Title: Meta-Clustering for Single-Cell Data Integration and Evaluation
Description: A workflow of (a) meta-clustering based on
inter-group similarity measures and (b) a ground-truth-free test metric to
assess the biological correctness of integration in real datasets. See Hu Z,
Ahmed A, Yau C (2021) <doi:10.1101/2021.03.29.437525> for
more details.
Author: Zhiyuan Hu [aut, cre] ,
Christopher Yau [aut]
Maintainer: Zhiyuan Hu <zhiyuan.cheryl.hu@gmail.com>
Diff between CIDER versions 0.99.0 dated 2021-11-19 and 0.99.1 dated 2022-09-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/evaluation.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Import Public Health Ontario's Ontario Marginalization Index
Description: The Ontario Marginalization Index is a socioeconomic model that is built on Statistics Canada census data.
The model consists of four dimensions: Residential Instability, Material Deprivation, Dependency and Ethnic Concentration.
Each of these dimensions are imported for a variety of geographic levels (DA, CD, etc.) for both the 2011 and 2016 administrations of the census (2021 pending).
These data sets contribute to community analysis of equity with respect to Ontario's Anti-Racism Act.
The Ontario Marginalization Index data is retrieved from the Public Health Ontario website: <https://www.publichealthontario.ca/en/data-and-analysis/health-equity/ontario-marginalization-index>.
The shapefile data is retrieved from the Statistics Canada website: <https://www12.statcan.gc.ca/census-recensement/2011/geo/bound-limit/bound-limit-eng.cfm>.
Author: William Conley [aut, cre]
Maintainer: William Conley <william@cconley.ca>
Diff between onmaRg versions 0.1.0 dated 2022-09-08 and 0.1.1 dated 2022-09-18
DESCRIPTION | 6 ++--- MD5 | 15 +++++++------- R/om_geo.R | 19 ++++++++++++++---- inst/doc/demo.R | 17 +++++++++------- inst/doc/demo.Rmd | 19 ++++++++++++------ inst/doc/demo.html | 48 ++++++++++++++++------------------------------- man/om_geo.Rd | 6 +++-- vignettes/REFERENCES.bib |only vignettes/demo.Rmd | 19 ++++++++++++------ 9 files changed, 83 insertions(+), 66 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/index.htm>.
Author: Christopher Endres [aut, cre]
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.7.0 dated 2022-08-08 and 0.7.1 dated 2022-09-18
DESCRIPTION | 10 +- MD5 | 31 ++++---- NAMESPACE | 4 + NEWS.md | 5 + R/nhanes.R | 135 ++++++++++++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/Introducing_nhanesA.R | 23 +++--- inst/doc/Introducing_nhanesA.Rmd | 32 ++++----- inst/doc/Introducing_nhanesA.html | 59 +++++++++++----- man/nhanesCodebook.Rd |only man/nhanesSearch.Rd | 2 man/nhanesSearchTableNames.Rd | 2 man/nhanesSearchVarName.Rd | 2 man/nhanesTableVars.Rd | 6 - man/nhanesTables.Rd | 2 man/nhanesTranslate.Rd | 2 vignettes/Introducing_nhanesA.Rmd | 32 ++++----- 17 files changed, 247 insertions(+), 100 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of spatial data. The package implements basic and high-level functions for raster data and for vector data operations such as intersections. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.
Author: Robert J. Hijmans [cre, aut] ,
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Dan Baston [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
Ben Fasoli [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ct [...truncated...]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 3.5-29 dated 2022-08-14 and 3.6-3 dated 2022-09-18
DESCRIPTION | 16 - MD5 | 112 ++++---- NEWS | 8 R/AAgeneric_functions.R | 1 R/GDALtransient.R | 246 +++++++++--------- R/approxNA.R | 8 R/canProcessInMemory.R | 1 R/clump.R | 5 R/coerce.R | 15 + R/connection.R | 6 R/contour.R | 6 R/cut.R | 2 R/density.R | 2 R/distanceRows.R | 2 R/drivers.R | 10 R/extractLines.R | 2 R/extractPoints.R | 8 R/extractPolygons.R | 2 R/gainoffset.R | 13 R/gdal.R | 68 ++--- R/gdalFormats.R | 15 - R/hdrEnvi.R | 8 R/hdrPRJ.R | 8 R/kml.R | 37 +- R/layerize.R | 1 R/makeProjString.R | 86 +++--- R/project.R | 10 R/projectRaster.R | 165 ++---------- R/projection.R | 4 R/raster.R | 1 R/rasterFromBIL.R | 2 R/rasterFromFile.R | 16 - R/rasterFromGDAL.R | 630 +++++++++++++++++++++++++----------------------- R/rasterFromIDRISI.R | 2 R/rasterOptions.R | 21 - R/readCellsGDAL.R | 216 ++++++++-------- R/readRasterBrick.R | 40 +-- R/readRasterLayer.R | 47 ++- R/sampleRegular.R | 160 ++++++------ R/stack.R | 6 R/update.R | 128 +++++---- R/writeAllGDAL.R | 17 - R/writeRaster.R | 6 R/writeStartStop.R | 4 R/writeStartStopGDAL.R | 165 ++++++++---- R/writeValues.R | 40 +-- man/brick.Rd | 4 man/dataType.Rd | 2 man/hdrFiles.Rd | 2 man/projectRaster.Rd | 28 -- man/projection.Rd | 4 man/raster.Rd | 4 man/sampleRegular.Rd | 3 man/shapefile.Rd | 4 man/writeFormats.Rd | 4 man/writeRaster.Rd | 12 man/writeValues.Rd | 3 57 files changed, 1247 insertions(+), 1191 deletions(-)
Title: Interface to the 'HDF5' Binary Data Format
Description: 'HDF5' is a data model, library and file format for storing
and managing large amounts of data. This package provides a nearly
feature complete, object oriented wrapper for the 'HDF5' API
<https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> using R6 classes.
