Tue, 30 Sep 2025

Package surveydown updated to version 0.13.3 with previous version 0.13.0 dated 2025-08-20

Title: Markdown-Based Programmable Surveys Using 'Quarto' and 'shiny'
Description: Generate programmable surveys using markdown and R code chunks. Surveys are composed of two files: a survey.qmd 'Quarto' file defining the survey content (pages, questions, etc), and an app.R file defining a 'shiny' app with global settings (libraries, database configuration, etc.) and server configuration options (e.g., conditional skipping / display, etc.). Survey data collected from respondents is stored in a 'PostgreSQL' database. Features include controls for conditional skip logic (skip to a page based on an answer to a question), conditional display logic (display a question based on an answer to a question), a customizable progress bar, and a wide variety of question types, including multiple choice (single choice and multiple choices), select, text, numeric, multiple choice buttons, text area, and dates. Because the surveys render into a 'shiny' app, designers can also leverage the reactive capabilities of 'shiny' to create dynamic and interactive surveys.
Author: John Paul Helveston [aut, cre, cph] , Pingfan Hu [aut, cph] , Bogdan Bunea [aut, cph] , Stefan Munnes [ctb]
Maintainer: John Paul Helveston <john.helveston@gmail.com>

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Package randomForestSRC updated to version 3.4.2 with previous version 3.4.1 dated 2025-06-07

Title: Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut], Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>

Diff between randomForestSRC versions 3.4.1 dated 2025-06-07 and 3.4.2 dated 2025-09-30

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Package ivo.table updated to version 0.7.0 with previous version 0.6 dated 2025-01-15

Title: Nicely Formatted Contingency Tables and Frequency Tables
Description: Nicely formatted frequency tables and contingency tables (1-way, 2-way, 3-way and 4-way tables), that can easily be exported to HTML or 'Office' documents. Designed to work with pipes.
Author: Mans Thulin [aut, cre], Kajsa Grind [aut], Stefan Furne [aut]
Maintainer: Mans Thulin <mans@statistikkonsult.com>

Diff between ivo.table versions 0.6 dated 2025-01-15 and 0.7.0 dated 2025-09-30

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Package stRoke updated to version 25.9.2 with previous version 25.9.1 dated 2025-09-02

Title: Clinical Stroke Research
Description: A collection of tools for clinical trial data management and analysis in research and teaching. The package is mainly collected for personal use, but any use beyond that is encouraged. This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added. Version follows months and year. See NEWS/Changelog for release notes. This package includes sampled data from the TALOS trial (Kraglund et al (2018) <doi:10.1161/STROKEAHA.117.020067>). The win_prob() function is based on work by Zou et al (2022) <doi:10.1161/STROKEAHA.121.037744>. The age_calc() function is based on work by Becker (2020) <doi:10.18637/jss.v093.i02>.
Author: Andreas Gammelgaard Damsbo [aut, cre]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>

Diff between stRoke versions 25.9.1 dated 2025-09-02 and 25.9.2 dated 2025-09-30

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Package RcppCWB updated to version 0.6.10 with previous version 0.6.9 dated 2025-09-27

Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>). The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>) and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>). See the file LICENSE.note for further information. The package includes modified code of the 'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre], Bernard Desgraupes [aut], Sylvain Loiseau [aut], Oliver Christ [ctb], Bruno Maximilian Schulze [ctb], Stephanie Evert [ctb], Arne Fitschen [ctb], Jeroen Ooms [ctb], Marius Bertram [ctb], Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>

Diff between RcppCWB versions 0.6.9 dated 2025-09-27 and 0.6.10 dated 2025-09-30

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Package openssl updated to version 2.3.4 with previous version 2.3.3 dated 2025-05-26

Title: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] , Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>

Diff between openssl versions 2.3.3 dated 2025-05-26 and 2.3.4 dated 2025-09-30

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New package writeAlizer with initial version 1.6.4
Package: writeAlizer
Title: Generate Predicted Writing Quality Scores
Version: 1.6.4
Date: 2025-09-23
Description: Imports variables from 'ReaderBench' (Dascalu et al., 2018)<doi:10.1007/978-3-319-66610-5_48>, 'Coh-Metrix' (McNamara et al., 2014)<doi:10.1017/CBO9780511894664>, and/or 'GAMET' (Crossley et al., 2019) <doi:10.17239/jowr-2019.11.02.01> output files; downloads predictive scoring models described in Mercer & Cannon (2022)<doi:10.31244/jero.2022.01.03> and Mercer et al.(2021)<doi:10.1177/0829573520987753>; and generates predicted writing quality and curriculum-based measurement (McMaster & Espin, 2007)<doi:10.1177/00224669070410020301> scores.
License: GPL-3
URL: https://github.com/shmercer/writeAlizer/
BugReports: https://github.com/shmercer/writeAlizer/issues
Depends: R (>= 2.10)
Imports: caret, digest, dplyr, glue, magrittr, stats, tidyselect, utils
Suggests: caretEnsemble, Cubist, earth, gbm, glmnet, kernlab, pls, randomForest, testthat (>= 3.1.0), withr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2025-09-23 18:59:25 UTC; shmer
Author: Sterett H. Mercer [aut, cre]
Maintainer: Sterett H. Mercer <sterett.mercer@ubc.ca>
Repository: CRAN
Date/Publication: 2025-09-30 08:40:02 UTC

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New package TwoDcDAPSA with initial version 0.1.0
Package: TwoDcDAPSA
Title: Calculate TwoDcDAPSA: PROs-Joint Contrast (PJC) Score and Quartiles
Version: 0.1.0
Description: Provides a calculator for the two-dimensional clinical Disease Activity index for Psoriatic Arthritis (TwoDcDAPSA), a principal component-derived measure that complements the conventional clinical DAPSA score. The TwoDcDAPSA captures residual variation in patient-reported outcomes (pain and patient global assessment) and joint counts (swollen and tender) after adjusting for standardized cDAPSA using natural spline coefficients derived from published models. Residuals are standardized and combined with fixed principal component loadings to yield a continuous PROs-Joint Contrast (PJC) score and quartile groupings. The package applies pre-specified coefficients and loadings to new datasets but does not estimate spline models or principal components itself.
License: MIT + file LICENSE
Depends: R (>= 3.6)
Imports: dplyr, splines, rlang
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-09-23 19:26:21 UTC; nmeng2
Author: Ning Meng [aut, cre], Ji Soo Kim [aut], Ana-Maria Orbai [aut], Scott L. Zeger [aut]
Maintainer: Ning Meng <nmeng2@jh.edu>
Repository: CRAN
Date/Publication: 2025-09-30 08:40:08 UTC

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New package twbparser with initial version 0.2.3
Package: twbparser
Title: Parse 'Tableau' Workbooks into Functional Data
Version: 0.2.3
Description: High-performance parsing of 'Tableau' workbook files into tidy data frames and dependency graphs for other visualization tools like R 'Shiny' or 'Power BI' replication.
License: MIT + file LICENSE
URL: https://prigasg.github.io/twbparser/, https://github.com/PrigasG/twbparser
BugReports: https://github.com/PrigasG/twbparser/issues
Depends: R (>= 4.2.0)
Imports: dplyr, igraph, purrr, R6, rlang, stringr, tibble, tidyr, withr, xml2
Suggests: cli, covr, ggraph, knitr, lintr, magrittr, optparse, rmarkdown, spelling, styler, testthat (>= 3.0.0), tidygraph, vctrs, zip
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2025-09-23 16:26:11 UTC; garthur
Author: George Arthur [aut, cre]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-30 08:30:02 UTC

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New package tidyusmacro with initial version 0.1.0
Package: tidyusmacro
Title: Downloading and Cleaning U.S. Macroeconomic Data
Version: 0.1.0
Description: Utilities to retrieve and tidy U.S. macroeconomic data series from public government data providers. Functions streamline access to series from the Federal Reserve Bank of St. Louis Federal Reserve Economic Data (FRED), the Bureau of Labor Statistics flat files, and the Bureau of Economic Analysis National Income and Product Accounts tables, then return consistent, tidy data frames ready for modeling and graphics. The package includes helpers for date alignment, log-linear projections, and common macro diagnostics, along with convenience plot builders for quick publication-quality charts.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
LazyData: true
Imports: dplyr, ggplot2, magrittr, purrr, readr, rlang, stringi, tidyr
NeedsCompilation: no
Packaged: 2025-09-24 03:37:40 UTC; mtkonczal
Author: Mike Konczal [aut, cre]
Maintainer: Mike Konczal <konczal@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-30 08:50:02 UTC

More information about tidyusmacro at CRAN
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New package streamsampler with initial version 0.1.0
Package: streamsampler
Title: Characterize and Subsample Stream Data
Version: 0.1.0
Description: Characterize daily stream discharge and water quality data and subsample water quality data. Provide dates, discharge, and water quality measurements and 'streamsampler' can find gaps, get summary statistics, and subsample according to common stream sampling protocols. Stream sampling protocols are described in Lee et al. (2016) <doi:10.1016/j.jhydrol.2016.08.059> and Lee et al. (2019) <doi:10.3133/sir20195084>.
License: CC0
URL: https://github.com/Kyle-Hurley/streamsampler
BugReports: https://github.com/Kyle-Hurley/streamsampler/issues
Encoding: UTF-8
Suggests: dataRetrieval (>= 2.7.16), knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 4.1)
LazyData: true
Imports: slider (>= 0.3.1), stats
VignetteBuilder: knitr
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits
NeedsCompilation: no
Packaged: 2025-09-23 12:25:18 UTC; kphur
Author: Kyle Hurley [aut, cre, cph] , Jeff Chanat [aut]
Maintainer: Kyle Hurley <kp.hurley87@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-30 08:30:09 UTC

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New package splineplot with initial version 0.1.1
Package: splineplot
Title: Visualization of Spline Effects in GAM and GLM Models
Version: 0.1.1
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Description: Creates 'ggplot2'-based visualizations of smooth effects from GAM (Generalized Additive Models) fitted with 'mgcv' and spline effects from GLM (Generalized Linear Models). Supports interaction terms and provides hazard ratio plots with histograms for survival analysis. Wood (2017, ISBN:9781498728331) provides comprehensive methodology for generalized additive models.
License: Apache License 2.0
Encoding: UTF-8
Imports: ggplot2 (>= 3.0.0), stats
Suggests: mgcv, survival, splines, testthat (>= 3.0.0), knitr, rmarkdown, covr, pkgdown
VignetteBuilder: knitr
URL: https://github.com/jinseob2kim/splineplot, https://jinseob2kim.github.io/splineplot/
BugReports: https://github.com/jinseob2kim/splineplot/issues
NeedsCompilation: no
Packaged: 2025-09-23 15:09:22 UTC; js
Author: Jinseob Kim [aut, cre] , Zarathu [cph, fnd]
Repository: CRAN
Date/Publication: 2025-09-30 08:30:14 UTC

More information about splineplot at CRAN
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New package SFHNV with initial version 0.1.0
Package: SFHNV
Title: Structural Forest for the Heterogeneous Newsvendor Model
Version: 0.1.0
Description: Implements the structural forest methodology for the heterogeneous newsvendor model. The package provides tools to prepare data, fit honest newsvendor trees and forests, and obtain point and distributional predictions for demand decisions under uncertainty.
URL: https://github.com/MurphyLiCN/SFHNV
License: MIT + file LICENSE
Depends: R (>= 3.6)
Imports: stats
Suggests: future.apply, testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-09-22 01:56:31 UTC; murphy
Author: Mengfei Li [aut, cre]
Maintainer: Mengfei Li <murphy.li.cn@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-30 08:50:14 UTC

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Package satin updated to version 1.2.0 with previous version 1.1.0 dated 2022-09-22

Title: Visualisation and Analysis of Ocean Data Derived from Satellites
Description: With 'satin' functions, visualisation, data extraction and further analysis like producing climatologies from several images, and anomalies of satellite derived ocean data can be easily done. Reading functions can import a user defined geographical extent of data stored in netCDF files. Currently supported ocean data sources include NASA's Oceancolor web page <https://oceancolor.gsfc.nasa.gov/>, sensors VIIRS-SNPP; MODIS-Terra; MODIS-Aqua; and SeaWiFS. Available variables from this source includes chlorophyll concentration, sea surface temperature (SST), and several others. Data sources specific for SST that can be imported too includes Pathfinder AVHRR <https://www.ncei.noaa.gov/products/avhrr-pathfinder-sst> and GHRSST <https://www.ghrsst.org/>. In addition, ocean productivity data produced by Oregon State University can also be handled previous conversion from HDF4 to HDF5 format. Many other ocean variables can be processed by importing netCDF data files from [...truncated...]
Author: Hector Villalobos [aut, cre] , Eduardo Gonzalez-Rodriguez [aut]
Maintainer: Hector Villalobos <hvillalo@ipn.mx>

Diff between satin versions 1.1.0 dated 2022-09-22 and 1.2.0 dated 2025-09-30

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Package rpaleoclim updated to version 1.1.0 with previous version 1.0.1 dated 2023-08-09

Title: Download Paleoclimate Data from 'PaleoClim'
Description: 'PaleoClim' <http://www.paleoclim.org> (Brown et al. 2019, <doi:10.1038/sdata.2018.254>) is a set of free, high resolution paleoclimate surfaces covering the whole globe. It includes data on surface temperature, precipitation and the standard bioclimatic variables commonly used in ecological modelling, derived from the 'HadCM3' general circulation model and downscaled to a spatial resolution of up to 2.5 minutes. Simulations are available for key time periods from the Late Holocene to mid-Pliocene. Data on current and Last Glacial Maximum climate is derived from 'CHELSA' (Karger et al. 2017, <doi:10.1038/sdata.2017.122>) and reprocessed by 'PaleoClim' to match their format; it is available at up to 30 seconds resolution. This package provides a simple interface for downloading 'PaleoClim' data in R, with support for caching and filtering retrieved data by period, resolution, and geographic extent.
Author: Joe Roe [aut, cre, cph]
Maintainer: Joe Roe <joe@joeroe.io>

Diff between rpaleoclim versions 1.0.1 dated 2023-08-09 and 1.1.0 dated 2025-09-30

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Package rmarchingcubes updated to version 0.1.4 with previous version 0.1.2 dated 2021-06-16

Title: Calculate 3D Contour Meshes Using the Marching Cubes Algorithm
Description: A port of the C++ routine for applying the marching cubes algorithm written by Thomas Lewiner et al. (2012) <doi:10.1080/10867651.2003.10487582> into an R package. The package supplies the contour3d() function, which takes a 3-dimensional array of voxel data and calculates the vertices, vertex normals, and faces for a 3d mesh representing the contour(s) at a given level.
Author: S. H. Wilks [aut, cre], Thomas Lewiner [aut]
Maintainer: S. H. Wilks <sam.wilks@unimelb.edu.au>

Diff between rmarchingcubes versions 0.1.2 dated 2021-06-16 and 0.1.4 dated 2025-09-30

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New package powergrid with initial version 0.5.0
Package: powergrid
Title: Power Analysis Across a Grid of Assumptions
Version: 0.5.0
Description: Evaluate a function across a grid of parameters. The function may be evaluated once, or many times for simulation. Parallel computing is facilitated. Utilities aim at performing analyses of power and sample size, allowing for easy search of minimum n (or min/max of any other parameter) to achieve a desired minimal level of power (or maximum of any other objective). Plotting functions are included that present the dependency of n and power in relation to further assumptions.
License: GPL-3
Encoding: UTF-8
Suggests: future.apply (>= 1.11.2), future (>= 1.33.2), knitr, rmarkdown, testthat (>= 3.0.0)
Imports: stats, methods
VignetteBuilder: knitr
URL: https://github.com/SwissClinicalTrialOrganisation/powergrid
BugReports: https://github.com/SwissClinicalTrialOrganisation/powergrid/issues
NeedsCompilation: no
Packaged: 2025-09-23 09:57:22 UTC; gilles
Author: Gilles Dutilh [aut, cre] , Richard Charles Allen [aut]
Maintainer: Gilles Dutilh <info@gillesdutilh.com>
Repository: CRAN
Date/Publication: 2025-09-30 08:20:02 UTC

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Package pollen updated to version 0.83.0 with previous version 0.82.0 dated 2021-12-03

Title: Analysis of Aerobiological Data
Description: Supports analysis of aerobiological data. Available features include determination of pollen season limits, replacement of outliers (Kasprzyk and Walanus (2014) <doi:10.1007/s10453-014-9332-8>), calculation of growing degree days (Baskerville and Emin (1969) <doi:10.2307/1933912>), and determination of the base temperature for growing degree days (Yang et al. (1995) <doi:10.1016/0168-1923(94)02185-M).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

Diff between pollen versions 0.82.0 dated 2021-12-03 and 0.83.0 dated 2025-09-30

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Package OSMscale updated to version 0.5.23 with previous version 0.5.22 dated 2025-07-27

Title: Add a Scale Bar to 'OpenStreetMap' Plots
Description: Functionality to handle and project lat-long coordinates, easily download background maps and add a correct scale bar to 'OpenStreetMap' plots in any map projection.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>

Diff between OSMscale versions 0.5.22 dated 2025-07-27 and 0.5.23 dated 2025-09-30

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New package houba with initial version 0.1.0
Package: houba
Title: Manipulation of (Large) Memory-Mapped Objects (Vectors, Matrices and Arrays)
Version: 0.1.0
Date: 2025-09-17
Maintainer: Herve Perdry <herve.perdry@universite-paris-saclay.fr>
Description: Manipulate data through memory-mapped files, as vectors, matrices or arrays. Basic arithmetic functions are implemented, but currently no matrix arithmetic. Can write and read descriptor files for compatibility with the 'bigmemory' package.
License: CeCILL-2
Encoding: UTF-8
Depends: methods
Imports: Rcpp (>= 1.0.11)
Suggests: knitr, bigmemory
VignetteBuilder: knitr
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2025-09-23 12:44:45 UTC; rv
Author: Herve Perdry [aut, cre], Juliette Meyniel [aut]
Repository: CRAN
Date/Publication: 2025-09-30 08:30:20 UTC

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Package GABB updated to version 0.3.10 with previous version 0.3.9 dated 2025-05-14

Title: Facilitation of Data Preparation and Plotting Procedures for RDA and PCA Analyses
Description: Help to the occasional R user for synthesis and enhanced graphical visualization of redundancy analysis (RDA) and principal component analysis (PCA) methods and objects. Inputs are : data frame, RDA (package 'vegan') and PCA (package 'FactoMineR') objects. Outputs are : synthesized results of RDA, displayed in console and saved in tables ; displayed and saved objects of PCA graphic visualization of individuals and variables projections with multiple graphic parameters.
Author: Gregoire Bianchetti [aut, cre]
Maintainer: Gregoire Bianchetti <auguste.blam@gmail.com>

Diff between GABB versions 0.3.9 dated 2025-05-14 and 0.3.10 dated 2025-09-30

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New package blox with initial version 0.0.1
Package: blox
Title: Block Diagonal Matrix Approximation
Version: 0.0.1
Maintainer: Jan O. Bauer <j.bauer@vu.nl>
Description: Finds the best block diagonal matrix approximation of a symmetric matrix. This can be exploited for divisive hierarchical clustering using singular vectors, named HC-SVD. The method is described in Bauer (202Xa) <doi:10.48550/arXiv.2308.06820>.
License: GPL (>= 2)
Imports: matrixStats, Rcpp, RcppArmadillo
Encoding: UTF-8
Suggests: corrplot, knitr, psych, testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2025-09-24 09:00:39 UTC; jan
Author: Jan O. Bauer [aut, cre]
Repository: CRAN
Date/Publication: 2025-09-30 09:00:13 UTC

