Title: Applying Landscape Genomic Methods on 'SNP' and 'Silicodart'
Data
Description: Provides landscape genomic functions to analyse 'SNP' (single nuclear
polymorphism) data, such as least cost path analysis and isolation by distance.
Therefore each sample needs to have coordinate data attached (lat/lon) to be
able to run most of the functions. 'dartR.spatial' is a package that belongs
to the 'dartRverse' suit of packages and depends on 'dartR.base' and 'dartR.data'.
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.spatial versions 0.78 dated 2023-11-14 and 1.0.3 dated 2025-08-21
DESCRIPTION | 16 - MD5 | 21 +- NAMESPACE | 6 R/gl.genleastcost.r | 93 ++++++--- R/gl.grm2.r | 2 R/gl.run.eems.r |only R/gl.spatial.autoCorr.r | 34 ++- R/gl2shp.r | 10 build |only man/gl.genleastcost.Rd | 65 +++--- man/gl.grm2.Rd | 176 ++++++++--------- man/gl.run.eems.Rd |only man/gl.spatial.autoCorr.Rd | 465 ++++++++++++++++++++++----------------------- 13 files changed, 478 insertions(+), 410 deletions(-)
Title: Visualising and Interpreting Statistical Models Fit to
Compositional Data
Description: Statistical models fit to compositional data are often difficult to interpret due to the sum to 1 constraint on data variables. 'DImodelsVis' provides novel visualisations tools to aid with the interpretation of models fit to compositional data. All visualisations in the package are created using the 'ggplot2' plotting framework and can be extended like every other 'ggplot' object.
Author: Rishabh Vishwakarma [aut, cre] ,
Caroline Brophy [aut],
Laura Byrne [aut],
Catherine Hurley [aut]
Maintainer: Rishabh Vishwakarma <vishwakr@tcd.ie>
Diff between DImodelsVis versions 1.0.1 dated 2024-02-26 and 1.0.2 dated 2025-08-21
DImodelsVis-1.0.1/DImodelsVis/R/Utilities.R |only DImodelsVis-1.0.2/DImodelsVis/DESCRIPTION | 24 DImodelsVis-1.0.2/DImodelsVis/MD5 | 207 - DImodelsVis-1.0.2/DImodelsVis/NAMESPACE | 358 +- DImodelsVis-1.0.2/DImodelsVis/NEWS.md | 11 DImodelsVis-1.0.2/DImodelsVis/R/ConditionalTernary.R | 26 DImodelsVis-1.0.2/DImodelsVis/R/GradientChange.R | 22 DImodelsVis-1.0.2/DImodelsVis/R/GroupedTernary.R | 85 DImodelsVis-1.0.2/DImodelsVis/R/ModelDiagnostics.R | 957 ++++-- DImodelsVis-1.0.2/DImodelsVis/R/ModelSelection.R | 256 + DImodelsVis-1.0.2/DImodelsVis/R/PredictionContributions.R | 159 - DImodelsVis-1.0.2/DImodelsVis/R/SanityChecks.R | 106 DImodelsVis-1.0.2/DImodelsVis/R/SimplexPath.R | 27 DImodelsVis-1.0.2/DImodelsVis/R/Ternary.R | 68 DImodelsVis-1.0.2/DImodelsVis/R/VisualiseEffects.R | 49 DImodelsVis-1.0.2/DImodelsVis/R/utilities.R |only DImodelsVis-1.0.2/DImodelsVis/README.md | 91 DImodelsVis-1.0.2/DImodelsVis/build/partial.rdb |binary DImodelsVis-1.0.2/DImodelsVis/build/vignette.rds |binary DImodelsVis-1.0.2/DImodelsVis/inst/WORDLIST | 25 DImodelsVis-1.0.2/DImodelsVis/inst/doc/DImodelsVis-with-DImodelsMulti-models.R |only DImodelsVis-1.0.2/DImodelsVis/inst/doc/DImodelsVis-with-DImodelsMulti-models.Rmd |only DImodelsVis-1.0.2/DImodelsVis/inst/doc/DImodelsVis-with-DImodelsMulti-models.html |only DImodelsVis-1.0.2/DImodelsVis/inst/doc/DImodelsVis-with-complex-models.R | 488 ++- DImodelsVis-1.0.2/DImodelsVis/inst/doc/DImodelsVis-with-complex-models.Rmd | 770 +++- DImodelsVis-1.0.2/DImodelsVis/inst/doc/DImodelsVis-with-complex-models.html | 1547 ++++++---- DImodelsVis-1.0.2/DImodelsVis/man/DImodelsVis-package.Rd | 460 +- DImodelsVis-1.0.2/DImodelsVis/man/Simplex_projection.Rd | 136 DImodelsVis-1.0.2/DImodelsVis/man/add_ID_terms.Rd | 98 DImodelsVis-1.0.2/DImodelsVis/man/add_add_var.Rd | 116 DImodelsVis-1.0.2/DImodelsVis/man/add_interaction_terms.Rd | 94 DImodelsVis-1.0.2/DImodelsVis/man/add_prediction.Rd | 298 - DImodelsVis-1.0.2/DImodelsVis/man/conditional_ternary.Rd | 352 +- DImodelsVis-1.0.2/DImodelsVis/man/conditional_ternary_data.Rd | 392 +- DImodelsVis-1.0.2/DImodelsVis/man/conditional_ternary_plot.Rd | 280 - DImodelsVis-1.0.2/DImodelsVis/man/copy_attributes.Rd | 122 DImodelsVis-1.0.2/DImodelsVis/man/custom_filter.Rd | 158 - DImodelsVis-1.0.2/DImodelsVis/man/figures/DImodelsVisWorkflowPackage.png |binary DImodelsVis-1.0.2/DImodelsVis/man/figures/DImodelsVisWorkflowPackage_old.png |only DImodelsVis-1.0.2/DImodelsVis/man/figures/README-cond-ternary-1.png |binary DImodelsVis-1.0.2/DImodelsVis/man/figures/README-effects-plot-1.png |binary DImodelsVis-1.0.2/DImodelsVis/man/figures/README-gradient-change-1.png |binary DImodelsVis-1.0.2/DImodelsVis/man/figures/README-model-diagnostics-1.png |binary DImodelsVis-1.0.2/DImodelsVis/man/figures/README-model-selection-1.png |binary DImodelsVis-1.0.2/DImodelsVis/man/figures/README-prediction-contributions-1.png |binary DImodelsVis-1.0.2/DImodelsVis/man/figures/README-simplex-path-1.png |binary DImodelsVis-1.0.2/DImodelsVis/man/get_colours.Rd | 70 DImodelsVis-1.0.2/DImodelsVis/man/get_equi_comms.Rd | 134 DImodelsVis-1.0.2/DImodelsVis/man/get_shades.Rd | 58 DImodelsVis-1.0.2/DImodelsVis/man/gradient_change.Rd | 392 +- DImodelsVis-1.0.2/DImodelsVis/man/gradient_change_data.Rd | 424 +- DImodelsVis-1.0.2/DImodelsVis/man/gradient_change_plot.Rd | 330 +- DImodelsVis-1.0.2/DImodelsVis/man/group_prop.Rd | 78 DImodelsVis-1.0.2/DImodelsVis/man/grouped_ternary.Rd | 374 +- DImodelsVis-1.0.2/DImodelsVis/man/grouped_ternary_data.Rd | 418 +- DImodelsVis-1.0.2/DImodelsVis/man/grouped_ternary_plot.Rd | 296 - DImodelsVis-1.0.2/DImodelsVis/man/model_diagnostics.Rd | 258 - DImodelsVis-1.0.2/DImodelsVis/man/model_diagnostics_data.Rd |only DImodelsVis-1.0.2/DImodelsVis/man/model_diagnostics_plot.Rd |only DImodelsVis-1.0.2/DImodelsVis/man/model_selection.Rd | 252 - DImodelsVis-1.0.2/DImodelsVis/man/model_selection_data.Rd |only DImodelsVis-1.0.2/DImodelsVis/man/model_selection_plot.Rd |only DImodelsVis-1.0.2/DImodelsVis/man/prediction_contributions.Rd | 396 +- DImodelsVis-1.0.2/DImodelsVis/man/prediction_contributions_data.Rd | 380 +- DImodelsVis-1.0.2/DImodelsVis/man/prediction_contributions_plot.Rd | 206 - DImodelsVis-1.0.2/DImodelsVis/man/simplex_path.Rd | 376 +- DImodelsVis-1.0.2/DImodelsVis/man/simplex_path_data.Rd | 334 +- DImodelsVis-1.0.2/DImodelsVis/man/simplex_path_plot.Rd | 246 - DImodelsVis-1.0.2/DImodelsVis/man/ternary_data.Rd | 362 +- DImodelsVis-1.0.2/DImodelsVis/man/ternary_plot.Rd | 342 +- DImodelsVis-1.0.2/DImodelsVis/man/theme_DI.Rd | 84 DImodelsVis-1.0.2/DImodelsVis/man/visualise_effects.Rd | 382 +- DImodelsVis-1.0.2/DImodelsVis/man/visualise_effects_data.Rd | 436 +- DImodelsVis-1.0.2/DImodelsVis/man/visualise_effects_plot.Rd | 216 - DImodelsVis-1.0.2/DImodelsVis/tests/testthat |only DImodelsVis-1.0.2/DImodelsVis/tests/testthat.R |only DImodelsVis-1.0.2/DImodelsVis/vignettes/DImodelsVis-with-DImodelsMulti-models.Rmd |only DImodelsVis-1.0.2/DImodelsVis/vignettes/DImodelsVis-with-complex-models.Rmd | 770 +++- 78 files changed, 8927 insertions(+), 6469 deletions(-)
Title: Experimental Data of Cascade Experiments in Genomics
Description: These experimental expression data (5 leukemic 'CLL' B-lymphocyte of aggressive form from 'GSE39411', <doi:10.1073/pnas.1211130110>), after B-cell receptor stimulation, are used as examples by packages such as the 'Cascade' one, a modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between CascadeData versions 1.4 dated 2022-11-28 and 1.5 dated 2025-08-21
DESCRIPTION | 21 +++++++++------- MD5 | 27 +++++++++++++------- NEWS.md | 5 +++ R/CascadeData-package.R | 39 +++++------------------------- R/Datasets.R | 37 ++++++++++++++++++++++++---- README.md | 58 +++++++++++++++++++++++++++------------------ build/partial.rdb |binary inst/CITATION | 36 ++++++++++++++++++++------- inst/_pkgdown.yml |only man/CascadeData-package.Rd | 40 ++++++++++--------------------- man/micro_S.Rd | 13 +++++++++- man/micro_US.Rd | 14 ++++++++++ tests |only 13 files changed, 173 insertions(+), 117 deletions(-)
Title: A Button-Based GUI for Financial and Economic Data Analysis
Description: A GUI designed to support the analysis of financial-economic time
series data.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between iClick versions 1.5 dated 2018-11-22 and 1.6 dated 2025-08-21
iClick-1.5/iClick/man/FFplusMOM.Rd |only iClick-1.5/iClick/man/IBM.Rd |only iClick-1.5/iClick/man/returnsDaily24.Rd |only iClick-1.5/iClick/man/world20.Rd |only iClick-1.6/iClick/DESCRIPTION | 21 ++++--- iClick-1.6/iClick/MD5 | 41 ++++++++----- iClick-1.6/iClick/NAMESPACE | 13 ++-- iClick-1.6/iClick/R/VisAssetPrice_Calendar.R | 39 ++++++++----- iClick-1.6/iClick/R/fin_GARCH.R |only iClick-1.6/iClick/R/fin_JFE.R |only iClick-1.6/iClick/R/fin_Portfolio.R |only iClick-1.6/iClick/R/fin_PortoflioMore.R |only iClick-1.6/iClick/R/fin_assetsSelection.R |only iClick-1.6/iClick/R/fin_getTWSE.fiveSecond.R |only iClick-1.6/iClick/R/fin_price.R |only iClick-1.6/iClick/R/fin_returns.R |only iClick-1.6/iClick/R/fin_utilities.R |only iClick-1.6/iClick/R/iClick_ARIMA.R | 7 +- iClick-1.6/iClick/R/iClick_GARCH.R | 50 ++++++++-------- iClick-1.6/iClick/R/iClick_VisAssetPrice.R | 78 ++++++++++++++++++++------ iClick-1.6/iClick/R/iClick_functions.R | 11 --- iClick-1.6/iClick/R/iClick_lm.R | 2 iClick-1.6/iClick/data/assetReturns.rda |only iClick-1.6/iClick/man/JFE.Rd |only iClick-1.6/iClick/man/calendarHeat.Rd | 13 +++- iClick-1.6/iClick/man/cutAndStack.Rd | 2 iClick-1.6/iClick/man/data-sets.Rd |only iClick-1.6/iClick/man/getTWSE.fiveSecond.Rd |only iClick-1.6/iClick/man/iClick.ARIMA.Rd | 10 --- iClick-1.6/iClick/man/riskOptimalPortfolio.Rd |only iClick-1.6/iClick/man/riskParityPortfolio.Rd |only 31 files changed, 175 insertions(+), 112 deletions(-)
Title: Data Access and Analytical Tools for 'VectorSurv' Users
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Diff between vectorsurvR versions 1.5.1 dated 2025-07-09 and 1.5.2 dated 2025-08-21
DESCRIPTION | 6 MD5 | 26 R/data.R | 8 R/getAbundance.R | 25 R/getAbundanceAnomaly.R | 2 data/sample_collections.rda |binary data/sample_pools.rda |binary inst/doc/vectorsurvR.R | 26 inst/doc/vectorsurvR.html | 2085 ++++++++++++++++++-------------------------- man/getAbundance.Rd | 2 man/getAbundanceAnomaly.Rd | 2 man/sample_collections.Rd | 3 man/sample_pools.Rd | 2 man/sample_spatial.Rd | 2 14 files changed, 945 insertions(+), 1244 deletions(-)
Title: Dump 'R' Package Source, Documentation, and Vignettes into One
File
Description: Dump source code, documentation and vignettes of an 'R'
package into a single file. Supports installed packages, tar.gz
archives, and package source directories. If the package is not
installed, only its source is automatically downloaded from CRAN for
processing. The output is a single plain text file or a character
vector, which is useful to ingest complete package documentation and
source into a large language model (LLM) or pass it further to other
tools, such as 'ragnar' <https://github.com/tidyverse/ragnar> to
create a Retrieval-Augmented Generation (RAG) workflow.
Author: Egor Kotov [aut, cre, cph]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between rdocdump versions 0.1.0 dated 2025-06-18 and 0.1.1 dated 2025-08-21
DESCRIPTION | 6 - MD5 | 24 ++--- NEWS.md | 4 R/extract_code.R | 51 +++++++---- R/to_txt.R | 17 ++- R/util_resolve_pkg_path.R | 66 +++++++++++++- README.md | 11 ++ inst/doc/rdocdump.html | 2 inst/schemaorg.json | 8 + man/rdd_extract_code.Rd | 31 +++--- man/rdd_to_txt.Rd | 5 - man/resolve_pkg_path.Rd | 5 - tests/testthat/test-to_txt.R | 194 ++++++++++++++++++++++++++++++++++++++++++- 13 files changed, 359 insertions(+), 65 deletions(-)
Title: Sensitivity Analysis Using Weighted Rank Statistics
Description: Performs a sensitivity analysis using weighted rank tests in observational studies with I blocks of size J; see Rosenbaum (2024) <doi:10.1080/01621459.2023.2221402>. The package can perform adaptive inference in block designs; see Rosenbaum (2012) <doi:10.1093/biomet/ass032>. The main functions are wgtRank(), wgtRankCI() and wgtRanktt().
Author: Paul Rosenbaum [aut, cre]
Maintainer: Paul Rosenbaum <rosenbaum@wharton.upenn.edu>
Diff between weightedRank versions 0.3.7 dated 2024-07-06 and 0.5.1 dated 2025-08-21
DESCRIPTION | 6 +- MD5 | 22 ++++---- R/estPower.R |only R/wgtRank.R | 144 ++++++++++++++++++++++++++++-------------------------- R/wgtRanktt.R | 55 +++++++++++++------- build/partial.rdb |binary man/dwgtRank.Rd | 6 +- man/estPower.Rd |only man/gwgtRank.Rd | 5 + man/wgtRank.Rd | 12 +++- man/wgtRankC.Rd | 14 +++-- man/wgtRankCI.Rd | 5 + man/wgtRanktt.Rd | 38 ++++++++++++-- 13 files changed, 188 insertions(+), 119 deletions(-)
Title: Foundations Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app/>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver," symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.19 dated 2025-03-18 and 1.20 dated 2025-08-21
DESCRIPTION | 15 ++++++++------- MD5 | 30 +++++++++++++++++++----------- NAMESPACE | 5 ++++- NEWS.md | 10 ++++++++++ R/prop.conf.R |only R/t_conf.R |only R/z.conf.R |only README.md | 4 ++-- data/caravan.RData |only data/datalist | 1 + inst/doc/liver-example.R | 4 ++-- inst/doc/liver-example.Rmd | 6 +++--- inst/doc/liver-example.html | 19 ++++++++++--------- man/caravan.Rd |only man/churn.Rd | 8 ++++---- man/liver-package.Rd | 5 +++-- man/prop.conf.Rd |only man/t_conf.Rd |only man/z.conf.Rd |only vignettes/liver-example.Rmd | 6 +++--- 20 files changed, 69 insertions(+), 44 deletions(-)
Title: A 'shiny' App for Reproducible QA/QC of Eddy Covariance Data
Description: An interactive 'shiny'-based tool for exploration and quality
assurance and quality control (QA/QC) of eddy covariance flux tower
data processing. It generates data-point removal code via
user-directed selection from a scatterplot, and can export a cleaned
.csv with removed points set to NA plus an R script for
reproducibility. Reference: Key (2025) <DOI:10.5281/zenodo.15597159>.
Author: Kesondra Key [aut, cre]
Maintainer: Kesondra Key <keyke@iu.edu>
Diff between fluxtools versions 0.4.0 dated 2025-07-20 and 0.5.0 dated 2025-08-21
fluxtools-0.4.0/fluxtools/inst/extdata |only fluxtools-0.4.0/fluxtools/man/run_flux_qaqc.Rd |only fluxtools-0.5.0/fluxtools/DESCRIPTION | 23 fluxtools-0.5.0/fluxtools/MD5 | 34 fluxtools-0.5.0/fluxtools/NAMESPACE | 4 fluxtools-0.5.0/fluxtools/NEWS.md | 26 fluxtools-0.5.0/fluxtools/R/prm.R |only fluxtools-0.5.0/fluxtools/R/run_app.R | 88 fluxtools-0.5.0/fluxtools/R/zzz.R | 14 fluxtools-0.5.0/fluxtools/README.md | 176 fluxtools-0.5.0/fluxtools/inst/CITATION | 32 fluxtools-0.5.0/fluxtools/inst/app/app.R | 3263 +++++++++------ fluxtools-0.5.0/fluxtools/inst/doc/introduction.R | 66 fluxtools-0.5.0/fluxtools/inst/doc/introduction.Rmd | 85 fluxtools-0.5.0/fluxtools/inst/doc/introduction.html | 2108 +++++++++ fluxtools-0.5.0/fluxtools/man/apply_prm.Rd |only fluxtools-0.5.0/fluxtools/man/figures/fluxtools-logo.png |binary fluxtools-0.5.0/fluxtools/man/get_prm_rules.Rd |only fluxtools-0.5.0/fluxtools/man/run_fluxtools.Rd |only fluxtools-0.5.0/fluxtools/tests |only fluxtools-0.5.0/fluxtools/vignettes/introduction.Rmd | 85 21 files changed, 4599 insertions(+), 1405 deletions(-)
Title: Hasse Diagram of the Layout Structure and Restricted Layout
Structure
Description: Returns a Hasse diagram of the layout structure (Bate and Chatfield (2016)) <doi:10.1080/00224065.2016.11918173> or the restricted layout structure (Bate and Chatfield (2016)) <doi:10.1080/00224065.2016.11918174> of an experimental design.
Author: Damianos Michaelides [aut, cre],
Simon Bate [aut],
Marion Chatfield [aut]
Maintainer: Damianos Michaelides <dm3g15@soton.ac.uk>
Diff between hassediagrams versions 1.0 dated 2025-06-11 and 1.1 dated 2025-08-21
DESCRIPTION | 8 +++---- MD5 | 44 ++++++++++++++++++++-------------------- R/analytical.R | 2 - R/concrete.R | 2 - R/dental.R | 4 +-- R/hasselayout.R | 41 +++++++++++++++++++++++++++----------- R/hasserls.R | 56 +++++++++++++++++++++++++++++++++++++++------------- R/human.R | 2 - R/itemlist.R | 16 +++++++++++--- build/partial.rdb |binary build/vignette.rds |binary data/analytical.rda |binary data/concrete.rda |binary data/dental.csv | 4 +-- data/dental.rda |binary data/human.rda |binary man/analytical.Rd | 2 - man/concrete.Rd | 2 - man/dental.Rd | 4 +-- man/hasselayout.Rd | 10 ++++----- man/hasserls.Rd | 16 ++++++++++++-- man/human.Rd | 2 - man/itemlist.Rd | 8 +++---- 23 files changed, 144 insertions(+), 79 deletions(-)
Title: 'teal' Modules for Standard Clinical Outputs
Description: Provides user-friendly tools for creating and customizing
clinical trial reports. By leveraging the 'teal' framework, this
package provides 'teal' modules to easily create an interactive panel
that allows for seamless adjustments to data presentation, thereby
streamlining the creation of detailed and accurate reports.
Author: Joe Zhu [aut] ,
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Mahmoud Hallal [aut],
Dawid Kaledkowski [aut, cre],
Rosemary Li [aut],
Heng Wang [aut],
Pawel Rucki [aut],
Nikolas Burkoff [aut],
Konrad Pag [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.modules.clinical versions 0.10.0 dated 2025-02-28 and 0.11.0 dated 2025-08-21
teal.modules.clinical-0.10.0/teal.modules.clinical/inst/css |only teal.modules.clinical-0.11.0/teal.modules.clinical/DESCRIPTION | 55 - teal.modules.clinical-0.11.0/teal.modules.clinical/MD5 | 352 +++++----- teal.modules.clinical-0.11.0/teal.modules.clinical/NAMESPACE | 3 teal.modules.clinical-0.11.0/teal.modules.clinical/NEWS.md | 16 teal.modules.clinical-0.11.0/teal.modules.clinical/R/arm_ref_comp.R | 4 teal.modules.clinical-0.11.0/teal.modules.clinical/R/facet_grid_formula.R | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/R/teal.modules.clinical.R | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_a_gee.R | 19 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_a_mmrm.R | 71 +- teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_barchart_simple.R | 49 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_ci.R | 23 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_forest_rsp.R | 29 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_forest_tte.R | 35 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_ipp.R | 44 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_km.R | 93 +- teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_lineplot.R | 53 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_pp_adverse_events.R | 70 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_pp_patient_timeline.R | 11 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_pp_therapy.R | 62 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_g_pp_vitals.R | 36 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_abnormality.R | 39 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_abnormality_by_worst_grade.R | 28 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_ancova.R | 49 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_binary_outcome.R | 96 +- teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_coxreg.R | 38 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_events.R | 79 +- teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_events_by_grade.R | 83 +- teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_events_patyear.R | 32 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_events_summary.R | 51 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_exposure.R | 30 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_glm_counts.R |only teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_logistic.R | 28 teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_mult_events.R | 46 - teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_pp_basic_info.R | 91 +- teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_pp_laboratory.R | 161 +--- teal.modules.clinical-0.11.0/teal.modules.clinical/R/tm_t_pp_medical_history.R | 11 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teal.modules.clinical-0.11.0/teal.modules.clinical/inst/doc/decorate-module-output.html | 16 teal.modules.clinical-0.11.0/teal.modules.clinical/inst/doc/generate_tmc_test_data.html | 4 teal.modules.clinical-0.11.0/teal.modules.clinical/inst/doc/quickstart_substitute.R | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/inst/doc/quickstart_substitute.Rmd | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/inst/doc/quickstart_substitute.html | 26 teal.modules.clinical-0.11.0/teal.modules.clinical/inst/doc/teal-modules-clinical.html | 4 teal.modules.clinical-0.11.0/teal.modules.clinical/man/arm_ref_comp_observer.Rd | 1 teal.modules.clinical-0.11.0/teal.modules.clinical/man/bracket_expr.Rd | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/man/check_arm_ref_comp.Rd | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/man/control_tte.Rd | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/man/default_total_label.Rd | 2 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| 2 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_g_ipp.Rd | 3 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_g_km.Rd | 14 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_g_lineplot.Rd | 3 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_laboratory.Rd | 6 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_logistic.Rd | 3 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_mult_events.Rd | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_shift_by_arm.Rd | 5 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_shift_by_arm_by_worst.Rd | 5 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_shift_by_grade.Rd | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_smq.Rd | 2 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_summary.Rd | 5 teal.modules.clinical-0.11.0/teal.modules.clinical/man/template_summary_by.Rd | 2 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teal.modules.clinical-0.11.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_basic_info.R | 8 teal.modules.clinical-0.11.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_laboratory.R | 18 teal.modules.clinical-0.11.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_medical_history.R | 12 teal.modules.clinical-0.11.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_prior_medication.R | 14 teal.modules.clinical-0.11.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_shift_by_arm.R | 10 teal.modules.clinical-0.11.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_shift_by_arm_by_worst.R | 14 teal.modules.clinical-0.11.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_shift_by_grade.R | 10 teal.modules.clinical-0.11.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_smq.R | 10 teal.modules.clinical-0.11.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_summary.R | 8 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More information about teal.modules.clinical at CRAN
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Title: Enhance 'Quarto' Project Workflows and Standards
Description: Streamlines 'Quarto' workflows by providing tools for consistent project setup and documentation. Enables portability through reusable metadata, automated project structure creation, and standardized templates. Features include enhanced project initialization, pre-formatted 'Quarto' documents, inclusion of 'Quarto' brand functionality, comprehensive data protection settings, custom styling, and structured documentation generation. Designed to improve efficiency and collaboration in R data science projects by reducing repetitive setup tasks while maintaining consistent formatting across multiple documents.
