Title: Retrieve Genomic and Clinical Data from CBioPortal Including
TCGA Data
Description: The Cancer Genome Atlas (TCGA) is a program aimed at improving our understanding of Cancer Biology. Several TCGA Datasets are available online. 'TCGAretriever' helps accessing and downloading TCGA data hosted on 'cBioPortal' via its Web Interface (see <https://www.cbioportal.org/> for more information).
Author: Damiano Fantini [aut, cre]
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between TCGAretriever versions 1.9.1 dated 2024-01-23 and 1.10.1 dated 2025-11-20
TCGAretriever-1.10.1/TCGAretriever/DESCRIPTION | 14 - TCGAretriever-1.10.1/TCGAretriever/MD5 | 38 +-- TCGAretriever-1.10.1/TCGAretriever/R/tcgaretriever_v_1_10_1.R |only TCGAretriever-1.10.1/TCGAretriever/build/vignette.rds |binary TCGAretriever-1.10.1/TCGAretriever/inst/doc/getting_started_with_TCGAretriever.R | 18 - TCGAretriever-1.10.1/TCGAretriever/inst/doc/getting_started_with_TCGAretriever.html | 107 ++++------ TCGAretriever-1.10.1/TCGAretriever/man/TCGAretriever-package.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/blcaOutputExamples.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/cb_query.Rd | 8 TCGAretriever-1.10.1/TCGAretriever/man/expand_cases.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/fetch_all_tcgadata.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_cancer_studies.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_cancer_types.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_case_lists.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_clinical_data.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_gene_identifiers.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_genetic_profiles.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_molecular_data.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/get_mutation_data.Rd | 2 TCGAretriever-1.10.1/TCGAretriever/man/make_groups.Rd | 2 TCGAretriever-1.9.1/TCGAretriever/R/tcgaretriever_v_1_9e.R |only 21 files changed, 108 insertions(+), 103 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385>, Wilson (2025) <DOI:10.1002/mrm.30462> and
spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 3.6.0 dated 2025-09-22 and 3.7.0 dated 2025-11-20
DESCRIPTION | 14 - MD5 | 62 +++-- NAMESPACE | 6 NEWS.md | 6 R/fit_svs.R | 103 +++++++-- R/fit_svs_edited.R | 320 +++++++++++++++++++++++++++--- R/fmrs.R | 25 ++ R/mol_parameters.R | 38 +++ R/mrs_data_display.R | 71 ++++-- R/mrs_data_proc.R | 196 +++++++++++++++--- R/mrs_read_nifti.R | 30 +- R/utils.R | 113 ++++++++++ inst/doc/spant-intro.html | 94 ++++---- inst/doc/spant-metabolite-simulation.html | 11 - inst/doc/spant-preprocessing.html | 4 inst/rmd/dataset_summary_svs_qa.Rmd | 52 ++-- inst/rmd/dyn_svs_report.Rmd | 5 inst/rmd/svs_edited_report.Rmd | 172 +++++++++++++++- inst/rmd/svs_report.Rmd | 4 man/add_noise_spec_snr.Rd | 11 - man/assign_dyns.Rd |only man/fit_svs.Rd | 15 + man/fit_svs_edited.Rd | 13 + man/fit_svs_edited_group_results.Rd |only man/fit_svs_group_results.Rd | 16 + man/lb_renoise.Rd |only man/match_files.Rd |only man/match_lineshape.Rd | 15 + man/paths2df.Rd |only man/preproc_svs.Rd | 8 man/preproc_svs_dataset.Rd | 6 man/segment_t1_fsl.Rd | 5 man/sim_asy_pvoigt.Rd | 2 man/stackplot.mrs_data.Rd | 6 man/trim_paths.Rd |only 35 files changed, 1173 insertions(+), 250 deletions(-)
Title: Mediation Analysis Confidence Intervals
Description: Computes confidence intervals for nonlinear functions of model
parameters (e.g., product of k coefficients) in single-level and multilevel
structural equation models. Methods include the distribution of the product,
Monte Carlo simulation, and bootstrap methods. It also performs the Model-Based
Constrained Optimization (MBCO) procedure for hypothesis testing of indirect
effects.
References:
Tofighi, D., and MacKinnon, D. P. (2011). RMediation: An R package for mediation
analysis confidence intervals. Behavior Research Methods, 43, 692-700.
