Title: A Functional Data Analysis Package for Spatial Single Cell Data
Description: Methods and tools for deriving spatial summary functions from single-cell imaging
data and performing functional data analyses. Functions can be applied to other single-cell
technologies such as spatial transcriptomics. Functional regression and functional principal component analysis methods
are in the 'refund' package <https://cran.r-project.org/package=refund> while calculation of the
spatial summary functions are from the 'spatstat' package <https://spatstat.org/>.
Author: Julia Wrobel [aut] ,
Alex Soupir [aut, cre]
Maintainer: Alex Soupir <alex.soupir@moffitt.org>
Diff between mxfda versions 0.2.2 dated 2024-10-07 and 0.2.2-1 dated 2025-02-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/run_sofr.R | 27 +++++++++++++++++++++------ README.md | 2 +- inst/doc/mx_fda.html | 7 +++---- inst/doc/mx_fpca.html | 2 +- inst/doc/mx_funreg.html | 2 +- 7 files changed, 37 insertions(+), 23 deletions(-)
Title: Hot-Spot Analysis with Simple Features
Description: Identify and understand clusters of points (typically representing
the locations of places or events) stored in simple-features (SF) objects.
This is useful for analysing, for example, hot-spots of crime events. The
package emphasises producing results from point SF data in a single step
using reasonable default values for all other arguments, to aid rapid data
analysis by users who are starting out. Functions available include kernel
density estimation (for details, see Yip (2020)
<doi:10.22224/gistbok/2020.1.12>), analysis of spatial association (Getis
and Ord (1992) <doi:10.1111/j.1538-4632.1992.tb00261.x>) and hot-spot
classification (Chainey (2020) ISBN:158948584X).
Author: Matt Ashby [aut, cre]
Maintainer: Matt Ashby <matthew.ashby@ucl.ac.uk>
Diff between sfhotspot versions 0.9.0 dated 2025-02-10 and 0.9.1 dated 2025-02-19
DESCRIPTION | 8 MD5 | 56 ++-- NEWS.md | 15 + R/autoplot.R | 30 +- R/count_points_in_polygons.R | 66 ++--- R/create_grid.R | 43 +-- R/get_cell_size.R |only R/gistar.R | 40 +-- R/hotspot_change.R | 114 ++++---- R/hotspot_classify.R | 136 +++++----- R/hotspot_classify_params.R | 24 - R/hotspot_count.R | 9 R/hotspot_dual_kde.R | 170 ++++++++----- R/hotspot_gistar.R | 52 ++-- R/hotspot_kde.R | 31 ++ R/kernel_density.R | 51 ++- R/set_bandwidth.R | 29 +- R/set_cell_size.R | 24 - R/validate_inputs.R | 321 ++++++++++++++++--------- README.md | 3 inst/doc/introduction.html | 20 - tests/testthat/test-count_points_in_polygons.R | 76 ++++- tests/testthat/test-create_grid.R | 13 - tests/testthat/test-get_cell_size.R |only tests/testthat/test-hotspot_change.R | 40 +++ tests/testthat/test-hotspot_dual_kde.R | 87 ++++++ tests/testthat/test-hotspot_kde.R | 14 + tests/testthat/test-kernel_density.R | 57 +++- tests/testthat/test-set_bandwidth.R | 13 - tests/testthat/test-validate_inputs.R | 46 +++ 30 files changed, 1033 insertions(+), 555 deletions(-)
Title: Calculation of the Water Deficit Index (WDI) and the Evaporative
Fraction (EF) on Rasters
Description: Calculates the Water Deficit Index (WDI) and the Evaporative Fraction (EF) using geospatial data,
such as fractional vegetation cover (FVC) and surface-air temperature difference (TS-TA).
Terms like "raster", "CRS" are part of standard geospatial terminology.
Author: Gaelle Hamelin [aut, cre]
Maintainer: Gaelle Hamelin <gaelle.hamelin@institut-agro.fr>
Diff between wdiEF versions 1.0.2 dated 2024-12-02 and 1.0.3 dated 2025-02-19
DESCRIPTION | 7 +++--- MD5 | 9 ++++--- NEWS.md |only R/calculate_EF.R | 63 +++++++++++++++++++++++++++--------------------------- R/calculate_WDI.R | 26 ++++++++++------------ R/zzz.R | 1 6 files changed, 54 insertions(+), 52 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.54 dated 2024-11-01 and 0.55 dated 2025-02-19
DESCRIPTION | 6 +++--- MD5 | 11 +++++++---- R/latex.R | 22 ++++++++++++---------- R/platforms.R |only R/tlmgr.R | 9 --------- man/latexmk.Rd | 5 +++-- tests/test-ci/test-dvi.tex |only tests/test-ci/test-latex.R |only 8 files changed, 25 insertions(+), 28 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems. See Mary C. Meyer (2013)<doi:10.1080/03610918.2012.659820> for more details.
Author: Mary C. Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between coneproj versions 1.19 dated 2024-06-11 and 1.20 dated 2025-02-19
ChangeLog | 4 + DESCRIPTION | 14 +++-- MD5 | 10 +-- R/coneproj.R | 8 +-- man/coneA.Rd | 144 +++++++++++++++++++++++++++---------------------------- src/coneproj.cpp | 30 ++++++++--- 6 files changed, 117 insertions(+), 93 deletions(-)
Title: Clustering and Simulation of Spherical Cauchy and PKBD Models
Description: Provides tools for estimation and clustering of spherical data, seamlessly integrated with the 'flexmix' package. Includes the necessary M-step implementations for both Poisson Kernel-Based Distribution (PKBD) and spherical Cauchy distribution. Additionally, the package provides random number generators for PKBD and spherical Cauchy distribution. Methods are based on Golzy M., Markatou M. (2020) <doi:10.1080/10618600.2020.1740713>, Kato S., McCullagh P. (2020) <doi:10.3150/20-bej1222> and Sablica L., Hornik K., Leydold J. (2023) <doi:10.1214/23-ejs2149>.
Author: Lukas Sablica [aut, cre] ,
Kurt Hornik [aut] ,
Bettina Gruen [aut] ,
Josef Leydold [aut]
Maintainer: Lukas Sablica <lsablica@wu.ac.at>
Diff between circlus versions 0.0.1 dated 2024-10-17 and 0.0.2 dated 2025-02-19
circlus-0.0.1/circlus/man/FLXMCpkbd.Rd |only circlus-0.0.1/circlus/man/FLXMRpkbd.Rd |only circlus-0.0.1/circlus/man/dpkbd.Rd |only circlus-0.0.1/circlus/man/rpkbd.Rd |only circlus-0.0.2/circlus/DESCRIPTION | 8 ++-- circlus-0.0.2/circlus/MD5 | 28 ++++++++-------- circlus-0.0.2/circlus/NAMESPACE | 8 ++-- circlus-0.0.2/circlus/R/Estimation.R | 50 ++++++++++++++--------------- circlus-0.0.2/circlus/R/PKBD_sample.R | 14 ++++---- circlus-0.0.2/circlus/man/FLXMCpkb.Rd |only circlus-0.0.2/circlus/man/FLXMCspcauchy.Rd | 2 - circlus-0.0.2/circlus/man/FLXMRpkb.Rd |only circlus-0.0.2/circlus/man/FLXMRspcauchy.Rd | 2 - circlus-0.0.2/circlus/man/dpkb.Rd |only circlus-0.0.2/circlus/man/rPKBD_Saw.Rd | 4 +- circlus-0.0.2/circlus/man/rpkb.Rd |only circlus-0.0.2/circlus/src/pkbd.cpp | 1 circlus-0.0.2/circlus/src/rpkbd.cpp | 2 - circlus-0.0.2/circlus/src/sCauchy.cpp | 2 - 19 files changed, 61 insertions(+), 60 deletions(-)
Title: Create Spreadsheet Publications Following Best Practice
Description: Generate spreadsheet publications that follow best practice
guidance from the UK government's Analysis Function, available at
<https://analysisfunction.civilservice.gov.uk/policy-store/releasing-statistics-in-spreadsheets/>,
with a focus on accessibility. See also the 'Python' package 'gptables'.
Author: Matt Dray [aut],
Tim Taylor [ctb],
Matt Kerlogue [ctb],
Crown Copyright [cph],
Olivia Box Power [cre, ctb]
Maintainer: Olivia Box Power <Olivia.BoxPower@dhsc.gov.uk>
Diff between aftables versions 1.0.1 dated 2025-02-19 and 1.0.2 dated 2025-02-19
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS.md | 2 +- inst/doc/aftables.html | 40 ++++++++++++++++++++-------------------- man/aftables-package.Rd | 2 +- 5 files changed, 32 insertions(+), 32 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.50 dated 2025-01-07 and 0.51 dated 2025-02-19
DESCRIPTION | 11 ++--- LICENSE | 2 MD5 | 34 ++++++++-------- NAMESPACE | 1 NEWS.md | 10 ++++ R/data-structure.R | 12 ++++- R/image.R | 23 ++++++----- R/io.R | 55 +++++++++++--------------- R/json.R | 90 ++++++++++++++++++++++++++++++++------------ R/record.R | 12 +++-- R/string.R | 16 +++++-- R/yaml.R | 2 inst/doc/xfun.html | 22 +++++----- man/download_file.Rd | 28 ++++++------- man/raw_string.Rd | 2 man/tojson.Rd | 32 ++++++++++++--- man/upload_imgur.Rd | 13 +++--- tests/test-cran/test-json.R | 29 ++++++-------- 18 files changed, 241 insertions(+), 153 deletions(-)
Title: Mine Metrics from Common Places on the Web
Description: Mine metrics on common places on the web through the power of their APIs (application programming interfaces).
It also helps make the data in a format that is easily used for a dashboard or other purposes.
There is an associated dashboard template and tutorials that are underdevelopment that help you
fully utilize 'metricminer'.
Author: Candace Savonen [aut, cre],
Howard Baek [aut]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between metricminer versions 0.5.1 dated 2024-02-02 and 1.0.0 dated 2025-02-19
metricminer-0.5.1/metricminer/man/get_all_ga_metrics.Rd |only metricminer-1.0.0/metricminer/DESCRIPTION | 14 metricminer-1.0.0/metricminer/MD5 | 113 +- metricminer-1.0.0/metricminer/NAMESPACE | 8 metricminer-1.0.0/metricminer/NEWS.md | 5 metricminer-1.0.0/metricminer/R/auth.R | 132 ++- metricminer-1.0.0/metricminer/R/citations.R |only metricminer-1.0.0/metricminer/R/github.R | 401 +++++++--- metricminer-1.0.0/metricminer/R/google-analytics.R | 214 +++-- metricminer-1.0.0/metricminer/R/google-forms.R | 38 metricminer-1.0.0/metricminer/R/scopes.R | 12 metricminer-1.0.0/metricminer/R/slido.R | 16 metricminer-1.0.0/metricminer/R/token-handlers.R | 4 metricminer-1.0.0/metricminer/R/utils-pipe.R |only metricminer-1.0.0/metricminer/R/utils.R | 15 metricminer-1.0.0/metricminer/R/write-data.R | 189 ++++ metricminer-1.0.0/metricminer/R/youtube.R | 17 metricminer-1.0.0/metricminer/README.md | 22 metricminer-1.0.0/metricminer/build/vignette.rds |binary metricminer-1.0.0/metricminer/inst/doc/example-data.html | 45 - metricminer-1.0.0/metricminer/inst/doc/getting-started.Rmd | 21 metricminer-1.0.0/metricminer/inst/doc/getting-started.html | 99 +- metricminer-1.0.0/metricminer/inst/extdata/_config_automation.yml |only metricminer-1.0.0/metricminer/man/app_set_up.Rd | 6 metricminer-1.0.0/metricminer/man/auth_from_secret.Rd | 28 metricminer-1.0.0/metricminer/man/authorize.Rd | 15 metricminer-1.0.0/metricminer/man/clean_ga_metrics.Rd | 6 metricminer-1.0.0/metricminer/man/clean_repo_metrics.Rd | 6 metricminer-1.0.0/metricminer/man/delete_creds.Rd | 6 metricminer-1.0.0/metricminer/man/get_citation_count.Rd |only metricminer-1.0.0/metricminer/man/get_config_file.Rd |only metricminer-1.0.0/metricminer/man/get_ga_metadata.Rd | 3 metricminer-1.0.0/metricminer/man/get_ga_properties.Rd | 2 metricminer-1.0.0/metricminer/man/get_ga_property_info.Rd |only metricminer-1.0.0/metricminer/man/get_ga_stats.Rd | 8 metricminer-1.0.0/metricminer/man/get_ga_user.Rd | 3 metricminer-1.0.0/metricminer/man/get_github.Rd | 4 metricminer-1.0.0/metricminer/man/get_github_metrics.Rd | 42 - metricminer-1.0.0/metricminer/man/get_github_repo_summary.Rd | 32 metricminer-1.0.0/metricminer/man/get_github_repo_timecourse.Rd | 32 metricminer-1.0.0/metricminer/man/get_github_user.Rd | 4 metricminer-1.0.0/metricminer/man/get_google_form.Rd | 4 metricminer-1.0.0/metricminer/man/get_multiple_forms.Rd | 9 metricminer-1.0.0/metricminer/man/get_multiple_ga_metrics.Rd |only metricminer-1.0.0/metricminer/man/get_multiple_repos_metrics.Rd | 45 - metricminer-1.0.0/metricminer/man/get_org_repo_list.Rd | 16 metricminer-1.0.0/metricminer/man/get_question_metadata.Rd | 2 metricminer-1.0.0/metricminer/man/get_slido_files.Rd | 5 metricminer-1.0.0/metricminer/man/get_timestamp_repo_metrics.Rd | 6 metricminer-1.0.0/metricminer/man/get_user_repo_list.Rd | 16 metricminer-1.0.0/metricminer/man/gh_repo_wrapper.Rd | 14 metricminer-1.0.0/metricminer/man/list_example_data.Rd | 1 metricminer-1.0.0/metricminer/man/pipe.Rd |only metricminer-1.0.0/metricminer/man/request_ga.Rd | 3 metricminer-1.0.0/metricminer/man/request_google_forms.Rd | 4 metricminer-1.0.0/metricminer/man/setup_folders.Rd |only metricminer-1.0.0/metricminer/man/write_playlist_details.Rd | 17 metricminer-1.0.0/metricminer/man/write_to_gsheet.Rd | 16 metricminer-1.0.0/metricminer/tests/testthat/test-calendly.R | 6 metricminer-1.0.0/metricminer/tests/testthat/test-citation.R |only metricminer-1.0.0/metricminer/tests/testthat/test-github.R | 13 metricminer-1.0.0/metricminer/tests/testthat/test-google-analytics.R | 11 metricminer-1.0.0/metricminer/vignettes/getting-started.Rmd | 21 63 files changed, 1251 insertions(+), 520 deletions(-)
Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.2.12 dated 2025-02-19 and 5.2.13 dated 2025-02-19
DESCRIPTION | 6 MD5 | 522 +++---- NAMESPACE | 1100 ++++++++-------- R/apis.R | 68 - R/audio.R | 368 ++--- R/cache.R | 334 ++-- R/chatgpt.R | 936 ++++++------- R/checks.R | 334 ++-- R/clusters.R | 694 +++++----- R/colour_palettes.R | 394 ++--- R/confidence.R | 172 +- R/correlations.R | 1116 ++++++++-------- R/cran.R | 176 +- R/credentials.R | 196 +- R/crossbrand.R | 682 +++++----- R/crossbrand2.R | 936 ++++++------- R/crosstab.R | 202 +-- R/currency.R | 146 +- R/dalex_explainers.R | 436 +++--- R/dataframe_str.R | 462 +++--- R/datasets.R | 160 +- R/dim_reduction.R | 336 ++--- R/distribution.R | 950 +++++++------- R/dropbox.R | 246 +-- R/encoding.R | 44 R/facebook.R | 1528 +++++++++++----------- R/family.R | 104 - R/forecasting.R | 710 +++++----- R/frequencies.R | 1724 ++++++++++++------------- R/gemini.R | 166 +- R/geodata.R | 524 +++---- R/google_analytics.R | 128 - R/google_sheets.R | 258 +-- R/google_trends.R | 380 ++--- R/hubspot.R | 398 ++--- R/hubspot_f1.R | 502 +++---- R/lares.R | 306 ++-- R/lasso.R | 264 +-- R/linkedin.R | 114 - R/logo.R | 98 - R/mails.R | 190 +- R/maze.R | 668 ++++----- R/missings.R | 260 +-- R/model_functions.R | 1956 ++++++++++++++--------------- R/model_metrics.R | 1232 +++++++++--------- R/model_plots.R | 2928 +++++++++++++++++++++---------------------- R/model_predict.R | 328 ++-- R/model_preprocessing.R | 490 +++---- R/numble.R | 54 R/object_detection.R | 120 - R/onehotencoding.R | 1052 +++++++-------- R/other_functions.R | 2262 ++++++++++++++++----------------- R/other_plots.R | 548 ++++---- R/outliers.R | 364 ++--- R/plot_scales.R | 224 +-- R/querieSQL.R | 64 R/robyn.R | 1583 ++++++++++++----------- R/rtistry.R | 96 - R/scrabble.R | 996 +++++++------- R/shapley.R | 538 ++++---- R/shiny.R | 2 R/slack.R | 92 - R/statusbar.R | 158 +- R/stocks.R | 3014 ++++++++++++++++++++++----------------------- R/sudoku.R | 178 +- R/surveys.R | 84 - R/text_mining.R | 1124 ++++++++-------- R/theme_lares.R | 820 ++++++------ R/tictoc.R | 188 +- R/trees.R | 298 ++-- R/twitter.R | 56 R/typeform.R | 98 - R/update.R | 74 - R/wordle.R | 596 ++++---- R/wrangling.R | 1750 +++++++++++++------------- R/x2y.R | 736 +++++----- R/zzz.R | 198 +- README.md | 146 +- inst/_pkgdown.yml | 20 inst/docs/config.yml | 28 inst/docs/stocksReport.Rmd | 160 +- man/ROC.Rd | 132 - man/autoline.Rd | 154 +- man/balance_data.Rd | 126 - man/bind_files.Rd | 114 - man/bring_api.Rd | 154 +- man/cache_write.Rd | 170 +- man/categ_reducer.Rd | 172 +- man/checks.Rd | 256 +-- man/chr2num.Rd | 142 +- man/ci_lower.Rd | 74 - man/ci_var.Rd | 72 - man/clean_text.Rd | 214 +-- man/clusterKmeans.Rd | 236 +-- man/clusterOptimalK.Rd | 116 - man/clusterVisualK.Rd | 86 - man/conf_mat.Rd | 144 +- man/corr.Rd | 208 +-- man/corr_cross.Rd | 218 +-- man/corr_var.Rd | 230 +-- man/cran_logs.Rd | 74 - man/crosstab.Rd | 146 +- man/dalex_local.Rd | 64 man/dalex_residuals.Rd | 48 man/dalex_variable.Rd | 88 - man/date_cuts.Rd | 102 - man/date_feats.Rd | 206 +-- man/db_download.Rd | 212 +-- man/db_upload.Rd | 174 +- man/df_str.Rd | 122 - man/dfr.Rd | 70 - man/dft.Rd | 98 - man/dist2d.Rd | 70 - man/distr.Rd | 268 ++-- man/errors.Rd | 132 - man/etf_sector.Rd | 68 - man/export_plot.Rd | 180 +- man/export_results.Rd | 196 +- man/fb_accounts.Rd | 144 +- man/fb_ads.Rd | 174 +- man/fb_creatives.Rd | 134 +- man/fb_insights.Rd | 294 ++-- man/fb_process.Rd | 114 - man/fb_report_check.Rd | 150 +- man/fb_rf.Rd | 306 ++-- man/fb_token.Rd | 116 - man/file_name.Rd | 156 +- man/filesGD.Rd | 86 - man/files_functions.Rd | 148 +- man/filterdata.Rd | 246 +-- man/font_exists.Rd | 138 +- man/forecast_arima.Rd | 162 +- man/formatColoured.Rd | 144 +- man/format_string.Rd | 324 ++-- man/freqs.Rd | 272 ++-- man/freqs_df.Rd | 178 +- man/freqs_list.Rd | 258 +-- man/freqs_plot.Rd | 180 +- man/gain_lift.Rd | 142 +- man/gemini_ask.Rd | 198 +- man/get_credentials.Rd | 268 ++-- man/get_currency.Rd | 88 - man/get_mp3.Rd | 174 +- man/get_tweets.Rd | 68 - man/gg_fill_customs.Rd | 162 +- man/glued.Rd | 192 +- man/google_sheets.Rd | 174 +- man/google_trends.Rd | 106 - man/gpt_ask.Rd | 352 ++--- man/gpt_prompter.Rd | 276 ++-- man/grepl_letters.Rd | 68 - man/grepm.Rd | 158 +- man/h2o_automl.Rd | 426 +++--- man/h2o_explainer.Rd | 140 +- man/h2o_results.Rd | 142 +- man/h2o_selectmodel.Rd | 154 +- man/h2o_shap.Rd | 154 +- man/haveInternet.Rd | 118 - man/holidays.Rd | 176 +- man/image_metadata.Rd | 112 - man/importxlsx.Rd | 114 - man/impute.Rd | 140 +- man/install_recommended.Rd | 38 man/ip_data.Rd | 156 +- man/iter_seeds.Rd | 84 - man/json2vector.Rd | 122 - man/lares-exports.Rd | 18 man/lares.Rd | 44 man/lares_logo.Rd | 36 man/lares_pal.Rd | 114 - man/lasso_vars.Rd | 188 +- man/left_right.Rd | 106 - man/li_auth.Rd | 88 - man/li_profile.Rd | 78 - man/list_cats.Rd | 134 +- man/listfiles.Rd | 152 +- man/loglossBinary.Rd | 58 man/mail_send.Rd | 218 +-- man/markdown2df.Rd | 120 - man/maze_solve.Rd | 182 +- man/missingness.Rd | 140 +- man/model_metrics.Rd | 248 +-- man/model_preprocess.Rd | 230 +-- man/move_files.Rd | 120 - man/mplot_conf.Rd | 180 +- man/mplot_cuts.Rd | 134 +- man/mplot_cuts_error.Rd | 128 - man/mplot_density.Rd | 138 +- man/mplot_full.Rd | 188 +- man/mplot_gain.Rd | 192 +- man/mplot_importance.Rd | 164 +- man/mplot_lineal.Rd | 118 - man/mplot_metrics.Rd | 104 - man/mplot_response.Rd | 186 +- man/mplot_roc.Rd | 174 +- man/mplot_splits.Rd | 158 +- man/mplot_topcats.Rd | 98 - man/msplit.Rd | 172 +- man/myip.Rd | 116 - man/ngrams.Rd | 98 - man/noPlot.Rd | 82 - man/normalize.Rd | 108 - man/num_abbr.Rd | 114 - man/ohe_commas.Rd | 140 +- man/ohse.Rd | 248 +-- man/outlier_tukey.Rd | 66 man/outlier_zscore.Rd | 68 - man/outlier_zscore_plot.Rd | 86 - man/plot_cats.Rd | 72 - man/plot_chord.Rd | 110 - man/plot_df.Rd | 72 - man/plot_nums.Rd | 80 - man/plot_palette.Rd | 82 - man/plot_survey.Rd | 74 - man/plot_timeline.Rd | 182 +- man/prophesize.Rd | 104 - man/quants.Rd | 132 - man/queryDB.Rd | 72 - man/queryGA.Rd | 158 +- man/quiet.Rd | 118 - man/read.file.Rd | 128 - man/reduce_pca.Rd | 128 - man/reduce_tsne.Rd | 102 - man/remove_stopwords.Rd | 82 - man/replaceall.Rd | 182 +- man/replacefactor.Rd | 114 - man/robyn_crossmmm.Rd | 250 +-- man/robyn_hypsbuilder.Rd | 126 - man/robyn_modelselector.Rd | 174 +- man/robyn_performance.Rd | 146 +- man/rtistry_sphere.Rd | 36 man/scale_x_comma.Rd | 208 +-- man/scrabble.Rd | 318 ++-- man/sentimentBreakdown.Rd | 110 - man/seq_surnames.Rd | 60 man/shap_var.Rd | 118 - man/slackSend.Rd | 124 - man/spread_list.Rd | 82 - man/statusbar.Rd | 182 +- man/stocks_hist.Rd | 170 +- man/stocks_report.Rd | 336 ++--- man/sudoku_solver.Rd | 96 - man/target_set.Rd | 56 man/textCloud.Rd | 112 - man/textFeats.Rd | 134 +- man/textTokenizer.Rd | 204 +-- man/theme_lares.Rd | 210 +-- man/tic.Rd | 200 +- man/topics_rake.Rd | 72 - man/tree_var.Rd | 254 +-- man/trim_mp3.Rd | 72 - man/try_require.Rd | 148 +- man/updateLares.Rd | 130 - man/vector2text.Rd | 132 - man/warnifnot.Rd | 118 - man/weighted_value.Rd | 102 - man/what_size.Rd | 146 +- man/winsorize.Rd | 64 man/wordle.Rd | 156 +- man/x2y.Rd | 256 +-- man/year_month.Rd | 110 - man/zerovar.Rd | 98 - 262 files changed, 35209 insertions(+), 35182 deletions(-)
Title: Kernel Functions and Tools for Machine Learning Applications
Description: Kernel functions for diverse types of data (including, but not
restricted to: nonnegative and real vectors, real matrices, categorical
and ordinal variables, sets, strings), plus other utilities like kernel
similarity, kernel Principal Components Analysis (PCA) and features'
importance for Support Vector Machines (SVMs), which expand other 'R'
packages like 'kernlab'.
Author: Elies Ramon [aut, cre, cph]
Maintainer: Elies Ramon <eramon@everlyrusher.com>
Diff between kerntools versions 1.1.0 dated 2024-10-25 and 1.2.0 dated 2025-02-19
DESCRIPTION | 6 MD5 | 49 +-- NAMESPACE | 4 NEWS.md | 15 R/importancies.R | 74 ++++ R/kernel_functions.R | 170 +++++++++- R/kernel_study.R | 22 - README.md | 7 inst/WORDLIST | 18 + inst/doc/Kernel-PCA-and-CIA.html | 12 inst/doc/Kernel-functions.R | 33 ++ inst/doc/Kernel-functions.Rmd | 131 +++++++- inst/doc/Kernel-functions.html | 534 +++++++++++++++++++++------------ inst/doc/kerntools.R | 14 inst/doc/kerntools.Rmd | 26 + inst/doc/kerntools.html | 198 +++++++----- man/Chi2.Rd |only man/KTA.Rd | 2 man/Laplace.Rd | 2 man/RBF.Rd | 2 man/aggregate_imp.Rd |only man/cLinear.Rd |only man/heatK.Rd | 3 tests/testthat/test-importancies.R | 23 + tests/testthat/test-kernel_functions.R | 77 ++++ vignettes/Kernel-functions.Rmd | 131 +++++++- vignettes/kerntools.Rmd | 26 + 27 files changed, 1240 insertions(+), 339 deletions(-)
Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical
data and the web. Offers simple, flexible tools for working with JSON in R, and
is particularly powerful for building pipelines and interacting with a web API.
The implementation is based on the mapping described in the vignette (Ooms, 2014).
In addition to converting JSON data from/to R objects, 'jsonlite' contains
functions to stream, validate, and prettify JSON data. The unit tests included
with the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] ,
Duncan Temple Lang [ctb],
Lloyd Hilaiel [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between jsonlite versions 1.8.9 dated 2024-09-20 and 1.9.0 dated 2025-02-19
jsonlite-1.8.9/jsonlite/src/modp_stdint.h |only jsonlite-1.9.0/jsonlite/DESCRIPTION | 6 ++--- jsonlite-1.9.0/jsonlite/MD5 | 17 +++++++--------- jsonlite-1.9.0/jsonlite/NEWS | 3 ++ jsonlite-1.9.0/jsonlite/build/vignette.rds |binary jsonlite-1.9.0/jsonlite/inst/doc/json-aaquickstart.html | 10 ++++----- jsonlite-1.9.0/jsonlite/inst/doc/json-mapping.pdf |binary jsonlite-1.9.0/jsonlite/man/stream_in.Rd | 2 - jsonlite-1.9.0/jsonlite/src/modp_numtoa.c | 5 ++-- jsonlite-1.9.0/jsonlite/src/modp_numtoa.h | 4 ++- 10 files changed, 26 insertions(+), 21 deletions(-)
Title: Viral Load and CD4 Lymphocytes Regression Models
Description: Provides a comprehensive framework for building, evaluating, and visualizing regression models for analyzing viral load and CD4 (Cluster of Differentiation 4) lymphocytes data. It leverages the principles of the tidymodels ecosystem of Max Kuhn and Hadley Wickham (2020) <https://www.tidymodels.org> to offer a user-friendly experience in model development. This package includes functions for data preprocessing, feature engineering, model training, tuning, and evaluation, along with visualization tools to enhance the interpretation of model results. It is specifically designed for researchers in biostatistics, computational biology, and HIV research who aim to perform reproducible and rigorous analyses to gain insights into disease dynamics. The main focus is on improving the understanding of the relationships between viral load, CD4 lymphocytes, and other relevant covariates to contribute to HIV research and the visibility of vulnerable seropositive populations.
Author: Juan Pablo Acuna Gonzalez [aut, cre]
Maintainer: Juan Pablo Acuna Gonzalez <acua6307@gmail.com>
Diff between viralmodels versions 1.3.1 dated 2024-10-18 and 1.3.3 dated 2025-02-19
DESCRIPTION | 6 +- MD5 | 32 ++++++------- NAMESPACE | 1 NEWS.md | 12 ++++- R/viralmodel.R | 64 +++++++++++++-------------- R/viralpreds.R | 88 +++++++++++++++++++++++++++++-------- R/viraltab.R | 89 ++++++++++++++++++++++---------------- R/viralvis.R | 60 ++++++++++++------------- man/viralmodel.Rd | 2 man/viralpreds.Rd | 24 +++++++--- man/viraltab.Rd | 11 +++- man/viralvis.Rd | 2 tests/testthat/_snaps/viraltab.md | 2 tests/testthat/test-viralmodel.R | 2 tests/testthat/test-viralpreds.R | 2 tests/testthat/test-viraltab.R | 4 - tests/testthat/test-viralvis.R | 3 - 17 files changed, 247 insertions(+), 157 deletions(-)
Title: Fitting and Simulating Mixtures of Watson Distributions
Description: Tools for fitting and simulating mixtures of Watson distributions.
The random sampling scheme of the package offers two sampling
algorithms that are based of the results of Sablica, Hornik and Leydold (2022)
<doi:10.1080/10618600.2024.2416521>.
What is more, the package offers a smart tool to combine these two methods,
and based on the selected parameters, it approximates the relative sampling
speed for both methods and picks the faster one. In addition, the package
offers a fitting function for the mixtures of Watson distribution, that
uses the expectation-maximization (EM) algorithm. Special features are
the possibility to use multiple variants of the E-step and M-step,
sparse matrices for the data representation and state of the art methods
for numerical evaluation of needed special functions using the results of
Sablica and Hornik (2022) <doi:10.1090/mcom/3690> and
Sablica and Hornik (2024) <doi:10.1016/j.jmaa.2024.128262>.
Author: Lukas Sablica [aut, cre] ,
Kurt Hornik [aut] ,
Josef Leydold [aut] ,
Gerard Jungman [ctb, cph] ,
Brian Gough [ctb, cph]
Maintainer: Lukas Sablica <lsablica@wu.ac.at>
Diff between watson versions 0.5 dated 2024-11-19 and 0.6 dated 2025-02-19
DESCRIPTION | 13 ++++++++----- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/RcppExports.R | 4 ++-- man/rmwat.Rd | 4 ++-- src/rwat.cpp | 8 ++++---- 6 files changed, 27 insertions(+), 18 deletions(-)
Title: An Analyzer of International Large Scale Assessments in
Education
Description: An easy way to analyze international large-scale assessments and surveys in education or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) while also allowing for analysis with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre],
Francesco Avvisati [aut],
Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>
Diff between Rrepest versions 1.5.3 dated 2025-02-17 and 1.5.4 dated 2025-02-19
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ R/coverage_daggers.R | 4 +--- R/data.R | 21 ++++++++++++++++++++- R/pv_rrepest_frequencies.R | 2 ++ R/repest_auxiliaries.R | 19 +++++++++++++++++++ data/talis18_tt3g23o_freq.rda |only man/coverage_daggers.Rd | 4 +--- man/talis18_tt3g23o_freq.Rd |only 9 files changed, 54 insertions(+), 16 deletions(-)
Title: Bayesian Dynamic Borrowing with Propensity Score
Description: A tool which aims to help evaluate the effect of external borrowing using an integrated approach described in Lewis et al., (2019) <doi:10.1080/19466315.2018.1497533> that combines propensity score and Bayesian dynamic borrowing methods.
