Wed, 01 Oct 2025

Package mgwnbr updated to version 0.3.0 with previous version 0.2.0 dated 2024-03-26

Title: Multiscale Geographically Weighted Negative Binomial Regression
Description: Fits a geographically weighted regression model with different scales for each covariate. Uses the negative binomial distribution as default, but also accepts the normal, Poisson, or logistic distributions. Can fit the global versions of each regression and also the geographically weighted alternatives with only one scale, since they are all particular cases of the multiscale approach. Hanchen Yu (2024). "Exploring Multiscale Geographically Weighted Negative Binomial Regression", Annals of the American Association of Geographers <doi:10.1080/24694452.2023.2289986>. Fotheringham AS, Yang W, Kang W (2017). "Multiscale Geographically Weighted Regression (MGWR)", Annals of the American Association of Geographers <doi:10.1080/24694452.2017.1352480>. Da Silva AR, Rodrigues TCV (2014). "Geographically Weighted Negative Binomial Regression - incorporating overdispersion", Statistics and Computing <doi:10.1007/s11222-013-9401-9>.
Author: Juliana Rosa [aut, cre], Jessica Vasconcelos [aut], Alan da Silva [aut]
Maintainer: Juliana Rosa <julianamrosa00@gmail.com>

Diff between mgwnbr versions 0.2.0 dated 2024-03-26 and 0.3.0 dated 2025-10-01

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Package MapperAlgo updated to version 1.0.5 with previous version 1.0.4 dated 2025-08-22

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>

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Package hydroloom updated to version 1.1.1 with previous version 1.1.0 dated 2024-08-26

Title: Utilities to Weave Hydrologic Fabrics
Description: A collection of utilities that support creation of network attributes for hydrologic networks. Methods and algorithms implemented are documented in Moore et al. (2019) <doi:10.3133/ofr20191096>), Cormen and Leiserson (2022) <ISBN:9780262046305> and Verdin and Verdin (1999) <doi:10.1016/S0022-1694(99)00011-6>.
Author: David Blodgett [aut, cre]
Maintainer: David Blodgett <dblodgett@usgs.gov>

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Package shrinkGPR updated to version 1.1.1 with previous version 1.1 dated 2025-08-19

Title: Scalable Gaussian Process Regression with Hierarchical Shrinkage Priors
Description: Efficient variational inference methods for fully Bayesian Gaussian Process Regression (GPR) models with hierarchical shrinkage priors, including the triple gamma prior for effective variable selection and covariance shrinkage in high-dimensional settings. The package leverages normalizing flows to approximate complex posterior distributions. For details on implementation, see Knaus (2025) <doi:10.48550/arXiv.2501.13173>.
Author: Peter Knaus [aut, cre]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>

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Package Rilostat updated to version 2.3.4 with previous version 2.3.1 dated 2025-03-10

Title: R Interface to ILOSTAT Open Data
Description: Provides tools to access, search, and manipulate ILO's ilostat database, including bulk download of statistical data, dictionary lookups, and table of contents.
Author: David Bescond [aut, cre] , Mabelin Villarreal-Fuentes [ctb] , ILO Department of Statistics [cph, fnd]
Maintainer: David Bescond <bescond@ilo.org>

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Package fluxtools updated to version 0.7.1 with previous version 0.7.0 dated 2025-09-18

Title: A 'shiny' App for Reproducible QA/QC of Eddy Covariance Data
Description: An interactive 'shiny'-based tool for exploration and quality assurance and quality control (QA/QC) of eddy covariance flux tower data processing. It generates data-point removal code via user-directed selection from a scatterplot, and can export a cleaned .csv with removed points set to NA plus an R script for reproducibility. Reference: Key (2025) <DOI:10.5281/zenodo.15597159>.
Author: Kesondra Key [aut, cre]
Maintainer: Kesondra Key <keyke@iu.edu>

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Package faux updated to version 1.2.3 with previous version 1.2.2 dated 2025-01-15

Title: Simulation for Factorial Designs
Description: Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://scienceverse.github.io/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.
Author: Lisa DeBruine [aut, cre, cph] , Anna Krystalli [ctb] , Andrew Heiss [ctb]
Maintainer: Lisa DeBruine <debruine@gmail.com>

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Package degradr updated to version 1.0.1 with previous version 1.0.0 dated 2025-08-25

Title: Estimating Remaining Useful Life with Linear Mixed Effects Models
Description: Provides tools for estimating the Remaining Useful Life (RUL) of degrading systems using linear mixed-effects models and creating a health index. It supports both univariate and multivariate degradation signals. For multivariate inputs, the signals are merged into a univariate health index prior to modeling. Linear and exponential degradation trajectories are supported (the latter using a log transformation). Remaining Useful Life (RUL) distributions are estimated using Bayesian updating for new units, enabling on-site predictive maintenance. Based on the methodology of Liu and Huang (2016) <doi:10.1109/TASE.2014.2349733>.
Author: Pedro Abraham Montoya Calzada [aut, cre, cph] , Rogelio Salinas Gutierrez [aut, cph] , Silvia Rodriguez-Narciso [aut, cph] , Netzahualcoyotl Castaneda-Leyva [aut, cph]
Maintainer: Pedro Abraham Montoya Calzada <pedroabraham.montoya@gmail.com>

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Package ClusROC updated to version 1.0.3 with previous version 1.0.2 dated 2022-11-17

