CRAN Package Updates Bot

CRAN updates: biostats fiodata #rstats

CRAN updates: tinycodet wakefield #rstats

CRAN updates: bioLeak easyViz multvardiv sate #rstats

CRAN: Package wkpool Establishes and maintains vertex pool topology for geometry handled by 'wk'. Segments are the atomic unit, vertices are shared via integer references into a pool. Topology is made discoverable via coincident vertex detection while not requiring modification of the input data. Topological data models follow principles described in Worboys and Duckham (2004, ISBN:978-0415283755). The edge-based topology geometry decomposed into vertices and directed edge pairs is a simplification of the quad-edge case in Guibas &amp; Stolfi (1985) &lt;<a href="https://doi.org/10.1145%2F282918.282923" target="_top">doi:10.1145/282918.282923</a>&gt;.

New CRAN package wkpool with initial version 0.3.0
#rstats
https://cran.r-project.org/package=wkpool

CRAN: Package rdkitpyr A task-oriented R interface to the 'RDKit' &lt;<a href="https://www.rdkit.org" target="_top">https://www.rdkit.org</a>&gt; library through its 'Python' API via 'reticulate'. The package offers high-level cheminformatics functionality, including molecule parsing, descriptor calculation, and fingerprint generation without replicating the native structure of 'RDKit'.

New CRAN package rdkitpyr with initial version 0.2.1
#rstats
https://cran.r-project.org/package=rdkitpyr

CRAN: Package llamaR Provides 'R' bindings to 'llama.cpp' for running Large Language Models ('LLMs') locally with optional 'Vulkan' GPU acceleration via 'ggmlR'. Supports model loading, text generation, 'tokenization', token-to-piece conversion, 'embeddings' (single and batch), encoder-decoder inference, low-level batch management, chat templates, 'LoRA' adapters, explicit backend/device selection, multi-GPU split, and 'NUMA' optimization. Includes a high-level 'ragnar'-compatible embedding provider ('embed_llamar'). Built on top of 'ggmlR' for efficient tensor operations.

New CRAN package llamaR with initial version 0.2.2
#rstats
https://cran.r-project.org/package=llamaR

CRAN: Package fdars Functional data analysis tools with a high-performance 'Rust' backend. Provides methods for functional data manipulation, depth computation, distance metrics, regression, and statistical testing. Supports both 1D functional data (curves) and 2D functional data (surfaces). Methods are described in Ramsay and Silverman (2005, ISBN:978-0-387-40080-8) "Functional Data Analysis" and Ferraty and Vieu (2006, ISBN:978-0-387-30369-7) "Nonparametric Functional Data Analysis".

New CRAN package fdars with initial version 0.3.3
#rstats
https://cran.r-project.org/package=fdars

CRAN: Package checkstring Validates common string formats including financial identifiers (ISIN, CUSIP, SEDOL, FIGI, IBAN, LEI), publication identifiers (ISBN, ISSN, DOI, ORCID), and general formats (email, UUID, URL, semver), with check digit verification where applicable.

New CRAN package checkstring with initial version 0.1.0
#rstats
https://cran.r-project.org/package=checkstring

CRAN: Package APCinteraction Provides novel nonparametric tests, 'APCSSA' and 'APCSSM', for interaction in two-way ANOVA designs with balanced replications using all possible comparisons. These statistics extend previous methods, allow greater flexibility, and demonstrate higher power in detecting interactions for non-normal data. The package includes optimized functions for computing these test statistics, generating interaction plots, and simulating their null distributions. The companion package 'APCinteractionData' is available on 'GitHub' &lt;<a href="https://github.com/tranbaokhue/APCinteractionData" target="_top">https://github.com/tranbaokhue/APCinteractionData</a>&gt;. Methods are described and compared empirically in Tran, Wagaman, Nguyen, Jacobson, and Hartlaub (2024) &lt;<a href="https://doi.org/10.48550%2FarXiv.2410.04700" target="_top">doi:10.48550/arXiv.2410.04700</a>&gt;.

New CRAN package APCinteraction with initial version 0.1.0
#rstats
https://cran.r-project.org/package=APCinteraction

CRAN updates: lme4 #rstats

CRAN updates: shinyMatrix sleev tidyILD #rstats

CRAN updates: asymmetry comat RcppGSL rjd3jars TauStar #rstats

CRAN updates: aire.zmvm ccLRforR DIDmultiplegtDYN systemfonts #rstats

CRAN readmissions: tidybins #rstats

CRAN updates: CSDownscale educabR lmerTest RcppParallel #rstats

CRAN updates: move2 #rstats

CRAN updates: babynamesIL exams.forge #rstats

CRAN: Package TriLLIEM Triad Log-Linear modelling of Imprinting Environmental interactions, and Maternal effects (TriLLIEM). This is an implementation of the log-linear model described in a series of papers, see for example Ainsworth et al. (2010) &lt;<a href="https://doi.org/10.1002%2Fgepi.20547" target="_top">doi:10.1002/gepi.20547</a>&gt;.

