Title: Threshold Indicator Taxa Analysis
Description: Uses indicator species scores across binary partitions of
a sample set to detect congruence in taxon-specific changes of abundance
and occurrence frequency along an environmental gradient as evidence of
an ecological community threshold. Relevant references include Baker and King
(2010) <doi:10.1111/j.2041-210X.2009.00007.x>, King and Baker (2010)
<doi:10.1899/09-144.1>, and Baker and King (2013) <doi:10.1899/12-142.1>.
Author: Matthew E. Baker [aut, cph] ,
Ryan S. King [aut, cph] ,
David Kahle [aut, cph, cre]
Maintainer: David Kahle <david@kahle.io>
Diff between TITAN2 versions 2.4.3 dated 2023-11-14 and 2.4.4 dated 2025-10-16
DESCRIPTION | 19 +++++++++++-------- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + R/TITAN2.R | 5 ++--- R/plot_cps.R | 2 +- R/plot_taxa_ridges.R | 33 ++++++++++++++++++--------------- README.md | 8 ++++---- build/vignette.rds |binary inst/doc/titan2-intro.R | 10 +++++----- inst/doc/titan2-intro.pdf |binary man/TITAN2.Rd | 3 +-- man/plot_taxa_ridges.Rd | 18 +++++++++--------- 12 files changed, 63 insertions(+), 58 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.8.0 dated 2025-09-23 and 0.8.1 dated 2025-10-16
DESCRIPTION | 6 MD5 | 44 ++-- NAMESPACE | 1 R/barplot.R | 15 - R/boxviolinplot.R | 434 +++++++++++++++++++++++++++++++++++------- R/dotplot.R | 5 R/heatmap.R | 305 +++++++++++++++++++++-------- R/jitterplot.R | 21 -- R/radarplot.R | 72 ++++++ R/volcanoplot.R | 10 man/BoxViolinPlot-internal.Rd | 8 man/BoxViolinPlotAtomic.Rd | 8 man/Heatmap.Rd | 35 ++- man/HeatmapAtomic.Rd | 9 man/JitterPlotAtomic.Rd | 4 man/RadarPlotAtomic.Rd | 6 man/VolcanoPlot.Rd | 4 man/VolcanoPlotAtomic.Rd | 3 man/boxviolinplot.Rd | 35 +++ man/heatmap-anno.Rd | 4 man/heatmap-layer.Rd | 23 ++ man/jitterplot.Rd | 6 man/radarplot.Rd | 9 23 files changed, 834 insertions(+), 233 deletions(-)
Title: Estimating Bivariate Dependency from Marginal Data
Description: Provides statistical methods for estimating bivariate dependency (correlation) from marginal summary statistics across multiple studies.
The package supports three modules: (1) bivariate correlation estimation for binary outcomes, (2) bivariate correlation estimation for continuous outcomes, and
(3) estimation of component-wise means and variances under a conditional two-component Gaussian mixture model for a continuous variable stratified by a binary class label.
These methods enable privacy-preserving joint estimation when individual-level data are unavailable.
The approaches are detailed in Shang, Tsao, and Zhang (2025a) <doi:10.48550/arXiv.2505.03995> and Shang, Tsao, and Zhang (2025b) <doi:10.48550/arXiv.2508.02057>.
Author: Longwen Shang [aut, cre],
Min Tsao [aut],
Xuekui Zhang [aut]
Maintainer: Longwen Shang <shanglongwen0918@gmail.com>
Diff between ebdm versions 1.1.0 dated 2025-07-17 and 3.0.0 dated 2025-10-16
DESCRIPTION | 16 ++++++++-------- MD5 | 17 +++++++++++------ NAMESPACE | 4 ++++ R/bin_example.R | 2 +- R/cor_bin.R | 10 ++++++++++ R/cor_cont.R | 8 ++++++++ R/est_mixture.R |only R/mixture_example.R |only data/mixture_example.rda |only man/bin_example.Rd | 2 +- man/est_mixture.Rd |only man/mixture_example.Rd |only 12 files changed, 43 insertions(+), 16 deletions(-)
Title: A Tidy Framework for Changepoint Detection Analysis
Description: Changepoint detection algorithms for R are widespread but have
different interfaces and reporting conventions.
This makes the comparative analysis of results difficult.
We solve this problem by providing a tidy, unified interface for several
different changepoint detection algorithms.
We also provide consistent numerical and graphical reporting leveraging
the 'broom' and 'ggplot2' packages.
Author: Benjamin S. Baumer [aut, cre, cph] ,
Biviana Marcela Suarez Sierra [aut] ,
Arrigo Coen [aut] ,
Carlos A. Taimal [aut] ,
Xueheng Shi [ctb]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>
Diff between tidychangepoint versions 1.0.1 dated 2025-07-09 and 1.0.2 dated 2025-10-16
tidychangepoint-1.0.1/tidychangepoint/R/segment_cga.R |only tidychangepoint-1.0.1/tidychangepoint/man/segment_cga.Rd |only tidychangepoint-1.0.2/tidychangepoint/DESCRIPTION | 8 - tidychangepoint-1.0.2/tidychangepoint/MD5 | 38 ++++----- tidychangepoint-1.0.2/tidychangepoint/NAMESPACE | 18 ++-- tidychangepoint-1.0.2/tidychangepoint/NEWS.md | 4 tidychangepoint-1.0.2/tidychangepoint/R/pkg-changepointGA.R | 42 ++++++---- tidychangepoint-1.0.2/tidychangepoint/R/segment.R | 8 - tidychangepoint-1.0.2/tidychangepoint/R/segment_cptga.R |only tidychangepoint-1.0.2/tidychangepoint/R/tidychangepoint-package.R | 4 tidychangepoint-1.0.2/tidychangepoint/README.md | 8 - tidychangepoint-1.0.2/tidychangepoint/inst/doc/tidychangepoint.html | 11 +- tidychangepoint-1.0.2/tidychangepoint/man/as.segmenter.Rd | 4 tidychangepoint-1.0.2/tidychangepoint/man/changepoints.Rd | 6 - tidychangepoint-1.0.2/tidychangepoint/man/fitness.Rd | 6 - tidychangepoint-1.0.2/tidychangepoint/man/model_args.Rd | 5 - tidychangepoint-1.0.2/tidychangepoint/man/model_name.Rd | 4 tidychangepoint-1.0.2/tidychangepoint/man/reexports.Rd | 8 - tidychangepoint-1.0.2/tidychangepoint/man/seg_params.Rd | 4 tidychangepoint-1.0.2/tidychangepoint/man/segment.Rd | 4 tidychangepoint-1.0.2/tidychangepoint/man/segment_cptga.Rd |only tidychangepoint-1.0.2/tidychangepoint/tests/testthat/test-changepointGA.R | 4 22 files changed, 106 insertions(+), 80 deletions(-)
More information about tidychangepoint at CRAN
Permanent link
Title: Power Analyses using Monte Carlo Simulations
Description: Provides a general purpose simulation-based power analysis
API for routine and customized simulation experimental designs.
The package focuses exclusively on Monte Carlo simulation experiment variants of
(expected) prospective power analyses,
criterion analyses, compromise analyses, sensitivity analyses, and
a priori/post-hoc analyses. The default simulation experiment functions defined within the package
provide stochastic variants of the power analysis subroutines in
G*Power 3.1 (Faul, Erdfelder, Buchner, and Lang, 2009) <doi:10.3758/brm.41.4.1149>,
along with various other parametric and non-parametric power analysis
applications (e.g., mediation analyses) and support for Bayesian power analysis
by way of Bayes factors or posterior probability evaluations.