Additionally, functionality is added so that 'HDF5' objects behave very
similar to their corresponding R counterparts.
Author: Holger Hoefling [aut, cre],
Mario Annau [aut],
Novartis Institute for BioMedical Research [cph]
Maintainer: Holger Hoefling <hhoeflin@gmail.com>
Diff between hdf5r versions 1.3.5 dated 2021-11-15 and 1.3.6 dated 2022-09-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 3 +++ R/factor_ext.R | 7 ++++--- build/vignette.rds |binary inst/doc/hdf5r.html | 18 +++++++++++++----- 6 files changed, 28 insertions(+), 16 deletions(-)
Title: Comparative Analysis with Annotation-Based Genomic Components
Description: A first-principle, phylogeny-aware comparative genomics tool for
investigating associations between terms used to annotate genomic
components (e.g., Pfam IDs, Gene Ontology terms,) with quantitative
or rank variables such as number of cell types, genome size, or
density of specific genomic elements. See the project website for
more information, documentation and examples.
Author: Francisco Lobo [aut],
Felipe Campelo [aut, cre],
Jorge Augusto Hongo [aut],
Giovanni Marques de Castro [aut],
Gabriel Almeida [sad, dnc]
Maintainer: Felipe Campelo <fcampelo@gmail.com>
Diff between CALANGO versions 1.0.10 dated 2022-03-12 and 1.0.12 dated 2022-09-18
DESCRIPTION | 8 MD5 | 133 NAMESPACE | 24 NEWS.md | 74 R/AddGenomeVectors.R | 188 - R/AnnotateResults.R | 38 R/CALANGO_brewer_pal.R | 1808 ++++++------- R/FileAddition.R | 72 R/FindContrasts.R | 236 - R/FindCorrelations.R | 144 - R/GenerateGenomeVector.R | 114 R/GenerateTree.R | 14 R/GroupElementCount.R | 70 R/activate_CRAN_dependencies_from_Rmd_reports.R | 32 R/check_bioc_dependencies.R | 40 R/check_inputs_correlation.R | 12 R/check_inputs_significance.R | 12 R/clean_data.R | 84 R/clean_data_correlation.R | 84 R/clean_data_significance.R | 92 R/do_analysis.R | 68 R/do_analysis_correlation.R | 274 - R/do_analysis_significance.R | 10 R/install_bioc_dependencies.R | 122 R/load_data.R | 158 - R/load_data_correlation.R | 327 +- R/load_data_significance.R | 196 - R/make_correlation_report.R | 358 +- R/make_report.R | 88 R/make_significance_report.R | 28 R/parse_GenomeMap.R | 12 R/print_results_correlations.R | 88 R/read_calango_file.R | 44 R/restore_relative_paths.R | 16 R/retrieve_calanguize_genomes.R | 124 R/retrieve_data_files.R | 128 R/run_CALANGO.R | 342 +- R/save_tsv_files.R | 114 R/set_absolute_paths.R | 60 R/utils_ontology_manipulation.R | 204 - README.md | 548 +-- build/vignette.rds |binary inst/CITATION |only inst/doc/CALANGO_Parameters.Rmd | 660 ++-- inst/doc/CALANGO_Parameters.html | 817 +++-- inst/extdata/report_files/_site.yml | 66 inst/extdata/report_files/about.Rmd | 44 inst/extdata/report_files/heatmap_phylo_norm.Rmd | 330 +- inst/extdata/report_files/heatmap_phylo_perc.Rmd | 282 +- inst/extdata/report_files/heatmap_phylo_raw.Rmd | 276 - inst/extdata/report_files/index.Rmd | 136 inst/extdata/report_files/q_value_scatter.Rmd | 108 inst/extdata/report_files/table.Rmd | 416 +- inst/scripts/count_GO_feature2GO.pl | 116 inst/scripts/count_GO_gene2GO.pl | 148 - inst/scripts/generate_symbolic_link.pl | 24 inst/scripts/parse_busco.pl | 76 inst/scripts/parse_interproscan_output.pl | 150 - inst/scripts/parse_interproscan_output_IPR.pl | 132 inst/scripts/parse_interproscan_output_feature2GO.pl | 140 - inst/scripts/parse_interproscan_output_gene2GO.pl | 190 - inst/scripts/parse_interproscan_output_gene2SUPERFAMILY.pl | 194 - man/install_bioc_dependencies.Rd | 76 man/make_report.Rd | 64 man/retrieve_calanguize_genomes.Rd | 88 man/retrieve_data_files.Rd | 96 man/run_CALANGO.Rd | 238 - vignettes/CALANGO_Parameters.Rmd | 660 ++-- 68 files changed, 6179 insertions(+), 5936 deletions(-)
Title: Robust Calibration of Imperfect Mathematical Models
Description: Implements full Bayesian analysis for calibrating mathematical models with new methodology for modeling the discrepancy function. It allows for emulation, calibration and prediction using complex mathematical model outputs and experimental data. See the reference: Mengyang Gu and Long Wang (2018) <arXiv:1707.08215>, Mengyang Gu, Fangzheng Xie and Long Wang (2021) <arXiv:1807.03829>, Mengyang Gu, Kyle Anderson and Erika McPhillips (2021) <arXiv:1810.11664>.
