Computational Methods

fastfocal v0.1.3: Provides a fast moving-window (“focal”) and buffer-based extraction for raster data using the terra package. Automatically selects between a C++ backend and a Fast Fourier Transform (FFT) backend depending on problem size. The FFT backend supports sum and mean. Other statistics are handled by terra. There are two vignettes: Benchmarking and Fast Multi-scale Raster Extraction and Moving Window Analysis with FFT.

GTRT v0.1.0: Provides a collection of functions for testing randomness (or mutual independence) in linear and circular data as proposed in Gehlot and Laha (2025a) and Gehlot and Laha (2025b). See the vignettes Randomness Tests for Circular Data and Randomness Tests for Linear Data.

rjuliabugs v0.1.0: Implements an interface to the JuliaBUGS.jl package for Bayesian inference using the BUGS modeling language. R users can run models in Julia and return results as familiar R objects. Visualization and posterior analysis are supported via the bayesplot and posterior packages. See README for an example.

Data

BioWorldR v0.1.0: Provides a curated collection of biodiversity and species-related datasets (birds, plants, reptiles, turtles, mammals, bees, marine data and related biological measurements), together with small utilities to load and explore them. The package aims to simplify reproducible workflows by packaging commonly used example datasets and metadata so they can be easily inspected, visualized, and used for teaching, testing, and prototyping analyses. See the vignette.

ecotourism v0.1.0: This is a collection of data files for exploring sightings of wild things, relative to weather and tourism patterns in Australia. There are eight vignettes, including Glowworms and Gouldian Finch.

ineapir v0.2.5: Provides access to open statistical data and metadata disseminated by the National Statistics Institute of Spain (INE). The functions return data frames with the requested information thanks to calls to the INE API. See README for information.

Decision Analysis

DUToolkit v1.0.2: Provides tools to help modelers and decision-makers effectively interpret and communicate decision risk when evaluating multiple policy options. It uses model outputs from uncertainty analysis for baseline scenarios and policy alternatives to generate visual representations of uncertainty and quantitative measures for assessing associated risks. See Wiggins et al. (2025) and the webpage for more details. There are six vignettes, including Calculating Risk and Introduction.

Ecology

ConSciR v0.3.0: Provides data science tools for conservation science, including methods for environmental data analysis, humidity calculations, sustainability metrics, engineering calculations, and data visualization. See Cosaert & Beltran et al. (2022) for background and the vignette for examples.

geospatialsuite v 0.1.0: Provides a toolkit for geospatio temporal analysis featuring 60+ vegetation indices, advanced raster visualization, universal spatial mapping, water quality analysis, CDL crop analysis, spatial interpolation, temporal analysis, and terrain analysis. Methods include vegetation indices calculations Rouse et al. (1974), water quality indices McFeeters (1996), and crop data layer analysis USDA NASS (2024). There are seven vignettes, including Getting Started and Water Quality Assessment.

streamsampler v0.1.0: Provides tools to characterize daily stream discharge and water quality data and subsample water quality data. Stream sampling protocols are described in Lee et al. (2016) and Lee et al. (2019). See the vignette for an introduction.

Epidemiology

epitraxr v0.5.0: Implements a tool for generating disease surveillance reports from data exported from EpiTrax, a central repository for epidemiological data used by public health officials. It provides functions to manipulate EpiTrax datasets, tailor reports to internal or public use, and export reports in csv, xlsx, or pdf formats. See the vignettes epitraxr and Piped Mode.

mitey v0.2.0: Provides methods to estimate serial intervals and time-varying case reproduction numbers from infectious disease outbreak data. Serial intervals measure the time between symptom onset in linked transmission pairs, while case reproduction numbers quantify how many secondary cases each infected individual generates over time. See Vink et al. (2014) and Wallinga & Lipsitch (2007) for background and the vignette for examples.