Additional functions for building
empirical power curves, reanalyzing simulation information, and
for increasing the precision of the resulting power
estimates are also included, each of which utilize similar API structures.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between Spower versions 0.4.0 dated 2025-09-05 and 0.5.0 dated 2025-10-16
DESCRIPTION | 11 MD5 | 126 +++---- R/Spower.R | 28 + R/SpowerBatch.R | 21 + R/SpowerCurve.R | 6 R/p_2r.R | 9 R/p_anova.test.R | 14 R/p_chisq.test.R | 16 R/p_glm.R | 10 R/p_kruskal.test.R | 8 R/p_ks.test.R | 11 R/p_lm.R2.R | 8 R/p_mauchly.test.R | 18 - R/p_mcnemar.test.R | 11 R/p_mediation.R | 8 R/p_prop.test.R | 19 - R/p_r.R | 20 - R/p_r.cat.R | 8 R/p_scale.R | 6 R/p_shapiro.test.R | 11 R/p_t.test.R | 67 ++-- R/p_var.test.R | 23 - R/p_wilcox.test.R | 9 R/util.R | 24 + README.md | 32 + build/vignette.rds |binary inst/doc/SpowerIntro.R | 3 inst/doc/SpowerIntro.Rmd | 90 ++--- inst/doc/SpowerIntro.html | 100 +++--- inst/doc/SpowerIntro_logicals.R | 100 +++--- inst/doc/SpowerIntro_logicals.Rmd | 377 ++++++++++++++++------ inst/doc/SpowerIntro_logicals.html | 514 +++++++++++++++++++++---------- inst/doc/Spower_TypeSM.R |only inst/doc/Spower_TypeSM.Rmd |only inst/doc/Spower_TypeSM.html |only inst/doc/gpower_examples.Rmd | 115 ++++-- inst/doc/gpower_examples.html | 121 ++++--- inst/intro.rds |binary inst/intro2.rds |binary inst/intro3.rds |only man/Spower.Rd | 37 +- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/p_2r.Rd | 7 man/p_anova.test.Rd | 7 man/p_chisq.test.Rd | 7 man/p_glm.Rd | 9 man/p_kruskal.test.Rd | 7 man/p_ks.test.Rd | 17 - man/p_lm.R2.Rd | 18 + man/p_mauchly.test.Rd | 15 man/p_mcnemar.test.Rd | 7 man/p_mediation.Rd | 7 man/p_prop.test.Rd | 7 man/p_r.Rd | 19 + man/p_r.cat.Rd | 7 man/p_scale.Rd | 6 man/p_shapiro.test.Rd | 8 man/p_t.test.Rd | 39 +- man/p_var.test.Rd | 7 man/p_wilcox.test.Rd | 9 vignettes/SpowerIntro.Rmd | 90 ++--- vignettes/SpowerIntro_logicals.Rmd | 377 ++++++++++++++++------ vignettes/Spower_TypeSM.Rmd |only vignettes/gpower_examples.Rmd | 115 ++++-- vignettes/precompile.R | 7 vignettes/precompileGpower.R |only 67 files changed, 1901 insertions(+), 872 deletions(-)
Title: Greedy Expected Posterior Loss
Description: Summarises a collection of partitions into a single optimal partition. The objective function is the expected posterior loss, and the minimisation is performed through a greedy algorithm described in Rastelli, R. and Friel, N. (2017) "Optimal Bayesian estimators for latent variable cluster models" <DOI:10.1007/s11222-017-9786-y>.
Author: Riccardo Rastelli [aut, cre]
Maintainer: Riccardo Rastelli <riccardoras@gmail.com>
Diff between GreedyEPL versions 1.2 dated 2021-09-02 and 1.3 dated 2025-10-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary man/MinimiseEPL.Rd | 8 ++++---- src/core_minimise_epl.cpp | 3 ++- 5 files changed, 14 insertions(+), 13 deletions(-)
Title: Generating Multi-Omics Datasets for Testing and Benchmarking
Description: Provides tools to simulate multi-omics datasets with predefined signal structures. The generated data can be used for testing, validating, and benchmarking integrative analysis methods such as factor models and clustering approaches. This version includes enhanced signal customization, visualization tools (scatter, histogram, 3D), MOFA-based analysis pipelines, PowerPoint export, and statistical profiling of datasets. Designed for both method development and teaching, SUMO supports real and synthetic data pipelines with interpretable outputs. Tini, Giulia, et al (2019) <doi:10.1093/bib/bbx167>.
Author: Bernard Isekah Osang'ir [aut, cre] ,
Ziv Shkedy [ctb],
Surya Gupta [ctb],
Juergen Claesen [ctb]
Maintainer: Bernard Isekah Osang'ir <Bernard.Osangir@sckcen.be>
Diff between SUMO versions 1.2.2 dated 2025-10-14 and 1.2.3 dated 2025-10-16
DESCRIPTION | 16 ++++++++-------- MD5 | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-)
Title: Imbalanced Resampling using SMOTE with Boosting (SMOTEWB)
Description: Provides the SMOTE with Boosting (SMOTEWB) algorithm. See
F. Sağlam, M. A. Cengiz (2022) <doi:10.1016/j.eswa.2022.117023>. It is a
SMOTE-based resampling technique which creates synthetic data on the links
between nearest neighbors. SMOTEWB uses boosting weights to determine where
to generate new samples and automatically decides the number of neighbors
for each sample. It is robust to noise and outperforms most of the
alternatives according to Matthew Correlation Coefficient metric.
Alternative resampling methods are also available in the package.
Author: Fatih Saglam [aut, cre]
Maintainer: Fatih Saglam <saglamf89@gmail.com>
Diff between SMOTEWB versions 1.2.2 dated 2025-05-22 and 1.2.5 dated 2025-10-16
DESCRIPTION | 8 +- MD5 | 54 ++++++++--------- R/ADASYN.R | 15 +--- R/BLSMOTE.R | 14 +--- R/GSMOTE.R | 14 +--- R/ROS.R | 16 +---- R/ROSE.R | 23 +++---- R/RSLSMOTE.R | 15 +--- R/RUS.R | 3 R/RWO.R | 15 +--- R/SLSMOTE.R | 14 +--- R/SMOTE.R | 16 ++--- R/SMOTEWB.R | 14 +--- R/generateGSMOTE.R | 2 R/generateRSLSMOTE.R | 2 R/generateSLSMOTE.R | 2 R/generateSMOTEWB.R | 2 man/ADASYN.Rd | 124 +++++++++++++++++++-------------------- man/BLSMOTE.Rd | 134 +++++++++++++++++++++--------------------- man/GSMOTE.Rd | 148 +++++++++++++++++++++++----------------------- man/ROS.Rd | 98 +++++++++++++++--------------- man/ROSE.Rd | 120 ++++++++++++++++++------------------- man/RSLSMOTE.Rd | 162 +++++++++++++++++++++++++-------------------------- man/RUS.Rd | 102 ++++++++++++++++---------------- man/RWO.Rd | 6 - man/SLSMOTE.Rd | 148 +++++++++++++++++++++++----------------------- man/SMOTE.Rd | 128 ++++++++++++++++++++-------------------- man/SMOTEWB.Rd | 7 -- 28 files changed, 687 insertions(+), 719 deletions(-)
Title: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over
Time
Description: Provide a range of functions with multiple criteria for cutting phylogenetic trees at any evolutionary depth. It enables users to cut trees in any orientation, such as rootwardly (from root to tips) and tipwardly (from tips to its root), or allows users to define a specific time interval of interest. It can also be used to create multiple tree pieces of equal temporal width. Moreover, it allows the assessment of novel temporal rates for various phylogenetic indexes, which can be quickly displayed graphically.
Author: Matheus Lima Araujo [aut, cre, cph] ,
Luiz Gabriel Souza e Souza Ferreira [aut] ,
Gabriel Nakamura [aut] ,
Marco Tulio Pacheco Coelho [aut] ,
Thiago Fernando Rangel [aut]
Maintainer: Matheus Lima Araujo <matheusaraujolima@live.com>
Diff between treesliceR versions 1.0.3 dated 2025-06-09 and 1.1.0 dated 2025-10-16
treesliceR-1.0.3/treesliceR/R/DR.R |only treesliceR-1.0.3/treesliceR/tests/testthat/test-DR.R |only treesliceR-1.1.0/treesliceR/DESCRIPTION |only treesliceR-1.1.0/treesliceR/LICENSE |only treesliceR-1.1.0/treesliceR/MD5 | 23 treesliceR-1.1.0/treesliceR/NAMESPACE |only treesliceR-1.1.0/treesliceR/NEWS.md |only treesliceR-1.1.0/treesliceR/R/CpB.R | 160 +--- treesliceR-1.1.0/treesliceR/R/CpB_RW.R | 124 --- treesliceR-1.1.0/treesliceR/R/CpD.R | 29 treesliceR-1.1.0/treesliceR/R/CpE.R | 44 - treesliceR-1.1.0/treesliceR/R/nodes_config.R | 10 treesliceR-1.1.0/treesliceR/R/r_phylo.R | 359 ++-------- treesliceR-1.1.0/treesliceR/README.md |only treesliceR-1.1.0/treesliceR/build |only treesliceR-1.1.0/treesliceR/data |only treesliceR-1.1.0/treesliceR/inst |only treesliceR-1.1.0/treesliceR/man |only treesliceR-1.1.0/treesliceR/vignettes/AllTrees_DR.png |only treesliceR-1.1.0/treesliceR/vignettes/AllTrees_turn.png |only treesliceR-1.1.0/treesliceR/vignettes/Intro-treesliceR.Rmd |only treesliceR-1.1.0/treesliceR/vignettes/OneTree_nest.png |binary treesliceR-1.1.0/treesliceR/vignettes/OneTree_sensitivity.png |only treesliceR-1.1.0/treesliceR/vignettes/OneTree_turn.png |only treesliceR-1.1.0/treesliceR/vignettes/Passeriformes-distribution.Rmd |only treesliceR-1.1.0/treesliceR/vignettes/Sliced_pas_tree.png |only 26 files changed, 194 insertions(+), 555 deletions(-)
Title: Analytical Methods for Stream DAGs
Description: Provides indices and tools for directed acyclic graphs (DAGs), particularly DAG representations of intermittent streams. A detailed introduction to the package can be found in the publication: "Non-perennial stream networks as directed acyclic graphs: The R-package streamDAG" (Aho et al., 2023) <doi:10.1016/j.envsoft.2023.105775>, and in the introductory package vignette.