Author: Kyle Grealis [aut, cre]
Maintainer: Kyle Grealis <kyleGrealis@icloud.com>
Diff between froggeR versions 0.5.1 dated 2025-07-22 and 0.5.2 dated 2025-08-21
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- README.md | 2 +- inst/doc/customizing-quarto.Rmd | 2 +- inst/doc/customizing-quarto.html | 2 +- inst/doc/hopping-into-quarto.Rmd | 10 +++++----- inst/doc/hopping-into-quarto.html | 12 ++++++------ inst/doc/quarto-workflow.Rmd | 2 +- inst/doc/quarto-workflow.html | 4 ++-- vignettes/customizing-quarto.Rmd | 2 +- vignettes/hopping-into-quarto.Rmd | 10 +++++----- vignettes/quarto-workflow.Rmd | 2 +- 12 files changed, 39 insertions(+), 39 deletions(-)
Title: Easy Visualization of Conditional Effects from Regression Models
Description: Offers a flexible and user-friendly interface for visualizing conditional
effects from a broad range of regression models, including mixed-effects and generalized
additive (mixed) models. Compatible model types include lm(), rlm(), glm(), glm.nb(),
and gam() (from 'mgcv'); nonlinear models via nls(); and generalized least squares via
gls(). Mixed-effects models with random intercepts and/or slopes can be fitted using
lmer(), glmer(), glmer.nb(), glmmTMB(), or gam() (from 'mgcv', via smooth terms).
Plots are rendered using base R graphics with extensive customization options.
Approximate confidence intervals for nls() models are computed using the delta method.
Robust standard errors for rlm() are computed using the sandwich estimator (Zeileis 2004)
<doi:10.18637/jss.v011.i10>. Methods for generalized additive models follow Wood (2017)
<doi:10.1201/9781315370279>. For linear mixed-effects models with 'lme4', see
Bates et al. (2015) <doi:10.18637/jss.v067.i01>. For mixe [...truncated...]
Author: Luca Corlatti [aut, cre]
Maintainer: Luca Corlatti <lucac1980@yahoo.it>
Diff between easyViz versions 1.0.0 dated 2025-07-22 and 1.1.0 dated 2025-08-21
easyViz-1.0.0/easyViz/R/easyViz_1.0.0.R |only easyViz-1.1.0/easyViz/DESCRIPTION | 20 +- easyViz-1.1.0/easyViz/MD5 | 9 easyViz-1.1.0/easyViz/NAMESPACE | 5 easyViz-1.1.0/easyViz/NEWS.md |only easyViz-1.1.0/easyViz/R/easyViz_1.1.0.R |only easyViz-1.1.0/easyViz/man/easyViz.Rd | 318 ++++++++++++++++++++++++-------- 7 files changed, 270 insertions(+), 82 deletions(-)
Title: Graded Response Model
Description: Simulation and analysis of graded response data with different types of estimators. Also, an interactive shiny application is provided with graphics for characteristic and information curves. Samejima (2018) <doi:10.1007/978-1-4757-2691-6_5>.
Author: Sooyong Lee [aut, cre],
Tiffany Whittaker [aut],
Laura Stapleton [aut]
Maintainer: Sooyong Lee <sooyongl09@gmail.com>
Diff between GRShiny versions 1.0.0 dated 2023-05-03 and 1.0.1 dated 2025-08-21
GRShiny-1.0.0/GRShiny/man/figures |only GRShiny-1.0.1/GRShiny/DESCRIPTION | 12 GRShiny-1.0.1/GRShiny/MD5 | 49 +-- GRShiny-1.0.1/GRShiny/R/GRShiny-package.r | 3 GRShiny-1.0.1/GRShiny/R/model_grm.r | 20 - GRShiny-1.0.1/GRShiny/R/plot.r | 14 - GRShiny-1.0.1/GRShiny/README.md | 6 GRShiny-1.0.1/GRShiny/build/vignette.rds |binary GRShiny-1.0.1/GRShiny/inst/doc/GRShiny.R | 4 GRShiny-1.0.1/GRShiny/inst/doc/GRShiny.Rmd | 4 GRShiny-1.0.1/GRShiny/inst/doc/GRShiny.html | 276 ++++++++++---------- GRShiny-1.0.1/GRShiny/man/ESplot.Rd | 98 +++---- GRShiny-1.0.1/GRShiny/man/FSplot.Rd | 98 +++---- GRShiny-1.0.1/GRShiny/man/GRShiny-package.Rd | 8 GRShiny-1.0.1/GRShiny/man/ICCplot.Rd | 112 ++++---- GRShiny-1.0.1/GRShiny/man/extract_est.Rd | 40 +- GRShiny-1.0.1/GRShiny/man/extract_fit.Rd | 40 +- GRShiny-1.0.1/GRShiny/man/genData.Rd | 58 ++-- GRShiny-1.0.1/GRShiny/man/genIRTpar.Rd | 54 +-- GRShiny-1.0.1/GRShiny/man/genLavSyn.Rd | 44 +-- GRShiny-1.0.1/GRShiny/man/infoPlot.Rd | 122 ++++---- GRShiny-1.0.1/GRShiny/man/runGRM.Rd | 16 - GRShiny-1.0.1/GRShiny/man/startGRshiny.Rd | 50 +-- GRShiny-1.0.1/GRShiny/tests/testthat.R | 8 GRShiny-1.0.1/GRShiny/tests/testthat/test-gendata.r | 9 GRShiny-1.0.1/GRShiny/vignettes/GRShiny.Rmd | 4 26 files changed, 592 insertions(+), 557 deletions(-)
Title: Forecasting Routines for Locally Stationary Wavelet Processes
Description: Implementation to perform forecasting of locally stationary wavelet processes by examining the local second order structure of the time series.
Author: Rebecca Killick [aut, cre],
Matt Nunes [aut],
Guy Nason [aut],
Marina Knight [aut],
Idris Eckley [ctb]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between forecastLSW versions 1.0 dated 2023-04-25 and 1.1.1 dated 2025-08-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 ++++- man/analyze.windanomaly.Rd | 2 +- man/forecastLSW-package.Rd | 4 ++-- man/forecastlpacf.Rd | 8 ++++---- 6 files changed, 20 insertions(+), 17 deletions(-)
Title: Deep Neural Network Tools for Probability and Statistic Models
Description: Contains a robust set of tools designed for constructing deep neural networks, which are highly adaptable with user-defined loss function and probability models. It includes several practical applications, such as the (deepAFT) model, which utilizes a deep neural network approach to enhance the accelerated failure time (AFT) model for survival data. Another example is the (deepGLM) model that applies deep neural network to the generalized linear model (glm), accommodating data types with continuous, categorical and Poisson distributions.
Author: Bingshu E. Chen [aut, cre],
Patrick Norman [aut, ctb],
Wenyu Jiang [ctb],
Wanlu Li [ctb]
Maintainer: Bingshu E. Chen <bingshu.chen@queensu.ca>
Diff between dnn versions 0.0.6 dated 2024-03-14 and 0.0.7 dated 2025-08-21
dnn-0.0.6/dnn/R/rSurv.R |only dnn-0.0.6/dnn/man/predict.deepAFT.Rd |only dnn-0.0.6/dnn/man/rSurv.Rd |only dnn-0.0.6/dnn/man/survfit.deepAFT.Rd |only dnn-0.0.7/dnn/DESCRIPTION | 12 - dnn-0.0.7/dnn/MD5 | 52 +++--- dnn-0.0.7/dnn/NAMESPACE | 11 - dnn-0.0.7/dnn/R/deepAFT.R | 26 ++- dnn-0.0.7/dnn/R/deepSurv.R | 198 ++++++++++++------------ dnn-0.0.7/dnn/R/dnn.R | 88 +++++------ dnn-0.0.7/dnn/R/dnnFit.R | 260 ++++++++++++++++---------------- dnn-0.0.7/dnn/R/ibs.deepAFT.R | 10 - dnn-0.0.7/dnn/R/residuals.dSurv.R | 264 +++++++++++++++++---------------- dnn-0.0.7/dnn/R/rmst.dSurv.R |only dnn-0.0.7/dnn/inst/CITATION | 6 dnn-0.0.7/dnn/man/bwdNN.Rd | 2 dnn-0.0.7/dnn/man/dNNmodel.Rd | 163 ++++++++++---------- dnn-0.0.7/dnn/man/deepAFT.Rd | 17 +- dnn-0.0.7/dnn/man/deepGLM.Rd | 21 +- dnn-0.0.7/dnn/man/deepSurv.Rd | 204 ++++++++++++------------- dnn-0.0.7/dnn/man/dnn-package.Rd | 10 - dnn-0.0.7/dnn/man/dnnControl.Rd | 10 - dnn-0.0.7/dnn/man/dnnFit.Rd | 20 +- dnn-0.0.7/dnn/man/ibs.deepAFT.Rd | 85 +++++----- dnn-0.0.7/dnn/man/mseIPCW.Rd | 80 +++++----- dnn-0.0.7/dnn/man/predict.dSurv.Rd |only dnn-0.0.7/dnn/man/print.Rd | 3 dnn-0.0.7/dnn/man/residuals.deepAFT.Rd | 90 +++++------ dnn-0.0.7/dnn/man/rmst.deepSurv.Rd |only dnn-0.0.7/dnn/man/survfit.dSurv.Rd |only dnn-0.0.7/dnn/src/dnn_lib.cpp | 14 + 31 files changed, 841 insertions(+), 805 deletions(-)
Title: Routines for Fit, Inference and Diagnostics in Linear L1 and LAD
Models
Description: Diagnostics for linear L1 regression (also known as LAD - Least Absolute Deviations), including: estimation, confidence intervals, tests of hypotheses, measures of leverage, methods of diagnostics for L1 regression, special diagnostics graphs and measures of leverage. The algorithms are based in Dielman (2005) <doi:10.1080/0094965042000223680>, Elian et al. (2000) <doi:10.1080/03610920008832518> and Dodge (1997) <doi:10.1006/jmva.1997.1666>. This package builds on the 'quantreg' package, which is a well-established package for tuning quantile regression models. There are also tests to verify if the errors have a Laplace distribution based on the work of Puig and Stephens (2000) <doi:10.2307/1270952>.
Author: Kevin Allan Sales Rodrigues [aut, cre] ,
Silvia Nagib Elian [ctb, ths]
Maintainer: Kevin Allan Sales Rodrigues <kevin.asr@outlook.com>
Diff between diagL1 versions 1.0.0 dated 2024-01-29 and 1.0.1 dated 2025-08-21
DESCRIPTION | 14 ++++----- MD5 | 48 +++++++++++++++---------------- R/HV_test.R | 8 +++-- R/LF_test.R | 10 ++++-- R/PIF.R | 5 +++ R/forwardSearch_regL1.R | 6 +-- R/fwd_regL1_methods.R | 8 ++--- R/regL1.R | 24 +++++++-------- R/regL1_het.R | 6 +-- build/partial.rdb |binary inst/CITATION | 26 ++++++++++++++-- man/HV_test.Rd | 7 ++-- man/LF_test.Rd | 9 +++-- man/PIF.Rd | 4 ++ man/class_to_regL1.Rd | 4 +- man/class_to_rq.Rd | 4 +- man/forwardSearch_regL1.Rd | 6 +-- man/plot.forwardSearch_regL1.Rd | 2 - man/print.forwardSearch_regL1.Rd | 2 - man/print.regL1.Rd | 2 - man/print.summary.forwardSearch_regL1.Rd | 2 - man/regL1.Rd | 6 +-- man/regL1_het.Rd | 6 +-- man/summary.forwardSearch_regL1.Rd | 2 - man/summary.regL1.Rd | 8 ++--- 25 files changed, 128 insertions(+), 91 deletions(-)
Title: Automate the Delineation of Urban River Spaces
Description: Provides tools to automate the morphological delineation of
riverside urban areas based on a method introduced in Forgaci (2018)
<doi:10.7480/abe.2018.31>. Delineation entails the identification of
corridor boundaries, segmentation of the corridor, and delineation of
the river space using two-dimensional spatial information from street
network data and digital elevation data in a projected CRS. The
resulting delineation can be used to characterise spatial phenomena
that can be related to the river as a central element.
Author: Claudiu Forgaci [aut, cre, cph] ,
Francesco Nattino [aut] ,
Fakhereh Alidoost [ctb] ,
Meiert Willem Grootes [ctb] ,
Netherlands eScience Center [fnd]
Maintainer: Claudiu Forgaci <c.forgaci@tudelft.nl>
Diff between rcrisp versions 0.1.4 dated 2025-07-04 and 0.2.0 dated 2025-08-21
rcrisp-0.1.4/rcrisp/man/dem_to_cog.Rd |only rcrisp-0.2.0/rcrisp/DESCRIPTION | 21 rcrisp-0.2.0/rcrisp/MD5 | 229 ++++----- rcrisp-0.2.0/rcrisp/NAMESPACE | 2 rcrisp-0.2.0/rcrisp/NEWS.md | 24 rcrisp-0.2.0/rcrisp/R/cache.R | 35 + rcrisp-0.2.0/rcrisp/R/corridor.R | 136 ++++- rcrisp-0.2.0/rcrisp/R/data.R | 4 rcrisp-0.2.0/rcrisp/R/delineate.R | 60 +- rcrisp-0.2.0/rcrisp/R/exampledata.R | 141 ++++- rcrisp-0.2.0/rcrisp/R/network.R | 176 +++++-- rcrisp-0.2.0/rcrisp/R/osmdata.R | 251 ++++++++-- rcrisp-0.2.0/rcrisp/R/rcrisp-package.R |only rcrisp-0.2.0/rcrisp/R/riverspace.R | 28 - rcrisp-0.2.0/rcrisp/R/segments.R | 91 +++ rcrisp-0.2.0/rcrisp/R/sf.R | 18 rcrisp-0.2.0/rcrisp/R/srr-stats-standards.R |only rcrisp-0.2.0/rcrisp/R/utils.R | 156 +++++- rcrisp-0.2.0/rcrisp/R/valley.R | 136 +++-- rcrisp-0.2.0/rcrisp/R/zzz.R | 1 rcrisp-0.2.0/rcrisp/README.md | 7 rcrisp-0.2.0/rcrisp/build/partial.rdb |only rcrisp-0.2.0/rcrisp/build/vignette.rds |binary rcrisp-0.2.0/rcrisp/data/bucharest_dambovita.rda |binary rcrisp-0.2.0/rcrisp/inst/doc/vig_01-method.R | 6 rcrisp-0.2.0/rcrisp/inst/doc/vig_01-method.Rmd | 9 rcrisp-0.2.0/rcrisp/inst/doc/vig_01-method.html | 9 rcrisp-0.2.0/rcrisp/inst/doc/vig_02-getting-osm-data.R | 92 +-- rcrisp-0.2.0/rcrisp/inst/doc/vig_02-getting-osm-data.Rmd | 113 ++-- rcrisp-0.2.0/rcrisp/inst/doc/vig_02-getting-osm-data.html | 105 +--- rcrisp-0.2.0/rcrisp/inst/doc/vig_03-network-preparation.R | 10 rcrisp-0.2.0/rcrisp/inst/doc/vig_03-network-preparation.Rmd | 11 rcrisp-0.2.0/rcrisp/inst/doc/vig_03-network-preparation.html | 12 rcrisp-0.2.0/rcrisp/inst/doc/vig_04-valley-delineation.R | 20 rcrisp-0.2.0/rcrisp/inst/doc/vig_04-valley-delineation.Rmd | 21 rcrisp-0.2.0/rcrisp/inst/doc/vig_04-valley-delineation.html | 16 rcrisp-0.2.0/rcrisp/inst/doc/vig_05-corridor-delineation.R | 21 rcrisp-0.2.0/rcrisp/inst/doc/vig_05-corridor-delineation.Rmd | 10 rcrisp-0.2.0/rcrisp/inst/doc/vig_05-corridor-delineation.html | 34 - rcrisp-0.2.0/rcrisp/inst/doc/vig_06-corridor-segmentation.R | 16 rcrisp-0.2.0/rcrisp/inst/doc/vig_06-corridor-segmentation.Rmd | 17 rcrisp-0.2.0/rcrisp/inst/doc/vig_06-corridor-segmentation.html | 10 rcrisp-0.2.0/rcrisp/inst/doc/vig_07-riverspace-delineation.R | 6 rcrisp-0.2.0/rcrisp/inst/doc/vig_07-riverspace-delineation.Rmd | 6 rcrisp-0.2.0/rcrisp/inst/doc/vig_07-riverspace-delineation.html | 10 rcrisp-0.2.0/rcrisp/man/add_weights.Rd | 3 rcrisp-0.2.0/rcrisp/man/as_bbox.Rd | 2 rcrisp-0.2.0/rcrisp/man/as_crs.Rd |only rcrisp-0.2.0/rcrisp/man/as_network.Rd | 18 rcrisp-0.2.0/rcrisp/man/bucharest_dambovita.Rd | 2 rcrisp-0.2.0/rcrisp/man/buffer.Rd | 2 rcrisp-0.2.0/rcrisp/man/build_river_network.Rd | 2 rcrisp-0.2.0/rcrisp/man/cap_corridor.Rd | 2 rcrisp-0.2.0/rcrisp/man/check_invalid_geometry.Rd | 4 rcrisp-0.2.0/rcrisp/man/clean_network.Rd | 6 rcrisp-0.2.0/rcrisp/man/clear_cache.Rd | 8 rcrisp-0.2.0/rcrisp/man/clip_and_filter.Rd | 2 rcrisp-0.2.0/rcrisp/man/combine_river_features.Rd | 8 rcrisp-0.2.0/rcrisp/man/corridor_edge.Rd | 2 rcrisp-0.2.0/rcrisp/man/corridor_end_points.Rd | 2 rcrisp-0.2.0/rcrisp/man/delineate.Rd | 35 + rcrisp-0.2.0/rcrisp/man/delineate_corridor.Rd | 51 +- rcrisp-0.2.0/rcrisp/man/delineate_riverspace.Rd | 14 rcrisp-0.2.0/rcrisp/man/delineate_segments.Rd | 19 rcrisp-0.2.0/rcrisp/man/delineate_valley.Rd | 7 rcrisp-0.2.0/rcrisp/man/filter_clusters.Rd | 3 rcrisp-0.2.0/rcrisp/man/filter_network.Rd | 4 rcrisp-0.2.0/rcrisp/man/find_intersections.Rd | 2 rcrisp-0.2.0/rcrisp/man/flatten_network.Rd | 9 rcrisp-0.2.0/rcrisp/man/get_corridor_edges.Rd | 2 rcrisp-0.2.0/rcrisp/man/get_dem.Rd | 16 rcrisp-0.2.0/rcrisp/man/get_dem_example_data.Rd | 18 rcrisp-0.2.0/rcrisp/man/get_example_cache_filepath.Rd |only rcrisp-0.2.0/rcrisp/man/get_example_data_file.Rd |only rcrisp-0.2.0/rcrisp/man/get_intersecting_edges.Rd | 5 rcrisp-0.2.0/rcrisp/man/get_osm_bb.Rd | 6 rcrisp-0.2.0/rcrisp/man/get_osm_buildings.Rd | 4 rcrisp-0.2.0/rcrisp/man/get_osm_city_boundary.Rd | 8 rcrisp-0.2.0/rcrisp/man/get_osm_example_data.Rd | 19 rcrisp-0.2.0/rcrisp/man/get_osm_railways.Rd | 10 rcrisp-0.2.0/rcrisp/man/get_osm_river.Rd | 10 rcrisp-0.2.0/rcrisp/man/get_osm_streets.Rd | 19 rcrisp-0.2.0/rcrisp/man/get_osmdata.Rd | 38 + rcrisp-0.2.0/rcrisp/man/get_river_aoi.Rd | 9 rcrisp-0.2.0/rcrisp/man/get_river_banks.Rd | 2 rcrisp-0.2.0/rcrisp/man/get_stac_asset_urls.Rd | 7 rcrisp-0.2.0/rcrisp/man/get_utm_zone.Rd | 2 rcrisp-0.2.0/rcrisp/man/get_valley_polygon_no_hole.Rd | 2 rcrisp-0.2.0/rcrisp/man/get_valley_polygon_raw.Rd | 2 rcrisp-0.2.0/rcrisp/man/initial_edges.Rd | 3 rcrisp-0.2.0/rcrisp/man/load_dem.Rd | 8 rcrisp-0.2.0/rcrisp/man/nearest_node.Rd | 6 rcrisp-0.2.0/rcrisp/man/osmdata_as_sf.Rd | 13 rcrisp-0.2.0/rcrisp/man/osmdata_query.Rd | 2 rcrisp-0.2.0/rcrisp/man/rcrisp-package.Rd |only rcrisp-0.2.0/rcrisp/man/reproject.Rd | 10 rcrisp-0.2.0/rcrisp/man/river_buffer.Rd | 2 rcrisp-0.2.0/rcrisp/man/select_nonintersecting_lines.Rd | 4 rcrisp-0.2.0/rcrisp/man/shortest_path.Rd | 4 rcrisp-0.2.0/rcrisp/man/split_by.Rd | 2 rcrisp-0.2.0/rcrisp/tests/testthat.R | 4 rcrisp-0.2.0/rcrisp/tests/testthat/helper-exampledata.R | 1 rcrisp-0.2.0/rcrisp/tests/testthat/helper-extended.R |only rcrisp-0.2.0/rcrisp/tests/testthat/test-autotest.R |only rcrisp-0.2.0/rcrisp/tests/testthat/test-cache.R | 14 rcrisp-0.2.0/rcrisp/tests/testthat/test-corridor.R | 95 +++ rcrisp-0.2.0/rcrisp/tests/testthat/test-delineate.R | 43 + rcrisp-0.2.0/rcrisp/tests/testthat/test-extended.R |only rcrisp-0.2.0/rcrisp/tests/testthat/test-network.R | 32 + rcrisp-0.2.0/rcrisp/tests/testthat/test-osmdata.R | 37 + rcrisp-0.2.0/rcrisp/tests/testthat/test-segments.R | 106 ++++ rcrisp-0.2.0/rcrisp/tests/testthat/test-utils.R | 115 ++++ rcrisp-0.2.0/rcrisp/tests/testthat/test-valley.R | 35 + rcrisp-0.2.0/rcrisp/vignettes/img/method-diagram.png |binary rcrisp-0.2.0/rcrisp/vignettes/vig_01-method.Rmd | 9 rcrisp-0.2.0/rcrisp/vignettes/vig_02-getting-osm-data.Rmd | 113 ++-- rcrisp-0.2.0/rcrisp/vignettes/vig_03-network-preparation.Rmd | 11 rcrisp-0.2.0/rcrisp/vignettes/vig_04-valley-delineation.Rmd | 21 rcrisp-0.2.0/rcrisp/vignettes/vig_05-corridor-delineation.Rmd | 10 rcrisp-0.2.0/rcrisp/vignettes/vig_06-corridor-segmentation.Rmd | 17 rcrisp-0.2.0/rcrisp/vignettes/vig_07-riverspace-delineation.Rmd | 6 121 files changed, 2401 insertions(+), 778 deletions(-)
Title: A 'ggplot2' Extension for Translating Plot Text
Description: Provides a simple way to translate text elements in 'ggplot2' plots using a dictionary-based approach.
Author: Mathias Leroy [aut, cre]
Maintainer: Mathias Leroy <mathias.leroy.rpkg@gmail.com>
Diff between ggtranslate versions 0.1.0 dated 2025-07-10 and 0.1.1 dated 2025-08-21
DESCRIPTION | 10 - LICENSE | 4 MD5 | 14 +- NAMESPACE | 18 ++- R/ggtranslate.R | 198 +++++++++++++++++++++----------------- README.md | 156 ++++++++++++++--------------- man/ggtranslate.Rd | 86 ++++++++-------- tests/testthat/test-ggtranslate.R | 71 +++++++++++-- 8 files changed, 319 insertions(+), 238 deletions(-)
Title: Download Data from the CSO 'PxStat' API
Description: Imports 'PxStat' data in JSON-stat format and (optionally) reshapes it into wide
format. The Central Statistics Office (CSO) is the national statistical institute of Ireland
and 'PxStat' is the CSOs online database of Official Statistics. This database contains current
and historical data series compiled from CSO statistical releases and is accessed at
<https://data.cso.ie>.
The CSO 'PxStat' Application Programming Interface (API), which is accessed in this package, provides
access to 'PxStat' data in JSON-stat format at <https://data.cso.ie>.
This dissemination tool allows developers machine to machine access to CSO 'PxStat' data.
Author: Eoin Horgan [aut] ,
Conor Crowley [aut, cre],
Vytas Vaiciulis [aut],
Mervyn O'Luing [aut],
James O'Rourke [aut]
Maintainer: Conor Crowley <conor.crowley@cso.ie>
Diff between csodata versions 1.5.0 dated 2024-05-29 and 1.5.1 dated 2025-08-21
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/cso_get_data.R | 7 +++++-- R/cso_get_toc.R | 7 +++++-- inst/doc/quick_start_guide.Rmd | 2 +- inst/doc/quick_start_guide.html | 23 ++++++++++++++--------- vignettes/quick_start_guide.Rmd | 2 +- 8 files changed, 44 insertions(+), 29 deletions(-)
Title: Accelerated Stability Kinetic Modelling
Description: Estimate the Šesták–Berggren kinetic model (degradation model) from experimental data.
A closed-form (analytic) solution to the degradation model is implemented as a non-linear fit,
allowing for the extrapolation of the degradation of a drug product - both in time and
temperature. Parametric bootstrap, with kinetic parameters drawn from the multivariate
t-distribution, and analytical formulae (the delta method) are available options to calculate
the confidence and prediction intervals.
The results (modelling, extrapolations and statistical intervals) can be visualised
with multiple plots. The examples illustrate the accelerated stability modelling in drugs and
vaccines development.
