Agriculture

manureshed v0.1.2: Implements a framework for analyzing agricultural nutrient balances across multiple spatial scales with integration of wastewater treatment plant effluent loads for both nitrogen and phosphorus. Supports classification of spatial units as nutrient sources, sinks, or balanced areas based on agricultural surplus and deficit calculations. Built-in datasets include agricultural nutrient balance data from NuGIS; The Fertilizer Institute and Plant Nutrition Canada, 1987-2016) and U.S. Environmental Protection Agency wastewater discharge ECHO Discharge Monitoring Report (2007-2016). See Akanbi et al. (2025) for the methodology. There are seven vignettes, including Getting Started and Advanced Features.

Artificial Intelligence

gooseR v0.1.1: Integrates Goose AI capabilities including memory management, visualization enhancements, and workflow automation. Save R objects to Goose memory, apply Block branding to visualizations, and manage data science project workflows. There are six vignettes, including Getting Started and Code Review and Testing.

pairwiseLLM v1.1.0: Provides a unified framework for generating, submitting, and analyzing pairwise comparisons of writing quality using large language models (LLMs). The package supports live and/or batch evaluation workflows across multiple providers (OpenAI, Anthropic, Google Gemini, Together AI, and locally-hosted Ollama models). Results can be modeled using Bradley–Terry (1952) or Elo rating methods as described in Clark et al. (2018) to derive writing quality scores. For information on the method of pairwise comparisons, see Thurstone (1927) and Heldsinger & Humphry (2010). There are three vignettes, including Getting Started and Advanced.

Audio Analysis

ReVAMP v1.0.1: Provides an interface to the Vamp audio analysis plugin system developed by Queen Mary University of London’s Centre for Digital Music that enables loading and running Vamp plugins for various audio analysis tasks, including tempo detection, onset detection, spectral analysis, and audio feature extraction. Supports mono and stereo audio with automatic channel adaptation and domain conversion. There is an Introduction and a vignette on Managing Plugin Paths.

Causal Inference

caugi v1.0.0: Implements a simple interface to build, structure, and examine causal relationships. There are five vignettes, including Getting Started and Visualizing Causal Graphs.

Computational Methods

bigPLSR v0.7.2: Provides fast partial least squares (PLS) for dense and out-of-core data that is optimized for bigmemory-backed matrices with streamed cross-products and chunked BLAS. For details, see Bertrand and Maumy (2023), Bertrand and Maumy (2023b), and Dayal and MacGregor (1997). Features include kernel logistic PLS with C++-accelerated alternating iteratively reweighted least squares (IRLS) updates, streamed reproducing kernel Hilbert space (RKHS) solvers with reusable centering statistics, and bootstrap diagnostics with graphical summaries for coefficients, scores, and cross-validation workflows. There are fourteen vignettes, including Automatic Algorithm Selection and Visualizing PLS Fits.

Ecology

ambiR v0.1.1: Provides functions to calculate AZTI’s Marine Biotic Index – AMBI of benthic fauna species according to their sensitivity to pollution. The Shannon Diversity Index H’ and the Danish benthic fauna quality index DKI (Dansk Kvalitetsindeks) can also be calculated, as well as the multivariate M-AMBI index. See Borja et al. (2000) for background. There are four vignettes, including Get Started and The AMBI index.

SHARK4R v1.0.3: Provides functions to retrieve, process, analyze, and quality-control marine physical, chemical, and biological data. The main focus is on Swedish monitoring data available through the SHARK database, with additional API support for Nordic Microalgae, Dyntaxa, World Register of Marine Species WoRMS, AlgaeBase, OBIS xylookup web service, and Intergovernmental Oceanographic Commission (IOC) – UNESCO databases on harmful algae and toxins. There are five vignettes including Quality Control of SHARK4R Data and Retrieve Data From SHARK.

Econometrics

gvcAnalyzer v0.1.1: Provides tools for decomposing Global Value Chain (GVC) participation and value-added trade. It implements the frameworks proposed by Borin and Mancini (2023) for source-based and sink-based decompositions, and by Borin, Mancini, and Taglioni (2025) for tripartite and output-based GVC measures. There are three vignettes including an Introduction and Trade vs Output Perspectives.