Author: Ken Aho [aut, cre],
Arya Legg [dtc, ctb],
Rob Ramos [dtc],
Maggi Kraft [dtc],
Charles T. Bond [dtc],
Rebecca L. Hale [dtc]
Maintainer: Ken Aho <ahoken@isu.edu>
Diff between streamDAG versions 1.5-9 dated 2025-01-14 and 1.6 dated 2025-10-16
DESCRIPTION | 8 - MD5 | 80 +++++++----- R/get.AIMS.data.R | 150 ++++++++++++----------- R/global.summary.R | 4 R/local_summary.R | 60 ++++----- R/spatial_plot.R | 235 ++++++++++++++++++++++--------------- build/vignette.rds |binary data/AIMS.node.coords.rda |binary data/dc_arc_pres_abs.rda |binary data/dc_lengths.rda |binary data/dc_node_pres_abs.rda |binary data/gj_coords16.rda |binary data/gj_lengths.rda |binary data/gj_lengths_piezo_full.rda |binary data/gj_node_pres_abs.rda |binary data/gj_node_pres_abs16.rda |binary data/jd_lengths.rda |binary data/jd_lengths_2023.rda |binary data/jd_lengths_full.rda |binary data/jd_node_pres_abs.rda |binary data/kon_coords.rda |binary data/kon_lengths.rda |binary data/mur_arc_pres_abs.rda |binary data/mur_coords.rda |binary data/mur_lengths.rda |binary data/mur_node_pres_abs.rda |binary data/mur_seasons_arc_pa.rda |binary inst/CITATION | 2 inst/doc/alpha-centrality.R |only inst/doc/alpha-centrality.Rnw |only inst/doc/alpha-centrality.pdf |only inst/doc/streamDAG.R | 16 +- inst/doc/streamDAG.html | 62 ++++----- man/get.AIMS.data.rd | 4 man/global.summary.Rd | 6 man/local.summary.Rd | 18 +- man/spatial.plot.Rd | 53 ++++---- vignettes/DAGs.pdf |only vignettes/Fig_1_alpha.png |only vignettes/GT1_01.png |only vignettes/GT3_2_1.png |only vignettes/MMEbst.bst |only vignettes/acyclic_cyclic1.png |only vignettes/alpha-centrality.Rnw |only vignettes/book.bib |only vignettes/connect_disc_stream1.png |only vignettes/simo1_DAG.pdf |only vignettes/simo_DAG.pdf |only 48 files changed, 385 insertions(+), 313 deletions(-)
Title: A Dynamic Bipartite Latent Space Model to Analyse Irish
Companies' Boards from 2003 to 2013
Description: Provides the dataset and an implementation of the method illustrated in Friel, N., Rastelli, R., Wyse, J. and Raftery, A.E. (2016) <DOI:10.1073/pnas.1606295113>.
Author: Riccardo Rastelli [aut, cre]
Maintainer: Riccardo Rastelli <riccardoras@gmail.com>
Diff between IrishDirectorates versions 1.4 dated 2019-08-29 and 1.5 dated 2025-10-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary src/Makevars | 3 ++- src/Makevars.win | 3 ++- src/RcppExports.cpp | 5 +++++ 6 files changed, 18 insertions(+), 11 deletions(-)
More information about IrishDirectorates at CRAN
Permanent link
Title: An Exponential Stochastic Block Model for Interaction Lengths
Description: Given a continuous-time dynamic network, this package allows one to fit a stochastic blockmodel where nodes belonging to the same group create interactions and non-interactions of similar lengths. This package implements the methodology described by R. Rastelli and M. Fop (2020) <doi:10.1007/s11634-020-00403-w>.
Author: Riccardo Rastelli [aut, cre] ,
Michael Fop [aut]
Maintainer: Riccardo Rastelli <riccardoras@gmail.com>
Diff between expSBM versions 1.3.5 dated 2019-10-15 and 1.3.6 dated 2025-10-16
DESCRIPTION | 15 ++++++++------- MD5 | 12 ++++++------ build/partial.rdb |binary man/expSBM-package.Rd | 2 +- src/Makevars | 2 +- src/Makevars.win | 2 +- src/RcppExports.cpp | 5 +++++ 7 files changed, 22 insertions(+), 16 deletions(-)
Title: User-Friendly PostgreSQL Connection Management
Description: Provides a user-friendly interface for managing PostgreSQL
database connection settings. The package supplies helper functions to
create, edit and load connection and option configuration files stored in a
user-specific directory using the 'odbc' and 'RPostgres' back ends. These
helpers make it easy to construct a reproducible connection string from a
configuration file, either by reading user-defined YAML files or by parsing
an environment variable.
Author: Bobby Fatemi [aut, cre]
Maintainer: Bobby Fatemi <bfatemi07@gmail.com>
Diff between rpgconn versions 0.3.1 dated 2025-08-21 and 0.3.2 dated 2025-10-16
DESCRIPTION | 8 MD5 | 13 - NEWS.md |only R/pgdbconn.R | 408 ++++++++++++++++++++--------------------- R/use-config.R | 107 +++++----- inst/WORDLIST | 2 man/pgdbconn.Rd | 8 tests/testthat/test-pgdbconn.R | 154 +++++++++------ 8 files changed, 379 insertions(+), 321 deletions(-)
Title: Retrieve Archived Web Pages from the 'Internet Archive'
Description: Scraping content from archived web pages stored in
the 'Internet Archive' (<https://archive.org>) using a systematic
workflow. Get an overview of the mementos available from the
respective homepage, retrieve the Urls and links of the page and
finally scrape the content. The final output is stored in tibbles,
which can be then easily used for further analysis.
Author: Lukas Isermann [aut, cre] ,
Konstantin Gavras [aut]
Maintainer: Lukas Isermann <lukas.isermann@uni-mannheim.de>
Diff between archiveRetriever versions 0.4.0 dated 2024-06-11 and 0.4.1 dated 2025-10-16
archiveRetriever-0.4.0/archiveRetriever/tests/testthat/Rplots.pdf |only archiveRetriever-0.4.1/archiveRetriever/DESCRIPTION | 16 archiveRetriever-0.4.1/archiveRetriever/MD5 | 67 archiveRetriever-0.4.1/archiveRetriever/NEWS.md | 7 archiveRetriever-0.4.1/archiveRetriever/R/archive_overview.R | 4 archiveRetriever-0.4.1/archiveRetriever/R/retrieve_links.R | 2 archiveRetriever-0.4.1/archiveRetriever/R/retrieve_urls.R | 4 archiveRetriever-0.4.1/archiveRetriever/R/scrape_urls.R | 2 archiveRetriever-0.4.1/archiveRetriever/README.md | 19 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links1.yml |10366 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links2.yml |10366 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links3.yml |10366 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links4.yml |10366 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links5.yml | 7340 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/retrieve_links6.yml |only archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url1.yml | 2872 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url2.yml | 2872 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url3.yml | 2884 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url4.yml | 2884 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url5.yml | 3587 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url6.yml | 4254 archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url7.yml |75307 +--------- archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url8.yml | 9095 - archiveRetriever-0.4.1/archiveRetriever/tests/fixtures/scrape_url9.yml | 5626 archiveRetriever-0.4.1/archiveRetriever/tests/testthat/_vcr |only archiveRetriever-0.4.1/archiveRetriever/tests/testthat/test_archive_overview.R | 3 archiveRetriever-0.4.1/archiveRetriever/tests/testthat/test_retrieve_links.R | 24 archiveRetriever-0.4.1/archiveRetriever/tests/testthat/test_retrieve_urls.R | 2 archiveRetriever-0.4.1/archiveRetriever/tests/testthat/test_scrape_urls.R | 9 29 files changed, 37748 insertions(+), 120596 deletions(-)
More information about archiveRetriever at CRAN
Permanent link
Title: Graphical User Interface with Integrated 'Diagrammer' for
'Lavaan'
Description: Provides a graphical user interface with an
integrated diagrammer for latent variable models from the 'lavaan' package.
It offers two core functions: first, lavaangui() launches a web application
that allows users to specify models by drawing path diagrams, fitting them,
assessing model fit, and more; second, plot_lavaan() creates
interactive path diagrams from models specified in 'lavaan'.
Karch (2024) <doi: 10.31234/osf.io/f4ary> contains a tutorial.
Author: Julian D. Karch [aut, cre, cph]
Maintainer: Julian D. Karch <j.d.karch@fsw.leidenuniv.nl>
Diff between lavaangui versions 0.2.6 dated 2025-08-19 and 0.3.0 dated 2025-10-16
lavaangui-0.2.6/lavaangui/inst/www/assets/index-f9f1a2f2.js |only lavaangui-0.3.0/lavaangui/DESCRIPTION | 12 ++-- lavaangui-0.3.0/lavaangui/MD5 | 17 +++--- lavaangui-0.3.0/lavaangui/NEWS.md | 31 ++++++------ lavaangui-0.3.0/lavaangui/R/miniSemPlot.R | 21 ++++---- lavaangui-0.3.0/lavaangui/R/serverLayout.R | 2 lavaangui-0.3.0/lavaangui/inst/www/assets/index-64e29f62.js |only lavaangui-0.3.0/lavaangui/inst/www/index.html | 26 +++++----- lavaangui-0.3.0/lavaangui/man/lavaangui.Rd | 2 lavaangui-0.3.0/lavaangui/man/plot_lavaan.Rd | 2 lavaangui-0.3.0/lavaangui/tests/manual/dofitFALSE.R |only 11 files changed, 63 insertions(+), 50 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.4.0 dated 2025-09-18 and 1.4.1 dated 2025-10-16
DESCRIPTION | 9 +- MD5 | 20 ++--- NEWS.md | 19 +++++ R/backend-dbplyr__duckdb_connection.R | 34 ++++----- R/release.R | 1 R/version.R | 2 src/duckdb.tar.xz |binary tests/testthat/_snaps/array.md | 2 tests/testthat/helper-skip.R |only tests/testthat/test-backend-dbplyr__duckdb_connection.R | 59 ++++++++++------ tests/testthat/test-duckdb-extensions.R |only tests/testthat/test-tbl__duckdb_connection.R | 9 ++ 12 files changed, 104 insertions(+), 51 deletions(-)
More information about sensitivityIxJ at CRAN
Permanent link
More information about QualityMeasure at CRAN
Permanent link
More information about dispersionIndicators at CRAN
Permanent link
More information about descsuppRplots at CRAN
Permanent link
Title: Bayesian Spatial Blind Source Separation
Description: Gibbs sampling for Bayesian spatial blind source separation (BSP-BSS). BSP-BSS is designed for spatially dependent signals in high dimensional and large-scale data, such as neuroimaging. The method assumes the expectation of the observed images as a linear mixture of multiple sparse and piece-wise smooth latent source signals, and constructs a Bayesian nonparametric prior by thresholding Gaussian processes. Details can be found in our paper: Wu, B., Guo, Y., & Kang, J. (2024). Bayesian spatial blind source separation via the thresholded gaussian process. Journal of the American Statistical Association, 119(545), 422-433.