Author: Mengyang Gu [aut, cre]
Maintainer: Mengyang Gu <mengyang@pstat.ucsb.edu>
Diff between RobustCalibration versions 0.5.2 dated 2022-01-11 and 0.5.3 dated 2022-09-18
CHANGELOG | 11 DESCRIPTION | 8 MD5 | 31 - NAMESPACE | 4 R/functions.R | 372 ++++++------- R/predict.R | 24 R/predict_MS.R | 1097 +++++++++++++++++++++------------------ R/rcalibration.R | 31 - R/rcalibration_MS.R | 81 ++ R/structure.R | 2 build/partial.rdb |binary man/Get_inv_all.Rd |only man/Log_marginal_post_delta.Rd |only man/Sample_delta.Rd |only man/predict_separable_2dim_MS.Rd |only man/rcalibration.Rd | 2 man/rcalibration_MS.Rd | 48 - man/separable_kernel.Rd |only src/functions.cpp | 30 - 19 files changed, 953 insertions(+), 788 deletions(-)
More information about RobustCalibration at CRAN
Permanent link
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut] ,
Vincent Arel-Bundock [aut, ctb]
,
Alex Hayes [rev]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.18.2 dated 2022-08-10 and 0.18.3 dated 2022-09-18
insight-0.18.2/insight/tests/testthat/test-get_modelmatrix-estimatr.R |only insight-0.18.3/insight/DESCRIPTION | 8 insight-0.18.3/insight/MD5 | 191 +++--- insight-0.18.3/insight/NAMESPACE | 18 insight-0.18.3/insight/NEWS.md | 56 +- insight-0.18.3/insight/R/check_if_installed.R | 16 insight-0.18.3/insight/R/clean_names.R | 15 insight-0.18.3/insight/R/colour_tools.R | 148 ++++- insight-0.18.3/insight/R/compute_variances.R | 30 - insight-0.18.3/insight/R/ellipsis_info.R | 2 insight-0.18.3/insight/R/export_table.R | 14 insight-0.18.3/insight/R/find_algorithm.R | 4 insight-0.18.3/insight/R/find_formula.R | 15 insight-0.18.3/insight/R/find_parameters.R | 4 insight-0.18.3/insight/R/find_parameters_other.R | 8 insight-0.18.3/insight/R/find_transformation.R | 1 insight-0.18.3/insight/R/format_message.R | 204 ++++++- insight-0.18.3/insight/R/format_number.R | 2 insight-0.18.3/insight/R/format_p.R | 3 insight-0.18.3/insight/R/format_table.R | 136 ++++ insight-0.18.3/insight/R/format_value.R | 67 ++ insight-0.18.3/insight/R/get_data.R | 82 ++ insight-0.18.3/insight/R/get_datagrid.R | 257 +++++++-- insight-0.18.3/insight/R/get_deviance.R | 2 insight-0.18.3/insight/R/get_df.R | 2 insight-0.18.3/insight/R/get_family.R | 6 insight-0.18.3/insight/R/get_loglikelihood.R | 28 - insight-0.18.3/insight/R/get_modelmatrix.R | 52 + insight-0.18.3/insight/R/get_parameters.R | 31 + insight-0.18.3/insight/R/get_parameters_bayesian.R | 8 insight-0.18.3/insight/R/get_parameters_htest.R | 2 insight-0.18.3/insight/R/get_parameters_others.R | 8 insight-0.18.3/insight/R/get_predicted.R | 47 + insight-0.18.3/insight/R/get_predicted_args.R | 12 insight-0.18.3/insight/R/get_predicted_ci.R | 8 insight-0.18.3/insight/R/get_predicted_fixedeffects.R | 2 insight-0.18.3/insight/R/get_predicted_gam.R | 19 insight-0.18.3/insight/R/get_predicted_methods.R | 8 insight-0.18.3/insight/R/get_predicted_mixed.R | 8 insight-0.18.3/insight/R/get_predicted_ordinal.R | 73 ++ insight-0.18.3/insight/R/get_predicted_other.R | 4 insight-0.18.3/insight/R/get_predicted_se.R | 23 insight-0.18.3/insight/R/get_priors.R | 2 insight-0.18.3/insight/R/get_random.R | 2 insight-0.18.3/insight/R/get_residuals.R | 10 insight-0.18.3/insight/R/get_statistic.R | 37 + insight-0.18.3/insight/R/get_varcov.R | 23 insight-0.18.3/insight/R/get_varcov_sandwich.R | 5 insight-0.18.3/insight/R/get_variances.R | 2 insight-0.18.3/insight/R/get_weights.R | 2 insight-0.18.3/insight/R/helper_functions.R | 4 insight-0.18.3/insight/R/is_converged.R | 2 insight-0.18.3/insight/R/is_model.R | 2 insight-0.18.3/insight/R/is_model_supported.R | 10 insight-0.18.3/insight/R/is_multivariate.R | 24 insight-0.18.3/insight/R/link_function.R | 9 insight-0.18.3/insight/R/link_inverse.R | 9 insight-0.18.3/insight/R/model_info.R | 100 ++- insight-0.18.3/insight/R/n_obs.R | 2 insight-0.18.3/insight/R/print_color.R | 9 insight-0.18.3/insight/R/text_remove_backticks.R | 4 insight-0.18.3/insight/R/utils_get_data.R | 33 - insight-0.18.3/insight/R/utils_model_info.R | 15 insight-0.18.3/insight/R/utils_object.R | 2 insight-0.18.3/insight/README.md | 43 - insight-0.18.3/insight/inst/doc/display.html | 279 ++++------ insight-0.18.3/insight/inst/doc/export.html | 13 insight-0.18.3/insight/inst/doc/insight.html | 13 insight-0.18.3/insight/man/export_table.Rd | 5 insight-0.18.3/insight/man/format_message.Rd | 92 +++ insight-0.18.3/insight/man/format_table.Rd | 5 insight-0.18.3/insight/man/get_datagrid.Rd | 110 +++ insight-0.18.3/insight/man/get_predicted.Rd | 42 + insight-0.18.3/insight/man/get_predicted_ci.Rd | 12 insight-0.18.3/insight/man/is_converged.Rd | 166 ++--- insight-0.18.3/insight/man/print_color.Rd | 9 insight-0.18.3/insight/tests/testthat/test-BayesFactorBF.R | 34 - insight-0.18.3/insight/tests/testthat/test-brms.R | 76 +- insight-0.18.3/insight/tests/testthat/test-coxph.R | 21 insight-0.18.3/insight/tests/testthat/test-export_table.R | 69 +- insight-0.18.3/insight/tests/testthat/test-fixest.R | 21 insight-0.18.3/insight/tests/testthat/test-formatting.R | 10 insight-0.18.3/insight/tests/testthat/test-gam.R | 11 insight-0.18.3/insight/tests/testthat/test-get_data.R | 24 insight-0.18.3/insight/tests/testthat/test-get_datagrid.R | 144 +++++ insight-0.18.3/insight/tests/testthat/test-get_modelmatrix.R |only insight-0.18.3/insight/tests/testthat/test-get_predicted-clm.R |only insight-0.18.3/insight/tests/testthat/test-get_predicted.R | 12 insight-0.18.3/insight/tests/testthat/test-get_varcov.R | 15 insight-0.18.3/insight/tests/testthat/test-is_model_supported.R |only insight-0.18.3/insight/tests/testthat/test-lm.R | 6 insight-0.18.3/insight/tests/testthat/test-lm_robust.R | 14 insight-0.18.3/insight/tests/testthat/test-lmer.R | 14 insight-0.18.3/insight/tests/testthat/test-marginaleffects.R | 2 insight-0.18.3/insight/tests/testthat/test-mlogit.R | 20 insight-0.18.3/insight/tests/testthat/test-mvrstanarm.R | 126 ++-- insight-0.18.3/insight/tests/testthat/test-rqss.R | 3 insight-0.18.3/insight/tests/testthat/test-utilities.R |only insight-0.18.3/insight/tests/testthat/test-vglm.R | 1 99 files changed, 2399 insertions(+), 945 deletions(-)
Title: Collect and Clean Hockey Stats
Description: Various functions to scrape hockey play-by-play data from the
<https://www.nhl.com/>. It also contains functions to scrape data from <https://www.hockey-reference.com/>,
including standings, player stats, and jersey number history.
Author: Daniel Morse [aut, cre]
Maintainer: Daniel Morse <danmorse8642@gmail.com>
Diff between hockeyR versions 1.0.0 dated 2022-08-22 and 1.2.0 dated 2022-09-18
hockeyR-1.0.0/hockeyR/R/get_team_roster.R |only hockeyR-1.0.0/hockeyR/man/fix_player_columns.Rd |only hockeyR-1.2.0/hockeyR/DESCRIPTION | 9 hockeyR-1.2.0/hockeyR/MD5 | 61 ++- hockeyR-1.2.0/hockeyR/NAMESPACE | 6 hockeyR-1.2.0/hockeyR/NEWS.md | 29 + hockeyR-1.2.0/hockeyR/R/calculate_individual.R |only hockeyR-1.2.0/hockeyR/R/calculate_on_ice.R |only hockeyR-1.2.0/hockeyR/R/calculate_toi.R |only hockeyR-1.2.0/hockeyR/R/calculate_xg.R |only hockeyR-1.2.0/hockeyR/R/fix_player_columns.R | 2 hockeyR-1.2.0/hockeyR/R/get_draft_class.R | 28 + hockeyR-1.2.0/hockeyR/R/get_game_ids.R | 23 + hockeyR-1.2.0/hockeyR/R/get_game_shifts.R | 6 hockeyR-1.2.0/hockeyR/R/get_standings.R |only hockeyR-1.2.0/hockeyR/R/get_team_rosters.R |only hockeyR-1.2.0/hockeyR/R/globals.R | 12 hockeyR-1.2.0/hockeyR/R/hockeyR-package.R |only hockeyR-1.2.0/hockeyR/R/prepare_xg_data.R |only hockeyR-1.2.0/hockeyR/R/scrape_game.R | 18 - hockeyR-1.2.0/hockeyR/R/sysdata.rda |binary hockeyR-1.2.0/hockeyR/R/utils-not_in.R |only hockeyR-1.2.0/hockeyR/README.md | 163 ++++++++-- hockeyR-1.2.0/hockeyR/build/vignette.rds |binary hockeyR-1.2.0/hockeyR/inst/doc/hockey-ref-scrapers.Rmd | 2 hockeyR-1.2.0/hockeyR/inst/doc/hockey-ref-scrapers.html | 15 hockeyR-1.2.0/hockeyR/inst/doc/hockeyR.html | 125 ++++--- hockeyR-1.2.0/hockeyR/man/calculate_individual.Rd |only hockeyR-1.2.0/hockeyR/man/calculate_on_ice.Rd |only hockeyR-1.2.0/hockeyR/man/calculate_toi.Rd |only