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New package ZIDW with initial version 0.1.0
Package: ZIDW
Version: 0.1.0
Date: 2025-09-22
Title: Zero-Inflated Discrete Weibull Models
Depends: R (>= 4.1.0)
Imports: DWreg, actuar, maxLik, COUNT, gtools, matrixcalc, DiscreteWeibull, dplyr, ggplot2, purrr, tibble
URL: https://github.com/dsy109/ZIDW
Description: Parameter estimation for zero-inflated discrete Weibull (ZIDW) regression models, the univariate setting, distribution functions, functions to generate randomized quantile residuals a pseudo R2, and plotting of rootograms. For more details, see Kalktawi (2017) <https://bura.brunel.ac.uk/handle/2438/14476>, Taconeli and Rodrigues de Lara (2022) <doi:10.1080/00949655.2021.2005597>, and Yeh and Young (2025) <doi:10.1080/03610918.2025.2464076>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2025-09-22 16:02:02 UTC; derekyoung
Author: Peng Yeh [aut], Derek S. Young [aut, cre]
Maintainer: Derek S. Young <derek.young@uky.edu>
Repository: CRAN
Date/Publication: 2025-09-30 07:20:22 UTC

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Package rstanarm updated to version 2.32.2 with previous version 2.32.1 dated 2024-01-18

Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut], Imad Ali [ctb], Sam Brilleman [ctb], Jacqueline Buros Novik [ctb] , AstraZeneca [ctb] , Trustees of Columbia University [cph], Simon Wood [cph] , R Core Deveopment Team [cph] , Douglas Bates [cph] , Martin Maechler [cph] , Ben Bolk [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

Diff between rstanarm versions 2.32.1 dated 2024-01-18 and 2.32.2 dated 2025-09-30

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New package rcldf with initial version 1.5.1
Package: rcldf
Title: Read Linguistic Data in the Cross Linguistic Data Format (CLDF)
Version: 1.5.1
Maintainer: Simon J. Greenhill <simon@simon.net.nz>
Description: Cross-Linguistic Data Format (CLDF) is a framework for storing cross-linguistic data, ensuring compatibility and ease of data exchange between different linguistic datasets see Forkel et al. (2018) <doi:10.1038/sdata.2018.205>. The 'rcldf' package is designed to facilitate the manipulation and analysis of these datasets by simplifying the loading, querying, and visualisation of CLDF datasets making it easier to conduct comparative linguistic analyses, manage language data, and apply statistical methods directly within R.
License: Apache License (>= 2.0)
Encoding: UTF-8
Imports: archive, bib2df (>= 1.1.1), csvwr, digest, dplyr, jsonlite, logger, magrittr, purrr, readr, remotes, rlang, tools, urltools, utils
Suggests: ggplot2, patchwork, testthat, mockthat, spelling, covr, knitr, rmarkdown, qpdf
URL: https://github.com/SimonGreenhill/rcldf
BugReports: https://github.com/SimonGreenhill/rcldf/issues
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-22 08:05:55 UTC; simon
Author: Simon J. Greenhill [aut, cre]
Repository: CRAN
Date/Publication: 2025-09-30 07:20:02 UTC

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New package radviz3d with initial version 2.3.0
Package: radviz3d
Title: 3D Radial Visualization
Version: 2.3.0
Description: Creating 3D radial visualizations of multivariate data. The package extends traditional radial coordinate visualization (RadViz) techniques to three-dimensional space, enabling enhanced exploration and analysis of high-dimensional datasets through interactive 3D plots. Zhu, Dai & Maitra (2022) <doi:10.1080/10618600.2021.2020129>.
Depends: R (>= 3.5.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: rgl (>= 0.100.19)
Suggests: MixSim, gtools
Author: Yifan Zhu [cre, aut], Fan Dai [aut], Ranjan Maitra [aut], Niraj Kunwar [aut], Gani Agadilov [aut]
Maintainer: Yifan Zhu <yifanzhu@iastate.edu>
NeedsCompilation: no
Packaged: 2025-09-23 07:12:54 UTC; yifanzhu
Repository: CRAN
Date/Publication: 2025-09-30 07:50:02 UTC

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New package OmopConstructor with initial version 0.1.0
Package: OmopConstructor
Title: Build Tables in the OMOP Common Data Model
Version: 0.1.0
Description: Provides functionality to construct standardised tables from health care data formatted according to the Observational Medical Outcomes Partnership (OMOP) Common Data Model. The package includes tools to build key tables such as observation period and drug era, among others.
License: Apache License (>= 2)
Encoding: UTF-8
Imports: cli, clock, dplyr, glue, omopgenerics, PatientProfiles, purrr, rlang, tidyr
Depends: R (>= 4.1)
Suggests: bookdown, CDMConnector, duckdb, ggplot2, gt, knitr, odbc, omock, OmopSketch, rmarkdown, RPostgres, stringr, testthat (>= 3.0.0), visOmopResults
URL: https://ohdsi.github.io/OmopConstructor/
BugReports: https://github.com/ohdsi/OmopConstructor/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-22 19:23:49 UTC; martics
Author: Marti Catala [aut, cre] , Elin Rowlands [ctb] , Cecilia Campanile [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Repository: CRAN
Date/Publication: 2025-09-30 07:20:28 UTC

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New package nonParQuantileCausality with initial version 0.1.0
Package: nonParQuantileCausality
Title: Nonparametric Causality in Quantiles Test
Version: 0.1.0
Author: Mehmet Balcilar [aut, cre]
Maintainer: Mehmet Balcilar <mehmet@mbalcilar.net>
Description: Implements the nonparametric causality-in-quantiles test (in mean or variance), returning a test object with an S3 plot() method. The current implementation uses one lag of each series (first-order Granger causality setup). Methodology is based on Balcilar, Gupta, and Pierdzioch (2016a) <doi:10.1016/j.resourpol.2016.04.004> and Balcilar et al. (2016) <doi:10.1007/s11079-016-9388-x>.
License: MIT + file LICENSE
URL: https://www.mbalcilar.net, https://github.com/mbalcilar/nonParQuantileCausality
Encoding: UTF-8
LazyData: true
LazyDataCompression: bzip2
Depends: R (>= 3.6)
Imports: stats, ggplot2, quantreg, KernSmooth
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-22 20:25:08 UTC; mbalcilar
Repository: CRAN
Date/Publication: 2025-09-30 07:20:08 UTC

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New package myownrobs with initial version 0.1.0
Package: myownrobs
Title: AI Coding Agent for 'RStudio'
Version: 0.1.0
Maintainer: Juan Cruz Rodriguez <jcrodriguez@unc.edu.ar>
Description: Provides an 'RStudio' extension with a chat interface for an AI coding agent to help users with R programming tasks.
License: MIT + file LICENSE
URL: https://myownrobs.github.io/myownrobs/, https://github.com/MyOwnRobs/myownrobs
BugReports: https://github.com/MyOwnRobs/myownrobs/issues
Encoding: UTF-8
Imports: fs, gargle, glue, httr2, jsonlite, mirai, rstudio.prefs, rstudioapi, shiny, tools, uuid, yaml
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-09-22 23:25:27 UTC; jcrodriguez
Author: Juan Cruz Rodriguez [aut, cre]
Repository: CRAN
Date/Publication: 2025-09-30 07:30:02 UTC

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New package mammalcol with initial version 0.2.9
Package: mammalcol
Title: Access to the List of Mammal Species of Colombia
Version: 0.2.9
Date: 2025-09-22
Maintainer: Diego J. Lizcano <dj.lizcano@gmail.com>
Description: The goal of 'mammalcol' is to provide easy access to a meticulously structured dataset of Colombian mammal species in R. The 2025 update includes comprehensive, detailed species accounts, and distribution information.
License: MIT + file LICENSE
URL: https://github.com/dlizcano/mammalcol, https://dlizcano.github.io/mammalcol/
BugReports: https://github.com/dlizcano/mammalcol/issues
Depends: R (>= 3.5.0)
Imports: ggplot2, magrittr, sf, geodata,
Suggests: dplyr, finch, knitr, readr, readxl, rmarkdown, stringr, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-22 16:51:35 UTC; usuario
Author: Diego J. Lizcano [aut, cre] , Cristian A. Cruz-Rodriguez [ctb, aut] , Andres F. Suarez-Castro [ctb, aut] , Baltazar Gonzalez [ctb, aut] , Alejandra Bonilla-Sanchez [ctb] , Camilo A. Calderon-Acevedo [ctb]
Repository: CRAN
Date/Publication: 2025-09-30 07:20:13 UTC

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New package foodwebr with initial version 1.0.0
Package: foodwebr
Title: Visualise Function Dependencies
Version: 1.0.0
Description: Easily create graphs of the inter-relationships between functions in an environment.
License: MIT + file LICENSE
URL: https://lewinfox.com/foodwebr/
BugReports: https://github.com/lewinfox/foodwebr/issues
Imports: cli, crayon, codetools, DiagrammeR, glue, rlang, stringr, tidygraph
Suggests: testthat
Encoding: UTF-8
Language: en-GB
NeedsCompilation: no
Packaged: 2025-09-23 04:44:26 UTC; lewin
Author: Lewin Appleton-Fox [aut, cre]
Maintainer: Lewin Appleton-Fox <lewin.a.f@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-30 07:30:07 UTC

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New package DyadRatios with initial version 1.2
Package: DyadRatios
Title: Dyad Ratios Algorithm
Version: 1.2
Date: 2025-09-22
Description: Estimates the Dyad Ratios Algorithm for pooling and smoothing poll estimates. The Dyad Ratios Algorithm smooths both forward and backward in time over polling results allowing differences in both question type and polling house. The result is an estimate of a single latent variable that describes the systematic trend over time in the (noisy) polling results. See James A. Stimson (2018) <doi:10.1177/0759106318761614> and the package's vignette for more details.
Depends: R (>= 3.5.0)
Imports: ggplot2, lubridate, stats
License: GPL (>= 2)
Encoding: UTF-8
Suggests: dplyr, rio, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-22 19:06:45 UTC; david
Author: Dave Armstrong [cre], James Stimson [aut]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-30 07:20:33 UTC

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New package docorator with initial version 0.5.0
Package: docorator
Title: Docorate (Decorate + Output) Displays
Version: 0.5.0
Description: A framework for creating production outputs. Users can frame a table, listing, or figure with headers and footers and save to an output file. Stores an intermediate 'docorator' object for reproducibility and rendering to multiple output types.
License: Apache License 2.0
Encoding: UTF-8
Imports: gt (>= 0.11.0), rmarkdown, rlang, cli, dplyr, rstudioapi, purrr, stringr, tidyr, lifecycle, png, knitr, withr, quarto
Suggests: rprojroot, testthat (>= 3.0.0), tfrmt, pdftools, ggplot2
VignetteBuilder: knitr
URL: https://GSK-Biostatistics.github.io/docorator/, https://github.com/GSK-Biostatistics/docorator
BugReports: https://github.com/GSK-Biostatistics/docorator/issues
Depends: R (>= 4.1.0)
NeedsCompilation: no
Packaged: 2025-09-22 15:38:15 UTC; bkrouse
Author: Becca Krouse [aut, cre], Shannon Haughton [aut], Seongbin Hong [aut], Dragoș Moldovan-Gruenfeld [aut], GlaxoSmithKline Research & Development Limited [cph, fnd]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Repository: CRAN
Date/Publication: 2025-09-30 07:10:02 UTC

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New package coglyphr with initial version 1.0.4
Package: coglyphr
Title: Compute Glyph Centers of Gravity from Image Data
Version: 1.0.4
Description: Computes the center of gravity (COG) of character-like binary images using three different methods. This package provides functions for estimating stroke-based, contour-based, and potential energy-based COG. It is useful for analyzing glyph structure in areas such as visual cognition research and font development. The contour-based method was originally proposed by Kotani et al. (2004) <https://ipsj.ixsq.nii.ac.jp/records/36793> and Kotani (2011) <https://shonan-it.repo.nii.ac.jp/records/2000243>, while the potential energy-based method was introduced by Kotani et al. (2006) <doi:10.11371/iieej.35.296>.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/mutopsy/coglyphr, https://mutopsy.github.io/coglyphr/
BugReports: https://github.com/mutopsy/coglyphr/issues
Depends: R (>= 4.4.0)
Imports: imager, dplyr, sp
LazyData: true
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-09-23 08:57:31 UTC; owner
Author: Hiroyuki Muto [aut, cre]
Maintainer: Hiroyuki Muto <mutopsy@omu.ac.jp>
Repository: CRAN
Date/Publication: 2025-09-30 08:00:11 UTC

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New package captain with initial version 1.1.1
Package: captain
Title: Running 'git' Pre-Commit Hooks
Version: 1.1.1
Description: Git hook scripts are useful for identifying simple issues before submission to code review. 'captain' (hook) is an R package to manage and run git pre-commit hooks.
License: MIT + file LICENSE
URL: https://github.com/alexym1/captain, https://alexym1.github.io/captain/
BugReports: https://github.com/alexym1/captain/issues
Depends: R (>= 4.1.0)
Imports: cli, fs, yaml
Suggests: devtools, covr, knitr, styler, testthat, withr
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-09-22 20:22:11 UTC; Admin
Author: Alex Yahiaoui Martinez [aut, cre]
Maintainer: Alex Yahiaoui Martinez <yahiaoui-martinez.alex@outlook.com>
Repository: CRAN
Date/Publication: 2025-09-30 07:20:18 UTC

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Package pdSpecEst updated to version 1.2.6 with previous version 1.2.4 dated 2020-01-08

Title: An Analysis Toolbox for Hermitian Positive Definite Matrices
Description: An implementation of data analysis tools for samples of symmetric or Hermitian positive definite matrices, such as collections of covariance matrices or spectral density matrices. The tools in this package can be used to perform: (i) intrinsic wavelet transforms for curves (1D) or surfaces (2D) of Hermitian positive definite matrices with applications to dimension reduction, denoising and clustering in the space of Hermitian positive definite matrices; and (ii) exploratory data analysis and inference for samples of positive definite matrices by means of intrinsic data depth functions and rank-based hypothesis tests in the space of Hermitian positive definite matrices.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>

Diff between pdSpecEst versions 1.2.4 dated 2020-01-08 and 1.2.6 dated 2025-09-30

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Package spatialEco updated to version 2.0-3 with previous version 2.0-2 dated 2023-11-17

Title: Spatial Analysis and Modelling Utilities
Description: Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.
Author: Jeffrey S. Evans [aut, cre] , Melanie A. Murphy [ctb], Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>

Diff between spatialEco versions 2.0-2 dated 2023-11-17 and 2.0-3 dated 2025-09-30

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Package prolsirm updated to version 0.1.1 with previous version 0.1.0 dated 2023-09-20

Title: Procrustes Matching for Latent Space Item Response Model
Description: Procrustes matching of the posterior samples of person and item latent positions from latent space item response models. The methods implemented in this package are based on work by Borg, I., Groenen, P. (1997, ISBN:978-0-387-94845-4), Jeon, M., Jin, I. H., Schweinberger, M., Baugh, S. (2021) <doi:10.1007/s11336-021-09762-5>, and Andrew, D. M., Kevin M. Q., Jong Hee Park. (2011) <doi:10.18637/jss.v042.i09>.
Author: Jinwen Luo [aut, cre] , Minjeong Jeon [aut]
Maintainer: Jinwen Luo <jevanluo@ucla.edu>

Diff between prolsirm versions 0.1.0 dated 2023-09-20 and 0.1.1 dated 2025-09-30

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Mon, 29 Sep 2025

Package SFDesign updated to version 0.1.3 with previous version 0.1.2 dated 2025-06-21

Title: Space-Filling Designs
Description: Construct various types of space-filling designs, including Latin hypercube designs, clustering-based designs, maximin designs, maximum projection designs, and uniform designs (Joseph 2016 <doi:10.1080/08982112.2015.1100447>). It also offers the option to optimize designs based on user-defined criteria. This work is supported by U.S. National Science Foundation grant DMS-2310637.
Author: Shangkun Wang [aut, cre], Roshan Joseph [aut]
Maintainer: Shangkun Wang <shangkunwang01@gmail.com>

Diff between SFDesign versions 0.1.2 dated 2025-06-21 and 0.1.3 dated 2025-09-29

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Package MSEtool updated to version 3.7.5 with previous version 3.7.4 dated 2025-06-04

Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre], Quang Huynh [aut], Tom Carruthers [aut], Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>

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Package geodata updated to version 0.6-6 with previous version 0.6-2 dated 2024-06-10

Title: Access Geographic Data
Description: Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.
Author: Robert J. Hijmans [cre, aut] , Marcia Barbosa [ctb] , Aniruddha Ghosh [ctb], Alex Mandel [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

Diff between geodata versions 0.6-2 dated 2024-06-10 and 0.6-6 dated 2025-09-29

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Package thematic updated to version 0.1.8 with previous version 0.1.7 dated 2025-06-19

Title: Unified and Automatic 'Theming' of 'ggplot2', 'lattice', and 'base' R Graphics
Description: Theme 'ggplot2', 'lattice', and 'base' graphics based on a few choices, including foreground color, background color, accent color, and font family. Fonts that aren't available on the system, but are available via download on 'Google Fonts', can be automatically downloaded, cached, and registered for use with the 'showtext' and 'ragg' packages.
Author: Carson Sievert [aut, cre] , Barret Schloerke [aut] , Joe Cheng [aut], Posit Software, PBC [cph, fnd]
Maintainer: Carson Sievert <carson@posit.co>

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Package rENA readmission to version 0.3.0 with previous version 0.2.7 dated 2024-02-23

Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016).
Author: Cody L Marquart [aut, cre] , Zachari Swiecki [aut], Wesley Collier [aut], Brendan Eagan [aut], Roman Woodward [aut], David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>

This is a re-admission after prior archival of version 0.2.7 dated 2024-02-23

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Package PortfolioTesteR updated to version 0.1.2 with previous version 0.1.1 dated 2025-09-22

Title: Test Investment Strategies with English-Like Code
Description: Design, backtest, and analyze portfolio strategies using simple, English-like function chains. Includes technical indicators, flexible stock selection, portfolio construction methods (equal weighting, signal weighting, inverse volatility, hierarchical risk parity), and a compact backtesting engine for portfolio returns, drawdowns, and summary metrics.
Author: Alberto Pallotta [aut, cre]
Maintainer: Alberto Pallotta <pallottaalberto@gmail.com>

Diff between PortfolioTesteR versions 0.1.1 dated 2025-09-22 and 0.1.2 dated 2025-09-29

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Package OpenStreetMap updated to version 0.4.1 with previous version 0.4.0 dated 2023-10-12

Title: Access to Open Street Map Raster Images
Description: Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite, and topographic map servers are directly supported. Additionally raster maps may be constructed using custom tile servers. Maps can be plotted using either base graphics, or ggplot2. This package is not affiliated with the OpenStreetMap.org mapping project.
Author: Ian Fellows [aut, cre], Jan-Peter Stotz [aut]
Maintainer: Ian Fellows <ian@fellstat.com>

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Package spsurvey updated to version 5.6.0 with previous version 5.5.1 dated 2024-01-09

Title: Spatial Sampling Design and Analysis
Description: A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that [...truncated...]
Author: Michael Dumelle [aut, cre] , Tom Kincaid [aut], Anthony R. Olsen [aut], Marc Weber [aut], Don Stevens [ctb], Denis White [ctb], Amanda M. Nahlik [ctb], Sarah Lehmann [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>

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Package delimtools updated to version 0.2.1 with previous version 0.2.0 dated 2025-03-31

Title: Helper Functions for Species Delimitation Analysis
Description: Helpers functions to process, analyse, and visualize the output of single locus species delimitation methods. For full functionality, please install suggested software at <https://legallab.github.io/delimtools/articles/install.html>.
Author: Pedro Bittencourt [aut, cre, cph] , Rupert Collins [aut, ctb, cph] , Tomas Hrbek [aut, ctb]
Maintainer: Pedro Bittencourt <pedro.sennabittencourt@gmail.com>

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Package bgmfiles updated to version 0.1.0 with previous version 0.0.6 dated 2016-08-10

Title: Example BGM Files for the Atlantis Ecosystem Model
Description: A collection of box-geometry model (BGM) files for the Atlantis ecosystem model. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model (see <http://atlantis.cmar.csiro.au/> for more information).
Author: Michael D. Sumner [aut, cre], Hadley Wickham [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

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Package Zseq updated to version 0.2.2 with previous version 0.2.1 dated 2022-09-07