Author: Bernard G Franq [aut, cph],
Ben Wells [ctb],
Alex Ball [cre],
Daniel Williams [ctb]
Maintainer: Alex Ball <alex_keith_ball@hotmail.com>
Diff between AccelStab versions 2.3.1 dated 2025-07-01 and 2.3.2 dated 2025-08-21
DESCRIPTION | 6 MD5 | 16 NEWS.md | 242 ++++++------- R/step1_sample_mvt.R | 880 ++++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/AccelStab.R | 59 ++- inst/doc/AccelStab.Rmd | 59 ++- inst/doc/AccelStab.html | 379 ++++++++++---------- vignettes/AccelStab.Rmd | 59 ++- 9 files changed, 892 insertions(+), 808 deletions(-)
Title: Vincent Van Gogh Colour Palette Generator
Description: Provides 'ggplot2'-compatible colour palettes inspired by Vincent van Gogh's paintings. Each palette contains five colours, manually selected by hexadecimal values.
Author: Cheryl Isabella [aut, cre]
Maintainer: Cheryl Isabella <cheryl.academic@gmail.com>
Diff between vangogh versions 0.1.1 dated 2022-05-27 and 0.1.2 dated 2025-08-21
vangogh-0.1.1/vangogh/R/scale.R |only vangogh-0.1.1/vangogh/R/utils.R |only vangogh-0.1.1/vangogh/inst/doc/vangogh.R |only vangogh-0.1.1/vangogh/inst/doc/vangogh.Rmd |only vangogh-0.1.1/vangogh/inst/doc/vangogh.html |only vangogh-0.1.1/vangogh/man/figures/README-Bedroom-1.png |only vangogh-0.1.1/vangogh/man/figures/README-CafeDeNuit-1.png |only vangogh-0.1.1/vangogh/man/figures/README-CafeTerrace-1.png |only vangogh-0.1.1/vangogh/man/figures/README-Chaise-1.png |only vangogh-0.1.1/vangogh/man/figures/README-Cypresses-1.png |only vangogh-0.1.1/vangogh/man/figures/README-Eglise-1.png |only vangogh-0.1.1/vangogh/man/figures/README-Irises-1.png |only vangogh-0.1.1/vangogh/man/figures/README-Landscape-1.png |only vangogh-0.1.1/vangogh/man/figures/README-Rest-1.png |only vangogh-0.1.1/vangogh/man/figures/README-SelfPortrait-1.png |only vangogh-0.1.1/vangogh/man/figures/README-Shoes-1.png |only vangogh-0.1.1/vangogh/man/figures/README-StarryNight-1.png |only vangogh-0.1.1/vangogh/man/figures/README-StarryRhone-1.png |only vangogh-0.1.1/vangogh/man/figures/README-SunflowersLondon-1.png |only vangogh-0.1.1/vangogh/man/figures/README-SunflowersMunich-1.png |only vangogh-0.1.1/vangogh/man/vangogh_pal.Rd |only vangogh-0.1.1/vangogh/vignettes/vangogh.Rmd |only vangogh-0.1.2/vangogh/DESCRIPTION | 27 vangogh-0.1.2/vangogh/LICENSE | 4 vangogh-0.1.2/vangogh/MD5 | 61 - vangogh-0.1.2/vangogh/NAMESPACE | 46 - vangogh-0.1.2/vangogh/NEWS.md | 34 vangogh-0.1.2/vangogh/R/palette_accessibility.R |only vangogh-0.1.2/vangogh/R/scales_vangogh.R |only vangogh-0.1.2/vangogh/R/theme_vangogh.R |only vangogh-0.1.2/vangogh/R/vangogh.R | 3 vangogh-0.1.2/vangogh/R/vangogh_interpolate.R |only vangogh-0.1.2/vangogh/README.md | 392 +++++++--- vangogh-0.1.2/vangogh/build/vignette.rds |binary vangogh-0.1.2/vangogh/inst/doc/van_gogh_palettes.Rmd |only vangogh-0.1.2/vangogh/inst/doc/van_gogh_palettes.html |only vangogh-0.1.2/vangogh/man/check_palette.Rd |only vangogh-0.1.2/vangogh/man/compare_palettes.Rd |only vangogh-0.1.2/vangogh/man/figures/logo.png |only vangogh-0.1.2/vangogh/man/safe_vangogh_palette.Rd |only vangogh-0.1.2/vangogh/man/scale_color_vangogh.Rd | 78 - vangogh-0.1.2/vangogh/man/scale_fill_vangogh.Rd | 52 - vangogh-0.1.2/vangogh/man/theme_vangogh.Rd |only vangogh-0.1.2/vangogh/man/vangogh.Rd | 38 vangogh-0.1.2/vangogh/man/vangogh_colors.Rd |only vangogh-0.1.2/vangogh/man/vangogh_export.Rd |only vangogh-0.1.2/vangogh/man/vangogh_interpolate.Rd |only vangogh-0.1.2/vangogh/man/vangogh_palette_info.Rd |only vangogh-0.1.2/vangogh/man/vangogh_suggest.Rd |only vangogh-0.1.2/vangogh/man/viz_palette.Rd | 62 - vangogh-0.1.2/vangogh/vignettes/van_gogh_palettes.Rmd |only 51 files changed, 490 insertions(+), 307 deletions(-)
Title: Statistical Process Control for Stochastic Textured Surfaces
Description: Provides statistical process control tools for stochastic
textured surfaces. The current version supports the following tools:
(1) generic modeling of stochastic textured surfaces.
(2) local defect monitoring and diagnostics in stochastic
textured surfaces, which was proposed by Bui and Apley (2018a)
<doi:10.1080/00401706.2017.1302362>.
(3) global change monitoring in the nature of stochastic
textured surfaces, which was proposed by Bui and Apley (2018b)
<doi:10.1080/00224065.2018.1507559>.
(4) computation of dissimilarity matrix of stochastic textured
surface images, which was proposed by Bui and Apley (2019b)
<doi:10.1016/j.csda.2019.01.019>.
Author: Anh Tuan Bui [aut, cre],
Daniel W. Apley [ths]
Maintainer: Anh Tuan Bui <atbui@u.northwestern.edu>
Diff between spc4sts versions 0.6.3 dated 2022-05-24 and 0.6.5 dated 2025-08-21
DESCRIPTION | 23 ++++++++++++++++------- MD5 | 6 +++--- inst/CITATION | 13 +++++++------ man/surfacemodel.Rd | 8 ++++---- 4 files changed, 30 insertions(+), 20 deletions(-)
Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks
(walk, bike, public transport and car) using 'R5', the Rapid Realistic
Routing on Real-world and Reimagined networks engine
<https://github.com/conveyal/r5>. The package allows users to generate
detailed routing analysis or calculate travel time and monetary cost matrices
using seamless parallel computing on top of the R5 Java machine. While R5
is developed by Conveyal, the package r5r is independently developed
by a team at the Institute for Applied Economic Research (Ipea) with
contributions from collaborators. Apart from the documentation in this
package, users will find additional information on R5 documentation at
<https://docs.conveyal.com/>. Although we try to keep new releases of
r5r in synchrony with R5, the development of R5 follows Conveyal's
independent update process. Hence, users should confirm the R5 version
implied by the Conveyal user manual (see
<https://docs.conveyal.com/changelog>) correspon [...truncated...]
Author: Marcus Saraiva [aut] ,
Rafael H. M. Pereira [aut, cre] ,
Daniel Herszenhut [aut] ,
Alex Magnus [aut],
Matthew Wigginton Bhagat-Conway [aut] ,
Carlos Kaue Vieira Braga [ctb] ,
Luyu Liu [ctb] ,
Daniel Snow [ctb],
Ipea - Institute for Applied Economic R [...truncated...]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between r5r versions 2.2.0 dated 2025-05-22 and 2.3.0 dated 2025-08-21
r5r-2.2.0/r5r/R/r5r.R |only r5r-2.2.0/r5r/tests/tests_rafa/test-set_road_speed.R |only r5r-2.2.0/r5r/tests/tests_rafa/v7.0_vs_7.1.R |only r5r-2.2.0/r5r/tests/testthat/test-setup_r5.R |only r5r-2.3.0/r5r/DESCRIPTION | 29 r5r-2.3.0/r5r/MD5 | 282 +- r5r-2.3.0/r5r/NAMESPACE | 4 r5r-2.3.0/r5r/NEWS.md | 30 r5r-2.3.0/r5r/R/accessibility.R | 79 r5r-2.3.0/r5r/R/arrival_travel_time_matrix.R |only r5r-2.3.0/r5r/R/build_network.R |only r5r-2.3.0/r5r/R/detailed_itineraries.R | 72 r5r-2.3.0/r5r/R/download_r5.R | 206 +- r5r-2.3.0/r5r/R/expanded_travel_time_matrix.R | 74 r5r-2.3.0/r5r/R/fare_structure.R | 39 r5r-2.3.0/r5r/R/find_snap.R | 31 r5r-2.3.0/r5r/R/isochrone.R | 32 r5r-2.3.0/r5r/R/java_utils.R | 68 r5r-2.3.0/r5r/R/onLoad.R | 24 r5r-2.3.0/r5r/R/pareto_frontier.R | 57 r5r-2.3.0/r5r/R/r5r-package.R |only r5r-2.3.0/r5r/R/r5r_network.R |only r5r-2.3.0/r5r/R/set.R | 246 +- r5r-2.3.0/r5r/R/setup_r5.R | 234 -- r5r-2.3.0/r5r/R/stop_r5.R | 22 r5r-2.3.0/r5r/R/street_network_to_sf.R | 35 r5r-2.3.0/r5r/R/transit_network_to_sf.R | 32 r5r-2.3.0/r5r/R/travel_time_matrix.R | 95 r5r-2.3.0/r5r/R/utils.R | 299 ++- r5r-2.3.0/r5r/build/vignette.rds |binary r5r-2.3.0/r5r/inst/doc/accessibility.R | 258 +- r5r-2.3.0/r5r/inst/doc/accessibility.Rmd | 450 ++-- r5r-2.3.0/r5r/inst/doc/accessibility.html | 82 r5r-2.3.0/r5r/inst/doc/detailed_itineraries.R | 118 - 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r5r-2.3.0/r5r/tests/testthat/test-scenarios_LTS.R |only r5r-2.3.0/r5r/tests/testthat/test-scenarios_car_speeds.R |only r5r-2.3.0/r5r/tests/testthat/test-set_max_lts.R | 208 +- r5r-2.3.0/r5r/tests/testthat/test-set_max_rides.R | 340 +-- r5r-2.3.0/r5r/tests/testthat/test-set_monte_carlo_draws.R | 614 +++--- r5r-2.3.0/r5r/tests/testthat/test-set_n_threads.R | 6 r5r-2.3.0/r5r/tests/testthat/test-set_percentiles.R | 338 +-- r5r-2.3.0/r5r/tests/testthat/test-set_progress.R | 24 r5r-2.3.0/r5r/tests/testthat/test-set_speed.R | 466 ++-- r5r-2.3.0/r5r/tests/testthat/test-set_time_window.R | 452 ++-- r5r-2.3.0/r5r/tests/testthat/test-set_verbose.R | 24 r5r-2.3.0/r5r/tests/testthat/test-setup_fare_structure.R | 328 +-- r5r-2.3.0/r5r/tests/testthat/test-stop_r5.R | 26 r5r-2.3.0/r5r/tests/testthat/test-street_network_to_sf.R | 8 r5r-2.3.0/r5r/tests/testthat/test-transit_network_to_sf.R | 38 r5r-2.3.0/r5r/tests/testthat/test-travel_time_matrix.R | 14 r5r-2.3.0/r5r/tests/testthat/test-utils.R | 6 r5r-2.3.0/r5r/tests/testthat/test-write_fare_structure.R | 68 r5r-2.3.0/r5r/vignettes/accessibility.Rmd | 450 ++-- r5r-2.3.0/r5r/vignettes/detailed_itineraries.Rmd | 354 +-- r5r-2.3.0/r5r/vignettes/faq.Rmd | 208 +- r5r-2.3.0/r5r/vignettes/fare_structure.Rmd | 990 +++++----- r5r-2.3.0/r5r/vignettes/isochrones.Rmd | 412 ++-- r5r-2.3.0/r5r/vignettes/pareto_frontier.Rmd | 489 ++-- r5r-2.3.0/r5r/vignettes/r5r.Rmd | 104 - r5r-2.3.0/r5r/vignettes/scenarios.Rmd |only r5r-2.3.0/r5r/vignettes/time_window.Rmd | 414 ++-- r5r-2.3.0/r5r/vignettes/travel_time_matrix.Rmd | 382 ++- 165 files changed, 9973 insertions(+), 8467 deletions(-)
Title: MAP-Bayesian Estimation of PK Parameters
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in 'mrgsolve', typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format. The performance of the package was described by Le Louedec et al (2021) <doi:10.1002/psp4.12689>.
Author: Felicien Le Louedec [aut, cre] ,
Kyle T Baron [ctb] ,
Laura Morvan [ctb]
Maintainer: Felicien Le Louedec <felicienlelouedec@proton.me>
Diff between mapbayr versions 0.10.0 dated 2023-07-17 and 0.10.1 dated 2025-08-21
DESCRIPTION | 12 MD5 | 218 +-- NAMESPACE | 312 ++--- NEWS.md | 8 R/augment.R | 320 ++--- R/data.R | 12 R/data_helpers.R | 1488 +++++++++++++------------- R/deprecations.R | 60 - R/eta.R | 212 +-- R/exmodel.R | 198 +-- R/mapbayest.R | 332 ++--- R/mapbayest_check_and_preprocess.R | 918 ++++++++-------- R/mapbayest_ofv_computation.R | 266 ++-- R/mapbayest_optimization.R | 358 +++--- R/mapbayest_postprocess.R | 178 +-- R/mapbayests.R | 662 +++++------ R/merge.R | 110 - R/modelaveraging.R | 2 R/pcvpc.R | 1 R/read_mrgsolve_model.R | 374 +++--- R/use_posterior.R | 160 +- R/vs_nonmem.R | 360 +++--- R/zzz_utils.R | 144 +- README.md | 892 +++++++-------- build/partial.rdb |binary data/est001.rda |binary inst/exmodel/data_to_fit001.csv | 74 - inst/exmodel/data_to_fit006.csv | 106 - inst/exmodel/data_to_fit301.csv | 170 +- inst/exmodel/data_to_fit401.csv | 114 - inst/exmodel/mrg_001.cpp | 78 - inst/exmodel/mrg_006.cpp | 94 - inst/exmodel/mrg_301.cpp | 86 - inst/exmodel/mrg_401.cpp | 108 - inst/nm001/run001.mod | 106 - inst/nm001/run001.phi | 18 inst/run20eta.phi | 26 man/add_covariates.Rd | 142 +- man/adm_rows.Rd | 240 ++-- man/as.data.frame.mapbayests.Rd | 38 man/augment.Rd | 38 man/augment.mapbayests.Rd | 116 +- man/check_mapbayr_model.Rd | 60 - man/compute_ofv.Rd | 94 - man/data_helpers.Rd | 112 - man/deprecations.Rd | 56 man/do_mapbayr_sim.Rd | 134 +- man/est001.Rd | 38 man/eta.Rd | 68 - man/exmodel_exdata.Rd | 132 +- man/filter.mrgmod.Rd | 54 man/get_x.Rd | 158 +- man/hist.mapbayests.Rd | 84 - man/mapbayest.Rd | 228 +-- man/mapbayr_plot.Rd | 110 - man/mapbayr_vpc.Rd | 142 +- man/model_averaging.Rd | 2 man/obs_rows.Rd | 222 +-- man/parse_datehour.Rd | 98 - man/plot.mapbayests.Rd | 72 - man/preprocess.ofv.Rd | 106 - man/preprocess.optim.Rd | 68 - man/print.mapbayests.Rd | 38 man/reexports.Rd | 32 man/use_posterior.Rd | 106 - man/vs_nonmem.Rd | 214 +-- man/x_cmt.Rd | 70 - tests/testthat.R | 8 tests/testthat/test-add_covariates.R | 116 +- tests/testthat/test-adm_lines.R | 320 ++--- tests/testthat/test-augment.R | 266 ++-- tests/testthat/test-blq.R | 48 tests/testthat/test-check_mapbayr_data.R | 168 +- tests/testthat/test-check_mapbayr_model.R | 386 +++--- tests/testthat/test-check_mapbayr_modeldata.R | 112 - tests/testthat/test-compute_ofv.R | 426 +++---- tests/testthat/test-covariance.R | 28 tests/testthat/test-data_helpers.R | 670 +++++------ tests/testthat/test-deprecations.R | 30 tests/testthat/test-eta.R | 94 - tests/testthat/test-exmodels.R | 126 +- tests/testthat/test-fill_eta.R | 42 tests/testthat/test-get_data.R | 42 tests/testthat/test-get_eta.R | 206 +-- tests/testthat/test-get_param.R | 188 +-- tests/testthat/test-get_phi.R | 64 - tests/testthat/test-hist.R | 225 +-- tests/testthat/test-mapbayr_sim.R | 140 +- tests/testthat/test-mdv_egal_0.R | 100 - tests/testthat/test-merge.R | 104 - tests/testthat/test-methods.R | 4 tests/testthat/test-modelaveraging.R | 314 ++--- tests/testthat/test-multi-ID.R | 72 - tests/testthat/test-newini2.R | 46 tests/testthat/test-no_data.R | 54 tests/testthat/test-obs_lines.R | 206 +-- tests/testthat/test-output.R | 106 - tests/testthat/test-parse_datehour.R | 60 - tests/testthat/test-pcvpc.R | 148 +- tests/testthat/test-plot.R | 178 +-- tests/testthat/test-post_mapbay_tab.R | 36 tests/testthat/test-preprocess.R | 30 tests/testthat/test-preprocess.optim.R | 94 - tests/testthat/test-progress.R | 38 tests/testthat/test-read_mrgsolve_model.R | 320 ++--- tests/testthat/test-reset-conditions.R | 436 +++---- tests/testthat/test-select_eta.R | 134 +- tests/testthat/test-use_posterior.R | 8 tests/testthat/test-verbose.R | 16 tests/testthat/test-vs_nonmem.R | 170 +- 110 files changed, 9029 insertions(+), 8999 deletions(-)
Title: Weather Forecast Verification
Description: Utilities for verifying discrete, continuous and probabilistic forecasts, and forecasts expressed as parametric distributions are included.
Author: Eric Gilleland [aut, cre] ,
Matt Pocernich [ctb],
Sabrina Wahl [ctb],
Ronald Frenette [ctb]
Maintainer: Eric Gilleland <eric.gilleland@colostate.edu>
Diff between verification versions 1.44 dated 2024-11-28 and 1.45 dated 2025-08-21
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++++--- NAMESPACE | 3 ++- R/pdpropper.R |only R/powerdiverger.R |only man/pdpropper.Rd |only man/powerdiverger.Rd |only man/verify-internal.Rd | 3 +++ 8 files changed, 19 insertions(+), 10 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 0.15.1 dated 2025-07-10 and 0.16.0 dated 2025-08-21
torch-0.15.1/torch/tools/torchgen/inst/declaration/Declarations-2.5.1.yaml |only torch-0.16.0/torch/DESCRIPTION | 6 torch-0.16.0/torch/MD5 | 61 - torch-0.16.0/torch/NEWS.md | 8 torch-0.16.0/torch/R/RcppExports.R | 92 ++ torch-0.16.0/torch/R/gen-method.R | 6 torch-0.16.0/torch/R/gen-namespace.R | 304 ++++++++- torch-0.16.0/torch/R/install.R | 40 - torch-0.16.0/torch/R/nn-loss.R | 6 torch-0.16.0/torch/R/tensor.R | 6 torch-0.16.0/torch/R/utils.R | 10 torch-0.16.0/torch/R/wrapers.R | 16 torch-0.16.0/torch/build/partial.rdb |binary torch-0.16.0/torch/configure.win | 2 torch-0.16.0/torch/inst/doc/installation.Rmd | 10 torch-0.16.0/torch/inst/doc/installation.html | 12 torch-0.16.0/torch/inst/include/lantern/lantern.h | 94 ++- torch-0.16.0/torch/inst/po/fr/LC_MESSAGES/R-torch.mo |binary torch-0.16.0/torch/inst/po/fr/LC_MESSAGES/torch.mo |only torch-0.16.0/torch/man/install_torch.Rd | 3 torch-0.16.0/torch/man/nn_triplet_margin_loss.Rd | 4 torch-0.16.0/torch/man/nn_triplet_margin_with_distance_loss.Rd | 2 torch-0.16.0/torch/man/torch_repeat_interleave.Rd | 2 torch-0.16.0/torch/po/R-fr.po | 162 ++--- torch-0.16.0/torch/po/R-torch.pot | 142 ++-- torch-0.16.0/torch/src/RcppExports.cpp | 313 +++++++++- torch-0.16.0/torch/src/gen-namespace.cpp | 126 +++- torch-0.16.0/torch/tests/testthat/test-gen-method.R | 10 torch-0.16.0/torch/tools/torchgen/R/cpp.R | 8 torch-0.16.0/torch/tools/torchgen/R/r.R | 4 torch-0.16.0/torch/tools/torchgen/R/utils.R | 2 torch-0.16.0/torch/tools/torchgen/inst/declaration/Declarations-2.7.1.yaml |only torch-0.16.0/torch/vignettes/installation.Rmd | 10 33 files changed, 1109 insertions(+), 352 deletions(-)
Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. We also provide functions for sample size determination and estimation of diagnostic accuracy measures. We also include graphical tools. The statistical methodology used here can be found in Perez-Jaume et al (2017) <doi:10.18637/jss.v082.i04> and in Skaltsa et al (2010, 2012) <doi:10.1002/bimj.200900294>, <doi:10.1002/sim.4369>.
Author: Sara Perez-Jaume [aut, cre],
Natalia Pallares [aut],
Konstantina Skaltsa [aut]
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.9.4 dated 2024-04-12 and 2.9.5 dated 2025-08-21
ThresholdROC-2.9.4/ThresholdROC/data/AD.txt.gz |only ThresholdROC-2.9.4/ThresholdROC/data/chemo.txt.gz |only ThresholdROC-2.9.5/ThresholdROC/DESCRIPTION | 8 - ThresholdROC-2.9.5/ThresholdROC/MD5 | 36 ++-- ThresholdROC-2.9.5/ThresholdROC/R/ThresholdROC-2states.R | 2 ThresholdROC-2.9.5/ThresholdROC/R/diagnostic.R | 38 ++++- ThresholdROC-2.9.5/ThresholdROC/data/AD.txt |only ThresholdROC-2.9.5/ThresholdROC/data/chemo.txt |only ThresholdROC-2.9.5/ThresholdROC/man/SS.Rd | 6 ThresholdROC-2.9.5/ThresholdROC/man/diagnostic.Rd | 21 +- ThresholdROC-2.9.5/ThresholdROC/man/lines-thres2.Rd | 14 - ThresholdROC-2.9.5/ThresholdROC/man/lines-thres3.Rd | 16 +- ThresholdROC-2.9.5/ThresholdROC/man/plot-thres2.Rd | 18 +- ThresholdROC-2.9.5/ThresholdROC/man/plot-thres3.Rd | 24 +-- ThresholdROC-2.9.5/ThresholdROC/man/plotCostROC.Rd | 10 - ThresholdROC-2.9.5/ThresholdROC/man/secondDer2.Rd | 2 ThresholdROC-2.9.5/ThresholdROC/man/secondDer3.Rd | 4 ThresholdROC-2.9.5/ThresholdROC/man/thres2.Rd | 113 ++++++++------- ThresholdROC-2.9.5/ThresholdROC/man/thres3.Rd | 102 +++++++------ ThresholdROC-2.9.5/ThresholdROC/man/thresTH2.Rd | 4 ThresholdROC-2.9.5/ThresholdROC/man/thresTH3.Rd | 7 21 files changed, 250 insertions(+), 175 deletions(-)
Title: An Alternative to the Hodrick-Prescott Filter
Description: In the working paper titled "Why You Should Never Use the Hodrick-Prescott Filter", James D. Hamilton proposes a new alternative to economic time series filtering. The neverhpfilter package provides functions and data for reproducing his work. Hamilton (2017) <doi:10.3386/w23429>.
Author: Justin M. Shea [aut, cre]
Maintainer: Justin M. Shea <jshea01@uic.edu>
This is a re-admission after prior archival of version 0.4-0 dated 2021-06-18
Diff between neverhpfilter versions 0.4-0 dated 2021-06-18 and 0.5-0 dated 2025-08-21
DESCRIPTION | 20 - MD5 | 118 +++++------ NEWS.md | 36 +++ R/EXPGSC1.R | 21 -- R/FEDFUNDS.R | 35 +-- R/GCEC1.R | 21 -- R/GDPC1.R | 19 - R/GDPDEF.R | 32 +-- R/GPDIC1.R | 30 +- R/GS10.R | 32 +-- R/Hamilton_table_2.R | 35 ++- R/IMPGSC1.R | 30 +- R/PAYEMS.R | 39 +-- R/PCECC96.R | 28 +- R/SP500.R | 117 +++++------ R/UNRATENSA.R | 30 +- R/USREC.R | 100 +++------ R/yth_filter.R | 177 ++++++++-------- R/yth_glm.R | 77 +++---- README.md | 6 build/vignette.rds |binary data/EXPGSC1.RData |binary data/FEDFUNDS.RData |binary data/GCEC1.RData |binary data/GDPC1.RData |binary data/GDPDEF.RData |binary data/GPDIC1.RData |binary data/GS10.RData |binary data/IMPGSC1.RData |binary data/PAYEMS.RData |binary data/PCECC96.RData |binary data/SP500.RData |binary data/UNRATENSA.RData |binary data/USREC.RData |binary inst/doc/Getting-started.R | 45 ---- inst/doc/Getting-started.Rmd | 32 +-- inst/doc/Getting-started.html | 315 ------------------------------ inst/doc/Reproducing-Hamilton.R | 88 -------- inst/doc/Reproducing-Hamilton.Rmd | 15 - inst/doc/Reproducing-Hamilton.html | 388 ------------------------------------- inst/tinytest/test_yth_filter.R | 45 ++++ inst/tinytest/test_yth_glm.R | 25 ++ man/EXPGSC1.Rd | 17 - man/FEDFUNDS.Rd | 35 +-- man/GCEC1.Rd | 17 - man/GDPC1.Rd | 15 - man/GDPDEF.Rd | 26 +- man/GPDIC1.Rd | 24 +- man/GS10.Rd | 33 +-- man/Hamilton_table_2.Rd | 25 +- man/IMPGSC1.Rd | 26 +- man/PAYEMS.Rd | 29 +- man/PCECC96.Rd | 22 +- man/SP500.Rd | 97 ++++----- man/UNRATENSA.Rd | 24 +- man/USREC.Rd | 100 +++------ man/yth_filter.Rd | 77 +++---- man/yth_glm.Rd | 60 ++--- vignettes/Getting-started.Rmd | 32 +-- vignettes/Reproducing-Hamilton.Rmd | 15 - 60 files changed, 906 insertions(+), 1724 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predicti [...truncated...]
