.R | 3 rcrisp-0.3.0/rcrisp/R/osmdata.R | 136 +++++++---- rcrisp-0.3.0/rcrisp/R/segments.R | 2 rcrisp-0.3.0/rcrisp/README.md | 73 +++++ rcrisp-0.3.0/rcrisp/build/vignette.rds |binary rcrisp-0.3.0/rcrisp/inst/csl |only rcrisp-0.3.0/rcrisp/inst/doc/getting-started.R |only rcrisp-0.3.0/rcrisp/inst/doc/getting-started.Rmd |only rcrisp-0.3.0/rcrisp/inst/doc/getting-started.html |only rcrisp-0.3.0/rcrisp/inst/doc/vig_02-getting-osm-data.R | 8 rcrisp-0.3.0/rcrisp/inst/doc/vig_02-getting-osm-data.Rmd | 8 rcrisp-0.3.0/rcrisp/inst/doc/vig_02-getting-osm-data.html | 36 +- rcrisp-0.3.0/rcrisp/inst/doc/vig_03-network-preparation.html | 4 rcrisp-0.3.0/rcrisp/man/figures/README-example-1.png |binary rcrisp-0.3.0/rcrisp/man/get_osm_river_centerline.Rd |only rcrisp-0.3.0/rcrisp/man/get_osm_river_surface.Rd |only rcrisp-0.3.0/rcrisp/man/get_river_aoi.Rd | 7 rcrisp-0.3.0/rcrisp/tests/testthat/test-corridor.R | 23 + rcrisp-0.3.0/rcrisp/tests/testthat/test-osmdata.R | 73 ++++- rcrisp-0.3.0/rcrisp/tests/testthat/test-segments.R | 2 rcrisp-0.3.0/rcrisp/tests/testthat/test-valley.R | 16 + rcrisp-0.3.0/rcrisp/vignettes/getting-started.Rmd |only rcrisp-0.3.0/rcrisp/vignettes/references.bib | 10 rcrisp-0.3.0/rcrisp/vignettes/vig_02-getting-osm-data.Rmd | 8 29 files changed, 358 insertions(+), 132 deletions(-)
Title: Powerful 'SAS' Inspired Concepts for more Efficient Bigger
Outputs
Description: The main goal is to make descriptive evaluations easier to create bigger and more complex outputs in less time with less code. Introducing format containers with multilabels <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p06ciqes4eaqo6n0zyqtz9p21nfb.htm>, a more powerful summarise which is capable to output every possible combination of the provided grouping variables in one go <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p0jvbbqkt0gs2cn1lo4zndbqs1pe.htm>, tabulation functions which can create any table in different styles <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/n1ql5xnu0k3kdtn11gwa5hc7u435.htm> and other more readable functions. The code is optimized to work fast even with datasets of over a million observations.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between qol versions 1.0.1 dated 2025-10-10 and 1.0.2 dated 2025-10-14
qol-1.0.1/qol/man/figures/tabulation.PNG |only qol-1.0.2/qol/DESCRIPTION | 10 qol-1.0.2/qol/MD5 | 42 - qol-1.0.2/qol/NEWS.md | 42 - qol-1.0.2/qol/R/any_table.R | 83 +- qol-1.0.2/qol/R/conversion.R | 2 qol-1.0.2/qol/R/crosstabs.R | 1 qol-1.0.2/qol/R/dummy_data.R | 302 ++++---- qol-1.0.2/qol/R/frequencies.R | 3 qol-1.0.2/qol/R/qol.R | 2 qol-1.0.2/qol/R/summarise_plus.R | 37 - qol-1.0.2/qol/README.md | 442 ++++++------ qol-1.0.2/qol/man/figures/tabulation.png |only qol-1.0.2/qol/man/qol-package.Rd | 3 qol-1.0.2/qol/tests/testthat/test-any_table.R | 12 qol-1.0.2/qol/tests/testthat/test-conversion.R | 34 qol-1.0.2/qol/tests/testthat/test-crosstabs.R | 756 ++++++++++----------- qol-1.0.2/qol/tests/testthat/test-frequencies.R | 660 +++++++++--------- qol-1.0.2/qol/tests/testthat/test-if_else.R | 216 +++--- qol-1.0.2/qol/tests/testthat/test-recode.R | 448 ++++++------ qol-1.0.2/qol/tests/testthat/test-small_helpers.R | 76 +- qol-1.0.2/qol/tests/testthat/test-split_by.R | 118 +-- qol-1.0.2/qol/tests/testthat/test-summarise_plus.R | 45 - 23 files changed, 1711 insertions(+), 1623 deletions(-)
Title: Intracardiac Electrograms
Description: A system for importing electrophysiological signal, based
on the 'Waveform Database (WFDB)' software package, written by Moody et al
2022 <doi:10.13026/gjvw-1m31>. A wrapper for utilizing 'WFDB' functions for
reading and writing signal data, as well as functions for visualization and
analysis are provided. A stable and broadly compatible class for working
with signal data, supporting the reading in of cardiac electrophysiological
files such as intracardiac electrograms, is introduced.