Title: Integer Sequence Generator
Description: Generates well-known integer sequences. 'gmp' package is adopted for computing with arbitrarily large numbers. Every function has hyperlink to its corresponding item in OEIS (The On-Line Encyclopedia of Integer Sequences) in the function help page. For interested readers, see Sloane and Plouffe (1995, ISBN:978-0125586306).
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>

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Package psgp updated to version 0.3-25 with previous version 0.3-24 dated 2025-09-26

Title: Projected Spatial Gaussian Process Methods
Description: Implements projected sparse Gaussian process Kriging ('Ingram et. al.', 2008, <doi:10.1007/s00477-007-0163-9>) as an additional method for the 'intamap' package. More details on implementation ('Barillec et. al.', 2010, <doi:10.1016/j.cageo.2010.05.008>).
Author: Ben Ingram [aut, cre] , Remi Barillec [aut], Jon Olav Skoien [aut]
Maintainer: Ben Ingram <ingrambr.work@gmail.com>

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Package oceanmap readmission to version 0.1.7 with previous version 0.1.6 dated 2023-11-10

Title: A Plotting Toolbox for 2D Oceanographic Data
Description: Plotting toolbox for 2D oceanographic data (satellite data, sea surface temperature, chlorophyll, ocean fronts & bathymetry). Recognized classes and formats include netcdf, Raster, '.nc' and '.gz' files.
Author: Robert K. Bauer [aut, cre]
Maintainer: Robert K. Bauer <marine.biologging@gmail.com>

This is a re-admission after prior archival of version 0.1.6 dated 2023-11-10

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Package EntropicStatistics readmission to version 0.1.3 with previous version 0.1.1 dated 2025-08-25

Title: Functions Based on Entropic Statistics
Description: Methods for data analysis from an entropic perspective. These methods are nonparametric and perform well on non-ordinal data. Currently includes 'HeatMap()' for visualizing distributional characteristics among multiple populations (groups).
Author: Jialin Zhang [aut, cph, cre]
Maintainer: Jialin Zhang <jzhang@math.msstate.edu>

This is a re-admission after prior archival of version 0.1.1 dated 2025-08-25

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Package ColombiAPI updated to version 0.3.0 with previous version 0.2.0 dated 2025-09-17

Title: Access Colombian Data via APIs and Curated Datasets
Description: Provides a comprehensive interface to access diverse public data about Colombia through multiple APIs and curated datasets. The package integrates four different APIs: 'API-Colombia' for Colombian-specific data including geography, culture, tourism, and government information; 'World Bank API' for economic and demographic indicators; 'Nager.Date' for public holidays; and 'REST Countries API' for general country information. The package enables users to explore various aspects of Colombia such as geographic locations, cultural attractions, economic indicators, demographic data, and public holidays. Additionally, 'ColombiAPI' includes curated datasets covering Bogota air stations, business and holiday dates, public schools, Colombian coffee exports, cannabis licenses, Medellin rainfall, malls in Bogota, as well as datasets on indigenous languages, student admissions and school statistics, forest liana mortality, municipal and regional data, connectivity and digital infrastructure, progra [...truncated...]
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>

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Package clusterability readmission to version 0.2.1.0 with previous version 0.1.1.0 dated 2020-03-04

Title: Performs Tests for Cluster Tendency of a Data Set
Description: Test for cluster tendency (clusterability) of a data set. The methods implemented - reducing the data set to a single dimension using principal component analysis or computing pairwise distances, and performing a multimodality test like the Dip Test or Silverman's Critical Bandwidth Test - are described in Adolfsson, Ackerman, and Brownstein (2019) <doi:10.1016/j.patcog.2018.10.026>. Such methods can inform whether clustering algorithms are appropriate for a data set.
Author: Zachariah Neville [aut, cre], Naomi Brownstein [aut], Maya Ackerman [aut], Andreas Adolfsson [aut]
Maintainer: Zachariah Neville <zachariahneville@outlook.com>

This is a re-admission after prior archival of version 0.1.1.0 dated 2020-03-04

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Package ubms updated to version 1.2.8 with previous version 1.2.7 dated 2024-10-01

Title: Bayesian Models for Data from Unmarked Animals using 'Stan'
Description: Fit Bayesian hierarchical models of animal abundance and occurrence via the 'rstan' package, the R interface to the 'Stan' C++ library. Supported models include single-season occupancy, dynamic occupancy, and N-mixture abundance models. Covariates on model parameters are specified using a formula-based interface similar to package 'unmarked', while also allowing for estimation of random slope and intercept terms. References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Ken Kellner [cre, aut]
Maintainer: Ken Kellner <contact@kenkellner.com>

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Package spCP updated to version 1.4.0 with previous version 1.3 dated 2022-09-05

Title: Spatially Varying Change Points
Description: Implements a spatially varying change point model with unique intercepts, slopes, variance intercepts and slopes, and change points at each location. Inference is within the Bayesian setting using Markov chain Monte Carlo (MCMC). The response variable can be modeled as Gaussian (no nugget), probit or Tobit link and the five spatially varying parameter are modeled jointly using a multivariate conditional autoregressive (MCAR) prior. The MCAR is a unique process that allows for a dissimilarity metric to dictate the local spatial dependencies. Full details of the package can be found in the accompanying vignette. Furthermore, the details of the package can be found in the corresponding paper published in Spatial Statistics by Berchuck et al (2019): "A spatially varying change points model for monitoring glaucoma progression using visual field data", <doi:10.1016/j.spasta.2019.02.001>.
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>

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Package sentopics updated to version 0.7.5 with previous version 0.7.4 dated 2024-09-20

Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of textual data. The package implements a fast Gibbs sampling estimation of Latent Dirichlet Allocation (Griffiths and Steyvers (2004) <doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He, Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of helpers and visualizations to analyze the result of topic modeling. The framework also allows enriching topic models with dates and externally computed sentiment measures. A flexible aggregation scheme enables the creation of time series of sentiment or topical proportions from the enriched topic models. Moreover, a novel method jointly aggregates topic proportions and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre] , Samuel Borms [ctb] , Chengua Lin [cph] , Yulan He [cph] , Jose Bernardo [cph] , David Robinson [cph] ), Julia Silge [cph] , ORCID: <https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>

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Package jackalope updated to version 1.1.6 with previous version 1.1.5 dated 2023-11-28

Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator
Description: Simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina <https://www.illumina.com/> and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. 'jackalope' can simulate single, paired-end, or mate-pair Illumina reads, as well as PacBio reads. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/polymerase chain reaction (PCR) duplicates. Simulating Illumina sequencing is based on ART by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>. PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>. All outputs can be written t [...truncated...]
Author: Lucas A. Nell [cph, aut, cre]
Maintainer: Lucas A. Nell <lucnell@gmail.com>

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Package ggRtsy updated to version 1.2.1 with previous version 0.1.0 dated 2023-09-15

Title: Add Some Van Gogh Colors and Overlay Colors on Your 'ggplot()'
Description: Works with 'ggplot2' to add a Van Gogh color palette to the user’s repertoire. It also has a function that work alongside 'ggplot2' to create more interesting data visualizations and add contextual information to the user’s plots.
Author: Katelyn Diaz [aut, cre] , Silas Weden [aut], Tess Goldmann [aut], Aushanae Haller [edt] , Kathleen Hablutzel [edt]
Maintainer: Katelyn Diaz <katndiaz@gmail.com>

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Package PEPBVS updated to version 2.2 with previous version 2.1 dated 2024-11-12

Title: Bayesian Variable Selection using Power-Expected-Posterior Prior
Description: Performs Bayesian variable selection under normal linear models for the data with the model parameters following as prior distributions either the power-expected-posterior (PEP) or the intrinsic (a special case of the former) (Fouskakis and Ntzoufras (2022) <doi: 10.1214/21-BA1288>, Fouskakis and Ntzoufras (2020) <doi: 10.3390/econometrics8020017>). The prior distribution on model space is the uniform over all models or the uniform on model dimension (a special case of the beta-binomial prior). The selection is performed by either implementing a full enumeration and evaluation of all possible models or using the Markov Chain Monte Carlo Model Composition (MC3) algorithm (Madigan and York (1995) <doi: 10.2307/1403615>). Complementary functions for hypothesis testing, estimation and predictions under Bayesian model averaging, as well as, plotting and printing the results are also provided. The results can be compared to the ones obtained under other well-known priors on [...truncated...]
Author: Konstantina Charmpi [aut, cre], Dimitris Fouskakis [aut], Ioannis Ntzoufras [aut]
Maintainer: Konstantina Charmpi <xarmpi.kon@gmail.com>

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Package MR.RGM updated to version 0.0.5 with previous version 0.0.4 dated 2025-03-03

Title: Multivariate Bidirectional Mendelian Randomization Networks
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. The resulting Graph visually represents these causal connections, showing directed edges with effect sizes labeled. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. In [...truncated...]
Author: Bitan Sarkar [aut, cre], Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>

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Package fdesigns updated to version 1.2 with previous version 1.1 dated 2025-06-17

Title: Optimal Experimental Designs for Dynamic/Functional Models
Description: Optimal experimental designs for functional linear and functional generalised linear models, for scalar responses and profile/dynamic factors. The designs are optimised using the coordinate exchange algorithm. The methods are discussed by Michaelides (2023) <https://eprints.soton.ac.uk/474982/1/Thesis_DamianosMichaelides_Final_pdfa_1_.pdf>.
Author: Damianos Michaelides [aut, cre], Antony Overstall [aut], Dave Woods [aut]
Maintainer: Damianos Michaelides <dm3g15@soton.ac.uk>

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Package bioimagetools updated to version 1.1.9 with previous version 1.1.8 dated 2022-05-28

Title: Tools for Microscopy Imaging
Description: Tools for 3D imaging, mostly for biology/microscopy. Read and write TIFF stacks. Functions for segmentation, filtering and analyzing 3D point patterns.
Author: Volker Schmid [aut, cre], Priyanka Kukreja [ctb], Fabian Scheipl [ctb]
Maintainer: Volker Schmid <stats@volkerschmid.de>

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Package RAthena updated to version 2.6.3 with previous version 2.6.1 dated 2022-12-20

Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this 'Python' 'Boto3' Software Development Kit ('SDK') <https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package optconerrf updated to version 1.0.1 with previous version 1.0.0 dated 2025-09-09

Title: Optimal Monotone Conditional Error Functions
Description: Design and analysis of confirmatory adaptive clinical trials using the optimal conditional error framework according to Brannath and Bauer (2004) <doi:10.1111/j.0006-341X.2004.00221.x>. An extension to the optimal conditional error function using interim estimates as described in Brannath and Dreher (2024) <doi:10.48550/arXiv.2402.00814> and functions to ensure that the resulting conditional error function is non-increasing are also available.
Author: Morten Dreher [aut, cre], Werner Brannath [aut, cph] , Cornelia Ursula Kunz [ctb] , Johanna zur Verth [aut]
Maintainer: Morten Dreher <morten.dreher@outlook.de>

Diff between optconerrf versions 1.0.0 dated 2025-09-09 and 1.0.1 dated 2025-09-29

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Package kinesis updated to version 0.3.1 with previous version 0.3.0 dated 2025-09-05

Title: 'shiny' Applications for the 'tesselle' Packages
Description: A collection of 'shiny' applications for the 'tesselle' packages <https://www.tesselle.org/>. This package provides applications for archaeological data analysis and visualization. These mainly, but not exclusively, include applications for chronological modelling (e.g. matrix seriation, aoristic analysis) and count data analysis (e.g. diversity measures, compositional data analysis).
Author: Nicolas Frerebeau [aut, cre] , Brice Lebrun [art] , Universite Bordeaux Montaigne [fnd] , CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>

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Package khroma updated to version 1.17.0 with previous version 1.16.0 dated 2025-02-25

Title: Colour Schemes for Scientific Data Visualization
Description: Color schemes ready for each type of data (qualitative, diverging or sequential), with colors that are distinct for all people, including color-blind readers. This package provides an implementation of Paul Tol (2018) and Fabio Crameri (2018) <doi:10.5194/gmd-11-2541-2018> color schemes for use with 'graphics' or 'ggplot2'. It provides tools to simulate color-blindness and to test how well the colors of any palette are identifiable. Several scientific thematic schemes (geologic timescale, land cover, FAO soils, etc.) are also implemented.
Author: Nicolas Frerebeau [aut, cre] , Brice Lebrun [art] , Vincent Arel-Bundock [ctb] , Ulrik Stervbo [ctb] , Universite Bordeaux Montaigne [fnd] , CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>

Diff between khroma versions 1.16.0 dated 2025-02-25 and 1.17.0 dated 2025-09-29

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New package whapi with initial version 0.0.2
Package: whapi
Title: R Client for 'whapi.cloud'
Version: 0.0.2
Date: 2025-09-10
Description: Provides an 'R' interface to the 'Whapi' 'API' <https://whapi.cloud>, enabling sending and receiving 'WhatsApp' messages directly from 'R'. Functions include sending text, images, documents, stickers, geographic locations, and interactive messages (buttons and lists). Also includes 'webhook' parsing utilities and channel health checks.
License: MIT + file LICENSE
URL: https://github.com/StrategicProjects/whapi/
BugReports: https://github.com/StrategicProjects/whapi/issues/
Depends: R (>= 4.2.0)
Imports: httr2 (>= 1.0.0), cli (>= 3.6.0), tibble (>= 3.2.0), purrr (>= 1.0.0), stringr (>= 1.5.0), stringi, dplyr, readr, lubridate (>= 1.9.0), jsonlite (>= 1.8.0), mime, openssl
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, pkgdown
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-09-22 11:21:29 UTC; leite
Author: Andre Leite [aut, cre], Hugo Vaconcelos [aut], Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Repository: CRAN
Date/Publication: 2025-09-29 17:00:02 UTC

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New package SHAPBoost with initial version 1.0.0
Package: SHAPBoost
Title: The SHAPBoost Feature Selection Algorithm
Version: 1.0.0
Description: The implementation of SHAPBoost, a boosting-based feature selection technique that ranks features iteratively based on Shapley values.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: xgboost, SHAPforxgboost, methods, caret, Matrix
Suggests: flare, survival
URL: https://github.com/O-T-O-Z/SHAPBoost-R
BugReports: https://github.com/O-T-O-Z/SHAPBoost-R/issues
NeedsCompilation: no
Packaged: 2025-09-22 09:04:24 UTC; o.t.ozyilmaz
Author: Oemer Tarik Oezyilmaz [aut, cre, cph] , Tamas Szili-Toeroek [aut, cph]
Maintainer: Oemer Tarik Oezyilmaz <o.t.ozyilmaz@umcg.nl>
Repository: CRAN
Date/Publication: 2025-09-29 16:40:02 UTC

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Package rdracor updated to version 1.0.6 with previous version 1.0.5 dated 2025-08-27

Title: Access to the 'DraCor' API
Description: Provide an interface for 'Drama Corpora Project' ('DraCor') API: <https://dracor.org/documentation/api>.
Author: Ivan Pozdniakov [aut, cre]
Maintainer: Ivan Pozdniakov <bucherr@yandex.ru>

Diff between rdracor versions 1.0.5 dated 2025-08-27 and 1.0.6 dated 2025-09-29

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Package bioseq updated to version 0.1.5 with previous version 0.1.4 dated 2022-09-06

Title: A Toolbox for Manipulating Biological Sequences
Description: Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences). Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>. Provides a collection of functions to perform biological conversion among classes (transcription, translation) and basic operations on sequences (detection, selection and replacement based on positions or patterns). The package also provides functions to import and export sequences from and to other package formats.
Author: Francois Keck [aut, cre, cph]
Maintainer: Francois Keck <francois.keck@gmail.com>

Diff between bioseq versions 0.1.4 dated 2022-09-06 and 0.1.5 dated 2025-09-29

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New package BOP2FE with initial version 1.0.3
Package: BOP2FE
Title: Bayesian Optimal Phase II Design with Futility and Efficacy Stopping Boundaries
Version: 1.0.3
Description: Bayesian optimal design with futility and efficacy stopping boundaries (BOP2-FE) is a novel statistical framework for single-arm Phase II clinical trials. It enables early termination for efficacy when interim data are promising, while explicitly controlling Type I and Type II error rates. The design supports a variety of endpoint structures, including single binary endpoints, nested endpoints, co-primary endpoints, and joint monitoring of efficacy and toxicity. The package provides tools for enumerating stopping boundaries prior to trial initiation and for conducting simulation studies to evaluate the design’s operating characteristics. Users can flexibly specify design parameters to suit their specific applications. For methodological details, refer to Xu et al. (2025) <doi:10.1080/10543406.2025.2558142>.
BugReports: https://github.com/belayb/BOP2FE/issues
License: MIT + file LICENSE
Encoding: UTF-8
Imports: gridExtra, patchwork, ggplot2, stats, utils
Suggests: spelling
Language: en-US
URL: https://github.com/belayb/BOP2FE
NeedsCompilation: no
Packaged: 2025-09-22 09:45:47 UTC; A4044038
Author: Belay Birlie Yimer [aut, cre], Xinling Xu [aut], Atsuki Hashimoto [aut], Gosuke Homma [aut], Kentaro Takeda [aut]
Maintainer: Belay Birlie Yimer <belayabyimer@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-29 16:40:07 UTC

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Package workspace updated to version 0.1.6 with previous version 0.1.5 dated 2025-09-11

Title: Manage Collections of Datasets and Objects
Description: Create, store, read and manage structured collections of datasets and other objects using a 'workspace', then bundle it into a compressed archive. Using open and interoperable formats makes it possible to exchange bundled data from 'R' to other languages such as 'Python' or 'Julia'. Multiple formats are supported 'Parquet', 'JSON', 'yaml', spatial data and raster data are supported.
Author: Eli Daniels [aut, cre], David Gohel [aut], ArData [cph, fnd]
Maintainer: Eli Daniels <eli.daniels@ardata.fr>

Diff between workspace versions 0.1.5 dated 2025-09-11 and 0.1.6 dated 2025-09-29

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Package SpatMCA updated to version 1.0.7 with previous version 1.0.4 dated 2023-11-21

Title: Regularized Spatial Maximum Covariance Analysis
Description: Provide regularized maximum covariance analysis incorporating smoothness, sparseness and orthogonality of couple patterns by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D (Wang and Huang, 2018 <doi:10.1002/env.2481>).
Author: Wen-Ting Wang [aut, cre] , Hsin-Cheng Huang [aut]
Maintainer: Wen-Ting Wang <egpivo@gmail.com>

Diff between SpatMCA versions 1.0.4 dated 2023-11-21 and 1.0.7 dated 2025-09-29

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Package PracTools updated to version 1.7 with previous version 1.6.1 dated 2025-05-11

Title: Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs, sample sizes in two-phase designs, and a stopping rule for ending data collection. A number of example data sets are included.
Author: Richard Valliant [aut, cre], Jill A. Dever [ctb], Frauke Kreuter [ctb], George Zipf [aut]
Maintainer: Richard Valliant <valliant@umich.edu>

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Package glmmrBase updated to version 1.1.0 with previous version 1.0.2 dated 2025-07-22

Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models. Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models, non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily, robust and bias-corrected standard error estimation, power calculation, data simulation, and more. See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>

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Package epiR updated to version 2.0.87 with previous version 2.0.86 dated 2025-08-31

Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] , Evan Sergeant [aut], Cord Heuer [ctb], Telmo Nunes [ctb], Cord Heuer [ctb], Jonathon Marshall [ctb], Javier Sanchez [ctb], Ron Thornton [ctb], Jeno Reiczigel [ctb], Jim Robison-Cox [ctb], Paola Sebastiani [ctb], Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>

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Package tilemaps updated to version 0.2.1 with previous version 0.2.0 dated 2020-07-10

Title: Generate Tile Maps
Description: Implements an algorithm for generating maps, known as tile maps, in which each region is represented by a single tile of the same shape and size. The algorithm was first proposed in "Generating Tile Maps" by Graham McNeill and Scott Hale (2017) <doi:10.1111/cgf.13200>. Functions allow users to generate, plot, and compare square or hexagon tile maps.
Author: Kaelyn Rosenberg [aut, cre]
Maintainer: Kaelyn Rosenberg <kaerosenberg@gmail.com>

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Package ASML updated to version 1.1.0 with previous version 1.0.0 dated 2025-02-19