Author: Isaac Gravestock [cre, ctb],
Craig Gower-Page [aut],
Matt Secrest [ctb],
Yichen Lu [aut],
Aijing Lin [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between psborrow versions 0.2.1 dated 2023-03-03 and 0.2.2 dated 2025-02-19
DESCRIPTION | 6 +-- MD5 | 10 +++--- NEWS.md | 4 ++ R/apply_mcmc.R | 2 - build/vignette.rds |binary tests/testthat/test-apply_mcmc.R | 63 +++++++++++++++++++++++++++++++++++++++ 6 files changed, 76 insertions(+), 9 deletions(-)
Title: Miscellaneous Functions for Metabarcoding Analysis
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Author: Adrien Taudiere [aut, cre, cph]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Diff between MiscMetabar versions 0.12.1 dated 2025-01-29 and 0.14.1 dated 2025-02-19
DESCRIPTION | 6 MD5 | 124 +-- NAMESPACE | 6 NEWS.md | 15 R/MiscMetabar-package.R | 2 R/alpha_div_test.R | 4 R/beta_div_test.R | 20 R/blast.R | 392 ++++++++-- R/dada_phyloseq.R | 245 +++++- R/miscellanous.R | 5 R/plot_functions.R | 24 R/targets_misc.R | 2 R/taxonomy.R |only R/vsearch.R | 41 - inst/doc/MiscMetabar.html | 34 inst/extdata/100_sp_UNITE_sh_general_release_dynamic_dadaSpecies.fasta |only man/LCBD_pq.Rd | 2 man/SRS_curve_pq.Rd | 2 man/add_blast_info.Rd | 2 man/add_new_taxonomy_pq.Rd | 29 man/adonis_pq.Rd | 2 man/ancombc_pq.Rd | 4 man/assign_blastn.Rd |only man/assign_dada2.Rd |only man/assign_idtaxa.Rd | 10 man/assign_sintax.Rd | 17 man/assign_vsearch_lca.Rd | 17 man/blast_pq.Rd | 8 man/blast_to_derep.Rd | 4 man/blast_to_phyloseq.Rd | 5 man/chimera_removal_vs.Rd | 2 man/diff_fct_diff_class.Rd | 2 man/dist_bycol.Rd | 2 man/filter_asv_blast.Rd | 4 man/format2dada2.Rd |only man/format2dada2_species.Rd |only man/format2sintax.Rd |only man/get_file_extension.Rd | 3 man/ggaluv_pq.Rd | 2 man/ggbetween_pq.Rd | 2 man/ggscatt_pq.Rd | 2 man/glmutli_pq.Rd | 2 man/hill_curves_pq.Rd | 2 man/hill_test_rarperm_pq.Rd | 2 man/lulu_pq.Rd | 2 man/multipatt_pq.Rd | 2 man/plot_LCBD_pq.Rd | 2 man/plot_SCBD_pq.Rd | 2 man/plot_tsne_pq.Rd | 2 man/postcluster_pq.Rd | 2 man/read_pq.Rd | 2 man/resolve_vector_ranks.Rd |only man/sample_data_with_new_names.Rd | 2 man/save_pq.Rd | 2 man/tbl_sum_samdata.Rd | 2 man/tbl_sum_taxtable.Rd | 2 man/track_wkflow.Rd | 2 man/treemap_pq.Rd | 2 man/tsne_pq.Rd | 2 man/umap_pq.Rd | 2 man/upset_pq.Rd | 2 man/upset_test_pq.Rd | 2 man/vs_search_global.Rd | 6 man/write_pq.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test_vsearch.R | 4 vignettes/bibliography.bib | 18 67 files changed, 842 insertions(+), 269 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.5.0 dated 2025-01-07 and 0.5.1 dated 2025-02-19
DESCRIPTION | 6 +- MD5 | 28 +++++----- NEWS.md | 6 ++ R/build_schedule_entry.R | 1 R/roxy_maestro.R | 4 - R/run_schedule.R | 2 R/utils.R | 9 +-- inst/doc/maestro-1-quick-start.html | 8 +-- inst/doc/maestro-2-motivation-concepts.html | 3 - inst/doc/maestro-3-use-cases.html | 3 - inst/doc/maestro-4-advanced-scheduling.html | 11 +--- inst/doc/maestro-5-directed-acyclic-graphs.html | 22 ++++---- inst/doc/maestro-6-logging.html | 63 +++++++++++------------- man/convert_to_seconds.Rd | 2 man/parse_rounding_unit.Rd | 2 15 files changed, 86 insertions(+), 84 deletions(-)
Title: A Fast and Light Package to Compute Polygenic Risk Scores
Description: Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".
Author: Guillermo Reales [aut, cre] ,
Chris Wallace [aut] ,
Olly Burren [ctb]
Maintainer: Guillermo Reales <gr440@cam.ac.uk>
Diff between RapidoPGS versions 2.3.0 dated 2023-10-13 and 2.3.1 dated 2025-02-19
DESCRIPTION | 8 MD5 | 39 +- NEWS.md | 14 R/data.R | 8 R/rapfunc.R | 12 README.md | 10 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 2 inst/doc/Computing_RapidoPGSmulti.R | 26 - inst/doc/Computing_RapidoPGSmulti.html | 503 +++++++++++++++++++++----- inst/doc/Computing_RapidoPGSsingle.R | 36 - inst/doc/Computing_RapidoPGSsingle.Rmd | 2 inst/doc/Computing_RapidoPGSsingle.html | 599 +++++++++++++++++++++++--------- man/EUR_ld.blocks19.Rd | 2 man/EUR_ld.blocks38.Rd | 2 man/michailidou19.Rd | 2 man/michailidou38.Rd | 2 man/rapidopgs_multi.Rd | 2 man/rapidopgs_single.Rd | 2 vignettes/Computing_RapidoPGSsingle.Rmd | 2 21 files changed, 933 insertions(+), 340 deletions(-)
Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.2.11 dated 2025-01-09 and 5.2.12 dated 2025-02-19
lares-5.2.11/lares/man/outlier_turkey.Rd |only lares-5.2.12/lares/DESCRIPTION | 6 - lares-5.2.12/lares/MD5 | 37 ++++---- lares-5.2.12/lares/NAMESPACE | 3 lares-5.2.12/lares/R/cache.R | 12 +- lares-5.2.12/lares/R/google_analytics.R | 3 lares-5.2.12/lares/R/lares.R | 2 lares-5.2.12/lares/R/outliers.R | 5 - lares-5.2.12/lares/R/robyn.R | 108 ++++++++++++++++++++++---- lares-5.2.12/lares/R/stocks.R | 21 ++--- lares-5.2.12/lares/man/cache_write.Rd | 5 + lares-5.2.12/lares/man/outlier_tukey.Rd |only lares-5.2.12/lares/man/outlier_zscore.Rd | 2 lares-5.2.12/lares/man/outlier_zscore_plot.Rd | 2 lares-5.2.12/lares/man/queryGA.Rd | 3 lares-5.2.12/lares/man/robyn_hypsbuilder.Rd | 1 lares-5.2.12/lares/man/robyn_marginal.Rd |only lares-5.2.12/lares/man/robyn_modelselector.Rd | 1 lares-5.2.12/lares/man/robyn_performance.Rd | 5 + lares-5.2.12/lares/man/stocks_report.Rd | 7 - lares-5.2.12/lares/man/winsorize.Rd | 2 21 files changed, 164 insertions(+), 61 deletions(-)
Title: Robust Trimmed Clustering
Description: Provides functions for robust trimmed clustering. The methods are
described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>,
Fritz et al. (2012) <doi:10.18637/jss.v047.i12>,
Garcia-Escudero et al. (2011) <doi:10.1007/s11222-010-9194-z> and others.
Author: Valentin Todorov [aut, cre] ,
Luis Angel Garcia Escudero [aut],
Agustin Mayo Iscar [aut],
Javier Crespo Guerrero [aut],
Heinrich Fritz [aut]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between tclust versions 2.0-5 dated 2024-10-15 and 2.1-0 dated 2025-02-19
ChangeLog | 15 + DESCRIPTION | 10 MD5 | 29 +- NAMESPACE | 5 R/RcppExports.R | 85 +++++++ R/print.tclust.R | 3 R/randIndex.R |only R/tclust.R | 40 +-- R/tclustIC.R | 4 man/estepRR.Rd |only man/randIndex.Rd |only src/RcppExports.cpp | 36 ++- src/rlg.cpp | 2 src/tclust.cpp | 560 +++++++++++++++++++++++++++++------------------- src/tkmeans.cpp | 2 tests/ttclust.R | 18 + tests/ttclust.Rout.save | 328 ++++++++++++++++++---------- 17 files changed, 752 insertions(+), 385 deletions(-)
Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marti Catala [ctb] ,
Xihang Chen [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [ctb] ,
Danielle Newby [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 3.3.2 dated 2025-01-28 and 3.4.0 dated 2025-02-19
DESCRIPTION | 14 - MD5 | 36 +-- R/drugCodes.R | 62 +++--- R/getRoutes.R | 121 ++++++------ R/mockVocabRef.R | 98 +++++----- R/runSearch.R | 4 R/stratifyByRoute.R | 267 +++++++++++++--------------- R/subsetOnRouteCategory.R | 190 +++++++++---------- R/summariseCodeUse.R | 56 +++++ inst/doc/a04_Vocab_based_codelists.html | 57 ----- man/getDrugIngredientCodes.Rd | 3 man/summariseCodeUse.Rd | 5 tests/testthat/test-codesFrom.R | 5 tests/testthat/test-dbms.R | 5 tests/testthat/test-drugCodes.R | 5 tests/testthat/test-findUnmappedCodes.R | 5 tests/testthat/test-getCandidateCodes.R | 4 tests/testthat/test-subsetOnRouteCategory.R | 58 +++--- tests/testthat/test-summariseCodeUse.R | 85 ++++++++ 19 files changed, 583 insertions(+), 497 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: Extending the Newman Studentized Range Statistic to
Transcriptomics
Description: Extends the classical Newman studentized range statistic
in various ways that can be applied to genome-scale transcriptomic
or other expression data.
Author: Zachary B. Abrams [aut],
Greg Gershkowitz [aut],
Anoushka Joglekar [aut],
Chao Liu [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NewmanOmics versions 1.0.11 dated 2024-04-28 and 1.0.13 dated 2025-02-19
NewmanOmics-1.0.11/NewmanOmics/tests/01-bankedTest.R |only NewmanOmics-1.0.11/NewmanOmics/tests/01-bankedTest.Rout.save |only NewmanOmics-1.0.11/NewmanOmics/tests/03-betamix.R |only NewmanOmics-1.0.11/NewmanOmics/tests/03-betamix.Rout.save |only NewmanOmics-1.0.13/NewmanOmics/DESCRIPTION | 23 NewmanOmics-1.0.13/NewmanOmics/MD5 | 18 NewmanOmics-1.0.13/NewmanOmics/R/02-betamix3.R | 13 NewmanOmics-1.0.13/NewmanOmics/build/vignette.rds |binary NewmanOmics-1.0.13/NewmanOmics/data/GSE6631.rda |binary NewmanOmics-1.0.13/NewmanOmics/data/LungPair.rda |binary NewmanOmics-1.0.13/NewmanOmics/inst/doc/newmanomics.html | 287 +++++------ NewmanOmics-1.0.13/NewmanOmics/man/02-pairedStat.Rd | 4 12 files changed, 181 insertions(+), 164 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut],
Youngsun Park [aut] ,
Hyungwoo Jo [aut],
Jeongmin Seo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.6.1 dated 2025-01-08 and 1.6.3 dated 2025-02-19
DESCRIPTION | 8 MD5 | 32 - NAMESPACE | 1 NEWS.md | 9 R/coxph.R | 248 ++++++++---- R/forestcox.R | 108 ++++- R/forestglm.R | 46 ++ R/jsBasicGadget.R | 16 R/jsPropensityGadget.R | 48 +- R/jsRepeatedGadget.R | 48 +- R/jsSurveyGadget.R | 654 ++++++++++++++++----------------- R/kaplan.R | 134 ++++-- inst/doc/jsmodule.html | 4 inst/doc/jsmodule_subgroup_cmprsk.html | 4 man/coxModule.Rd | 8 man/forestcoxServer.Rd | 8 man/kaplanModule.Rd | 8 17 files changed, 835 insertions(+), 549 deletions(-)
Title: Frequently Used Functions for Easy R Programming
Description: Some utility functions for validation and data manipulation. These functions can be helpful to reduce internal codes everywhere in package development.
Author: Yuchen Li [aut, cre]
Maintainer: Yuchen Li <ycli1995@outlook.com>
Diff between easy.utils versions 0.0.5 dated 2024-09-24 and 0.1.0 dated 2025-02-19
easy.utils-0.0.5/easy.utils/R/All_S3_Generics.R |only easy.utils-0.0.5/easy.utils/R/color_palettes.R |only easy.utils-0.0.5/easy.utils/man/checkColorMap.Rd |only easy.utils-0.0.5/easy.utils/man/pal_discrete.Rd |only easy.utils-0.0.5/easy.utils/man/setColor.Rd |only easy.utils-0.1.0/easy.utils/DESCRIPTION | 11 +++++------ easy.utils-0.1.0/easy.utils/MD5 | 13 ++++--------- easy.utils-0.1.0/easy.utils/NAMESPACE | 8 -------- easy.utils-0.1.0/easy.utils/NEWS.md | 5 +++++ easy.utils-0.1.0/easy.utils/man/easy.utils-package.Rd | 2 +- 10 files changed, 15 insertions(+), 24 deletions(-)
Title: Biologically Explainable Machine Learning Framework
Description: Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <doi:10.48550/arXiv.1712.00336>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.
Author: Shunjie Zhang [aut, cre],
Junfang Chen [aut]
Maintainer: Shunjie Zhang <zhang.shunjie@qq.com>
Diff between BioM2 versions 1.1.0 dated 2024-09-20 and 1.1.1 dated 2025-02-19
DESCRIPTION | 6 ++-- MD5 | 8 ++--- R/BioM2.R | 78 +++++++++++++++++++++++++++++++++++-------------------- man/BioM2.Rd | 3 ++ man/baseModel.Rd | 2 - 5 files changed, 62 insertions(+), 35 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut] ,
Kurt Hornik [aut, cre] ,
Artifex Software, Inc. [ctb, cph]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tm versions 0.7-15 dated 2024-11-18 and 0.7-16 dated 2025-02-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/NEWS.Rd | 7 +++++++ inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary man/Source.Rd | 1 - 6 files changed, 16 insertions(+), 10 deletions(-)
Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate functions,
and fitters for consensus relations.
Author: David Meyer [aut] ,
Kurt Hornik [aut, cre] ,
Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between relations versions 0.6-14 dated 2024-11-13 and 0.6-15 dated 2025-02-19
DESCRIPTION | 12 +++++---- MD5 | 16 ++++++------- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++ inst/doc/relations.Rnw | 2 - inst/doc/relations.pdf |binary man/choice.Rd | 4 ++- man/consensus.Rd | 58 ++++++++++++++++++++++++++---------------------- vignettes/relations.Rnw | 2 - 9 files changed, 58 insertions(+), 42 deletions(-)
Title: Construct and Visualize TDA Mapper Graphs
Description: Topological data analysis (TDA) is a method of data analysis that
uses techniques from topology to analyze high-dimensional data. Here we
implement Mapper, an algorithm from this area developed by Singh, Mémoli and
Carlsson (2007) which generalizes the concept of a
Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.
Author: George Clare Kennedy [aut, cre]
Maintainer: George Clare Kennedy <george-clarekennedy@uiowa.edu>
Diff between mappeR versions 2.0.0 dated 2025-02-16 and 2.0.1 dated 2025-02-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/clusterer_farm.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between cgam versions 1.22 dated 2025-02-17 and 1.23 dated 2025-02-19
ChangeLog | 5 +- DESCRIPTION | 8 +-- MD5 | 8 +-- R/cgam.R | 124 +++++++++++++++++++++++++++---------------------------- man/plotpersp.Rd | 6 +- 5 files changed, 77 insertions(+), 74 deletions(-)
Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis,
including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>],
calculation of relatedness coefficients using path-tracing methods
[Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>],
inference of relatedness, pedigree conversion, and simulation of multi-generational family data
[Lyu et al. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview,
see Garrison et al. (2025) <doi:10.21105/joss.06203>.
Author: S. Mason Garrison [aut, cre] ,
Michael D. Hunter [aut] ,
Xuanyu Lyu [aut] ,
Rachel N. Good [ctb],
Jonathan D. Trattner [aut] ,
S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between BGmisc versions 1.3.2 dated 2024-06-18 and 1.3.3 dated 2025-02-19
BGmisc-1.3.2/BGmisc/tests/testthat/test-clean.X |only BGmisc-1.3.3/BGmisc/DESCRIPTION | 19 BGmisc-1.3.3/BGmisc/MD5 | 94 - BGmisc-1.3.3/BGmisc/NEWS.md | 11 BGmisc-1.3.3/BGmisc/R/buildPedigree.R | 18 BGmisc-1.3.3/BGmisc/R/checkIDs.R | 12 BGmisc-1.3.3/BGmisc/R/checkSex.R | 24 BGmisc-1.3.3/BGmisc/R/computeRelatedness.R | 2 BGmisc-1.3.3/BGmisc/R/convertPedigree.R | 448 ++++-- BGmisc-1.3.3/BGmisc/R/readPedigree.R | 431 +++--- BGmisc-1.3.3/BGmisc/R/simulatePedigree.R | 4 BGmisc-1.3.3/BGmisc/R/summarizePedigree.R | 210 +- BGmisc-1.3.3/BGmisc/R/tweakPedigree.R | 4 BGmisc-1.3.3/BGmisc/README.md | 2 BGmisc-1.3.3/BGmisc/build/partial.rdb |only BGmisc-1.3.3/BGmisc/build/vignette.rds |binary BGmisc-1.3.3/BGmisc/inst/doc/analyticrelatedness.html | 18 BGmisc-1.3.3/BGmisc/inst/doc/modelingrelatedness.html | 188 +- BGmisc-1.3.3/BGmisc/inst/doc/network.html | 80 - BGmisc-1.3.3/BGmisc/inst/doc/pedigree.html | 14 BGmisc-1.3.3/BGmisc/inst/doc/validation.R | 201 +- BGmisc-1.3.3/BGmisc/inst/doc/validation.Rmd | 197 +- BGmisc-1.3.3/BGmisc/inst/doc/validation.html | 779 +++++------ BGmisc-1.3.3/BGmisc/man/BGmisc-package.Rd | 2 BGmisc-1.3.3/BGmisc/man/calculateSummaryDT.Rd | 5 BGmisc-1.3.3/BGmisc/man/checkSex.Rd | 24 BGmisc-1.3.3/BGmisc/man/compute_transpose.Rd |only BGmisc-1.3.3/BGmisc/man/ped2add.Rd | 26 BGmisc-1.3.3/BGmisc/man/ped2ce.Rd | 4 BGmisc-1.3.3/BGmisc/man/ped2cn.Rd | 26 BGmisc-1.3.3/BGmisc/man/ped2com.Rd | 26 BGmisc-1.3.3/BGmisc/man/ped2fam.Rd | 5 BGmisc-1.3.3/BGmisc/man/ped2graph.Rd | 5 BGmisc-1.3.3/BGmisc/man/ped2maternal.Rd | 5 BGmisc-1.3.3/BGmisc/man/ped2mit.Rd | 26 BGmisc-1.3.3/BGmisc/man/ped2paternal.Rd | 5 BGmisc-1.3.3/BGmisc/man/recodeSex.Rd | 17 BGmisc-1.3.3/BGmisc/man/repairSex.Rd | 17 BGmisc-1.3.3/BGmisc/man/summarizeFamilies.Rd | 16 BGmisc-1.3.3/BGmisc/man/summarizeMatrilines.Rd | 16 BGmisc-1.3.3/BGmisc/man/summarizePatrilines.Rd | 16 BGmisc-1.3.3/BGmisc/man/summarizePedigrees.Rd | 36 BGmisc-1.3.3/BGmisc/tests/testthat.R | 1 BGmisc-1.3.3/BGmisc/tests/testthat/Rplots.pdf |binary BGmisc-1.3.3/BGmisc/tests/testthat/test-convertPedigree.R |only BGmisc-1.3.3/BGmisc/tests/testthat/test-identifyModel.R | 3 BGmisc-1.3.3/BGmisc/tests/testthat/test-networks.R | 212 -- BGmisc-1.3.3/BGmisc/tests/testthat/test-readPedigrees.R | 18 BGmisc-1.3.3/BGmisc/tests/testthat/test-summarizePedigrees.R | 75 - BGmisc-1.3.3/BGmisc/vignettes/validation.Rmd | 197 +- 50 files changed, 1989 insertions(+), 1550 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.5.5.1 dated 2025-01-20 and 1.5.6 dated 2025-02-19
gpboost-1.5.5.1/gpboost/tests/testthat/_snaps |only gpboost-1.5.6/gpboost/DESCRIPTION | 8 gpboost-1.5.6/gpboost/MD5 | 36 gpboost-1.5.6/gpboost/R/GPModel.R | 33 gpboost-1.5.6/gpboost/R/gpb.cv.R | 56 - gpboost-1.5.6/gpboost/configure.ac | 2 gpboost-1.5.6/gpboost/demo/GPBoost_algorithm.R | 22 gpboost-1.5.6/gpboost/demo/compare_usage_lme4_gpboost.R | 3 gpboost-1.5.6/gpboost/demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 5 gpboost-1.5.6/gpboost/src/CG_utils.cpp | 39 gpboost-1.5.6/gpboost/src/Vecchia_utils.cpp | 4 gpboost-1.5.6/gpboost/src/include/GPBoost/CG_utils.h | 28 gpboost-1.5.6/gpboost/src/include/GPBoost/cov_fcts.h | 294 +++-- gpboost-1.5.6/gpboost/src/include/GPBoost/likelihoods.h | 494 ++++++---- gpboost-1.5.6/gpboost/src/include/GPBoost/re_comp.h | 22 gpboost-1.5.6/gpboost/src/include/GPBoost/re_model_template.h | 97 + gpboost-1.5.6/gpboost/src/include/GPBoost/utils.h | 8 gpboost-1.5.6/gpboost/src/objective/regression_objective.hpp | 2 gpboost-1.5.6/gpboost/tests/testthat/test_GPModel_gaussian_process.R | 268 ++--- gpboost-1.5.6/gpboost/tests/testthat/test_GPModel_non_Gaussian_data.R | 50 - 20 files changed, 884 insertions(+), 587 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully
configurable HTTP/FTP requests where responses can be processed in memory, on
disk, or streaming via the callback or connection interfaces. Some knowledge
of 'libcurl' is recommended; for a more-user-friendly web client see the
'httr2' package which builds on this package with http specific tools and logic.
Author: Jeroen Ooms [aut, cre] ,
Hadley Wickham [ctb],
Posit Software, PBC [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between curl versions 6.2.0 dated 2025-01-23 and 6.2.1 dated 2025-02-19
DESCRIPTION | 6 +- MD5 | 30 +++++----- NAMESPACE | 1 NEWS | 7 ++ R/echo.R | 23 +++++--- R/multi_download.R | 2 R/options.R | 3 - R/utilities.R | 22 +++++-- inst/doc/intro.html | 98 +++++++++++++++++------------------ man/multi_download.Rd | 2 src/curl-common.h | 1 src/dryrun.c |only src/init.c | 2 src/multi.c | 9 --- src/utils.c | 10 ++- tests/testthat/test-errors.R |only tests/testthat/test-multi-download.R | 4 + 17 files changed, 125 insertions(+), 95 deletions(-)
Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP API
from R functions using the annotations in the R documentation around your
functions.
Author: Barret Schloerke [cre, aut] ,
Jeff Allen [aut, ccp],
Bruno Tremblay [ctb],
Frans van Dunne [ctb],
Sebastiaan Vandewoude [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between plumber versions 1.2.2 dated 2024-03-25 and 1.3.0 dated 2025-02-19
plumber-1.2.2/plumber/build |only plumber-1.2.2/plumber/inst/validate_api_spec |only plumber-1.3.0/plumber/DESCRIPTION | 13 - plumber-1.3.0/plumber/MD5 | 66 +++--- plumber-1.3.0/plumber/NAMESPACE | 8 plumber-1.3.0/plumber/NEWS.md | 26 ++ plumber-1.3.0/plumber/R/find-port.R | 100 ++++++---- plumber-1.3.0/plumber/R/openapi-spec.R | 1 plumber-1.3.0/plumber/R/options_plumber.R | 2 plumber-1.3.0/plumber/R/parse-body.R | 72 +++++-- plumber-1.3.0/plumber/R/plumber-step.R | 15 + plumber-1.3.0/plumber/R/plumber.R | 41 ++-- plumber-1.3.0/plumber/R/pr.R | 2 plumber-1.3.0/plumber/R/pr_set.R | 14 + plumber-1.3.0/plumber/R/serializer.R | 86 +++++++- plumber-1.3.0/plumber/R/utils.R | 3 plumber-1.3.0/plumber/R/validate_api_spec.R | 97 +++------ plumber-1.3.0/plumber/README.md | 12 - plumber-1.3.0/plumber/inst/WORDLIST | 15 - plumber-1.3.0/plumber/man/Plumber.Rd | 6 plumber-1.3.0/plumber/man/endpoint_serializer.Rd | 4 plumber-1.3.0/plumber/man/forward.Rd | 14 + plumber-1.3.0/plumber/man/parsers.Rd | 9 plumber-1.3.0/plumber/man/pr_set_debug.Rd | 14 + plumber-1.3.0/plumber/man/serializers.Rd | 28 ++ plumber-1.3.0/plumber/man/validate_api_spec.Rd | 18 + plumber-1.3.0/plumber/tests/spelling.R | 3 plumber-1.3.0/plumber/tests/testthat/files/include/test.html | 14 - plumber-1.3.0/plumber/tests/testthat/test-find-port.R | 52 +++-- plumber-1.3.0/plumber/tests/testthat/test-parse-body.R | 38 +++ plumber-1.3.0/plumber/tests/testthat/test-plumber-run.R | 41 ---- plumber-1.3.0/plumber/tests/testthat/test-plumber.R | 7 plumber-1.3.0/plumber/tests/testthat/test-serializer-device.R | 13 + plumber-1.3.0/plumber/tests/testthat/test-serializer-excel.R |only plumber-1.3.0/plumber/tests/testthat/test-shared-secret.R | 2 35 files changed, 531 insertions(+), 305 deletions(-)
Title: Tabulate P.L. 94-171 Redistricting Data Summary Files
Description: Tools to process legacy format summary redistricting data files
produced by the United States Census Bureau pursuant to P.L. 94-171. These
files are generally available earlier but are difficult to work with as-is.
Author: Cory McCartan [aut, cre],
Christopher T. Kenny [aut]
Maintainer: Cory McCartan <mccartan@psu.edu>
Diff between PL94171 versions 1.1.2 dated 2022-09-11 and 1.1.3 dated 2025-02-19
DESCRIPTION | 12 +-- MD5 | 24 +++---- NEWS.md | 3 R/pl_get_baf.R | 2 R/pl_select_standard.R | 4 - R/pl_subset.R | 2 build/vignette.rds |binary inst/doc/PL94171.R | 18 ++--- inst/doc/PL94171.html | 152 +++++++++++++++++++++++----------------------- man/PL94171-package.Rd | 2 man/pl_get_baf.Rd | 2 man/pl_select_standard.Rd | 2 man/pl_subset.Rd | 2 13 files changed, 117 insertions(+), 108 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-26 24.2.0
2023-12-19 23.12.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-28 1.1
2022-04-13 1.0
Title: Modeling Workflows
Description: Managing both a 'parsnip' model and its data preparation steps,
such as a model formula or recipe from 'recipes', can often be challenging.
The goal of 'workflows' is to streamline this process by bundling the
model with its data preparation, all within the same object.
Author: Davis Vaughan [aut],
Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between workflows versions 1.1.4 dated 2024-02-19 and 1.2.0 dated 2025-02-18
DESCRIPTION | 30 +- MD5 | 134 ++++++------ NAMESPACE | 23 ++ NEWS.md | 20 + R/action.R | 11 - R/broom.R | 9 R/butcher.R | 16 + R/control.R | 5 R/extract.R | 50 +++- R/fit-action-model.R | 37 ++- R/fit.R | 44 +++- R/generics.R | 8 R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/pre-action-case-weights.R | 22 +- R/pre-action-formula.R | 35 ++- R/pre-action-recipe.R | 45 ++-- R/pre-action-variables.R | 33 ++- R/predict.R | 13 - R/pull.R | 2 R/reexports.R | 12 + R/sparsevctrs.R |only R/stage.R | 18 + R/survival-censoring-weights.R | 2 R/utils.R | 19 + R/workflow.R | 16 - R/workflows-package.R | 2 R/zzz.R | 4 README.md | 4 build/vignette.rds |binary inst/doc/stages.Rmd | 4 inst/doc/stages.html | 247 ----------------------- man/add_formula.Rd | 6 man/add_recipe.Rd | 2 man/extract-workflow.Rd | 12 + man/fit-workflow.Rd | 2 man/glance.workflow.Rd | 2 man/is_trained_workflow.Rd | 2 man/predict-workflow.Rd | 2 man/reexports.Rd | 7 man/workflow-extractors.Rd | 2 man/workflow.Rd | 2 man/workflows-internals.Rd | 2 man/workflows-package.Rd | 2 tests/testthat/_snaps/control.md | 2 tests/testthat/_snaps/fit-action-model.md | 2 tests/testthat/_snaps/pre-action-case-weights.md | 25 -- tests/testthat/_snaps/pre-action-formula.md | 2 tests/testthat/_snaps/pre-action-recipe.md | 2 tests/testthat/_snaps/pre-action-variables.md | 2 tests/testthat/_snaps/pull.md | 10 tests/testthat/_snaps/sparsevctrs.md |only tests/testthat/_snaps/workflow.md | 10 tests/testthat/helper-sparsevctrs.R |only tests/testthat/test-broom.R | 5 tests/testthat/test-butcher.R | 2 tests/testthat/test-extract.R | 42 +++ tests/testthat/test-fit-action-model.R | 2 tests/testthat/test-fit.R | 2 tests/testthat/test-generics.R | 4 tests/testthat/test-pre-action-case-weights.R | 19 + tests/testthat/test-pre-action-formula.R | 2 tests/testthat/test-pre-action-recipe.R | 2 tests/testthat/test-pre-action-variables.R | 5 tests/testthat/test-predict.R | 5 tests/testthat/test-printing.R | 2 tests/testthat/test-pull.R | 2 tests/testthat/test-sparsevctrs.R |only tests/testthat/test-workflow.R | 2 vignettes/extras/getting-started.Rmd | 14 - vignettes/stages.Rmd | 4 71 files changed, 567 insertions(+), 510 deletions(-)
Title: Global Optimization by Differential Evolution in C++
Description: An efficient C++ based implementation of the 'DEoptim'
function which performs global optimization by differential evolution.
Its creation was motivated by trying to see if the old approximation "easier,
shorter, faster: pick any two" could in fact be extended to achieving all
three goals while moving the code from plain old C to modern C++. The
initial version did in fact do so, but a good part of the gain was due to
an implicit code review which eliminated a few inefficiencies which have
since been eliminated in 'DEoptim'.
Author: Dirk Eddelbuettel [aut, cre] ,
David Ardia [aut] ,
Katharine Mullen [aut] ,
Brian Peterson [aut] ,
Joshua Ulrich [aut] ,
Kris Boudt [ctb] ,
Rainer Storn [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDE versions 0.1.7 dated 2022-12-20 and 0.1.8 dated 2025-02-18
ChangeLog | 27 +++++++++++++++++++++++++++ DESCRIPTION | 27 ++++++++++++++++++++------- MD5 | 14 +++++++------- README.md | 9 +++++---- build/vignette.rds |binary inst/doc/RcppDE.pdf |binary src/Makevars | 4 +--- src/devol.cpp | 10 +++++----- 8 files changed, 65 insertions(+), 26 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 3.0.3 dated 2025-01-18 and 3.0.4 dated 2025-02-18
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 7 +++++++ R/focei.R | 4 +++- R/hook.R | 9 +++++++++ R/nlmixr2_md5.R | 2 +- R/preProcessCovariatesPresent.R | 1 + tests/testthat/test-addCwres.R | 36 ++++++++++++++++++++++++++++++++++++ tests/testthat/test-cwres-3.0.3.qs |only 9 files changed, 68 insertions(+), 12 deletions(-)
Title: Interpreting Latent Variables with AI
Description: A small package designed for interpreting continuous and categorical latent variables. You provide a data set with a latent variable you want to understand and some other explanatory variables. It provides a description of the latent variable based on the explanatory variables. It also provides a name to the latent variable.
Author: Nel Herve [aut],
Sebastien Le [aut, cre]
Maintainer: Sebastien Le <sebastien.le@institut-agro.fr>
Diff between NaileR versions 1.2.1 dated 2024-11-11 and 1.2.2 dated 2025-02-18
DESCRIPTION | 12 +- MD5 | 44 ++++---- NAMESPACE | 8 + R/datasets.R | 40 +++---- R/globals.R | 4 R/nail_catdes.R | 100 +++++++++++++++++- R/nail_qda.R | 232 +++++++++++++++++++------------------------- README.md | 10 + data/atomic_habit.rda |binary data/atomic_habit_clust.rda |binary man/agri_studies.Rd | 2 man/beard_cont.Rd | 2 man/beard_wide.Rd | 4 man/boss.Rd | 2 man/fabric.Rd | 4 man/glossophobia.Rd | 2 man/local_food.Rd | 2 man/nail_catdes.Rd | 6 + man/nail_qda.Rd | 3 man/nutriscore.Rd | 3 man/quality.Rd | 5 man/rorschach.Rd | 12 -- man/waste.Rd | 2 23 files changed, 285 insertions(+), 214 deletions(-)
Title: Multivariate (Dynamic) Generalized Additive Models
Description: Fit Bayesian Dynamic Generalized Additive Models to multivariate observations. Users can build nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2022) <doi:10.1111/2041-210X.13974>.
Author: Nicholas J Clark [aut, cre] ,
Sarah Heaps [ctb] ,
Scott Pease [ctb] ,
Matthijs Hollanders [ctb]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Diff between mvgam versions 1.1.3 dated 2024-09-03 and 1.1.4 dated 2025-02-18
mvgam-1.1.3/mvgam/R/RW.R |only mvgam-1.1.3/mvgam/vignettes/trend_formulas.html |only mvgam-1.1.4/mvgam/DESCRIPTION | 41 mvgam-1.1.4/mvgam/MD5 | 428 - mvgam-1.1.4/mvgam/NAMESPACE | 39 mvgam-1.1.4/mvgam/NEWS.md | 100 mvgam-1.1.4/mvgam/R/add_MACor.R | 843 ++ mvgam-1.1.4/mvgam/R/add_base_dgam_lines.R | 834 +- mvgam-1.1.4/mvgam/R/add_binomial.R | 462 - mvgam-1.1.4/mvgam/R/add_nmixture.R | 1366 +-- mvgam-1.1.4/mvgam/R/add_residuals.R | 4 mvgam-1.1.4/mvgam/R/add_stan_data.R | 1442 +-- mvgam-1.1.4/mvgam/R/add_trend_lines.R | 1584 ++-- mvgam-1.1.4/mvgam/R/add_tweedie_lines.R | 120 mvgam-1.1.4/mvgam/R/as.data.frame.mvgam.R | 36 mvgam-1.1.4/mvgam/R/backends.R | 11 mvgam-1.1.4/mvgam/R/compute_edf.R | 252 mvgam-1.1.4/mvgam/R/conditional_effects.R | 16 mvgam-1.1.4/mvgam/R/data_grids.R | 186 mvgam-1.1.4/mvgam/R/dynamic.R | 4 mvgam-1.1.4/mvgam/R/ensemble.R | 381 - mvgam-1.1.4/mvgam/R/evaluate_mvgams.R | 159 mvgam-1.1.4/mvgam/R/families.R | 3224 ++++---- mvgam-1.1.4/mvgam/R/fevd.mvgam.R |only mvgam-1.1.4/mvgam/R/forecast.mvgam.R | 123 mvgam-1.1.4/mvgam/R/formula.mvgam.R | 4 mvgam-1.1.4/mvgam/R/get_linear_predictors.R | 368 - mvgam-1.1.4/mvgam/R/get_monitor_pars.R | 70 mvgam-1.1.4/mvgam/R/get_mvgam_priors.R | 161 mvgam-1.1.4/mvgam/R/globals.R | 49 mvgam-1.1.4/mvgam/R/gp.R | 1609 ++-- mvgam-1.1.4/mvgam/R/gratia_methods.R | 99 mvgam-1.1.4/mvgam/R/hindcast.mvgam.R | 3 mvgam-1.1.4/mvgam/R/how_to_cite.R |only mvgam-1.1.4/mvgam/R/index-mvgam.R | 59 mvgam-1.1.4/mvgam/R/interpret_mvgam.R | 8 mvgam-1.1.4/mvgam/R/irf.mvgam.R | 34 mvgam-1.1.4/mvgam/R/jsdgam.R |only mvgam-1.1.4/mvgam/R/lfo_cv.mvgam.R | 949 +- mvgam-1.1.4/mvgam/R/logLik.mvgam.R | 387 - mvgam-1.1.4/mvgam/R/loo.mvgam.R | 13 mvgam-1.1.4/mvgam/R/lv_correlations.R | 9 mvgam-1.1.4/mvgam/R/marginaleffects.mvgam.R | 101 mvgam-1.1.4/mvgam/R/mcmc_plot.mvgam.R | 11 mvgam-1.1.4/mvgam/R/model.frame.mvgam.R | 233 mvgam-1.1.4/mvgam/R/monotonic.R | 830 +- mvgam-1.1.4/mvgam/R/mvgam-package.R |only mvgam-1.1.4/mvgam/R/mvgam.R | 4328 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Title: An R Package to Extend 'ACER ConQuest'
Description: Extends 'ACER ConQuest' through a family of functions
designed to improve graphical outputs and help with advanced analysis
(e.g., differential item functioning). Allows R users to call
'ACER ConQuest' from within R and read 'ACER ConQuest' System Files
(generated by the command `put` <https://conquestmanual.acer.org/s4-00.html#put>).