Title: ROC Analysis in Three-Class Classification Problems for Clustered Data
Description: Statistical methods for ROC surface analysis in three-class classification problems for clustered data and in presence of covariates. In particular, the package allows to obtain covariate-specific point and interval estimation for: (i) true class fractions (TCFs) at fixed pairs of thresholds; (ii) the ROC surface; (iii) the volume under ROC surface (VUS); (iv) the optimal pairs of thresholds. Methods considered in points (i), (ii) and (iv) are proposed and discussed in To et al. (2022) <doi:10.1177/09622802221089029>. Referring to point (iv), three different selection criteria are implemented: Generalized Youden Index (GYI), Closest to Perfection (CtP) and Maximum Volume (MV). Methods considered in point (iii) are proposed and discussed in Xiong et al. (2018) <doi:10.1177/0962280217742539>. Visualization tools are also provided. We refer readers to the articles cited above for all details.
Author: Duc-Khanh To [aut, cre] , Gianfranco Adimari [ctb], Monica Chiogna [ctb]
Maintainer: Duc-Khanh To <tdkhanh@hcmus.edu.vn>

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Package bbk updated to version 0.8.0 with previous version 0.7.0 dated 2025-08-25

Title: Client for Central Bank APIs
Description: A client for retrieving data and metadata from major central bank APIs. It supports access to the 'Bundesbank SDMX Web Service API' (<https://www.bundesbank.de/en/statistics/time-series-databases/help-for-sdmx-web-service/web-service-interface-data>), the 'Swiss National Bank Data Portal' (<https://data.snb.ch/en>), the 'European Central Bank Data Portal API' (<https://data.ecb.europa.eu/help/api/overview>), the 'Bank of England Interactive Statistical Database' (<https://www.bankofengland.co.uk/boeapps/database>), the 'Banco de España API' (<https://www.bde.es/webbe/en/estadisticas/recursos/api-estadisticas-bde.html>), the 'Banque de France Web Service' (<https://webstat.banque-france.fr/en/pages/guide-migration-api/>), and 'Bank of Canada Valet API' (<https://www.bankofcanada.ca/valet/docs>).
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>

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Package SEQTaRget updated to version 1.0.1 with previous version 1.0.0 dated 2025-09-17

Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases. The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies, can be used to estimate observational analogs of intention-to-treat and per-protocol effects, and can adjust for potential selection bias induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] , Alejandro Szmulewicz [aut] , Tom Palmer [aut] , Miguel Hernan [aut] , The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryanodea@hsph.harvard.edu>

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Package qad updated to version 1.0.6 with previous version 1.0.5 dated 2025-07-02

Title: Quantification of Asymmetric Dependence
Description: A copula-based measure for quantifying asymmetry in dependence and associations. Documentation and theory about 'qad' is provided by the paper by Junker, Griessenberger & Trutschnig (2021, <doi:10.1016/j.csda.2020.107058>), and the paper by Trutschnig (2011, <doi:10.1016/j.jmaa.2011.06.013>).
Author: Thimo Kasper [aut], Florian Griessenberger [aut], Robert R. Junker [aut], Valentin Petzel [aut], Wolfgang Trutschnig [aut], Lea Maislinger [cre]
Maintainer: Lea Maislinger <lea.maislinger@plus.ac.at>

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Package MultiTraits updated to version 0.6.0 with previous version 0.5.0 dated 2025-04-20

Title: Analyzing and Visualizing Multidimensional Plant Traits
Description: Implements analytical methods for multidimensional plant traits, including Competitors-Stress tolerators-Ruderals strategy analysis using leaf traits, Leaf-Height-Seed strategy analysis, Niche Periodicity Table analysis, and Trait Network analysis. Provides functions for data analysis, visualization, and network metrics calculation. Methods are based on Grime (1974) <doi:10.1038/250026a0>, Pierce et al. (2017) <doi:10.1111/1365-2435.12882>, Westoby (1998) <doi:10.1023/A:1004327224729>, Winemiller et al. (2015) <doi:10.1111/ele.12462>, He et al. (2020) <doi:10.1016/j.tree.2020.06.003>.
Author: Yan He [aut, cre], Zhaogang Liu [aut], Jiangshan Lai [aut], Lingfeng Mao [aut]
Maintainer: Yan He <heyan@njfu.edu.cn>

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Package ggredist updated to version 0.0.4 with previous version 0.0.3 dated 2025-08-29

Title: Scales, Geometries, and Extensions of 'ggplot2' for Election Mapping
Description: Provides 'ggplot2' extensions for political map making. Implements new geometries for groups of simple feature geometries. Adds palettes and scales for red to blue color mapping and for discrete maps. Implements tools for easy label generation and placement, automatic map coloring, and themes.
Author: Cory McCartan [aut], Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>

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Package aion updated to version 1.6.0 with previous version 1.5.0 dated 2025-04-29

Title: Archaeological Time Series
Description: A toolkit for archaeological time series and time intervals. This package provides a system of classes and methods to represent and work with archaeological time series and time intervals. Dates are represented as "rata die" and can be converted to (virtually) any calendar defined by Reingold and Dershowitz (2018) <doi:10.1017/9781107415058>. This packages offers a simple API that can be used by other specialized packages.
Author: Nicolas Frerebeau [aut, cre] , Joe Roe [aut] , Brice Lebrun [art] , Universite Bordeaux Montaigne [fnd] , CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>

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Package tikatuwq updated to version 0.5.1 with previous version 0.4.6 dated 2025-09-22

Title: Water Quality Analysis Tools for the Brazilian Context
Description: Tools to import, clean, validate, and analyze freshwater quality data in Brazil. Implements water quality indices including the Water Quality Index (WQI/IQA), the Trophic State Index (TSI/IET) after Carlson (1977) <doi:10.4319/lo.1977.22.2.0361> and Lamparelli (2004) <https://www.teses.usp.br/teses/disponiveis/41/41134/tde-20032006-075813/publico/TeseLamparelli2004.pdf>, and the National Sanitation Foundation Water Quality Index (NSF WQI) <doi:10.1007/s11157-023-09650-7>. The package also checks compliance with Brazilian standard CONAMA Resolution 357/2005 <https://conama.mma.gov.br/?id=450&option=com_sisconama&task=arquivo.download> and generates reproducible reports for routine monitoring workflows.
Author: Vinicius Saraiva Santos [aut, cre]
Maintainer: Vinicius Saraiva Santos <vinisaraiva@gmail.com>