Title: Algorithm Portfolio Selection with Machine Learning
Description: A wrapper for machine learning (ML) methods to select among a portfolio of algorithms based on the value of a key performance indicator (KPI). A number of features is used to adjust a model to predict the value of the KPI for each algorithm, then, for a new value of the features the KPI is estimated and the algorithm with the best one is chosen. To learn it can use the regression methods in 'caret' package or a custom function defined by the user. Several graphics available to analyze the results obtained. This library has been used in Ghaddar et al. (2023) <doi:10.1287/ijoc.2022.0090>).
Author: Brais Gonzalez-Rodriguez [aut, cre] , Ignacio Gomez-Casares [aut] , Beatriz Pateiro-Lopez [aut] , Julio Gonzalez-Diaz [aut] , Maria Caseiro-Arias [ctb], Antonio Farina-Elorza [ctb], Manuel Timiraos-Lopez [ctb]
Maintainer: Brais Gonzalez-Rodriguez <brais.gonzalez.rodriguez@uvigo.gal>

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Package tinytable updated to version 0.14.0 with previous version 0.13.0 dated 2025-08-19

Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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 tinytable-0.14.0/tinytable/R/save_tt.R                                                                    |   42 
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 tinytable-0.14.0/tinytable/R/tabulator_data.R                                                             |    2 
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 tinytable-0.14.0/tinytable/inst/tinytest/test-i_j.R                                                       |    3 
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Package openxlsx2 updated to version 1.20 with previous version 1.19 dated 2025-08-25

Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by providing a high level interface to writing, styling and editing worksheets.
Author: Jordan Mark Barbone [aut] , Jan Marvin Garbuszus [aut, cre], Olivier Roy [ctb], openxlsx authors [cph] , Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>

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Package conMItion updated to version 0.2.1 with previous version 0.2.0 dated 2025-07-14

Title: Conditional Mutual Information Estimation for Multi-Omics Data
Description: The biases introduced in association measures, particularly mutual information, are influenced by factors such as tumor purity, mutation burden, and hypermethylation. This package provides the estimation of conditional mutual information (CMI) and its statistical significance with a focus on its application to multi-omics data. Utilizing B-spline functions (inspired by Daub et al. (2004) <doi:10.1186/1471-2105-5-118>), the package offers tools to estimate the association between heterogeneous multi- omics data, while removing the effects of confounding factors. This helps to unravel complex biological interactions. In addition, it includes methods to evaluate the statistical significance of these associations, providing a robust framework for multi-omics data integration and analysis. This package is ideal for researchers in computational biology, bioinformatics, and systems biology seeking a comprehensive tool for understanding interdependencies in omics data.
Author: Gaojianyong Wang [aut, cre]
Maintainer: Gaojianyong Wang <gjywang@gmail.com>

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Package timeordered updated to version 1.0.2 with previous version 1.0.1 dated 2024-09-15

Title: Time-Ordered and Time-Aggregated Network Analyses
Description: Approaches for incorporating time into network analysis. Methods include: construction of time-ordered networks (temporal graphs); shortest-time and shortest-path-length analyses; resource spread calculations; data resampling and rarefaction for null model construction; reduction to time-aggregated networks with variable window sizes; application of common descriptive statistics to these networks; vector clock latencies; and plotting functionalities. The package supports <doi:10.1371/journal.pone.0020298>.
Author: Benjamin Wong Blonder [aut, cre]
Maintainer: Benjamin Wong Blonder <benjamin.blonder@berkeley.edu>

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Package soundgen updated to version 2.7.4 with previous version 2.7.3 dated 2025-07-17

Title: Sound Synthesis and Acoustic Analysis
Description: Performs parametric synthesis of sounds with harmonic and noise components such as animal vocalizations or human voice. Also offers tools for audio manipulation and acoustic analysis, including pitch tracking, spectral analysis, audio segmentation, pitch and formant shifting, etc. Includes four interactive web apps for synthesizing and annotating audio, manually correcting pitch contours, and measuring formant frequencies. Reference: Anikin (2019) <doi:10.3758/s13428-018-1095-7>.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <andrey.anikin@cogsci.se>

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Package Rparadox updated to version 0.1.5 with previous version 0.1.2 dated 2025-09-22

Title: Read Paradox Database Files into R
Description: Provides a simple and efficient way to read data from Paradox database files (.db) directly into R as modern 'tibble' data frames. It uses the underlying 'pxlib' C library, to handle the low-level file format details and provides a clean, user-friendly R interface.
Author: Daniil Popov [aut, cre]
Maintainer: Daniil Popov <popov.daniil@gmail.com>

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Package rFIA updated to version 1.1.2 with previous version 1.1.1 dated 2025-03-10

Title: Estimation of Forest Variables using the FIA Database
Description: The goal of 'rFIA' is to increase the accessibility and use of the United States Forest Services (USFS) Forest Inventory and Analysis (FIA) Database by providing a user-friendly, open source toolkit to easily query and analyze FIA Data. Designed to accommodate a wide range of potential user objectives, 'rFIA' simplifies the estimation of forest variables from the FIA Database and allows all R users (experts and newcomers alike) to unlock the flexibility inherent to the Enhanced FIA design. Specifically, 'rFIA' improves accessibility to the spatial-temporal estimation capacity of the FIA Database by producing space-time indexed summaries of forest variables within user-defined population boundaries. Direct integration with other popular R packages (e.g., 'dplyr', 'tidyr', and 'sf') facilitates efficient space-time query and data summary, and supports common data representations and API design. The package implements design-based estimation procedures outlined by Bechtold & Patterson [...truncated...]
Author: Jeffrey Doser [aut, cre], Hunter Stanke [aut], Andrew Finley [aut]
Maintainer: Jeffrey Doser <jwdoser@ncsu.edu>

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Package occCite readmission to version 0.6.1 with previous version 0.6.0 dated 2025-06-16

Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] , Cory Merow [aut] , Brian Maitner [aut] , Jamie M. Kass [aut] , Vijay Barve [aut] , Robert P. Guralnick [aut] , Damiano Oldoni [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/407>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>

This is a re-admission after prior archival of version 0.6.0 dated 2025-06-16

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Package NHSRplotthedots updated to version 0.2.2 with previous version 0.1.0 dated 2021-11-03

Title: Draw XmR Charts for NHS 'Making Data Count' Programme
Description: Provides tools for drawing Statistical Process Control (SPC) charts. This package supports the NHS 'Making Data Count' programme, and allows users to draw XmR charts, use change points and apply rules with summary indicators for when rules are breached.
Author: Tom Smith [cre, aut], Christopher Reading [aut], Simon Wellesley-Miller [aut], Zoe Turner [aut] , Tom Jemmett [aut] , Chris Mainey [aut] , John MacKintosh [aut], Marcos Fabietti [aut], Fran Barton [aut] , NHS-R community [cph]
Maintainer: Tom Smith <thomas.smith103@nhs.net>

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Package mwa updated to version 0.5.0 with previous version 0.4.4 dated 2022-04-26

Title: Causal Inference in Spatiotemporal Event Data
Description: Implementation of Matched Wake Analysis (mwa) for studying causal relationships in spatiotemporal event data, introduced by Schutte and Donnay (2014) <doi:10.1016/j.polgeo.2014.03.001>.
Author: Sebastian Schutte [aut], Karsten Donnay [aut, cre]
Maintainer: Karsten Donnay <kdonnay@gmx.net>

Diff between mwa versions 0.4.4 dated 2022-04-26 and 0.5.0 dated 2025-09-29

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Package JMbayes updated to version 0.9-0 with previous version 0.8-85 dated 2020-01-08

Title: Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Author: Dimitris Rizopoulos [aut, cre]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>

Diff between JMbayes versions 0.8-85 dated 2020-01-08 and 0.9-0 dated 2025-09-29

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Package IPMRF readmission to version 1.3 with previous version 1.2 dated 2017-08-09

Title: Intervention in Prediction Measure for Random Forests
Description: Computes intervention in prediction measure for assessing variable importance for random forests. See details at I. Epifanio (2017) <DOI:10.1186/s12859-017-1650-8>.
Author: Irene Epifanio [aut, cre], Stefano Nembrini [aut], Aleix Alcacer [aut], Vicente Bolos [aut]
Maintainer: Irene Epifanio <epifanio@uji.es>

This is a re-admission after prior archival of version 1.2 dated 2017-08-09

Diff between IPMRF versions 1.2 dated 2017-08-09 and 1.3 dated 2025-09-29

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Package getRad updated to version 0.2.2 with previous version 0.2.1 dated 2025-08-25

Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for aeroecological research directly into R. With 'getRad' you can access data from several sources in Europe and the US and standardize it to facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] , Pieter Huybrechts [aut] ), Peter Desmet [aut] ), Cecilia Nilsson [ctb] , Alexander Tedeschi [ctb] , Hidde Leijnse [ctb] , Bart Hoekstra [ctb] , University of Amsterdam [cph] , Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>

Diff between getRad versions 0.2.1 dated 2025-08-25 and 0.2.2 dated 2025-09-29

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Package fastpos updated to version 0.6.0 with previous version 0.5.1 dated 2022-08-15

Title: Finds the Critical Sequential Point of Stability for a Pearson Correlation
Description: Finds the critical sample size ("critical point of stability") for a correlation to stabilize in Schoenbrodt and Perugini's definition of sequential stability (see <doi:10.1016/j.jrp.2013.05.009>).
Author: Johannes Titz [aut, cre, cph]
Maintainer: Johannes Titz <johannes.titz@gmail.com>

Diff between fastpos versions 0.5.1 dated 2022-08-15 and 0.6.0 dated 2025-09-29

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Package ExpDE updated to version 0.2.0 with previous version 0.1.4 dated 2018-01-10

Title: Modular Differential Evolution for Experimenting with Operators
Description: Modular implementation of the Differential Evolution algorithm for experimenting with different types of operators.
Author: Felipe Campelo [aut, cre], Moises Botelho [aut]
Maintainer: Felipe Campelo <f.campelo@bristol.ac.uk>

Diff between ExpDE versions 0.1.4 dated 2018-01-10 and 0.2.0 dated 2025-09-29

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Package copBasic updated to version 2.2.9 with previous version 2.2.8 dated 2025-06-27

Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations for bicopula theory. The lower, upper, product, and select other bicopula are implemented along with operations including the diagonal, survival copula, dual of a copula, co-copula, and numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical derivatives and inverses of a bicopula are provided through which simulation is implemented. Bicopula composition, convex combination, asymmetry extension, and products also are provided. Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau, Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer- Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and positive/negative quadrant dependency, left (right) increasing (decreasing) are available. Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>

Diff between copBasic versions 2.2.8 dated 2025-06-27 and 2.2.9 dated 2025-09-29

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More information about copBasic at CRAN
Permanent link

Package bhpm readmission to version 1.8.1 with previous version 1.7 dated 2020-04-01

Title: Bayesian Hierarchical Poisson Models for Multiple Grouped Outcomes with Clustering
Description: Bayesian hierarchical methods for the detection of differences in rates of related outcomes for multiple treatments for clustered observations (Carragher et al. (2020) <doi:10.1002/sim.8563>). This software was developed for the Precision Drug Theraputics: Risk Prediction in Pharmacoepidemiology project as part of a Rutherford Fund Fellowship at Health Data Research (UK), Medical Research Council (UK) award reference MR/S003967/1 (<https://gtr.ukri.org/>). Principal Investigator: Raymond Carragher.
Author: Raymond Carragher [aut, cre]
Maintainer: Raymond Carragher <rcarragh@gmail.com>

This is a re-admission after prior archival of version 1.7 dated 2020-04-01

Diff between bhpm versions 1.7 dated 2020-04-01 and 1.8.1 dated 2025-09-29

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Package profile updated to version 1.0.4 with previous version 1.0.3 dated 2022-08-22

Title: Read, Manipulate, and Write Profiler Data
Description: Defines a data structure for profiler data, and methods to read and write from the 'Rprof' and 'pprof' file formats.
Author: Kirill Mueller [aut, cre] , R Consortium [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>

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Package enaho updated to version 0.2.5 with previous version 0.2.0 dated 2025-07-23

Title: Encuesta Nacional de Hogares (Peruvian Home National Survey)
Description: Descarga, lee y analiza bases de la Encuesta Nacional de Hogares (ENAHO) y otras encuestas del Instituto Nacional de Estadística e Informática (INEI) del Perú. (Downloads, reads, and combines data from the Peruvian Home National Survey and other surveys from the National Institute for Statistics (INEI).)
Author: Andres Christiansen [aut, cre]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>

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Sun, 28 Sep 2025

Package intsurv updated to version 0.3.0 with previous version 0.2.2 dated 2021-01-08

Title: Integrative Survival Modeling
Description: Contains implementations of the integrative Cox model with uncertain event times proposed by Wang, et al. (2020) <doi:10.1214/19-AOAS1287>, the regularized Cox cure rate model with uncertain event status proposed by Wang, et al. (2023) <doi:10.1007/s12561-023-09374-w>, and other survival analysis routines including the Cox cure rate model proposed by Kuk and Chen (1992) <doi:10.1093/biomet/79.3.531> via an EM algorithm proposed by Sy and Taylor (2000) <doi:10.1111/j.0006-341X.2000.00227.x>, the regularized Cox cure rate model with elastic net penalty following Masud et al. (2018) <doi:10.1177/0962280216677748>.
Author: Wenjie Wang [aut, cre] , Kun Chen [ths] , Jun Yan [ths]
Maintainer: Wenjie Wang <wang@wwenjie.org>

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Package rotations updated to version 1.6.6 with previous version 1.6.5 dated 2023-12-07

Title: Working with Rotation Data
Description: Tools for working with rotational data, including simulation from the most commonly used distributions on SO(3), methods for different Bayes, mean and median type estimators for the central orientation of a sample, confidence/credible regions for the central orientation based on those estimators and a novel visualization technique for rotation data. Most recently, functions to identify potentially discordant (outlying) values have been added. References: Bingham, Melissa A. and Nordman, Dan J. and Vardeman, Steve B. (2009), Bingham, Melissa A and Vardeman, Stephen B and Nordman, Daniel J (2009), Bingham, Melissa A and Nordman, Daniel J and Vardeman, Stephen B (2010), Leon, C.A. and Masse, J.C. and Rivest, L.P. (2006), Hartley, R and Aftab, K and Trumpf, J. (2011), Stanfill, Bryan and Genschel, Ulrike and Hofmann, Heike (2013), Maonton, Jonathan (2004), Mardia, KV and Jupp, PE (2000, ISBN:9780471953333), Rancourt, D. and Rivest, L.P. and Asselin, J. (2000), Chang, Ted and Rivest, Loui [...truncated...]
Author: Bryan Stanfill [aut, cre], Heike Hofmann [aut], Ulrike Genschel [aut], Aymeric Stamm [ctb] , Luciano Selzer [ctb]
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>

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Package hesim updated to version 0.5.6 with previous version 0.5.5 dated 2024-09-18

Title: Health Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for parameterizing, simulating, and analyzing health economic simulation models. The package supports cohort discrete time state transition models (Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>, N-state partitioned survival models (Glasziou et al. 1990) <doi:10.1002/sim.4780091106>, and individual-level continuous time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>, encompassing both Markov (time-homogeneous and time-inhomogeneous) and semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is quantified with standard graphical and tabular summaries of a probabilistic sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>, <doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table make individual-patient simulation, probabilistic sensitivity analysis, and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre], Jeroen P. Jansen [aut], Mark Clements [aut], R Core Team [ctb]
Maintainer: Devin Incerti <devin.incerti@gmail.com>

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 hesim-0.5.6/hesim/MD5                                                                                |  212 +++++-----
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 hesim-0.5.6/hesim/src/apply_rr.cpp                                                                   |    6 
 hesim-0.5.6/hesim/src/ctstm.cpp                                                                      |    2 
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 hesim-0.5.6/hesim/src/psm.cpp                                                                        |    2 
 hesim-0.5.6/hesim/src/statevals.cpp                                                                  |    2 
 hesim-0.5.6/hesim/src/test-utils.cpp                                                                 |   10 
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Package constants updated to version 2022.0 with previous version 1.0.1 dated 2021-02-25

Title: Reference on Constants, Units and Uncertainty
Description: CODATA internationally recommended values of the fundamental physical constants, provided as symbols for direct use within the R language. Optionally, the values with uncertainties and/or units are also provided if the 'errors', 'units' and/or 'quantities' packages are installed. The Committee on Data for Science and Technology (CODATA) is an interdisciplinary committee of the International Council for Science which periodically provides the internationally accepted set of values of the fundamental physical constants. This package contains the "2022 CODATA" version, published on May 2024: Eite Tiesinga, Peter J. Mohr, David B. Newell, and Barry N. Taylor (2024) <https://physics.nist.gov/cuu/Constants/>.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>

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Package shinyNotes updated to version 0.0.3 with previous version 0.0.2 dated 2023-02-19

Title: Shiny Module for Taking Free-Form Notes
Description: An enterprise-targeted scalable and customizable 'shiny' module providing an easy way to incorporate free-form note taking or discussion boards into applications. The package includes a 'shiny' module that can be included in any 'shiny' application to create a panel containing searchable, editable text broken down by section headers. Can be used with a local 'SQLite' database, or a compatible remote database of choice.
Author: Daniel Kovtun [cre, aut]
Maintainer: Daniel Kovtun <quantumfusetrader@gmail.com>

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Package seededlda updated to version 1.4.3 with previous version 1.4.2 dated 2025-01-07

Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>. Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph], Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>

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Package prefio readmission to version 0.2.0 with previous version 0.1.1 dated 2023-09-07

Title: Structures for Preference Data
Description: Convenient structures for creating, sourcing, reading, writing and manipulating ordinal preference data. Methods for writing to/from PrefLib formats. See Nicholas Mattei and Toby Walsh "PrefLib: A Library of Preference Data" (2013) <doi:10.1007/978-3-642-41575-3_20>.
Author: Floyd Everest [aut, cre] , Heather Turner [aut] , Damjan Vukcevic [aut]
Maintainer: Floyd Everest <me@floydeverest.com>

This is a re-admission after prior archival of version 0.1.1 dated 2023-09-07

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Package extrafontdb updated to version 1.1 with previous version 1.0 dated 2012-06-11

Title: Holding the Database for the 'extrafont' Package
Description: It is meant to be used with the 'extrafont' package. The 'extrafont' package contains the code to install and use fonts, while the 'extrafontdb' package contains the font database.
Author: Winston Chang [aut], Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>

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Package spsUtil updated to version 0.2.2.1 with previous version 0.2.2 dated 2021-10-30

Title: 'systemPipeShiny' Utility Functions
Description: The systemPipeShiny (SPS) framework comes with many useful utility functions. However, installing the whole framework is heavy and takes some time. If you like only a few useful utility functions from SPS, install this package is enough.
Author: Le Zhang [aut, cre]
Maintainer: Le Zhang <lezhang100@gmail.com>

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Package slcm updated to version 0.1.1 with previous version 0.1.0 dated 2023-08-12

Title: Sparse Latent Class Model for Cognitive Diagnosis
Description: Perform a Bayesian estimation of the exploratory Sparse Latent Class Model for Binary Data described by Chen, Y., Culpepper, S. A., and Liang, F. (2020) <doi:10.1007/s11336-019-09693-2>.
Author: James Joseph Balamuta [aut, cre, cph] , Steven Andrew Culpepper [aut, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package gslnls updated to version 1.4.2 with previous version 1.4.1 dated 2025-01-17

Title: GSL Multi-Start Nonlinear Least-Squares Fitting
Description: An R interface to weighted nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Robust nonlinear regression can be performed using various robust loss functions, in which case the optimization problem is solved by iterative reweighted least squares (IRLS). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>

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Package camtrapR updated to version 3.0.0 with previous version 2.3.1 dated 2025-09-02