Requires 'ACER ConQuest' version 5.40 or later.
A demonstration version can be downloaded from <https://shop.acer.org/acer-conquest-5.html>.
Author: Dan Cloney [aut, cre] ,
Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>
Diff between conquestr versions 1.3.4 dated 2024-07-24 and 1.4.5 dated 2025-02-18
DESCRIPTION | 17 MD5 | 204 - NEWS.md | 33 R/ReadConQuestLibrary.R | 200 - R/ReadConQuestState.R | 13 R/conquestr.R | 26 R/conquestrFunc.R | 55 R/generateHelpers.R | 300 + R/generateItems.R |only R/itanalHelpers.R | 581 ++- README.md | 11 build/vignette.rds |binary inst/doc/data-cleaning-functions-in-conquestr.R | 6 inst/doc/data-cleaning-functions-in-conquestr.Rmd | 48 inst/doc/data-cleaning-functions-in-conquestr.html | 515 --- inst/doc/generateResponses.html | 58 inst/doc/intro-to-conquestr.html | 16 inst/doc/itanal-in-conquestr.R | 6 inst/doc/itanal-in-conquestr.Rmd | 68 inst/doc/itanal-in-conquestr.html | 31 inst/doc/plotting.html | 12 inst/doc/responseProbs.html | 12 inst/doc/test_item_review_sheet_markdown.html | 3261 ++++++++++++++++++++- inst/extdata/ex1.cqc | 4 inst/extdata/mysysfile.cqs |binary inst/extdata/mysysfile_v26.cqs |only man/ConQuestRout.Rd | 11 man/ReadADesignMatrices.Rd | 2 man/ReadAllCaseEstimates.Rd | 2 man/ReadAllGroupsData.Rd | 2 man/ReadAllResponseData.Rd | 2 man/ReadAllY.Rd | 2 man/ReadAnchor.Rd | 2 man/ReadAnchorList.Rd | 2 man/ReadBDesignMatrices.Rd | 2 man/ReadBandDefine.Rd | 2 man/ReadBandDefinesList.Rd | 2 man/ReadBitSet.Rd | 2 man/ReadBoolean.Rd | 2 man/ReadCDesignMatrices.Rd | 2 man/ReadCategorise.Rd | 2 man/ReadCategoriseList.Rd | 2 man/ReadCodeList.Rd | 2 man/ReadDataRecord.Rd | 2 man/ReadDouble.Rd | 2 man/ReadDoubleList.Rd | 2 man/ReadEstimatesRecord.Rd | 2 man/ReadFit.Rd | 2 man/ReadFitList.Rd | 2 man/ReadGExportOptions.Rd | 2 man/ReadGExportOptionsList.Rd | 2 man/ReadGraph.Rd | 2 man/ReadGroupsOneCase.Rd | 2 man/ReadHistory.Rd | 2 man/ReadIRecode.Rd | 2 man/ReadIRecodeList.Rd | 2 man/ReadImplicitVar.Rd | 2 man/ReadInteger.Rd | 2 man/ReadIntegerList.Rd | 2 man/ReadIntegerListList.Rd | 2 man/ReadItemSet.Rd | 2 man/ReadItemSetList.Rd | 2 man/ReadKeyList.Rd | 2 man/ReadLabel.Rd | 2 man/ReadLabelList.Rd | 2 man/ReadLookUp.Rd | 2 man/ReadLookUpList.Rd | 2 man/ReadMatrix.Rd | 2 man/ReadMatrixList.Rd | 2 man/ReadMatrixVars.Rd | 2 man/ReadNamedStringList.Rd |only man/ReadParameters.Rd | 2 man/ReadParametersList.Rd | 2 man/ReadPoint.Rd | 2 man/ReadRandomStructure.Rd | 2 man/ReadRegression.Rd | 2 man/ReadRegressionList.Rd | 2 man/ReadRegressionListLeg.Rd | 2 man/ReadResponse.Rd | 2 man/ReadResponseList.Rd | 2 man/ReadSeries.Rd | 2 man/ReadString.Rd | 2 man/ReadStringList.Rd | 2 man/ReadTerms.Rd | 2 man/ReadTermsList.Rd | 2 man/ReadVarInfo.Rd | 2 man/ReadVarList.Rd | 2 man/ReadVariable.Rd | 2 man/ReadVariableList.Rd | 2 man/ReadYOneCase.Rd | 2 man/fmtCqItanal.Rd | 3 man/genItems.Rd | 67 man/genItems_deltaDots.Rd |only man/genItems_taus.Rd |only man/getCqHist.Rd | 20 man/getCqItanal.Rd | 12 man/makeItemDfs.Rd |only man/makeItemList.Rd | 4 man/simplep.Rd | 2 tests/testthat/test-ConQuestRout.R | 2 tests/testthat/test-ConQuestSys.R |only tests/testthat/test-genHelpers.R | 12 tests/testthat/test-genItems.R |only tests/testthat/test-getCqItanal.R | 8 tests/testthat/test-plotItemMap.R | 4 vignettes/data-cleaning-functions-in-conquestr.Rmd | 48 vignettes/itanal-in-conquestr.Rmd | 68 107 files changed, 4541 insertions(+), 1321 deletions(-)
Title: Sample Size Estimation for Bio-Equivalence Trials Through
Simulation
Description: Sample size estimation for bio-equivalence trials is supported through a simulation-based approach
that extends the Two One-Sided Tests (TOST) procedure. The methodology provides flexibility in
hypothesis testing, accommodates multiple treatment comparisons, and accounts for correlated endpoints.
Users can model complex trial scenarios, including parallel and crossover designs, intra-subject variability,
and different equivalence margins. Monte Carlo simulations enable accurate estimation of power and type I error
rates, ensuring well-calibrated study designs. The statistical framework builds on established methods for
equivalence testing and multiple hypothesis testing in bio-equivalence studies, as described in Schuirmann (1987)
<doi:10.1007/BF01068419>, Mielke et al. (2018) <doi:10.1080/19466315.2017.1371071>, Shieh (2022)
<doi:10.1371/journal.pone.0269128>, and Sozu et al. (2015) <doi:10.1007/978-3-319-22005-5>.
Comprehensive documentation and vignettes guid [...truncated...]
Author: Thomas Debray [aut, cre] ,
Johanna Munoz [aut],
Dewi Amaliah [ctb],
Wei Wei [ctb],
Marian Mitroiu [ctb],
Scott McDonald [ctb],
Biogen Inc [cph, fnd]
Maintainer: Thomas Debray <tdebray@fromdatatowisdom.com>
Diff between SimTOST versions 1.0.1 dated 2025-02-18 and 1.0.2 dated 2025-02-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ src/RcppExports.cpp | 36 ++++++++++++++++++------------------ src/module.cpp | 18 +++++++++--------- 5 files changed, 41 insertions(+), 34 deletions(-)
Title: Linear Model Evaluation with Randomized Residuals in a
Permutation Procedure
Description: Linear model calculations are made for many random versions of data.
Using residual randomization in a permutation procedure, sums of squares are
calculated over many permutations to generate empirical probability distributions
for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many
permutations can be used for various procedures including pairwise tests, prediction, classification, and
model comparison. This package should provide most tools one could need for the analysis of
high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre] ,
Dean Adams [aut]
Maintainer: Michael Collyer <mlcollyer@gmail.com>
Diff between RRPP versions 2.1.1 dated 2025-02-09 and 2.1.2 dated 2025-02-18
DESCRIPTION | 9 ++++----- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/RRPP.utils.r | 2 +- inst/CITATION | 2 +- inst/doc/ANOVA.vs.MANOVA.html | 4 ++-- inst/doc/Using.RRPP.html | 4 ++-- 7 files changed, 22 insertions(+), 17 deletions(-)
Title: Visualize the Climate Scenario Alignment of a Financial
Portfolio
Description: Create plots to visualize the alignment of a corporate
lending financial portfolio to climate change scenarios based on
climate indicators (production and emission intensities) across key
climate relevant sectors of the 'PACTA' methodology (Paris Agreement Capital
Transition Assessment; <https://www.transitionmonitor.com/>).
Financial institutions use 'PACTA' to study how their capital
allocation decisions align with climate change mitigation goals.
Author: Monika Furdyna [aut, ctr, cre]
,
Mauro Lepore [aut, ctr] ,
Alex Axthelm [aut, ctr] ,
RMI [cph, fnd]
Maintainer: Monika Furdyna <monika.furdyna@gmail.com>
Diff between r2dii.plot versions 0.5.0 dated 2025-02-12 and 0.5.1 dated 2025-02-18
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NEWS.md | 4 ++++ R/prep_trajectory.R | 2 ++ data/data_dictionary.rda |binary man/prep_trajectory.Rd | 3 ++- tests/testthat/test-data_dictionary.R |only 7 files changed, 19 insertions(+), 11 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on
'Windows', 'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between ps versions 1.8.1 dated 2024-10-28 and 1.9.0 dated 2025-02-18
DESCRIPTION | 6 MD5 | 28 ++-- NEWS.md | 8 + R/low-level.R | 18 +- R/ps.R | 319 ++++++++++++++++++++++++++++++++++++++++------- configure | 2 man/ps.Rd | 50 ++++++- man/ps_memory_info.Rd | 2 src/api-posix.c | 10 + src/api-windows.c | 6 src/dummy.c | 1 src/init.c | 1 src/ps.h | 1 tests/testthat/helpers.R | 2 tests/testthat/test-ps.R | 6 15 files changed, 387 insertions(+), 73 deletions(-)
Title: Penalized Linear Mixed Models for Correlated Data
Description: Fits penalized linear mixed models that correct for
unobserved confounding factors. 'plmmr' infers and corrects for the
presence of unobserved confounding effects such as population
stratification and environmental heterogeneity. It then fits a linear
model via penalized maximum likelihood. Originally designed for the
multivariate analysis of single nucleotide polymorphisms (SNPs)
measured in a genome-wide association study (GWAS), 'plmmr' eliminates
the need for subpopulation-specific analyses and post-analysis p-value
adjustments. Functions for the appropriate processing of 'PLINK'
files are also supplied. For examples, see the package homepage.
<https://pbreheny.github.io/plmmr/>.
Author: Tabitha K. Peter [aut] ,
Anna C. Reisetter [aut] ,
Patrick J. Breheny [aut, cre] ,
Yujing Lu [aut]
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>
Diff between plmmr versions 4.1.0 dated 2024-10-23 and 4.2.0 dated 2025-02-18
plmmr-4.1.0/plmmr/R/file_sans_ext.R |only plmmr-4.1.0/plmmr/R/index_std_X.R |only plmmr-4.1.0/plmmr/R/untransform_filebacked.R |only plmmr-4.1.0/plmmr/man/file_sans_ext.Rd |only plmmr-4.1.0/plmmr/man/index_std_X.Rd |only plmmr-4.1.0/plmmr/man/untransform_filebacked.Rd |only plmmr-4.2.0/plmmr/DESCRIPTION | 8 plmmr-4.2.0/plmmr/MD5 | 89 ++++----- plmmr-4.2.0/plmmr/NAMESPACE | 1 plmmr-4.2.0/plmmr/NEWS.md | 40 ++-- plmmr-4.2.0/plmmr/R/construct_variance.R | 5 plmmr-4.2.0/plmmr/R/create_design_filebacked.R | 4 plmmr-4.2.0/plmmr/R/cv-plmm.R | 235 +++++++++--------------- plmmr-4.2.0/plmmr/R/cvf.R | 121 +++++++----- plmmr-4.2.0/plmmr/R/plmm.R | 172 +++++++---------- plmmr-4.2.0/plmmr/R/plmm_checks.R | 36 ++- plmmr-4.2.0/plmmr/R/plmm_fit.R | 62 +----- plmmr-4.2.0/plmmr/R/plmm_format.R | 63 +++--- plmmr-4.2.0/plmmr/R/plmm_prep.R | 39 --- plmmr-4.2.0/plmmr/R/plmmr-package.R | 1 plmmr-4.2.0/plmmr/R/plot-cv-plmm.R | 12 - plmmr-4.2.0/plmmr/R/predict-plmm.R | 115 ++++++----- plmmr-4.2.0/plmmr/R/predict_within_cv.R | 63 +----- plmmr-4.2.0/plmmr/R/print-summary-cv-plmm.R | 2 plmmr-4.2.0/plmmr/R/rotate_filebacked.R | 2 plmmr-4.2.0/plmmr/R/standardize_filebacked.R | 3 plmmr-4.2.0/plmmr/R/summary-cv-plmm.R | 2 plmmr-4.2.0/plmmr/R/untransform.R | 27 ++ plmmr-4.2.0/plmmr/R/untransform_delim.R |only plmmr-4.2.0/plmmr/R/untransform_in_memory.R | 1 plmmr-4.2.0/plmmr/R/untransform_plink.R |only plmmr-4.2.0/plmmr/R/zzz.R |only plmmr-4.2.0/plmmr/README.md | 3 plmmr-4.2.0/plmmr/build/partial.rdb |binary plmmr-4.2.0/plmmr/build/vignette.rds |binary plmmr-4.2.0/plmmr/inst/CITATION | 16 + plmmr-4.2.0/plmmr/inst/doc/getting-started.html | 6 plmmr-4.2.0/plmmr/man/cv_plmm.Rd | 35 --- plmmr-4.2.0/plmmr/man/cvf.Rd | 4 plmmr-4.2.0/plmmr/man/plmm.Rd | 73 +++---- plmmr-4.2.0/plmmr/man/plmm_checks.Rd | 3 plmmr-4.2.0/plmmr/man/plmm_fit.Rd | 44 ---- plmmr-4.2.0/plmmr/man/plmm_format.Rd | 18 + plmmr-4.2.0/plmmr/man/plmm_prep.Rd | 7 plmmr-4.2.0/plmmr/man/predict.plmm.Rd | 20 +- plmmr-4.2.0/plmmr/man/predict_within_cv.Rd | 30 --- plmmr-4.2.0/plmmr/man/summary.cv_plmm.Rd | 2 plmmr-4.2.0/plmmr/man/untransform.Rd | 17 + plmmr-4.2.0/plmmr/man/untransform_delim.Rd |only plmmr-4.2.0/plmmr/man/untransform_plink.Rd |only plmmr-4.2.0/plmmr/src/big_standardize.cpp | 18 + 51 files changed, 654 insertions(+), 745 deletions(-)
Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Maximilian Muecke [aut, cre] ,
Damir Pulatov [aut],
Michel Lang [aut] ,
Marc Becker [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3cluster versions 0.1.10 dated 2024-10-03 and 0.1.11 dated 2025-02-18
mlr3cluster-0.1.10/mlr3cluster/tests/testthat/Rplots.pdf |only mlr3cluster-0.1.11/mlr3cluster/DESCRIPTION | 28 +- mlr3cluster-0.1.11/mlr3cluster/MD5 | 95 ++++------ mlr3cluster-0.1.11/mlr3cluster/NEWS.md | 11 - mlr3cluster-0.1.11/mlr3cluster/R/LearnerClust.R | 19 +- mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustAffinityPropagation.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustAgnes.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustDiana.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustFeatureless.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustHclust.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustMclust.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustMeanShift.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustMiniBatchKMeans.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustPAM.R | 5 mlr3cluster-0.1.11/mlr3cluster/R/MeasureClust.R | 20 +- mlr3cluster-0.1.11/mlr3cluster/R/PredictionClust.R | 3 mlr3cluster-0.1.11/mlr3cluster/R/PredictionDataClust.R | 4 mlr3cluster-0.1.11/mlr3cluster/R/as_prediction_clust.R | 7 mlr3cluster-0.1.11/mlr3cluster/R/as_task_clust.R | 4 mlr3cluster-0.1.11/mlr3cluster/R/zzz.R | 4 mlr3cluster-0.1.11/mlr3cluster/README.md | 78 ++++---- mlr3cluster-0.1.11/mlr3cluster/build/partial.rdb |binary mlr3cluster-0.1.11/mlr3cluster/man/mlr3cluster-package.Rd | 5 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/helper_expectations.R | 16 - mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_LearnerClust.R | 2 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_agnes.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_ap.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_bico.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_birch.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_cmeans.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_cobweb.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan_fpc.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_diana.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_em.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_fanny.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_featureless.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_ff.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_hclust.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_hdbscan.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_kkmeans.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_kmeans.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_mbatchkmeans.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_mclust.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_meanshift.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_optics.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_pam.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_simplekmeans.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_xmeans.R | 6 49 files changed, 251 insertions(+), 220 deletions(-)
Title: Statistical Tools for the Analysis of Psychophysical Data
Description: Tools for the analysis of psychophysical data in R. This package allows to estimate the Point of Subjective Equivalence (PSE)
and the Just Noticeable Difference (JND), either from a psychometric function or from a Generalized Linear Mixed Model (GLMM).
Additionally, the package allows plotting the fitted models and the response data, simulating psychometric functions of different shapes, and simulating data sets.
For a description of the use of GLMMs applied to psychophysical data, refer to Moscatelli et al. (2012).
Author: Alessandro Moscatelli [aut, cre]
,
Priscilla Balestrucci [aut]
Maintainer: Alessandro Moscatelli <moskante@gmail.com>
Diff between MixedPsy versions 1.1.0 dated 2021-11-08 and 1.2.0 dated 2025-02-18
DESCRIPTION | 11 +-- MD5 | 24 ++++--- NAMESPACE | 13 +++ R/PsySimulate.R | 163 +++++++++++++++++++++++++++--------------------- R/mix_utils.R | 4 - R/psych_utils.R | 2 R/psych_utils_multi.R |only R/xplode.R | 6 - man/PsySimulate.Rd | 59 ++++++++++------- man/PsychInterpolate.Rd |only man/PsychModels.Rd |only man/PsychParameters.Rd |only man/PsychShape.Rd | 2 man/pseMer.Rd | 4 - man/xplode.Rd | 6 - 15 files changed, 173 insertions(+), 121 deletions(-)
Title: Meta-Analysis for Detecting Genotype x Environment Associations
Description: Provides functions to perform all steps of genome-wide
association meta-analysis for studying Genotype x Environment
interactions, from collecting the data to the manhattan plot. The
procedure accounts for the potential correlation between studies. In
addition to the Fixed and Random models, one can investigate the
relationship between QTL effects and some qualitative or quantitative
covariate via the test of contrast and the meta-regression,
respectively. The methodology is available from: (De Walsche, A., et
al. (2023) \doi{10.1101/2023.03.01.530237}).
Author: Annaig De Walsche [aut, cre] ,
Tristan Mary-Huard [aut]
Maintainer: Annaig De Walsche <annaig.de-walsche@inrae.fr>
Diff between metaGE versions 1.1.0 dated 2024-07-31 and 1.2.0 dated 2025-02-18
DESCRIPTION | 10 ++--- MD5 | 26 ++++++------- R/metaGEfit.R | 3 + R/metaGEmatcor.R | 60 ++++++++++++++++++------------ R/metaGEplot.R | 22 +++++++---- R/metaGEtest.R | 4 +- inst/doc/metaGE-vignette.html | 84 +++++++++++++++++++++--------------------- man/FastKerFdr.Rd | 11 +++++ man/metaGE.cor.Rd | 5 +- man/metaGE.fit.Rd | 3 + man/metaGE.heatmap.Rd | 2 + man/metaGE.manhattan.Rd | 11 +++-- man/metaGE.pvalplot.Rd | 2 + man/metaGE.test.Rd | 4 +- 14 files changed, 144 insertions(+), 103 deletions(-)
Title: A Logging Utility Focus on Clinical Trial Programming Workflows
Description: A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
Author: Nathan Kosiba [aut, cre],
Thomas Bermudez [aut],
Ben Straub [aut],
Michael Rimler [aut],
Nicholas Masel [aut],
Sam Parmar [aut],
GSK/Atorus JPT [cph, fnd]
Maintainer: Nathan Kosiba <nhkosiba@gmail.com>
Diff between logrx versions 0.3.1 dated 2024-04-11 and 0.3.2 dated 2025-02-18
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 3 +++ build/vignette.rds |binary inst/doc/approved.html | 30 ++++++++++++++++-------------- inst/doc/execution.R | 16 ++++++++-------- inst/doc/execution.html | 5 +++-- inst/doc/logrx.R | 2 +- inst/doc/logrx.html | 5 +++-- inst/doc/options.html | 2 ++ tests/testthat/test-get.R | 19 ++++++++++--------- tests/testthat/test-writer.R | 27 ++++++++++++++------------- 12 files changed, 75 insertions(+), 64 deletions(-)
Title: Calculate Genetic Interactions for Paired CRISPR Targets
Description: Helps find meaningful patterns in complex genetic experiments. First gimap takes data from paired CRISPR (Clustered regularly interspaced short palindromic repeats) screens that has been pre-processed to counts table of paired gRNA (guide Ribonucleic Acid) reads. The input data will have cell counts for how well cells grow (or don't grow) when different genes or pairs of genes are disabled. The output of the 'gimap' package is genetic interaction scores which are the distance between the observed CRISPR score and the expected CRISPR score. The expected CRISPR scores are what we expect for the CRISPR values to be for two unrelated genes. The further away an observed CRISPR score is from its expected score the more we suspect genetic interaction. The work in this package is based off of original research from the Alice Berger lab at Fred Hutchinson Cancer Center (2021) <doi:10.1016/j.celrep.2021.109597>.
Author: Candace Savonen [aut, cre],
Phoebe Parrish [aut],
Kate Isaac [aut],
Howard Baek [aut],
Daniel Grosso [aut],
Siobhan O'Brien [aut],
Alice Berger [aut]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between gimap versions 1.0.1 dated 2025-02-03 and 1.0.2 dated 2025-02-18
DESCRIPTION | 6 +- MD5 | 34 ++++++------ NEWS.md | 7 ++ R/02-gimap_filter.R | 108 ++++++++++++++-------------------------- R/03-annotate.R | 7 +- R/utils.R | 2 inst/doc/quick-start.Rmd | 18 ++++++ inst/doc/quick-start.html | 90 +++++++++++++++++++-------------- inst/doc/timepoint-example.Rmd | 18 ++++++ inst/doc/timepoint-example.html | 96 ++++++++++++++++++++--------------- inst/doc/treatment_example.Rmd | 18 ++++++ inst/doc/treatment_example.html | 108 ++++++++++++++++++++++------------------ man/gimap_annotate.Rd | 2 man/gimap_filter.Rd | 16 ++--- man/qc_filter_zerocounts.Rd | 2 vignettes/quick-start.Rmd | 18 ++++++ vignettes/timepoint-example.Rmd | 18 ++++++ vignettes/treatment_example.Rmd | 18 ++++++ 18 files changed, 359 insertions(+), 227 deletions(-)
Title: Benchmark and Frontier Analysis Using DEA and SFA
Description: Methods for frontier
analysis, Data Envelopment Analysis (DEA), under different
technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+),
and using different efficiency measures (input based, output based,
hyperbolic graph, additive, super, and directional efficiency). Peers
and slacks are available, partial price information can be included,
and optimal cost, revenue and profit can be calculated. Evaluation of
mergers is also supported. Methods for graphing the technology sets
are also included. There is also support for comparative methods based
on Stochastic Frontier Analyses (SFA) and for convex nonparametric
least squares of convex functions (STONED). In general, the methods
can be used to solve not only standard models, but also many other
model variants. It complements the book, Bogetoft and Otto,
Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of
course also be used as a stand-alone package.
Author: Peter Bogetoft [aut],
Lars Otto [aut, cre]
Maintainer: Lars Otto <larsot23@gmail.com>
Diff between Benchmarking versions 0.32 dated 2024-03-13 and 0.33 dated 2025-02-18
Benchmarking-0.32/Benchmarking/R/Benchmarking.R |only Benchmarking-0.33/Benchmarking/DESCRIPTION | 18 ++++++++++++----- Benchmarking-0.33/Benchmarking/MD5 | 17 +++++++--------- Benchmarking-0.33/Benchmarking/NEWS | 9 +++++++- Benchmarking-0.33/Benchmarking/R/bootStat.R | 6 ++--- Benchmarking-0.33/Benchmarking/R/profit.R | 3 +- Benchmarking-0.33/Benchmarking/R/sfa.R | 2 - Benchmarking-0.33/Benchmarking/man/eladder.Rd | 12 +++++++---- Benchmarking-0.33/Benchmarking/man/sfa.Rd | 25 ++++++++++++------------ Benchmarking-0.33/Benchmarking/man/stoned.Rd | 10 +++++++-- 10 files changed, 64 insertions(+), 38 deletions(-)
Title: Measure Climate Scenario Alignment of Corporate Loans
Description: These tools help you to assess if a corporate lending
portfolio aligns with climate goals. They summarize key climate
indicators attributed to the portfolio (e.g. production, emission
factors), and calculate alignment targets based on climate scenarios.
They implement in R the last step of the free software 'PACTA' (Paris
Agreement Capital Transition Assessment;
<https://www.transitionmonitor.com/>). Financial institutions use 'PACTA'
to study how their capital allocation decisions align with climate
change mitigation goals.
Author: Jacob Kastl [aut, cre, ctr] ,
Alex Axthelm [aut, ctr] ,
Jackson Hoffart [aut, ctr] ,
Mauro Lepore [aut, ctr] ,
Klaus Hogedorn [aut],
Nicky Halterman [aut],
RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>
Diff between r2dii.analysis versions 0.5.0 dated 2025-02-13 and 0.5.1 dated 2025-02-18
DESCRIPTION | 10 +-- MD5 | 19 +++--- NEWS.md | 4 + R/join_abcd_scenario.R | 37 ++++++++----- R/target_market_share.R | 2 R/utils.R | 9 +-- data/data_dictionary.rda |binary man/join_abcd_scenario.Rd | 8 +- tests/testthat/test-data_dictionary.R |only tests/testthat/test-join_abcd_scenario.R | 36 ++++++++++++ tests/testthat/test-summarize_weighted_production.R | 56 +++++++++++++++++++- 11 files changed, 145 insertions(+), 36 deletions(-)
More information about r2dii.analysis at CRAN
Permanent link
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Lucas Mation [aut]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between enderecobr versions 0.4.0 dated 2025-01-14 and 0.4.1 dated 2025-02-18
DESCRIPTION | 6 ++--- MD5 | 14 +++++------ NEWS.md | 12 ++++++++++ R/padronizar_ceps.R | 8 +++++- R/padronizar_numeros.R | 4 ++- tests/testthat/_snaps/padronizar_enderecos.md | 31 ++++++++++++++++++++++++++ tests/testthat/test-padronizar_enderecos.R | 27 ++++++++++++++++++++++ tests/testthat/test-padronizar_numeros.R | 1 8 files changed, 90 insertions(+), 13 deletions(-)
Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre],
Muhammed Ali Yilmaz [aut],
Ozgur Asar [ctb],
Ozlem Ilk [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between AID versions 3.0 dated 2024-11-22 and 3.1 dated 2025-02-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/boxcoxmeta.R | 10 +++++----- R/boxcoxnc.R | 8 ++++---- 4 files changed, 16 insertions(+), 16 deletions(-)
Title: Assesses the Quality of Estimates Made by Complex Sample Designs
Description: Assesses the quality of estimates made by complex sample designs,
following the methodology developed by the National Institute of Statistics Chile (2020, <https://www.ine.cl/docs/default-source/institucionalidad/buenas-pr%C3%A1cticas/clasificaciones-y-estandares/est%C3%A1ndar-evaluaci%C3%B3n-de-calidad-de-estimaciones-publicaci%C3%B3n-27022020.pdf>)
and by Economic Commission for Latin America and
Caribbean (2020, <https://repositorio.cepal.org/bitstream/handle/11362/45681/1/S2000293_es.pdf>), (2024, <https://repositorio.cepal.org/server/api/core/bitstreams/f04569e6-4f38-42e7-a32b-e0b298e0ab9c/content>).
Author: Klaus Lehmann [aut, cre],
Ricardo Pizarro [aut],
Ignacio Agloni [ctb],
Andrea Lopez [ctb],
Javiera Preuss [ctb]
Maintainer: Klaus Lehmann <klehmann@fen.uchile.cl>
Diff between calidad versions 0.6.0 dated 2024-10-16 and 0.7.0 dated 2025-02-18
DESCRIPTION | 13 +- MD5 | 28 ++-- NEWS.md | 5 R/create_external.R | 14 +- R/create_internal.R | 68 +++++++--- R/data.R | 35 +++++ data/enusc_2023.rda |only inst/doc/tutorial.R | 8 + inst/doc/tutorial.Rmd | 12 + inst/doc/tutorial.html | 240 ++++++++++++++++++++------------------ man/create_prop.Rd | 5 man/create_prop_internal.Rd | 5 man/enusc.Rd | 2 man/enusc_2023.Rd |only tests/testthat/test-create_prop.R | 91 ++++++++++++++ vignettes/tutorial.Rmd | 12 + 16 files changed, 376 insertions(+), 162 deletions(-)
More information about UAHDataScienceSF at CRAN
Permanent link
Title: Manage Data from Cardiopulmonary Exercise Testing
Description: Import, process, summarize and visualize raw data from
metabolic carts. See Robergs, Dwyer, and Astorino (2010) <doi:10.2165/11319670-000000000-00000> for more details on data processing.
Author: Simon Nolte [aut, cre] ,
Manuel Ramon [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/541>),
James Hunter [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/541>)
Maintainer: Simon Nolte <s.nolte@dshs-koeln.de>
Diff between spiro versions 0.2.1 dated 2023-08-14 and 0.2.3 dated 2025-02-18
DESCRIPTION | 8 LICENSE | 2 MD5 | 67 NEWS.md | 24 R/spiro-package.R | 14 R/spiro.R | 4 R/spiro_get.R | 30 R/spiro_plot.R | 41 R/spiro_raw.R | 6 README.md | 45 build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/import_processing.R | 90 inst/doc/import_processing.Rmd | 66 inst/doc/import_processing.html | 18 inst/doc/summarizing_plotting.R | 9 inst/doc/summarizing_plotting.Rmd | 9 inst/doc/summarizing_plotting.html | 20 man/spiro-package.Rd | 24 man/spiro.Rd | 4 tests/testthat/_snaps/spiro_plot/basic.svg | 4188 ++++++++++---------- tests/testthat/_snaps/spiro_plot/bsmooth.svg | 4188 ++++++++++---------- tests/testthat/_snaps/spiro_plot/color.svg | 5414 +++++++++++++------------- tests/testthat/_snaps/spiro_plot/grid.svg | 1468 +++---- tests/testthat/_snaps/spiro_plot/hr.svg | 5414 +++++++++++++------------- tests/testthat/_snaps/spiro_plot/style.svg | 4188 ++++++++++---------- tests/testthat/_snaps/spiro_plot/theme.svg | 4188 ++++++++++---------- tests/testthat/_snaps/spiro_plot/tsmooth.svg | 4194 ++++++++++---------- tests/testthat/_snaps/spiro_plot/vertline.svg | 4212 ++++++++++---------- tests/testthat/_snaps/spiro_summary.md | 2 tests/testthat/test-spiro_raw.R | 1 tests/testthat/test_spiro_plot.R | 3 vignettes/import_processing.Rmd | 66 vignettes/summarizing_plotting.Rmd | 9 35 files changed, 19045 insertions(+), 18972 deletions(-)
Title: Non-Interactive Spatial Tools for Raster Processing and
Visualization
Description: S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.
