Title: Calculate Textures from Grey-Level Co-Occurrence Matrices
(GLCMs)
Description: Enables calculation of image textures (Haralick 1973)
<doi:10.1109/TSMC.1973.4309314> from grey-level co-occurrence matrices
(GLCMs). Supports processing images that cannot fit in memory.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff <azvoleff@conservation.org>
Diff between glcm versions 1.6.5 dated 2020-02-26 and 1.6.6 dated 2025-11-11
DESCRIPTION | 14 ++++---- MD5 | 31 +++++++++---------- NAMESPACE | 2 - NEWS | 4 ++ R/glcm-package.R | 60 +++++++++++++++++-------------------- R/glcm.R | 9 ++++- README.md | 9 ++--- data/test_raster.RData |binary man/L5TSR_1986.Rd | 18 +++++------ man/calc_glcm_edge.Rd |only man/expected_textures_3x3_1x1.Rd | 12 +++---- man/expected_textures_5x3_n1xn2.Rd | 12 +++---- man/expected_textures_5x7_2x3.Rd | 12 +++---- man/glcm-package.Rd | 38 ++++++++++++++--------- man/test_raster.Rd | 2 - src/RcppExports.cpp | 5 +++ src/calc_texture.cpp | 7 ++-- 17 files changed, 129 insertions(+), 106 deletions(-)
Title: Interface for Multilevel Regression and Poststratification
Description: Dual interfaces, graphical and programmatic, designed for
intuitive applications of Multilevel Regression and Poststratification (MRP).
Users can apply the method to a variety of datasets, from electronic health records
to sample survey data, through an end-to-end Bayesian data analysis workflow.
The package provides robust tools for data cleaning, exploratory analysis,
flexible model building, and insightful result visualization. For more details, see
Si et al. (2020) <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2020002/article/00003-eng.pdf?st=iF1_Fbrh>
and Si (2025) <doi:10.1214/24-STS932>.
Author: Toan Tran [cre, aut, cph],
Jonah Gabry [aut, cph],
Yajuan Si [aut, cph]
Maintainer: Toan Tran <trannttoan97@gmail.com>
Diff between shinymrp versions 0.9.0 dated 2025-10-09 and 0.9.1 dated 2025-11-11
shinymrp-0.9.0/shinymrp/vignettes/data/model.qs |only shinymrp-0.9.0/shinymrp/vignettes/data/workflow.qs |only shinymrp-0.9.1/shinymrp/DESCRIPTION | 8 shinymrp-0.9.1/shinymrp/MD5 | 53 ++--- shinymrp-0.9.1/shinymrp/NEWS.md | 11 + shinymrp-0.9.1/shinymrp/R/example.R | 4 shinymrp-0.9.1/shinymrp/R/fct_data.R | 67 ++++-- shinymrp-0.9.1/shinymrp/R/mod_analyze_model.R | 10 - shinymrp-0.9.1/shinymrp/R/mod_analyze_upload.R | 60 +++--- shinymrp-0.9.1/shinymrp/R/model.R | 8 shinymrp-0.9.1/shinymrp/R/utils.R | 2 shinymrp-0.9.1/shinymrp/R/utils_server.R | 1 shinymrp-0.9.1/shinymrp/README.md | 6 shinymrp-0.9.1/shinymrp/build/partial.rdb |binary shinymrp-0.9.1/shinymrp/build/vignette.rds |binary shinymrp-0.9.1/shinymrp/inst/doc/example.R | 4 shinymrp-0.9.1/shinymrp/inst/doc/example.Rmd | 4 shinymrp-0.9.1/shinymrp/inst/doc/example.html | 4 shinymrp-0.9.1/shinymrp/inst/doc/workflow.R | 8 shinymrp-0.9.1/shinymrp/inst/doc/workflow.Rmd | 10 - shinymrp-0.9.1/shinymrp/inst/doc/workflow.html | 100 ++++------ shinymrp-0.9.1/shinymrp/man/MRPModel-method-save.Rd | 4 shinymrp-0.9.1/shinymrp/tests/testthat/test-data-processing.R | 29 ++ shinymrp-0.9.1/shinymrp/tests/testthat/test-example.R | 4 shinymrp-0.9.1/shinymrp/tests/testthat/test-mrp-model.R | 2 shinymrp-0.9.1/shinymrp/vignettes/data/model.qs2 |only shinymrp-0.9.1/shinymrp/vignettes/data/workflow.qs2 |only shinymrp-0.9.1/shinymrp/vignettes/example.Rmd | 4 shinymrp-0.9.1/shinymrp/vignettes/spatial_prior.html |only shinymrp-0.9.1/shinymrp/vignettes/workflow.Rmd | 10 - 30 files changed, 233 insertions(+), 180 deletions(-)
Title: Map Image Classification Efficacy
Description: Map image classification efficacy (MICE) adjusts the accuracy rate relative to a random classification baseline (Shao et al. (2021)<doi:10.1109/ACCESS.2021.3116526> and Tang et al. (2024)<doi:10.1109/TGRS.2024.3446950>). Only the proportions from the reference labels are considered, as opposed to the proportions from the reference and predictions, as is the case for the Kappa statistic. This package offers means to calculate MICE and adjusted versions of class-level user's accuracy (i.e., precision) and producer's accuracy (i.e., recall) and F1-scores. Class-level metrics are aggregated using macro-averaging. Functions are also made available to estimate confidence intervals using bootstrapping and statistically compare two classification results.
Author: Aaron Maxwell [aut, cre, cph],
Sarah Farhadpour [aut]
Maintainer: Aaron Maxwell <Aaron.Maxwell@mail.wvu.edu>
Diff between micer versions 0.2.0 dated 2025-01-20 and 0.2.1 dated 2025-11-11
DESCRIPTION | 13 +-- MD5 | 16 ++-- R/micer.R | 14 +--- inst/doc/micerExamples.R | 5 - inst/doc/micerExamples.Rmd | 7 -- inst/doc/micerExamples.html | 144 +++++++++++++++++++++----------------------- man/miceCI.Rd | 5 - man/miceCompare.Rd | 7 -- vignettes/micerExamples.Rmd | 7 -- 9 files changed, 95 insertions(+), 123 deletions(-)
Title: Feature Selection in R
Description: Feature subset selection algorithms modularized in search algorithms and measure utilities.
Author: Alfonso Jimenez-Vilchez [aut, cre] ,
Francisco Aragon-Royon [aut] ,
Adan M. Rodriguez [aut],
Antonio Arauzo-Azofra [aut] ,
Jose Manuel Benitez [aut]
Maintainer: Alfonso Jimenez-Vilchez <i52jivia@uco.es>
Diff between FSinR versions 2.0.9 dated 2025-10-23 and 2.0.10 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ NEWS.md | 4 ++++ build/partial.rdb |binary inst/REFERENCES.bib | 2 +- inst/doc/FSinR.html | 12 ++++++------ inst/doc/methods.html | 34 ++++++++++++++++++++++------------ 8 files changed, 48 insertions(+), 30 deletions(-)
Title: Coarsened Mixtures of Hierarchical Skew Kernels
Description: Bayesian fit of a Dirichlet Process Mixture with hierarchical multivariate skew normal kernels and coarsened posteriors. For more information, see Gorsky, Chan and Ma (2024) <doi:10.1214/22-BA1356>.
Author: S. Gorsky [aut, cre],
C. Chan [ctb],
L. Ma [ctb]
Maintainer: S. Gorsky <sgorsky@umass.edu>
Diff between COMIX versions 1.0.0 dated 2022-11-23 and 1.0.1 dated 2025-11-11
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- build/vignette.rds |binary src/Makevars | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: A Tool for Semi-Automating the Statistical Disclosure Control of
Research Outputs
Description: A Tool for Semi-Automating the Statistical Disclosure Control of Research Outputs.
Author: Jim Smith [cre, ctb] ,
Maha Albashir [aut, ctb],
Richard John Preen [aut, ctb]
Maintainer: Jim Smith <James.Smith@uwe.ac.uk>
Diff between acro versions 0.1.5 dated 2025-07-03 and 0.1.6 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++++++------ NEWS.md | 6 ++++++ R/create_virtualenv.R | 7 ++++--- README.md | 14 ++++++++++++-- inst/INSTALL.md |only inst/Images/settingpython-rstudio-step0.png |only inst/Images/settingpython-rstudio-step1.png |only inst/Images/settingpython-rstudio-step2.png |only inst/Images/settingpython-rstudio-step3.png |only inst/WORDLIST | 12 ++++++++++++ inst/binder |only tests/testthat/Rplots.pdf |binary 13 files changed, 52 insertions(+), 15 deletions(-)
Title: Proteomics Data Analysis and Modeling Tools
Description: A comprehensive, user-friendly package for label-free proteomics data analysis and machine learning-based modeling. Data generated from 'MaxQuant' can be easily used to conduct differential expression analysis, build predictive models with top protein candidates, and assess model performance. promor includes a suite of tools for quality control, visualization, missing data imputation (Lazar et. al. (2016) <doi:10.1021/acs.jproteome.5b00981>), differential expression analysis (Ritchie et. al. (2015) <doi:10.1093/nar/gkv007>), and machine learning-based modeling (Kuhn (2008) <doi:10.18637/jss.v028.i05>).
Author: Chathurani Ranathunge [aut, cre, cph]
Maintainer: Chathurani Ranathunge <caranathunge86@gmail.com>
This is a re-admission after prior archival of version 0.2.1 dated 2023-07-17
Diff between promor versions 0.2.1 dated 2023-07-17 and 0.2.2 dated 2025-11-11
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/handleNA.R | 23 ++++++----------------- README.md | 2 +- inst/doc/intro_to_promor.R | 4 ++-- man/impute_na.Rd | 20 ++++---------------- man/impute_plot.Rd | 2 +- tests/testthat/test-protein_analysis.R | 19 ------------------- 9 files changed, 34 insertions(+), 70 deletions(-)
Title: Native Access Medical Record Retriever for High Yield Analytics
Description: A toolkit for medical records data analysis. The 'naryn'
package implements an efficient data structure for storing medical
records, and provides a set of functions for data extraction,
manipulation and analysis.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Ben Gilat [aut],
Netta Mendelson-Cohen [ctb],
Rami Jaschek [ctb],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between naryn versions 2.6.30 dated 2024-09-27 and 2.6.31 dated 2025-11-11
DESCRIPTION | 9 MD5 | 16 NEWS.md | 5 R/db.R | 2 R/filter.R | 5 inst/doc/advanced.html | 1199 ++++++++++++++++++++++++++++++++++++++----------- man/emr_db.connect.Rd | 2 src/NRTest.cpp | 2 src/naryn.cpp | 18 9 files changed, 980 insertions(+), 278 deletions(-)
Title: Machine Learning Modelling for Everyone
Description: A minimal library specifically designed to make the estimation of
Machine Learning (ML) techniques as easy and accessible as possible,
particularly within the framework of the Knowledge Discovery in
Databases (KDD) process in data mining. The package provides
essential tools to structure and execute each stage of a predictive
or classification modeling workflow, aligning closely with the
fundamental steps of the KDD methodology, from data selection and
preparation, through model building and tuning, to the
interpretation and evaluation of results using Sensitivity Analysis.
The 'MLwrap' workflow is organized into four core steps;
preprocessing(), build_model(), fine_tuning(), and
sensitivity_analysis(). These steps correspond, respectively, to
data preparation and transformation, model construction,
hyperparameter optimization, and sensitivity analysis. The user can
access comprehensive model evaluation results including fit
assessment metrics, plots, predictions, and performance diagn [...truncated...]