hockeyR-1.2.0/hockeyR/man/calculate_xg.Rd |only hockeyR-1.2.0/hockeyR/man/figures/README-shot-plot-example-1.png |binary hockeyR-1.2.0/hockeyR/man/get_game_ids.Rd | 14 hockeyR-1.2.0/hockeyR/man/get_standings.Rd |only hockeyR-1.2.0/hockeyR/man/get_team_rosters.Rd | 2 hockeyR-1.2.0/hockeyR/man/hockeyR-package.Rd |only hockeyR-1.2.0/hockeyR/man/not_in.Rd |only hockeyR-1.2.0/hockeyR/man/prepare_xg_data.Rd |only hockeyR-1.2.0/hockeyR/man/scrape_game.Rd | 2 hockeyR-1.2.0/hockeyR/vignettes/hockey-ref-scrapers.Rmd | 2 hockeyR-1.2.0/hockeyR/vignettes/man/figures/vignettes-rosters-1.png |binary 41 files changed, 383 insertions(+), 136 deletions(-)
Title: Analytical Tool for Aquatic Respirometry
Description: Calculates metabolic rate of fish and other aquatic organisms measured using
an intermittent-flow respirometry approach. The tool is used to run a set of graphical
QC tests of raw respirometry data, correct it for background respiration and chamber
effect, filter and extract target values of absolute and mass-specific metabolic rate.
Experimental design should include background respiration tests and measuring of one
or more metabolic rate traits. The R package is ideally integrated with the pump
controller 'PumpResp' and the DO meter 'SensResp' (open-source hardware by FishResp).
Raw respirometry data can be also imported from 'AquaResp' (free software), 'AutoResp'
('LoligoSystems'), 'OxyView' ('PreSens'), 'Pyro Oxygen Logger' ('PyroScience') and
'Q-box Aqua' ('QubitSystems'). More information about the R package 'FishResp'is
available in the publication by Morozov et al. (2019) <doi:10.1093/conphys/coz003>.
Author: Sergey Morozov [aut, cre],
Scott McCairns [aut, ths],
Juha Merila [ths],
Federico Calboli [ctb],
Jenni Prokkola [dtc],
Stephen White [dtc],
Daniel Montgomery [dtc],
Laura Almodovar-Acevedo [dtc],
Niclas Kolm [dtc],
Alexander Kotrschal [dtc],
Erik Gil [...truncated...]
Maintainer: Sergey Morozov <sergey.morozov@helsinki.fi>
Diff between FishResp versions 1.1.0 dated 2021-05-11 and 1.1.1 dated 2022-09-18
DESCRIPTION | 8 - MD5 | 8 - NEWS.md | 18 ++- R/import.meas.R | 313 +++++++++++++++++++++++++++++++---------------------- man/import.meas.Rd | 9 + 5 files changed, 222 insertions(+), 134 deletions(-)
Title: Solutions for Common Problems in Base R
Description: Contains functions for solving commonly encountered problems while
programming in R. This package is intended to provide a lightweight
supplement to Base R, and will be useful for almost any R user.
Author: David Bosak [aut, cre],
Andrew Simmons [aut],
Duong Tran [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between common versions 1.0.3 dated 2022-08-18 and 1.0.4 dated 2022-09-18
common-1.0.3/common/man/images/common1.png |only common-1.0.3/common/man/images/gift.png |only common-1.0.3/common/man/images/libr_blue.png |only common-1.0.4/common/DESCRIPTION | 6 common-1.0.4/common/MD5 | 44 +++-- common-1.0.4/common/NAMESPACE | 2 common-1.0.4/common/NEWS.md | 7 common-1.0.4/common/R/common.R | 2 common-1.0.4/common/R/other_functions.R | 18 ++ common-1.0.4/common/R/string_functions.R |only common-1.0.4/common/R/subsc.R | 2 common-1.0.4/common/R/supsc.R | 2 common-1.0.4/common/R/symbol.R |only common-1.0.4/common/README.md | 16 +- common-1.0.4/common/inst/doc/common.R | 17 +- common-1.0.4/common/inst/doc/common.Rmd | 70 +++++++- common-1.0.4/common/inst/doc/common.html | 88 ++++++++--- common-1.0.4/common/man/common.Rd | 2 common-1.0.4/common/man/images/archive |only common-1.0.4/common/man/images/common_new.png |only common-1.0.4/common/man/images/symbol.png |only common-1.0.4/common/man/spaces.Rd |only common-1.0.4/common/man/subsc.Rd | 5 common-1.0.4/common/man/supsc.Rd | 5 common-1.0.4/common/man/symbol.Rd |only common-1.0.4/common/tests/testthat/test-other_functions.R | 110 ++++++++++++++ common-1.0.4/common/vignettes/common.Rmd | 70 +++++++- 27 files changed, 378 insertions(+), 88 deletions(-)
Title: User-Friendly GUI Plotting Tools
Description: Create a user-friendly plotting GUI for R.
