Fri, 03 Oct 2025

Package isoorbi updated to version 1.5.2 with previous version 1.3.1 dated 2024-08-27

Title: Process Orbitrap Isotopocule Data
Description: Read and process isotopocule data from an Orbitrap Isotope Solutions mass spectrometer. Citation: Kantnerova et al. (Nature Protocols, 2024).
Author: Caj Neubauer [aut, cre, cph] , Sebastian Kopf [aut] , Kristyna Kantnerova [aut]
Maintainer: Caj Neubauer <caj.neubauer@colorado.edu>

Diff between isoorbi versions 1.3.1 dated 2024-08-27 and 1.5.2 dated 2025-10-03

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Package dscore updated to version 2.0.0 with previous version 1.11.0 dated 2025-09-26

Title: D-Score for Child Development
Description: The D-score summarizes a child's performance on developmental milestones into a single number. Its key feature is its generic nature. The method does not depend on a specific measurement instrument. The statistical method underlying the D-score is described in van Buuren et al. (2025) <doi:10.1177/01650254241294033>. This package implements model keys to convert milestone scores to D-scores; maps instrument-specific item names to a generic 9-position naming convention; computes D-scores and their precision from a child's milestone scores; and converts D-scores to Development-for-Age Z-scores (DAZ) using age-conditional reference standards.
Author: Stef van Buuren [cre, aut], Iris Eekhout [aut], Arjan Huizing [aut], Jonathan Seiden [aut]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>

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New package BioMoR with initial version 0.1.0
Package: BioMoR
Title: Bioinformatics Modeling with Recursion and Autoencoder-Based Ensemble
Version: 0.1.0
Description: Tools for bioinformatics modeling using recursive transformer-inspired architectures, autoencoders, random forests, XGBoost, and stacked ensemble models. Includes utilities for cross-validation, calibration, benchmarking, and threshold optimization in predictive modeling workflows. The methodology builds on ensemble learning (Breiman 2001 <doi:10.1023/A:1010933404324>), gradient boosting (Chen and Guestrin 2016 <doi:10.1145/2939672.2939785>), autoencoders (Hinton and Salakhutdinov 2006 <doi:10.1126/science.1127647>), and recursive transformer efficiency approaches such as Mixture-of-Recursions (Bae et al. 2025 <doi:10.48550/arXiv.2507.10524>).
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: caret, recipes, themis, xgboost, magrittr, dplyr, pROC
Suggests: randomForest, testthat (>= 3.0.0), PRROC, ggplot2, purrr, tibble, yardstick, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-27 09:30:29 UTC; apple
Author: MD. Arshad [aut, cre]
Maintainer: MD. Arshad <arshad10867c@gmail.com>
Repository: CRAN
Date/Publication: 2025-10-03 13:50:02 UTC

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New package adcontabil with initial version 1.0.4
Package: adcontabil
Version: 1.0.4
Title: Accounting Analysis
Description: Provides methods for processing corporate balance sheets with a focus on the Brazilian reporting format. Includes data standardization, classification by accounting categories, and aggregation of values. Supports accounting and financial analyses of companies, improving efficiency and ensuring reproducibility of empirical studies.
License: MIT + file LICENSE
URL: https://github.com/LissandroSousa/adcontabil.R
BugReports: https://github.com/LissandroSousa/adcontabil.R/issues
Imports: dplyr, magrittr, stringi, data.table
Encoding: UTF-8
NeedsCompilation: no
Depends: R (>= 4.1.0)
Packaged: 2025-09-26 22:39:29 UTC; USER
Author: Lissandro Costa de Sousa [cre, aut], Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Costa de Sousa <lisandrosousa54@gmail.com>
Repository: CRAN
Date/Publication: 2025-10-03 13:10:02 UTC

