Tue, 18 Feb 2025

Package calidad updated to version 0.7.0 with previous version 0.6.0 dated 2024-10-16

Title: Assesses the Quality of Estimates Made by Complex Sample Designs
Description: Assesses the quality of estimates made by complex sample designs, following the methodology developed by the National Institute of Statistics Chile (2020, <https://www.ine.cl/docs/default-source/institucionalidad/buenas-pr%C3%A1cticas/clasificaciones-y-estandares/est%C3%A1ndar-evaluaci%C3%B3n-de-calidad-de-estimaciones-publicaci%C3%B3n-27022020.pdf>) and by Economic Commission for Latin America and Caribbean (2020, <https://repositorio.cepal.org/bitstream/handle/11362/45681/1/S2000293_es.pdf>), (2024, <https://repositorio.cepal.org/server/api/core/bitstreams/f04569e6-4f38-42e7-a32b-e0b298e0ab9c/content>).
Author: Klaus Lehmann [aut, cre], Ricardo Pizarro [aut], Ignacio Agloni [ctb], Andrea Lopez [ctb], Javiera Preuss [ctb]
Maintainer: Klaus Lehmann <klehmann@fen.uchile.cl>

Diff between calidad versions 0.6.0 dated 2024-10-16 and 0.7.0 dated 2025-02-18

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New package UAHDataScienceSF with initial version 1.0.0
Package: UAHDataScienceSF
Version: 1.0.0
Title: Interactive Statistical Learning Functions
Description: An educational toolkit for learning statistical concepts through interactive exploration. Provides functions for basic statistics (mean, variance, etc.) and probability distributions with step-by-step explanations and interactive learning modes. Each function can be used for simple calculations, detailed learning with explanations, or interactive practice with feedback.
License: MIT + file LICENSE
Imports: stats, magick (>= 2.7.3), crayon (>= 1.3.4)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-02-17 15:31:07 UTC; andriy
Author: Carlos Javier Hellin Asensio [aut], Jose Manuel Gomez Caceres [aut], Dennis Monheimius [aut], Eduardo Benito [aut], Juan Jose Cuadrado [aut], Andriy Protsak Protsak [aut, cre], Universidad de Alcala de Henares [cph]
Maintainer: Andriy Protsak Protsak <andriy.protsak@edu.uah.es>
Repository: CRAN
Date/Publication: 2025-02-18 11:10:07 UTC

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Package spiro updated to version 0.2.3 with previous version 0.2.1 dated 2023-08-14

Title: Manage Data from Cardiopulmonary Exercise Testing
Description: Import, process, summarize and visualize raw data from metabolic carts. See Robergs, Dwyer, and Astorino (2010) <doi:10.2165/11319670-000000000-00000> for more details on data processing.
Author: Simon Nolte [aut, cre] , Manuel Ramon [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/541>), James Hunter [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/541>)
Maintainer: Simon Nolte <s.nolte@dshs-koeln.de>

Diff between spiro versions 0.2.1 dated 2023-08-14 and 0.2.3 dated 2025-02-18

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New package musicXML with initial version 1.0.1
Package: musicXML
Title: Data Sonification using 'musicXML'
Version: 1.0.1
Description: A set of tools to facilitate data sonification and handle the 'musicXML' format <https://usermanuals.musicxml.com/MusicXML/Content/XS-MusicXML.htm>. Several classes are defined for basic musical objects such as note pitch, note duration, note, measure and score. Moreover, sonification utilities functions are provided, e.g. to map data into musical attributes such as pitch, loudness or duration. A typical sonification workflow hence looks like: get data; map them to musical attributes; create and write the 'musicXML' score, which can then be further processed using specialized music software (e.g. 'MuseScore', 'GuitarPro', etc.). Examples can be found in the blog <https://globxblog.github.io/>, the presentation by Renard and Le Bescond (2022, <https://hal.science/hal-03710340v1>) or the poster by Renard et al. (2023, <https://hal.inrae.fr/hal-04388845v1>).
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: xml2
Suggests: knitr, rmarkdown, tidyr, gganimate, av
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-17 18:07:18 UTC; brenard
Author: Benjamin Renard [aut, cre, cph] , INRAE [fnd], European Commission [fnd]
Maintainer: Benjamin Renard <benjamin.renard@inrae.fr>
Repository: CRAN
Date/Publication: 2025-02-18 11:10:02 UTC

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New package fishgrowth with initial version 1.0.1
Package: fishgrowth
Version: 1.0.1
Date: 2025-02-18
Title: Fit Growth Curves to Fish Data
Depends: R (>= 2.10), RTMB
Suggests: areaplot
LazyData: yes
Description: Fit growth models to otoliths and/or tagging data, using the 'RTMB' package and maximum likelihood. The otoliths (or similar measurements of age) provide direct observed coordinates of age and length. The tagging data provide information about the observed length at release and length at recapture at a later time, where the age at release is unknown and estimated as a vector of parameters. The growth models provided by this package can be fitted to otoliths only, tagging data only, or a combination of the two. Growth variability can be modelled as constant or increasing with length.
License: GPL-3
URL: https://github.com/arni-magnusson/fishgrowth
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-18 03:53:41 UTC; arnim
Author: Arni Magnusson [aut, cre], Mark Maunder [aut]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-18 11:20:02 UTC

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Package ursa updated to version 3.11.3 with previous version 3.11.2 dated 2025-01-14

Title: Non-Interactive Spatial Tools for Raster Processing and Visualization
Description: S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.
Author: Nikita Platonov [aut, cre]
Maintainer: Nikita Platonov <platonov@sev-in.ru>

Diff between ursa versions 3.11.2 dated 2025-01-14 and 3.11.3 dated 2025-02-18

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New package SimTOST with initial version 1.0.1
Package: SimTOST
Title: Sample Size Estimation for Bio-Equivalence Trials Through Simulation
Version: 1.0.1
Description: Sample size estimation for bio-equivalence trials is supported through a simulation-based approach that extends the Two One-Sided Tests (TOST) procedure. The methodology provides flexibility in hypothesis testing, accommodates multiple treatment comparisons, and accounts for correlated endpoints. Users can model complex trial scenarios, including parallel and crossover designs, intra-subject variability, and different equivalence margins. Monte Carlo simulations enable accurate estimation of power and type I error rates, ensuring well-calibrated study designs. The statistical framework builds on established methods for equivalence testing and multiple hypothesis testing in bio-equivalence studies, as described in Schuirmann (1987) <doi:10.1007/BF01068419>, Mielke et al. (2018) <doi:10.1080/19466315.2017.1371071>, Shieh (2022) <doi:10.1371/journal.pone.0269128>, and Sozu et al. (2015) <doi:10.1007/978-3-319-22005-5>. Comprehensive documentation and vignettes guid [...truncated...]
License: Apache License (>= 2)
Encoding: UTF-8
Imports: MASS, Rcpp (>= 1.0.13), data.table, matrixcalc, parallel
Suggests: PowerTOST, ggplot2, kableExtra, knitr, rmarkdown, testthat (>= 3.0.0), tibble, tinytest
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo
URL: https://smartdata-analysis-and-statistics.github.io/SimTOST/
NeedsCompilation: yes
Packaged: 2025-02-17 11:37:16 UTC; Thomas
Author: Thomas Debray [aut, cre] , Johanna Munoz [aut], Dewi Amaliah [ctb], Wei Wei [ctb], Marian Mitroiu [ctb], Scott McDonald [ctb], Biogen Inc [cph, fnd]
Maintainer: Thomas Debray <tdebray@fromdatatowisdom.com>
Repository: CRAN
Date/Publication: 2025-02-18 10:10:14 UTC

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New package rb3 with initial version 0.0.12
Package: rb3
Title: Download and Parse Public Data Released by B3 Exchange
Description: Download and parse public files released by B3 and convert them into useful formats and data structures common to data analysis practitioners.
Version: 0.0.12
License: MIT + file LICENSE
Depends: R (>= 4.1.0),
Imports: bizdays, stringr, proto, cli, readr, dplyr, rvest, httr, jsonlite, purrr, ascii, rlang, methods, yaml, digest, base64enc, XML, readxl, tidyr
Suggests: testthat, knitr, DT, miniUI, shiny, xtable, rmarkdown, ggplot2, covr, scales, magrittr, tibble, withr, vcr (>= 0.6.0)
BugReports: https://github.com/ropensci/rb3/issues
URL: https://github.com/ropensci/rb3, http://ropensci.github.io/rb3/
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-16 18:57:35 UTC; root
Author: Wilson Freitas [aut, cre], Marcelo Perlin [aut]
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-18 10:10:02 UTC

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Package ProtE updated to version 1.0.3 with previous version 1.0.2 dated 2025-02-17

Title: Processing Proteomics Data, Statistical Analysis and Visualization
Description: The 'Proteomics Eye' ('ProtE') offers a comprehensive and intuitive framework for the univariate analysis of label-free proteomics data. By integrating essential data wrangling and processing steps into a single function, 'ProtE' streamlines pairwise statistical comparisons for categorical variables. It provides quality checks and generates publication-ready visualizations, enabling efficient and robust data analysis. 'ProtE' is compatible with proteomics data outputs from 'MaxQuant' (Cox & Mann, (2008) <doi:10.1038/nbt.1511>), 'DIA-NN' (Demichev et al., (2020) <doi:10.1038/s41592-019-0638-x>), and 'Proteome Discoverer' (Thermo Fisher Scientific, version 2.5). The package leverages 'ggplot2' for visualization (Wickham, (2016) <doi:10.1007/978-3-319-24277-4>) and 'limma' for statistical analysis (Ritchie et al., (2015) <doi:10.1093/nar/gkv007>).
Author: Theodoros Margelos [aut, cre, cph], Rafael Stroggilos [ctb, cph]
Maintainer: Theodoros Margelos <ted.margelos02@gmail.com>

Diff between ProtE versions 1.0.2 dated 2025-02-17 and 1.0.3 dated 2025-02-18

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New package logos with initial version 0.1.0
Package: logos
Title: Access to the Hebrew, Greek, and English Version of the Bible
Version: 0.1.0
Maintainer: JP Monteagudo <jpmonteagudo2014@gmail.com>
Description: Access to the Greek New Testament (27 books) and the Old Testament (39 books) and allow users to do textual analysis on the data. The New and Old Testament have been provided in their original languages, Greek and Hebrew, respectively. Additionally, the Revised American Standard Bible is also provided for users who'd rather use a word–for–word modern English translation.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/jpmonteagudo28/logos
BugReports: https://github.com/jpmonteagudo28/logos/issues
LazyData: true
Depends: R (>= 4.1)
Suggests: testthat (>= 3.0.0)
Imports: dplyr
NeedsCompilation: no
Packaged: 2025-02-17 13:25:23 UTC; jpmonteagudo
Author: JP Monteagudo [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-02-18 10:10:06 UTC

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New package datamedios with initial version 1.1.0
Package: datamedios
Title: Scraping Chilean Media
Version: 1.1.0
Maintainer: Exequiel Trujillo <exequiel.trujillo@ug.uchile.cl>
Description: A system for extracting news from Chilean media, specifically through Web Scapping from Chilean media. The package allows for news searches using search phrases and date filters, and returns the results in a structured format, ready for analysis. Additionally, it includes functions to clean the extracted data, visualize it, and store it in databases. All of this can be done automatically, facilitating the collection and analysis of relevant information from Chilean media.
License: MIT + file LICENSE
Encoding: UTF-8
Language: es-ES
Depends: R (>= 4.1)
Suggests: rcmdcheck
Imports: dplyr, httr, magrittr, jsonlite, utils, tidyverse, wordcloud2, tidytext, lubridate, rvest, stringr, xml2, purrr, DT, ggplot2
NeedsCompilation: no
Packaged: 2025-02-16 21:20:50 UTC; ismae
Author: Exequiel Trujillo [aut, cre, cph, fnd], Ismael Aguayo [aut, fnd], Klaus Lehmann [aut, fnd]
Repository: CRAN
Date/Publication: 2025-02-18 10:10:10 UTC

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New package correlatio with initial version 0.1.0
Package: correlatio
Title: Visualize Details Behind Pearson's Correlation Coefficient
Version: 0.1.0
Description: Helps visualizing what is summarized in Pearson's correlation coefficient. That is, it visualizes its main constituent, namely the distances of the single values to their respective mean. The visualization thereby shows what the etymology of the word correlation contains: In pairwise combination, bringing back (see package Vignette for more details). I hope that the 'correlatio' package may benefit some people in understanding and critically evaluating what Pearson's correlation coefficient summarizes in a single number, i.e., to what degree and why Pearson's correlation coefficient may (or may not) be warranted as a measure of association.
License: MIT + file LICENSE
Repository: CRAN
URL: https://github.com/mmiche/correlatio
Encoding: UTF-8
Imports: Rdpack, stats, ggplot2, tibble
Depends: R (>= 4.0.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
BugReports: https://github.com/mmiche/correlatio/issues
NeedsCompilation: no
Packaged: 2025-02-17 14:51:36 UTC; mmiche
Author: Marcel Miche [aut, cre]
Maintainer: Marcel Miche <marcel.miche.predictme@gmail.com>
Date/Publication: 2025-02-18 10:20:10 UTC

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Package clarabel updated to version 0.10.0 with previous version 0.9.0.1 dated 2024-09-03

Title: Interior Point Conic Optimization Solver
Description: A versatile interior point solver that solves linear programs (LPs), quadratic programs (QPs), second-order cone programs (SOCPs), semidefinite programs (SDPs), and problems with exponential and power cone constraints (<https://clarabel.org/stable/>). For quadratic objectives, unlike interior point solvers based on the standard homogeneous self-dual embedding (HSDE) model, Clarabel handles quadratic objective without requiring any epigraphical reformulation of its objective function. It can therefore be significantly faster than other HSDE-based solvers for problems with quadratic objective functions. Infeasible problems are detected using using a homogeneous embedding technique.
Author: Balasubramanian Narasimhan [aut, cre], Paul Goulart [aut, cph], Yuwen Chen [aut], Hiroaki Yutani [ctb] , David Zimmermann-Kollenda [ctb] , Hiroaki Yutani [ctb] , The authors of the dependency Rust crates [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>

Diff between clarabel versions 0.9.0.1 dated 2024-09-03 and 0.10.0 dated 2025-02-18

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Package XLConnect updated to version 1.2.0 with previous version 1.1.0 dated 2024-08-22

Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], The Apache Software Foundation [ctb, cph] , Graph Builder [ctb, cph] , Brett Woolridge [ctb, cph]
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>

Diff between XLConnect versions 1.1.0 dated 2024-08-22 and 1.2.0 dated 2025-02-18

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New package PiC with initial version 1.0.3
Package: PiC
Title: Pointcloud Interactive Computation for Forest Structure Analysis
Version: 1.0.3
Description: Provides advanced algorithms for analyzing pointcloud data in forestry applications. Key features include fast voxelization of large datasets; segmentation of point clouds into forest floor, understorey, canopy, and wood components. The package enables efficient processing of large-scale forest pointcloud data, offering insights into forest structure, connectivity, and fire risk assessment. Algorithms to analyze pointcloud data (.xyz input file). For more details, see Ferrara & Arrizza (2025) <https://hdl.handle.net/20.500.14243/533471>. For single tree segmentation details, see Ferrara et al. (2018) <doi:10.1016/j.agrformet.2018.04.008>.
License: GPL (>= 3)
Depends: R (>= 4.3)
Imports: collapse, data.table, dbscan, dplyr, foreach, magrittr, stats, tictoc
Suggests: ggplot2, testthat (>= 3.0.0), withr
Encoding: UTF-8
URL: https://github.com/rupppy/PiC
BugReports: https://github.com/rupppy/PiC/issues
NeedsCompilation: no
Packaged: 2025-02-17 09:39:57 UTC; robertoferrara
Author: Roberto Ferrara [aut, cre] , Stefano Arrizza [aut]
Maintainer: Roberto Ferrara <roberto.ferrara@cnr.it>
Repository: CRAN
Date/Publication: 2025-02-18 10:00:02 UTC

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New package Dogoftest with initial version 0.1
Package: Dogoftest
Title: Distributed Online Goodness-of-Fit Tests for Distributed Datasets
Date: 2025-02-15
Version: 0.1
Description: Distributed Online Goodness-of-Fit Test can process the distributed datasets. The philosophy of the package is described in Guo G.(2024) <doi:10.1016/j.apm.2024.115709>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-02-15 09:53:56 UTC; ASUS
Author: Guangbao Guo [aut, cre] , Di Chang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-02-18 10:00:05 UTC