<doi:10.3758/s13428-011-0076-x>;
Tofighi, D., and Kelley, K. (2020). Improved inference in mediation analysis: Introducing the model-based constrained optimization procedure.
Psychological Methods, 25(4), 496-515. <doi:10.1037/met0000259>;
Tofighi, D. (2020). Bootstrap Model-Based Constrained Optimization Tests of
Indirect Effects. Frontiers in Psychology, 10, 2989.
<doi:10.3389/fpsyg.2019.02989>.
Author: Davood Tofighi [aut, cre]
Maintainer: Davood Tofighi <dtofighi@gmail.com>
Diff between RMediation versions 1.2.2 dated 2023-05-11 and 1.3.0 dated 2025-11-20
DESCRIPTION | 60 +++++++---- LICENSE |only MD5 | 79 ++++++++------- NAMESPACE | 74 ++++++++++---- NEWS.md | 19 +++ R/RMediation.R |only R/ci.R | 222 ++++++++++++++++++++++++++++++++++--------- R/confintAsymp.R | 160 +++++++++++++++---------------- R/confintMC.R | 237 ++++++++++++++++++++++------------------------ R/mbco.R | 146 ++++++++++++++-------------- R/mbco_asymp.R | 7 - R/mbco_parametric.R | 20 ++- R/mbco_semi.R | 29 +++-- R/medci.R | 228 ++++++++++++++++++++++++++++---------------- R/medciAsymp.R | 14 +- R/medciMC.R | 22 ++-- R/medciMeeker.R | 23 ++-- R/memory_exp.R | 1 R/pMC.R | 100 +++++++++++++------ R/pprodnormal.R | 66 +++++------- R/pprodnormalMC.R | 33 +++--- R/pprodnormalMeeker.R | 37 +++---- R/qMC.R | 98 ++++++++++++------- R/qprodnormal.R | 85 ++++++---------- R/qprodnormalMC.R | 31 +++--- R/qprodnormalMeeker.R | 103 +++++++++---------- R/tidy_logLik.R |only README.md | 94 +++++++++++++++++- build/partial.rdb |binary inst/WORDLIST |only man/RMediation-package.Rd | 13 ++ man/ci.Rd | 28 +++-- man/figures |only man/mbco.Rd | 39 +++---- man/medci.Rd | 11 +- man/pMC.Rd | 9 - man/pprodnormal.Rd | 2 man/qMC.Rd | 9 - man/qprodnormal.Rd | 16 +-- man/reexports.Rd |only man/tidy_logLik.Rd |only tests |only 42 files changed, 1268 insertions(+), 847 deletions(-)
Title: Tools for Managing Imaging FlowCytobot (IFCB) Data
Description: A comprehensive suite of tools for managing, processing, and
analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports
quality control, geospatial analysis, and preparation of IFCB data for
publication in databases like <https://www.gbif.org>,
<https://www.obis.org>, <https://emodnet.ec.europa.eu/en>,
<https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package
integrates with the MATLAB 'ifcb-analysis' tool, which is described in
Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides
features for working with raw, manually classified, and machine
learning–classified image datasets. Key functionalities include image
extraction, particle size distribution analysis, taxonomic data
handling, and biomass concentration calculations, essential for
plankton research.