Epidemiology

MetaRVM v1.0.1: Simulates respiratory virus epidemics using meta-population compartmental models. Following Fadikar et. al. (2025) it implements a stochastic SEIRD (Susceptible-Exposed-Infected-Recovered-Dead) framework with demographic stratification by age, race, and geographic zones that supports complex epidemiological scenarios including asymptomatic and presymptomatic transmission, hospitalization dynamics, vaccination schedules, and time-varying contact patterns via mixing matrices. There are four vignettes including Getting Started and Running a Simulation.

sitrep v0.4.0: Loads the complete sitrep ecosystem for applied epidemiology analysis. This package provides report templates and automatically loads companion packages, including epitabulate (for epidemiological tables), epidict (for data dictionaries), epikit (for epidemiological utilities), and apyramid (for age-sex pyramids). There are seven vignettes including Origin Story and Guide: Measles Outbreak report.

Genetics

EZbakR v0.1.0: A complete rewrite and reimagining of bakR, Vock et al. (2025), designed to support a wide array of analyses of nucleotide recoding RNA-seq datasets of any type, including TimeLapse-seq/SLAM-seq/TUC-seq, Start-TimeLapse-seq, TT-TimeLapse-seq, and subcellular NR-seq. It extends standard NR-seq standard NR-seq mutational modeling to support multi-label analyses, and implements an improved hierarchical model to better account for transcript-to-transcript variance in metabolic label incorporation, and also generalized dynamical systems modeling of NR-seq data to support analyses of premature mRNA processing and flow between subcellular compartments. There are seven vignettes, including Quickstart and Linear Modeling.

gpyramid v0.0.1: Provides functions to identify efficient crossing schemes for gene pyramiding and calculates the cost of crossing in terms of the number of individuals and generations, which has been theoretically formulated by Servin et al. (2004). The package has been designed for selecting appropriate parental genotypes and finding the most efficient crossing scheme for gene pyramiding, especially for plant breeding. There is an Introduction and a Tutorial.

phylospatial v1.2.1: Provides functions to analyze spatial phylogenetic diversity patterns. Use your data on an evolutionary tree and geographic distributions of the terminal taxa to compute diversity and endemism metrics, test significance with null model randomization, analyze community turnover and biotic regionalization, and perform spatial conservation prioritizations. All functions support quantitative community data in addition to binary data. There are four vignettes, including phylospatial data and Prioritization.

Genomics

CimpleG v1.0.1: Provides a method for the detection of small CpG methylation signatures used for cell-type classification and deconvolution that is time efficient and performs as well as top performing methods for cell-type classification of blood cells and other somatic cells. Predictions are based on a single DNA methylation site per cell type, but users can also select more sites if they so wish. Users can train cell type classifiers and directly apply these in a deconvolution of cell mixes context. See Maié et al. (2023) for details and the vignettes Genetic signatures and Quickly save and load large objects.

Machine Learning

LBBNN v0.1.4: Implements an interface to the LibTorch backend to provide latent binary Bayesian neural networks via torch. Supports mean-field variational inference as well as flexible variational posteriors using normalizing flows. The standard LBBNN implementation follows Hubin and Storvik (2024) and uses the local reparametrization trick as in Skaaret-Lund et al. (2024). Input-skip connections are implemented as described in Høyheim et al. (2025). See the vignette to get started.

snic v0.6.1: Implements the Simple Non-Iterative Clustering algorithm for superpixel segmentation of multi-band images, as introduced by Achanta and Susstrunk (2017), and supports both standard image arrays and geospatial raster objects, with a design that can be extended to other spatial data frameworks. The algorithm groups adjacent pixels into compact, coherent regions based on spectral similarity and spatial proximity. A high-performance implementation supports images with arbitrary spectral bands. See the vignettes about Arrays and SpatRaster segmentation pipelines.

Mathematics

algebraic.dist v0.1.0: Provides an algebra over probability distributions enabling composition, sampling, and automatic simplification to closed forms. Supports normal, exponential, multivariate normal, and empirical distributions with operations like addition and subtraction that automatically simplify when mathematical identities apply (e.g., the sum of independent normal distributions is normal).

Mediation Analysis

wsMed v1.0.2: Provides tools for within-subject mediation analysis using structural equation modeling to examine how changes in an outcome variable between two conditions are mediated through one or more variables. Supports within-subject mediation analysis using the lavaan package by Rosseel (2012), and extends Monte Carlo confidence interval estimation to missing data scenarios using the semmcci package by Pesigan and Cheung (2023). There are six vignettes, including wsMed and GenerateModelIP.