Author: John Wambaugh [aut, cre] ,
Sarah Davidson-Fritz [aut] ,
Robert Pearce [aut] ,
Caroline Ring [aut] ,
Greg Honda [aut] ,
Mark Sfeir [aut],
Matt Linakis [aut] ,
Dustin Kapraun [aut] ,
Kimberly Truong [aut] ,
Colin Thomson [aut] ,
Meredith Scherer [aut] [...truncated...]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 2.7.0 dated 2025-07-23 and 2.7.1 dated 2025-08-21
httk-2.7.0/httk/man/chem.invivo.PK.data.Rd |only httk-2.7.0/httk/man/load_honda2023.Rd |only httk-2.7.0/httk/tests/solve_dermal_crude_test.R |only httk-2.7.0/httk/tests/solve_dermal_crude_test.Rout |only httk-2.7.1/httk/DESCRIPTION | 13 httk-2.7.1/httk/LICENSE |only httk-2.7.1/httk/MD5 | 150 +- httk-2.7.1/httk/NAMESPACE | 1 httk-2.7.1/httk/NEWS.md | 131 +- httk-2.7.1/httk/R/add_chemtable.R | 8 httk-2.7.1/httk/R/armitage.R | 4 httk-2.7.1/httk/R/benchmark_httk.R | 22 httk-2.7.1/httk/R/calc_css.R | 2 httk-2.7.1/httk/R/calc_kair.R | 2 httk-2.7.1/httk/R/convert_units.R | 26 httk-2.7.1/httk/R/data.R | 198 --- httk-2.7.1/httk/R/export_pbtk_jarnac.R | 41 httk-2.7.1/httk/R/export_pbtk_sbml.R | 23 httk-2.7.1/httk/R/get_2023pfasinfo.R | 2 httk-2.7.1/httk/R/list_models.R | 50 httk-2.7.1/httk/R/load_honda2023.R | 39 httk-2.7.1/httk/R/modelinfo_1comp.R | 9 httk-2.7.1/httk/R/modelinfo_1comppfas.R | 14 httk-2.7.1/httk/R/modelinfo_1tri_pbtk.R | 9 httk-2.7.1/httk/R/modelinfo_3comp.R | 9 httk-2.7.1/httk/R/modelinfo_3comp2.R | 9 httk-2.7.1/httk/R/modelinfo_3compss.R | 9 httk-2.7.1/httk/R/modelinfo_armitage.R | 28 httk-2.7.1/httk/R/modelinfo_dermal.R | 9 httk-2.7.1/httk/R/modelinfo_dermal_1subcomp.R | 9 httk-2.7.1/httk/R/modelinfo_fetal_pbtk.R | 9 httk-2.7.1/httk/R/modelinfo_gas_pbtk.R | 9 httk-2.7.1/httk/R/modelinfo_pbtk.R | 9 httk-2.7.1/httk/R/modelinfo_schmitt.R | 9 httk-2.7.1/httk/R/modelinfo_sumclearances.R | 9 httk-2.7.1/httk/R/modelinfo_sumclearancespfas.R | 12 httk-2.7.1/httk/R/parameterize_1tri_pbtk.R | 2 httk-2.7.1/httk/R/parameterize_armitage.R | 12 httk-2.7.1/httk/R/parameterize_kramer.R | 10 httk-2.7.1/httk/R/solve_1tri_pbtk.R | 2 httk-2.7.1/httk/R/solve_dermal_pbtk.R | 4 httk-2.7.1/httk/R/solve_fetal_pbtk.R | 2 httk-2.7.1/httk/R/solve_full_pregnancy.R | 2 httk-2.7.1/httk/R/solve_model.R | 33 httk-2.7.1/httk/README.md | 5 httk-2.7.1/httk/build/partial.rdb |binary httk-2.7.1/httk/build/vignette.rds |binary httk-2.7.1/httk/data/Tables.RData |binary httk-2.7.1/httk/inst/doc/V1_IntroToHTTK.Rmd | 1 httk-2.7.1/httk/inst/doc/V1_IntroToHTTK.html | 15 httk-2.7.1/httk/inst/doc/Va_Pearce2017.html | 22 httk-2.7.1/httk/inst/doc/Vb_Ring2017.html | 4 httk-2.7.1/httk/inst/doc/Ve_Truong2025.html | 4 httk-2.7.1/httk/inst/doc/Vf_WambaughSubmitted.html | 4 httk-2.7.1/httk/inst/doc/Vg_MeadeSubmitted.html | 6 httk-2.7.1/httk/inst/doc/Vh_SchererSubmitted.R | 334 +++-- httk-2.7.1/httk/inst/doc/Vh_SchererSubmitted.Rmd | 450 +++++-- httk-2.7.1/httk/inst/doc/Vh_SchererSubmitted.html | 1229 +++++++++++---------- httk-2.7.1/httk/man/calc_css.Rd | 2 httk-2.7.1/httk/man/calc_kair.Rd | 2 httk-2.7.1/httk/man/export_pbtk_jarnac.Rd | 16 httk-2.7.1/httk/man/export_pbtk_sbml.Rd | 16 httk-2.7.1/httk/man/get_2023pfasinfo.Rd | 2 httk-2.7.1/httk/man/httk-package.Rd | 1 httk-2.7.1/httk/man/httk.performance.Rd | 2 httk-2.7.1/httk/man/list_models.Rd | 7 httk-2.7.1/httk/man/load_honda2025.Rd |only httk-2.7.1/httk/man/parameterize_1tri_pbtk.Rd | 2 httk-2.7.1/httk/man/solve_1tri_pbtk.Rd | 2 httk-2.7.1/httk/man/solve_dermal_pbtk.Rd | 4 httk-2.7.1/httk/man/solve_fetal_pbtk.Rd | 2 httk-2.7.1/httk/man/solve_full_pregnancy.Rd | 2 httk-2.7.1/httk/src/dermal_1subcomp.c | 27 httk-2.7.1/httk/src/model_gas_pbtk.c | 8 httk-2.7.1/httk/tests/solve_dermal_test.R |only httk-2.7.1/httk/tests/solve_dermal_test.Rout.save |only httk-2.7.1/httk/tests/solve_gas_test.R | 2 httk-2.7.1/httk/tests/solve_gas_test.Rout.save | 20 httk-2.7.1/httk/vignettes/V1_IntroToHTTK.Rmd | 1 httk-2.7.1/httk/vignettes/Vh_SchererSubmitted.Rmd | 450 +++++-- 80 files changed, 2137 insertions(+), 1446 deletions(-)
Title: Fit Multivariate Diversity-Interactions Models with Repeated
Measures
Description: An add-on package to 'DImodels' for the fitting of biodiversity and ecosystem function relationship study data with multiple ecosystem function responses and/or time points. This package uses the multivariate and repeated measures Diversity-Interactions (DI) methods developed by Kirwan et al. (2009) <doi:10.1890/08-1684.1>, Finn et al. (2013) <doi:10.1111/1365-2664.12041>, and Dooley et al. (2015) <doi:10.1111/ele.12504>.
Author: Laura Byrne [aut, cre] ,
Rishabh Vishwakarma [aut],
Rafael de Andrade Moral [aut],
Caroline Brophy [aut]
Maintainer: Laura Byrne <Laura.Byrne.Work@outlook.com>
Diff between DImodelsMulti versions 1.1.1 dated 2024-05-08 and 1.2.0 dated 2025-08-21
DImodelsMulti-1.1.1/DImodelsMulti/R/DImulti_Compos.R |only DImodelsMulti-1.1.1/DImodelsMulti/R/DImulti_compare.R |only DImodelsMulti-1.1.1/DImodelsMulti/R/DImulti_simulateData.R |only DImodelsMulti-1.2.0/DImodelsMulti/DESCRIPTION | 15 DImodelsMulti-1.2.0/DImodelsMulti/MD5 | 63 - DImodelsMulti-1.2.0/DImodelsMulti/R/DImodelsMulti_HelpFile.R | 2 DImodelsMulti-1.2.0/DImodelsMulti/R/DImulti_fit.R | 132 ++ DImodelsMulti-1.2.0/DImodelsMulti/README.md |only DImodelsMulti-1.2.0/DImodelsMulti/build/vignette.rds |binary DImodelsMulti-1.2.0/DImodelsMulti/data/Belgium.rda |only DImodelsMulti-1.2.0/DImodelsMulti/data/Belgium_MV.rda |only DImodelsMulti-1.2.0/DImodelsMulti/data/Belgium_RM.rda |only DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_commonErrors.R | 72 - DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_commonErrors.Rmd | 4 DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_commonErrors.html | 20 DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_onTheta.R | 28 DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_onTheta.Rmd | 4 DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_onTheta.html | 13 DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_prediction.R | 4 DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_prediction.html | 10 DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_workflow.R | 26 DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_workflow.Rmd | 12 DImodelsMulti-1.2.0/DImodelsMulti/inst/doc/DImulti_workflow.html | 449 ++++------ DImodelsMulti-1.2.0/DImodelsMulti/man/Belgium.Rd |only DImodelsMulti-1.2.0/DImodelsMulti/man/Belgium_MV.Rd |only DImodelsMulti-1.2.0/DImodelsMulti/man/Belgium_RM.Rd |only DImodelsMulti-1.2.0/DImodelsMulti/man/DImodelsMulti.Rd | 2 DImodelsMulti-1.2.0/DImodelsMulti/man/DImulti.Rd | 18 DImodelsMulti-1.2.0/DImodelsMulti/man/dataBEL.Rd | 19 DImodelsMulti-1.2.0/DImodelsMulti/man/dataSWE.Rd | 28 DImodelsMulti-1.2.0/DImodelsMulti/man/figures |only DImodelsMulti-1.2.0/DImodelsMulti/man/simMV.Rd | 5 DImodelsMulti-1.2.0/DImodelsMulti/man/simMVRM.Rd | 5 DImodelsMulti-1.2.0/DImodelsMulti/man/simRM.Rd | 9 DImodelsMulti-1.2.0/DImodelsMulti/vignettes/DImulti_commonErrors.Rmd | 4 DImodelsMulti-1.2.0/DImodelsMulti/vignettes/DImulti_onTheta.Rmd | 4 DImodelsMulti-1.2.0/DImodelsMulti/vignettes/DImulti_workflow.Rmd | 12 37 files changed, 540 insertions(+), 420 deletions(-)
Title: Spatial and Environmental Blocking for K-Fold and LOO
Cross-Validation
Description: Creating spatially or environmentally separated folds for cross-validation to provide a robust error estimation in spatially structured environments; Investigating and visualising the effective range of spatial autocorrelation in continuous raster covariates and point samples to find an initial realistic distance band to separate training and testing datasets spatially described in Valavi, R. et al. (2019) <doi:10.1111/2041-210X.13107>.
Author: Roozbeh Valavi [aut, cre] ,
Jane Elith [aut],
Jose Lahoz-Monfort [aut],
Ian Flint [aut],
Gurutzeta Guillera-Arroita [aut]
Maintainer: Roozbeh Valavi <valavi.r@gmail.com>
This is a re-admission after prior archival of version 3.1-6 dated 2025-06-23
Diff between blockCV versions 3.1-6 dated 2025-06-23 and 3.2-0 dated 2025-08-21
DESCRIPTION | 16 - MD5 | 57 +-- R/RcppExports.R | 4 R/checks.R | 10 R/cv_block_size.R | 5 R/cv_buffer.R | 40 -- R/cv_cluster.R | 2 R/cv_nndm.R | 2 R/cv_plot.R | 50 +-- R/cv_similarity.R | 131 ++++++-- R/cv_spatial.R | 79 ++--- R/cv_spatial_autocor.R | 115 ++++--- R/utils.R |only inst/doc/tutorial_1.R | 4 inst/doc/tutorial_1.Rmd | 7 inst/doc/tutorial_1.html | 98 ++---- inst/doc/tutorial_2.html | 4 man/cv_similarity.Rd | 42 ++ src/Lightweight_matrix.h |only src/RcppExports.cpp | 15 src/nndm.cpp | 241 ++++++--------- src/similarity.cpp |only tests/testthat/test-cv_buffer.R | 253 ++++++++-------- tests/testthat/test-cv_cluster.R | 228 +++++++------- tests/testthat/test-cv_nndm.R | 278 ++++++++--------- tests/testthat/test-cv_plot.R | 29 - tests/testthat/test-cv_similarity.R | 71 +++- tests/testthat/test-cv_spatial.R | 485 ++++++++++++++++--------------- tests/testthat/test-cv_spatial_autocor.R | 156 ++++----- tests/testthat/test-v2-functions.R | 312 ++++++++++--------- vignettes/tutorial_1.Rmd | 7 31 files changed, 1453 insertions(+), 1288 deletions(-)
Title: JAR Dependency for MCMC Using 'BEAST'
Description: Provides JAR to perform Markov chain Monte Carlo (MCMC) inference using
the popular Bayesian Evolutionary Analysis by Sampling Trees 'BEAST X' software
library of Baele et al (2025) <doi:10.1038/s41592-025-02751-x>. 'BEAST X' supports
auto-tuning Metropolis-Hastings, slice, Hamiltonian Monte Carlo and Sequential Monte
Carlo sampling for a large variety of composable standard and phylogenetic
statistical models using high performance computing. By placing the 'BEAST X' JAR in
this package, we offer an efficient distribution system for 'BEAST X' use by other R
packages using CRAN.
Author: Marc A. Suchard [aut, cre, cph],
Andrew Rambaut [cph],
Alexei J. Drummond [cph]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between BeastJar versions 10.5.0 dated 2025-07-19 and 10.5.1 dated 2025-08-21
.aspell |only DESCRIPTION | 10 ++++++---- MD5 | 20 +++++++++++--------- NEWS.md | 8 ++++++++ R/BeastJar.R | 6 +++--- R/Utilities.R | 2 +- build |only inst/COPYRIGHTS | 2 +- inst/java/beast.jar |binary man/BeastJar-package.Rd |only man/BeastJar.Rd | 3 +-- man/supportsJava8.Rd | 2 +- tests/testthat/test-installation.R | 8 ++++++++ 13 files changed, 40 insertions(+), 21 deletions(-)
Title: Read, Validate, Analyze, and Map GTFS Feeds
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.
Author: Flavio Poletti [aut, cre],
Daniel Herszenhut [aut] ,
Mark Padgham [aut],
Tom Buckley [aut],
Danton Noriega-Goodwin [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb], [...truncated...]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>
Diff between tidytransit versions 1.7.0 dated 2024-10-18 and 1.7.1 dated 2025-08-21
DESCRIPTION | 16 ++-- MD5 | 105 +++++++++++++-------------- NAMESPACE | 25 ++++++ NEWS.md | 7 + R/dates.R | 28 +++---- R/filters.R | 44 ++++++----- R/frequencies.R | 35 ++++----- R/geo.R | 73 +++++++++++-------- R/io.R | 9 ++ R/raptor.R | 5 - R/service.R | 38 ++++----- R/spatial.R | 64 +++++++++------- R/summary.R | 4 - R/sysdata.rda |binary R/time.R | 6 + R/travel_times.R | 30 +++++-- R/validate_gtfs.R | 12 +-- build/vignette.rds |binary data/gtfs_duke.rda |binary inst/doc/frequency.R | 6 - inst/doc/frequency.Rmd | 6 - inst/doc/frequency.html | 4 - inst/doc/introduction.R | 52 ++++++++----- inst/doc/introduction.Rmd | 24 ++++-- inst/doc/introduction.html | 142 ++++++++++++++++++------------------- inst/doc/servicepatterns.R | 36 +++++---- inst/doc/servicepatterns.Rmd | 38 +++++---- inst/doc/servicepatterns.html | 78 +++++++++++--------- inst/doc/timetable.R | 8 +- inst/doc/timetable.Rmd | 8 +- inst/doc/timetable.html | 26 +++--- inst/extdata/mobilitydata.rds |only man/filter_feed_by_area.Rd | 2 man/filter_feed_by_date.Rd | 3 man/filter_feed_by_stops.Rd | 2 man/filter_feed_by_trips.Rd | 2 man/gtfs_as_sf.Rd | 2 man/gtfs_duke.Rd | 2 man/gtfs_transform.Rd | 2 man/json_to_sf.Rd | 4 - man/set_servicepattern.Rd | 7 + man/shapes_as_sf.Rd | 2 man/stop_group_distances.Rd | 5 + man/stops_as_sf.Rd | 2 man/validate_gtfs.Rd | 2 man/write_gtfs.Rd | 10 ++ tests/testthat/test-raptor.R | 2 tests/testthat/test-service.R | 3 tests/testthat/test-spatial.R | 6 + tests/testthat/test-travel_times.R | 7 + vignettes/frequency.Rmd | 6 - vignettes/introduction.Rmd | 24 ++++-- vignettes/servicepatterns.Rmd | 38 +++++---- vignettes/timetable.Rmd | 8 +- 54 files changed, 633 insertions(+), 437 deletions(-)
Title: Probabilistic Numerical Modelling of Sediment Properties
Description: A flexible framework for definition and application of time/depth-
based rules for sets of parameters for single grains that can be used to
create artificial sediment profiles. Such profiles can be used for virtual
sample preparation and synthetic, for instance, luminescence measurements.
Author: Michael Dietze [aut, cre] ,
Sebastian Kreutzer [aut]
Maintainer: Michael Dietze <michael.dietze@uni-goettingen.de>
Diff between sandbox versions 0.2.1 dated 2022-02-25 and 0.2.2 dated 2025-08-21
DESCRIPTION | 20 +++++++++++--------- MD5 | 20 ++++++++++---------- R/get_RuleBook.R | 2 +- R/measure_SAR_OSL.R | 2 +- R/sandbox-package.R | 1 + R/set_Rule.R | 2 +- build/partial.rdb |binary man/get_RuleBook.Rd | 2 +- man/measure_SAR_OSL.Rd | 2 +- man/sandbox-package.Rd | 8 ++++++++ man/set_Rule.Rd | 2 +- 11 files changed, 36 insertions(+), 25 deletions(-)
Title: Access to the 'RESOURCECODE' Hindcast Database
Description: Utility functions to download data from the 'RESOURCECODE'
hindcast database of sea-states, time series of sea-state parameters
and time series of 1D and 2D wave spectra. See
<https://resourcecode.ifremer.fr> for more details about the available
data. Also provides facilities to plot and analyse downloaded data,
such as computing the sea-state parameters from both the 1D and 2D
surface elevation variance spectral density.
Author: Nicolas Raillard [aut, cre]
Maintainer: Nicolas Raillard <nicolas.raillard@ifremer.fr>
Diff between resourcecode versions 0.2.1 dated 2024-12-03 and 0.3.0 dated 2025-08-21
DESCRIPTION | 16 MD5 | 76 +- NAMESPACE | 3 NEWS.md | 11 R/data.R | 46 - R/download_data.R | 71 +- R/orbital_speed.R | 25 R/plots.R | 36 - R/specta_data_ploting.R | 190 +++--- R/specta_data_processing.R | 94 +-- R/spectral_data_download.R | 703 ++++++++++++----------- R/utils.R | 747 ++++++++++++++++++------- README.md | 29 build/vignette.rds |binary inst/CITATION | 22 inst/doc/resourcecode.html | 2 man/closest_point_field.Rd | 2 man/closest_point_spec.Rd | 4 man/compute_orbital_speeds.Rd | 4 man/compute_sea_state_1d_spectrum.Rd | 36 - man/compute_sea_state_2d_spectrum.Rd | 36 - man/convert_spectrum_2d1d.Rd | 72 +- man/cut_directions.Rd |only man/cut_seasons.Rd |only man/figures/README-data_fetcher-1.png |binary man/figures/README-plot-bathymetry-1.png |binary man/get_parameters.Rd | 4 man/mean_direction.Rd |only man/plot_2d_specta.Rd | 4 man/resourcecode-package.Rd | 1 man/rscd_dir.Rd | 46 - man/rscd_freq.Rd | 48 - man/rscd_mapplot.Rd | 2 tests/testthat.R | 24 tests/testthat/Rplots.pdf |binary tests/testthat/test-data_download.R | 147 ++-- tests/testthat/test-orbital_speed.R | 56 - tests/testthat/test-plots.R | 9 tests/testthat/test-spectral_data_processing.R | 77 +- tests/testthat/test-test_cut_seasons.R |only tests/testthat/test-test_utils.R | 57 + 41 files changed, 1662 insertions(+), 1038 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [ctb] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Clif [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.43 dated 2025-04-15 and 0.44 dated 2025-08-21
DESCRIPTION | 26 ++++++++++++++------------ MD5 | 12 +++++++----- R/html.R | 4 ++-- build/vignette.rds |binary inst/resources/gitbook/css/style.css | 2 +- tests/testthat/resources |only tests/testthat/test-html.R | 24 ++++++++++++++++++++++++ 7 files changed, 48 insertions(+), 20 deletions(-)
Title: Extremal Dependence Models
Description: A set of procedures for parametric and non-parametric modelling of the dependence structure of multivariate extreme-values is provided. The statistical inference is performed with non-parametric estimators, likelihood-based estimators and Bayesian techniques. It adapts the methodologies of Beranger and Padoan (2015) <doi:10.48550/arXiv.1508.05561>, Marcon et al. (2016) <doi:10.1214/16-EJS1162>, Marcon et al. (2017) <doi:10.1002/sta4.145>, Marcon et al. (2017) <doi:10.1016/j.jspi.2016.10.004> and Beranger et al. (2021) <doi:10.1007/s10687-019-00364-0>. This package also allows for the modelling of spatial extremes using flexible max-stable processes. It provides simulation algorithms and fitting procedures relying on the Stephenson-Tawn likelihood as per Beranger at al. (2021) <doi:10.1007/s10687-020-00376-1>.
Author: Boris Beranger [aut],
Simone Padoan [cre, aut],
Giulia Marcon [aut],
Steven G. Johnson [ctb] ,
Rudolf Schuerer [ctb] ,
Brian Gough [ctb] ,
Alec G. Stephenson [ctb],
Anne Sabourin [ctb] ,
Philippe Naveau [ctb]
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between ExtremalDep versions 0.0.4-5 dated 2025-06-29 and 1.0.0 dated 2025-08-21
DESCRIPTION | 8 MD5 | 154 - R/0_sim.R | 167 - R/ConfidenceBands.R | 168 - R/ConvexityConstraints.R | 473 +-- R/Densities.R | 114 R/Dependence.R | 298 +- R/Distributions.R | 377 +- R/ExtremalDep.R | 2 R/Madogram.R | 42 R/PAMfmado.R | 72 R/UnivExtremeQ.R | 154 - R/adaptIntegrate.R | 74 R/beed.R | 520 ++- R/dExtDep.R | 2987 ++++++++++++---------- R/dGEV.R | 99 R/diagnostics.R | 104 R/dim_ExtDep.R | 109 R/fExtDep.R | 1082 ++++---- R/fExtDepSpat.R | 6120 +++++++++++++++++++++++++---------------------- R/fExtDep_np.R | 2388 +++++++++--------- R/fGEV.R | 339 +- R/loglikelihood.R | 182 - R/output_functions.R | 105 R/pExtDep.R | 1031 ++++--- R/plot_ExpDep.np.R | 1670 ++++++------ R/plot_ExtDep.R | 1046 ++++---- R/rExtDep.R | 381 +- R/rExtDepSpat.R | 824 +++--- R/returns.R | 86 R/utilities.R | 185 - README.md | 6 man/ExtQ.Rd | 250 + man/MilanPollution.Rd | 21 man/PAMfmado.Rd | 61 man/PrecipFrance.Rd | 24 man/StdErr.Rd | 35 man/Wind.Rd | 27 man/WindSpeedGust.Rd | 38 man/angular.Rd | 100 man/angular.plot.Rd | 8 man/beed.Rd | 28 man/beed.boot.Rd | 14 man/beed.confband.Rd | 14 man/bic.Rd | 9 man/dExtDep.Rd | 40 man/dGEV.Rd | 63 man/desn.Rd | 24 man/dest.Rd | 26 man/diagnostics.Rd | 127 man/dim_ExtDep.Rd | 77 man/dmesn.Rd | 113 man/dmest.Rd | 104 man/ellipse.Rd | 89 man/est.Rd | 36 man/fExtDep.Rd | 248 - man/fExtDep.np.Rd | 319 +- man/fExtDepSpat.Rd | 132 - man/fGEV.Rd | 109 man/heat.Rd | 47 man/index.ExtDep.Rd | 129 man/lambda.HR.Rd | 47 man/logReturns.Rd | 18 man/madogram.Rd | 147 - man/method.Rd | 27 man/model.Rd | 25 man/pExtDep.Rd | 126 man/pFailure.Rd | 110 man/pickands.plot.Rd | 37 man/pollution.Rd | 97 man/rExtDep.Rd | 101 man/rExtDepSpat.Rd | 152 - man/returns.Rd | 160 - man/returns.plot.Rd | 99 man/simplex.Rd | 56 man/tic.Rd | 33 man/trans2GEV.Rd | 37 man/trans2UFrechet.Rd | 53 78 files changed, 13515 insertions(+), 11489 deletions(-)
Title: Compare Raster Images Side by Side with a Slider
Description: Create a side-by-side view of raster(image)s with an interactive
slider to switch between regions of the images. This can be especially useful
for image comparison of the same region at different time stamps.