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New package decompML with initial version 0.1.1
Package: decompML
Title: Decomposition Based Machine Learning Model
Version: 0.1.1
Maintainer: Kapil Choudhary <kapiliasri@gmail.com>
Description: The hybrid model is a highly effective forecasting approach that integrates decomposition techniques with machine learning to enhance time series prediction accuracy. Each decomposition technique breaks down a time series into multiple intrinsic mode functions (IMFs), which are then individually modeled and forecasted using machine learning algorithms. The final forecast is obtained by aggregating the predictions of all IMFs, producing an ensemble output for the time series. The performance of the developed models is evaluated using international monthly maize price data, assessed through metrics such as root mean squared error (RMSE), mean absolute percentage error (MAPE), and mean absolute error (MAE). For method details see Choudhary, K. et al. (2023). <https://ssca.org.in/media/14_SA44052022_R3_SA_21032023_Girish_Jha_FINAL_Finally.pdf>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: forecast, nnfor, Rlibeemd, VMDecomp
Depends: R (>= 3.5)
NeedsCompilation: no
Packaged: 2025-02-12 10:43:18 UTC; kapil
Author: Girish Kumar Jha [aut, ctb], Kapil Choudhary [aut, cre], Rajender Parsad [ctb], Ronit Jaiswal [ctb], Rajeev Ranjan Kumar [ctb], P Venkatesh [ctb], Dwijesh Chandra Mishra [ctb]
Repository: CRAN
Date/Publication: 2025-02-18 09:40:02 UTC

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Package fastQR (with last version 1.0.0) was removed from CRAN

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

2025-02-04 1.0.0

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Package TransProR updated to version 1.0.3 with previous version 1.0.2 dated 2025-02-14

Title: Analysis and Visualization of Multi-Omics Data
Description: A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10. [...truncated...]
Author: Dongyue Yu [aut, cre, cph]
Maintainer: Dongyue Yu <yudongyue@mail.nankai.edu.cn>

Diff between TransProR versions 1.0.2 dated 2025-02-14 and 1.0.3 dated 2025-02-18

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Package sae.projection updated to version 0.1.2 with previous version 0.1.1 dated 2025-02-15

Title: Small Area Estimation Using Model-Assisted Projection Method
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Author: Ridson Al Farizal P [aut, cre, cph] , Azka Ubaidillah [aut] , Silvi Ajeng Larasati [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>

Diff between sae.projection versions 0.1.1 dated 2025-02-15 and 0.1.2 dated 2025-02-18

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Package dartRverse updated to version 1.0.6 with previous version 1.0.2 dated 2024-05-24

Title: Install and Load the 'dartRverse' Suits of Packages
Description: Provides a single function that supports the installation of all packages belonging to the 'dartRverse'. The 'dartRverse' is a set of packages that work together to analyse SNP (single nuclear polymorphism) data. All packages aim to have a similar 'look and feel' and are based on the same type of data structure ('genlight'), with additional metadata for loci and individuals (samples). For more information visit the 'GitHub' pages <https://github.com/green-striped-gecko/dartRverse>.
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [aut], Oliver Berry [aut]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>

Diff between dartRverse versions 1.0.2 dated 2024-05-24 and 1.0.6 dated 2025-02-18

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New package dartR.captive with initial version 1.0.2
Package: dartR.captive
Title: Analysing 'SNP' Data to Support Captive Breeding
Version: 1.0.2
Date: 2025-02-17
Description: Functions are provided that facilitate the analysis of SNP (single nucleotide polymorphism) data to answer questions regarding captive breeding and relatedness between individuals. 'dartR.captive' is part of the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.
Encoding: UTF-8
Depends: R (>= 3.5), adegenet (>= 2.0.0), dartR.base, dartR.data, dartR.sim
Imports: methods, utils, crayon, ggplot2, patchwork, stringr, data.table
Suggests: SIBER, gplots, fields, igraph, reshape2, rrBLUP, scales, spelling
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2025-02-17 22:50:08 UTC; s425824
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb], Eric Archer [ctb], Sam Amini [ctb]
URL: https://green-striped-gecko.github.io/dartR/
BugReports: https://groups.google.com/g/dartr?pli=1
Language: en-US
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2025-02-18 08:20:05 UTC

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Package cardx updated to version 0.2.3 with previous version 0.2.2 dated 2024-11-27

Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects. The package supplements the simple ARD functions from the 'cards' package, exporting functions to put statistical results in the ARD format. These objects are used and re-used to construct summary tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] , Abinaya Yogasekaram [aut], Emily de la Rua [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

Diff between cardx versions 0.2.2 dated 2024-11-27 and 0.2.3 dated 2025-02-18

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Package iNEXT.3D updated to version 1.0.8 with previous version 1.0.7 dated 2025-01-22

Title: Interpolation and Extrapolation for Three Dimensions of Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D) of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional diversity (FD). This package provides functions to compute standardized 3D diversity estimates with a common sample size or sample coverage. A unified framework based on Hill numbers and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates are in the same units of species/lineage equivalents and can be meaningfully compared. The package features size- and coverage-based rarefaction and extrapolation sampling curves to facilitate rigorous comparison of 3D diversity across individual assemblages. Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021) <doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre], KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>

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Mon, 17 Feb 2025

Package RConics updated to version 1.1.2 with previous version 1.1.1 dated 2022-03-11

Title: Computations on Conics
Description: Solve some conic related problems (intersection of conics with lines and conics, arc length of an ellipse, polar lines, etc.).
Author: Emanuel Huber [aut, cre]
Maintainer: Emanuel Huber <emanuel.huber@pm.me>

Diff between RConics versions 1.1.1 dated 2022-03-11 and 1.1.2 dated 2025-02-17

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Package cata updated to version 0.1.0.26 with previous version 0.1.0.7 dated 2024-10-08

Title: Analysis of Check-All-that-Apply (CATA) Data
Description: Package contains functions for analyzing check-all-that-apply (CATA) data from consumer and sensory tests. Cochran's Q test, McNemar's test, and Penalty-Lift analysis are provided; for details, see Meyners, Castura & Carr (2013) <doi:10.1016/j.foodqual.2013.06.010>. Cluster analysis can be performed using b-cluster analysis, then evaluated using various measures; for details, see Castura, Meyners, Varela & Næs (2022) <doi:10.1016/j.foodqual.2022.104564>. Methods are adapted to cluster consumers based on their product-related hedonic responses; for details, see Castura, Meyners, Pohjanheimo, Varela & Næs (2023) <doi:10.1111/joss.12860>.
Author: J.C. Castura [aut, cre, ctb]
Maintainer: J.C. Castura <jcastura@compusense.com>

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Package UAHDataScienceUC updated to version 1.0.1 with previous version 1.0.0 dated 2025-02-17

Title: Learn Clustering Techniques Through Examples and Code
Description: A comprehensive educational package combining clustering algorithms with detailed step-by-step explanations. Provides implementations of both traditional (hierarchical, k-means) and modern (Density-Based Spatial Clustering of Applications with Noise (DBSCAN), Gaussian Mixture Models (GMM), genetic k-means) clustering methods as described in Ezugwu et. al., (2022) <doi:10.1016/j.engappai.2022.104743>. Includes educational datasets highlighting different clustering challenges, based on 'scikit-learn' examples (Pedregosa et al., 2011) <https://jmlr.csail.mit.edu/papers/v12/pedregosa11a.html>. Features detailed algorithm explanations, visualizations, and weighted distance calculations for enhanced learning.
Author: Eduardo Ruiz Sabajanes [aut], Roberto Alcantara [aut], Juan Jose Cuadrado Gallego [aut] , Andriy Protsak Protsak [aut, cre], Universidad de Alcala [cph]
Maintainer: Andriy Protsak Protsak <andriy.protsak@edu.uah.es>

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Package geocodebr updated to version 0.1.1 with previous version 0.1.0 dated 2025-02-12

Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O pacote é baseado em conjuntos de dados espaciais abertos de endereços brasileiros, utilizando principalmente o Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro de Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia do Brasil. (A simple and efficient method for geolocating data in Brazil. The package is based on open spatial datasets of Brazilian addresses, primarily using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE), published by the Instituto Brasileiro de Geografia e Estatística (IBGE), Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre] , Daniel Herszenhut [aut] , Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>

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Package fdasrvf updated to version 2.3.6 with previous version 2.3.5 dated 2025-02-11

Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and unidimensional functions using the square-root velocity framework (Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] , Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>

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Package cards updated to version 0.5.0 with previous version 0.4.0 dated 2024-11-27

Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards Consortium) compliant Analysis Results Data objects. These objects are used and re-used to construct summary tables, visualizations, and written reports. The package also exports utilities for working with these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] , Becca Krouse [aut], Emily de la Rua [aut], F. Hoffmann-La Roche AG [cph, fnd], GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

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Package blocklength updated to version 0.2.0 with previous version 0.1.5 dated 2022-03-02

Title: Select an Optimal Block-Length to Bootstrap Dependent Data (Block Bootstrap)
Description: A set of functions to select the optimal block-length for a dependent bootstrap (block-bootstrap). Includes the Hall, Horowitz, and Jing (1995) <doi:10.1093/biomet/82.3.561> subsampling-based cross-validation method, the Politis and White (2004) <doi:10.1081/ETC-120028836> Spectral Density Plug-in method, including the Patton, Politis, and White (2009) <doi:10.1080/07474930802459016> correction, and the Lahiri, Furukawa, and Lee (2007) <doi:10.1016/j.stamet.2006.08.002> nonparametric plug-in method, with a corresponding set of S3 plot methods.
Author: Alec Stashevsky [aut, cre] , Sergio Armella [ctb]
Maintainer: Alec Stashevsky <alec@alecstashevsky.com>

Diff between blocklength versions 0.1.5 dated 2022-03-02 and 0.2.0 dated 2025-02-17

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Package BaseSet updated to version 1.0.0 with previous version 0.9.0 dated 2023-08-22

Title: Working with Sets the Tidy Way
Description: Implements a class and methods to work with sets, doing intersection, union, complementary sets, power sets, cartesian product and other set operations in a "tidy" way. These set operations are available for both classical sets and fuzzy sets. Import sets from several formats or from other several data structures.
Author: Lluis Revilla Sancho [aut, cre, cph] , Zebulun Arendsee [rev], Jennifer Chang [rev]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>

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Package sgboost updated to version 0.2.0 with previous version 0.1.3 dated 2024-05-19

Title: Sparse-Group Boosting
Description: Sparse-group boosting to be used in conjunction with the 'mboost' for modeling grouped data. Applicable to all sparse-group lasso type problems where within-group and between-group sparsity is desired. Interprets and visualizes individual variables and groups.
Author: Fabian Obster [aut, cre, cph]
Maintainer: Fabian Obster <fabian.obster@unibw.de>

Diff between sgboost versions 0.1.3 dated 2024-05-19 and 0.2.0 dated 2025-02-17

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Package NNS updated to version 11.1 with previous version 11.0 dated 2025-01-10

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: 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>

Diff between NNS versions 11.0 dated 2025-01-10 and 11.1 dated 2025-02-17

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Permanent link

Package MLE updated to version 1.4 with previous version 1.3 dated 2024-12-16

Title: Maximum Likelihood Estimation of Various Univariate and Multivariate Distributions
Description: Several functions for maximum likelihood estimation of various univariate and multivariate distributions. The list includes more than 100 functions for univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.
Author: Michail Tsagris [aut, cre], Sofia Piperaki [aut], Muhammad Imran [ctb], Rafail Vargiakakis [aut], Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

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Package cgam updated to version 1.22 with previous version 1.21 dated 2023-08-10

Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut], Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>

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Package readsparse updated to version 0.1.5-8 with previous version 0.1.5-6 dated 2023-11-27

Title: Read and Write Sparse Matrices in 'SVMLight' and 'LibSVM' Formats
Description: Read and write labelled sparse matrices in text format as used by software such as 'SVMLight', 'LibSVM', 'ThunderSVM', 'LibFM', 'xLearn', 'XGBoost', 'LightGBM', and others. Supports labelled data for regression, classification (binary, multi-class, multi-label), and ranking (with 'qid' field), and can handle header metadata and comments in files.
Author: David Cortes [aut, cre, cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

Diff between readsparse versions 0.1.5-6 dated 2023-11-27 and 0.1.5-8 dated 2025-02-17

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Package ProtE updated to version 1.0.2 with previous version 1.0.1 dated 2025-01-15

Title: Processing Proteomics Data, Statistical Analysis and Visualization
Description: The 'Proteomics Eye' ('ProtE') offers a comprehensive and intuitive framework for the univariate analysis of label-free proteomics data. By integrating essential data wrangling and processing steps into a single function, 'ProtE' streamlines pairwise statistical comparisons for categorical variables. It provides quality checks and generates publication-ready visualizations, enabling efficient and robust data analysis. 'ProtE' is compatible with proteomics data outputs from 'MaxQuant' (Cox & Mann, (2008) <doi:10.1038/nbt.1511>), 'DIA-NN' (Demichev et al., (2020) <doi:10.1038/s41592-019-0638-x>), and 'Proteome Discoverer' (Thermo Fisher Scientific, version 2.5). The package leverages 'ggplot2' for visualization (Wickham, (2016) <doi:10.1007/978-3-319-24277-4>) and 'limma' for statistical analysis (Ritchie et al., (2015) <doi:10.1093/nar/gkv007>).
Author: Theodoros Margelos [aut, cre, cph], Rafael Stroggilos [ctb, cph]
Maintainer: Theodoros Margelos <ted.margelos02@gmail.com>

Diff between ProtE versions 1.0.1 dated 2025-01-15 and 1.0.2 dated 2025-02-17

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New package nimbleAPT with initial version 1.0.7
Package: nimbleAPT
Title: Adaptive Parallel Tempering for 'NIMBLE'
Version: 1.0.7
Encoding: UTF-8
Date: 2025-02-17
Maintainer: David Pleydell <david.pleydell@inrae.fr>
URL: https://github.com/DRJP/nimbleAPT
Description: Functions for adaptive parallel tempering (APT) with NIMBLE models. Adapted from 'Lacki' & 'Miasojedow' (2016) <DOI:10.1007/s11222-015-9579-0> and 'Miasojedow, Moulines and Vihola' (2013) <DOI:10.1080/10618600.2013.778779>.
License: BSD_3_clause + file LICENSE
Copyright: See COPYRIGHTS file.
Depends: R (>= 3.1.2), nimble
Imports: methods
Suggests: knitr, rmarkdown, coda
VignetteBuilder: knitr
Note: The APT samplers within this package were adapted from MCMC samplers provided in the NIMBLE package (https://github.com/nimble-dev/nimble) and developed by the cited members of the NIMBLE Development Team. The adaptations for APT included in this package were the work of the package developer. Many thanks to the NIMBLE Development Team for their support during the development of this package.
NeedsCompilation: no
Packaged: 2025-02-17 11:08:02 UTC; pleydell
Author: David Pleydell [aut, cre, cph] , Daniel Turek [cph] , Perry de Valpine [cph] , Christopher Paciorek [cph] , Nick Michaud [cph]
Repository: CRAN
Date/Publication: 2025-02-17 13:10:02 UTC

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New package UAHDataScienceUC with initial version 1.0.0
Package: UAHDataScienceUC
Title: Learn Clustering Techniques Through Examples and Code
Version: 1.0.0
Description: A comprehensive educational package combining clustering algorithms with detailed step-by-step explanations. Provides implementations of both traditional (hierarchical, k-means) and modern (DBSCAN, GMM, genetic k-means) clustering methods as described in Ezugwu et. al., (2022) <doi:10.1016/j.engappai.2022.104743>. Includes educational datasets highlighting different clustering challenges, based on 'scikit-learn' examples (Pedregosa et al., 2011) <https://jmlr.csail.mit.edu/papers/v12/pedregosa11a.html>. Features detailed algorithm explanations, visualizations, and weighted distance calculations for enhanced learning.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.3.0)
Imports: proxy (>= 0.4-27), cli (>= 3.6.1)
Suggests: deldir (>= 1.0-9), knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2025-02-14 18:35:25 UTC; andriy
Author: Eduardo Ruiz Sabajanes [aut], Roberto Alcantara [aut], Juan Jose Cuadrado Gallego [aut] , Andriy Protsak Protsak [aut, cre], Universidad de Alcala [cph]
Maintainer: Andriy Protsak Protsak <andriy.protsak@edu.uah.es>
Repository: CRAN
Date/Publication: 2025-02-17 12:20:02 UTC

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Package pxmake updated to version 0.15.1 with previous version 0.14.2 dated 2025-01-22

Title: Make PX-Files in R
Description: Create PX-files from scratch or read and modify existing ones. Includes a function for every PX keyword, making metadata manipulation simple and human-readable.
Author: Johan Ejstrud [cre, aut], Lars Pedersen [aut], Statistics Greenland [cph]
Maintainer: Johan Ejstrud <johan@ejstrud.com>

Diff between pxmake versions 0.14.2 dated 2025-01-22 and 0.15.1 dated 2025-02-17

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Package OPL updated to version 1.0.1 with previous version 1.0.0 dated 2025-02-03

Title: Optimal Policy Learning
Description: Provides functions for optimal policy learning in socioeconomic applications helping users to learn the most effective policies based on data in order to maximize empirical welfare. Specifically, 'OPL' allows to find "treatment assignment rules" that maximize the overall welfare, defined as the sum of the policy effects estimated over all the policy beneficiaries. Documentation about 'OPL' is provided by several international articles via Athey et al (2021, <doi:10.3982/ECTA15732>), Kitagawa et al (2018, <doi:10.3982/ECTA13288>), Cerulli (2022, <doi:10.1080/13504851.2022.2032577>), the paper by Cerulli (2021, <doi:10.1080/13504851.2020.1820939>) and the book by Gareth et al (2013, <doi:10.1007/978-1-4614-7138-7>).
Author: Federico Brogi [aut, cre], Barbara Guardabascio [aut], Giovanni Cerulli [aut]
Maintainer: Federico Brogi <federicobrogi@gmail.com>