Author: Anish S. Shah [aut, cre, cph] ,
Darren Seaney [ctb]
Maintainer: Anish S. Shah <shah.in.boots@gmail.com>
Diff between EGM versions 0.1.0 dated 2024-05-23 and 0.1.1 dated 2025-10-14
EGM-0.1.0/EGM/LICENSE |only EGM-0.1.0/EGM/R/egm-package.R |only EGM-0.1.0/EGM/R/lspro.R |only EGM-0.1.0/EGM/R/shiny.R |only EGM-0.1.0/EGM/inst/extdata/lspro-avnrt.txt |only EGM-0.1.0/EGM/inst/extdata/lspro-pac-svt.txt |only EGM-0.1.0/EGM/man/lspro.Rd |only EGM-0.1.0/EGM/tests/testthat/egm.qrs |only EGM-0.1.0/EGM/tests/testthat/egm.txt |only EGM-0.1.0/EGM/tests/testthat/test-lspro.R |only EGM-0.1.0/EGM/tests/testthat/test-shiny.R |only EGM-0.1.1/EGM/DESCRIPTION | 41 +++--- EGM-0.1.1/EGM/MD5 | 126 ++++++++++++-------- EGM-0.1.1/EGM/NAMESPACE | 32 ++++- EGM-0.1.1/EGM/NEWS.md | 19 ++- EGM-0.1.1/EGM/R/EGM-package.R |only EGM-0.1.1/EGM/R/bard.R |only EGM-0.1.1/EGM/R/cpp11.R |only EGM-0.1.1/EGM/R/ecg.R |only EGM-0.1.1/EGM/R/egm.R | 6 EGM-0.1.1/EGM/R/fwave.R |only EGM-0.1.1/EGM/R/ggm.R | 57 +++++---- EGM-0.1.1/EGM/R/muse.R | 33 +++-- EGM-0.1.1/EGM/R/prucka.R |only EGM-0.1.1/EGM/R/wfdb-annotation.R | 7 + EGM-0.1.1/EGM/R/wfdb-io.R | 10 - EGM-0.1.1/EGM/R/window.R |only EGM-0.1.1/EGM/R/zzz.R | 6 EGM-0.1.1/EGM/README.md | 7 + EGM-0.1.1/EGM/build/partial.rdb |binary EGM-0.1.1/EGM/build/vignette.rds |binary EGM-0.1.1/EGM/inst/CITATION |only EGM-0.1.1/EGM/inst/doc/getting-started.R | 8 - EGM-0.1.1/EGM/inst/doc/getting-started.Rmd | 12 - EGM-0.1.1/EGM/inst/doc/getting-started.html | 51 ++++---- EGM-0.1.1/EGM/inst/doc/segmentation-guide.R | 10 - EGM-0.1.1/EGM/inst/doc/segmentation-guide.html | 5 EGM-0.1.1/EGM/inst/doc/wfdb-guide.R | 2 EGM-0.1.1/EGM/inst/doc/wfdb-guide.html | 16 +- EGM-0.1.1/EGM/inst/extdata/bard-avnrt.txt |only EGM-0.1.1/EGM/inst/extdata/bard-pac-svt.txt |only EGM-0.1.1/EGM/man/EGM-package.Rd | 13 +- EGM-0.1.1/EGM/man/EGM-vctrs.Rd | 2 EGM-0.1.1/EGM/man/add_annotations.Rd |only EGM-0.1.1/EGM/man/analyze_atrial_signal.Rd |only EGM-0.1.1/EGM/man/annotators.Rd |only EGM-0.1.1/EGM/man/as_ecg.Rd |only EGM-0.1.1/EGM/man/bard.Rd |only EGM-0.1.1/EGM/man/c.windowed.Rd |only EGM-0.1.1/EGM/man/calculate_approximate_entropy.Rd |only