Author: Javier Martinez Garcia [aut] ,
Juan Jose Montano Moreno [ctb] ,
Albert Sese [cre, ctb]
Maintainer: Albert Sese <albert.sese@uib.es>
Diff between MLwrap versions 0.2.2 dated 2025-11-05 and 0.2.3 dated 2025-11-11
DESCRIPTION | 12 +- MD5 | 18 +-- R/InterpretableML.R | 6 - R/permutation_feature_importance.R | 218 +++++++++++++++++++++++++++++++------ R/table_utils.R | 47 ++++--- README.md | 2 build/partial.rdb |binary man/sensitivity_analysis.Rd | 6 - man/table_pfi_results.Rd | 26 +--- man/table_shap_results.Rd | 23 ++- 10 files changed, 257 insertions(+), 101 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.3.5 dated 2025-11-07 and 0.3.6 dated 2025-11-11
DESCRIPTION | 14 +++++++------- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 10 ++++++++-- R/cms_download_subset.r | 10 +--------- R/cms_login.r | 3 +-- R/translate.R | 2 +- inst/doc/translate.R | 6 ++++-- inst/doc/translate.Rmd | 6 ++++-- inst/doc/translate.html | 6 ++++-- man/account.Rd | 2 +- man/cms_download_native.Rd | 2 +- man/cms_download_subset.Rd | 12 +----------- man/cms_translate.Rd | 2 +- man/cms_wmts.Rd | 2 +- tests/testthat.R | 1 - tests/testthat/test_subset.r | 1 + vignettes/translate.Rmd | 6 ++++-- 17 files changed, 56 insertions(+), 61 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Grain-Size Statistics and Description of Sediment
Description: Full descriptive statistics, physical description of sediment,
metric or phi sieves. Includes a Shiny web application for
interactive grain size analysis and visualization.
Author: Regis K. Gallon [aut, cre] ,
Jerome Fournier [aut]
Maintainer: Regis K. Gallon <regis.gallon@lecnam.net>
Diff between G2Sd versions 2.1.5 dated 2015-12-07 and 2.2 dated 2025-11-11
G2Sd-2.1.5/G2Sd/data/coord_gran.rda |only G2Sd-2.1.5/G2Sd/inst/extdata/www/R_logo.png |only G2Sd-2.1.5/G2Sd/inst/extdata/www/bootstrap3.css |only G2Sd-2.1.5/G2Sd/inst/extdata/www/cnrs.gif |only G2Sd-2.1.5/G2Sd/inst/extdata/www/mnhn.gif |only G2Sd-2.1.5/G2Sd/man/coord_gran.Rd |only G2Sd-2.2/G2Sd/DESCRIPTION | 33 G2Sd-2.2/G2Sd/MD5 | 41 G2Sd-2.2/G2Sd/NAMESPACE | 44 G2Sd-2.2/G2Sd/NEWS | 18 G2Sd-2.2/G2Sd/R/G2Sd-internal.R | 1068 +++++++++++------------- G2Sd-2.2/G2Sd/R/grandistrib.R | 83 + G2Sd-2.2/G2Sd/R/granplot.R | 292 +++++- G2Sd-2.2/G2Sd/R/granstat.R | 215 ++-- G2Sd-2.2/G2Sd/README.md |only G2Sd-2.2/G2Sd/inst/CITATION | 11 G2Sd-2.2/G2Sd/inst/INDEX | 16 G2Sd-2.2/G2Sd/inst/extdata/server.R | 880 ++++++++++++++++--- G2Sd-2.2/G2Sd/inst/extdata/ui.R | 442 ++++++++- G2Sd-2.2/G2Sd/inst/extdata/www/G2SdLogo.png |only G2Sd-2.2/G2Sd/inst/extdata/www/cnam_logo.png |only G2Sd-2.2/G2Sd/man/G2Sd-package.Rd | 102 +- G2Sd-2.2/G2Sd/man/grandistrib.Rd | 96 +- G2Sd-2.2/G2Sd/man/granplot.Rd | 20 G2Sd-2.2/G2Sd/man/granstat.Rd | 245 ++--- G2Sd-2.2/G2Sd/man/granulo.Rd | 56 - 26 files changed, 2413 insertions(+), 1249 deletions(-)
Title: Test Robustness with Directed Acyclic Graphs
Description: Provides robustness checks to align estimands with the identification
that they require. Given a 'dagitty' object and a model specification,
'DAGassist' classifies variables by causal roles, flags problematic controls,
and generates a report comparing the original model with minimal and canonical
adjustment sets. Exports publication-grade reports in 'LaTeX', 'Word', 'Excel',
'dotwhisker', or plain text/'markdown'. 'DAGassist' is built on 'dagitty', an
'R' package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for
creating and analyzing DAGs. Methods draw on Pearl (2009) <doi:10.1017/CBO9780511803161>
and Textor et al. (2016) <doi:10.1093/ije/dyw341>.
Author: Graham Goff [aut, cre] ,
Michael Denly [aut]
Maintainer: Graham Goff <goffgrahamc@gmail.com>
Diff between DAGassist versions 0.2.4 dated 2025-09-21 and 0.2.7 dated 2025-11-11
DESCRIPTION | 36 - MD5 | 57 +-- NAMESPACE | 1 NEWS.md | 31 + R/assist.R | 817 ++++++++++++++++++++++++++++++++----------- R/assist_helpers.R | 173 ++++++++- R/classify.R | 273 +++++++------- R/dotwhisker.R |only R/export_helpers.R | 18 R/report_excel.R | 33 + R/report_latex.R | 224 ++++++++--- R/report_text.R | 65 ++- R/report_word.R | 36 + R/validate.R | 21 - README.md | 71 ++- inst/doc/get-started.R | 115 +++--- inst/doc/get-started.Rmd | 186 ++++++--- inst/doc/get-started.html | 616 ++++++++++++++++---------------- inst/doc/making-reports.R | 50 ++ inst/doc/making-reports.Rmd | 74 +++ inst/doc/making-reports.html | 406 +++++++++++++++++++-- inst/doc/quick-tour.R | 29 + inst/doc/quick-tour.Rmd | 34 + inst/doc/quick-tour.html | 48 +- man/DAGassist.Rd | 147 +++++-- man/art |only man/classify_nodes.Rd | 61 +-- man/figures/logo.png |only vignettes/get-started.Rmd | 186 ++++++--- vignettes/making-reports.Rmd | 74 +++ vignettes/quick-tour.Rmd | 34 + 31 files changed, 2752 insertions(+), 1164 deletions(-)
Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, rational expectations, endogenous targeting and model renormalization, structural stability, stochastic simulation and forecast, optimal control, by A. Luciani (2022) <doi:10.13140/RG.2.2.31160.83202>.
Author: Andrea Luciani [aut, cre] ,
Roberto Stok [aut],
Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>
Diff between bimets versions 4.1.1 dated 2025-10-30 and 4.1.2 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/bimets_ts_functions.R | 2 +- README.md | 10 +++++----- inst/doc/bimets.pdf |binary inst/doc/frb2bimets.pdf |binary man/MDL.Rd | 4 ++-- man/RENORM.Rd | 2 +- man/SIMULATE.Rd | 4 ++-- man/STOCHSIMULATE.Rd | 2 +- man/bimets-package.Rd | 6 ++---- 12 files changed, 35 insertions(+), 31 deletions(-)
Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] ,
Riccardo Corradin [aut],
Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Diff between BayesChange versions 2.1.2 dated 2025-11-05 and 2.1.3 dated 2025-11-11
DESCRIPTION | 6 MD5 | 52 ++-- NAMESPACE | 48 ++-- NEWS.md | 2 R/BayesChange-package.R | 24 +- inst/doc/tutorial.html | 209 ++++++++++--------- man/BayesChange-package.Rd | 58 ++--- man/ClustCpObj.Rd | 104 ++++----- man/DetectCpObj.Rd | 116 +++++------ man/clust_cp.Rd | 358 +++++++++++++++++----------------- man/clust_cp_epi.Rd | 186 ++++++++--------- man/clust_cp_multi.Rd | 160 +++++++-------- man/clust_cp_uni.Rd | 128 ++++++------ man/detect_cp.Rd | 288 +++++++++++++-------------- man/detect_cp_multi.Rd | 134 ++++++------ man/detect_cp_uni.Rd | 118 +++++------ man/plot.ClustCpObj.Rd | 174 ++++++++-------- man/plot.DetectCpObj.Rd | 110 +++++----- man/posterior_estimate.ClustCpObj.Rd | 116 +++++------ man/posterior_estimate.DetectCpObj.Rd | 106 +++++----- man/posterior_estimate.Rd | 24 +- man/print.ClustCpObj.Rd | 64 +++--- man/print.DetectCpObj.Rd | 62 ++--- man/sim_epi_data.Rd | 72 +++--- man/summary.ClustCpObj.Rd | 64 +++--- man/summary.DetectCpObj.Rd | 64 +++--- tests/testthat.R | 24 +- 27 files changed, 1444 insertions(+), 1427 deletions(-)
Title: Marginal Structural Models with Latent Class Growth Analysis of
Treatment Trajectories
Description: Implements marginal structural models combined with a latent class growth analysis framework for assessing the causal effect of treatment trajectories. Based on the approach described in "Marginal Structural Models with Latent Class Growth Analysis of Treatment Trajectories" Diop, A., Sirois, C., Guertin, J.R., Schnitzer, M.E., Candas, B., Cossette, B., Poirier, P., Brophy, J., Mésidor, M., Blais, C. and Hamel, D., (2023) <doi:10.1177/09622802231202384>.