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Package PRECAST updated to version 1.7 with previous version 1.6.6 dated 2025-03-27

Title: Embedding and Clustering with Alignment for Spatial Omics Datasets
Description: An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.
Author: Wei Liu [aut, cre], Yi Yang [aut], Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>

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Package meteospain updated to version 0.2.2 with previous version 0.2.1 dated 2025-07-01

Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG, Meteoclimatic...).
Author: Victor Granda [aut, cre] , Miquel de Caceres [ctb] , Aitor Ameztegui [ctb] , Luis Franco [ctb], Ruben Fernandez-Casal [ctb]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>

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Package climate updated to version 1.2.4 with previous version 1.2.3 dated 2025-04-23

Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories: OGIMET (<http://ogimet.com/index.phtml.en>), University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>), Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>), and National Oceanic & Atmospheric Administration (NOAA). This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] , Arkadiusz Glogowski [aut] , Jakub Nowosad [aut] , IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>

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Package systemfonts updated to version 1.3.1 with previous version 1.3.0 dated 2025-09-30

Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries on Windows, macOS and Linux for finding font files that can then be used further by e.g. graphic devices. The main use is intended to be from compiled code but 'systemfonts' also provides access from R.
Author: Thomas Lin Pedersen [aut, cre] , Jeroen Ooms [aut] , Devon Govett [aut] , Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>

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Package redist updated to version 4.3.1 with previous version 4.3.0 dated 2025-07-08

Title: Simulation Methods for Legislative Redistricting
Description: Enables researchers to sample redistricting plans from a pre-specified target distribution using Sequential Monte Carlo and Markov Chain Monte Carlo algorithms. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. Tools for analysis such as computation of various summary statistics and plotting functionality are also included. The package implements the SMC algorithm of McCartan and Imai (2023) <doi:10.1214/23-AOAS1763>, the enumeration algorithm of Fifield, Imai, Kawahara, and Kenny (2020) <doi:10.1080/2330443X.2020.1791773>, the Flip MCMC algorithm of Fifield, Higgins, Imai and Tarr (2020) <doi:10.1080/10618600.2020.1739532>, the Merge-split/Recombination algorithms of Carter et al. (2019) <doi:10.48550/arXiv.1911.01503> and DeFord et al. (2021) <doi:10.1162/99608f92.eb30390f>, and the Short-burst optimization algorithm of Cannon et al. (2020) < [...truncated...]
Author: Christopher T. Kenny [aut, cre] , Cory McCartan [aut] , Ben Fifield [aut] , Kosuke Imai [aut] , Jun Kawahara [ctb], Alexander Tarr [ctb], Michael Higgins [ctb]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>

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Package PatientProfiles updated to version 1.4.3 with previous version 1.4.2 dated 2025-07-09

Title: Identify Characteristics of Patients in the OMOP Common Data Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] , Yuchen Guo [aut] , Mike Du [aut] , Kim Lopez-Guell [aut] , Edward Burn [aut] , Nuria Mercade-Besora [aut] , Xintong Li [ctb] , Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>

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Package lpirfs updated to version 0.2.5 with previous version 0.2.4 dated 2025-03-18

Title: Local Projections Impulse Response Functions
Description: Provides functions to estimate and visualize linear as well as nonlinear impulse responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>. The methods and the package are explained in detail in Adämmer (2019) <doi:10.32614/RJ-2019-052>.
Author: Philipp Adaemmer [aut, cre] , James P. LeSage [ctb], Mehmet Balcilar [ctb], Jon Danielsson [ctb]
Maintainer: Philipp Adaemmer <philipp.adaemmer@uni-greifswald.de>

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Package CB2 updated to version 1.3.6 with previous version 1.3.4 dated 2020-07-24

Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyunhwanjeong@icloud.com>

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Package Asiaverse (with last version 0.1.0) was removed from CRAN

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2022-09-09 1.0.0

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Package multilevLCA updated to version 2.1.1 with previous version 2.1.0 dated 2025-09-22

Title: Estimates and Plots Single-Level and Multilevel Latent Class Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al. (2025) <doi:10.1080/00273171.2025.2473935>.
Author: Roberto Di Mari [aut, cre], Johan Lyrvall [aut], Zsuzsa Bakk [ctb], Jennifer Oser [ctb], Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>

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Package geneviewer updated to version 0.1.11 with previous version 0.1.10 dated 2025-01-10

Title: Gene Cluster Visualizations
Description: Provides tools for plotting gene clusters and transcripts by importing data from GenBank, FASTA, and GFF files. It performs BLASTP and MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>; Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on gene arrow maps. Extensive customization options are available, including legends, labels, annotations, scales, colors, tooltips, and more.
Author: Niels van der Velden [aut, cre]
Maintainer: Niels van der Velden <n.s.j.vandervelden@gmail.com>

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Package cylcop updated to version 0.2.1 with previous version 0.2.0 dated 2022-10-29

Title: Circular-Linear Copulas with Angular Symmetry for Movement Data
Description: Classes (S4) of circular-linear, symmetric copulas with corresponding methods, extending the 'copula' package. These copulas are especially useful for modeling correlation in discrete-time movement data. Methods for density, (conditional) distribution, random number generation, bivariate dependence measures and fitting parameters using maximum likelihood and other approaches. The package also contains methods for visualizing movement data and copulas.
Author: Florian Hodel [aut, cre]
Maintainer: Florian Hodel <florian.hodel@yahoo.com>

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Package RchivalTag readmission to version 0.2.2 with previous version 0.1.9 dated 2023-11-10

