Title: Download 'Qualtrics' Survey Data
Description: Provides functions to access survey results directly into R
using the 'Qualtrics' API. 'Qualtrics'
<https://www.qualtrics.com/about/> is an online survey and data
collection software platform. See <https://api.qualtrics.com/> for
more information about the 'Qualtrics' API. This package is
community-maintained and is not officially supported by 'Qualtrics'.
Author: Jasper Ginn [aut],
Jackson Curtis [ctb],
Shaun Jackson [ctb],
Samuel Kaminsky [ctb],
Eric Knudsen [ctb],
Joseph O'Brien [aut],
Daniel Seneca [ctb],
Julia Silge [aut, cre] ,
Phoebe Wong [ctb]
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between qualtRics versions 3.2.1 dated 2024-08-16 and 3.2.2 dated 2025-08-22
qualtRics-3.2.1/qualtRics/tests/fixtures/colmap_fetch.yml |only qualtRics-3.2.1/qualtRics/tests/fixtures/extract_colmap.yml |only qualtRics-3.2.1/qualtRics/tests/fixtures/fetch_one_qid.yml |only qualtRics-3.2.1/qualtRics/tests/fixtures/fetch_survey.yml |only qualtRics-3.2.1/qualtRics/tests/fixtures/fetch_survey_custom.yml |only qualtRics-3.2.1/qualtRics/tests/fixtures/fetch_survey_exclude.yml |only qualtRics-3.2.1/qualtRics/tests/testthat/_snaps/api-credentials.md |only qualtRics-3.2.1/qualtRics/tests/testthat/test-api-credentials.R |only qualtRics-3.2.2/qualtRics/DESCRIPTION | 8 qualtRics-3.2.2/qualtRics/MD5 | 70 - qualtRics-3.2.2/qualtRics/NEWS.md | 6 qualtRics-3.2.2/qualtRics/R/checks.R | 2 qualtRics-3.2.2/qualtRics/R/fetch_survey.R | 2 qualtRics-3.2.2/qualtRics/build/vignette.rds |binary qualtRics-3.2.2/qualtRics/inst/doc/qualtRics.R | 58 - qualtRics-3.2.2/qualtRics/inst/doc/qualtRics.html | 9 qualtRics-3.2.2/qualtRics/tests/fixtures/column_map.yml | 123 +- qualtRics-3.2.2/qualtRics/tests/fixtures/fetch_description.yml | 535 +++------- qualtRics-3.2.2/qualtRics/tests/fixtures/fetch_description_legacy.yml | 411 +------ qualtRics-3.2.2/qualtRics/tests/fixtures/metadata.yml | 106 + qualtRics-3.2.2/qualtRics/tests/fixtures/metadata_flow.yml | 106 + qualtRics-3.2.2/qualtRics/tests/fixtures/survey_questions.yml | 106 + qualtRics-3.2.2/qualtRics/tests/testthat/helper-qualtRics.R | 33 qualtRics-3.2.2/qualtRics/tests/testthat/test-all-mailinglists.R | 8 qualtRics-3.2.2/qualtRics/tests/testthat/test-all-surveys.R | 18 qualtRics-3.2.2/qualtRics/tests/testthat/test-check-params.R | 25 qualtRics-3.2.2/qualtRics/tests/testthat/test-column_map.R | 6 qualtRics-3.2.2/qualtRics/tests/testthat/test-extract-colmap.R | 16 qualtRics-3.2.2/qualtRics/tests/testthat/test-fetch-description.R | 84 - qualtRics-3.2.2/qualtRics/tests/testthat/test-fetch-distribution-history.R | 16 qualtRics-3.2.2/qualtRics/tests/testthat/test-fetch-distributions.R | 14 qualtRics-3.2.2/qualtRics/tests/testthat/test-fetch-id.R | 51 qualtRics-3.2.2/qualtRics/tests/testthat/test-fetch-mailinglist.R | 29 qualtRics-3.2.2/qualtRics/tests/testthat/test-fetch-survey.R | 189 +-- qualtRics-3.2.2/qualtRics/tests/testthat/test-generate-url.R | 54 - qualtRics-3.2.2/qualtRics/tests/testthat/test-list-distribution-links.R | 8 qualtRics-3.2.2/qualtRics/tests/testthat/test-metadata.R | 28 qualtRics-3.2.2/qualtRics/tests/testthat/test-qualtrics-api-request.R | 89 - qualtRics-3.2.2/qualtRics/tests/testthat/test-read-survey.R | 29 qualtRics-3.2.2/qualtRics/tests/testthat/test-survey-questions.R | 9 40 files changed, 1002 insertions(+), 1246 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot
Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [ctb] ,
Wenping Wang [aut],
Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2plot versions 3.0.2 dated 2025-06-25 and 3.0.3 dated 2025-08-22
nlmixr2plot-3.0.2/nlmixr2plot/tests/testthat/test-add.R |only nlmixr2plot-3.0.3/nlmixr2plot/DESCRIPTION | 6 nlmixr2plot-3.0.3/nlmixr2plot/MD5 | 11 - nlmixr2plot-3.0.3/nlmixr2plot/NAMESPACE | 3 nlmixr2plot-3.0.3/nlmixr2plot/NEWS.md | 5 nlmixr2plot-3.0.3/nlmixr2plot/R/nlmixr2PlotList.R | 70 +++++----- nlmixr2plot-3.0.3/nlmixr2plot/tests/testthat/test-nlmixr2PlotList.R | 70 +++++++++- 7 files changed, 112 insertions(+), 53 deletions(-)
Title: Analysis of Clinical Trials with the Desirability of Outcome
Ranking Methodology
Description: Statistical methods and related graphical representations for the Desirability of Outcome Ranking (DOOR) methodology. The DOOR is a paradigm for the design, analysis, interpretation of clinical trials and other research studies based on the patient centric benefit risk evaluation. The package provides functions for generating summary statistics from individual level/summary level datasets, conduct DOOR probability-based inference, and visualization of the results. For more details of DOOR methodology, see Hamasaki and Evans (2025) <doi:10.1201/9781003390855>. For more explanation of the statistical methods and the graphics, see the technical document and user manual of the DOOR 'Shiny' apps at <https://methods.bsc.gwu.edu>.
Author: Yijie He [aut, cre],
Qihang Wu [ctb],
Toshimitsu Hamasaki [ctb]
Maintainer: Yijie He <yih148@gwu.edu>
Diff between door versions 0.0.2 dated 2025-07-08 and 0.0.3 dated 2025-08-22
DESCRIPTION | 6 +- MD5 | 6 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-plots.R | 116 +++++++++++++++++++++++--------------------- 4 files changed, 68 insertions(+), 60 deletions(-)
Title: Model Wrappers for Discriminant Analysis
Description: Bindings for additional classification models for use with
the 'parsnip' package. Models include flavors of discriminant
analysis, such as linear (Fisher (1936)
<doi:10.1111/j.1469-1809.1936.tb02137.x>), regularized (Friedman
(1989) <doi:10.1080/01621459.1989.10478752>), and flexible (Hastie,
Tibshirani, and Buja (1994) <doi:10.1080/01621459.1994.10476866>), as
well as naive Bayes classifiers (Hand and Yu (2007)
<doi:10.1111/j.1751-5823.2001.tb00465.x>).
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between discrim versions 1.0.1 dated 2023-03-08 and 1.0.2 dated 2025-08-22
discrim-1.0.1/discrim/R/aaa.R |only discrim-1.0.1/discrim/tests/testthat/_snaps/naive-Bayes.md |only discrim-1.0.1/discrim/tests/testthat/_snaps/naive-Bayes_naivebayes.md |only discrim-1.0.1/discrim/tests/testthat/test-flexible.R |only discrim-1.0.1/discrim/tests/testthat/test-linear-fda.R |only discrim-1.0.2/discrim/DESCRIPTION | 31 + discrim-1.0.2/discrim/LICENSE | 2 discrim-1.0.2/discrim/MD5 | 80 ++-- discrim-1.0.2/discrim/NEWS.md | 4 discrim-1.0.2/discrim/R/data.R | 12 discrim-1.0.2/discrim/R/discrim-package.R | 5 discrim-1.0.2/discrim/R/discrim_flexible_data.R | 31 - discrim-1.0.2/discrim/R/discrim_linear_data.R | 122 +++---- discrim-1.0.2/discrim/R/discrim_quad_data.R | 62 +-- discrim-1.0.2/discrim/R/discrim_regularized_data.R | 29 - discrim-1.0.2/discrim/R/helpers.R | 90 +++-- discrim-1.0.2/discrim/R/misc.R | 6 discrim-1.0.2/discrim/R/naive_Bayes_data.R | 49 +-- discrim-1.0.2/discrim/R/zzz.R |only discrim-1.0.2/discrim/README.md | 10 discrim-1.0.2/discrim/inst/WORDLIST | 47 -- discrim-1.0.2/discrim/man/discrim-package.Rd | 16 discrim-1.0.2/discrim/man/figures/README-example-1.png |binary discrim-1.0.2/discrim/man/figures/logo.png |only discrim-1.0.2/discrim/man/fit_regularized_linear.Rd | 18 - discrim-1.0.2/discrim/man/parabolic.Rd | 12 discrim-1.0.2/discrim/man/rmd/example.Rmd | 15 discrim-1.0.2/discrim/tests/spelling.R | 3 discrim-1.0.2/discrim/tests/testthat/_snaps/flexible-earth.md |only discrim-1.0.2/discrim/tests/testthat/_snaps/linear-lda.md | 12 discrim-1.0.2/discrim/tests/testthat/_snaps/linear-sparsediscrim.md | 5 discrim-1.0.2/discrim/tests/testthat/_snaps/linear.md |only discrim-1.0.2/discrim/tests/testthat/_snaps/quad-qda.md | 30 + discrim-1.0.2/discrim/tests/testthat/_snaps/rda.md | 2 discrim-1.0.2/discrim/tests/testthat/_snaps/regularized.md |only discrim-1.0.2/discrim/tests/testthat/helper-objects.R | 140 +++++++- discrim-1.0.2/discrim/tests/testthat/test-flexible-earth.R |only discrim-1.0.2/discrim/tests/testthat/test-linear-lda.R | 128 ++++--- discrim-1.0.2/discrim/tests/testthat/test-linear-ridge.R |only discrim-1.0.2/discrim/tests/testthat/test-linear-sda.R | 37 +- discrim-1.0.2/discrim/tests/testthat/test-linear-sparsediscrim.R | 161 +++++----- discrim-1.0.2/discrim/tests/testthat/test-linear.R |only discrim-1.0.2/discrim/tests/testthat/test-naive-Bayes.R | 151 ++++----- discrim-1.0.2/discrim/tests/testthat/test-naive-Bayes_naivebayes.R | 153 ++++----- discrim-1.0.2/discrim/tests/testthat/test-quad-qda.R | 115 +++---- discrim-1.0.2/discrim/tests/testthat/test-quad-sparsediscrim.R | 114 +++---- discrim-1.0.2/discrim/tests/testthat/test-rda.R | 99 +++--- discrim-1.0.2/discrim/tests/testthat/test-regularized.R |only 48 files changed, 993 insertions(+), 798 deletions(-)
Title: Simulating Differential Equations with Data
Description: Designed to support the visualization, numerical computation,
qualitative analysis, model-data fusion, and stochastic simulation for
autonomous systems of differential equations. Euler and Runge-Kutta methods
are implemented, along with tools to visualize the two-dimensional
phaseplane. Likelihood surfaces and a simple Markov Chain Monte Carlo
parameter estimator can be used for model-data fusion of differential
equations and empirical models. The Euler-Maruyama method is provided for
simulation of stochastic differential equations. The package was originally
written for internal use to support teaching by Zobitz, and refined to
support the text "Exploring modeling with data and differential equations
using R" by John Zobitz (2021) <https://jmzobitz.github.io/ModelingWithR/index.html>.
Author: John Zobitz [aut, cre]
Maintainer: John Zobitz <zobitz@augsburg.edu>
Diff between demodelr versions 1.0.1 dated 2022-09-16 and 2.0.0 dated 2025-08-22
DESCRIPTION | 12 - MD5 | 28 +-- NEWS.md | 6 R/compute_likelihood.R | 34 ++-- R/euler.R | 10 - R/euler_stochastic.R | 14 - R/global_temperature.R | 2 R/mcmc_analyze.R | 95 +++++------ R/mcmc_estimate.R | 385 ++++++++++++++++++++++------------------------ R/phaseplane.R | 54 +++--- R/rk4.R | 22 +- man/global_temperature.Rd | 2 man/mcmc_analyze.Rd | 2 man/mcmc_estimate.Rd | 2 man/phaseplane.Rd | 8 15 files changed, 340 insertions(+), 336 deletions(-)
Title: Relational Data from the 'Star Wars' API for Learning and
Teaching
Description: Provides data about the 'Star Wars' movie franchise in a set
of relational tables or as a complete 'DuckDB' database. All data was
collected from the open source 'Star Wars' API.
Author: Garrick Aden-Buie [aut, cre]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between starwarsdb versions 0.1.2 dated 2020-11-02 and 0.1.3 dated 2025-08-22
DESCRIPTION | 28 +++---- MD5 | 39 +++++----- NEWS.md | 4 + R/data.R | 15 +--- README.md | 100 +++++++++++++-------------- man/figures/README-starwars-data-model-1.svg |only man/films.Rd | 2 man/films_people.Rd | 2 man/films_planets.Rd | 2 man/films_vehicles.Rd | 2 man/people.Rd | 2 man/pilots.Rd | 2 man/planets.Rd | 2 man/roxygen/templates/swapi.R | 2 man/schema.Rd | 16 ++-- man/species.Rd | 2 man/starwars_db.Rd | 12 +-- man/starwars_dm.Rd | 4 - man/starwarsdb-package.Rd | 2 man/vehicles.Rd | 2 tests/testthat/test-dm.R | 19 +++-- 21 files changed, 133 insertions(+), 126 deletions(-)
Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl],
Paul Pearson [ctb],
Daniel Muellner [ctb],
Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>
Diff between MapperAlgo versions 1.0.3 dated 2025-06-20 and 1.0.4 dated 2025-08-22
DESCRIPTION | 10 LICENSE | 2 MD5 | 50 ++-- NAMESPACE | 2 R/Cluster.R | 332 +++++++++++++++---------------- R/ConvertLevelsets.R | 66 +++--- R/Cover.R | 76 +++---- R/EdgeVertices.R | 98 ++++----- R/MapperAlgo.R | 279 ++++++++++++++------------ R/Plotter.R | 114 ++++++---- R/SimplicialComplex.R | 86 ++++---- R/zzz.R | 2 README.md | 173 +++++++--------- man/MapperAlgo.Rd | 97 ++++----- man/MapperPlotter.Rd | 48 ++-- man/cluster_cutoff_at_first_empty_bin.Rd | 42 +-- man/cover_points.Rd | 74 +++--- man/find_best_k_for_kmeans.Rd | 42 +-- man/mapperEdges.Rd | 36 +-- man/mapperVertices.Rd | 40 +-- man/perform_clustering.Rd | 56 ++--- man/simplcial_complex.Rd | 68 +++--- man/to_lsfi.Rd | 38 +-- man/to_lsmi.Rd | 38 +-- tests/testthat.R | 24 +- tests/testthat/test-MapperAlgo.R | 6 26 files changed, 968 insertions(+), 931 deletions(-)
Title: Self-Validated Ensemble Models with Elastic Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM, Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using Elastic Net regression via 'glmnet' (Friedman et al. <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). \\Code for the whole model test was taken from the supplementary material of Karl (2024). Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 1.4.0 dated 2025-08-18 and 1.5.3 dated 2025-08-22
DESCRIPTION | 8 MD5 | 23 R/SVEMnet.R | 292 ++-- R/glmnet_with_cv.R | 20 R/predict.svem_lasso.R | 92 + inst/doc/SVEMnet_vignette.R | 17 inst/doc/SVEMnet_vignette.Rmd | 185 -- inst/doc/SVEMnet_vignette.html | 2572 +++++------------------------------------ man/SVEMnet.Rd | 192 +-- man/glmnet_with_cv.Rd | 4 man/predict.svem_model.Rd | 27 vignettes/SVEMnet_vignette.Rmd | 185 -- vignettes/bic_sim.R |only 13 files changed, 776 insertions(+), 2841 deletions(-)
Title: Spatial Navigation Strategy Analysis
Description: A toolkit for the analysis of paths from spatial tracking experiments and calculation of goal-finding strategies.
This package is centered on an approach using machine learning for path classification.
Author: Rupert Overall [aut, cre]
Maintainer: Rupert Overall <rtrack@rupertoverall.net>
Diff between Rtrack versions 2.0.3 dated 2023-12-11 and 2.0.4 dated 2025-08-22
DESCRIPTION | 17 +- MD5 | 60 +++---- NAMESPACE | 2 NEWS.md | 14 + R/calculate_apa_metrics.R | 34 ++-- R/calculate_barnes_metrics.R | 40 ++--- R/calculate_mwm_metrics.R | 30 +-- R/calculate_nor_metrics.R | 18 +- R/calculate_oft_metrics.R | 28 +-- R/call_strategy.R | 2 R/check_experiment.R | 101 +++++++------ R/export_data.R | 2 R/export_results.R | 12 + R/identify_track_format.R | 69 +++++--- R/plot_density.R | 66 +++++--- R/plot_path.R | 15 + R/plot_strategies.R | 151 ++++++++++++++----- R/plot_variable.R | 171 +++++++++++++++------- R/read_apa_path.R | 14 - R/read_arena.R | 334 +++++++++++++++++++++++++++++-------------- R/read_experiment.R | 37 +++- R/read_json.R | 5 R/read_oft_path.R | 2 R/read_raw_coordinate_data.R | 111 +++++++++++--- R/shapes.R | 61 +++++-- R/sysdata.rda |binary README.md | 7 man/plot_density.Rd | 11 + man/plot_path.Rd | 5 man/plot_strategies.Rd | 33 +++- man/plot_variable.Rd | 39 +++-- 31 files changed, 1003 insertions(+), 488 deletions(-)
Title: Spatial Dispersion Index (SDI) Family of Metrics for
Spatial/Geographic Networks
Description: Spatial Dispersion Index (SDI) is a generalized measurement index, or rather a family of indices to evaluate spatial dispersion of movements/flows in a network in a problem neutral way as described in: Gencer (2023) <doi:10.1007/s12061-023-09545-8>. This package computes and optionally visualizes this index with minimal hassle.
Author: Mehmet Gencer [aut, cre, cph] ,
Muecahit Zor [aut],
Engin Hengirmen [aut]
Maintainer: Mehmet Gencer <mehmetgencer@yahoo.com>
Diff between rSDI versions 0.2.1 dated 2024-05-30 and 0.2.2 dated 2025-08-22
DESCRIPTION | 14 +++--- MD5 | 18 ++++---- NEWS.md | 6 ++ R/plotSDI.R | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/rSDI.R | 31 ++------------ inst/doc/rSDI.Rmd | 32 ++------------- inst/doc/rSDI.html | 110 ++++++++++++++++++++--------------------------------- vignettes/rSDI.Rmd | 32 ++------------- 10 files changed, 82 insertions(+), 165 deletions(-)
Title: Many Ways to Make, Modify, Mark, and Measure Myriad Networks
Description: Many tools for making, modifying, marking, measuring,
and motifs and memberships of many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
on directed, multiplex, multimodal, signed, and other networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Christian Steglich [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 1.5.1 dated 2025-06-23 and 1.6.0 dated 2025-08-22
manynet-1.5.1/manynet/R/map_autograph.R |only manynet-1.5.1/manynet/R/map_layouts.R |only manynet-1.5.1/manynet/R/map_palettes.R |only manynet-1.5.1/manynet/R/map_plot.R |only manynet-1.5.1/manynet/R/map_theme.R |only manynet-1.5.1/manynet/R/reexports_ggplot2.R |only manynet-1.5.1/manynet/man/depth_first_recursive_search.Rd |only manynet-1.5.1/manynet/man/map_graphr.Rd |only manynet-1.5.1/manynet/man/map_graphs.Rd |only manynet-1.5.1/manynet/man/map_grapht.Rd |only manynet-1.5.1/manynet/man/map_layout_configuration.Rd |only manynet-1.5.1/manynet/man/map_layout_partition.Rd |only manynet-1.5.1/manynet/man/map_palettes.Rd |only manynet-1.5.1/manynet/man/map_scales.Rd |only manynet-1.5.1/manynet/man/map_themes.Rd |only manynet-1.5.1/manynet/tests/testthat/test-map_autograph.R |only manynet-1.5.1/manynet/tests/testthat/test-map_theme.R |only manynet-1.6.0/manynet/DESCRIPTION | 29 +-- manynet-1.6.0/manynet/MD5 | 93 ++++------- manynet-1.6.0/manynet/NAMESPACE | 97 ----------- manynet-1.6.0/manynet/NEWS.md | 42 +++++ manynet-1.6.0/manynet/R/make_generate.R | 12 - manynet-1.6.0/manynet/R/make_play.R | 5 manynet-1.6.0/manynet/R/make_read.R | 2 manynet-1.6.0/manynet/R/manip_correlation.R | 3 manynet-1.6.0/manynet/R/manip_format.R | 1 manynet-1.6.0/manynet/R/manip_reformed.R | 37 ++-- manynet-1.6.0/manynet/R/manip_ties.R | 2 manynet-1.6.0/manynet/R/manynet-defunct.R | 76 ++++----- manynet-1.6.0/manynet/R/manynet-tutorials.R | 6 manynet-1.6.0/manynet/R/manynet-utils.R | 15 - manynet-1.6.0/manynet/R/mark_ties.R | 28 +-- manynet-1.6.0/manynet/R/measure_centrality.R | 8 manynet-1.6.0/manynet/R/measure_features.R | 52 +++++- manynet-1.6.0/manynet/R/member_components.R | 3 manynet-1.6.0/manynet/R/member_core.R | 34 +++- manynet-1.6.0/manynet/README.md | 108 ------------- manynet-1.6.0/manynet/man/defunct.Rd | 42 ----- manynet-1.6.0/manynet/man/make_cran.Rd | 2 manynet-1.6.0/manynet/man/make_learning.Rd | 3 manynet-1.6.0/manynet/man/make_play.Rd | 2 manynet-1.6.0/manynet/man/make_random.Rd | 4 manynet-1.6.0/manynet/man/make_stochastic.Rd | 8 manynet-1.6.0/manynet/man/manip_paths.Rd | 5 manynet-1.6.0/manynet/man/manip_permutation.Rd | 4 manynet-1.6.0/manynet/man/manip_project.Rd | 3 manynet-1.6.0/manynet/man/manip_reformat.Rd | 1 manynet-1.6.0/manynet/man/manip_ties.Rd | 2 manynet-1.6.0/manynet/man/mark_core.Rd | 13 + manynet-1.6.0/manynet/man/mark_ties.Rd | 4 manynet-1.6.0/manynet/man/mark_triangles.Rd | 24 +- manynet-1.6.0/manynet/man/measure_central_between.Rd | 4 manynet-1.6.0/manynet/man/measure_central_close.Rd | 4 manynet-1.6.0/manynet/man/measure_features.Rd | 28 ++- manynet-1.6.0/manynet/man/reexports.Rd | 13 - manynet-1.6.0/manynet/tests/testthat/test-manip_reformed.R | 12 + 56 files changed, 331 insertions(+), 500 deletions(-)
Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Toolbox to process raw data from closed loop flux chamber (or tent)
setups into ecosystem gas fluxes usable for analysis. It goes from a
data frame of gas concentration over time (which can contain several
measurements) and a meta data file indicating which measurement was done
when, to a data frame of ecosystem gas fluxes including quality diagnostics.
Organized with one function per step, maximizing user flexibility and backwards
compatibility. Different models to estimate the fluxes from the raw data are
available: exponential as described in
Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, exponential as described in
Hutchinson and Mosier (1981) <doi:10.2136/sssaj1981.03615995004500020017x>,
quadratic, and linear. Other functions include quality assessment,
plotting for visual check, calculation of fluxes based on the setup
specific parameters (chamber size, plot area, ...), gross primary production
and transpiration rate calculation, and light response curves.
Author: Joseph Gaudard [aut, cre] ,
Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between fluxible versions 1.2.6 dated 2025-06-24 and 1.3.0 dated 2025-08-22
DESCRIPTION | 30 MD5 | 280 NAMESPACE | 11 NEWS.md | 48 R/data-co2_conc_mid_missing.R | 1 R/data-co2_conc_missing.R | 1 R/data-co2_df_missing.R | 1 R/data-record_liahovden.R | 2 R/data-slopes0_temp.R | 3 R/data-wet_conc.R |only R/flux_calc.R | 24 R/flux_check_item.R | 1 R/flux_cut.R | 5 R/flux_diff.R |only R/flux_drygas.R |only R/flux_fit_type.R | 1 R/flux_fitting.R | 62 R/flux_fitting_exptz.R | 1 R/flux_fitting_hm.R | 1 R/flux_fitting_lm.R | 1 R/flux_fitting_quadratic.R | 1 R/flux_fitting_zhao18.R | 1 R/flux_fun_check.R | 1 R/flux_gep.R | 8 R/flux_gpp.R | 17 R/flux_lrc.R | 53 R/flux_match.R | 45 R/flux_match_col.R | 3 R/flux_match_fixed.R | 1 R/flux_param_exp.R | 10 R/flux_param_kappamax.R | 10 R/flux_param_lm.R | 10 R/flux_param_qua.R | 10 R/flux_plot.R | 148 R/flux_plot_exp.R | 19 R/flux_plot_flag.R | 3 R/flux_plot_lin.R | 5 R/flux_plot_longpdf.R |only R/flux_plot_pdf.R |only R/flux_plot_quadratic.R | 5 R/flux_print_plot.R |only R/flux_quality.R | 4 R/flux_quality_exp.R | 1 R/flux_quality_kappamax.R | 1 R/flux_quality_lm.R | 1 R/flux_quality_qua.R | 1 R/flux_units.R | 6 R/stupeflux.R | 10 README.md | 125 build/vignette.rds |binary data/co2_df_short.rda |binary data/co2_liahovden.rda |binary data/record_liahovden.rda |binary data/record_short.rda |binary data/wet_conc.rda |only inst/CITATION | 6 inst/doc/data-prep.R | 16 inst/doc/data-prep.Rmd | 57 inst/doc/data-prep.html | 154 inst/doc/fluxible.R | 92 inst/doc/fluxible.Rmd | 243 inst/doc/fluxible.html | 511 inst/doc/li7500.R |only inst/doc/li7500.Rmd |only inst/doc/li7500.html |only inst/doc/two-gases.Rmd | 2 inst/doc/two-gases.html | 6 man/co2_conc_mid_missing.Rd | 2 man/co2_conc_missing.Rd | 2 man/co2_df_missing.Rd | 2 man/figures/README-short-example-1.png |binary man/figures/logo.png |only man/flux_calc.Rd | 10 man/flux_check_item.Rd | 1 man/flux_cut.Rd | 1 man/flux_diff.Rd |only man/flux_drygas.Rd |only man/flux_fit_type.Rd | 1 man/flux_fitting.Rd | 14 man/flux_fitting_exptz.Rd | 1 man/flux_fitting_hm.Rd | 1 man/flux_fitting_lm.Rd | 1 man/flux_fitting_quadratic.Rd | 1 man/flux_fitting_zhao18.Rd | 1 man/flux_fun_check.Rd | 1 man/flux_gep.Rd | 8 man/flux_gpp.Rd | 4 man/flux_lrc.Rd | 13 man/flux_match.Rd | 21 man/flux_match_col.Rd | 3 man/flux_match_fixed.Rd | 1 man/flux_param_exp.Rd | 5 man/flux_param_kappamax.Rd | 5 man/flux_param_lm.Rd | 5 man/flux_param_qua.Rd | 5 man/flux_plot.Rd | 33 man/flux_plot_exp.Rd | 5 man/flux_plot_flag.Rd | 1 man/flux_plot_lin.Rd | 1 man/flux_plot_longpdf.Rd |only man/flux_plot_pdf.Rd |only man/flux_plot_quadratic.Rd | 1 man/flux_print_plot.Rd |only man/flux_quality_exp.Rd | 1 man/flux_quality_kappamax.Rd | 1 man/flux_quality_lm.Rd | 1 man/flux_quality_qua.Rd | 1 man/flux_units.Rd | 5 man/fluxible-package.Rd | 4 man/record_liahovden.Rd | 2 man/slopes0_temp.Rd | 4 man/stupeflux.Rd | 10 man/wet_conc.Rd |only tests/testthat/_snaps/flux_calc.md | 57 tests/testthat/_snaps/flux_diff.md |only tests/testthat/_snaps/flux_drygas.md |only tests/testthat/_snaps/flux_fitting.md | 33 tests/testthat/_snaps/flux_gpp.md | 6 tests/testthat/_snaps/flux_lrc.md | 56 tests/testthat/_snaps/flux_match.md | 2 tests/testthat/_snaps/flux_plot.md | 49 tests/testthat/_snaps/flux_plot/ggssave-and-print.svg |only tests/testthat/_snaps/flux_plot/longpdf-and-print.svg |only tests/testthat/_snaps/flux_plot/plot-as-an-object.svg | 3336 +-- tests/testthat/_snaps/flux_plot/plot-for-exp-hm-fit.svg | 8466 ++++----- tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit-with-mid-missing-data.svg | 7788 ++++----- tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit.svg | 8472 ++++----- tests/testthat/_snaps/flux_plot/plot-for-exp-zhao18-fit-with-mid-missing-data.svg | 7782 ++++----- tests/testthat/_snaps/flux_plot/plot-for-kappamax-fit.svg | 8476 +++++----- tests/testthat/_snaps/flux_plot/plot-for-linear-fit.svg | 3336 +-- tests/testthat/_snaps/flux_plot/plot-for-quadratic-fit-with-mid-missing-data.svg | 7770 ++++----- tests/testthat/_snaps/flux_plot/plot-with-custom-facet-id.svg |only tests/testthat/_snaps/flux_quality.md | 9 tests/testthat/test-flux_calc.R | 42 tests/testthat/test-flux_diff.R |only tests/testthat/test-flux_drygas.R |only tests/testthat/test-flux_fit_type.R | 6 tests/testthat/test-flux_fitting.R | 96 tests/testthat/test-flux_gpp.R | 37 tests/testthat/test-flux_lrc.R | 34 tests/testthat/test-flux_match.R | 105 tests/testthat/test-flux_plot.R | 158 tests/testthat/test-flux_quality.R | 4 tests/testthat/test-flux_units.R | 9 vignettes/data-prep.Rmd | 57 vignettes/ex_data/field_campaign/1_2000_east_1_day_a-2023-12-14T105700.txt | 102 vignettes/ex_data/field_campaign/1_2000_east_1_day_photo-2023-12-14T105344.txt | 122 vignettes/ex_data/field_campaign/1_2000_east_1_night_a-2023-12-11T220205.txt | 88 vignettes/ex_data/li7500 |only vignettes/fluxible.Rmd | 243 vignettes/li7500.Rmd |only vignettes/tent_peru.jpg |only vignettes/two-gases.Rmd | 2 153 files changed, 30161 insertions(+), 28820 deletions(-)
Title: Line Plots that Pop
Description: A set of geometries to make line plots a little bit nicer. Use
along with 'ggplot2' to:
- Improve the clarity of line plots with many overlapping lines
- Draw more realistic worms.