Author: Nikita Platonov [aut, cre]
Maintainer: Nikita Platonov <platonov@sev-in.ru>
Diff between ursa versions 3.11.2 dated 2025-01-14 and 3.11.3 dated 2025-02-18
DESCRIPTION | 14 -- MD5 | 181 ++++++++++++++------------- NAMESPACE | 5 NEWS.md | 31 ++++ R/classCRS.R | 77 ++++++++++- R/classRaster.Extract.R | 21 ++- R/classRaster_as.matrix.R | 6 R/classRaster_hist.R | 2 R/colorize.R | 3 R/compose_close.R | 10 + R/compose_legend.R | 2 R/conn.open_gdal.R | 3 R/conn.read_gdal.R | 3 R/cubehelix.R | 4 R/glance.R | 2 R/legend_colorbar.R | 2 R/legend_mtext.R | 2 R/panel_annotation.R | 4 R/panel_coastline.R | 2 R/panel_contour.R | 2 R/panel_graticule.R | 4 R/panel_new.R | 9 - R/panel_plot.R | 4 R/panel_raster.R | 18 +- R/panel_scalebar.R | 2 R/polygonize.R | 3 R/spatial_write.R | 18 ++ R/unix |only R/ursa_blank.R | 2 R/windows |only R/xxx.geomap.R | 18 +- R/xxx.panel_basemap.R | 4 R/xxx.panel_cluster.R | 10 + R/xxx.panel_legend.R | 2 R/xxx.spatialize.R | 3 R/yyy.cache.R | 2 R/yyy.getPrm.R | 254 +++++++++++++++++++-------------------- R/yyy.tile.R | 2 R/yyy.util.R | 96 ++++++++++++++ R/zzz.R | 2 inst/requisite/browseURL.html |only inst/requisite/coast-l.rds |binary man/Ops.band_stat.Rd | 2 man/Ops.focal_mean.Rd | 2 man/Ops.focal_special.Rd | 2 man/Ops.global_group.Rd | 2 man/Ops.local_group.Rd | 2 man/allocate.Rd | 2 man/chunk.Rd | 2 man/classCRS.Rd | 2 man/classColorTable.Rd | 2 man/classConnection.Rd | 2 man/classGrid.Rd | 2 man/classRaster.Extract.Rd | 2 man/classRaster_GroupGeneric.Rd | 2 man/classRaster_as.data.frame.Rd | 2 man/classRaster_as.table.Rd | 2 man/classRaster_c.Rd | 2 man/classRaster_is.na.Rd | 2 man/classRaster_length.Rd | 2 man/classRaster_names.Rd | 2 man/classRaster_sort.Rd | 2 man/classRaster_summary.Rd | 2 man/codec.Rd | 2 man/compose_close.Rd | 2 man/compose_design.Rd | 2 man/compose_open.Rd | 2 man/compose_panel.Rd | 2 man/conn.create_any.Rd | 2 man/conn.open_gdal.Rd | 2 man/conn.write_envi.Rd | 2 man/cubehelix.Rd | 2 man/display_rgb.Rd | 2 man/display_stack.Rd | 2 man/get_earthdata.Rd | 2 man/identify.Rd | 2 man/legend_align.Rd | 2 man/package_raster.Rd | 2 man/package_sf.Rd | 2 man/panel_coastline.Rd | 2 man/panel_contour.Rd | 2 man/panel_new.Rd | 2 man/panel_raster.Rd | 2 man/panel_scalebar.Rd | 2 man/progressBar.Rd | 2 man/regrid.Rd | 2 man/session.Rd | 2 man/temporal_mean.Rd | 2 man/trackline.Rd | 2 man/ursa_as.Rd | 2 man/ursa_blank.Rd | 2 man/ursa_crs.Rd | 2 man/ursa_new.Rd | 2 93 files changed, 591 insertions(+), 340 deletions(-)
Title: Processing Proteomics Data, Statistical Analysis and
Visualization
Description: The 'Proteomics Eye' ('ProtE') offers a comprehensive and intuitive framework for the univariate analysis of label-free proteomics data. By integrating essential data wrangling and processing steps into a single function, 'ProtE' streamlines pairwise statistical comparisons for categorical variables. It provides quality checks and generates publication-ready visualizations, enabling efficient and robust data analysis. 'ProtE' is compatible with proteomics data outputs from 'MaxQuant' (Cox & Mann, (2008) <doi:10.1038/nbt.1511>), 'DIA-NN' (Demichev et al., (2020) <doi:10.1038/s41592-019-0638-x>), and 'Proteome Discoverer' (Thermo Fisher Scientific, version 2.5). The package leverages 'ggplot2' for visualization (Wickham, (2016) <doi:10.1007/978-3-319-24277-4>) and 'limma' for statistical analysis (Ritchie et al., (2015) <doi:10.1093/nar/gkv007>).
Author: Theodoros Margelos [aut, cre, cph],
Rafael Stroggilos [ctb, cph]
Maintainer: Theodoros Margelos <ted.margelos02@gmail.com>
Diff between ProtE versions 1.0.2 dated 2025-02-17 and 1.0.3 dated 2025-02-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 2 ++ R/DIAnn.R | 2 +- R/new_vers_PD.R | 2 +- R/path_res.R | 2 +- 6 files changed, 13 insertions(+), 11 deletions(-)
Title: Interior Point Conic Optimization Solver
Description: A versatile interior point solver that solves linear programs (LPs), quadratic programs (QPs), second-order cone programs (SOCPs), semidefinite programs (SDPs), and problems with exponential and power cone constraints (<https://clarabel.org/stable/>). For quadratic objectives, unlike interior point solvers based on the standard homogeneous self-dual embedding (HSDE) model, Clarabel handles quadratic objective without requiring any epigraphical reformulation of its objective function. It can therefore be significantly faster than other HSDE-based solvers for problems with quadratic objective functions. Infeasible problems are detected using using a homogeneous embedding technique.
Author: Balasubramanian Narasimhan [aut, cre],
Paul Goulart [aut, cph],
Yuwen Chen [aut],
Hiroaki Yutani [ctb] ,
David Zimmermann-Kollenda [ctb] ,
Hiroaki Yutani [ctb] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between clarabel versions 0.9.0.1 dated 2024-09-03 and 0.10.0 dated 2025-02-18
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 27 +++++++++++++++------------ NEWS.md | 9 +++++++++ R/clarabel.R | 6 +++++- build/vignette.rds |binary configure | 6 +++++- configure.win |only inst/doc/clarabel.html | 5 +++-- man/clarabel_control.Rd | 3 +++ src/Makevars.in | 6 +++++- src/Makevars.win | 4 +--- src/rust/Cargo.lock |only src/rust/Cargo.toml | 10 +++++++--- src/rust/cargo_vendor_config.toml | 11 ++++++++++- src/rust/vendor.tar.xz |binary tools |only 16 files changed, 78 insertions(+), 32 deletions(-)
Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut],
Martin Studer [cre],
The Apache Software Foundation [ctb, cph] ,
Graph Builder [ctb, cph] ,
Brett Woolridge [ctb, cph]
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>
Diff between XLConnect versions 1.1.0 dated 2024-08-22 and 1.2.0 dated 2025-02-18
XLConnect-1.1.0/XLConnect/inst/java/XLConnect-3.0.0-SNAPSHOT.jar |only XLConnect-1.2.0/XLConnect/DESCRIPTION | 6 +- XLConnect-1.2.0/XLConnect/MD5 | 18 +++--- XLConnect-1.2.0/XLConnect/NEWS | 11 ++-- XLConnect-1.2.0/XLConnect/R/onLoad.R | 26 +++++----- XLConnect-1.2.0/XLConnect/build/vignette.rds |binary XLConnect-1.2.0/XLConnect/inst/COPYRIGHTS | 2 XLConnect-1.2.0/XLConnect/inst/doc/XLConnect.pdf |binary XLConnect-1.2.0/XLConnect/inst/doc/XLConnectImpatient.pdf |binary XLConnect-1.2.0/XLConnect/inst/java/XLConnect-3.1.0.jar |only XLConnect-1.2.0/XLConnect/inst/java/log4j2.system.properties | 3 - 11 files changed, 35 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-04 1.0.0
Title: Analysis and Visualization of Multi-Omics Data
Description: A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10. [...truncated...]
Author: Dongyue Yu [aut, cre, cph]
Maintainer: Dongyue Yu <yudongyue@mail.nankai.edu.cn>
Diff between TransProR versions 1.0.2 dated 2025-02-14 and 1.0.3 dated 2025-02-18
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 1 - R/CircosFruits.R | 3 --- inst/doc/TransProR.html | 4 ++-- 5 files changed, 12 insertions(+), 16 deletions(-)
Title: Small Area Estimation Using Model-Assisted Projection Method
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Author: Ridson Al Farizal P [aut, cre, cph]
,
Azka Ubaidillah [aut] ,
Silvi Ajeng Larasati [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>
Diff between sae.projection versions 0.1.1 dated 2025-02-15 and 0.1.2 dated 2025-02-18
sae.projection-0.1.1/sae.projection/R/Projection_rf.R |only sae.projection-0.1.1/sae.projection/R/Projection_rf_CorrectedBias.R |only sae.projection-0.1.1/sae.projection/man/Projection_rf.Rd |only sae.projection-0.1.1/sae.projection/man/Projection_rf_CorrectedBias.Rd |only sae.projection-0.1.2/sae.projection/DESCRIPTION | 6 sae.projection-0.1.2/sae.projection/MD5 | 22 sae.projection-0.1.2/sae.projection/NAMESPACE | 25 sae.projection-0.1.2/sae.projection/R/data.R | 256 +-- sae.projection-0.1.2/sae.projection/R/proj_random_forest.R |only sae.projection-0.1.2/sae.projection/R/projection.R | 688 +++++----- sae.projection-0.1.2/sae.projection/README.md | 502 +++---- sae.projection-0.1.2/sae.projection/data/df_susenas_sep2020.rda |binary sae.projection-0.1.2/sae.projection/man/df_susenas_sep2020.Rd | 2 sae.projection-0.1.2/sae.projection/man/proj_random_forest.Rd |only sae.projection-0.1.2/sae.projection/man/projection_rf.Rd |only sae.projection-0.1.2/sae.projection/man/projection_rf_CorrectedBias.Rd |only 16 files changed, 751 insertions(+), 750 deletions(-)
More information about sae.projection at CRAN
Permanent link
Title: Install and Load the 'dartRverse' Suits of Packages
Description: Provides a single function that supports the installation of all packages
belonging to the 'dartRverse'. The 'dartRverse' is a set of packages that work
together to analyse SNP (single nuclear polymorphism) data. All packages aim to have a similar 'look and feel'
and are based on the same type of data structure ('genlight'), with additional
metadata for loci and individuals (samples). For more information visit the
'GitHub' pages <https://github.com/green-striped-gecko/dartRverse>.
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Peter J. Unmack [aut],
Oliver Berry [aut]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartRverse versions 1.0.2 dated 2024-05-24 and 1.0.6 dated 2025-02-18
DESCRIPTION | 12 +++---- MD5 | 8 +++- NAMESPACE | 28 ++++++++++------ R/gl.download.binary.r |only man/dartRverse_install.Rd | 76 +++++++++++++++++++++++----------------------- man/gl.download.binary.Rd |only 6 files changed, 66 insertions(+), 58 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] ,
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.2.2 dated 2024-11-27 and 0.2.3 dated 2025-02-18
cardx-0.2.2/cardx/tests/spelling.R |only cardx-0.2.3/cardx/DESCRIPTION | 21 cardx-0.2.3/cardx/MD5 | 57 - cardx-0.2.3/cardx/NAMESPACE | 1 cardx-0.2.3/cardx/NEWS.md | 22 cardx-0.2.3/cardx/R/ard_categorical.survey.design.R | 9 cardx-0.2.3/cardx/R/ard_categorical_ci.R | 391 ++++++++-- cardx-0.2.3/cardx/R/ard_categorical_max.R |only cardx-0.2.3/cardx/R/ard_missing.survey.design.R | 7 cardx-0.2.3/cardx/R/ard_survival_survfit.R | 20 cardx-0.2.3/cardx/R/proportion_ci.R | 21 cardx-0.2.3/cardx/README.md | 36 cardx-0.2.3/cardx/inst/WORDLIST | 2 cardx-0.2.3/cardx/man/ard_categorical_ci.Rd | 15 cardx-0.2.3/cardx/man/ard_categorical_ci.survey.design.Rd | 4 cardx-0.2.3/cardx/man/ard_categorical_max.Rd |only cardx-0.2.3/cardx/man/ard_survival_survfit.Rd | 3 cardx-0.2.3/cardx/man/cardx-package.Rd | 2 cardx-0.2.3/cardx/man/dot-strata_normal_quantile.Rd | 6 cardx-0.2.3/cardx/man/dot-update_weights_strat_wilson.Rd | 4 cardx-0.2.3/cardx/man/proportion_ci.Rd | 13 cardx-0.2.3/cardx/tests/testthat.R | 2 cardx-0.2.3/cardx/tests/testthat/_snaps/ard_categorical.survey.design.md | 16 cardx-0.2.3/cardx/tests/testthat/_snaps/ard_categorical_max.md |only cardx-0.2.3/cardx/tests/testthat/_snaps/ard_proportion_ci.md | 26 cardx-0.2.3/cardx/tests/testthat/_snaps/ard_survival_survfit.md | 24 cardx-0.2.3/cardx/tests/testthat/_snaps/proportion_ci.md | 57 + cardx-0.2.3/cardx/tests/testthat/test-ard_categorical.survey.design.R | 52 + cardx-0.2.3/cardx/tests/testthat/test-ard_categorical_ci.data.frame.R | 319 +++++++- cardx-0.2.3/cardx/tests/testthat/test-ard_categorical_max.R |only cardx-0.2.3/cardx/tests/testthat/test-ard_missing.survey.design.R | 33 cardx-0.2.3/cardx/tests/testthat/test-ard_survival_survfit.R | 9 32 files changed, 994 insertions(+), 178 deletions(-)
Title: Interpolation and Extrapolation for Three Dimensions of
Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from
genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D)
of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional
diversity (FD). This package provides functions to compute standardized 3D diversity estimates
with a common sample size or sample coverage. A unified framework based on Hill numbers
and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates
are in the same units of species/lineage equivalents and can be meaningfully compared.
The package features size- and coverage-based rarefaction and extrapolation sampling
curves to facilitate rigorous comparison of 3D diversity across individual assemblages.
Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021)
<doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.3D versions 1.0.7 dated 2025-01-22 and 1.0.8 dated 2025-02-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 5 +++++ R/ChaoUtility_Fun.R | 24 ++++++++++++++++-------- R/CommonFun.R | 2 +- inst/doc/Introduction.pdf |binary 6 files changed, 30 insertions(+), 17 deletions(-)
Title: Computations on Conics
Description: Solve some conic related problems (intersection of conics with lines and conics, arc length of an ellipse, polar lines, etc.).
Author: Emanuel Huber [aut, cre]
Maintainer: Emanuel Huber <emanuel.huber@pm.me>
Diff between RConics versions 1.1.1 dated 2022-03-11 and 1.1.2 dated 2025-02-17
DESCRIPTION | 11 +++++------ MD5 | 6 +++--- R/conicMatrixToEllipse.R | 3 ++- README.md | 4 +++- 4 files changed, 13 insertions(+), 11 deletions(-)
Title: Analysis of Check-All-that-Apply (CATA) Data
Description: Package contains functions for analyzing check-all-that-apply (CATA) data from consumer and sensory tests. Cochran's Q test, McNemar's test, and Penalty-Lift analysis are provided; for details, see Meyners, Castura & Carr (2013) <doi:10.1016/j.foodqual.2013.06.010>. Cluster analysis can be performed using b-cluster analysis, then evaluated using various measures; for details, see Castura, Meyners, Varela & Næs (2022) <doi:10.1016/j.foodqual.2022.104564>. Methods are adapted to cluster consumers based on their product-related hedonic responses; for details, see Castura, Meyners, Pohjanheimo, Varela & Næs (2023) <doi:10.1111/joss.12860>.
Author: J.C. Castura [aut, cre, ctb]
Maintainer: J.C. Castura <jcastura@compusense.com>
Diff between cata versions 0.1.0.7 dated 2024-10-08 and 0.1.0.26 dated 2025-02-17
cata-0.1.0.26/cata/DESCRIPTION | 10 cata-0.1.0.26/cata/MD5 | 47 +- cata-0.1.0.26/cata/NAMESPACE | 4 cata-0.1.0.26/cata/R/cata-internal.R | 4 cata-0.1.0.26/cata/R/cata.R | 448 +++++++++++------------ cata-0.1.0.26/cata/R/evalClusterQuality.R | 40 -- cata-0.1.0.26/cata/R/ocov.R |only cata-0.1.0.26/cata/R/plift.R |only cata-0.1.0.26/cata/build/partial.rdb |binary cata-0.1.0.26/cata/data/bread.rda |binary cata-0.1.0.26/cata/man/ARI.Rd | 18 cata-0.1.0.26/cata/man/barray.Rd | 18 cata-0.1.0.26/cata/man/bcluster.Rd | 9 cata-0.1.0.26/cata/man/bcluster.h.Rd | 4 cata-0.1.0.26/cata/man/cochranQ.Rd | 30 - cata-0.1.0.26/cata/man/code.topk.Rd | 6 cata-0.1.0.26/cata/man/evaluateClusterQuality.Rd | 14 cata-0.1.0.26/cata/man/getb.Rd | 8 cata-0.1.0.26/cata/man/homogeneity.Rd | 6 cata-0.1.0.26/cata/man/mad.dist.Rd |only cata-0.1.0.26/cata/man/madperm.Rd |only cata-0.1.0.26/cata/man/mcnemarQ.Rd | 17 cata-0.1.0.26/cata/man/plift.Rd |only cata-0.1.0.26/cata/man/rv.coef.Rd | 8 cata-0.1.0.26/cata/man/toMatrix.Rd | 14 cata-0.1.0.26/cata/man/toWideMatrix.Rd | 14 cata-0.1.0.7/cata/R/pLift.R |only cata-0.1.0.7/cata/man/pLift.Rd |only 28 files changed, 364 insertions(+), 355 deletions(-)
Title: Learn Clustering Techniques Through Examples and Code
Description: A comprehensive educational package combining clustering algorithms with
detailed step-by-step explanations. Provides implementations of both traditional
(hierarchical, k-means) and modern (Density-Based Spatial Clustering of Applications with Noise (DBSCAN),
Gaussian Mixture Models (GMM), genetic k-means) clustering methods
as described in Ezugwu et. al., (2022) <doi:10.1016/j.engappai.2022.104743>.
Includes educational datasets highlighting different clustering challenges, based on
'scikit-learn' examples (Pedregosa et al., 2011)
<https://jmlr.csail.mit.edu/papers/v12/pedregosa11a.html>. Features detailed
algorithm explanations, visualizations, and weighted distance calculations for
enhanced learning.
Author: Eduardo Ruiz Sabajanes [aut],
Roberto Alcantara [aut],
Juan Jose Cuadrado Gallego [aut]
,
Andriy Protsak Protsak [aut, cre],
Universidad de Alcala [cph]
Maintainer: Andriy Protsak Protsak <andriy.protsak@edu.uah.es>
Diff between UAHDataScienceUC versions 1.0.0 dated 2025-02-17 and 1.0.1 dated 2025-02-17
DESCRIPTION | 9 MD5 | 12 - NEWS.md | 5 R/divisive_clustering.R | 5 inst/doc/UAHDataScienceUC.html | 408 ++++++++++++++++++++--------------------- man/divisive_clustering.Rd | 5 man/gaussian_mixture.Rd | 21 -- 7 files changed, 233 insertions(+), 232 deletions(-)
More information about UAHDataScienceUC at CRAN
Permanent link
Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian
Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O
pacote é baseado em conjuntos de dados espaciais abertos de endereços
brasileiros, utilizando principalmente o Cadastro Nacional de Endereços para
Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro de
Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia do
Brasil. (A simple and efficient method for geolocating data in Brazil. The
package is based on open spatial datasets of Brazilian addresses, primarily
using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE),
published by the Instituto Brasileiro de Geografia e Estatística (IBGE),
Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre]
,
Daniel Herszenhut [aut] ,
Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geocodebr versions 0.1.0 dated 2025-02-12 and 0.1.1 dated 2025-02-17
DESCRIPTION | 6 - MD5 | 39 ++++----- NAMESPACE | 1 NEWS.md | 7 + R/cache.R | 36 ++++++-- R/geocodebr.R | 17 --- README.md | 13 ++- build/vignette.rds |binary inst/doc/geocodebr.R | 6 - inst/doc/geocodebr.Rmd | 12 ++ inst/doc/geocodebr.html | 112 +++++++++++++------------- man/create_index.Rd | 24 ++--- man/definir_campos.Rd | 132 +++++++++++++++---------------- man/deletar_pasta_cache.Rd | 38 ++++---- man/listar_dados_cache.Rd | 48 +++++------ man/listar_pasta_cache.Rd | 42 ++++----- man/update_input_db.Rd | 44 +++++----- tests/tests_rafa/benchmark_LIKE.R | 20 ++-- tests/tests_rafa/teste_geocodebr_1km.csv |only tests/testthat/test-cache.R | 3 vignettes/geocodebr.Rmd | 12 ++ 21 files changed, 325 insertions(+), 287 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.3.5 dated 2025-02-11 and 2.3.6 dated 2025-02-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 ++++- R/jointfPCA.R | 6 ++++++ src/bayesian.cpp | 2 +- 5 files changed, 19 insertions(+), 10 deletions(-)
Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards
Consortium) compliant Analysis Results Data objects. These objects are
used and re-used to construct summary tables, visualizations, and
written reports. The package also exports utilities for working with
these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] ,
Becca Krouse [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cards versions 0.4.0 dated 2024-11-27 and 0.5.0 dated 2025-02-17
cards-0.4.0/cards/man/label_cards.Rd |only cards-0.4.0/cards/tests/spelling.R |only cards-0.4.0/cards/tests/testthat/test-label_cards.R |only cards-0.5.0/cards/DESCRIPTION | 17 cards-0.5.0/cards/MD5 | 127 +- cards-0.5.0/cards/NAMESPACE | 3 cards-0.5.0/cards/NEWS.md | 24 cards-0.5.0/cards/R/apply_fmt_fn.R | 31 cards-0.5.0/cards/R/ard_attributes.R | 1 cards-0.5.0/cards/R/ard_categorical.R | 107 ++ cards-0.5.0/cards/R/ard_complex.R | 1 cards-0.5.0/cards/R/ard_continuous.R | 5 cards-0.5.0/cards/R/ard_hierarchical.R | 41 cards-0.5.0/cards/R/ard_stack_hierarchical.R | 1 cards-0.5.0/cards/R/ard_strata.R | 3 cards-0.5.0/cards/R/default_stat_labels.R | 2 cards-0.5.0/cards/R/deprecated.R |only cards-0.5.0/cards/R/eval_capture_conditions.R | 1 cards-0.5.0/cards/R/options.R |only cards-0.5.0/cards/R/print.R | 1 cards-0.5.0/cards/R/print_ard_conditions.R | 27 cards-0.5.0/cards/R/rename_ard_groups.R |only cards-0.5.0/cards/R/round5.R | 2 cards-0.5.0/cards/R/selectors.R | 10 cards-0.5.0/cards/R/tidy_ard_order.R | 43 cards-0.5.0/cards/R/tidy_as_ard.R | 1 cards-0.5.0/cards/README.md | 432 +++++++++- cards-0.5.0/cards/inst/WORDLIST | 5 cards-0.5.0/cards/man/ard_categorical.Rd | 33 cards-0.5.0/cards/man/ard_complex.Rd | 3 cards-0.5.0/cards/man/ard_continuous.Rd | 2 cards-0.5.0/cards/man/ard_dichotomous.Rd | 31 cards-0.5.0/cards/man/ard_hierarchical.Rd | 52 - cards-0.5.0/cards/man/ard_missing.Rd | 2 cards-0.5.0/cards/man/ard_stack_hierarchical.Rd | 5 cards-0.5.0/cards/man/ard_strata.Rd | 1 cards-0.5.0/cards/man/cards.options.Rd |only cards-0.5.0/cards/man/deprecated.Rd |only cards-0.5.0/cards/man/dot-calculate_tabulation_statistics.Rd | 10 cards-0.5.0/cards/man/dot-cli_condition_messaging.Rd | 2 cards-0.5.0/cards/man/dot-process_denominator.Rd | 6 cards-0.5.0/cards/man/dot-rename_last_group_as_variable.Rd | 4 cards-0.5.0/cards/man/eval_capture_conditions.Rd | 1 cards-0.5.0/cards/man/label_round.Rd |only cards-0.5.0/cards/man/print.card.Rd | 1 cards-0.5.0/cards/man/print_ard_conditions.Rd | 7 cards-0.5.0/cards/man/rename_ard_groups.Rd |only cards-0.5.0/cards/man/round5.Rd | 2 cards-0.5.0/cards/man/selectors.Rd | 2 cards-0.5.0/cards/man/tidy_ard_order.Rd | 12 cards-0.5.0/cards/tests/testthat/_snaps/ard_categorical.md | 79 - cards-0.5.0/cards/tests/testthat/_snaps/ard_hierarchical.md | 8 cards-0.5.0/cards/tests/testthat/_snaps/ard_stack_hierarchical.md | 24 cards-0.5.0/cards/tests/testthat/_snaps/ard_strata.md | 22 cards-0.5.0/cards/tests/testthat/_snaps/bind_ard.md | 120 -- cards-0.5.0/cards/tests/testthat/_snaps/options.md |only cards-0.5.0/cards/tests/testthat/_snaps/print.md | 14 cards-0.5.0/cards/tests/testthat/_snaps/print_ard_conditions.md | 29 cards-0.5.0/cards/tests/testthat/_snaps/rename_ard_columns.md | 47 - cards-0.5.0/cards/tests/testthat/_snaps/rename_ard_groups.md |only cards-0.5.0/cards/tests/testthat/_snaps/tidy_ard_row_order.md |only cards-0.5.0/cards/tests/testthat/test-ard_categorical.R | 253 +++++ cards-0.5.0/cards/tests/testthat/test-ard_hierarchical.R | 12 cards-0.5.0/cards/tests/testthat/test-ard_stack.R | 10 cards-0.5.0/cards/tests/testthat/test-ard_stack_hierarchical.R | 5 cards-0.5.0/cards/tests/testthat/test-bind_ard.R | 1 cards-0.5.0/cards/tests/testthat/test-label_round.R |only cards-0.5.0/cards/tests/testthat/test-options.R |only cards-0.5.0/cards/tests/testthat/test-print_ard_conditions.R | 30 cards-0.5.0/cards/tests/testthat/test-rename_ard_columns.R | 5 cards-0.5.0/cards/tests/testthat/test-rename_ard_groups.R |only cards-0.5.0/cards/tests/testthat/test-tidy_ard_column_order.R | 15 cards-0.5.0/cards/tests/testthat/test-tidy_ard_row_order.R |only 73 files changed, 1310 insertions(+), 425 deletions(-)
Title: Select an Optimal Block-Length to Bootstrap Dependent Data
(Block Bootstrap)
Description: A set of functions to select the optimal block-length for a
dependent bootstrap (block-bootstrap). Includes the Hall, Horowitz, and Jing
(1995) <doi:10.1093/biomet/82.3.561> subsampling-based cross-validation method, the
Politis and White (2004) <doi:10.1081/ETC-120028836> Spectral Density
Plug-in method, including the Patton, Politis, and White (2009)
<doi:10.1080/07474930802459016> correction, and the Lahiri, Furukawa, and Lee
(2007) <doi:10.1016/j.stamet.2006.08.002> nonparametric plug-in method, with
a corresponding set of S3 plot methods.
Author: Alec Stashevsky [aut, cre] ,
Sergio Armella [ctb]
Maintainer: Alec Stashevsky <alec@alecstashevsky.com>
Diff between blocklength versions 0.1.5 dated 2022-03-02 and 0.2.0 dated 2025-02-17
DESCRIPTION | 21 MD5 | 53 NAMESPACE | 14 NEWS.md | 95 - R/hhj.R | 750 ++++---- R/nppi.R |only R/plot.hhj.R | 130 - R/plot.nppi.R |only R/plot.pwsd.R | 156 - R/pwsd.R | 522 +++--- README.md | 531 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/tuning-parameters.R | 274 +-- inst/doc/tuning-parameters.Rmd | 542 +++--- inst/doc/tuning-parameters.html | 3412 +++++++++++++++++++++++++++++++++++----- man/figures/README-hhj-1.svg | 604 +++---- man/figures/README-hhj-2.svg | 604 +++---- man/figures/README-nppi-1.svg |only man/figures/README-pwsd-1.svg | 520 +++--- man/hhj.Rd | 2 man/nppi.Rd |only man/plot.nppi.Rd |only tests/testthat.R | 8 tests/testthat/Rplots.pdf |only tests/testthat/test-hhj.R | 164 - tests/testthat/test-nppi.R |only tests/testthat/test-plots.R | 70 tests/testthat/test-pwsd.R | 126 - vignettes/references.bib | 244 +- vignettes/tuning-parameters.Rmd | 542 +++--- 31 files changed, 6085 insertions(+), 3299 deletions(-)
Title: Working with Sets the Tidy Way
Description: Implements a class and methods to work with sets, doing
intersection, union, complementary sets, power sets, cartesian product
and other set operations in a "tidy" way. These set operations are
available for both classical sets and fuzzy sets. Import sets from
several formats or from other several data structures.
Author: Lluis Revilla Sancho [aut, cre, cph]
,
Zebulun Arendsee [rev],
Jennifer Chang [rev]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between BaseSet versions 0.9.0 dated 2023-08-22 and 1.0.0 dated 2025-02-17
BaseSet-0.9.0/BaseSet/R/utils-pipe.R |only BaseSet-0.9.0/BaseSet/man/pipe.Rd |only BaseSet-0.9.0/BaseSet/man/tidy.Rd |only BaseSet-0.9.0/BaseSet/tests/testthat/test-gmt.R |only BaseSet-0.9.0/BaseSet/tests/testthat/test-toimplement.R |only BaseSet-1.0.0/BaseSet/DESCRIPTION | 42 - BaseSet-1.0.0/BaseSet/LICENSE | 2 BaseSet-1.0.0/BaseSet/MD5 | 235 ++++---- BaseSet-1.0.0/BaseSet/NAMESPACE | 13 BaseSet-1.0.0/BaseSet/NEWS.md | 11 BaseSet-1.0.0/BaseSet/R/AllGenerics.R | 26 BaseSet-1.0.0/BaseSet/R/GeneSetCollection.R | 62 +- BaseSet-1.0.0/BaseSet/R/c.R | 1 BaseSet-1.0.0/BaseSet/R/complement.R | 20 BaseSet-1.0.0/BaseSet/R/data_frame.R | 1 BaseSet-1.0.0/BaseSet/R/elements.R | 15 BaseSet-1.0.0/BaseSet/R/extract.R | 65 +- BaseSet-1.0.0/BaseSet/R/names.R | 320 +++++++----- BaseSet-1.0.0/BaseSet/R/obo.R | 11 BaseSet-1.0.0/BaseSet/R/set.R | 15 BaseSet-1.0.0/BaseSet/R/size.R | 11 BaseSet-1.0.0/BaseSet/R/tidy-set.R | 11 BaseSet-1.0.0/BaseSet/README.md | 2 BaseSet-1.0.0/BaseSet/build/vignette.rds |binary BaseSet-1.0.0/BaseSet/inst/WORDLIST | 4 BaseSet-1.0.0/BaseSet/inst/doc/BaseSet.html | 92 +-- BaseSet-1.0.0/BaseSet/inst/doc/advanced.R | 312 +++++------ BaseSet-1.0.0/BaseSet/inst/doc/advanced.Rmd | 8 BaseSet-1.0.0/BaseSet/inst/doc/advanced.html | 131 +++- BaseSet-1.0.0/BaseSet/inst/doc/fuzzy.html | 54 +- BaseSet-1.0.0/BaseSet/man/TidySet-class.Rd | 6 BaseSet-1.0.0/BaseSet/man/activate.Rd | 6 BaseSet-1.0.0/BaseSet/man/add_column.Rd | 6 BaseSet-1.0.0/BaseSet/man/add_relation.Rd | 6 BaseSet-1.0.0/BaseSet/man/arrange_.Rd | 6 BaseSet-1.0.0/BaseSet/man/cartesian.Rd | 6 BaseSet-1.0.0/BaseSet/man/complement.Rd | 24 BaseSet-1.0.0/BaseSet/man/complement_element.Rd | 8 BaseSet-1.0.0/BaseSet/man/complement_set.Rd | 8 BaseSet-1.0.0/BaseSet/man/dimnames.TidySet.Rd |only BaseSet-1.0.0/BaseSet/man/element_size.Rd | 6 BaseSet-1.0.0/BaseSet/man/elements.Rd | 19 BaseSet-1.0.0/BaseSet/man/extract-TidySet.Rd | 3 BaseSet-1.0.0/BaseSet/man/filter_.Rd | 6 BaseSet-1.0.0/BaseSet/man/group.Rd | 4 BaseSet-1.0.0/BaseSet/man/group_by_.Rd | 4 BaseSet-1.0.0/BaseSet/man/incidence.Rd | 6 BaseSet-1.0.0/BaseSet/man/intersection.Rd | 6 BaseSet-1.0.0/BaseSet/man/is.fuzzy.Rd | 6 BaseSet-1.0.0/BaseSet/man/is_nested.Rd | 6 BaseSet-1.0.0/BaseSet/man/move_to.Rd | 6 BaseSet-1.0.0/BaseSet/man/mutate_.Rd | 6 BaseSet-1.0.0/BaseSet/man/nElements.Rd | 10 BaseSet-1.0.0/BaseSet/man/nRelations.Rd | 6 BaseSet-1.0.0/BaseSet/man/nSets.Rd | 10 BaseSet-1.0.0/BaseSet/man/name_elements-set.Rd | 14 BaseSet-1.0.0/BaseSet/man/name_elements.Rd | 30 - BaseSet-1.0.0/BaseSet/man/name_sets-set.Rd | 12 BaseSet-1.0.0/BaseSet/man/name_sets.Rd | 34 - BaseSet-1.0.0/BaseSet/man/names.TidySet.Rd |only BaseSet-1.0.0/BaseSet/man/power_set.Rd | 6 BaseSet-1.0.0/BaseSet/man/pull_.Rd | 6 BaseSet-1.0.0/BaseSet/man/relations.Rd | 6 BaseSet-1.0.0/BaseSet/man/remove_column.Rd | 6 BaseSet-1.0.0/BaseSet/man/remove_element.Rd | 6 BaseSet-1.0.0/BaseSet/man/remove_relation.Rd | 6 BaseSet-1.0.0/BaseSet/man/remove_set.Rd | 6 BaseSet-1.0.0/BaseSet/man/rename_elements.Rd | 10 BaseSet-1.0.0/BaseSet/man/rename_set.Rd | 10 BaseSet-1.0.0/BaseSet/man/select_.Rd | 6 BaseSet-1.0.0/BaseSet/man/set_size.Rd | 6 BaseSet-1.0.0/BaseSet/man/sets.Rd | 21 BaseSet-1.0.0/BaseSet/man/size.Rd | 2 BaseSet-1.0.0/BaseSet/man/subtract.Rd | 10 BaseSet-1.0.0/BaseSet/man/tidySet.Rd | 31 + BaseSet-1.0.0/BaseSet/man/union.Rd | 6 BaseSet-1.0.0/BaseSet/tests/testthat.R | 8 BaseSet-1.0.0/BaseSet/tests/testthat/test-GMT.R |only BaseSet-1.0.0/BaseSet/tests/testthat/test-activate.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-add_relation.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-add_relations.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-adjacency.R | 12 BaseSet-1.0.0/BaseSet/tests/testthat/test-arrange.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-cartesian.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-complement.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-data_frame.R | 6 BaseSet-1.0.0/BaseSet/tests/testthat/test-df2TS.R | 4 BaseSet-1.0.0/BaseSet/tests/testthat/test-element_size.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-elements.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-extract.R | 51 + BaseSet-1.0.0/BaseSet/tests/testthat/test-filter.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-group.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-group_by.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-head.R |only BaseSet-1.0.0/BaseSet/tests/testthat/test-incidence.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-independent.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-intersection.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-length.R | 8 BaseSet-1.0.0/BaseSet/tests/testthat/test-move_to.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-mutate.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-name.R | 18 BaseSet-1.0.0/BaseSet/tests/testthat/test-naming.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-nested.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-operations.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-power_set.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-print.R | 1 BaseSet-1.0.0/BaseSet/tests/testthat/test-pull.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-relations.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-remove_column.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-remove_element.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-remove_relation.R | 23 BaseSet-1.0.0/BaseSet/tests/testthat/test-remove_set.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-rename.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-select.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-setAs.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-set_size.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-sets.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-size.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-subtract.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-tidy.R | 34 - BaseSet-1.0.0/BaseSet/tests/testthat/test-tidyset.R | 2 BaseSet-1.0.0/BaseSet/tests/testthat/test-union.R | 2 BaseSet-1.0.0/BaseSet/vignettes/advanced.Rmd | 8 123 files changed, 1235 insertions(+), 884 deletions(-)
Title: Sparse-Group Boosting
Description: Sparse-group boosting to be used in conjunction with the 'mboost' for modeling grouped data.