Title: Analyzing and Interactive Visualization of Archival Tagging Data
Description: A set of functions to generate, access and analyze standard data products from archival tagging data.
Author: Robert K. Bauer [aut, cre]
Maintainer: Robert K. Bauer <marine.biologging@gmail.com>

This is a re-admission after prior archival of version 0.1.9 dated 2023-11-10

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Package checkglobals updated to version 0.1.4 with previous version 0.1.3 dated 2025-02-06

Title: Static Analysis of R-Code Dependencies
Description: A minimal R-package to approximately detect global and imported functions or variables from R-source code or R-packages by static code analysis.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>

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Package radiant.model updated to version 1.6.8 with previous version 1.6.7 dated 2024-10-11

Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic regression, naive Bayes, neural networks, classification and regression trees, model evaluation, collaborative filtering, decision analysis, and simulation. The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant.model versions 1.6.7 dated 2024-10-11 and 1.6.8 dated 2025-10-01

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Package patterncausality updated to version 0.2.3 with previous version 0.2.2 dated 2025-09-04

Title: Pattern Causality Algorithm
Description: Pattern causality is a novel approach for detecting the hidden causality in the complex system.
Author: Stavros Stavroglou [aut, cre] , Athanasios Pantelous [aut] , Hui Wang [aut]
Maintainer: Stavros Stavroglou <stavros.k.stavroglou@gmail.com>

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Package fireexposuR readmission to version 1.2.0 with previous version 1.1.0 dated 2025-05-27

Title: Compute and Visualize Wildfire Exposure
Description: Methods for computing and visualizing wildfire ignition exposure and directional vulnerability that are published in a series of scientific publications are automated by the functions in this package. See Beverly et al. (2010) <doi:10.1071/WF09071>, Beverly et al. (2021) <doi:10.1007/s10980-020-01173-8>, and Beverly and Forbes (2023) <doi:10.1007/s11069-023-05885-3> for background and methodology.
Author: Air Forbes [aut, cre] , Jennifer Beverly [ths]
Maintainer: Air Forbes <heyairf@gmail.com>

This is a re-admission after prior archival of version 1.1.0 dated 2025-05-27

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Package dartR.base updated to version 1.0.7 with previous version 1.0.5 dated 2025-03-03

Title: Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Description: Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism') and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility', maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages. To install the other packages, we recommend to install the 'dartRverse' package, that su [...truncated...]
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Diana Robledo-Ruiz [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb], Eric Archer [ctb], Ching Ching Lau [ [...truncated...]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>

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Package confidenceCurves updated to version 0.2.0 with previous version 0.1.0 dated 2025-08-19

Title: Frequentist Confidence Analysis for Clinical Trials
Description: Frequentist confidence analysis answers the question: How confident are we in a particular treatment effect? This package calculates the frequentist confidence in a treatment effect of interest given observed data, and returns the family of confidence curves associated with that data.
Author: Freda Werdiger [aut, cre]
Maintainer: Freda Werdiger <freda.werdiger@unimelb.edu.au>

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Package bage updated to version 0.9.6 with previous version 0.9.4 dated 2025-07-20

Title: Bayesian Estimation and Forecasting of Age-Specific Rates
Description: Fast Bayesian estimation and forecasting of age-specific rates, probabilities, and means, based on 'Template Model Builder'.
Author: John Bryant [aut, cre], Junni Zhang [aut], Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>

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Package VertexWiseR updated to version 1.4.2 with previous version 1.4.1 dated 2025-08-19

Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal Surface
Description: Provides functions to run statistical analyses on surface-based neuroimaging data, computing measures including cortical thickness and surface area of the whole-brain and of the hippocampi. It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12' preprocessed datasets and 'HippUnfold' hippocampal segmentation outputs for a given sample by restructuring the data values into a single file. The single file can then be used by the package for analyses independently from its base dataset and without need for its access.
Author: Junhong Yu [aut] , Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>

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Package stepmetrics updated to version 1.0.3 with previous version 1.0.1 dated 2025-09-16

Title: Calculate Step and Cadence Metrics from Wearable Data
Description: Provides functions to calculate step- and cadence-based metrics from timestamped accelerometer and wearable device data. Supports CSV and AGD files from 'ActiGraph' devices, CSV files from 'Fitbit' devices, and step counts derived with R package 'GGIR' <https://github.com/wadpac/GGIR>, with automatic handling of epoch lengths from 1 to 60 seconds. Metrics include total steps, cadence peaks, minutes and steps in predefined cadence bands, and time and steps in moderate-to-vigorous physical activity (MVPA). Methods and thresholds are informed by the literature, e.g., Tudor-Locke and Rowe (2012) <doi:10.2165/11599170-000000000-00000>, Barreira et al. (2012) <doi:10.1249/MSS.0b013e318254f2a3>, and Tudor-Locke et al. (2018) <doi:10.1136/bjsports-2017-097628>. The package record is also available on Zenodo (2023) <doi:10.5281/zenodo.7858094>.
Author: Jairo H Migueles [aut, cre], Elroy J Aguiar [fnd] , University of Alabama [fnd]
Maintainer: Jairo H Migueles <jairo@jhmigueles.com>

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Package pvEBayes updated to version 0.1.2 with previous version 0.1.1 dated 2025-07-10

Title: Empirical Bayes Methods for Pharmacovigilance
Description: A suite of empirical Bayes methods to use in pharmacovigilance. Contains various model fitting and post-processing functions. For more details see Tan et al. (2025) <doi:10.48550/arXiv.2502.09816>, Koenker and Mizera (2014) <doi:10.1080/01621459.2013.869224> and Efron (2016) <doi:10.1093/biomet/asv068>.
Author: Yihao Tan [aut, cre] , Marianthi Markatou [aut] , Saptarshi Chakraborty [aut] , Raktim Mukhopadhyay [aut]
Maintainer: Yihao Tan <yihaotan@buffalo.edu>