Author: Jacob Scott [aut, cre]
Maintainer: Jacob Scott <jscott2718@gmail.com>
Diff between ggborderline versions 0.2.0 dated 2022-10-25 and 0.3.0 dated 2025-08-22
DESCRIPTION | 18 +++++++------- MD5 | 8 +++--- NEWS.md | 8 ++++-- R/geom-borderpath.R | 31 ++++++++++++++++++++++++ man/geom_borderpath.Rd | 63 +++++++++++++++++++++++++++++++++++++++---------- 5 files changed, 102 insertions(+), 26 deletions(-)
Title: R Client for 'Via Foundry' API
Description: 'Via Foundry' API provides streamlined tools for interacting with and extracting data from structured responses, particularly for use cases involving hierarchical data from Foundry's API. It includes functions to fetch and parse process-level and file-level metadata, allowing users to efficiently query and manipulate nested data structures. Key features include the ability to list all unique process names, retrieve file metadata for specific or all processes, and dynamically load or download files based on their type. With built-in support for handling various file formats (e.g., tabular and non-tabular files) and seamless integration with API through authentication, this package is designed to enhance workflows involving large-scale data management and analysis. Robust error handling and flexible configuration ensure reliable performance across diverse data environments. Please consult the documentation for the API endpoint for your installation.
Author: Alper Kucukural [aut, cre],
Via Scientific [aut, cph]
Maintainer: Alper Kucukural <alper@viascientific.com>
Diff between viafoundry versions 1.0.0 dated 2025-01-13 and 1.0.1 dated 2025-08-22
DESCRIPTION | 8 - MD5 | 81 ++++++++++--- NAMESPACE | 55 ++++++++ NEWS.md | 7 + R/auth.R | 24 ++- R/client.R | 65 +++++++--- R/metadata.R |only R/proccess.R |only R/reports.R | 261 +++++++++++++++++++++++++++++++++++++----- README.md | 200 ++++++++++++++++++++++++++++++-- inst |only man/addFilesToDataset.Rd |only man/authenticate.Rd | 10 - man/call_endpoint.Rd | 16 +- man/checkProcessUsage.Rd |only man/createCanvas.Rd |only man/createCollection.Rd |only man/createField.Rd |only man/createMenuGroup.Rd |only man/createParameter.Rd |only man/createProcess.Rd |only man/createProcessConfig.Rd |only man/deleteCanvas.Rd |only man/deleteCollection.Rd |only man/deleteData.Rd |only man/deleteField.Rd |only man/deleteParameter.Rd |only man/deleteProcess.Rd |only man/duplicateProcess.Rd |only man/filterParameters.Rd |only man/getAllFileNames.Rd | 8 - man/getAllReportPaths.Rd |only man/getCanvas.Rd |only man/getCanvasFields.Rd |only man/getCollection.Rd |only man/getCollectionFields.Rd |only man/getData.Rd |only man/getField.Rd |only man/getFieldsForCollection.Rd |only man/getFileNames.Rd | 2 man/getMenuGroupByName.Rd |only man/getPipelineParameters.Rd |only man/getProcess.Rd |only man/getProcessRevisions.Rd |only man/getReportDirs.Rd |only man/get_bearer_token.Rd | 2 man/listMenuGroups.Rd |only man/listParameters.Rd |only man/listProcesses.Rd |only man/load_config.Rd | 2 man/login.Rd | 2 man/prepareSessionHistory.Rd |only man/searchCanvas.Rd |only man/searchCollections.Rd |only man/searchData.Rd |only man/searchDatasetFiles.Rd |only man/searchFields.Rd |only man/updateCanvas.Rd |only man/updateCollection.Rd |only man/updateData.Rd |only man/updateField.Rd |only man/updateMenuGroup.Rd |only man/updateParameter.Rd |only man/updateProcess.Rd |only man/uploadReportFile.Rd |only man/uploadSessionHistory.Rd |only 66 files changed, 640 insertions(+), 103 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There
is also an experimental extension for survival analysis, clustering
and general, example-specific cost-sensitive learning. Generic
resampling, including cross-validation, bootstrapping and subsampling.
Hyperparameter tuning with modern optimization techniques, for single-
and multi-objective problems. Filter and wrapper methods for feature
selection. Extension of basic learners with additional operations
common in machine learning, also allowing for easy nested resampling.
Most operations can be parallelized.
Author: Bernd Bischl [aut] ,
Michel Lang [aut] ,
Lars Kotthoff [aut],
Patrick Schratz [aut] ,
Julia Schiffner [aut],
Jakob Richter [aut],
Zachary Jones [aut],
Giuseppe Casalicchio [aut] ,
Mason Gallo [aut],
Jakob Bossek [ctb] ,
Erich Studerus [ctb] ,
Leonard [...truncated...]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr versions 2.19.2 dated 2024-06-12 and 2.19.3 dated 2025-08-22
mlr-2.19.2/mlr/R/getResampleExtract.R |only mlr-2.19.3/mlr/DESCRIPTION | 33 mlr-2.19.3/mlr/MD5 | 43 mlr-2.19.3/mlr/NAMESPACE | 2364 ++++++++++----------- mlr-2.19.3/mlr/NEWS.md | 4 mlr-2.19.3/mlr/R/BaseWrapper.R | 2 mlr-2.19.3/mlr/R/ResampleInstances.R | 31 mlr-2.19.3/mlr/R/TuneControlMBO.R | 2 mlr-2.19.3/mlr/R/batchmark.R | 4 mlr-2.19.3/mlr/R/extractFDAFeaturesMethods.R | 2 mlr-2.19.3/mlr/R/getClassWeightParam.R | 2 mlr-2.19.3/mlr/build/partial.rdb |binary mlr-2.19.3/mlr/build/vignette.rds |binary mlr-2.19.3/mlr/man/TuneMultiCritControl.Rd | 2 mlr-2.19.3/mlr/man/batchmark.Rd | 4 mlr-2.19.3/mlr/man/getClassWeightParam.Rd | 2 mlr-2.19.3/mlr/man/getLearnerParamSet.Rd | 2 mlr-2.19.3/mlr/man/getParamSet.Rd | 2 mlr-2.19.3/mlr/man/instantiateResampleInstance.Rd |only mlr-2.19.3/mlr/man/makeBaseWrapper.Rd | 2 mlr-2.19.3/mlr/man/makeExtractFDAFeatMethod.Rd | 2 mlr-2.19.3/mlr/man/makeModelMultiplexerParamSet.Rd | 2 mlr-2.19.3/mlr/man/makeTuneControlMBO.Rd | 2 mlr-2.19.3/mlr/tests/testthat/xgboost.model |only 24 files changed, 1278 insertions(+), 1229 deletions(-)
Title: Create Visualisations for BART Models
Description: Investigating and visualising Bayesian Additive Regression Tree (BART) (Chipman, H. A., George, E. I., & McCulloch, R. E. 2010) <doi:10.1214/09-AOAS285> model fits. We construct conventional plots to analyze a model’s performance and stability as well as create new tree-based plots to analyze variable importance, interaction, and tree structure. We employ Value Suppressing Uncertainty Palettes (VSUP) to construct heatmaps that display variable importance and interactions jointly using colour scale to represent posterior uncertainty. Our visualisations are designed to work with the most popular BART R packages available, namely 'BART' Rodney Sparapani and Charles Spanbauer and Robert McCulloch 2021 <doi:10.18637/jss.v097.i01>, 'dbarts' (Vincent Dorie 2023) <https://CRAN.R-project.org/package=dbarts>, and 'bartMachine' (Adam Kapelner and Justin Bleich 2016) <doi:10.18637/jss.v070.i04>.
Author: Alan Inglis [aut, cre],
Andrew Parnell [aut],
Catherine Hurley [aut],
Claus Wilke [ctb]
Maintainer: Alan Inglis <alan.inglis@mu.ie>
Diff between bartMan versions 0.1.1 dated 2024-07-24 and 0.2.0 dated 2025-08-22
DESCRIPTION | 12 - MD5 | 21 +- NAMESPACE | 25 +++ R/VSUP.R | 402 +++++++++++++++++++++++++++++++++++++++++++++++++++- R/bartDiag.R | 14 + R/extractTreeData.R | 20 ++ R/localProcedure.R | 69 ++++---- R/permVimp.R | 57 ++++--- R/permVint.R | 103 +++++-------- R/treeBarPlot.R | 289 ++++++++++++++++++++----------------- R/viviBartPlot.R | 18 +- inst |only 12 files changed, 743 insertions(+), 287 deletions(-)
Title: Build and Tune Several Models
Description: Frequently one needs a convenient way to build and tune
several models in one go.The goal is to provide a number of machine learning convenience
functions. It provides the ability to build, tune and obtain predictions of
several models in one function. The models are built using functions from
'caret' with easier to read syntax.
Kuhn(2014) <doi:10.48550/arXiv.1405.6974>.
Author: Nelson Gonzabato [aut, cre]
Maintainer: Nelson Gonzabato <gonzabato@hotmail.com>
Diff between manymodelr versions 0.3.9 dated 2025-03-20 and 0.4.0 dated 2025-08-22
DESCRIPTION | 14 ++--- MD5 | 77 ++++++++++++++-------------- NAMESPACE | 63 ++++++++++++++++++---- R/add_model_predictions.R | 23 ++++---- R/agg_by_group.R | 1 R/extract_model_info.R | 18 ++---- R/get_mode.R | 50 +++++++++--------- R/get_var_corr.R | 23 ++++---- R/get_var_corr_.R | 25 ++++----- R/globals.R | 2 R/helpers.R | 14 ++--- R/imports.R |only R/multi_model_1.R | 35 +++++------- R/na_replace.R | 22 ++++---- R/plot_corr.R | 7 +- R/report_model.R | 4 - R/rowdiff.R | 24 ++++---- R/zzz.R | 1 build/vignette.rds |binary inst/doc/correlations.html | 16 +---- inst/doc/correlations.rmd | 2 inst/doc/manymodelr_vignette.R | 4 - inst/doc/manymodelr_vignette.html | 11 ++-- inst/doc/manymodelr_vignette.rmd | 4 - inst/doc/misc.html | 4 - inst/doc/modeling.R | 4 - inst/doc/modeling.html | 8 +- inst/doc/modeling.rmd | 4 - man/add_model_predictions.Rd | 2 man/add_model_residuals.Rd | 2 man/get_var_corr.Rd | 2 man/get_var_corr_.Rd | 2 man/multi_model_1.Rd | 4 - man/rowdiff.Rd | 4 - tests/testthat/test_add_model_predictions.R | 18 +++--- tests/testthat/test_na_replace.R | 2 tests/testthat/test_plot_corr.R | 6 +- vignettes/correlations.rmd | 2 vignettes/manymodelr_vignette.rmd | 4 - vignettes/modeling.rmd | 4 - 40 files changed, 264 insertions(+), 248 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Includes implementation for the kidney hierarchical composite endpoint as defined in Heerspink HL et al (2023) “Development and validation of a new hierarchical composite end point for clinical trials of kidney disease progression” (Journal of the American Society of Nephrology 34 (2): 2025–2038, <doi:10.1681/ASN.0000000000000243>). Win odds, also called Wilcoxon-Mann-Whitney or success odds, is the main analysis method. Other win statistics (win probability, win ratio, net benefit) are also implemented in the univariate case, provided there is no censoring. The win probability analysis is based on the Brunner-Munzel test and uses the DeLong-DeLong-Clarke-Pearson variance estimator, as described by Brunner and Konietschke (2025) in “An unbiased rank-based estimator of the Mann–Whitney variance including the case of ties” (Statistical Papers 66 (1): 20, <doi:10.1007/s00362-024-01635-0>). Stratification and covariate adju [...truncated...]
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.8.0 dated 2025-07-11 and 0.8.5 dated 2025-08-22
DESCRIPTION | 6 - MD5 | 64 +++++----- NAMESPACE | 1 NEWS.md | 11 + R/IWP.R | 7 - R/as_hce.data.frame.R | 13 +- R/calcWINS_data_frame.R | 28 ++++ R/calcWINS_formula.R | 1 R/calcWINS_hce.R | 1 R/hce.R | 74 +++++++----- R/regWO_data_frame.R | 2 R/simKHCE.R | 27 +++- R/simORD.R | 2 R/stratWO_data_frame.R | 4 R/summaryWO_adhce.R |only R/summaryWO_hce.R | 5 inst/doc/Introduction.R | 29 +++- inst/doc/Introduction.Rmd | 48 +++++--- inst/doc/Introduction.html | 250 ++++++++++++++++++++++-------------------- inst/doc/Wins.html | 8 - inst/doc/hce.html | 8 - inst/doc/maraca.html | 10 - man/as_hce.data.frame.Rd | 9 + man/calcWINS.data.frame.Rd | 24 +++- man/calcWINS.formula.Rd | 1 man/calcWINS.hce.Rd | 1 man/hce.Rd | 53 +++++--- man/simKHCE.Rd | 15 ++ man/simORD.Rd | 2 man/summaryWO.adhce.Rd |only man/summaryWO.hce.Rd | 1 tests/testthat/test-test-WO.R | 61 ++++++++++ vignettes/Introduction.Rmd | 48 +++++--- vignettes/REFERENCES.bib | 12 -- 34 files changed, 528 insertions(+), 298 deletions(-)
Title: Two One-Sided Tests (TOST) Equivalence Testing
Description: Two one-sided tests (TOST) procedure to test equivalence for t-tests, correlations, differences between proportions, and meta-analyses, including power analysis for t-tests and correlations. Allows you to specify equivalence bounds in raw scale units or in terms of effect sizes. See: Lakens (2017) <doi:10.1177/1948550617697177>.
Author: Daniel Lakens [aut],
Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between TOSTER versions 0.8.4 dated 2025-02-06 and 0.8.6 dated 2025-08-22
DESCRIPTION | 8 MD5 | 181 ++++----- NEWS.md | 10 R/boot_compare_cor.R | 96 +++- R/boot_compare_smd.R | 391 +++++++++++++------ R/boot_cor_test.R | 115 ++++- R/boot_log_TOST.R | 107 ++++- R/boot_ses_calc.R | 146 ++++++- R/boot_smd_calc.R | 107 ++++- R/boot_t_TOST.R | 112 ++++- R/boot_t_test.R | 122 +++++- R/brunner_munzel.R | 16 R/compare_cor.R | 96 +++- R/compare_smd.R | 123 +++++- R/cor_test.R | 91 +++- R/corsum_test.R | 82 +++- R/equ_anova.R | 85 +++- R/equ_ftest.R | 84 +++- R/htest.R | 52 +- R/htest_helpers.R | 78 ++- R/log_TOST.R | 26 + R/others.R | 16 R/plot_corr.R | 76 +++ R/plot_pes.R | 95 ++++ R/plot_smd.R | 123 +++++- R/powerTOSTanova.R | 179 ++++++-- R/power_t_TOST.R | 2 R/rbs.R | 2 R/ses_calc.R | 97 ++++ R/simple_htest.R | 141 +++++-- R/smd_calc.R | 77 +++ R/t_TOST.R | 132 ++++-- R/tsum_TOST.R | 109 ++++- R/wilcox_TOST.R | 19 build/partial.rdb |binary build/vignette.rds |binary inst/doc/IntroTOSTt.R | 92 ++-- inst/doc/IntroTOSTt.Rmd | 249 ++++++++---- inst/doc/IntroTOSTt.html | 742 ++++++++++++++++++++++--------------- inst/doc/IntroductionToTOSTER.html | 4 inst/doc/SMD_calcs.html | 18 inst/doc/correlations.R | 68 ++- inst/doc/correlations.Rmd | 157 +++++-- inst/doc/correlations.html | 391 ++++++++++++------- inst/doc/robustTOST.R | 2 inst/doc/robustTOST.Rmd | 271 ++++++++++++- inst/doc/robustTOST.html | 653 ++++++++++++++++++++++++++++---- inst/doc/the_ftestTOSTER.R | 53 ++ inst/doc/the_ftestTOSTER.Rmd | 230 +++++++++-- inst/doc/the_ftestTOSTER.html | 520 +++++++++++++++++++------ man/as_htest.Rd | 52 +- man/boot_compare_cor.Rd | 128 +++++- man/boot_compare_smd.Rd | 165 ++++++-- man/boot_cor_test.Rd | 135 +++++- man/boot_log_TOST.Rd | 101 +++-- man/boot_ses_calc.Rd | 122 +++++- man/boot_smd_calc.Rd | 120 +++++ man/boot_t_TOST.Rd | 104 +++-- man/boot_t_test.Rd | 129 +++++- man/brunner_munzel.Rd | 6 man/compare_cor.Rd | 120 ++++- man/compare_smd.Rd | 121 +++++- man/corsum_test.Rd | 102 ++++- man/datatosttwoprop.Rd | 1 man/equ_anova.Rd | 77 ++- man/equ_ftest.Rd | 78 ++- man/extract_r_paired.Rd | 4 man/htest-helpers.Rd | 72 ++- man/log_TOST.Rd | 19 man/plot_cor.Rd | 79 +++ man/plot_pes.Rd | 96 ++++ man/plot_smd.Rd | 128 +++++- man/power_eq_f.Rd | 76 +++ man/power_t_TOST.Rd | 2 man/rbs.Rd | 2 man/ses_calc.Rd | 93 +++- man/simple_htest.Rd | 122 ++++-- man/smd_calc.Rd | 85 +++- man/t_TOST.Rd | 116 ++++- man/tsum_TOST.Rd | 108 +++-- man/twoprop_test.Rd | 11 man/wilcox_TOST.Rd | 10 man/z_cor_test.Rd | 90 +++- tests/testthat/Rplots.pdf |only tests/testthat/test-bootTOST.R | 11 tests/testthat/test-log.R | 17 tests/testthat/test-tTOST.R | 16 tests/testthat/test-wilcox.R | 33 + vignettes/IntroTOSTt.Rmd | 249 ++++++++---- vignettes/correlations.Rmd | 157 +++++-- vignettes/robustTOST.Rmd | 271 ++++++++++++- vignettes/the_ftestTOSTER.Rmd | 230 +++++++++-- 92 files changed, 8075 insertions(+), 2229 deletions(-)
Title: User-Friendly R Package for Supervised Machine Learning
Pipelines
Description: An interface to build machine learning models for
classification and regression problems. 'mikropml' implements the ML
pipeline described by Topçuoğlu et al. (2020)
<doi:10.1128/mBio.00434-20> with reasonable default options for data
preprocessing, hyperparameter tuning, cross-validation, testing, model
evaluation, and interpretation steps. See the website
<https://www.schlosslab.org/mikropml/> for more information,
documentation, and examples.
Author: Beguem Topcuoglu [aut] ,
Zena Lapp [aut] ,
Kelly Sovacool [aut, cre] ,
Evan Snitkin [aut] ,
Jenna Wiens [aut] ,
Patrick Schloss [aut] ,
Nick Lesniak [ctb] ,
Courtney Armour [ctb] ,
Sarah Lucas [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between mikropml versions 1.6.1 dated 2023-08-21 and 1.6.2 dated 2025-08-22
DESCRIPTION | 103 +++++++++-------------- MD5 | 56 ++++++------ NEWS.md | 7 + R/checks.R | 8 - R/cross_val.R | 2 R/hyperparameters.R | 2 R/partition.R | 6 - R/plot.R | 4 R/run_ml.R | 4 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/otu_mini_bin_results_rf.rda |binary inst/doc/introduction.R | 134 +++++++++++++++---------------- inst/doc/introduction.html | 13 +-- inst/doc/paper.R | 4 inst/doc/paper.html | 7 - man/check_all.Rd | 7 - man/check_training_frac.Rd | 4 man/create_grouped_data_partition.Rd | 4 man/create_grouped_k_multifolds.Rd | 2 man/get_partition_indices.Rd | 2 man/set_hparams_glmnet.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-checks.R | 5 - tests/testthat/test-feature_importance.R | 123 +--------------------------- tests/testthat/test-plot.R | 6 - tests/testthat/test-run_ml.R | 27 +++--- tests/testthat/test-train.R | 6 - 29 files changed, 206 insertions(+), 334 deletions(-)
Title: Desirability Functions for Multiparameter Optimization
Description: In-line functions for multivariate optimization via
desirability functions (Derringer and Suich, 1980,
<doi:10.1080/00224065.1980.11980968>) with easy use within 'dplyr'
pipelines.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between desirability2 versions 0.1.0 dated 2025-07-22 and 0.2.0 dated 2025-08-22
DESCRIPTION | 6 ++-- MD5 | 21 +++++++-------- NAMESPACE | 1 NEWS.md | 13 +++++++++ R/checks.R | 21 ++++++++++++++- R/desirability.R | 2 - R/tune.R | 47 ++++++++++++++++++++++------------ man/desirability.Rd | 2 - man/make_desirability_cols.Rd |only tests/testthat/_snaps/desirability.md | 10 +++---- tests/testthat/test-desirability.R | 2 - tests/testthat/test-use-data.R | 31 ++++++++++++++++++++++ 12 files changed, 118 insertions(+), 38 deletions(-)
Title: Automatic Plotting of Many Graphs
Description: Visual exploration and presentation of networks should not be difficult.
This package includes functions for plotting networks and network-related metrics with sensible and pretty defaults.
It includes 'ggplot2'-based plot methods for many popular network package classes.
It also includes some novel layout algorithms, and options for straightforward, consistent themes.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between autograph versions 0.1.2 dated 2025-07-02 and 0.2.0 dated 2025-08-22
autograph-0.1.2/autograph/R/map_layout_layered.R |only autograph-0.1.2/autograph/R/map_layout_matching.R |only autograph-0.1.2/autograph/R/map_palettes.R |only autograph-0.1.2/autograph/R/map_theme.R |only autograph-0.1.2/autograph/man/layout_tbl_graph_layered.Rd |only autograph-0.1.2/autograph/man/layout_tbl_graph_matching.Rd |only autograph-0.1.2/autograph/man/map_themes.Rd |only autograph-0.1.2/autograph/tests/testthat/_snaps |only autograph-0.2.0/autograph/DESCRIPTION | 16 + autograph-0.2.0/autograph/MD5 | 52 ++++- autograph-0.2.0/autograph/NAMESPACE | 90 ++++++++++ autograph-0.2.0/autograph/NEWS.md | 27 +++ autograph-0.2.0/autograph/R/autograph_utilities.R |only autograph-0.2.0/autograph/R/layout_configurational.R |only autograph-0.2.0/autograph/R/layout_grid.R |only autograph-0.2.0/autograph/R/layout_layered.R |only autograph-0.2.0/autograph/R/layout_matching.R |only autograph-0.2.0/autograph/R/layout_partition.R |only autograph-0.2.0/autograph/R/layout_valence.R |only autograph-0.2.0/autograph/R/map_autograph.R |only autograph-0.2.0/autograph/R/plot_manydata.R |only autograph-0.2.0/autograph/R/plot_manynet.R | 20 +- autograph-0.2.0/autograph/R/theme_palettes.R |only autograph-0.2.0/autograph/R/theme_scales.R |only autograph-0.2.0/autograph/R/theme_set.R |only autograph-0.2.0/autograph/README.md | 79 ++++++++ autograph-0.2.0/autograph/build |only autograph-0.2.0/autograph/man/ag_call.Rd | 2 autograph-0.2.0/autograph/man/depth_first_recursive_search.Rd |only autograph-0.2.0/autograph/man/layout_configuration.Rd |only autograph-0.2.0/autograph/man/layout_layered.Rd |only autograph-0.2.0/autograph/man/layout_matching.Rd |only autograph-0.2.0/autograph/man/layout_partition.Rd |only autograph-0.2.0/autograph/man/layout_valence.Rd |only autograph-0.2.0/autograph/man/map_graphr.Rd |only autograph-0.2.0/autograph/man/map_graphs.Rd |only autograph-0.2.0/autograph/man/map_grapht.Rd |only autograph-0.2.0/autograph/man/map_scales.Rd |only autograph-0.2.0/autograph/man/match_color.Rd | 2 autograph-0.2.0/autograph/man/plus-.ggplot.Rd |only autograph-0.2.0/autograph/man/theme_scales.Rd |only autograph-0.2.0/autograph/man/theme_set.Rd |only autograph-0.2.0/autograph/tests/testthat/test-layout_partition.R |only autograph-0.2.0/autograph/tests/testthat/test-map_autograph.R |only autograph-0.2.0/autograph/tests/testthat/test-map_theme.R |only 45 files changed, 253 insertions(+), 35 deletions(-)
Title: Sequential Pairwise Online Rating Techniques
Description: Calculates ratings for two-player or
multi-player challenges. Methods included in package such as are able to
estimate ratings (players strengths) and their evolution in time, also able to
predict output of challenge. Algorithms are based on Bayesian Approximation
Method, and they don't involve any matrix inversions nor likelihood estimation.
Parameters are updated sequentially, and computation doesn't require any
additional RAM to make estimation feasible. Additionally, base of the package
is written in C++ what makes sport computation even faster. Methods used in the
package refer to Mark E. Glickman (1999)
<https://www.glicko.net/research/glicko.pdf>;
Mark E. Glickman (2001) <doi:10.1080/02664760120059219>;
Ruby C. Weng, Chih-Jen Lin (2011) <https://www.jmlr.org/papers/volume12/weng11a/weng11a.pdf>;
W. Penny, Stephen J. Roberts (1999) <doi:10.1109/IJCNN.1999.832603>.
Author: Dawid Kaledkowski [aut, cre]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@gmail.com>
Diff between sport versions 0.2.1 dated 2024-01-08 and 0.2.2 dated 2025-08-22
DESCRIPTION | 21 +- MD5 | 32 ++- NEWS.md | 7 R/RcppExports.R | 40 +--- build/vignette.rds |binary inst/doc/sport_in_r.R | 4 inst/doc/sport_in_r.html | 352 +++++++++++++++++++++--------------------- inst/doc/the_theory.Rmd | 4 inst/doc/the_theory.html | 238 ++++++++++++++-------------- tests/testthat/_snaps |only tests/testthat/test_dbl_run.R | 2 tests/testthat/test_output.R | 18 -- tests/testthat/test_predict.R | 2 tests/testthat/test_rating.R | 1 tests/testthat/test_terms.R | 2 tests/testthat/test_utils.R | 2 vignettes/the_theory.Rmd | 4 17 files changed, 351 insertions(+), 378 deletions(-)
Title: Manual Tours, Manual Control of Dynamic Projections of Numeric
Multivariate Data
Description: Data visualization tours animates linear projection
of multivariate data as its basis (ie. orientation) changes. The 'spinifex'
packages generates paths for manual tours by manipulating the contribution of
a single variable at a time Cook & Buja (1997)
<doi:10.1080/10618600.1997.10474754>. Other types of tours, such as grand
(random walk) and guided (optimizing some objective function) are available
in the 'tourr' package Wickham et al. <doi:10.18637/jss.v040.i02>.