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New package topologyR with initial version 0.1.1
Package: topologyR
Title: Topological Connectivity Analysis for Numeric Data
Version: 0.1.1
Description: Description: Implementation of topological data analysis methods based on graph-theoretic approaches for discovering topological structures in data. The core algorithm constructs topological spaces from graphs following Nada et al. (2018) <doi:10.1002/mma.5096> "New types of topological structures via graphs".
License: MIT + file LICENSE
URL: https://github.com/IsadoreNabi/topologyR
BugReports: https://github.com/IsadoreNabi/topologyR/issues
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: ggplot2, stats, utils
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-09-26 02:18:30 UTC; ROG
Author: Jose Mauricio Gomez Julian [aut, cre]
Maintainer: Jose Mauricio Gomez Julian <isadore.nabi@pm.me>
Repository: CRAN
Date/Publication: 2025-10-03 12:20:02 UTC

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Package distrom updated to version 1.0.2 with previous version 1.0.1 dated 2022-03-28

Title: Distributed Multinomial Regression
Description: Fast distributed/parallel estimation for multinomial logistic regression via Poisson factorization and the 'gamlr' package. For details see: Taddy (2015, AoAS), Distributed Multinomial Regression, <doi:10.48550/arXiv.1311.6139>.
Author: Matt Taddy [aut], Nelson Rayl [cre]
Maintainer: Nelson Rayl <nelsonrayl14@gmail.com>

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New package CORPlot with initial version 1.0.2
Package: CORPlot
Title: Cumulative Odds Ratio Plot
Version: 1.0.2
Description: Create cumulative odds ratio plot to visually inspect the proportional odds assumption from the proportional odds model.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/Yongxi-Long/CORPlot
BugReports: https://github.com/Yongxi-Long/CORPlot/issues
Suggests: testthat (>= 3.0.0)
Depends: R (>= 3.5)
LazyData: true
Imports: ggplot2, knitr, stats, VGAM
NeedsCompilation: no
Packaged: 2025-09-26 14:25:18 UTC; ylong
Author: Yongxi Long [aut, cre, cph]
Maintainer: Yongxi Long <y.long@lumc.nl>
Repository: CRAN
Date/Publication: 2025-10-03 12:50:02 UTC

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Package TDLM updated to version 1.1.3 with previous version 1.1.2 dated 2025-05-06

Title: Systematic Comparison of Trip Distribution Laws and Models
Description: The main purpose of this package is to propose a rigorous framework to fairly compare trip distribution laws and models as described in Lenormand et al. (2016) <doi:10.1016/j.jtrangeo.2015.12.008>.
Author: Maxime Lenormand [aut, cre]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>

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Package primerTree updated to version 1.1.0 with previous version 1.0.6 dated 2022-04-05

Title: Visually Assessing the Specificity and Informativeness of Primer Pairs
Description: Identifies potential target sequences for a given set of primers and generates phylogenetic trees annotated with the taxonomies of the predicted amplification products.
Author: Jim Hester [aut], Matt Cannon [aut, cre]
Maintainer: Matt Cannon <matthewvc1@gmail.com>

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More information about primerTree at CRAN
Permanent link

Package fastymd updated to version 0.1.4 with previous version 0.1.3 dated 2025-05-12

Title: Fast Utilities for Year Month Day Objects
Description: A collection of utility functions for working with Year Month Day objects. Includes functions for fast parsing of numeric and character input based on algorithms described in Hinnant, H. (2021) <https://howardhinnant.github.io/date_algorithms.html> as well as a branchless calculation of leap years by Jerichaux (2025) <https://stackoverflow.com/a/79564914>.
Author: Tim Taylor [aut, cre] , Howard Hinnant [aut] , jerichaux [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

Diff between fastymd versions 0.1.3 dated 2025-05-12 and 0.1.4 dated 2025-10-03

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Package drclust updated to version 0.1.1 with previous version 0.1 dated 2024-04-22

