Regularly spaced grids containing continuous data are transformed to contour polygons. A grid can be defined by a data.frame (x, y, value), an sf object or a raster from terra'.

This is a tool for epidemiologist, medical data analyst, medical or public health professionals. It contains three domains of functions: 1) data management, 2) statistical analysis and 3) calculating epidemiological measures.

Optimizing regular numeric problems in optically stimulated luminescence dating, such as: equivalent dose calculation, dose rate determination, growth curve fitting, decay curve decomposition, statistical age model optimization, and statistical plot visualization.

Automatically calculate direct, indirect, and total effects for piecewise structural equation models, comprising lists of fitted models representing structured equations (Lefcheck, 2016 <doi:10/f8s8rb>). Confidence intervals are provided via bootstrapping.

Extension of the snow package supporting fault tolerant and reproducible applications, as well as supporting easy-to-use parallel programming - only one function is needed. Dynamic cluster size is also available.

S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.

This package implements the sparse clustering methods of Witten and Tibshirani (2010): "A framework for feature selection in clustering"; published in Journal of the American Statistical Association 105(490): 713-726.

Download TIGER/Line shapefiles from the United States Census Bureau (<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>) and load into R as sf objects.

Dimensionality reduction (DR) is widely used in many domain for analyzing and visualizing high-dimensional data. tidydr provides uniform output and is compatible with multiple methods, including prcomp', mds', Rtsne'. etc.

This package provides a set of general functions that I have used in various projects and other R packages. Miscellaneous operations on data frames, matrices and vectors, ROC and PR statistics.

Inference methods for state-space models, relying on the Kalman Filter or on Viking (Variational Bayesian VarIance tracKING). See J. de Vilmarest (2022) <https://theses.hal.science/tel-03716104/>.

This package implements inferential and graphic procedures for the semiparametric proportional means regression of weighted composite endpoint of recurrent event and death (Mao and Lin, 2016, <doi:10.1093/biostatistics/kxv050>).

This is a collection of some useful functions when dealing with text data. Currently it only contains a very efficient function of decoding HTML entities in character vectors by Rcpp routine.

This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.

R-escape streamlines gene set enrichment analysis for single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize GSEA across individual cells.

This package provides a package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package.

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.

This is a package for estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.

Inspired by the the futile.logger R package and logging Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.

The DuckDB project is an embedded analytical data management system with support for the Structured Query Language (SQL). This package includes all of DuckDB and an R Database Interface (DBI) connector.

This package provides a ggplot2 extension that enables the rendering of complex formatted plot labels (titles, subtitles, facet labels, axis labels, etc.). Text boxes with automatic word wrap are also supported.

This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.

This package lets you manage configuration values across multiple environments (e.g. development, test, production). It reads values using a function that determines the current environment and returns the appropriate value.