Author: Anders Torstensson [aut, cre] ,
Kendra Hayashi [ctb] ,
Jamie Enslein [ctb],
Raphael Kudela [ctb] ,
Alle Lie [ctb] ,
Jayme Smith [ctb] ,
DTO-BioFlow [fnd] ,
SBDI [fnd]
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Diff between iRfcb versions 0.5.2 dated 2025-09-03 and 0.6.0 dated 2025-11-20
DESCRIPTION | 11 LICENSE | 4 LICENSE.note | 64 MD5 | 414 ++-- NAMESPACE | 394 ++-- NEWS.md | 22 R/defunct.R | 56 R/iRfcb-package.R | 72 R/ifcb_adjust_classes.R | 96 - R/ifcb_annotate_batch.R | 350 +-- R/ifcb_convert_filenames.R | 140 - R/ifcb_correct_annotation.R | 224 +- R/ifcb_count_mat_annotations.R | 266 +- R/ifcb_create_class2use.R | 96 - R/ifcb_create_empty_manual_file.R | 142 - R/ifcb_create_manifest.R | 126 - R/ifcb_download_dashboard_data.R | 769 ++++---- R/ifcb_download_dashboard_metadata.R |only R/ifcb_download_test_data.R | 284 +-- R/ifcb_download_whoi_plankton.R | 352 +-- R/ifcb_extract_annotated_images.R | 324 +-- R/ifcb_extract_biovolumes.R | 676 +++---- R/ifcb_extract_classified_images.R | 278 +-- R/ifcb_extract_pngs.R | 340 +-- R/ifcb_get_ecotaxa_example.R | 80 R/ifcb_get_ferrybox_data.R | 390 ++-- R/ifcb_get_mat_names.R | 82 R/ifcb_get_mat_variable.R | 110 - R/ifcb_get_runtime.R | 156 - R/ifcb_get_shark_colnames.R | 76 R/ifcb_get_shark_example.R | 48 R/ifcb_get_trophic_type.R | 160 - R/ifcb_helper_functions.R | 1560 ++++++++--------- R/ifcb_is_diatom.R | 122 - R/ifcb_is_in_basin.R | 180 - R/ifcb_is_near_land.R | 462 ++--- R/ifcb_list_dashboard_bins.R |only R/ifcb_match_taxa_names.R | 214 +- R/ifcb_merge_manual.R | 406 ++-- R/ifcb_prepare_whoi_plankton.R | 590 +++--- R/ifcb_psd.R | 432 ++-- R/ifcb_psd_plot.R | 265 +- R/ifcb_py_install.R | 196 +- R/ifcb_read_features.R | 132 - R/ifcb_read_hdr_data.R | 202 +- R/ifcb_read_mat.R | 122 - R/ifcb_read_summary.R | 336 +-- R/ifcb_replace_mat_values.R | 148 - R/ifcb_run_image_gallery.R | 58 R/ifcb_summarize_biovolumes.R | 307 +-- R/ifcb_summarize_class_counts.R | 280 +-- R/ifcb_summarize_png_counts.R | 360 +-- R/ifcb_summarize_png_metadata.R | 175 - R/ifcb_volume_analyzed.R | 130 - R/ifcb_volume_analyzed_from_adc.R | 160 - R/ifcb_which_basin.R | 192 +- R/ifcb_zip_matlab.R | 586 +++--- R/ifcb_zip_pngs.R | 380 ++-- R/zzz.R | 144 - README.md | 217 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 inst/WORDLIST | 508 +++-- inst/doc/a-general-tutorial.R | 304 +-- inst/doc/a-general-tutorial.Rmd | 500 ++--- inst/doc/a-general-tutorial.html | 1475 ++++++++-------- inst/doc/qc-tutorial.R | 435 ++-- inst/doc/qc-tutorial.Rmd | 615 +++--- inst/doc/qc-tutorial.html | 1338 +++++++------- inst/exdata/MATLAB-template.md | 232 +- inst/exdata/README-template.md | 36 inst/exdata/ecotaxa_table_minimum.tsv | 10 inst/exdata/ecotaxa_table_with_classification.tsv | 22 inst/exdata/ecotaxa_table_without_classification.tsv | 18 inst/exdata/example.txt | 6 inst/exdata/example_ferrybox.txt | 6 inst/exdata/example_table_ifcb.tsv | 12 inst/python/create_manual_mat.py | 78 inst/python/edit_manual_file.py | 32 inst/python/psd.py | 878 +++++---- inst/python/read_mat_file.py | 150 - inst/python/replace_value_in_classlist.py | 56 inst/python/requirements.txt | 6 inst/python/save_class2use_to_mat.py | 20 inst/python/start_mc_adjust_classes_user_training.py | 62 inst/shiny/ifcb_image_gallery/server.R | 290 +-- inst/shiny/ifcb_image_gallery/ui.R | 66 man/create_package_manifest.Rd | 50 man/defunct.Rd | 32 man/figures/lifecycle-archived.svg | 42 man/figures/lifecycle-defunct.svg | 42 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-maturing.svg | 42 man/figures/lifecycle-questioning.svg | 42 man/figures/lifecycle-soft-deprecated.