Medical Statistics

cifmodeling v0.9.8: Implements a publication-ready toolkit for modern survival and competing risks analysis with a minimal, formula-based interface. Both nonparametric estimation and direct polytomous regression of cumulative incidence functions (CIFs) are supported. Functions estimate survival and CIF curves, produce high-quality graphics with risk tables, censoring and competing-risk marks, and multi-panel or inset layouts. All core functions adopt a formula-and-data syntax and return tidy and extensible outputs. Key numerical routines are implemented in C++. There are seven vignettes including Overview and Examples.

Medical Statistics Continued

eVCGsampler v0.9.2: Provides a principled framework for sampling Virtual Control Group (VCG) using energy distance-based covariate balancing, offers visualization tools to assess covariate balance, and includes a permutation test to evaluate the statistical significance of observed deviations. See the vignette.

fgdiR v0.1.0: provides tools for computing the Functional Gait Deviation Index, a novel index for quantifying gait pathology using multivariate functional principal component analysis and supports analysis at the level of both legs combined, individual legs, and individual joints/planes. It includes functions for functional data preprocessing, multivariate functional principal component decomposition, FGDI computation, and visualization of gait abnormality scores. See Minhas et al. (2025) for background and the vignettes Amputee Gait Analysis and Parkinson Gait Analysis.

Pharma

aNCA v0.1.0: Provides an interactive shiny application for performing non-compartmental analysis on pre-clinical and clinical pharmacokinetic data and provides interactive visualizations, CDISC outputs (ADNCA, PP, ADPP) and configurable TLGs (tables, listings, and graphs). Methods and core estimators are described in Denney, Duvvuri, and Buckeridge (2015). There are three vignettes, including a User Guide and Adding new TLGs.

httkexamples v0.0.1: Provide examples as vignettes using High throughput toxicokinetics (HTTK) methods to solve various problems in bioinformatics, toxicology, and exposure science. In accordance with Davidson-Fritz et al. (2025), whenever a new HTTK model is developed, the code to generate the figures evaluating that model is added as a new vignette. HTTKis the combination of chemical-specific in vitro measurements or in silico predictions and generic mathematical models, to predict absorption, distribution, metabolism, and excretion by the body. See Pearce et al. (2017) and Breen et al. (2021) for background. There are thirteen vignettes including HTTK Basics and Generating subpopulations.

Statistics

distionary v0.1.0: Provides functions to create and evaluate probability distribution objects from a variety of families or define custom distributions and automatically compute distributional properties, even when they have not been specified. This package supports statistical modeling and simulations, and forms the core of the probaverse suite of R packages. There are three vignettes, including Evaluate a Distribution and Specifying Your Own Distribution.

jollofR v0.6.5: Provides functions to automatically disaggregate small-area population estimates by demographic groups (e.g., age, sex, race, marital status, educational level, etc) along with the estimates of uncertainty, using advanced Bayesian statistical modelling approaches based on integrated nested Laplace approximation (INLA) Rue et al. (2009), and stochastic partial differential equation methods Lindgren et al. (2011), hierarchical Bayesian modeling frameworks for small area estimation as described in Leasure et al. (2020), and Nnanatu et al. (2025). See README for package details and examples.

PSsurvival v0.2.0: Implements propensity score weighting methods for estimating counterfactual survival functions, marginal hazard ratios, and weighted Kaplan-Meier and cumulative risk curves in observational studies with time-to-event outcomes. Supports binary and multiple treatment groups with inverse probability of treatment weighting, overlap weighting, and average treatment effect on the treated, and includes symmetric trimming (Crump extension) for extreme propensity scores. Implements variance estimation via analytical M-estimation or bootstrap. Methods based on Li et al. (2018), Li & Li (2019), and Cheng et al. (2022). See the vignette.

quantbayes v0.1.0: Implements the Quantification Evidence Standard algorithm for computing Bayesian evidence sufficiency from binary evidence matrices and provides posterior estimates, credible intervals, percentiles, and optional visual summaries. The method is universal, reproducible, and independent of any specific clinical or rule-based framework. See The Quantitative Omics Epidemiology Group et al. (2025) for details and the vignette for examples.

tipse v1.2: Implements tipping point sensitivity analysis for time-to-event endpoints under different missing data scenarios, as described in Oodally et al. (2025). Supports both model-based and model-free imputation, multiple imputation workflows, plausibility assessment, and visualizations. Enables robust assessment for regulatory and exploratory analyses. See the vignette.

weightedsurv v0.1.0: Provides survival analysis functions with support for time-dependent and subject-specific (e.g., propensity score) weighting. Implements weighted estimation for Cox models, Kaplan-Meier survival curves, and treatment differences with point-wise and simultaneous confidence bands. Includes restricted mean survival time comparisons evaluated across all potential truncation times with both point-wise and simultaneous confidence bands. See Cole & Hernán (2004) for methodological background and the vignette for examples.