'spinifex' builds on 'tourr' and can render tours with 'gganimate' and
'plotly' graphics, and allows for exporting as an .html widget and as an .gif,
respectively. This work is fully discussed in Spyrison & Cook (2020)
<doi:10.32614/RJ-2020-027>.
Author: Nicholas Spyrison [aut, cre] ,
Dianne Cook [aut, ths]
Maintainer: Nicholas Spyrison <spyrison@gmail.com>
Diff between spinifex versions 0.3.8 dated 2025-01-08 and 0.3.9 dated 2025-08-22
DESCRIPTION | 13 LICENSE | 2 MD5 | 145 ++-- NAMESPACE | 131 +-- NEWS.md | 7 R/0_util.r | 2 R/1_manual_tour.r | 734 ++++++++++----------- R/2_ggproto_visualize.r | 20 R/8_run_app.r | 90 +- R/9_spinifex-depricated.r | 20 R/spinifex-package.r | 2 R/zDepricated_2_render.r | 710 ++++++++++---------- R/zDepricated_3_visualize.r | 888 +++++++++++++------------- README.md | 154 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting_started_with_spinifex.html | 24 inst/doc/ggproto_api.Rmd | 598 ++++++++--------- inst/doc/ggproto_api.html | 20 inst/shiny_apps/radial_tour/rsconnect |only inst/shiny_apps/radial_tour/ui.R | 164 ++-- man/BreastCancer_na.rm.Rd | 152 ++-- man/PimaIndiansDiabetes_long.Rd | 136 +-- man/PimaIndiansDiabetes_wide.Rd | 128 +-- man/animate_gganimate.Rd | 162 ++-- man/append_fixed_y.Rd | 120 +-- man/array2df.Rd | 110 +-- man/basis_guided.Rd | 92 +- man/basis_onpp.Rd | 104 +-- man/basis_pca.Rd | 64 - man/create_manip_space.Rd | 90 +- man/facet_wrap_tour.Rd | 120 +-- man/ggtour.Rd | 214 +++--- man/is_orthonormal.Rd | 52 - man/manual_tour.Rd | 196 ++--- man/penguins_na.rm.Rd | 134 +-- man/play_manual_tour.Rd | 192 ++--- man/play_tour_path.Rd | 146 ++-- man/plot_pca.Rd | 62 - man/plot_pca_scree.Rd | 56 - man/proto_basis.Rd | 224 +++--- man/proto_default.Rd | 150 ++-- man/proto_density.Rd | 172 ++--- man/proto_density2d.Rd | 130 +-- man/proto_frame_cor2.Rd | 92 +- man/proto_hex.Rd | 140 ++-- man/proto_highlight.Rd | 208 +++--- man/proto_hline0.Rd | 114 +-- man/proto_origin.Rd | 140 ++-- man/proto_point.Rd | 158 ++-- man/proto_text.Rd | 154 ++-- man/proto_text_repel.Rd | 164 ++-- man/render_.Rd | 158 ++-- man/render_gganimate.Rd | 170 ++-- man/render_plotly.Rd | 120 +-- man/rotate_manip_space.Rd | 104 +-- man/run_app.Rd | 52 - man/save_history.Rd | 152 ++-- man/scale_sd.Rd | 44 - man/spinifex-deprecated.Rd | 92 +- man/spinifex.Rd | 66 - man/theme_spinifex.Rd | 50 - man/view_frame.Rd | 170 ++-- man/view_manip_space.Rd | 124 +-- man/weather.Rd | 168 ++-- man/wine.Rd | 138 ++-- tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/test-0_util.R | 2 tests/testthat/test-1_manual_tour.R | 104 +-- tests/testthat/test-2_ggproto_visualize.r | 100 +- tests/testthat/test-zDepricated_2_render.R | 2 tests/testthat/test-zDepricated_3_visualize.r | 8 vignettes/ggproto_api.Rmd | 598 ++++++++--------- 74 files changed, 5176 insertions(+), 5160 deletions(-)
Title: Error Detection in Science
Description: Test published summary statistics for consistency
(Brown and Heathers, 2017, <doi:10.1177/1948550616673876>;
Allard, 2018, <https://aurelienallard.netlify.app/post/anaytic-grimmer-possibility-standard-deviations/>;
Heathers and Brown, 2019, <https://osf.io/5vb3u/>).
The package also provides infrastructure for implementing new
error detection techniques.
Author: Lukas Jung [aut, cre],
Aurelien Allard [ctb],
Nicolas Roman Posner [ctb]
Maintainer: Lukas Jung <jung-lukas@gmx.net>
Diff between scrutiny versions 0.5.0 dated 2024-09-22 and 0.6.0 dated 2025-08-22
DESCRIPTION | 28 +++++--- MD5 | 88 ++++++++++++++------------- NAMESPACE | 3 NEWS.md | 23 +++++++ R/debit-plot.R | 3 R/debit-table.R | 8 +- R/function-factory-helpers.R | 20 ++++-- R/function-map-seq.R | 8 ++ R/function-map-total-n.R | 15 +++- R/function-map.R | 98 +++++++++++++++++++------------ R/grim.R | 60 +++++++++++------- R/odds-ratio-map.R |only R/restore-zeros.R | 34 ++++++++-- R/seq-predicates.R | 79 +++++++++++++++++------- R/unround.R | 2 R/utils.R | 48 ++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/consistency-tests-in-depth.R | 96 +++++++++++++++--------------- inst/doc/consistency-tests-in-depth.html | 12 +-- inst/doc/consistency-tests-simple.html | 2 inst/doc/debit.R | 4 + inst/doc/debit.html | 26 ++++---- inst/doc/devtools.html | 2 inst/doc/duplicates.Rmd | 4 - inst/doc/duplicates.html | 15 ++-- inst/doc/grim.R | 14 ++++ inst/doc/grim.Rmd | 6 - inst/doc/grim.html | 22 +++--- inst/doc/grimmer.R | 10 +++ inst/doc/grimmer.html | 10 +-- inst/doc/rounding-in-depth.html | 56 ++++++++--------- inst/doc/rounding-options.Rmd | 6 - inst/doc/rounding-options.html | 13 +--- inst/doc/wrangling.html | 2 man/absorb_key_args.Rd |only man/check_args_disabled.Rd |only man/check_factory_dots.Rd |only man/restore_zeros.Rd | 5 - man/scrutiny-package.Rd | 1 tests/testthat/Rplots.pdf |only tests/testthat/helper-expectations.R |only tests/testthat/test-decimal-places.R | 2 tests/testthat/test-restore-zeros.R | 9 ++ tests/testthat/test-seq-predicates.R | 6 - vignettes/duplicates.Rmd | 4 - vignettes/grim.Rmd | 6 - vignettes/rounding-options.Rmd | 6 - 48 files changed, 537 insertions(+), 319 deletions(-)
Title: Axis Invariant Scatter Pie Plots
Description: Extends 'ggplot2' to help replace points in a scatter plot with pie-chart glyphs showing the relative proportions of different categories. The pie glyphs are independent of the axes and plot dimensions, to prevent distortions when the plot dimensions are changed.
Author: Rishabh Vishwakarma [aut, cre] ,
Caroline Brophy [aut],
Catherine Hurley [aut]
Maintainer: Rishabh Vishwakarma <vishwakr@tcd.ie>
Diff between PieGlyph versions 1.0.0 dated 2024-06-28 and 1.1.0 dated 2025-08-22
DESCRIPTION | 12 MD5 | 96 +-- NAMESPACE | 137 ++--- NEWS.md | 10 R/PieGlyph-package.R | 154 ++--- R/aaa_utils_ggiraph.R |only R/aaa_utils_ggplot2.R |only R/aaa_utils_grid.R |only R/geom_pie_glyph.R | 18 R/geom_pie_interactive.R | 23 R/pie_grob.R | 6 build/vignette.rds |binary inst/doc/PieGlyph.R | 16 inst/doc/PieGlyph.Rmd | 16 inst/doc/PieGlyph.html | 48 + inst/doc/interactive-pie-glyphs.Rmd | 608 +++++++++++------------ inst/doc/interactive-pie-glyphs.html | 48 + inst/doc/multinomial-classification-example.R | 2 inst/doc/multinomial-classification-example.Rmd | 2 inst/doc/multinomial-classification-example.html | 4 inst/doc/pie-lollipop-example.R | 4 inst/doc/pie-lollipop-example.Rmd | 4 inst/doc/pie-lollipop-example.html | 6 inst/doc/spatial-example.R | 8 inst/doc/spatial-example.Rmd | 8 inst/doc/spatial-example.html | 10 inst/doc/time-series-example.R | 10 inst/doc/time-series-example.Rmd | 10 inst/doc/time-series-example.html | 12 inst/doc/unusual-situations.R | 20 inst/doc/unusual-situations.Rmd | 20 inst/doc/unusual-situations.html | 20 man/PieGlyph-package.Rd | 186 +++---- man/draw_key_pie.Rd | 50 - man/geom_pie_glyph.Rd | 390 +++++++------- man/geom_pie_interactive.Rd | 170 +++--- man/pieGrob.Rd | 202 +++---- man/scale_radius_continuous.Rd | 246 ++++----- man/upgradeUnit.unit.list.Rd |only tests/testthat.R | 15 tests/testthat/Rplots.pdf |binary tests/testthat/test-geom-pie-glyph.R | 39 + tests/testthat/test-geom_pie_interactive.R | 114 ++++ tests/testthat/test-pie-grob.R | 10 vignettes/PieGlyph.Rmd | 16 vignettes/interactive-pie-glyphs.Rmd | 608 +++++++++++------------ vignettes/multinomial-classification-example.Rmd | 2 vignettes/pie-lollipop-example.Rmd | 4 vignettes/spatial-example.Rmd | 8 vignettes/time-series-example.Rmd | 10 vignettes/unusual-situations.Rmd | 20 51 files changed, 1814 insertions(+), 1608 deletions(-)
Title: Fast, Easy, and Visual Bayesian Inference
Description: Accelerate Bayesian analytics workflows in 'R' through interactive modelling,
visualization, and inference. Define probabilistic graphical models using directed
acyclic graphs (DAGs) as a unifying language for business stakeholders, statisticians,
and programmers. This package relies on interfacing with the 'numpyro' python package.
Author: Adam Fleischhacker [aut, cre, cph],
Daniela Dapena [ctb],
Rose Nguyen [ctb],
Jared Sharpe [ctb]
Maintainer: Adam Fleischhacker <ajf@udel.edu>
Diff between causact versions 0.5.7 dated 2025-01-15 and 0.5.8 dated 2025-08-22
DESCRIPTION | 6 MD5 | 16 NEWS.md | 5 R/data.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/narrative-to-insight-with-causact.html | 694 ------------------------ man/corruptDF.Rd | 2 tests/testthat/test-dag_plot.R | 2 9 files changed, 22 insertions(+), 707 deletions(-)
Title: Biclustering with Missing Data
Description: Biclustering is a statistical learning technique that simultaneously
partitions and clusters rows and columns of a data matrix. Since the solution
space of biclustering is in infeasible to completely search with current
computational mechanisms, this package uses a greedy heuristic. The algorithm
featured in this package is, to the best our knowledge, the first biclustering
algorithm to work on data with missing values. Li, J., Reisner, J., Pham, H.,
Olafsson, S., and Vardeman, S. (2020) Biclustering with Missing Data. Information
Sciences, 510, 304–316.
Author: John Reisner [cre, aut, cph],
Hieu Pham [ctb, cph],
Jing Li [ctb, cph]
Maintainer: John Reisner <johntreisner@gmail.com>
Diff between biclustermd versions 0.2.3 dated 2021-06-17 and 0.2.4 dated 2025-08-22
DESCRIPTION | 6 LICENSE | 4 MD5 | 178 ++--- NAMESPACE | 122 +-- R/as.Biclust.R | 162 ++-- R/autoplot.biclustermd.R | 362 +++++----- R/autoplot.biclustermd_sim.R | 144 ++-- R/autoplot.biclustermd_sse.R | 56 - R/biclustermd-package.R | 14 R/biclustermd.R | 772 +++++++++++------------ R/binary_vector_gen.R | 22 R/cell_heatmap.R | 88 +- R/cell_mse.R | 118 +-- R/cluster_iteration_sum_sse.R | 58 - R/col.names.R | 20 R/col.names.biclustermd.R | 46 - R/col_cluster_names.R | 54 - R/compare_biclusters.R | 148 ++-- R/fill_empties_P.R | 162 ++-- R/fill_empties_Q.R | 174 ++--- R/format_partition.R | 64 - R/gather.biclustermd.R | 228 +++--- R/globalvars.R | 34 - R/jaccard.R | 78 +- R/mse_heatmap.R | 70 +- R/part_matrix_to_vector.R | 34 - R/partition_gen.R | 96 +- R/partition_gen_by_p.R | 36 - R/position_finder.R | 22 R/print.R | 80 +- R/reorder_biclust.R | 28 R/rep_biclustermd.R | 258 +++---- R/results_heatmap.R | 268 ++++---- R/row.names.biclustermd.R | 46 - R/row_cluster_names.R | 54 - R/runtimes.R | 48 - R/synthetic.R | 10 R/tune_biclustermd.R | 426 ++++++------ README.md | 170 ++--- build/vignette.rds |binary inst/doc/Airports.R | 182 ++--- inst/doc/Airports.Rmd | 320 ++++----- inst/doc/Airports.html | 933 ++++++++++++++++++---------- man/as.Biclust.Rd | 86 +- man/autoplot.biclustermd.Rd | 150 ++-- man/autoplot.biclustermd_sim.Rd | 88 +- man/autoplot.biclustermd_sse.Rd | 62 - man/biclustermd-package.Rd | 20 man/biclustermd.Rd | 254 +++---- man/binary_vector_gen.Rd | 38 - man/cell_heatmap.Rd | 60 - man/cell_mse.Rd | 58 - man/cluster_iteration_sum_sse.Rd | 42 - man/col.names.Rd | 28 man/col.names.biclustermd.Rd | 54 - man/col_cluster_names.Rd | 64 - man/compare_biclusters.Rd | 70 +- man/fill_empties_P.Rd | 46 - man/fill_empties_Q.Rd | 46 - man/format_partition.Rd | 34 - man/gather.biclustermd.Rd | 112 +-- man/jaccard_similarity.Rd | 46 - man/mse_heatmap.Rd | 64 - man/part_matrix_to_vector.Rd | 36 - man/partition_gen.Rd | 38 - man/partition_gen_by_p.Rd | 42 - man/position_finder.Rd | 34 - man/print.biclustermd.Rd | 32 man/reorder_biclust.Rd | 34 - man/rep_biclustermd.Rd | 204 +++--- man/results_heatmap.Rd | 88 +- man/row.names.biclustermd.Rd | 54 - man/row_cluster_names.Rd | 64 - man/runtimes.Rd | 72 +- man/synthetic.Rd | 34 - man/tune_biclustermd.Rd | 224 +++--- tests/testthat.R | 8 tests/testthat/test-autoplot_biclustermd.R | 97 +- tests/testthat/test-autoplot_similarities.R | 76 +- tests/testthat/test-autoplot_sse.R | 16 tests/testthat/test-biclustermd.R | 190 ++--- tests/testthat/test-col.names.R | 50 - tests/testthat/test-gather.R | 72 +- tests/testthat/test-part_matrix_to_vec.R | 38 - tests/testthat/test-partition_gen.R | 46 - tests/testthat/test-partition_gen_by_p.R | 78 +- tests/testthat/test-row.names.R | 50 - tests/testthat/test-sse.R | 106 +-- tests/testthat/test-synthetic.R | 10 vignettes/Airports.Rmd | 320 ++++----- 90 files changed, 5002 insertions(+), 4728 deletions(-)
Title: Species Distribution Models with Tidymodels
Description: Fit species distribution models (SDMs) using the 'tidymodels' framework,
which provides a standardised interface to define models and process their
outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects,
models and metrics specific to SDMs,
as well as a number of specialised functions to process occurrences
for contemporary and palaeo datasets. The full
functionalities of the package are described
in Leonardi et al. (2023) <doi:10.1101/2023.07.24.550358>.
Author: Michela Leonardi [aut],
Margherita Colucci [aut],
Andrea Vittorio Pozzi [aut],
Eleanor M.L. Scerri [aut],
Ben Tupper [ctb],
Andrea Manica [aut, cre]
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidysdm versions 1.0.0 dated 2025-03-05 and 1.0.2 dated 2025-08-22
DESCRIPTION | 14 - MD5 | 119 +++++++-------- NAMESPACE | 2 NEWS.md | 6 R/autoplot_simple_ensemble.R | 4 R/blockcv2rsample.R | 2 R/calib_class_thresh.R | 2 R/dist_pres_vs_bg.R | 2 R/explain_tidysdm.R | 8 - R/predict_raster.R | 131 ++++++++++++----- R/predict_simple_ensemble.R | 4 R/sdm_spec_boost_tree.R | 2 R/tidysdm-package.R | 1 R/utils-pipe.R | 4 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/lacerta.rda |binary data/lacerta_ensemble.rda |binary data/lacerta_rep_ens.rda |binary data/lacertidae_background.rda |binary inst/WORDLIST | 2 inst/doc/a0_tidysdm_overview.html | 144 ++++++++++-------- inst/doc/a1_palaeodata_application.html | 32 ++-- inst/doc/a2_tidymodels_additions.html | 96 +++++++----- inst/doc/a3_troubleshooting.R | 11 - inst/doc/a3_troubleshooting.Rmd | 37 +++- inst/doc/a3_troubleshooting.html | 198 ++++++++++++++++---------- inst/extdata/lacerta_climate_future_10m.rds |binary inst/extdata/lacerta_climate_present_10m.rds |binary inst/extdata/lacerta_land_mask.rds |binary inst/extdata/lacerta_thin_all_vars.rds |binary man/autoplot.simple_ensemble.Rd | 4 man/blockcv2rsample.Rd | 2 man/calib_class_thresh.Rd | 2 man/dist_pres_vs_bg.Rd | 3 man/explain_tidysdm.Rd | 8 - man/pipe.Rd | 2 man/predict_raster.Rd | 13 + man/sdm_spec_boost_tree.Rd | 2 tests/spelling.R | 9 - tests/testthat/Rplots.pdf |binary tests/testthat/test_blockcv2rsample.R | 2 tests/testthat/test_calib_class_thresh.R | 1 tests/testthat/test_clamp_predictors.R | 2 tests/testthat/test_dist_pres_vs_bg.R | 2 tests/testthat/test_explain_tidysdm.R | 3 tests/testthat/test_extrapol_mess.R | 2 tests/testthat/test_filter_collinear.R | 3 tests/testthat/test_overlap_niche.R | 1 tests/testthat/test_predict_raster.R |only tests/testthat/test_predict_repeat_ensemble.R | 3 tests/testthat/test_predict_simple_ensemble.R | 1 tests/testthat/test_recipe_sf.R | 12 + tests/testthat/test_repeat_ensemble.R | 1 tests/testthat/test_sample_background_time.R | 1 tests/testthat/test_sample_pseudoabs_time.R | 1 tests/testthat/test_simple_ensemble.R | 2 tests/testthat/test_thin_by_cell_time.R | 1 tests/testthat/test_thin_by_dist_time.R | 1 vignettes/a3_troubleshooting.Rmd | 37 +++- 61 files changed, 588 insertions(+), 356 deletions(-)
Title: Tools to Conduct Meteorological Normalisation and Counterfactual
Modelling for Air Quality Data
Description: An integrated set of tools to allow data users to conduct
meteorological normalisation and counterfactual modelling for air quality
data. The meteorological normalisation technique uses predictive random
forest models to remove variation of pollutant concentrations so trends and
interventions can be explored in a robust way. For examples, see
Grange et al. (2018) <doi:10.5194/acp-18-6223-2018> and
Grange and Carslaw (2019) <doi:10.1016/j.scitotenv.2018.10.344>. The random
forest models can also be used for counterfactual or business as usual (BAU)
modelling by using the models to predict, from the model's perspective, the
future. For an example, see Grange et al. (2021) <doi:10.5194/acp-2020-1171>.
Author: Stuart K. Grange [cre, aut]
Maintainer: Stuart K. Grange <s.k.grange@gmail.com>
Diff between rmweather versions 0.2.62 dated 2025-02-20 and 0.2.63 dated 2025-08-22
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- tests/testthat/test_02_rmw_functions.R | 11 ++++++----- 3 files changed, 14 insertions(+), 12 deletions(-)
Title: Principal Component Analysis (PCA) Tool on Protein Expression
Data
Description: Analysis of protein expression data can be done through Principal Component Analysis (PCA), and this R package is designed to streamline the analysis. This package enables users to perform PCA and it generates biplot and scree plot for advanced graphical visualization. Optionally, it supports grouping/clustering visualization with PCA loadings and confidence ellipses. With this R package, researchers can quickly explore complex protein datasets, interpret variance contributions, and visualize sample clustering through intuitive biplots. For more details, see Jolliffe (2001) <doi:10.1007/b98835>, Gabriel (1971) <doi:10.1093/biomet/58.3.453>, Zhang et al. (2024) <doi:10.1038/s41467-024-53239-9>, and Anandan et al. (2022) <doi:10.1038/s41598-022-07781-5>.
Author: Paul Angelo C. Manlapaz [aut, cre]
Maintainer: Paul Angelo C. Manlapaz <pacmanlapaz@gmail.com>
Diff between ProteinPCA versions 0.1.0 dated 2025-04-12 and 0.1.1 dated 2025-08-22
DESCRIPTION | 21 +++++++-------------- MD5 | 2 +- 2 files changed, 8 insertions(+), 15 deletions(-)
Title: Fits Models Inside the Database
Description: Uses 'dplyr' and 'tidyeval' to fit statistical models inside
the database. It currently supports KMeans and linear regression
models.
Author: Edgar Ruiz [aut],
Max Kuhn [aut, cre]
Maintainer: Max Kuhn <max@posit.co>
Diff between modeldb versions 0.3.0 dated 2023-11-01 and 0.3.1 dated 2025-08-22
DESCRIPTION | 8 - MD5 | 26 +++--- NEWS.md | 4 README.md | 137 +++++++++++++++++++++++----------- build/vignette.rds |binary inst/doc/kmeans.html | 28 +++--- inst/doc/linear-regression.R | 2 inst/doc/linear-regression.html | 10 +- man/modeldb-package.Rd | 5 + tests/testthat/test-as-parsed-model.R | 2 tests/testthat/test_dummy_var.R | 2 tests/testthat/test_kmeans.R | 2 tests/testthat/test_kmeans_viz.R | 7 - tests/testthat/test_lr.R | 2 14 files changed, 141 insertions(+), 94 deletions(-)
Title: Compute Scores for Different Implicit Measures
Description: A tool for computing the scores for the Implicit Association Test
(IAT; Greenwald, McGhee & Schwartz (1998) <doi:10.1037/0022-3514.74.6.1464>)
and the Single Category-IAT (SC-IAT: Karpinski & Steinman
(2006) <doi:10.1037/0022-3514.91.1.16>). Functions for preparing the data
(both for the IAT and the SC-IAT), plotting the results, and obtaining a
table with the scores of implicit measures descriptive statistics are
provided.
Author: Ottavia M. Epifania [aut, cre],
Pasquale Anselmi [ctb],
Egidio Robusto [ctb]
Maintainer: Ottavia M. Epifania <otta.epifania@gmail.com>
Diff between implicitMeasures versions 0.3.0 dated 2025-07-10 and 0.3.1 dated 2025-08-22
DESCRIPTION | 6 ++--- MD5 | 26 ++++++++++++------------ NEWS.md | 8 +------ inst/doc/IAT-example.html | 8 +++---- inst/doc/SC-IAT-example.html | 6 ++--- inst/doc/implicitMeasures.html | 4 +-- tests/testthat/test-IAT_rel_descript_d.R | 2 - tests/testthat/test-clean_iat.R | 5 +--- tests/testthat/test-compute_iat-replicate.R | 14 ++++++++++-- tests/testthat/test-compute_iat.R | 4 +-- tests/testthat/test-compute_sciat-replicate.R | 6 +---- tests/testthat/test-compute_sciat.R | 2 - tests/testthat/test-d_density_d_plot.R | 16 +++++++------- tests/testthat/test-multi_dscore_multi_dsciat.R | 10 ++++----- 14 files changed, 59 insertions(+), 58 deletions(-)
More information about implicitMeasures at CRAN
Permanent link
Title: Extracts Knowledge from 'Git' Repositories
Description: Scan multiple 'Git' repositories, pull specified files content and process it with large language models. You can summarize the content in specific way, extract information and data, or find answers to your questions about the repositories. The output can be stored in vector database and used for semantic search or as a part of a RAG (Retrieval Augmented Generation) prompt.
Author: Kamil Wais [aut, cre],
Krystian Igras [aut],
Maciej Banas [aut]
Maintainer: Kamil Wais <kamil.wais@gmail.com>
Diff between GitAI versions 0.1.1 dated 2025-05-20 and 0.1.2 dated 2025-08-22
GitAI-0.1.1/GitAI/inst/demo-app/rsconnect |only GitAI-0.1.2/GitAI/DESCRIPTION | 7 GitAI-0.1.2/GitAI/MD5 | 107 - GitAI-0.1.2/GitAI/NAMESPACE | 28 GitAI-0.1.2/GitAI/NEWS.md | 12 GitAI-0.1.2/GitAI/R/GitAI-package.R | 26 GitAI-0.1.2/GitAI/R/GitAI.R | 200 +- GitAI-0.1.2/GitAI/R/Pinecone.R | 472 ++--- GitAI-0.1.2/GitAI/R/VectorDatabase.R | 62 GitAI-0.1.2/GitAI/R/add_files.R | 32 GitAI-0.1.2/GitAI/R/add_metadata.R | 96 - GitAI-0.1.2/GitAI/R/find_records.R | 38 GitAI-0.1.2/GitAI/R/global.R | 2 GitAI-0.1.2/GitAI/R/initialize_project.R | 18 GitAI-0.1.2/GitAI/R/process_content.R | 58 GitAI-0.1.2/GitAI/R/process_repos.R | 222 +- GitAI-0.1.2/GitAI/R/run_demo.R | 12 GitAI-0.1.2/GitAI/R/set_database.R | 58 GitAI-0.1.2/GitAI/R/set_llm.R | 104 - GitAI-0.1.2/GitAI/R/set_repos.R | 98 - GitAI-0.1.2/GitAI/R/test-helpers.R | 568 +++--- GitAI-0.1.2/GitAI/R/verbose.R | 74 GitAI-0.1.2/GitAI/README.md | 258 +- GitAI-0.1.2/GitAI/build/vignette.rds |binary GitAI-0.1.2/GitAI/inst/demo-app/app.R | 124 - GitAI-0.1.2/GitAI/inst/doc/building-shiny-app-chatbot.R | 342 +-- GitAI-0.1.2/GitAI/inst/doc/building-shiny-app-chatbot.Rmd | 514 ++--- GitAI-0.1.2/GitAI/inst/doc/building-shiny-app-chatbot.html | 1155 ++++++------- GitAI-0.1.2/GitAI/man/GitAI-package.Rd | 44 GitAI-0.1.2/GitAI/man/add_files.Rd | 40 GitAI-0.1.2/GitAI/man/find_records.Rd | 42 GitAI-0.1.2/GitAI/man/initialize_project.Rd | 34 GitAI-0.1.2/GitAI/man/is_verbose.Rd | 30 GitAI-0.1.2/GitAI/man/missing_deps_note_fix.Rd | 30 GitAI-0.1.2/GitAI/man/process_repos.Rd | 44 GitAI-0.1.2/GitAI/man/set_database.Rd | 36 GitAI-0.1.2/GitAI/man/set_github_repos.Rd | 46 GitAI-0.1.2/GitAI/man/set_gitlab_repos.Rd | 46 GitAI-0.1.2/GitAI/man/set_llm.Rd | 52 GitAI-0.1.2/GitAI/man/set_prompt.Rd | 38 GitAI-0.1.2/GitAI/man/verbose_off.Rd | 24 GitAI-0.1.2/GitAI/man/verbose_on.Rd | 24 GitAI-0.1.2/GitAI/tests/testthat.R | 26 GitAI-0.1.2/GitAI/tests/testthat/setup.R | 180 +- GitAI-0.1.2/GitAI/tests/testthat/test-Pinecone.R | 192 +- GitAI-0.1.2/GitAI/tests/testthat/test-VectorDatabase.R | 20 GitAI-0.1.2/GitAI/tests/testthat/test-add_files.R | 52 GitAI-0.1.2/GitAI/tests/testthat/test-add_metadata.R | 42 GitAI-0.1.2/GitAI/tests/testthat/test-initialize_project.R | 20 GitAI-0.1.2/GitAI/tests/testthat/test-process_content.R | 98 - GitAI-0.1.2/GitAI/tests/testthat/test-process_repos.R | 52 GitAI-0.1.2/GitAI/tests/testthat/test-set_database.R | 48 GitAI-0.1.2/GitAI/tests/testthat/test-set_llm.R | 230 +- GitAI-0.1.2/GitAI/tests/testthat/test-set_repos.R | 32 GitAI-0.1.2/GitAI/vignettes/building-shiny-app-chatbot.Rmd | 514 ++--- 55 files changed, 3363 insertions(+), 3360 deletions(-)
Title: Create Images of Volumetric Brain Data in NIfTI Format Using
'ggplot2' Syntax
Description: A 'ggplot2'-consistent approach to generating 2D displays of volumetric brain imaging data.