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/iRfcb-package.Rd | 72 man/ifcb_adjust_classes.Rd | 94 - man/ifcb_annotate_batch.Rd | 176 - man/ifcb_convert_filenames.Rd | 84 man/ifcb_correct_annotation.Rd | 152 - man/ifcb_count_mat_annotations.Rd | 122 - man/ifcb_create_class2use.Rd | 86 man/ifcb_create_empty_manual_file.Rd | 126 - man/ifcb_create_manifest.Rd | 84 man/ifcb_download_dashboard_data.Rd | 191 +- man/ifcb_download_dashboard_metadata.Rd |only man/ifcb_download_test_data.Rd | 110 - man/ifcb_download_whoi_plankton.Rd | 94 - man/ifcb_extract_annotated_images.Rd | 192 +- man/ifcb_extract_biovolumes.Rd | 255 +- man/ifcb_extract_classified_images.Rd | 184 +- man/ifcb_extract_pngs.Rd | 144 - man/ifcb_get_ecotaxa_example.Rd | 76 man/ifcb_get_ferrybox_data.Rd | 108 - man/ifcb_get_mat_names.Rd | 86 man/ifcb_get_mat_variable.Rd | 114 - man/ifcb_get_runtime.Rd | 68 man/ifcb_get_shark_colnames.Rd | 62 man/ifcb_get_shark_example.Rd | 48 man/ifcb_get_trophic_type.Rd | 74 man/ifcb_is_diatom.Rd | 108 - man/ifcb_is_in_basin.Rd | 86 man/ifcb_is_near_land.Rd | 164 - man/ifcb_list_dashboard_bins.Rd |only man/ifcb_match_taxa_names.Rd | 116 - man/ifcb_merge_manual.Rd | 162 - man/ifcb_prepare_whoi_plankton.Rd | 234 +- man/ifcb_psd.Rd | 257 +- man/ifcb_psd_plot.Rd | 134 - man/ifcb_py_install.Rd | 106 - man/ifcb_read_features.Rd | 82 man/ifcb_read_hdr_data.Rd | 84 man/ifcb_read_mat.Rd | 78 man/ifcb_read_summary.Rd | 108 - man/ifcb_replace_mat_values.Rd | 106 - man/ifcb_run_image_gallery.Rd | 56 man/ifcb_summarize_biovolumes.Rd | 245 +- man/ifcb_summarize_class_counts.Rd | 110 - man/ifcb_summarize_png_counts.Rd | 128 - man/ifcb_summarize_png_metadata.Rd | 75 man/ifcb_volume_analyzed.Rd | 78 man/ifcb_volume_analyzed_from_adc.Rd | 80 man/ifcb_which_basin.Rd | 86 man/ifcb_zip_matlab.Rd | 190 +- man/ifcb_zip_pngs.Rd | 136 - man/process_ifcb_string.Rd | 70 man/read_hdr_file.Rd | 34 man/retrieve_worms_records.Rd | 74 man/split_large_zip.Rd | 56 man/summarize_TBclass.Rd | 48 man/vol2C_lgdiatom.Rd | 54 man/vol2C_nondiatom.Rd | 54 tests/spelling.R | 6 tests/testthat.R | 24 tests/testthat/helper.R | 251 +- tests/testthat/setup-venv.R | 39 tests/testthat/test-defunct.R | 14 tests/testthat/test-ifcb_adjust_classes.R | 96 - tests/testthat/test-ifcb_annotate_batch.R | 266 +- tests/testthat/test-ifcb_convert_filenames.R | 202 +- tests/testthat/test-ifcb_correct_annotation.R | 466 ++--- tests/testthat/test-ifcb_count_mat_annotations.R | 142 - tests/testthat/test-ifcb_create_class2use.R | 46 tests/testthat/test-ifcb_create_empty_manual_file.R | 136 - tests/testthat/test-ifcb_create_manifest.R | 202 +- tests/testthat/test-ifcb_download_dashboard_data.R | 322 +-- tests/testthat/test-ifcb_download_dashboard_metadata.R |only tests/testthat/test-ifcb_download_test_data.R | 89 tests/testthat/test-ifcb_download_whoi_plankton.R | 42 tests/testthat/test-ifcb_extract_annotated_images.R | 304 +-- tests/testthat/test-ifcb_extract_biovolumes.R | 430 ++-- tests/testthat/test-ifcb_extract_classified_images.R | 482 ++--- tests/testthat/test-ifcb_extract_pngs.R | 150 - tests/testthat/test-ifcb_get_ecotaxa_example.R | 76 tests/testthat/test-ifcb_get_ferrybox_data.R | 339 +-- tests/testthat/test-ifcb_get_mat_names.R | 80 tests/testthat/test-ifcb_get_mat_variable.R | 112 - tests/testthat/test-ifcb_get_runtime.R | 158 - tests/testthat/test-ifcb_get_shark_colnames.R | 74 tests/testthat/test-ifcb_get_shark_example.R | 58 tests/testthat/test-ifcb_get_trophic_type.R | 80 tests/testthat/test-ifcb_is_diatom.R | 92 - tests/testthat/test-ifcb_is_in_basin.R | 118 - tests/testthat/test-ifcb_is_near_land.R | 160 - tests/testthat/test-ifcb_list_dashboard_bins.R |only tests/testthat/test-ifcb_match_taxa_names.R | 64 tests/testthat/test-ifcb_merge_manual.R | 266 +- tests/testthat/test-ifcb_prepare_whoi_plankton.R | 294 +-- tests/testthat/test-ifcb_psd.R | 226 +- tests/testthat/test-ifcb_psd_plot.R | 178 + tests/testthat/test-ifcb_py_install.R | 116 - tests/testthat/test-ifcb_read_features.R | 108 - tests/testthat/test-ifcb_read_hdr_data.R | 150 - tests/testthat/test-ifcb_read_summary.R | 220 +- tests/testthat/test-ifcb_replace_mat_values.R | 280 +-- tests/testthat/test-ifcb_run_image_gallery.R | 34 tests/testthat/test-ifcb_summarize_biovolumes.R | 230 +- tests/testthat/test-ifcb_summarize_class_counts.R | 88 tests/testthat/test-ifcb_summarize_png_counts.R | 226 +- tests/testthat/test-ifcb_summarize_png_metadata.R | 126 - tests/testthat/test-ifcb_volume_analyzed.R | 94 - tests/testthat/test-ifcb_volume_analyzed_from_adc.R | 78 tests/testthat/test-ifcb_which_basin.R | 130 - tests/testthat/test-ifcb_zip_matlab.R | 206 +- tests/testthat/test-ifcb_zip_pngs.R | 146 - vignettes/a-general-tutorial.Rmd | 500 ++--- vignettes/qc-tutorial.Rmd | 615 +++--- 211 files changed, 19368 insertions(+), 18875 deletions(-)
Title: Functionalities for the 'INLA' Package
Description: Contain code to work with a C struct, in short
cgeneric, to define a Gaussian Markov random (GMRF) model.
The cgeneric contain code to specify GMRF elements such as
the graph and the precision matrix, and also the initial and
prior for its parameters, useful for model inference.
It can be accessed from a C program and is the recommended
way to implement new GMRF models in the 'INLA' package
(<https://www.r-inla.org>).
The 'INLAtools' implement functions to evaluate
each one of the model specifications from R.
The implemented functionalities leverage the use
of 'cgeneric' models and provide a way to debug
the code as well to work with the prior for the
model parameters and to sample from it.
A very useful functionality is the Kronecker product method
that creates a new model from multiple cgeneric models.
It also works with the rgeneric, the R version of the
cgeneric intended to easy try implementation of new GMRF models.
The Kronecker between two cgeneric models was used in
Sterr [...truncated...]
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAtools versions 0.0.4 dated 2025-06-23 and 0.0.5 dated 2025-11-20
INLAtools-0.0.4/INLAtools/man/cgeneric.Rd |only INLAtools-0.0.4/INLAtools/man/rgeneric.Rd |only INLAtools-0.0.4/INLAtools/tests |only INLAtools-0.0.5/INLAtools/DESCRIPTION | 44 ++ INLAtools-0.0.5/INLAtools/MD5 | 48 +-- INLAtools-0.0.5/INLAtools/NAMESPACE | 21 + INLAtools-0.0.5/INLAtools/R/Matrix.R | 33 +- INLAtools-0.0.5/INLAtools/R/aaa_classes.R | 18 - INLAtools-0.0.5/INLAtools/R/aaa_methods.R | 35 +- INLAtools-0.0.5/INLAtools/R/cgeneric.R | 281 +++++++++++-------- INLAtools-0.0.5/INLAtools/R/cgeneric_generic0.R | 28 - INLAtools-0.0.5/INLAtools/R/cgeneric_kronecker.R | 281 ++++++++++++++----- INLAtools-0.0.5/INLAtools/R/cgeneric_utils.R | 85 +++-- INLAtools-0.0.5/INLAtools/R/rgeneric.R | 60 ++-- INLAtools-0.0.5/INLAtools/R/utils.R | 18 - INLAtools-0.0.5/INLAtools/demo |only INLAtools-0.0.5/INLAtools/man/cgeneric-class.Rd | 123 +++++--- INLAtools-0.0.5/INLAtools/man/cgeneric_generic0.Rd | 2 INLAtools-0.0.5/INLAtools/man/extraconstr.Rd | 10 INLAtools-0.0.5/INLAtools/man/is.zero.Rd | 14 INLAtools-0.0.5/INLAtools/man/multi_generic_model.Rd |only INLAtools-0.0.5/INLAtools/man/rgeneric-class.Rd | 64 +++- INLAtools-0.0.5/INLAtools/src/INLAtools.h | 8 INLAtools-0.0.5/INLAtools/src/cgeneric_generic0.c | 19 - INLAtools-0.0.5/INLAtools/src/cgeneric_get.c | 27 - INLAtools-0.0.5/INLAtools/src/cgeneric_kronecker.c | 127 +++++--- 26 files changed, 857 insertions(+), 489 deletions(-)
Title: Gini-Based Composite Indicators
Description: An implementation of Gini-based weighting approaches in constructing composite indicators, providing functionalities for normalization, aggregation, and ranking comparison.