EGM-0.1.1/EGM/man/calculate_dominant_frequency.Rd |only EGM-0.1.1/EGM/man/detect_QRS.Rd |only EGM-0.1.1/EGM/man/ecg.Rd |only EGM-0.1.1/EGM/man/egm.Rd | 2 EGM-0.1.1/EGM/man/extract_f_waves.Rd |only EGM-0.1.1/EGM/man/format.windowed.Rd |only EGM-0.1.1/EGM/man/interpolate_signal.Rd |only EGM-0.1.1/EGM/man/is_windowed.Rd |only EGM-0.1.1/EGM/man/lapply.windowed.Rd |only EGM-0.1.1/EGM/man/muse.Rd | 5 EGM-0.1.1/EGM/man/print.windowed.Rd |only EGM-0.1.1/EGM/man/prucka.Rd |only EGM-0.1.1/EGM/man/standardize_windows.Rd |only EGM-0.1.1/EGM/man/sub-.windowed.Rd |only EGM-0.1.1/EGM/man/time_normalize_windows.Rd |only EGM-0.1.1/EGM/man/validate_ecg_data.Rd |only EGM-0.1.1/EGM/man/wfdb.Rd | 6 EGM-0.1.1/EGM/man/wfdb_io.Rd | 5 EGM-0.1.1/EGM/man/window.Rd |only EGM-0.1.1/EGM/man/windowed.Rd |only EGM-0.1.1/EGM/src |only EGM-0.1.1/EGM/tests/testthat/300.hea | 6 EGM-0.1.1/EGM/tests/testthat/bard-egm.dat |only EGM-0.1.1/EGM/tests/testthat/bard-egm.hea |only EGM-0.1.1/EGM/tests/testthat/bard-egm.qrs |only EGM-0.1.1/EGM/tests/testthat/bard-egm.txt |only EGM-0.1.1/EGM/tests/testthat/egm.hea | 2 EGM-0.1.1/EGM/tests/testthat/prucka.inf |only EGM-0.1.1/EGM/tests/testthat/prucka.txt |only EGM-0.1.1/EGM/tests/testthat/test-bard.R |only EGM-0.1.1/EGM/tests/testthat/test-channels.R | 4 EGM-0.1.1/EGM/tests/testthat/test-ecg.R |only EGM-0.1.1/EGM/tests/testthat/test-egm.R | 8 - EGM-0.1.1/EGM/tests/testthat/test-fwave.R |only EGM-0.1.1/EGM/tests/testthat/test-ggm.R | 34 ++--- EGM-0.1.1/EGM/tests/testthat/test-muse.R | 2 EGM-0.1.1/EGM/tests/testthat/test-prucka.R |only EGM-0.1.1/EGM/tests/testthat/test-wfdb-io.R | 29 ++-- EGM-0.1.1/EGM/tests/testthat/test-wfdb-structures.R | 2 EGM-0.1.1/EGM/tests/testthat/test-window.R |only EGM-0.1.1/EGM/vignettes/getting-started.Rmd | 12 - 91 files changed, 363 insertions(+), 217 deletions(-)
Title: Model Consistent Lasso Estimation Through the Bootstrap
Description: Implements the bolasso algorithm for consistent variable selection
and estimation accuracy. Includes support for many parallel backends via the
future package. For details see: Bach (2008),
'Bolasso: model consistent Lasso estimation through the bootstrap',
<doi:10.48550/arXiv.0804.1302>.