Author: Awa Diop [aut, cre],
Denis Talbot [aut]
Maintainer: Awa Diop <awa.diop.2@ulaval.ca>
Diff between trajmsm versions 0.1.4 dated 2025-06-16 and 0.1.5 dated 2025-11-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/trajmsm_ipw.R | 1 - 3 files changed, 5 insertions(+), 6 deletions(-)
Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between slendr versions 1.2.0 dated 2025-07-31 and 1.3.0 dated 2025-11-11
slendr-1.2.0/slendr/inst/extdata/models/introgression/__pycache__/script.cpython-312.pyc |only slendr-1.3.0/slendr/DESCRIPTION | 13 - slendr-1.3.0/slendr/MD5 | 130 +++++----- slendr-1.3.0/slendr/NAMESPACE | 1 slendr-1.3.0/slendr/NEWS.md | 12 slendr-1.3.0/slendr/R/interface.R | 1 slendr-1.3.0/slendr/R/shiny.R | 83 +++--- slendr-1.3.0/slendr/R/tree-sequences.R | 28 +- slendr-1.3.0/slendr/R/visualization.R | 46 +-- slendr-1.3.0/slendr/R/zzz.R | 6 slendr-1.3.0/slendr/build/partial.rdb |binary slendr-1.3.0/slendr/build/vignette.rds |binary slendr-1.3.0/slendr/inst/doc/vignette-01-tutorial.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-01-tutorial.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-01-tutorial.html | 28 +- slendr-1.3.0/slendr/inst/doc/vignette-02-grid-model.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-02-grid-model.Rmd | 4 slendr-1.3.0/slendr/inst/doc/vignette-02-grid-model.html | 16 - slendr-1.3.0/slendr/inst/doc/vignette-03-interactions.R | 6 slendr-1.3.0/slendr/inst/doc/vignette-03-interactions.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-03-interactions.html | 4 slendr-1.3.0/slendr/inst/doc/vignette-04-nonspatial-models.R | 6 slendr-1.3.0/slendr/inst/doc/vignette-04-nonspatial-models.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-04-nonspatial-models.html | 2 slendr-1.3.0/slendr/inst/doc/vignette-05-tree-sequences.R | 12 slendr-1.3.0/slendr/inst/doc/vignette-05-tree-sequences.Rmd | 12 slendr-1.3.0/slendr/inst/doc/vignette-05-tree-sequences.html | 10 slendr-1.3.0/slendr/inst/doc/vignette-06-locations.R | 8 slendr-1.3.0/slendr/inst/doc/vignette-06-locations.Rmd | 10 slendr-1.3.0/slendr/inst/doc/vignette-06-locations.html | 22 - slendr-1.3.0/slendr/inst/doc/vignette-07-engines.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-07-engines.Rmd | 4 slendr-1.3.0/slendr/inst/doc/vignette-07-engines.html | 10 slendr-1.3.0/slendr/inst/doc/vignette-08-nonslendr-tskit.R | 8 slendr-1.3.0/slendr/inst/doc/vignette-08-nonslendr-tskit.Rmd | 8 slendr-1.3.0/slendr/inst/doc/vignette-08-nonslendr-tskit.html | 4 slendr-1.3.0/slendr/inst/doc/vignette-10-tracts.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-10-tracts.Rmd | 4 slendr-1.3.0/slendr/inst/doc/vignette-10-tracts.html | 6 slendr-1.3.0/slendr/inst/doc/vignette-11-extensions.R | 6 slendr-1.3.0/slendr/inst/doc/vignette-11-extensions.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-11-extensions.html | 4 slendr-1.3.0/slendr/inst/extdata/models/introgression/__pycache__/script.cpython-313.pyc |only slendr-1.3.0/slendr/inst/extdata/models/introgression/checksums.tsv | 2 slendr-1.3.0/slendr/inst/extdata/models/introgression/ranges.rds |binary slendr-1.3.0/slendr/inst/extdata/models/introgression/script.py | 4 slendr-1.3.0/slendr/inst/extdata/models/introgression/script.slim | 44 +-- slendr-1.3.0/slendr/inst/extdata/models/introgression_msprime.trees |binary slendr-1.3.0/slendr/inst/extdata/models/introgression_slim.trees |binary slendr-1.3.0/slendr/inst/extdata/models/msprime.trees |binary slendr-1.3.0/slendr/inst/scripts/script.slim | 42 +-- slendr-1.3.0/slendr/man/plot_map.Rd | 5 slendr-1.3.0/slendr/tests/testthat/afs_Linux.tsv.gz |binary slendr-1.3.0/slendr/tests/testthat/distances.tsv.gz |binary slendr-1.3.0/slendr/tests/testthat/test-interaction-changes.R | 2 slendr-1.3.0/slendr/tests/testthat/test-msprime-geneflow.R | 2 slendr-1.3.0/slendr/tests/testthat/test-msprime.R | 2 slendr-1.3.0/slendr/vignettes/vignette-01-tutorial.Rmd | 6 slendr-1.3.0/slendr/vignettes/vignette-02-grid-model.Rmd | 4 slendr-1.3.0/slendr/vignettes/vignette-03-interactions.Rmd | 6 slendr-1.3.0/slendr/vignettes/vignette-04-nonspatial-models.Rmd | 6 slendr-1.3.0/slendr/vignettes/vignette-05-tree-sequences.Rmd | 12 slendr-1.3.0/slendr/vignettes/vignette-06-locations.Rmd | 10 slendr-1.3.0/slendr/vignettes/vignette-07-engines.Rmd | 4 slendr-1.3.0/slendr/vignettes/vignette-08-nonslendr-tskit.Rmd | 8 slendr-1.3.0/slendr/vignettes/vignette-10-tracts.Rmd | 4 slendr-1.3.0/slendr/vignettes/vignette-11-extensions.Rmd | 6 67 files changed, 344 insertions(+), 379 deletions(-)
Title: Plots for the Quantitative Analysis of Textual Data
Description: Plotting functions for visualising textual data. Extends 'quanteda' and
related packages with plot methods designed specifically for text data, textual statistics,
and models fit to textual data. Plot types include word clouds, lexical dispersion plots,
scaling plots, network visualisations, and word 'keyness' plots.
Author: Kenneth Benoit [cre, aut, cph] ,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Adam Obeng [aut] ,
Stefan Mueller [aut] ,
Akitaka Matsuo [aut] ,
Ian Fellows [cph] ),
European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda.textplots versions 0.96 dated 2025-09-03 and 0.96.1 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/textplot_keyness.R | 2 +- R/textplot_xray.R | 10 ++++++---- README.md | 8 +++----- man/textplot_xray.Rd | 7 ++++--- 6 files changed, 23 insertions(+), 22 deletions(-)
More information about quanteda.textplots at CRAN
Permanent link
Title: Access and Analyse Data from the 'CVD Prevent' API
Description: Provides an R interface to the 'CVD Prevent' application
programming interface (API), allowing users to retrieve and analyse
cardiovascular disease prevention data from primary care records
across England. The Cardiovascular Disease Prevention Audit
(CVDPREVENT) automatically extracts routinely held GP health data to
support national reporting and improvement initiatives. See the API
documentation for details:
<https://bmchealthdocs.atlassian.net/wiki/spaces/CP/pages/317882369/CVDPREVENT+API+Documentation>.
Author: Craig Parylo [aut, cre, cph] ,
Cardiovascular Disease Prevention Audit [ant]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between cvdprevent versions 0.2.3 dated 2025-11-05 and 0.2.4 dated 2025-11-11
DESCRIPTION | 6 MD5 | 15 NAMESPACE | 1 NEWS.md | 64 R/cvd_memoise.R | 62 README.md | 20 build/vignette.rds |binary inst/doc/using_cvdprevent.html | 4182 ++++++++++++++++++++--------------------- man/cvd_clear_cache.Rd |only 9 files changed, 2213 insertions(+), 2137 deletions(-)
Title: Statistical Analysis of Contingency Tables
Description: Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
Author: Morten Wang Fagerland [aut],
Stian Lydersen [ctb],
Petter Laake [ctb],
Waldir Leoncio [cre],
Ole Christian Lingjaerde [trl],
Brad J. Biggerstaff [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between contingencytables versions 3.0.1 dated 2024-08-29 and 3.1.0 dated 2025-11-11
DESCRIPTION | 9 MD5 | 225 ++++++------ NEWS.md | 6 R/Adjusted_inv_sinh_CI_OR_2x2.R | 1 R/Adjusted_inv_sinh_CI_ratio_2x2.R | 1 R/Adjusted_log_CI_2x2.R | 1 R/AgrestiCaffo_CI_2x2.R | 1 R/BaptistaPike_exact_conditional_CI_2x2.R | 1 R/BaptistaPike_midP_CI_2x2.R | 1 R/CochranMantelHaenszel_test_stratified_2x2.R | 1 R/Cornfield_exact_conditional_CI_2x2.R | 1 R/Cornfield_midP_CI_2x2.R | 1 R/Exact_unconditional_test_2x2.R | 23 - R/Fisher_exact_test_2x2.R | 7 R/Fisher_midP_test_2x2.R | 1 R/Gart_adjusted_logit_CI_2x2.R | 1 R/Independence_smoothed_logit_CI_2x2.R | 1 R/Inv_sinh_CI_OR_2x2.R | 1 R/Inv_sinh_CI_ratio_2x2.R | 1 R/Katz_log_CI_2x2.R | 1 R/Koopman_asymptotic_score_CI_2x2.R | 1 R/LR_test_2x2.R | 1 R/MOVER_R_Wilson_CI_OR_2x2.R | 1 R/MOVER_R_Wilson_CI_ratio_2x2.R | 1 R/MantelHaenszel_estimate_stratified_2x2.R | 1 R/McNemar_asymptotic_test_CC_paired_2x2.R | 1 R/McNemar_asymptotic_test_paired_2x2.R | 1 R/Mee_asymptotic_score_CI_2x2.R | 1 R/MiettinenNurminen_asymptotic_score_CI_OR_2x2.R | 1 R/MiettinenNurminen_asymptotic_score_CI_difference_2x2.R | 1 R/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.R | 1 R/Newcombe_hybrid_score_CI_2x2.R | 1 R/Newcombe_square_and_add_CI_paired_2x2.R | 1 R/Pearson_LR_test_common_effect_stratified_2x2.R | 1 R/Pearson_chi_squared_test_2x2.R | 4 R/Pearson_chi_squared_test_CC_2x2.R | 1 R/PriceBonett_approximate_Bayes_CI_2x2.R | 1 R/Transformed_Blaker_exact_CI_paired_2x2.R | 1 R/Transformed_Clopper_Pearson_exact_CI_paired_2x2.R | 1 R/Transformed_Clopper_Pearson_midP_CI_paired_2x2.R | 1 R/Uncorrected_asymptotic_score_CI_2x2.R | 1 R/Wald_CI_2x2.R | 1 R/Wald_CI_AgrestiMin_paired_2x2.R | 1 R/Wald_CI_CC_2x2.R | 1 R/Wald_CI_OR_paired_2x2.R | 1 R/Wald_CI_ratio_paired_2x2.R | 1 R/Wald_test_and_CI_common_diff_stratified_2x2.R | 1 R/Wald_test_and_CI_common_ratio_stratified_2x2.R | 1 R/Woolf_logit_CI_2x2.R | 1 R/Z_unpooled_test_2x2.R | 1 R/chapters.R | 15 R/the_2x2_table_CIs_OR.R | 1 R/the_2x2_table_CIs_difference.R | 1 R/the_2x2_table_CIs_ratio.R | 1 R/the_2x2_table_tests.R | 1 R/the_paired_2x2_table_CIs_OR.R | 1 man/Adjusted_inv_sinh_CI_OR_2x2.Rd | 8 man/Adjusted_inv_sinh_CI_ratio_2x2.Rd | 8 man/Adjusted_log_CI_2x2.Rd | 8 man/AgrestiCaffo_CI_2x2.Rd | 8 man/BaptistaPike_exact_conditional_CI_2x2.Rd | 8 man/BaptistaPike_midP_CI_2x2.Rd | 8 man/CochranMantelHaenszel_test_stratified_2x2.Rd | 8 man/Cornfield_exact_conditional_CI_2x2.Rd | 8 man/Cornfield_midP_CI_2x2.Rd | 8 man/Exact_unconditional_test_2x2.Rd | 8 man/Fisher_exact_test_2x2.Rd | 8 man/Fisher_midP_test_2x2.Rd | 8 man/Gart_adjusted_logit_CI_2x2.Rd | 8 man/Independence_smoothed_logit_CI_2x2.Rd | 8 man/Inv_sinh_CI_OR_2x2.Rd | 8 man/Inv_sinh_CI_ratio_2x2.Rd | 8 man/Katz_log_CI_2x2.Rd | 8 man/Koopman_asymptotic_score_CI_2x2.Rd | 8 man/LR_test_2x2.Rd | 8 man/MOVER_R_Wilson_CI_OR_2x2.Rd | 8 man/MOVER_R_Wilson_CI_ratio_2x2.Rd | 8 man/MantelHaenszel_estimate_stratified_2x2.Rd | 8 man/McNemar_asymptotic_test_CC_paired_2x2.Rd | 8 man/McNemar_asymptotic_test_paired_2x2.Rd | 8 man/Mee_asymptotic_score_CI_2x2.Rd | 8 man/MiettinenNurminen_asymptotic_score_CI_OR_2x2.Rd | 8 man/MiettinenNurminen_asymptotic_score_CI_difference_2x2.Rd | 8 man/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.Rd | 8 man/Newcombe_hybrid_score_CI_2x2.Rd | 8 man/Newcombe_square_and_add_CI_paired_2x2.Rd | 8 man/Pearson_LR_test_common_effect_stratified_2x2.Rd | 8 man/Pearson_chi_squared_test_2x2.Rd | 8 man/Pearson_chi_squared_test_CC_2x2.Rd | 8 man/PriceBonett_approximate_Bayes_CI_2x2.Rd | 8 man/Transformed_Blaker_exact_CI_paired_2x2.Rd | 8 man/Transformed_Clopper_Pearson_exact_CI_paired_2x2.Rd | 8 man/Transformed_Clopper_Pearson_midP_CI_paired_2x2.Rd | 8 man/Uncorrected_asymptotic_score_CI_2x2.Rd | 8 man/Wald_CI_2x2.Rd | 8 man/Wald_CI_AgrestiMin_paired_2x2.Rd | 8 man/Wald_CI_CC_2x2.Rd | 8 man/Wald_CI_OR_paired_2x2.Rd | 8 man/Wald_CI_ratio_paired_2x2.Rd | 8 man/Wald_test_and_CI_common_diff_stratified_2x2.Rd | 8 man/Wald_test_and_CI_common_ratio_stratified_2x2.Rd | 8 man/Woolf_logit_CI_2x2.Rd | 8 man/Z_unpooled_test_2x2.Rd | 8 man/chap10.Rd | 8 man/chap4.Rd | 8 man/chap8.Rd | 8 man/the_2x2_table_CIs_OR.Rd | 8 man/the_2x2_table_CIs_difference.Rd | 8 man/the_2x2_table_CIs_ratio.Rd | 8 man/the_2x2_table_tests.Rd | 8 man/the_paired_2x2_table_CIs_OR.Rd | 8 tests/testthat/Rplots.pdf |only tests/testthat/test-ch4.R | 18 tests/testthat/test-validation.R | 4 114 files changed, 667 insertions(+), 133 deletions(-)
More information about contingencytables at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-15 0.2.4
2018-04-30 0.2.3
2016-04-29 0.2.2
2015-07-17 0.2
2014-01-12 0.1
Title: Power Analysis for Research Experiments
Description: Provides tools for calculating statistical power for experiments
analyzed using linear mixed models. It supports standard designs, including
randomized block, split-plot, and Latin Square designs, while offering flexibility
to accommodate a variety of other complex study designs.