Diff between OPL versions 1.0.0 dated 2025-02-03 and 1.0.1 dated 2025-02-17

 DESCRIPTION  |    8 -
 MD5          |    4 
 R/opl_lc_c.R |  400 +++++++++++++++++++++++++++++------------------------------
 3 files changed, 206 insertions(+), 206 deletions(-)

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New package MissCP with initial version 0.1.1
Package: MissCP
Title: Change Point Detection with Missing Values
Version: 0.1.1
Author: Yanxi Liu [aut, cre], Abolfazl Safikhani [aut]
Maintainer: Yanxi Liu <liuyanxi@ufl.edu>
Description: A four step change point detection method that can detect break points with the presence of missing values proposed by Liu and Safikhani (2023) <https://drive.google.com/file/d/1a8sV3RJ8VofLWikTDTQ7W4XJ76cEj4Fg/view?usp=drive_link>.
License: GPL-2
Encoding: UTF-8
Imports: stats, graphics, mvtnorm, factoextra, Rcpp, ggplot2, glmnet
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-02-17 11:48:51 UTC; yanxiliu
Repository: CRAN
Date/Publication: 2025-02-17 12:30:07 UTC

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New package fishstat with initial version 2024.1.0.1
Package: fishstat
Version: 2024.1.0.1
Date: 2025-02-14
Title: Global Fishery and Aquaculture Statistics
Depends: R (>= 3.5.0)
Suggests: areaplot
LazyData: yes
Description: The Food and Agriculture Organization of the United Nations (FAO) FishStat database is the leading source of global fishery and aquaculture statistics and provides unique information for sector analysis and monitoring. This package provides the global production data from all fisheries and aquaculture in R format, ready for analysis.
License: CC BY-NC-SA 4.0
URL: https://www.fao.org/fishery/en/fishstat, https://github.com/sofia-taf/fishstat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-02-14 07:13:54 UTC; arnim
Author: Arni Magnusson [aut, cre], Rishi Sharma [aut], FAO [cph]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-17 12:50:02 UTC

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New package chatRater with initial version 1.0.0
Package: chatRater
Title: Rating Text Using Large Language Models
Version: 1.0.0
Date: 2025-02-14
Maintainer: Shiyang Zheng <Shiyang.Zheng@nottingham.ac.uk>
Description: Generates ratings for textual stimuli using large language models. It allows users to evaluate idioms and similar texts by combining context, prompts, and stimulus inputs. The package supports both 'OpenAI' and 'DeepSeek' APIs by enabling users to switch models simply by specifying the model parameter. It implements methods for constructing the request payload and parsing numeric ratings from the model outputs.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: tidyverse, openai, httr, jsonlite
Suggests: testthat
NeedsCompilation: no
Packaged: 2025-02-14 16:08:28 UTC; admin
Author: Shiyang Zheng [aut, cre]
Repository: CRAN
Date/Publication: 2025-02-17 12:10:01 UTC

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New package UAHDataScienceSC with initial version 1.0.0
Package: UAHDataScienceSC
Title: Learn Supervised Classification Methods Through Examples and Code
Version: 1.0.0
Description: Supervised classification methods, which (if asked) can provide step-by-step explanations of the algorithms used, as described in PK Josephine et. al., (2021) <doi:10.59176/kjcs.v1i1.1259>; and datasets to test them on, which highlight the strengths and weaknesses of each technique.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.3.0)
Imports: cli (>= 3.6.1)
Suggests: knitr, rmarkdown
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2025-02-14 15:13:26 UTC; andriy
Author: Victor Amador Padilla [aut], Juan Jose Cuadrado Gallego [ctb] , Andriy Protsak Protsak [aut, cre], Universidad de Alcala [cph]
Maintainer: Andriy Protsak Protsak <andriy.protsak@edu.uah.es>
Repository: CRAN
Date/Publication: 2025-02-17 12:00:09 UTC

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New package simqi with initial version 0.1.0
Package: simqi
Title: Simulate Quantities of Interest from Regression Models
Version: 0.1.0
Depends: R (>= 3.5.0)
Maintainer: Steve Miller <steve@svmiller.com>
Description: This is an all-encompassing suite to facilitate the simulation of so-called quantities of interest by way of a multivariate normal distribution of the regression model's coefficients and variance-covariance matrix.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: stevemisc, tibble, methods
NeedsCompilation: no
Packaged: 2025-02-14 14:48:22 UTC; steve
Author: Steve Miller [aut, cre]
Repository: CRAN
Date/Publication: 2025-02-17 12:00:02 UTC

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Package Rrepest updated to version 1.5.3 with previous version 1.5.2 dated 2025-02-10

Title: An Analyzer of International Large Scale Assessments in Education
Description: An easy way to analyze international large-scale assessments and surveys in education or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) while also allowing for analysis with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre], Francesco Avvisati [aut], Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>

Diff between Rrepest versions 1.5.2 dated 2025-02-10 and 1.5.3 dated 2025-02-17

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 NAMESPACE               |    1 +
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 R/coverage_daggers.R    |only
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 7 files changed, 63 insertions(+), 30 deletions(-)

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New package rpcss with initial version 0.1.0
Package: rpcss
Title: Constitution of Core Collections by Principal Component Scoring Strategy
Version: 0.1.0
Description: Generate a Core Collection with Principal Component Scoring Strategy (PCSS) using qualitative and/or quantitative trait data according to Hamon and Noirot (1990) <https://www.documentation.ird.fr/hor/fdi:36506>, Noirot et al. (1996) <doi:10.2307/2527837> and Noirot et al. (2003) <https://www.documentation.ird.fr/hor/fdi:010031886>.
License: GPL-2 | GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
BuildManual: TRUE
Imports: dplyr, FactoMineR, ggplot2, ggrepel, gslnls, mathjaxr, methods, Rdpack, stats, tidyr, utils
Suggests: EvaluateCore, factoextra, knitr, rmarkdown, pander
Copyright: 2024-2025, ICAR-NBPGR
URL: https://github.com/aravind-j/rpcss, https://aravind-j.github.io/rpcss/
BugReports: https://github.com/aravind-j/rpcss/issues
NeedsCompilation: no
Packaged: 2025-02-14 04:37:22 UTC; Aravind-DGC
Author: J. Aravind [aut, cre] , ICAR-NBGPR [cph]
Maintainer: J. Aravind <j.aravind@icar.gov.in>
Repository: CRAN
Date/Publication: 2025-02-17 11:50:02 UTC

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New package indexr with initial version 0.2.2
Package: indexr
Title: A Thoughtful Saver of Results
Version: 0.2.2
Date: 2025-02-14
Description: Helps with the thoughtful saving, reading, and management of result files (using 'rds' files). The core functions take a list of parameters that are used to generate a unique hash to save results under. Then, the same parameter list can be used to read those results back in. This is helpful to avoid clunky file naming when running a large number of simulations. Additionally, helper functions are available for compiling a flat file of parameters of saved results, monitoring result usage, and cleaning up unwanted or unused results. For more information, visit the 'indexr' homepage <https://lharris421.github.io/indexr/>.
BugReports: https://github.com/lharris421/indexr/issues
License: GPL-3
URL: https://lharris421.github.io/indexr/, https://github.com/lharris421/indexr
Encoding: UTF-8
Imports: stringr, readr, dplyr, digest, glue, methods
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-02-14 15:01:45 UTC; loganharris
Author: Logan Harris [aut, cre]
Maintainer: Logan Harris <logan-harris@uiowa.edu>
Repository: CRAN
Date/Publication: 2025-02-17 12:00:05 UTC

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New package flint with initial version 0.0.1
Package: flint
Version: 0.0.1
VersionNote: sync configure.ac
Date: 2025-02-14
Title: Fast Library for Number Theory
Description: An R interface to 'FLINT' <https://flintlib.org/>, a C library for number theory. 'FLINT' extends GNU 'MP' <https://gmplib.org/> and GNU 'MPFR' <https://www.mpfr.org/> with support for arithmetic in standard rings (the integers, the integers modulo n, the rational, p-adic, real, and complex numbers) as well as vectors, matrices, polynomials, and power series over rings. 'FLINT' implements midpoint-radius interval arithmetic, also known as ball arithmetic, in the real and complex numbers, enabling computation in arbitrary precision with rigorous propagation of errors; see Johansson (2017) <doi:10.1109/TC.2017.2690633>. Finally, 'FLINT' provides ball arithmetic implementations of many special mathematical functions, with high coverage of reference works such as the NIST Digital Library of Mathematical Functions <https://dlmf.nist.gov/>. The R interface defines S4 classes, generic functions, and methods for representation and basic operations as well as p [...truncated...]
License: GPL (>= 2)
URL: https://github.com/jaganmn/flint
BugReports: https://github.com/jaganmn/flint/issues
Depends: R (>= 4.3), methods
Imports: stats
SystemRequirements: gmp, mpfr (>= 3.1), flint (>= 3)
SystemRequirementsNote: purely informational as we use configure tests
NeedsCompilation: yes
Packaged: 2025-02-13 22:34:03 UTC; mikael
Author: Mikael Jagan [aut, cre]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Repository: CRAN
Date/Publication: 2025-02-17 11:30:03 UTC

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New package changepointGA with initial version 0.1.0
Package: changepointGA
Title: Changepoint Detection via Modified Genetic Algorithm
Version: 0.1.0
Date: 2025-01-21
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...]
License: MIT + file LICENSE
Depends: R (>= 4.3.0)
Imports: foreach, doParallel, Rcpp, RcppArmadillo, clue, stats
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/mli171/changepointGA
BugReports: https://github.com/mli171/changepointGA/issues
Suggests: knitr, rmarkdown
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-02-13 21:49:58 UTC; mo
Author: Mo Li [aut, cre]
Maintainer: Mo Li <mo.li@louisiana.edu>
Repository: CRAN
Date/Publication: 2025-02-17 11:30:16 UTC

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New package BigDataPE with initial version 0.0.95
Package: BigDataPE
Title: Secure and Intuitive Access to 'BigDataPE' 'API' Datasets
Version: 0.0.95
Date: 2025-02-13
Description: Designed to simplify the process of retrieving datasets from the 'Big Data PE' platform using secure token-based authentication. It provides functions for securely storing, retrieving, and managing tokens associated with specific datasets, as well as fetching and processing data using the 'httr2' package.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: dplyr, tibble, httr2
URL: <https://github.com/StrategicProjects/bigdatape>
NeedsCompilation: no
Packaged: 2025-02-14 13:36:49 UTC; leite
Author: Andre Leite [aut, cre], Hugo Vaconcelos [aut], Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Repository: CRAN
Date/Publication: 2025-02-17 12:00:12 UTC

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New package BaHZING with initial version 1.0.0
Package: BaHZING
Title: Bayesian Hierarchical Zero-Inflated Negative Binomial Regression with G-Computation
Version: 1.0.0
Description: A Bayesian model for examining the association between environmental mixtures and all Taxa measured in a hierarchical microbiome dataset in a single integrated analysis. Compared with analyzing the associations of environmental mixtures with each Taxa individually, 'BaHZING' controls Type 1 error rates and provides more stable effect estimates when dealing with small sample sizes.
License: GPL (>= 3)
Depends: R (>= 4.1.0), rjags (>= 4.0.0)
Imports: bayestestR, dplyr, magrittr, phyloseq, pscl, R2jags, stats, stringr, tidyr
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
SystemRequirements: JAGS 4.x.y (http://mcmc-jags.sourceforge.net)
NeedsCompilation: no
Packaged: 2025-02-13 20:53:48 UTC; jagoodri
Author: Hailey Hampson [aut], Jesse Goodrich [aut, cre] , Hongxu Wang [aut], Tanya Alderete [ctb], Shardul Nazirkar [ctb], David Conti [aut]
Maintainer: Jesse Goodrich <jagoodri@usc.edu>
Repository: CRAN
Date/Publication: 2025-02-17 11:20:07 UTC

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New package polykde with initial version 1.0.0
Package: polykde
Title: Polyspherical Kernel Density Estimation
Version: 1.0.0
Date: 2025-02-13
Description: Kernel density estimation on the polysphere, hypersphere, and circle. Includes functions for density estimation, regression estimation, ridge estimation, bandwidth selection, kernels, samplers, and homogeneity tests. Companion package to García-Portugués and Meilán-Vila (2024) <doi:10.48550/arXiv.2411.04166> and García-Portugués and Meilán-Vila (2023) <doi:10.1007/978-3-031-32729-2_4>.
License: GPL-3
Imports: abind, doFuture, foreach, future, gsl, movMF, progressr, Rcpp (>= 1.0.8.3), RcppProgress, rotasym, sphunif
Suggests: alphashape3d, DirStats, FixedPoint, ks, manipulate, numDeriv, optimParallel, testthat, viridis, rgl, scatterplot3d, sdetorus, smacof
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
URL: https://github.com/egarpor/polykde
BugReports: https://github.com/egarpor/polykde/issues
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-02-13 19:14:03 UTC; Eduardo
Author: Eduardo Garcia-Portugues [aut, cre] , Andrea Meilan-Vila [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Repository: CRAN
Date/Publication: 2025-02-17 11:00:01 UTC

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2018-05-30 0.1.0

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2013-03-02 1.1.0
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2025-01-27 0.2.1
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2021-11-17 1.1.0
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2015-08-01 0.1-4
2015-07-11 0.1-3
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Package pathfindR updated to version 2.4.2 with previous version 2.4.1 dated 2024-05-04

Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. 'pathfindR' also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in 'pathfindR' are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR [...truncated...]
Author: Ege Ulgen [cre, cph] , Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>

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Package gdverse updated to version 1.3-2 with previous version 1.3-1 dated 2024-12-14

Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial stratified heterogeneity, while also taking into account local spatial dependencies, spatial interpretability, complex spatial interactions, and robust spatial stratification. Additionally, it supports the spatial stratified heterogeneity family established in academic literature.
Author: Wenbo Lv [aut, cre, cph] , Yangyang Lei [aut] , Fangmei Liu [aut] , Jianwu Yan [aut] , Yongze Song [aut] , Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>

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Package survivalSL updated to version 0.97.1 with previous version 0.97 dated 2025-01-29

Title: Super Learner for Survival Prediction from Censored Data
Description: Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.
Author: Yohann Foucher [aut, cre] , Camille Sabathe [aut]
Maintainer: Yohann Foucher <yohann.foucher@univ-poitiers.fr>

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Package rstanemax updated to version 0.1.9 with previous version 0.1.8 dated 2025-02-05

Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] , Danielle Navarro [aut] , Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>

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Package FLORAL updated to version 0.4.0 with previous version 0.3.0 dated 2024-08-20

Title: Fit Log-Ratio Lasso Regression for Compositional Data
Description: Log-ratio Lasso regression for continuous, binary, and survival outcomes with (longitudinal) compositional features. See Fei and others (2024) <doi:10.1016/j.crmeth.2024.100899>.
Author: Teng Fei [aut, cre, cph] , Tyler Funnell [aut] , Nicholas Waters [aut] , Sandeep Raj [aut]
Maintainer: Teng Fei <feit1@mskcc.org>

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Package nlmixr2extra updated to version 3.0.2 with previous version 3.0.1 dated 2024-10-29

Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for support functions like preconditioned fits <doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate selection.
Author: Matthew Fidler [aut, cre] , Vipul Mann [aut], Vishal Sarsani [aut] , Christian Bartels [ctb], Bill Denney [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>

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Sun, 16 Feb 2025

Package waywiser updated to version 0.6.1 with previous version 0.6.0 dated 2024-06-27

Title: Ergonomic Methods for Assessing Spatial Models
Description: Assessing predictive models of spatial data can be challenging, both because these models are typically built for extrapolating outside the original region represented by training data and due to potential spatially structured errors, with "hot spots" of higher than expected error clustered geographically due to spatial structure in the underlying data. Methods are provided for assessing models fit to spatial data, including approaches for measuring the spatial structure of model errors, assessing model predictions at multiple spatial scales, and evaluating where predictions can be made safely. Methods are particularly useful for models fit using the 'tidymodels' framework. Methods include Moran's I ('Moran' (1950) <doi:10.2307/2332142>), Geary's C ('Geary' (1954) <doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995) <doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from 'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement m [...truncated...]
Author: Michael Mahoney [aut, cre] , Lucas Johnson [ctb] , Virgilio Gomez-Rubio [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/571>), Jakub Nowosad [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/571 [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>

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Package EFAfactors updated to version 1.2.1 with previous version 1.2.0 dated 2025-01-07

Title: Determining the Number of Factors in Exploratory Factor Analysis
Description: Provides a collection of standard factor retention methods in Exploratory Factor Analysis (EFA), making it easier to determine the number of factors. Traditional methods such as the scree plot by Cattell (1966) <doi:10.1207/s15327906mbr0102_10>, Kaiser-Guttman Criterion (KGC) by Guttman (1954) <doi:10.1007/BF02289162> and Kaiser (1960) <doi:10.1177/001316446002000116>, and flexible Parallel Analysis (PA) by Horn (1965) <doi:10.1007/BF02289447> based on eigenvalues form PCA or EFA are readily available. This package also implements several newer methods, such as the Empirical Kaiser Criterion (EKC) by Braeken and van Assen (2017) <doi:10.1037/met0000074>, Comparison Data (CD) by Ruscio and Roche (2012) <doi:10.1037/a0025697>, and Hull method by Lorenzo-Seva et al. (2011) <doi:10.1080/00273171.2011.564527>, as well as some AI-based methods like Comparison Data Forest (CDF) by Goretzko and Ruscio (2024) <doi:10.3758/s13428-023-02122-4> and F [...truncated...]
Author: Haijiang Qin [aut, cre, cph] , Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>