Author: Tim Appelhans [cre, aut],
Stefan Woellauer [aut]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between slideview versions 0.2.0 dated 2022-04-11 and 0.2.1 dated 2025-08-21
DESCRIPTION | 14 MD5 | 18 NAMESPACE | 3 NEWS | 15 NEWS.md | 8 R/raster.R | 31 - R/slideView.R | 565 ++++++++++++++++++++--------- inst/htmlwidgets/slideView.js | 58 +- inst/htmlwidgets/slideView_style/style.css | 217 +++++------ man/slideView.Rd | 112 +++-- 10 files changed, 654 insertions(+), 387 deletions(-)
Title: Read and Write C3D Motion Capture Files
Description: A wrapper for the 'EZC3D' library to work with C3D motion capture data.
Author: Simon Nolte [aut, cre] ,
Benjamin Michaud [cph] ,
German Sport University Cologne [fnd] ,
Aymeric Stamm [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/686>),
July Pilowsky [rev] for rOpenSci, see
<https://github.com/rop [...truncated...]
Maintainer: Simon Nolte <s.nolte@dshs-koeln.de>
Diff between c3dr versions 0.1.5 dated 2025-05-22 and 0.2.0 dated 2025-08-21
DESCRIPTION | 6 LICENSE | 4 MD5 | 46 - NEWS.md | 12 R/read.R | 4 R/write.R | 17 README.md | 15 build/vignette.rds |binary inst/CITATION | 4 inst/doc/c3dr.R | 7 inst/doc/c3dr.html | 15 inst/doc/c3dr.qmd | 11 inst/extdata/LICENSE.txt | 1348 ++++++++++++++++++++--------------------- man/c3d_read.Rd | 4 man/c3d_write.Rd | 17 src/ezc3d/Parameters.cpp | 6 src/ezc3d/Points.cpp | 1 src/ezc3d/RotationsInfo.cpp | 15 src/read.cpp | 48 + src/write.cpp | 50 + tests/testthat/_snaps/print.md | 64 - tests/testthat/_snaps/read.md | 542 ++++++++-------- tests/testthat/test-write.R | 27 vignettes/c3dr.qmd | 11 24 files changed, 1233 insertions(+), 1041 deletions(-)
Title: Custom 'xaringan' CSS Themes
Description: Create beautifully color-coordinated and customized themes
for your 'xaringan' slides, without writing any CSS. Complete your
slide theme with 'ggplot2' themes that match the font and colors used
in your slides. Customized styles can be created directly in your
slides' 'R Markdown' source file or in a separate external script.
Author: Garrick Aden-Buie [aut, cre]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between xaringanthemer versions 0.4.3 dated 2024-09-15 and 0.4.4 dated 2025-08-21
DESCRIPTION | 9 ++--- LICENSE | 2 - MD5 | 24 ++++++------- NEWS.md | 6 +++ R/ggplot2.R | 9 +++-- build/vignette.rds |binary inst/doc/ggplot2-themes.R | 54 ++++++++++++------------------- inst/doc/ggplot2-themes.Rmd | 73 +++++++++++++++++------------------------- inst/doc/ggplot2-themes.html | 74 +++++++++++++++++++------------------------ inst/doc/xaringanthemer.R | 52 +++++++++++++++--------------- inst/doc/xaringanthemer.html | 9 ++--- man/scale_xaringan.Rd | 8 +++- vignettes/ggplot2-themes.Rmd | 73 +++++++++++++++++------------------------- 13 files changed, 182 insertions(+), 211 deletions(-)
More information about xaringanthemer at CRAN
Permanent link
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.10 dated 2025-06-17 and 1.3.11 dated 2025-08-21
DESCRIPTION | 6 +- MD5 | 50 ++++++++--------- R/MAplotW.R | 22 +++---- R/VolcanoPlotW.R | 13 +++- R/checkForLegLoc.R | 4 - R/convertPlotCoordPix.R | 2 R/histW.R | 21 +++++-- R/imageW.R | 116 ++++++++++++++++++++++------------------- R/partitionPlot.R | 2 R/plotBy2Groups.R | 6 +- R/plotW2Leg.R | 2 R/staggerdCountsPlot.R | 4 - R/vioplotW.R | 3 - build/vignette.rds |binary inst/doc/wrGraphVignette1.R | 2 inst/doc/wrGraphVignette1.Rmd | 8 +- inst/doc/wrGraphVignette1.html | 94 +++++++++++++++------------------ man/checkForLegLoc.Rd | 2 man/convertPlotCoordPix.Rd | 2 man/histW.Rd | 14 +++- man/imageW.Rd | 19 ++++-- man/partitionPlot.Rd | 2 man/plotBy2Groups.Rd | 2 man/plotW2Leg.Rd | 2 man/staggerdCountsPlot.Rd | 2 vignettes/wrGraphVignette1.Rmd | 8 +- 26 files changed, 224 insertions(+), 184 deletions(-)
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which
are a collection of UCSC-hosted public databases such as TCGA, ICGC,
TARGET, GTEx, CCLE, and others. Databases are normalized so they can
be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] ,
Xue-Song Liu [aut] ,
Martin Morgan [ctb],
Christine Stawitz [rev] ,
Carl Ganz [rev]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaTools versions 1.4.8 dated 2022-06-20 and 1.6.1 dated 2025-08-21
UCSCXenaTools-1.4.8/UCSCXenaTools/R/shiny.R |only UCSCXenaTools-1.4.8/UCSCXenaTools/man/XenaShiny.Rd |only UCSCXenaTools-1.6.1/UCSCXenaTools/DESCRIPTION | 16 UCSCXenaTools-1.6.1/UCSCXenaTools/MD5 | 46 - UCSCXenaTools-1.6.1/UCSCXenaTools/NAMESPACE | 2 UCSCXenaTools-1.6.1/UCSCXenaTools/NEWS.md | 21 UCSCXenaTools-1.6.1/UCSCXenaTools/R/XenaFilter.R | 92 +- UCSCXenaTools-1.6.1/UCSCXenaTools/R/XenaHub-class.R | 19 UCSCXenaTools-1.6.1/UCSCXenaTools/R/XenaQuery.R | 2 UCSCXenaTools-1.6.1/UCSCXenaTools/R/XenaQueryProbeMap.R | 2 UCSCXenaTools-1.6.1/UCSCXenaTools/R/api_inner.R | 3 UCSCXenaTools-1.6.1/UCSCXenaTools/R/dynamics.R |only UCSCXenaTools-1.6.1/UCSCXenaTools/R/fetch.R | 1 UCSCXenaTools-1.6.1/UCSCXenaTools/README.md | 182 +--- UCSCXenaTools-1.6.1/UCSCXenaTools/build/vignette.rds |binary UCSCXenaTools-1.6.1/UCSCXenaTools/data/XenaData.rda |binary UCSCXenaTools-1.6.1/UCSCXenaTools/inst/CITATION | 8 UCSCXenaTools-1.6.1/UCSCXenaTools/inst/doc/USCSXenaTools.R | 14 UCSCXenaTools-1.6.1/UCSCXenaTools/inst/doc/USCSXenaTools.Rmd | 14 UCSCXenaTools-1.6.1/UCSCXenaTools/inst/doc/USCSXenaTools.html | 438 ++++------ UCSCXenaTools-1.6.1/UCSCXenaTools/inst/queries/datasetSources.xq |only UCSCXenaTools-1.6.1/UCSCXenaTools/inst/queries/datasetStatus.xq |only UCSCXenaTools-1.6.1/UCSCXenaTools/man/UCSCXenaTools-dynamic.Rd |only UCSCXenaTools-1.6.1/UCSCXenaTools/man/XenaHub.Rd | 4 UCSCXenaTools-1.6.1/UCSCXenaTools/man/fetch.Rd | 12 UCSCXenaTools-1.6.1/UCSCXenaTools/tests/testthat/test-full-tests.R | 25 UCSCXenaTools-1.6.1/UCSCXenaTools/vignettes/USCSXenaTools.Rmd | 14 27 files changed, 415 insertions(+), 500 deletions(-)
Title: SDTM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Study Data Tabulation Model (SDTM) datasets from the
Clinical Data Interchange Standards Consortium (CDISC) pilot project
used for testing and developing Analysis Data Model (ADaM) datasets
inside the pharmaverse family of packages. SDTM dataset specifications
are described in the CDISC SDTM implementation guide, accessible by
creating a free account on <https://www.cdisc.org/>.
Author: Lina Patil [aut, cre],
Stefan Bundfuss [aut] ,
Fanny Gautier [aut] ,
Edoardo Mancini [aut] ,
Tomoyuki Namai [aut],
Vinh Nguyen [aut],
Vladyslav Shuliar [aut] ,
Cytel Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline LLC [cph, fnd]
Maintainer: Lina Patil <lina.patil@cytel.com>
Diff between pharmaversesdtm versions 1.3.0 dated 2025-07-04 and 1.3.1 dated 2025-08-21
DESCRIPTION | 41 ++++++++++++++++++----------------------- MD5 | 13 ++++++++----- NEWS.md | 18 ++++++++++++++++++ README.md | 17 ++++++++++++----- inst/WORDLIST | 14 ++++++++++++++ man/figures/cytel_logo.png |only man/figures/gsk_logo.png |only man/figures/roche_logo.png |only man/pharmaversesdtm-package.Rd | 18 ++++++++++-------- 9 files changed, 80 insertions(+), 41 deletions(-)
More information about pharmaversesdtm at CRAN
Permanent link
Title: Retrieval, Analysis and Visualization of Air Traffic Data
Description: Provides functionalities and data structures to retrieve, analyze and visualize aviation
data. It includes a client interface to the 'OpenSky' API <https://opensky-network.org>. It allows
retrieval of flight information, as well as aircraft state vectors.
Author: Rafael Ayala [aut, cre] ,
Daniel Ayala [aut] ,
David Ruiz [aut] ,
Aleix Selles [aut],
Lara Selles Vidal [aut]
Maintainer: Rafael Ayala <rafaelayalahernandez@gmail.com>
Diff between openSkies versions 1.2.1 dated 2024-04-03 and 1.2.2 dated 2025-08-21
DESCRIPTION | 26 +++++++-- MD5 | 31 ++++++----- README.md |only build/vignette.rds |binary inst/doc/openSkies.R | 108 ++++++++++++++++++++--------------------- inst/doc/openSkies.Rmd | 4 - inst/doc/openSkies.html | 43 ++++++++++++++-- man/ADSBDecoder.Rd | 2 man/clusterRoutes.Rd | 6 +- man/openSkiesAircraft.Rd | 4 - man/openSkiesAirport.Rd | 4 - man/openSkiesFlight.Rd | 4 - man/openSkiesRoute.Rd | 4 - man/openSkiesStateVector.Rd | 4 - man/openSkiesStateVectorSet.Rd | 4 - tests/runTests.R | 15 +++++ vignettes/openSkies.Rmd | 4 - 17 files changed, 162 insertions(+), 101 deletions(-)
Title: Latent Transition Cognitive Diagnosis Model with Covariates
Description: Implementation of the three-step approach of (latent transition) cognitive diagnosis model (CDM) with covariates. This approach can be used for single time-point situations (cross-sectional data) and multiple time-point situations (longitudinal data) to investigate how the covariates are associated with attribute mastery. For multiple time-point situations, the three-step approach of latent transition CDM with covariates allows researchers to assess changes in attribute mastery status and to evaluate the covariate effects on both the initial states and transition probabilities over time using latent logistic regression. Because stepwise approaches often yield biased estimates, correction for classification error probabilities (CEPs) is considered in this approach. The three-step approach for latent transition CDM with covariates involves the following steps: (1) fitting a CDM to the response data without covariates at each time point separately, (2) assigning examinees to latent states [...truncated...]
Author: Qianru Liang [aut, cre, cph] ,
Jimmy de la Torre [aut] ,
Jingping Du [ctb]
Maintainer: Qianru Liang <liangqr@jnu.edu.cn>
Diff between LTCDM versions 1.0.0 dated 2024-05-15 and 1.1.0 dated 2025-08-21
DESCRIPTION | 14 ++++++++------ MD5 | 15 ++++++++++----- NAMESPACE | 2 ++ NEWS.md |only R/CEP_1t.R |only R/step3_1t.R |only R/step3_est.R | 2 +- R/update.class.R | 1 + man/CEP_1t.Rd |only man/step3_1t.Rd |only man/update_class.Rd | 1 + 11 files changed, 23 insertions(+), 12 deletions(-)
Title: Probabilistic Models to Analyze and Gaussianize Heavy-Tailed,
Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze
skewed, heavy-tailed data. It is based on an input/output system, where the
output random variable (RV) Y is a non-linearly transformed version of an input
RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed).
The transformed RV Y has a Lambert W x F distribution. This package contains
functions to model and analyze skewed, heavy-tailed data the Lambert Way:
simulate random samples, estimate parameters, compute quantiles, and plot/
print results nicely. The most useful function is 'Gaussianize',
which works similarly to 'scale', but actually makes the data Gaussian.
A do-it-yourself toolkit allows users to define their own Lambert W x
'MyFavoriteDistribution' and use it in their analysis right away.
Author: Georg M. Goerg [aut, cre]
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between LambertW versions 0.6.9-1 dated 2023-11-30 and 0.6.9-2 dated 2025-08-21
DESCRIPTION | 13 - MD5 | 20 +- NEWS.md | 4 R/LambertW-package.R | 5 R/bootstrap.R | 2 build/vignette.rds |binary inst/doc/lambertw-overview.R | 22 +-- inst/doc/lambertw-overview.html | 218 ++++++++++++------------------ man/LambertW-package.Rd | 13 + man/bootstrap.Rd | 2 tests/testthat/test_analyze_convergence.R | 5 11 files changed, 141 insertions(+), 163 deletions(-)
Title: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site
Motifs
Description: A comprehensive suite of helper functions designed to facilitate the analysis of genomic annotations from the 'GENCODE' database <https://www.gencodegenes.org/>, supporting both human and mouse genomes. This toolkit enables users to extract, filter, and analyze a wide range of annotation features including genes, transcripts, exons, and introns across different 'GENCODE' releases. It provides functionality for cross-version comparisons, allowing researchers to systematically track annotation updates, structural changes, and feature-level differences between releases. In addition, the package can generate high-quality FASTA files containing donor and acceptor splice site motifs, which are formatted for direct input into the 'MaxEntScan' tool (Yeo and Burge, 2004 <doi:10.1089/1066527041410418>), enabling accurate calculation of splice site strength scores.
Author: Monah Abou Alezz [aut, cre, cph] ,
Lorenzo Salviati [ctb],
Roberta Alfieri [ctb],
Silvia Bione [ctb]
Maintainer: Monah Abou Alezz <aboualezz.monah@hsr.it>
Diff between GencoDymo2 versions 1.0.2 dated 2025-07-14 and 1.0.3 dated 2025-08-21
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/globals.R | 3 ++- R/utils.R | 14 +++++++------- inst/doc/GencoDymo2_vignette.R | 2 +- inst/doc/GencoDymo2_vignette.Rmd | 4 ++-- inst/doc/GencoDymo2_vignette.html | 16 ++++++++-------- man/compare_release.Rd | 6 +++--- vignettes/GencoDymo2_vignette.Rmd | 4 ++-- 10 files changed, 42 insertions(+), 36 deletions(-)
Title: Cluster Origin-Destination Flow Data
Description: Provides functionality for clustering
origin-destination (OD) pairs, representing desire lines (or flows).
This includes creating distance matrices between OD pairs and passing
distance matrices to a clustering algorithm. See the academic paper
Tao and Thill (2016) <doi:10.1111/gean.12100>
for more details on spatial clustering of flows.
See the paper on delineating demand-responsive operating areas
by Mahfouz et al. (2025) <doi:10.1016/j.urbmob.2025.100135>
for an example of how this package can be used to cluster flows for
applied transportation research.
Author: Hussein Mahfouz [aut, cre] ,
Robin Lovelace [aut]
Maintainer: Hussein Mahfouz <husseinmahfouz93@gmail.com>
Diff between flowcluster versions 0.1.0 dated 2025-07-05 and 0.2.1 dated 2025-08-21
DESCRIPTION | 19 ++-- MD5 | 17 ++- NAMESPACE | 1 NEWS.md |only R/clustering.R | 4 R/linestring_aggregation.R |only README.md | 116 +++++++++++++++++++++++++-- inst/WORDLIST | 4 man/aggregate_clustered_flows.Rd |only man/dbscan_sensitivity.Rd | 6 - man/figures/cluster_aggregated_results.png |only tests/testthat/test-linestring_aggregation.R |only 12 files changed, 142 insertions(+), 25 deletions(-)
Title: View 3D Raster Cubes Interactively
Description: Creates a 3D data cube view of a RasterStack/Brick, typically a
collection/array of RasterLayers (along z-axis) with the same geographical
extent (x and y dimensions) and resolution, provided by package 'raster'.
Slices through each dimension (x/y/z), freely adjustable in location,
are mapped to the visible sides of the cube. The cube can be freely rotated.
Zooming and panning can be used to focus on different areas of the cube.
Author: Tim Appelhans [cre, aut],
Stefan Woellauer [aut],
three.js authors [ctb, cph]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between cubeview versions 0.2.4 dated 2025-04-12 and 0.4.1 dated 2025-08-21
DESCRIPTION | 12 ++-- MD5 | 16 ++--- NAMESPACE | 7 -- NEWS | 7 ++ NEWS.md | 7 ++ R/cubeView.R | 125 +++++++++++++++++++++++++------------------ README.md | 4 - inst/htmlwidgets/cubeView.js | 10 +-- man/cubeview.Rd | 27 ++++++++- 9 files changed, 135 insertions(+), 80 deletions(-)
Title: Analyze Clustered Data using the Cluster Bootstrap
Description: Provides functionality for the analysis of clustered data using the cluster bootstrap.
Author: Mathijs Deen [aut, cre],
Mark de Rooij [aut]
Maintainer: Mathijs Deen <dev@mathijsdeen.com>
Diff between ClusterBootstrap versions 1.1.2 dated 2021-02-16 and 2.0.0 dated 2025-08-21
ClusterBootstrap-1.1.2/ClusterBootstrap/R/additional_exports.R |only ClusterBootstrap-1.1.2/ClusterBootstrap/R/clusbootemm.R |only ClusterBootstrap-1.1.2/ClusterBootstrap/R/clusbootglm_internals.R |only ClusterBootstrap-1.1.2/ClusterBootstrap/R/clusbootglm_s3_methods.R |only ClusterBootstrap-1.1.2/ClusterBootstrap/R/permutationtest.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/DESCRIPTION | 21 +-- ClusterBootstrap-2.0.0/ClusterBootstrap/MD5 | 57 ++++++---- ClusterBootstrap-2.0.0/ClusterBootstrap/NAMESPACE | 12 +- ClusterBootstrap-2.0.0/ClusterBootstrap/NEWS | 26 ++++ ClusterBootstrap-2.0.0/ClusterBootstrap/R/clusbootglm.R | 23 ++-- ClusterBootstrap-2.0.0/ClusterBootstrap/R/clusbootglm_sample_glm.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/clusbootsample.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/clusjackglm.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/clusterBootstrap.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/clusterResample.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/coef.clusbootglm.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/confint.clusbootglm.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/confint.clusterBootstrap.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/confint_types.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/emm.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/onAttach.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/plot.clusbootemm.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/plot.clusbootptest.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/predict.clusbootglm.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/printpbmessage.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/ptest.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/summary.clusbootemm.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/summary.clusbootglm.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/R/zzz.R |only ClusterBootstrap-2.0.0/ClusterBootstrap/README.md |only ClusterBootstrap-2.0.0/ClusterBootstrap/inst/CITATION | 26 ++-- ClusterBootstrap-2.0.0/ClusterBootstrap/man/clusbootsample.Rd | 2 ClusterBootstrap-2.0.0/ClusterBootstrap/man/clusterBootstrap.Rd |only ClusterBootstrap-2.0.0/ClusterBootstrap/man/clusterResample.Rd |only ClusterBootstrap-2.0.0/ClusterBootstrap/man/coef.clusbootglm.Rd | 2 ClusterBootstrap-2.0.0/ClusterBootstrap/man/confint.clusbootglm.Rd | 2 ClusterBootstrap-2.0.0/ClusterBootstrap/man/confint.clusterBootstrap.Rd |only ClusterBootstrap-2.0.0/ClusterBootstrap/man/emm.Rd | 6 - ClusterBootstrap-2.0.0/ClusterBootstrap/man/plot.clusbootemm.Rd | 16 ++ ClusterBootstrap-2.0.0/ClusterBootstrap/man/plot.clusbootptest.Rd | 2 ClusterBootstrap-2.0.0/ClusterBootstrap/man/predict.clusbootglm.Rd |only ClusterBootstrap-2.0.0/ClusterBootstrap/man/ptest.Rd | 4 ClusterBootstrap-2.0.0/ClusterBootstrap/man/summary.clusbootemm.Rd | 2 ClusterBootstrap-2.0.0/ClusterBootstrap/man/summary.clusbootglm.Rd | 2 44 files changed, 135 insertions(+), 68 deletions(-)
More information about ClusterBootstrap at CRAN
Permanent link
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 4.4.49 dated 2025-06-15 and 4.4.51 dated 2025-08-21
DESCRIPTION | 8 +- MD5 | 81 ++++++++++++++-------------- R/alldiffs.findLSD.v1.r | 7 +- R/alldiffs.v4.r | 6 +- R/choose.r | 6 +- R/reml4.v13.r | 65 +++++++++++++--------- build/partial.rdb |binary inst/NEWS.Rd | 9 +++ inst/doc/LadybirdEMMs.asreml.pdf |binary inst/doc/LadybirdEMMs.lm.pdf |binary inst/doc/Wheat.analysis.pdf |binary inst/doc/Wheat.infoCriteria.pdf |binary inst/doc/WheatSpatialModels.pdf |binary inst/doc/asremlPlus-manual.pdf |binary man/allDifferences.data.frame.Rd | 3 - man/chooseModel.asrtests.Rd | 31 +++++----- man/findLSDminerrors.alldiffs.Rd | 3 - man/linTransform.alldiffs.Rd | 3 - man/pairdiffsTransform.alldiffs.Rd | 3 - man/predictPlus.asreml.Rd | 39 ++++++------- man/predictPresent.asreml.Rd | 34 ++++++----- man/recalcLSD.alldiffs.Rd | 3 - man/recalcWaldTab.asrtests.Rd | 35 ++++++------ man/redoErrorIntervals.alldiffs.Rd | 3 - man/subset.alldiffs.Rd | 2 man/testranfix.asrtests.Rd | 35 ++++++------ tests/testthat/data/summ703.rda |binary tests/testthat/test3Selection.r | 8 +- tests/testthat/test3Variofaces.r | 2 tests/testthat/test3alldiffs.r | 2 tests/testthat/test41Selection.r | 8 +- tests/testthat/test41Variofaces.r | 2 tests/testthat/test41alldiffs.asr.r | 6 +- tests/testthat/test42EstimateV.r | 4 - tests/testthat/test42Selection.r | 8 +- tests/testthat/test42SpatialModels.r | 8 +- tests/testthat/test42Variofaces.r | 2 tests/testthat/test42WheatSpatialVignette.r | 4 - tests/testthat/test42WheatVignette.r | 34 +++++------ tests/testthat/test42alldiffsasr.r | 6 +- tests/testthat/test42glm.r | 4 - tests/testthat/testthat-problems.rds |only 42 files changed, 258 insertions(+), 216 deletions(-)
Title: Interface to 'TensorFlow Probability'
Description: Interface to 'TensorFlow Probability', a 'Python' library built on 'TensorFlow'
that makes it easy to combine probabilistic models and deep learning on modern hardware ('TPU', 'GPU').
'TensorFlow Probability' includes a wide selection of probability distributions and bijectors, probabilistic layers,
variational inference, Markov chain Monte Carlo, and optimizers such as Nelder-Mead, BFGS, and SGLD.
