'ECOS' Plugin for the 'R' Optimization Infrastructure

Enhances the 'R' Optimization Infrastructure ('ROI') package with the Embedded Conic Solver ('ECOS') for solving conic optimization problems.

Fast Fixed-Effects Estimations

Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), instrumental variables (IV), generalized linear models (GLM), maximum likelihood estimation (ML), and the negative binomial. The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Bergé, Butts, McDermott (2026) . Further provides tools to export and view the results of several estimations with intuitive design to change the standard-errors.

Genetic Tools for Colony Management

Provides genetic tools for colony management and is a derivation of the work in Amanda Vinson and Michael J Raboin (2015) < https://pmc.ncbi.nlm.nih.gov/articles/PMC4671785/> "A Practical Approach for Designing Breeding Groups to Maximize Genetic Diversity in a Large Colony of Captive Rhesus Macaques ('Macaca' 'mulatto')". It provides a 'Shiny' application with an exposed API. The application supports five groups of functions: (1) Quality control of studbooks contained in text files or 'Excel' workbooks and of pedigrees within 'LabKey' Electronic Health Records (EHR); (2) Creation of pedigrees from a list of animals using the 'LabKey' EHR integration; (3) Creation and display of an age by sex pyramid plot of the living animals within the designated pedigree; (4) Generation of genetic value analysis reports; and (5) Creation of potential breeding groups with and without proscribed sex ratios and defined maximum kinships.

Efficient Serialization of R Objects

Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.

Bayesian Additive Regression Trees

An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.

Functional Guilds, Invasion Status, Endemism, and Rarity of Ants

Provides functions for the analysis of ant communities, aiming to standardize workflows in myrmecology. The package automates the assignment of species to functional guilds based on trophic strategies, feeding habits, and foraging behavior, using established classification frameworks (Silva et al., 2015 ; Silvestre et al., 2003 ; Delabie et al., 2000 < https://www.researchgate.net/publication/44961742_Sampling_Ground-Dwelling_Ants_Case_Studies_from_the_World%27s_Rain_Forests>), and also includes a novel classification system implemented within the package, developed from ant species occurring in urban environments. It also includes routines to flag exotic species of Brazil (Vieira, 2025, unpublished master's thesis), identify endemic species (Silva et al., 2025 ), and classify species rarity and rarity forms of the Atlantic Forest (Silva et al., 2024 ). The package reduces manual effort and improves reproducibility, supporting research and biodiversity management of Neotropical ant communities.

Infrastructure for Ordering Objects Using Seriation

Infrastructure for ordering objects with an implementation of several seriation/sequencing/ordination techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) .

Access and Analyse Data from the 'CVD Prevent' API

Provides an R interface to the 'CVD Prevent' application programming interface (API), allowing users to retrieve and analyse cardiovascular disease prevention data from primary care records across England. The Cardiovascular Disease Prevention Audit (CVDPREVENT) automatically extracts routinely held GP health data to support national reporting and improvement initiatives. See the API documentation for details: < https://bmchealthdocs.atlassian.net/wiki/spaces/CP/pages/317882369/CVDPREVENT+API+Documentation>.

Evolutionary Learning of Globally Optimal Trees

Commonly used classification and regression tree methods like the CART algorithm are recursive partitioning methods that build the model in a forward stepwise search. Although this approach is known to be an efficient heuristic, the results of recursive tree methods are only locally optimal, as splits are chosen to maximize homogeneity at the next step only. An alternative way to search over the parameter space of trees is to use global optimization methods like evolutionary algorithms. The 'evtree' package implements an evolutionary algorithm for learning globally optimal classification and regression trees in R. CPU and memory-intensive tasks are fully computed in C++ while the 'partykit' package is leveraged to represent the resulting trees in R, providing unified infrastructure for summaries, visualizations, and predictions.

Nonparametric Preprocessing for Parametric Causal Inference

Selects matched samples of the original treated and control groups with similar covariate distributions -- can be used to match exactly on covariates, to match on propensity scores, or perform a variety of other matching procedures. The package also implements a series of recommendations offered in Ho, Imai, King, and Stuart (2007) . (The 'gurobi' package, which is not on CRAN, is optional and comes with an installation of the Gurobi Optimizer, available at < https://www.gurobi.com>.)