Diff between EFAfactors versions 1.2.0 dated 2025-01-07 and 1.2.1 dated 2025-02-16

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Package rsparse updated to version 0.5.3 with previous version 0.5.2 dated 2024-06-28

Title: Statistical Learning on Sparse Matrices
Description: Implements many algorithms for statistical learning on sparse matrices - matrix factorizations, matrix completion, elastic net regressions, factorization machines. Also 'rsparse' enhances 'Matrix' package by providing methods for multithreaded <sparse, dense> matrix products and native slicing of the sparse matrices in Compressed Sparse Row (CSR) format. List of the algorithms for regression problems: 1) Elastic Net regression via Follow The Proximally-Regularized Leader (FTRL) Stochastic Gradient Descent (SGD), as per McMahan et al(, <doi:10.1145/2487575.2488200>) 2) Factorization Machines via SGD, as per Rendle (2010, <doi:10.1109/ICDM.2010.127>) List of algorithms for matrix factorization and matrix completion: 1) Weighted Regularized Matrix Factorization (WRMF) via Alternating Least Squares (ALS) - paper by Hu, Koren, Volinsky (2008, <doi:10.1109/ICDM.2008.22>) 2) Maximum-Margin Matrix Factorization via ALS, paper by Rennie, Srebro (2005, <doi:10.1145/110 [...truncated...]
Author: Dmitriy Selivanov [aut, cre, cph] , David Cortes [ctb], Drew Schmidt [ctb] , Wei-Chen Chen [ctb]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>

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Package pqrBayes updated to version 1.1.0 with previous version 1.0.5 dated 2025-02-05

Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing sparse priors to impose exact sparsity leads to efficient Bayesian shrinkage estimation, variable selection and statistical inference. In this package, we have implemented robust Bayesian variable selection with spike-and-slab priors under high-dimensional linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular, valid robust Bayesian inferences under both models in the presence of heavy-tailed errors can be validated on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms of the proposed and alternative models are implemented in C++.
Author: Kun Fan [aut], Cen Wu [aut, cre], Jie Ren [aut], Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>

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Package modEvA updated to version 3.29 with previous version 3.23 dated 2024-11-24

Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre], Jennifer A. Brown [aut], Alberto Jimenez-Valverde [aut], Raimundo Real [aut], Oswald van Ginkel [ctb], Jurica Levatic [ctb], Victoria Formoso-Freire [ctb], Andres Baselga [ctb], Carola Gomez-Rodriguez [ctb], Jose Carlos [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>

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Package mappeR updated to version 2.0.0 with previous version 1.3.0 dated 2024-10-30

Title: Construct and Visualize TDA Mapper Graphs
Description: Topological data analysis (TDA) is a method of data analysis that uses techniques from topology to analyze high-dimensional data. Here we implement Mapper, an algorithm from this area developed by Singh, Mémoli and Carlsson (2007) which generalizes the concept of a Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.
Author: George Clare Kennedy [aut, cre]
Maintainer: George Clare Kennedy <george-clarekennedy@uiowa.edu>

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Package jmvReadWrite updated to version 0.4.10 with previous version 0.4.9 dated 2025-01-16

Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi' (<https://www.jamovi.org>) aims to make statistical analyses easy and intuitive. 'jamovi' produces syntax that can directly be used in R (in connection with the R-package 'jmv'). Having import / export routines for the data files 'jamovi' produces ('.omv') permits an easy transfer of data and analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre, cph]
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>

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Package CCAMLRGIS updated to version 4.2.1 with previous version 4.2.0 dated 2024-10-15

Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant to the activities of the Commission for the Conservation of Antarctic Marine Living Resources. Provides two categories of functions: load functions and create functions. Load functions are used to import existing spatial layers from the online CCAMLR GIS such as the ASD boundaries. Create functions are used to create layers from user data such as polygons and grids.
Author: Stephane Thanassekos [aut, cre], Keith Reid [aut], Lucy Robinson [aut], Michael D. Sumner [ctb], Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <stephane.thanassekos@ccamlr.org>

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Package assessor updated to version 1.1.1 with previous version 1.1.0 dated 2024-04-03

Title: Assessment Tools for Regression Models with Discrete and Semicontinuous Outcomes
Description: Provides assessment tools for regression models with discrete and semicontinuous outcomes proposed in Yang (2023) <doi:10.48550/arXiv.2308.15596>. It calculates the double probability integral transform (DPIT) residuals, constructs QQ plots of residuals and the ordered curve for assessing mean structures.
Author: Lu Yang [aut], Jeonghwan Lee [cre, aut]
Maintainer: Jeonghwan Lee <lee03938@umn.edu>

Diff between assessor versions 1.1.0 dated 2024-04-03 and 1.1.1 dated 2025-02-16

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Package asremlPlus updated to version 4.4.46 with previous version 4.4.43 dated 2024-12-10

Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>

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Package PhenotypeR updated to version 0.1.3 with previous version 0.1.2 dated 2025-02-05

Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model. Diagnostics are run at the database, code list, cohort, and population level to assess whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] , Marti Catala [aut] , Xihang Chen [aut] , Marta Alcalde-Herraiz [aut] , Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>

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Package nanonext updated to version 1.5.1 with previous version 1.5.0 dated 2025-01-27

Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library for reliable, high-performance messaging over in-process, IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and service discovery. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing. Intuitive 'aio' objects resolve automatically when asynchronous operations complete, and synchronisation primitives allow R to wait upon events signalled by concurrent threads.
Author: Charlie Gao [aut, cre] , Hibiki AI Limited [cph], R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>

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Package rjaf updated to version 0.1.2 with previous version 0.1.1 dated 2024-12-08

Title: Regularized Joint Assignment Forest with Treatment Arm Clustering
Description: Personalized assignment to one of many treatment arms via regularized and clustered joint assignment forests as described in Ladhania, Spiess, Ungar, and Wu (2023) <doi:10.48550/arXiv.2311.00577>. The algorithm pools information across treatment arms: it considers a regularized forest-based assignment algorithm based on greedy recursive partitioning that shrinks effect estimates across arms; and it incorporates a clustering scheme that combines treatment arms with consistently similar outcomes.
Author: Wenbo Wu [aut, cph] , Xinyi Zhang [aut, cre, cph] , Jann Spiess [aut, cph] , Rahul Ladhania [aut, cph]
Maintainer: Xinyi Zhang <zhang.xinyi@nyu.edu>

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Package urlshorteneR updated to version 1.6.0 with previous version 1.5.7 dated 2022-08-22

Title: R Wrapper for the 'Bit.ly' and 'Is.gd'/'v.gd' URL Shortening Services
Description: Allows using two URL shortening services, which also provide expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth 2.0) and 'is.gd' (no API key).
Author: John Malc [aut, cre] , Andrea Dodet [ctb] , Stephen Synchronicity [ctb]
Maintainer: John Malc <cincenko@outlook.com>

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Package subincomeR updated to version 0.3.0 with previous version 0.2.2 dated 2024-12-19

Title: Access to Global Sub-National Income Data
Description: Provides access to granular sub-national income data from the MCC-PIK Database Of Sub-national Economic Output (DOSE). The package downloads and processes the data from its open repository on 'Zenodo' (<https://zenodo.org/records/13773040>). Functions are provided to fetch data at multiple geographic levels, match coordinates to administrative regions, and access associated geometries.
Author: Pablo Garcia Guzman [aut, cre, cph]
Maintainer: Pablo Garcia Guzman <garciagp@ebrd.com>

Diff between subincomeR versions 0.2.2 dated 2024-12-19 and 0.3.0 dated 2025-02-16

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Package CohortConstructor updated to version 0.3.5 with previous version 0.3.4 dated 2025-01-17

Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] , Marti Catala [aut] , Nuria Mercade-Besora [aut] , Marta Alcalde-Herraiz [aut] , Mike Du [aut] , Yuchen Guo [aut] , Xihang Chen [aut] , Kim Lopez-Guell [aut] , Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>

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Package nda updated to version 0.2.4 with previous version 0.1.15 dated 2024-10-14

Title: Generalized Network-Based Dimensionality Reduction and Analysis
Description: Non-parametric dimensionality reduction function. Reduction with and without feature selection. Plot functions. Automated feature selections. Kosztyan et. al. (2024) <doi:10.1016/j.eswa.2023.121779>.
Author: Zsolt T. Kosztyan [aut, cre], Marcell T. Kurbucz [aut], Attila I. Katona [aut], Zahid Khan [aut]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>

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Package gibasa updated to version 1.1.2 with previous version 1.1.1 dated 2024-07-05

Title: An Alternative 'Rcpp' Wrapper of 'MeCab'
Description: A plain 'Rcpp' wrapper for 'MeCab' that can segment Chinese, Japanese, and Korean text into tokens. The main goal of this package is to provide an alternative to 'tidytext' using morphological analysis.
Author: Akiru Kato [aut, cre], Shogo Ichinose [aut], Taku Kudo [aut], Jorge Nocedal [ctb], Nippon Telegraph and Telephone Corporation [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>

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Package ColombiAPI updated to version 0.1.1 with previous version 0.1.0 dated 2025-01-09

Title: Access Colombia's Public Data via 'API-Colombia'
Description: Provides a seamless interface to access diverse public data about Colombia through the 'API-Colombia', a RESTful API. The package enables users to explore various aspects of Colombia, including general information, geography, and cultural insights. It includes five API-related functions to retrieve data on topics such as Colombia's general information, airports, departments, regions, and presidents. Additionally, 'ColombiAPI' offers a built-in function to view the datasets available within the package. The package also includes curated datasets covering Bogota air stations, business and holiday dates, public schools, Colombian coffee exports, cannabis licenses, Medellin rainfall, and malls in Bogota, making it a comprehensive tool for exploring Colombia's data. For more details on the 'API-Colombia', see <https://api-colombia.com/>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>

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Sat, 15 Feb 2025

Package divo updated to version 1.0.2 with previous version 1.0.1 dated 2019-12-16

Title: Tools for Analysis of Diversity and Similarity in Biological Systems
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in a population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
Author: Christoph Sadee [aut], Maciej Pietrzak [aut, cre], Michal Seweryn [aut], Cankun Wang [aut], Grzegorz Rempala [aut]
Maintainer: Maciej Pietrzak <pietrzak.20@osu.edu>

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Package fixr updated to version 0.2.0 with previous version 0.1.0 dated 2023-04-20

Title: Fixing Data Made Easy for Statistical Analysis
Description: A set of functions that facilitate basic data manipulation and cleaning for statistical analysis including functions for finding and fixing duplicate rows and columns, missing values, outliers, and special characters in column and row names and functions for checking data consistency, distribution, quality, reliability, and structure.
Author: Ambu Vijayan [aut, cre] , J. Sreekumar [aut]
Maintainer: Ambu Vijayan <ambuvjyn@gmail.com>

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Package aqp updated to version 2.2 with previous version 2.1.0 dated 2024-10-19

Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>

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 aqp-2.2/aqp/R/slab.R                                                    |    1 
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Package deBif updated to version 0.1.9 with previous version 0.1.8 dated 2023-12-04

Title: Bifurcation Analysis of Ordinary Differential Equation Systems
Description: Shiny application that performs bifurcation and phaseplane analysis of systems of ordinary differential equations. The package allows for computation of equilibrium curves as a function of a single free parameter, detection of transcritical, saddle-node and hopf bifurcation points along these curves, and computation of curves representing these transcritical, saddle-node and hopf bifurcation points as a function of two free parameters. The shiny-based GUI allows visualization of the results in both 2D- and 3D-plots. The implemented methods for solution localisation and curve continuation are based on the book "Elements of applied bifurcation theory" (Kuznetsov, Y. A., 1995; ISBN: 0-387-94418-4).
Author: Andre M. de Roos [aut, cre]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>

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Package TDAvec updated to version 0.1.4 with previous version 0.1.3 dated 2022-10-31

Title: Vector Summaries of Persistence Diagrams
Description: Provides tools for computing various vector summaries of persistence diagrams studied in Topological Data Analysis. For improved computational efficiency, all code for the vector summaries is written in 'C++' using the 'Rcpp' and 'RcppArmadillo' packages.
Author: Umar Islambekov [aut], Aleksei Luchinsky [aut, cre]
Maintainer: Aleksei Luchinsky <aluchi@bgsu.edu>

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Package openxlsx2 updated to version 1.13 with previous version 1.12 dated 2024-12-19

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 patterncausality updated to version 0.2.1 with previous version 0.2.0 dated 2025-01-09

Title: Pattern Causality Algorithm
Description: A comprehensive package for detecting and analyzing causal relationships in complex systems using pattern-based approaches. Key features include state space reconstruction, pattern identification, and causality strength evaluation.
Author: Stavros Stavroglou [aut] , Athanasios Pantelous [aut] , Hui Wang [aut, cre]
Maintainer: Hui Wang <huiw1128@gmail.com>

Diff between patterncausality versions 0.2.0 dated 2025-01-09 and 0.2.1 dated 2025-02-15

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Package sae.projection updated to version 0.1.1 with previous version 0.1.0 dated 2024-12-19

Title: Small Area Estimation Using Model-Assisted Projection Method
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Author: Ridson Al Farizal P [aut, cre, cph] , Azka Ubaidillah [aut] , Silvi Ajeng Larasati [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>

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Package rix updated to version 0.15.2 with previous version 0.14.4 dated 2025-01-21

Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] , Philipp Baumann [aut] , David Watkins [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/625>), Jacob Wujiciak-Jens [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>

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Package dtreg updated to version 1.1.1 with previous version 1.1.0 dated 2024-12-02

Title: Interact with Data Type Registries and Create Machine-Readable Data
Description: You can load a schema from a DTR (data type registry) as an R object. Use this schema to write your data in JSON-LD (JavaScript Object Notation for Linked Data) format to make it machine readable.
Author: Olga Lezhnina [aut, cre] , Manuel Prinz [aut] , Markus Stocker [aut] , Open Research Knowledge Graph Project and Contributors [cph]
Maintainer: Olga Lezhnina <olga.lezhnina@tib.eu>

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Package rolog updated to version 0.9.20 with previous version 0.9.18 dated 2024-07-09

Title: Query 'SWI'-'Prolog' from R
Description: This R package connects to SWI-Prolog, <https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to prolog (consult, query/submit, once, findall).
Author: Matthias Gondan [aut, com, cre] , European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>

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Package IceSat2R updated to version 1.0.7 with previous version 1.0.6 dated 2024-08-17

Title: ICESat-2 Altimeter Data using R
Description: Programmatic connection to the 'OpenAltimetry API' <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global Geolocated Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice Freeboard), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects altimetry data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice freeboard, and vegetation canopy height begu [...truncated...]
Author: Lampros Mouselimis [aut, cre] , OpenAltimetry.org [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

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Package flexsurvcure updated to version 1.3.3 with previous version 1.3.1 dated 2022-11-01

Title: Flexible Parametric Cure Models
Description: Flexible parametric mixture and non-mixture cure models for time-to-event data.
Author: Jordan Amdahl [aut, cre]
Maintainer: Jordan Amdahl <jrdnmdhl@gmail.com>

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Package MapperAlgo updated to version 1.0.2 with previous version 1.0.1 dated 2024-12-08

Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl], Paul Pearson [ctb], Daniel Muellner [ctb], Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>

Diff between MapperAlgo versions 1.0.1 dated 2024-12-08 and 1.0.2 dated 2025-02-15

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Package r2redux updated to version 1.0.18 with previous version 1.0.17 dated 2023-11-28

Title: R2 Statistic
Description: R2 statistic for significance test. Variance and covariance of R2 values used to assess the 95% CI and p-value of the R2 difference.
Author: Hong Lee [aut, cph], Moksedul Momin [aut, cre, cph]
Maintainer: Moksedul Momin <cvasu.momin@gmail.com>

Diff between r2redux versions 1.0.17 dated 2023-11-28 and 1.0.18 dated 2025-02-15

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Package oneinfl updated to version 1.0.1 with previous version 1.0.0 dated 2025-02-06

Title: Estimates OIPP and OIZTNB Regression Models
Description: Estimates one-inflated positive Poisson (OIPP) and one-inflated zero-truncated negative binomial (OIZTNB) regression models. A suite of ancillary statistical tools are also provided, including: estimation of positive Poisson (PP) and zero-truncated negative binomial (ZTNB) models; marginal effects and their standard errors; diagnostic likelihood ratio and Wald tests; plotting; predicted counts and expected responses; and random variate generation. The models and tools, as well as four applications, are shown in Godwin, R. T. (2024). "One-inflated zero-truncated count regression models" arXiv preprint <doi:10.48550/arXiv.2402.02272>.
Author: Ryan T. Godwin [aut, cre]
Maintainer: Ryan T. Godwin <ryan.godwin@umanitoba.ca>