Time Series

bpvars v1.0: Provides Bayesian estimation and forecasting of dynamic panel data using Bayesian Panel Vector Autoregressions with hierarchical prior distributions. Models include country-specific VARs that share a global prior distribution that extends the model by Jarociński (2010). Functions provide model specification, estimation, and forecasting routines, facilitating coherent workflows and reproducibility and includes automated pseudo-out-of-sample forecasting and computation of forecasting performance measures and algorithms written in C++. See README to get started.

gctsc V0.1.3: Implements Gaussian copula models for count time series. Includes simulation utilities, likelihood approximation, maximum-likelihood estimation, residual diagnostics, and predictive inference. Implements the Time Series Minimax Exponential Tilting method, an adaptation of Minimax Exponential Tilting Botev, 2017, and the Vecchia-based tilting framework of Cao and Katzfuss (2025). Also provides a linear-cost implementation of the Geweke–Hajivassiliou–Keane simulator inspired by Masarotto and Varin (2012), and the Continuous Extension approximation of Nguyen and De Oliveira (2025). See the vignette.

Utilities

fjoin v0.1.0: Extends data.table join functionality to work with any data frame class, and provides a familiar x/y-style interface, enabling broad use across R. Offers NA-safe matching by default, on-the-fly column selection, multiple match-handling on both sides, x or y row order, and a row origin indicator. Performs inner, left, right, full, semi- and anti-joins with equality and inequality conditions, plus cross joins. Specific support for data.table, (grouped) tibble, and sf/sfc objects and their attributes; returns a plain data frame otherwise. Avoids data-copying of inputs and outputs. Allows displaying the data.table code instead of (or as well as) executing it. See the vignette.

meetupr v0.3.1: Provides programmatic access to the Meetup GraphQL API enabling users to retrieve information about groups, events, and members from Meetup. Supports authentication via OAuth2 and includes functions for common queries and data manipulation tasks. There are four vignettes, including Getting Started and Meetup API Schema Introspection.

odiffr v0.5.1: Implements R bindings to odiff, a pixel-by-pixel image comparison tool. Supports PNG, JPEG, WEBP, and TIFF with configurable thresholds, antialiasing detection, and region ignoring. Requires system installation of odiff. Ideal for visual regression testing in automated workflows. See the vignette.

svgedit v1.0.0: Provides functions to edit SVG files created in Inkscape by replacing placeholders (e.g., a rectangle element or {} in a text box by ggplot2 objects, images, or text. This helps automate the creation of figures with complex layouts. See the vignette.

taskqueue v0.2.0: Implements a task queue system for asynchronous parallel computing using PostgreSQL as a backend. Designed for embarrassingly parallel problems where tasks do not communicate with each other. Dynamically distributes tasks to workers, handles uneven load balancing, and allows new workers to join at any time. Particularly useful for running large numbers of independent tasks on high-performance computing (HPC) clusters with SLURM https://slurm.schedmd.com/ job schedulers.

yaml12 v0.1.0: Provides a fast, correct, safe, and ergonomic YAML 1.2 parser and generator written in Rust, enabling conversion between YAML and simple R objects with full support for multi-document streams, tags, anchors, and aliases. Offers opt-in handlers for custom tag behavior and round-trips common R data structures. Implements the YAML 1.2.2 specification. There are two vignettes, YAML in 2 minutes and YAML Tags.

Visualization

blockr.ggplot v0.1.0: Extends blockr.core with interactive blocks for data visualization using ggplot2. Users can build charts through a graphical interface without writing code directly. Includes common chart types (bar charts, line charts, pie charts, scatter plots) as well as statistical plots (boxplots, histograms, density plots, violin plots) with rich customization options and intuitive user interfaces. See the vignette.

mapycusmaximus v1.0.0: Provides focus-glue-context fisheye transformations to two-dimensional coordinates and spatial vector geometries. Implements a smooth radial distortion that enlarges a focal region, transitions through a glue ring, and preserves outside context. Methods build on generalized fisheye views and focus+context mapping. See Furnas (1986), Furnas (2006), and Yamamoto et al. (2009) for details and the vignette for examples.