Efficient coordinate ascent algorithm for fitting regularization paths for linear models penalized by Spike-and-Slab LASSO of Rockova and George (2018) <doi:10.1080/01621459.2016.1260469>.

Fetch data on targeted public investments from Plataforma +Brasil (SICONV) <http://plataformamaisbrasil.gov.br/>, the responsible system for requests, execution, and monitoring of federal discretionary transfers in Brazil.

Selects invalid instruments amongst a candidate of potentially bad instruments. The algorithm selects potentially invalid instruments and provides an estimate of the causal effect between exposure and outcome.

Set of tools aimed at wrapping some of the functionalities of the packages tools, utils and codetools into a nicer format so that an IDE can use them.

All data in the book "Statistical Methods in Biology" by Welham et al. (2015) <doi:10.1201/b17336> with a corresponding documentation and illustrative analysis of the data.

An extension to the R tidy data environment for automated machine learning. The package allows fitting and cross validation of linear regression and classification algorithms on grouped data.

Tidy standardized mean differences ('SMDs'). tidysmd uses the smd package to calculate standardized mean differences for variables in a data frame, returning the results in a tidy format.

Identifies the optimal confidence level to represent the results of a set of pairwise tests as suggested by Armstrong and Poirier (2025) <doi:10.1017/pan.2024.24>.

Assesses evidence for Zipf's Law of Abbreviation in animal vocalisation using IDs, note class and note duration. The package also provides a web plot function for visualisation.

Fits MIDAS denoising autoencoder models for multiple imputation of missing data, generates multiply-imputed datasets, computes imputation means, and runs Rubin's rules regression analysis. Wraps the MIDAS2 Python engine via a local FastAPI server over HTTP', so no reticulate dependency is needed at runtime. Methods are described in Lall and Robinson (2022) <doi:10.1017/pan.2020.49> and Lall and Robinson (2023) <doi:10.18637/jss.v107.i09>.

The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.

This package provides a flexible framework for implementing hierarchical access control in shiny applications. Features include user permission management through a two-tier system of access panels and units, pluggable shiny module for administrative interfaces, and support for multiple storage backends (local, AWS S3', Posit Connect'). The system enables fine-grained control over application features, with built-in audit trails and user management capabilities. Integrates seamlessly with Posit Connect's authentication system.

Supports automated Markov chain Monte Carlo for arbitrarily structured correlation matrices. The user supplies data, a correlation matrix in symbolic form, the current state of the chain, a function that computes the log likelihood, and a list of prior distributions. The package's flagship function then carries out a parameter-at-a-time update of all correlation parameters, and returns the new state. The method is presented in Hughes (2023), in preparation.

Package runonce helps automating the saving of long-running code to help running the same code multiple times. If you run some long-running code once, it saves the result in a file on disk. Then, if the result already exists, i.e. if the code has already been run and its output has already been saved, it just reads the result from the stored file instead of running the code again.

Flay analyzes code for structural similarities. Differences in literal values, variable, class, method names, whitespace, programming style, braces vs do/end, etc are all ignored. Making this totally rad.

The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.

This is a package for fast Non-negative Matrix Factorization (NMF) with automatic rank-determination for dimension reduction of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and similar.

This package performs score test using saddlepoint approximation to estimate the null distribution. It also prepares summary statistics for meta-analysis and performs meta-analysis to combine multiple association results.

This package provides auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).

16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin.

Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.

Anytime-valid sequential estimation of the p-value of a test calibrated by Monte-Carlo simulation, as described in Stoepker & Castro (2024) <doi:10.48550/arXiv.2409.18908>.

This package provides low-level R bindings to the Anime.js library (<https://animejs.com>), enabling the creation of browser-native SVG and HTML animations via the htmlwidgets framework.

Grafts the extinct bird species from the Avotrex database (Sayol et al., in review) on to the BirdTree phylogenies <https://birdtree.org>, using a set of different commands.