Author: Ben Wu [aut, cre],
Ying Guo [aut],
Jian Kang [aut]
Maintainer: Ben Wu <wuben@ruc.edu.cn>
Diff between BSPBSS versions 1.0.5 dated 2022-11-25 and 1.0.6 dated 2025-10-16
DESCRIPTION | 8 ++--- MD5 | 8 ++--- inst/doc/BSPBSS-vignette.html | 64 +++++++++++++++++++++++------------------- src/Makevars | 1 src/Makevars.win | 2 - 5 files changed, 44 insertions(+), 39 deletions(-)
More information about BayesianDisaggregation at CRAN
Permanent link
Title: Stochastic Data Envelopment Analysis
Description: Set of functions for Stochastic Data Envelopment Analysis. Chance constrained versions of radial, directional and additive DEA models are implemented, as long as super-efficiency models. See: Cooper, W.W.; Deng, H.; Huang, Z.; Li, S.X. (2002). <doi:10.1057/palgrave.jors.2601433>, Bolós, V.J.; Benítez, R.; Coll-Serrano, V. (2024) <doi:10.1016/j.orp.2024.100307>.
Author: Vicente Bolos [aut, cre],
Vicente Coll-Serrano [aut],
Rafael Benitez Suarez [aut]
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between SdeaR versions 1.0.0 dated 2025-09-14 and 1.0.1 dated 2025-10-16
DESCRIPTION | 6 - MD5 | 28 ++++---- R/modelstoch_additive.R | 33 +++++++--- R/modelstoch_additive_p.R | 33 +++++++--- R/modelstoch_addsupereff.R | 17 ++++- R/modelstoch_dir.R | 138 +++++++++++++++++++++++++++--------------- R/modelstoch_dir_dd.R | 137 +++++++++++++++++++++++++++-------------- R/modelstoch_radial.R | 138 +++++++++++++++++++++++++++--------------- build/partial.rdb |binary man/modelstoch_additive.Rd | 4 + man/modelstoch_additive_p.Rd | 4 + man/modelstoch_addsupereff.Rd | 4 + man/modelstoch_dir.Rd | 6 + man/modelstoch_dir_dd.Rd | 6 + man/modelstoch_radial.Rd | 6 + 15 files changed, 380 insertions(+), 180 deletions(-)
Title: Gene Set Enrichment Meta-Analysis
Description: Performing the different steps of gene set enrichment meta-analysis. It provides different functions that allow the application of meta-analysis based on the combination of effect sizes from different pathways in different studies to obtain significant pathways that are common to all of them.
Author: Juan Antonio Villatoro-Garcia [aut, cre],
Pablo Jurado-Bascon [aut],
Pedro Carmona-Saez [aut]
Maintainer: Juan Antonio Villatoro-Garcia <juanantoniovillatorogarcia@gmail.com>
This is a re-admission after prior archival of version 0.99.3 dated 2024-10-14
Diff between GSEMA versions 0.99.3 dated 2024-10-14 and 0.99.4 dated 2025-10-16
DESCRIPTION | 14 ++--- MD5 | 12 ++-- NAMESPACE | 1 R/createObjectMApath.R | 56 +++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/GSEMA.html | 129 ++++++++++++++++++++++--------------------------- 7 files changed, 103 insertions(+), 109 deletions(-)
Title: Process Control and Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyze data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson [aut, cre]
Maintainer: Oskar Hansson <oskhan@ous-hf.no>
Diff between strvalidator versions 2.4.1 dated 2023-07-16 and 2.4.2 dated 2025-10-16
DESCRIPTION | 16 +++++++++------ MD5 | 46 ++++++++++++++++++++++---------------------- NEWS | 12 ++++++++++- R/calculateAllele.R | 3 +- R/calculateSpike.R | 3 +- R/calculateStatistics.r | 3 +- R/combine_gui.r | 6 +---- R/editData_gui.r | 5 ++-- R/ggsave_gui.r | 8 ++----- R/plotDistribution_gui.r | 4 +-- R/plotGroups_gui.r | 3 +- R/strvalidator-package.r | 35 +++++++++++++++++---------------- build/partial.rdb |binary man/calculateAllele.Rd | 2 - man/calculateSpike.Rd | 2 - man/calculateStatistics.Rd | 2 - man/combine_gui.Rd | 2 - man/editData_gui.Rd | 4 +-- man/ggsave_gui.Rd | 4 +-- man/plotDistribution_gui.Rd | 2 - man/plotGroups_gui.Rd | 2 - man/ref51.Rd | 2 - man/ref52.Rd | 2 - man/strvalidator-package.Rd | 33 +++++++++++++++++++++---------- 24 files changed, 114 insertions(+), 87 deletions(-)
Title: Robust Regression and Estimation Through Maximum Mean
Discrepancy Minimization
Description: The functions in this package compute robust estimators by minimizing a kernel-based distance known as MMD (Maximum Mean Discrepancy) between the sample and a statistical model. Recent works proved that these estimators enjoy a universal consistency property, and are extremely robust to outliers. Various optimization algorithms are implemented: stochastic gradient is available for most models, but the package also allows gradient descent in a few models for which an exact formula is available for the gradient. In terms of distribution fit, a large number of continuous and discrete distributions are available: Gaussian, exponential, uniform, gamma, Poisson, geometric, etc. In terms of regression, the models available are: linear, logistic, gamma, beta and Poisson.
Alquier, P. and Gerber, M. (2024) <doi:10.1093/biomet/asad031>
Cherief-Abdellatif, B.-E. and Alquier, P. (2022) <doi:10.3150/21-BEJ1338>.
Author: Pierre Alquier [aut, cre] ,
Mathieu Gerber [aut]
Maintainer: Pierre Alquier <pierre.alquier.stat@gmail.com>
Diff between regMMD versions 0.0.2 dated 2025-10-15 and 0.0.3 dated 2025-10-16
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/estimation_function.R | 5 +++-- R/models_Gaussian.R | 8 ++++++-- R/models_beta.R | 4 ++-- R/models_continuous_uniform.R | 8 ++++---- R/models_gamma.R | 4 ++-- R/models_multidim_Dirac.R | 4 ++-- R/models_multidim_Gaussian.R | 16 ++++++++-------- build/partial.rdb |binary 10 files changed, 39 insertions(+), 34 deletions(-)
Title: Board Game Graphics
Description: Functions to make board game graphics with the 'ggplot2', 'grid', 'rayrender', 'rayvertex', and 'rgl' packages. Specializes in game diagrams, animations, and "Print & Play" layouts for the 'piecepack' <https://www.ludism.org/ppwiki> but can make graphics for other board game systems. Includes configurations for several public domain game systems such as checkers, (double-18) dominoes, go, 'piecepack', playing cards, etc.