Author: Tomasz Kalinowski [ctb, cre],
Sigrid Keydana [aut],
Daniel Falbel [ctb],
Kevin Kuo [ctb] ,
RStudio [cph]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>
Diff between tfprobability versions 0.15.1 dated 2022-09-01 and 0.15.2 dated 2025-08-21
DESCRIPTION | 10 MD5 | 456 ++++++++--------- NEWS.md | 6 R/bijector-methods.R | 8 R/distribution-layers.R | 3 R/distribution-methods.R | 32 - R/distributions.R | 5 R/initializers.R | 2 R/install.R | 2 R/mcmc-functions.R | 4 R/mcmc-kernels.R | 12 R/package.R | 8 R/sts-functions.R | 6 build/vignette.rds |binary inst/doc/hamiltonian_monte_carlo.R | 190 +++---- inst/doc/hamiltonian_monte_carlo.html | 280 +++++----- inst/doc/layer_dense_variational.R | 252 ++++----- inst/doc/layer_dense_variational.html | 348 ++++++------ man/initializer_blockwise.Rd | 2 man/install_tfprobability.Rd | 7 man/layer_independent_normal.Rd | 3 man/mcmc_no_u_turn_sampler.Rd | 2 man/mcmc_sample_chain.Rd | 4 man/mcmc_simple_step_size_adaptation.Rd | 2 man/mcmc_transformed_transition_kernel.Rd | 2 man/sts_additive_state_space_model.Rd | 14 man/sts_autoregressive.Rd | 12 man/sts_autoregressive_state_space_model.Rd | 12 man/sts_constrained_seasonal_state_space_model.Rd | 14 man/sts_decompose_by_component.Rd | 2 man/sts_dynamic_linear_regression.Rd | 12 man/sts_dynamic_linear_regression_state_space_model.Rd | 12 man/sts_fit_with_hmc.Rd | 2 man/sts_forecast.Rd | 2 man/sts_linear_regression.Rd | 14 man/sts_local_level.Rd | 12 man/sts_local_level_state_space_model.Rd | 12 man/sts_local_linear_trend.Rd | 12 man/sts_local_linear_trend_state_space_model.Rd | 12 man/sts_seasonal.Rd | 12 man/sts_seasonal_state_space_model.Rd | 12 man/sts_semi_local_linear_trend.Rd | 12 man/sts_semi_local_linear_trend_state_space_model.Rd | 12 man/sts_smooth_seasonal.Rd | 12 man/sts_smooth_seasonal_state_space_model.Rd | 12 man/sts_sparse_linear_regression.Rd | 14 man/sts_sum.Rd | 14 man/tfb_absolute_value.Rd | 20 man/tfb_affine.Rd | 18 man/tfb_affine_linear_operator.Rd | 20 man/tfb_affine_scalar.Rd | 20 man/tfb_ascending.Rd | 20 man/tfb_batch_normalization.Rd | 20 man/tfb_blockwise.Rd | 20 man/tfb_chain.Rd | 20 man/tfb_cholesky_outer_product.Rd | 20 man/tfb_cholesky_to_inv_cholesky.Rd | 20 man/tfb_correlation_cholesky.Rd | 20 man/tfb_cumsum.Rd | 20 man/tfb_discrete_cosine_transform.Rd | 20 man/tfb_exp.Rd | 18 man/tfb_expm1.Rd | 18 man/tfb_ffjord.Rd | 20 man/tfb_fill_scale_tri_l.Rd | 20 man/tfb_fill_triangular.Rd | 20 man/tfb_forward.Rd | 6 man/tfb_forward_log_det_jacobian.Rd | 6 man/tfb_glow.Rd | 20 man/tfb_gompertz_cdf.Rd | 20 man/tfb_gumbel.Rd | 18 man/tfb_gumbel_cdf.Rd | 18 man/tfb_identity.Rd | 20 man/tfb_inline.Rd | 20 man/tfb_inverse.Rd | 4 man/tfb_inverse_log_det_jacobian.Rd | 4 man/tfb_invert.Rd | 20 man/tfb_iterated_sigmoid_centered.Rd | 20 man/tfb_kumaraswamy.Rd | 18 man/tfb_kumaraswamy_cdf.Rd | 18 man/tfb_lambert_w_tail.Rd | 20 man/tfb_masked_autoregressive_default_template.Rd | 20 man/tfb_masked_autoregressive_flow.Rd | 20 man/tfb_masked_dense.Rd | 20 man/tfb_matrix_inverse_tri_l.Rd | 20 man/tfb_matvec_lu.Rd | 20 man/tfb_normal_cdf.Rd | 20 man/tfb_ordered.Rd | 20 man/tfb_pad.Rd | 20 man/tfb_permute.Rd | 20 man/tfb_power_transform.Rd | 20 man/tfb_rational_quadratic_spline.Rd | 20 man/tfb_rayleigh_cdf.Rd | 20 man/tfb_real_nvp.Rd | 18 man/tfb_real_nvp_default_template.Rd | 18 man/tfb_reciprocal.Rd | 20 man/tfb_reshape.Rd | 20 man/tfb_scale.Rd | 18 man/tfb_scale_matvec_diag.Rd | 20 man/tfb_scale_matvec_linear_operator.Rd | 20 man/tfb_scale_matvec_lu.Rd | 20 man/tfb_scale_matvec_tri_l.Rd | 20 man/tfb_scale_tri_l.Rd | 20 man/tfb_shift.Rd | 18 man/tfb_shifted_gompertz_cdf.Rd | 18 man/tfb_sigmoid.Rd | 20 man/tfb_sinh.Rd | 18 man/tfb_sinh_arcsinh.Rd | 18 man/tfb_softmax_centered.Rd | 20 man/tfb_softplus.Rd | 20 man/tfb_softsign.Rd | 20 man/tfb_split.Rd | 20 man/tfb_square.Rd | 20 man/tfb_tanh.Rd | 20 man/tfb_transform_diagonal.Rd | 20 man/tfb_transpose.Rd | 20 man/tfb_weibull.Rd | 16 man/tfb_weibull_cdf.Rd | 16 man/tfd_autoregressive.Rd | 26 man/tfd_batch_reshape.Rd | 26 man/tfd_bates.Rd | 26 man/tfd_bernoulli.Rd | 26 man/tfd_beta.Rd | 24 man/tfd_beta_binomial.Rd | 24 man/tfd_binomial.Rd | 26 man/tfd_categorical.Rd | 26 man/tfd_cauchy.Rd | 26 man/tfd_cdf.Rd | 2 man/tfd_chi.Rd | 24 man/tfd_chi2.Rd | 24 man/tfd_cholesky_lkj.Rd | 26 man/tfd_continuous_bernoulli.Rd | 26 man/tfd_covariance.Rd | 2 man/tfd_cross_entropy.Rd | 2 man/tfd_deterministic.Rd | 26 man/tfd_dirichlet.Rd | 24 man/tfd_dirichlet_multinomial.Rd | 24 man/tfd_empirical.Rd | 26 man/tfd_entropy.Rd | 2 man/tfd_exp_gamma.Rd | 26 man/tfd_exp_inverse_gamma.Rd | 26 man/tfd_exponential.Rd | 26 man/tfd_gamma.Rd | 24 man/tfd_gamma_gamma.Rd | 24 man/tfd_gaussian_process.Rd | 24 man/tfd_gaussian_process_regression_model.Rd | 24 man/tfd_generalized_normal.Rd | 26 man/tfd_geometric.Rd | 26 man/tfd_gumbel.Rd | 26 man/tfd_half_cauchy.Rd | 26 man/tfd_half_normal.Rd | 26 man/tfd_hidden_markov_model.Rd | 26 man/tfd_horseshoe.Rd | 26 man/tfd_independent.Rd | 26 man/tfd_inverse_gamma.Rd | 26 man/tfd_inverse_gaussian.Rd | 26 man/tfd_johnson_s_u.Rd | 26 man/tfd_joint_distribution_named.Rd | 24 man/tfd_joint_distribution_named_auto_batched.Rd | 24 man/tfd_joint_distribution_sequential.Rd | 24 man/tfd_joint_distribution_sequential_auto_batched.Rd | 24 man/tfd_kl_divergence.Rd | 2 man/tfd_kumaraswamy.Rd | 26 man/tfd_laplace.Rd | 26 man/tfd_linear_gaussian_state_space_model.Rd | 26 man/tfd_lkj.Rd | 26 man/tfd_log_cdf.Rd | 2 man/tfd_log_logistic.Rd | 26 man/tfd_log_normal.Rd | 26 man/tfd_log_prob.Rd | 2 man/tfd_log_survival_function.Rd | 2 man/tfd_logistic.Rd | 26 man/tfd_mean.Rd | 2 man/tfd_mixture.Rd | 24 man/tfd_mixture_same_family.Rd | 24 man/tfd_mode.Rd | 2 man/tfd_multinomial.Rd | 26 man/tfd_multivariate_normal_diag.Rd | 24 man/tfd_multivariate_normal_diag_plus_low_rank.Rd | 24 man/tfd_multivariate_normal_full_covariance.Rd | 26 man/tfd_multivariate_normal_linear_operator.Rd | 26 man/tfd_multivariate_normal_tri_l.Rd | 26 man/tfd_multivariate_student_t_linear_operator.Rd | 26 man/tfd_negative_binomial.Rd | 26 man/tfd_normal.Rd | 26 man/tfd_one_hot_categorical.Rd | 26 man/tfd_pareto.Rd | 26 man/tfd_pixel_cnn.Rd | 26 man/tfd_poisson.Rd | 24 man/tfd_poisson_log_normal_quadrature_compound.Rd | 24 man/tfd_power_spherical.Rd | 26 man/tfd_prob.Rd | 2 man/tfd_probit_bernoulli.Rd | 26 man/tfd_quantile.Rd | 2 man/tfd_quantized.Rd | 26 man/tfd_relaxed_bernoulli.Rd | 26 man/tfd_relaxed_one_hot_categorical.Rd | 26 man/tfd_sample.Rd | 2 man/tfd_sample_distribution.Rd | 26 man/tfd_sinh_arcsinh.Rd | 26 man/tfd_skellam.Rd | 26 man/tfd_spherical_uniform.Rd | 26 man/tfd_stddev.Rd | 2 man/tfd_student_t.Rd | 24 man/tfd_student_t_process.Rd | 24 man/tfd_survival_function.Rd | 2 man/tfd_transformed_distribution.Rd | 26 man/tfd_triangular.Rd | 26 man/tfd_truncated_cauchy.Rd | 26 man/tfd_truncated_normal.Rd | 26 man/tfd_uniform.Rd | 26 man/tfd_variance.Rd | 2 man/tfd_variational_gaussian_process.Rd | 26 man/tfd_vector_diffeomixture.Rd | 26 man/tfd_vector_exponential_diag.Rd | 26 man/tfd_vector_exponential_linear_operator.Rd | 26 man/tfd_vector_laplace_diag.Rd | 26 man/tfd_vector_laplace_linear_operator.Rd | 26 man/tfd_vector_sinh_arcsinh_diag.Rd | 26 man/tfd_von_mises.Rd | 24 man/tfd_von_mises_fisher.Rd | 26 man/tfd_weibull.Rd | 26 man/tfd_wishart.Rd | 24 man/tfd_wishart_linear_operator.Rd | 26 man/tfd_wishart_tri_l.Rd | 26 man/tfd_zipf.Rd | 28 - tests/testthat/helper-utils.R | 1 tests/testthat/test-distribution-layers.R | 1 tests/testthat/test-distributions.R | 7 tests/testthat/test-vi-functions.R | 2 229 files changed, 2798 insertions(+), 2785 deletions(-)
Title: Advanced and Parallel Random Number Generation via 'TRNG'
Description: Embeds sources and headers from Tina's Random
Number Generator ('TRNG') C++ library. Exposes some functionality for
easier access, testing and benchmarking into R. Provides examples of
how to use parallel RNG with 'RcppParallel'. The methods and
techniques behind 'TRNG' are illustrated in the package vignettes and
examples. Full documentation is available in Bauke (2021)
<https://github.com/rabauke/trng4/blob/v4.23.1/doc/trng.pdf>.
Author: Riccardo Porreca [aut, cre],
Roland Schmid [aut],
Mirai Solutions GmbH [cph],
Heiko Bauke [ctb, cph]
Maintainer: Riccardo Porreca <riccardo.porreca@mirai-solutions.com>
Diff between rTRNG versions 4.23.1-2 dated 2022-03-14 and 4.23.1-4 dated 2025-08-21
DESCRIPTION | 8 MD5 | 56 +- NEWS.md | 14 R/LdFlags.R | 1 R/TRNG.Engine.R | 2 R/rTRNG-package.R | 13 README.md | 41 -- build/vignette.rds |binary inst/demos/skeletonFiles/Makevars | 1 inst/demos/skeletonFiles/Makevars.win | 1 inst/doc/mcMat.R | 6 inst/doc/mcMat.Rmd | 3 inst/doc/mcMat.html | 665 +++++++++++++++++++++++----------- inst/doc/rTRNG.R | 2 inst/doc/rTRNG.Rmd | 7 inst/doc/rTRNG.html | 505 +++++++++++++++++++------ man/TRNG.Engine.Rd | 2 man/rTRNG-package.Rd | 13 man/rbinom_trng.Rd | 4 man/rlnorm_trng.Rd | 4 man/rnorm_trng.Rd | 4 man/rpois_trng.Rd | 4 man/runif_trng.Rd | 4 src/Makevars | 1 src/Makevars.win | 1 vignettes/code/mcMat.cpp | 2 vignettes/code/mcMatParallel.cpp | 2 vignettes/mcMat.Rmd | 3 vignettes/rTRNG.Rmd | 7 29 files changed, 932 insertions(+), 444 deletions(-)
Title: Neat and Painless Statistical Reporting
Description: User-friendly, clear and simple statistics, primarily for
publication in psychological science. The main functions are wrappers for
other packages, but there are various additions as well. Every relevant step
from data aggregation to reportable printed statistics is covered for basic
experimental designs.
Author: Gaspar Lukacs [aut, cre] ,
Bennett Kleinberg [ctb] ,
Johnny van Doorn [ctb]
Maintainer: Gaspar Lukacs <lkcsgaspar@gmail.com>
Diff between neatStats versions 1.13.3 dated 2022-12-07 and 1.13.5 dated 2025-08-21
DESCRIPTION | 18 LICENSE | 2 MD5 | 120 +- NAMESPACE | 60 - R/aggr_neat.R | 466 +++---- R/anova_neat.R | 1832 +++++++++++++++--------------- R/ci_from_p.R | 138 +- R/dems_neat.R | 734 ++++++------ R/enum.R | 92 - R/excl_neat.R | 262 ++-- R/imports.R | 4 R/internal.R | 2440 ++++++++++++++++++++--------------------- R/mean_ci.R | 72 - R/mon_neat.R | 214 +-- R/neatStats.R | 26 R/norm_tests.R | 608 +++++----- R/path_neat.R | 70 - R/peek_neat.R | 580 ++++----- R/plot_neat.R | 1814 +++++++++++++++--------------- R/props_neat.R | 1202 ++++++++++---------- R/rbind_loop.R | 286 ++-- R/read_dir.R | 286 ++-- R/ro.R | 124 +- R/roc_neat.R | 766 ++++++------ R/sd_ci.R | 54 R/se.R | 26 R/t_neat.R | 1762 ++++++++++++++--------------- R/table_neat.R | 306 ++--- R/var_tests.R | 332 ++--- R/zzz.R | 4 README.md | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/example_pipeline.Rmd | 816 ++++++------- inst/doc/example_pipeline.html | 343 ++--- man/aggr_neat.Rd | 316 ++--- man/anova_neat.Rd | 876 +++++++------- man/ci_from_p.Rd | 132 +- man/corr_neat.Rd | 240 ++-- man/dems_neat.Rd | 302 ++--- man/enum.Rd | 82 - man/excl_neat.Rd | 174 +- man/mean_ci.Rd | 66 - man/mon_conv.Rd | 90 - man/mon_neat.Rd | 58 man/neatStats-package.Rd | 70 - man/norm_tests.Rd | 178 +- man/path_neat.Rd | 58 man/peek_neat.Rd | 276 ++-- man/plot_neat.Rd | 828 ++++++------- man/props_neat.Rd | 560 ++++----- man/rbind_loop.Rd | 262 ++-- man/read_dir.Rd | 182 +-- man/ro.Rd | 104 - man/roc_neat.Rd | 266 ++-- man/sd_ci.Rd | 56 man/se.Rd | 48 man/t_neat.Rd | 618 +++++----- man/table_neat.Rd | 218 +-- man/var_tests.Rd | 162 +- vignettes/example_pipeline.Rmd | 816 ++++++------- 61 files changed, 11456 insertions(+), 11453 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Ben Wilson [aut, cre],
Matei Zaharia [aut],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Ben Wilson <benjamin.wilson@databricks.com>
Diff between mlflow versions 2.22.1 dated 2025-06-17 and 3.2.0 dated 2025-08-21
DESCRIPTION | 44 +++++++++++++++++++---------------- MD5 | 18 +++++++------- NAMESPACE | 1 R/cast-utils.R |only R/model-registry.R | 20 +++++++-------- R/project-param.R | 11 +++----- R/tracking-experiments.R | 2 - man/mlflow-package.Rd | 3 +- tests/testthat/test-cast-utils.R |only tests/testthat/test-model-registry.R | 2 - tests/testthat/test-model.R | 4 +-- 11 files changed, 56 insertions(+), 49 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous and continuous response data using latent factor by both 1PL LSIRM and 2PL LSIRM as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>. It includes original 1PL LSIRM and 2PL LSIRM provided for binary response data and its extension for continuous response data. Bayesian model selection with spike-and-slab prior and method for dealing data with missing value under missing at random, missing completely at random are also supported. Various diagnostic plots are available to inspect the latent space and summary of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 1.3.6 dated 2025-08-18 and 1.3.7 dated 2025-08-21
DESCRIPTION | 8 MD5 | 4 R/diagnostic.lsirm.R | 417 +++++++++++++++++++++++---------------------------- 3 files changed, 196 insertions(+), 233 deletions(-)
Title: Fits a Collection of Curves to Single-Cohort Decomposition Data
Description: Fit different model forms to single-cohort litter
decomposition data (mass remaining through time) using likelihood-based
estimation. Models span simple empirical to process-motivated forms with
differing numbers of free parameters. Provides parameter estimates,
uncertainty, and tools for model comparison/selection. Based on
Cornwell & Weedon (2013) <doi:10.1111/2041-210X.12138>.
Author: Will Cornwell [aut, cre] ,
James Weedon [aut],
Guofang Liu [ctb]
Maintainer: Will Cornwell <wcornwell@gmail.com>
Diff between litterfitter versions 0.1.3 dated 2023-08-29 and 0.1.4 dated 2025-08-21
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Title: Parsing, Computation, and Diagnostics for Greenhouse Gas
Measurements
Description: Parse static-chamber greenhouse gas measurement
files generated by a variety of instruments; compute flux rates using
multi-observation metadata; and generate diagnostic metrics and plots.
Designed to be easy to integrate into reproducible scientific workflows.
Author: Stephanie Wilson [cre] ,
Ben Bond-Lamberty [aut] ,
Genevieve Noyce [ctb] ,
Roberta Bittencourt Peixoto [ctb] ,
Patrick Megonigal [ctb] ,
Smithsonian Institution [cph, fnd]
Maintainer: Stephanie Wilson <sjw22120@gmail.com>
This is a re-admission after prior archival of version 1.1.0 dated 2025-06-21
Diff between fluxfinder versions 1.1.0 dated 2025-06-21 and 1.2.0 dated 2025-08-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 +++--- R/qaqc.R | 1 + 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Support for Compiling Examination Tasks using the 'exams'
Package
Description: The main aim is to further facilitate the creation of exercises based on the package 'exams'
by Grün, B., and Zeileis, A. (2009) <doi:10.18637/jss.v029.i10>. Creating effective student exercises
involves challenges such as creating appropriate data sets and ensuring access to intermediate values
for accurate explanation of solutions. The functionality includes the generation of univariate and
bivariate data including simple time series, functions for theoretical distributions and their approximation,
statistical and mathematical calculations for tasks in basic statistics courses as well as general tasks
such as string manipulation, LaTeX/HTML formatting and the editing of XML task files for 'Moodle'.
Author: Sigbert Klinke [aut, cre]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Diff between exams.forge versions 1.0.10 dated 2024-07-10 and 1.0.11 dated 2025-08-21
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Title: Generate and Simulate Deterministic Compartmental Models
Description: R package to build and simulate deterministic compartmental models that can be non-Markovian. Length of stay in each compartment can be defined to follow a parametric distribution (d_exponential(), d_gamma(), d_weibull(), d_lognormal()) or a non-parametric distribution (nonparametric()). Other supported types of transition from one compartment to another includes fixed transition (constant()), multinomial (multinomial()), fixed transition probability (transprob()).
Author: Thinh Ong [aut, cph] ,
Anh Phan [aut, cre] ,
Marc Choisy [aut] ,
Niels Lohman [ctb],
Bjoern Hoehrmann [ctb],
Florian Loitsch [ctb],
Ingo Berg [ctb]
Maintainer: Anh Phan <anhptq@oucru.org>
Diff between denim versions 1.2.1 dated 2025-06-02 and 1.2.2 dated 2025-08-21
denim-1.2.1/denim/src/Distribution.cpp |only denim-1.2.1/denim/src/Distribution.h |only denim-1.2.1/denim/src/DistributionConstant.cpp |only denim-1.2.1/denim/src/DistributionConstant.h |only denim-1.2.1/denim/src/DistributionDiscreteExponential.cpp |only denim-1.2.1/denim/src/DistributionDiscreteExponential.h |only denim-1.2.1/denim/src/DistributionDiscreteGamma.cpp |only denim-1.2.1/denim/src/DistributionDiscreteGamma.h |only denim-1.2.1/denim/src/DistributionDiscreteWeibull.cpp |only denim-1.2.1/denim/src/DistributionDiscreteWeibull.h |only denim-1.2.1/denim/src/DistributionLogNormal.cpp |only denim-1.2.1/denim/src/DistributionLogNormal.h |only denim-1.2.1/denim/src/DistributionMathExpression.cpp |only denim-1.2.1/denim/src/DistributionMathExpression.h |only denim-1.2.1/denim/src/DistributionNonparametric.cpp |only denim-1.2.1/denim/src/DistributionNonparametric.h |only denim-1.2.1/denim/src/DistributionParametric.cpp |only denim-1.2.1/denim/src/DistributionParametric.h |only denim-1.2.1/denim/src/DistributionTransitionProb.cpp |only denim-1.2.1/denim/src/DistributionTransitionProb.h |only denim-1.2.2/denim/DESCRIPTION | 13 denim-1.2.2/denim/MD5 | 153 denim-1.2.2/denim/NAMESPACE | 2 denim-1.2.2/denim/NEWS.md | 2 denim-1.2.2/denim/R/denim.R | 2 denim-1.2.2/denim/R/distribution.R | 111 denim-1.2.2/denim/R/dsl.R | 4 denim-1.2.2/denim/R/helpers.R | 10 denim-1.2.2/denim/R/model.R | 18 denim-1.2.2/denim/R/simulators.R | 11 denim-1.2.2/denim/README.md | 36 denim-1.2.2/denim/build/vignette.rds |binary denim-1.2.2/denim/inst/doc/deSolve_to_denim.R | 4 denim-1.2.2/denim/inst/doc/deSolve_to_denim.Rmd | 28 denim-1.2.2/denim/inst/doc/deSolve_to_denim.html | 62 denim-1.2.2/denim/inst/doc/denim.R | 229 denim-1.2.2/denim/inst/doc/denim.Rmd | 314 - denim-1.2.2/denim/inst/doc/denim.html | 3529 -------------- denim-1.2.2/denim/inst/doc/denim_dsl.R | 66 denim-1.2.2/denim/inst/doc/denim_dsl.Rmd | 95 denim-1.2.2/denim/inst/doc/denim_dsl.html | 368 - denim-1.2.2/denim/inst/doc/multinomial.R | 10 denim-1.2.2/denim/inst/doc/multinomial.Rmd | 26 denim-1.2.2/denim/inst/doc/multinomial.html | 26 denim-1.2.2/denim/inst/doc/nonparametric.R | 4 denim-1.2.2/denim/inst/doc/nonparametric.Rmd | 10 denim-1.2.2/denim/inst/doc/nonparametric.html | 18 denim-1.2.2/denim/man/d_exponential.Rd | 2 denim-1.2.2/denim/man/d_gamma.Rd | 2 denim-1.2.2/denim/man/d_lognormal.Rd | 2 denim-1.2.2/denim/man/d_weibull.Rd | 2 denim-1.2.2/denim/man/denim-package.Rd | 2 denim-1.2.2/denim/man/denim_dsl.Rd | 4 denim-1.2.2/denim/man/figures/README-example-plot-1.png |binary denim-1.2.2/denim/man/mathexpr.Rd | 4 denim-1.2.2/denim/man/nonparametric.Rd | 4 denim-1.2.2/denim/man/sim.Rd | 9 denim-1.2.2/denim/src/Compartment.cpp | 125 denim-1.2.2/denim/src/Compartment.h | 20 denim-1.2.2/denim/src/Model.cpp | 2 denim-1.2.2/denim/src/ModelJSON.cpp | 108 denim-1.2.2/denim/src/ModelJSON.h | 16 denim-1.2.2/denim/src/Transition.cpp |only denim-1.2.2/denim/src/Transition.h |only denim-1.2.2/denim/src/TransitionConstant.cpp |only denim-1.2.2/denim/src/TransitionConstant.h |only denim-1.2.2/denim/src/TransitionDiscreteExponential.cpp |only denim-1.2.2/denim/src/TransitionDiscreteExponential.h |only denim-1.2.2/denim/src/TransitionDiscreteGamma.cpp |only denim-1.2.2/denim/src/TransitionDiscreteGamma.h |only denim-1.2.2/denim/src/TransitionDiscreteWeibull.cpp |only denim-1.2.2/denim/src/TransitionDiscreteWeibull.h |only denim-1.2.2/denim/src/TransitionLogNormal.cpp |only denim-1.2.2/denim/src/TransitionLogNormal.h |only denim-1.2.2/denim/src/TransitionMathExpression.cpp |only denim-1.2.2/denim/src/TransitionMathExpression.h |only denim-1.2.2/denim/src/TransitionNonparametricDist.cpp |only denim-1.2.2/denim/src/TransitionNonparametricDist.h |only denim-1.2.2/denim/src/TransitionParametricDist.cpp |only denim-1.2.2/denim/src/TransitionParametricDist.h |only denim-1.2.2/denim/src/TransitionProb.cpp |only denim-1.2.2/denim/src/TransitionProb.h |only denim-1.2.2/denim/src/helpers.cpp | 4 denim-1.2.2/denim/src/simcm.cpp | 14 denim-1.2.2/denim/src/simcm.h | 2 denim-1.2.2/denim/src/test-denim.cpp | 46 denim-1.2.2/denim/tests/testthat/test-denim_dsl.R | 4 denim-1.2.2/denim/vignettes/deSolve_to_denim.Rmd | 28 denim-1.2.2/denim/vignettes/denim.Rmd | 314 - denim-1.2.2/denim/vignettes/denim_dsl.Rmd | 95 denim-1.2.2/denim/vignettes/images |only denim-1.2.2/denim/vignettes/multinomial.Rmd | 26 denim-1.2.2/denim/vignettes/nonparametric.Rmd | 10 denim-1.2.2/denim/vignettes/references.bib | 61 94 files changed, 1451 insertions(+), 4606 deletions(-)
Title: Preformatted Maps of Norway that Don't Need Geolibraries
Description: Provides datasets containing preformatted maps of Norway at
the county, municipality, and ward (Oslo only) level for redistricting in
2024, 2020, 2018, and 2017. Multiple layouts are provided (normal, split,
and with an insert for Oslo), allowing the user to rapidly create choropleth
maps of Norway without any geolibraries.