Author: Daniel Molitor [aut, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between bolasso versions 0.3.0 dated 2024-12-08 and 0.4.0 dated 2025-10-14
DESCRIPTION | 10 ++++---- MD5 | 32 ++++++++++++++------------ NAMESPACE | 1 NEWS.md | 13 ++++++++++ R/bolasso.R | 14 ++++++++++- R/bolasso_fast.R | 7 +++-- R/plot.R | 36 ++++++++++++++++++++++-------- R/utils.R | 23 +++++++++++++++---- README.md | 31 +++++++++++++++---------- man/bolasso.Rd | 3 ++ man/bootstrap_samples.Rd |only man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-16-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary tests/testthat/test-plots.R |only 18 files changed, 119 insertions(+), 51 deletions(-)
Title: Use 'nlmixr2' to Interact with Open Source and Commercial
Software
Description: Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019)
<doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can
get/install the 'lixoftConnectors' package in the 'Monolix' installation, as
described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When
'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up
command line usage.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [aut] ,
Theodoros Papathanasiou [ctb],
Nook Fulloption [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between babelmixr2 versions 0.1.9 dated 2025-08-31 and 0.1.10 dated 2025-10-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/WORDLIST | 21 +++++++++++++++++++-- tests/testthat/test-units.R | 37 ++++++++++++++++++++++++++----------- 5 files changed, 56 insertions(+), 20 deletions(-)
Title: Obtain and Visualize Spectral Reflectance Data for Earth Surface
Polygons
Description: Tools for obtaining, processing, and visualizing spectral reflectance data for the user-defined land or water surface classes for visual exploring in which wavelength the classes differ. Input should be a shapefile with polygons of surface classes (it might be different habitat types, crops, vegetation, etc.). The Sentinel-2 L2A satellite mission optical bands pixel data are obtained through the Google Earth Engine service (<https://earthengine.google.com/>) and used as a source of spectral data.
Author: Oleh Prylutskyi [aut, cre],
Dariia Shyriaieva [ctb],
Vladimir Mikryukov [ctb]
Maintainer: Oleh Prylutskyi <oleh.prylutskyi@gmail.com>
Diff between spectralR versions 0.1.3 dated 2023-08-24 and 0.1.4 dated 2025-10-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/spectral.curves.plot.R | 10 +++++----- R/stat.summary.plot.R | 18 +++++++++--------- R/violin.plot.R | 4 ++-- README.md | 4 ++++ man/spectralR.Rd | 2 +- 8 files changed, 36 insertions(+), 28 deletions(-)
Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses. See e.g. Halekoh and Højsgaard, (2005,
<doi:10.18637/jss.v015.i02>), for details.
Author: Soeren Hoejsgaard [aut, cre, cph],
Ulrich Halekoh [aut, cph],
Jun Yan [aut, cph],
Claus Thorn Ekstroem [ctb]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between geepack versions 1.3.12 dated 2024-09-23 and 1.3.13 dated 2025-10-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary inst/CITATION | 14 ++++++++++++++ inst/doc/geepack-manual.pdf |binary 5 files changed, 21 insertions(+), 7 deletions(-)
Title: Double Constrained Correspondence Analysis for Trait-Environment
Analysis in Ecology
Description: Double constrained correspondence analysis (dc-CA) analyzes
(multi-)trait (multi-)environment ecological data by using the 'vegan'
package and native R code. Throughout the two step algorithm of ter Braak
et al. (2018) is used. This algorithm combines and extends community-
(sample-) and species-level analyses, i.e. the usual community weighted
means (CWM)-based regression analysis and the species-level analysis of
species-niche centroids (SNC)-based regression analysis. The two steps use
canonical correspondence analysis to regress the abundance data on to the
traits and (weighted) redundancy analysis to regress the CWM of the
orthonormalized traits on to the environmental predictors. The function
dc_CA() has an option to divide the abundance data of a site by the site
total, giving equal site weights. This division has the advantage that the
multivariate analysis corresponds with an unweighted (multi-trait)
community-level analysis, instead of being weighted. The first step of
the al [...truncated...]