Applicable to all sparse-group lasso type problems where within-group and between-group sparsity is desired.
Interprets and visualizes individual variables and groups.
Author: Fabian Obster [aut, cre, cph]
Maintainer: Fabian Obster <fabian.obster@unibw.de>
Diff between sgboost versions 0.1.3 dated 2024-05-19 and 0.2.0 dated 2025-02-17
DESCRIPTION | 6 MD5 | 25 +-- NAMESPACE | 7 NEWS.md | 8 + R/balance.R |only R/create_formula.R | 21 +- R/get_coef.R | 6 R/plot_path.R | 278 +++++++++++++++++------------------ inst/doc/sgboost.html | 182 +++++++++++----------- man/balance.Rd |only man/create_formula.Rd | 3 tests/spelling.R | 9 - tests/testthat/test-create_formula.R | 15 + tests/testthat/test-plot_path.R | 9 - tests/testthat/test-test-balance.R |only 15 files changed, 306 insertions(+), 263 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 11.0 dated 2025-01-10 and 11.1 dated 2025-02-17
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++-------- NAMESPACE | 3 ++ R/Causation.R | 13 ++++------ R/Numerical_Differentiation.R | 28 +++++++++++----------- R/SD_Cluster.R |only R/gvload.R | 2 - README.md | 4 +-- inst/doc/NNSvignette_Comparing_Distributions.R | 28 +++++++++++----------- inst/doc/NNSvignette_Comparing_Distributions.Rmd | 12 +++++++-- inst/doc/NNSvignette_Comparing_Distributions.html | 26 ++++++++++++++++++-- man/NNS.SD.cluster.Rd |only vignettes/NNSvignette_Comparing_Distributions.Rmd | 12 +++++++-- 13 files changed, 101 insertions(+), 57 deletions(-)
Title: Maximum Likelihood Estimation of Various Univariate and
Multivariate Distributions
Description: Several functions for maximum likelihood estimation of various univariate and multivariate distributions. The list includes more than 100 functions for univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.
Author: Michail Tsagris [aut, cre],
Sofia Piperaki [aut],
Muhammad Imran [ctb],
Rafail Vargiakakis [aut],
Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MLE versions 1.3 dated 2024-12-16 and 1.4 dated 2025-02-17
DESCRIPTION | 16 ++-- MD5 | 44 ++++++------ R/circ.mle.R | 2 R/colcens.mle.R | 13 +++ R/colcirc.mle.R | 109 +++++++++++++++++++++++++++++++ R/coldisc.mle.R | 169 ++++++++++++++++++++++++++++++++++++++++++++++++- R/colpositive.mle.R | 133 ++++++++++++++++++++++++++++++++++++++ R/colprop.mle.R | 76 ++++++++++++++++++++++ R/colreal.mle.R | 96 +++++++++++++++++++++++++-- R/disc.mle.R | 2 R/prop.mle.R | 2 man/MLE-package.Rd | 9 +- man/circ.mle.Rd | 8 +- man/colcens.mle.Rd | 12 +-- man/colcirc.mle.Rd | 43 ++++++++++-- man/coldisc.mle.Rd | 33 +++++++-- man/colpositive.mle.Rd | 6 - man/colprop.mle.Rd | 17 ++++ man/colreal.mle.Rd | 21 ++++-- man/disc.mle.Rd | 6 - man/hspher.mle.Rd | 10 +- man/prop.mle.Rd | 2 man/real.mle.Rd | 5 + 23 files changed, 742 insertions(+), 92 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between cgam versions 1.21 dated 2023-08-10 and 1.22 dated 2025-02-17
ChangeLog | 7 DESCRIPTION | 14 MD5 | 20 - NAMESPACE | 2 R/cgam.R | 761 ++++++++++++++++++++++++++++++++++++++++++++-------- R/cgamm.R | 5 man/ShapeSelect.Rd | 2 man/cgam.Rd | 2 man/plotpersp.Rd | 10 man/predict.cgam.Rd | 8 man/shapes.Rd | 2 11 files changed, 698 insertions(+), 135 deletions(-)
Title: Read and Write Sparse Matrices in 'SVMLight' and 'LibSVM'
Formats
Description: Read and write labelled sparse matrices in text format as used by
software such as 'SVMLight', 'LibSVM', 'ThunderSVM', 'LibFM', 'xLearn', 'XGBoost', 'LightGBM',
and others. Supports labelled data for regression, classification (binary, multi-class, multi-label),
and ranking (with 'qid' field), and can handle header metadata and comments in files.
Author: David Cortes [aut, cre, cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between readsparse versions 0.1.5-6 dated 2023-11-27 and 0.1.5-8 dated 2025-02-17
DESCRIPTION | 14 +++++++++----- MD5 | 14 +++++++------- R/RcppExports.R | 4 ++++ R/read_sparse.R | 4 +++- man/read.sparse.Rd | 2 ++ src/RcppExports.cpp | 10 ++++++++++ src/Rwrapper.cpp | 10 ++++++++++ tests/testthat/test-read-write.R | 20 ++++++++++++++++++++ 8 files changed, 65 insertions(+), 13 deletions(-)
Title: Processing Proteomics Data, Statistical Analysis and
Visualization
Description: The 'Proteomics Eye' ('ProtE') offers a comprehensive and intuitive framework for the univariate analysis of label-free proteomics data. By integrating essential data wrangling and processing steps into a single function, 'ProtE' streamlines pairwise statistical comparisons for categorical variables. It provides quality checks and generates publication-ready visualizations, enabling efficient and robust data analysis. 'ProtE' is compatible with proteomics data outputs from 'MaxQuant' (Cox & Mann, (2008) <doi:10.1038/nbt.1511>), 'DIA-NN' (Demichev et al., (2020) <doi:10.1038/s41592-019-0638-x>), and 'Proteome Discoverer' (Thermo Fisher Scientific, version 2.5). The package leverages 'ggplot2' for visualization (Wickham, (2016) <doi:10.1007/978-3-319-24277-4>) and 'limma' for statistical analysis (Ritchie et al., (2015) <doi:10.1093/nar/gkv007>).
Author: Theodoros Margelos [aut, cre, cph],
Rafael Stroggilos [ctb, cph]
Maintainer: Theodoros Margelos <ted.margelos02@gmail.com>
Diff between ProtE versions 1.0.1 dated 2025-01-15 and 1.0.2 dated 2025-02-17
DESCRIPTION | 14 +- MD5 | 38 ++--- NAMESPACE | 11 - NEWS.md | 4 R/DIAnn.R | 176 ++++++++++--------------- R/max_quant.R | 103 +++++++++----- R/new_vers_PD.R | 117 ++++++++-------- R/path_res.R | 124 ++++++++++------- README.md | 18 +- inst/doc/Workflow.Rmd | 8 - inst/doc/Workflow.html | 18 +- inst/doc/informations.Rmd | 14 +- inst/doc/informations.html | 20 +- inst/extdata/report.pg_matrix.tsv | 262 +++++++++++++++++++------------------- man/dianno.Rd | 9 + man/maximum_quantum.Rd | 8 + man/pd_multi.Rd | 17 ++ man/pd_single.Rd | 7 - vignettes/Workflow.Rmd | 8 - vignettes/informations.Rmd | 14 +- 20 files changed, 525 insertions(+), 465 deletions(-)
More information about UAHDataScienceUC at CRAN
Permanent link
Title: Make PX-Files in R
Description: Create PX-files from scratch or read and modify existing ones.
Includes a function for every PX keyword, making metadata manipulation
simple and human-readable.
Author: Johan Ejstrud [cre, aut],
Lars Pedersen [aut],
Statistics Greenland [cph]
Maintainer: Johan Ejstrud <johan@ejstrud.com>
Diff between pxmake versions 0.14.2 dated 2025-01-22 and 0.15.1 dated 2025-02-17
DESCRIPTION | 12 MD5 | 80 +-- NEWS.md | 22 R/classification.R | 28 - R/data.R | 1 R/data_df.R | 30 - R/documentation.R | 4 R/excel.R | 49 +- R/helper_functions.R | 11 R/metadata_df.R | 1 R/modify_helpers.R | 44 + R/modify_languages.R | 11 R/modify_variable1.R | 4 R/note_warning_error.R | 21 R/px.R | 32 + R/px_base_tables.R | 39 + R/px_file.R | 63 +- R/r_script.R |only README.md | 484 ++++++++++---------- build/vignette.rds |binary data/px_keywords.rda |binary inst/doc/first-px-file.html | 42 - inst/doc/micro-files.R | 8 inst/doc/micro-files.html | 26 - inst/extdata |only man/convert_df_to_code.Rd |only man/convert_value_to_code.Rd |only man/px.Rd | 19 man/px_classification.Rd | 28 - man/px_keywords.Rd | 1 man/px_save.Rd | 9 man/save_px_as_r_script.Rd |only man/save_px_as_xlsx.Rd | 5 man/validate_px_arguments.Rd | 13 man/validate_px_save_arguments.Rd | 6 tests/testthat/fixtures/px/multilingual_no_codes.px |only tests/testthat/test-50-px.R | 7 tests/testthat/test-51-pxsave.R | 9 tests/testthat/test-52-px-ordering.R |only tests/testthat/test-53-pxjob-px-pxsave.R | 1 tests/testthat/test-55-modify-cells1.R | 22 tests/testthat/test-55-modify-cells2.R | 11 tests/testthat/test-74-pxsave-to-R-preserves.R |only tests/testthat/test-91-micromake.R | 6 44 files changed, 697 insertions(+), 452 deletions(-)
Title: Optimal Policy Learning
Description: Provides functions for optimal policy learning in socioeconomic applications helping users to learn the most effective policies based
on data in order to maximize empirical welfare. Specifically, 'OPL' allows to find "treatment assignment rules" that maximize the overall
welfare, defined as the sum of the policy effects estimated over all the policy beneficiaries. Documentation about 'OPL' is provided by
several international articles via Athey et al (2021, <doi:10.3982/ECTA15732>), Kitagawa et al (2018, <doi:10.3982/ECTA13288>),
Cerulli (2022, <doi:10.1080/13504851.2022.2032577>), the paper by Cerulli (2021, <doi:10.1080/13504851.2020.1820939>)
and the book by Gareth et al (2013, <doi:10.1007/978-1-4614-7138-7>).
Author: Federico Brogi [aut, cre],
Barbara Guardabascio [aut],
Giovanni Cerulli [aut]
Maintainer: Federico Brogi <federicobrogi@gmail.com>
Diff between OPL versions 1.0.0 dated 2025-02-03 and 1.0.1 dated 2025-02-17
DESCRIPTION | 8 - MD5 | 4 R/opl_lc_c.R | 400 +++++++++++++++++++++++++++++------------------------------ 3 files changed, 206 insertions(+), 206 deletions(-)
More information about UAHDataScienceSC at CRAN
Permanent link
Title: An Analyzer of International Large Scale Assessments in
Education
Description: An easy way to analyze international large-scale assessments and surveys in education or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) while also allowing for analysis with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre],
Francesco Avvisati [aut],
Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>
Diff between Rrepest versions 1.5.2 dated 2025-02-10 and 1.5.3 dated 2025-02-17
DESCRIPTION | 16 ++++------------ MD5 | 10 ++++++---- NAMESPACE | 1 + R/average.R | 24 +++++++++++++++++++++--- R/coverage_column.R | 42 +++++++++++++++++++++++++++++++----------- R/coverage_daggers.R |only man/coverage_daggers.Rd |only 7 files changed, 63 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-30 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-27 0.2.1
2025-01-08 0.1.3
2024-11-08 0.1.2
2024-11-02 0.1.1
2024-10-03 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-03 0.2
2021-07-09 0.1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-28 0.1-7
2016-11-20 0.1-6
2016-09-04 0.1-5
2015-08-01 0.1-4
2015-07-11 0.1-3
2015-07-08 0.1-2
2014-05-13 0.1-1
2014-05-04 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-10 0.3.0
2023-07-09 0.2.1
2023-06-04 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-17 1.1.0
2021-09-16 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-11 1.0.7
2023-01-27 1.0.6
2022-01-05 1.0.5
2021-09-20 1.0.4
2020-01-08 1.0.3
2019-08-30 1.0.1
2019-08-30 1.0.2
2019-08-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-31 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-29 0.4.47
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-28 1.1.9
2015-02-10 1.1.8
2013-07-09 1.1.7
2013-04-29 1.1.6
2013-03-02 1.1.0
2012-02-20 0.99.19
2012-02-08 0.99.18
2012-01-18 0.99.17
2011-12-02 0.99.15
2011-11-17 0.99.14
2011-11-15 0.99.13
2011-11-09 0.99.12
2011-11-04 0.99.11
2011-06-15 0.99.9
2011-06-07 0.99.8
2011-06-04 0.99.7
2011-04-24 0.99.6
2011-04-14 0.99.4
2011-04-12 0.99.2
2011-03-31 0.99.0
2011-03-07 0.9.3
2010-12-08 0.9.2
2010-09-29 0.9.1
2010-09-09 0.9.0
2010-05-19 0.1.6
2009-12-14 0.1.5
2009-11-13 0.1.3
2009-10-20 0.1.2
2009-07-24 0.1.0
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
'pathfindR' also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in 'pathfindR' are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 2.4.1 dated 2024-05-04 and 2.4.2 dated 2025-02-17
DESCRIPTION | 20 +-- MD5 | 52 ++++---- NEWS.md | 7 + R/active_snw_search.R | 2 R/data_generation.R | 6 - R/utility.R | 2 R/visualization.R | 6 - build/vignette.rds |binary inst/doc/comparing_results.R | 20 +-- inst/doc/comparing_results.html | 10 - inst/doc/intro_vignette.R | 190 +++++++++++++++---------------- inst/doc/intro_vignette.html | 194 +++++++++++++++----------------- inst/doc/manual_execution.R | 124 ++++++++++---------- inst/doc/manual_execution.html | 12 +- inst/doc/non_hs_analysis.R | 160 +++++++++++++------------- inst/doc/non_hs_analysis.html | 203 ++++++++++++++++++++++++---------- inst/doc/obtain_data.R | 64 +++++----- inst/doc/obtain_data.Rmd | 4 inst/doc/obtain_data.html | 46 ++++--- inst/doc/visualization_vignette.R | 98 ++++++++-------- inst/doc/visualization_vignette.html | 26 ++-- man/active_snw_search.Rd | 2 man/get_gene_sets_list.Rd | 4 man/get_mgsigdb_gsets.Rd | 2 man/input_processing.Rd | 2 tests/testthat/test-data_generation.R | 16 +- vignettes/obtain_data.Rmd | 4 27 files changed, 685 insertions(+), 591 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial stratified heterogeneity, while also taking into account local spatial dependencies, spatial interpretability, complex spatial interactions, and robust spatial stratification. Additionally, it supports the spatial stratified heterogeneity family established in academic literature.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.3-1 dated 2024-12-14 and 1.3-2 dated 2025-02-17
gdverse-1.3-1/gdverse/R/gd_bestunidisc.R |only gdverse-1.3-1/gdverse/man/gd_bestunidisc.Rd |only gdverse-1.3-1/gdverse/man/shuffle_vector.Rd |only gdverse-1.3-2/gdverse/DESCRIPTION | 12 gdverse-1.3-2/gdverse/MD5 | 180 +- gdverse-1.3-2/gdverse/NAMESPACE | 4 gdverse-1.3-2/gdverse/NEWS.md | 173 +- gdverse-1.3-2/gdverse/R/gd.R | 178 +- gdverse-1.3-2/gdverse/R/gd_optunidisc.R |only gdverse-1.3-2/gdverse/R/geodetector.R | 35 gdverse-1.3-2/gdverse/R/gozh.R | 462 +++--- gdverse-1.3-2/gdverse/R/idsa.R | 5 gdverse-1.3-2/gdverse/R/lesh.R | 2 gdverse-1.3-2/gdverse/R/opgd.R | 266 +-- gdverse-1.3-2/gdverse/R/pid_idsa.R | 107 - gdverse-1.3-2/gdverse/R/psd_pseudop.R | 68 - gdverse-1.3-2/gdverse/R/r_interact_py.R | 3 gdverse-1.3-2/gdverse/R/rgd.R | 2 gdverse-1.3-2/gdverse/R/rid.R | 2 gdverse-1.3-2/gdverse/R/robustdisc.R | 27 gdverse-1.3-2/gdverse/R/sesu_gozh.R | 3 gdverse-1.3-2/gdverse/R/sesu_opgd.R | 3 gdverse-1.3-2/gdverse/R/spade.R | 2 gdverse-1.3-2/gdverse/R/spd_lesh.R | 239 +-- gdverse-1.3-2/gdverse/R/srs_geodetecor.R | 13 gdverse-1.3-2/gdverse/R/srsgd.R | 194 +- gdverse-1.3-2/gdverse/R/utils.R | 30 gdverse-1.3-2/gdverse/R/zzz.R | 7 gdverse-1.3-2/gdverse/build/vignette.rds |binary gdverse-1.3-2/gdverse/inst/doc/consistency.Rmd |only gdverse-1.3-2/gdverse/inst/doc/consistency.html |only gdverse-1.3-2/gdverse/inst/doc/gd.Rmd | 879 ++++++------- gdverse-1.3-2/gdverse/inst/doc/gd.html | 149 +- gdverse-1.3-2/gdverse/inst/doc/idsa.Rmd | 22 gdverse-1.3-2/gdverse/inst/doc/idsa.html | 80 - gdverse-1.3-2/gdverse/inst/doc/opgd.Rmd | 432 +++--- gdverse-1.3-2/gdverse/inst/doc/opgd.html | 112 - gdverse-1.3-2/gdverse/inst/doc/rgdrid.Rmd | 11 gdverse-1.3-2/gdverse/inst/doc/rgdrid.html | 26 gdverse-1.3-2/gdverse/inst/doc/sesu.Rmd | 18 gdverse-1.3-2/gdverse/inst/doc/sesu.html | 48 gdverse-1.3-2/gdverse/inst/doc/shegd.Rmd | 403 +++-- gdverse-1.3-2/gdverse/inst/doc/shegd.html | 87 - gdverse-1.3-2/gdverse/inst/doc/spade.Rmd | 20 gdverse-1.3-2/gdverse/inst/doc/spade.html | 78 - gdverse-1.3-2/gdverse/man/cpsd_disc.Rd | 29 gdverse-1.3-2/gdverse/man/factor_detector.Rd | 9 gdverse-1.3-2/gdverse/man/figures/gd/fd-1.png |binary gdverse-1.3-2/gdverse/man/figures/gd/gd_all-1.png |binary gdverse-1.3-2/gdverse/man/figures/idsa/idsa_modeling-1.png |binary gdverse-1.3-2/gdverse/man/figures/opgd/opgd_plot-1.png |binary gdverse-1.3-2/gdverse/man/figures/rgdrid/rgd_id-1.png |binary gdverse-1.3-2/gdverse/man/figures/rgdrid/rid_plot-1.png |binary gdverse-1.3-2/gdverse/man/figures/shegd/gozh_bi-1.png |binary gdverse-1.3-2/gdverse/man/figures/shegd/gozh_uni-1.png |binary gdverse-1.3-2/gdverse/man/figures/shegd/lesh-1.png |binary gdverse-1.3-2/gdverse/man/figures/shegd/lesh_only-1.png |binary gdverse-1.3-2/gdverse/man/figures/shegd/lesh_own-1.png |binary gdverse-1.3-2/gdverse/man/figures/spade/spade-1.png |binary gdverse-1.3-2/gdverse/man/gd.Rd | 2 gdverse-1.3-2/gdverse/man/gd_optunidisc.Rd |only gdverse-1.3-2/gdverse/man/gen_permutations.Rd |only gdverse-1.3-2/gdverse/man/geodetector.Rd | 2 gdverse-1.3-2/gdverse/man/gozh.Rd | 2 gdverse-1.3-2/gdverse/man/gozh_detector.Rd | 4 gdverse-1.3-2/gdverse/man/idsa.Rd | 5 gdverse-1.3-2/gdverse/man/lesh.Rd | 2 gdverse-1.3-2/gdverse/man/opgd.Rd | 4 gdverse-1.3-2/gdverse/man/plot.factor_detector.Rd | 4 gdverse-1.3-2/gdverse/man/rgd.Rd | 2 gdverse-1.3-2/gdverse/man/rid.Rd | 2 gdverse-1.3-2/gdverse/man/risk_detector.Rd | 5 gdverse-1.3-2/gdverse/man/robust_disc.Rd | 12 gdverse-1.3-2/gdverse/man/sesu_gozh.Rd | 3 gdverse-1.3-2/gdverse/man/sesu_opgd.Rd | 3 gdverse-1.3-2/gdverse/man/spade.Rd | 2 gdverse-1.3-2/gdverse/man/spd_lesh.Rd | 4 gdverse-1.3-2/gdverse/man/srs_geodetector.Rd | 2 gdverse-1.3-2/gdverse/man/srsgd.Rd | 2 gdverse-1.3-2/gdverse/vignettes/consistency.Rmd |only gdverse-1.3-2/gdverse/vignettes/consistency.Rmd.orig |only gdverse-1.3-2/gdverse/vignettes/gd.Rmd | 879 ++++++------- gdverse-1.3-2/gdverse/vignettes/gd.Rmd.orig | 2 gdverse-1.3-2/gdverse/vignettes/idsa.Rmd | 22 gdverse-1.3-2/gdverse/vignettes/idsa.Rmd.orig | 2 gdverse-1.3-2/gdverse/vignettes/opgd.Rmd | 432 +++--- gdverse-1.3-2/gdverse/vignettes/opgd.Rmd.orig | 17 gdverse-1.3-2/gdverse/vignettes/precompile.R | 3 gdverse-1.3-2/gdverse/vignettes/rgdrid.Rmd | 11 gdverse-1.3-2/gdverse/vignettes/rgdrid.Rmd.orig | 7 gdverse-1.3-2/gdverse/vignettes/sesu.Rmd | 18 gdverse-1.3-2/gdverse/vignettes/sesu.Rmd.orig | 2 gdverse-1.3-2/gdverse/vignettes/shegd.Rmd | 403 +++-- gdverse-1.3-2/gdverse/vignettes/shegd.Rmd.orig | 2 gdverse-1.3-2/gdverse/vignettes/spade.Rmd | 20 gdverse-1.3-2/gdverse/vignettes/spade.Rmd.orig | 2 96 files changed, 3259 insertions(+), 3045 deletions(-)
Title: Super Learner for Survival Prediction from Censored Data
Description: Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.
Author: Yohann Foucher [aut, cre] ,
Camille Sabathe [aut]
Maintainer: Yohann Foucher <yohann.foucher@univ-poitiers.fr>
Diff between survivalSL versions 0.97 dated 2025-01-29 and 0.97.1 dated 2025-02-17
DESCRIPTION | 6 +- MD5 | 46 ++++++++--------- R/LIB_AFTgamma.R | 2 R/LIB_AFTggamma.R | 2 R/LIB_AFTllogis.R | 2 R/LIB_AFTweibull.R | 2 R/LIB_COXall.R | 2 R/LIB_PHexponential.R | 2 R/LIB_PHgompertz.R | 2 R/LIB_PHspline.R | 2 R/survivalSL.R | 131 ++++++++++++++++++++++++++++---------------------- R/tuneCOXen.R | 15 ++++- R/tuneCOXlasso.R | 17 ++++-- R/tuneCOXridge.R | 14 ++++- R/tunePHspline.R | 9 ++- R/tunePLANN.R | 8 ++- R/tuneSNN.R | 8 ++- man/survivalSL.Rd | 11 ++-- man/tuneCOXen.Rd | 11 ++-- man/tuneCOXlasso.Rd | 12 ++-- man/tuneCOXridge.Rd | 7 +- man/tunePHspline.Rd | 5 + man/tunePLANN.Rd | 5 + man/tuneSNN.Rd | 7 +- 24 files changed, 197 insertions(+), 131 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] ,
Danielle Navarro [aut] ,
Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between rstanemax versions 0.1.8 dated 2025-02-05 and 0.1.9 dated 2025-02-17
DESCRIPTION | 8 +- MD5 | 34 ++++---- NAMESPACE | 7 + NEWS.md | 6 + R/log_lik.R |only R/posterior_predict.R | 62 ++++++++++------ R/rstanemax-package.R | 1 R/yyy.R | 5 + README.md | 33 +++++--- build/vignette.rds |binary inst/doc/emaxmodel.html | 108 ++++++++++++++-------------- man/figures/README-unnamed-chunk-3-1.png |binary man/log_lik.Rd |only man/posterior_predict.Rd | 12 ++- src/Makevars.win |only tests/testthat/test-log_lik.R |only tests/testthat/test-set_prior.R | 6 - tests/testthat/test-stan_emax.R | 4 + tests/testthat/test-stan_emax_binary.R | 9 ++ tests/testthat/test-tidybayes_integration.R | 16 +--- 20 files changed, 180 insertions(+), 131 deletions(-)
Title: Fit Log-Ratio Lasso Regression for Compositional Data
Description: Log-ratio Lasso regression for continuous, binary, and survival outcomes with (longitudinal) compositional features. See Fei and others (2024) <doi:10.1016/j.crmeth.2024.100899>.
Author: Teng Fei [aut, cre, cph] ,
Tyler Funnell [aut] ,
Nicholas Waters [aut] ,
Sandeep Raj [aut]
Maintainer: Teng Fei <feit1@mskcc.org>
Diff between FLORAL versions 0.3.0 dated 2024-08-20 and 0.4.0 dated 2025-02-17
DESCRIPTION | 14 MD5 | 53 NAMESPACE | 77 NEWS.md | 10 R/FLORAL.R | 2280 +++++----- R/LogRatioGEE.R | 111 R/RcppExports.R | 94 R/coxsplit.R | 43 R/simu.R | 1032 ++-- R/utils.R |only README.md | 364 - build/vignette.rds |binary inst/WORDLIST | 86 inst/doc/Using-FLORAL-for-Microbiome-Analysis.R | 162 inst/doc/Using-FLORAL-for-Microbiome-Analysis.Rmd | 322 - inst/doc/Using-FLORAL-for-Microbiome-Analysis.html | 1212 ++--- inst/doc/Using-FLORAL-for-survival-models-with-longitudinal-microbiome-data.R | 78 inst/doc/Using-FLORAL-for-survival-models-with-longitudinal-microbiome-data.html | 885 +-- inst/doc/Using-FLORAL-with-phyloseq.R |only inst/doc/Using-FLORAL-with-phyloseq.Rmd |only inst/doc/Using-FLORAL-with-phyloseq.html |only man/FLORAL.Rd | 9 man/a.FLORAL.Rd | 3 man/mcv.FLORAL.Rd | 3 man/phy_to_floral_data.Rd |only man/simu.Rd | 20 src/pgee.cpp | 34 tests/spelling.R | 6 tests/testthat/test-utils.R |only vignettes/Using-FLORAL-for-Microbiome-Analysis.Rmd | 322 - vignettes/Using-FLORAL-with-phyloseq.Rmd |only 31 files changed, 3759 insertions(+), 3461 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra
Support Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
support functions like preconditioned fits
<doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate
selection.
Author: Matthew Fidler [aut, cre] ,
Vipul Mann [aut],
Vishal Sarsani [aut] ,
Christian Bartels [ctb],
Bill Denney [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2extra versions 3.0.1 dated 2024-10-29 and 3.0.2 dated 2025-02-17
DESCRIPTION | 6 - MD5 | 14 +-- NEWS.md | 4 R/computingutil.R | 12 ++ R/profile.R | 11 ++ README.md | 223 +++++----------------------------------------------- inst/tools/build.R | 20 +++- man/profileFixed.Rd | 3 8 files changed, 70 insertions(+), 223 deletions(-)
Title: Ergonomic Methods for Assessing Spatial Models
Description: Assessing predictive models of spatial data can be
challenging, both because these models are typically built for
extrapolating outside the original region represented by training data
and due to potential spatially structured errors, with "hot spots" of
higher than expected error clustered geographically due to spatial
structure in the underlying data. Methods are provided for assessing
models fit to spatial data, including approaches for measuring the
spatial structure of model errors, assessing model predictions at
multiple spatial scales, and evaluating where predictions can be made
safely. Methods are particularly useful for models fit using the
'tidymodels' framework. Methods include Moran's I ('Moran' (1950)
<doi:10.2307/2332142>), Geary's C ('Geary' (1954)
<doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from
'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement
m [...truncated...]
Author: Michael Mahoney [aut, cre] ,
Lucas Johnson [ctb] ,
Virgilio Gomez-Rubio [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/571>),
Jakub Nowosad [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/571 [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between waywiser versions 0.6.0 dated 2024-06-27 and 0.6.1 dated 2025-02-16
waywiser-0.6.0/waywiser/tests/testthat/_snaps/multi_scale.md |only waywiser-0.6.1/waywiser/DESCRIPTION | 8 - waywiser-0.6.1/waywiser/MD5 | 69 ++++------ waywiser-0.6.1/waywiser/NEWS.md | 6 waywiser-0.6.1/waywiser/R/multi_scale.R | 2 waywiser-0.6.1/waywiser/R/tidy_importance.R | 3 waywiser-0.6.1/waywiser/build/partial.rdb |binary waywiser-0.6.1/waywiser/build/vignette.rds |binary waywiser-0.6.1/waywiser/inst/doc/multi-scale-assessment.html | 12 - waywiser-0.6.1/waywiser/inst/doc/residual-autocorrelation.html | 6 waywiser-0.6.1/waywiser/inst/doc/waywiser.html | 56 ++++---- waywiser-0.6.1/waywiser/inst/srr_template_spatial_yardstick.R | 66 ++++++--- waywiser-0.6.1/waywiser/man/figures/README-unnamed-chunk-5-1.png |binary waywiser-0.6.1/waywiser/tests/testthat/_snaps/area_of_applicability.md | 18 +- waywiser-0.6.1/waywiser/tests/testthat/_snaps/misc.md | 9 + waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_global_geary_c.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_global_geary_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_global_moran_i.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_global_moran_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_geary_c.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_geary_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_getis_ord_g.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_getis_ord_g_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_moran_i.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/_snaps/srr-ww_local_moran_pvalue.md | 31 ++++ waywiser-0.6.1/waywiser/tests/testthat/test-multi_scale.R | 5 waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_global_geary_c.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_global_geary_pvalue.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_global_moran_i.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_global_moran_pvalue.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_geary_c.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_geary_pvalue.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_getis_ord_g.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_getis_ord_g_pvalue.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_moran_i.R | 66 ++++++--- waywiser-0.6.1/waywiser/tests/testthat/test-srr-ww_local_moran_pvalue.R | 66 ++++++--- 36 files changed, 948 insertions(+), 282 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 1.2.0 dated 2025-01-07 and 1.2.1 dated 2025-02-16
DESCRIPTION | 8 ++-- MD5 | 75 ++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS.md | 6 +++ R/CD.R | 28 +++++++------- R/CDF.R | 60 +++++++++++++++++++------------- R/EFAhclust.R | 16 ++++---- R/EFAindex.R | 4 +- R/EFAkmeans.R | 16 ++++---- R/EFAscreet.R | 4 +- R/EFAvote.R | 2 - R/EKC.R | 20 +++++----- R/GenData.R | 7 ++- R/Hull.R | 20 +++++----- R/KGC.R | 16 ++++---- R/PA.R | 20 +++++----- R/extractor.feature.DNN.R | 4 +- R/extractor.feature.FF.R | 32 +++++++++++++---- R/factor.analysis.R | 26 +++++++++---- man/CD.Rd | 28 +++++++------- man/CDF.Rd | 6 ++- man/EFAhclust.Rd | 16 ++++---- man/EFAindex.Rd | 4 +- man/EFAkmeans.Rd | 16 ++++---- man/EFAscreet.Rd | 4 +- man/EFAvote.Rd | 2 - man/EKC.Rd | 20 +++++----- man/GenData.Rd | 4 +- man/Hull.Rd | 20 +++++----- man/KGC.Rd | 16 ++++---- man/PA.Rd | 20 +++++----- man/extractor.feature.DNN.Rd | 4 +- man/extractor.feature.FF.Rd | 4 +- man/factor.analysis.Rd | 16 ++++---- src/Makevars | 2 - src/Makevars.win | 2 - tests/building.R | 2 - tests/testthat/demo_simulate.R | 14 +++---- tests/testthat/demo_simulate2.R |only 39 files changed, 306 insertions(+), 259 deletions(-)
Title: Statistical Learning on Sparse Matrices
Description: Implements many algorithms for statistical learning on
sparse matrices - matrix factorizations, matrix completion,
elastic net regressions, factorization machines.
Also 'rsparse' enhances 'Matrix' package by providing methods for
multithreaded <sparse, dense> matrix products and native slicing of
the sparse matrices in Compressed Sparse Row (CSR) format.
List of the algorithms for regression problems:
1) Elastic Net regression via Follow The Proximally-Regularized Leader (FTRL)
Stochastic Gradient Descent (SGD), as per McMahan et al(, <doi:10.1145/2487575.2488200>)
2) Factorization Machines via SGD, as per Rendle (2010, <doi:10.1109/ICDM.2010.127>)
List of algorithms for matrix factorization and matrix completion:
1) Weighted Regularized Matrix Factorization (WRMF) via Alternating Least
Squares (ALS) - paper by Hu, Koren, Volinsky (2008, <doi:10.1109/ICDM.2008.22>)
2) Maximum-Margin Matrix Factorization via ALS, paper by Rennie, Srebro
(2005, <doi:10.1145/110 [...truncated...]
Author: Dmitriy Selivanov [aut, cre, cph]
,
David Cortes [ctb],
Drew Schmidt [ctb] ,
Wei-Chen Chen [ctb]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between rsparse versions 0.5.2 dated 2024-06-28 and 0.5.3 dated 2025-02-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/model_LinearFlow.R | 1 - R/zzz.R | 24 ++++++++++-------------- README.md | 4 ++-- man/LinearFlow.Rd | 1 - src/utils.cpp | 4 ++-- 7 files changed, 23 insertions(+), 29 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing sparse priors to
impose exact sparsity leads to efficient Bayesian shrinkage estimation, variable
selection and statistical inference. In this package, we have implemented robust
Bayesian variable selection with spike-and-slab priors under high-dimensional
linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and
Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying
coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular,
valid robust Bayesian inferences under both models in the presence of heavy-tailed errors
can be validated on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms
of the proposed and alternative models are implemented in C++.