Rnaught v0.1.0: Provides a collection of methods for estimating the basic reproduction number (R0) of infectious diseases, and includes a shiny application and datasets for Canadian national and provincial COVID-19 case counts from Berry et al. (2021). See Fisman et al. (2013), Bettencourt & Ribeiro (2008), and White & Pagano (2008) for the models implemented. There are three vignettes, including Introduction and Sequential Bayes.

vaxineR v0.1.0: Provides tools to analyze vaccine coverage data and simulate potential disease outbreak scenarios and to calculate key epidemiological metrics, such as the effective reproduction number (Re), outbreak probabilities, and expected infection counts based on county-level vaccination rates, disease characteristics, and vaccine effectiveness. The package includes historical kindergarten vaccination data for Florida counties. See the vignette.

Finance

PortfolioTesteR v0.1.3: Provides functions to design, backtest, and analyze portfolio strategies using simple, English-like function chains. Includes technical indicators, flexible stock selection, portfolio construction methods (equal weighting, signal weighting, inverse volatility, hierarchical risk parity), and a compact backtesting engine for portfolio returns, drawdowns, and summary metrics. There are three vignettes, including Getting Started and ML Strategies.

Rmfrac v0.1.1: Provides functions to simulate fractional and multifractional processes along with a shinyapp for interactive exploration. Functions simulate Brownian and fractional Brownian motions, bridges and Gaussian Haar-based multifractional processes (GHBMP), and Hurst functions. See Ayache, Olenko and Samarakoon (2025) doi:10.48550/arXiv.2503.07286 for background and README to get started.

Genomics

cellGeometry v0.5.4: Provides tools for the deconvolution of bulk RNA-Sequencing data into proportions of cells based on a reference single-cell RNA-Sequencing dataset using high-dimensional geometric methodology. See the vignettes quickstart and Deconvolution with the brain atlas’.

MicrobTiSDA v0.1.0: Provides a framework for microbiome time-series analysis and tools specifically designed for analyzing longitudinal microbiome data that integrate seven functional modules. See Fisher (2014) for more details on inferences involving interspecies interactions and the vignette for examples.

Machine Learning

causalDT v1.0.0: Implements a novel machine learning method for estimating interpretable subgroups with heterogeneous treatment effects. CDT allows researchers to fit any machine learning model (or metalearner) to estimate heterogeneous treatment effects for each individual, and then “distills” these predicted heterogeneous treatment effects into interpretable subgroups by fitting an ordinary decision tree to predict the previously-estimated heterogeneous treatment effects. See Huang, Tang, and Kenney (2025) for details and README for an example.

Machine Learning (continued)

polarisR v0.1.4: Provides an interactive platform for exploring high-dimensional datasets, diagnosing the quality of embeddings and comparing different NLDR methods such as t-SNE and UMAP. It also implements a shiny application There is an Introduction and a vignette on Tips, Requirements, and Support.

SemanticDistance v0.1.1: Implements tools to clean and format language transcripts based on a series of transformations such as lemmatize words, omit stopwords, and split strings across rows). Functions compute two distinct metrics of cosine semantic distance which reflect pairwise cosine distance between different elements or chunks of a language sample. Guided by user-specified options, the package tools can process stories, dialogues, word lists and more. There are five vignettes including Dialogues and Monologues.

Mathematics

ricci v0.1.1: Provides a compact interface for performing tensor calculations by allowing upper and lower index labeling of arrays. Ricci calculus conventions implicitly trigger contractions and diagonal subsetting. Features include explicit tensor operations, such as addition, subtraction and multiplication of tensors via the standard operators, raising and lowering indices, taking symmetric or antisymmetric tensor parts, the Kronecker product, the Levi Civita epsilon, the Christoffel symbols, the Riemann ans Ricci tensors. See README and the vignettes ricci and Tensor Fields.

Medical Applications

diegr v0.1.0: Provides tools to visualize high-density electroencephalography (HD-EEG) data through interactive plots and animations, enabling exploratory and communicative analysis of temporal-spatial brain signals. See the vignette.

Epoch v1.0.3: Provides tools for working with iEEG matrix data, including downloading curated iEEG data from The Open Science Framework (OSF), making new objects, processing, and visualizing the data. See the vignette.

optconerrf v1.0.1: Provides tools to design and analyze confirmatory adaptive clinical trials using the optimal conditional error framework of Brannath and Bauer (2004) and the extensions of Brannath and Dreher (2024). There is an Introduction and a vignette, Using Constraints and Interim Estimates for the Optimal Conditional Error Function.