Author: Cajo J.F ter Braak [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between douconca versions 1.2.3 dated 2025-05-09 and 1.2.4 dated 2025-10-14
DESCRIPTION | 10 - MD5 | 36 ++-- NEWS.md | 12 + R/FS.dcca.R | 2 R/FS.wrda.R | 6 R/fCWM_SNC.R | 2 R/ipfN2marginals.R | 38 +++- R/utils.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/douconca.html | 338 ++++++++++++++++++--------------------- inst/tinytest/anova_dccaDivT |binary inst/tinytest/test_anova.dcca.R | 2 inst/tinytest/test_anova.dccav.R | 2 inst/tinytest/test_dccav.R | 4 inst/tinytest/test_ipf2N2.R | 2 man/FS.dcca.Rd | 3 man/FS.wrda.Rd | 4 man/ipf2N2.Rd | 17 + 19 files changed, 257 insertions(+), 222 deletions(-)
Title: 'WhiteboxTools' R Frontend
Description: An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. [...truncated...]
Author: Qiusheng Wu [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <brown.andrewg@gmail.com>
Diff between whitebox versions 2.4.0 dated 2024-05-27 and 2.4.2 dated 2025-10-14
whitebox-2.4.0/whitebox/man/sample_dem_data.Rd |only whitebox-2.4.2/whitebox/DESCRIPTION | 15 whitebox-2.4.2/whitebox/MD5 | 54 whitebox-2.4.2/whitebox/NAMESPACE | 1 whitebox-2.4.2/whitebox/NEWS.md | 18 whitebox-2.4.2/whitebox/R/wbt.R | 144 whitebox-2.4.2/whitebox/R/wbt_source.R | 222 + whitebox-2.4.2/whitebox/R/whitebox-package.R | 49 whitebox-2.4.2/whitebox/README.md | 35 whitebox-2.4.2/whitebox/build/partial.rdb |binary whitebox-2.4.2/whitebox/build/vignette.rds |binary whitebox-2.4.2/whitebox/data/wbttoolparameters.rda |binary whitebox-2.4.2/whitebox/data/wbttools.rda |binary whitebox-2.4.2/whitebox/inst/CITATION | 6 whitebox-2.4.2/whitebox/inst/WORDLIST | 16 whitebox-2.4.2/whitebox/inst/doc/datasets.html | 468 +- whitebox-2.4.2/whitebox/inst/doc/demo.R | 6 whitebox-2.4.2/whitebox/inst/doc/demo.html | 1611 +++++----- whitebox-2.4.2/whitebox/inst/doc/wbt-method.html | 444 +- whitebox-2.4.2/whitebox/inst/extdata/STATSGO2.cpg |only whitebox-2.4.2/whitebox/inst/extdata/STATSGO2.dbf |only whitebox-2.4.2/whitebox/inst/extdata/STATSGO2.prj |only whitebox-2.4.2/whitebox/inst/extdata/STATSGO2.shp |only whitebox-2.4.2/whitebox/inst/extdata/STATSGO2.shx |only whitebox-2.4.2/whitebox/man/extdata-gis.Rd |only whitebox-2.4.2/whitebox/man/figures/README-terra-plot-facc-1.jpeg |binary whitebox-2.4.2/whitebox/man/wbt_source.Rd | 27 whitebox-2.4.2/whitebox/man/wbttoolparameters.Rd | 2 whitebox-2.4.2/whitebox/man/wbttools.Rd | 2 whitebox-2.4.2/whitebox/man/whitebox-package.Rd | 2 whitebox-2.4.2/whitebox/tests/testthat.R | 8 whitebox-2.4.2/whitebox/tests/testthat/test-wbt_source.R |only 32 files changed, 1708 insertions(+), 1422 deletions(-)
Title: Spatial Coverage Sampling and Random Sampling from Compact
Geographical Strata
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means. See Walvoort et al. (2010)
<doi:10.1016/j.cageo.2010.04.005> for details.
Author: Dennis Walvoort [aut, cre, cph] ,
Dick Brus [aut, cph] ,
Jaap de Gruijter [aut, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between spcosa versions 0.4-4 dated 2025-06-29 and 0.4-5 dated 2025-10-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/methods_plot.R | 43 ++++++++++++++----------------------------- inst/NEWS.Rd | 6 ++++++ 4 files changed, 27 insertions(+), 36 deletions(-)
Title: Additional Tools for Developing Spatially Explicit Discrete
Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling
tools for developing cellular automata, dynamic raster models, and
agent based models in 'SpaDES'. Included are various methods for
spatial spreading, spatial agents, GIS operations, random map
generation, and others. See '?SpaDES.tools' for an categorized
overview of these additional tools. The suggested package 'NLMR' can
be installed from the following repository:
(<https://PredictiveEcology.r-universe.dev>).