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New package plotlsirm with initial version 0.1.3
Package: plotlsirm
Title: Plot Toolkit for Latent Space Item Response Models
Version: 0.1.3
Description: Provides publication‑quality and interactive plots for exploring the posterior output of Latent Space Item Response Models, including Posterior Interaction Profiles, radar charts, 2‑D latent maps, and item‑similarity heat maps. The methods implemented in this package are based on work by Jeon, M., Jin, I. H., Schweinberger, M., Baugh, S. (2021) <doi:10.1007/s11336-021-09762-5>.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: ggplot2 (>= 3.4), rlang, dplyr, tidyr, patchwork, scales, grid
Suggests: plotly, testthat (>= 3.0.0), spelling
URL: https://github.com/jevanluo/plotlsirm
BugReports: https://github.com/jevanluo/plotlsirm/issues
Author: Jinwen Luo [aut, cre] , Minjeong Jeon [aut]
Maintainer: Jinwen Luo <jevanluo@ucla.edu>
NeedsCompilation: no
Packaged: 2025-09-24 20:18:55 UTC; jevan
Repository: CRAN
Date/Publication: 2025-10-01 07:10:02 UTC

More information about plotlsirm at CRAN
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New package PhytoIn with initial version 0.2.0
Package: PhytoIn
Title: Vegetation Analysis and Forest Inventory
Version: 0.2.0
Description: Provides functions and example datasets for phytosociological analysis, forest inventory, biomass and carbon estimation, and visualization of vegetation data. Includes functions to compute structural parameters [phytoparam(), summary.param(), stats()], estimate above-ground biomass and carbon [AGB()], stratify wood volume by diameter at breast height (DBH) classes [stratvol()], generate collector and rarefaction curves [collector.curve(), rarefaction()], and visualize basal areas on quadrat maps [BAplot(), including rectangular plots and individual coordinates]. Several example datasets are provided to demonstrate the functionality of these tools. For more details see FAO (1981, ISBN:92-5-101132-X) "Manual of forest inventory", IBGE (2012, ISBN:9788524042720) "Manual técnico da vegetação brasileira" and Heringer et al. (2020) "Phytosociology in R: A routine to estimate phytosociological parameters" <doi:10.22533/at.ed.3552009033>.
Depends: R (>= 3.5.0)
Imports: ggplot2, ggforce, packcircles, BIOMASS, scales, utils, stats
Suggests: httr2, spelling
License: GPL-3
URL: https://github.com/PhytoIn/PhytoIn
BugReports: https://github.com/PhytoIn/PhytoIn/issues
Encoding: UTF-8
LazyData: true
Language: en-US
NeedsCompilation: no
Packaged: 2025-09-24 17:21:04 UTC; raspe
Author: Rodrigo Augusto Santinelo Pereira [aut, cre]
Maintainer: Rodrigo Augusto Santinelo Pereira <raspereira@usp.br>
Repository: CRAN
Date/Publication: 2025-10-01 07:10:13 UTC

More information about PhytoIn at CRAN
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Package nanonext updated to version 1.7.1 with previous version 1.7.0 dated 2025-09-01

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] , Posit Software, PBC [cph, fnd] , Hibiki AI Limited [cph], R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>

Diff between nanonext versions 1.7.0 dated 2025-09-01 and 1.7.1 dated 2025-10-01

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New package LePage with initial version 1.0
Package: LePage
Title: LePage Type Tests
Version: 1.0
Date: 2025-09-25
Author: Michail Tsagris [aut, cre], Abid Hussain [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Depends: R (>= 4.0)
Imports: Rfast, stats
Suggests: Rfast2
Description: Location and scale hypothesis testing using the LePage test and variants of its as proposed by Hussain A. and Tsagris M. (2025), <doi:10.48550/arXiv.2509.19126>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2025-09-25 05:27:59 UTC; mtsag
Repository: CRAN
Date/Publication: 2025-10-01 07:30:09 UTC

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Package ggDNAvis updated to version 0.3.0 with previous version 0.2.1 dated 2025-09-21

Title: 'ggplot2'-Based Tools for Visualising DNA Sequences and Modifications
Description: Uses 'ggplot2' to visualise either (a) a single DNA/RNA sequence split across multiple lines, (b) multiple DNA/RNA sequences, each occupying a whole line, or (c) base modifications such as DNA methylation called by modified bases models in Dorado or Guppy. Functions starting with visualise_<something>() are the main plotting functions, and functions starting with extract_<something>() are key helper functions for reading files and reformatting data. Source code is available at <https://github.com/ejade42/ggDNAvis> and a full non-expert user guide is available at <https://ejade42.github.io/ggDNAvis/>.
Author: Evelyn Jade [aut, cre, cph]
Maintainer: Evelyn Jade <evelynjade42@gmail.com>

Diff between ggDNAvis versions 0.2.1 dated 2025-09-21 and 0.3.0 dated 2025-10-01

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 NEWS.md                                                                    |   26 ++
 R/dna_tools.R                                                              |   83 +++++++-
 R/ggDNAvis-package.R                                                       |   17 -
 R/visualise_methylation.R                                                  |    2 
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 man/convert_base_to_number.Rd                                              |    2 
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Package GEint readmission to version 1.1 with previous version 1.0 dated 2022-05-18