Author: Kai Wang [aut, cre, cph] ,
Mutian Niu [aut, cph]
Maintainer: Kai Wang <kai.wang@usys.ethz.ch>
Diff between pwr4exp versions 1.0.0 dated 2025-03-17 and 1.0.1 dated 2025-11-11
DESCRIPTION | 11 ++-- MD5 | 48 ++++++++++++------- NAMESPACE | 20 ++++++++ NEWS.md | 8 ++- R/corClasses.R |only R/df_utils.R | 6 +- R/mkdesign.R | 22 ++++++-- R/standard_designs.R | 6 +- R/utils.R | 125 ++++++++++++++++++++++++++++++++++---------------- build/vignette.rds |binary inst/CITATION | 14 +++-- inst/doc/pwr4exp.R | 4 - inst/doc/pwr4exp.Rmd | 6 +- inst/doc/pwr4exp.html | 23 ++++----- man/corAR1.Rd |only man/corARMA.Rd |only man/corCAR1.Rd |only man/corClasses.Rd |only man/corCompSymm.Rd |only man/corExp.Rd |only man/corGaus.Rd |only man/corLin.Rd |only man/corRatio.Rd |only man/corSpher.Rd |only man/corSymm.Rd |only man/create_designs.Rd | 4 - man/df.lsd.Rd | 4 - man/mkRTrms.Rd | 6 +- man/mkStruct.Rd | 4 - man/mkdesign.Rd | 9 ++- vignettes/pwr4exp.Rmd | 6 +- 31 files changed, 213 insertions(+), 113 deletions(-)
Title: Evolutionary Transcriptomics
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) <doi:10.1093/bioinformatics/btx835>). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.
Author: Hajk-Georg Drost [aut, cre] ,
Stefan Manolache [aut, ctb] ,
Jaruwatana Sodai Lotharukpong [aut, ctb] ,
Nikola Kalabova [aut, ctb] ,
Filipa Martins Costa [aut, ctb],
Kristian K Ullrich [aut, ctb]
Maintainer: Hajk-Georg Drost <hajk-georg.drost@tuebingen.mpg.de>
Diff between myTAI versions 2.3.3 dated 2025-11-07 and 2.3.4 dated 2025-11-11
DESCRIPTION | 8 - MD5 | 74 +++++++-------- NEWS.md | 10 +- R/plot_contribution.R | 13 ++ R/plot_gene_heatmap.R | 17 --- R/taxid.R | 32 ++++++ README.md | 12 -- inst/doc/myTAI.Rmd | 1 inst/doc/myTAI.html | 2 inst/doc/other-strata.Rmd | 1 inst/doc/other-strata.html | 4 inst/doc/phylo-expression-object.R | 12 +- inst/doc/phylo-expression-object.Rmd | 13 +- inst/doc/phylo-expression-object.html | 160 ++++++++++++---------------------- inst/doc/phylostratigraphy.Rmd | 9 + inst/doc/phylostratigraphy.html | 20 ++-- inst/doc/tai-breaker.Rmd | 1 inst/doc/tai-gallery.Rmd | 1 inst/doc/tai-gallery.html | 72 +++++++-------- inst/doc/tai-stats.Rmd | 1 inst/doc/tai-stats.html | 56 +++++------ inst/doc/tai-transform.Rmd | 3 inst/doc/tai-transform.html | 20 ++-- inst/doc/taxonomy.R | 30 +++--- inst/doc/taxonomy.Rmd | 31 ++++-- inst/doc/taxonomy.html | 52 ++++++----- man/dot-plot_gene_heatmap_impl.Rd | 3 man/plot_gene_heatmap.Rd | 3 tests/testthat/test-plotting.R | 15 +++ vignettes/myTAI.Rmd | 1 vignettes/other-strata.Rmd | 1 vignettes/phylo-expression-object.Rmd | 13 +- vignettes/phylostratigraphy.Rmd | 9 + vignettes/tai-breaker.Rmd | 1 vignettes/tai-gallery.Rmd | 1 vignettes/tai-stats.Rmd | 1 vignettes/tai-transform.Rmd | 3 vignettes/taxonomy.Rmd | 31 ++++-- 38 files changed, 384 insertions(+), 353 deletions(-)
Title: Automatic Processing of Terrestrial-Based Technologies Point
Cloud Data for Forestry Purposes
Description: Process automation of point cloud data derived from terrestrial-based technologies such as Terrestrial Laser Scanner (TLS) or Mobile Laser Scanner. 'FORTLS' enables (i) detection of trees and estimation of tree-level attributes (e.g. diameters and heights), (ii) estimation of stand-level variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories at stand-level, and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2022, <doi:10.1016/j.envsoft.2022.105337>).
Author: Juan Alberto Molina-Valero [aut, cph, cre],
Adela Martinez-Calvo [aut, com],
Maria Jose Ginzo Villamayor [aut, com],
Juan Gabriel Alvarez-Gonzalez [aut, ths],
Fernando Montes [aut],
Cesar Perez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <jamolinavalero@gmail.com>
Diff between FORTLS versions 1.6.0 dated 2025-07-29 and 1.6.1 dated 2025-11-11
FORTLS-1.6.0/FORTLS/R/geometric.features.R |only FORTLS-1.6.0/FORTLS/man/geometric.features.Rd |only FORTLS-1.6.0/FORTLS/man/geometric_features_point.Rd |only FORTLS-1.6.0/FORTLS/man/sort_sublists.Rd |only FORTLS-1.6.0/FORTLS/man/subset_matrix_by_indices.Rd |only FORTLS-1.6.0/FORTLS/src/geometric.features.cpp |only FORTLS-1.6.1/FORTLS/DESCRIPTION | 18 FORTLS-1.6.1/FORTLS/MD5 | 72 - FORTLS-1.6.1/FORTLS/R/RcppExports.R | 8 FORTLS-1.6.1/FORTLS/R/auxiliary.functions.R | 142 +- FORTLS-1.6.1/FORTLS/R/install_fortls_python_deps.R | 3 FORTLS-1.6.1/FORTLS/R/normalize.R | 12 FORTLS-1.6.1/FORTLS/R/tree.detection.multi.scan.R | 216 --- FORTLS-1.6.1/FORTLS/R/tree.detection.several.plots.R | 15 FORTLS-1.6.1/FORTLS/R/tree.detection.single.scan.R | 238 --- FORTLS-1.6.1/FORTLS/README.md | 5 FORTLS-1.6.1/FORTLS/build/partial.rdb |binary FORTLS-1.6.1/FORTLS/build/vignette.rds |binary FORTLS-1.6.1/FORTLS/inst/doc/plot_design_optimization.R | 2 FORTLS-1.6.1/FORTLS/inst/doc/plot_design_optimization.Rmd | 4 FORTLS-1.6.1/FORTLS/inst/doc/plot_design_optimization.html | 8 FORTLS-1.6.1/FORTLS/inst/doc/stand_level.Rmd | 4 FORTLS-1.6.1/FORTLS/inst/doc/stand_level.html | 4 FORTLS-1.6.1/FORTLS/inst/doc/tree_level.R | 78 - FORTLS-1.6.1/FORTLS/inst/doc/tree_level.Rmd | 88 - FORTLS-1.6.1/FORTLS/inst/doc/tree_level.html | 875 +++++++------ FORTLS-1.6.1/FORTLS/man/Rioja.data.Rd | 2 FORTLS-1.6.1/FORTLS/man/Rioja.simulations.Rd | 12 FORTLS-1.6.1/FORTLS/man/geometric_features_dist.Rd |only FORTLS-1.6.1/FORTLS/man/geometric_features_knn.Rd |only FORTLS-1.6.1/FORTLS/man/normalize.Rd | 5 FORTLS-1.6.1/FORTLS/man/tree.detection.multi.scan.Rd | 12 FORTLS-1.6.1/FORTLS/man/tree.detection.several.plots.Rd | 11 FORTLS-1.6.1/FORTLS/man/tree.detection.single.scan.Rd | 8 FORTLS-1.6.1/FORTLS/src/RcppExports.cpp | 88 - FORTLS-1.6.1/FORTLS/src/geometric_features_dist.cpp |only FORTLS-1.6.1/FORTLS/src/geometric_features_knn.cpp |only FORTLS-1.6.1/FORTLS/vignettes/plot_design_optimization.Rmd | 4 FORTLS-1.6.1/FORTLS/vignettes/stand_level.Rmd | 4 FORTLS-1.6.1/FORTLS/vignettes/tree.list.multi.tls.csv | 40 FORTLS-1.6.1/FORTLS/vignettes/tree.list.single.tls.csv | 27 FORTLS-1.6.1/FORTLS/vignettes/tree_level.Rmd | 88 - 42 files changed, 1024 insertions(+), 1069 deletions(-)
Title: Diagnosis of Metabolic Dysfunction Associated Fatty Liver
Disease
Description: The latest guidelines proposed by International Expert Consensus are used for the clinical diagnosis of Metabolic Associated Fatty Liver Disease (MAFLD). The new definition takes hepatic steatosis (determined by elastography or histology or biomarker-based fatty liver index) as a major criterion. In addition, race, gender, body mass index (BMI), waist circumference (WC), fasting plasma glucose (FPG), systolic blood pressure (SBP), diastolic blood pressure (DBP), triglycerides (TG), high-density lipoprotein cholesterol (HDLC), homeostatic model assessment of insulin resistance (HOMAIR), high sensitive c-reactive protein (HsCRP) for the diagnosis of MAFLD. Each parameter has to be interpreted based on the proposed cut-offs, making the diagnosis slightly complex and error-prone. This package is developed by incorporating the latest international expert consensus guidelines, and it will aid in the easy and quick diagnosis of MAFLD based on FibroScan in busy healthcare settings and also for [...truncated...]
Author: Jagadish Ramasamy [aut, cre]
Maintainer: Jagadish Ramasamy <iamjagankmr@gmail.com>
Diff between MAFLD versions 3.0.0 dated 2025-09-14 and 4.0.0 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/MAFLD.R | 11 ++++++++++- R/data.R | 1 + README.md | 8 ++++++-- data/x.rda |binary man/x.Rd | 1 + 8 files changed, 33 insertions(+), 14 deletions(-)
More information about SelectBoost.beta at CRAN
Permanent link
Title: Visualising How Nonlinear Dimension Reduction Warps Your Data
Description: To construct a model in 2-D space from 2-D nonlinear
dimension reduction data and then lift it to the high-dimensional
space. Additionally, provides tools to visualise the model overlay the
data in 2-D and high-dimensional space. Furthermore, provides
summaries and diagnostics to evaluate the nonlinear dimension
reduction layout.