New CRAN package TriLLIEM with initial version 0.1.0
#rstats
https://cran.r-project.org/package=TriLLIEM

CRAN: Package scPairs Discovers synergistic gene pairs in single-cell RNA-seq and spatial transcriptomics data. Unlike conventional pairwise co-expression analyses that rely on a single correlation metric, scPairs integrates 14 complementary metrics across five orthogonal evidence layers to compute a composite synergy score with optional permutation-based significance testing. The five evidence layers span cell-level co-expression (Pearson, Spearman, biweight midcorrelation, mutual information, ratio consistency), neighbourhood-aware smoothing (KNN-smoothed correlation, neighbourhood co-expression, cluster pseudo-bulk, cross-cell-type, neighbourhood synergy), prior biological knowledge (GO/KEGG co-annotation Jaccard, pathway bridge score), trans-cellular interaction, and spatial co-variation (Lee's L, co-location quotient). This multi-scale design enables researchers to move beyond simple co-expression towards a comprehensive characterisation of cooperative gene regulation at transcriptomic and spatial resolution. For more information, see the package documentation at &lt;<a href="https://github.com/zhaoqing-wang/scPairs" target="_top">https://github.com/zhaoqing-wang/scPairs</a>&gt;.

New CRAN package scPairs with initial version 0.1.8
#rstats
https://cran.r-project.org/package=scPairs

CRAN: Package RSQLite.toolkit A lightweight wrapper around the 'RSQLite' package for streamlined loading of data from tabular files (i,e. text delimited files like Comma Separated Values and Tab Separated Values, Microsoft Excel, and Arrow Inter-process Communication files) in 'SQLite' databases. Includes helper functions for inspecting the structure of the input files, and some functions to simplify activities on the 'SQLite' tables.

New CRAN package RSQLite.toolkit with initial version 0.1.1
#rstats
https://cran.r-project.org/package=RSQLite.toolkit

CRAN: Package reliacoef Calculates and compares various reliability coefficients for unidimensional and multidimensional scales. Supported unidimensional estimators include coefficient alpha, congeneric reliability, the Gilmer-Feldt coefficient, Feldt's classical congeneric reliability, Hancock's H, Heise-Bohrnstedt's omega, Kaiser-Caffrey's alpha, and Ten Berge and Zegers' mu series. Multidimensional estimators include stratified alpha, maximal reliability, correlated factors reliability, second-order factor reliability, and bifactor reliability. See Cho (2021) &lt;<a href="https://doi.org/10.1007%2Fs11336-021-09801-1" target="_top">doi:10.1007/s11336-021-09801-1</a>&gt;, Cho (2024) &lt;<a href="https://doi.org/10.1037%2Fmet0000475" target="_top">doi:10.1037/met0000475</a>&gt;, Cho (2025) &lt;<a href="https://doi.org/10.1037%2Fmet0000525" target="_top">doi:10.1037/met0000525</a>&gt;.

New CRAN package reliacoef with initial version 1.0.1
#rstats
https://cran.r-project.org/package=reliacoef

CRAN: Package epiviz Tools for making epidemiological reporting easier with consistent static and dynamic charts and maps. Builds on 'ggplot2' for static visualizations as described in Wickham (2016) &lt;<a href="https://doi.org/10.1007%2F978-3-319-24277-4" target="_top">doi:10.1007/978-3-319-24277-4</a>&gt; and 'plotly' for interactive visualizations as described in Sievert (2020) &lt;<a href="https://doi.org/10.1201%2F9780429447273" target="_top">doi:10.1201/9780429447273</a>&gt;.

New CRAN package epiviz with initial version 0.1.2
#rstats
https://cran.r-project.org/package=epiviz

CRAN: Package AV1R Converts legacy microscopy video formats (H.264/H.265, AVI/MJPEG, TIFF stacks) to the modern 'AV1' codec with minimal quality loss. Typical use cases include compressing large TIFF stacks from confocal microscopy and time-lapse experiments from hundreds of gigabytes to manageable sizes, re-encoding MP4 files exported from 'CellProfiler', 'ImageJ'/'Fiji', and microscope software with approximately 2x better compression at the same visual quality, and converting legacy AVI (MJPEG) and H.265 recordings to a single patent-free format suited for long-term archival. Automatically selects the best available backend: GPU hardware acceleration via 'Vulkan' 'VK_KHR_VIDEO_ENCODE_AV1' (tested on AMD RDNA4; bundled headers, builds with any 'Vulkan' SDK &gt;= 1.3.275), with automatic fallback to CPU encoding through 'FFmpeg' and 'SVT-AV1'. Audio tracks are preserved automatically. Provides a simple R API for batch conversion of entire experiment folders.

New CRAN package AV1R with initial version 0.1.2
#rstats
https://cran.r-project.org/package=AV1R

CRAN readmissions: multinet #rstats

CRAN updates: emmeans later PulmoDataSets vectorsurvR #rstats

CRAN updates: cgam isotree lessR renv ssdtools textclean #rstats

CRAN removals: event neuroimaGene pdxTrees #rstats

CRAN updates: copulaSFM reappraised #rstats

CRAN updates: emplikCS #rstats

CRAN updates: climate did2s #rstats