Title: Camera Trap Data Management and Analysis Framework
Description: Management and analysis of camera trap wildlife data through an integrated workflow. Provides functions for image/video organization and metadata extraction, species/individual identification. Creates detection histories for occupancy and spatial capture-recapture analyses, with support for multi-season studies. Includes tools for fitting community occupancy models in JAGS and NIMBLE, and an interactive dashboard for survey data visualization and analysis. Features visualization of species distributions and activity patterns, plus export capabilities for GIS and reports. Emphasizes automation and reproducibility while maintaining flexibility for different study designs.
Author: Juergen Niedballa [aut, cre] , Alexandre Courtiol [aut] , Rahel Sollmann [aut] , John Mathai [ctb], Seth Timothy Wong [ctb] , An The Truong Nguyen [ctb] , Azlan bin Mohamed [ctb] , Andrew Tilker [ctb] , Roshan Guharajan [ctb] , Ioannis Alexiou [ctb] [...truncated...]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>

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Package aidar (with last version 1.0.5) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-01-26 1.0.5
2013-12-11 1.0.0

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Package fgdr (with last version 1.1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-02-21 1.1.1
2020-09-30 1.1.0
2020-05-06 1.0.1
2019-10-11 1.0.0

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Package jstor (with last version 0.3.11) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2023-08-16 0.3.11
2021-12-08 0.3.10

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Package rmarkdown updated to version 2.30 with previous version 2.29 dated 2024-11-04

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] , Christophe Dervieux [aut] , Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] , Andrew Dun [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>

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Package lingtypology updated to version 1.1.24 with previous version 1.1.23 dated 2025-08-18

Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] , Kirill Koncha [ctb] , Mikhail Leonov [ctb], Anna Smirnova [ctb], Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>

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Package TreeDist updated to version 2.11.0 with previous version 2.10.1 dated 2025-08-25

Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; the Hierarchical Mutual Information (Perotti et al. 2015) <doi:10.1103/PhysRevE.92.062825>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands o [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg] , Roy Jonker [prg, cph], Yong Yang [ctb, cph], Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

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Package spatstat updated to version 3.4-1 with previous version 3.4-0 dated 2025-07-25

Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images. Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] , Rolf Turner [aut] , Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package SpatPCA updated to version 1.3.8 with previous version 1.3.5 dated 2023-11-13

Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigen-functions by using the alternating direction method of multipliers algorithm (Wang and Huang, 2017, <DOI:10.1080/10618600.2016.1157483>). The method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D.
Author: Wen-Ting Wang [aut, cre] , Hsin-Cheng Huang [aut]
Maintainer: Wen-Ting Wang <egpivo@gmail.com>

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Package litteR updated to version 1.0.2 with previous version 1.0.1 dated 2025-07-04

Title: Litter Analysis
Description: Data sets on various litter types like beach litter, riverain litter, floating litter, and seafloor litter are rapidly growing. This package offers a simple user interface to analyse these litter data in a consistent and reproducible way. It also provides functions to facilitate several kinds of litter analysis, e.g., trend analysis, power analysis, and baseline analysis. Under the hood, these functions are also used by the user interface. See Schulz et al. (2019) <doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual for 'RStudio' and 'litteR'.
Author: Dennis Walvoort [aut, cre, cph], Willem van Loon [aut, cph], Rijkswaterstaat - The Netherlands [cph, fnd, dtc]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>

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Package hdMTD updated to version 0.1.2 with previous version 0.1.1 dated 2025-08-27

Title: Inference for High-Dimensional Mixture Transition Distribution Models
Description: Estimates parameters in Mixture Transition Distribution (MTD) models, a class of high-order Markov chains. The set of relevant pasts (lags) is selected using either the Bayesian Information Criterion or the Forward Stepwise and Cut algorithms. Other model parameters (e.g. transition probabilities and oscillations) can be estimated via maximum likelihood estimation or the Expectation-Maximization algorithm. Additionally, 'hdMTD' includes a perfect sampling algorithm that generates samples of an MTD model from its invariant distribution. For theory, see Ost & Takahashi (2023) <http://jmlr.org/papers/v24/22-0266.html>.
Author: Maiara Gripp [aut, cre], Guilherme Ost [ths], Giulio Iacobelli [ths]
Maintainer: Maiara Gripp <maiara@dme.ufrj.br>

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Package changepointGA updated to version 0.1.3 with previous version 0.1.1 dated 2025-05-22

Title: Changepoint Detection via Modified Genetic Algorithm
Description: The Genetic Algorithm (GA) is used to perform changepoint analysis in time series data. The package also includes an extended island version of GA, as described in Lu, Lund, and Lee (2010, <doi:10.1214/09-AOAS289>). By mimicking the principles of natural selection and evolution, GA provides a powerful stochastic search technique for solving combinatorial optimization problems. In 'changepointGA', each chromosome represents a changepoint configuration, including the number and locations of changepoints, hyperparameters, and model parameters. The package employs genetic operators—selection, crossover, and mutation—to iteratively improve solutions based on the given fitness (objective) function. Key features of 'changepointGA' include encoding changepoint configurations in an integer format, enabling dynamic and simultaneous estimation of model hyperparameters, changepoint configurations, and associated parameters. The detailed algorithmic implementation can be found in the package [...truncated...]
Author: Mo Li [aut, cre], QiQi Lu [aut]
Maintainer: Mo Li <mo.li@louisiana.edu>

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Package hexDensity updated to version 1.4.10 with previous version 1.4.9 dated 2025-06-07

Title: Fast Kernel Density Estimation with Hexagonal Grid
Description: Kernel density estimation with hexagonal grid for bivariate data. Hexagonal grid has many beneficial properties like equidistant neighbours and less edge bias, making it better for spatial analyses than the more commonly used rectangular grid. Carr, D. B. et al. (1987) <doi:10.2307/2289444>. Diggle, P. J. (2010) <doi:10.1201/9781420072884>. Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>. Jones, M. C. (1993) <doi:10.1007/BF00147776>.
Author: Quoc Hoang Nguyen [aut, cre] , Yunshun Chen [aut] , Dan Carr [ctb], binning routine ported by Nicholas Lewin-Koh [ctb], Martin Maechler [ctb]
Maintainer: Quoc Hoang Nguyen <nguyen.q@wehi.edu.au>

Diff between hexDensity versions 1.4.9 dated 2025-06-07 and 1.4.10 dated 2025-09-28

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Package spatstat.model updated to version 3.4-2 with previous version 3.4-0 dated 2025-07-23

Title: Parametric Statistical Modelling and Inference for the 'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Supports parametric modelling, formal statistical inference, and model validation. Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] , Rolf Turner [aut, cph] , Ege Rubak [aut, cph] , Kasper Klitgaard Berthelsen [ctb], Achmad Choiruddin [ctb, cph], Jean-Francois Coeurjolly [ctb], Ottmar Cronie [ctb], Tilman Davies [ctb], Julian Gilbey [ctb], Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package hgwrr updated to version 0.6-2 with previous version 0.6-1 dated 2024-11-16

Title: Hierarchical and Geographically Weighted Regression
Description: This model divides coefficients into three types, i.e., local fixed effects, global fixed effects, and random effects (Hu et al., 2022)<doi:10.1177/23998083211063885>. If data have spatial hierarchical structures (especially are overlapping on some locations), it is worth trying this model to reach better fitness.
Author: Yigong Hu [aut, cre], Richard Harris [aut], Richard Timmerman [aut]
Maintainer: Yigong Hu <yigong.hu@bristol.ac.uk>

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Sat, 27 Sep 2025

Package sasLM updated to version 0.10.7 with previous version 0.10.6 dated 2025-07-23

Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that. Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>

Diff between sasLM versions 0.10.6 dated 2025-07-23 and 0.10.7 dated 2025-09-27

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Package dina updated to version 2.0.2 with previous version 2.0.0 dated 2019-02-01

Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy "And" Gate (DINA) cognitive diagnostic model parameters using the Gibbs sampler described by Culpepper (2015) <doi:10.3102/1076998615595403>.
Author: Steven Andrew Culpepper [aut, cph] , James Joseph Balamuta [aut, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package tugboat updated to version 0.1.3 with previous version 0.1.1 dated 2024-12-17

Title: Build a Docker Image from a Directory or Project
Description: Simple utilities to generate a Dockerfile from a directory or project, build the corresponding Docker image, and push the image to DockerHub.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>

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Package sirt updated to version 4.2-133 with previous version 4.1-15 dated 2024-02-05

Title: Supplementary Item Response Theory Models
Description: Supplementary functions for item response models aiming to complement existing R packages. The functionality includes among others multidimensional compensatory and noncompensatory IRT models (Reckase, 2009, <doi:10.1007/978-0-387-89976-3>), MCMC for hierarchical IRT models and testlet models (Fox, 2010, <doi:10.1007/978-1-4419-0742-4>), NOHARM (McDonald, 1982, <doi:10.1177/014662168200600402>), Rasch copula model (Braeken, 2011, <doi:10.1007/s11336-010-9190-4>; Schroeders, Robitzsch & Schipolowski, 2014, <doi:10.1111/jedm.12054>), faceted and hierarchical rater models (DeCarlo, Kim & Johnson, 2011, <doi:10.1111/j.1745-3984.2011.00143.x>), ordinal IRT model (ISOP; Scheiblechner, 1995, <doi:10.1007/BF02301417>), DETECT statistic (Stout, Habing, Douglas & Kim, 1996, <doi:10.1177/014662169602000403>), local structural equation modeling (LSEM; Hildebrandt, Luedtke, Robitzsch, Sommer & Wilhelm, 2016, <doi:10.1080/00273171.20 [...truncated...]
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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 R/IRT.expectedCounts.mirt.R                           |    8 
 R/IRT.mle.R                                           |    4 
 R/RcppExports.R                                       |   26 
 R/amh_plot.R                                          |    9 
 R/anova_sirt.R                                        |   42 -
 R/attach.environment.sirt.R                           |   18 
 R/automatic.recode.R                                  |    4 
 R/brm.irf.R                                           |    4 
 R/brm.sim.R                                           |    7 
 R/btm.R                                               |   16 
 R/categorize.R                                        |    6 
 R/ccov.np.R                                           |   15 
 R/ccov_np_compute_ccov_sum_score.R                    |    4 
 R/cfa_meas_inv.R                                      |    4 
 R/class.accuracy.rasch.R                              |    8 
 R/conf.detect.R                                       |    4 
 R/create.ccov.R                                       |    4 
 R/data.prep.R                                         |   16 
 R/data.recode.sirt.R                                  |    4 
 R/data.wide2long.R                                    |   18 
 R/decategorize.R                                      |    6 
 R/detect.index.R                                      |   14 
 R/dexppow.R                                           |    3 
 R/dif.logisticregression.R                            |   67 +-
 R/dif.strata.variance.R                               |    9 
 R/dirichlet.simul.R                                   |    4 
 R/dmlavaan_est_model.R                                |    5 
 R/dmlavaan_est_model_bread_matrix_score_derivatives.R |    9 
 R/dmlavaan_est_model_parameterTable.R                 |    7 
 R/dmlavaan_joint_parameterTable.R                     |    4 
 R/dmlavaan_se_bootstrap.R                             |   11 
 R/dmlavaan_se_sandwich.R                              |    6 
 R/eigenvalues.manymatrices.R                          |   14 
 R/equating.rasch.jackknife.R                          |   10 
 R/expl.detect.R                                       |   22 
 R/f1d.irt.R                                           |    4 
 R/fit.adisop.R                                        |   16 
 R/fit.gradedresponse.R                                |   23 
 R/fit.gradedresponse_alg.R                            |    6 
 R/gom_em_calc_theta.R                                 |    6 
 R/gom_em_est_b.R                                      |   10 
 R/gom_em_est_covariance.R                             |    4 
 R/gom_em_est_lambda.R                                 |   14 
 R/invariance.alignment.R                              |  150 ++++-
 R/invariance_alignment_cfa_config.R                   |   10 
 R/invariance_alignment_cfa_config_estimate.R          |   10 
 R/invariance_alignment_proc_labels.R                  |    6 
 R/invariance_alignment_simulate.R                     |   18 
 R/likelihood_adjustment.R                             |   50 -
 R/likelihood_adjustment_aux.R                         |    6 
 R/linking.haberman.R                                  |    6 
 R/linking.haberman.lq.R                               |   87 ++
 R/linking.haebara.R                                   |   10 
 R/linking.robust.R                                    |    4 
 R/linking_2groups.R                                   |only
 R/linking_2groups_haebara_fun.R                       |only
 R/linking_2groups_haebara_grad.R                      |only
 R/linking_2groups_numerical_gradient.R                |only
 R/linking_2groups_power_loss.R                        |only
 R/linking_2groups_stocking_lord_fun.R                 |only
 R/linking_2groups_stocking_lord_grad.R                |only
 R/linking_2groups_vector_with_names.R                 |only
 R/linking_haberman_als.R                              |    8 
 R/linking_haberman_als_residual_weights.R             |   10 
 R/linking_haberman_als_vcov.R                         |    9 
 R/linking_haberman_compute_lts_mean.R                 |    8 
 R/linking_haberman_itempars_prepare.R                 |    6 
 R/linking_haberman_lq_pw_create_design.R              |only
 R/linking_haberman_lq_pw_le.R                         |only
 R/linking_haberman_lq_pw_le_arrange_Vgamma.R          |only
 R/linking_haberman_lq_pw_le_grad.R                    |only
 R/linking_haberman_lq_pw_le_hess_delta.R              |only
 R/linking_haberman_lq_pw_le_hess_gamma.R              |only
 R/linking_haebara_gradient_function_R.R               |    6 
 R/linking_haebara_optim_function_R.R                  |    9 
 R/locpolycor.R                                        |only
 R/locpolycor_est_polycor_itempair.R                   |only
 R/locpolycor_est_polycor_opt_fun.R                    |only
 R/locpolycor_est_thresh_grad_fun.R                    |only
 R/locpolycor_est_thresh_item.R                        |only
 R/locpolycor_est_thresh_opt_fun.R                     |only
 R/lq_fit.R                                            |   49 +
 R/lsdm.R                                              |    6 
 R/lsdm_est_logist_quant.R                             |   12 
 R/lsem.MGM.stepfunctions.R                            |    4 
 R/lsem.bootstrap.R                                    |    9 
 R/lsem.estimate.R                                     |   57 +
 R/lsem.permutationTest.R                              |   11 
 R/lsem.test.R                                         |   32 -
 R/lsem_aggregate_statistics.R                         |only
 R/lsem_bootstrap_draw_bootstrap_sample.R              |   22 
 R/lsem_estimate_proc_args.R                           |   12 
 R/lsem_fit_initial_model.R                            |    7 
 R/lsem_fit_initial_model_sufficient_statistics.R      |   36 -
 R/lsem_fitsem.R                                       |   42 -
 R/lsem_fitsem_compute_sufficient_statistics.R         |   61 +-
 R/lsem_fitsem_joint_estimation_prepare_partable.R     |   14 
 R/lsem_fitsem_raw_data_define_pseudo_weights.R        |    4 
 R/lsem_group_moderator.R                              |   32 -
 R/lsem_local_weights.R                                |   94 ++-
 R/lsem_parameter_summary.R                            |    4 
 R/lsem_residualize.R                                  |  134 +++-
 R/m_est.R                                             |   12 
 R/mcmc.2pno.R                                         |    4 
 R/mcmc.2pno_alg.R                                     |    5 
 R/mcmc.2pnoh.R                                        |   64 +-
 R/mcmc_3pno_testlet_draw_itempars.R                   |   27 
 R/mcmc_Rhat.R                                         |    9 
 R/mcmc_WaldTest.R                                     |    8 
 R/mcmc_as_formula.R                                   |    6 
 R/mcmc_confint.R                                      |   11 
 R/mcmc_derivedPars.R                                  |    6 
 R/mcmc_plot.R                                         |    9 
 R/mcmc_rename_define_symbols.R                        |    6 
 R/mcmc_rename_helper.R                                |    8 
 R/mcmc_rename_parameter_names.R                       |    6 
 R/mcmc_rename_undo_parameter_names.R                  |    4 
 R/mcmc_summary.R                                      |   21 
 R/mcmc_summary_print_information_criteria.R           |   18 
 R/mcmclist2coda.R                                     |    4 
 R/mgsem.R                                             |    4 
 R/mgsem_bdiag.R                                       |    6 
 R/mgsem_cd_opt.R                                      |    4 
 R/mgsem_create_index.R                                |    6 
 R/mgsem_duplication_matrix.R                          |    6 
 R/mgsem_evaluate_penalties.R                          |    6 
 R/mgsem_grad_fun.R                                    |    6 
 R/mgsem_list_elements_est_total_implied.R             |    4 
 R/mgsem_loglike_suffstat_derivative.R                 |   16 
 R/mgsem_opt_fun.R                                     |    4 
 R/mgsem_output_proc_casewise_likelihood.R             |    4 
 R/mgsem_output_proc_residuals.R                       |    4 
 R/mgsem_partable2model.R                              |    4 
 R/mgsem_proc_data.R                                   |    4 
 R/mgsem_proc_model.R                                  |   12 
 R/mgsem_proc_model_is_B.R                             |    4 
 R/mgsem_proc_model_partable_define_index.R            |    6 
 R/mgsem_proc_model_update_penalties_matrix.R          |    4 
 R/mgsem_proc_suffstat.R                               |    4 
 R/mgsem_suffstat_covariance_matrix.R                  |   13 
 R/mgsem_vcov_me.R                                     |    8 
 R/mirt.specify.partable.R                             |    7 
 R/nedelsky.irf.R                                      |    6 
 R/nedelsky.sim.R                                      |    6 
 R/noharm.sirt.R                                       |    4 
 R/noharm_sirt_efa_rotated_solution.R                  |    4 
 R/noharm_sirt_optim_function.R                        |   19 
 R/noharm_sirt_optim_function_R.R                      |    9 
 R/noharm_sirt_optim_gradient.R                        |   32 -
 R/noharm_sirt_optim_gradient_R.R                      |   11 
 R/noharm_sirt_optim_gradient_R_der_gamma_item.R       |   21 
 R/noharm_sirt_optim_gradient_R_der_gamma_item_pair.R  |   21 
 R/noharm_sirt_partable_extract_par.R                  |    4 
 R/noharm_sirt_partable_include_par.R                  |    6 
 R/noharm_sirt_preproc.R                               |   65 +-
 R/noharm_sirt_preproc_parameter_table_matrix.R        |    9 
 R/noharm_sirt_preproc_pattern_matrix.R                |    4 
 R/normal2.cw.R                                        |    2 
 R/package_version_date.R                              |    6 
 R/parmsummary_extend.R                                |   17 
 R/pbivnorm2.R                                         |   34 -
 R/rasch.copula3.R                                     |   10 
 R/rasch.pairwise.itemcluster.R                        |   11 
 R/rasch_jml_update_b.R                                |    7 
 R/rasch_mirtlc_est_a.R                                |   11 
 R/rasch_pairwise_iterations.R                         |    4 
 R/rasch_pairwise_optimize.R                           |    7 
 R/rasch_pairwise_optimize_opt_fun_terms2.R            |   10 
 R/resp_groupwise.R                                    |    4 
 R/rexppow.R                                           |   10 
 R/rm.facets.R                                         |   37 -
 R/rm_determine_fixed_tau_parameters.R                 |    4 
 R/rm_facets_center_value_aggregate.R                  |    4 
 R/rm_facets_pp_mle.R                                  |    5 
 R/rm_facets_pp_mle_calc_ll.R                          |    5 
 R/rm_numdiff_index.R                                  |   14 
 R/rm_pcm_calcprobs.R                                  |    8 
 R/rm_posterior.R                                      |    4 
 R/rm_proc_create_pseudoraters.R                       |    8 
 R/rm_proc_data.R                                      |   22 
 R/rm_smooth_distribution.R                            |    4 
 R/rm_trim_increments_mstep.R                          |    5 
 R/rmvn.R                                              |    4 
 R/sia.sirt.R                                          |   24 
 R/sia_sirt_remove_transitive.R                        |    6 
 R/sim.rasch.dep.R                                     |    8 
 R/sim.raschtype.R                                     |    6 
 R/sirt_EAP.R                                          |    4 
 R/sirt_MAP.R                                          |    4 
 R/sirt_add_list_elements.R                            |    4 
 R/sirt_logit_to_probs.R                               |    4 
 R/sirt_matrix_lower_to_upper.R                        |    4 
 R/sirt_max.R                                          |only
 R/sirt_optimizer.R                                    |    4 
 R/sirt_pem_collect_parameters.R                       |    4 
 R/sirt_pem_create_parameter_index.R                   |    4 
 R/sirt_rbind_fill.R                                   |    6 
 R/sirt_rename_list_entry.R                            |    6 
 R/smirt_postproc.R                                    |   33 -
 R/sqrt_diag.R                                         |   13 
 R/sqrt_diag_positive.R                                |only
 R/summary.gom.em.R                                    |    5 
 R/summary.lsem.R                                      |    5 
 R/summary.lsem.permutationTest.R                      |    4 
 R/summary_round_helper.R                              |    4 
 R/tam2mirt_fix.R                                      |   58 -
 R/tam2mirt_freed.R                                    |   78 +-
 R/testlet.marginalized.R                              |    6 
 R/tetrachoric2.R                                      |   44 -
 R/truescore.irt.R                                     |   10 
 R/truescore_irt_irf.R                                 |    6 
 R/unidim.csn.R                                        |    8 
 R/wle.rasch.jackknife.R                               |    8 
 R/write.format2.R                                     |   15 
 R/write.fwf2.R                                        |   10 
 R/xxirt.R                                             |   76 +-
 R/xxirt_EAP.R                                         |    8 
 R/xxirt_classprobs_lca.R                              |    4 
 R/xxirt_classprobs_lca_init_par.R                     |    8 
 R/xxirt_compute_casewise_likelihood.R                 |   14 
 R/xxirt_compute_itemprobs.R                           |   28 
 R/xxirt_compute_likelihood.R                          |   20 
 R/xxirt_compute_posterior.R                           |   18 
 R/xxirt_compute_priorDistribution.R                   |    7 
 R/xxirt_compute_prior_Theta_from_x.R                  |    3 
 R/xxirt_compute_prob_item_from_x.R                    |    7 
 R/xxirt_createDiscItem.R                              |   11 
 R/xxirt_createItemList.R                              |   13 
 R/xxirt_createParTable.R                              |   19 
 R/xxirt_createThetaDistribution.R                     |   11 
 R/xxirt_data_proc.R                                   |   10 
 R/xxirt_em_algorithm.R                                |   38 -
 R/xxirt_em_args_extract.R                             |only
 R/xxirt_hessian.R                                     |    8 
 R/xxirt_ic.R                                          |   13 
 R/xxirt_ic_compute_criteria.R                         |   16 
 R/xxirt_irf_lca_init_par.R                            |    6 
 R/xxirt_mstep_ThetaParameters.R                       |   32 -
 R/xxirt_mstep_itemParameters.R                        |   63 +-
 R/xxirt_mstep_itemParameters_evalPrior.R              |    4 
 R/xxirt_newton_raphson.R                              |   68 +-
 R/xxirt_nr_grad_fun_R.R                               |    6 
 R/xxirt_nr_grad_fun_Rcpp.R                            |   52 +
 R/xxirt_nr_grad_fun_numapprox.R                       |   14 
 R/xxirt_nr_grad_fun_pml_casewise.R                    |only
 R/xxirt_nr_opt_fun_pml_casewise.R                     |only
 R/xxirt_nr_optim_fun.R                                |   27 
 R/xxirt_nr_pml_grad_fun.R                             |only
 R/xxirt_nr_pml_more_arguments.R                       |only
 R/xxirt_nr_pml_opt_fun.R                              |only
 R/xxirt_nr_pml_opt_fun_R.R                            |only
 R/xxirt_nr_pml_preproc_data.R                         |only
 R/xxirt_partable_extract_freeParameters.R             |    2 
 R/xxirt_postproc_parameters.R                         |   16 
 R/xxirt_prepare_response_data.R                       |    6 
 R/xxirt_proc_ParTable.R                               |   10 
 R/xxirt_sandwich_pml.R                                |only
 R/xxirt_simulate.R                                    |   10 
 R/xxirt_summary_parts.R                               |   24 
 build/partial.rdb                                     |binary
 data/data.pisa2006Read.rda                            |only
 data/datalist                                         |    1 
 inst/CITATION                                         |    3 
 inst/NEWS                                             |   40 +
 man/R2conquest.Rd                                     |    4 
 man/data.pisa2006Read.Rd                              |only
 man/data.pisaMath.Rd                                  |    4 
 man/invariance.alignment.Rd                           |   33 +
 man/linking.haberman.Rd                               |   48 +
 man/linking_2groups.Rd                                |only
 man/locpolycor.Rd                                     |only
 man/lq_fit.Rd                                         |    5 
 man/lsem.estimate.Rd                                  |   15 
 man/lsem.test.Rd                                      |    8 
 man/matrixfunctions.sirt.Rd                           |    5 
 man/xxirt.Rd                                          |  275 +++++++++
 man/xxirt_createParTable.Rd                           |    5 
 man/xxirt_createThetaDistribution.Rd                  |    5 
 src/Makevars                                          |    2 
 src/Makevars.win                                      |    2 
 src/RcppExports.cpp                                   |  123 +++-
 src/sirt_rcpp_invariance_alignment.cpp                |   18 
 src/sirt_rcpp_polychoric2.cpp                         |    8 
 src/sirt_rcpp_rm_sdt.cpp                              |   27 
 src/sirt_rcpp_xxirt.cpp                               |  369 ++++++++++++
 289 files changed, 3292 insertions(+), 1725 deletions(-)