Author: Trevor L. Davis [aut, cre] ,
Linux Foundation [dtc] ,
Delapouite <https://delapouite.com/> [ill] ,
Creative Commons [ill] ` uses "license badges"
from Creative Commons to describe the generated print-and-play
file's license)
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
This is a re-admission after prior archival of version 1.15.1 dated 2025-05-08
Diff between piecepackr versions 1.15.1 dated 2025-05-08 and 1.15.3 dated 2025-10-16
DESCRIPTION | 8 MD5 | 156 - NAMESPACE | 1 NEWS.md | 9 R/aabb_piece.R | 63 R/animate_piece.R | 459 +++-- R/basicPieceGrob.R | 749 +++++---- R/cropmarkGrob.R | 473 +++-- R/crosshairGrob.R | 509 +++--- R/game_systems.R | 1935 +++++++++++++----------- R/geom_piece.R | 323 ++-- R/hooks.R | 8 R/install_ppverse.R | 27 R/op_transform.R | 390 ++-- R/piece-rayrender.R | 196 +- R/piece3d-rgl.R | 249 ++- R/pieceGrob-grid.R | 508 ++++-- R/piece_mesh-rayvertex.R | 211 +- R/piecepackr-defunct.R | 20 R/pmap_piece.R | 162 +- R/pp_cfg.R | 1402 ++++++++++------- R/pp_shape.R | 716 ++++---- R/render_piece.R | 550 ++++-- R/save_piece_images.R | 275 +-- R/save_piece_obj.R | 1895 +++++++++++++---------- R/save_print_and_play.R | 281 +-- R/sysdata.rda |binary R/utils-bleed-grobs.R | 159 + R/utils-boards.R | 869 ++++++---- R/utils-cache.R | 31 R/utils-composite.R | 458 +++-- R/utils-d10.R | 644 ++++--- R/utils-d12.R | 370 ++-- R/utils-d20.R | 410 ++--- R/utils-d4.R | 658 ++++---- R/utils-d6.R | 155 - R/utils-d8.R | 465 +++-- R/utils-font.R | 139 - R/utils-fudge.R | 94 - R/utils-geometry.R | 298 +-- R/utils-grid.R | 26 R/utils-grobCoords.R | 64 R/utils-mat-grobs.R | 198 +- R/utils-misc.R | 389 ++-- R/utils-op-grobs.R | 1466 ++++++++++-------- R/utils-opt.R | 1193 ++++++++------ R/utils-pips.R | 1322 +++++++++------- R/utils-pnp-4x6.R | 226 +- R/utils-pnp-letter-bleed.R | 720 +++++--- R/utils-pnp-letter-both.R | 315 ++- R/utils-pnp-letter-compact.R | 888 ++++++----- R/utils-token.R | 678 ++++---- R/utils-transformation.R | 160 + R/utils-xyz.R | 74 R/zzz.R | 22 README.md | 93 - data/spdx_license_list.rda |binary man/geom_piece.Rd | 4 man/piece.Rd | 32 man/piece3d.Rd | 2 man/piece_mesh.Rd | 41 man/render_piece.Rd | 2 man/save_piece_obj.Rd | 2 man/scale_piece.Rd | 10 tests/testthat/_snaps/geom_piece/geom-piece.svg | 1 tests/testthat/test-animate_piece.R | 63 tests/testthat/test-cache.R | 28 tests/testthat/test-crop_marks.R | 56 tests/testthat/test-crosshairs.R | 41 tests/testthat/test-defunct.R | 32 tests/testthat/test-game_systems.R | 868 +++++++--- tests/testthat/test-geom_piece.R | 51 tests/testthat/test-obj.R | 247 +-- tests/testthat/test-op_transform.R | 299 ++- tests/testthat/test-options.R | 344 ++-- tests/testthat/test-pieceGrob.R | 812 +++++----- tests/testthat/test-pp_shape.R | 184 +- tests/testthat/test-ppverse.R | 5 tests/testthat/test-render_piece.R | 140 + 79 files changed, 15965 insertions(+), 11458 deletions(-)
Title: Robust Image Rendering Support for 'ggplot2'
Description: A 'ggplot2' extension that enables robust image grobs in
panels and theme elements.
Author: Sebastian Carl [aut, cre, cph]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between ggpath versions 1.1.0 dated 2025-09-17 and 1.1.1 dated 2025-10-16
DESCRIPTION | 6 +-- MD5 | 15 +++++---- NEWS.md | 6 +++ R/theme_element.R | 41 +++++++++++++++++++++++--- tests/testthat/_snaps/theme-elements/p1.svg | 6 +-- tests/testthat/_snaps/theme-elements/p2.svg | 6 +-- tests/testthat/_snaps/theme-elements/p5.svg |only tests/testthat/_snaps/theme-elements/p6.svg |only tests/testthat/_snaps/theme-elements/p7.svg |only tests/testthat/test-theme-elements.R | 43 ++++++++++++++++++++++++++++ 10 files changed, 102 insertions(+), 21 deletions(-)
Title: Smoother Change Tracking and Versioning for R Packages
Description: Streamlines the process of updating changelogs (NEWS.md)
and versioning R packages developed in git repositories.
Author: Kirill Mueller [aut, cre, cph] ,
Patrick Schratz [aut] ,
Maelle Salmon [ctb]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between fledge versions 0.1.2 dated 2024-02-18 and 0.1.3 dated 2025-10-16
DESCRIPTION | 17 +++++++------ MD5 | 18 +++++++------- NEWS.md | 5 +++ R/enc.R | 2 - build/vignette.rds |binary inst/doc/demo.R | 4 +-- inst/doc/demo.html | 54 +++++++++++++++++++++---------------------- inst/doc/fledge.html | 3 +- inst/doc/internals.html | 3 +- man/get_top_level_commits.Rd | 2 - 10 files changed, 58 insertions(+), 50 deletions(-)
Title: Bayesian Estimation and Forecasting of Age-Specific Rates
Description: Fast Bayesian estimation and forecasting of age-specific
rates, probabilities, and means, based on 'Template Model Builder'.
Author: John Bryant [aut, cre],
Junni Zhang [aut],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between bage versions 0.9.7 dated 2025-10-07 and 0.9.8 dated 2025-10-16
DESCRIPTION | 6 MD5 | 52 +-- NEWS.md | 28 ++ R/bage_mod-functions.R | 1 R/util.R | 2 inst/TMB-version | 2 inst/doc/vig01_intro.R | 4 inst/doc/vig01_intro.Rmd | 8 inst/doc/vig01_intro.html | 160 ++++++------ inst/doc/vig05_bdef.html | 64 ++-- inst/doc/vig06_mortality.R | 14 - inst/doc/vig06_mortality.Rmd | 16 - inst/doc/vig06_mortality.html | 91 +++--- inst/doc/vig07_simulation.R | 7 inst/doc/vig07_simulation.Rmd | 8 inst/doc/vig07_simulation.html | 37 -- inst/doc/vig09_covariates.R | 10 inst/doc/vig09_covariates.Rmd | 15 - inst/doc/vig09_covariates.html | 406 +++++++++++++++---------------- inst/doc/vig10_datamod.html | 38 +- tests/testthat/test-bage_mod-functions.R | 17 + tests/testthat/test-bage_mod-methods.R | 15 - tests/testthat/test-make-outputs.R | 44 +-- vignettes/vig01_intro.Rmd | 8 vignettes/vig06_mortality.Rmd | 16 - vignettes/vig07_simulation.Rmd | 8 vignettes/vig09_covariates.Rmd | 15 - 27 files changed, 543 insertions(+), 549 deletions(-)
Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to
'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R
using the 'libtorch' library. Also supports low-level tensor operations and
'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph],
Javier Luraschi [aut],
Dmitriy Selivanov [ctb],
Athos Damiani [ctb],
Christophe Regouby [ctb],
Krzysztof Joachimiak [ctb],
Hamada S. Badr [ctb],
Sebastian Fischer [ctb],
Maximilian Pichler [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torch versions 0.16.0 dated 2025-08-21 and 0.16.1 dated 2025-10-16
torch-0.16.0/torch/inst/doc/distributions.R |only torch-0.16.0/torch/inst/doc/distributions.Rmd |only torch-0.16.0/torch/inst/doc/distributions.html |only torch-0.16.0/torch/inst/doc/extending-autograd.R |only torch-0.16.0/torch/inst/doc/extending-autograd.Rmd |only torch-0.16.0/torch/inst/doc/extending-autograd.html |only torch-0.16.0/torch/inst/doc/indexing.R |only torch-0.16.0/torch/inst/doc/indexing.Rmd |only torch-0.16.0/torch/inst/doc/indexing.html |only torch-0.16.0/torch/inst/doc/loading-data.R |only torch-0.16.0/torch/inst/doc/loading-data.Rmd |only torch-0.16.0/torch/inst/doc/loading-data.html |only torch-0.16.0/torch/inst/doc/python-to-r.R |only torch-0.16.0/torch/inst/doc/python-to-r.Rmd |only torch-0.16.0/torch/inst/doc/python-to-r.html |only torch-0.16.0/torch/inst/doc/serialization.R |only torch-0.16.0/torch/inst/doc/serialization.Rmd |only torch-0.16.0/torch/inst/doc/serialization.html |only torch-0.16.0/torch/inst/doc/tensor-creation.R |only torch-0.16.0/torch/inst/doc/tensor-creation.Rmd |only torch-0.16.0/torch/inst/doc/tensor-creation.html |only torch-0.16.0/torch/inst/doc/torchscript.R |only torch-0.16.0/torch/inst/doc/torchscript.Rmd |only torch-0.16.0/torch/inst/doc/torchscript.html |only torch-0.16.0/torch/inst/doc/using-autograd.R |only torch-0.16.0/torch/inst/doc/using-autograd.Rmd |only torch-0.16.0/torch/inst/doc/using-autograd.html |only torch-0.16.0/torch/vignettes/distributions.Rmd |only torch-0.16.0/torch/vignettes/extending-autograd.Rmd |only torch-0.16.0/torch/vignettes/indexing.Rmd |only torch-0.16.0/torch/vignettes/loading-data.Rmd |only torch-0.16.0/torch/vignettes/python-to-r.Rmd |only torch-0.16.0/torch/vignettes/serialization.Rmd |only torch-0.16.0/torch/vignettes/tensor-creation.Rmd |only torch-0.16.0/torch/vignettes/torchscript.Rmd |only torch-0.16.0/torch/vignettes/using-autograd.Rmd |only torch-0.16.1/torch/DESCRIPTION | 6 +- torch-0.16.1/torch/MD5 | 54 +++----------------- torch-0.16.1/torch/NEWS.md | 4 + torch-0.16.1/torch/R/ignite.R | 2 torch-0.16.1/torch/R/install.R | 35 +++++++++++- torch-0.16.1/torch/R/utils-data-sampler.R | 5 - torch-0.16.1/torch/build/partial.rdb |binary torch-0.16.1/torch/build/vignette.rds |binary torch-0.16.1/torch/man/sampler.Rd | 5 - torch-0.16.1/torch/tools/renamelib.R | 2 46 files changed, 54 insertions(+), 59 deletions(-)
Title: Select Sparse Geoadditive Models for Spatial Prediction
Description: A model building procedure to build parsimonious geoadditive model from a large number of covariates. Continuous, binary and ordered categorical responses are supported. The model building is based on component wise gradient boosting with linear effects, smoothing splines and a smooth spatial surface to model spatial autocorrelation. The resulting covariate set after gradient boosting is further reduced through backward elimination and aggregation of factor levels. The package provides a model based bootstrap method to simulate prediction intervals for point predictions. A test data set of a soil mapping case study in Berne (Switzerland) is provided. Nussbaum, M., Walthert, L., Fraefel, M., Greiner, L., and Papritz, A. (2017) <doi:10.5194/soil-3-191-2017>.