Author: Jayani P. Gamage [aut, cre] ,
Dianne Cook [aut] ,
Paul Harrison [aut] ,
Michael Lydeamore [aut] ,
Thiyanga S. Talagala [aut]
Maintainer: Jayani P. Gamage <jayanilakshika76@gmail.com>
Diff between quollr versions 0.3.13 dated 2025-09-23 and 1.0.1 dated 2025-11-11
quollr-0.3.13/quollr/man/plot_rmse_layouts.Rd |only quollr-1.0.1/quollr/DESCRIPTION | 6 quollr-1.0.1/quollr/MD5 | 52 - quollr-1.0.1/quollr/NAMESPACE | 2 quollr-1.0.1/quollr/NEWS.md | 2 quollr-1.0.1/quollr/R/prediction.R | 28 quollr-1.0.1/quollr/data/scurve_plts.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse2.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse3.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse4.rda |binary quollr-1.0.1/quollr/inst/doc/quollr4algo.html | 321 ++++++---- quollr-1.0.1/quollr/inst/doc/quollr5summary.html | 2 quollr-1.0.1/quollr/inst/doc/quollr6bestbinwidth.R | 8 quollr-1.0.1/quollr/inst/doc/quollr6bestbinwidth.Rmd | 14 quollr-1.0.1/quollr/inst/doc/quollr6bestbinwidth.html | 32 quollr-1.0.1/quollr/inst/doc/quollr7bestfit.R | 4 quollr-1.0.1/quollr/inst/doc/quollr7bestfit.Rmd | 10 quollr-1.0.1/quollr/inst/doc/quollr7bestfit.html | 21 quollr-1.0.1/quollr/man/gen_diffbin1_errors.Rd | 4 quollr-1.0.1/quollr/man/glance.highd_vis_model.Rd | 2 quollr-1.0.1/quollr/man/plot_hbe_layouts.Rd |only quollr-1.0.1/quollr/src/prediction.cpp | 6 quollr-1.0.1/quollr/tests/testthat/_snaps/prediction.md | 54 - quollr-1.0.1/quollr/tests/testthat/test-prediction.R | 4 quollr-1.0.1/quollr/vignettes/quollr6bestbinwidth.Rmd | 14 quollr-1.0.1/quollr/vignettes/quollr7bestfit.Rmd | 10 quollr-1.0.1/quollr/vignettes/quollr7bestfit_files/figure-html/unnamed-chunk-3-1.png |binary 28 files changed, 345 insertions(+), 251 deletions(-)
Title: Efficient Evaluation of Quadratic Forms
Description: A range of quadratic forms are evaluated, using efficient methods.
Unnecessary transposes are not performed. Complex values are handled
consistently.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between quadform versions 0.0-2 dated 2024-05-14 and 0.0-4 dated 2025-11-11
quadform-0.0-2/quadform/build |only quadform-0.0-2/quadform/inst |only quadform-0.0-4/quadform/DESCRIPTION | 12 +-- quadform-0.0-4/quadform/MD5 | 15 +--- quadform-0.0-4/quadform/NAMESPACE | 40 ++++++++++- quadform-0.0-4/quadform/NEWS.md | 12 +++ quadform-0.0-4/quadform/R/quadform.R | 108 +++++++++++++++++++++++-------- quadform-0.0-4/quadform/README.md | 18 ++--- quadform-0.0-4/quadform/man/quad.form.Rd | 106 +++++++++++++++--------------- 9 files changed, 206 insertions(+), 105 deletions(-)
Title: Estimate Bayesian Multilevel Models for Compositional Data
Description: Implement Bayesian multilevel modelling for compositional data.
Compute multilevel compositional data and
perform log-ratio transforms at between and within-person levels,
fit Bayesian multilevel models for compositional predictors and outcomes,
and run post-hoc analyses such as isotemporal substitution models.
References:
Le, Stanford, Dumuid, and Wiley (2025) <doi:10.1037/met0000750>,
Le, Dumuid, Stanford, and Wiley (2025) <doi:10.1080/00273171.2025.2565598>.
Author: Flora Le [aut, cre] ,
Joshua F. Wiley [aut]
Maintainer: Flora Le <floralebui@gmail.com>
This is a re-admission after prior archival of version 1.3.2 dated 2025-05-25
Diff between multilevelcoda versions 1.3.2 dated 2025-05-25 and 1.3.3 dated 2025-11-11
multilevelcoda-1.3.2/multilevelcoda/R/substitution-bsubmargins.R |only multilevelcoda-1.3.2/multilevelcoda/R/substitution-sub-margins.R |only multilevelcoda-1.3.2/multilevelcoda/R/substitution-wsubmargins.R |only multilevelcoda-1.3.2/multilevelcoda/man/bsubmargins.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/build.basesub.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/create_substitution.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/print.summary.complr.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/submargins.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/update.complr.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/wsubmargins.Rd |only multilevelcoda-1.3.3/multilevelcoda/DESCRIPTION | 16 multilevelcoda-1.3.3/multilevelcoda/MD5 | 184 multilevelcoda-1.3.3/multilevelcoda/NAMESPACE | 33 multilevelcoda-1.3.3/multilevelcoda/NEWS.md | 11 multilevelcoda-1.3.3/multilevelcoda/R/brmcoda-methods.R | 91 multilevelcoda-1.3.3/multilevelcoda/R/brmcoda.R | 107 multilevelcoda-1.3.3/multilevelcoda/R/build.R | 338 + multilevelcoda-1.3.3/multilevelcoda/R/complr-methods.R | 144 multilevelcoda-1.3.3/multilevelcoda/R/complr.R | 465 +- multilevelcoda-1.3.3/multilevelcoda/R/get.R |only multilevelcoda-1.3.3/multilevelcoda/R/internal.R | 127 multilevelcoda-1.3.3/multilevelcoda/R/optimise.R |only multilevelcoda-1.3.3/multilevelcoda/R/pivot-coord.R | 371 - multilevelcoda-1.3.3/multilevelcoda/R/plot.R | 169 multilevelcoda-1.3.3/multilevelcoda/R/posterior.R | 397 - multilevelcoda-1.3.3/multilevelcoda/R/shiny.R | 484 +- multilevelcoda-1.3.3/multilevelcoda/R/substitution-bsub.R | 41 multilevelcoda-1.3.3/multilevelcoda/R/substitution-bsubmargin.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution-helpers.R | 2310 +++++----- multilevelcoda-1.3.3/multilevelcoda/R/substitution-sub.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution-submargin.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution-wsub.R | 39 multilevelcoda-1.3.3/multilevelcoda/R/substitution-wsubmargin.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution.R | 438 + multilevelcoda-1.3.3/multilevelcoda/R/summary.R | 373 - multilevelcoda-1.3.3/multilevelcoda/R/update.R | 164 multilevelcoda-1.3.3/multilevelcoda/README.md | 5 multilevelcoda-1.3.3/multilevelcoda/build/vignette.rds |binary multilevelcoda-1.3.3/multilevelcoda/inst/doc/B-composition-MLM.Rmd | 60 multilevelcoda-1.3.3/multilevelcoda/inst/doc/B-composition-MLM.html | 60 multilevelcoda-1.3.3/multilevelcoda/inst/doc/C-composition-MMLM.Rmd | 62 multilevelcoda-1.3.3/multilevelcoda/inst/doc/C-composition-MMLM.html | 60 multilevelcoda-1.3.3/multilevelcoda/inst/doc/D-substitution.Rmd | 24 multilevelcoda-1.3.3/multilevelcoda/inst/doc/D-substitution.html | 24 multilevelcoda-1.3.3/multilevelcoda/man/VarCorr.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/as.data.frame.complr.Rd | 5 multilevelcoda-1.3.3/multilevelcoda/man/brmcoda.Rd | 40 multilevelcoda-1.3.3/multilevelcoda/man/bsub.Rd | 60 multilevelcoda-1.3.3/multilevelcoda/man/bsubmargin.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/build.base.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/build.rg.Rd | 16 multilevelcoda-1.3.3/multilevelcoda/man/coef.brmcoda.Rd | 12 multilevelcoda-1.3.3/multilevelcoda/man/compilr.Rd | 14 multilevelcoda-1.3.3/multilevelcoda/man/complr.Rd | 47 multilevelcoda-1.3.3/multilevelcoda/man/fitted.brmcoda.Rd | 30 multilevelcoda-1.3.3/multilevelcoda/man/fixef.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/get-substitution.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/get_sbp.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/get_variables.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/mcmc_plot.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/mean.complr.Rd | 12 multilevelcoda-1.3.3/multilevelcoda/man/model.frame.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/nobs.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/pairs.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/pivot_coord.Rd | 35 multilevelcoda-1.3.3/multilevelcoda/man/pivot_coord_refit.Rd | 33 multilevelcoda-1.3.3/multilevelcoda/man/pivot_coord_rotate.Rd | 29 multilevelcoda-1.3.3/multilevelcoda/man/plot.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/plot.substitution.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/predict.brmcoda.Rd | 35 multilevelcoda-1.3.3/multilevelcoda/man/print.brmcoda.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/print.complr.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/print.substitution.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/ranef.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/residuals.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/sub.Rd | 60 multilevelcoda-1.3.3/multilevelcoda/man/submargin.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/substitution.Rd | 75 multilevelcoda-1.3.3/multilevelcoda/man/summary.brmcoda.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/summary.complr.Rd | 18 multilevelcoda-1.3.3/multilevelcoda/man/summary.pivot_coord.Rd | 14 multilevelcoda-1.3.3/multilevelcoda/man/summary.substitution.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/update.brmcoda.Rd | 21 multilevelcoda-1.3.3/multilevelcoda/man/var.complr.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/vcov.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/wsub.Rd | 60 multilevelcoda-1.3.3/multilevelcoda/man/wsubmargin.Rd |only multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-bayesfactors.R | 8 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-brmcoda.R | 12 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-bsub.R | 68 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-bsubmargins.R | 48 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-complr.R | 12 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-plotcoda.R | 4 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-submargins.R | 42 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-substitution.R | 20 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-update.R | 58 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-wsub.R | 100 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-wsubmargins.R | 48 multilevelcoda-1.3.3/multilevelcoda/vignettes/B-composition-MLM.Rmd | 60 multilevelcoda-1.3.3/multilevelcoda/vignettes/B-composition-MLM.Rmd.orig | 30 multilevelcoda-1.3.3/multilevelcoda/vignettes/C-composition-MMLM.Rmd | 62 multilevelcoda-1.3.3/multilevelcoda/vignettes/C-composition-MMLM.Rmd.orig | 10 multilevelcoda-1.3.3/multilevelcoda/vignettes/D-substitution.Rmd | 24 multilevelcoda-1.3.3/multilevelcoda/vignettes/D-substitution.Rmd.orig | 6 104 files changed, 4295 insertions(+), 3642 deletions(-)
More information about multilevelcoda at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-10 1.14.6.4
Title: Provides Batch Functions and Visualisation for Basic Statistical
Procedures
Description: Designed to streamline data analysis and statistical testing, reducing the length of R
scripts while generating well-formatted outputs in 'pdf', 'Microsoft Word', and 'Microsoft Excel'
formats. In essence, the package contains functions which are sophisticated wrappers around
existing R functions that are called by using 'f_' (user f_riendly) prefix followed by the normal
function name. This first version of the 'rfriend' package focuses primarily on data exploration,
including tools for creating summary tables, f_summary(), performing data transformations,
f_boxcox() in part based on 'MASS/boxcox' and 'rcompanion', and f_bestNormalize()
which wraps and extends functionality from the 'bestNormalize' package. Furthermore, 'rfriend'
can automatically (or on request) generate visualizations such as boxplots, f_boxplot(),
QQ-plots, f_qqnorm(), histograms f_hist(), and density plots. Additionally, the package includes
four statistical test functions: f_aov(), f_kruskal_test(), f_glm(), f_c [...truncated...]