In addition, one purpose of creating the R package is to facilitate third-party software to call R for drawing, for example, 'Phoenix WinNonlin' software calls R to draw the drug concentration versus time curve.
Author: Fu Yongchao <3212418315@qq.com>
Maintainer: Fu Yongchao <3212418315@qq.com>
Diff between guiplot versions 0.2.0 dated 2022-03-07 and 0.2.1 dated 2022-09-18
DESCRIPTION | 10 +-- MD5 | 18 +++--- NAMESPACE | 6 ++ NEWS | 5 + R/colClass_as.R |only R/guiplot.R | 32 ++++++++++- R/guiplotServer.R | 146 ++++++++++++++++++++++++++++++++++++++++++++++++++--- R/guiplotUI.R | 41 +++++++++----- man/PK.Rd | 18 +++--- man/colClass_as.Rd |only man/guiplot.Rd | 70 ++++++++++++------------- 11 files changed, 265 insertions(+), 81 deletions(-)
Title: Retrieve and Plot Google n-Gram Data
Description: Retrieve and plot word frequencies through time from the "Google
Ngram Viewer" <https://books.google.com/ngrams>.
Author: Sean Carmody [aut, cre, cph]
Maintainer: Sean Carmody <seancarmody@gmail.com>
Diff between ngramr versions 1.8.0 dated 2022-09-17 and 1.8.1 dated 2022-09-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/ngram.R | 3 ++- tests/testthat/test-ngramr.R | 21 +++++++-------------- 5 files changed, 22 insertions(+), 23 deletions(-)
Title: Phylogenetic Reconstruction and Analysis
Description: Allows for estimation of phylogenetic trees and networks
using Maximum Likelihood, Maximum Parsimony, distance methods and
Hadamard conjugation (Schliep 2011). Offers methods for tree comparison,
model selection and visualization of phylogenetic networks as described in
Schliep et al. (2017).
Author: Klaus Schliep [aut, cre] ,
Emmanuel Paradis [aut] ,
Leonardo de Oliveira Martins [aut]
,
Alastair Potts [aut],
Tim W. White [aut],
Cyrill Stachniss [ctb],
Michelle Kendall [ctb],
Keren Halabi [ctb],
Richel Bilderbeek [ctb],
Kristin Winchell [ctb],
Li [...truncated...]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.9.0 dated 2022-06-16 and 2.10.0 dated 2022-09-18
DESCRIPTION | 16 MD5 | 188 ++++---- NAMESPACE | 4 NEWS | 35 + R/Densi.R | 23 - R/RcppExports.R | 8 R/ancestral_pml.R | 39 - R/bab.R | 2 R/baseFreq.R | 2 R/bipart.R |only R/bootstrap.R | 55 -- R/candidate_tree.R |only R/cladePar.R | 5 R/discrete.gamma.R | 7 R/distTree.R | 110 +++-- R/fitch64.R | 4 R/hash_phylo.R |only R/image_phyDat.R |only R/mast.R | 8 R/modelTest.R | 10 R/networx.R | 35 - R/parsimony.R | 29 - R/phyDat.R | 389 ++---------------- R/phyDat2.R | 5 R/phyDat_conversion.R |only R/phylo.R | 606 ++++++++++++---------------- R/pmlMix.R | 30 - R/pmlPart.R | 6 R/pml_bb.R |only R/pml_control.R |only R/pml_generics.R |only R/read.nexus.splits.R | 12 R/splits.R | 3 R/splitsNetwork.R | 3 R/transferBootstrap.R | 47 +- R/treeRearrangement.R | 88 ---- R/treedist.R | 29 - R/zzz.R | 3 README.md | 2 TODO |only build/vignette.rds |binary inst/doc/AdvancedFeatures.R | 49 +- inst/doc/AdvancedFeatures.Rmd | 115 +++-- inst/doc/AdvancedFeatures.html | 309 ++++++++++---- inst/doc/Ancestral.html | 40 - inst/doc/IntertwiningTreesAndNetworks.R | 31 - inst/doc/IntertwiningTreesAndNetworks.Rmd | 31 - inst/doc/IntertwiningTreesAndNetworks.html | 54 +- inst/doc/Networx.html | 25 - inst/doc/Trees.R | 148 ++++-- inst/doc/Trees.Rmd | 222 ++++++---- inst/doc/Trees.html | 623 ++++++++++++++++++----------- inst/extdata/trees/H3N2_NA_20.csv |only inst/extdata/trees/H3N2_NA_20.fasta |only inst/extdata/trees/seqfile.txt |only inst/extdata/trees/tree.txt |only inst/tinytest/test_bootstrap.R | 7 inst/tinytest/test_candidate_tree.R |only inst/tinytest/test_dist_tree.R | 4 inst/tinytest/test_hash.R |only inst/tinytest/test_modelTest.R | 40 + inst/tinytest/test_parsimony.R | 2 inst/tinytest/test_phyDat.R | 22 - inst/tinytest/test_pml.R | 41 + inst/tinytest/test_pmlMix.R | 42 + man/Ancestors.Rd | 4 man/CI.Rd | 5 man/addConfidences.Rd | 9 man/as.phyDat.Rd |only man/as.splits.Rd | 3 man/baseFreq.Rd | 2 man/consensusNet.Rd | 3 man/densiTree.Rd | 23 - man/designTree.Rd | 17 man/discrete.gamma.Rd | 4 man/figures/logo.png |only man/identify.networx.Rd | 3 man/image.phyDat.Rd |only man/mast.Rd | 6 man/parsimony.Rd | 23 - man/phangorn-internal.Rd | 11 man/phangorn-package.Rd | 4 man/phyDat.Rd | 125 +---- man/plot.networx.Rd | 4 man/plotBS.Rd | 5 man/pml.Rd | 11 man/pml.control.Rd | 18 man/pml.fit.Rd | 7 man/pmlCluster.Rd | 3 man/pmlPart.Rd | 3 man/pml_bb.Rd |only man/read.nexus.splits.Rd | 13 man/splitsNetwork.Rd | 6 man/transferBootstrap.Rd |only man/treedist.Rd | 5 src/RcppExports.cpp | 75 +-- src/ml.c | 4 src/phangorn_utils.cpp | 46 ++ src/phangorn_utils.h | 2 src/sprdist.c | 4 vignettes/AdvancedFeatures.Rmd | 115 +++-- vignettes/IntertwiningTreesAndNetworks.Rmd | 31 - vignettes/Trees.RData |binary vignettes/Trees.Rmd | 222 ++++++---- vignettes/phangorn.bib | 64 ++ 105 files changed, 2451 insertions(+), 2037 deletions(-)
Title: Open Source Geometry Engine ('GEOS') R API
Description: Provides an R API to the Open Source Geometry Engine
('GEOS') library (<https://libgeos.org/>) and a vector format
with which to efficiently store 'GEOS' geometries. High-performance functions
to extract information from, calculate relationships between, and
transform geometries are provided. Finally, facilities to import
and export geometry vectors to other spatial formats are provided.