Author: Madlene Nussbaum [cre, aut],
Andreas Papritz [ths]
Maintainer: Madlene Nussbaum <m.nussbaum@uu.nl>
Diff between geoGAM versions 0.1-3 dated 2023-11-14 and 0.1-4 dated 2025-10-16
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/geoGAM.Rd | 14 +++++++------- man/methods.geoGAM.Rd | 6 +++--- man/predict.geoGAM.Rd | 8 ++++---- 5 files changed, 23 insertions(+), 23 deletions(-)
Title: moDel Agnostic Language for Exploration and eXplanation
Description: Any unverified black box model is the path to failure. Opaqueness leads to distrust.
Distrust leads to ignoration. Ignoration leads to rejection.
DALEX package xrays any model and helps to explore and explain its behaviour.
Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance. But such black-box models usually lack direct interpretability.
DALEX package contains various methods that help to understand the link between input variables
and model output. Implemented methods help to explore the model on the level of a single instance
as well as a level of the whole dataset.
All model explainers are model agnostic and can be compared across different models.
DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration.
Find more details in (Biecek 2018) <https://jmlr.org/papers/v19/18 [...truncated...]
Author: Przemyslaw Biecek [aut, cre] ,
Szymon Maksymiuk [aut] ,
Hubert Baniecki [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 2.5.2 dated 2025-07-27 and 2.5.3 dated 2025-10-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/misc_theme_drwhy.R | 12 ++++++------ R/plot_model_diagnostics.R | 2 +- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Predict and Visualize Population-Level Changes in Allele
Frequencies in Response to Climate Change
Description: Methods (<doi:10.7717/peerj.11534>) are provided of calibrating and predicting shifts in allele frequencies through redundancy analysis ('vegan::rda()') and generalized additive models ('mgcv::gam()'). Visualization functions for predicted changes in allele frequencies include 'shift.dot.ggplot()', 'shift.pie.ggplot()', 'shift.moon.ggplot()', 'shift.waffle.ggplot()' and 'shift.surf.ggplot()' that are made with input data sets that are prepared by helper functions for each visualization method. Examples in the documentation show how to prepare animated climate change graphics through a time series with the 'gganimate' package. Function 'amova.rda()' shows how Analysis of Molecular Variance can be directly conducted with the results from redundancy analysis.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between AlleleShift versions 1.1-2 dated 2023-10-28 and 1.1-3 dated 2025-10-16
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- inst/ChangeLog | 7 +++++++ man/count.model.Rd | 15 ++++++++------- 4 files changed, 24 insertions(+), 15 deletions(-)
Title: Interpolation and Extrapolation for Three Dimensions of
Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from
genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D)
of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional
diversity (FD). This package provides functions to compute standardized 3D diversity estimates
with a common sample size or sample coverage. A unified framework based on Hill numbers
and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates
are in the same units of species/lineage equivalents and can be meaningfully compared.
The package features size- and coverage-based rarefaction and extrapolation sampling
curves to facilitate rigorous comparison of 3D diversity across individual assemblages.
Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021)
<doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb],
PoYen Chuang [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.3D versions 1.0.10 dated 2025-07-02 and 1.0.11 dated 2025-10-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 2 ++ R/FD_Fun.R | 3 +++ R/PD_Fun.R | 1 + R/TD_Fun.R | 3 ++- inst/doc/Introduction.pdf |binary 7 files changed, 17 insertions(+), 10 deletions(-)
Title: Optimal Assignment of Students to Groups
Description: Integer programming models to assign students to groups by maximising
diversity within groups, or by maximising preference scores for topics.
Author: Vik Gopal [aut, cre],
Kevin Lam [aut],
Ju Xue [ctb],
National University of Singapore [cph]
Maintainer: Vik Gopal <vik.gopal@nus.edu.sg>
Diff between grouper versions 0.3.1 dated 2025-07-09 and 0.5.0 dated 2025-10-16
DESCRIPTION | 6 LICENSE | 4 MD5 | 98 +- NAMESPACE | 18 NEWS.md | 36 - R/data.R | 115 ++- R/extract_fns.R | 435 ++++++------ R/model_prep.R | 262 +++---- R/post_process.R | 134 +-- R/utils-pipe.R | 28 R/zzz.R | 2 README.md | 60 - build/vignette.rds |binary data/dba_gc_ex003.rda |only data/dba_gc_ex004.rda |only inst/doc/a-related-work.R | 12 inst/doc/a-related-work.Rmd | 356 +++++----- inst/doc/a-related-work.html | 1010 +++++++++++++++--------------- inst/doc/b-diversity-skill.R | 12 inst/doc/b-diversity-skill.Rmd | 260 +++---- inst/doc/b-diversity-skill.html | 788 +++++++++++------------ inst/doc/c-subgroups-preference.R | 12 inst/doc/c-subgroups-preference.Rmd | 238 +++---- inst/doc/c-subgroups-preference.html | 766 +++++++++++----------- inst/doc/d-sanity-checks.R | 195 +++-- inst/doc/d-sanity-checks.Rmd | 387 ++++++----- inst/doc/d-sanity-checks.html | 1176 +++++++++++++++++++---------------- inst/extdata/dba_params_ex001.yml | 12 inst/extdata/dba_params_ex003.yml |only inst/extdata/dba_params_ex004.yml |only inst/extdata/pba_params_ex002.yml | 14 inst/shiny |only man/assign_groups.Rd | 78 +- man/dba_gc_ex001.Rd | 58 - man/dba_gc_ex003.Rd |only man/dba_gc_ex004.Rd |only man/extract_params_yaml.Rd | 82 +- man/extract_student_info.Rd | 177 ++--- man/pba_gc_ex002.Rd | 54 - man/pba_prefmat_ex002.Rd | 50 - man/pipe.Rd | 40 - man/prepare_model.Rd | 66 - vignettes/a-related-work.Rmd | 356 +++++----- vignettes/b-diversity-skill.Rmd | 260 +++---- vignettes/c-subgroups-preference.Rmd | 238 +++---- vignettes/d-sanity-checks.Rmd | 387 ++++++----- vignettes/diversity_skill.R |only vignettes/diversity_skill.html |only vignettes/references.bib | 98 +- vignettes/related_work.R |only vignettes/related_work.html |only vignettes/sanity_checks.R |only vignettes/sanity_checks.html |only vignettes/subgroups_preference.R |only vignettes/subgroups_preference.html |only 55 files changed, 4392 insertions(+), 3988 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.3.6 dated 2025-09-17 and 2.3.7 dated 2025-10-16