Author: Sander H. van Delden [aut, cre]
Maintainer: Sander H. van Delden <plantmind@proton.me>
Diff between rfriend versions 1.0.0 dated 2025-07-16 and 2.0.0 dated 2025-11-11
DESCRIPTION | 8 - MD5 | 60 ++++---- NAMESPACE | 2 NEWS.md |only R/faov.R | 306 ++++++++++++++++++++++++++++--------------- R/fbestnormalize.R | 242 +++++++++++++++++++++++----------- R/fboxcox.R | 219 ++++++++++++++++++++---------- R/fboxplot.R | 139 ++++++++++++++----- R/fclear.R | 15 -- R/fcorplot.R | 252 +++++++++++++++++++++++------------ R/ffactors.R | 21 +- R/fglm.R | 183 ++++++++++++++++--------- R/fhist.R | 58 +++----- R/fkruskal_test.R | 204 +++++++++++++++++++--------- R/fmodel_compare.R | 2 R/fqqnorm.R | 57 +++----- R/fsummary.R | 125 ++++++++--------- R/helper_extract_extension.R |only R/helper_get_save_path.R |only R/import.R | 2 README.md |only man/f_aov.Rd | 23 +-- man/f_bestNormalize.Rd | 17 +- man/f_boxcox.Rd | 40 ++--- man/f_boxplot.Rd | 24 ++- man/f_corplot.Rd | 21 +- man/f_factors.Rd | 17 +- man/f_glm.Rd | 20 +- man/f_hist.Rd | 14 + man/f_kruskal_test.Rd | 25 +-- man/f_qqnorm.Rd | 14 + man/f_summary.Rd | 21 +- man/print.f_summary.Rd | 2 33 files changed, 1339 insertions(+), 794 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate and play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive. This package is the successor of 'ProTrackR' providing
better performance.
Author: Pepijn de Vries [aut, cre] ,
Olav Soerensen [aut]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR2 versions 0.0.5 dated 2024-11-09 and 0.1.0 dated 2025-11-11
DESCRIPTION | 21 MD5 | 177 +++--- NAMESPACE | 208 ++++--- NEWS.md | 88 +-- R/cell.R | 92 ++- R/command.R | 188 +++--- R/cpp11.R | 56 -- R/data.R | 32 - R/demo.R | 16 R/instrument.R | 131 ++-- R/mod_info.R | 61 ++ R/note.R | 198 +++---- R/pattern.R | 79 +- R/play.R |only R/render.R | 100 ++- R/s3.R | 186 +++--- R/samples.R | 290 +++++++++- R/select_ops.R | 649 ++++++++++++----------- README.md | 137 ++--- build/vignette.rds |binary inst/doc/ProTrackR_vs_ProTrackR2.R | 87 ++- inst/doc/ProTrackR_vs_ProTrackR2.Rmd | 293 ++++++---- inst/doc/ProTrackR_vs_ProTrackR2.html | 472 +++++------------ inst/doc/effect_commands.R | 72 ++ inst/doc/effect_commands.Rmd | 214 +++++-- inst/doc/effect_commands.html | 133 ++++ inst/doc/s3class.R | 2 inst/doc/s3class.Rmd | 607 +++++++++++----------- inst/doc/s3class.html | 110 +--- inst/doc/sel_assign.Rmd | 360 ++++++------- inst/doc/sel_assign.html | 44 - inst/mod.intro |binary man/ProTrackR2-package.Rd | 62 +- man/as_modplug_pattern.Rd | 56 +- man/as_pt2cell.Rd |only man/effect_commands.Rd | 48 - man/figures/logo.svg | 396 +++++++------- man/mod_info.Rd | 159 +++-- man/mod_io.Rd | 68 +- man/play.Rd | 119 ++-- man/pt2_cell.Rd | 68 +- man/pt2_command.Rd | 100 +-- man/pt2_demo.Rd | 36 - man/pt2_duration.Rd | 74 +- man/pt2_instrument.Rd | 98 +-- man/pt2_new_mod.Rd | 50 - man/pt2_new_pattern.Rd | 54 - man/pt2_note.Rd | 112 ++-- man/pt2_note_to_period.Rd | 68 +- man/pt2_pattern.Rd | 60 +- man/pt2_render.Rd | 112 ++-- man/pt2_render_options.Rd | 85 +-- man/pt2_sample.Rd | 60 +- man/pt2_sample_to_audio.Rd |only man/pt2_validate.Rd | 62 +- man/s3methods.Rd | 362 +++++++------ man/samp_io.Rd | 74 +- man/sample_properties.Rd |only man/select_assign.Rd | 160 +++-- src/cpp11.cpp | 140 +---- src/get_mod.cpp | 2 src/get_mod.h | 2 src/mod_header.cpp | 37 - src/mod_header.h | 4 src/mod_io.cpp | 26 src/mod_render.cpp | 29 - src/patterns.cpp | 24 src/pt2-clone.h |only src/pt2-clone/LICENSE.txt | 50 - src/pt2-clone/pt2_audio.c | 870 ++++++++++++++++---------------- src/pt2-clone/pt2_module_loader.c | 84 +-- src/pt2-clone/pt2_module_loader.h | 2 src/pt2-clone/pt2_sampler.c | 566 ++++++++++---------- src/pt2-clone/smploaders/pt2_load_wav.c | 9 src/pt_cell.cpp | 329 +----------- src/pt_cell.h | 5 src/pt_cleanup.cpp | 2 src/pt_init.cpp | 3 src/samp_io.cpp | 44 - src/samples.cpp | 87 +-- src/samples.h | 4 tests |only vignettes/ProTrackR_vs_ProTrackR2.Rmd | 293 ++++++---- vignettes/effect_commands.Rmd | 214 +++++-- vignettes/s3class.Rmd | 607 +++++++++++----------- vignettes/sel_assign.Rmd | 360 ++++++------- 86 files changed, 6044 insertions(+), 5395 deletions(-)
Title: Model Based Phylogenetic Analysis
Description: A collection of functions to do model-based phylogenetic analysis.
It includes functions to calculate community phylogenetic diversity,
to estimate correlations among functional traits while accounting for
phylogenetic relationships, and to fit phylogenetic generalized linear
mixed models. The Bayesian phylogenetic generalized linear mixed models
are fitted with the 'INLA' package (<https://www.r-inla.org>).
Author: Anthony Ives [aut],
Russell Dinnage [aut] ,
Lucas A. Nell [aut] ,
Matthew Helmus [aut],
Daijiang Li [aut, cre]
Maintainer: Daijiang Li <daijianglee@gmail.com>
Diff between phyr versions 1.1.0 dated 2020-12-18 and 1.1.3 dated 2025-11-11
DESCRIPTION | 17 MD5 | 61 +- NAMESPACE | 2 NEWS.md | 8 R/RcppExports.R | 28 + R/cor_phylo.R | 234 ++++++----- R/pglmm-utils.R | 262 ++++++++++-- R/pglmm.R | 25 - R/pglmm_compare.R | 8 R/utils.R | 1 README.md | 81 ++- build/vignette.rds |binary inst/doc/benchmarks.R | 246 +++++------ inst/doc/benchmarks.html | 728 ++++++++++++++++++++++------------ inst/doc/pglmm.html | 375 ++++++++++++++--- inst/doc/plot-re.html | 753 +++++++++++++++++++++++++----------- man/cor_phylo.Rd | 118 ++--- man/figures |only man/nobs.communityPGLMM.Rd | 4 man/pglmm-profile-LRT.Rd | 14 man/refit_boots.Rd | 12 man/simulate.communityPGLMM.Rd | 25 + src/RcppExports.cpp | 76 +++ src/binaryPGLMM.cpp | 2 src/cor_phylo.cpp | 544 +++++++++++++------------- src/cor_phylo.h | 157 ++----- tests/testthat/test-cor_phylo.R | 36 + tests/testthat/test-pcd.R | 16 tests/testthat/test-pglmm.R | 57 +- tests/testthat/test-pglmm_compare.R | 2 tests/testthat/test-psv.R | 6 tests/testthat/test_pglmm_utils.R | 24 - 32 files changed, 2522 insertions(+), 1400 deletions(-)
Title: Convert Addresses to Standard Inputs
Description: Efficient tools for parsing and standardizing Australian
addresses from textual data. It utilizes optimized algorithms to accurately identify and
extract components of addresses, such as street names, types, and postcodes, especially
for large batched data in contexts where sending addresses to internet services may be
slow or inappropriate. The core functionality is built on fast string processing techniques
to handle variations in address formats and abbreviations commonly found in Australian
address data. Designed for data scientists, urban planners, and logistics analysts, the
package facilitates the cleaning and normalization of address information, supporting
better data integration and analysis in urban studies, geography, and related fields.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between healthyAddress versions 0.4.5 dated 2025-01-08 and 0.5.1 dated 2025-11-11
DESCRIPTION | 12 - MD5 | 18 + NEWS.md | 4 R/HashStreetName.R | 94 ++++----- R/download_latlon_data.R | 142 +++++++-------- R/fillPostcodeStreets.R | 63 +++--- R/read_locality_by_postcode.R | 2 inst/extdata/LOCALITY_BY_POSTCODE.qdata |only inst/extdata/POSTCODE-STREET_TYPE_CODE-STREET_NAME.qdata |only man/download_latlon_data.Rd | 7 tests/tinytest.R | 10 - 11 files changed, 179 insertions(+), 173 deletions(-)
More information about healthyAddress at CRAN
Permanent link
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler/>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects.
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg [aut, cre],
Uku Raudvere [aut]
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.2.3 dated 2024-02-23 and 0.2.4 dated 2025-11-11
DESCRIPTION | 14 ++-- MD5 | 24 +++---- NAMESPACE | 1 R/gprofiler2.R | 107 ++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/gprofiler2.R | 60 +++++++++--------- inst/doc/gprofiler2.Rmd | 6 - inst/doc/gprofiler2.html | 154 ++++++++++++++++++++++++----------------------- inst/extdata |only man/gostplot.Rd | 3 man/gprofiler_request.Rd |only man/publish_gostplot.Rd | 3 man/publish_gosttable.Rd | 3 vignettes/gprofiler2.Rmd | 6 - 14 files changed, 218 insertions(+), 163 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 1.3.3 dated 2025-09-25 and 1.3.4 dated 2025-11-11
DESCRIPTION | 8 MD5 | 88 ++--- NEWS.md | 5 R/flux_fitting.R | 27 - R/flux_fitting_exptz.R | 9 R/flux_fitting_hm.R | 7 R/flux_fitting_lm.R | 7 R/flux_fitting_quadratic.R | 9 R/flux_fitting_zhao18.R | 9 R/flux_fortify.R | 10 R/flux_fortify_exp.R | 7 R/flux_fortify_lin.R | 5 R/flux_fortify_quadratic.R | 5 R/flux_param_exp.R | 12 R/flux_param_kappamax.R | 12 R/flux_param_lm.R | 12 R/flux_param_qua.R | 12 R/flux_plot.R | 2 R/flux_plot_flag.R | 2 README.md | 71 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 9 inst/doc/two-gases.html | 4 man/figures/README-short-example-1.png |binary man/figures/logo.png |binary man/flux_fitting.Rd | 4 man/flux_fitting_exptz.Rd | 4 man/flux_fitting_hm.Rd | 4 man/flux_fitting_lm.Rd | 5 man/flux_fitting_quadratic.Rd | 13 man/flux_fitting_zhao18.Rd | 4 man/flux_fortify_exp.Rd | 4 man/flux_fortify_lin.Rd | 4 man/flux_fortify_quadratic.Rd | 4 man/flux_param_exp.Rd | 4 man/flux_param_kappamax.Rd | 4 man/flux_param_lm.Rd | 4 man/flux_param_qua.Rd | 4 tests/testthat/_snaps/flux_fitting.md | 47 +- tests/testthat/_snaps/flux_plot.md | 32 ++ tests/testthat/_snaps/flux_plot/flux-diff-and-lm.svg |only tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-hm.svg |only tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-tz.svg |only tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-quadratic.svg |only tests/testthat/test-flux_fitting.R | 27 + tests/testthat/test-flux_plot.R | 158 ++++++++++ 47 files changed, 456 insertions(+), 202 deletions(-)
Title: Dynamic ICAR Spatiotemporal Factor Models
Description: Bayesian factor models are effective tools for dimension reduction. This is especially applicable to multivariate large-scale datasets. It allows researchers to understand the latent factors of the data which are the linear or non-linear combination of the variables. Dynamic Intrinsic Conditional Autocorrelative Priors (ICAR) Spatiotemporal Factor Models 'DIFM' package provides function to run Markov Chain Monte Carlo (MCMC), evaluation methods and visual plots from Shin and Ferreira (2023)<doi:10.1016/j.spasta.2023.100763>. Our method is a class of Bayesian factor model which can account for spatial and temporal correlations. By incorporating these correlations, the model can capture specific behaviors and provide predictions.