Author: Dewey Dunnington [aut, cre] ,
Edzer Pebesma [aut]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between geos versions 0.2.0 dated 2022-09-03 and 0.2.1 dated 2022-09-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/geos-writer.cpp | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'DDIwR', 'QCA' and 'venn'.
Interprets and translates, factorizes and negates SOP - Sum of Products
expressions, for both binary and multi-value crisp sets, and extracts
information (set names, set values) from those expressions. Other functions
perform various other checks if possibly numeric (even if all numbers reside
in a character vector) and coerce to numeric, or check if the numbers are
whole. It also offers, among many others, a highly versatile recoding
routine and a more flexible alternative to the base function 'with()'.
Some of the functions in this package use related functions from package
'QCA'. Users are encouraged to install that package despite not being listed
in the Imports field, due to circular dependency issues.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between admisc versions 0.29 dated 2022-06-20 and 0.30 dated 2022-09-18
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 2 +- R/asNumeric.R | 3 +++ R/compute.R | 31 +++++++++++++++++++++++-------- R/expand.R | 8 ++++++-- R/possibleNumeric.R | 3 +++ R/replaceText.R | 4 ++-- R/simplify.R | 8 ++++++-- R/string.R | 2 +- R/tagged.R | 2 +- R/translate.R | 9 ++++++--- R/using.R | 26 ++++++++++++++++++-------- R/wholeNumeric.R | 5 +---- build/partial.rdb |binary inst/ChangeLog | 6 ++++++ man/admisc_package.Rd | 4 ++-- 17 files changed, 99 insertions(+), 54 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-09 5.7.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-02 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-10 0.0.7
2018-05-22 0.0.6
2015-05-19 0.0.5
2015-01-08 0.0.4
2014-11-13 0.0.3
2014-07-12 0.0.2
2014-02-17 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-17 2.2.6
2020-04-03 2.2.5
2018-09-29 2.2.4
2018-06-29 2.2.3.1
2018-01-28 2.2.3
2018-01-21 2.2.2
2017-11-24 2.2.1
2017-11-15 2.2
2017-10-13 2.1
2017-08-31 2.0
2017-07-11 1.1
2017-07-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-02 1.0
Title: Angle-Based Large-Margin Classifiers
Description: Multi-category angle-based large-margin classifiers.
See Zhang and Liu (2014) <doi:10.1093/biomet/asu017> for details.