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Fri, 14 Feb 2025

Package ife updated to version 0.1.12 with previous version 0.1.0 dated 2024-11-08

Title: Influence Function Based Estimate Objects
Description: Implements an S7 class for estimates based on influence functions. Standard arithmetic operations are defined for the class.
Author: Nicholas Williams [aut, cre, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>

Diff between ife versions 0.1.0 dated 2024-11-08 and 0.1.12 dated 2025-02-14

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Package R6 updated to version 2.6.1 with previous version 2.6.0 dated 2025-02-12

Title: Encapsulated Classes with Reference Semantics
Description: Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.
Author: Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Winston Chang <winston@posit.co>

Diff between R6 versions 2.6.0 dated 2025-02-12 and 2.6.1 dated 2025-02-14

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Package nlive updated to version 0.7.0 with previous version 0.6.0 dated 2024-05-26

Title: Automated Estimation of Sigmoidal and Piecewise Linear Mixed Models
Description: Estimation of relatively complex nonlinear mixed-effects models, including the Sigmoidal Mixed Model and the Piecewise Linear Mixed Model with abrupt or smooth transition, through a single intuitive line of code and with automated generation of starting values.
Author: Maude Wagner [aut, cre] , Ana W. Capuano [aut], Emmanuelle Comets [ctb]
Maintainer: Maude Wagner <maude_wagner@rush.edu>

Diff between nlive versions 0.6.0 dated 2024-05-26 and 0.7.0 dated 2025-02-14

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Package PhylogeneticEM updated to version 1.8.0 with previous version 1.7.0 dated 2024-01-31

Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on phylogenies. Some tools to handle equivalent shifts configurations are also available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
Author: Paul Bastide [aut, cre], Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>

Diff between PhylogeneticEM versions 1.7.0 dated 2024-01-31 and 1.8.0 dated 2025-02-14

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Package nhdplusTools updated to version 1.3.1 with previous version 1.3.0 dated 2024-12-18

Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] , Mike Johnson [aut] , Marc Weber [ctb] , Josh Erickson [ctb], Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>

Diff between nhdplusTools versions 1.3.0 dated 2024-12-18 and 1.3.1 dated 2025-02-14

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Package torch updated to version 0.14.2 with previous version 0.14.1 dated 2025-02-03

Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph], Javier Luraschi [aut], Dmitriy Selivanov [ctb], Athos Damiani [ctb], Christophe Regouby [ctb], Krzysztof Joachimiak [ctb], Hamada S. Badr [ctb], Sebastian Fischer [ctb], Maximilian Pichler [ctb], RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>

Diff between torch versions 0.14.1 dated 2025-02-03 and 0.14.2 dated 2025-02-14

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New package TransProR with initial version 1.0.2
Package: TransProR
Title: Analysis and Visualization of Multi-Omics Data
Version: 1.0.2
Maintainer: Dongyue Yu <yudongyue@mail.nankai.edu.cn>
Description: A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10. [...truncated...]
Imports: magrittr, stats, dplyr, rlang, tibble, sva, DESeq2, utils, edgeR, limma, ggplot2, ggVennDiagram, ggdensity, ggpubr, ggtree, hrbrthemes, grid, ggraph, tidygraph, tidyr, stringr, geomtextpath, ggalt, ggnewscale, ggtreeExtra, Hmisc, circlize, graphics, spiralize, ComplexHeatmap, grDevices
Suggests: prettydoc, knitr, rmarkdown
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/SSSYDYSSS/TransProRBook
BugReports: https://github.com/SSSYDYSSS/TransProR/issues
LazyData: true
Depends: R (>= 4.3.0)
NeedsCompilation: no
Packaged: 2025-02-14 16:18:34 UTC; Yu
Author: Dongyue Yu [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-02-14 23:00:10 UTC

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Package TapeS updated to version 0.13.3 with previous version 0.13.2 dated 2025-01-22

Title: Tree Taper Curves and Sorting Based on 'TapeR'
Description: Providing new german-wide 'TapeR' Models and functions for their evaluation. Included are the most common tree species in Germany (Norway spruce, Scots pine, European larch, Douglas fir, Silver fir as well as European beech, Common/Sessile oak and Red oak). Many other species are mapped to them so that 36 tree species / groups can be processed. Single trees are defined by species code, one or multiple diameters in arbitrary measuring height and tree height. The functions then provide information on diameters along the stem, bark thickness, height of diameters, volume of the total or parts of the trunk and total and component above-ground biomass. It is also possible to calculate assortments from the taper curves. Uncertainty information is provided for diameter, volume and component biomass estimation.
Author: Christian Vonderach [aut, cre], Edgar Kublin [aut], Gerald Kaendler [aut]
Maintainer: Christian Vonderach <christian.vonderach@forst.bwl.de>

Diff between TapeS versions 0.13.2 dated 2025-01-22 and 0.13.3 dated 2025-02-14

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Package solvebio updated to version 2.15.1 with previous version 2.15.0 dated 2024-08-16

Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API. SolveBio is a biomedical knowledge hub that enables life science organizations to collect and harmonize the complex, disparate "multi-omic" data essential for today's R&D and BI needs.
Author: Tobi Guennel [aut, cre]
Maintainer: Tobi Guennel <tobi.guennel@precisionformedicine.com>

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Package jobqueue updated to version 1.3.1 with previous version 1.3.0 dated 2025-02-13

Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method which can be called to terminate the background job. Also provides timeouts and other mechanisms for automatically terminating a background job. The result of the expression is available synchronously via $result or asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] , Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>

Diff between jobqueue versions 1.3.0 dated 2025-02-13 and 1.3.1 dated 2025-02-14

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Package bootStateSpace updated to version 1.0.2 with previous version 1.0.1 dated 2025-01-22

Title: Bootstrap for State Space Models
Description: Provides a streamlined and user-friendly framework for bootstrapping 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>

Diff between bootStateSpace versions 1.0.1 dated 2025-01-22 and 1.0.2 dated 2025-02-14

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Package BayesChange updated to version 1.1.1 with previous version 1.1.0 dated 2025-02-13

Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] , Riccardo Corradin [aut], Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>

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Package simStateSpace updated to version 1.2.9 with previous version 1.2.8 dated 2025-01-23

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 rKIN updated to version 1.0.3 with previous version 1.0.2 dated 2023-10-02

Title: (Kernel) Isotope Niche Estimation
Description: Applies methods used to estimate animal homerange, but instead of geospatial coordinates, we use isotopic coordinates. The estimation methods include: 1) 2-dimensional bivariate normal kernel utilization density estimator, 2) bivariate normal ellipse estimator, and 3) minimum convex polygon estimator, all applied to stable isotope data. Additionally, functions to determine niche area, polygon overlap between groups and levels (confidence contours) and plotting capabilities.
Author: Shannon E Albeke [aut, cre]
Maintainer: Shannon E Albeke <salbeke@uwyo.edu>

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Package censored updated to version 0.3.3 with previous version 0.3.2 dated 2024-06-11

Title: 'parsnip' Engines for Survival Models
Description: Engines for survival models from the 'parsnip' package. These include parametric models (e.g., Jackson (2016) <doi:10.18637/jss.v070.i08>), semi-parametric (e.g., Simon et al (2011) <doi:10.18637/jss.v039.i05>), and tree-based models (e.g., Buehlmann and Hothorn (2007) <doi:10.1214/07-STS242>).
Author: Emil Hvitfeldt [aut] , Hannah Frick [aut, cre] , Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>

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Package epm updated to version 1.1.4 with previous version 1.1.3 dated 2024-09-13

Title: EcoPhyloMapper
Description: Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.
Author: Pascal Title [aut, cre] , Donald Swiderski [aut], Miriam Zelditch [aut]
Maintainer: Pascal Title <pascal.title@stonybrook.edu>

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Package transltr updated to version 0.1.0 with previous version 0.0.1 dated 2025-01-24

Title: Support Many Languages in R
Description: An object model for source text and translations. Find and extract translatable strings. Provide translations and seamlessly retrieve them at runtime.
Author: Jean-Mathieu Potvin [aut, cre, cph], Jerome Lavoue [ctb, fnd, rev]
Maintainer: Jean-Mathieu Potvin <jeanmathieupotvin@ununoctium.dev>

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Package spant updated to version 3.2.0 with previous version 3.1.0 dated 2024-12-17

Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] , Yong Wang [ctb], John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

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Package rxode2 updated to version 3.0.4 with previous version 3.0.3 dated 2024-12-15

Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] , Wenping Wang [aut], Alan Hindmarsh [ctb], Arun Srinivasan [ctb], Awad H. Al-Mohy [ctb], Bill Denney [ctb] , Cleve Moler [ctb], David Cooley [ctb], Drew Schmidt [ctb], Ernst Hairer [ctb], Gabriel Staples [ctb], Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>

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Package overturemapsr updated to version 0.1.0 with previous version 0.0.4 dated 2024-06-24

Title: Download Overture Maps Data in R
Description: Overture Maps offers free and open geospatial map data sourced from various providers and standardized to a common schema. This tool allows you to download Overture Maps data for a specific region of interest and convert it to several different file formats. For more information, visit <https://overturemaps.org/download/>.
Author: Dennis Irorere [aut, cre, cph]
Maintainer: Dennis Irorere <denironyx@gmail.com>

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Package EmpiricalCalibration updated to version 3.1.4 with previous version 3.1.3 dated 2024-09-30

Title: Routines for Performing Empirical Calibration of Observational Study Estimates
Description: Routines for performing empirical calibration of observational study estimates. By using a set of negative control hypotheses we can estimate the empirical null distribution of a particular observational study setup. This empirical null distribution can be used to compute a calibrated p-value, which reflects the probability of observing an estimated effect size when the null hypothesis is true taking both random and systematic error into account. A similar approach can be used to calibrate confidence intervals, using both negative and positive controls. For more details, see Schuemie et al. (2013) <doi:10.1002/sim.5925> and Schuemie et al. (2018) <doi:10.1073/pnas.1708282114>.
Author: Martijn Schuemie [aut, cre] , Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

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 src/RcppWrapper.cpp                                        |    2 
 tests/testthat/test-EmpiricalCalibrationUsingAsymptotics.R |   11 
 tests/testthat/test-LlrCalibration.R                       |  110 ++++----
 tests/testthat/test-asymptoticNull.R                       |    5 
 tests/testthat/test-empiricalCalibrationUsingMcmc.R        |    3 
 24 files changed, 238 insertions(+), 204 deletions(-)

More information about EmpiricalCalibration at CRAN
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Package SaturnCoefficient updated to version 1.4 with previous version 1.3 dated 2024-12-17

Title: Statistical Evaluation of UMAP Dimensionality Reductions
Description: A metric expressing the quality of a UMAP layout. This is a package that contains the Saturn_coefficient() function that reads an input matrix, its dimensionality reduction produced by UMAP, and evaluates the quality of this dimensionality reduction by producing a real value in the [0; 1] interval. We call this real value Saturn coefficient. A higher value means better dimensionality reduction; a lower value means worse dimensionality reduction. Reference: Davide Chicco et al. "The Saturn coefficient for evaluating the quality of UMAP dimensionality reduction results" (2025, in preparation).
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>

Diff between SaturnCoefficient versions 1.3 dated 2024-12-17 and 1.4 dated 2025-02-14

 DESCRIPTION            |    6 +++---
 MD5                    |    4 ++--
 R/Saturn_coefficient.r |    7 ++++---
 3 files changed, 9 insertions(+), 8 deletions(-)

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Package r2dii.match updated to version 0.4.0 with previous version 0.3.0 dated 2024-12-04

Title: Tools to Match Corporate Lending Portfolios with Climate Data
Description: These tools implement in R a fundamental part of the software 'PACTA' (Paris Agreement Capital Transition Assessment), which is a free tool that calculates the alignment between financial portfolios and climate scenarios (<https://www.transitionmonitor.com/>). Financial institutions use 'PACTA' to study how their capital allocation decisions align with climate change mitigation goals. This package matches data from corporate lending portfolios to asset level data from market-intelligence databases (e.g. power plant capacities, emission factors, etc.). This is the first step to assess if a financial portfolio aligns with climate goals.
Author: Jacob Kastl [aut, cre, ctr] , Alex Axthelm [aut, ctr] , Jackson Hoffart [aut, ctr] , Mauro Lepore [aut, ctr] , Klaus Hagedorn [aut], Florence Palandri [aut], Evgeny Petrovsky [aut], RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>

Diff between r2dii.match versions 0.3.0 dated 2024-12-04 and 0.4.0 dated 2025-02-14

 DESCRIPTION                      |   29 +++++++++++++++--------------
 MD5                              |   17 ++++++++++-------
 NEWS.md                          |    6 ++++++
 R/data_dictionary.R              |only
 README.md                        |    2 +-
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 man/r2dii.match-package.Rd       |    4 ++--
 tests/testthat.R                 |    2 ++
 tests/testthat/test-match_name.R |   27 +++++++++++++++++++++++++++
 tests/testthat/test-prioritize.R |   39 +++++++++++++++++++++++++++++++++++++++
 11 files changed, 102 insertions(+), 24 deletions(-)

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Package nlmixr2plot updated to version 3.0.1 with previous version 3.0.0 dated 2024-09-18

Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot Functions
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for 'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] , Bill Denney [ctb] , Wenping Wang [aut], Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>

Diff between nlmixr2plot versions 3.0.0 dated 2024-09-18 and 3.0.1 dated 2025-02-14

 DESCRIPTION               |    8 ++++----
 MD5                       |    9 +++++----
 NAMESPACE                 |    1 +
 NEWS.md                   |    4 ++++
 R/nlmixr2PlotList.R       |   37 +++++++++++++++++++++++++++++++++++++
 tests/testthat/test-add.R |only
 6 files changed, 51 insertions(+), 8 deletions(-)

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New package rangr with initial version 1.0.5
Package: rangr
Title: Mechanistic Simulation of Species Range Dynamics
Version: 1.0.5
Description: Integrates population dynamics and dispersal into a mechanistic virtual species simulator. The package can be used to study the effects of environmental change on population growth and range shifts. It allows for simple and straightforward definition of population dynamics (including positive density dependence), extensive possibilities for defining dispersal kernels, and the ability to generate virtual ecologist data. Learn more about the 'rangr' at <https://docs.ropensci.org/rangr/>.
License: MIT + file LICENSE
Imports: methods, parallel, pbapply, grDevices, graphics, stats, utils, zoo, terra, assertthat
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), covr, bookdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
URL: https://github.com/ropensci/rangr, https://docs.ropensci.org/rangr/, https://doi.org/10.1111/2041-210X.14475
BugReports: https://github.com/ropensci/rangr/issues
NeedsCompilation: no
Packaged: 2025-02-13 10:47:09 UTC; katar
Author: Katarzyna Markowska [aut, cre], Lechoslaw Kuczynski [aut], Tad Dallas [rev], Joanne Potts [rev]
Maintainer: Katarzyna Markowska <katarzyna.markowska@amu.edu.pl>
Repository: CRAN
Date/Publication: 2025-02-14 14:30:02 UTC

More information about rangr at CRAN
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Package pysparklyr updated to version 0.1.6 with previous version 0.1.5 dated 2024-06-24

Title: Provides a 'PySpark' Back-End for the 'sparklyr' Package
Description: It enables 'sparklyr' to integrate with 'Spark Connect', and 'Databricks Connect' by providing a wrapper over the 'PySpark' 'python' library.
Author: Edgar Ruiz [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Edgar Ruiz <edgar@posit.co>

Diff between pysparklyr versions 0.1.5 dated 2024-06-24 and 0.1.6 dated 2025-02-14

 DESCRIPTION                                  |    6 +--
 MD5                                          |   41 +++++++++++++--------------
 NEWS.md                                      |   19 ++++++++++++
 R/databricks-utils.R                         |   20 +++++++++----
 R/dplyr.R                                    |    6 +--
 R/ide-connections-pane.R                     |    6 +--
 R/python-install.R                           |    3 -
 R/python-use-envname.R                       |    2 -
 R/sparklyr-spark-apply.R                     |   13 +++++---
 R/sparklyr-spark-connect.R                   |   31 ++++++++++++--------
 R/start-stop-service.R                       |    4 ++
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 tests/testthat/test-databricks-utils.R       |    8 +++--
 tests/testthat/test-dplyr.R                  |   13 +++++---
 tests/testthat/test-ml-pipeline.R            |    2 +
 tests/testthat/test-sparklyr-spark-apply.R   |    1 
 tests/testthat/test-sparklyr-spark-connect.R |   18 +++++++++++
 22 files changed, 157 insertions(+), 70 deletions(-)

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Permanent link

New package PRMethods with initial version 0.1.0
Package: PRMethods
Title: D-Hondt, Sainte-Lague, and Modified Sainte-Lague Methods for Seat Allocation
Version: 0.1.0
Maintainer: Pau Bello Perez <paubelloperez@gmail.com>
Description: Calculates seat allocation using the D-Hondt method, Sainte-Lague method, and Modified Sainte-Lague method, all commonly used in proportional representation electoral systems. For more information on these methods, see Michael Gallagher (1991)<doi:10.1016/0261-3794(91)90004-C>.
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-13 11:47:57 UTC; paube
Author: Pau Bello Perez [aut, cre]
Repository: CRAN
Date/Publication: 2025-02-14 14:30:10 UTC