Author: Viet Duong Nguyen [aut, cre] ,
Chiara Gigliarano [aut] ,
Mariateresa Ciommi [aut]
Maintainer: Viet Duong Nguyen <viet-duong.nguyen@outlook.com>
Diff between giniCI versions 0.1.0 dated 2025-02-13 and 0.1.3 dated 2025-11-20
DESCRIPTION | 21 +++++++++++++-------- MD5 | 28 +++++++++++++++------------- NEWS.md |only R/bli.R | 2 +- R/giniCI-package.R | 4 ++-- R/giniCI.R | 12 ++++++++---- R/normalize.R | 4 ++-- R/summary.rankComp.R | 4 ++-- README.md |only build/vignette.rds |binary inst/doc/giniCI.pdf |binary man/bli.Rd | 2 +- man/giniCI-package.Rd | 4 ++-- man/giniCI.Rd | 12 ++++++++---- man/normalize.Rd | 4 ++-- man/summary.rankComp.Rd | 4 ++-- 16 files changed, 58 insertions(+), 43 deletions(-)
Title: Plotting Tools for Anyone Working in Deep Time
Description: Extends the functionality of other plotting packages (notably 'ggplot2')
to help facilitate the plotting of data over long time intervals, including,
but not limited to, geological, evolutionary, and ecological data. The
primary goal of 'deeptime' is to enable users to add highly customizable
timescales to their visualizations. Other functions are also included to
assist with other areas of deep time visualization.
Author: William Gearty [aut, cre]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between deeptime versions 2.2.0 dated 2025-06-19 and 2.3.0 dated 2025-11-20
deeptime-2.2.0/deeptime/man/getScaleData.Rd |only deeptime-2.2.0/deeptime/tests/testthat/_snaps/gggeo_scale |only deeptime-2.2.0/deeptime/tests/testthat/_snaps/ggplot4/gggeo_scale |only deeptime-2.3.0/deeptime/DESCRIPTION | 8 deeptime-2.3.0/deeptime/MD5 | 167 ++-- deeptime-2.3.0/deeptime/NAMESPACE | 11 deeptime-2.3.0/deeptime/NEWS.md | 22 deeptime-2.3.0/deeptime/R/coord_geo.R | 46 - deeptime-2.3.0/deeptime/R/data.R | 25 deeptime-2.3.0/deeptime/R/get_scale_data.R | 14 deeptime-2.3.0/deeptime/R/gggeo_scale.R | 363 ---------- deeptime-2.3.0/deeptime/R/gggeo_scale_old.R | 4 deeptime-2.3.0/deeptime/R/patterns.R | 55 + deeptime-2.3.0/deeptime/R/scales.R | 2 deeptime-2.3.0/deeptime/R/zzz.R | 2 deeptime-2.3.0/deeptime/README.md | 6 deeptime-2.3.0/deeptime/build/vignette.rds |binary deeptime-2.3.0/deeptime/data/FGDC_names.rda |only deeptime-2.3.0/deeptime/inst/CITATION | 16 deeptime-2.3.0/deeptime/inst/doc/coord.Rmd | 2 deeptime-2.3.0/deeptime/inst/doc/coord.html | 16 deeptime-2.3.0/deeptime/inst/doc/coord_geo.html | 19 deeptime-2.3.0/deeptime/inst/doc/geo.R | 4 deeptime-2.3.0/deeptime/inst/doc/geo.Rmd | 7 deeptime-2.3.0/deeptime/inst/doc/geo.html | 81 +- deeptime-2.3.0/deeptime/inst/doc/ggarrange2.html | 23 deeptime-2.3.0/deeptime/inst/doc/phylogenies.R | 15 deeptime-2.3.0/deeptime/inst/doc/phylogenies.Rmd | 26 deeptime-2.3.0/deeptime/inst/doc/phylogenies.html | 61 + deeptime-2.3.0/deeptime/inst/doc/time.html | 23 deeptime-2.3.0/deeptime/inst/doc/traits.html | 11 deeptime-2.3.0/deeptime/man/coord_geo.Rd | 39 - 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deeptime-2.3.0/deeptime/tests/testthat/test-gggeo_scale.R | 35 deeptime-2.3.0/deeptime/tests/testthat/test-patterns.R | 10 deeptime-2.3.0/deeptime/vignettes/coord.Rmd | 2 deeptime-2.3.0/deeptime/vignettes/geo.Rmd | 7 deeptime-2.3.0/deeptime/vignettes/phylogenies-6.png |only deeptime-2.3.0/deeptime/vignettes/phylogenies.Rmd | 26 87 files changed, 848 insertions(+), 1062 deletions(-)