Author: Hwasoo Shin [aut, cre],
Marco Ferreira [aut]
Maintainer: Hwasoo Shin <hshin2@hfhs.org>
Diff between DIFM versions 1.0 dated 2024-04-12 and 1.0.1 dated 2025-11-11
DESCRIPTION | 15 ++++----- MD5 | 14 ++++---- R/RcppExports.R | 15 ++------- build/partial.rdb |binary inst/doc/DIFMvignette.html | 24 +++++++------- src/marginal.d.cpp | 31 +++++++++---------- src/sigma2.simulation.cpp | 65 ++++++++++++++++++++-------------------- src/tau.simulation.cpp | 73 +++++++++++++++++++++++---------------------- 8 files changed, 117 insertions(+), 120 deletions(-)
Title: General Unified Threshold Model of Survival for Bees using
Bayesian Inference
Description: Tools to calibrate, validate, and make predictions with the
General Unified Threshold model of Survival adapted for Bee species. The
model is presented in the publication from Baas, J., Goussen, B., Miles, M.,
Preuss, T.G., Roessing, I. (2022) <doi:10.1002/etc.5423> and
Baas, J., Goussen, B., Taenzler, V., Roeben, V., Miles, M., Preuss, T.G.,
van den Berg, S., Roessink, I. (2024) <doi:10.1002/etc.5871>, and is based on the
GUTS framework Jager, T., Albert, C., Preuss, T.G. and Ashauer, R. (2011)
<doi:10.1021/es103092a>.
The authors are grateful to Bayer A.G. for its financial support.
Author: Benoit Goussen [aut] ,
Liubov Zakharova [ctb],
Carlo Romoli [aut, cre],
Bayer AG [cph, fnd],
ibacon GmbH [cph]
Maintainer: Carlo Romoli <carlo.romoli@ibacon.com>
Diff between BeeGUTS versions 1.3.0 dated 2024-10-23 and 1.4.0 dated 2025-11-11
DESCRIPTION | 26 +++++++-------- MD5 | 36 +++++++++++----------- NEWS.md | 3 + R/BeeGUTS-package.R | 29 +++++++++++++++++ R/ppc.R | 6 +++ README.md | 44 +++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary data/valBetacyfluthrinChronic.rda |only inst/doc/Tutorial.html | 43 ++++++++++++-------------- man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-example-5.png |binary man/ppc.beeSurvValidation.Rd | 6 +++ man/valBetacyfluthrinChronic.Rd |only vignettes/man/figures/Tutorial-example-2.png |binary vignettes/man/figures/Tutorial-example-3.png |binary vignettes/man/figures/Tutorial-example-4.png |binary vignettes/man/figures/Tutorial-example-5.png |binary 20 files changed, 118 insertions(+), 75 deletions(-)
Title: Value Added Receiver Operating Characteristics Curve
Description: A continuous version of the receiver operating characteristics (ROC) curve to assess both classification and continuity performances of biomarkers, diagnostic tests, or risk prediction models.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between varoc versions 0.4.0 dated 2025-06-21 and 1.0.0 dated 2025-11-11
varoc-0.4.0/varoc/R/tmd.R |only varoc-1.0.0/varoc/DESCRIPTION | 11 +- varoc-1.0.0/varoc/MD5 | 12 +-- varoc-1.0.0/varoc/NAMESPACE | 6 - varoc-1.0.0/varoc/R/tmd_ft.R |only varoc-1.0.0/varoc/R/varoc.R | 152 ++++++++++++++++++--------------------- varoc-1.0.0/varoc/R/varoc3d.R |only varoc-1.0.0/varoc/man/varoc.Rd | 43 ++++------- varoc-1.0.0/varoc/man/varoc3d.Rd |only 9 files changed, 105 insertions(+), 119 deletions(-)
Title: Identify and Measure Tree Rings on X-Ray Micro-Density Profiles
Description: Contains functions to identify tree-ring borders based on X-ray micro-density profiles and a Graphical User Interface (GUI) to visualize density profiles and correct tree-ring borders. Campelo F, Mayer K, Grabner M. (2019) <doi:10.1016/j.dendro.2018.11.002>.
Author: Filipe Campelo [aut, cre, cph],
Konrad Mayer [ctb]
Maintainer: Filipe Campelo <fcampelo@ci.uc.pt>
Diff between xRing versions 0.1.1 dated 2022-04-22 and 0.1.2 dated 2025-11-11
xRing-0.1.1/xRing/man/plot.Rd |only xRing-0.1.1/xRing/man/print.Rd |only xRing-0.1.2/xRing/DESCRIPTION | 28 ++--- xRing-0.1.2/xRing/MD5 | 75 +++++++-------- xRing-0.1.2/xRing/R/calibrateFilm.R | 4 xRing-0.1.2/xRing/R/detectRings.R | 2 xRing-0.1.2/xRing/R/imDisplay.R | 2 xRing-0.1.2/xRing/R/imRead.R | 6 - xRing-0.1.2/xRing/R/plot.R | 34 +++--- xRing-0.1.2/xRing/R/plotRings.R | 2 xRing-0.1.2/xRing/R/print.R | 24 ++-- xRing-0.1.2/xRing/R/toxRing.R | 2 xRing-0.1.2/xRing/R/toxRingList.R | 2 xRing-0.1.2/xRing/inst/img/AFO1046.1200dpi_AFO1046.RData |only xRing-0.1.2/xRing/man/PaPiRaw.Rd | 13 ++ xRing-0.1.2/xRing/man/PaPiSpan.Rd | 10 ++ xRing-0.1.2/xRing/man/addRing.Rd | 2 xRing-0.1.2/xRing/man/calibrateFilm.Rd | 2 xRing-0.1.2/xRing/man/combineFrag.Rd | 2 xRing-0.1.2/xRing/man/correctRings.Rd | 2 xRing-0.1.2/xRing/man/detectEwLw.Rd | 2 xRing-0.1.2/xRing/man/detectRings.Rd | 4 xRing-0.1.2/xRing/man/fitCalibrationModel.Rd | 6 - xRing-0.1.2/xRing/man/getBorders.Rd | 2 xRing-0.1.2/xRing/man/getDensity.Rd | 2 xRing-0.1.2/xRing/man/getRwls.Rd | 2 xRing-0.1.2/xRing/man/getSteps.Rd | 2 xRing-0.1.2/xRing/man/imCrop.Rd | 2 xRing-0.1.2/xRing/man/imDisplay.Rd | 4 xRing-0.1.2/xRing/man/imRead.Rd | 8 + xRing-0.1.2/xRing/man/measureProfiles.Rd | 2 xRing-0.1.2/xRing/man/plot.xRing.Rd |only xRing-0.1.2/xRing/man/plot.xRingList.Rd |only xRing-0.1.2/xRing/man/plotRings.Rd | 4 xRing-0.1.2/xRing/man/print.xRing.Rd |only xRing-0.1.2/xRing/man/print.xRingList.Rd |only xRing-0.1.2/xRing/man/removeRing.Rd | 2 xRing-0.1.2/xRing/man/selectProfiles.Rd | 2 xRing-0.1.2/xRing/man/setLastYear.Rd | 2 xRing-0.1.2/xRing/man/stepIncrease.Rd | 2 xRing-0.1.2/xRing/man/toxRing.Rd | 4 xRing-0.1.2/xRing/man/toxRingList.Rd | 4 42 files changed, 170 insertions(+), 98 deletions(-)
Title: Seamless Access to World Bank International Debt Statistics
(IDS)
Description: Access and analyze the World Bank's International Debt Statistics
(IDS) <https://www.worldbank.org/en/programs/debt-statistics/ids>.
IDS provides creditor-debtor relationships between countries, regions, and
institutions. 'wbids' enables users to download, process and work with IDS
series across multiple geographies, counterparts, and time periods.
Author: Teal Emery [aut, cre],
Teal Insights [cph],
Christoph Scheuch [aut] ,
Christopher Smith [ctb]
Maintainer: Teal Emery <lte@tealinsights.com>
Diff between wbids versions 1.1.0 dated 2025-09-04 and 1.1.1 dated 2025-11-11
DESCRIPTION | 6 LICENSE | 4 MD5 | 98 NAMESPACE | 46 NEWS.md | 5 R/global-variables.R | 24 R/ids_bulk.R | 562 +- R/ids_bulk_files.R | 79 R/ids_bulk_series.R | 82 R/ids_get.R | 1082 ++--- R/ids_list_counterparts.R | 58 R/ids_list_entities.R | 130 R/ids_list_series.R | 56 R/ids_list_series_topics.R | 48 R/perform_request.R | 208 R/read_bulk_info.R | 42 R/sysdata.R | 54 R/wbids-package.R | 26 README.md | 294 - build/vignette.rds |binary inst/doc/data-model.R | 94 inst/doc/data-model.html | 5729 +++++++++++++-------------- inst/doc/data-model.qmd | 250 - man/counterparts.Rd | 32 man/entities.Rd | 32 man/ids_bulk.Rd | 116 man/ids_bulk_files.Rd | 56 man/ids_bulk_series.Rd | 66 man/ids_get.Rd | 288 - man/ids_list_counterparts.Rd | 66 man/ids_list_entities.Rd | 88 man/ids_list_geographies.Rd | 90 man/ids_list_series.Rd | 64 man/ids_list_series_topics.Rd | 56 man/read_bulk_info.Rd | 32 man/series.Rd | 32 man/series_topics.Rd | 32 man/wbids-package.Rd | 70 tests/testthat.R | 24 tests/testthat/test-ids_bulk.R | 812 +-- tests/testthat/test-ids_bulk_files.R | 30 tests/testthat/test-ids_bulk_series.R | 30 tests/testthat/test-ids_get.R | 1292 +++--- tests/testthat/test-ids_list_counterparts.R | 20 tests/testthat/test-ids_list_entities.R | 48 tests/testthat/test-ids_list_series.R | 18 tests/testthat/test-ids_list_series_topics.R | 16 tests/testthat/test-perform_request.R | 230 - tests/testthat/test-read_bulk_info.R | 19 vignettes/data-model.qmd | 250 - 50 files changed, 6532 insertions(+), 6354 deletions(-)
Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation
(SLOPE): generalized linear models regularized with the sorted L1-norm
(Bogdan et al. 2015). Supported models include
ordinary least-squares regression, binomial regression, multinomial
regression, and Poisson regression. Both dense and sparse predictor
matrices are supported. In addition, the package features predictor
screening rules that enable fast and efficient solutions to high-dimensional
problems.