Title: Misspecified Models for Gene-Environment Interaction
Description: The first major functionality is to compute the bias in regression coefficients of misspecified linear gene-environment interaction models. The most generalized function for this objective is GE_bias(). However GE_bias() requires specification of many higher order moments of covariates in the model. If users are unsure about how to calculate/estimate these higher order moments, it may be easier to use GE_bias_normal_squaredmis(). This function places many more assumptions on the covariates (most notably that they are all jointly generated from a multivariate normal distribution) and is thus able to automatically calculate many of the higher order moments automatically, necessitating only that the user specify some covariances. There are also functions to solve for the bias through simulation and non-linear equation solvers; these can be used to check your work. Second major functionality is to implement the Bootstrap Inference with Correct Sandwich (BICS) testing procedure, which we ha [...truncated...]
Author: Ryan Sun [aut, cre], Richard Barfield [ctb]
Maintainer: Ryan Sun <ryansun.work@gmail.com>

This is a re-admission after prior archival of version 1.0 dated 2022-05-18

Diff between GEint versions 1.0 dated 2022-05-18 and 1.1 dated 2025-10-01

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Package fishgrowth updated to version 1.0.3 with previous version 1.0.2 dated 2025-04-08

Title: Fit Growth Curves to Fish Data
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.
Author: Arni Magnusson [aut, cre], Mark Maunder [aut]
Maintainer: Arni Magnusson <thisisarni@gmail.com>

Diff between fishgrowth versions 1.0.2 dated 2025-04-08 and 1.0.3 dated 2025-10-01

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 22 files changed, 521 insertions(+), 388 deletions(-)

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New package ExtendedABSurvTDC with initial version 0.1.0
Package: ExtendedABSurvTDC
Title: Survival Analysis using Indicators under Time Dependent Covariates
Version: 0.1.0
Author: Dr. Himadri Ghosh [aut, cre], Mr. Saikath Das [aut], Dr. Md Yeasin [aut], Dr. Debopam Rakshit [aut]
Maintainer: Dr. Himadri Ghosh <hghosh@gmail.com>
Description: Survival analysis is employed to model time-to-event data. This package examines the relationship between survival and one or more predictors, termed as covariates, which can include both treatment variables (e.g., season of birth, represented by indicator functions) and continuous variables. To this end, the Cox-proportional hazard (Cox-PH) model, introduced by Cox in 1972, is a widely applicable and commonly used method for survival analysis. This package enables the estimation of the effect of randomization for the treatment variable to account for potential confounders, providing adjustment when estimating the association with exposure. It accommodates both fixed and time-dependent covariates and computes survival probabilities for lactation periods in dairy animals. The package is built upon the algorithm developed by Klein and Moeschberger (2003) <DOI:10.1007/b97377>.
License: GPL-3
Encoding: UTF-8
Imports: stats, survival, readxl
NeedsCompilation: no
Packaged: 2025-09-24 13:21:56 UTC; YEASIN
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2025-10-01 07:10:18 UTC

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New package EpiPvr with initial version 0.0.1
Package: EpiPvr
Title: Estimating Plant Pathogen Epidemiology Parameters from Laboratory Assays
Version: 0.0.1
Description: Provides functions for estimating plant pathogen parameters from access period (AP) experiments. Separate functions are implemented for semi-persistently transmitted (SPT) and persistently transmitted (PT) pathogens. The common AP experiment exposes insect cohorts to infected source plants, healthy test plants, and intermediate plants (for PT pathogens). The package allows estimation of acquisition and inoculation rates during feeding, recovery rates, and latent progression rates (for PT pathogens). Additional functions support inference of epidemic risk from pathogen and local parameters, and also simulate AP experiment data. The functions implement probability models for epidemiological analysis, as derived in Donnelly et al. (2025), <doi:10.32942/X29K9P>. These models were originally implemented in the 'EpiPv' 'GitHub' package.
License: GPL-3
Encoding: UTF-8
Biarch: true
Depends: R (>= 3.5)
Imports: methods, stats, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.5.0), posterior
Suggests: bayesplot, knitr, rmarkdown, testthat (>= 3.0.0), ggplot2
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
VignetteBuilder: knitr
URL: https://CRAN.R-project.org/package=EpiPvr
LazyData: true
NeedsCompilation: yes
Packaged: 2025-09-25 00:22:14 UTC; ruair
Author: Ruairi Donnelly [aut, cre, cph]
Maintainer: Ruairi Donnelly <rd501@cam.ac.uk>
Repository: CRAN
Date/Publication: 2025-10-01 07:30:14 UTC

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New package descsuppR with initial version 1.2
Package: descsuppR
Version: 1.2
License: GPL-3
Title: Support Functions for (Reproducible) Descriptive Statistics
Description: Contains functions to help with generating tables with descriptive statistics. In addition, the package can display results of statistical tests for group comparisons. A wide range of test procedures is supported, and user-defined test functions can be incorporated.
Depends: foreach
Imports: plyr, descutils, tibble, dplyr, rlang, DescTools, nparcomp, rankFD, circular, glue, purrr
Suggests: roxygen2, survival, stringr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-09-24 18:38:18 UTC; kueck2
Author: Andreas Leha [aut], Fabian Kueck [aut, cre]
Maintainer: Fabian Kueck <fabian.kueck@med.uni-goettingen.de>
Repository: CRAN
Date/Publication: 2025-10-01 07:10:08 UTC

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Package CFtime updated to version 1.7.1 with previous version 1.7.0 dated 2025-08-23

Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast (CF) Metadata Conventions for climate and forecasting data. The CF Metadata Conventions is widely used for distributing files with climate observations or projections, including the Coupled Model Intercomparison Project (CMIP) data used by climate change scientists and the Intergovernmental Panel on Climate Change (IPCC). This package specifically allows the user to work with any of the CF-compliant calendars (many of which are not compliant with POSIXt). The CF time coordinate is formally defined in the CF Metadata Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.12/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>