More information about PRMethods at CRAN
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New package odbr with initial version 0.1.1
Package: odbr
Title: Download Data from Brazil's Origin Destination Surveys
Version: 0.1.1
Description: Download data from Brazil's Origin Destination Surveys. The package covers both data from household travel surveys, dictionaries of variables, and the spatial geometries of surveys conducted in different years and across various urban areas in Brazil. For some cities, the package will include enhanced versions of the data sets with variables "harmonized" across different years.
License: GPL (>= 3)
Depends: R (>= 2.10)
Imports: cli, data.table, fs, haven, piggyback, R.utils, sf
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.2.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
URL: https://hsvab.github.io/odbr/, https://github.com/hsvab/odbr
BugReports: https://github.com/hsvab/odbr/issues
Language: en-US
NeedsCompilation: no
Packaged: 2025-02-13 12:22:23 UTC; hsvab
Author: Haydee Svab [aut, cre], Beatriz Milz [aut] , Diego Rabatone Oliveira [aut], Rafael H. M. Pereira [aut]
Maintainer: Haydee Svab <hsvab@hsvab.eng.br>
Repository: CRAN
Date/Publication: 2025-02-14 14:50:07 UTC

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New package multilandr with initial version 1.0.0
Package: multilandr
Title: Landscape Analysis at Multiple Spatial Scales
Version: 1.0.0
Maintainer: Pablo Yair Huais <pablo.huais@unc.edu.ar>
Description: Provides a tidy workflow for landscape-scale analysis. 'multilandr' offers tools to generate landscapes at multiple spatial scales and compute landscape metrics, primarily using the 'landscapemetrics' package. It also features utility functions for plotting and analyzing multi-scale landscapes, exploring correlations between metrics, filtering landscapes based on specific conditions, generating landscape gradients for a given metric, and preparing datasets for further statistical analysis. Documentation about 'multilandr' is provided in an introductory vignette included in this package and in the paper by Huais (2024) <doi:10.1007/s10980-024-01930-z>; see citation("multilandr") for details.
License: GPL (>= 3)
Encoding: UTF-8
Imports: terra (>= 1.7-71), GGally (>= 2.2.1), ggplot2 (>= 3.5.1), tidyterra (>= 0.6.0), gridExtra (>= 2.3), landscapemetrics (>= 2.1.1), sf (>= 1.0-16), methods (>= 4.3.0)
Depends: R (>= 4.3.0)
LazyData: true
Suggests: knitr, parallel (>= 4.1.0), rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/phuais/multilandr
BugReports: https://github.com/phuais/multilandr/issues
NeedsCompilation: no
Packaged: 2025-02-13 15:17:38 UTC; pablo
Author: Pablo Yair Huais [aut, cre, cph]
Repository: CRAN
Date/Publication: 2025-02-14 14:50:10 UTC

More information about multilandr at CRAN
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New package guideR with initial version 0.1.0
Package: guideR
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Version: 0.1.0
Description: Companion package for the manual 'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at <https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous functions introduced in 'guide-R' to facilitate statistical analysis and manipulation of survey data.
License: GPL (>= 3)
URL: https://larmarange.github.io/guideR/, https://github.com/larmarange/guideR
BugReports: https://github.com/larmarange/guideR/issues
Depends: R (>= 4.2)
Imports: cli, dplyr, ggplot2, labelled, lifecycle, pak, patchwork, purrr, renv, rlang, scales, srvyr, tidyr, tidyselect
Encoding: UTF-8
Suggests: broom.helpers, FactoMineR, nnet, spelling, survey, testthat (>= 3.0.0)
Language: en-US
NeedsCompilation: no
Packaged: 2025-02-13 10:26:32 UTC; josep
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Repository: CRAN
Date/Publication: 2025-02-14 14:30:06 UTC

More information about guideR at CRAN
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New package ClusterGVis with initial version 0.1.2
Package: ClusterGVis
Title: One-Step to Cluster and Visualize Gene Expression Data
Version: 0.1.2
Description: Streamlining the clustering and visualization of time-series gene expression data from RNA-Seq experiments, this tool supports fuzzy c-means and k-means clustering algorithms. It is compatible with outputs from widely-used packages such as 'Seurat', 'Monocle', and 'WGCNA', enabling seamless downstream visualization and analysis. See Lokesh Kumar and Matthias E Futschik (2007) <doi:10.6026/97320630002005> for more details.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Depends: R (>= 2.10)
Imports: Biobase,circlize,clusterProfiler,colorRamps,ComplexHeatmap,dplyr,e1071, factoextra,ggplot2,grDevices,grid,magrittr,Matrix,methods,Mfuzz,purrr, reshape2,scales,SingleCellExperiment,stats,SummarizedExperiment,TCseq,tibble
Suggests: igraph, monocle, pheatmap, Seurat, WGCNA
BugReports: https://github.com/junjunlab/ClusterGVis/issues
NeedsCompilation: no
Packaged: 2025-02-13 11:34:18 UTC; 11389
Author: Jun Zhang [aut, cre]
Maintainer: Jun Zhang <3219030654@stu.cpu.edu.cn>
Repository: CRAN
Date/Publication: 2025-02-14 14:30:13 UTC

More information about ClusterGVis at CRAN
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Package ade4 updated to version 1.7-23 with previous version 1.7-22 dated 2023-02-06

Title: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stephane Dray [aut] , Anne-Beatrice Dufour [aut] , Jean Thioulouse [aut] , Daniel Chessel [ant], Thibaut Jombart [ctb], Sandrine Pavoine [ctb], Jean R. Lobry [ctb], Sebastien Ollier [ctb], Daniel Borcard [ctb], Pierre Legendre [ctb], Stephanie Bougea [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

Diff between ade4 versions 1.7-22 dated 2023-02-06 and 1.7-23 dated 2025-02-14

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 ade4-1.7-23/ade4/R/bca.coinertia.R          |    8 
 ade4-1.7-23/ade4/R/bca.rlq.R                |    8 
 ade4-1.7-23/ade4/R/betwitdpcoa.R            |   20 -
 ade4-1.7-23/ade4/R/cailliez.R               |    4 
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 ade4-1.7-23/ade4/R/dagnelie.test.R          |    8 
 ade4-1.7-23/ade4/R/disc.R                   |    6 
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 ade4-1.7-23/ade4/R/s.distri.R               |   10 
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 ade4-1.7-23/ade4/R/score.acm.R              |   20 -
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Package BAwiR updated to version 1.3.4 with previous version 1.3.3 dated 2025-01-21

Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>, <https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions of their respectives robots.txt files, when available. Box score data are available for the three leagues. Play-by-play data are also available for the Spanish league. Methods for analysis include a population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games, maps of nationalities, combinations of lineups, possessions-related variables, timeouts, performance by periods, personal fouls and offensive rebounds. Please see Vinue (2020) <doi:10.1089/big.2018.0124> and Vinue (2024) [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>

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Package antaresEditObject updated to version 0.9.0 with previous version 0.7.1 dated 2024-09-27

Title: Edit an 'Antares' Simulation
Description: Edit an 'Antares' simulation before running it : create new areas, links, thermal clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings. 'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.
Author: Tatiana Vargas [aut, cre], Frederic Breant [ctb], Victor Perrier [ctb], Baptiste Seguinot [ctb], Benoit Thieurmel [ctb], Titouan Robert [ctb], Jalal-Edine Zawam [ctb], Etienne Sanchez [ctb], Janus De Bondt [ctb], Assil Mansouri [ctb], Abdallah Mahoud [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>

Diff between antaresEditObject versions 0.7.1 dated 2024-09-27 and 0.9.0 dated 2025-02-14

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Package unnest (with last version 0.0.6) was removed from CRAN

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

2024-10-19 0.0.6
2023-12-03 0.0.5
2023-01-08 0.0.4
2021-09-23 0.0.3
2020-09-22 0.0.2

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Package unigd (with last version 0.1.2) was removed from CRAN

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

2024-06-05 0.1.2
2024-03-25 0.1.1
2024-01-25 0.1.0

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Package RClickhouse (with last version 0.6.9) was removed from CRAN

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

2024-01-19 0.6.9

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Package httpgd (with last version 2.0.2) was removed from CRAN

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

2024-06-05 2.0.2
2024-03-11 2.0.1

Permanent link
Package IOHexperimenter (with last version 0.1.4) was removed from CRAN

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

2020-09-01 0.1.4
2020-06-24 0.1.3
2020-06-23 0.1.2

Permanent link
Package adelie updated to version 1.0.6 with previous version 1.0.2 dated 2024-09-03

Title: Group Lasso and Elastic Net Solver for Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire group lasso and group elastic net regularization path for GLMs, multinomial, the Cox model and multi-task Gaussian models. Similar to the R package 'glmnet' in scope of models, and in computational speed. This package provides R bindings to the C++ code underlying the corresponding Python package 'adelie'. These bindings offer a general purpose group elastic net solver, a wide range of matrix classes that can exploit special structure to allow large-scale inputs, and an assortment of generalized linear model classes for fitting various types of data. The package is an implementation of Yang, J. and Hastie, T. (2024) <doi:10.48550/arXiv.2405.08631>.
Author: James Yang [aut, cph], Trevor Hastie [aut, cph, cre], Balasubramanian Narasimhan [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>

Diff between adelie versions 1.0.2 dated 2024-09-03 and 1.0.6 dated 2025-02-14

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 adelie-1.0.6/adelie/DESCRIPTION                                                                            |   16 
 adelie-1.0.6/adelie/MD5                                                                                    |  388 ++-
 adelie-1.0.6/adelie/NAMESPACE                                                                              |   13 
 adelie-1.0.6/adelie/R/adelie-package.R                                                                     |    1 
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 adelie-1.0.6/adelie/R/glm.R                                                                                |   24 
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 adelie-1.0.6/adelie/R/state.R                                                                              |   43 
 adelie-1.0.6/adelie/R/utilities.R                                                                          |   18 
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 adelie-1.0.6/adelie/inst/adelie/adelie/cv.py                                                               |   63 
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 adelie-1.0.6/adelie/inst/adelie/adelie/io.py                                                               |   10 
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Package teal.logger updated to version 0.3.2 with previous version 0.3.1 dated 2025-01-22

Title: Logging Setup for the 'teal' Family of Packages
Description: Utilizing the 'logger' framework to record events within a package, specific to 'teal' family of packages. Supports logging namespaces, hierarchical logging, various log destinations, vectorization, and more.
Author: Dawid Kaledkowski [aut, cre], Konrad Pagacz [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>

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Package teal.code updated to version 0.6.1 with previous version 0.6.0 dated 2025-01-27

Title: Code Storage and Execution Class for 'teal' Applications
Description: Introduction of 'qenv' S4 class, that facilitates code execution and reproducibility in 'teal' applications.
Author: Dawid Kaledkowski [aut, cre], Aleksander Chlebowski [aut], Marcin Kosinski [aut], Pawel Rucki [aut], Nikolas Burkoff [aut], Mahmoud Hallal [aut], Maciej Nasinski [aut], Konrad Pagacz [aut], Junlue Zhao [aut], Chendi Liao [rev], Dony Unardi [rev], F. [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>

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Package rgrass updated to version 0.5-2 with previous version 0.5-1 dated 2025-02-03

Title: Interface Between 'GRASS' Geographical Information System and 'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Author: Roger Bivand [aut] , Sebastian Jeworutzki [ctb] , Rainer Krug [ctb] , Robin Lovelace [ctb] , Markus Neteler [ctb] , Steven Pawley [cre, aut] , Floris Vanderhaeghe [ctb]
Maintainer: Steven Pawley <dr.stevenpawley@gmail.com>

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Thu, 13 Feb 2025

Package parsnip updated to version 1.3.0 with previous version 1.2.1 dated 2024-03-22

Title: A Common API to Modeling and Analysis Functions
Description: A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', 'H2O', etc).
Author: Max Kuhn [aut, cre], Davis Vaughan [aut], Emil Hvitfeldt [ctb], Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>

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Package omopgenerics updated to version 1.0.0 with previous version 0.4.1 dated 2024-12-05

Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic pipelines that query the OMOP (Observational Medical Outcomes Partnership) common data model.
Author: Marti Catala [aut, cre] , Edward Burn [aut] , Mike Du [ctb] , Yuchen Guo [ctb] , Adam Black [ctb] , Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>

Diff between omopgenerics versions 0.4.1 dated 2024-12-05 and 1.0.0 dated 2025-02-13

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Package epiomics updated to version 1.2.0 with previous version 1.1.0 dated 2024-02-26

Title: Analysis of Omics Data in Observational Studies
Description: A collection of fast and flexible functions for analyzing omics data in observational studies. Multiple different approaches for integrating multiple environmental/genetic factors, omics data, and/or phenotype data are implemented. This includes functions for performing omics wide association studies with one or more variables of interest as the exposure or outcome; a function for performing a meet in the middle analysis for linking exposures, omics, and outcomes (as described by Chadeau-Hyam et al., (2010) <doi:10.3109/1354750X.2010.533285>); and a function for performing a mixtures analysis across all omics features using quantile-based g-Computation (as described by Keil et al., (2019) <doi:10.1289/EHP5838>).
Author: Jesse Goodrich [aut, cre]
Maintainer: Jesse Goodrich <jagoodri@usc.edu>

Diff between epiomics versions 1.1.0 dated 2024-02-26 and 1.2.0 dated 2025-02-13

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Package r2dii.analysis updated to version 0.5.0 with previous version 0.4.0 dated 2024-03-26

Title: Measure Climate Scenario Alignment of Corporate Loans
Description: These tools help you to assess if a corporate lending portfolio aligns with climate goals. They summarize key climate indicators attributed to the portfolio (e.g. production, emission factors), and calculate alignment targets based on climate scenarios. They implement in R the last step of the free software 'PACTA' (Paris Agreement Capital Transition Assessment; <https://www.transitionmonitor.com/>). Financial institutions use 'PACTA' to study how their capital allocation decisions align with climate change mitigation goals.
Author: Jacob Kastl [aut, cre, ctr] , Alex Axthelm [aut, ctr] , Jackson Hoffart [aut, ctr] , Mauro Lepore [aut, ctr] , Klaus Hogedorn [aut], Nicky Halterman [aut], RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>

Diff between r2dii.analysis versions 0.4.0 dated 2024-03-26 and 0.5.0 dated 2025-02-13

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Package mkin updated to version 1.2.9 with previous version 1.2.6 dated 2023-10-14

Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006, 2014). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using automatically generated C functions. Non-constant errors can be taken into account using variance by variable or two-component error models <doi:10.3390/environments6120124>. Hierarchical degradation models can be fitted using nonlinear mixed-effects model packages as a back end <doi:10.3390/environments8080071>. Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke [aut, cre, cph] , Katrin Lindenberger [ctb] ), Rene Lehmann [ctb] and invilr), Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <johannes.ranke@jrwb.de>

Diff between mkin versions 1.2.6 dated 2023-10-14 and 1.2.9 dated 2025-02-13

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Package automap updated to version 1.1-16 with previous version 1.1-12 dated 2024-09-03

Title: Automatic Interpolation Package
Description: An automatic interpolation is done by automatically estimating the variogram and then calling gstat. An overview is given by Hiemstra et al (2008) <doi:10.1016/j.cageo.2008.10.011>.
Author: Paul Hiemstra [aut], Jon Olav Skoien [aut, cre]
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>

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Package micromapST updated to version 3.1.0 with previous version 3.0.4 dated 2024-10-26

Title: Linked Micromap Plots for U. S. and Other Geographic Areas
Description: Provides the users with the ability to quickly create linked micromap plots for a collection of geographic areas. Linked micromap plots are visualizations of geo-referenced data that link statistical graphics to an organized series of small maps or graphic images. The Help description contains examples of how to use the 'micromapST' function. Contained in this package are border group datasets to support creating linked micromap plots for the 50 U.S. states and District of Columbia (51 areas), the U. S. 20 Seer Registries, the 105 counties in the state of Kansas, the 62 counties of New York, the 24 counties of Maryland, the 29 counties of Utah, the 32 administrative areas in China, the 218 administrative areas in the UK and Ireland (for testing only), the 25 districts in the city of Seoul South Korea, and the 52 counties on the Africa continent. A border group dataset contains the boundaries related to the data level areas, a second layer boundaries, a top or third layer boundary, a pa [...truncated...]
Author: Jim Pearson [aut, cre, cph], Dan Carr [aut, cph], Linda Pickle [ctb, cph]
Maintainer: Jim Pearson <jbpearson353@gmail.com>

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Package lightgbm updated to version 4.6.0 with previous version 4.5.0 dated 2024-07-26

Title: Light Gradient Boosting Machine
Description: Tree based algorithms can be improved by introducing boosting frameworks. 'LightGBM' is one such framework, based on Ke, Guolin et al. (2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>. This package offers an R interface to work with it. It is designed to be distributed and efficient with the following advantages: 1. Faster training speed and higher efficiency. 2. Lower memory usage. 3. Better accuracy. 4. Parallel learning supported. 5. Capable of handling large-scale data. In recognition of these advantages, 'LightGBM' has been widely-used in many winning solutions of machine learning competitions. Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple m [...truncated...]
Author: Yu Shi [aut], Guolin Ke [aut], Damien Soukhavong [aut], James Lamb [aut, cre], Qi Meng [aut], Thomas Finley [aut], Taifeng Wang [aut], Wei Chen [aut], Weidong Ma [aut], Qiwei Ye [aut], Tie-Yan Liu [aut], Nikita Titov [aut], Yachen Yan [ctb], Microsof [...truncated...]
Maintainer: James Lamb <jaylamb20@gmail.com>