More information about sirt at CRAN
Permanent link

Package silviculture updated to version 0.2.0 with previous version 0.1.0 dated 2025-05-29

Title: Utility Functions for Forest Inventory and Silviculture
Description: Perform common dendrometry operations such as inventory preparing, and inventory data analysis.
Author: Adrian Cidre Gonzalez [aut, cre], Aitor Vazquez Veloso [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>

Diff between silviculture versions 0.1.0 dated 2025-05-29 and 0.2.0 dated 2025-09-27

 silviculture-0.1.0/silviculture/R/biomass.R                            |only
 silviculture-0.1.0/silviculture/R/dendrometry-summary.R                |only
 silviculture-0.1.0/silviculture/R/dendrometry.R                        |only
 silviculture-0.1.0/silviculture/R/globals.R                            |only
 silviculture-0.1.0/silviculture/R/inventory.R                          |only
 silviculture-0.1.0/silviculture/R/lidar.R                              |only
 silviculture-0.1.0/silviculture/R/volume.R                             |only
 silviculture-0.1.0/silviculture/man/Inventory.Rd                       |only
 silviculture-0.1.0/silviculture/man/SampleSize.Rd                      |only
 silviculture-0.1.0/silviculture/man/calc_dominant_height.Rd            |only
 silviculture-0.2.0/silviculture/DESCRIPTION                            |   27 +
 silviculture-0.2.0/silviculture/MD5                                    |  156 +++++++---
 silviculture-0.2.0/silviculture/NAMESPACE                              |   63 ++--
 silviculture-0.2.0/silviculture/NEWS.md                                |   66 ++++
 silviculture-0.2.0/silviculture/R/deprecated-funs.R                    |only
 silviculture-0.2.0/silviculture/R/inventory-summary.R                  |only
 silviculture-0.2.0/silviculture/R/metrics-lidar.R                      |only
 silviculture-0.2.0/silviculture/R/metrics-stand-density.R              |only
 silviculture-0.2.0/silviculture/R/metrics-stand-level.R                |only
 silviculture-0.2.0/silviculture/R/metrics-tree-level.R                 |only
 silviculture-0.2.0/silviculture/R/predict-biomass.R                    |only
 silviculture-0.2.0/silviculture/R/predict-height.R                     |only
 silviculture-0.2.0/silviculture/R/sample-size.R                        |only
 silviculture-0.2.0/silviculture/R/silviculture-package.R               |only
 silviculture-0.2.0/silviculture/R/sysdata.rda                          |binary
 silviculture-0.2.0/silviculture/R/treatment-thinning.R                 |only
 silviculture-0.2.0/silviculture/R/utils-not-exported.R                 |  133 ++++++++
 silviculture-0.2.0/silviculture/R/zzz.R                                |   25 +
 silviculture-0.2.0/silviculture/README.md                              |    5 
 silviculture-0.2.0/silviculture/build/partial.rdb                      |binary
 silviculture-0.2.0/silviculture/data/biomass_models.rda                |binary
 silviculture-0.2.0/silviculture/data/inventory_samples.rda             |binary
 silviculture-0.2.0/silviculture/inst                                   |only
 silviculture-0.2.0/silviculture/man/calc_accumulated_trees.Rd          |only
 silviculture-0.2.0/silviculture/man/calc_dominant_metric.Rd            |only
 silviculture-0.2.0/silviculture/man/calc_n_cost.Rd                     |only
 silviculture-0.2.0/silviculture/man/calc_n_optimal.Rd                  |only
 silviculture-0.2.0/silviculture/man/calc_n_prop.Rd                     |only
 silviculture-0.2.0/silviculture/man/calc_n_simple.Rd                   |   48 +--
 silviculture-0.2.0/silviculture/man/eq_biomass_cudjoe_2024.Rd          |only
 silviculture-0.2.0/silviculture/man/eq_biomass_dieguez_aranda_2009.Rd  |only
 silviculture-0.2.0/silviculture/man/eq_biomass_manrique_2017.Rd        |only
 silviculture-0.2.0/silviculture/man/eq_biomass_menendez_2022.Rd        |only
 silviculture-0.2.0/silviculture/man/eq_biomass_montero_2005.Rd         |only
 silviculture-0.2.0/silviculture/man/eq_biomass_ruiz_peinado_2011.Rd    |only
 silviculture-0.2.0/silviculture/man/eq_biomass_ruiz_peinado_2012.Rd    |only
 silviculture-0.2.0/silviculture/man/eq_hd_vazquez_veloso_2025.Rd       |only
 silviculture-0.2.0/silviculture/man/figures/lifecycle-deprecated.svg   |only
 silviculture-0.2.0/silviculture/man/figures/lifecycle-experimental.svg |only
 silviculture-0.2.0/silviculture/man/figures/lifecycle-stable.svg       |only
 silviculture-0.2.0/silviculture/man/figures/lifecycle-superseded.svg   |only
 silviculture-0.2.0/silviculture/man/figures/logo.png                   |binary
 silviculture-0.2.0/silviculture/man/lid_fcov.Rd                        |   66 ++--
 silviculture-0.2.0/silviculture/man/lid_lhdi.Rd                        |   58 +--
 silviculture-0.2.0/silviculture/man/plot.Rd                            |   38 +-
 silviculture-0.2.0/silviculture/man/silv_basal_area.Rd                 |  108 +++---
 silviculture-0.2.0/silviculture/man/silv_biomass.Rd                    |  142 ++++-----
 silviculture-0.2.0/silviculture/man/silv_density_hart.Rd               |only
 silviculture-0.2.0/silviculture/man/silv_density_ntrees_ha.Rd          |only
 silviculture-0.2.0/silviculture/man/silv_density_sdi.Rd                |only
 silviculture-0.2.0/silviculture/man/silv_diametric_class.Rd            |   90 ++---
 silviculture-0.2.0/silviculture/man/silv_dominant_height.Rd            |  118 +++----
 silviculture-0.2.0/silviculture/man/silv_lorey_height.Rd               |   87 ++---
 silviculture-0.2.0/silviculture/man/silv_ntrees_ha.Rd                  |   85 ++---
 silviculture-0.2.0/silviculture/man/silv_predict_biomass.Rd            |only
 silviculture-0.2.0/silviculture/man/silv_predict_height.Rd             |only
 silviculture-0.2.0/silviculture/man/silv_sample_size.Rd                |  103 +++---
 silviculture-0.2.0/silviculture/man/silv_sample_size_simple.Rd         |only
 silviculture-0.2.0/silviculture/man/silv_sample_size_stratified.Rd     |only
 silviculture-0.2.0/silviculture/man/silv_spacing_index.Rd              |   98 +++---
 silviculture-0.2.0/silviculture/man/silv_sqrmean_diameter.Rd           |   84 ++---
 silviculture-0.2.0/silviculture/man/silv_stand_basal_area.Rd           |only
 silviculture-0.2.0/silviculture/man/silv_stand_dominant_diameter.Rd    |only
 silviculture-0.2.0/silviculture/man/silv_stand_dominant_height.Rd      |only
 silviculture-0.2.0/silviculture/man/silv_stand_lorey_height.Rd         |only
 silviculture-0.2.0/silviculture/man/silv_stand_qmean_diameter.Rd       |only
 silviculture-0.2.0/silviculture/man/silv_summary.Rd                    |  148 ++++-----
 silviculture-0.2.0/silviculture/man/silv_treatment_thinning.Rd         |only
 silviculture-0.2.0/silviculture/man/silv_tree_basal_area.Rd            |only
 silviculture-0.2.0/silviculture/man/silv_tree_dclass.Rd                |only
 silviculture-0.2.0/silviculture/man/silv_tree_volume.Rd                |only
 silviculture-0.2.0/silviculture/man/silv_volume.Rd                     |  104 +++---
 silviculture-0.2.0/silviculture/man/silviculture-package.Rd            |only
 83 files changed, 1097 insertions(+), 755 deletions(-)

More information about silviculture at CRAN
Permanent link

Package RcppCWB updated to version 0.6.9 with previous version 0.6.8 dated 2025-07-17

Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>). The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>) and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>). See the file LICENSE.note for further information. The package includes modified code of the 'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre], Bernard Desgraupes [aut], Sylvain Loiseau [aut], Oliver Christ [ctb], Bruno Maximilian Schulze [ctb], Stephanie Evert [ctb], Arne Fitschen [ctb], Jeroen Ooms [ctb], Marius Bertram [ctb], Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>

Diff between RcppCWB versions 0.6.8 dated 2025-07-17 and 0.6.9 dated 2025-09-27

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Package photobiologyLEDs updated to version 0.5.3 with previous version 0.5.2 dated 2023-11-01

Title: Spectral Data for Light-Emitting-Diodes
Description: Spectral emission data for some frequently used light emitting diodes available as electronic components. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] , Shafiuddin Ahmed [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

Diff between photobiologyLEDs versions 0.5.2 dated 2023-11-01 and 0.5.3 dated 2025-09-27

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Package mpactr readmission to version 0.3.1 with previous version 0.3.0 dated 2025-09-07

Title: Correction of Preprocessed MS Data
Description: An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) <doi:10.1021/acs.analchem.2c04632>). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.
Author: Allison Mason [aut] , Gregory Johnson [aut] , Patrick Schloss [aut, cre, cph]
Maintainer: Patrick Schloss <pschloss@umich.edu>

This is a re-admission after prior archival of version 0.3.0 dated 2025-09-07

Diff between mpactr versions 0.3.0 dated 2025-09-07 and 0.3.1 dated 2025-09-27

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Package errum updated to version 0.0.4 with previous version 0.0.3 dated 2020-03-20

Title: Exploratory Reduced Reparameterized Unified Model Estimation
Description: Perform a Bayesian estimation of the exploratory reduced reparameterized unified model (ErRUM) described by Culpepper and Chen (2018) <doi:10.3102/1076998618791306>.
Author: James Joseph Balamuta [aut, cre, cph] , Steven Andrew Culpepper [aut, cph] , Jeffrey A. Douglas [aut]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

Diff between errum versions 0.0.3 dated 2020-03-20 and 0.0.4 dated 2025-09-27

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More information about errum at CRAN
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Package DistatisR updated to version 1.1.2 with previous version 1.1.1 dated 2022-12-05

Title: DiSTATIS Three Way Metric Multidimensional Scaling
Description: Implement DiSTATIS and CovSTATIS (three-way multidimensional scaling). DiSTATIS and CovSTATIS are used to analyze multiple distance/covariance matrices collected on the same set of observations. These methods are based on Abdi, H., Williams, L.J., Valentin, D., & Bennani-Dosse, M. (2012) <doi:10.1002/wics.198>.
Author: Derek Beaton [aut, ctb], Ju-Chi Yu [aut, ctb], Vincent Guillemot [aut, ctb], Herve Abdi [aut, cre]
Maintainer: Herve Abdi <herve@utdallas.edu>

Diff between DistatisR versions 1.1.1 dated 2022-12-05 and 1.1.2 dated 2025-09-27

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Package CopernicusMarine updated to version 0.3.1 with previous version 0.3.0 dated 2025-09-11

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 0.3.0 dated 2025-09-11 and 0.3.1 dated 2025-09-27

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Package BayesMultiMode updated to version 0.7.4 with previous version 0.7.3 dated 2024-10-31

Title: Bayesian Mode Inference
Description: A two-step Bayesian approach for mode inference following Cross, Hoogerheide, Labonne and van Dijk (2024) <doi:10.1016/j.econlet.2024.111579>). First, a mixture distribution is fitted on the data using a sparse finite mixture (SFM) Markov chain Monte Carlo (MCMC) algorithm. The number of mixture components does not have to be known; the size of the mixture is estimated endogenously through the SFM approach. Second, the modes of the estimated mixture at each MCMC draw are retrieved using algorithms specifically tailored for mode detection. These estimates are then used to construct posterior probabilities for the number of modes, their locations and uncertainties, providing a powerful tool for mode inference.
Author: Nalan Bastuerk [aut], Jamie Cross [aut], Peter de Knijff [aut], Lennart Hoogerheide [aut], Paul Labonne [aut, cre], Herman van Dijk [aut]
Maintainer: Paul Labonne <labonnepaul@gmail.com>

Diff between BayesMultiMode versions 0.7.3 dated 2024-10-31 and 0.7.4 dated 2025-09-27

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Package AmigaFFH updated to version 0.4.8 with previous version 0.4.7 dated 2025-01-08

Title: Commodore Amiga File Format Handler
Description: Modern software often poorly support older file formats. This package intends to handle many file formats that were native to the antiquated Commodore Amiga machine. This package focuses on file types from the older Amiga operating systems (<= 3.0). It will read and write specific file formats and coerces them into more contemporary data.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>

Diff between AmigaFFH versions 0.4.7 dated 2025-01-08 and 0.4.8 dated 2025-09-27

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Package secr updated to version 5.3.0 with previous version 5.2.4 dated 2025-06-13

Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] , Philipp Jund [ctb] , David Fletcher [ctb] , Yan Ru Choo [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

Diff between secr versions 5.2.4 dated 2025-06-13 and 5.3.0 dated 2025-09-27

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Package tci updated to version 0.2.1 with previous version 0.2.0 dated 2022-08-15

Title: Target Controlled Infusion (TCI)
Description: Implementation of target-controlled infusion algorithms for compartmental pharmacokinetic and pharmacokinetic-pharmacodynamic models. Jacobs (1990) <doi:10.1109/10.43622>; Marsh et al. (1991) <doi:10.1093/bja/67.1.41>; Shafer and Gregg (1993) <doi:10.1007/BF01070999>; Schnider et al. (1998) <doi:10.1097/00000542-199805000-00006>; Abuhelwa, Foster, and Upton (2015) <doi:10.1016/j.vascn.2015.03.004>; Eleveld et al. (2018) <doi:10.1016/j.bja.2018.01.018>.
Author: Ryan Jarrett [aut, cre]
Maintainer: Ryan Jarrett <ryantjarrett@gmail.com>

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Package gdistance updated to version 1.6.5 with previous version 1.6.4 dated 2023-06-19

Title: Distances and Routes on Geographical Grids
Description: Provides classes and functions to calculate various distance measures and routes in heterogeneous geographic spaces represented as grids. The package implements measures to model dispersal histories first presented by van Etten and Hijmans (2010) <doi:10.1371/journal.pone.0012060>. Least-cost distances as well as more complex distances based on (constrained) random walks can be calculated. The distances implemented in the package are used in geographical genetics, accessibility indicators, and may also have applications in other fields of geospatial analysis.
Author: Jacob van Etten [aut] , Kaue de Sousa [ctb] , Andrew Marx [cre, ctb]
Maintainer: Andrew Marx <ajm.rpackages@gmail.com>

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Package bgms updated to version 0.1.6.0 with previous version 0.1.4.2 dated 2024-12-05