DESCRIPTION | 6 LICENSE | 4 MD5 | 284 - NAMESPACE | 102 NEWS.md | 568 +-- R/Engine.R | 44 R/EngineGraphQL.R | 401 +- R/EngineGraphQLGitHub.R | 1516 +++----- R/EngineGraphQLGitLab.R | 1564 ++++---- R/EngineRest.R | 225 - R/EngineRestGitHub.R | 626 +-- R/EngineRestGitLab.R | 1357 +++---- R/GQLQueryGitHub.R | 632 +-- R/GQLQueryGitLab.R | 636 +-- R/GitHost.R | 3188 ++++++++--------- R/GitHostGitHub.R | 705 ++- R/GitHostGitLab.R | 965 ++--- R/GitStats-package.R | 22 R/GitStats.R | 2142 +++++------ R/get_commits.R | 242 - R/get_files.R | 208 - R/get_issues.R | 250 - R/get_orgs.R | 78 R/get_release_logs.R | 78 R/get_repos.R | 390 +- R/get_users.R | 82 R/gitstats_functions.R | 166 R/global.R | 26 R/message_handler.R | 76 R/set_host.R | 168 R/test_helpers.R | 516 +- R/utils-pipe.R | 28 R/utils.R | 146 README.md | 372 - build/vignette.rds |binary inst/WORDLIST | 80 inst/doc/get_repos_with_code.R | 74 inst/doc/get_repos_with_code.Rmd | 110 inst/doc/get_repos_with_code.html | 779 ++-- inst/doc/set_hosts.R | 118 inst/doc/set_hosts.Rmd | 298 - inst/doc/set_hosts.html | 1001 ++--- man/create_gitstats.Rd | 34 man/get_commits.Rd | 104 man/get_commits_stats.Rd | 94 man/get_files.Rd | 204 - man/get_issues.Rd | 112 man/get_issues_stats.Rd | 94 man/get_orgs.Rd | 76 man/get_release_logs.Rd | 94 man/get_repos.Rd | 158 man/get_repos_trees.Rd | 116 man/get_repos_urls.Rd | 130 man/get_storage.Rd | 78 man/get_users.Rd | 78 man/is_verbose.Rd | 28 man/pipe.Rd | 40 man/set_github_host.Rd | 116 man/set_gitlab_host.Rd | 118 man/show_orgs.Rd | 38 man/verbose_off.Rd | 34 man/verbose_on.Rd | 34 tests/spelling.R | 6 tests/testthat.R | 24 tests/testthat/_snaps/00-get_orgs-GitHub.md | 52 tests/testthat/_snaps/00-get_orgs-GitLab.md | 214 - tests/testthat/_snaps/00-get_orgs-GitStats.md | 14 tests/testthat/_snaps/01-get_repos-GitHub.md | 154 tests/testthat/_snaps/01-get_repos-GitLab.md | 170 tests/testthat/_snaps/01-get_repos-GitStats.md | 30 tests/testthat/_snaps/02-get_commits-GitHub.md | 14 tests/testthat/_snaps/02-get_commits-GitLab.md | 34 tests/testthat/_snaps/02-get_commits-GitStats.md | 42 tests/testthat/_snaps/03-get_files_structure-GitHub.md | 110 tests/testthat/_snaps/03-get_files_structure-GitLab.md | 23 tests/testthat/_snaps/03-get_repos_trees-GitStats.md | 36 tests/testthat/_snaps/04-get_files_content-GitHub.md | 29 tests/testthat/_snaps/04-get_files_content-GitLab.md | 80 tests/testthat/_snaps/05-get_files.md | 24 tests/testthat/_snaps/06-get_issues-GitHub.md | 14 tests/testthat/_snaps/06-get_issues-GitLab.md | 14 tests/testthat/_snaps/06-get_issues-GitStats.md | 34 tests/testthat/_snaps/get_commits_stats.md | 10 tests/testthat/_snaps/get_issues_stats.md | 10 tests/testthat/_snaps/get_release-GitHub.md | 14 tests/testthat/_snaps/get_release-GitLab.md | 46 tests/testthat/_snaps/get_release-GitStats.md | 34 tests/testthat/_snaps/get_urls_repos-GitHub.md | 42 tests/testthat/_snaps/get_urls_repos-GitStats.md | 16 tests/testthat/_snaps/get_user-GitHub.md | 14 tests/testthat/_snaps/get_user-GitLab.md | 14 tests/testthat/_snaps/get_users-GitStats.md | 16 tests/testthat/_snaps/helpers.md | 130 tests/testthat/_snaps/set_host.md | 287 - tests/testthat/_snaps/z-GitStats.md | 180 tests/testthat/helper-error-fixtures.R | 206 - tests/testthat/helper-expect-responses.R | 648 +-- tests/testthat/helper-expect-tables.R | 226 - tests/testthat/helper-fixtures.R | 2134 +++++------ tests/testthat/helper.R | 154 tests/testthat/setup.R | 125 tests/testthat/test-00-api-requests.R | 238 - tests/testthat/test-00-get_orgs-GitHub.R | 338 - tests/testthat/test-00-get_orgs-GitLab.R | 944 ++--- tests/testthat/test-00-get_orgs-GitStats.R | 134 tests/testthat/test-00-graphql_errors.R | 58 tests/testthat/test-01-get_repos-GitHub.R | 1481 ++++--- tests/testthat/test-01-get_repos-GitLab.R | 1184 +++--- tests/testthat/test-01-get_repos-GitStats.R | 364 - tests/testthat/test-02-get_commits-GitHub.R | 467 +- tests/testthat/test-02-get_commits-GitLab.R | 386 +- tests/testthat/test-02-get_commits-GitStats.R | 246 - tests/testthat/test-03-get_files_structure-GitHub.R | 772 +--- tests/testthat/test-03-get_files_structure-GitLab.R | 557 +- tests/testthat/test-03-get_repos_trees-GitStats.R | 160 tests/testthat/test-04-get_files-REST-GitHub.R | 74 tests/testthat/test-04-get_files-REST-GitLab.R | 96 tests/testthat/test-04-get_files_content-GitHub.R | 320 - tests/testthat/test-04-get_files_content-GitLab.R | 505 +- tests/testthat/test-05-get_files.R | 224 - tests/testthat/test-06-get_issues-GitHub.R | 467 +- tests/testthat/test-06-get_issues-GitLab.R | 407 +- tests/testthat/test-06-get_issues-GitStats.R | 222 - tests/testthat/test-GitHost-helpers.R | 138 tests/testthat/test-get_commits_stats.R | 68 tests/testthat/test-get_issues_stats.R | 67 tests/testthat/test-get_release-GitHub.R | 262 - tests/testthat/test-get_release-GitLab.R | 304 - tests/testthat/test-get_release-GitStats.R | 156 tests/testthat/test-get_storage.R | 98 tests/testthat/test-get_urls_repos-GitHub.R | 652 +-- tests/testthat/test-get_urls_repos-GitLab.R | 384 +- tests/testthat/test-get_urls_repos-GitStats.R | 278 - tests/testthat/test-get_user-GitHub.R | 90 tests/testthat/test-get_user-GitLab.R | 94 tests/testthat/test-get_users-GitStats.R | 120 tests/testthat/test-helpers.R | 442 +- tests/testthat/test-set_host.R | 396 +- tests/testthat/test-show_orgs.R | 12 tests/testthat/test-utils.R | 62 tests/testthat/test-z-GitStats.R | 288 - vignettes/get_repos_with_code.Rmd | 110 vignettes/set_hosts.Rmd | 298 - 143 files changed, 20892 insertions(+), 20548 deletions(-)
Title: Tools for Post-Processing Predicted Values
Description: Models can be improved by post-processing class
probabilities, by: recalibration, conversion to hard probabilities,
assessment of equivocal zones, and other activities. 'probably'
contains tools for conducting these operations as well as calibration
tools and conformal inference techniques for regression models.