Title: Statistical Inference and Prediction of Annotations in
Phylogenetic Trees
Description: Implements a parsimonious evolutionary model to analyze and
predict gene-functional annotations in phylogenetic trees as described in Vega
Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on
computational efficiency, 'aphylo' makes it possible to estimate pooled
phylogenetic models, including thousands (hundreds) of annotations (trees) in
the same run. The package also provides the tools for visualization of
annotated phylogenies, calculation of posterior probabilities (prediction)
and goodness-of-fit assessment featured in Vega Yon et al. (2021).
Author: George Vega Yon [aut, cre] ,
National Cancer Institute [fnd] ,
USC Biostatistics [cph]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
This is a re-admission after prior archival of version 0.3-4 dated 2024-12-03
Diff between aphylo versions 0.3-4 dated 2024-12-03 and 0.3-5 dated 2025-11-20
DESCRIPTION | 11 MD5 | 28 build/vignette.rds |binary configure | 1402 +++++++++++++++++++++++++--------------- configure.ac | 10 inst/doc/example.R | 22 inst/doc/example.html | 28 man/figures/MCMC-1.png |binary man/figures/MCMC-2.png |binary man/figures/MLE-1.png |binary man/figures/Predict-1.png |binary man/figures/get-offspring-1.png |binary man/figures/get-offspring-2.png |binary src/Makevars.in | 2 src/Makevars.win | 4 15 files changed, 945 insertions(+), 562 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.4.1 dated 2025-11-06 and 1.4.2 dated 2025-11-20
DESCRIPTION | 14 +++++++------- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 3 +++ NEWS | 14 ++++++++++---- R/do_possession_stats.R | 11 +++++++++-- R/get_four_factors_plot.R | 6 +++--- R/get_roster_age_profile.R | 29 ++++++++++++++++++++--------- R/get_shooting_plot.R | 5 ++++- R/get_sticker.R |only data/acb_age_profile_data_2526.RData |binary data/acb_sticker_data_2526.RData |only inst/doc/BAwiR.html | 4 ++-- inst/doc/BAwiR_pbp.html | 4 ++-- inst/doc/BAwiR_sc.html | 4 ++-- man/acb_sticker_data_2526.Rd |only man/get_four_factors_plot.Rd | 2 +- man/get_shooting_plot.Rd | 3 +++ man/get_sticker.Rd |only 18 files changed, 83 insertions(+), 46 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Warick Brown [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Martin Hazelton [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oeh [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.6-0 dated 2025-09-20 and 3.6-1 dated 2025-11-20
DESCRIPTION | 8 +- MD5 | 54 +++++++-------- NEWS | 32 +++++++++ R/diagram.R | 8 +- R/funxy.R | 2 R/hyperframe.R | 6 - R/hypersub.R | 2 R/layered.R | 6 - R/listof.R | 4 - R/marks.R | 2 R/morphology.R | 2 R/nnfun.R | 4 - R/owin2mask.R | 6 - R/pp3.R | 4 - R/psp.R | 2 R/quadratcount.R | 4 - R/solist.R | 12 +-- R/split.ppp.R | 2 R/symbolmap.R | 2 R/tess.R | 160 ++++++++++++++++++++++++++++++--------------- R/tessfun.R | 2 R/texture.R | 2 R/wingeom.R | 4 - inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/as.im.Rd | 9 ++ man/macros/defns.Rd | 3 man/owin2mask.Rd | 5 - 28 files changed, 228 insertions(+), 121 deletions(-)
Title: Number-Theoretic Functions
Description: Provides number-theoretic functions for factorization, prime
numbers, twin primes, primitive roots, modular logarithm and
inverses, extended GCD, Farey series and continued fractions.