Title: Simultaneous Clustering and (or) Dimensionality Reduction
Description: Methods for simultaneous clustering and dimensionality reduction such as: Double k-means, Reduced k-means, Factorial k-means, Clustering with Disjoint PCA but also methods for exclusively dimensionality reduction: Disjoint PCA, Disjoint FA. The statistical methods implemented refer to the following articles: de Soete G., Carroll J. (1994) "K-means clustering in a low-dimensional Euclidean space" <doi:10.1007/978-3-642-51175-2_24> ; Vichi M. (2001) "Double k-means Clustering for Simultaneous Classification of Objects and Variables" <doi:10.1007/978-3-642-59471-7_6> ; Vichi M., Kiers H.A.L. (2001) "Factorial k-means analysis for two-way data" <doi:10.1016/S0167-9473(00)00064-5> ; Vichi M., Saporta G. (2009) "Clustering and disjoint principal component analysis" <doi:10.1016/j.csda.2008.05.028> ; Vichi M. (2017) "Disjoint factor analysis with cross-loadings" <doi:10.1007/s11634-016-0263-9>.
Author: Ionel Prunila [aut, cre], Maurizio Vichi [aut]
Maintainer: Ionel Prunila <ionel.prunila@uniroma1.it>

Diff between drclust versions 0.1 dated 2024-04-22 and 0.1.1 dated 2025-10-03

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Permanent link

Package devtools updated to version 2.4.6 with previous version 2.4.5 dated 2022-10-11

Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut], Jim Hester [aut], Winston Chang [aut], Jennifer Bryan [aut, cre] , Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>

Diff between devtools versions 2.4.5 dated 2022-10-11 and 2.4.6 dated 2025-10-03

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Package roptim updated to version 0.1.7 with previous version 0.1.6 dated 2022-08-06

Title: General Purpose Optimization in R using C++
Description: Perform general purpose optimization in R using C++. A unified wrapper interface is provided to call C functions of the five optimization algorithms ('Nelder-Mead', 'BFGS', 'CG', 'L-BFGS-B' and 'SANN') underlying optim().
Author: Yi Pan [aut, cre]
Maintainer: Yi Pan <ypan1988@gmail.com>

Diff between roptim versions 0.1.6 dated 2022-08-06 and 0.1.7 dated 2025-10-03

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Permanent link

Package HMDHFDplus updated to version 2.0.8 with previous version 2.0.6 dated 2025-01-21

Title: Read Human Mortality Database and Human Fertility Database Data from the Web
Description: Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<https://www.fertilitydata.org>), The Japanese Mortality Database (<https://www.ipss.go.jp/p-toukei/JMD/index-en.html>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Author: Tim Riffe [aut, cre], Carl Boe [aut], Jason Hilton [aut], Josh Goldstein [ctb], Stephen Holzman [ctb], Sam Hyun Yoo [ctb]
Maintainer: Tim Riffe <tim.riffe@gmail.com>

Diff between HMDHFDplus versions 2.0.6 dated 2025-01-21 and 2.0.8 dated 2025-10-03

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Package HandTill2001 updated to version 1.0.3 with previous version 1.0.2 dated 2025-05-24

Title: Multiple Class Area under ROC Curve
Description: An S4 implementation of Eq. (3) and Eq. (7) by David J. Hand and Robert J. Till (2001) <DOI:10.1023/A:1010920819831>.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

Diff between HandTill2001 versions 1.0.2 dated 2025-05-24 and 1.0.3 dated 2025-10-03

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Package fdasrvf updated to version 2.4.2 with previous version 2.4.1 dated 2025-09-23

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>

Diff between fdasrvf versions 2.4.1 dated 2025-09-23 and 2.4.2 dated 2025-10-03

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Package DR.SC updated to version 3.6 with previous version 3.5 dated 2025-03-29

Title: Joint Dimension Reduction and Spatial Clustering
Description: Joint dimension reduction and spatial clustering is conducted for Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
Author: Wei Liu [aut, cre], Yi Yang [aut], Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>