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Package CASMI updated to version 2.0.0 with previous version 1.2.2 dated 2024-02-16

Title: 'CASMI'-Based Functions
Description: Contains Coverage Adjusted Standardized Mutual Information ('CASMI')-based functions. 'CASMI' is a fundamental concept of a series of methods. For more information about 'CASMI' and 'CASMI'-related methods, please refer to the corresponding publications (e.g., a feature selection method, Shi, J., Zhang, J., & Ge, Y. (2019) <doi:10.3390/e21121179>, and a dataset quality measurement method, Shi, J., Zhang, J., & Ge, Y. (2019) <doi:10.1109/ICHI.2019.8904553>) or contact the package author for the latest updates.
Author: Jingyi Shi [aut, cre, cph, ctb], Shirli Arndt [aut], Jialin Zhang [ctb]
Maintainer: Jingyi (Catherine) Shi <jshi@math.msstate.edu>

Diff between CASMI versions 1.2.2 dated 2024-02-16 and 2.0.0 dated 2025-02-13

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Package wikkitidy updated to version 0.1.14 with previous version 0.1.13 dated 2024-08-17

Title: Tidy Analysis of Wikipedia
Description: Access 'Wikipedia' through the several 'MediaWiki' APIs (<https://www.mediawiki.org/wiki/API>), as well as through the 'XTools' API (<https://www.mediawiki.org/wiki/XTools/API>). Ensure your API calls are correct, and receive results in tidy tibbles.
Author: Michael Falk [aut, cre, cph]
Maintainer: Michael Falk <michaelgfalk@gmail.com>

Diff between wikkitidy versions 0.1.13 dated 2024-08-17 and 0.1.14 dated 2025-02-13

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Package reveneraR updated to version 1.0.0 with previous version 0.1.2 dated 2022-08-06

Title: Connect to Your 'Revenera' (Formerly 'Revulytics') Data
Description: Facilitates making a connection to the 'Revenera' API and executing various queries. You can use it to get event data and metadata. The 'Revenera' documentation is available at <https://rui-api.redoc.ly/>. This package is not supported by 'Flexera' (owner of the software).
Author: Chris Umphlett [aut, cre], Avinash Panigrahi [aut]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>

Diff between reveneraR versions 0.1.2 dated 2022-08-06 and 1.0.0 dated 2025-02-13

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Package IsoplotRgui updated to version 6.5 with previous version 6.4 dated 2024-10-19

Title: Web Interface to 'IsoplotR'
Description: Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Author: Pieter Vermeesch [aut, cre], Tim Band [ctb]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between IsoplotRgui versions 6.4 dated 2024-10-19 and 6.5 dated 2025-02-13

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Package rtpcr updated to version 2.0.1 with previous version 2.0.0 dated 2024-07-07

Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to calculate the fold change (FC, Delta Delta Ct method) or relative expression (RE, Delta Ct method). The functions further provide standard errors and confidence intervals for means, a [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>

Diff between rtpcr versions 2.0.0 dated 2024-07-07 and 2.0.1 dated 2025-02-13

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Package rcompanion updated to version 2.5.0 with previous version 2.4.36 dated 2024-05-27

Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support Summary and Analysis of Extension Program Evaluation in R, and An R Companion for the Handbook of Biological Statistics. Vignettes are available at <https://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>

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Package Colossus updated to version 1.2 with previous version 1.1.4.2 dated 2024-10-21

Title: "Risk Model Regression and Analysis with Complex Non-Linear Models"
Description: Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Gray competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grant 80NSSC19M0161 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric Giunta [aut, cre] , Amir Bahadori [ctb] , Dan Andresen [ctb], Linda Walsh [ctb] , Benjamin French [ctb] , Lawrence Dauer [ctb], John Boice Jr [ctb] , Kansas State University [cph], NASA [fnd], NCRP [fnd], NRC [fnd]
Maintainer: Eric Giunta <egiunta@ksu.edu>

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Package statConfR updated to version 0.2.0 with previous version 0.1.1 dated 2024-04-25

Title: Models of Decision Confidence and Measures of Metacognition
Description: Provides fitting functions and other tools for decision confidence and metacognition researchers, including meta-d'/d', often considered to be the gold standard to measure metacognitive efficiency, and information-theoretic measures of metacognition. Also allows to fit several static models of decision making and confidence.
Author: Manuel Rausch [aut, cre] , Sascha Meyen [aut] , Sebastian Hellmann [aut]
Maintainer: Manuel Rausch <manuel.rausch@hochschule-rhein-waal.de>

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Package groqR updated to version 0.0.3 with previous version 0.0.1 dated 2024-09-20

Title: A Coding Assistant using the Fast AI Inference 'Groq'
Description: A comprehensive suite of functions and 'RStudio' Add-ins leveraging the capabilities of open-source Large Language Models (LLMs) to support R developers. These functions offer a range of utilities, including text rewriting, translation, and general query capabilities. Additionally, the programming-focused functions provide assistance with debugging, translating, commenting, documenting, and unit testing code, as well as suggesting variable and function names, thereby streamlining the development process.
Author: Gabriel Kaiser [aut, cre]
Maintainer: Gabriel Kaiser <quantresearch.gk@gmail.com>

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Package dawaR updated to version 0.3.0 with previous version 0.2.7 dated 2024-12-07

Title: An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Description: Functions for interacting with all sections of the official 'Danish Address Web API' (also known as 'DAWA') <https://api.dataforsyningen.dk>. The development of this package is completely independent from the government agency, Klimadatastyrelsen, who maintains the API.
Author: Aleksander Bang-Larsen [aut, cre, cph] , Agency of Climate Data [ctb]
Maintainer: Aleksander Bang-Larsen <contact@aleksanderbl.dk>

Diff between dawaR versions 0.2.7 dated 2024-12-07 and 0.3.0 dated 2025-02-13

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 dawaR-0.3.0/dawaR/R/utils.R                                                                             |    7 
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Package spacetime updated to version 1.3-3 with previous version 1.3-2 dated 2024-09-04

Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [aut, cre] , Benedikt Graeler [ctb], Tom Gottfried [ctb], Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package phenopix updated to version 2.4.5 with previous version 2.4.4 dated 2024-01-19

Title: Process Digital Images of a Vegetation Cover
Description: A collection of functions to process digital images, depict greenness index trajectories and extract relevant phenological stages.
Author: Gianluca Filippa [aut, cre], Edoardo Cremonese [aut], Mirco Migliavacca [aut], Marta Galvagno [aut], Matthias Folker [aut], Andrew D. Richardson [aut], Enrico Tomelleri [aut]
Maintainer: Gianluca Filippa <gian.filippa@gmail.com>

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Package fluxible updated to version 1.0.0 with previous version 0.0.1 dated 2024-08-27

Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Processes the raw data from closed loop flux chamber (or tent) setups into ecosystem gas fluxes usable for analysis. It goes from a data frame of gas concentration over time (which can contain several measurements) and a meta data file indicating which measurement was done when, to a data frame of ecosystem gas fluxes including quality diagnostics. Functions provided include different models (exponential as described in Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, quadratic and linear) to estimate the fluxes from the raw data, quality assessment, plotting for visual check and calculation of fluxes based on the setup specific parameters (chamber size, plot area, ...).
Author: Joseph Gaudard [aut, cre] , Paul Efren Santos-Andrade [aut], Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>

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Package mlr3torch updated to version 0.2.1 with previous version 0.2.0 dated 2025-02-07

Title: Deep Learning with 'mlr3'
Description: Deep Learning library that extends the mlr3 framework by building upon the 'torch' package. It allows to conveniently build, train, and evaluate deep learning models without having to worry about low level details. Custom architectures can be created using the graph language defined in 'mlr3pipelines'.
Author: Sebastian Fischer [cre, aut] , Bernd Bischl [ctb] , Lukas Burk [ctb] , Martin Binder [aut], Florian Pfisterer [ctb] , Carson Zhang [ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>

Diff between mlr3torch versions 0.2.0 dated 2025-02-07 and 0.2.1 dated 2025-02-13

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Package mnet updated to version 0.1.4 with previous version 0.1.2 dated 2023-06-07

Title: Modeling Group Differences and Moderation Effects in Statistical Network Models
Description: A toolbox for modeling manifest and latent group differences and moderation effects in various statistical network models.
Author: Jonas Haslbeck [aut, cre]
Maintainer: Jonas Haslbeck <jonashaslbeck@protonmail.com>

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Package collegeScorecard updated to version 0.2.0 with previous version 0.1.0 dated 2024-07-29

Title: US College Scorecard Data
Description: Provides a tidied subset of the US College Scorecard dataset, containing institutional characteristics, enrollment, student aid, costs, and student outcomes at institutions of higher education in the United States.
Author: Garrick Aden-Buie [aut, cre, cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>

Diff between collegeScorecard versions 0.1.0 dated 2024-07-29 and 0.2.0 dated 2025-02-13

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Package webdav updated to version 0.1.4 with previous version 0.1.3 dated 2025-01-08

Title: A Simple Interface for Interacting with 'WebDAV' Servers
Description: An easy-to-use interface for interacting with 'WebDAV' servers, including 'OwnCloud'. It simplifies the use of 'WebDAV' methods such as COPY, MKCOL, MOVE, and others. With built-in authentication and request handling, it allows for easy management of files and directories over the 'WebDAV' protocol.
Author: Andre Leite [aut, cre], Hugo Vaconcelos [aut], Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>

Diff between webdav versions 0.1.3 dated 2025-01-08 and 0.1.4 dated 2025-02-13

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New package DBCVindex with initial version 1.3
Encoding: UTF-8
Package: DBCVindex
Title: Calculates the Density-Based Clustering Validation (DBCV) Index
Version: 1.3
Description: A metric called 'Density-Based Clustering Validation index' (DBCV) index to evaluate clustering results, following the <https://github.com/pajaskowiak/clusterConfusion/blob/main/R/dbcv.R> 'R' implementation by Pablo Andretta Jaskowiak. Original 'DBCV' index article: Moulavi, D., Jaskowiak, P. A., Campello, R. J., Zimek, A., and Sander, J. (April 2014), "Density-based clustering validation", Proceedings of SDM 2014 -- the 2014 SIAM International Conference on Data Mining (pp. 839-847), <doi:10.1137/1.9781611973440.96>.
Depends: R (>= 4.0.0)
License: GPL-3
URL: https://github.com/davidechicco/DBCVindex
BugReports: https://github.com/davidechicco/DBCVindex/issues
Imports: qpdf
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-13 09:54:20 UTC; davide
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Repository: CRAN
Date/Publication: 2025-02-13 13:22:01 UTC

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Package CvmortalityMult updated to version 1.0.9 with previous version 1.0.8 dated 2025-02-06

Title: Cross-Validation for Multi-Population Mortality Models
Description: Implementation of cross-validation method for testing the forecasting accuracy of several multi-population mortality models. The family of multi-population includes several multi-population mortality models proposed through the actuarial and demography literature. The package includes functions for fitting and forecast the mortality rates of several populations. Additionally, we include functions for testing the forecasting accuracy of different multi-population models. References. Atance, D., Debon, A., and Navarro, E. (2020) <doi:10.3390/math8091550>. Bergmeir, C. & Benitez, J.M. (2012) <doi:10.1016/j.ins.2011.12.028>. Debon, A., Montes, F., & Martinez-Ruiz, F. (2011) <doi:10.1007/s13385-011-0043-z>. Lee, R.D. & Carter, L.R. (1992) <doi:10.1080/01621459.1992.10475265>. Russolillo, M., Giordano, G., & Haberman, S. (2011) <doi:10.1080/03461231003611933>. Santolino, M. (2023) <doi:10.3390/risks11100170>.
Author: David Atance [aut, cre] , Ana Debon [aut]
Maintainer: David Atance <david.atance@uah.es>

Diff between CvmortalityMult versions 1.0.8 dated 2025-02-06 and 1.0.9 dated 2025-02-13

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New package zonebuilder with initial version 0.1.0
Package: zonebuilder
Title: Create and Explore Geographic Zoning Systems
Version: 0.1.0
Description: Functions, documentation and example data to help divide geographic space into discrete polygons (zones). The package supports new zoning systems that are documented in the accompanying paper, "ClockBoard: A zoning system for urban analysis", by Lovelace et al. (2022) <doi:10.5311/JOSIS.2022.24.172>. The functions are motivated by research into the merits of different zoning systems (Openshaw, 1977) <doi:10.1068/a090169>. A flexible ClockBoard zoning system is provided, which breaks-up space by concentric rings and radial lines emanating from a central point. By default, the diameter of the rings grow according to the triangular number sequence (Ross & Knott, 2019) <doi:10.1080/26375451.2019.1598687> with the first 4 doughnuts (or annuli) measuring 1, 3, 6, and 10 km wide. These annuli are subdivided into equal segments (12 by default), creating the visual impression of a dartboard. Zones are labelled according to distance to the centre and angular distance from N [...truncated...]
License: GPL-3
BugReports: https://github.com/zonebuilders/zonebuilder/issues
Depends: R (>= 3.5.0)
Imports: sf, RColorBrewer, graphics, grDevices
Suggests: knitr, rmarkdown, tmap, tmaptools, dplyr, lwgeom, leaflet, covr, bookdown
VignetteBuilder: knitr
URL: https://github.com/zonebuilders/zonebuilder, https://zonebuilders.github.io/zonebuilder/
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2025-02-13 12:03:52 UTC; robin
Author: Robin Lovelace [aut, cre] , Martijn Tennekes [aut]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-13 12:40:02 UTC

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Package RQdeltaCT updated to version 1.3.2 with previous version 1.3.0 dated 2024-04-17

Title: Relative Quantification of Gene Expression using Delta Ct Methods
Description: The commonly used methods for relative quantification of gene expression levels obtained in real-time PCR (Polymerase Chain Reaction) experiments are the delta Ct methods, encompassing 2^-dCt and 2^-ddCt methods, originally proposed by Kenneth J. Livak and Thomas D. Schmittgen (2001) <doi:10.1006/meth.2001.1262>. The main idea is to normalise gene expression values using endogenous control gene, present gene expression levels in linear form by using the 2^-(value)^ transformation, and calculate differences in gene expression levels between groups of samples (or technical replicates of a single sample). The 'RQdeltaCT' package offers functions that cover both methods for comparison of either independent groups of samples or groups with paired samples, together with importing expression datasets, performing multi-step quality control of data, enabling numerous data visualisations, enrichment of the standard workflow with additional useful analyses (correlation analysis, Receiver Op [...truncated...]
Author: Daniel Zalewski [aut, cre]
Maintainer: Daniel Zalewski <daniel.piotr.zalewski@gmail.com>

Diff between RQdeltaCT versions 1.3.0 dated 2024-04-17 and 1.3.2 dated 2025-02-13

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Package fitPoly updated to version 4.0.0 with previous version 3.0.0 dated 2018-03-16

Title: Genotype Calling for Bi-Allelic Marker Assays
Description: Genotyping assays for bi-allelic markers (e.g. SNPs) produce signal intensities for the two alleles. 'fitPoly' assigns genotypes (allele dosages) to a collection of polyploid samples based on these signal intensities. 'fitPoly' replaces the older package 'fitTetra' that was limited (a.o.) to only tetraploid populations whereas 'fitPoly' accepts any ploidy level. Reference: Voorrips RE, Gort G, Vosman B (2011) <doi:10.1186/1471-2105-12-172>. New functions added on conversion of data from SNP array software formats, drawing of XY-scatterplots with or without genotype colors, checking against expected F1 segregation patterns, comparing results from two different assays (probes) for the same SNP, recovery from a saveMarkerModels() crash.
Author: Roeland E. Voorrips [aut], Gerrit Gort [aut], Alejandro Therese Navarro [aut], Giorgio Tumino [aut, cre]
Maintainer: Giorgio Tumino <giorgio.tumino@wur.nl>

Diff between fitPoly versions 3.0.0 dated 2018-03-16 and 4.0.0 dated 2025-02-13

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New package tomledit with initial version 0.1.0
Package: tomledit
Title: Parse, Read, and Edit 'TOML'
Version: 0.1.0
Description: A toolkit for working with 'TOML' files in R while preserving formatting, comments, and structure. 'tomledit' enables serialization of R objects such as lists, data.frames, numeric, logical, and date vectors.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en
SystemRequirements: Cargo (Rust's package manager), rustc
Depends: R (>= 4.1.0)
Imports: rlang (>= 1.1.0)
URL: https://josiahparry.github.io/tomledit/
NeedsCompilation: yes
Packaged: 2025-02-12 21:55:35 UTC; josiahparry
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-13 11:30:03 UTC