Display data from multiple NIfTI images using standard 'ggplot2' conventions such scales, limits, and
themes to control the appearance of displays. The resulting plots are returned as 'patchwork' objects,
inheriting from 'ggplot', allowing for any standard modifications of display aesthetics supported by 'ggplot2'.
Author: Michael Hallquist [aut, cre]
Maintainer: Michael Hallquist <michael.hallquist@gmail.com>
Diff between ggbrain versions 0.9.0 dated 2025-03-19 and 0.9.1 dated 2025-08-22
DESCRIPTION | 11 MD5 | 28 +- NEWS.md | 6 R/ggbrain_label.R | 3 R/ggbrain_layer.R | 3 R/ggbrain_panel.R | 3 build/vignette.rds |binary inst/doc/ggbrain_introduction.html | 200 ++++++++------- inst/doc/ggbrain_labels.R | 8 inst/doc/ggbrain_labels.Rmd | 8 inst/doc/ggbrain_labels.html | 473 ++++++++++++------------------------- man/ggplot_add.ggbrain_label.Rd | 4 man/ggplot_add.ggbrain_layer.Rd | 4 man/ggplot_add.ggbrain_panel.Rd | 4 vignettes/ggbrain_labels.Rmd | 8 15 files changed, 323 insertions(+), 440 deletions(-)
Title: Tidy Flowchart Generator
Description: Creates participant flow diagrams directly from a dataframe. Representing the flow of participants through each stage of a study, especially in clinical trials, is essential to assess the generalisability and validity of the results. This package provides a set of functions that can be combined with a pipe operator to create all kinds of flowcharts from a data frame in an easy way.
Author: Pau Satorra [aut, cre] ,
Joao Carmezim [aut] ,
Natalia Pallares [aut] ,
Cristian Tebe [aut] ,
Kenneth Taylor [aut]
Maintainer: Pau Satorra <psatorra@igtp.cat>
Diff between flowchart versions 0.8.0 dated 2025-04-23 and 0.9.0 dated 2025-08-22
DESCRIPTION | 19 - MD5 | 85 +++-- NAMESPACE | 1 NEWS.md | 20 + R/as_fc.R | 111 ++++++- R/fc_draw.R | 76 +++-- R/fc_export.R | 87 +++--- R/fc_filter.R | 261 +++++++++++++----- R/fc_split.R | 232 ++++++++++------ R/fc_stack.R | 2 R/fc_theme.R |only R/fc_view.R | 2 R/utils.R | 41 ++ README.md | 7 build/vignette.rds |binary inst/doc/flowchart.R | 271 ------------------ inst/doc/flowchart.Rmd | 393 --------------------------- inst/doc/flowchart.html | 506 +++-------------------------------- man/as_fc.Rd | 57 +++ man/fc_draw.Rd | 39 +- man/fc_export.Rd | 21 - man/fc_filter.Rd | 90 ++++-- man/fc_modify.Rd | 4 man/fc_split.Rd | 54 ++- man/fc_stack.Rd | 2 man/fc_theme.Rd |only man/fc_view.Rd | 6 man/format_percentage.Rd |only man/quiet_prettyNum.Rd | 2 man/replace_num_in_expr.Rd | 6 man/safo.Rd | 44 +-- man/update_numbers.Rd | 4 man/update_y_stack_unite.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/as_fc.md | 2 tests/testthat/_snaps/fc_export.md | 2 tests/testthat/_snaps/fc_filter.md | 4 tests/testthat/_snaps/fc_split.md | 2 tests/testthat/_snaps/utils.md | 13 tests/testthat/test-as_fc.R | 12 tests/testthat/test-fc_filter.R | 54 +++ tests/testthat/test-fc_split.R | 68 ++++ tests/testthat/test-fc_theme.R |only tests/testthat/test.pdf |binary tests/testthat/testthat-problems.rds |only vignettes/flowchart.Rmd | 393 --------------------------- 46 files changed, 1101 insertions(+), 1894 deletions(-)
Title: Interactive 'shiny' Dashboard for 'nlmixr2'
Description: An R shiny user interface for the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) package,
designed to simplify the modeling process for users. Additionally, this package includes supplementary functions
to further enhances the usage of 'nlmixr2'.
Author: Richard Hooijmaijers [aut, cre, cph],
Teun Post [aut, cph],
LAPP Consultants [fnd, cph],
Matthew Fidler [ctb],
Veerle van Leemput [ctb]
Maintainer: Richard Hooijmaijers <richardhooijmaijers@gmail.com>
Diff between shinyMixR versions 0.5.1 dated 2025-07-18 and 0.5.2 dated 2025-08-22
DESCRIPTION | 6 ++--- MD5 | 16 +++++++++++--- NEWS.md | 4 +++ tests/testthat/_snaps |only tests/testthat/test-fit_plot.R | 24 +++++++++++----------- tests/testthat/test-gof_plot.R | 44 ++++++++++++++++++++++------------------- 6 files changed, 55 insertions(+), 39 deletions(-)
Title: Functions for Diffusing Function Documentations into 'Roxygen'
Comments
Description: Efficient diffusing of content across function documentations. Sections, parameters or dot parameters are extracted from function documentations and turned into valid Rd character strings, which are ready to diffuse into the 'roxygen' comments of another function by inserting inline code.
Author: Xiurui Zhu [aut, cre]
Maintainer: Xiurui Zhu <zxr6@163.com>
Diff between roclang versions 0.2.2 dated 2023-05-26 and 0.2.3 dated 2025-08-22
DESCRIPTION | 6 LICENSE | 4 MD5 | 28 - NAMESPACE | 34 - NEWS.md | 7 R/package-roclang.R | 40 - R/roc_eval_functions.R | 224 +++++----- R/roc_text_functions.R | 702 ++++++++++++++++----------------- README.md | 32 - man/extract_roc_text.Rd | 246 +++++------ man/roc_eval_text.Rd | 92 ++-- man/roclang-package.Rd | 58 +- tests/testthat.R | 8 tests/testthat/test-extract_roc_text.R | 2 tests/testthat/test-roc_eval_text.R | 32 - 15 files changed, 761 insertions(+), 754 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Data-driven approach for arriving at person-specific time series models. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. See Gates & Molenaar (2012) <doi:10.1016/j.neuroimage.2012.06.026>.
Author: Stephanie Lane [aut, trl],
Kathleen M Gates [aut, cre, ccp],
Zachary Fisher [aut],
Cara Arizmendi [aut],
Peter Molenaar [aut, ccp],
Edgar Merkle [ctb],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Teague Henry [ctb],
Kelly Duffy [ctb],
Lan Luo [ctb],
[...truncated...]
Maintainer: Kathleen M Gates <gateskm@email.unc.edu>
Diff between gimme versions 0.9.1 dated 2025-06-26 and 0.9.2 dated 2025-08-22
DESCRIPTION | 16 ++++++++------ MD5 | 32 ++++++++++++++-------------- R/count.excellent.R | 18 +++++++++++----- R/determine.subgroups.R | 5 ++-- R/gimme.R | 48 ++++++++++++++++++++++++++++++++++++------- R/highest.mi.R | 22 +++++++++++++++++-- R/indiv.search.R | 21 +++++++++++++++++- R/search.paths.ind.R | 30 +++++++++++++++++++++++--- R/setup.R | 7 ------ R/summaryPathsCounts.R | 9 +++----- inst/doc/gimme_vignette.html | 4 +-- man/count.excellent.Rd | 16 +++++++++++++- man/gimmeSEM.Rd | 18 +++++++++++++++- man/highest.mi.Rd | 18 +++++++++++++++- man/indiv.search.Rd | 24 ++++++++++++++++++++- man/search.paths.ind.Rd | 18 +++++++++++++++- tests/testthat/test-gimme.R | 38 +++++++++++++++++----------------- 17 files changed, 261 insertions(+), 83 deletions(-)
Title: Coalescent-Based Simulation of Ecological Communities
Description: Coalescent-Based Simulation of Ecological Communities as proposed
by Munoz et al. (2018) <doi:10.1111/2041-210X.12918>. The package includes
a tool for estimating parameters of community assembly by using Approximate
Bayesian Computation.
Author: Francois Munoz [aut, cre],
Matthias Grenie [aut],
Pierre Denelle [aut],
Adrien Taudiere [ctb],
Fabien Laroche [ctb],
Caroline Tucker [ctb],
Cyrille Violle [ctb]
Maintainer: Francois Munoz <francois.munoz@hotmail.fr>
Diff between ecolottery versions 1.0.1 dated 2025-04-14 and 1.0.2 dated 2025-08-22
DESCRIPTION | 6 MD5 | 16 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 8 - inst/doc/Barro_Colorado.Rmd | 4 inst/doc/Barro_Colorado.html | 6 inst/doc/coalesc_vignette.html | 278 ++++++++++++++++++++--------------------- vignettes/Barro_Colorado.Rmd | 4 9 files changed, 161 insertions(+), 161 deletions(-)
Title: Mapping Data for 'usmap' Package
Description: Provides a container for data used by the 'usmap' package.
The data used by 'usmap' has been extracted into this package so that the
file size of the 'usmap' package can be reduced greatly. The data in this
package will be updated roughly once per year as new map data files are
provided by the US Census Bureau.
Author: Paolo Di Lorenzo [aut, cre]
Maintainer: Paolo Di Lorenzo <paolo@dilorenzo.org>
Diff between usmapdata versions 0.6.0 dated 2025-06-14 and 1.0.0 dated 2025-08-22
DESCRIPTION | 8 +-- MD5 | 62 +++++++++++++-------------- NEWS.md | 20 ++++++++ R/create-us-map.R | 43 ++++++++++++++++-- R/fips-data.R | 3 - R/us-map.R | 59 +++++++++++++------------ R/usmapdata-package.R | 10 ++-- README.md | 2 inst/extdata/2021/us_counties.gpkg |binary inst/extdata/2021/us_counties_centroids.gpkg |binary inst/extdata/2021/us_states.gpkg |binary inst/extdata/2021/us_states_centroids.gpkg |binary inst/extdata/2022/us_counties.gpkg |binary inst/extdata/2022/us_counties_centroids.gpkg |binary inst/extdata/2022/us_states.gpkg |binary inst/extdata/2022/us_states_centroids.gpkg |binary inst/extdata/2023/us_counties.gpkg |binary inst/extdata/2023/us_counties_centroids.gpkg |binary inst/extdata/2023/us_states.gpkg |binary inst/extdata/2023/us_states_centroids.gpkg |binary inst/extdata/2024/us_counties.gpkg |binary inst/extdata/2024/us_counties_centroids.gpkg |binary inst/extdata/2024/us_states.gpkg |binary inst/extdata/2024/us_states_centroids.gpkg |binary man/centroid_labels.Rd | 6 -- man/create_us_map.Rd | 12 ++++- man/fips_data.Rd | 4 - man/select_map_year.Rd | 2 man/us_map.Rd | 10 +--- man/usmapdata.Rd | 6 +- tests/testthat/test-fips-data.R | 18 +++---- tests/testthat/test-usmap.R | 24 +++++++--- 32 files changed, 175 insertions(+), 114 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg] ,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.9.2 dated 2025-01-11 and 2.10.0 dated 2025-08-22
DESCRIPTION | 20 MD5 | 203 +- NAMESPACE | 4 NEWS.md | 521 ++--- R/Information.R | 745 +++---- R/Islands.R | 156 - R/MSTSegments.R | 158 - R/Plot3.R | 168 - R/RcppExports.R | 187 + R/Reduce.R | 134 - R/TreeDist-package.R | 286 +- R/kmeanspp.R | 208 +- R/lap.R | 130 - R/median.R | 172 - R/parallel.R | 158 - R/plot.R | 150 - R/tree_distance_info.R | 23 R/tree_distance_kendall-colijn.R | 456 ++-- R/tree_distance_mast.R | 220 +- R/tree_distance_msi.R | 94 R/tree_distance_nni.R | 332 +-- R/tree_distance_nye.R | 15 R/tree_distance_path.R | 216 +- R/tree_distance_rf.R | 16 R/tree_distance_spr.R | 312 +-- R/tree_distance_utilities.R | 89 R/tree_information.R | 708 +++---- R/trustworthiness.R | 154 - R/zzz.R | 56 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 148 - inst/REFERENCES.bib | 1414 +++++++------- inst/doc/Generalized-RF.Rmd | 586 ++--- inst/doc/Robinson-Foulds.Rmd | 718 +++---- inst/doc/Using-TreeDist.html | 6 inst/doc/compare-treesets.html | 1076 ---------- inst/doc/different-leaves.Rmd | 194 - inst/doc/landscapes.Rmd | 256 +- inst/doc/landscapes.html | 4 inst/doc/treespace.Rmd | 942 ++++----- inst/doc/treespace.html | 8 inst/doc/using-distances.R | 4 inst/treespace/app.R | 2964 +++++++++++++++--------------- man/CalculateTreeDistance.Rd | 60 man/CompareAll.Rd | 106 - man/Entropy.Rd | 61 man/Islands.Rd | 158 - man/JaccardRobinsonFoulds.Rd | 288 +- man/KMeansPP.Rd | 110 - man/KendallColijn.Rd | 286 +- man/LAPJV.Rd | 126 - man/MSTSegments.Rd | 170 - man/MapTrees.Rd | 250 +- man/MappingQuality.Rd | 112 - man/MatchingSplitDistance.Rd | 204 +- man/NormalizeInfo.Rd | 192 - man/NyeSimilarity.Rd | 280 +- man/PathDist.Rd | 172 - man/ReduceTrees.Rd | 102 - man/ReportMatching.Rd | 54 man/Robinson-Foulds.Rd | 324 +-- man/SPRDist.Rd | 168 - man/SpectralEigens.Rd | 102 - man/StartParallel.Rd | 126 - man/TreeDist-package.Rd | 290 +- man/TreeDistance.Rd | 642 +++--- man/cluster-statistics.Rd | 212 +- man/entropy_int.Rd |only man/median.multiPhylo.Rd | 188 - src/RcppExports.cpp | 78 src/day_1985.cpp | 138 - src/information.h | 44 src/ints.h | 15 src/lap.cpp | 275 +- src/mast.cpp | 2 src/nni_distance.cpp | 15 src/path_vector.cpp | 80 src/reduce_tree.h | 2 src/spr.cpp | 16 src/tree_distance_functions.cpp | 121 - src/tree_distances.cpp | 594 ++---- src/tree_distances.h | 532 +++++ tests/benchmark/benchmark.R | 36 tests/testthat/test-Islands.R | 38 tests/testthat/test-MSTSegments.R | 94 tests/testthat/test-Plot3.R | 56 tests/testthat/test-cluster_stats.R | 170 - tests/testthat/test-day_1985.cpp.r | 130 - tests/testthat/test-information.R | 185 - tests/testthat/test-kmeanspp.R | 60 tests/testthat/test-lap.R | 679 +++--- tests/testthat/test-plot.R | 74 tests/testthat/test-spectral_clustering.R | 24 tests/testthat/test-split_info.R | 124 - tests/testthat/test-tree_distance.R | 1 tests/testthat/test-tree_distance_kc.R | 120 - tests/testthat/test-tree_distance_path.R | 66 vignettes/Generalized-RF.Rmd | 586 ++--- vignettes/Robinson-Foulds.Rmd | 718 +++---- vignettes/different-leaves.Rmd | 194 - vignettes/landscapes.Rmd | 256 +- vignettes/treespace.Rmd | 942 ++++----- 103 files changed, 12516 insertions(+), 13143 deletions(-)
Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>,
an open source software library for numerical computation using data
flow graphs. Nodes in the graph represent mathematical operations,
while the graph edges represent the multidimensional data arrays
(tensors) communicated between them. The flexible architecture allows
you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop,
server, or mobile device with a single 'API'. 'TensorFlow' was originally
developed by researchers and engineers working on the Google Brain Team
within Google's Machine Intelligence research organization for the
purposes of conducting machine learning and deep neural networks research,
but the system is general enough to be applicable in a wide variety
of other domains as well.
Author: JJ Allaire [aut, cph],
Tomasz Kalinowski [ctb, cph, cre],
Daniel Falbel [ctb, cph],
Dirk Eddelbuettel [ctb, cph],
Yuan Tang [aut, cph] ,
Nick Golding [ctb, cph],
Google Inc. [ctb, cph] ,
Posit, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@posit.co>
Diff between tensorflow versions 2.16.0 dated 2024-04-15 and 2.20.0 dated 2025-08-22
DESCRIPTION | 12 - MD5 | 30 +-- NAMESPACE | 4 NEWS.md | 21 +- R/arguments.R | 2 R/generics.R | 14 + R/help.R | 16 + R/install.R | 297 ++++++++++++++++++++++++++-------- R/package.R | 29 +++ R/reexports.R | 3 R/tensorboard.R | 2 man/install_tensorflow.Rd | 85 ++++++--- man/parse_arguments.Rd | 2 man/reexports.Rd | 3 tests/testthat/test-generic-methods.R | 2 tests/testthat/test-types.R | 16 + 16 files changed, 412 insertions(+), 126 deletions(-)
Title: Simulation-Based Power Analysis for Factorial Designs
Description: Functions to perform simulations of ANOVA designs of up to three factors. Calculates the observed power and average observed effect size for all main effects and interactions in the ANOVA, and all simple comparisons between conditions. Includes functions for analytic power calculations and additional helper functions that compute effect sizes for ANOVA designs, observed error rates in the simulations, and functions to plot power curves. Please see Lakens, D., & Caldwell, A. R. (2021). "Simulation-Based Power Analysis for Factorial Analysis of Variance Designs". <doi:10.1177/2515245920951503>.
Author: Aaron Caldwell [aut, cre],
Daniel Lakens [aut],
Lisa DeBruine [ctb],
Jonathon Love [ctb],
Frederik Aust [ctb]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between Superpower versions 0.2.4 dated 2025-06-24 and 0.2.4.1 dated 2025-08-22
DESCRIPTION | 6 +- MD5 | 20 +++--- NEWS.md | 12 +++- build/vignette.rds |binary inst/doc/ANCOVAs.html | 77 ++++++++++++++++---------- inst/doc/compromise_power.html | 20 +++--- inst/doc/emmeans_power.html | 111 ++++++++++++++++++-------------------- inst/doc/intro_to_superpower.html | 4 - inst/doc/more_anova_designs.R | 10 +-- inst/doc/more_anova_designs.html | 32 +++++----- tests/testthat/test-morey.R | 2 11 files changed, 159 insertions(+), 135 deletions(-)
Title: Compositional Data Analysis
Description: Methods for analysis of compositional data including robust
methods (<doi:10.1007/978-3-319-96422-5>), imputation of missing values (<doi:10.1016/j.csda.2009.11.023>), methods to replace
rounded zeros (<doi:10.1080/02664763.2017.1410524>, <doi:10.1016/j.chemolab.2016.04.011>, <doi:10.1016/j.csda.2012.02.012>),
count zeros (<doi:10.1177/1471082X14535524>),
methods to deal with essential zeros (<doi:10.1080/02664763.2016.1182135>), (robust) outlier
detection for compositional data, (robust) principal component analysis for
compositional data, (robust) factor analysis for compositional data, (robust)
discriminant analysis for compositional data (Fisher rule), robust regression
with compositional predictors, functional data analysis (<doi:10.1016/j.csda.2015.07.007>) and p-splines (<doi:10.1016/j.csda.2015.07.007>),
contingency (<doi:10.1080/03610926.2013.824980>)
and compositional tables (<doi:10.1111/sjos.12326>, <doi: [...truncated...]
Author: Matthias Templ [aut, cre] ,
Karel Hron [aut] ,
Peter Filzmoser [aut] ,
Kamila Facevicova [ctb],
Petra Kynclova [ctb],
Jan Walach [ctb],
Veronika Pintar [ctb],
Jiajia Chen [ctb],
Dominika Miksova [ctb],
Bernhard Meindl [ctb],
Alessandra Menafoglio [ct [...truncated...]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between robCompositions versions 2.4.1 dated 2023-08-25 and 2.4.2 dated 2025-08-22
DESCRIPTION | 28 +-- MD5 | 149 +++++++++---------- NAMESPACE | 10 - R/aDist.R | 108 ++++++++----- R/clustCoDa.R | 37 +++- R/daFisher.R | 9 - R/dataSets.R | 263 +++++++++++++++++++++++----------- R/imputeBDLs.R | 21 ++ R/imputeUDLs.R | 1 R/intTab.R | 2 R/lmCoDaX.R | 2 R/pls_pb.R |only R/rSDev.test.R | 150 +++++++++---------- R/robCompositions-package.R | 2 R/spca_logrs.R |only R/splineDensity.R | 21 ++ R/weightedPivotCoord.R | 10 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/imputation.pdf |binary inst/doc/robCompositions-overview.pdf |binary man/GDPsatis.Rd | 2 man/aDist.Rd | 4 man/ageCatWorld.Rd | 2 man/alcohol.Rd | 2 man/alcoholreg.Rd | 2 man/arcticLake.Rd | 2 man/cancer.Rd | 2 man/cancerMN.Rd | 2 man/coffee.Rd | 2 man/economy.Rd | 2 man/educFM.Rd | 2 man/efsa.Rd | 2 man/election.Rd | 2 man/electionATbp.Rd | 2 man/employment2.Rd | 2 man/employment_df.Rd | 2 man/expenditures.Rd | 2 man/expendituresEU.Rd | 2 man/fBPUpChi_PLS.Rd |only man/foodbalance.Rd | 124 +++++++++++++++- man/gemas.Rd | 2 man/gjovik.Rd | 2 man/govexp.Rd | 2 man/haplogroups.Rd | 37 ++-- man/honey.Rd | 2 man/instw.Rd | 17 +- man/intTab.Rd | 2 man/isic32.Rd | 2 man/laborForce.Rd | 2 man/landcover.Rd | 2 man/lifeExpGdp.Rd | 2 man/machineOperators.Rd | 2 man/manu_abs.Rd | 2 man/mcad.Rd | 2 man/mortality.Rd | 2 man/mortality_tab.Rd | 2 man/nutrients.Rd | 2 man/nutrients_branded.Rd | 2 man/payments.Rd | 2 man/phd.Rd | 2 man/phd_totals.Rd | 2 man/pls_pb.Rd |only man/precipitation.Rd | 2 man/production.Rd | 2 man/rSDev.test.Rd | 2 man/rcodes.Rd | 2 man/saffron.Rd | 2 man/skyeLavas.Rd | 2 man/smoothSplines.Rd | 13 + man/socExp.Rd | 2 man/spca_logrs.Rd |only man/teachingStuff.Rd | 2 man/trondelagC.Rd | 2 man/trondelagO.Rd | 2 man/unemployed.Rd | 2 man/weightedPivotCoord.Rd | 10 - src/density_estimation.cpp | 1 78 files changed, 712 insertions(+), 401 deletions(-)
More information about robCompositions at CRAN
Permanent link
Title: Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information
returned online by Google Trends is provided. Trends (number of
hits) over the time as well as geographic representation of the
results can be displayed.
Author: Philippe Massicotte [aut, cre],
Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>
Diff between gtrendsR versions 1.5.1 dated 2022-05-23 and 1.5.2 dated 2025-08-22
DESCRIPTION | 8 MD5 | 32 + NEWS.md | 4 R/countries.R | 2 R/gtrends.R | 65 ++- R/related_queries.R | 119 +++---- R/related_topics.R | 90 +---- R/setHandleParameters.R | 14 R/top_rising_search.R |only R/zzz.R | 442 ++++++++++++++++++++------ README.md | 10 inst/tinytest/test_encoding_does_not_change.R | 9 inst/tinytest/test_gprop.R | 4 inst/tinytest/test_not_empty_results.R | 10 inst/tinytest/test_timespans.R | 16 man/countries.Rd | 2 man/extract_top_rising.Rd |only tests/tinytest.R | 1 18 files changed, 549 insertions(+), 279 deletions(-)
Title: Bindings to 'GDAL'
Description: API bindings to the Geospatial Data Abstraction Library ('GDAL',
<https://gdal.org>). Implements the 'GDAL' Raster and Vector Data Models.
Bindings are implemented with 'Rcpp' modules. Exposed C++ classes and
stand-alone functions wrap much of the 'GDAL' API and provide additional
functionality. Calling signatures resemble the native C, C++ and Python APIs
provided by the 'GDAL' project. Class 'GDALRaster' encapsulates a
'GDALDataset' and its raster band objects. Class 'GDALVector' encapsulates
an 'OGRLayer' and the 'GDALDataset' that contains it. Initial bindings are
provided to the unified 'gdal' command line interface added in 'GDAL' 3.11.
C++ stand-alone functions provide bindings to most 'GDAL' "traditional"
raster and vector utilities, including 'OGR' facilities for vector
geoprocessing, several algorithms, as well as the Geometry API ('GEOS' via
'GDAL' headers), the Spatial Reference Systems API, and methods for
coordinate transformation. Bindings to the Virtual Systems In [...truncated...]