Author: Eliot J B McIntire [aut] ,
Alex M Chubaty [aut, cre] ,
Yong Luo [ctb],
Ceres Barros [ctb] ,
Steve Cumming [ctb],
Jean Marchal [ctb],
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Diff between SpaDES.tools versions 2.0.8 dated 2025-10-11 and 2.0.9 dated 2025-10-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/distanceFromEachPoint.R | 5 +++-- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: 'R' Bindings for 'TMB'
Description: Native 'R' interface to 'TMB' (Template Model Builder) so models can be written entirely in 'R' rather than 'C++'. Automatic differentiation, to any order, is available for a rich subset of 'R' features, including linear algebra for dense and sparse matrices, complex arithmetic, Fast Fourier Transform, probability distributions and special functions. 'RTMB' provides easy access to model fitting and validation following the principles of Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. M. (2016) <DOI:10.18637/jss.v070.i05> and Thygesen, U.H., Albertsen, C.M., Berg, C.W. et al. (2017) <DOI:10.1007/s10651-017-0372-4>.
Author: Kasper Kristensen [aut, cre]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between RTMB versions 1.7 dated 2025-01-10 and 1.8 dated 2025-10-14
DESCRIPTION | 11 - MD5 | 79 +++++----- NAMESPACE | 12 + R/00roxygen.R | 61 +++++-- R/RcppExports.R | 84 +++++++--- R/advector.R | 117 +++++++++++++-- R/bessel.R |only R/distributions.R | 70 +-------- R/expAv.R | 50 ++++-- R/interpol.R | 50 +++++- R/methods.R | 104 +++++++++++++ R/mvgauss.R | 9 + build/vignette.rds |binary inst/doc/RTMB-advanced.html | 30 +-- inst/doc/RTMB-introduction.R | 45 +++++ inst/doc/RTMB-introduction.html | 269 +++++++++++++++++++++++----------- inst/doc/RTMB-introduction.rmd | 79 ++++++++++ inst/include/RTMB.h | 24 ++- inst/include/RTMB_stubs.cpp | 5 inst/tinytest/test-bessel.R |only inst/tinytest/test-distributions.R | 23 ++ inst/tinytest/test-spline.R | 11 + man/ADmatrix.Rd | 26 +++ man/ADvector.Rd | 26 +++ man/Distributions.Rd | 134 ++++++++++++----- man/Interpolation.Rd | 12 - man/RTMB-package.Rd | 20 +- man/Simulation.Rd | 29 ++- man/Tape.Rd | 18 ++ man/expAv.Rd | 25 ++- src/RTMB.cpp | 5 src/RTMB.h | 24 ++- src/RTMB_tape.cpp | 114 +++++++++----- src/RcppExports.cpp | 285 +++++++++++++++++++++++++------------ src/bessel.cpp |only src/distributions.cpp | 68 +------- src/expAv.cpp |only src/interpol.cpp | 13 - src/lapack.cpp | 2 src/math.cpp | 41 +---- src/misc.cpp | 28 ++- src/subset.cpp |only vignettes/RTMB-introduction.rmd | 79 ++++++++++ 43 files changed, 1483 insertions(+), 599 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition
Examination Survey (NHANES) website <https://www.cdc.gov/nchs/nhanes/>.