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New package rchroma with initial version 0.1.0
Package: rchroma
Title: A Client for 'ChromaDB'
Version: 0.1.0
Description: Client for 'ChromaDB', a vector database for storing and querying embeddings. This package provides a convenient interface to interact with the REST API of 'ChromaDB' <https://docs.trychroma.com>.
License: MIT + file LICENSE
URL: https://github.com/cynkra/rchroma
BugReports: https://github.com/cynkra/rchroma/issues
Language: en-US
Encoding: UTF-8
Imports: httr2 (>= 1.0.0)
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, covr, spelling
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-02-13 04:22:40 UTC; david
Author: David Schoch [aut, cre] , Christoph Sax [aut], cynkra LLC [cph]
Maintainer: David Schoch <david@schochastics.net>
Repository: CRAN
Date/Publication: 2025-02-13 11:30:09 UTC

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New package PerMallows with initial version 1.14
Package: PerMallows
Title: Permutations and Mallows Distributions
Version: 1.14
Date: 2025-02-11
Description: Includes functions to work with the Mallows and Generalized Mallows Models. The considered distances are Kendall's-tau, Cayley, Hamming and Ulam and it includes functions for making inference, sampling and learning such distributions, some of which are novel in the literature. As a by-product, PerMallows also includes operations for permutations, paying special attention to those related with the Kendall's-tau, Cayley, Ulam and Hamming distances. It is also possible to generate random permutations at a given distance, or with a given number of inversions, or cycles, or fixed points or even with a given length on LIS (longest increasing subsequence).
License: GPL (>= 2)
Depends: R (>= 4.0)
Imports: utils
LinkingTo: Rcpp
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-02-13 09:21:59 UTC; ekhi
Author: Ekhine Irurozki [aut, cre], Borja Calvo [aut], Jose A. Lozano [aut]
Maintainer: Ekhine Irurozki <irurozki@telecom-paris.fr>
Repository: CRAN
Date/Publication: 2025-02-13 11:20:05 UTC

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Package IsoplotR updated to version 6.5 with previous version 6.4 dated 2024-10-19

Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington', 'Ludwig' and Omnivariant Generalised Least-Squares ('OGLS') approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isoch [...truncated...]
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between IsoplotR versions 6.4 dated 2024-10-19 and 6.5 dated 2025-02-13

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 12 files changed, 249 insertions(+), 183 deletions(-)

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New package IFTPredictor with initial version 0.1.0
Package: IFTPredictor
Title: Predictions Using Item-Focused Tree Models
Version: 0.1.0
Author: Muditha L. Bodawatte Gedara [aut, cre], Barret A. Monchka [aut], Lisa M. Lix [aut]
Maintainer: Muditha L. Bodawatte Gedara <muditha.lakmali.1993@gmail.com>
Description: This function predicts item response probabilities and item responses using the item-focused tree model. The item-focused tree model combines logistic regression with recursive partitioning to detect Differential Item Functioning in dichotomous items. The model applies partitioning rules to the data, splitting it into homogeneous subgroups, and uses logistic regression within each subgroup to explain the data. Differential Item Functioning detection is achieved by examining potential group differences in item response patterns. This method is useful for understanding how different predictors, such as demographic or psychological factors, influence item responses across subgroups.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: DIFtree
Suggests: devtools, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2025-02-13 04:19:09 UTC; mudithalakmali
Repository: CRAN
Date/Publication: 2025-02-13 11:30:28 UTC

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New package fracARMA with initial version 0.1.0
Package: fracARMA
Title: Fractionally Integrated ARMA Model
Version: 0.1.0
Maintainer: Muhammed Irshad M <irshadmiitm@gmail.com>
Description: Implements fractional differencing with Autoregressive Moving Average models to analyse long-memory time series data. Traditional ARIMA models typically use integer values for differencing, which are suitable for time series with short memory or anti-persistent behaviour. In contrast, the Fractional ARIMA model allows fractional differencing, enabling it to effectively capture long memory characteristics in time series data. The ‘fracARMA’ package is user-friendly and allows users to manually input the fractional differencing parameter, which can be obtained using various estimators such as the GPH estimator, Sperio method, or Wavelet method and many. Additionally, the package enables users to directly feed the time series data, AR order, MA order, fractional differencing parameter, and the proportion of training data as a split ratio, all in a single command. The package is based on the reference from the paper of Irshad and others (2024, <doi:10.22271/maths.2024.v9.i6b.19 [...truncated...]
Encoding: UTF-8
License: GPL-3
Imports: forecast, fracdiff
NeedsCompilation: no
Packaged: 2025-02-12 18:30:01 UTC; irshad m
Author: Muhammed Irshad M [aut, cre], Dr. Kader Ali Sarkar [aut], Dr. Digvijay Singh Dhakre [aut], Prof. Debasis Bhattacharaya [aut]
Repository: CRAN
Date/Publication: 2025-02-13 11:20:02 UTC

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Package dials updated to version 1.4.0 with previous version 1.3.0 dated 2024-07-30

Title: Tools for Creating Tuning Parameter Values
Description: Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.
Author: Max Kuhn [aut], Hannah Frick [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>

Diff between dials versions 1.3.0 dated 2024-07-30 and 1.4.0 dated 2025-02-13

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Package tourr updated to version 1.2.4 with previous version 1.2.0 dated 2024-04-19

Title: Tour Methods for Multivariate Data Visualisation
Description: Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.
Author: Hadley Wickham [aut, ctb] , Dianne Cook [aut, cre] , Nick Spyrison [ctb] , Ursula Laa [ctb] , H. Sherry Zhang [ctb] , Stuart Lee [ctb]
Maintainer: Dianne Cook <dicook@monash.edu>

Diff between tourr versions 1.2.0 dated 2024-04-19 and 1.2.4 dated 2025-02-13

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New package swash with initial version 1.0.0
Package: swash
Title: Swash-Backwash Model for the Single Epidemic Wave
Version: 1.0.0
Date: 2025-02-12
Author: Thomas Wieland [aut, cre]
Maintainer: Thomas Wieland <geowieland@googlemail.com>
Description: The Swash-Backwash Model for the Single Epidemic Wave was developed by Cliff and Haggett (2006) <doi:10.1007/s10109-006-0027-8> to model the velocity of spread of infectious diseases across space. This package enables the calculation of the Swash-Backwash Model for user-supplied panel data on regional infections. The package also provides additional functions for bootstrap confidence intervals and data management.
License: GPL (>= 2)
Imports: methods
NeedsCompilation: no
Packaged: 2025-02-12 08:32:40 UTC; thoma
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-02-13 10:30:02 UTC

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Package singleRcapture updated to version 0.2.3 with previous version 0.2.2 dated 2025-02-04

Title: Single-Source Capture-Recapture Models
Description: Implementation of single-source capture-recapture methods for population size estimation using zero-truncated, zero-one truncated and zero-truncated one-inflated Poisson, Geometric and Negative Binomial regression as well as Zelterman's and Chao's regression. Package includes point and interval estimators for the population size with variances estimated using analytical or bootstrap method. Details can be found in: van der Heijden et all. (2003) <doi:10.1191/1471082X03st057oa>, Böhning and van der Heijden (2019) <doi:10.1214/18-AOAS1232>, Böhning et al. (2020) Capture-Recapture Methods for the Social and Medical Sciences or Böhning and Friedl (2021) <doi:10.1007/s10260-021-00556-8>.
Author: Piotr Chlebicki [aut, ctb] , Maciej Beresewicz [aut, cre]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>

Diff between singleRcapture versions 0.2.2 dated 2025-02-04 and 0.2.3 dated 2025-02-13

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New package sgdGMF with initial version 1.0
Package: sgdGMF
Title: Estimation of Generalized Matrix Factorization Models via Stochastic Gradient Descent
Version: 1.0
Date: 2025-01-28
Description: Efficient framework to estimate high-dimensional generalized matrix factorization models using penalized maximum likelihood under a dispersion exponential family specification. Either deterministic and stochastic methods are implemented for the numerical maximization. In particular, the package implements the stochastic gradient descent algorithm with a block-wise mini-batch strategy to speed up the computations and an efficient adaptive learning rate schedule to stabilize the convergence. All the theoretical details can be found in Castiglione et al. (2024, <doi:10.48550/arXiv.2412.20509>). Other methods considered for the optimization are the alternated iterative re-weighted least squares and the quasi-Newton method with diagonal approximation of the Fisher information matrix discussed in Kidzinski et al. (2022, <http://jmlr.org/papers/v23/20-1104.html>).
License: MIT + file LICENSE
Imports: Rcpp (>= 1.0.10), RcppArmadillo, RSpectra, parallel, doParallel, foreach, MASS, SuppDists, methods, generics, reshape2, ggpubr, viridisLite
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 4.0.0), ggplot2
Suggests: testthat (>= 3.0.0), Rtsne, dplyr, knitr, rmarkdown
Encoding: UTF-8
URL: https://github.com/CristianCastiglione/sgdGMF
BugReports: https://github.com/CristianCastiglione/sgdGMF/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-02-12 10:42:15 UTC; crist
Author: Cristian Castiglione [aut, cre] , Davide Risso [ctb] , Alexandre Segers [ctb]
Maintainer: Cristian Castiglione <cristian_castiglione@libero.it>
Repository: CRAN
Date/Publication: 2025-02-13 10:30:06 UTC

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Package rqPen updated to version 4.1.3 with previous version 4.1.2 dated 2024-10-29

Title: Penalized Quantile Regression
Description: Performs penalized quantile regression with LASSO, elastic net, SCAD and MCP penalty functions including group penalties. In addition, offers a group penalty that provides consistent variable selection across quantiles. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC. Below URL provides a link to a work in progress vignette.
Author: Ben Sherwood [aut, cre], Shaobo Li [aut], Adam Maidman [aut]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>

Diff between rqPen versions 4.1.2 dated 2024-10-29 and 4.1.3 dated 2025-02-13

 DESCRIPTION       |    8 -
 MD5               |   12 -
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 7 files changed, 208 insertions(+), 198 deletions(-)

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Package jobqueue updated to version 1.3.0 with previous version 1.0.1 dated 2025-01-30

Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method which can be called to terminate the background job. Also provides timeouts and other mechanisms for automatically terminating a background job. The result of the expression is available synchronously via $result or asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] , Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>

Diff between jobqueue versions 1.0.1 dated 2025-01-30 and 1.3.0 dated 2025-02-13

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 19 files changed, 372 insertions(+), 175 deletions(-)

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New package giniCI with initial version 0.1.0
Package: giniCI
Title: Gini-Based Composite Indicators
Version: 0.1.0
Maintainer: Viet Duong Nguyen <viet-duong.nguyen@outlook.com>
Description: An implementation of Gini-based weighting approaches in constructing composite indicators, providing functionalities for normalization, aggregation, and ranking comparison.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: DescTools (>= 0.99.57), ggplot2 (>= 3.5.1), ggrepel (>= 0.9.6), ggpubr (>= 0.6.0)
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2025-02-12 15:48:08 UTC; Duong Nguyen
Author: Viet Duong Nguyen [aut, cre] , Chiara Gigliarano [aut] , Mariateresa Ciommi [aut]
Repository: CRAN
Date/Publication: 2025-02-13 10:30:10 UTC

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New package evesim with initial version 1.0.0
Package: evesim
Title: Evolution Emulator: Species Diversification under an Evolutionary Relatedness Dependent Scenario
Version: 1.0.0
Description: Evolutionary relatedness dependent diversification simulation powered by the 'Rcpp' back-end 'SimTable'.
License: MIT + file LICENSE
Depends: R (>= 4.4.0)
Imports: Rcpp, RcppParallel
Encoding: UTF-8
SystemRequirements: C++17
LinkingTo: Rcpp (>= 1.0.11), RcppParallel
URL: http://qtj.me/evesim/
NeedsCompilation: yes
Packaged: 2025-02-12 14:08:36 UTC; tianj
Author: Tianjian Qin [aut, cre], Hanno Hildenbrandt [aut] , Luis Valente [aut, ths], Rampal Etienne [aut, ths]
Maintainer: Tianjian Qin <t.qin@rug.nl>
Repository: CRAN
Date/Publication: 2025-02-13 10:30:14 UTC

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New package BayesChange with initial version 1.1.0
Package: BayesChange
Title: Bayesian Methods for Change Points Analysis
Version: 1.1.0
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
License: GPL (>= 3)
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo, RcppGSL
Imports: Rcpp
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/lucadanese/BayesChange
BugReports: https://github.com/lucadanese/BayesChange/issues
NeedsCompilation: yes
Packaged: 2025-02-12 09:49:13 UTC; LUCA
Author: Luca Danese [aut, cre, cph] , Riccardo Corradin [aut], Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Repository: CRAN
Date/Publication: 2025-02-13 10:30:17 UTC

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New package ptetools with initial version 1.0.0
Package: ptetools
Title: Panel Treatment Effects Tools
Version: 1.0.0
URL: https://github.com/bcallaway11/ptetools
BugReports: https://github.com/bcallaway11/ptetools/issues
Description: Generic code for estimating treatment effects with panel data. The idea is to break into separate steps organizing the data, looping over groups and time periods, computing group-time average treatment effects, and aggregating group-time average treatment effects. Often, one is able to implement a new identification/estimation procedure by simply replacing the step on estimating group-time average treatment effects. See several different examples of this approach in the package documentation.
License: GPL-3
Encoding: UTF-8
Imports: BMisc (>= 1.4.7), Matrix, ggplot2, DRDID, tidyr, dplyr, pbapply, splines2
Suggests: testthat (>= 3.0.0), did
NeedsCompilation: no
Packaged: 2025-02-11 21:19:36 UTC; bmc43193
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Repository: CRAN
Date/Publication: 2025-02-13 10:00:01 UTC

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New package NLPwavelet with initial version 1.0
Package: NLPwavelet
Title: Bayesian Wavelet Analysis Using Non-Local Priors
Version: 1.0
Date: 2025-02-09
Description: Performs Bayesian wavelet analysis using individual non-local priors as described in Sanyal & Ferreira (2017) <DOI:10.1007/s13571-016-0129-3> and non-local prior mixtures as described in Sanyal (2025) <DOI:10.48550/arXiv.2501.18134>.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.14), wavethresh
LinkingTo: Rcpp, RcppArmadillo
URL: https://nilotpalsanyal.github.io/NLPwavelet/
BugReports: https://github.com/nilotpalsanyal/NLPwavelet/issues
Repository: CRAN
NeedsCompilation: yes
Packaged: 2025-02-11 22:59:56 UTC; nsanyal
Author: Nilotpal Sanyal [aut, cre]
Maintainer: Nilotpal Sanyal <nsanyal@utep.edu>
Date/Publication: 2025-02-13 10:00:06 UTC

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New package VARcpDetectOnline with initial version 0.2.0
Package: VARcpDetectOnline
Title: Sequential Change Point Detection for High-Dimensional VAR Models
Version: 0.2.0
Description: Implements the algorithm introduced in Tian, Y., and Safikhani, A. (2024) <doi:10.5705/ss.202024.0182>, "Sequential Change Point Detection in High-dimensional Vector Auto-regressive Models". This package provides tools for detecting change points in the transition matrices of VAR models, effectively identifying shifts in temporal and cross-correlations within high-dimensional time series data.
Encoding: UTF-8
LazyData: true
Imports: MASS, corpcor, Matrix, glmnet, doParallel, stats
Suggests: ggplot2
License: GPL-2 | file LICENSE
URL: https://github.com/Helloworld9293/VARcpDetectOnline
BugReports: https://github.com/Helloworld9293/VARcpDetectOnline/issues
NeedsCompilation: no
Packaged: 2025-02-12 18:06:25 UTC; AAA
Author: Yuhan Tian [aut, cre], Abolfazl Safikhani [aut]
Maintainer: Yuhan Tian <yuhan.tian@ufl.edu>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-02-13 08:40:02 UTC

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New package FPDclustering with initial version 2.3.4
Package: FPDclustering
Title: PD-Clustering and Related Methods
Version: 2.3.4
Date: 2025-02-12
Maintainer: Cristina Tortora <grikris1@gmail.com>
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution-free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership under the constraint that the product of the probability and the distance of each point to any cluster center is a constant. PD-clustering is a flexible method that can be used with elliptical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different sizes. GPDC and TPDC use a dissimilarity measure based on densities. Factor PD-clustering (FPDC) is a factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high-dimensional data sets.
Depends: ThreeWay,mvtnorm,R (>= 4.1.0)
Imports: ExPosition, cluster,rootSolve, MASS, klaR, GGally, ggplot2, ggeasy
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2025-02-12 18:28:45 UTC; 011543324
Repository: CRAN
Date/Publication: 2025-02-13 08:40:06 UTC
Author: Cristina Tortora [aut, cre, cph], Noe Vidales [aut], Francesco Palumbo [aut], Tina Kalra [aut], Paul D. McNicholas [fnd]

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Package tidyquant updated to version 1.0.11 with previous version 1.0.10 dated 2025-01-08

Title: Tidy Quantitative Financial Analysis
Description: Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

Diff between tidyquant versions 1.0.10 dated 2025-01-08 and 1.0.11 dated 2025-02-13

 DESCRIPTION                               |    6 +++---
 MD5                                       |    6 +++---
 NEWS.md                                   |    4 ++++
 tests/testthat/test-tq_get_stock_prices.R |    4 ++--
 4 files changed, 12 insertions(+), 8 deletions(-)

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