Author: Chris Toney [aut, cre] ,
Michael D. Sumner [ctb],
Frank Warmerdam [ctb, cph] ,
Even Rouault [ctb, cph] ,
Marius Appel [ctb, cph] ,
Daniel James [ctb, cph] ,
Peter Dimov [ctb, cph]
Maintainer: Chris Toney <jctoney@gmail.com>
Diff between gdalraster versions 2.1.0 dated 2025-07-14 and 2.2.0 dated 2025-08-22
gdalraster-2.1.0/gdalraster/inst/doc/vector-api-overview.R |only gdalraster-2.1.0/gdalraster/inst/doc/vector-api-overview.Rmd |only gdalraster-2.1.0/gdalraster/inst/doc/vector-api-overview.html |only gdalraster-2.1.0/gdalraster/vignettes/vector-api-overview.Rmd |only gdalraster-2.2.0/gdalraster/DESCRIPTION | 34 - gdalraster-2.2.0/gdalraster/MD5 | 145 +++--- gdalraster-2.2.0/gdalraster/NEWS.md | 32 + gdalraster-2.2.0/gdalraster/R/RcppExports.R | 21 gdalraster-2.2.0/gdalraster/R/cmb_table.R | 10 gdalraster-2.2.0/gdalraster/R/gdal_cli.R |only gdalraster-2.2.0/gdalraster/R/gdal_helpers.R | 43 - gdalraster-2.2.0/gdalraster/R/gdal_rat.R | 6 gdalraster-2.2.0/gdalraster/R/gdal_util.R | 4 gdalraster-2.2.0/gdalraster/R/gdalalg.R |only gdalraster-2.2.0/gdalraster/R/gdalraster.R | 56 +- gdalraster-2.2.0/gdalraster/R/gdalraster_proc.R | 44 - gdalraster-2.2.0/gdalraster/R/gdalvector.R | 226 +++++----- gdalraster-2.2.0/gdalraster/R/geom.R | 18 gdalraster-2.2.0/gdalraster/R/ogr_define.R | 39 + gdalraster-2.2.0/gdalraster/R/ogr_manage.R | 6 gdalraster-2.2.0/gdalraster/R/ogr_reproject.R | 11 gdalraster-2.2.0/gdalraster/R/running_stats.R | 2 gdalraster-2.2.0/gdalraster/R/transform.R | 2 gdalraster-2.2.0/gdalraster/R/vsifile.R | 18 gdalraster-2.2.0/gdalraster/README.md | 78 ++- gdalraster-2.2.0/gdalraster/build/vignette.rds |binary gdalraster-2.2.0/gdalraster/configure | 18 gdalraster-2.2.0/gdalraster/configure.ac | 2 gdalraster-2.2.0/gdalraster/inst/COPYRIGHTS | 27 - gdalraster-2.2.0/gdalraster/inst/doc/gdal-config-quick-ref.html | 2 gdalraster-2.2.0/gdalraster/inst/doc/raster-api-tutorial.html | 42 + gdalraster-2.2.0/gdalraster/inst/doc/raster-attribute-tables.html | 110 ++-- gdalraster-2.2.0/gdalraster/inst/extdata/storml_elev.tif |binary gdalraster-2.2.0/gdalraster/inst/extdata/storml_elev_orig.tif |only gdalraster-2.2.0/gdalraster/man/CmbTable-class.Rd | 10 gdalraster-2.2.0/gdalraster/man/GDALAlg-class.Rd |only gdalraster-2.2.0/gdalraster/man/GDALRaster-class.Rd | 56 +- gdalraster-2.2.0/gdalraster/man/GDALVector-class.Rd | 226 +++++----- gdalraster-2.2.0/gdalraster/man/RunningStats-class.Rd | 2 gdalraster-2.2.0/gdalraster/man/VSIFile-class.Rd | 18 gdalraster-2.2.0/gdalraster/man/autoCreateWarpedVRT.Rd | 2 gdalraster-2.2.0/gdalraster/man/buildRAT.Rd | 6 gdalraster-2.2.0/gdalraster/man/calc.Rd | 8 gdalraster-2.2.0/gdalraster/man/dem_proc.Rd | 12 gdalraster-2.2.0/gdalraster/man/fillNodata.Rd | 16 gdalraster-2.2.0/gdalraster/man/gdal_cli.Rd |only gdalraster-2.2.0/gdalraster/man/gdalraster-package.Rd | 6 gdalraster-2.2.0/gdalraster/man/getCreationOptions.Rd | 20 gdalraster-2.2.0/gdalraster/man/get_pixel_line.Rd | 5 gdalraster-2.2.0/gdalraster/man/inspectDataset.Rd | 18 gdalraster-2.2.0/gdalraster/man/ogr_define.Rd | 12 gdalraster-2.2.0/gdalraster/man/ogr_manage.Rd | 4 gdalraster-2.2.0/gdalraster/man/ogr_reproject.Rd | 11 gdalraster-2.2.0/gdalraster/man/read_ds.Rd | 4 gdalraster-2.2.0/gdalraster/src/RcppExports.cpp | 16 gdalraster-2.2.0/gdalraster/src/gdal_exp.cpp | 16 gdalraster-2.2.0/gdalraster/src/gdalalg.cpp |only gdalraster-2.2.0/gdalraster/src/gdalalg.h |only gdalraster-2.2.0/gdalraster/src/gdalraster.cpp | 59 +- gdalraster-2.2.0/gdalraster/src/gdalraster.h | 21 gdalraster-2.2.0/gdalraster/src/gdalvector.cpp | 11 gdalraster-2.2.0/gdalraster/src/gdalvector.h | 5 gdalraster-2.2.0/gdalraster/src/rcpp_util.cpp | 56 +- gdalraster-2.2.0/gdalraster/src/rcpp_util.h | 8 gdalraster-2.2.0/gdalraster/src/vsifile.cpp | 15 gdalraster-2.2.0/gdalraster/tests/testthat/test-GDALAlg-class.R |only gdalraster-2.2.0/gdalraster/tests/testthat/test-GDALRaster-class.R | 16 gdalraster-2.2.0/gdalraster/tests/testthat/test-GDALVector-class.R | 8 gdalraster-2.2.0/gdalraster/tests/testthat/test-display.R | 2 gdalraster-2.2.0/gdalraster/tests/testthat/test-gdal_cli.R |only gdalraster-2.2.0/gdalraster/tests/testthat/test-gdal_create.R | 2 gdalraster-2.2.0/gdalraster/tests/testthat/test-gdal_exp.R | 18 gdalraster-2.2.0/gdalraster/tests/testthat/test-gdal_helpers.R | 7 gdalraster-2.2.0/gdalraster/tests/testthat/test-gdal_util.R | 4 gdalraster-2.2.0/gdalraster/tests/testthat/test-gdal_vsi.R | 10 gdalraster-2.2.0/gdalraster/tests/testthat/test-gdalraster_proc.R | 14 gdalraster-2.2.0/gdalraster/tests/testthat/test-geom.R | 10 gdalraster-2.2.0/gdalraster/tests/testthat/test-ogr_reproject.R | 39 + gdalraster-2.2.0/gdalraster/tests/testthat/test-s3_methods.R | 11 gdalraster-2.2.0/gdalraster/tests/testthat/test-srs_api.R | 2 80 files changed, 1006 insertions(+), 776 deletions(-)
Title: Algorithm Driven Statistical Analysis for Researchers without
Coding Skills
Description: Support functions for R-based 'EQUAL-STATS' software which automatically classifies the data and performs appropriate statistical tests. 'EQUAL-STATS' software is a shiny application with an user-friendly interface to perform complex statistical analysis. Gurusamy,K (2024)<doi:10.5281/zenodo.13354162>.
Author: Kurinchi Gurusamy [aut, cre]
Maintainer: Kurinchi Gurusamy <k.gurusamy@ucl.ac.uk>
Diff between EQUALSTATS versions 0.5.0 dated 2024-09-23 and 0.5.1 dated 2025-08-22
DESCRIPTION | 13 +++++-------- MD5 | 4 ++-- R/function.Survival_Analysis.R | 4 ++-- 3 files changed, 9 insertions(+), 12 deletions(-)
Title: Convolution-Closed Models for Count Time Series
Description: Useful tools for fitting, validating, and forecasting of practical convolution-closed time series models for low counts are provided. Marginal distributions of the data can be modelled via Poisson and Generalized Poisson innovations. Regression effects can be incorporated through time varying innovation rates. The models are described in Jung and Tremayne (2011) <doi:10.1111/j.1467-9892.2010.00697.x> and the model assessment tools are presented in Czado et al. (2009) <doi:10.1111/j.1541-0420.2009.01191.x> and, Tsay (1992) <doi:10.2307/2347612>.
Author: Manuel Huth [aut, cre],
Robert C. Jung [aut],
Andy Tremayne [aut]
Maintainer: Manuel Huth <manuel.huth@yahoo.com>
Diff between coconots versions 2.0.1 dated 2025-07-24 and 2.0.2 dated 2025-08-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/cocoReg.R | 8 +++++++- R/cocoSim.R | 12 ++++++++++++ R/predict.coco.R | 17 ++++++++++------- R/utils.R | 2 +- man/cocoSim.Rd | 11 +++++++++++ 7 files changed, 51 insertions(+), 19 deletions(-)
Title: Canadian Forest Fire Danger Rating System
Description: This project provides a group of new functions to calculate
the outputs of the two main components of the Canadian Forest Fire
Danger Rating System (CFFDRS) Van Wagner and Pickett (1985)
<https://ostrnrcan-dostrncan.canada.ca/entities/publication/29706108-2891-4e5d-a59a-a77c96bc507c>) at various time
scales: the Fire Weather Index (FWI) System Wan Wagner (1985)
<https://ostrnrcan-dostrncan.canada.ca/entities/publication/d96e56aa-e836-4394-ba29-3afe91c3aa6c> and the Fire Behaviour
Prediction (FBP) System Forestry Canada Fire Danger Group (1992)
<https://cfs.nrcan.gc.ca/pubwarehouse/pdfs/10068.pdf>. Some functions
have two versions, table and raster based.
Author: Xianli Wang [aut],
Alan Cantin [aut],
Marc-Andre Parisien [aut],
Mike Wotton [aut],
Kerry Anderson [aut],
Brett Moore [cre, aut],
Tom Schiks [aut],
Mike Flannigan [aut]
Maintainer: Brett Moore <Brett.Moore@nrcan-rncan.gc.ca>
Diff between cffdrs versions 1.9.0 dated 2024-02-22 and 1.9.2 dated 2025-08-22
DESCRIPTION | 37 +- MD5 | 86 ++-- NEWS.md | 16 R/Slopecalc.r | 23 - R/back_rate_of_spread.r | 2 R/cffdrs-package.R | 6 R/fbpRaster.r | 1 R/fine_fuel_moisture_code.r | 7 R/fire_behaviour_prediction.r | 3 R/gfmcRaster.R | 1 R/grass_fuel_moisture.r | 2 R/grass_fuel_moisture_code.r | 2 R/hourly_fine_fuel_moisture_code.r | 6 R/initial_spread_index.r | 2 README.md | 4 man/cffdrs-package.Rd | 4 man/fbpRaster.Rd | 1 man/fire_season.Rd | 2 man/gfmcRaster.Rd | 1 tests/testthat/data/BackRateOfSpread.csv | 8 tests/testthat/data/HourlyFineFuelMoistureCode.csv | 174 ++++----- tests/testthat/data/InitialSpreadIndex.csv | 378 ++++++++++----------- tests/testthat/data/Slope.csv | 194 +++++----- tests/testthat/data/fbpRaster_test1.tif |binary tests/testthat/data/fbpRaster_test2.tif |binary tests/testthat/data/fbpRaster_test3.tif |binary tests/testthat/data/fbpRaster_test4.tif |binary tests/testthat/data/fbpRaster_test5.tif |binary tests/testthat/data/fbp_01.csv | 2 tests/testthat/data/fbp_02.csv | 2 tests/testthat/data/fbp_03.csv | 2 tests/testthat/data/fbp_04.csv | 2 tests/testthat/data/fbp_05.csv | 2 tests/testthat/data/fbp_06.csv | 2 tests/testthat/data/fbp_07.csv | 2 tests/testthat/data/fwiRaster_test1_and_2.tif |binary tests/testthat/data/fwiRaster_test3.tif |binary tests/testthat/data/fwi_11.csv | 2 tests/testthat/data/gfmcRaster_test1.tif |binary tests/testthat/data/gfmcRaster_test2.tif |binary tests/testthat/data/hffmcRaster_test1.tif |binary tests/testthat/data/hffmcRaster_test2.tif |binary tests/testthat/data/hffmcRaster_test3.tif |binary tests/testthat/test_fbp.r | 12 44 files changed, 505 insertions(+), 483 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of Data
and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package, introduced in Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>, can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>.
Various risk estimation and anonymization methods are included. Note that the package
includes a graphical user interface published in Meindl and Templ (2019) <doi:10.3390/a12090191> that allows to use various methods of this
package.
Author: Matthias Templ [aut, cre] ,
Bernhard Meindl [aut],
Alexander Kowarik [aut] ,
Johannes Gussenbauer [aut],
Organisation For Economic Co-Operation And Development [cph] code code for rank swapping,
mdav-microaggregation, suda2 and other risk
measures [...truncated...]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 5.7.8 dated 2024-03-11 and 5.7.9 dated 2025-08-22
DESCRIPTION | 18 - MD5 | 38 +- NEWS | 5 R/dUtility.R | 101 +++---- R/localSuppression.R | 237 +++++++++++------- R/modRisk.R | 393 +++++++++++++++---------------- R/pram.R | 26 +- R/recordSwap.R | 54 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/sdcMicro.html | 4 man/dUtility.Rd | 29 ++ man/il_additional.Rd | 2 man/localSuppression.Rd | 104 ++++---- man/modRisk.Rd | 15 - man/pram.Rd | 6 man/print.localSuppression.Rd | 2 man/sdcMicro-package.Rd | 2 tests/testthat/test_recordSwap_inputs.R | 2 tests/testthat/test_recordSwap_outputs.R | 18 - 20 files changed, 579 insertions(+), 477 deletions(-)
Title: Bayesian Dynamic Borrowing with Propensity Score
Description: A tool which aims to help evaluate the effect of external borrowing using an integrated approach described in Lewis et al., (2019) <doi:10.1080/19466315.2018.1497533> that combines propensity score and Bayesian dynamic borrowing methods.
Author: Isaac Gravestock [cre, ctb],
Craig Gower-Page [aut],
Matt Secrest [ctb],
Yichen Lu [aut],
Aijing Lin [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between psborrow versions 0.2.3 dated 2025-06-23 and 0.2.4 dated 2025-08-22
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/get_summary.R | 2 +- man/ps_message.Rd | 6 ++++-- man/set_cov.Rd | 6 ++++-- man/set_event.Rd | 6 ++++-- 7 files changed, 26 insertions(+), 16 deletions(-)
Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of segments shared identical-by-descent (IBD) by
pedigree members. Using sex specific recombination rates along the
human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'pedsuite' collection of packages for pedigree analysis.
A detailed presentation of the 'pedsuite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdsim2 versions 2.3.0 dated 2025-07-22 and 2.3.1 dated 2025-08-22
DESCRIPTION | 10 ++-- MD5 | 18 ++++---- NEWS.md | 23 ++++++++-- R/karyogram.R | 86 ++++++++++++++++++++--------------------- R/plotSegmentDistribution.R | 66 +++++++++++++++++-------------- R/utils.R | 1 inst/shiny/R/plot-functions.R | 9 ++-- inst/shiny/R/utils.R | 8 +++ inst/shiny/app.R | 12 ++--- man/plotSegmentDistribution.Rd | 2 10 files changed, 131 insertions(+), 104 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] ,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.15.0 dated 2025-07-21 and 1.16.0 dated 2025-08-22
DESCRIPTION | 11 MD5 | 257 - NAMESPACE | 991 ++--- NEWS.md | 28 R/AddTip.R | 550 +- R/ClusterTable.R | 238 - R/Consensus.R | 285 - R/ConsistentSplits.R |only R/Decompose.R | 328 - R/DropTip.R | 633 +-- R/LongBranchScore.R |only R/MatchStrings.R | 66 R/PathLengths.R | 92 R/PhyToString.R | 275 - R/RcppExports-manual.R | 64 R/RcppExports.R | 24 R/Reweight.R | 220 - R/RoguePlot.R | 574 +-- R/SplitFunctions.R | 902 ++-- R/Splits.R | 1209 +++--- R/Support.R | 390 +- R/TopologyOnly.R | 79 R/Treeness.R |only R/data.R | 180 R/helper_functions.R | 378 +- R/parse_files.R | 1822 ++++----- R/phylo.R | 644 +-- R/tree_descendants.R | 293 - R/tree_generation.R | 1134 +++--- R/tree_numbering.R | 1323 +++---- R/tree_properties.R | 1152 +++--- R/tree_rearrangement.R | 1285 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 702 +-- inst/WORDLIST | 247 - inst/apa-old-doi-prefix.csl | 3172 ++++++++--------- inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.Rmd | 428 +- inst/doc/load-data.html | 4 inst/doc/load-trees.html | 4 inst/include/TreeTools/ClusterTable.h | 301 + inst/include/TreeTools/SplitList.h | 133 inst/include/TreeTools/assert.h | 2 inst/include/TreeTools/keep_tip.h | 2 inst/include/TreeTools/renumber_tree.h | 779 +--- inst/include/TreeTools/root_tree.h | 130 inst/include/TreeTools/types.h | 4 man/AddTip.Rd | 282 - man/AncestorEdge.Rd | 106 man/ClusterTable.Rd | 155 man/ConsensusWithout.Rd | 208 - man/Decompose.Rd | 166 man/DescendantEdges.Rd | 178 man/DropTip.Rd | 265 - man/EdgeAncestry.Rd | 124 man/EndSentence.Rd | 64 man/GenerateTree.Rd | 188 - man/ListAncestors.Rd | 218 - man/LongBranch.Rd |only man/MakeTreeBinary.Rd | 109 man/MatchEdges.Rd | 132 man/MatchStrings.Rd | 80 man/MatrixToPhyDat.Rd | 150 man/MorphoBankDecode.Rd | 58 man/NSplits.Rd | 166 man/NTip.Rd | 134 man/Neworder.Rd | 128 man/NodeNumbers.Rd | 108 man/PathLengths.Rd | 108 man/PhyToString.Rd | 212 - man/ReadCharacters.Rd | 288 - man/Reorder.Rd | 560 +-- man/Reweight.Rd | 156 man/RightmostCharacter.Rd | 72 man/RootTree.Rd | 192 - man/SplitConsistent.Rd |only man/SplitFrequency.Rd | 214 - man/SplitsInBinaryTree.Rd | 156 man/Subsplit.Rd | 95 man/Subtree.Rd | 124 man/TipLabels.Rd | 246 - man/TopologyOnly.Rd | 47 man/TreeIsRooted.Rd | 80 man/TreeShape.Rd | 322 - man/Treeness.Rd |only man/TrivialSplits.Rd | 95 man/TrivialTree.Rd | 126 man/Unquote.Rd | 64 man/brewer.Rd | 66 man/match.Splits.Rd | 128 man/match.multiPhylo.Rd | 144 man/sapply64.Rd | 164 src/RcppExports.cpp | 90 src/as_newick.cpp | 2 src/consensus.cpp | 124 src/descendant_edges.cpp | 111 src/int_to_tree.cpp | 4 src/path_lengths.cpp | 71 src/splits.cpp | 398 +- src/splits_to_tree.cpp | 80 src/tips_in_splits.cpp | 48 src/tree_shape.cpp | 4 tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg | 106 tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg | 82 tests/testthat/_snaps/Support/labelsplits-nameless.svg | 172 tests/testthat/_snaps/Support/labelsplits-names.svg | 148 tests/testthat/test-AddTip.R | 356 - tests/testthat/test-ClusterTable.R | 198 - tests/testthat/test-Decompose.R | 118 tests/testthat/test-DropTip.R | 481 +- tests/testthat/test-LongBranchScore.R |only tests/testthat/test-MatchStrings.R | 26 tests/testthat/test-PathLengths.R | 67 tests/testthat/test-PhyToString.R | 136 tests/testthat/test-ReadTntTree.R | 290 - tests/testthat/test-Reweight.R | 92 tests/testthat/test-RoguePlot.R | 310 - tests/testthat/test-SplitConsistent.R |only tests/testthat/test-SplitFunctions.R | 452 +- tests/testthat/test-Splits.R | 1083 ++--- tests/testthat/test-Support.R | 116 tests/testthat/test-TopologyOnly.R | 49 tests/testthat/test-Treeness.R |only tests/testthat/test-consensus.R | 220 - tests/testthat/test-helper_functions.R | 22 tests/testthat/test-match.R | 58 tests/testthat/test-parsers.R | 426 +- tests/testthat/test-split_analysis.R | 22 tests/testthat/test-tree_generation.R | 438 +- tests/testthat/test-tree_properties.R | 360 - tests/testthat/test-tree_rearrange.R | 825 ++-- tests/testthat/testdata/nonPreCons.nex | 48 vignettes/load-data.Rmd | 428 +- 134 files changed, 18474 insertions(+), 17604 deletions(-)
Title: Assessing Package Risk Metrics
Description: Provides a structured approach to assess the quality and trustworthiness of R packages
(documentation, testing, popularity, dependencies), supporting informed decisions in production
or research by highlighting strengths and potential risks in adoption or development.
Author: Edward Gillian [cre, aut] ,
Hugo Bottois [aut] ,
Paulin Charliquart [aut],
Andre Couturier [aut],
Sanofi [cph, fnd]
Maintainer: Edward Gillian <edward.gillian-ext@sanofi.com>
Diff between risk.assessr versions 2.0.0 dated 2025-07-10 and 2.0.1 dated 2025-08-22
DESCRIPTION | 6 - MD5 | 36 +++++----- NEWS.md | 12 +++ build/vignette.rds |binary inst/doc/create-your-weights-profile.html | 2 tests/testthat/test-assess_examples.R | 22 +++++- tests/testthat/test-assess_export_help.R | 15 +++- tests/testthat/test-assess_exports.R | 15 +++- tests/testthat/test-assess_news.R | 15 +++- tests/testthat/test-assess_news_current.R | 15 +++- tests/testthat/test-assess_pkg.R | 40 ++++++++++- tests/testthat/test-check_suggested_exp_funcs.R | 79 +++++++++++++++++++--- tests/testthat/test-create_traceability_matrix.R | 54 ++++++++++++--- tests/testthat/test-get_pkg_license.R | 30 +++++++- tests/testthat/test-parse_dcf_dependencies.R | 15 +++- tests/testthat/test-run_coverage.R | 80 ++++++++++++++++++++--- tests/testthat/test-run_covr.R | 17 ++++ tests/testthat/test-run_rcmdcheck.R | 63 +++++++++++++++--- tests/testthat/test-set_up_pkg.R | 22 +----- 19 files changed, 436 insertions(+), 102 deletions(-)
Title: Prior Diagnostics and Sensitivity Analysis
Description: Provides functions for prior and likelihood sensitivity analysis in Bayesian models. Currently it implements methods to determine the sensitivity of the posterior to power-scaling perturbations of the prior and likelihood.
Author: Noa Kallioinen [aut, cre, cph],
Topi Paananen [aut],
Paul-Christian Buerkner [aut],
Aki Vehtari [aut],
Frank Weber [ctb]
Maintainer: Noa Kallioinen <noa.kallioinen@aalto.fi>
Diff between priorsense versions 1.1.0 dated 2025-04-10 and 1.1.1 dated 2025-08-22
priorsense-1.1.0/priorsense/tests/testthat/test_brm.R |only priorsense-1.1.1/priorsense/DESCRIPTION | 14 priorsense-1.1.1/priorsense/MD5 | 76 priorsense-1.1.1/priorsense/NEWS.md | 4 priorsense-1.1.1/priorsense/R/additional_divergence_measures.R | 70 priorsense-1.1.1/priorsense/R/cjs.R | 9 priorsense-1.1.1/priorsense/R/create_priorsense_data.R | 22 priorsense-1.1.1/priorsense/R/find_alpha_threshold.R | 17 priorsense-1.1.1/priorsense/R/log_lik_draws.R | 12 priorsense-1.1.1/priorsense/R/log_prior_draws.R | 20 priorsense-1.1.1/priorsense/R/plots.R | 1127 +++++----- priorsense-1.1.1/priorsense/R/powerscale.R | 37 priorsense-1.1.1/priorsense/R/powerscale_sensitivity.R | 2 priorsense-1.1.1/priorsense/R/print.R | 3 priorsense-1.1.1/priorsense/R/priorsense-package.R | 44 priorsense-1.1.1/priorsense/R/scale_draws.R | 6 priorsense-1.1.1/priorsense/R/scaled_log_ratio.R | 2 priorsense-1.1.1/priorsense/R/srr-stats-standards.R | 36 priorsense-1.1.1/priorsense/R/summarise_draws.R | 32 priorsense-1.1.1/priorsense/R/weighted_diagnostics.R | 4 priorsense-1.1.1/priorsense/R/weighted_quantities.R | 51 priorsense-1.1.1/priorsense/R/whiten_draws.R | 4 priorsense-1.1.1/priorsense/build/vignette.rds |binary priorsense-1.1.1/priorsense/inst/doc/powerscaling.html | 147 + priorsense-1.1.1/priorsense/inst/doc/priorsense_with_jags.R | 1 priorsense-1.1.1/priorsense/inst/doc/priorsense_with_jags.html | 143 + priorsense-1.1.1/priorsense/inst/doc/priorsense_with_jags.qmd | 2 priorsense-1.1.1/priorsense/man/create-priorsense-data.Rd | 15 priorsense-1.1.1/priorsense/man/log_lik_draws.Rd | 3 priorsense-1.1.1/priorsense/man/log_prior_draws.Rd | 7 priorsense-1.1.1/priorsense/man/powerscale_plots.Rd | 3 priorsense-1.1.1/priorsense/man/priorsense-package.Rd | 23 priorsense-1.1.1/priorsense/tests/testthat.R | 1 priorsense-1.1.1/priorsense/tests/testthat/test_cjs.R | 1 priorsense-1.1.1/priorsense/tests/testthat/test_conjugate.R |only priorsense-1.1.1/priorsense/tests/testthat/test_plots.R | 34 priorsense-1.1.1/priorsense/tests/testthat/test_powerscale.R | 89 priorsense-1.1.1/priorsense/tests/testthat/test_rstan.R | 10 priorsense-1.1.1/priorsense/tests/testthat/test_whiten_draws.R | 3 priorsense-1.1.1/priorsense/vignettes/priorsense_with_jags.qmd | 2 40 files changed, 1326 insertions(+), 750 deletions(-)
Title: Multivariate Outlier Detection and Imputation for Incomplete
Survey Data
Description: Algorithms for multivariate outlier detection when missing values
occur. Algorithms are based on Mahalanobis distance or data depth.
Imputation is based on the multivariate normal model or uses nearest
neighbour donors. The algorithms take sample designs, in particular
weighting, into account. The methods are described in Bill and Hulliger
(2016) <doi:10.17713/ajs.v45i1.86>.
Author: Beat Hulliger [aut, cre],
Martin Sterchi [ctb],
Tobias Schoch [ctb]
Maintainer: Beat Hulliger <beat.hulliger@fhnw.ch>
Diff between modi versions 0.1.2 dated 2023-03-14 and 0.1.3 dated 2025-08-22
DESCRIPTION | 8 - MD5 | 23 +- NAMESPACE | 2 R/data.R | 5 R/modi-package.R |only R/modi.R | 1 build/partial.rdb |only build/vignette.rds |binary inst/doc/modi_vignette.R | 54 +++--- inst/doc/modi_vignette.html | 343 ++++++++++++++++++++++---------------------- man/lival.Rd | 5 man/modi-package.Rd |only man/modi.Rd | 63 +++----- tests/testthat/Rplots.pdf |binary 14 files changed, 254 insertions(+), 250 deletions(-)
Title: Statistical Methods for the Analysis of Excess Lifetimes
Description: A collection of parametric and nonparametric methods for the analysis of survival data. Parametric families implemented include Gompertz-Makeham, exponential and generalized Pareto models and extended models. The package includes an implementation of the nonparametric maximum likelihood estimator for arbitrary truncation and censoring pattern based on Turnbull (1976) <doi:10.1111/j.2517-6161.1976.tb01597.x>, along with graphical goodness-of-fit diagnostics. Parametric models for positive random variables and peaks over threshold models based on extreme value theory are described in Rootzén and Zholud (2017) <doi:10.1007/s10687-017-0305-5>; Belzile et al. (2021) <doi:10.1098/rsos.202097> and Belzile et al. (2022) <doi:10.1146/annurev-statistics-040120-025426>.
Author: Leo Belzile [aut, cre]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between longevity versions 1.2.1 dated 2025-07-03 and 1.2.2 dated 2025-08-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/plots.R | 10 ++-------- R/threshstab.R | 39 ++++----------------------------------- inst/doc/introduction.html | 4 ++-- inst/doc/nonparametric.html | 4 ++-- 6 files changed, 18 insertions(+), 55 deletions(-)
Title: Extended Evolutionary and Genetic Algorithms
Description: Implementation of a scalable, highly configurable, and
e(x)tended architecture for (e)volutionary and (g)enetic (a)lgorithms.
Multiple representations (binary, real-coded, permutation, and
derivation-tree), a rich collection of genetic operators,
as well as an extended processing pipeline are provided
for genetic algorithms (Goldberg, D. E. (1989, ISBN:0-201-15767-5)),
differential evolution (Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005)
<doi:10.1007/3-540-31306-0>), simulated annealing (Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7)), grammar-based genetic programming
(Geyer-Schulz (1997, ISBN:978-3-7908-0830-X)), grammatical evolution
(Ryan, C., O'Neill, M., and Collins, J. J. (2018) <doi:10.1007/978-3-319-78717-6>),
and grammatical differential evolution (O'Neill, M. and Brabazon, A. (2006) in
Arabinia, H. (2006, ISBN:978-193-241596-3).
All algorithms reuse basic adaptive mechanisms for performance optimization.
Sequential or parallel execution ( [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xega versions 0.9.0.12 dated 2025-07-30 and 0.9.0.17 dated 2025-08-22
DESCRIPTION | 12 +++++++----- MD5 | 20 ++++++++++---------- NEWS | 38 ++++++++++++++++++++++++++++++++++++++ R/sgXCrossoverFactory.R | 2 +- R/xegaRerun.R | 42 ++++++++++++++++++++++++++++++++++++++---- R/xegaRun.R | 26 ++++++++++++++++++-------- R/xegaVersion.R | 4 ++-- man/sgXCrossoverFactory.Rd | 2 +- man/xegaReRun.Rd | 14 ++++++++++++-- man/xegaRun.Rd | 12 +++++++----- tests/testthat/test-xega.R | 10 +++++----- 11 files changed, 139 insertions(+), 43 deletions(-)
Title: Statistical Framework for in Vivo Drug Combination Studies
Description: A framework for evaluating drug combination effects in preclinical in vivo studies.
'SynergyLMM' provides functions to analyze longitudinal tumor growth experiments using mixed-effects models,
perform time-resolved analyses of synergy and antagonism, evaluate model diagnostics and performance,
and assess both post-hoc and a priori statistical power.
The calculation of drug combination synergy follows the statistical framework provided by Demidenko and Miller (2019, <doi:10.1371/journal.pone.0224137>).