Author: Richard Aubrey White [aut, cre] ,
Chi Zhang [aut] ,
CSIDS [cph]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between csmaps versions 2023.5.22 dated 2023-05-23 and 2025.8.21 dated 2025-08-21
csmaps-2023.5.22/csmaps/inst/doc/naming_scheme.R |only csmaps-2023.5.22/csmaps/inst/doc/naming_scheme.Rmd |only csmaps-2023.5.22/csmaps/inst/doc/naming_scheme.html |only csmaps-2023.5.22/csmaps/vignettes/naming_scheme.Rmd |only csmaps-2025.8.21/csmaps/DESCRIPTION | 22 csmaps-2025.8.21/csmaps/LICENSE | 2 csmaps-2025.8.21/csmaps/MD5 | 116 - csmaps-2025.8.21/csmaps/NAMESPACE | 1 csmaps-2025.8.21/csmaps/NEWS.md | 14 csmaps-2025.8.21/csmaps/R/data_norway_county.R | 93 + csmaps-2025.8.21/csmaps/R/data_norway_position_title_insert_oslo.R | 2 csmaps-2025.8.21/csmaps/R/data_oslo_ward.R | 4 csmaps-2025.8.21/csmaps/README.md | 32 csmaps-2025.8.21/csmaps/build/vignette.rds |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2017_default_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2017_default_sf.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2017_insert_oslo_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2019_default_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2019_default_sf.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2019_insert_oslo_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2020_default_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2020_default_sf.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2020_insert_oslo_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2020_split_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2024_default_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2024_default_sf.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2024_insert_oslo_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_map_b2024_split_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2017_default_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2017_insert_oslo_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2019_default_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2019_insert_oslo_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2020_default_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2020_insert_oslo_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2020_split_dt.rda |only csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2024_default_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2024_insert_oslo_dt.rda |binary csmaps-2025.8.21/csmaps/data/nor_county_position_geolabels_b2024_split_dt.rda |only csmaps-2025.8.21/csmaps/data/oslo_ward_position_geolabels_b2020_default_dt.rda |binary csmaps-2025.8.21/csmaps/data/oslo_ward_position_geolabels_b2024_default_dt.rda |binary csmaps-2025.8.21/csmaps/inst/doc/csmaps.R | 19 csmaps-2025.8.21/csmaps/inst/doc/csmaps.Rmd | 23 csmaps-2025.8.21/csmaps/inst/doc/csmaps.html | 78 - csmaps-2025.8.21/csmaps/inst/doc/customization.R | 106 - csmaps-2025.8.21/csmaps/inst/doc/customization.Rmd | 120 - csmaps-2025.8.21/csmaps/inst/doc/customization.html | 503 +++--- csmaps-2025.8.21/csmaps/inst/doc/layout.R | 63 csmaps-2025.8.21/csmaps/inst/doc/layout.Rmd | 122 + csmaps-2025.8.21/csmaps/inst/doc/layout.html | 227 ++ csmaps-2025.8.21/csmaps/inst/doc/sf_interactive.R | 2 csmaps-2025.8.21/csmaps/inst/doc/sf_interactive.html | 766 +++++++--- csmaps-2025.8.21/csmaps/man/figures/@eaDir/logo.png@SynoEAStream |binary csmaps-2025.8.21/csmaps/man/figures/logo.png |binary csmaps-2025.8.21/csmaps/man/nor_county_map_bxxxx_default_dt.Rd | 16 csmaps-2025.8.21/csmaps/man/nor_county_map_bxxxx_default_sf.Rd | 2 csmaps-2025.8.21/csmaps/man/nor_county_map_bxxxx_insert_oslo_dt.Rd | 22 csmaps-2025.8.21/csmaps/man/nor_county_map_bxxxx_split_dt.Rd | 55 csmaps-2025.8.21/csmaps/man/nor_xxx_position_title_insert_oslo_bxxxx_insert_oslo_dt.Rd | 2 csmaps-2025.8.21/csmaps/man/oslo_ward_map_bxxxx_default_dt.Rd | 4 csmaps-2025.8.21/csmaps/vignettes/csmaps.Rmd | 23 csmaps-2025.8.21/csmaps/vignettes/customization.Rmd | 120 - csmaps-2025.8.21/csmaps/vignettes/layout.Rmd | 122 + 62 files changed, 1754 insertions(+), 927 deletions(-)
Title: Compositional Data Analysis
Description: Provides functions for the consistent analysis of compositional
data (e.g. portions of substances) and positive numbers (e.g. concentrations)
in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.
Author: K. Gerald van den Boogaart [aut, cre],
Raimon Tolosana-Delgado [aut],
Matevz Bren [aut]
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between compositions versions 2.0-8 dated 2024-01-31 and 2.0-9 dated 2025-08-21
ChangeLog | 3 DESCRIPTION | 25 - MD5 | 24 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/UsingCompositions.pdf |binary inst/doc/compositions_v2.Rmd | 4 inst/doc/compositions_v2.html | 850 ++++++++++++++++++++--------------------- man/codadendrogram.Rd | 8 man/kingtetrahedron.Rd | 4 man/pairwisePlot.Rd | 4 man/pwlrPlot.Rd | 8 vignettes/compositions_v2.Rmd | 4 13 files changed, 474 insertions(+), 460 deletions(-)
Title: Caught by the Fuzz! - A Minimalistic Fuzz-Test Runner
Description: A simple runner for fuzz-testing functions in an R package's
public interface. Fuzz testing helps identify functions lacking sufficient
argument validation, and uncovers problematic inputs that, while valid by
function signature, may cause issues within the function body.
Author: Marco Colombo [aut, cre]
Maintainer: Marco Colombo <mar.colombo13@gmail.com>
Diff between CBTF versions 0.4.0 dated 2025-08-19 and 0.5.0 dated 2025-08-21
DESCRIPTION | 8 +- MD5 | 39 ++++++----- NAMESPACE | 2 NEWS.md | 27 +++++++ R/CBTF-package.R | 27 +++++-- R/fuzz.R | 143 +++++++++++++++++++++++++++++------------- R/inputs.R | 48 ++++++++++++-- R/misc.R | 20 ----- R/summary.R | 28 +++++--- README.md | 129 ++++++++++++++++++++++++++++++++----- man/CBTF-package.Rd | 28 +++++--- man/fuzz.Rd | 34 +++++---- man/length.cbtf.Rd | 6 - man/namify.Rd |only man/summary.cbtf.Rd | 7 +- man/test_inputs.Rd | 14 ++-- man/whitelist.Rd |only tests/testthat/_snaps |only tests/testthat/setup.R | 4 + tests/testthat/test_fuzz.R | 90 ++++++++++++++++++++------ tests/testthat/test_inputs.R | 6 + tests/testthat/test_summary.R | 12 ++- 22 files changed, 487 insertions(+), 185 deletions(-)
Title: Design and Analyze Choice-Based Conjoint Experiments
Description: Design and evaluate choice-based conjoint survey experiments. Generate a variety of survey designs, including random designs, frequency-based designs, and D-optimal designs, as well as "labeled" designs (also known as "alternative-specific designs"), designs with "no choice" options, and designs with dominant alternatives removed. Conveniently inspect and compare designs using a variety of metrics, including design balance, overlap, and D-error, and simulate choice data for a survey design either randomly or according to a utility model defined by user-provided prior parameters. Conduct a power analysis for a given survey design by estimating the same model on different subsets of the data to simulate different sample sizes. Bayesian D-efficient designs using the 'cea' and 'modfed' methods are obtained using the 'idefix' package by Traets et al (2020) <doi:10.18637/jss.v096.i03>. Choice simulation and model estimation in power analyses are handled using the 'logitr' package by He [...truncated...]
Author: John Helveston [cre, aut, cph]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between cbcTools versions 0.6.2 dated 2025-07-17 and 0.6.3 dated 2025-08-21
DESCRIPTION | 6 MD5 | 42 - NEWS.md | 4 R/design_greedy.R | 951 ++++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/choices.html | 10 inst/doc/design.R | 6 inst/doc/design.Rmd | 22 inst/doc/design.html | 75 +-- inst/doc/getting-started.html | 221 ++++----- inst/doc/power.html | 14 inst/doc/priors.html | 6 inst/doc/profiles.html | 4 tests/testthat/test_choices.R | 18 tests/testthat/test_comparison.R | 19 tests/testthat/test_decode.R | 17 tests/testthat/test_design.R | 13 tests/testthat/test_inspection.R | 25 - tests/testthat/test_power.R | 34 + tests/testthat/test_priors.R | 20 tests/testthat/test_profiles.R | 12 vignettes/design.Rmd | 22 22 files changed, 875 insertions(+), 666 deletions(-)
Title: Analysis of Massive SNP Arrays
Description: Easy-to-use, efficient, flexible and scalable tools for analyzing
massive SNP arrays. Privé et al. (2018) <doi:10.1093/bioinformatics/bty185>.
Author: Florian Prive [aut, cre],
Michael Blum [ths],
Hugues Aschard [ths],
Bjarni Johann Vilhjalmsson [ths]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between bigsnpr versions 1.12.18 dated 2024-11-26 and 1.12.21 dated 2025-08-21
DESCRIPTION | 12 +-- MD5 | 62 ++++++++++---------- NAMESPACE | 1 NEWS.md | 4 + R/bed-mult-vec.R | 2 R/bed-projectPCA.R | 1 R/bed-tcrossprodSelf.R | 2 R/binom-scaling.R | 6 + R/clumping.R | 2 R/corr.R | 7 +- R/impute.R | 3 R/man-qq-gc.R | 2 R/read-bgen.R | 2 R/read-plink.R | 4 - R/utils-assert.R | 19 +++--- inst/WORDLIST | 3 man/bed-mat-acc.Rd | 74 +++++++++++------------ man/bed_projectPCA.Rd | 2 man/snp_asGeneticPos2.Rd | 96 +++++++++++++++---------------- man/snp_autoSVD.Rd | 2 man/snp_clumping.Rd | 2 man/snp_cor.Rd | 5 + man/snp_ld_scores.Rd | 5 + man/snp_readBGEN.Rd | 2 man/snp_readBed.Rd | 4 - tests/testthat/test-2-autoSVD.R | 2 tests/testthat/test-2-bed-clumping-SVD.R | 16 ++++- tests/testthat/test-2-corr.R | 2 tests/testthat/test-2-ld-scores.R | 2 tests/testthat/test-2-pca-project.R | 4 + tests/testthat/test-5-bed-prod-vec.R | 2 tests/testthat/test-9-Fst.R | 8 +- 32 files changed, 205 insertions(+), 155 deletions(-)
Title: Applied Statistical Time Series Analysis
Description: Contains data sets and scripts for analyzing time series in both the frequency and time domains including state space modeling as well as supporting the texts Time Series Analysis and Its Applications: With R Examples (5th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2025, <DOI:10.1007/978-3-031-70584-7>, and Time Series: A Data Analysis Approach Using R (2nd ed). Chapman-Hall, 2026, <https://www.routledge.com/Time-Series-A-Data-Analysis-Approach-Using-R/Shumway-Stoffer/p/book/9781041031642>. Most scripts are designed to require minimal input to produce aesthetically pleasing output for ease of use in live demonstrations and course work.
Author: David Stoffer [aut, cre],
Nicky Poison [ctb, mus, spy]
Maintainer: David Stoffer <stoffer@pitt.edu>
Diff between astsa versions 2.2 dated 2025-01-15 and 2.3 dated 2025-08-21
DESCRIPTION | 10 +-- MD5 | 152 ++++++++++++++++++++++++++------------------------- NAMESPACE | 34 ++++++----- R/ARMAtoAR.R | 2 R/ESS.R | 9 ++- R/FDR.R | 2 R/LagReg.R | 8 +- R/QQnorm.R | 50 +++++++++------- R/SV.mcmc.R | 21 +++---- R/SigExtract.R | 24 ++++---- R/acf1.R | 15 ++--- R/acf2.R | 20 ++---- R/acfm.r | 46 +++++++-------- R/ar.boot.r | 38 ++++-------- R/ar.mcmc.r | 59 ++++++------------- R/arma.spec.R | 92 +++++++++++++++--------------- R/astsa.col.r | 25 ++++++-- R/bart.R | 4 - R/ccf2.R | 14 +--- R/detrend.R | 4 - R/ffbs.R | 32 +++++----- R/lag1.plot.R | 9 +-- R/lag2.plot.R | 11 ++- R/mvspec.R | 140 +++++++++++++++++++++++++++++++++++++++------- R/pre.white.R | 5 + R/sarima.R | 38 ++++++------ R/sarima.for.R | 56 +++++++++--------- R/sarima.sim.R | 10 ++- R/scatter.hist.r | 6 +- R/spec.ic.r | 4 - R/specenv.R | 4 - R/ssm.R | 6 +- R/stoch.reg.R | 6 ++ R/test.linear.R | 10 +-- R/trend.R | 15 +++-- R/tspairs.r |only R/tsplot.R | 2 R/ttable.r |only R/zzz.R | 59 +++++++++++++++++++ README.md | 27 ++++----- build/partial.rdb |binary data/USpop20.rda |only man/ARMAtoAR.Rd | 3 - man/EM.Rd | 8 +- man/ESS.Rd | 20 ++++-- man/Hare.Rd | 6 +- man/Kfilter.Rd | 17 ++--- man/Ksmooth.Rd | 26 +++----- man/Lynx.Rd | 6 +- man/QQnorm.Rd | 13 ++-- man/SigExtract.Rd | 4 + man/USpop.Rd | 3 + man/USpop20.Rd |only man/WBC.Rd | 2 man/acf1.Rd | 6 +- man/acf2.Rd | 6 +- man/acfm.Rd | 8 +- man/ar.boot.Rd | 22 ++++--- man/ar.mcmc.Rd | 19 +++--- man/ar1miss.Rd | 16 +++++ man/arma.spec.Rd | 4 - man/astsa-package.Rd | 45 ++++++++------- man/astsa.col.Rd | 84 ++++++++++++++++++++++------ man/ccf2.Rd | 10 +-- man/climhyd.Rd | 4 + man/cpg.Rd | 2 man/lag1.plot.Rd | 8 ++ man/lag2.plot.Rd | 10 ++- man/mvspec.Rd | 35 ++++++++--- man/sarima.Rd | 53 ++++++++++------- man/sarima.for.Rd | 31 ++++++++-- man/sarima.sim.Rd | 4 + man/scatter.hist.Rd | 8 ++ man/sleep1.Rd | 7 -- man/sleep2.Rd | 7 -- man/spec.ic.Rd | 7 +- man/trend.Rd | 7 +- man/tspairs.Rd |only man/ttable.Rd |only man/varve.Rd | 6 ++ 80 files changed, 937 insertions(+), 649 deletions(-)
Title: Seasonal Analysis of Health Data
Description: Routines for the seasonal analysis of health data, including
regression models, time-stratified case-crossover, plotting functions
and residual checks, see Barnett and Dobson (2010) ISBN
978-3-642-10748-1. Thanks to Yuming Guo for checking the
case-crossover code.
Author: Adrian Barnett [aut, cre] ,
Peter Baker [aut] ,
Oliver Hughes [aut]
Maintainer: Adrian Barnett <a.barnett@qut.edu.au>
Diff between season versions 0.3.15 dated 2022-03-21 and 0.3.16 dated 2025-08-21
season-0.3.15/season/R/nochars.R |only season-0.3.15/season/man/cipolygon.Rd |only season-0.3.15/season/man/nochars.Rd |only season-0.3.15/season/man/plotCircle.Rd |only season-0.3.15/season/man/plotCircular.Rd |only season-0.3.15/season/man/plotMonth.Rd |only season-0.3.15/season/man/summary.Cosinor.Rd |only season-0.3.16/season/DESCRIPTION | 41 - season-0.3.16/season/MD5 | 94 +- season-0.3.16/season/NAMESPACE | 5 season-0.3.16/season/NEWS.md |only season-0.3.16/season/R/casecross.R | 8 season-0.3.16/season/R/cipolygon.R | 11 season-0.3.16/season/R/cosinor.R | 6 season-0.3.16/season/R/monthglm.R | 56 - season-0.3.16/season/R/plot.Cosinor.R | 2 season-0.3.16/season/R/plot.Monthmean.R | 2 season-0.3.16/season/R/plot.monthglm.R | 4 season-0.3.16/season/R/plot.nonlintest.R | 2 season-0.3.16/season/R/plotCircle.R | 2 season-0.3.16/season/R/plotCircular.R | 8 season-0.3.16/season/R/plotMonth.R | 2 season-0.3.16/season/R/print.Cosinor.R | 2 season-0.3.16/season/R/print.Monthmean.R | 2 season-0.3.16/season/R/print.casecross.R | 4 season-0.3.16/season/R/print.monthglm.R | 2 season-0.3.16/season/R/print.nonlintest.R | 2 season-0.3.16/season/R/print.nsCosinor.R | 2 season-0.3.16/season/R/print.summary.Cosinor.R | 2 season-0.3.16/season/R/print.summary.nsCosinor.R | 2 season-0.3.16/season/R/season-package.R | 27 season-0.3.16/season/R/seasrescheck.R | 2 season-0.3.16/season/R/sinusoid.R | 2 season-0.3.16/season/R/summary.Cosinor.R | 6 season-0.3.16/season/R/summary.casecross.R | 2 season-0.3.16/season/R/summary.monthglm.R | 2 season-0.3.16/season/R/summary.nsCosinor.R | 2 season-0.3.16/season/R/wtest.R | 2 season-0.3.16/season/R/yrfraction.R | 2 season-0.3.16/season/build/vignette.rds |binary season-0.3.16/season/inst/CITATION | 43 - season-0.3.16/season/inst/doc/season-vignette.R | 28 season-0.3.16/season/inst/doc/season-vignette.Rmd | 24 season-0.3.16/season/inst/doc/season-vignette.html | 811 ++++++++++++++------- season-0.3.16/season/man/casecross.Rd | 6 season-0.3.16/season/man/cosinor.Rd | 6 season-0.3.16/season/man/monthglm.Rd | 6 season-0.3.16/season/man/season-package.Rd | 10 season-0.3.16/season/man/seasrescheck.Rd | 2 season-0.3.16/season/man/sinusoid.Rd | 2 season-0.3.16/season/man/wtest.Rd | 2 season-0.3.16/season/vignettes/season-vignette.Rmd | 24 52 files changed, 801 insertions(+), 471 deletions(-)
Title: Estimating Means, Standard Deviations and Visualising
Distributions using Quantiles
Description: Implements a novel density-based approach for estimating unknown means, visualizing distributions,
and meta-analyses of quantiles. A detailed vignettes with example datasets and code to prepare data and analyses is available at <https://bookdown.org/a2delivera/metaquant/>.
The methods are described in the pre-print by De Livera, Prendergast and Kumaranathunga (2024, <doi:10.48550/arXiv.2411.10971>).
Author: Udara Kumaranathunga [cre],
Alysha De Livera [aut],
Luke Prendergast [aut]
Maintainer: Udara Kumaranathunga <U.Kumaranathunga@latrobe.edu.au>
Diff between metaquant versions 0.1.1 dated 2025-02-11 and 0.1.2 dated 2025-08-21
metaquant-0.1.1/metaquant/R/est.mean.2g.R |only metaquant-0.1.1/metaquant/R/est.sd.2g.R |only metaquant-0.1.1/metaquant/man/est.mean.2g.Rd |only metaquant-0.1.1/metaquant/man/est.sd.2g.Rd |only metaquant-0.1.2/metaquant/DESCRIPTION | 6 metaquant-0.1.2/metaquant/MD5 | 26 +- metaquant-0.1.2/metaquant/NAMESPACE | 5 metaquant-0.1.2/metaquant/R/est.mean.R | 216 ++++++++++++++++-- metaquant-0.1.2/metaquant/R/est.sd.R | 8 metaquant-0.1.2/metaquant/R/helper.functions.R | 160 ------------- metaquant-0.1.2/metaquant/R/plotdist.R | 10 metaquant-0.1.2/metaquant/build |only metaquant-0.1.2/metaquant/man/est.density.five.Rd |only metaquant-0.1.2/metaquant/man/est.density.minq2max.Rd |only metaquant-0.1.2/metaquant/man/est.density.q1q2q3.Rd |only metaquant-0.1.2/metaquant/man/est.mean.Rd | 18 - metaquant-0.1.2/metaquant/man/est.sd.Rd | 4 metaquant-0.1.2/metaquant/man/plotdist.Rd | 2 18 files changed, 245 insertions(+), 210 deletions(-)
Title: Collection of Data Structures
Description: A collection of functions to generate a large variety of
structures in high dimensions. These data structures are useful for
testing, validating, and improving algorithms used in dimensionality
reduction, clustering, machine learning, and visualization.
Author: Jayani P. Gamage [aut, cre] ,
Dianne Cook [aut] ,
Paul Harrison [aut] ,
Michael Lydeamore [aut] ,
Thiyanga S. Talagala [aut]
Maintainer: Jayani P. Gamage <jayanilakshika76@gmail.com>
Diff between cardinalR versions 0.1.1 dated 2024-04-16 and 0.1.10 dated 2025-08-21
cardinalR-0.1.1/cardinalR/R/circulars.R |only cardinalR-0.1.1/cardinalR/R/clustering.R |only cardinalR-0.1.1/cardinalR/R/grid.R |only cardinalR-0.1.1/cardinalR/R/highd_obj.R |only cardinalR-0.1.1/cardinalR/R/mobius_clust.R |only cardinalR-0.1.1/cardinalR/R/nonlinear.R |only cardinalR-0.1.1/cardinalR/R/s_curve.R |only cardinalR-0.1.1/cardinalR/R/triangular.R |only cardinalR-0.1.1/cardinalR/data/mobius_clust_data.rda |only cardinalR-0.1.1/cardinalR/data/mobius_clust_tsne_param1.rda |only cardinalR-0.1.1/cardinalR/data/mobius_clust_tsne_param2.rda |only cardinalR-0.1.1/cardinalR/data/mobius_clust_tsne_param3.rda |only cardinalR-0.1.1/cardinalR/data/mobius_clust_umap_param1.rda |only cardinalR-0.1.1/cardinalR/data/mobius_clust_umap_param2.rda |only cardinalR-0.1.1/cardinalR/data/mobius_clust_umap_param3.rda |only cardinalR-0.1.1/cardinalR/man/cell_cycle.Rd |only cardinalR-0.1.1/cardinalR/man/clust_diff_shapes.Rd |only cardinalR-0.1.1/cardinalR/man/clust_diff_shapes_pts.Rd |only cardinalR-0.1.1/cardinalR/man/conic_spiral_3d.Rd |only cardinalR-0.1.1/cardinalR/man/conic_spiral_3d_row.Rd |only cardinalR-0.1.1/cardinalR/man/cube_3d.Rd |only cardinalR-0.1.1/cardinalR/man/curv_2d.Rd |only cardinalR-0.1.1/cardinalR/man/curvy_branch.Rd |only cardinalR-0.1.1/cardinalR/man/curvy_branch_clust.Rd |only cardinalR-0.1.1/cardinalR/man/curvy_branch_clust_bkg.Rd |only cardinalR-0.1.1/cardinalR/man/curvy_cycle.Rd |only cardinalR-0.1.1/cardinalR/man/curvy_tree.Rd |only cardinalR-0.1.1/cardinalR/man/diff_sphere.Rd |only cardinalR-0.1.1/cardinalR/man/dini_surface_3d.Rd |only cardinalR-0.1.1/cardinalR/man/dini_surface_3d_row.Rd |only cardinalR-0.1.1/cardinalR/man/eight_branch.Rd |only cardinalR-0.1.1/cardinalR/man/four_branch.Rd |only cardinalR-0.1.1/cardinalR/man/four_long_clust.Rd |only cardinalR-0.1.1/cardinalR/man/four_long_clust_bkg.Rd |only cardinalR-0.1.1/cardinalR/man/gau_clust.Rd |only cardinalR-0.1.1/cardinalR/man/gau_clust_diff.Rd |only cardinalR-0.1.1/cardinalR/man/gau_curvy_clust.Rd |only cardinalR-0.1.1/cardinalR/man/gau_curvy_clust_bkg.Rd |only cardinalR-0.1.1/cardinalR/man/gen_bkg_noise.Rd |only cardinalR-0.1.1/cardinalR/man/gen_noise_dims.Rd |only cardinalR-0.1.1/cardinalR/man/mirror_scurves.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_5d.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_5d_row.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_clust.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_clust_data.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_clust_tsne_param1.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_clust_tsne_param2.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_clust_tsne_param3.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_clust_umap_param1.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_clust_umap_param2.Rd |only cardinalR-0.1.1/cardinalR/man/mobius_clust_umap_param3.Rd |only cardinalR-0.1.1/cardinalR/man/nonlinear_2d.Rd |only cardinalR-0.1.1/cardinalR/man/nonlinear_connect.Rd |only cardinalR-0.1.1/cardinalR/man/nonlinear_mirror.Rd |only cardinalR-0.1.1/cardinalR/man/one_doublet.Rd |only cardinalR-0.1.1/cardinalR/man/one_doublet_bkg.Rd |only cardinalR-0.1.1/cardinalR/man/one_doublet_diff_patterns.Rd |only cardinalR-0.1.1/cardinalR/man/one_doublet_diff_var_clust.Rd |only cardinalR-0.1.1/cardinalR/man/one_doublet_four_clusts.Rd |only cardinalR-0.1.1/cardinalR/man/one_grid.Rd |only cardinalR-0.1.1/cardinalR/man/one_grid_bkg.Rd |only cardinalR-0.1.1/cardinalR/man/plane.Rd |only cardinalR-0.1.1/cardinalR/man/plane_2d_hole.Rd |only cardinalR-0.1.1/cardinalR/man/roman_surface_3d.Rd |only cardinalR-0.1.1/cardinalR/man/roman_surface_3d_row.Rd |only cardinalR-0.1.1/cardinalR/man/scurve.Rd |only cardinalR-0.1.1/cardinalR/man/scurve_hole.Rd |only cardinalR-0.1.1/cardinalR/man/seven_branch.Rd |only cardinalR-0.1.1/cardinalR/man/sine_curve.Rd |only cardinalR-0.1.1/cardinalR/man/sphere.Rd |only cardinalR-0.1.1/cardinalR/man/spiral_3d.Rd |only 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cardinalR-0.1.10/cardinalR/tests/testthat/test-trigonometric.R |only cardinalR-0.1.10/cardinalR/tests/testthat/test-util.R | 168 cardinalR-0.1.10/cardinalR/vignettes/main_function.Rmd |only cardinalR-0.1.10/cardinalR/vignettes/quollr1sample.Rmd | 112 280 files changed, 2920 insertions(+), 15975 deletions(-)
Title: Package Admix for Admixture (aka Contamination) Models
Description: Implements techniques to estimate the unknown quantities
related to two-component admixture models, where the two components
can belong to any distribution (note that in the case of multinomial
mixtures, the two components must belong to the same family).