Title: Bayesian Analysis of Networks of Binary and/or Ordinal Variables
Description: Bayesian variable selection methods for analyzing the structure of a Markov random field model for a network of binary and/or ordinal variables.
Author: Maarten Marsman [aut, cre] , Giuseppe Arena [ctb] , Karoline Huth [ctb] , Nikola Sekulovski [ctb] , Don van den Bergh [ctb]
Maintainer: Maarten Marsman <m.marsman@uva.nl>

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Package parallelDist updated to version 0.2.7 with previous version 0.2.6 dated 2022-02-03

Title: Parallel Distance Matrix Computation using Multiple Threads
Description: A fast parallelized alternative to R's native 'dist' function to calculate distance matrices for continuous, binary, and multi-dimensional input matrices, which supports a broad variety of 41 predefined distance functions from the 'stats', 'proxy' and 'dtw' R packages, as well as user- defined functions written in C++. For ease of use, the 'parDist' function extends the signature of the 'dist' function and uses the same parameter naming conventions as distance methods of existing R packages. The package is mainly implemented in C++ and leverages the 'RcppParallel' package to parallelize the distance computations with the help of the 'TinyThread' library. Furthermore, the 'Armadillo' linear algebra library is used for optimized matrix operations during distance calculations. The curiously recurring template pattern (CRTP) technique is applied to avoid virtual functions, which improves the Dynamic Time Warping calculations while the implementation stays flexible enough to support differe [...truncated...]
Author: Alexander Eckert [aut, cre], Lucas Godoy [ctb], Srikanth KS [ctb]
Maintainer: Alexander Eckert <info@alexandereckert.com>

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Package photobiologySun updated to version 0.5.1 with previous version 0.5.0 dated 2024-04-01

Title: Data for Sunlight Spectra
Description: Data for the extraterrestrial solar spectral irradiance and ground level solar spectral irradiance and irradiance. In addition data for shade light under vegetation and irradiance time series from different broadband sensors. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, trl, cre] , T. Matthew Robson [ctb] , Saara M. Hartiakinen [ctb] , Anders Lindfors [ctb], Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package cccp updated to version 0.3-3 with previous version 0.3-2 dated 2025-07-30

Title: Cone Constrained Convex Problems
Description: Routines for solving convex optimization problems with cone constraints by means of interior-point methods. The implemented algorithms are partially ported from CVXOPT, a Python module for convex optimization (see <https://cvxopt.org> for more information).
Author: Bernhard Pfaff [aut, cre], Lieven Vandenberghe [cph] , Martin Andersen [cph] , Joachim Dahl [cph]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>

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Package comtradr updated to version 1.0.4 with previous version 1.0.3 dated 2024-11-15

Title: Interface with the United Nations Comtrade API
Description: Interface with and extract data from the United Nations 'Comtrade' API <https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping data for a variety of commodities, these functions allow for easy API query and data returned as a tidy data frame.
Author: Paul Bochtler [aut, cre, cph] , Harriet Goers [aut], Chris Muir [aut], Alicia Schep [rev] , Rafael Hellwig [rev] , Ernest Guevarra [rev] , Nicholas Potter [rev] , Juergen Amann [ctb]
Maintainer: Paul Bochtler <paulbochtler.gh@gmail.com>

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Package cNORM updated to version 3.5.0 with previous version 3.4.1 dated 2025-05-11

Title: Continuous Norming
Description: A comprehensive toolkit for generating continuous test norms in psychometrics and biometrics, and analyzing model fit. The package offers both distribution-free modeling using Taylor polynomials and parametric modeling using the beta-binomial and the 'Sinh-Arcsinh' distribution. Originally developed for achievement tests, it is applicable to a wide range of mental, physical, or other test scores dependent on continuous or discrete explanatory variables. The package provides several advantages: It minimizes deviations from representativeness in subsamples, interpolates between discrete levels of explanatory variables, and significantly reduces the required sample size compared to conventional norming per age group. cNORM enables graphical and analytical evaluation of model fit, accommodates a wide range of scales including those with negative and descending values, and even supports conventional norming. It generates norm tables including confidence intervals. It also includes methods f [...truncated...]
Author: Alexandra Lenhard [aut] , Wolfgang Lenhard [cre, aut] , Sebastian Gary [aut], WPS publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>

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Package ORION updated to version 1.0.4 with previous version 1.0.3 dated 2022-02-07

Title: Ordinal Relations
Description: Functions to handle ordinal relations reflected within the feature space. Those function allow to search for ordinal relations in multi-class datasets. One can check whether proposed relations are reflected in a specific feature representation. Furthermore, it provides functions to filter, organize and further analyze those ordinal relations.
Author: L Lausser [aut], LM Schaefer [aut], R Szekely [aut], HA Kestler [aut, cre]
Maintainer: HA Kestler <hans.kestler@uni-ulm.de>

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Package treestructure updated to version 0.7.0 with previous version 0.1.0 dated 2020-02-17

Title: Detect Population Structure Within Phylogenetic Trees
Description: Algorithms for detecting population structure from the history of coalescent events recorded in phylogenetic trees. This method classifies each tip and internal node of a tree into disjoint sets characterized by similar coalescent patterns.
Author: Erik Volz [aut, cre] , Fabricia F. Nascimento [ctb] , Vinicius B. Franceschi [ctb]
Maintainer: Erik Volz <erik.volz@gmail.com>

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Package plume updated to version 0.3.0 with previous version 0.2.5 dated 2024-09-02

Title: A Simple Author Handler for Scientific Writing
Description: Handles and formats author information in scientific writing in 'R Markdown' and 'Quarto'. 'plume' provides easy-to-use and flexible tools for inserting author data in 'YAML' as well as generating author and contribution lists (among others) as strings from tabular data.
Author: Arnaud Gallou [aut, cre, cph]
Maintainer: Arnaud Gallou <arangacas@gmail.com>

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Package ETRep updated to version 1.2.1 with previous version 1.2.0 dated 2025-06-05

Title: Analysis of Elliptical Tubes Under the Relative Curvature Condition
Description: Analysis of elliptical tubes with applications in biological modeling. The package is based on the references: Taheri, M., Pizer, S. M., & Schulz, J. (2024) "The Mean Shape under the Relative Curvature Condition." Journal of Computational and Graphical Statistics <doi:10.1080/10618600.2025.2535600> and arXiv <doi:10.48550/arXiv.2404.01043>. Mohsen Taheri Shalmani (2024) "Shape Statistics via Skeletal Structures", PhD Thesis, University of Stavanger, Norway <doi:10.13140/RG.2.2.34500.23685>. Key features include constructing discrete elliptical tubes, calculating transformations, validating structures under the Relative Curvature Condition (RCC), computing means, and generating simulations. Supports intrinsic and non-intrinsic mean calculations and transformations, size estimation, plotting, and random sample generation based on a reference tube. The intrinsic approach relies on the interior path of the original non-convex space, incorporating the RCC, while the no [...truncated...]
Author: Mohsen Taheri Shalmani [aut, cre] , Joern Schulz [aut], Stephen M. Pizer [aut]
Maintainer: Mohsen Taheri Shalmani <MohsenTaheriShalmani@gmail.com>

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Package structSSI readmission to version 1.2.0 with previous version 1.1.1 dated 2015-05-05

Title: Multiple Testing for Hypotheses with Hierarchical or Group Structure
Description: Performs multiple testing corrections that take specific structure of hypotheses into account, as described in Sankaran & Holmes (2014) <doi:10.18637/jss.v059.i13>.
Author: Kris Sankaran [aut, cre]
Maintainer: Kris Sankaran <ksankaran@wisc.edu>

This is a re-admission after prior archival of version 1.1.1 dated 2015-05-05

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New package spuriouscorrelations with initial version 0.1
Package: spuriouscorrelations
Title: Datasets with Strong and Spurious Correlations
Version: 0.1
Description: Provides datasets from Vigen (2015) <https://web.archive.org/web/20230607181247/https%3A/tylervigen.com/spurious-correlations> rescued from the Internet Wayback Machine. These should be preserved for statistics introductory courses as these make it very clear that correlation is not causation.
License: CC0
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2025-09-21 13:40:21 UTC; pacha
Author: Tyler Vigen [cph], Mauricio Vargas Sepulveda [aut, cre]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-27 08:30:02 UTC

More information about spuriouscorrelations at CRAN
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New package ppks with initial version 1.0
Package: ppks
Title: Permutation Based Paired Kolmogorov-Smirnov Test
Version: 1.0
Date: 2025-09-21
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Depends: R (>= 4.0)
Imports: Rfast, stats
Suggests: Rfast2
Description: Permutation based Kolmogorov-Smirnov test for paired samples. The test was proposed by Wang W.S., Amsler C. and Schmidt, P. (2025) <doi:10.1007/s00181-025-02779-0>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2025-09-21 08:34:58 UTC; mtsag
Repository: CRAN
Date/Publication: 2025-09-27 08:20:02 UTC

More information about ppks at CRAN
Permanent link

New package DEmixR with initial version 0.1.1
Package: DEmixR
Title: Fit Two-Component Normal and Lognormal Mixture Models
Version: 0.1.1
Description: Fits, bootstraps, and evaluates two-component normal and lognormal mixture models. Includes diagnostic plots and statistical evaluation of mixture model fits using differential evolution optimization.
Imports: DEoptim (>= 2.0.0), pbapply (>= 1.0.0), parallelly (>= 1.0.0)
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-21 18:17:46 UTC; mac
Author: Farrokh Habibzadeh [aut, cre]
Maintainer: Farrokh Habibzadeh <farrokh.habibzadeh@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-27 08:40:08 UTC

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New package BioWorldR with initial version 0.1.0
Package: BioWorldR
Title: A Curated Collection of Biodiversity and Species Datasets and Utilities
Version: 0.1.0
Maintainer: Juan David Monroy <monroyjuandavid773@gmail.com>
Description: Provides a curated collection of biodiversity and species-related datasets (birds, plants, reptiles, turtles, mammals, bees, marine data and related biological measurements), together with small utilities to load and explore them. The package gathers data sourced from public repositories (including Kaggle and well-known ecological/biological R packages) and standardizes access for researchers, educators, and data analysts working on biodiversity, biogeography, ecology and comparative biology. It aims to simplify reproducible workflows by packaging commonly used example datasets and metadata so they can be easily inspected, visualized, and used for teaching, testing, and prototyping analyses.
License: GPL-3
URL: https://github.com/Monroy31039/BioWorld, https://Monroy31039.github.io/BioWorld/
BugReports: https://github.com/Monroy31039/BioWorld/issues
Encoding: UTF-8
LazyData: true
Suggests: ggplot2, dplyr, testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-20 22:03:03 UTC; monro
Author: Juan David Monroy [aut, cre]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-09-27 08:10:02 UTC

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Package galisats updated to version 2.2.0 with previous version 2.0.2 dated 2025-09-11

Title: Configuration of Jupiter's Four Largest Satellites
Description: Calculate, plot and animate the configuration of Jupiter's four largest satellites (known as Galilean satellites) for a given date and time (UTC - Coordinated Universal Time). The galsat() function returns numerical values of the satellites’ positions. x – the apparent rectangular coordinate of the satellite with respect to the center of Jupiter’s disk in the equatorial plane in the units of Jupiter’s equatorial radius; X is positive toward the west, y – the apparent rectangular coordinate of the satellite with respect to the center of Jupiter’s disk from the equatorial plane in the units of Jupiter’s equatorial radius; Y is positive toward the north. For more details see Meeus (1988, ISBN 0-943396-22-0) "Astronomical Formulae for Calculators". The galsat_animate() function creates an animation of the Galilean satellites' positions. You provide the starting time, duration, the time step between frames, and the pause between frames. The function delta_t() returns the value of delta-T in [...truncated...]
Author: Lech Jaszowski [aut, cre, cph]
Maintainer: Lech Jaszowski <lech.jaszowski@interia.pl>

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Package checkdown updated to version 0.0.13 with previous version 0.0.12 dated 2023-10-27

Title: Check-Fields and Check-Boxes for 'rmarkdown'
Description: Creates auto-grading check-fields and check-boxes for 'rmarkdown' or 'quarto' HTML. It can be used in class, when teacher share materials and tasks, so students can solve some problems and check their work. In contrast to the 'learnr' package, the 'checkdown' package works serverlessly without 'shiny'.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>

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Package cIRT updated to version 1.3.3 with previous version 1.3.2 dated 2022-02-21

Title: Choice Item Response Theory
Description: Jointly model the accuracy of cognitive responses and item choices within a Bayesian hierarchical framework as described by Culpepper and Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package contains the datasets used within the analysis of the paper.
Author: Steven Andrew Culpepper [aut, cph] , James Joseph Balamuta [aut, cph, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package rrum updated to version 0.2.2 with previous version 0.2.1 dated 2023-11-29

Title: Bayesian Estimation of the Reduced Reparameterized Unified Model with Gibbs Sampling
Description: Implementation of Gibbs sampling algorithm for Bayesian Estimation of the Reduced Reparameterized Unified Model ('rrum'), described by Culpepper and Hudson (2017) <doi: 10.1177/0146621617707511>.
Author: Steven Andrew Culpepper [aut, cph] , Aaron Hudson [aut, cph] , James Joseph Balamuta [aut, cph, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package ohoegdm updated to version 0.1.1 with previous version 0.1.0 dated 2022-02-24

Title: Ordinal Higher-Order Exploratory General Diagnostic Model for Polytomous Data
Description: Perform a Bayesian estimation of the ordinal exploratory Higher-order General Diagnostic Model (OHOEGDM) for Polytomous Data described by Culpepper, S. A. and Balamuta, J. J. (2021) <doi:10.1080/00273171.2021.1985949>.
Author: Steven Andrew Culpepper [aut, cph] , James Joseph Balamuta [aut, cre, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package edina updated to version 0.1.2 with previous version 0.1.1 dated 2020-03-25

Title: Bayesian Estimation of an Exploratory Deterministic Input, Noisy and Gate Model
Description: Perform a Bayesian estimation of the exploratory deterministic input, noisy and gate (EDINA) cognitive diagnostic model described by Chen et al. (2018) <doi:10.1007/s11336-017-9579-4>.
Author: James Joseph Balamuta [aut, cre, cph] , Steven Andrew Culpepper [aut, cph] , Jeffrey A. Douglas [aut]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package agena.ai updated to version 1.1.2 with previous version 1.1.1 dated 2023-09-26

Title: R Wrapper for 'agena.ai' API
Description: An R wrapper for 'agena.ai' <https://www.agena.ai> which provides users capabilities to work with 'agena.ai' using the R environment. Users can create Bayesian network models from scratch or import existing models in R and export to 'agena.ai' cloud or local API for calculations. Note: running calculations requires a valid 'agena.ai' API license (past the initial trial period of the local API).
Author: Erhan Pisirir [aut], Eugene Dementiev [aut, cre], Martin Neil [aut, cph]
Maintainer: Eugene Dementiev <support@agenarisk.com>

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Fri, 26 Sep 2025

Package terra updated to version 1.8-70 with previous version 1.8-60 dated 2025-07-21

Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] , Marcia Barbosa [ctb] , Roger Bivand [ctb] , Andrew Brown [ctb] , Michael Chirico [ctb] , Emanuele Cordano [ctb] , Krzysztof Dyba [ctb] , Edzer Pebesma [ctb] , Barry Rowlingson [ctb] , Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

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Package soilDB updated to version 2.8.13 with previous version 2.8.12 dated 2025-08-29

Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut] , Jay Skovlin [aut], Stephen Roecker [aut], Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>

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Package MRMCaov updated to version 0.3.1 with previous version 0.3.0 dated 2023-01-10

Title: Multi-Reader Multi-Case Analysis of Variance
Description: Estimation and comparison of the performances of diagnostic tests in multi-reader multi-case studies where true case statuses (or ground truths) are known and one or more readers provide test ratings for multiple cases. Reader performance metrics are provided for area under and expected utility of ROC curves, likelihood ratio of positive or negative tests, and sensitivity and specificity. ROC curves can be estimated empirically or with binormal or binormal likelihood-ratio models. Statistical comparisons of diagnostic tests are based on the ANOVA model of Obuchowski-Rockette and the unified framework of Hillis (2005) <doi:10.1002/sim.2024>. The ANOVA can be conducted with data from a full factorial, nested, or partially paired study design; with random or fixed readers or cases; and covariances estimated with the DeLong method, jackknifing, or an unbiased method. Smith and Hillis (2020) <doi:10.1117/12.2549075>.
Author: Brian J Smith [aut, cre], Stephen L Hillis [aut], Lorenzo L Pesce [ctb]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>

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Package liver updated to version 1.22 with previous version 1.21 dated 2025-09-07

Title: Foundations Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver," symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] , Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>

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Package archeofrag updated to version 1.2.3 with previous version 1.2.0 dated 2025-03-27

Title: Spatial Analysis in Archaeology from Refitting Fragments
Description: Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, visualise, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. A series of published empirical datasets is included. Documentation about 'archeofrag' is provided by a vignette and by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by the 'archeofrag.gui' R package, a companion GUI application available at <https://analytics.huma-num.fr/Sebast [...truncated...]
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>

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Package V8 updated to version 8.0.0 with previous version 7.0.0 dated 2025-09-01

Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript and WebAssembly engine. This package can be compiled either with V8 version 6 and up or NodeJS when built as a shared library.
Author: Jeroen Ooms [aut, cre] , George Stagg [ctb] , Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>

Diff between V8 versions 7.0.0 dated 2025-09-01 and 8.0.0 dated 2025-09-26

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Package SqlRender updated to version 1.19.4 with previous version 1.19.3 dated 2025-08-19

Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle', 'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake', 'Azure Synapse Analytics Dedicated', 'Apache Spark', 'SQLite', and 'InterSystems IRIS'.
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

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Package SIMPLE.REGRESSION updated to version 0.2.7 with previous version 0.2.6 dated 2025-06-20

Title: OLS, Moderated, Logistic, and Count Regressions Made Simple
Description: Provides SPSS- and SAS-like output for least squares multiple regression, logistic regression, and count variable regressions. Detailed output is also provided for OLS moderated regression, interaction plots, and Johnson-Neyman regions of significance. The output includes standardized coefficients, partial and semi-partial correlations, collinearity diagnostics, plots of residuals, and detailed information about simple slopes for interactions. The output for some functions includes Bayes Factors and, if requested, regression coefficients from Bayesian Markov Chain Monte Carlo analyses. There are numerous options for model plots. The REGIONS_OF_SIGNIFICANCE function also provides Johnson-Neyman regions of significance and plots of interactions for both lm and lme models. There is also a function for partial and semipartial correlations and a function for conducting Cohen's set correlation analyses.
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>

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Package Rttf2pt1 updated to version 1.3.14 with previous version 1.3.13 dated 2025-09-24

Title: 'ttf2pt1' Program
Description: Contains the program 'ttf2pt1', for use with the 'extrafont' package. This product includes software developed by the 'TTF2PT1' Project and its contributors.
Author: Winston Chang [aut], Andrew Weeks [aut], Frank M. Siegert [aut], Mark Heath [aut], Thomas Henlick [aut], Sergey Babkin [aut], Turgut Uyar [aut], Rihardas Hepas [aut], Szalay Tamas [aut], Johan Vromans [aut], Petr Titera [aut], Lei Wang [aut], Chen Xi [...truncated...]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>

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Package RSA updated to version 0.10.8 with previous version 0.10.6 dated 2023-01-12

Title: Response Surface Analysis
Description: Advanced response surface analysis. The main function RSA computes and compares several nested polynomial regression models (full second- or third-order polynomial, shifted and rotated squared difference model, rising ridge surfaces, basic squared difference model, asymmetric or level-dependent congruence effect models). The package provides plotting functions for 3d wireframe surfaces, interactive 3d plots, and contour plots. Calculates many surface parameters (a1 to a5, principal axes, stationary point, eigenvalues) and provides standard, robust, or bootstrapped standard errors and confidence intervals for them.
Author: Felix Schoenbrodt [cre, aut], Sarah Humberg [aut]
Maintainer: Felix Schoenbrodt <felix@nicebread.de>

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Package remify updated to version 3.2.9 with previous version 3.2.8 dated 2025-01-29