Author: Christopher Endres [aut] ,
Laha Ale [aut] ,
Robert Gentleman [aut] ,
Deepayan Sarkar [aut, cre]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between nhanesA versions 1.4 dated 2025-09-10 and 1.4.1 dated 2025-10-14
nhanesA-1.4.1/nhanesA/DESCRIPTION | 18 +++-- nhanesA-1.4.1/nhanesA/MD5 | 48 +++++++-------- nhanesA-1.4.1/nhanesA/R/nhanes.R | 50 ++++++++++------ nhanesA-1.4.1/nhanesA/R/nhanes_codebook.R | 13 ++-- nhanesA-1.4.1/nhanesA/R/nhanes_constants.R | 2 nhanesA-1.4.1/nhanesA/R/nhanes_manifest.R | 16 +++-- nhanesA-1.4.1/nhanesA/R/nhanes_search.R | 39 +++++++----- nhanesA-1.4.1/nhanesA/R/nhanes_tables.R | 32 +++++----- nhanesA-1.4.1/nhanesA/R/nhanes_translate.R | 15 +++- nhanesA-1.4.1/nhanesA/README.md | 2 nhanesA-1.4.1/nhanesA/inst/doc/Introducing_nhanesA.html | 4 - nhanesA-1.4.1/nhanesA/inst/doc/UsingSurveyWeights.html | 8 +- nhanesA-1.4.1/nhanesA/man/figures/logo.png |only nhanesA-1.4.1/nhanesA/man/nhanes.Rd | 10 +-- nhanesA-1.4.1/nhanesA/man/nhanesCodebook.Rd | 13 ++-- nhanesA-1.4.1/nhanesA/man/nhanesDXA.Rd | 12 ++- nhanesA-1.4.1/nhanesA/man/nhanesFromURL.Rd | 11 ++- nhanesA-1.4.1/nhanesA/man/nhanesManifest.Rd | 15 +++- nhanesA-1.4.1/nhanesA/man/nhanesSearch.Rd | 14 ++-- nhanesA-1.4.1/nhanesA/man/nhanesSearchTableNames.Rd | 14 ++-- nhanesA-1.4.1/nhanesA/man/nhanesSearchVarName.Rd | 10 +-- nhanesA-1.4.1/nhanesA/man/nhanesTableSummary.Rd | 7 +- nhanesA-1.4.1/nhanesA/man/nhanesTableVars.Rd | 14 ++-- nhanesA-1.4.1/nhanesA/man/nhanesTables.Rd | 18 +++-- nhanesA-1.4.1/nhanesA/man/nhanesTranslate.Rd | 15 +++- nhanesA-1.4/nhanesA/man/figures/nhanesAsticker.png |only 26 files changed, 244 insertions(+), 156 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.36 dated 2025-09-26 and 4.38 dated 2025-10-14
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 36 ++++++++++++++++++++++++++++++++++++ R/cleanCoords.R | 8 ++++---- R/getRegion.R | 33 +++++++++++++++++++-------------- R/gridRecords.R | 4 ++-- R/timer.R | 43 +++++++++++++++++++++++++++++++++---------- man/cleanCoords.Rd | 8 ++++---- man/fuzzyRangeChange.Rd | 14 +++++++------- man/fuzzySim-package.Rd | 4 ++-- man/getRegion.Rd | 12 ++++++------ man/gridRecords.Rd | 2 +- man/timer.Rd | 16 +++++++++++----- 13 files changed, 141 insertions(+), 71 deletions(-)
Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters) first started as an open source project with support of Haag-Streit in 2010. It specifies basic functions that allow many visual field tests to be constructed. As of February 2022 it is fully implemented on the Haag-Streit Octopus 900 and 'CrewT ImoVifa' ('Topcon Tempo') with partial implementations on the Centervue Compass, Kowa AP 7000 and Android phones. It also has a cousin: the R package 'visualFields', which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin [cre, aut, cph] ,
David Lawson [ctb, cph],
Ivan Marin-Franch [ctb, cph],
Matthias Muller [ctb],
Jonathan Denniss [ctb, cph],
Astrid Zeman [ctb],
Giovanni Montesano [ctb]
Maintainer: Andrew Turpin <andrew.turpin@lei.org.au>
Diff between OPI versions 3.0.4 dated 2025-04-09 and 3.0.5 dated 2025-10-14
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 3 +++ R/Compass.r | 2 ++ R/Display.r | 2 ++ R/ImoVifa.r | 2 ++ R/KowaAP7000Client.r | 2 ++ R/MAIA.r | 2 ++ R/PhoneHMD.r | 2 ++ R/PicoVR.r | 2 ++ 10 files changed, 30 insertions(+), 13 deletions(-)