The implementation and analysis of linear mixed-effect models is based on the methods described by Pinheiro and Bates (2000, <doi:10.1007/b98882>),
and Gałecki and Burzykowski (2013, <doi:10.1007/978-1-4614-3900-4>).
Author: Rafael Romero-Becerra [aut, cre] ,
Zhi Zhao [ctb],
Tero Aittokallio [ctb]
Maintainer: Rafael Romero-Becerra <r.r.becerra@medisin.uio.no>
Diff between SynergyLMM versions 1.1.0 dated 2025-07-29 and 1.1.1 dated 2025-08-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ man/figures/logo.png |binary tests/testthat/test-plot_SynergyLMM.R | 4 ++-- 5 files changed, 17 insertions(+), 9 deletions(-)
Title: Sparse Marginal Epistasis Test
Description: The Sparse Marginal Epistasis Test is a computationally efficient
genetics method which detects statistical epistasis in complex traits;
see Stamp et al. (2025, <doi:10.1101/2025.01.11.632557>) for details.
Author: Julian Stamp [cre, aut] ,
Lorin Crawford [aut] ,
sriramlab [cph]
Maintainer: Julian Stamp <julian.d.stamp@gmail.com>
Diff between smer versions 0.0.1 dated 2025-01-16 and 0.0.2 dated 2025-08-22
smer-0.0.1/smer/inst/include |only smer-0.0.2/smer/DESCRIPTION | 19 +- smer-0.0.2/smer/MD5 | 75 +--------- smer-0.0.2/smer/NEWS.md | 6 smer-0.0.2/smer/README.md | 12 + smer-0.0.2/smer/build/vignette.rds |binary smer-0.0.2/smer/inst/doc/smer.R | 2 smer-0.0.2/smer/inst/doc/smer.Rmd | 2 smer-0.0.2/smer/inst/doc/smer.html | 49 +++--- smer-0.0.2/smer/inst/doc/study-erythroid-differentiation-data.html | 56 +++---- smer-0.0.2/smer/inst/doc/tutorial-create-mask-file.html | 56 +++---- smer-0.0.2/smer/inst/doc/tutorial-memory-optimization.html | 56 +++---- smer-0.0.2/smer/inst/doc/tutorial-simulate-traits.html | 58 +++---- smer-0.0.2/smer/vignettes/smer.Rmd | 2 14 files changed, 179 insertions(+), 214 deletions(-)
Title: Access Color Names Using a Standardized Nomenclature
Description: A curated set of colors that are called using
a standardized syntax: saturation + hue + lightness. For example,
"brightblue4" and "mutedred2". Functions exists to return individual colors
by name or to build palettes across or within hues. Most functions allow you
to visualize the palettes in addition to returning the desired hex codes.
Author: Jake Riley [aut, cre]
Maintainer: Jake Riley <rjake@sas.upenn.edu>
Diff between simplecolors versions 0.1.2 dated 2023-08-31 and 0.1.3 dated 2025-08-22
DESCRIPTION | 11 +++++---- MD5 | 28 ++++++++++++------------- NEWS.md | 4 +++ R/build_colors.R | 3 -- R/build_palettes.R | 5 ++-- build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/intro.R | 42 +++++++++++++++++++------------------- inst/doc/intro.html | 22 +++++++++---------- man/sc.Rd | 3 ++ man/sc_across.Rd | 3 ++ man/sc_within.Rd | 3 ++ man/show_colors.Rd | 4 --- man/simplecolors.Rd | 3 +- tests/testthat/test-show_colors.R | 2 - 15 files changed, 74 insertions(+), 60 deletions(-)
Title: Animated Biplots
Description: Create animated biplots that enables dynamic visualisation of temporal or sequential changes in multivariate data by animating a single biplot across the levels of a time variable. It builds on objects from the 'biplotEZ' package, Lubbe S, le Roux N, Nienkemper-Swanepoel J, Ganey R, Buys R, Adams Z, Manefeldt P (2024) <doi:10.32614/CRAN.package.biplotEZ>, allowing users to create animated biplots that reveal how both samples and variables evolve over time.
Author: Raeesa Ganey [aut, cre, cph] ,
Johane Nienkemper-Swanepoel [aut, cph]
Maintainer: Raeesa Ganey <raeesa.ganey@wits.ac.za>
Diff between moveEZ versions 1.0.3 dated 2025-07-05 and 1.1.0 dated 2025-08-22
moveEZ-1.0.3/moveEZ/man/reflect_biplot.Rd |only moveEZ-1.1.0/moveEZ/DESCRIPTION | 7 moveEZ-1.1.0/moveEZ/MD5 | 34 ++-- moveEZ-1.1.0/moveEZ/NAMESPACE | 1 moveEZ-1.1.0/moveEZ/NEWS.md | 5 moveEZ-1.1.0/moveEZ/R/evaluation_func.R |only moveEZ-1.1.0/moveEZ/R/globals.R | 2 moveEZ-1.1.0/moveEZ/R/plot.R | 73 ++++++-- moveEZ-1.1.0/moveEZ/R/utility.R | 27 --- moveEZ-1.1.0/moveEZ/README.md | 2 moveEZ-1.1.0/moveEZ/inst/doc/moveEZ.R | 45 +++-- moveEZ-1.1.0/moveEZ/inst/doc/moveEZ.Rmd | 82 ++++++++- moveEZ-1.1.0/moveEZ/inst/doc/moveEZ.html | 227 +++++++++++++++++++++++---- moveEZ-1.1.0/moveEZ/man/evaluation.Rd |only moveEZ-1.1.0/moveEZ/man/moveEZ-package.Rd | 7 moveEZ-1.1.0/moveEZ/man/moveplot.Rd | 3 moveEZ-1.1.0/moveEZ/man/moveplot2.Rd | 3 moveEZ-1.1.0/moveEZ/man/moveplot3.Rd | 6 moveEZ-1.1.0/moveEZ/vignettes/moveEZ.Rmd | 82 ++++++++- moveEZ-1.1.0/moveEZ/vignettes/references.bib |only 20 files changed, 469 insertions(+), 137 deletions(-)
Title: Rolling and Expanding Statistics
Description: Fast and efficient computation of rolling and expanding statistics for time-series data.
Author: Jason Foster [aut, cre]
Maintainer: Jason Foster <jason.j.foster@gmail.com>
Diff between roll versions 1.1.7 dated 2024-04-05 and 1.2.0 dated 2025-08-22
DESCRIPTION | 15 MD5 | 24 NEWS.md | 6 R/roll.R | 8 README.md | 1 build/partial.rdb |binary inst/include/roll_mat.h | 4815 ++++++++++++++++++++++----------------------- inst/include/roll_vec.h | 4043 +++++++++++++++++++------------------ man/roll_median.Rd | 4 man/roll_quantile.Rd | 4 src/roll.cpp | 273 +- tests/testthat/test-roll.R | 15 tests/testthat/test-zoo.R | 8 13 files changed, 4704 insertions(+), 4512 deletions(-)
Title: Causal Moderated Mediation Analysis
Description: Causal moderated mediation analysis using the methods proposed by Qin and Wang (2023) <doi:10.3758/s13428-023-02095-4>. Causal moderated mediation analysis is crucial for investigating how, for whom, and where a treatment is effective by assessing the heterogeneity of mediation mechanism across individuals and contexts. This package enables researchers to estimate and test the conditional and moderated mediation effects, assess their sensitivity to unmeasured pre-treatment confounding, and visualize the results. The package is built based on the quasi-Bayesian Monte Carlo method, because it has relatively better performance at small sample sizes, and its running speed is the fastest. The package is applicable to a treatment of any scale, a binary or continuous mediator, a binary or continuous outcome, and one or more moderators of any scale.
Author: Xu Qin [aut, cre, cph],
Lijuan Wang [ctb]
Maintainer: Xu Qin <xuqin@pitt.edu>
Diff between moderate.mediation versions 0.0.11 dated 2025-04-03 and 0.0.12 dated 2025-08-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/moderate.mediation.R | 11 +++++------ 3 files changed, 11 insertions(+), 12 deletions(-)
More information about moderate.mediation at CRAN
Permanent link
Title: Genetic Population Level Functions
Description: This collection of gene representation-independent functions
implements the population layer of extended evolutionary and genetic
algorithms and its support. The population layer consists of functions
for initializing, logging, observing, evaluating a population of genes,
as well as of computing the next population. For parallel evaluation of a
population of genes 4 execution models - named Sequential, MultiCore,
FutureApply, and Cluster - are provided. They are implemented by
configuring the lapply() function. The execution model FutureApply can be
externally configured as recommended by Bengtsson (2021)
<doi:10.32614/RJ-2021-048>. Configurable acceptance rules and cooling
schedules (see Kirkpatrick, S., Gelatt, C. D. J, and Vecchi, M. P. (1983)
<doi:10.1126/science.220.4598.671>, and Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7) offer simulated annealing or greedy randomized
approximate search procedure elements. Adaptive crossover and mutation
rates depending on po [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaPopulation versions 1.0.0.8 dated 2025-07-30 and 1.0.0.10 dated 2025-08-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ R/configuration.R | 8 ++++---- 4 files changed, 14 insertions(+), 10 deletions(-)
More information about xegaPopulation at CRAN
Permanent link
Title: Genetic Operations for Grammar-Based Genetic Programming
Description: An implementation of
the representation-dependent gene level operations of grammar-based
genetic programming with genes which are derivation trees
of a context-free grammar: Initialization of a gene with a
complete random derivation tree, decoding of a derivation tree.
Crossover is implemented by exchanging subtrees. Depth-bounds
for the minimal and the maximal depth of the roots of the subtrees
exchanged by crossover can be set.
Mutation is implemented by replacing a subtree by a random subtree.
The depth of the random subtree and the insertion node are
configurable. For details,
see Geyer-Schulz (1997, ISBN:978-3-7908-0830-X).
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaGpGene versions 1.0.0.2 dated 2025-04-17 and 1.0.0.3 dated 2025-08-22
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NEWS | 6 ++++++ R/xegaGpCrossover.R | 12 ++++++------ R/xegaGpMutate.R | 4 ++-- 5 files changed, 25 insertions(+), 18 deletions(-)
Title: Penalised Likelihood Estimation of a Covariance Matrix
Description: Penalised likelihood estimation of a covariance matrix via the ridge-regularised covglasso estimator described in Cibinel et al. (2024) <doi:10.48550/arXiv.2410.02403>. Based on the 'C++' code of the 'R' package 'covglasso' (by Michael Fop, <https://orcid.org/0000-0003-3936-2757>) and the 'R' code of 'icf' (by Mathias Drton, <https://orcid.org/0000-0001-5614-3025>) within the 'R' package 'ggm'.
Author: Luca Cibinel [cre, aut] ,
Alberto Roverato [aut] ,
Veronica Vinciotti [aut]
Maintainer: Luca Cibinel <lcibinel@gmail.com>
Diff between gicf versions 1.0 dated 2025-05-16 and 1.0.1 dated 2025-08-22
DESCRIPTION | 23 ++++++++++------------- MD5 | 7 ++++--- README.md |only build/partial.rdb |binary src/gicf.cpp | 23 +++++++++++++---------- 5 files changed, 27 insertions(+), 26 deletions(-)
Title: Disaggregation Modelling
Description: Fits disaggregation regression models using 'TMB' ('Template Model
Builder'). When the response data are aggregated to polygon level but
the predictor variables are at a higher resolution, these models can be
useful. Regression models with spatial random fields. The package is
described in detail in Nandi et al. (2023) <doi:10.18637/jss.v106.i11>.
Author: Anita Nandi [aut] ,
Tim Lucas [aut, cre] ,
Rohan Arambepola [aut],
Andre Python [aut] ,
Simon Smart [ctb]
Maintainer: Tim Lucas <timcdlucas@gmail.com>
Diff between disaggregation versions 0.4.0 dated 2024-10-02 and 0.4.1 dated 2025-08-22
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/build_mesh.R | 2 +- build/vignette.rds |binary inst/doc/disaggregation.html | 16 ++++++++-------- 5 files changed, 19 insertions(+), 19 deletions(-)
More information about disaggregation at CRAN
Permanent link
Title: Standardize Dates in Different Formats or with Missing Data
Description: There are many different formats dates are commonly
represented with: the order of day, month, or year can differ,
different separators ("-", "/", or whitespace) can be used, months can
be numerical, names, or abbreviations and year given as two digits or
four. 'datefixR' takes dates in all these different formats and
converts them to R's built-in date class. If 'datefixR' cannot
standardize a date, such as because it is too malformed, then the user
is told which date cannot be standardized and the corresponding ID for
the row. 'datefixR' also allows the imputation of missing days and
months with user-controlled behavior.
Author: Nathan Constantine-Cooke [aut, cre] ,
Jonathan Kitt [ctb, trl],
Antonio J. Perez-Luque [ctb, trl] ,
Daniel Possenriede [ctb, trl] ,
Michal Lauer [ctb, trl],
Kaique dos S. Alves [rev] ,
Al-Ahmadgaid B. Asaad [rev] ,
Anatoly Tsyplenkov [ctb, trl] ,
Chi [...truncated...]
Maintainer: Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>
Diff between datefixR versions 1.7.0 dated 2024-09-08 and 2.0.0 dated 2025-08-22
datefixR-1.7.0/datefixR/R/RcppExports.R |only datefixR-1.7.0/datefixR/R/fix_date.R |only datefixR-1.7.0/datefixR/R/fix_dates.R |only datefixR-1.7.0/datefixR/R/months.R |only datefixR-1.7.0/datefixR/man/fix_date.Rd |only datefixR-1.7.0/datefixR/man/fix_dates.Rd |only datefixR-1.7.0/datefixR/src/RcppExports.cpp |only datefixR-1.7.0/datefixR/src/code.cpp |only datefixR-1.7.0/datefixR/src/translate.h |only datefixR-1.7.0/datefixR/tests/testthat/_snaps/fix_date.md |only datefixR-1.7.0/datefixR/tests/testthat/_snaps/fix_dates.md |only datefixR-1.7.0/datefixR/tests/testthat/_snaps/mac-4.2/app_1 |only datefixR-1.7.0/datefixR/tests/testthat/_snaps/mac-4.3/app_1 |only datefixR-1.7.0/datefixR/tests/testthat/test_fix_date.R |only datefixR-1.7.0/datefixR/tests/testthat/test_fix_dates.R |only datefixR-2.0.0/datefixR/DESCRIPTION | 45 - datefixR-2.0.0/datefixR/MD5 | 112 +-- datefixR-2.0.0/datefixR/NAMESPACE | 3 datefixR-2.0.0/datefixR/NEWS.md | 36 - datefixR-2.0.0/datefixR/R/datefixR-package.R | 1 datefixR-2.0.0/datefixR/R/extendr-wrappers.R |only datefixR-2.0.0/datefixR/R/fix_date_char.R | 216 +++++- datefixR-2.0.0/datefixR/R/fix_date_df.R | 332 +++++++-- datefixR-2.0.0/datefixR/R/internal.R | 343 --------- datefixR-2.0.0/datefixR/R/shinyapp.R | 34 datefixR-2.0.0/datefixR/README.md | 338 +++++++-- datefixR-2.0.0/datefixR/build/vignette.rds |binary datefixR-2.0.0/datefixR/configure |only datefixR-2.0.0/datefixR/configure.win |only datefixR-2.0.0/datefixR/inst/CITATION | 2 datefixR-2.0.0/datefixR/inst/WORDLIST | 17 datefixR-2.0.0/datefixR/inst/doc/datefixR.R | 104 ++- datefixR-2.0.0/datefixR/inst/doc/datefixR.Rmd | 252 ++++++- datefixR-2.0.0/datefixR/inst/doc/datefixR.html | 346 ++++++++-- datefixR-2.0.0/datefixR/inst/doc/internationalization.R |only datefixR-2.0.0/datefixR/inst/doc/internationalization.Rmd |only datefixR-2.0.0/datefixR/inst/doc/internationalization.html |only datefixR-2.0.0/datefixR/inst/doc/shiny_app.R |only datefixR-2.0.0/datefixR/inst/doc/shiny_app.Rmd |only datefixR-2.0.0/datefixR/inst/doc/shiny_app.html |only datefixR-2.0.0/datefixR/man/fix_date_app.Rd | 4 datefixR-2.0.0/datefixR/man/fix_date_char.Rd | 143 ++-- datefixR-2.0.0/datefixR/man/fix_date_df.Rd | 166 +++- datefixR-2.0.0/datefixR/po/datefixR.pot | 20 datefixR-2.0.0/datefixR/src/Makevars.in |only datefixR-2.0.0/datefixR/src/Makevars.win.in |only datefixR-2.0.0/datefixR/src/datefixR-win.def |only datefixR-2.0.0/datefixR/src/entrypoint.c |only datefixR-2.0.0/datefixR/src/rust |only datefixR-2.0.0/datefixR/tests/spelling.R | 3 datefixR-2.0.0/datefixR/tests/test_zz.R | 13 datefixR-2.0.0/datefixR/tests/testthat/_snaps/mac-4.5 |only datefixR-2.0.0/datefixR/tests/testthat/_snaps/shiny/app_1/001_.png |binary datefixR-2.0.0/datefixR/tests/testthat/_snaps/shiny/app_1/003_.png |binary datefixR-2.0.0/datefixR/tests/testthat/test_app_1.R | 128 +++ datefixR-2.0.0/datefixR/tests/testthat/test_fix_date_app.R | 4 datefixR-2.0.0/datefixR/tests/testthat/test_fix_date_char.R | 64 + datefixR-2.0.0/datefixR/tests/testthat/test_fix_date_df.R | 128 +++ datefixR-2.0.0/datefixR/tests/testthat/test_languages.R | 11 datefixR-2.0.0/datefixR/tools |only datefixR-2.0.0/datefixR/vignettes/datefixR.Rmd | 252 ++++++- datefixR-2.0.0/datefixR/vignettes/internationalization.Rmd |only datefixR-2.0.0/datefixR/vignettes/shiny_app.Rmd |only 63 files changed, 2198 insertions(+), 919 deletions(-)
Title: Binary Gene Operations for Genetic Algorithms
Description: Representation-dependent gene level operations of a
genetic algorithm with binary coded genes:
Initialization of random binary genes, several gene maps for
binary genes, several mutation operators, several crossover
operators with 1 and 2 kids, replication
pipelines for 1 and 2 kids, and, last but not least, function
factories for configuration.
See Goldberg, D. E. (1989, ISBN:0-201-15767-5).
For crossover operators, see
Syswerda, G. (1989, ISBN:1-55860-066-3),
Spears, W. and De Jong, K. (1991, ISBN:1-55860-208-9).
For mutation operators, see
Stanhope, S. A. and Daida, J. M. (1996, ISBN:0-18-201-031-7).
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaGaGene versions 1.0.0.4 dated 2025-07-28 and 1.0.0.5 dated 2025-08-22
DESCRIPTION | 8 +-- MD5 | 8 +-- NAMESPACE | 1 NEWS | 10 ++++ R/xegaOperatorPipelines.R | 98 +++++++++++++++++----------------------------- 5 files changed, 57 insertions(+), 68 deletions(-)
Title: Gene Operations for Real-Coded Genes
Description: Representation-dependent gene-level operations
for genetic and evolutionary algorithms with real-coded genes
are collected in this package. The common feature of the gene
operations is that all of them are useful for derivation-free
optimization algorithms. At the moment the package
implements initialization, mutation, crossover, and replication
operations for differential evolution as described in
Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005)
<doi:10.1007/3-540-31306-0>. In addition, several (more recent)
methods for determining the scale factor are provided.
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaDfGene versions 1.0.0.5 dated 2025-07-29 and 1.0.0.7 dated 2025-08-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 14 ++++++++++++-- R/xegaDfReplicate.R | 21 +++++++++++++-------- man/xegaDfReplicateGeneDE.Rd | 3 +++ man/xegaDfReplicateGeneDEPipeline.Rd | 2 +- 7 files changed, 40 insertions(+), 21 deletions(-)
Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'Openai', 'Gemini','Mistral' and local models via 'Ollama' into R workflows. The package supports text and media-based interactions, interactive message history, batch request APIs, and a tidy, pipeline-oriented interface for streamlined integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://aistudio.google.com/>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre],
Jia Zhang [ctb]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between tidyllm versions 0.3.4 dated 2025-03-27 and 0.3.5 dated 2025-08-22
DESCRIPTION | 6 MD5 | 70 ++++-- NAMESPACE | 8 NEWS.md | 106 +++++---- R/api_claude.R | 352 ++++++++++++++++++++++++++++++ R/api_gemini.R | 395 +++++++++++++++++++++++++++++++++- R/api_openai.R | 6 R/api_perplexity.R | 184 +++++++++------ inst/doc/tidyllm.Rmd | 2 inst/doc/tidyllm.html | 3 man/check_gemini_batch.Rd |only man/claude_chat.Rd | 5 man/claude_delete_file.Rd |only man/claude_file_metadata.Rd |only man/claude_list_files.Rd |only man/claude_upload_file.Rd |only man/fetch_gemini_batch.Rd |only man/gemini_chat.Rd | 2 man/list_gemini_batches.Rd |only man/openai_chat.Rd | 2 man/perplexity_chat.Rd | 72 ++++-- man/send_gemini_batch.Rd |only man/send_openai_batch.Rd | 2 tests/testthat/claude |only tests/testthat/deepseek |only tests/testthat/groq |only tests/testthat/list_openai_batches |only tests/testthat/mistral |only tests/testthat/mistral_embedding |only tests/testthat/ollama |only tests/testthat/ollama_embedding |only tests/testthat/openai |only tests/testthat/openai_embedding |only tests/testthat/openai_models |only tests/testthat/openai_schema_multiple |only tests/testthat/openai_schema_single |only tests/testthat/perplexity |only tests/testthat/test_api_claude.R | 56 ++++ tests/testthat/test_api_deepseek.R | 28 ++ tests/testthat/test_api_gemini.R | 83 ++++++- tests/testthat/test_api_groq.R | 45 +++ tests/testthat/test_api_mistral.R | 84 ++++++- tests/testthat/test_api_ollama.R | 59 ++++- tests/testthat/test_api_openai.R | 261 ++++++++++++++++++++++ tests/testthat/test_api_perplexity.R | 34 ++ tests/testthat/test_api_voyage.R |only tests/testthat/voyage_embedding_text |only vignettes/tidyllm.Rmd | 2 48 files changed, 1642 insertions(+), 225 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 0.11.0 dated 2025-08-21 and 0.11.1 dated 2025-08-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 3 ++- 3 files changed, 8 insertions(+), 7 deletions(-)
More information about teal.modules.clinical at CRAN
Permanent link
Title: Analysis of Functional and Phylogenetic Patterns in
Metacommunities
Description: Analysis of metacommunities based on functional traits and
phylogeny of the community components. The functions that are offered here
implement for the R environment methods that have been available in the
'SYNCSA' application written in C++ (by Valerio Pillar, available at
<http://ecoqua.ecologia.ufrgs.br/SYNCSA.html>).
Author: Vanderlei Julio Debastiani [aut, cre]
Maintainer: Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>
This is a re-admission after prior archival of version 1.3.4 dated 2020-01-09
Diff between SYNCSA versions 1.3.4 dated 2020-01-09 and 1.3.5 dated 2025-08-22
SYNCSA-1.3.4/SYNCSA/R/cor.mantel.R |only SYNCSA-1.3.4/SYNCSA/R/cor.matrix2.R |only SYNCSA-1.3.4/SYNCSA/R/cor.procrustes.R |only SYNCSA-1.3.4/SYNCSA/R/pro.matrix2.R |only SYNCSA-1.3.4/SYNCSA/R/procrustes.partial.R |only SYNCSA-1.3.5/SYNCSA/DESCRIPTION | 34 +- SYNCSA-1.3.5/SYNCSA/MD5 | 104 +++--- SYNCSA-1.3.5/SYNCSA/NAMESPACE | 19 - SYNCSA-1.3.5/SYNCSA/R/CollectNames.R | 4 SYNCSA-1.3.5/SYNCSA/R/ProgressBAR.R | 4 SYNCSA-1.3.5/SYNCSA/R/cent.norm.R | 4 SYNCSA-1.3.5/SYNCSA/R/coinertia.partial.syncsa.R |only SYNCSA-1.3.5/SYNCSA/R/coinertia.syncsa.R |only SYNCSA-1.3.5/SYNCSA/R/cor.matrix.R | 10 SYNCSA-1.3.5/SYNCSA/R/cor.matrix.bf.R |only SYNCSA-1.3.5/SYNCSA/R/cor.matrix.rao.R |only SYNCSA-1.3.5/SYNCSA/R/matmult.syncsa.R | 11 SYNCSA-1.3.5/SYNCSA/R/matrix.p.R | 30 + SYNCSA-1.3.5/SYNCSA/R/matrix.t.R | 26 - SYNCSA-1.3.5/SYNCSA/R/matrix.w.transformation.R |only SYNCSA-1.3.5/SYNCSA/R/matrix.x.R | 85 +++-- SYNCSA-1.3.5/SYNCSA/R/optimal.R | 73 +++- SYNCSA-1.3.5/SYNCSA/R/organize.syncsa.R | 42 ++ SYNCSA-1.3.5/SYNCSA/R/part.cor.R | 4 SYNCSA-1.3.5/SYNCSA/R/permut.row.matrix.R | 4 SYNCSA-1.3.5/SYNCSA/R/permut.vector.R | 4 SYNCSA-1.3.5/SYNCSA/R/print.syncsa.R | 18 - SYNCSA-1.3.5/SYNCSA/R/pro.matrix.bf.R |only SYNCSA-1.3.5/SYNCSA/R/pro.matrix.partial.R | 10 SYNCSA-1.3.5/SYNCSA/R/pro.matrix.rao.R |only SYNCSA-1.3.5/SYNCSA/R/procrustes.partial.syncsa.R |only SYNCSA-1.3.5/SYNCSA/R/procrustes.syncsa.R | 4 SYNCSA-1.3.5/SYNCSA/R/rao.diversity.R | 72 +++- SYNCSA-1.3.5/SYNCSA/R/rv.matrix.R |only SYNCSA-1.3.5/SYNCSA/R/rv.matrix.bf.R |only SYNCSA-1.3.5/SYNCSA/R/rv.matrix.partial.R |only SYNCSA-1.3.5/SYNCSA/R/rv.matrix.rao.R |only SYNCSA-1.3.5/SYNCSA/R/syncsa.R | 333 +++++++++++++-------- SYNCSA-1.3.5/SYNCSA/R/syncsa.obs.R |only SYNCSA-1.3.5/SYNCSA/R/var.dummy.R | 2 SYNCSA-1.3.5/SYNCSA/R/var.type.R | 6 SYNCSA-1.3.5/SYNCSA/inst/CITATION | 18 - SYNCSA-1.3.5/SYNCSA/man/ADRS.Rd | 6 SYNCSA-1.3.5/SYNCSA/man/CollectNames.Rd | 4 SYNCSA-1.3.5/SYNCSA/man/ProgressBAR.Rd | 4 SYNCSA-1.3.5/SYNCSA/man/cent.norm.Rd | 4 SYNCSA-1.3.5/SYNCSA/man/coinertia.syncsa.Rd |only SYNCSA-1.3.5/SYNCSA/man/cor.matrix.Rd | 106 +++++- SYNCSA-1.3.5/SYNCSA/man/matmult.syncsa.Rd | 9 SYNCSA-1.3.5/SYNCSA/man/matrix.p.Rd | 19 - SYNCSA-1.3.5/SYNCSA/man/matrix.t.Rd | 18 - SYNCSA-1.3.5/SYNCSA/man/matrix.w.transformation.Rd |only SYNCSA-1.3.5/SYNCSA/man/matrix.x.Rd | 22 - SYNCSA-1.3.5/SYNCSA/man/optimal.Rd | 6 SYNCSA-1.3.5/SYNCSA/man/organize.syncsa.Rd | 12 SYNCSA-1.3.5/SYNCSA/man/part.cor.Rd | 4 SYNCSA-1.3.5/SYNCSA/man/permut.row.matrix.Rd | 4 SYNCSA-1.3.5/SYNCSA/man/permut.vector.Rd | 4 SYNCSA-1.3.5/SYNCSA/man/procrustes.syncsa.Rd | 9 SYNCSA-1.3.5/SYNCSA/man/rao.diversity.Rd | 34 +- SYNCSA-1.3.5/SYNCSA/man/syncsa.Rd | 88 ++++- SYNCSA-1.3.5/SYNCSA/man/var.dummy.Rd | 2 SYNCSA-1.3.5/SYNCSA/man/var.type.Rd | 6 63 files changed, 866 insertions(+), 416 deletions(-)
Title: Sea Currents to Connectivity Transformation
Description: Transformation of sea currents to connectivity data. Two files of
horizontal and vertical currents flows are transformed into connectivity data
in the form of 'sfnetwork', shapefile, edge list and adjacency matrix. An
application example is shown at Nagkoulis et al. (2025)
<doi:10.1016/j.dib.2024.111268>.