Diff between CFtime versions 1.7.0 dated 2025-08-23 and 1.7.1 dated 2025-10-01

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New package bakerrr with initial version 0.1.0
Package: bakerrr
Title: Background-Parallel Jobs
Version: 0.1.0
Description: Easily launch, track, and control functions as background-parallel jobs. Includes robust utilities for job status, error handling, resource monitoring, and result collection. Designed for scalable workflows in interactive and automated settings (local or remote). Integrates with multiple backends; supports flexible automation pipelines and live job tracking. For more information, see <https://anirbanshaw24.github.io/bakerrr/>.
License: MIT + file LICENSE
URL: https://github.com/anirbanshaw24/bakerrr
BugReports: https://github.com/anirbanshaw24/bakerrr/issues
Depends: R (>= 4.1.0)
Imports: callr, carrier, cli, config, fs, glue, mirai, purrr, S7
Suggests: covr, DT, htmltools, knitr, lintr, qpdf, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2025-09-25 10:40:26 UTC; shawa11
Author: Anirban Shaw [aut, cre]
Maintainer: Anirban Shaw <anirbanshaw24@gmail.com>
Repository: CRAN
Date/Publication: 2025-10-01 07:40:02 UTC

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New package readepi with initial version 1.0.1
Package: readepi
Title: Read Data from Relational Database Management Systems and Health Information Systems
Version: 1.0.1
Description: Import Data from Relational Database Management Systems (RDBMS) and Health Information Systems ('HIS'). The current version of the package supports importing data from RDBMS including 'MS SQL', 'MySQL', 'PostGRESQL', and 'SQLite', as well as from two HIS platforms: 'DHIS2' and 'SORMAS'.
License: MIT + file LICENSE
URL: https://epiverse-trace.github.io/readepi/, https://github.com/epiverse-trace/readepi/, https://github.com/epiverse-trace/readepi
BugReports: https://github.com/epiverse-trace/readepi/issues
Depends: R (>= 4.1.0)
Imports: checkmate, cli, DBI, dplyr, httr2, odbc, pool, purrr, RMySQL, RSQLite, tidyr
Suggests: cyclocomp, DiagrammeR, httptest, kableExtra, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
SystemRequirements: odbc, libmariadbclient-dev
NeedsCompilation: no
Packaged: 2025-09-24 13:08:48 UTC; karimmane
Author: Karim Mane [aut, cre, cph] , Emmanuel Kabuga [ctb] , Bubacarr Bah [ctb] , Bankole Ahadzie [ctb], Nuredin Mohammed [ctb], Abdoelnaser Degoot [ctb], Hugo Gruson [rev] , Pratik Gupte [rev] , Andree Valle-Campos [rev] , London School of Hygiene and Tropi [...truncated...]
Maintainer: Karim Mane <karim.mane@lshtm.ac.uk>
Repository: CRAN
Date/Publication: 2025-10-01 07:00:02 UTC

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Package predict3d updated to version 0.1.6 with previous version 0.1.5 dated 2024-04-04

Title: Draw Three Dimensional Predict Plot Using Package 'rgl'
Description: Draw 2 dimensional and three dimensional plot for multiple regression models using package 'ggplot2' and 'rgl'. Supports linear models (lm), generalized linear models (glm) and local polynomial regression fittings (loess).
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>

Diff between predict3d versions 0.1.5 dated 2024-04-04 and 0.1.6 dated 2025-10-01

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 man/fit2newdata.Rd      |    2 +-
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 11 files changed, 76 insertions(+), 58 deletions(-)

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New package FDOTT with initial version 0.1.0
Package: FDOTT
Title: Optimal Transport Based Testing in Factorial Design
Version: 0.1.0
Date: 2025-09-24
Description: Perform optimal transport based tests in factorial designs as introduced in Groppe et al. (2025) <doi:10.48550/arXiv.2509.13970> via the FDOTT() function. These tests are inspired by ANOVA and its nonparametric counterparts. They allow for testing linear relationships in factorial designs between finitely supported probability measures on a metric space. Such relationships include equality of all measures (no treatment effect), interaction effects between a number of factors, as well as main and simple factor effects.
License: GPL (>= 3)
Imports: Rcpp (>= 1.0.12), ROI, future.apply, progressr, transport, slam, rrapply, stats, methods
Depends: R (>= 4.1)
Suggests: ROI.plugin.glpk, future
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2025-09-24 13:04:29 UTC; mgroppe
Author: Michel Groppe [aut, cre], Linus Niemoeller [aut]
Maintainer: Michel Groppe <michel.groppe@uni-goettingen.de>
Repository: CRAN
Date/Publication: 2025-10-01 07:00:20 UTC

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New package eDNAfuns with initial version 0.1.0
Package: eDNAfuns
Title: Working with Metabarcoding Data in a Tidy Format
Version: 0.1.0
Description: A series of R functions that come in handy while working with metabarcoding data. The reasoning of doing this is to have the same functions we use all the time stored in a curated, reproducible way. In a way it is all about putting together the grammar of the 'tidyverse' from Wickham et al.(2019) <doi:10.21105/joss.01686> with the functions we have used in community ecology compiled in packages like 'vegan' from Dixon (2003) <doi:10.1111/j.1654-1103.2003.tb02228.x> and 'phyloseq' McMurdie & Holmes (2013) <doi:10.1371/journal.pone.0061217>. The package includes functions to read sequences from FAST(A/Q) into a tibble ('fasta_reader' and 'fastq_reader'), to process 'cutadapt' Martin (2011) <doi:10.14806/ej.17.1.200> 'info-file' output. When it comes to sequence counts across samples, the package works with the long format in mind (a three column 'tibble' with Sample, Sequence and counts ), with functions to move from there to the wider format.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: insect, testthat, tidyverse, knitr, rmarkdown
Imports: dplyr, googlesheets4, phyloseq, purrr, rlang, tibble, tidyr, vegan, ggplot2, vroom, Biostrings, stringr, tidyselect, readr
Depends: R (>= 4.1.0)
NeedsCompilation: no
Packaged: 2025-09-24 10:08:22 UTC; RG.5015511
Author: Ramon Gallego Simon [aut, cre]
Maintainer: Ramon Gallego Simon <ramongallego@gmail.com>
Repository: CRAN
Date/Publication: 2025-10-01 07:00:09 UTC