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.0.5 dated 2025-02-05 and 1.1.0 dated 2025-02-16
pqrBayes-1.0.5/pqrBayes/R/Robust.R |only pqrBayes-1.0.5/pqrBayes/R/select.VC.R |only pqrBayes-1.0.5/pqrBayes/man/print.VCselect.Rd |only pqrBayes-1.0.5/pqrBayes/man/select.VC.Rd |only pqrBayes-1.1.0/pqrBayes/DESCRIPTION | 28 - pqrBayes-1.1.0/pqrBayes/MD5 | 68 ++- pqrBayes-1.1.0/pqrBayes/NAMESPACE | 24 - pqrBayes-1.1.0/pqrBayes/NEWS.md |only pqrBayes-1.1.0/pqrBayes/R/NonRobust.R | 150 ++++---- pqrBayes-1.1.0/pqrBayes/R/NonRobust_vc.R |only pqrBayes-1.1.0/pqrBayes/R/RcppExports.R | 16 pqrBayes-1.1.0/pqrBayes/R/Robust_vc.R |only pqrBayes-1.1.0/pqrBayes/R/coverage.R | 62 --- pqrBayes-1.1.0/pqrBayes/R/coverage_lin.R |only pqrBayes-1.1.0/pqrBayes/R/coverage_vc.R |only pqrBayes-1.1.0/pqrBayes/R/data.R | 40 +- pqrBayes-1.1.0/pqrBayes/R/estimation.R | 107 +----- pqrBayes-1.1.0/pqrBayes/R/estimation_lin.R |only pqrBayes-1.1.0/pqrBayes/R/estimation_vc.R |only pqrBayes-1.1.0/pqrBayes/R/nonrobust_lin.R |only pqrBayes-1.1.0/pqrBayes/R/pqrBayes-package.R | 120 +++--- pqrBayes-1.1.0/pqrBayes/R/pqrBayes.R | 194 ++++++----- pqrBayes-1.1.0/pqrBayes/R/pqrBayes_lin.R |only pqrBayes-1.1.0/pqrBayes/R/pqrBayes_vc.R |only pqrBayes-1.1.0/pqrBayes/R/predict.pqrBayes.R | 152 ++------ pqrBayes-1.1.0/pqrBayes/R/predict_lin.R |only pqrBayes-1.1.0/pqrBayes/R/predict_vc.R |only pqrBayes-1.1.0/pqrBayes/R/print.pqrBayes.R | 105 +++-- pqrBayes-1.1.0/pqrBayes/R/robust_lin.R |only pqrBayes-1.1.0/pqrBayes/R/select.pqrBayes.R |only pqrBayes-1.1.0/pqrBayes/R/select_lin.R |only pqrBayes-1.1.0/pqrBayes/R/select_vc.R |only pqrBayes-1.1.0/pqrBayes/README.md | 334 +++++++++++-------- pqrBayes-1.1.0/pqrBayes/data/data.rda |binary pqrBayes-1.1.0/pqrBayes/man/coverage.Rd | 18 - pqrBayes-1.1.0/pqrBayes/man/data.Rd | 36 +- pqrBayes-1.1.0/pqrBayes/man/estimation.pqrBayes.Rd | 20 - pqrBayes-1.1.0/pqrBayes/man/pqrBayes-package.Rd | 24 - pqrBayes-1.1.0/pqrBayes/man/pqrBayes.Rd | 76 ++-- pqrBayes-1.1.0/pqrBayes/man/predict.pqrBayes.Rd | 33 - pqrBayes-1.1.0/pqrBayes/man/print.pqrBayes.Rd | 6 pqrBayes-1.1.0/pqrBayes/man/print.pqrBayes.select.Rd |only pqrBayes-1.1.0/pqrBayes/man/select.pqrBayes.Rd |only pqrBayes-1.1.0/pqrBayes/src/BL.cpp |only pqrBayes-1.1.0/pqrBayes/src/BLSS.cpp |only pqrBayes-1.1.0/pqrBayes/src/BQL.cpp |only pqrBayes-1.1.0/pqrBayes/src/BQLSS.cpp |only pqrBayes-1.1.0/pqrBayes/src/RcppExports.cpp | 114 ++++++ 48 files changed, 907 insertions(+), 820 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Jose Carlos [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.23 dated 2024-11-24 and 3.29 dated 2025-02-16
DESCRIPTION | 8 - MD5 | 48 +++++----- NAMESPACE | 5 - NEWS | 118 +++++++++++++++++++++++++ R/AUC.R | 70 ++++++++------- R/Boyce.R | 231 +++++++++++++++++++++++++------------------------- R/MillerCalib.R | 88 +++++++++---------- R/RsqGLM.R | 7 - R/lollipop.R | 93 ++++++++++++++------ R/optiPair.R | 141 +++++++++++++++--------------- R/optiThresh.R | 22 +--- R/plotCoeffs.R |only R/similarity.R | 4 R/threshMeasures.R | 6 - R/varImp.R | 151 +++++++++++++++++--------------- man/AUC.Rd | 4 man/Boyce.Rd | 160 +++++++++++++++++----------------- man/MillerCalib.Rd | 186 ++++++++++++++++++++-------------------- man/RMSE.Rd | 114 ++++++++++++------------ man/evaluate.Rd | 10 +- man/lollipop.Rd | 42 +++++---- man/modEvA-package.Rd | 4 man/optiPair.Rd | 165 ++++++++++++++++++----------------- man/optiThresh.Rd | 178 +++++++++++++++++++------------------- man/plotCoeffs.Rd |only man/varImp.Rd | 4 26 files changed, 1028 insertions(+), 831 deletions(-)
Title: Construct and Visualize TDA Mapper Graphs
Description: Topological data analysis (TDA) is a method of data analysis that
uses techniques from topology to analyze high-dimensional data. Here we
implement Mapper, an algorithm from this area developed by Singh, Mémoli and
Carlsson (2007) which generalizes the concept of a
Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.
Author: George Clare Kennedy [aut, cre]
Maintainer: George Clare Kennedy <george-clarekennedy@uiowa.edu>
Diff between mappeR versions 1.3.0 dated 2024-10-30 and 2.0.0 dated 2025-02-16
mappeR-1.3.0/mappeR/R/stats_hub.R |only mappeR-1.3.0/mappeR/man/run_cluster_machine.Rd |only mappeR-1.3.0/mappeR/man/run_mapper.Rd |only mappeR-2.0.0/mappeR/DESCRIPTION | 6 mappeR-2.0.0/mappeR/LICENSE | 4 mappeR-2.0.0/mappeR/MD5 | 95 - mappeR-2.0.0/mappeR/NAMESPACE | 45 mappeR-2.0.0/mappeR/NEWS.md | 93 + mappeR-2.0.0/mappeR/R/art_studio.R | 112 +- mappeR-2.0.0/mappeR/R/baskin_robbins.R | 294 +++--- mappeR-2.0.0/mappeR/R/cartography_chamber.R | 530 +++++----- mappeR-2.0.0/mappeR/R/cluster_factory.R | 421 ++++---- mappeR-2.0.0/mappeR/R/clusterer_farm.R |only mappeR-2.0.0/mappeR/R/mappeR-package.R | 36 mappeR-2.0.0/mappeR/R/quilting_hut.R | 278 ++--- mappeR-2.0.0/mappeR/R/viewmaster-library.R | 56 - mappeR-2.0.0/mappeR/README.md | 586 ++++++------ mappeR-2.0.0/mappeR/man/assemble_mapper_object.Rd |only mappeR-2.0.0/mappeR/man/check_in_interval.Rd | 34 mappeR-2.0.0/mappeR/man/compute_tightness.Rd | 44 mappeR-2.0.0/mappeR/man/convert_to_clusters.Rd | 34 mappeR-2.0.0/mappeR/man/create_1D_mapper_object.Rd | 91 - mappeR-2.0.0/mappeR/man/create_ball_mapper_object.Rd | 58 - mappeR-2.0.0/mappeR/man/create_balls.Rd | 72 - mappeR-2.0.0/mappeR/man/create_bins.Rd | 42 mappeR-2.0.0/mappeR/man/create_clusterball_mapper_object.Rd | 83 - mappeR-2.0.0/mappeR/man/create_mapper_object.Rd | 112 +- mappeR-2.0.0/mappeR/man/create_single_bin.Rd | 42 mappeR-2.0.0/mappeR/man/create_width_balanced_cover.Rd | 70 - mappeR-2.0.0/mappeR/man/cut_dendrogram.Rd | 44 mappeR-2.0.0/mappeR/man/eccentricity_filter.Rd | 60 - mappeR-2.0.0/mappeR/man/get_bin_vector.Rd | 34 mappeR-2.0.0/mappeR/man/get_cluster_sizes.Rd | 34 mappeR-2.0.0/mappeR/man/get_cluster_tightness_vector.Rd | 38 mappeR-2.0.0/mappeR/man/get_clustered_data.Rd | 34 mappeR-2.0.0/mappeR/man/get_clusters.Rd | 44 mappeR-2.0.0/mappeR/man/get_edge_weights.Rd | 48 mappeR-2.0.0/mappeR/man/get_hierarchical_clusters.Rd | 40 mappeR-2.0.0/mappeR/man/get_raw_clusters.Rd |only mappeR-2.0.0/mappeR/man/get_tallest_branch.Rd | 34 mappeR-2.0.0/mappeR/man/hierarchical_clusterer.Rd |only mappeR-2.0.0/mappeR/man/is_in_ball.Rd | 34 mappeR-2.0.0/mappeR/man/mappeR-package.Rd | 46 mappeR-2.0.0/mappeR/man/mapper_object_to_igraph.Rd | 56 - mappeR-2.0.0/mappeR/man/process_dendrograms.Rd | 44 mappeR-2.0.0/mappeR/man/run_link.Rd | 38 mappeR-2.0.0/mappeR/man/subset_dists.Rd | 38 mappeR-2.0.0/mappeR/tests/testthat.R | 24 mappeR-2.0.0/mappeR/tests/testthat/test-binning.R | 50 - mappeR-2.0.0/mappeR/tests/testthat/test-covering.R | 176 +-- mappeR-2.0.0/mappeR/tests/testthat/test-igraph.R | 12 mappeR-2.0.0/mappeR/tests/testthat/test-inputs.R | 112 +- 52 files changed, 2143 insertions(+), 2135 deletions(-)
Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi'
(<https://www.jamovi.org>) aims to make statistical analyses easy and
intuitive. 'jamovi' produces syntax that can directly be used in R (in
connection with the R-package 'jmv'). Having import / export routines for
the data files 'jamovi' produces ('.omv') permits an easy transfer of
data and analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre, cph]
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>
Diff between jmvReadWrite versions 0.4.9 dated 2025-01-16 and 0.4.10 dated 2025-02-16
DESCRIPTION | 6 MD5 | 24 +-- NEWS.md | 12 + R/describe_omv.R | 195 ++++++++++++++------------- R/globals.R | 94 ++++++++++--- R/read_omv.R | 279 +++++++++++++++++++--------------------- R/write_omv.R | 147 +++++++++------------ README.md | 4 inst/CITATION | 2 inst/doc/jmvReadWrite.html | 8 - tests/testthat/test-globals.R | 39 ++++- tests/testthat/test-read_omv.R | 163 +++++++++++++++++------ tests/testthat/test-write_omv.R | 94 ++++++++++++- 13 files changed, 653 insertions(+), 414 deletions(-)
Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant
to the activities of the Commission for the Conservation of Antarctic Marine Living
Resources. Provides two categories of functions: load functions and create functions.
Load functions are used to import existing spatial layers from the online CCAMLR GIS
such as the ASD boundaries. Create functions are used to create layers from user data
such as polygons and grids.
Author: Stephane Thanassekos [aut, cre],
Keith Reid [aut],
Lucy Robinson [aut],
Michael D. Sumner [ctb],
Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <stephane.thanassekos@ccamlr.org>
Diff between CCAMLRGIS versions 4.2.0 dated 2024-10-15 and 4.2.1 dated 2025-02-16
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 7 +++++++ R/add_Cscale.R | 2 +- R/add_col.R | 4 ++-- R/add_labels.R | 2 +- R/create_Arrow.R | 5 +++++ R/load.R | 1 + README.md | 2 +- build/vignette.rds |binary data/Coast.RData |binary inst/doc/CCAMLRGIS.html | 4 ++-- man/add_Cscale.Rd | 2 +- man/add_col.Rd | 4 ++-- man/add_labels.Rd | 2 +- 15 files changed, 42 insertions(+), 29 deletions(-)
Title: Assessment Tools for Regression Models with Discrete and
Semicontinuous Outcomes
Description: Provides assessment tools for regression models with discrete and semicontinuous outcomes proposed in Yang (2023) <doi:10.48550/arXiv.2308.15596>. It calculates the double probability integral transform (DPIT) residuals, constructs QQ plots of residuals and the ordered curve for assessing mean structures.
Author: Lu Yang [aut],
Jeonghwan Lee [cre, aut]
Maintainer: Jeonghwan Lee <lee03938@umn.edu>
Diff between assessor versions 1.1.0 dated 2024-04-03 and 1.1.1 dated 2025-02-16
assessor-1.1.0/assessor/LICENSE |only assessor-1.1.1/assessor/DESCRIPTION | 12 ++++++------ assessor-1.1.1/assessor/MD5 | 6 ++++-- assessor-1.1.1/assessor/R/bballHR.R |only assessor-1.1.1/assessor/data/bballHR.rda |only assessor-1.1.1/assessor/man/bballHR.Rd |only 6 files changed, 10 insertions(+), 8 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Procedures are available for choosing models that
conform to the hierarchy or marginality principle, for fitting and choosing between
two-dimensional spatial models using correlation, natural cubic smoothing spline and
P-spline models. A history of the fitting of a sequence of models is kept in a data frame.
Also used to compute functions and contrasts of, to investigate differences between and
to plot predictions obtained using any model fitting function. The content falls into
the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model
selection and description functions, (iv) Model diagnostics and simulation functions,
(v) Prediction production and presentation functions, (vi) Response transformation
functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions
(for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.4.43 dated 2024-12-10 and 4.4.46 dated 2025-02-16
asremlPlus-4.4.43/asremlPlus/R/reml4.v11.r |only asremlPlus-4.4.43/asremlPlus/R/spatial.funcs.v10.r |only asremlPlus-4.4.43/asremlPlus/R/spatial.utilities.v3.r |only asremlPlus-4.4.46/asremlPlus/DESCRIPTION | 8 asremlPlus-4.4.46/asremlPlus/MD5 | 52 +-- asremlPlus-4.4.46/asremlPlus/R/REMLRTIC.v4.r | 14 asremlPlus-4.4.46/asremlPlus/R/asremlPlusObjUtils.r | 3 asremlPlus-4.4.46/asremlPlus/R/asremlPlusUtilities.r | 93 ++++- asremlPlus-4.4.46/asremlPlus/R/choose.r | 2 asremlPlus-4.4.46/asremlPlus/R/psplineUtilities.v2.R | 2 asremlPlus-4.4.46/asremlPlus/R/reml4.v13.r |only asremlPlus-4.4.46/asremlPlus/R/spatial.funcs.v11.r |only asremlPlus-4.4.46/asremlPlus/R/spatial.utilities.v4.r |only asremlPlus-4.4.46/asremlPlus/build/partial.rdb |binary asremlPlus-4.4.46/asremlPlus/inst/NEWS.Rd | 18 + asremlPlus-4.4.46/asremlPlus/inst/doc/LadybirdEMMs.asreml.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/LadybirdEMMs.lm.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/Wheat.analysis.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/Wheat.infoCriteria.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/WheatSpatialModels.pdf |binary asremlPlus-4.4.46/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-4.4.46/asremlPlus/man/newfit.asreml.Rd | 16 asremlPlus-4.4.46/asremlPlus/man/setvarianceterms.call.Rd | 28 + asremlPlus-4.4.46/asremlPlus/tests/testthat/data/summ703.rda |binary asremlPlus-4.4.46/asremlPlus/tests/testthat/test42EstimateV.r | 36 +- asremlPlus-4.4.46/asremlPlus/tests/testthat/test42GeneticCane.R | 19 - asremlPlus-4.4.46/asremlPlus/tests/testthat/test42REMLRTIC.r | 2 asremlPlus-4.4.46/asremlPlus/tests/testthat/test42Selection.r | 117 +++++- asremlPlus-4.4.46/asremlPlus/tests/testthat/test42SpatialModels.r | 172 +++++++--- asremlPlus-4.4.46/asremlPlus/tests/testthat/test42WheatSpatialVignette.r | 6 30 files changed, 426 insertions(+), 162 deletions(-)
Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model. Diagnostics
are run at the database, code list, cohort, and population level to assess
whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Marta Alcalde-Herraiz [aut] ,
Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between PhenotypeR versions 0.1.2 dated 2025-02-05 and 0.1.3 dated 2025-02-16
DESCRIPTION | 8 - MD5 | 40 ++--- inst/doc/a01_DatabaseDiagnostics.R | 2 inst/doc/a01_DatabaseDiagnostics.Rmd | 2 inst/doc/a01_DatabaseDiagnostics.html | 224 +++++++++++++++---------------- inst/doc/a02_CodelistDiagnostics.R | 2 inst/doc/a02_CodelistDiagnostics.Rmd | 2 inst/doc/a02_CodelistDiagnostics.html | 228 ++++++++++++++++---------------- inst/doc/a03_CohortDiagnostics.R | 2 inst/doc/a03_CohortDiagnostics.Rmd | 2 inst/doc/a03_CohortDiagnostics.html | 220 +++++++++++++++--------------- inst/doc/a04_MatchedDiagnostics.R | 2 inst/doc/a04_MatchedDiagnostics.Rmd | 2 inst/doc/a05_PopulationDiagnostics.R | 2 inst/doc/a05_PopulationDiagnostics.Rmd | 2 inst/doc/a05_PopulationDiagnostics.html | 226 +++++++++++++++---------------- vignettes/a01_DatabaseDiagnostics.Rmd | 2 vignettes/a02_CodelistDiagnostics.Rmd | 2 vignettes/a03_CohortDiagnostics.Rmd | 2 vignettes/a04_MatchedDiagnostics.Rmd | 2 vignettes/a05_PopulationDiagnostics.Rmd | 2 21 files changed, 488 insertions(+), 488 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library for reliable, high-performance messaging over in-process,
IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability
Protocols', a standard for common communications patterns including
publish/subscribe, request/reply and service discovery. As its own threaded
concurrency framework, provides a toolkit for asynchronous programming and
distributed computing. Intuitive 'aio' objects resolve automatically when
asynchronous operations complete, and synchronisation primitives allow R to
wait upon events signalled by concurrent threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 1.5.0 dated 2025-01-27 and 1.5.1 dated 2025-02-16
nanonext-1.5.0/nanonext/cleanup.ucrt |only nanonext-1.5.0/nanonext/configure.ucrt |only nanonext-1.5.0/nanonext/src/Makevars.ucrt |only nanonext-1.5.0/nanonext/src/Makevars.win |only nanonext-1.5.1/nanonext/DESCRIPTION | 8 - nanonext-1.5.1/nanonext/MD5 | 64 +++++----- nanonext-1.5.1/nanonext/NAMESPACE | 1 nanonext-1.5.1/nanonext/NEWS.md | 10 + nanonext-1.5.1/nanonext/R/aio.R | 4 nanonext-1.5.1/nanonext/R/context.R | 4 nanonext-1.5.1/nanonext/R/listdial.R | 8 - nanonext-1.5.1/nanonext/R/nanonext-package.R | 10 + nanonext-1.5.1/nanonext/R/stream.R | 16 ++ nanonext-1.5.1/nanonext/R/sync.R | 60 --------- nanonext-1.5.1/nanonext/README.md | 20 +-- nanonext-1.5.1/nanonext/cleanup.win |only nanonext-1.5.1/nanonext/configure | 6 nanonext-1.5.1/nanonext/configure.win |only nanonext-1.5.1/nanonext/man/dial.Rd | 4 nanonext-1.5.1/nanonext/man/listen.Rd | 4 nanonext-1.5.1/nanonext/man/lock.Rd | 48 ------- nanonext-1.5.1/nanonext/man/pipe_notify.Rd | 14 -- nanonext-1.5.1/nanonext/man/recv_aio.Rd | 4 nanonext-1.5.1/nanonext/man/reply.Rd | 4 nanonext-1.5.1/nanonext/man/stream.Rd | 18 ++ nanonext-1.5.1/nanonext/src/aio.c | 26 ++-- nanonext-1.5.1/nanonext/src/comms.c | 34 ++--- nanonext-1.5.1/nanonext/src/init.c | 4 nanonext-1.5.1/nanonext/src/nanonext.h | 11 - nanonext-1.5.1/nanonext/src/ncurl.c | 10 - nanonext-1.5.1/nanonext/src/nng-110.tar.xz |binary nanonext-1.5.1/nanonext/src/proto.c | 21 +-- nanonext-1.5.1/nanonext/src/sync.c | 163 +++------------------------ nanonext-1.5.1/nanonext/src/thread.c | 6 nanonext-1.5.1/nanonext/src/utils.c | 34 ++--- nanonext-1.5.1/nanonext/tests/tests.R | 35 ----- 36 files changed, 217 insertions(+), 434 deletions(-)
Title: Regularized Joint Assignment Forest with Treatment Arm
Clustering
Description: Personalized assignment to one of many treatment arms via regularized and clustered joint assignment forests as described in Ladhania, Spiess, Ungar, and Wu (2023) <doi:10.48550/arXiv.2311.00577>. The algorithm pools information across treatment arms: it considers a regularized forest-based assignment algorithm based on greedy recursive partitioning that shrinks effect estimates across arms; and it incorporates a clustering scheme that combines treatment arms with consistently similar outcomes.
Author: Wenbo Wu [aut, cph] ,
Xinyi Zhang [aut, cre, cph] ,
Jann Spiess [aut, cph] ,
Rahul Ladhania [aut, cph]
Maintainer: Xinyi Zhang <zhang.xinyi@nyu.edu>
Diff between rjaf versions 0.1.1 dated 2024-12-08 and 0.1.2 dated 2025-02-16
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 1 + R/residualize.R | 9 +++++---- R/rjaf.R | 40 +++++++++++++++++++++++++++------------- man/residualize.Rd | 7 ++++--- man/rjaf.Rd | 15 +++++++++------ src/rjaf.cpp | 10 ++++++++-- tests/testthat/test-rjaf.R | 2 +- 9 files changed, 66 insertions(+), 40 deletions(-)
Title: R Wrapper for the 'Bit.ly' and 'Is.gd'/'v.gd' URL Shortening
Services
Description: Allows using two URL shortening services, which also provide
expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth 2.0) and 'is.gd' (no API key).
Author: John Malc [aut, cre] ,
Andrea Dodet [ctb] ,
Stephen Synchronicity [ctb]
Maintainer: John Malc <cincenko@outlook.com>
Diff between urlshorteneR versions 1.5.7 dated 2022-08-22 and 1.6.0 dated 2025-02-16
urlshorteneR-1.5.7/urlshorteneR/tests/testthat/test-GitHubIssue9.R |only urlshorteneR-1.6.0/urlshorteneR/DESCRIPTION | 24 - urlshorteneR-1.6.0/urlshorteneR/MD5 | 9 urlshorteneR-1.6.0/urlshorteneR/NEWS | 2 urlshorteneR-1.6.0/urlshorteneR/build/vignette.rds |binary urlshorteneR-1.6.0/urlshorteneR/inst/doc/Tutorial.html | 208 +++++----- 6 files changed, 125 insertions(+), 118 deletions(-)
Title: Access to Global Sub-National Income Data
Description: Provides access to granular sub-national income data from the
MCC-PIK Database Of Sub-national Economic Output (DOSE). The package
downloads and processes the data from its open repository on 'Zenodo'
(<https://zenodo.org/records/13773040>). Functions are provided to
fetch data at multiple geographic levels, match coordinates to
administrative regions, and access associated geometries.
Author: Pablo Garcia Guzman [aut, cre, cph]
Maintainer: Pablo Garcia Guzman <garciagp@ebrd.com>
Diff between subincomeR versions 0.2.2 dated 2024-12-19 and 0.3.0 dated 2025-02-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/getDOSE.R | 4 ++-- README.md | 13 ++++++++++++- inst/doc/regional-convergence.html | 8 ++++---- man/figures/map.png |binary 7 files changed, 35 insertions(+), 16 deletions(-)
Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde-Herraiz [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Xihang Chen [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortConstructor versions 0.3.4 dated 2025-01-17 and 0.3.5 dated 2025-02-16
DESCRIPTION | 10 MD5 | 118 - NAMESPACE | 2 R/benchmark.R |only R/collapseCohorts.R | 207 +-- R/conceptCohort.R | 1182 ++++++++--------- R/copyCohorts.R |only R/demographicsCohort.R | 139 +- R/exitAtColumnDate.R | 580 ++++---- R/exitAtDate.R | 444 +++--- R/intersectCohorts.R | 1086 ++++++++-------- R/matchCohorts.R | 863 ++++++------ R/measurementCohort.R | 566 ++++---- R/padCohortDate.R | 646 ++++----- R/requireCohortIntersect.R | 355 ++--- R/requireConceptIntersect.R | 43 R/requireDateRange.R | 430 +++--- R/requireDeathFlag.R | 246 +-- R/requireDemographics.R | 1305 +++++++++---------- R/requireIsEntry.R | 443 +++--- R/requireMinCohortCount.R | 146 +- R/requireTableIntersect.R | 289 ++-- R/sampleCohorts.R | 167 +- R/stratifyCohorts.R | 491 +++---- R/subsetCohorts.R | 125 - R/sysdata.rda |binary R/trimDemographics.R | 833 ++++++------ R/unionCohorts.R | 208 +-- R/yearCohorts.R | 404 +++--- README.md | 4 inst/doc/a02_cohort_table_requirements.html | 20 inst/doc/a03_require_demographics.html | 20 inst/doc/a04_require_intersections.html | 20 inst/doc/a06_concatanate_cohorts.R | 13 inst/doc/a06_concatanate_cohorts.Rmd | 177 +- inst/doc/a06_concatanate_cohorts.html | 1746 +++++++------------------- inst/doc/a07_filter_cohorts.html | 24 inst/doc/a08_split_cohorts.R | 20 inst/doc/a08_split_cohorts.Rmd | 26 inst/doc/a08_split_cohorts.html | 88 - inst/doc/a09_combine_cohorts.R | 16 inst/doc/a09_combine_cohorts.Rmd | 19 inst/doc/a11_benchmark.R | 1 inst/doc/a11_benchmark.Rmd | 1 inst/doc/a11_benchmark.html | 440 +++--- man/benchmarkCohortConstructor.Rd |only man/copyCohorts.Rd |only man/measurementCohort.Rd | 2 tests/testthat/test-benchmark.R |only tests/testthat/test-collapseCohorts.R | 540 ++++---- tests/testthat/test-conceptCohort.R | 3 tests/testthat/test-copyCohorts.R |only tests/testthat/test-exitAtDate.R | 431 +++--- tests/testthat/test-measurementCohort.R | 16 tests/testthat/test-requireCohortIntersect.R | 724 +++++----- tests/testthat/test-requireConceptIntersect.R | 734 +++++----- tests/testthat/test-requireDateRange.R | 6 tests/testthat/test-requireIsEntry.R | 539 ++++---- tests/testthat/test-sampleCohorts.R | 30 vignettes/a06_concatanate_cohorts.Rmd | 177 +- vignettes/a08_split_cohorts.Rmd | 26 vignettes/a09_combine_cohorts.Rmd | 19 vignettes/a11_benchmark.Rmd | 1 63 files changed, 8334 insertions(+), 8877 deletions(-)
More information about CohortConstructor at CRAN
Permanent link
Title: Generalized Network-Based Dimensionality Reduction and Analysis
Description: Non-parametric dimensionality reduction function. Reduction with and without feature selection. Plot functions. Automated feature selections. Kosztyan et. al. (2024) <doi:10.1016/j.eswa.2023.121779>.
Author: Zsolt T. Kosztyan [aut, cre],
Marcell T. Kurbucz [aut],
Attila I. Katona [aut],
Zahid Khan [aut]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between nda versions 0.1.15 dated 2024-10-14 and 0.2.4 dated 2025-02-16
DESCRIPTION | 8 MD5 | 42 - NAMESPACE | 8 R/biplot.nda.R | 14 R/fitted.ndrlm.R |only R/nda.R | 1431 +++++++++++++++++++++++++++++++++++++++++++++++-- R/ndr.R | 65 +- R/ndrlm.R |only R/plot.nda.R | 170 ++--- R/plot.ndrlm.R |only R/predict.nda.R |only R/predict.ndrlm.R |only R/print.nda.R | 8 R/print.ndrlm.R |only R/residuals.ndrlm.R |only R/summary.nda.R | 8 R/summary.ndrlm.R |only inst/NEWS | 24 man/fitted.ndrlm.Rd |only man/fs.dmred.Rd | 4 man/nda.Rd | 5 man/ndr.Rd | 211 ++++--- man/ndrlm.Rd |only man/plot.nda.Rd | 125 ++-- man/plot.ndrlm.Rd |only man/predict.nda.Rd |only man/predict.ndrlm.Rd |only man/print.ndrlm.Rd |only man/residuals.ndrlm.Rd |only man/summary.ndrlm.Rd |only 30 files changed, 1761 insertions(+), 362 deletions(-)
Title: An Alternative 'Rcpp' Wrapper of 'MeCab'
Description: A plain 'Rcpp' wrapper for 'MeCab' that can segment Chinese,
Japanese, and Korean text into tokens. The main goal of this package
is to provide an alternative to 'tidytext' using morphological
analysis.
Author: Akiru Kato [aut, cre],
Shogo Ichinose [aut],
Taku Kudo [aut],
Jorge Nocedal [ctb],
Nippon Telegraph and Telephone Corporation [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>
Diff between gibasa versions 1.1.1 dated 2024-07-05 and 1.1.2 dated 2025-02-16
DESCRIPTION | 19 +++++----- MD5 | 42 +++++++++++----------- NEWS.md | 5 ++ R/RcppExports.R | 73 ++++++++++++++++++++++++++++---------- R/bind_tf_idf2.R | 8 ++-- R/mute_tokens.R | 2 - R/prettify.R | 2 - R/tokenize.R | 33 ++++++++++++----- R/utils.R | 11 +++-- README.md | 77 ++++++++++++----------------------------- build/partial.rdb |binary man/dictionary_info.Rd | 35 ++++++++++++++++-- man/get_transition_cost.Rd | 15 ++++--- man/gibasa-package.Rd | 2 - man/is_blank.Rd | 4 +- man/mute_tokens.Rd | 2 - man/posDebugRcpp.Rd | 12 +++--- man/posParallelRcpp.Rd | 15 ++++--- man/transition_cost.Rd | 14 ++++--- src/posDebug.cpp | 60 +++++++++++++++++++++++++------ src/posParallel.cpp | 17 +++++---- tests/testthat/test-tokenize.R | 24 +++++++++--- 22 files changed, 292 insertions(+), 180 deletions(-)
Title: Access Colombia's Public Data via 'API-Colombia'
Description: Provides a seamless interface to access diverse public data about
Colombia through the 'API-Colombia', a RESTful API. The package enables users
to explore various aspects of Colombia, including general information,
geography, and cultural insights. It includes five API-related functions to
retrieve data on topics such as Colombia's general information, airports,
departments, regions, and presidents. Additionally, 'ColombiAPI' offers a
built-in function to view the datasets available within the package. The
package also includes curated datasets covering Bogota air stations,
business and holiday dates, public schools, Colombian coffee exports,
cannabis licenses, Medellin rainfall, and malls in Bogota, making it a
comprehensive tool for exploring Colombia's data. For more details on the
'API-Colombia', see <https://api-colombia.com/>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ColombiAPI versions 0.1.0 dated 2025-01-09 and 0.1.1 dated 2025-02-16
DESCRIPTION | 8 +-- MD5 | 50 +++++++++++----------- R/colombiapi-package.R | 2 R/data-documentation.R | 2 R/get_Colombia_info.R | 2 R/get_airports_list.R | 12 ++++- R/get_departments_list.R | 2 R/get_presidents_list.R | 2 R/get_regions_list.R | 2 R/utils.R | 2 R/view_datasets.R | 2 inst/CITATION | 2 tests/testthat/test-Bogota_airstations_df.R | 2 tests/testthat/test-Bogota_business_Date.R | 2 tests/testthat/test-Bogota_holidays_Date.R | 2 tests/testthat/test-Bogota_malls_tbl_df.R | 2 tests/testthat/test-Cannabis_Licenses_tbl_df.R | 2 tests/testthat/test-Colombia_coffee_tbl_df.R | 2 tests/testthat/test-Medellin_rain_tbl_df.R | 2 tests/testthat/test-Tulua_Public_Schools_tbl_df.R | 2 tests/testthat/test-get_Colombia_info.R | 2 tests/testthat/test-get_airports_list.R | 6 +- tests/testthat/test-get_departments_list.R | 2 tests/testthat/test-get_presidents_list.R | 2 tests/testthat/test-get_regions_list.R | 2 tests/testthat/test-view_datasets.R | 2 26 files changed, 64 insertions(+), 56 deletions(-)
Title: Tools for Analysis of Diversity and Similarity in Biological
Systems
Description: A set of tools for empirical analysis of diversity (a number
and frequency of different types in a population) and similarity
(a number and frequency of shared types in two populations) in
biological or ecological systems.
Author: Christoph Sadee [aut],
Maciej Pietrzak [aut, cre],
Michal Seweryn [aut],
Cankun Wang [aut],
Grzegorz Rempala [aut]
Maintainer: Maciej Pietrzak <pietrzak.20@osu.edu>
Diff between divo versions 1.0.1 dated 2019-12-16 and 1.0.2 dated 2025-02-15
DESCRIPTION | 38 +++++++++++++++++++++++++++++++------- MD5 | 22 +++++++++++----------- build/vignette.rds |binary inst/doc/divo-Manual.Rnw | 3 ++- inst/doc/divo-Manual.pdf |binary inst/doc/divo-Vignette.Rnw | 4 ++-- inst/doc/divo-Vignette.pdf |binary man/TCR.Data.Rd | 24 ++++++++++++++++-------- man/li.Rd | 32 ++++++++++++++++++++++++-------- src/OL_read.c | 1 + vignettes/divo-Manual.Rnw | 3 ++- vignettes/divo-Vignette.Rnw | 4 ++-- 12 files changed, 91 insertions(+), 40 deletions(-)
Title: Fixing Data Made Easy for Statistical Analysis
Description: A set of functions that facilitate basic data manipulation and cleaning for statistical analysis including functions for finding and fixing duplicate rows and columns, missing values, outliers, and special characters in column and row names and functions for checking data consistency, distribution, quality, reliability, and structure.