Includes Legendre and Jacobi symbols, some divisor functions,
Euler's Phi function, etc.
Author: Hans Werner Borchers [aut],
Hans W. Borchers [cre]
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between numbers versions 0.8-5 dated 2022-11-23 and 0.9-2 dated 2025-11-20
DESCRIPTION | 20 +++++--- MD5 | 20 +++++--- NAMESPACE | 6 +- NEWS | 16 ++++++ R/contFrac.R | 125 ++++++++++++++++++++++++++++++++++++++++------------- R/modNthroot.R |only R/polygonal.R |only R/progression.R |only build/partial.rdb |binary man/cf2num.Rd | 99 +++++++++++++++++++++++++++++++---------- man/divisors.Rd | 17 +++++++ man/modNthroot.Rd |only man/polygonal.Rd |only man/progression.Rd |only 14 files changed, 233 insertions(+), 70 deletions(-)
Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Matrix
Description: Implements a constrained version of hierarchical agglomerative
clustering, in which each observation is associated to a position, and only
adjacent clusters can be merged. Typical application fields in
bioinformatics include Genome-Wide Association Studies or Hi-C data
analysis, where the similarity between items is a decreasing function of
their genomic distance. Taking advantage of this feature, the implemented
algorithm is time and memory efficient. This algorithm is described in
Ambroise et al (2019) <doi:10.1186/s13015-019-0157-4>.
Author: Christophe Ambroise [aut],
Shubham Chaturvedi [aut],
Alia Dehman [aut],
Pierre Neuvial [aut, cre] ,
Guillem Rigaill [aut],
Nathalie Vialaneix [aut] ,
Gabriel Hoffman [aut]
Maintainer: Pierre Neuvial <pierre.neuvial@math.univ-toulouse.fr>
Diff between adjclust versions 0.6.10 dated 2024-10-08 and 0.6.11 dated 2025-11-20
DESCRIPTION | 14 - MD5 | 28 +-- NEWS.md | 18 +- R/adjclust.R | 2 R/plotSim.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/hicClust.R | 24 +- inst/doc/hicClust.html | 288 +++++++++++++++++++++++--------- inst/doc/notesCHAC.R | 8 inst/doc/notesCHAC.html | 386 +++++++++++++++++++++++++++++-------------- inst/doc/snpClust.html | 285 +++++++++++++++++++------------ man/adjClust.Rd | 2 man/plotSim.Rd | 2 tests/testthat/test_modify.R | 10 - 15 files changed, 713 insertions(+), 356 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.20.0 dated 2025-09-17 and 0.21.0 dated 2025-11-20
adbcdrivermanager-0.20.0/adbcdrivermanager/src/c/vendor/portable-snippets/safe-math.h |only adbcdrivermanager-0.21.0/adbcdrivermanager/DESCRIPTION | 6 adbcdrivermanager-0.21.0/adbcdrivermanager/MD5 | 20 +- adbcdrivermanager-0.21.0/adbcdrivermanager/R/driver_void.R | 1 adbcdrivermanager-0.21.0/adbcdrivermanager/R/helpers.R | 9 - adbcdrivermanager-0.21.0/adbcdrivermanager/man/adbc_driver_load.Rd | 3 adbcdrivermanager-0.21.0/adbcdrivermanager/man/read_adbc.Rd | 7 adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/driver/postgresql/bind_stream.h | 6 adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/driver/postgresql/copy/reader.h | 40 +++- adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/driver/postgresql/statement.cc | 18 +- adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/driver_manager/adbc_driver_manager.cc | 89 +++++++--- adbcdrivermanager-0.21.0/adbcdrivermanager/src/c/vendor/portable-snippets/include |only 12 files changed, 147 insertions(+), 52 deletions(-)
More information about adbcdrivermanager at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-24 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-31 0.2.0