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New package boxTest with initial version 0.1.0
Package: boxTest
Title: Boxplot and Significance Test for Two Groups
Version: 0.1.0
Description: Provides functions to create side-by-side boxplots for a continuous variable grouped by a two-level categorical variable, check normality assumptions using the Shapiro-Wilk test (Shapiro and Wilk (1965) <doi:10.2307/2333709>), and perform appropriate statistical tests such as the independent two-sample t-test (Student (1908) <doi:10.1093/biomet/6.1.1>) or the Mann–Whitney U test ( Mann–Whitney (1947) <doi:10.1214/aoms/1177730491>). Returns a publication-ready plot and test statistics including test statistic, degrees of freedom, and p-value.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: ggplot2, dplyr, stats, rlang
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-24 11:39:52 UTC; arka
Author: Arkaprabha Sau [aut, cre], Santanu Phadikar [aut], Ishita Bhakta [aut]
Maintainer: Arkaprabha Sau <arka.doctor@gmail.com>
Repository: CRAN
Date/Publication: 2025-10-01 07:00:16 UTC

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New package BlockwiseRankTest with initial version 0.1.0
Package: BlockwiseRankTest
Title: Block-Wise Rank in Similarity Graph Edge-Count Two-Sample Test (BRISE)
Version: 0.1.0
Maintainer: Kejian Zhang <kejianzhang@u.nus.edu>
Description: Implements the Block-wise Rank in Similarity Graph Edge-count test (BRISE), a rank-based two-sample test designed for block-wise missing data. The method constructs (pattern) pair-wise similarity graphs and derives quadratic test statistics with asymptotic chi-square distribution or permutation-based p-values. It provides both vectorized and congregated versions for flexible inference. The methodology is described in Zhang, Liang, Maile, and Zhou (2025) <doi:10.48550/arXiv.2508.17411>.
License: GPL (>= 2)
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: stats
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-09-24 10:54:58 UTC; keenov
Author: Kejian Zhang [aut, cre], Doudou Zhou [aut]
Repository: CRAN
Date/Publication: 2025-10-01 07:00:26 UTC

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Package PathwayVote updated to version 0.1.2 with previous version 0.1.1 dated 2025-06-25

Title: Robust Pathway Enrichment for DNA Methylation Studies Using Ensemble Voting
Description: Performs pathway enrichment analysis using a voting-based framework that integrates CpG–gene regulatory information from expression quantitative trait methylation (eQTM) data. For a grid of top-ranked CpGs and filtering thresholds, gene sets are generated and refined using an entropy-based pruning strategy that balances information richness, stability, and probe bias correction. In particular, gene lists dominated by genes with disproportionately high numbers of CpG mappings are penalized to mitigate active probe bias—a common artifact in methylation data analysis. Enrichment results across parameter combinations are then aggregated using a voting scheme, prioritizing pathways that are consistently recovered under diverse settings and robust to parameter perturbations.
Author: Yinan Zheng [aut, cre]
Maintainer: Yinan Zheng <y-zheng@northwestern.edu>

Diff between PathwayVote versions 0.1.1 dated 2025-06-25 and 0.1.2 dated 2025-10-01

 DESCRIPTION         |   10 -
 MD5                 |   10 -
 NAMESPACE           |    5 
 R/pathway-vote.R    |  278 ++++++++++++++++++++++++++++++++++----------------
 R/utils.R           |  287 ++++++++++++++++++++++++++++++----------------------
 man/pathway_vote.Rd |   50 +++++----
 6 files changed, 404 insertions(+), 236 deletions(-)

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Package jstable updated to version 1.3.18 with previous version 1.3.17 dated 2025-09-03

Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] , Zarathu [cph, fnd], Yoonkyoung Jeon [aut], Jaehun Shon [aut], Hyojong Myung [aut], Hyungwoo Jo [aut], Sungho Choi [aut], Jaewoong Heo [aut], Mingu Jee [aut], Yujeong Yoon [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

Diff between jstable versions 1.3.17 dated 2025-09-03 and 1.3.18 dated 2025-10-01

 DESCRIPTION                                   |   20 ++++++------
 MD5                                           |   16 ++++-----
 NAMESPACE                                     |    1 
 NEWS.md                                       |    4 ++
 R/cox2.R                                      |   43 ++++++++++++++++++++++++--
 R/forestcox.R                                 |    4 +-
 inst/doc/jstable.html                         |   28 ++++++++--------
 inst/doc/jstable_competing_risk_analysis.html |    4 +-
 inst/doc/jstable_options.html                 |    4 +-
 9 files changed, 86 insertions(+), 38 deletions(-)

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Package jskm updated to version 0.5.20 with previous version 0.5.16 dated 2025-08-19

Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] , yoonkyoung Chun [aut], Zarathu [cph, fnd], sungho Choi [aut], Mingu Jee [aut], Wonbin Hahn [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

Diff between jskm versions 0.5.16 dated 2025-08-19 and 0.5.20 dated 2025-10-01

 DESCRIPTION        |   14 +++++-----
 MD5                |   14 +++++-----
 NEWS.md            |    3 ++
 R/jskm.R           |   73 +++++++++++++++++++++++++++++++++++++++++++----------
 R/svyjskm.R        |   73 ++++++++++++++++++++++++++++++++++++++++++-----------
 inst/doc/jskm.html |   32 +++++++++++------------
 man/jskm.Rd        |    3 ++
 man/svyjskm.Rd     |    3 ++
 8 files changed, 158 insertions(+), 57 deletions(-)

More information about jskm at CRAN
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