Author: Wenjie Wang [aut, cre] ,
Eli Lilly and Company [cph]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between abclass versions 0.3.0 dated 2022-05-28 and 0.4.0 dated 2022-09-18
abclass-0.3.0/abclass/src/Makevars.win |only abclass-0.4.0/abclass/DESCRIPTION | 12 abclass-0.4.0/abclass/MD5 | 142 - abclass-0.4.0/abclass/NAMESPACE | 13 abclass-0.4.0/abclass/NEWS.md | 32 abclass-0.4.0/abclass/R/RcppExports.R | 196 +- abclass-0.4.0/abclass/R/abclass.R | 118 - abclass-0.4.0/abclass/R/abclass_engine.R |only abclass-0.4.0/abclass/R/bic.R |only abclass-0.4.0/abclass/R/coef.R | 120 + abclass-0.4.0/abclass/R/cv.abclass.R |only abclass-0.4.0/abclass/R/cv.supclass.R |only abclass-0.4.0/abclass/R/et.abclass.R |only abclass-0.4.0/abclass/R/predict.R | 180 + abclass-0.4.0/abclass/R/supclass.R |only abclass-0.4.0/abclass/R/utils.R | 59 abclass-0.4.0/abclass/README.md | 183 - abclass-0.4.0/abclass/inst/CITATION | 2 abclass-0.4.0/abclass/inst/examples/ex-abclass.R | 14 abclass-0.4.0/abclass/inst/examples/ex-supclass.R |only abclass-0.4.0/abclass/inst/include/abclass.h | 16 abclass-0.4.0/abclass/inst/include/abclass/Abclass.h | 186 + abclass-0.4.0/abclass/inst/include/abclass/AbclassGroup.h |only abclass-0.4.0/abclass/inst/include/abclass/AbclassGroupLasso.h | 482 ++-- abclass-0.4.0/abclass/inst/include/abclass/AbclassGroupMCP.h | 494 ++--- abclass-0.4.0/abclass/inst/include/abclass/AbclassGroupSCAD.h | 508 ++--- abclass-0.4.0/abclass/inst/include/abclass/AbclassNet.h | 437 ++-- abclass-0.4.0/abclass/inst/include/abclass/Boost.h |only abclass-0.4.0/abclass/inst/include/abclass/BoostGroupLasso.h | 80 abclass-0.4.0/abclass/inst/include/abclass/BoostGroupMCP.h | 81 abclass-0.4.0/abclass/inst/include/abclass/BoostGroupSCAD.h | 81 abclass-0.4.0/abclass/inst/include/abclass/BoostNet.h | 80 abclass-0.4.0/abclass/inst/include/abclass/Control.h |only abclass-0.4.0/abclass/inst/include/abclass/HingeBoost.h |only abclass-0.4.0/abclass/inst/include/abclass/HingeBoostGroupLasso.h | 78 abclass-0.4.0/abclass/inst/include/abclass/HingeBoostGroupMCP.h | 78 abclass-0.4.0/abclass/inst/include/abclass/HingeBoostGroupSCAD.h | 78 abclass-0.4.0/abclass/inst/include/abclass/HingeBoostNet.h | 78 abclass-0.4.0/abclass/inst/include/abclass/Logistic.h |only abclass-0.4.0/abclass/inst/include/abclass/LogisticGroupLasso.h | 50 abclass-0.4.0/abclass/inst/include/abclass/LogisticGroupMCP.h | 51 abclass-0.4.0/abclass/inst/include/abclass/LogisticGroupSCAD.h | 51 abclass-0.4.0/abclass/inst/include/abclass/LogisticNet.h | 50 abclass-0.4.0/abclass/inst/include/abclass/Lum.h |only abclass-0.4.0/abclass/inst/include/abclass/LumGroupLasso.h | 98 - abclass-0.4.0/abclass/inst/include/abclass/LumGroupMCP.h | 100 - abclass-0.4.0/abclass/inst/include/abclass/LumGroupSCAD.h | 101 - abclass-0.4.0/abclass/inst/include/abclass/LumNet.h | 100 - abclass-0.4.0/abclass/inst/include/abclass/template_cv.h | 165 - abclass-0.4.0/abclass/inst/include/abclass/template_et.h |only abclass-0.4.0/abclass/inst/include/abclass/utils.h | 59 abclass-0.4.0/abclass/inst/tinytest/test-abclass.R | 119 + abclass-0.4.0/abclass/inst/tinytest/test-cv.abclass.R |only abclass-0.4.0/abclass/inst/tinytest/test-cv.supclass.R |only abclass-0.4.0/abclass/inst/tinytest/test-et.abclass.R |only abclass-0.4.0/abclass/inst/tinytest/test-supclass.R |only abclass-0.4.0/abclass/man/abclass.Rd | 76 abclass-0.4.0/abclass/man/coef.abclass.Rd | 17 abclass-0.4.0/abclass/man/coef.supclass.Rd |only abclass-0.4.0/abclass/man/cv.abclass.Rd |only abclass-0.4.0/abclass/man/cv.supclass.Rd |only abclass-0.4.0/abclass/man/et.abclass.Rd |only abclass-0.4.0/abclass/man/predict.abclass.Rd | 22 abclass-0.4.0/abclass/man/predict.supclass.Rd |only abclass-0.4.0/abclass/man/supclass.Rd |only abclass-0.4.0/abclass/src/RcppExports.cpp | 966 ++++++++-- abclass-0.4.0/abclass/src/boost_group_lasso.cpp | 90 abclass-0.4.0/abclass/src/boost_group_mcp.cpp | 92 abclass-0.4.0/abclass/src/boost_group_scad.cpp | 92 abclass-0.4.0/abclass/src/boost_net.cpp | 77 abclass-0.4.0/abclass/src/cross_validation.cpp |only abclass-0.4.0/abclass/src/export-helpers.h | 180 - abclass-0.4.0/abclass/src/hinge_boost_group_lasso.cpp | 90 abclass-0.4.0/abclass/src/hinge_boost_group_mcp.cpp | 92 abclass-0.4.0/abclass/src/hinge_boost_group_scad.cpp | 92 abclass-0.4.0/abclass/src/hinge_boost_net.cpp | 77 abclass-0.4.0/abclass/src/logistic_group_lasso.cpp | 84 abclass-0.4.0/abclass/src/logistic_group_mcp.cpp | 86 abclass-0.4.0/abclass/src/logistic_group_scad.cpp | 86 abclass-0.4.0/abclass/src/logistic_net.cpp | 71 abclass-0.4.0/abclass/src/lum_group_lasso.cpp | 92 abclass-0.4.0/abclass/src/lum_group_mcp.cpp | 94 abclass-0.4.0/abclass/src/lum_group_scad.cpp | 94 abclass-0.4.0/abclass/src/lum_net.cpp | 79 abclass-0.4.0/abclass/src/predict.cpp | 144 - 85 files changed, 4150 insertions(+), 3415 deletions(-)