TrialSimulator v1.3.0: Implements tools to simulate phase II and/or phase III clinical trials including carrying out graphical testing procedure and combination test under group sequential design. It supports various types of endpoints and adaptive strategies. There are eleven vignettes including: An Example of Simulating a Trial with Adaptive Design and Simulate Correlated Progression-Free Survival and Overall Survival as Endpoints.

Programming

kerasnip v0.0.3: Provides a seamless bridge between the keras and the tidymodels frameworks that allows for the dynamic creation of parsnip model specifications for keras models. There are eight vignettes, including Transfer Learning with Keras Applications and Tidymodels Workflow with Functional Keras Models.

Statistics

eFCM v1.0: Implements the exponential Factor Copula Model (eFCM) of Castro-Camilo & Huser (2020) for spatial extremes, with tools for dependence estimation, tail inference, and visualization. The package supports likelihood-based inference, Gaussian process modeling via Matérn covariance functions, and bootstrap uncertainty quantification. See the vignette for an example.

inphr v0.0.1: Provides functions for performing null hypothesis testing on samples of persistence diagrams using the theory of permutations. Inputs can be either samples of persistence diagrams themselves or vectorizations. In the former case, they are embedded in a metric space using either the Bottleneck or Wasserstein distance. In the latter case, persistence data becomes functional data. See Pini & Vantini (2017) and Lovato et al. (2020) for background and look here for an example.

ordinalTables v1.0.0.3: Provides over 340 functions to fit a variety of models to two-way tables with ordered categories. Most models apply to tables with correlated ordered response categories. There is a particular focus on rater data and models for rescore tables. Functions are organized by the last name of the primary author of the source article suggesting the model. There are five vignettes, including Goodman’s Analysis of Association and Models to Fit Square Tables.

SLGP v1.0.0: Provides tools for conditional and spatially dependent density estimation using spatial logistic Gaussian processes. Probability densities are represented through finite-rank Gaussian process priors transformed via a spatial logistic density transformation. Functions include density prediction, quantile and moment estimation, sampling methods, and preprocessing. See Leonard (1978), Lenk (1988), and other references provided for background. There is an introduction and an additional vignette.

Utilities

houba v0.1.0: Provides tools to manipulate data through memory-mapped files, as vectors, matrices, or arrays. Basic arithmetic functions are implemented. It also includes functions to write and read descriptor files for compatibility with the bigmemory package. See the vignette.

memshare v1.0.2: Extends R with a mechanism for efficient parallel data access by utilizing C++ shared memory. Large data objects can be accessed and manipulated directly from R without redundant copying, providing both speed and memory efficiency. See README to get started.

plumber2 v0.1.0: Provides tools to automatically create a web server from annotated R files or by building it up programmatically. Includes automatic OpenAPI documentation, input handling, asynchronous evaluation, and plugin support. There are ten vignettes, including Get Started and Programmatic Usage.

Visualization

clockplot v0.8.3: Provides a novel visualization technique for plotting time stamped events on a 24-hour circular clock face. This is particularly useful for analyzing daily patterns, event clustering, and gaps in temporal data. See the vignettes clockplot and clockchart construction.

ggDNAvis v0.3.0: Use `ggplot2 to visualize a single DNA/RNA sequence split across multiple lines, multiple DNA/RNA sequences, each occupying a whole line, or base modifications such as DNA methylation called by modified bases models in Dorado or Guppy. See the non-expert user guide.

isocubes v1.0.0: Provides functions for visualizing voxel data using fixed viewpoint isometric cubes for each data point. There are four vignettes, including Animated Isosurface and Heightmaps.

radviz3d v2.3.0: Extends traditional radial coordinate visualization techniques to three-dimensional space for enhanced exploration and analysis of high-dimensional datasets through interactive 3D plots. See Zhu, Dai & Maitra (2022) for background and README for examples.

regress3d v1.0.0: Provides functions that use plotly to plot regression surfaces and marginal effects in three dimensions. See README.

splineplot v0.1.1: Provides functions to create ggplot2visualizations of smooth effects from GAM (Generalized Additive Models) fitted with mgcv. Supports interaction terms and provides hazard ratio plots with histograms for survival analysis. See the vignette.