Author: Nikolaos Nagkoulis [aut] ,
Christos Adam [aut, cre] ,
Ioannis G. Mamoutos [aut] ,
Antonios D. Mazaris [aut] ,
Stelios Katsanevakis [aut]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between SeaGraphs versions 0.1.2 dated 2025-05-30 and 0.1.3 dated 2025-08-22
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 8 ++++++++ README.md | 7 ++++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.Rmd | 8 -------- inst/doc/Introduction.html | 6 ------ vignettes/Introduction.Rmd | 8 -------- 9 files changed, 26 insertions(+), 35 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph] ,
Finnish Biodiversity Information Facility [cph] ,
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.9.10 dated 2025-04-15 and 0.9.11 dated 2025-08-22
DESCRIPTION | 20 MD5 | 71 NEWS.md | 8 R/finbif_occurrence_load.R | 162 R/sysdata.rda |binary README.md | 4 build/vignette.rds |binary man/finbif-package.Rd | 3 tests/fixtures/finbif_cache_db_timeout.yml | 157 tests/fixtures/finbif_cache_file_timeout.yml | 157 tests/fixtures/finbif_cache_timeout.yml | 157 tests/fixtures/finbif_check_taxa.yml | 45 tests/fixtures/finbif_collections.yml |14934 ++++----- tests/fixtures/finbif_informal_groups.yml | 22 tests/fixtures/finbif_last_mod1.yml | 26 tests/fixtures/finbif_last_mod2.yml | 26 tests/fixtures/finbif_last_mod3.yml | 26 tests/fixtures/finbif_metadata.yml | 781 tests/fixtures/finbif_occurrence.yml |16212 +++++----- tests/fixtures/finbif_occurrence_aggregate.yml | 136 tests/fixtures/finbif_occurrence_api_error.yml | 22 tests/fixtures/finbif_occurrence_compute_var_from_id_zero_rows.yml |15201 ++++----- tests/fixtures/finbif_occurrence_dates.yml | 255 tests/fixtures/finbif_occurrence_load.yml | 416 tests/fixtures/finbif_occurrence_print.yml | 70 tests/fixtures/finbif_occurrence_select_local_area.yml | 24 tests/fixtures/finbif_taxa.yml | 45 tests/testthat/HBF.12943.zip |only tests/testthat/_snaps/caching.md | 93 tests/testthat/_snaps/finbif_collections.md | 368 tests/testthat/_snaps/finbif_metadata.md | 4 tests/testthat/_snaps/finbif_occurrence.md | 111 tests/testthat/_snaps/finbif_occurrence_load.md | 609 tests/testthat/helper.R | 2 tests/testthat/laji-data-new-col.tsv | 1 tests/testthat/laji-data.tsv | 1 tests/testthat/test-finbif_occurrence_load.R | 19 37 files changed, 25583 insertions(+), 24605 deletions(-)
Title: Preprocessing Tools for Clinical Trial Data
Description: A collection of functions to preprocess data and organize
them in a format amenable to use by chevron.
Author: Liming Li [aut] ,
Benoit Falquet [aut] ,
Xiaoli Duan [ctb],
Pawel Rucki [ctb],
Joe Zhu [cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between dunlin versions 0.1.10 dated 2025-04-14 and 0.1.11 dated 2025-08-22
DESCRIPTION | 24 ++++++++++-------------- MD5 | 9 ++++++--- NAMESPACE | 1 + NEWS.md | 4 ++++ R/subject_level_flag.R |only man/subject_level_flag.Rd |only tests/testthat/test-subject_level_flag.R |only 7 files changed, 21 insertions(+), 17 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: CRAN Team [ctb, cre] ,
Duncan Temple Lang [aut] ,
Tomas Kalibera [ctb],
Ivan Krylov [ctb]
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between XML versions 3.99-0.18 dated 2025-01-01 and 3.99-0.19 dated 2025-08-22
DESCRIPTION | 15 +++++++++------ MD5 | 4 ++-- src/DocParse.c | 5 ++++- 3 files changed, 15 insertions(+), 9 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.13.1 dated 2025-04-01 and 1.13.3 dated 2025-08-22
DESCRIPTION | 6 MD5 | 86 - R/combineMultFilterNAimput.R | 6 R/convAASeq2mass.R | 7 R/corColumnOrder.R | 11 R/countNoOfCommonPeptides.R | 36 R/extrSpeciesAnnot.R | 2 R/extractTestingResults.R | 20 R/getUPS1acc.R | 46 R/inspectSpeciesIndic.R | 2 R/plotROC.R | 19 R/readAlphaPeptFile.R | 4 R/readDiaNNFile.R | 4 R/readDiaNNPeptides.R | 4 R/readFragpipeFile.R | 4 R/readIonbotPeptides.R | 244 +- R/readMassChroQFile.R | 4 R/readMaxQuantFile.R | 20 R/readMaxQuantPeptides.R | 169 - R/readProlineFile.R | 68 R/readProteomeDiscovererFile.R | 704 ++++---- R/readProteomeDiscovererPeptides.R | 142 - R/readSampleMetaData.R | 845 +++++++-- R/readWombatNormFile.R | 4 R/shortSoftwName.R | 18 R/summarizeForROC.R | 6 R/testRobustToNAimputation.R | 23 build/vignette.rds |binary inst/doc/wrProteoVignette1.R | 13 inst/doc/wrProteoVignette1.Rmd | 45 inst/doc/wrProteoVignette1.html | 327 +-- inst/doc/wrProteoVignetteUPS1.R | 121 - inst/doc/wrProteoVignetteUPS1.Rmd | 173 +- inst/doc/wrProteoVignetteUPS1.html | 2896 +++++++++++++++------------------- man/convAASeq2mass.Rd | 5 man/countNoOfCommonPeptides.Rd | 2 man/dot-checkSetupGroups.Rd | 13 man/dot-extrSpecPref.Rd | 5 man/getUPS1acc.Rd | 16 man/readProteomeDiscovererPeptides.Rd | 2 man/readSampleMetaData.Rd | 9 man/shortSoftwName.Rd | 14 vignettes/wrProteoVignette1.Rmd | 45 vignettes/wrProteoVignetteUPS1.Rmd | 173 +- 44 files changed, 3392 insertions(+), 2971 deletions(-)
Title: Test Surveys by Simulating Spatially-Correlated Populations
Description: Simulate age-structured populations that vary in space and time and
explore the efficacy of a range of built-in or user-defined sampling
protocols to reproduce the population parameters of the known population.
(See Regular et al. (2020) <doi:10.1371/journal.pone.0232822> for more
details).
Author: Paul Regular [aut, cre] ,
Jonathan Babyn [ctb],
Greg Robertson [ctb]
Maintainer: Paul Regular <Paul.Regular@dfo-mpo.gc.ca>
Diff between SimSurvey versions 0.1.6 dated 2023-09-19 and 0.1.7 dated 2025-08-22
SimSurvey-0.1.6/SimSurvey/R/pipe.R |only SimSurvey-0.1.6/SimSurvey/man/reexports.Rd |only SimSurvey-0.1.7/SimSurvey/DESCRIPTION | 18 - SimSurvey-0.1.7/SimSurvey/MD5 | 101 +++---- SimSurvey-0.1.7/SimSurvey/NAMESPACE | 3 SimSurvey-0.1.7/SimSurvey/NEWS.md | 6 SimSurvey-0.1.7/SimSurvey/R/data.R | 26 - SimSurvey-0.1.7/SimSurvey/R/helper.R | 10 SimSurvey-0.1.7/SimSurvey/R/icc.R | 12 SimSurvey-0.1.7/SimSurvey/R/make_grid.R | 35 +- SimSurvey-0.1.7/SimSurvey/R/plot_sim.R | 139 ++++----- SimSurvey-0.1.7/SimSurvey/R/run_strat.R | 138 ++++----- SimSurvey-0.1.7/SimSurvey/R/sim_dist.R | 157 +++++------ SimSurvey-0.1.7/SimSurvey/R/sim_dist_spde.R | 120 +++----- SimSurvey-0.1.7/SimSurvey/R/sim_pop.R | 223 ++++++++-------- SimSurvey-0.1.7/SimSurvey/R/sim_survey.R | 193 ++++++------- SimSurvey-0.1.7/SimSurvey/R/test_surveys.R | 150 +++++----- SimSurvey-0.1.7/SimSurvey/R/vis_sim.R | 22 - SimSurvey-0.1.7/SimSurvey/build/partial.rdb |only SimSurvey-0.1.7/SimSurvey/build/vignette.rds |binary SimSurvey-0.1.7/SimSurvey/inst/doc/custom_closures.R | 30 +- SimSurvey-0.1.7/SimSurvey/inst/doc/custom_closures.html | 11 SimSurvey-0.1.7/SimSurvey/man/convert_N.Rd | 11 SimSurvey-0.1.7/SimSurvey/man/dot-Q.Rd | 25 - SimSurvey-0.1.7/SimSurvey/man/error_stats.Rd | 14 - SimSurvey-0.1.7/SimSurvey/man/expand_surveys.Rd | 17 - SimSurvey-0.1.7/SimSurvey/man/group_lengths.Rd | 12 SimSurvey-0.1.7/SimSurvey/man/icc.Rd | 11 SimSurvey-0.1.7/SimSurvey/man/land.Rd | 4 SimSurvey-0.1.7/SimSurvey/man/make_grid.Rd | 31 +- SimSurvey-0.1.7/SimSurvey/man/make_mesh.Rd | 29 +- SimSurvey-0.1.7/SimSurvey/man/object_size.Rd | 9 SimSurvey-0.1.7/SimSurvey/man/plot_trend.Rd | 46 +-- SimSurvey-0.1.7/SimSurvey/man/round_sim.Rd | 6 SimSurvey-0.1.7/SimSurvey/man/run_strat.Rd | 45 +-- SimSurvey-0.1.7/SimSurvey/man/sim_R.Rd | 64 ++-- SimSurvey-0.1.7/SimSurvey/man/sim_abundance.Rd | 91 +++--- SimSurvey-0.1.7/SimSurvey/man/sim_ays_covar.Rd | 23 - SimSurvey-0.1.7/SimSurvey/man/sim_ays_covar_spde.Rd | 62 ++-- SimSurvey-0.1.7/SimSurvey/man/sim_distribution.Rd | 51 +-- SimSurvey-0.1.7/SimSurvey/man/sim_logistic.Rd | 11 SimSurvey-0.1.7/SimSurvey/man/sim_nlf.Rd | 114 ++++---- SimSurvey-0.1.7/SimSurvey/man/sim_parabola.Rd | 25 - SimSurvey-0.1.7/SimSurvey/man/sim_sets.Rd | 36 +- SimSurvey-0.1.7/SimSurvey/man/sim_survey.Rd | 86 +++--- SimSurvey-0.1.7/SimSurvey/man/sim_survey_parallel.Rd | 102 +++---- SimSurvey-0.1.7/SimSurvey/man/sim_vonB.Rd | 27 - SimSurvey-0.1.7/SimSurvey/man/strat_data.Rd | 20 - SimSurvey-0.1.7/SimSurvey/man/strat_error.Rd | 29 +- SimSurvey-0.1.7/SimSurvey/man/strat_means.Rd | 28 -- SimSurvey-0.1.7/SimSurvey/man/survey_grid.Rd | 20 - SimSurvey-0.1.7/SimSurvey/man/test_surveys.Rd | 164 +++++------ SimSurvey-0.1.7/SimSurvey/man/vis_sim.Rd | 21 - 53 files changed, 1314 insertions(+), 1314 deletions(-)
Title: Visualizing the Elements Within Bio-Sequences
Description: Visualizing the types and distribution of elements within
bio-sequences. At the same time, We have developed a geom layer,
geom_rrect(), that can generate rounded rectangles. No external references
are used in the development of this package.
Author: Shiqi Zhao [aut, cre, cph]
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Diff between BioVizSeq versions 1.0.3 dated 2025-04-11 and 1.0.4 dated 2025-08-22
DESCRIPTION | 9 - MD5 | 70 +++++++----- NAMESPACE | 113 ++++++++++---------- NEWS.md | 16 +- R/ProtParam_calc.R |only R/combi_plot2.R |only R/gff_plot.R | 166 +++++++++++++++++++++++++++++- R/globalvariables.R | 4 R/meme_plot.R | 4 R/plantcare_plot.R | 2 R/smart_plot.R | 14 +- README.md | 46 +++++++- inst/extdata/idpep2.fa |only inst/shinyapp/app.R | 15 ++ inst/shinyapp/global.R | 4 inst/shinyapp/script/mod_advplot.R | 118 +++++++++++++++------ inst/shinyapp/script/mod_advplot2.R | 93 ++++++++++++---- inst/shinyapp/script/mod_cddplot.R | 20 ++- inst/shinyapp/script/mod_geneinfo.R |only inst/shinyapp/script/mod_gffplot.R | 20 ++- inst/shinyapp/script/mod_memeplot.R | 20 ++- inst/shinyapp/script/mod_pfamplot.R | 20 ++- inst/shinyapp/script/mod_plantcareplot.R | 20 ++- inst/shinyapp/script/mod_plantcareplot2.R | 20 ++- inst/shinyapp/script/mod_plot.R | 22 ++- inst/shinyapp/script/mod_protparam.R |only inst/shinyapp/script/mod_smartplot.R | 20 ++- inst/shinyapp/www/html/README.html | 60 ++++++++-- man/ProtParam_calc.Rd |only man/combi_p2.Rd |only man/figures/README-adv_plot-1.png |binary man/figures/README-gff_one-1.png |binary man/figures/README-gff_step-1.png |binary man/figures/README-meme_one-1.png |binary man/figures/README-meme_step-1.png |binary man/figures/README-plantcare_one-1.png |binary man/figures/README-plantcare_step-1.png |binary man/gff_statistics.Rd |only man/meme_plot.Rd | 1 man/meme_seq.Rd | 1 40 files changed, 678 insertions(+), 220 deletions(-)
Title: Power Analyses for SEM
Description: Provides a-priori, post-hoc, and compromise power-analyses
for structural equation models (SEM).
Author: Morten Moshagen [aut, cre] ,
Martina Bader [aut]
Maintainer: Morten Moshagen <morten.moshagen@uni-ulm.de>
Diff between semPower versions 2.1.1 dated 2024-09-29 and 2.1.3 dated 2025-08-22
semPower-2.1.1/semPower/R/convenienceFunctions.R |only semPower-2.1.3/semPower/DESCRIPTION | 11 +- semPower-2.1.3/semPower/MD5 | 60 +++++++++------ semPower-2.1.3/semPower/NEWS | 16 +++- semPower-2.1.3/semPower/R/cf_arma.R |only semPower-2.1.3/semPower/R/cf_autoreg.R |only semPower-2.1.3/semPower/R/cf_bifactor.R |only semPower-2.1.3/semPower/R/cf_cfa.R |only semPower-2.1.3/semPower/R/cf_clpm.R |only semPower-2.1.3/semPower/R/cf_lav.R |only semPower-2.1.3/semPower/R/cf_lgcm.R |only semPower-2.1.3/semPower/R/cf_li.R |only semPower-2.1.3/semPower/R/cf_mediation.R |only semPower-2.1.3/semPower/R/cf_mi.R |only semPower-2.1.3/semPower/R/cf_path.R |only semPower-2.1.3/semPower/R/cf_regression.R |only semPower-2.1.3/semPower/R/cf_riclpm.R |only semPower-2.1.3/semPower/R/helperFunctions.R | 4 - semPower-2.1.3/semPower/R/onAttach.R | 2 semPower-2.1.3/semPower/R/output.R | 4 - semPower-2.1.3/semPower/R/semPower-package.R | 2 semPower-2.1.3/semPower/R/simulate.R | 14 ++- semPower-2.1.3/semPower/R/zUnitTests.R | 34 ++++++++ semPower-2.1.3/semPower/README.md | 2 semPower-2.1.3/semPower/build/vignette.rds |binary semPower-2.1.3/semPower/man/semPower.powerARMA.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerAutoreg.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerBifactor.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerCFA.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerCLPM.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerLGCM.Rd | 11 ++ semPower-2.1.3/semPower/man/semPower.powerLI.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerLav.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerMI.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerMediation.Rd | 61 +++++++++------- semPower-2.1.3/semPower/man/semPower.powerPath.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerRICLPM.Rd | 4 - semPower-2.1.3/semPower/man/semPower.powerRegression.Rd | 4 - 38 files changed, 174 insertions(+), 91 deletions(-)
Title: A Simple Framework to Analyse Population and Landscape Genetic
Data
Description: Provides beginner friendly framework to analyse population genetic
data. Based on 'adegenet' objects it uses 'knitr' to create comprehensive reports on spatial genetic data.
For detailed information how to use the package refer to the comprehensive
tutorials or visit <http://www.popgenreport.org/>.
Author: Bernd Gruber [aut, cre],
Aaron Adamack [aut]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between PopGenReport versions 3.1 dated 2023-10-11 and 3.1.3 dated 2025-08-22
DESCRIPTION | 10 +++--- MD5 | 50 +++++++++++++++++----------------- R/allel.rich.r | 2 - R/allele.dist.r | 2 - R/datasets.R | 2 - R/gd.kosman.r | 2 - R/gd.smouse.r | 2 - R/genleastcost.r | 4 +- R/landgenreport.r | 4 +- R/null.all.r | 2 - R/popgenreport.r | 21 ++++++-------- R/read.genetable.r | 10 +++--- build/vignette.rds |binary inst/doc/PopGenReportIntroduction.pdf |binary inst/doc/Tutorial_landgenreport.pdf |binary inst/doc/Tutorial_optimizer.pdf |binary man/allel.rich.Rd | 2 - man/allele.dist.Rd | 2 - man/bilby.Rd | 2 - man/gd.kosman.Rd | 2 - man/gd.smouse.Rd | 2 - man/genleastcost.Rd | 4 +- man/landgenreport.Rd | 4 +- man/null.all.Rd | 2 - man/popgenreport.Rd | 23 ++++++--------- man/read.genetable.Rd | 10 +++--- 26 files changed, 80 insertions(+), 84 deletions(-)
Title: Statistical Inference via Lancaster Correlation
Description: Implementation of the methods described in Holzmann, Klar (2024) <doi: 10.1111/sjos.12733>.
Lancaster correlation is a correlation coefficient which equals the
absolute value of the Pearson correlation for the bivariate normal distribution,
and is equal to or slightly less than the maximum correlation coefficient
for a variety of bivariate distributions. Rank and moment-based estimators and
corresponding confidence intervals are implemented, as well as independence
tests based on these statistics.
Author: Bernhard Klar [aut, cre] ,
Hajo Holzmann [aut],
Lucas Iglesias [ctb]
Maintainer: Bernhard Klar <bernhard.klar@kit.edu>
Diff between lancor versions 0.1.2 dated 2024-05-02 and 0.1.3 dated 2025-08-22
lancor-0.1.2/lancor/R/ace.test.R |only lancor-0.1.2/lancor/man/ace.test.Rd |only lancor-0.1.3/lancor/DESCRIPTION | 38 +++++++++------- lancor-0.1.3/lancor/MD5 | 27 +++++------ lancor-0.1.3/lancor/R/Sigma.est.R | 29 ++++++++++++ lancor-0.1.3/lancor/R/lcor.R | 64 ++++++++++++++++++++++++++++ lancor-0.1.3/lancor/R/lcor.ci.R | 47 ++++++++++++++++++++ lancor-0.1.3/lancor/R/lcor.comp.R | 41 ++++++++++++++++++ lancor-0.1.3/lancor/R/lcor.test.R | 35 +++++++++++++++ lancor-0.1.3/lancor/README.md | 62 ++++++++++++++++++++++++++- lancor-0.1.3/lancor/build |only lancor-0.1.3/lancor/man/Sigma.est.Rd | 35 +++++++++------ lancor-0.1.3/lancor/man/lcor.Rd | 65 ++++++++++++++++++++++------ lancor-0.1.3/lancor/man/lcor.ci.Rd | 79 ++++++++++++++++++++++------------- lancor-0.1.3/lancor/man/lcor.comp.Rd | 45 +++++++++++-------- lancor-0.1.3/lancor/man/lcor.test.Rd | 60 +++++++++++++++----------- 16 files changed, 496 insertions(+), 131 deletions(-)
Title: Continuous Time Meta-Analysis ('CoTiMA')
Description: The 'CoTiMA' package performs meta-analyses of correlation matrices of repeatedly measured variables taken from
studies that used different time intervals. Different time intervals between measurement occasions impose problems for
meta-analyses because the effects (e.g. cross-lagged effects) cannot be simply aggregated, for example, by means of common
fixed or random effects analysis. However, continuous time math, which is applied in 'CoTiMA', can be used to extrapolate or
intrapolate the results from all studies to any desired time lag. By this, effects obtained in studies that used different
time intervals can be meta-analyzed. 'CoTiMA' fits models to empirical data using the structural equation model (SEM) package
'ctsem', the effects specified in a SEM are related to parameters that are not directly included in the model (i.e.,
continuous time parameters; together, they represent the continuous time structural equation model, CTSEM). Statistical
model comparisons and significance [...truncated...]
Author: Christian Dormann [aut, cph],
Markus Homberg [aut, com, cre],
Olga Diener [ctb],
Christina Guthier [ctb],
Manuel Voelkle [ctb]
Maintainer: Markus Homberg <cotima@uni-mainz.de>
Diff between CoTiMA versions 0.8.0 dated 2024-04-25 and 1.0.2 dated 2025-08-22
CoTiMA-0.8.0/CoTiMA/build |only CoTiMA-0.8.0/CoTiMA/inst/doc |only CoTiMA-0.8.0/CoTiMA/vignettes |only CoTiMA-1.0.2/CoTiMA/DESCRIPTION | 25 CoTiMA-1.0.2/CoTiMA/MD5 | 312 ++++---- CoTiMA-1.0.2/CoTiMA/NAMESPACE | 6 CoTiMA-1.0.2/CoTiMA/R/ctmaAllInvFit.R | 12 CoTiMA-1.0.2/CoTiMA/R/ctmaBiG.R | 240 +++--- CoTiMA-1.0.2/CoTiMA/R/ctmaEmpCov.R | 4 CoTiMA-1.0.2/CoTiMA/R/ctmaEqual.R | 113 ++- CoTiMA-1.0.2/CoTiMA/R/ctmaFit.R | 363 ++++++--- CoTiMA-1.0.2/CoTiMA/R/ctmaGenData.R |only CoTiMA-1.0.2/CoTiMA/R/ctmaInit.R | 332 ++------- CoTiMA-1.0.2/CoTiMA/R/ctmaLabels.R | 2 CoTiMA-1.0.2/CoTiMA/R/ctmaMMtoCINT.R |only CoTiMA-1.0.2/CoTiMA/R/ctmaOTL.R |only CoTiMA-1.0.2/CoTiMA/R/ctmaOptimizeFit.R | 509 +++++++++++--- CoTiMA-1.0.2/CoTiMA/R/ctmaOptimizeInit.R | 2 CoTiMA-1.0.2/CoTiMA/R/ctmaPlotCtsemMod.R | 141 ++- CoTiMA-1.0.2/CoTiMA/R/ctmaPrep.R | 43 - CoTiMA-1.0.2/CoTiMA/R/ctmaScaleInits.R | 7 CoTiMA-1.0.2/CoTiMA/R/ctmaShapeRawData.R | 23 CoTiMA-1.0.2/CoTiMA/R/ctmaStanctArgs.R | 55 - CoTiMA-1.0.2/CoTiMA/data/A128.rda |binary CoTiMA-1.0.2/CoTiMA/data/A313.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMABiG_D_BO.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAFullFit_3.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAFullFit_6.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAFullFit_6_new.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAFullInv23Fit_6.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAFullInvEq23Fit_6.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAInitFit_3.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAInitFit_6.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAInitFit_6_NUTS.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAInitFit_6_new.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAInitFit_D_BO.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAMod1onFullFit_6.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAMod1onFullFit_6_cats12.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAMod2on23Fit_6.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAPart134Inv3Fit_6.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAPower_D_BO.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAStanctArgs.rda |only CoTiMA-1.0.2/CoTiMA/data/CoTiMAstudyList_3.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAstudyList_6.rda |binary CoTiMA-1.0.2/CoTiMA/data/CoTiMAstudyList_6_new.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageM1.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageM128.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageM18.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageM201.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageM313.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageM32.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageM4.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageSD1.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageSD128.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageSD18.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageSD201.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageSD313.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageSD32.rda |binary CoTiMA-1.0.2/CoTiMA/data/ageSD4.rda |binary CoTiMA-1.0.2/CoTiMA/data/alphas128.rda |binary CoTiMA-1.0.2/CoTiMA/data/alphas313.rda |binary CoTiMA-1.0.2/CoTiMA/data/burnout1.rda |binary 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|binary CoTiMA-1.0.2/CoTiMA/data/pairwiseN128.rda |binary CoTiMA-1.0.2/CoTiMA/data/pubList_8.rda |binary CoTiMA-1.0.2/CoTiMA/data/rawData228.rda |binary CoTiMA-1.0.2/CoTiMA/data/recodeVariables128.rda |binary CoTiMA-1.0.2/CoTiMA/data/results128.rda |binary CoTiMA-1.0.2/CoTiMA/data/sampleSize1.rda |binary CoTiMA-1.0.2/CoTiMA/data/sampleSize128.rda |binary CoTiMA-1.0.2/CoTiMA/data/sampleSize18.rda |binary CoTiMA-1.0.2/CoTiMA/data/sampleSize201.rda |binary CoTiMA-1.0.2/CoTiMA/data/sampleSize313.rda |binary CoTiMA-1.0.2/CoTiMA/data/sampleSize32.rda |binary CoTiMA-1.0.2/CoTiMA/data/sampleSize4.rda |binary CoTiMA-1.0.2/CoTiMA/data/source1.rda |binary CoTiMA-1.0.2/CoTiMA/data/source128.rda |binary CoTiMA-1.0.2/CoTiMA/data/source18.rda |binary CoTiMA-1.0.2/CoTiMA/data/source201.rda |binary CoTiMA-1.0.2/CoTiMA/data/source313.rda |binary CoTiMA-1.0.2/CoTiMA/data/source4.rda |binary CoTiMA-1.0.2/CoTiMA/data/targetVariables1.rda |binary CoTiMA-1.0.2/CoTiMA/data/targetVariables128.rda |binary CoTiMA-1.0.2/CoTiMA/data/targetVariables313.rda |binary CoTiMA-1.0.2/CoTiMA/data/targetVariables4.rda |binary CoTiMA-1.0.2/CoTiMA/data/variableNames128.rda |binary CoTiMA-1.0.2/CoTiMA/data/variableNames18.rda |binary CoTiMA-1.0.2/CoTiMA/data/variableNames201.rda |binary CoTiMA-1.0.2/CoTiMA/data/variableNames32.rda |binary CoTiMA-1.0.2/CoTiMA/inst/guide |only CoTiMA-1.0.2/CoTiMA/man/ctmaAllInvFit.Rd | 2 CoTiMA-1.0.2/CoTiMA/man/ctmaBiG.Rd | 8 CoTiMA-1.0.2/CoTiMA/man/ctmaFit.Rd | 9 CoTiMA-1.0.2/CoTiMA/man/ctmaGenData.Rd |only CoTiMA-1.0.2/CoTiMA/man/ctmaInit.Rd | 4 CoTiMA-1.0.2/CoTiMA/man/ctmaMMtoCINT.Rd |only CoTiMA-1.0.2/CoTiMA/man/ctmaOTL.Rd |only CoTiMA-1.0.2/CoTiMA/man/ctmaOptimizeFit.Rd | 25 CoTiMA-1.0.2/CoTiMA/man/ctmaOptimizeInit.Rd | 2 CoTiMA-1.0.2/CoTiMA/man/ctmaPlotCtsemMod.Rd | 16 CoTiMA-1.0.2/CoTiMA/man/ctmaPrep.Rd | 3 CoTiMA-1.0.2/CoTiMA/man/ctmaScaleInits.Rd | 7 162 files changed, 1375 insertions(+), 890 deletions(-)
Title: Estimation of the Number of Fatalities from Carcass Searches
Description: The number of bird or bat fatalities from collisions with buildings, towers or wind energy turbines can be estimated based on carcass searches and experimentally assessed carcass persistence times and searcher efficiency. Functions for estimating the probability that a bird or bat that died is found by a searcher are provided. Further functions calculate the posterior distribution of the number of fatalities based on the number of carcasses found and the estimated detection probability.