Author: Ambu Vijayan [aut, cre] ,
J. Sreekumar [aut]
Maintainer: Ambu Vijayan <ambuvjyn@gmail.com>
Diff between fixr versions 0.1.0 dated 2023-04-20 and 0.2.0 dated 2025-02-15
fixr-0.1.0/fixr/man/find_duplicate_cols.Rd |only fixr-0.2.0/fixr/DESCRIPTION | 14 ++--- fixr-0.2.0/fixr/MD5 | 8 +-- fixr-0.2.0/fixr/NAMESPACE | 1 fixr-0.2.0/fixr/NEWS.md |only fixr-0.2.0/fixr/R/find_duplicate_cols.R | 75 +++++++++++------------------ 6 files changed, 40 insertions(+), 58 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre],
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.1.0 dated 2024-10-19 and 2.2 dated 2025-02-15
aqp-2.1.0/aqp/R/profile_compare.R |only aqp-2.1.0/aqp/man/profile_compare.Rd |only aqp-2.1.0/aqp/tests/testthat/test-profile_compare.R |only aqp-2.2/aqp/DESCRIPTION | 16 aqp-2.2/aqp/MD5 | 196 +-- aqp-2.2/aqp/NAMESPACE | 13 aqp-2.2/aqp/NEWS.md | 11 aqp-2.2/aqp/R/NCSP.R | 7 aqp-2.2/aqp/R/SoilProfileCollection-coercion.R | 6 aqp-2.2/aqp/R/SoilProfileCollection-methods.R | 3 aqp-2.2/aqp/R/SoilProfileCollection-slice-methods.R | 1 aqp-2.2/aqp/R/accumulateDepths.R | 3 aqp-2.2/aqp/R/accuracy_uncertainty.R | 23 aqp-2.2/aqp/R/addBracket.R | 14 aqp-2.2/aqp/R/aggregateColor.R | 72 - aqp-2.2/aqp/R/aggregateColorPlot.R |only aqp-2.2/aqp/R/aqp-package.R | 15 aqp-2.2/aqp/R/colorChart.R | 124 +- aqp-2.2/aqp/R/colorContrast.R | 5 aqp-2.2/aqp/R/colorContrastPlot.R | 5 aqp-2.2/aqp/R/colorQuantiles.R | 12 aqp-2.2/aqp/R/combine.R | 133 +- aqp-2.2/aqp/R/data-documentation.R | 43 aqp-2.2/aqp/R/dice.R | 2 aqp-2.2/aqp/R/equivalentMunsellChips.R | 1 aqp-2.2/aqp/R/evalGenHz.R | 20 aqp-2.2/aqp/R/generalize.hz.R | 14 aqp-2.2/aqp/R/huePositionCircle.R | 15 aqp-2.2/aqp/R/hzTransitionProbabilities.R | 35 aqp-2.2/aqp/R/invertLabelColor.R | 2 aqp-2.2/aqp/R/munsell2rgb.R | 10 aqp-2.2/aqp/R/parseMunsell.R | 5 aqp-2.2/aqp/R/plotMultipleSPC.R | 2 aqp-2.2/aqp/R/plotProfileDendrogram.R |only aqp-2.2/aqp/R/plotSPC.R | 27 aqp-2.2/aqp/R/plot_distance_graph.R | 2 aqp-2.2/aqp/R/previewColors.R | 7 aqp-2.2/aqp/R/quickSPC.R | 15 aqp-2.2/aqp/R/random_profile.R | 9 aqp-2.2/aqp/R/segment.R | 2 aqp-2.2/aqp/R/slab.R | 1 aqp-2.2/aqp/R/soilColorSignature.R | 6 aqp-2.2/aqp/R/soilPalette.R | 14 aqp-2.2/aqp/R/spec2Munsell.R | 42 aqp-2.2/aqp/R/texture.R | 235 ++-- aqp-2.2/aqp/build/partial.rdb |binary aqp-2.2/aqp/build/vignette.rds |binary aqp-2.2/aqp/data/wilson2022.rda |binary aqp-2.2/aqp/demo/aqp.R | 2 aqp-2.2/aqp/inst/WORDLIST | 2 aqp-2.2/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.R | 256 ++-- aqp-2.2/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.Rmd | 144 +- aqp-2.2/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 294 ++--- aqp-2.2/aqp/inst/doc/Munsell-color-conversion.R | 2 aqp-2.2/aqp/inst/doc/Munsell-color-conversion.Rmd | 2 aqp-2.2/aqp/inst/doc/Munsell-color-conversion.html | 2 aqp-2.2/aqp/inst/doc/NCSP.R | 10 aqp-2.2/aqp/inst/doc/NCSP.Rmd | 14 aqp-2.2/aqp/inst/doc/NCSP.html | 57 - aqp-2.2/aqp/inst/doc/aqp-overview.R | 2 aqp-2.2/aqp/inst/doc/aqp-overview.Rmd | 2 aqp-2.2/aqp/inst/doc/label-placement.R | 94 - aqp-2.2/aqp/inst/doc/label-placement.Rmd | 11 aqp-2.2/aqp/inst/doc/label-placement.html | 521 ++++------ aqp-2.2/aqp/inst/doc/missing-data.R | 6 aqp-2.2/aqp/inst/doc/missing-data.Rmd | 8 aqp-2.2/aqp/inst/doc/missing-data.html | 38 aqp-2.2/aqp/inst/doc/new-in-aqp-2.R | 2 aqp-2.2/aqp/inst/doc/new-in-aqp-2.Rmd | 2 aqp-2.2/aqp/man/accumulateDepths.Rd | 3 aqp-2.2/aqp/man/addDiagnosticBracket.Rd | 2 aqp-2.2/aqp/man/aggregateColor.Rd | 58 - aqp-2.2/aqp/man/aggregateColorPlot.Rd |only aqp-2.2/aqp/man/colorChart.Rd | 112 +- aqp-2.2/aqp/man/evalGenHZ.Rd | 7 aqp-2.2/aqp/man/generalize.hz.Rd | 7 aqp-2.2/aqp/man/hzTransitionProbabilities.Rd | 35 aqp-2.2/aqp/man/jacobs2000.Rd | 13 aqp-2.2/aqp/man/munsell2rgb.Rd | 6 aqp-2.2/aqp/man/parseMunsell.Rd | 4 aqp-2.2/aqp/man/plotMultipleSPC.Rd | 2 aqp-2.2/aqp/man/plotProfileDendrogram.Rd |only aqp-2.2/aqp/man/plot_distance_graph.Rd | 2 aqp-2.2/aqp/man/previewColors.Rd | 2 aqp-2.2/aqp/man/random_profile.Rd | 7 aqp-2.2/aqp/man/soilPalette.Rd | 3 aqp-2.2/aqp/man/soilTextureColorPal.Rd | 70 - aqp-2.2/aqp/man/sp3.Rd | 2 aqp-2.2/aqp/man/spec2Munsell.Rd | 44 aqp-2.2/aqp/man/wilson2022.Rd | 148 +- aqp-2.2/aqp/tests/testthat/Rplots.pdf |binary aqp-2.2/aqp/tests/testthat/test-DT-tbl.R | 6 aqp-2.2/aqp/tests/testthat/test-aggregateColor.R | 2 aqp-2.2/aqp/tests/testthat/test-color-signature.R | 6 aqp-2.2/aqp/tests/testthat/test-genhz.R | 1 aqp-2.2/aqp/tests/testthat/test-plotProfileDendrogram.R |only aqp-2.2/aqp/vignettes/Introduction-to-SoilProfileCollection-Objects.Rmd | 144 +- aqp-2.2/aqp/vignettes/Munsell-color-conversion.Rmd | 2 aqp-2.2/aqp/vignettes/NCSP.Rmd | 14 aqp-2.2/aqp/vignettes/aqp-overview.Rmd | 2 aqp-2.2/aqp/vignettes/label-placement.Rmd | 11 aqp-2.2/aqp/vignettes/missing-data.Rmd | 8 aqp-2.2/aqp/vignettes/new-in-aqp-2.Rmd | 2 103 files changed, 1551 insertions(+), 1813 deletions(-)
Title: Bifurcation Analysis of Ordinary Differential Equation Systems
Description: Shiny application that performs bifurcation and phaseplane analysis of systems of ordinary
differential equations. The package allows for computation of equilibrium curves as a function of
a single free parameter, detection of transcritical, saddle-node and hopf bifurcation points along
these curves, and computation of curves representing these transcritical, saddle-node and hopf
bifurcation points as a function of two free parameters. The shiny-based GUI allows visualization
of the results in both 2D- and 3D-plots. The implemented methods for solution localisation and curve
continuation are based on the book "Elements of applied bifurcation theory" (Kuznetsov, Y. A., 1995;
ISBN: 0-387-94418-4).
Author: Andre M. de Roos [aut, cre]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>
Diff between deBif versions 0.1.8 dated 2023-12-04 and 0.1.9 dated 2025-02-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 +++++++- R/bif1parplot.R | 22 +++++++++++----------- build/vignette.rds |binary 5 files changed, 26 insertions(+), 20 deletions(-)
Title: Vector Summaries of Persistence Diagrams
Description: Provides tools for computing various vector summaries of persistence diagrams studied in Topological Data Analysis. For improved computational efficiency,
all code for the vector summaries is written in 'C++' using the 'Rcpp' and 'RcppArmadillo' packages.
Author: Umar Islambekov [aut],
Aleksei Luchinsky [aut, cre]
Maintainer: Aleksei Luchinsky <aluchi@bgsu.edu>
Diff between TDAvec versions 0.1.3 dated 2022-10-31 and 0.1.4 dated 2025-02-15
TDAvec-0.1.3/TDAvec/NEWS.md |only TDAvec-0.1.3/TDAvec/man/computeECC.Rd |only TDAvec-0.1.3/TDAvec/man/computeNL.Rd |only TDAvec-0.1.3/TDAvec/man/computePES.Rd |only TDAvec-0.1.3/TDAvec/man/computePI.Rd |only TDAvec-0.1.3/TDAvec/man/computePL.Rd |only TDAvec-0.1.3/TDAvec/man/computePS.Rd |only TDAvec-0.1.3/TDAvec/man/computeVAB.Rd |only TDAvec-0.1.3/TDAvec/man/computeVPB.Rd |only TDAvec-0.1.3/TDAvec/src/ECC.cpp |only TDAvec-0.1.3/TDAvec/src/NL.cpp |only TDAvec-0.1.3/TDAvec/src/PES.cpp |only TDAvec-0.1.3/TDAvec/src/PI.cpp |only TDAvec-0.1.3/TDAvec/src/PL.cpp |only TDAvec-0.1.3/TDAvec/src/PS.cpp |only TDAvec-0.1.3/TDAvec/src/VAB.cpp |only TDAvec-0.1.3/TDAvec/src/VPB.cpp |only TDAvec-0.1.4/TDAvec/DESCRIPTION | 37 - TDAvec-0.1.4/TDAvec/MD5 | 66 + TDAvec-0.1.4/TDAvec/NAMESPACE | 7 TDAvec-0.1.4/TDAvec/R/RcppExports.R | 56 + TDAvec-0.1.4/TDAvec/README.md | 57 - TDAvec-0.1.4/TDAvec/build/vignette.rds |binary TDAvec-0.1.4/TDAvec/inst/doc/TDAvec_vignette.R | 115 --- TDAvec-0.1.4/TDAvec/inst/doc/TDAvec_vignette.Rmd | 206 ++--- TDAvec-0.1.4/TDAvec/inst/doc/TDAvec_vignette.html | 581 +++++++--------- TDAvec-0.1.4/TDAvec/man/computeAlgebraicFunctions.Rd |only TDAvec-0.1.4/TDAvec/man/computeBettiCurve.Rd |only TDAvec-0.1.4/TDAvec/man/computeComplexPolynomial.Rd |only TDAvec-0.1.4/TDAvec/man/computeEulerCharacteristic.Rd |only TDAvec-0.1.4/TDAvec/man/computeLimits.Rd |only TDAvec-0.1.4/TDAvec/man/computeNormalizedLife.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistenceBlock.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistenceImage.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistenceLandscape.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistenceSilhouette.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistentEntropy.Rd |only TDAvec-0.1.4/TDAvec/man/computeStats.Rd |only TDAvec-0.1.4/TDAvec/man/computeTemplateFunction.Rd |only TDAvec-0.1.4/TDAvec/man/computeTropicalCoordinates.Rd |only TDAvec-0.1.4/TDAvec/src/AlgebraicFunctions.cpp |only TDAvec-0.1.4/TDAvec/src/BettiCurve.cpp |only TDAvec-0.1.4/TDAvec/src/ComplexPolynomial.cpp |only TDAvec-0.1.4/TDAvec/src/EulerCharacteristic.cpp |only TDAvec-0.1.4/TDAvec/src/Limits.cpp |only TDAvec-0.1.4/TDAvec/src/Makevars |only TDAvec-0.1.4/TDAvec/src/NormalizedLife.cpp |only TDAvec-0.1.4/TDAvec/src/PersistenceBlock.cpp |only TDAvec-0.1.4/TDAvec/src/PersistenceImage.cpp |only TDAvec-0.1.4/TDAvec/src/PersistenceLandscape.cpp |only TDAvec-0.1.4/TDAvec/src/PersistenceSilhouette.cpp |only TDAvec-0.1.4/TDAvec/src/PersistentEntropy.cpp |only TDAvec-0.1.4/TDAvec/src/RcppExports.cpp | 235 ++++-- TDAvec-0.1.4/TDAvec/src/Stats.cpp |only TDAvec-0.1.4/TDAvec/src/TemplateFunction.cpp |only TDAvec-0.1.4/TDAvec/src/TropicalCoordinates.cpp |only TDAvec-0.1.4/TDAvec/vignettes/TDAvec_vignette.Rmd | 206 ++--- 57 files changed, 718 insertions(+), 848 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.12 dated 2024-12-19 and 1.13 dated 2025-02-15
openxlsx2-1.12/openxlsx2/man/figures/badge.png |only openxlsx2-1.12/openxlsx2/man/figures/badge.svg |only openxlsx2-1.13/openxlsx2/DESCRIPTION | 6 openxlsx2-1.13/openxlsx2/LICENSE | 2 openxlsx2-1.13/openxlsx2/MD5 | 181 openxlsx2-1.13/openxlsx2/NAMESPACE | 1 openxlsx2-1.13/openxlsx2/NEWS.md | 30 openxlsx2-1.13/openxlsx2/R/RcppExports.R | 12 openxlsx2-1.13/openxlsx2/R/asserts.R | 11 openxlsx2-1.13/openxlsx2/R/baseXML.R | 24 openxlsx2-1.13/openxlsx2/R/class-comment.R | 4 openxlsx2-1.13/openxlsx2/R/class-sheet-data.R | 13 openxlsx2-1.13/openxlsx2/R/class-workbook-wrappers.R | 5 openxlsx2-1.13/openxlsx2/R/class-workbook.R | 542 openxlsx2-1.13/openxlsx2/R/class-worksheet.R | 10 openxlsx2-1.13/openxlsx2/R/converters.R | 2 openxlsx2-1.13/openxlsx2/R/helper-functions.R | 399 openxlsx2-1.13/openxlsx2/R/openxlsx2-package.R | 2 openxlsx2-1.13/openxlsx2/R/pugixml.R | 6 openxlsx2-1.13/openxlsx2/R/read.R | 23 openxlsx2-1.13/openxlsx2/R/utils.R | 28 openxlsx2-1.13/openxlsx2/R/wb_functions.R | 76 openxlsx2-1.13/openxlsx2/R/wb_load.R | 50 openxlsx2-1.13/openxlsx2/R/wb_styles.R | 523 openxlsx2-1.13/openxlsx2/R/write.R | 61 openxlsx2-1.13/openxlsx2/R/write_xlsx.R | 31 openxlsx2-1.13/openxlsx2/R/xl_open.R | 7 openxlsx2-1.13/openxlsx2/README.md | 6 openxlsx2-1.13/openxlsx2/build/vignette.rds |binary openxlsx2-1.13/openxlsx2/inst/AUTHORS | 5 openxlsx2-1.13/openxlsx2/inst/WORDLIST | 138 openxlsx2-1.13/openxlsx2/inst/doc/conditional-formatting.R | 34 openxlsx2-1.13/openxlsx2/inst/doc/conditional-formatting.Rmd | 40 openxlsx2-1.13/openxlsx2/inst/doc/conditional-formatting.html | 118 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_charts_manual.Rmd | 2 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_charts_manual.html | 5 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_formulas_manual.R | 2 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_formulas_manual.Rmd | 2 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_formulas_manual.html | 12 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_read_to_df.Rmd | 4 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_read_to_df.html | 4 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_style_manual.R | 8 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_style_manual.Rmd | 8 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_style_manual.html | 235 openxlsx2-1.13/openxlsx2/inst/extdata/hex_icon.R |only openxlsx2-1.13/openxlsx2/inst/include/pugixml/pugiconfig.hpp | 11 openxlsx2-1.13/openxlsx2/inst/include/pugixml/pugixml.cpp | 829 - openxlsx2-1.13/openxlsx2/inst/include/pugixml/pugixml.hpp | 121 openxlsx2-1.13/openxlsx2/man/create_border.Rd | 50 openxlsx2-1.13/openxlsx2/man/create_cell_style.Rd | 67 openxlsx2-1.13/openxlsx2/man/create_dxfs_style.Rd | 7 openxlsx2-1.13/openxlsx2/man/create_fill.Rd | 31 openxlsx2-1.13/openxlsx2/man/create_font.Rd | 48 openxlsx2-1.13/openxlsx2/man/create_numfmt.Rd | 17 openxlsx2-1.13/openxlsx2/man/create_shape.Rd |only openxlsx2-1.13/openxlsx2/man/dims_helper.Rd | 2 openxlsx2-1.13/openxlsx2/man/figures/logo.png |only openxlsx2-1.13/openxlsx2/man/fmt_txt.Rd | 5 openxlsx2-1.13/openxlsx2/man/openxlsx2-package.Rd | 2 openxlsx2-1.13/openxlsx2/man/wb_add_border.Rd | 3 openxlsx2-1.13/openxlsx2/man/wb_add_formula.Rd | 2 openxlsx2-1.13/openxlsx2/man/wb_dims.Rd | 2 openxlsx2-1.13/openxlsx2/man/write_xlsx.Rd | 8 openxlsx2-1.13/openxlsx2/man/xl_open.Rd | 4 openxlsx2-1.13/openxlsx2/src/RcppExports.cpp | 35 openxlsx2-1.13/openxlsx2/src/helper_functions.cpp | 352 openxlsx2-1.13/openxlsx2/src/load_workbook.cpp | 115 openxlsx2-1.13/openxlsx2/src/openxlsx2.h | 192 openxlsx2-1.13/openxlsx2/src/openxlsx2_types.h | 94 openxlsx2-1.13/openxlsx2/src/pugi.cpp | 212 openxlsx2-1.13/openxlsx2/src/strings_xml.cpp | 36 openxlsx2-1.13/openxlsx2/src/styles_xml.cpp | 312 openxlsx2-1.13/openxlsx2/src/write_file.cpp | 175 openxlsx2-1.13/openxlsx2/src/xlsb.cpp | 6789 +++++----- openxlsx2-1.13/openxlsx2/src/xlsb_defines.h | 1866 +- openxlsx2-1.13/openxlsx2/src/xlsb_funs.h | 2166 +-- openxlsx2-1.13/openxlsx2/tests/testthat/test-class-workbook.R | 4 openxlsx2-1.13/openxlsx2/tests/testthat/test-conditional_formatting.R | 4 openxlsx2-1.13/openxlsx2/tests/testthat/test-date_time_conversion.R | 4 openxlsx2-1.13/openxlsx2/tests/testthat/test-formulas.R | 42 openxlsx2-1.13/openxlsx2/tests/testthat/test-helper-functions.R | 30 openxlsx2-1.13/openxlsx2/tests/testthat/test-pugi_cpp.R | 20 openxlsx2-1.13/openxlsx2/tests/testthat/test-read_from_created_wb.R | 11 openxlsx2-1.13/openxlsx2/tests/testthat/test-read_xlsb.R | 37 openxlsx2-1.13/openxlsx2/tests/testthat/test-save.R | 53 openxlsx2-1.13/openxlsx2/tests/testthat/test-utils.R | 13 openxlsx2-1.13/openxlsx2/tests/testthat/test-wb_functions.R | 6 openxlsx2-1.13/openxlsx2/tests/testthat/test-wb_styles.R | 6 openxlsx2-1.13/openxlsx2/tests/testthat/test-write.R | 50 openxlsx2-1.13/openxlsx2/vignettes/conditional-formatting.Rmd | 40 openxlsx2-1.13/openxlsx2/vignettes/openxlsx2_charts_manual.Rmd | 2 openxlsx2-1.13/openxlsx2/vignettes/openxlsx2_formulas_manual.Rmd | 2 openxlsx2-1.13/openxlsx2/vignettes/openxlsx2_read_to_df.Rmd | 4 openxlsx2-1.13/openxlsx2/vignettes/openxlsx2_style_manual.Rmd | 8 94 files changed, 8938 insertions(+), 7623 deletions(-)
Title: Pattern Causality Algorithm
Description: A comprehensive package for detecting and analyzing causal relationships in complex systems using pattern-based approaches. Key features include state space reconstruction, pattern identification, and causality strength evaluation.
Author: Stavros Stavroglou [aut] ,
Athanasios Pantelous [aut] ,
Hui Wang [aut, cre]
Maintainer: Hui Wang <huiw1128@gmail.com>
Diff between patterncausality versions 0.2.0 dated 2025-01-09 and 0.2.1 dated 2025-02-15
DESCRIPTION | 6 MD5 | 56 +++---- R/PC.Mk.II.Full.Details.R | 3 R/PC.Mk.II.Lightweight.R | 3 R/natureOfCausality.R | 13 + R/optimalParametersSearch.R | 5 R/pcAccuracy.R | 7 R/pcCV.R | 71 ++++++--- R/pcCrossMatrix.R | 10 - R/pcMatrix.R | 9 - R/pc_full_details_utils.R | 5 R/pc_lightweight_utils.R | 69 ++++---- R/signatureSpace.R | 22 ++ README.md | 81 +++++++--- inst/doc/advanced.html | 20 +- inst/doc/dynamic.html | 6 inst/doc/matrix.html | 6 inst/doc/patterncausality.R | 6 inst/doc/patterncausality.Rmd | 32 +++- inst/doc/patterncausality.html | 53 +++++- inst/doc/series.html | 318 ++++++++++++++++++++--------------------- man/optimalParametersSearch.Rd | 3 man/pcAccuracy.Rd | 3 man/pcCrossMatrix.Rd | 3 man/pcCrossValidation.Rd | 5 man/pcFullDetails.Rd | 3 man/pcLightweight.Rd | 3 man/pcMatrix.Rd | 3 vignettes/patterncausality.Rmd | 32 +++- 29 files changed, 517 insertions(+), 339 deletions(-)
More information about patterncausality at CRAN
Permanent link
Title: Small Area Estimation Using Model-Assisted Projection Method
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Author: Ridson Al Farizal P [aut, cre, cph]
,
Azka Ubaidillah [aut] ,
Silvi Ajeng Larasati [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>
Diff between sae.projection versions 0.1.0 dated 2024-12-19 and 0.1.1 dated 2025-02-15
DESCRIPTION | 14 +++-- MD5 | 18 +++++-- NAMESPACE | 6 ++ R/Projection_rf.R |only R/Projection_rf_CorrectedBias.R |only R/data.R | 88 +++++++++++++++++++++++++++++++++++++ R/projection.R | 10 +++- data/df_susenas_mar2020.rda |only data/df_susenas_sep2020.rda |only man/Projection_rf.Rd |only man/Projection_rf_CorrectedBias.Rd |only man/df_susenas_mar2020.Rd |only man/df_susenas_sep2020.Rd |only man/projection.Rd | 12 ++--- 14 files changed, 129 insertions(+), 19 deletions(-)
More information about sae.projection at CRAN
Permanent link
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.14.4 dated 2025-01-21 and 0.15.2 dated 2025-02-15
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Title: Interact with Data Type Registries and Create Machine-Readable
Data
Description: You can load a schema from a DTR (data type registry) as an R
object. Use this schema to write your data in JSON-LD (JavaScript
Object Notation for Linked Data) format to make it machine readable.
Author: Olga Lezhnina [aut, cre] ,
Manuel Prinz [aut] ,
Markus Stocker [aut] ,
Open Research Knowledge Graph Project and Contributors [cph]
Maintainer: Olga Lezhnina <olga.lezhnina@tib.eu>
Diff between dtreg versions 1.1.0 dated 2024-12-02 and 1.1.1 dated 2025-02-15
DESCRIPTION | 7 MD5 | 62 +-- NEWS.md | 6 R/helpers.R | 4 R/load_datatype.R | 2 R/to_jsonld.R | 6 README.md | 18 inst/doc/dtreg.R | 200 +++++---- inst/doc/dtreg.Rmd | 274 ++++++++----- inst/doc/dtreg.html | 362 +++++++++++------- inst/extdata/ePIC-21-T11909-286991b26f02d58ee490.json | 2 inst/extdata/ePIC-21-T11909-37182ecfb4474942e255.json | 2 inst/extdata/ePIC-21-T11909-3f64a93eef69d721518f.json | 2 inst/extdata/ePIC-21-T11909-437807f8d1a81b5138a3.json | 2 inst/extdata/ePIC-21-T11909-5b66cb584b974b186f37.json | 2 inst/extdata/ePIC-21-T11909-5e782e67e70d0b2a022a.json | 2 inst/extdata/ePIC-21-T11909-6e3e29ce3ba5a0b9abfe.json | 2 inst/extdata/ePIC-21-T11909-abef9f1c0d48853f3e51.json | 2 inst/extdata/ePIC-21-T11909-b9335ce2c99ed87735a6.json | 2 inst/extdata/ePIC-21-T11909-c6b413ba96ba477b5dca.json | 2 inst/extdata/ePIC-21-T11909-c6e19df3b52ab8d855a9.json | 2 inst/extdata/ePIC-21-T11909-feeb33ad3e4440682a4d.json |only man/load_datatype.Rd | 2 man/show_fields.Rd | 4 man/to_jsonld.Rd | 4 tests/testthat/helper-mocked.R |only tests/testthat/test-extract_epic.R | 23 - tests/testthat/test-extract_orkg.R | 3 tests/testthat/test-helpers.R | 6 tests/testthat/test-load_datatype.R | 5 tests/testthat/test-request_dtr.R | 8 tests/testthat/test-to_jsonld.R | 7 vignettes/dtreg.Rmd | 274 ++++++++----- 33 files changed, 763 insertions(+), 536 deletions(-)
Title: Query 'SWI'-'Prolog' from R
Description: This R package connects to SWI-Prolog, <https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to prolog (consult, query/submit, once, findall).
Author: Matthias Gondan [aut, com, cre] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rolog versions 0.9.18 dated 2024-07-09 and 0.9.20 dated 2025-02-15
rolog-0.9.18/rolog/tests |only rolog-0.9.20/rolog/DESCRIPTION | 12 rolog-0.9.20/rolog/MD5 | 18 rolog-0.9.20/rolog/NEWS.md | 9 rolog-0.9.20/rolog/README.md | 111 +---- rolog-0.9.20/rolog/build/vignette.rds |binary rolog-0.9.20/rolog/inst/doc/rolog.html | 717 ++++++++++++++++----------------- rolog-0.9.20/rolog/src/Makevars | 4 rolog-0.9.20/rolog/src/Makevars.win | 2 rolog-0.9.20/rolog/src/crolog.cpp | 153 ++++++- 10 files changed, 571 insertions(+), 455 deletions(-)
Title: ICESat-2 Altimeter Data using R
Description: Programmatic connection to the 'OpenAltimetry API' <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global Geolocated Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice Freeboard), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects altimetry data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice freeboard, and vegetation canopy height begu [...truncated...]
Author: Lampros Mouselimis [aut, cre] ,
OpenAltimetry.org [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between IceSat2R versions 1.0.6 dated 2024-08-17 and 1.0.7 dated 2025-02-15
DESCRIPTION | 10 +-- MD5 | 28 ++++---- NEWS.md | 7 ++ R/mission_orbits.R | 34 ++++++++++ README.md | 13 ++-- build/vignette.rds |binary data/RGT_cycle_14.rda |binary data/ne_10m_glaciated_areas.rda |binary inst/data_files/technical_specs_urls.csv | 60 +++++++++---------- inst/doc/IceSat-2_Atlas_products_PDF.pdf |binary inst/doc/IceSat-2_Mission_Orbits_PDF.pdf |binary inst/doc/IceSat-2_Virtual_File_System_Orbits_PDF.pdf |binary tests/testthat/test-API_utils.R | 8 ++ tests/testthat/test-get_Atlas_data.R | 10 ++- tests/testthat/test-mission_orbits.R | 17 +++-- 15 files changed, 122 insertions(+), 65 deletions(-)
Title: Flexible Parametric Cure Models
Description: Flexible parametric mixture and non-mixture cure models for time-to-event data.
Author: Jordan Amdahl [aut, cre]
Maintainer: Jordan Amdahl <jrdnmdhl@gmail.com>
Diff between flexsurvcure versions 1.3.1 dated 2022-11-01 and 1.3.3 dated 2025-02-15
DESCRIPTION | 10 +- MD5 | 18 ++-- NEWS.md | 6 + R/flexsurvcure.R | 12 +- R/mixture.r | 2 R/nonmixture.R | 4 build/vignette.rds |binary inst/doc/flexsurvcure.R | 10 +- inst/doc/flexsurvcure.html | 198 +++++++++++++++++++++++---------------------- man/flexsurvcure.Rd | 10 +- 10 files changed, 141 insertions(+), 129 deletions(-)
Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl],
Paul Pearson [ctb],
Daniel Muellner [ctb],
Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>
Diff between MapperAlgo versions 1.0.1 dated 2024-12-08 and 1.0.2 dated 2025-02-15
DESCRIPTION | 9 +- MD5 | 16 ++-- NAMESPACE | 4 + R/Cluster.R | 158 ++++++++++++++++++++++--------------------- R/MapperAlgo.R | 92 ++++++++++++++++--------- README.md | 33 ++++++-- man/MapperAlgo.Rd | 10 +- man/figures/Performance1.png |only man/figures/Performance2.png |only man/perform_clustering.Rd | 3 10 files changed, 189 insertions(+), 136 deletions(-)
Title: R2 Statistic
Description: R2 statistic for significance test. Variance and covariance of R2 values used to assess the 95% CI and p-value of the R2 difference.
Author: Hong Lee [aut, cph],
Moksedul Momin [aut, cre, cph]
Maintainer: Moksedul Momin <cvasu.momin@gmail.com>
Diff between r2redux versions 1.0.17 dated 2023-11-28 and 1.0.18 dated 2025-02-15
r2redux-1.0.17/r2redux/tests |only r2redux-1.0.18/r2redux/DESCRIPTION | 6 +++--- r2redux-1.0.18/r2redux/MD5 | 6 ++---- r2redux-1.0.18/r2redux/R/r_diff.r | 14 +++++--------- 4 files changed, 10 insertions(+), 16 deletions(-)
Title: Estimates OIPP and OIZTNB Regression Models
Description: Estimates one-inflated positive Poisson (OIPP) and
one-inflated zero-truncated negative binomial (OIZTNB) regression
models. A suite of ancillary statistical tools are also provided,
including: estimation of positive Poisson (PP) and zero-truncated
negative binomial (ZTNB) models; marginal effects and their standard
errors; diagnostic likelihood ratio and Wald tests; plotting;
predicted counts and expected responses; and random variate
generation. The models and tools, as well as four applications, are
shown in Godwin, R. T. (2024). "One-inflated zero-truncated count
regression models" arXiv preprint <doi:10.48550/arXiv.2402.02272>.
Author: Ryan T. Godwin [aut, cre]
Maintainer: Ryan T. Godwin <ryan.godwin@umanitoba.ca>
Diff between oneinfl versions 1.0.0 dated 2025-02-06 and 1.0.1 dated 2025-02-15
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/dEdq_nb.R | 5 +++-- R/dEdq_pois.R | 5 +++-- R/margins.R | 10 +++++----- R/summary-oneinfl.R | 4 ++-- 7 files changed, 29 insertions(+), 20 deletions(-)
Title: Influence Function Based Estimate Objects
Description: Implements an S7 class for estimates based on influence functions.
Standard arithmetic operations are defined for the class.
Author: Nicholas Williams [aut, cre, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between ife versions 0.1.0 dated 2024-11-08 and 0.1.12 dated 2025-02-14
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NAMESPACE | 2 ++ NEWS.md |only R/ife.R | 7 +++++-- R/influence_func_estimand.R | 20 ++++++++++++++++---- README.md | 22 +++++++++++++--------- man/ife_constructor.Rd | 14 ++++++++++++-- tests/testthat/test-validator.R | 4 ++++ 9 files changed, 63 insertions(+), 27 deletions(-)
Title: Encapsulated Classes with Reference Semantics
Description: Creates classes with reference semantics, similar to R's
built-in reference classes. Compared to reference classes, R6 classes
are simpler and lighter-weight, and they are not built on S4 classes
so they do not require the methods package. These classes allow public
and private members, and they support inheritance, even when the
classes are defined in different packages.
Author: Winston Chang [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Winston Chang <winston@posit.co>
Diff between R6 versions 2.6.0 dated 2025-02-12 and 2.6.1 dated 2025-02-14
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md | 8 ++++++-- R/r6_class.R | 5 +++-- tests/testthat/test-dollarnames.R |only 5 files changed, 16 insertions(+), 10 deletions(-)
Title: Automated Estimation of Sigmoidal and Piecewise Linear Mixed
Models
Description: Estimation of relatively complex nonlinear mixed-effects models, including the Sigmoidal Mixed Model and the Piecewise Linear Mixed Model with abrupt or smooth transition, through a single intuitive line of code and with automated generation of starting values.