Estimation methods depend on the assumptions made on the unknown
component density; see Bordes and Vandekerkhove (2010)
<doi:10.3103/S1066530710010023>, Patra and Sen (2016)
<doi:10.1111/rssb.12148>, and Milhaud, Pommeret, Salhi, Vandekerkhove
(2024) <doi:10.3150/23-BEJ1593>. In practice, one can estimate both
the mixture weight and the unknown component density in a wide variety
of frameworks. On top of that, hypothesis tests can be performed in
one and two-sample contexts to test the unknown component density (see
Milhaud, Pommeret, Salhi and Vandekerkhove (2022)
<doi:10.1016/j.jspi.2021.05.010>, and Milhaud, Pommeret, Salhi,
Vandekerkhove (2024) <doi:10.3150/23-BEJ1593>). Finally, clustering of
unknown [...truncated...]
Author: Xavier Milhaud [aut, cre],
Pierre Vandekerkhove [ctb],
Denys Pommeret [ctb],
Yahia Salhi [ctb]
Maintainer: Xavier Milhaud <xavier.milhaud.research@gmail.com>
Diff between admix versions 2.4.2 dated 2025-07-05 and 2.4.3 dated 2025-08-21
admix-2.4.2/admix/R/decontaminated_density.R |only admix-2.4.2/admix/man/getmixingWeight.Rd |only admix-2.4.2/admix/man/getmixtData.Rd |only admix-2.4.3/admix/DESCRIPTION | 6 admix-2.4.3/admix/MD5 | 101 ++++++------ admix-2.4.3/admix/NAMESPACE | 16 + admix-2.4.3/admix/R/IBM_k_samples_test.R | 39 ++-- admix-2.4.3/admix/R/admix_cluster.R | 21 +- admix-2.4.3/admix/R/admix_estim.R | 39 +--- admix-2.4.3/admix/R/admix_model.R | 15 + admix-2.4.3/admix/R/admix_test.R | 16 + admix-2.4.3/admix/R/decontaminated_dist.R |only admix-2.4.3/admix/R/estim_BVdk.R | 25 +- admix-2.4.3/admix/R/estim_IBM.R | 39 ++-- admix-2.4.3/admix/R/estim_PS.R | 13 - admix-2.4.3/admix/R/extractors.R |only admix-2.4.3/admix/R/gaussianity_test.R | 13 - admix-2.4.3/admix/R/orthobasis_test.R | 15 - admix-2.4.3/admix/R/twoComp_mixt.R | 17 +- admix-2.4.3/admix/R/utils.R | 29 +-- admix-2.4.3/admix/build/partial.rdb |binary admix-2.4.3/admix/inst/doc/admixture-clustering.Rmd | 10 - admix-2.4.3/admix/inst/doc/admixture-clustering.html | 10 - admix-2.4.3/admix/inst/doc/admixture-weight-estimation.R | 16 - admix-2.4.3/admix/inst/doc/admixture-weight-estimation.Rmd | 16 - admix-2.4.3/admix/inst/doc/admixture-weight-estimation.html | 46 ++--- admix-2.4.3/admix/inst/doc/test-hypothesis.Rmd | 12 - admix-2.4.3/admix/inst/doc/test-hypothesis.html | 12 - admix-2.4.3/admix/man/IBM_k_samples_test.Rd | 13 - admix-2.4.3/admix/man/admix_cluster.Rd | 18 +- admix-2.4.3/admix/man/admix_estim.Rd | 7 admix-2.4.3/admix/man/admix_test.Rd | 4 admix-2.4.3/admix/man/decontaminated_cdf.Rd | 8 admix-2.4.3/admix/man/decontaminated_density.Rd | 12 - admix-2.4.3/admix/man/detect_support_type.Rd |only admix-2.4.3/admix/man/estim_BVdk.Rd | 12 - admix-2.4.3/admix/man/estim_IBM.Rd | 13 - admix-2.4.3/admix/man/estim_PS.Rd | 5 admix-2.4.3/admix/man/gaussianity_test.Rd | 2 admix-2.4.3/admix/man/get_cluster_members.Rd |only admix-2.4.3/admix/man/get_cluster_sizes.Rd |only admix-2.4.3/admix/man/get_discrepancy_id.Rd |only admix-2.4.3/admix/man/get_discrepancy_matrix.Rd |only admix-2.4.3/admix/man/get_discrepancy_rank.Rd |only admix-2.4.3/admix/man/get_known_component.Rd |only admix-2.4.3/admix/man/get_mixing_weights.Rd |only admix-2.4.3/admix/man/get_mixture_data.Rd |only admix-2.4.3/admix/man/get_statistic_components.Rd |only admix-2.4.3/admix/man/get_tabulated_dist.Rd |only admix-2.4.3/admix/man/is_equal_knownComp.Rd |only admix-2.4.3/admix/man/orthobasis_test.Rd | 4 admix-2.4.3/admix/man/plot.admix_model.Rd | 5 admix-2.4.3/admix/man/plot.decontaminated_density.Rd | 20 +- admix-2.4.3/admix/man/print.decontaminated_density.Rd | 2 admix-2.4.3/admix/man/reject_nullHyp.Rd |only admix-2.4.3/admix/man/summary.decontaminated_density.Rd | 2 admix-2.4.3/admix/man/twoComp_mixt.Rd | 12 - admix-2.4.3/admix/man/which_rank.Rd |only admix-2.4.3/admix/vignettes/admixture-clustering.Rmd | 10 - admix-2.4.3/admix/vignettes/admixture-weight-estimation.Rmd | 16 - admix-2.4.3/admix/vignettes/test-hypothesis.Rmd | 12 - 61 files changed, 381 insertions(+), 322 deletions(-)
Title: R Interface to W3C Markup Validation Services
Description: R interface to a W3C Markup Validation service.
See <https://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between W3CMarkupValidator versions 0.1-7 dated 2023-02-06 and 0.2-0 dated 2025-08-21
DESCRIPTION | 10 - MD5 | 12 - NAMESPACE | 10 - R/w3c.R | 348 ++++++++++++++++++++----------------- man/w3c_markup_validate.Rd | 93 +++++---- man/w3c_markup_validate_baseurl.Rd | 2 man/w3c_markup_validate_db.Rd | 33 ++- 7 files changed, 281 insertions(+), 227 deletions(-)
More information about W3CMarkupValidator at CRAN
Permanent link
Title: Handling and Manipulating Remote Sensing Data
Description: Herein, we provide a broad variety of functions which are useful
for handling, manipulating, and visualizing satellite-based remote sensing
data. These operations range from mere data import and layer handling (eg
subsetting), over Raster* typical data wrangling (eg crop, extend), to more
sophisticated (pre-)processing tasks typically applied to satellite imagery
(eg atmospheric and topographic correction). This functionality is
complemented by a full access to the satellite layers' metadata at any
stage and the documentation of performed actions in a separate log file.
Currently available sensors include Landsat 4-5 (TM), 7 (ETM+), and 8
(OLI/TIRS Combined), and additional compatibility is ensured for the Landsat
Global Land Survey data set.
Author: Thomas Nauss [aut],
Hanna Meyer [aut],
Tim Appelhans [aut],
Florian Detsch [aut, cre]
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between satellite versions 1.0.5 dated 2024-02-10 and 1.0.6 dated 2025-08-21
DESCRIPTION | 29 LICENSE | 2 MD5 | 214 - NAMESPACE | 220 - NEWS | 147 NEWS.md | 147 R/AAAsatelliteClasses.R | 132 R/RcppExports.R | 30 R/alignGeometry.R | 216 - R/brick.R | 102 R/calcAtmosCorr.R | 437 +- R/calcDODN.R | 138 R/calcEarthSunDist.R | 138 R/calcPathRadDOS.R | 470 +-- R/calcTOAIrradModel.R | 302 - R/calcTOAIrradRadRef.R | 218 - R/calcTOAIrradTable.R | 256 - R/calcTopoCorr.R | 286 - R/compFilePathLandsat.R | 222 - R/compMetaLandsat.R | 336 +- R/convRad2BT.R | 178 - R/convRad2Ref.R | 238 - R/convRef2RadLinear.R | 60 R/convSC2Rad.R | 226 - R/convSC2Ref.R | 256 - R/crop.R | 162 - R/demTools.R | 176 - R/extend.R | 152 R/lutInfo.R | 316 +- R/maskInvarFeatures.R | 252 - R/names.R | 102 R/plot.R | 168 - R/print.R | 32 R/satInfo.R | 1526 +++++----- R/satellite-package.R | 116 R/satellite.R | 238 - R/show.R | 12 R/stack.R | 106 R/subset.R | 184 - R/sysdata.rda |binary README.md | 70 build/partial.rdb |binary build/vignette.rds |binary data/l7.rda |binary data/l8.rda |binary inst/doc/landsat-calibration.R | 22 inst/doc/landsat-calibration.Rmd | 88 inst/doc/landsat-calibration.html | 787 ++--- inst/doc/satellite.R | 78 inst/doc/satellite.Rmd | 226 - inst/doc/satellite.html | 1241 ++++---- inst/extdata/LC08_L1TP_195025_20130707_20170503_01_T1_MTL.txt | 450 +- inst/extdata/LE07_L1TP_195025_20010730_20170204_01_T1_MTL.txt | 480 +-- inst/testdata/LC8/LC81950252013188LGN00_MTL.txt | 412 +- inst/testdata/LE7/LE71950252001211EDC00_MTL.txt | 376 +- inst/testdata/LT05/LT05_L1TP_167055_20000309_20161214_01_T1_MTL.txt | 388 +- man/Satellite-class.Rd | 18 man/SatelliteInfo-class.Rd | 46 man/SatelliteLayers-class.Rd | 30 man/SatelliteLog-class.Rd | 30 man/SatelliteMetaData-class.Rd | 30 man/alignGeometry.Rd | 108 man/brick.Rd | 60 man/calcAtmosCorr.Rd | 287 - man/calcDODN.Rd | 100 man/calcEarthSunDist.Rd | 114 man/calcPathRadDOS.Rd | 316 +- man/calcTOAIrradModel.Rd | 178 - man/calcTOAIrradRadRef.Rd | 146 man/calcTOAIrradTable.Rd | 148 man/calcTopoCorr.Rd | 142 man/compFilePathLandsat.Rd | 88 man/compMetaLandsat.Rd | 116 man/convRad2BT.Rd | 94 man/convRad2Ref.Rd | 132 man/convRef2RadLinear.Rd | 68 man/convSC2Rad.Rd | 128 man/convSC2Ref.Rd | 140 man/crop.Rd | 114 man/demTools.Rd | 98 man/extend.Rd | 98 man/l7.Rd | 48 man/l8.Rd | 50 man/lutInfo.Rd | 214 - man/maskInvarFeatures.Rd | 146 man/names.Rd | 62 man/plot.Rd | 84 man/satInfo.Rd | 760 ++-- man/satellite-package.Rd | 66 man/satellite.Rd | 124 man/stack.Rd | 60 man/subset.Rd | 84 tests/testthat.R | 138 tests/testthat/test-calcAtmosCorr.R | 156 - tests/testthat/test-calcDODN.R | 50 tests/testthat/test-calcEarthSunDist.R | 36 tests/testthat/test-calcPathRadDOS.R | 122 tests/testthat/test-calcTOAIrradModel.R | 82 tests/testthat/test-calcTOAIrradRadRef.R | 138 tests/testthat/test-calcTOAIrradTable.R | 84 tests/testthat/test-compMetaLandsat.R | 252 - tests/testthat/test-extend.R | 64 tests/testthat/test-maskInvarFeatures.R | 40 tests/testthat/test-satInfo.R | 40 tests/testthat/test-satInvarFeatures.R | 30 tests/testthat/test-satellite.R | 224 - vignettes/landsat-calibration.Rmd | 88 vignettes/satellite.Rmd | 226 - 108 files changed, 9744 insertions(+), 9713 deletions(-)
Title: A Simple Router for HTTP and WebSocket Requests
Description: In order to make sure that web request ends up in the correct
handler function a router is often used. 'routr' is a package implementing a
simple but powerful routing functionality for R based servers. It is a fully
functional 'fiery' plugin, but can also be used with other 'httpuv' based
servers.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between routr versions 0.4.1 dated 2022-08-19 and 1.0.0 dated 2025-08-21
routr-0.4.1/routr/R/ressource_route.R |only routr-0.4.1/routr/man/Route.Rd |only routr-1.0.0/routr/DESCRIPTION | 24 routr-1.0.0/routr/MD5 | 87 ++ routr-1.0.0/routr/NAMESPACE | 34 - routr-1.0.0/routr/NEWS.md | 35 + routr-1.0.0/routr/R/aaa.R | 20 routr-1.0.0/routr/R/asset_route.R |only routr-1.0.0/routr/R/import-standalone-obj-type.R |only routr-1.0.0/routr/R/import-standalone-types-check.R |only routr-1.0.0/routr/R/openapi_route.R |only routr-1.0.0/routr/R/redirector.R |only routr-1.0.0/routr/R/report_route.R |only routr-1.0.0/routr/R/resource_route.R |only routr-1.0.0/routr/R/route.R | 364 +++++++----- routr-1.0.0/routr/R/routestack.R | 301 ++++++--- routr-1.0.0/routr/R/routr-package.R | 8 routr-1.0.0/routr/R/shared_secret_route.R |only routr-1.0.0/routr/R/sizelimit_route.R | 26 routr-1.0.0/routr/R/tidy_api.R |only routr-1.0.0/routr/README.md | 10 routr-1.0.0/routr/man/AssetRoute.Rd |only routr-1.0.0/routr/man/Route-class.Rd |only routr-1.0.0/routr/man/RouteStack.Rd | 208 +++++- routr-1.0.0/routr/man/asset_route.Rd |only routr-1.0.0/routr/man/figures/lifecycle-deprecated.svg |only routr-1.0.0/routr/man/figures/lifecycle-experimental.svg |only routr-1.0.0/routr/man/figures/lifecycle-stable.svg |only routr-1.0.0/routr/man/figures/lifecycle-superseded.svg |only routr-1.0.0/routr/man/openapi_route.Rd |only routr-1.0.0/routr/man/register_report_format.Rd |only routr-1.0.0/routr/man/report_info.Rd |only routr-1.0.0/routr/man/report_route.Rd |only routr-1.0.0/routr/man/resource_route.Rd |only routr-1.0.0/routr/man/ressource_route.Rd | 117 --- routr-1.0.0/routr/man/route.Rd |only routr-1.0.0/routr/man/route_add.Rd |only routr-1.0.0/routr/man/route_merge.Rd |only routr-1.0.0/routr/man/route_stack.Rd |only routr-1.0.0/routr/man/routr-package.Rd | 2 routr-1.0.0/routr/man/shared_secret_route.Rd |only routr-1.0.0/routr/man/sizelimit_route.Rd | 15 routr-1.0.0/routr/tests/testthat.R | 8 routr-1.0.0/routr/tests/testthat/_snaps |only routr-1.0.0/routr/tests/testthat/fixtures |only routr-1.0.0/routr/tests/testthat/test-asset_route.R |only routr-1.0.0/routr/tests/testthat/test-openapi_route.R |only routr-1.0.0/routr/tests/testthat/test-redirector.R |only routr-1.0.0/routr/tests/testthat/test-report_route.R |only routr-1.0.0/routr/tests/testthat/test-resource_route.R |only routr-1.0.0/routr/tests/testthat/test-route.R | 41 - routr-1.0.0/routr/tests/testthat/test-routestack.R | 98 ++- routr-1.0.0/routr/tests/testthat/test-shared_secret_route.R |only routr-1.0.0/routr/tests/testthat/test-sizelimit_route.R |only routr-1.0.0/routr/tests/testthat/test-tidy_api.R |only 55 files changed, 875 insertions(+), 523 deletions(-)
Title: Patient Reported Outcomes Regression Analysis
Description: It offers a wide variety of techniques, such as graphics, recoding, or regression models, for a comprehensive analysis of patient-reported outcomes (PRO). Especially novel is the broad range of regression models based on the beta-binomial distribution useful for analyzing binomial data with over-dispersion in cross-sectional, longitudinal, or multidimensional response studies (see Najera-Zuloaga J., Lee D.-J. and Arostegui I. (2019) <doi:10.1002/bimj.201700251>).
Author: Josu Najera-Zuloaga [aut, cre],
Dae-Jin Lee [aut],
Inmaculada Arostegui [aut]
Maintainer: Josu Najera-Zuloaga <josu.najera@ehu.eus>
Diff between PROreg versions 1.3 dated 2024-03-13 and 1.3.1 dated 2025-08-21
DESCRIPTION | 22 ++ MD5 | 8 - man/BBmm.Rd | 388 ++++++++++++++++++++++++++-------------------------- man/HRQoLplot.Rd | 6 man/summary.BBmm.Rd | 206 +++++++++++++-------------- 5 files changed, 322 insertions(+), 308 deletions(-)
Title: Power Simulation for Sequential Analyses and Multiple Hypotheses
Description: Calculates, via simulation, power and appropriate stopping
alpha boundaries (and/or futility bounds) for sequential analyses (i.e.,
group sequential design) as well as for multiple hypotheses (multiple tests
included in an analysis), given any specified global error rate. This enables
the sequential use of practically any significance test, as long as the
underlying data can be simulated in advance to a reasonable approximation.
Lukács (2022) <doi:10.21105/joss.04643>.
Author: Gaspar Lukacs [aut, cre]
Maintainer: Gaspar Lukacs <lkcsgaspar@gmail.com>
Diff between POSSA versions 0.6.4 dated 2023-04-22 and 0.6.5 dated 2025-08-21
DESCRIPTION | 10 LICENSE | 2 MD5 | 82 - NAMESPACE | 24 R/POSSA.R | 30 R/get_p.R | 148 +- R/imports.R | 2 R/internal.R | 416 +++--- R/pow.R | 2164 ++++++++++++++++---------------- R/print.possa_pow_df.R | 602 ++++----- R/print.possa_sim_df.R | 316 ++-- R/sim.R | 1064 ++++++++-------- README.md | 2 build/vignette.rds |binary inst/doc/v_1_intro.R | 76 - inst/doc/v_1_intro.Rmd | 1238 +++++++++--------- inst/doc/v_1_intro.html | 2233 +++++++++++++++++----------------- inst/doc/v_2_multiple_hypotheses.R | 336 ++--- inst/doc/v_2_multiple_hypotheses.Rmd | 1162 ++++++++--------- inst/doc/v_2_multiple_hypotheses.html | 2009 +++++++++++++++--------------- inst/doc/v_3_examples.R | 88 - inst/doc/v_3_examples.Rmd | 1252 +++++++++---------- inst/doc/v_3_examples.html | 2011 +++++++++++++++--------------- inst/doc/v_4_benchmarking.R | 118 - inst/doc/v_4_benchmarking.Rmd | 288 ++-- inst/doc/v_4_benchmarking.html | 965 +++++++------- man/POSSA-package.Rd | 60 man/get_p.Rd | 114 - man/pow.Rd | 546 ++++---- man/print.possa_pow_df.Rd | 66 - man/print.possa_pow_list.Rd | 64 man/print.possa_sim_df.Rd | 88 - man/sim.Rd | 448 +++--- tests/testthat.R | 8 tests/testthat/test_1_ttests.R | 302 ++-- tests/testthat/test_2_factors.R | 202 +-- tests/testthat/test_5_aov.R | 340 ++--- tests/testthat/test_get_p.R | 342 ++--- vignettes/v_1_intro.Rmd | 1238 +++++++++--------- vignettes/v_2_multiple_hypotheses.Rmd | 1162 ++++++++--------- vignettes/v_3_examples.Rmd | 1252 +++++++++---------- vignettes/v_4_benchmarking.Rmd | 288 ++-- 42 files changed, 11581 insertions(+), 11577 deletions(-)
Title: Additions and Extensions of the 'VGAM' Package
Description: Extending the functionalities of the 'VGAM' package with
additional functions and datasets. At present, 'VGAMextra'
comprises new family functions (ffs) to estimate several time
series models by maximum likelihood using Fisher scoring,
unlike popular packages in CRAN relying on optim(), including
ARMA-GARCH-like models, the Order-(p, d, q) ARIMAX model (non-
seasonal), the Order-(p) VAR model, error correction models
for cointegrated time series, and ARMA-structures with Student-t
errors. For independent data, new ffs to estimate the inverse-
Weibull, the inverse-gamma, the generalized beta of the second
kind and the general multivariate normal distributions are
available. In addition, 'VGAMextra' incorporates new VGLM-links
for the mean-function, and the quantile-function (as an alternative
to ordinary quantile modelling) of several 1-parameter distributions,
that are compatible with the class of VGLM/VGAM family functions.
Currently, only fixed-effects models are implemented. All fun [...truncated...]
Author: Victor Miranda [aut, cre, cph],
Thomas Yee [ctb, ths, cph]
Maintainer: Victor Miranda <victor.miranda@aut.ac.nz>
Diff between VGAMextra versions 0.0-7 dated 2025-02-12 and 0.0-8 dated 2025-08-21
DESCRIPTION | 8 +-- MD5 | 26 +++++------ NEWS | 8 ++- R/AR.studentt.ff.R | 2 R/TSfamilyARIMAX.R | 14 ------ R/TSfamilyARMAX.R | 2 R/TSfamilyLog.R | 45 ++++--------------- R/TSfamilyNegBin.R | 106 ++++++----------------------------------------- R/TSfamilyPoisson.R | 35 +++++---------- R/TSfamilyVGLM.INGARCH.R | 24 +++------- R/TSfamilyYulesimon.R | 62 +++++++-------------------- R/Truncnormalff.R | 4 - R/uninormalff.R | 1 man/ARIMAXff.Rd | 2 14 files changed, 94 insertions(+), 245 deletions(-)
Title: Generating Various Numerical Representation Schemes for Protein
Sequences
Description: Comprehensive toolkit for generating various numerical
features of protein sequences described in Xiao et al. (2015)
<DOI:10.1093/bioinformatics/btv042>. For full functionality,
the software 'ncbi-blast+' is needed, see
<https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html>
for more information.
Author: Nan Xiao [aut, cre] ,
Qing-Song Xu [aut],
Dong-Sheng Cao [aut],
Sebastian Mueller [ctb]
Maintainer: Nan Xiao <me@nanx.me>
Diff between protr versions 1.7-4 dated 2024-09-11 and 1.7-5 dated 2025-08-21
DESCRIPTION | 11 -- MD5 | 14 +- NEWS.md | 7 + README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/protr.R | 286 ++++++++++++++++++++++++++-------------------------- inst/doc/protr.html | 2 8 files changed, 164 insertions(+), 158 deletions(-)
Title: Likelihood Based Inference
Description: Maximum likelihood estimation and likelihood ratio test are essential for modern statistics. This package supports in calculating likelihood based inference.
Reference: Pawitan Y. (2001, ISBN:0-19-850765-8).
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between LBI versions 0.2.2 dated 2025-01-22 and 0.2.3 dated 2025-08-21
LBI-0.2.2/LBI/inst/doc/LBI-manual.pdf |only LBI-0.2.3/LBI/DESCRIPTION | 6 +++--- LBI-0.2.3/LBI/MD5 | 18 +++++++++--------- LBI-0.2.3/LBI/R/LBCIvar.R | 2 +- LBI-0.2.3/LBI/R/LInorm.R | 2 +- LBI-0.2.3/LBI/R/LInormVar.R | 2 +- LBI-0.2.3/LBI/R/LIvRatio.R | 2 +- LBI-0.2.3/LBI/R/LIvar.R | 2 +- LBI-0.2.3/LBI/R/LIvtest.R | 2 +- LBI-0.2.3/LBI/inst/NEWS.Rd | 6 ++++++ LBI-0.2.3/LBI/inst/doc/LBI_0.2.3.pdf |only 11 files changed, 24 insertions(+), 18 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package 'arules' with various visualization
techniques for association rules and itemsets. The package also
includes several interactive visualizations for rule exploration.
Michael Hahsler (2017) <doi:10.32614/RJ-2017-047>.
Author: Michael Hahsler [aut, cre, cph] ,
Giallanza Tyler [ctb],
Sudheer Chelluboina [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.5.3 dated 2024-04-26 and 1.5.4 dated 2025-08-21
DESCRIPTION | 46 +++--- MD5 | 36 ++--- NEWS.md | 9 + R/ggplot2.R | 140 +++++++++----------- R/ggraph.R | 4 R/inspectDT.R | 4 R/plot.R | 241 +++++++++++++++--------------------- R/ruleExplorer.R | 31 +--- R/rules2matrix.R | 13 - README.md | 11 - build/partial.rdb |binary build/vignette.rds |binary inst/README_files/graph-1.png |binary inst/README_files/scatterplot-1.png |binary inst/doc/arulesViz.pdf |binary man/inspectDT.Rd | 4 man/plot_arulesViz.Rd | 1 man/ruleExplorer.Rd | 19 +- tests/testthat.R | 8 - 19 files changed, 252 insertions(+), 315 deletions(-)
Title: The Echelon Analysis and the Detection of Spatial Clusters using
Echelon Scan Method
Description: Functions for the echelon analysis proposed by Myers et al. (1997) <doi:10.1023/A:1018518327329>, and the detection of spatial clusters using echelon scan method proposed by Kurihara (2003) <doi:10.20551/jscswabun.15.2_171>.
Author: Fumio Ishioka [aut, cre]
Maintainer: Fumio Ishioka <fishioka@okayama-u.ac.jp>
Diff between echelon versions 0.3.1 dated 2025-03-20 and 0.4.0 dated 2025-08-21
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++------- NAMESPACE | 4 +-- NEWS.md | 4 +++ R/e.echebin.r | 11 ++++++-- R/e.echenor.r |only R/e.echepoi.r | 11 ++++++-- R/e_main.monte.r | 38 +++++++++++++++++++++++++++- man/echebin.Rd | 73 ++++++++++++++++++++++++++++++++++--------------------- man/echelon.Rd | 2 - man/echenor.Rd |only man/echepoi.Rd | 61 +++++++++++++++++++++++++++++---------------- 12 files changed, 159 insertions(+), 73 deletions(-)