Author: Fraenzi Korner-Nievergelt [aut, cre],
Ivo Niermann [aut],
Oliver Behr [aut],
Matthew A. Etterson [aut],
Robert Brinkmann [aut],
Pius Korner [aut],
Barbara Hellriegel [aut],
Tobias Roth [aut],
Manuela M. P. Huso [aut],
Dan Dalthorp [aut]
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@oikostat.ch>
Diff between carcass versions 1.7 dated 2023-10-03 and 1.9 dated 2025-08-22
DESCRIPTION | 52 +++++++++++++++++++++++++++++++++++++++++------ MD5 | 6 ++--- man/persistence.prob.Rd | 4 --- man/search.efficiency.Rd | 4 +-- 4 files changed, 52 insertions(+), 14 deletions(-)
Title: Bayesian Evaluation of Variant Involvement in Mendelian Disease
Description: A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework - 'A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases', Greene et al 2017 <doi:10.1016/j.ajhg.2017.05.015>.
Author: Daniel Greene [aut, cre]
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between BeviMed versions 6.0 dated 2025-04-29 and 7.0 dated 2025-08-22
DESCRIPTION | 8 - MD5 | 34 ++--- R/RcppExports.R | 4 R/convenience.R | 53 +++------ R/functions.R | 32 ++++- R/generics.R | 17 -- inst/doc/Guide.Rnw | 5 inst/doc/Guide.pdf |binary inst/doc/Intro.html | 4 inst/doc/vcf.html | 4 man/bevimed.Rd | 3 man/bevimed_m.Rd | 3 man/bevimed_polytomous.Rd | 3 man/call_cpp.Rd | 6 + src/RcppExports.cpp | 10 + src/sampling.cpp | 266 +++++++++++++++++++++++++++++++++------------- src/sampling.h | 2 vignettes/Guide.Rnw | 5 18 files changed, 302 insertions(+), 157 deletions(-)
Title: Detection of Evolutionary Shifts in Both Optimal Value and
Variance
Description: Implements statistical methods for detecting evolutionary shifts
in both the optimal trait value (mean) and evolutionary diffusion variance.
The method uses an L1-penalized optimization framework to identify branches
where shifts occur, and the shift magnitudes. It also supports the
inclusion of measurement error. For more details, see Zhang, Ho, and Kenney (2023) <doi:10.48550/arXiv.2312.17480>.
Author: Wensha Zhang [aut, cre],
Lam Si Tung Ho [aut],
Toby Kenney [aut]
Maintainer: Wensha Zhang <wn209685@dal.ca>
Diff between ShiVa versions 1.0.1 dated 2025-07-22 and 1.0.2 dated 2025-08-22
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- R/ShiVa.R | 5 ++- README.md | 2 - inst/doc/ShiVa-example.Rmd | 2 - inst/doc/ShiVa-example.html | 65 +++++++++++++++++++++++--------------------- vignettes/ShiVa-example.Rmd | 2 - 7 files changed, 50 insertions(+), 44 deletions(-)
Title: Data Sets Useful for Modeling Examples
Description: Data sets used for demonstrating or testing model-related
packages are contained in this package.
Author: Max Kuhn [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between modeldata versions 1.5.0 dated 2025-07-31 and 1.5.1 dated 2025-08-22
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/leaf_id_flavia.R | 4 ++-- R/simulations.R | 6 +++--- data/leaf_id_flavia.rda |binary man/leaf_id_flavia.Rd | 4 ++-- man/sim_classification.Rd | 6 +++--- 8 files changed, 24 insertions(+), 20 deletions(-)
Title: Data Analysis for IP Addresses and Networks
Description: Classes and functions for working with IP (Internet Protocol)
addresses and networks, inspired by the Python 'ipaddress' module.
Offers full support for both IPv4 and IPv6 (Internet Protocol versions
4 and 6) address spaces. It is specifically designed to work well with
the 'tidyverse'.
Author: David Hall [aut, cre]
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between ipaddress versions 1.0.2 dated 2023-12-01 and 1.0.3 dated 2025-08-22
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/ip-data.html | 6 +++--- inst/doc/recipes.html | 28 ++++++++++++++-------------- tests/testthat/_snaps/country_networks.md | 2 +- tests/testthat/test-country_networks.R | 18 +++++++++++++++++- tests/testthat/test-ip_to_hostname.R | 2 +- 9 files changed, 53 insertions(+), 33 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie [aut, cre],
Balasubramanian Narasimhan [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.22-5 dated 2024-09-12 and 1.22-6 dated 2025-08-22
gam-1.22-5/gam/tests/testthat/test_results/gam-1.20-results.RDS |only gam-1.22-6/gam/DESCRIPTION | 8 +- gam-1.22-6/gam/MD5 | 8 +- gam-1.22-6/gam/src/gam_init.c | 8 ++ gam-1.22-6/gam/tests/testthat/test_example.R | 28 +++++----- gam-1.22-6/gam/tests/testthat/test_results/gam-results.RDS |only 6 files changed, 30 insertions(+), 22 deletions(-)
Title: Pharmacometric Modeling
Description: Facilitate Pharmacokinetic (PK) and Pharmacodynamic (PD) modeling
and simulation with powerful tools for Nonlinear Mixed-Effects (NLME)
modeling. The package provides access to the same advanced Maximum Likelihood
algorithms used by the NLME-Engine in the Phoenix platform. These tools support
a range of analyses, from parametric methods to individual and pooled data, and
support integrated use within the Pirana pharmacometric workbench
<doi:10.1002/psp4.70067>. Execution is supported both locally or on
remote machines.
Author: James Craig [aut, cre],
Michael Tomashevskiy [aut],
Vitalii Nazarov [aut],
Shuhua Hu [ctb],
Soltanshahi Fred [aut],
Certara USA, Inc. [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Diff between Certara.RsNLME versions 3.0.1 dated 2024-11-20 and 3.1.0 dated 2025-08-22
Certara.RsNLME-3.0.1/Certara.RsNLME/man/DosePoint-class.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/NlmeModelAbsorption-class.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/NlmeModelParameterization-class.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/NlmeModelType-class.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/NlmeRandParamsMapping-class.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/NlmeRandomEffectBlock.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/NlmeRandomEffectValues-class.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/NlmeStructuralParameter-class.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/SecondaryParameter-class.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/addTablesToColumnMapping.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/generatePMLModel.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/initializeRandomEffectsBlock.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/randomOccasionalBlockStatement.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/structuralParam-set.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/man/updateErrorModel.Rd |only Certara.RsNLME-3.0.1/Certara.RsNLME/tests/testthat/_snaps/covar.md |only Certara.RsNLME-3.1.0/Certara.RsNLME/DESCRIPTION | 13 Certara.RsNLME-3.1.0/Certara.RsNLME/MD5 | 285 - Certara.RsNLME-3.1.0/Certara.RsNLME/NAMESPACE | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/R/GenerateParamsfile.R | 119 Certara.RsNLME-3.1.0/Certara.RsNLME/R/NlmeColumnMapping.r | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/R/NlmeCovariateParameter.r | 411 + Certara.RsNLME-3.1.0/Certara.RsNLME/R/NlmeModelAbsorption.R | 1 Certara.RsNLME-3.1.0/Certara.RsNLME/R/NlmeModelParameterization.R | 1 Certara.RsNLME-3.1.0/Certara.RsNLME/R/NlmeModelType.R | 1 Certara.RsNLME-3.1.0/Certara.RsNLME/R/NlmeParallelHost.R | 99 Certara.RsNLME-3.1.0/Certara.RsNLME/R/NlmeRandParamsMapping.R | 1 Certara.RsNLME-3.1.0/Certara.RsNLME/R/NlmeRandomEffectBlock.r | 6 Certara.RsNLME-3.1.0/Certara.RsNLME/R/RandomEffectsMethods.R | 58 Certara.RsNLME-3.1.0/Certara.RsNLME/R/SimpleNlmeJob.R | 30 Certara.RsNLME-3.1.0/Certara.RsNLME/R/acceptAllEffects.R | 20 Certara.RsNLME-3.1.0/Certara.RsNLME/R/addInfusion.R | 13 Certara.RsNLME-3.1.0/Certara.RsNLME/R/addLabel.R | 12 Certara.RsNLME-3.1.0/Certara.RsNLME/R/addTablesToColumnMapping.R | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/R/bootstrap.r | 4 Certara.RsNLME-3.1.0/Certara.RsNLME/R/colMapping.R | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/R/copyModel.R | 24 Certara.RsNLME-3.1.0/Certara.RsNLME/R/covariateModel.R | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/R/covariateNames.R | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/R/create_model_from_metamodel.R | 5 Certara.RsNLME-3.1.0/Certara.RsNLME/R/create_model_info.R | 4 Certara.RsNLME-3.1.0/Certara.RsNLME/R/dosing.r | 58 Certara.RsNLME-3.1.0/Certara.RsNLME/R/editModel.R | 8 Certara.RsNLME-3.1.0/Certara.RsNLME/R/engine_params.r | 2084 ++++++---- 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Certara.RsNLME-3.1.0/Certara.RsNLME/R/shotgunSearch.R | 10 Certara.RsNLME-3.1.0/Certara.RsNLME/R/sortfit.R | 8 Certara.RsNLME-3.1.0/Certara.RsNLME/R/stepwiseSearch.R | 14 Certara.RsNLME-3.1.0/Certara.RsNLME/R/structural_param.r | 10 Certara.RsNLME-3.1.0/Certara.RsNLME/R/vpc.r | 103 Certara.RsNLME-3.1.0/Certara.RsNLME/inst/extdata/mmdlInfusionTest/nlmeargs.txt | 21 Certara.RsNLME-3.1.0/Certara.RsNLME/man/NlmeEngineExtraParams-class.Rd | 265 + Certara.RsNLME-3.1.0/Certara.RsNLME/man/NlmeEngineExtraParams.Rd |only Certara.RsNLME-3.1.0/Certara.RsNLME/man/NlmeJobStatus.Rd | 50 Certara.RsNLME-3.1.0/Certara.RsNLME/man/NlmeParallelHost-class.Rd | 52 Certara.RsNLME-3.1.0/Certara.RsNLME/man/NlmePmlModel-class.Rd | 8 Certara.RsNLME-3.1.0/Certara.RsNLME/man/NlmeStrucParamStyle.Rd | 2 Certara.RsNLME-3.1.0/Certara.RsNLME/man/NlmeVpcParams-class.Rd | 29 Certara.RsNLME-3.1.0/Certara.RsNLME/man/RunProfilePertubation.Rd | 53 Certara.RsNLME-3.1.0/Certara.RsNLME/man/acceptAllEffects.Rd | 20 Certara.RsNLME-3.1.0/Certara.RsNLME/man/addADDL.Rd | 14 Certara.RsNLME-3.1.0/Certara.RsNLME/man/addCovariate.Rd | 38 Certara.RsNLME-3.1.0/Certara.RsNLME/man/addDoseCycle.Rd | 9 Certara.RsNLME-3.1.0/Certara.RsNLME/man/addExtraDef.Rd | 5 Certara.RsNLME-3.1.0/Certara.RsNLME/man/addInfusion.Rd | 13 Certara.RsNLME-3.1.0/Certara.RsNLME/man/addLabel.Rd | 12 Certara.RsNLME-3.1.0/Certara.RsNLME/man/addMDV.Rd | 9 Certara.RsNLME-3.1.0/Certara.RsNLME/man/addSecondary.Rd | 7 Certara.RsNLME-3.1.0/Certara.RsNLME/man/addSteadyState.Rd | 12 Certara.RsNLME-3.1.0/Certara.RsNLME/man/bootstrap.Rd | 4 Certara.RsNLME-3.1.0/Certara.RsNLME/man/cancelJob.Rd | 66 Certara.RsNLME-3.1.0/Certara.RsNLME/man/colMapping.Rd | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/man/copyModel.Rd | 24 Certara.RsNLME-3.1.0/Certara.RsNLME/man/covariateModel.Rd | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/man/covariateNames.Rd | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/man/createModelInfo.Rd | 4 Certara.RsNLME-3.1.0/Certara.RsNLME/man/create_model_from_metamodel.Rd | 5 Certara.RsNLME-3.1.0/Certara.RsNLME/man/dataMapping.Rd | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/man/doseNames.Rd | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/man/editModel.Rd | 8 Certara.RsNLME-3.1.0/Certara.RsNLME/man/engineParams.Rd | 375 + Certara.RsNLME-3.1.0/Certara.RsNLME/man/extraDoseLines.Rd | 4 Certara.RsNLME-3.1.0/Certara.RsNLME/man/extraDoseNames.Rd | 4 Certara.RsNLME-3.1.0/Certara.RsNLME/man/extract_mmdl.Rd | 4 Certara.RsNLME-3.1.0/Certara.RsNLME/man/fitmodel.Rd | 7 Certara.RsNLME-3.1.0/Certara.RsNLME/man/fixedEffect.Rd | 6 Certara.RsNLME-3.1.0/Certara.RsNLME/man/getRandomEffectNames.Rd | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/man/getThetas.Rd | 11 Certara.RsNLME-3.1.0/Certara.RsNLME/man/hostParams.Rd | 67 Certara.RsNLME-3.1.0/Certara.RsNLME/man/initFixedEffects.Rd | 99 Certara.RsNLME-3.1.0/Certara.RsNLME/man/listCovariateEffectNames.Rd | 16 Certara.RsNLME-3.1.0/Certara.RsNLME/man/loadModel.Rd | 22 Certara.RsNLME-3.1.0/Certara.RsNLME/man/modelVariableNames.Rd | 2 Certara.RsNLME-3.1.0/Certara.RsNLME/man/obtain_NLMELicense.Rd | 14 Certara.RsNLME-3.1.0/Certara.RsNLME/man/parse_NLMEHosts.Rd | 12 Certara.RsNLME-3.1.0/Certara.RsNLME/man/pkmodel.Rd | 3 Certara.RsNLME-3.1.0/Certara.RsNLME/man/print.NlmeParallelHost.Rd | 16 Certara.RsNLME-3.1.0/Certara.RsNLME/man/print.NlmePmlModel.Rd | 4 Certara.RsNLME-3.1.0/Certara.RsNLME/man/print.SimpleNlmeJob.Rd | 26 Certara.RsNLME-3.1.0/Certara.RsNLME/man/profilePertubate.Rd | 55 Certara.RsNLME-3.1.0/Certara.RsNLME/man/randomEffect.Rd | 8 Certara.RsNLME-3.1.0/Certara.RsNLME/man/removeCovariate.Rd | 10 Certara.RsNLME-3.1.0/Certara.RsNLME/man/remove_NLMELicense.Rd | 11 Certara.RsNLME-3.1.0/Certara.RsNLME/man/run_metamodel.Rd | 15 Certara.RsNLME-3.1.0/Certara.RsNLME/man/saveModel.Rd | 17 Certara.RsNLME-3.1.0/Certara.RsNLME/man/saveUpdatedMetamodel.Rd | 68 Certara.RsNLME-3.1.0/Certara.RsNLME/man/shotgunSearch.Rd | 10 Certara.RsNLME-3.1.0/Certara.RsNLME/man/simmodel.Rd | 15 Certara.RsNLME-3.1.0/Certara.RsNLME/man/sortfit.Rd | 8 Certara.RsNLME-3.1.0/Certara.RsNLME/man/stepwiseSearch.Rd | 14 Certara.RsNLME-3.1.0/Certara.RsNLME/man/vpcmodel.Rd | 61 Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/2sort_Ind_unix/sortby/residuals.csv | 224 - Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/2sort_Ind_windows/sortby/residuals.csv | 224 - Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/NlmeParallelHost.md | 2 Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/add_multi_occ_no_ranef_occ2 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/add_multi_occ_no_ranef_occ3 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/after_occ2 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/after_occ3 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/block_option_no |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/block_remove_4 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/block_remove_cl2 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/block_remove_v2 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/block_remove_v2_v3 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/diag_option_no |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/diag_remove_4 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/diag_remove_single_v2 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/diag_remove_v2_v3 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/diag_remove_v3_cl3 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/extract_mmdl/multArgs.txt1 | 8 Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/extract_mmdl/multArgs.txt2 | 8 Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/extract_mmdl/nlmeargs.txt | 6 Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/no_extra_plus_on_no_ranef |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/no_orphan_plus_multi_param |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/no_orphan_plus_remove_occ1 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/no_orphan_plus_remove_occ2 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/option_no_block |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/option_no_diag |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/remove_cl_from_block |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/remove_consecutive_no_ranef_v2_v3 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/remove_consecutive_no_ranef_v_v2 |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/remove_v2_from_block |only Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/_snaps/writeColumnMapping.md | 245 - Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/test_NlmeEngineExtraparams.r | 702 ++- Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/test_NlmeParallelHost.r | 2 Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/test_covar.r | 687 +++ Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/test_random_effects.r | 11 Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/test_simple_estimation.r | 2 Certara.RsNLME-3.1.0/Certara.RsNLME/tests/testthat/test_vpc.r | 2 164 files changed, 6306 insertions(+), 3336 deletions(-)
More information about Certara.RsNLME at CRAN
Permanent link
Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut],
Egill Fridgeirsson [aut],
Martijn Schuemie [aut, cre],
Marc A. Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between Andromeda versions 1.1.0 dated 2025-07-24 and 1.1.1 dated 2025-08-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/Object.R | 1 + inst/doc/UsingAndromeda.html | 6 +++--- 5 files changed, 20 insertions(+), 11 deletions(-)
Title: Structured Messages and Options
Description: Provides a structured framework for consistent user
communication and configuration management for package developers.
Author: Aksel Thomsen [aut, cre],
Mathias Lerbech Jeppesen [aut],
Cervan Girard [aut],
Kristian Troejelsgaard [aut],
Lovemore Gakava [aut],
Steffen Falgreen Larsen [aut],
Vladimir Obucina [aut],
Novo Nordisk A/S [cph]
Maintainer: Aksel Thomsen <oath@novonordisk.com>
Diff between zephyr versions 0.1.2 dated 2025-03-13 and 0.1.3 dated 2025-08-22
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/options.R | 41 +++++++++++++++++++++++++++++++---------- README.md | 3 ++- man/get_option.Rd | 13 ++++++++++++- tests/testthat/test-options.R | 16 +++++++++++++++- 7 files changed, 74 insertions(+), 22 deletions(-)
Title: Easily Create Production-Ready Rich Text Format (RTF) Tables and
Figures
Description: Create production-ready Rich Text Format (RTF) tables and figures
with flexible format.
Author: Yilong Zhang [aut],
Siruo Wang [aut],
Simiao Ye [aut],
Fansen Kong [aut],
Brian Lang [aut],
Benjamin Wang [aut, cre],
Nan Xiao [ctb],
Madhusudhan Ginnaram [ctb],
Ruchitbhai Patel [ctb],
Huei-Ling Chen [ctb],
Peikun Wu [ctb],
Uday Preetham Palukuru [c [...truncated...]
Maintainer: Benjamin Wang <benjamin.wang@merck.com>
Diff between r2rtf versions 1.1.4 dated 2025-03-11 and 1.2.0 dated 2025-08-22
DESCRIPTION | 6 - MD5 | 59 +++++----- NEWS.md | 13 ++ R/as_rtf_paragraph.R | 6 - R/content_create.R | 25 +++- R/conversion.R | 87 ++++++++++------ R/data.R | 6 - R/dictionary.R | 30 ++++- R/obj_rtf_text.R | 4 R/rtf_colheader.R | 10 + R/rtf_encode_figure.R | 2 R/rtf_encode_table.R | 2 R/rtf_footnote.R | 6 - R/rtf_page.R | 40 ++++--- R/rtf_source.R | 6 - R/rtf_strwidth.R | 5 R/rtf_table_content.R | 4 R/rtf_text.R | 6 - R/rtf_title.R | 20 ++- inst/doc/r2rtf-cran.html | 4 man/r2rtf_HAMD17.Rd | 6 - man/rtf_colheader.Rd | 3 man/rtf_page.Rd | 5 man/rtf_subline.Rd | 3 man/rtf_title.Rd | 3 tests/testthat/test-independent-testing-conversion.R | 2 tests/testthat/test-independent-testing-dictionary.R | 19 +++ tests/testthat/test-independent-testing-i18n.R |only tests/testthat/test-independent-testing-rtf_colheader.R | 14 ++ tests/testthat/test-independent-testing-rtf_page.R | 17 +++ tests/testthat/test-independent-testing-rtf_title.R | 21 +++ 31 files changed, 322 insertions(+), 112 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] ,
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] ,
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] ,
Timothy Waterhouse [ctb] ,
Kyle Meyer [ctb],
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 1.5.2 dated 2024-10-18 and 1.6.1 dated 2025-08-22
DESCRIPTION | 33 +++++++------ MD5 | 79 +++++++++++++++++-------------- NAMESPACE | 10 +++ NEWS.md | 86 ++++++++++++++++++++++++++++++++++ R/Aaaa.R | 17 ++++++ R/class_mrgmod.R | 23 ++++++++- R/compile.R | 4 - R/custom-tol.R |only R/handle_spec_block.R | 18 +++++++ R/matlist.R | 40 ++++++++------- R/modspec.R | 10 --- R/mread.R | 24 ++++----- R/mwrite.R | 2 R/print.R | 12 +++- R/update.R | 19 +------ inst/base/databox_cpp.h | 14 +++-- inst/base/modelheader.h | 2 inst/base/mrgsolv.h | 12 ++-- inst/base/mrgsolve-evtools-regimen.h | 13 +++-- inst/base/mrgsolve-evtools.h | 16 ++++++ inst/include/datarecord.h | 2 inst/include/mrgsolve.h | 2 man/as.list-mrgmod-method.Rd | 4 + man/custom_tol.Rd |only man/get_tol.Rd |only man/matlist_ops.Rd | 6 +- man/mrgmod-class.Rd | 8 +++ man/reset_tol.Rd |only man/use_custom_tol.Rd |only src/LSODA.cpp | 28 ++++++----- src/LSODA.h | 7 +- src/datarecord.cpp | 47 +++++++++++++----- src/devtran.cpp | 28 ++++++++--- src/lsoda_functions.h | 35 +++++++++++++ src/mrgsolve.cpp | 9 ++- src/odeproblem.cpp | 8 +-- tests/testthat/nm/1005-omega-skip.mod |only tests/testthat/test-as_list_mrgmod.R | 6 +- tests/testthat/test-modspec.R | 21 ++++++++ tests/testthat/test-mread.R | 10 +++ tests/testthat/test-mwrite.R | 43 ++++++++++++++++- tests/testthat/test-nmxml.R | 8 +++ tests/testthat/test-opts.R | 1 tests/testthat/test-tolerances.R |only 44 files changed, 531 insertions(+), 176 deletions(-)
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax, using the approach presented in Cheung and Cheung
(2024) <doi:10.3758/s13428-023-02224-z>. Can also form bootstrap
confidence intervals by doing bootstrapping only once and reusing the
bootstrap estimates in all subsequent computations. Supports bootstrap
confidence intervals for standardized (partially or completely) indirect
effects, conditional effects, and conditional indirect effects as described
in Cheung (2009) <doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui,
and Vong (2022) <doi:10.1037/hea0001188>. Model fitting can be done by
structural equation modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut] ,
Rong Wei Sun [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.2.9 dated 2025-06-21 and 0.3.1 dated 2025-08-22
DESCRIPTION | 21 MD5 | 102 - NAMESPACE | 4 NEWS.md | 46 R/boot2est_lavaan.R | 40 R/cond_indirect.R | 17 R/find_product.R | 18 R/get_prod.R | 12 R/index_mome.R | 13 R/indirect.R | 17 R/lav_data_used.R | 18 R/lavaan2lm_list.R | 8 R/lavaan_helpers.R | 32 R/print_indirect_list.R | 42 R/q_functions_helpers.R | 114 + R/q_functions_helpers_lavaan.R |only R/q_mediation.R | 1280 +++++++++++++++++---- R/q_mediation_plot.R |only R/q_mediation_plot_helpers.R |only README.md | 2 inst/doc/do_boot.Rmd | 20 inst/doc/do_boot.html | 24 inst/doc/do_mc.Rmd | 2 inst/doc/do_mc.html | 4 inst/doc/do_mc_lavaan_mi.Rmd | 2 inst/doc/do_mc_lavaan_mi.html | 4 inst/doc/manymome.Rmd | 2 inst/doc/manymome.html | 4 inst/doc/med_lav.Rmd | 7 inst/doc/med_lav.html | 23 inst/doc/med_lm.Rmd | 7 inst/doc/med_lm.html | 51 inst/doc/mod_levels.html | 4 inst/doc/mome_lm.Rmd | 2 inst/doc/mome_lm.html | 4 man/cond_indirect.Rd | 11 man/get_prod.Rd | 8 man/index_of_mome.Rd | 7 man/indirect_i.Rd | 8 man/manymome-package.Rd | 5 man/plot.q_mediation.Rd |only man/q_mediation.Rd | 289 ++++ tests/testthat/test_find_product_skip_indicators.R |only tests/testthat/test_q_fct_mediation_model.R |only tests/testthat/test_q_fct_mediation_plot_sem.R |only tests/testthat/test_q_fct_mediation_sem.R |only tests/testthat/test_q_fct_mediation_sem_lm2lav.R |only tests/testthat/test_q_fct_mediation_sem_mc.R |only vignettes/articles/med_mg.Rmd | 7 vignettes/articles/q_mediation.Rmd | 204 ++- vignettes/do_boot.Rmd | 20 vignettes/do_mc.Rmd | 2 vignettes/do_mc_lavaan_mi.Rmd | 2 vignettes/manymome.Rmd | 2 vignettes/med_lav.Rmd | 7 vignettes/med_lm.Rmd | 7 vignettes/mome_lm.Rmd | 2 57 files changed, 2021 insertions(+), 506 deletions(-)
Title: Local Partial Autocorrelation Function Estimation for Locally
Stationary Wavelet Processes
Description: Provides the method for computing the local partial autocorrelation function for locally stationary wavelet time series from Killick, Knight, Nason, Eckley (2020) <doi:10.1214/20-EJS1748>.
Author: Rebecca Killick [aut, cre],
Guy Nason [aut],
Marina Knight [aut],
Matt Nunes [aut],
Idris Eckley [ctb]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between lpacf versions 1.0.1 dated 2023-05-12 and 1.0.2 dated 2025-08-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ man/lpacf-package.Rd | 4 ++-- man/lpacf.Epan.Rd | 2 +- man/lpacf.Rd | 2 +- man/print.lpacf.Rd | 1 + man/summary.lpacf.Rd | 20 ++++++++++++++++++-- 8 files changed, 38 insertions(+), 17 deletions(-)
Title: Less Code, More Results
Description: Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis (facet) graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.4.4 dated 2025-06-16 and 4.4.5 dated 2025-08-22
lessR-4.4.4/lessR/R/sort_by.R |only lessR-4.4.4/lessR/man/sort_by.Rd |only lessR-4.4.5/lessR/DESCRIPTION | 10 lessR-4.4.5/lessR/MD5 | 60 - lessR-4.4.5/lessR/NAMESPACE | 7 lessR-4.4.5/lessR/NEWS.md | 57 + lessR-4.4.5/lessR/R/Plot.R | 283 ++++--- lessR-4.4.5/lessR/R/STL.R | 89 +- lessR-4.4.5/lessR/R/date.infer.R |only lessR-4.4.5/lessR/R/order_by.R | 8 lessR-4.4.5/lessR/R/pc.main.R | 1 lessR-4.4.5/lessR/R/plt.by.legend.R | 11 lessR-4.4.5/lessR/R/plt.forecast.R | 838 +++++++++++++++------- lessR-4.4.5/lessR/R/plt.lattice.R | 10 lessR-4.4.5/lessR/R/plt.main.R | 51 - lessR-4.4.5/lessR/R/plt.time.R | 17 lessR-4.4.5/lessR/R/style.R | 2 lessR-4.4.5/lessR/R/train_test.R | 12 lessR-4.4.5/lessR/R/zzz.R | 51 + lessR-4.4.5/lessR/R/zzz_ts.R |only lessR-4.4.5/lessR/build/vignette.rds |binary lessR-4.4.5/lessR/data/dataStockPrice.rda |binary lessR-4.4.5/lessR/inst/doc/intro.R | 6 lessR-4.4.5/lessR/inst/doc/intro.Rmd | 11 lessR-4.4.5/lessR/inst/doc/intro.html | 439 ++++++----- lessR-4.4.5/lessR/inst/shiny_apps/BarChart/app.R | 26 lessR-4.4.5/lessR/inst/shiny_apps/Histogram/app.R | 64 - lessR-4.4.5/lessR/man/PieChart.Rd | 4 lessR-4.4.5/lessR/man/Plot.Rd | 195 +++-- lessR-4.4.5/lessR/man/STL.Rd | 42 - lessR-4.4.5/lessR/man/reshape_long.Rd | 1 lessR-4.4.5/lessR/man/train_test.Rd | 17 lessR-4.4.5/lessR/vignettes/intro.Rmd | 11 33 files changed, 1496 insertions(+), 827 deletions(-)