Author: Maude Wagner [aut, cre] ,
Ana W. Capuano [aut],
Emmanuelle Comets [ctb]
Maintainer: Maude Wagner <maude_wagner@rush.edu>
Diff between nlive versions 0.6.0 dated 2024-05-26 and 0.7.0 dated 2025-02-14
DESCRIPTION | 10 +++++----- MD5 | 8 +++++--- NAMESPACE | 12 ++++++++++++ R/globals.R | 5 ++++- R/nlive.splines.R |only man/nlive.splines.Rd |only 6 files changed, 26 insertions(+), 9 deletions(-)
Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and
Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
Author: Paul Bastide [aut, cre],
Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>
Diff between PhylogeneticEM versions 1.7.0 dated 2024-01-31 and 1.8.0 dated 2025-02-14
DESCRIPTION | 11 MD5 | 46 +-- NAMESPACE | 1 NEWS.md | 8 R/estimateEM.R | 301 ++++++++++++++------- R/generic_functions.R | 1 R/model_selection.R | 1 R/plot_functions.R | 2 build/vignette.rds |binary inst/doc/monkeys.R | 36 +- inst/doc/monkeys.Rmd | 2 inst/doc/monkeys.html | 400 +--------------------------- inst/doc/tutorial.R | 28 - inst/doc/tutorial.Rmd | 2 inst/doc/tutorial.html | 72 ----- man/PhyloEM.Rd | 6 man/estimateEM.Rd | 2 man/merge_alpha_grids.Rd |only man/plot.PhyloEM.Rd | 2 man/plot.equivalent_shifts.Rd | 2 man/plot.params_process.Rd | 2 tests/testthat/test-utilities-merge_alpha.R |only tests/testthat/test-utilities-rotations.R | 65 ++++ vignettes/monkeys.Rmd | 2 vignettes/tutorial.Rmd | 2 25 files changed, 388 insertions(+), 606 deletions(-)
More information about PhylogeneticEM at CRAN
Permanent link
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 1.3.0 dated 2024-12-18 and 1.3.1 dated 2025-02-14
nhdplusTools-1.3.0/nhdplusTools/man/discover_nldi_characteristics.Rd |only nhdplusTools-1.3.0/nhdplusTools/man/get_nldi_characteristics.Rd |only nhdplusTools-1.3.1/nhdplusTools/DESCRIPTION | 8 nhdplusTools-1.3.1/nhdplusTools/MD5 | 44 nhdplusTools-1.3.1/nhdplusTools/NAMESPACE | 3 nhdplusTools-1.3.1/nhdplusTools/NEWS.md | 6 nhdplusTools-1.3.1/nhdplusTools/R/A_nhdplusTools.R | 1050 +-- nhdplusTools-1.3.1/nhdplusTools/R/arcrest_tools.R | 462 - nhdplusTools-1.3.1/nhdplusTools/R/downloading_tools.R | 3 nhdplusTools-1.3.1/nhdplusTools/R/get_hydro.R | 67 nhdplusTools-1.3.1/nhdplusTools/R/get_nldi.R | 78 nhdplusTools-1.3.1/nhdplusTools/inst/doc/get_3dhp_data.html | 95 nhdplusTools-1.3.1/nhdplusTools/inst/doc/get_data_overview.html | 3397 +++++++++- nhdplusTools-1.3.1/nhdplusTools/inst/doc/nhdplusTools.html | 3012 ++++++++ nhdplusTools-1.3.1/nhdplusTools/inst/doc/nhdplushr.html | 4 nhdplusTools-1.3.1/nhdplusTools/inst/doc/plot_nhdplus.html | 87 nhdplusTools-1.3.1/nhdplusTools/man/download_nhdplushr.Rd | 3 nhdplusTools-1.3.1/nhdplusTools/man/get_3dhp.Rd | 4 nhdplusTools-1.3.1/nhdplusTools/man/get_huc.Rd | 2 nhdplusTools-1.3.1/nhdplusTools/man/get_nhdphr.Rd |only nhdplusTools-1.3.1/nhdplusTools/man/query_usgs_arcrest.Rd | 8 nhdplusTools-1.3.1/nhdplusTools/tests/testthat/test_01_get_nldi.R | 36 nhdplusTools-1.3.1/nhdplusTools/tests/testthat/test_arcrest.R | 8 nhdplusTools-1.3.1/nhdplusTools/tests/testthat/test_geoconnex.R | 4 nhdplusTools-1.3.1/nhdplusTools/tests/testthat/test_get_nhdphr.R |only 25 files changed, 7253 insertions(+), 1128 deletions(-)
Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to
'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R
using the 'libtorch' library. Also supports low-level tensor operations and
'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph],
Javier Luraschi [aut],
Dmitriy Selivanov [ctb],
Athos Damiani [ctb],
Christophe Regouby [ctb],
Krzysztof Joachimiak [ctb],
Hamada S. Badr [ctb],
Sebastian Fischer [ctb],
Maximilian Pichler [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torch versions 0.14.1 dated 2025-02-03 and 0.14.2 dated 2025-02-14
DESCRIPTION | 6 +- MD5 | 16 ++--- NEWS.md | 4 + R/install.R | 2 build/partial.rdb |binary configure.win | 2 inst/doc/tensor-creation.html | 8 +- inst/doc/torchscript.html | 112 ++++++++++++++++++++--------------------- inst/include/lantern/lantern.h | 28 ---------- 9 files changed, 78 insertions(+), 100 deletions(-)
Title: Tree Taper Curves and Sorting Based on 'TapeR'
Description: Providing new german-wide 'TapeR' Models and functions for their
evaluation. Included are the most common tree species in Germany (Norway
spruce, Scots pine, European larch, Douglas fir, Silver fir as well as
European beech, Common/Sessile oak and Red oak). Many other species are mapped
to them so that 36 tree species / groups can be processed. Single trees are
defined by species code, one or multiple diameters in arbitrary measuring
height and tree height. The functions then provide information on diameters
along the stem, bark thickness, height of diameters, volume of the total or
parts of the trunk and total and component above-ground biomass. It is also
possible to calculate assortments from the taper curves. Uncertainty
information is provided for diameter, volume and component biomass estimation.
Author: Christian Vonderach [aut, cre],
Edgar Kublin [aut],
Gerald Kaendler [aut]
Maintainer: Christian Vonderach <christian.vonderach@forst.bwl.de>
Diff between TapeS versions 0.13.2 dated 2025-01-22 and 0.13.3 dated 2025-02-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/sysdata.rda |binary build/partial.rdb |binary inst/doc/tapes.R | 14 +++++++------- inst/doc/tapes.html | 4 ++-- 7 files changed, 22 insertions(+), 18 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
Author: Tobi Guennel [aut, cre]
Maintainer: Tobi Guennel <tobi.guennel@precisionformedicine.com>
Diff between solvebio versions 2.15.0 dated 2024-08-16 and 2.15.1 dated 2025-02-14
DESCRIPTION | 15 +++++++-------- MD5 | 2 +- 2 files changed, 8 insertions(+), 9 deletions(-)
Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method
which can be called to terminate the background job. Also provides timeouts
and other mechanisms for automatically terminating a background job. The
result of the expression is available synchronously via $result or
asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between jobqueue versions 1.3.0 dated 2025-02-13 and 1.3.1 dated 2025-02-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 3 +-- tests/testthat/test-job.r | 2 +- tests/testthat/test-queue.r | 12 ++++++------ tests/testthat/test-worker.r | 17 +++++++++-------- 6 files changed, 26 insertions(+), 26 deletions(-)
Title: Bootstrap for State Space Models
Description: Provides a streamlined and user-friendly framework
for bootstrapping in state space models,
particularly when the number of subjects/units (n) exceeds one,
a scenario commonly encountered in social and behavioral sciences.
For an introduction to state space models in social and behavioral sciences,
refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between bootStateSpace versions 1.0.1 dated 2025-01-22 and 1.0.2 dated 2025-02-14
DESCRIPTION | 6 - MD5 | 108 +++++++++--------- NEWS.md | 8 + R/bootStateSpace-coef-fit-dynr-dot.R | 4 R/bootStateSpace-dynr-data-dot.R | 2 R/bootStateSpace-dynr-dynamics-dot.R | 20 +-- R/bootStateSpace-dynr-initial-dot.R | 12 -- R/bootStateSpace-dynr-measurement-dot.R | 16 +- R/bootStateSpace-dynr-noise-dot.R | 14 +- R/bootStateSpace-formula-lin-sde-dot.R | 41 ++---- R/bootStateSpace-formula-ou-dot.R | 97 +++++++--------- R/bootStateSpace-formula-var-dot.R | 41 ++---- R/bootStateSpace-label-full-dot.R | 28 ++-- R/bootStateSpace-label-sym-dot.R | 46 +++---- R/bootStateSpace-lambda-label-dot.R | 14 +- R/bootStateSpace-methods.R | 32 +---- R/bootStateSpace-pb-ci-dot.R | 4 R/bootStateSpace-pb-coef-dynr-dot.R | 24 +--- R/bootStateSpace-pb-ssm-fixed-fork-dot.R | 8 - R/bootStateSpace-pb-ssm-fixed-prep-dynr-dot.R | 14 +- R/bootStateSpace-pb-ssm-fixed-serial-dot.R | 8 - R/bootStateSpace-pb-ssm-fixed-socket-dot.R | 8 - R/bootStateSpace-pb-ssm-fixed.R | 24 +++- R/bootStateSpace-pb-ssm-lin-sde-fixed-fork-dot.R | 8 - R/bootStateSpace-pb-ssm-lin-sde-fixed-prep-dynr-dot.R | 14 +- R/bootStateSpace-pb-ssm-lin-sde-fixed-serial-dot.R | 8 - R/bootStateSpace-pb-ssm-lin-sde-fixed-socket-dot.R | 8 - R/bootStateSpace-pb-ssm-lin-sde-fixed.R | 21 ++- R/bootStateSpace-pb-ssm-ou-fixed-fork-dot.R | 8 - R/bootStateSpace-pb-ssm-ou-fixed-prep-dynr-dot.R | 14 +- R/bootStateSpace-pb-ssm-ou-fixed-serial-dot.R | 8 - R/bootStateSpace-pb-ssm-ou-fixed-socket-dot.R | 8 - R/bootStateSpace-pb-ssm-ou-fixed.R | 21 ++- R/bootStateSpace-pb-ssm-var-fixed-fork-dot.R | 8 - R/bootStateSpace-pb-ssm-var-fixed-prep-dynr-dot.R | 14 +- R/bootStateSpace-pb-ssm-var-fixed-serial-dot.R | 8 - R/bootStateSpace-pb-ssm-var-fixed-socket-dot.R | 8 - R/bootStateSpace-pb-ssm-var-fixed.R | 21 ++- R/bootStateSpace-vec-2-full-mat-dot.R | 2 R/bootStateSpace-vec-2-mat-dot.R | 27 ++-- R/bootStateSpace-vec-2-sym-mat-dot.R | 2 R/linearAlgebra-vec-dot.R | 2 R/linearAlgebra-vech-dot.R | 14 +- R/nBootstrap-bc-ci-dot.R | 12 -- R/nBootstrap-bc-probs-dot.R | 6 - R/nBootstrap-ci-format-dot.R | 2 R/nBootstrap-pc-ci-dot.R | 12 -- R/nBootstrap-pc-probs-dot.R | 8 - R/nBootstrap-z0-dot.R | 10 - R/nBootstrap-z1-dot.R | 4 R/simStateSpace-long-dot.R | 10 - man/PBSSMFixed.Rd | 7 + man/PBSSMLinSDEFixed.Rd | 7 + man/PBSSMOUFixed.Rd | 7 + man/PBSSMVARFixed.Rd | 7 + 55 files changed, 431 insertions(+), 464 deletions(-)
More information about bootStateSpace at CRAN
Permanent link
Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] ,
Riccardo Corradin [aut],
Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Diff between BayesChange versions 1.1.0 dated 2025-02-13 and 1.1.1 dated 2025-02-14
DESCRIPTION | 6 - MD5 | 26 ++--- NEWS.md | 2 inst/doc/tutorial.R | 134 ++++++++++++++--------------- inst/doc/tutorial.Rmd | 38 ++++---- inst/doc/tutorial.html | 112 +++--------------------- src/Makevars | 11 +- src/code.cpp | 21 +--- tests/testthat/test-test-clust_cp_epi.R | 7 - tests/testthat/test-test-clust_cp_multi.R | 41 ++------ tests/testthat/test-test-clust_cp_uni.R | 25 +---- tests/testthat/test-test-detect_cp_multi.R | 18 +-- tests/testthat/test-test-detect_cp_uni.R | 21 +--- vignettes/tutorial.Rmd | 38 ++++---- 14 files changed, 183 insertions(+), 317 deletions(-)
Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework
for simulating data in state space models,
particularly when the number of subjects/units (n) exceeds one,
a scenario commonly encountered in social and behavioral sciences.
For an introduction to state space models in social and behavioral sciences,
refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between simStateSpace versions 1.2.8 dated 2025-01-23 and 1.2.9 dated 2025-02-14
simStateSpace-1.2.8/simStateSpace/R/linearAlgebra-vec-dot.R |only simStateSpace-1.2.8/simStateSpace/R/linearAlgebra-vech-dot.R |only simStateSpace-1.2.9/simStateSpace/DESCRIPTION | 6 simStateSpace-1.2.9/simStateSpace/MD5 | 82 +++++----- simStateSpace-1.2.9/simStateSpace/NAMESPACE | 2 simStateSpace-1.2.9/simStateSpace/NEWS.md | 6 simStateSpace-1.2.9/simStateSpace/R/RcppExports.R | 4 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-lin-sde-cov.R |only simStateSpace-1.2.9/simStateSpace/R/simStateSpace-lin-sde-mean.R |only simStateSpace-1.2.9/simStateSpace/R/simStateSpace-long-dot.R | 10 - simStateSpace-1.2.9/simStateSpace/R/simStateSpace-methods-simstatespace.R | 14 - simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-fixed.R | 4 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-i-vary.R | 4 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-lin-growth-i-vary.R | 4 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-lin-growth.R | 12 - simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-lin-sde-fixed.R | 2 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-lin-sde-i-vary.R | 4 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-ou-fixed.R | 2 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-ou-i-vary.R | 4 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-var-fixed.R | 4 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-sim-ssm-var-i-vary.R | 4 simStateSpace-1.2.9/simStateSpace/R/simStateSpace-wide-dot.R | 2 simStateSpace-1.2.9/simStateSpace/man/LinSDE2SSM.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/LinSDECov.Rd |only simStateSpace-1.2.9/simStateSpace/man/LinSDEMean.Rd |only simStateSpace-1.2.9/simStateSpace/man/SimBetaN.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/SimPhiN.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/SimSSMFixed.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/SimSSMIVary.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/SimSSMLinGrowth.Rd | 10 - simStateSpace-1.2.9/simStateSpace/man/SimSSMLinGrowthIVary.Rd | 4 simStateSpace-1.2.9/simStateSpace/man/SimSSMLinSDEFixed.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/SimSSMLinSDEIVary.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/SimSSMOUFixed.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/SimSSMOUIVary.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/SimSSMVARFixed.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/SimSSMVARIVary.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/TestPhi.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/TestStability.Rd | 2 simStateSpace-1.2.9/simStateSpace/man/TestStationarity.Rd | 2 simStateSpace-1.2.9/simStateSpace/src/RcppExports.cpp | 14 + simStateSpace-1.2.9/simStateSpace/src/source.cpp | 13 + simStateSpace-1.2.9/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-cov.R |only simStateSpace-1.2.9/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-mean.R |only simStateSpace-1.2.9/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-growth.R | 8 simStateSpace-1.2.9/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-sde-i-vary.R | 62 +++++++ 46 files changed, 210 insertions(+), 99 deletions(-)
Title: (Kernel) Isotope Niche Estimation
Description: Applies methods used to estimate animal homerange, but
instead of geospatial coordinates, we use isotopic coordinates. The estimation
methods include: 1) 2-dimensional bivariate normal kernel utilization density
estimator, 2) bivariate normal ellipse estimator, and 3) minimum convex polygon
estimator, all applied to stable isotope data. Additionally, functions to
determine niche area, polygon overlap between groups and levels (confidence
contours) and plotting capabilities.
Author: Shannon E Albeke [aut, cre]
Maintainer: Shannon E Albeke <salbeke@uwyo.edu>
Diff between rKIN versions 1.0.2 dated 2023-10-02 and 1.0.3 dated 2025-02-14
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/plotKIN.R | 2 +- build/vignette.rds |binary 4 files changed, 9 insertions(+), 9 deletions(-)
Title: 'parsnip' Engines for Survival Models
Description: Engines for survival models from the 'parsnip' package. These
include parametric models (e.g., Jackson (2016)
<doi:10.18637/jss.v070.i08>), semi-parametric (e.g., Simon et al
(2011) <doi:10.18637/jss.v039.i05>), and tree-based models (e.g.,
Buehlmann and Hothorn (2007) <doi:10.1214/07-STS242>).
Author: Emil Hvitfeldt [aut] ,
Hannah Frick [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>
Diff between censored versions 0.3.2 dated 2024-06-11 and 0.3.3 dated 2025-02-14
DESCRIPTION | 15 ++- MD5 | 43 ++++++---- NEWS.md | 7 + R/censored-package.R | 30 ++++++- R/survival_reg-data.R | 51 ++++++------ R/survival_reg-flexsurv.R | 43 ++++++++++ R/survival_reg-survival.R | 42 ++-------- README.md | 26 +++--- tests/testthat/_snaps/bag_tree-rpart.md | 8 ++ tests/testthat/_snaps/boost_tree-mboost.md |only tests/testthat/_snaps/decision_tree-partykit.md |only tests/testthat/_snaps/decision_tree-rpart.md |only tests/testthat/_snaps/proportional_hazards-survival.md | 8 ++ tests/testthat/_snaps/rand_forest-aorsf.md |only tests/testthat/_snaps/rand_forest-partykit.md |only tests/testthat/test-bag_tree-rpart.R | 31 +++++-- tests/testthat/test-boost_tree-mboost.R | 34 ++++++-- tests/testthat/test-decision_tree-partykit.R | 32 ++++++-- tests/testthat/test-decision_tree-rpart.R | 46 ++++++++--- tests/testthat/test-proportional_hazards-survival.R | 40 +++++++--- tests/testthat/test-rand_forest-aorsf.R | 47 +++++++++-- tests/testthat/test-rand_forest-partykit.R | 32 +++++--- tests/testthat/test-survival_reg-flexsurv.R | 67 ++++++++--------- tests/testthat/test-survival_reg-flexsurvspline.R | 58 ++++++-------- tests/testthat/test-survival_reg-survival.R | 39 +++++++-- 25 files changed, 458 insertions(+), 241 deletions(-)
Title: EcoPhyloMapper
Description: Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.
Author: Pascal Title [aut, cre] ,
Donald Swiderski [aut],
Miriam Zelditch [aut]
Maintainer: Pascal Title <pascal.title@stonybrook.edu>
Diff between epm versions 1.1.3 dated 2024-09-13 and 1.1.4 dated 2025-02-14
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/addTraits.R | 12 +++++++++++- R/plot.epmGrid.R | 6 +++++- R/plotDispersionField.R | 6 +++++- R/plotSpRange.R | 6 +++++- build/partial.rdb |binary man/plot.Rd | 2 +- man/plotDispersionField.Rd | 2 +- man/plotSpRange.Rd | 2 +- 10 files changed, 41 insertions(+), 19 deletions(-)
Title: Support Many Languages in R
Description: An object model for source text and translations. Find and extract
translatable strings. Provide translations and seamlessly retrieve them at
runtime.
Author: Jean-Mathieu Potvin [aut, cre, cph],
Jerome Lavoue [ctb, fnd, rev]
Maintainer: Jean-Mathieu Potvin <jeanmathieupotvin@ununoctium.dev>
Diff between transltr versions 0.0.1 dated 2025-01-24 and 0.1.0 dated 2025-02-14
transltr-0.0.1/transltr/R/constants.R |only transltr-0.0.1/transltr/R/translate-is-call.R |only transltr-0.0.1/transltr/R/translate.R |only transltr-0.0.1/transltr/man/translate-is-call.Rd |only transltr-0.0.1/transltr/man/translate.Rd |only transltr-0.0.1/transltr/tests/testthat/_snaps/constants.md |only transltr-0.0.1/transltr/tests/testthat/_snaps/normalize.md |only transltr-0.0.1/transltr/tests/testthat/_snaps/translate.md |only transltr-0.0.1/transltr/tests/testthat/test-constants.R |only transltr-0.0.1/transltr/tests/testthat/test-translate-is-call.R |only transltr-0.0.1/transltr/tests/testthat/test-translate.R |only transltr-0.1.0/transltr/DESCRIPTION | 26 transltr-0.1.0/transltr/MD5 | 155 ++--- transltr-0.1.0/transltr/NAMESPACE | 2 transltr-0.1.0/transltr/NEWS.md | 73 ++ transltr-0.1.0/transltr/R/aaa.R |only transltr-0.1.0/transltr/R/assert.R | 34 - transltr-0.1.0/transltr/R/class-location.R | 32 - transltr-0.1.0/transltr/R/class-text.R | 133 ++-- transltr-0.1.0/transltr/R/class-translator.R | 245 +++----- transltr-0.1.0/transltr/R/find-source-in-exprs.R | 122 ++-- transltr-0.1.0/transltr/R/find-source.R | 210 ++++-- transltr-0.1.0/transltr/R/flat.R | 26 transltr-0.1.0/transltr/R/hash.R | 35 + transltr-0.1.0/transltr/R/language.R | 5 transltr-0.1.0/transltr/R/normalize.R | 93 +-- transltr-0.1.0/transltr/R/serialize.R | 98 +-- transltr-0.1.0/transltr/R/text-io.R | 3 transltr-0.1.0/transltr/R/translator-io.R | 36 - transltr-0.1.0/transltr/R/transltr-package.R | 21 transltr-0.1.0/transltr/R/utils-format-vector.R | 48 - transltr-0.1.0/transltr/R/utils-strings.R | 31 - transltr-0.1.0/transltr/R/zzz.R | 16 transltr-0.1.0/transltr/README.md | 44 + transltr-0.1.0/transltr/inst |only transltr-0.1.0/transltr/man/assert.Rd | 40 - transltr-0.1.0/transltr/man/class-location-ranges.Rd | 6 transltr-0.1.0/transltr/man/class-location.Rd | 11 transltr-0.1.0/transltr/man/class-text.Rd | 107 +-- transltr-0.1.0/transltr/man/class-translator.Rd | 301 +++++----- transltr-0.1.0/transltr/man/constants.Rd | 43 - transltr-0.1.0/transltr/man/find-source-in-file.Rd | 81 +- transltr-0.1.0/transltr/man/find-source.Rd | 201 ++++-- transltr-0.1.0/transltr/man/flat.Rd | 20 transltr-0.1.0/transltr/man/hash.Rd | 13 transltr-0.1.0/transltr/man/language.Rd | 8 transltr-0.1.0/transltr/man/normalize.Rd | 48 - transltr-0.1.0/transltr/man/serialize.Rd | 39 - transltr-0.1.0/transltr/man/text-io.Rd | 11 transltr-0.1.0/transltr/man/translator-io.Rd | 44 - transltr-0.1.0/transltr/man/transltr-package.Rd | 18 transltr-0.1.0/transltr/man/utils-format-vector.Rd | 55 - transltr-0.1.0/transltr/man/utils-strings.Rd | 25 transltr-0.1.0/transltr/tests/testthat/_mocks/find-source/r-script1.R | 35 - transltr-0.1.0/transltr/tests/testthat/_mocks/find-source/r-script2.R | 34 - transltr-0.1.0/transltr/tests/testthat/_mocks/find-source/r-script3 | 11 transltr-0.1.0/transltr/tests/testthat/_mocks/find-source/r-script4.R |only transltr-0.1.0/transltr/tests/testthat/_snaps/class-text.md | 44 - transltr-0.1.0/transltr/tests/testthat/_snaps/class-translator.md | 54 + transltr-0.1.0/transltr/tests/testthat/_snaps/find-source.md | 27 transltr-0.1.0/transltr/tests/testthat/_snaps/serialize.md | 73 ++ transltr-0.1.0/transltr/tests/testthat/_snaps/translator-io.md | 6 transltr-0.1.0/transltr/tests/testthat/_snaps/translator-io/translations-write-el.txt | 4 transltr-0.1.0/transltr/tests/testthat/_snaps/translator-io/translator-write-el.txt | 4 transltr-0.1.0/transltr/tests/testthat/_snaps/translator-io/translator-write-es.txt | 4 transltr-0.1.0/transltr/tests/testthat/_snaps/translator-io/translator-write-fr.txt | 4 transltr-0.1.0/transltr/tests/testthat/_snaps/translator-io/translator-write-translator.yml | 6 transltr-0.1.0/transltr/tests/testthat/_snaps/utils-strings.md | 26 transltr-0.1.0/transltr/tests/testthat/test-aaa.R |only transltr-0.1.0/transltr/tests/testthat/test-assert.R | 40 - transltr-0.1.0/transltr/tests/testthat/test-class-location.R | 18 transltr-0.1.0/transltr/tests/testthat/test-class-text.R | 77 -- transltr-0.1.0/transltr/tests/testthat/test-class-translator.R | 86 +- transltr-0.1.0/transltr/tests/testthat/test-find-source-in-exprs.R | 123 ++-- transltr-0.1.0/transltr/tests/testthat/test-find-source.R | 88 +- transltr-0.1.0/transltr/tests/testthat/test-flat.R | 10 transltr-0.1.0/transltr/tests/testthat/test-language.R | 8 transltr-0.1.0/transltr/tests/testthat/test-normalize.R | 179 ++--- transltr-0.1.0/transltr/tests/testthat/test-serialize.R | 186 +++--- transltr-0.1.0/transltr/tests/testthat/test-text-io.R | 4 transltr-0.1.0/transltr/tests/testthat/test-translator-io.R | 55 - transltr-0.1.0/transltr/tests/testthat/test-utils-map.R | 8 transltr-0.1.0/transltr/tests/testthat/test-utils-stop.R | 3 transltr-0.1.0/transltr/tests/testthat/test-utils-strings.R | 50 + transltr-0.1.0/transltr/tests/testthat/test-uuid.R | 6 transltr-0.1.0/transltr/tests/testthat/test-zzz.R | 22 86 files changed, 2051 insertions(+), 1803 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> 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 3.1.0 dated 2024-12-17 and 3.2.0 dated 2025-02-14
DESCRIPTION | 13 +- MD5 | 42 ++++---- NAMESPACE | 3 NEWS.md | 8 + R/amp_scaling.R | 6 + R/cli_utils.R |only R/fit_display.R | 2 R/fit_svs.R | 179 ++++++++++++++++++++++++++++++-------- R/fitting.R | 16 ++- R/fmrs.R | 12 +- R/interactive_plotting.R | 2 R/mrs_read_dicom.R | 9 + R/qm_simulation.R | 2 inst/cli_scripts |only inst/doc/spant-intro.html | 130 +++++++++++++-------------- inst/doc/spant-preprocessing.html | 4 inst/rmd/dyn_svs_report.Rmd | 23 ++++ inst/rmd/svs_report.Rmd | 118 +++++++++++++++++++------ man/fit_svs.Rd | 33 +++++-- man/get_hrf.Rd |only man/install_cli.Rd |only man/one_page_pdf.Rd | 2 man/ortho3.Rd | 2 man/sim_basis.Rd | 2 24 files changed, 427 insertions(+), 181 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 3.0.3 dated 2024-12-15 and 3.0.4 dated 2025-02-14
DESCRIPTION | 6 MD5 | 56 +-- NAMESPACE | 4 NEWS.md | 10 R/CTS.R | 4 R/rxUiGet.R | 39 ++ R/rxode-options.R | 4 R/rxode2_md5.R | 2 R/rxrandom.R | 61 +++ data/rxReservedKeywords.rda |binary data/rxResidualError.rda |binary data/rxSyntaxFunctions.rda |binary inst/doc/rxode2-syntax.html | 712 ++++++++++++++++++++++++++---------------- inst/include/rxode2parseVer.h | 4 man/rxUdfUi.Rd | 5 man/rxUiGet.Rd | 6 man/rxnbinom.Rd | 6 man/rxode2.Rd | 77 +--- src/RcppExports.cpp | 4 src/codegen.h | 4 src/cvPost.cpp | 1 src/expandGrid.cpp | 2 src/init.c | 2 src/rxData.cpp | 2 src/rxnbinom.h |only src/rxthreefry.cpp | 52 +-- src/rxthreefry.h | 1 tests/testthat/test-nesting.R |only tests/testthat/test-random.R | 93 +++++ tests/testthat/test-udf.R | 3 30 files changed, 771 insertions(+), 389 deletions(-)
Title: Download Overture Maps Data in R
Description: Overture Maps offers free and open geospatial map data sourced from various providers and standardized to a common schema. This tool allows you to download Overture Maps data for a specific region of interest and convert it to several different file formats. For more information, visit <https://overturemaps.org/download/>.
Author: Dennis Irorere [aut, cre, cph]
Maintainer: Dennis Irorere <denironyx@gmail.com>
Diff between overturemapsr versions 0.0.4 dated 2024-06-24 and 0.1.0 dated 2025-02-14
overturemapsr-0.0.4/overturemapsr/man/get_all_overture_types.Rd |only overturemapsr-0.1.0/overturemapsr/DESCRIPTION | 9 overturemapsr-0.1.0/overturemapsr/MD5 | 21 - overturemapsr-0.1.0/overturemapsr/NAMESPACE | 7 overturemapsr-0.1.0/overturemapsr/NEWS.md | 22 + overturemapsr-0.1.0/overturemapsr/R/core.R | 116 ++++++++-- overturemapsr-0.1.0/overturemapsr/R/utils.R | 6 overturemapsr-0.1.0/overturemapsr/README.md | 23 + overturemapsr-0.1.0/overturemapsr/man/dataset_path.Rd | 13 - overturemapsr-0.1.0/overturemapsr/man/get_all_overture_schema_types.Rd |only overturemapsr-0.1.0/overturemapsr/man/get_dataset_metadata.Rd |only overturemapsr-0.1.0/overturemapsr/man/record_batch_reader.Rd | 11 overturemapsr-0.1.0/overturemapsr/tests/testthat/test-1-core.R | 6 13 files changed, 173 insertions(+), 61 deletions(-)
Title: Routines for Performing Empirical Calibration of Observational
Study Estimates
Description: Routines for performing empirical calibration of observational
study estimates. By using a set of negative control hypotheses we can
estimate the empirical null distribution of a particular observational
study setup. This empirical null distribution can be used to compute a
calibrated p-value, which reflects the probability of observing an
estimated effect size when the null hypothesis is true taking both random
and systematic error into account. A similar approach can be used to
calibrate confidence intervals, using both negative and positive controls.
For more details, see Schuemie et al. (2013) <doi:10.1002/sim.5925> and
Schuemie et al. (2018) <doi:10.1073/pnas.1708282114>.
Author: Martijn Schuemie [aut, cre] ,
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between EmpiricalCalibration versions 3.1.3 dated 2024-09-30 and 3.1.4 dated 2025-02-14
DESCRIPTION | 8 MD5 | 46 +-- NEWS.md | 13 R/ConfidenceIntervalCalibration.R | 2 R/Data.R | 2 R/EmpiricalCalibration.R | 2 R/EmpiricalCalibrationUsingAsymptotics.R | 11 R/EmpiricalCalibrationUsingMcmc.R | 9 R/Evaluation.R | 2 R/ExpectedSystematicError.R | 30 +- R/Likelihoods.R | 2 R/LlrCalibration.R | 2 R/MaxSprtCriticalValues.R | 2 R/Plots.R | 2 R/Simulation.R | 2 inst/doc/EmpiricalCiCalibrationVignette.pdf |binary inst/doc/EmpiricalMaxSprtCalibrationVignette.R | 176 ++++++------- inst/doc/EmpiricalMaxSprtCalibrationVignette.pdf |binary inst/doc/EmpiricalPCalibrationVignette.pdf |binary src/RcppWrapper.cpp | 2 tests/testthat/test-EmpiricalCalibrationUsingAsymptotics.R | 11 tests/testthat/test-LlrCalibration.R | 110 ++++---- tests/testthat/test-asymptoticNull.R | 5 tests/testthat/test-empiricalCalibrationUsingMcmc.R | 3 24 files changed, 238 insertions(+), 204 deletions(-)
More information about EmpiricalCalibration at CRAN
Permanent link
Title: Statistical Evaluation of UMAP Dimensionality Reductions
Description: A metric expressing the quality of a UMAP layout. This is a
package that contains the Saturn_coefficient() function that reads an
input matrix, its dimensionality reduction produced by UMAP, and
evaluates the quality of this dimensionality reduction by producing a
real value in the [0; 1] interval. We call this real value Saturn
coefficient. A higher value means better dimensionality reduction; a
lower value means worse dimensionality reduction.
Reference: Davide Chicco et al. "The Saturn coefficient for evaluating
the quality of UMAP dimensionality reduction results" (2025, in preparation).
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Diff between SaturnCoefficient versions 1.3 dated 2024-12-17 and 1.4 dated 2025-02-14
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/Saturn_coefficient.r | 7 ++++--- 3 files changed, 9 insertions(+), 8 deletions(-)
More information about SaturnCoefficient at CRAN
Permanent link
Title: Tools to Match Corporate Lending Portfolios with Climate Data
Description: These tools implement in R a fundamental part of the software
'PACTA' (Paris Agreement Capital Transition Assessment), which is a
free tool that calculates the alignment between financial portfolios
and climate scenarios (<https://www.transitionmonitor.com/>). Financial
institutions use 'PACTA' to study how their capital allocation
decisions align with climate change mitigation goals. This package
matches data from corporate lending portfolios to asset level data
from market-intelligence databases (e.g. power plant capacities,
emission factors, etc.). This is the first step to assess if a
financial portfolio aligns with climate goals.
Author: Jacob Kastl [aut, cre, ctr] ,
Alex Axthelm [aut, ctr] ,
Jackson Hoffart [aut, ctr] ,
Mauro Lepore [aut, ctr] ,
Klaus Hagedorn [aut],
Florence Palandri [aut],
Evgeny Petrovsky [aut],
RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>
Diff between r2dii.match versions 0.3.0 dated 2024-12-04 and 0.4.0 dated 2025-02-14
DESCRIPTION | 29 +++++++++++++++-------------- MD5 | 17 ++++++++++------- NEWS.md | 6 ++++++ R/data_dictionary.R |only README.md | 2 +- data |only man/data_dictionary.Rd |only man/r2dii.match-package.Rd | 4 ++-- tests/testthat.R | 2 ++ tests/testthat/test-match_name.R | 27 +++++++++++++++++++++++++++ tests/testthat/test-prioritize.R | 39 +++++++++++++++++++++++++++++++++++++++ 11 files changed, 102 insertions(+), 24 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot
Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [ctb] ,
Wenping Wang [aut],
Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2plot versions 3.0.0 dated 2024-09-18 and 3.0.1 dated 2025-02-14
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 1 + NEWS.md | 4 ++++ R/nlmixr2PlotList.R | 37 +++++++++++++++++++++++++++++++++++++ tests/testthat/test-add.R |only 6 files changed, 51 insertions(+), 8 deletions(-)