Diff between DR.SC versions 3.5 dated 2025-03-29 and 3.6 dated 2025-10-03

 DR.SC-3.5/DR.SC/build/partial.rdb           |only
 DR.SC-3.5/DR.SC/data/datalist               |only
 DR.SC-3.5/DR.SC/man/genspatialdata.Rd       |only
 DR.SC-3.6/DR.SC/DESCRIPTION                 |   15 -
 DR.SC-3.6/DR.SC/MD5                         |   69 ++---
 DR.SC-3.6/DR.SC/NAMESPACE                   |    4 
 DR.SC-3.6/DR.SC/R/RcppExports.R             |    8 
 DR.SC-3.6/DR.SC/R/main.R                    |  343 ++++++++++++++--------------
 DR.SC-3.6/DR.SC/README.md                   |    3 
 DR.SC-3.6/DR.SC/build/vignette.rds          |binary
 DR.SC-3.6/DR.SC/data/seu.rda                |only
 DR.SC-3.6/DR.SC/inst/doc/DR-SC.R            |    2 
 DR.SC-3.6/DR.SC/inst/doc/DR-SC.Rmd          |    4 
 DR.SC-3.6/DR.SC/inst/doc/DR-SC.html         |  185 ++++++++-------
 DR.SC-3.6/DR.SC/inst/doc/DR.SC.DLPFC.R      |    8 
 DR.SC-3.6/DR.SC/inst/doc/DR.SC.DLPFC.Rmd    |   10 
 DR.SC-3.6/DR.SC/inst/doc/DR.SC.DLPFC.html   |  332 +++++++++++++++------------
 DR.SC-3.6/DR.SC/inst/doc/DR.SC.Simu.R       |   10 
 DR.SC-3.6/DR.SC/inst/doc/DR.SC.Simu.Rmd     |   54 ++--
 DR.SC-3.6/DR.SC/inst/doc/DR.SC.Simu.html    |  294 +++++++++++++-----------
 DR.SC-3.6/DR.SC/man/DR.SC.Rd                |    4 
 DR.SC-3.6/DR.SC/man/DR.SC.fit.Rd            |    4 
 DR.SC-3.6/DR.SC/man/FindSVGs.Rd             |    2 
 DR.SC-3.6/DR.SC/man/RunWPCA.Rd              |    2 
 DR.SC-3.6/DR.SC/man/drscPlot.Rd             |    2 
 DR.SC-3.6/DR.SC/man/getAdj.Rd               |    4 
 DR.SC-3.6/DR.SC/man/mbicPlot.Rd             |    2 
 DR.SC-3.6/DR.SC/man/selectModel.Rd          |    4 
 DR.SC-3.6/DR.SC/man/seu_sim.Rd              |only
 DR.SC-3.6/DR.SC/man/sp_means_Rcpp.Rd        |   38 +--
 DR.SC-3.6/DR.SC/man/sp_sums_Rcpp.Rd         |   38 +--
 DR.SC-3.6/DR.SC/man/spatialPlotClusters.Rd  |    2 
 DR.SC-3.6/DR.SC/man/topSVGs.Rd              |    2 
 DR.SC-3.6/DR.SC/src/RcppExports.cpp         |   33 --
 DR.SC-3.6/DR.SC/src/simulDRcluster_main.cpp |   54 ++++
 DR.SC-3.6/DR.SC/vignettes/DR-SC.Rmd         |    4 
 DR.SC-3.6/DR.SC/vignettes/DR.SC.DLPFC.Rmd   |   10 
 DR.SC-3.6/DR.SC/vignettes/DR.SC.Simu.Rmd    |   54 ++--
 38 files changed, 855 insertions(+), 745 deletions(-)

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Package bookdown updated to version 0.45 with previous version 0.44 dated 2025-08-21

Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] , Christophe Dervieux [ctb] , JJ Allaire [ctb], Albert Kim [ctb], Alessandro Samuel-Rosa [ctb], Andrzej Oles [ctb], Atsushi Yasumoto [ctb] , Aust Frederik [ctb] , Bastiaan Quast [ctb], Ben Marwick [ctb], Chester Ismay [ctb], Clif [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between bookdown versions 0.44 dated 2025-08-21 and 0.45 dated 2025-10-03

 DESCRIPTION                   |    6 +++---
 MD5                           |    6 +++---
 R/html.R                      |    2 +-
 tests/testthat/test-gitbook.R |   24 ++++++++++++++++++++++++
 4 files changed, 31 insertions(+), 7 deletions(-)

More information about bookdown at CRAN
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Package cesR (with last version 0.1.0) was removed from CRAN

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

2021-11-23 0.1.0

Permanent link
Package glmtree (with last version 0.3.1) was removed from CRAN

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

2024-03-06 0.3.1
2020-10-03 0.2
2019-10-06 0.1

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