Author: Max Kuhn [aut, cre],
Davis Vaughan [aut],
Edgar Ruiz [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between probably versions 1.1.1 dated 2025-07-30 and 1.2.0 dated 2025-10-16
probably-1.1.1/probably/R/cal-estimate-multinom.R |only probably-1.1.1/probably/R/conformal_infer.R |only probably-1.1.1/probably/tests/testthat/_snaps/bound-prediction.md |only probably-1.1.1/probably/tests/testthat/_snaps/cal-estimate.md |only probably-1.1.1/probably/tests/testthat/_snaps/cal-plot.md |only probably-1.1.1/probably/tests/testthat/_snaps/conformal-intervals-quantile.md |only probably-1.1.1/probably/tests/testthat/_snaps/conformal-intervals-split.md |only probably-1.1.1/probably/tests/testthat/_snaps/conformal-intervals.md |only probably-1.1.1/probably/tests/testthat/_snaps/make-class-pred.md |only probably-1.1.1/probably/tests/testthat/_snaps/threshold-perf.md |only probably-1.1.1/probably/tests/testthat/test-bound-prediction.R |only probably-1.1.1/probably/tests/testthat/test-cal-estimate.R |only probably-1.1.1/probably/tests/testthat/test-cal-plot.R |only probably-1.1.1/probably/tests/testthat/test-conformal-intervals-quantile.R |only probably-1.1.1/probably/tests/testthat/test-conformal-intervals-split.R |only probably-1.1.1/probably/tests/testthat/test-conformal-intervals.R |only probably-1.1.1/probably/tests/testthat/test-make-class-pred.R |only probably-1.1.1/probably/tests/testthat/test-threshold-perf.R |only probably-1.2.0/probably/DESCRIPTION | 20 probably-1.2.0/probably/MD5 | 161 +-- probably-1.2.0/probably/NAMESPACE | 4 probably-1.2.0/probably/NEWS.md | 6 probably-1.2.0/probably/R/bound_prediction.R | 15 probably-1.2.0/probably/R/butcher.R |only probably-1.2.0/probably/R/cal-apply-binary.R | 20 probably-1.2.0/probably/R/cal-apply-impl.R | 5 probably-1.2.0/probably/R/cal-apply.R | 70 - probably-1.2.0/probably/R/cal-estimate-beta.R | 86 - probably-1.2.0/probably/R/cal-estimate-isotonic.R | 29 probably-1.2.0/probably/R/cal-estimate-linear.R | 65 - probably-1.2.0/probably/R/cal-estimate-logistic.R | 8 probably-1.2.0/probably/R/cal-estimate-multinomial.R |only probably-1.2.0/probably/R/cal-estimate-none.R | 63 - probably-1.2.0/probably/R/cal-estimate-utils.R | 99 +- probably-1.2.0/probably/R/cal-plot-breaks.R | 212 ++-- probably-1.2.0/probably/R/cal-plot-logistic.R | 184 ++-- probably-1.2.0/probably/R/cal-plot-regression.R | 60 - probably-1.2.0/probably/R/cal-plot-utils.R | 104 +- probably-1.2.0/probably/R/cal-plot-windowed.R | 230 ++--- probably-1.2.0/probably/R/cal-utils.R | 5 probably-1.2.0/probably/R/cal-validate.R | 448 +++++----- probably-1.2.0/probably/R/class-pred.R | 15 probably-1.2.0/probably/R/conformal_infer_cv.R | 35 probably-1.2.0/probably/R/conformal_infer_full.R |only probably-1.2.0/probably/R/conformal_infer_quantile.R | 14 probably-1.2.0/probably/R/conformal_infer_split.R | 28 probably-1.2.0/probably/R/make_class_pred.R | 36 probably-1.2.0/probably/R/printing.R | 8 probably-1.2.0/probably/R/probably-package.R | 23 probably-1.2.0/probably/R/threshold_perf.R | 21 probably-1.2.0/probably/R/utils.R | 4 probably-1.2.0/probably/R/vctrs-compat.R | 8 probably-1.2.0/probably/R/zzz.R | 24 probably-1.2.0/probably/build/vignette.rds |binary probably-1.2.0/probably/inst/doc/equivocal-zones.html | 9 probably-1.2.0/probably/inst/doc/where-to-use.html | 9 probably-1.2.0/probably/man/cal_estimate_multinomial.Rd | 4 probably-1.2.0/probably/man/control_conformal_full.Rd | 2 probably-1.2.0/probably/man/inf_conformal-butcher.Rd |only probably-1.2.0/probably/man/int_conformal_cv.Rd | 2 probably-1.2.0/probably/man/int_conformal_full.Rd | 73 + probably-1.2.0/probably/man/int_conformal_quantile.Rd | 2 probably-1.2.0/probably/man/int_conformal_split.Rd | 2 probably-1.2.0/probably/man/predict.int_conformal_full.Rd | 10 probably-1.2.0/probably/man/probably-package.Rd | 2 probably-1.2.0/probably/man/required_pkgs.cal_object.Rd | 4 probably-1.2.0/probably/man/required_pkgs.int_conformal_cv.Rd |only probably-1.2.0/probably/tests/testthat/_snaps/bound_prediction.md |only probably-1.2.0/probably/tests/testthat/_snaps/cal-estimate-isotonic.md | 17 probably-1.2.0/probably/tests/testthat/_snaps/cal-estimate-linear.md | 35 probably-1.2.0/probably/tests/testthat/_snaps/cal-plot-breaks.md |only probably-1.2.0/probably/tests/testthat/_snaps/cal-plot-logistic.md |only probably-1.2.0/probably/tests/testthat/_snaps/cal-plot-regression.md |only probably-1.2.0/probably/tests/testthat/_snaps/cal-plot-windowed.md |only probably-1.2.0/probably/tests/testthat/_snaps/conformal_infer_cv.md |only probably-1.2.0/probably/tests/testthat/_snaps/conformal_infer_full.md |only probably-1.2.0/probably/tests/testthat/_snaps/conformal_infer_quantile.md |only probably-1.2.0/probably/tests/testthat/_snaps/conformal_infer_split.md |only probably-1.2.0/probably/tests/testthat/_snaps/make_class_pred.md |only probably-1.2.0/probably/tests/testthat/_snaps/threshold_perf.md |only probably-1.2.0/probably/tests/testthat/helper-cal.R | 29 probably-1.2.0/probably/tests/testthat/test-bound_prediction.R |only probably-1.2.0/probably/tests/testthat/test-butcher.R |only probably-1.2.0/probably/tests/testthat/test-cal-apply-binary.R |only probably-1.2.0/probably/tests/testthat/test-cal-apply-multi.R |only probably-1.2.0/probably/tests/testthat/test-cal-apply-regression.R |only probably-1.2.0/probably/tests/testthat/test-cal-apply.R | 84 - probably-1.2.0/probably/tests/testthat/test-cal-estimate-beta.R | 5 probably-1.2.0/probably/tests/testthat/test-cal-estimate-isotonic.R | 55 + probably-1.2.0/probably/tests/testthat/test-cal-estimate-linear.R | 72 - probably-1.2.0/probably/tests/testthat/test-cal-estimate-logistic.R | 48 - probably-1.2.0/probably/tests/testthat/test-cal-estimate-multinomial.R | 50 - probably-1.2.0/probably/tests/testthat/test-cal-estimate-none.R | 5 probably-1.2.0/probably/tests/testthat/test-cal-plot-breaks.R |only probably-1.2.0/probably/tests/testthat/test-cal-plot-logistic.R |only probably-1.2.0/probably/tests/testthat/test-cal-plot-regression.R |only probably-1.2.0/probably/tests/testthat/test-cal-plot-windowed.R |only probably-1.2.0/probably/tests/testthat/test-cal-validate-multiclass.R | 20 probably-1.2.0/probably/tests/testthat/test-cal-validate.R | 210 ++++ probably-1.2.0/probably/tests/testthat/test-class-pred.R | 20 probably-1.2.0/probably/tests/testthat/test-conformal_infer_cv.R |only probably-1.2.0/probably/tests/testthat/test-conformal_infer_full.R |only probably-1.2.0/probably/tests/testthat/test-conformal_infer_quantile.R |only probably-1.2.0/probably/tests/testthat/test-conformal_infer_split.R |only probably-1.2.0/probably/tests/testthat/test-make_class_pred.R |only probably-1.2.0/probably/tests/testthat/test-threshold_perf.R |only 106 files changed, 1780 insertions(+), 1099 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It works with data from a Freesurfer analysis (cortical thickness,
volumes, local gyrification index, surface area), diffusion tensor
tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from
DPABI). It contains a graphical user interface for graph visualization and
data exploration, along with several functions for generating useful
figures.
Author: Christopher G. Watson [aut, cre]
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 3.1.0 dated 2024-04-04 and 3.1.1 dated 2025-10-16
DESCRIPTION | 14 ++-- MD5 | 136 +++++++++++++++++++++---------------------- NEWS.md | 7 ++ R/plot_global.R | 2 R/sysdata.rda |binary build/partial.rdb |binary data/aal116.rda |binary data/aal2.120.rda |binary data/aal2.94.rda |binary data/aal90.rda |binary data/brainnetome.rda |binary data/brainsuite.rda |binary data/craddock200.rda |binary data/destrieux.rda |binary data/destrieux.scgm.rda |binary data/dk.rda |binary data/dk.scgm.rda |binary data/dkt.rda |binary data/dkt.scgm.rda |binary data/dosenbach160.rda |binary data/gordon333.rda |binary data/hcp_mmp1.0.rda |binary data/hoa112.rda |binary data/lpba40.rda |binary data/power264.rda |binary man/Bootstrapping.Rd | 38 +++++++----- man/NBS.Rd | 43 +++++++++---- man/attributes.Rd | 19 ++++-- man/brainGraph.Rd | 14 ++++ man/brainGraphList.Rd | 81 ++++++++++++++++++------- man/brainGraph_permute.Rd | 67 ++++++++++++++------- man/brain_atlases.Rd | 42 ++++++++++++- man/centr_betw_comm.Rd | 3 man/centr_lev.Rd | 3 man/correlation_matrices.Rd | 38 ++++++++---- man/count_edges.Rd | 7 +- man/create_mats.Rd | 16 +++-- man/efficiency.Rd | 13 +++- man/glm.Rd | 60 +++++++++++++----- man/glm_brainGraphList.Rd | 62 ++++++++++++++----- man/glm_design.Rd | 20 ++++-- man/glm_fit.Rd | 88 ++++++++++++++++++++------- man/glm_graph_plots.Rd | 64 ++++++++++++++------ man/glm_helpers.Rd | 14 +++- man/import_scn.Rd | 21 ++++-- man/individ_contrib.Rd | 24 ++++--- man/inverse.Rd | 10 ++- man/make_auc_brainGraph.Rd | 3 man/make_brainGraph.Rd | 99 ++++++++++++++++++++++--------- man/make_ego_brainGraph.Rd | 7 +- man/matrix_utils.Rd | 3 man/mean_distance_wt.Rd | 10 ++- man/mediation.Rd | 42 ++++++++++--- man/mtpc.Rd | 69 +++++++++++++++------ man/plot.brainGraph.Rd | 32 +++++++--- man/plot.brainGraphList.Rd | 10 +-- man/plot_brainGraph_multi.Rd | 33 +++++++--- man/plot_global.Rd | 14 +++- man/plot_rich_norm.Rd | 16 +++-- man/plot_vertex_measures.Rd | 13 +++- man/plot_volumetric.Rd | 21 ++++-- man/random_graphs.Rd | 49 +++++++++++---- man/randomise.Rd | 38 ++++++++++-- man/residuals.Rd | 29 +++++---- man/rich_club.Rd | 8 +- man/rich_club_attrs.Rd | 5 - man/robustness.Rd | 8 +- man/vertex_roles.Rd | 9 ++ man/write_brainnet.Rd | 9 ++ 69 files changed, 1007 insertions(+), 426 deletions(-)