Title: Processing and Transforming Relational Event History Data
Description: Efficiently processes relational event history data and transforms them into formats suitable for other packages. The primary objective of this package is to convert event history data into a format that integrates with the packages in 'remverse' and is compatible with various analytical tools (e.g., computing network statistics, estimating tie-oriented or actor-oriented social network models). Second, it can also transform the data into formats compatible with other packages out of 'remverse'. The package processes the data for two types of temporal social network models: tie-oriented modeling framework (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) and actor-oriented modeling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>).
Author: Giuseppe Arena [aut, cre] , Rumana Lakdawala [ctb], Marlyne Meijerink-Bosman [ctb], Diana Karimova [ctb], Fabio Generoso Vieira [ctb], Mahdi Shafiee Kamalabad [ctb], Roger Leenders [ctb], Joris Mulder [ctb]
Maintainer: Giuseppe Arena <g.arena@uva.nl>

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Package papaja updated to version 0.1.4 with previous version 0.1.3 dated 2024-10-24

Title: Prepare American Psychological Association Journal Articles with R Markdown
Description: Tools to create dynamic, submission-ready manuscripts, which conform to American Psychological Association manuscript guidelines. We provide R Markdown document formats for manuscripts (PDF and Word) and revision letters (PDF). Helper functions facilitate reporting statistical analyses or create publication-ready tables and plots.
Author: Frederik Aust [aut, cre] , Marius Barth [aut] , Birk Diedenhofen [ctb], Christoph Stahl [ctb], Joseph V. Casillas [ctb], Rudolf Siegel [ctb]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>

Diff between papaja versions 0.1.3 dated 2024-10-24 and 0.1.4 dated 2025-09-26

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Package fuzzySim updated to version 4.36 with previous version 4.34 dated 2025-09-08

Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut], Alba Estrada [ctb], Paul Melloy [ctb], Jose Carlos Guerrero [fnd], A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>

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Package CausalImpact updated to version 1.4.1 with previous version 1.3.0 dated 2022-11-09

Title: Inferring Causal Effects using Bayesian Structural Time-Series Models
Description: Implements a Bayesian approach to causal impact estimation in time series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>. See the package documentation on GitHub <https://google.github.io/CausalImpact/> to get started.
Author: Kay H. Brodersen [aut], Alain Hauser [aut, cre]
Maintainer: Alain Hauser <alhauser@google.com>

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Package blosc updated to version 0.1.2 with previous version 0.1.1 dated 2025-09-11

Title: Compress and Decompress Data Using the 'BLOSC' Library
Description: Arrays of structured data types can require large volumes of disk space to store. 'Blosc' is a library that provides a fast and efficient way to compress such data. It is often applied in storage of n-dimensional arrays, such as in the case of the geo-spatial 'zarr' file format. This package can be used to compress and decompress data using 'Blosc'.
Author: Pepijn de Vries [aut, cre] , Chris Maiwald [cph], Alexander Gessler [cph]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>

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Package Analitica updated to version 2.0.0 with previous version 1.8.5 dated 2025-06-27

Title: Exploratory Data Analysis, Group Comparison Tools, and Other Procedures
Description: Provides a comprehensive set of tools for descriptive statistics, graphical data exploration, outlier detection, homoscedasticity testing, and multiple comparison procedures. Includes manual implementations of Levene's test, Bartlett's test, and the Fligner-Killeen test, as well as post hoc comparison methods such as Tukey, Scheffé, Games-Howell, Brunner-Munzel, and others. This version introduces two new procedures: the Jonckheere-Terpstra trend test and the Jarque-Bera test with Glinskiy's (2024) correction. Designed for use in teaching, applied statistical analysis, and reproducible research.
Author: Carlos Jimenez-Gallardo [aut, cre]
Maintainer: Carlos Jimenez-Gallardo <carlos.jimenez@ufrontera.cl>

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Package unmarked updated to version 1.5.1 with previous version 1.5.0 dated 2025-02-10

Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Richard Chandler [aut], Ken Kellner [cre, aut], Ian Fiske [aut], David Miller [aut], Andy Royle [aut], Jeff Hostetler [aut], Rebecca Hutchinson [aut], Adam Smith [aut], Lea Pautrel [aut], Marc Kery [ctb], Mike Meredith [ctb], Auriel Fournier [ctb], A [...truncated...]
Maintainer: Ken Kellner <contact@kenkellner.com>

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Package tabxplor updated to version 1.3.1 with previous version 1.3.0 dated 2025-03-09

Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data exploration, by creating them, manipulating them, and adding color helpers to highlight important informations (differences from totals, comparisons between lines or columns, contributions to variance, confidence intervals, odds ratios, etc.). All functions are pipe-friendly and render data frames which can be easily manipulated. In the same time, time-taking operations are done with 'data.table' to go faster with big dataframes. Tables can be exported with formats and colors to 'Excel', plot and html.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>

Diff between tabxplor versions 1.3.0 dated 2025-03-09 and 1.3.1 dated 2025-09-26

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Package survAUC updated to version 1.4-0 with previous version 1.3-0 dated 2024-09-09

Title: Estimators of Prediction Accuracy for Time-to-Event Data
Description: Provides a variety of functions to estimate time-dependent true/false positive rates and AUC curves from a set of censored survival data.
Author: Sergej Potapov [aut], Werner Adler [aut], Matthias Schmid [aut], Frederic Bertrand [cre, aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>

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Package strucchangeRcpp updated to version 1.5-4-1.0.1 with previous version 1.5-4-1.0.0 dated 2024-10-17

Title: Testing, Monitoring, and Dating Structural Changes: C++ Version
Description: A fast implementation with additional experimental features for testing, monitoring and dating structural changes in (linear) regression models. 'strucchangeRcpp' features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g. cumulative/moving sum, recursive/moving estimates) and F statistics, respectively. These methods are described in Zeileis et al. (2002) <doi:10.18637/jss.v007.i02>. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals, and their magnitude as well as the model fit can be evaluated using a variety of statistical measures.
Author: Dainius Masiliunas [aut, cre] , Achim Zeileis [aut] , Marius Appel [aut], Friedrich Leisch [aut], Kurt Hornik [aut], Christian Kleiber [aut], Andrei Mirt [ctb] , Bruce Hansen [ctb], Edgar C. Merkle [ctb], Nikolaus Umlauf [ctb]
Maintainer: Dainius Masiliunas <pastas4@gmail.com>

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Package simStateSpace updated to version 1.2.11 with previous version 1.2.10 dated 2025-03-29

Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework for simulating data in state space models, particularly when the number of subjects/units (n) exceeds one, a scenario commonly encountered in social and behavioral sciences. For an introduction to state space models in social and behavioral sciences, refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>

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Package rio updated to version 1.2.4 with previous version 1.2.3 dated 2024-09-25

Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data format from the file extension, reasonable defaults are used for data import and export, web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly, and fast import packages are used where appropriate. An additional convenience function, 'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut], Chung-hong Chan [aut, cre] , David Schoch [aut] , Geoffrey CH Chan [ctb], Thomas J. Leeper [aut] , Christopher Gandrud [ctb], Andrew MacDonald [ctb], Ista Zahn [ctb], Stanislaus Stadlmann [ctb], Ruaridh Williamson [ctb], Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>

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Package plspm updated to version 0.6.0 with previous version 0.5.2 dated 2025-08-18

Title: Partial Least Squares Path Modeling (PLS-PM)
Description: Partial Least Squares Path Modeling (PLS-PM), Tenenhaus, Esposito Vinzi, Chatelin, Lauro (2005) <doi:10.1016/j.csda.2004.03.005>, analysis for both metric and non-metric data, as well as REBUS analysis, Esposito Vinzi, Trinchera, Squillacciotti, and Tenenhaus (2008) <doi:10.1002/asmb.728>.
Author: Gaston Sanchez [aut], Laura Trinchera [aut], Giorgio Russolillo [aut], Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>

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Package photobiology updated to version 0.14.0 with previous version 0.13.2 dated 2025-07-31

Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] , Titta K. Kotilainen [ctb] , Glenn Davis [ctb], Agnese Fazio [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package NNS updated to version 11.6 with previous version 11.5 dated 2025-08-20

Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre], Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

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Package neonUtilities updated to version 3.0.2 with previous version 3.0.1 dated 2025-08-28

Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb], Christine Laney [aut, ctb], Nathan Mietkiewicz [aut, ctb], Eric Sokol [aut, ctb], Kaelin Cawley [aut, ctb], NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>

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Package graphon updated to version 0.3.6 with previous version 0.3.5 dated 2021-08-13

Title: A Collection of Graphon Estimation Methods
Description: Provides a not-so-comprehensive list of methods for estimating graphon, a symmetric measurable function, from a single or multiple of observed networks. For a detailed introduction on graphon and popular estimation techniques, see the paper by Orbanz, P. and Roy, D.M.(2014) <doi:10.1109/TPAMI.2014.2334607>. It also contains several auxiliary functions for generating sample networks using various network models and graphons.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>

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Package dosearch updated to version 1.0.12 with previous version 1.0.11 dated 2024-07-16

Title: Causal Effect Identification from Multiple Incomplete Data Sources
Description: Identification of causal effects from arbitrary observational and experimental probability distributions via do-calculus and standard probability manipulations using a search-based algorithm by Tikka, Hyttinen and Karvanen (2021) <doi:10.18637/jss.v099.i05>. Allows for the presence of mechanisms related to selection bias (Bareinboim and Tian, 2015) <doi:10.1609/aaai.v29i1.9679>, transportability (Bareinboim and Pearl, 2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>, missing data (Mohan, Pearl, and Tian, 2013) <http://ftp.cs.ucla.edu/pub/stat_ser/r410.pdf>) and arbitrary combinations of these. Also supports identification in the presence of context-specific independence (CSI) relations through labeled directed acyclic graphs (LDAG). For details on CSIs see (Corander et al., 2019) <doi:10.1016/j.apal.2019.04.004>.
Author: Santtu Tikka [aut, cre] , Antti Hyttinen [ctb] , Juha Karvanen [ctb]
Maintainer: Santtu Tikka <santtuth@gmail.com>

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Package dexter updated to version 1.7.0 with previous version 1.6.2 dated 2025-06-10

Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut], Timo Bechger [aut], Jesse Koops [aut, cre], Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>

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Package womblR updated to version 1.0.6 with previous version 1.0.5 dated 2022-09-05

Title: Spatiotemporal Boundary Detection Model for Areal Unit Data
Description: Implements a spatiotemporal boundary detection model with a dissimilarity metric for areal data with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC). The response variable can be modeled as Gaussian (no nugget), probit or Tobit link and spatial correlation is introduced at each time point through a conditional autoregressive (CAR) prior. Temporal correlation is introduced through a hierarchical structure and can be specified as exponential or first-order autoregressive. Full details of the package can be found in the accompanying vignette. Furthermore, the details of the package can be found in "Diagnosing Glaucoma Progression with Visual Field Data Using a Spatiotemporal Boundary Detection Method", by Berchuck et al (2019) <doi:10.1080/01621459.2018.1537911>.
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>

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Package rly updated to version 1.7.7 with previous version 1.7.4 dated 2022-05-08

Title: Tools to Create Formal Language Parser
Description: R implementation of the common parsing tools 'lex' and 'yacc'.
Author: Marek Jagielski [aut, cre, cph], David M. Beazley [aut, cph], Yasutaka Tanaka [ctb], Henrico Witvliet [ctb]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>

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Package comat updated to version 0.9.6 with previous version 0.9.5 dated 2023-11-28

Title: Creates Co-Occurrence Matrices of Spatial Data
Description: Builds co-occurrence matrices based on spatial raster data. It includes creation of weighted co-occurrence matrices (wecoma) and integrated co-occurrence matrices (incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>).
Author: Jakub Nowosad [aut, cre] , Maximillian H.K. Hesselbarth [ctb] , get_unique_values, and rcpp_get_coma functions), Marco Sciaini [ctb] , get_unique_values, and rcpp_get_coma functions), Sebastian Hanss [ctb] , get_unique_values, and rcpp_get_coma funct [...truncated...]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

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Package autothresholdr updated to version 1.4.3 with previous version 1.4.2 dated 2023-12-13

Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Algorithms for automatically finding appropriate thresholds for numerical data, with special functions for thresholding images. Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users. See <https://imagej.net/plugins/auto-threshold> and Landini et al. (2017) <DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl] , Luis Alvarez [ctb] , Sergi Padilla-Parra [ctb, ths] , Gabriel Landini [ctb, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package ArchaeoPhases updated to version 2.1.0 with previous version 2.0 dated 2024-06-16

Title: Post-Processing of Markov Chain Monte Carlo Simulations for Chronological Modelling
Description: Statistical analysis of archaeological dates and groups of dates. This package allows to post-process Markov Chain Monte Carlo (MCMC) simulations from 'ChronoModel' <https://chronomodel.com/>, 'Oxcal' <https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal' <https://bcal.shef.ac.uk/>. It provides functions for the study of rhythms of the long term from the posterior distribution of a series of dates (tempo and activity plot). It also allows the estimation and visualization of time ranges from the posterior distribution of groups of dates (e.g. duration, transition and hiatus between successive phases) as described in Philippe and Vibet (2020) <doi:10.18637/jss.v093.c01>.
Author: Anne Philippe [aut, cre] , Marie-Anne Vibet [aut] , Nicolas Frerebeau [aut] , Thomas S. Dye [ctb] , Nantes Universite [fnd] , Universite Bordeaux Montaigne [fnd] , CNRS [fnd]
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>

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Package psgp updated to version 0.3-24 with previous version 0.3-23 dated 2025-07-17

Title: Projected Spatial Gaussian Process Methods
Description: Implements projected sparse Gaussian process Kriging ('Ingram et. al.', 2008, <doi:10.1007/s00477-007-0163-9>) as an additional method for the 'intamap' package. More details on implementation ('Barillec et. al.', 2010, <doi:10.1016/j.cageo.2010.05.008>).
Author: Ben Ingram [aut, cre] , Remi Barillec [aut], Jon Olav Skoien [aut]
Maintainer: Ben Ingram <ingrambr.work@gmail.com>

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Package sharpshootR updated to version 2.4 with previous version 2.3.3 dated 2025-04-17

Title: A Soil Survey Toolkit
Description: A collection of data processing, visualization, and export functions to support soil survey operations. Many of the functions build on the `SoilProfileCollection` S4 class provided by the aqp package, extending baseline visualization to more elaborate depictions in the context of spatial and taxonomic data. While this package is primarily developed by and for the USDA-NRCS, in support of the National Cooperative Soil Survey, the authors strive for generalization sufficient to support any soil survey operation. Many of the included functions are used by the SoilWeb suite of websites and movile applications. These functions are provided here, with additional documentation, to enable others to replicate high quality versions of these figures for their own purposes.
Author: Dylan Beaudette [cre, aut], Jay Skovlin [aut], Stephen Roecker [aut], Andrew Brown [aut], USDA-NRCS Soil Survey Staff [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>

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Package eye updated to version 1.3.0 with previous version 1.2.1 dated 2021-09-04

Title: Analysis of Eye Data
Description: There is no ophthalmic researcher who has not had headaches from the handling of visual acuity entries. Different notations, untidy entries. This shall now be a matter of the past. Eye makes it as easy as pie to work with VA data - easy cleaning, easy conversion between Snellen, logMAR, ETDRS letters, and qualitative visual acuity shall never pester you again. The eye package automates the pesky task to count number of patients and eyes, and can help to clean data with easy re-coding for right and left eyes. It also contains functions to help reshaping eye side specific variables between wide and long format. Visual acuity conversion is based on Schulze-Bonsel et al. (2006) <doi:10.1167/iovs.05-0981>, Gregori et al. (2010) <doi:10.1097/iae.0b013e3181d87e04>, Beck et al. (2003) <doi:10.1016/s0002-9394(02)01825-1> and Bach (2007) <https://michaelbach.de/sci/acuity.html>.
Author: Tjebo Heeren [aut, cre] , Antoine Fabri [ctb]
Maintainer: Tjebo Heeren <tjebo@gmx.de>

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 eye-1.3.0/eye/MD5                           |   68 -
 eye-1.3.0/eye/NAMESPACE                     |    6 
 eye-1.3.0/eye/NEWS.md                       |   33 
 eye-1.3.0/eye/R/eye.R                       |    2 
 eye-1.3.0/eye/R/reveal.R                    |    6 
 eye-1.3.0/eye/R/str_helper.R                |   26 
 eye-1.3.0/eye/R/va.R                        |  145 +-
 eye-1.3.0/eye/R/va_cleaner.R                |   64 -
 eye-1.3.0/eye/R/va_methods.R                |   15 
 eye-1.3.0/eye/README.md                     |  215 ++-
 eye-1.3.0/eye/build/vignette.rds            |binary
 eye-1.3.0/eye/inst/CITATION                 |    6 
 eye-1.3.0/eye/inst/doc/eye.R                |   20 
 eye-1.3.0/eye/inst/doc/eye.Rmd              |   27 
 eye-1.3.0/eye/inst/doc/eye.html             | 1573 ++++++++++++++++++----------
 eye-1.3.0/eye/man/VAwrapper.Rd              |    2 
 eye-1.3.0/eye/man/clean_va.Rd               |    7 
 eye-1.3.0/eye/man/convertQuali.Rd           |   18 
 eye-1.3.0/eye/man/eye.Rd                    |    6 
 eye-1.3.0/eye/man/eye_codes.Rd              |    2 
 eye-1.3.0/eye/man/plausibility_methods.Rd   |    2 
 eye-1.3.0/eye/man/reveal_methods.Rd         |    5 
 eye-1.3.0/eye/man/reveal_split.Rd           |    4 
 eye-1.3.0/eye/man/set_eye_strings.Rd        |   23 
 eye-1.3.0/eye/man/snellen_steps.Rd          |    2 
 eye-1.3.0/eye/man/va.Rd                     |   80 -
 eye-1.3.0/eye/man/va_methods.Rd             |    2 
 eye-1.3.0/eye/man/va_mixed.Rd               |   25 
 eye-1.3.0/eye/man/which_va.Rd               |    4 
 eye-1.3.0/eye/tests/testthat/test-eyes.R    |    1 
 eye-1.3.0/eye/tests/testthat/test-reveal.R  |    2 
 eye-1.3.0/eye/tests/testthat/test-va.R      |   54 
 eye-1.3.0/eye/tests/testthat/test_cleanVA.r |only
 eye-1.3.0/eye/vignettes/eye.Rmd             |   27 
 36 files changed, 1671 insertions(+), 828 deletions(-)

More information about eye at CRAN
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Package rbi.helpers updated to version 0.4.1 with previous version 0.4.0 dated 2023-08-24

Title: 'rbi' Helper Functions
Description: Contains a collection of helper functions to use with 'rbi', the R interface to 'LibBi', described in Murray et al. (2015) <doi:10.18637/jss.v067.i10>. It contains functions to adapt the proposal distribution and number of particles in particle Markov-Chain Monte Carlo, as well as calculating the Deviance Information Criterion (DIC) and converting between times in 'LibBi' results and R time/dates.
Author: Sebastian Funk [aut, cre]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>

Diff between rbi.helpers versions 0.4.0 dated 2023-08-24 and 0.4.1 dated 2025-09-26

 DESCRIPTION                    |   20 +++++++---
 MD5                            |   38 ++++++++++----------
 NEWS.md                        |    4 ++
 R/acceptance_rate.R            |    6 +--
 R/adapt_particles.R            |    6 +--
 R/adapt_proposal.R             |   11 +++--
 R/get_mvn_params.r             |    4 +-
 R/times.r                      |   10 ++---
 R/update_proposal.r            |    6 +--
 build/vignette.rds             |binary
 inst/doc/rbi.helpers.R         |   76 ++++++++++++++++++++---------------------
 inst/doc/rbi.helpers.html      |    1 
 man/acceptance_rate.Rd         |    4 +-
 man/adapt_particles.Rd         |    6 +--
 man/adapt_proposal.Rd          |    6 +--
 man/get_mvn_params.Rd          |    4 +-
 man/numeric_to_time.Rd         |    2 -
 man/update_proposal.Rd         |    4 +-
 tests/testthat/test-adapt.r    |    4 --
 tests/testthat/test-proposal.r |    2 -
 20 files changed, 111 insertions(+), 103 deletions(-)

More information about rbi.helpers at CRAN
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