Author: Johan Larsson [aut, cre] ,
Jonas Wallin [aut] ,
Malgorzata Bogdan [aut] ,
Ewout van den Berg [aut],
Chiara Sabatti [aut],
Emmanuel Candes [aut],
Evan Patterson [aut],
Weijie Su [aut],
Jakub Kala [aut],
Krystyna Grzesiak [aut],
Mathurin Massias [aut], [...truncated...]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between SLOPE versions 1.1.0 dated 2025-10-30 and 1.2.0 dated 2025-11-11
DESCRIPTION | 6 - MD5 | 47 +++++++------- NEWS.md | 26 ++++++++ R/plot.R | 2 R/regularization_weights.R | 2 R/slope.R | 4 - README.md | 60 +++++++++++++++--- inst/CITATION | 99 +++++++++++-------------------- inst/WORDLIST | 4 + inst/doc/introduction.html | 6 - inst/doc/solvers.html | 8 +- inst/include/slope/cv.h | 11 ++- inst/include/slope/eigen_compat.h |only inst/include/slope/folds.h | 7 +- inst/include/slope/math.h | 4 - inst/include/slope/ols.h | 4 - inst/include/slope/slope.h | 74 +++++++++++++++++++---- inst/include/slope/solvers/hybrid_cd.h | 3 inst/include/slope/solvers/pgd.h | 4 - inst/include/slope/utils.h | 40 +++++++++++- man/SLOPE.Rd | 2 man/figures/README-unnamed-chunk-5-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/regularizationWeights.Rd | 2 src/rcpp_slope.cpp | 16 ++++- tests/testthat/test-coef.R | 26 ++++++++ 26 files changed, 318 insertions(+), 139 deletions(-)
Title: Tools for Information-Based Feature Selection and Scoring
Description: A toolbox of fast, native and parallel implementations of various information-based importance criteria estimators and feature selection filters based on them, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <https://www.jmlr.org/papers/v13/brown12a.html>.
Contains, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <https://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between praznik versions 11.0.0 dated 2022-05-20 and 12.0.0 dated 2025-11-11
praznik-11.0.0/praznik/R/pure.R |only praznik-11.0.0/praznik/tests/testthat |only praznik-11.0.0/praznik/tests/testthat.R |only praznik-12.0.0/praznik/DESCRIPTION | 16 ++++----- praznik-12.0.0/praznik/MD5 | 50 +++++++++++++++-------------- praznik-12.0.0/praznik/NAMESPACE | 1 praznik-12.0.0/praznik/R/transforms.R | 30 +++++++++++++++++ praznik-12.0.0/praznik/inst/CITATION | 24 ++++--------- praznik-12.0.0/praznik/inst/NEWS | 4 ++ praznik-12.0.0/praznik/inst/tinytest |only praznik-12.0.0/praznik/man/tspTransform.Rd |only praznik-12.0.0/praznik/src/cmis.h | 6 +-- praznik-12.0.0/praznik/src/hs.h | 4 +- praznik-12.0.0/praznik/src/ims.h | 2 - praznik-12.0.0/praznik/src/jmis.h | 4 +- praznik-12.0.0/praznik/src/kt.h | 4 +- praznik-12.0.0/praznik/src/minmaxs.h | 4 +- praznik-12.0.0/praznik/src/mis.h | 4 +- praznik-12.0.0/praznik/src/praznik.c | 5 ++ praznik-12.0.0/praznik/src/shared.h | 4 +- praznik-12.0.0/praznik/src/trips.h | 2 - praznik-12.0.0/praznik/src/tsp.h |only praznik-12.0.0/praznik/tests/tinytest.R |only 23 files changed, 98 insertions(+), 66 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.2 dated 2025-10-13 and 1.3.3 dated 2025-11-11
DESCRIPTION | 8 MD5 | 38 - NAMESPACE | 1 NEWS.md | 7 R/OMOPGenerics-package.R | 1 R/assert.R | 5 R/classCdmReference.R | 19 R/classCdmTable.R | 10 R/classConceptSetExpression.R | 32 - R/compute.R | 108 +-- R/exportConceptSetExpression.R | 2 R/exportSummarisedResult.R | 18 R/importConceptSetExpression.R | 17 R/logger.R | 47 - inst/doc/logging.html | 52 - inst/doc/summarised_result.html | 886 +++++++++++++++---------------- man/assertLogical.Rd | 3 man/exportSummarisedResult.Rd | 5 tests/testthat/test-logger.R | 6 tests/testthat/test-methodComputeTable.R | 11 20 files changed, 647 insertions(+), 629 deletions(-)
Title: Modelling of Extreme Values
Description: Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes (Dombry, Engelke and Oesting, 2016, <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.
Author: Leo Belzile [aut, cre] ,
Jennifer L. Wadsworth [aut],
Paul J. Northrop [aut] ,
Raphael Huser [aut] ,
Scott D. Grimshaw [aut] ,
Jin Zhang [ctb],
Michael A. Stephens [ctb],
Art B. Owen [ctb]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between mev versions 2.0 dated 2025-10-22 and 2.1 dated 2025-11-11
DESCRIPTION | 6 MD5 | 50 ++--- NAMESPACE | 7 NEWS.md | 25 ++ R/NCdiag.R | 2 R/coefvariation.R | 14 - R/extgp.R | 363 ++++++++++++++++++++++++++++++++------ R/infomattest.R | 41 +++- R/penultimate.R | 91 +++++++-- R/pickands.R | 4 R/tailindex.R | 23 +- R/threshold.R | 240 +++++++++++++++---------- R/thselect.R | 114 +++++++++++ R/vartymetric.R | 29 ++- inst/doc/mev-vignette.html | 10 - inst/tinytest/test-distribution.R | 122 ++++++++++++ inst/tinytest/test-egp.R | 268 ++++++++++++++-------------- man/egpdist.Rd | 3 man/smith.penult.Rd | 74 +++++-- man/thselect.cbm.Rd |only man/thselect.egp.Rd |only man/thselect.rbm.Rd | 5 man/thselect.sdinfo.Rd | 4 man/thselect.vmetric.Rd | 17 + man/tstab.cv.Rd | 14 - man/tstab.egp.Rd | 13 + man/tstab.gpd.Rd | 4 27 files changed, 1160 insertions(+), 383 deletions(-)
Title: Ecological Trajectory Analysis
Description: Analysis of temporal changes (i.e. dynamics) of ecological entities, defined as trajectories on a chosen multivariate space, by providing a set of
trajectory metrics and visual representations [De Caceres et al. (2019) <doi:10.1002/ecm.1350>;
and Sturbois et al. (2021) <doi:10.1016/j.ecolmodel.2020.109400>]. Includes functions
to estimate metrics for individual trajectories (length, directionality, angles, ...) as well as
metrics to relate pairs of trajectories (dissimilarity and convergence). Functions are also
provided to estimate the ecological quality of ecosystem with respect to reference conditions
[Sturbois et al. (2023) <doi:10.1002/ecs2.4726>].
Author: Miquel De Caceres [aut, cre] ,
Nicolas Djeghri [aut] ,
Anthony Sturbois [aut] ,
Javier De la Casa [ctb]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between ecotraj versions 1.1.1 dated 2025-08-28 and 1.2.0 dated 2025-11-11
DESCRIPTION | 15 ++-- MD5 | 30 ++++++--- NAMESPACE | 10 ++- NEWS.md | 5 + R/cycleShiftArrows.R |only R/ecotraj-package.R | 5 - R/trajectoryComparison.R | 121 ++++++++++++++++++++++++++++++++------- R/trajectoryConvergencePlot.R |only R/trajectoryCyclical.R | 4 - R/trajectoryCyclicalPlots.R | 6 - R/trajectoryRMA.R |only R/trajectoryRMAPlot.R |only build/partial.rdb |binary man/cycleShiftArrows.Rd |only man/trajectoryComparison.Rd | 25 +++++++- man/trajectoryConvergencePlot.Rd |only man/trajectoryCyclical.Rd | 4 - man/trajectoryCyclicalPlots.Rd | 6 - man/trajectoryRMA.Rd |only man/trajectoryRMAPlot.Rd |only 20 files changed, 176 insertions(+), 55 deletions(-)
Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used
in marketing and micro-econometrics applications.
The package includes:
Bayes Regression (univariate or multivariate dep var),
Bayes Seemingly Unrelated Regression (SUR),
Binary and Ordinal Probit,
Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit,
Negative Binomial (Poisson) Regression,
Multivariate Mixtures of Normals (including clustering),
Dirichlet Process Prior Density Estimation with normal base,
Hierarchical Linear Models with normal prior and covariates,
Hierarchical Linear Models with a mixture of normals prior and covariates,
Hierarchical Multinomial Logits with a mixture of normals prior
and covariates,
Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates,
Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data,
Bayesian treatment of linear instrumental variables models,
Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as i [...truncated...]
Author: Peter Rossi [aut, cre],
Robert McCulloch [ctb],
Wayne Taylor [ctb],
Dan Yavorsky [ctb]
Maintainer: Peter Rossi <perossichi@gmail.com>
Diff between bayesm versions 3.1-6 dated 2023-09-23 and 3.1-7 dated 2025-11-11
DESCRIPTION | 21 +- MD5 | 33 ++-- NEWS.md |only build/vignette.rds |binary data/Scotch.rda |binary data/bank.rda |binary data/camera.RData |binary data/cheese.rda |binary data/customerSat.rda |binary data/detailing.rda |binary data/margarine.rda |binary data/orangeJuice.rda |binary data/tuna.rda |binary inst/doc/Constrained_MNL_Vignette.R | 32 ++-- inst/doc/Constrained_MNL_Vignette.html | 249 ++++++++++++++++----------------- inst/doc/bayesm_Overview_Vignette.R | 64 ++++---- inst/doc/bayesm_Overview_Vignette.html | 221 ++++++++++++++--------------- src/clusterMix_rcpp_loop.cpp | 2 18 files changed, 311 insertions(+), 311 deletions(-)
Title: Genetic Relatedness Between Polyclonal Infections
Description: An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results.
Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.
Author: Inna Gerlovina [aut, cre]
Maintainer: Inna Gerlovina <innager@berkeley.edu>
Diff between dcifer versions 1.2.1 dated 2023-12-12 and 1.5.0 dated 2025-11-11
DESCRIPTION | 13 ++-- MD5 | 57 +++++++++--------- NAMESPACE | 1 NEWS.md | 18 +++++ R/data.R | 3 R/ibd.R | 131 ++++++++++++++++++++++++++++--------------- R/plot.R | 99 ++++++++++++++++++++++---------- R/prep.R | 80 +++++++++++++++----------- R/probUxUy.R | 40 ++++--------- build/vignette.rds |binary inst/doc/vignetteDcifer.R | 72 ++++++++++++----------- inst/doc/vignetteDcifer.Rmd | 41 ++++++------- inst/doc/vignetteDcifer.pdf |binary man/dsmp.Rd | 3 man/format.Rd | 14 ++-- man/getCOI.Rd | 2 man/ibdDat.Rd | 10 ++- man/ibdEstM.Rd | 6 + man/ibdPair.Rd | 6 + man/matchAfreq.Rd | 15 +++- man/mixMat.Rd |only man/plotColorbar.Rd | 3 man/plotRel.Rd | 36 ++++++----- src/logr.c | 21 ++++-- src/pUxUy.c | 75 +++++++++++++++++------- src/pUxUy0.c | 42 ++++++++++--- src/pUxUy0M1.c | 82 ++++++++++++++++++++------ src/pUxUyEqr.c | 55 ++++++++++++++---- src/pUxUyM1.c | 105 ++++++++++++++++++++++++---------- vignettes/vignetteDcifer.Rmd | 41 ++++++------- 30 files changed, 691 insertions(+), 380 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-27 0.2.0
2023-08-21 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-12 0.1.1