Convex Partition is a black-box optimisation algorithm for single objective real-parameters functions. The basic principle is to progressively estimate and exploit a regression tree similar to a CART (Classification and Regression Tree) of the objective function. For more details see de Paz (2024) <doi:10.1007/978-3-031-62836-8_3> and Loh (2011) <doi:10.1002/widm.8> .

Estimation of one- and two-sided confidence intervals via the numerical inversion of the cumulative distribution function of a statistic's sampling distribution. For more details, see section 9.2.3 of Casella and Berger (2002) <ISBN:0534243126>.

CHAP-GWAS (Chromosomal Haplotype-Integrated Genome-Wide Association Study) provides a dynamically adaptive framework for genome-wide association studies (GWAS) that integrates chromosome-scale haplotypes with single nucleotide polymorphism (SNP) analysis. The method identifies and extends haplotype variants based on their phenotypic associations rather than predefined linkage blocks, enabling high-resolution detection of quantitative trait loci (QTL). By leveraging long-range phased haplotype information, CHAP-GWAS improves statistical power and offers a more comprehensive view of the genetic architecture underlying complex traits.

Use three methods to estimate parameters from a mediation analysis with a binary misclassified mediator. These methods correct for the problem of "label switching" using Youden's J criteria. A detailed description of the analysis methods is available in Webb and Wells (2024), "Effect estimation in the presence of a misclassified binary mediator" <doi:10.48550/arXiv.2407.06970>.

Hierarchical and partitioning algorithms to cluster blocks of variables. The partitioning algorithm includes an option called noise cluster to set aside atypical blocks of variables. Different thresholds per cluster can be sets. The CLUSTATIS method (for quantitative blocks) (Llobell, Cariou, Vigneau, Labenne & Qannari (2020) <doi:10.1016/j.foodqual.2018.05.013>, Llobell, Vigneau & Qannari (2019) <doi:10.1016/j.foodqual.2019.02.017>) and the CLUSCATA method (for Check-All-That-Apply data) (Llobell, Cariou, Vigneau, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2018.09.006>, Llobell, Giacalone, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2019.05.017>) are the core of this package. The CATATIS methods allows to compute some indices and tests to control the quality of CATA data. Multivariate analysis and clustering of subjects for quantitative multiblock data, CATA, RATA, Free Sorting and JAR experiments are available. Clustering of rows in multi-block context (notably with ClusMB strategy) is also included.

The issue of overlapping regions in multidimensional data arises when different classes or clusters share similar feature representations, making it challenging to delineate distinct boundaries between them accurately. This package provides methods for detecting and visualizing these overlapping regions using partitional clustering techniques based on nearest neighbor distances.

This package implements lasso and ridge regression for dichotomised outcomes (<doi:10.1080/02664763.2023.2233057>), i.e., numerical outcomes that were transformed to binary outcomes. Such artificial binary outcomes indicate whether an underlying measurement is greater than a threshold.

Implement tableGrob object as a clickable image map. The clickableImageMap package is designed to be more convenient and more configurable than the edit() function. Limitations that I have encountered with edit() are cannot control (1) positioning (2) size (3) appearance and formatting of fonts In contrast, when the table is implemented as a tableGrob', all of these features are controllable. In particular, the ggplot2 grid system allows exact positioning of the table relative to other graphics etc.

This package implements the conditionally symmetric multidimensional Gaussian mixture model (csmGmm) for large-scale testing of composite null hypotheses in genetic association applications such as mediation analysis, pleiotropy analysis, and replication analysis. In such analyses, we typically have J sets of K test statistics where K is a small number (e.g. 2 or 3) and J is large (e.g. 1 million). For each one of the J sets, we want to know if we can reject all K individual nulls. Please see the vignette for a quickstart guide. The paper describing these methods is "Testing a Large Number of Composite Null Hypotheses Using Conditionally Symmetric Multidimensional Gaussian Mixtures in Genome-Wide Studies" by Sun R, McCaw Z, & Lin X (Journal of the American Statistical Association 2025, <doi:10.1080/01621459.2024.2422124>).

Easily create color-coded (choropleth) maps in R. No knowledge of cartography or shapefiles needed; go directly from your geographically identified data to a highly customizable map with a single line of code! Supported geographies: U.S. states, counties, census tracts, and zip codes, world countries and sub-country regions (e.g., provinces, prefectures, etc.).

This package provides a comprehensive reproducibility framework designed for R and bioinformatics workflows. Automatically captures the entire analysis environment including R session info, package versions, external tool versions ('Samtools', STAR', BWA', etc.), conda environments, reference genomes, data provenance with smart checksumming for large files, parameter choices, random seeds, and hardware specifications. Generates executable scripts with Docker', Singularity', and renv configurations. Integrates with workflow managers ('Nextflow', Snakemake', WDL', CWL') to ensure complete reproducibility of computational research workflows.

This package provides functions for testing if the covariance structure of 2-dimensional data (e.g. samples of surfaces X_i = X_i(s,t)) is separable, i.e. if covariance(X) = C_1 x C_2. A complete descriptions of the implemented tests can be found in the paper Aston, John A. D.; Pigoli, Davide; Tavakoli, Shahin. Tests for separability in nonparametric covariance operators of random surfaces. Ann. Statist. 45 (2017), no. 4, 1431--1461. <doi:10.1214/16-AOS1495> <https://projecteuclid.org/euclid.aos/1498636862> <arXiv:1505.02023>.

Different approaches to censored or truncated regression with conditional heteroscedasticity are provided. First, continuous distributions can be used for the (right and/or left censored or truncated) response with separate linear predictors for the mean and variance. Second, cumulative link models for ordinal data (obtained by interval-censoring continuous data) can be employed for heteroscedastic extended logistic regression (HXLR). In the latter type of models, the intercepts depend on the thresholds that define the intervals. Infrastructure for working with censored or truncated normal, logistic, and Student-t distributions, i.e., d/p/q/r functions and distributions3 objects.

Google's Compact Language Detector 3 is a neural network model for language identification and the successor of cld2 (available from CRAN). The algorithm is still experimental and takes a novel approach to language detection with different properties and outcomes. It can be useful to combine this with the Bayesian classifier results from cld2'. See <https://github.com/google/cld3#readme> for more information.

Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.

Variance estimation on indicators of income concentration and poverty using complex sample survey designs. Wrapper around the survey package.

This package implements a Ward-like hierarchical clustering algorithm including soft spatial/geographical constraints.

Imports and cleans opencovid19-fr <https://github.com/opencovid19-fr/data> data on COVID-19 in France.

Easily cache and retrieve computation results. The package works seamlessly across interactive R sessions, R scripts and Rmarkdown documents.

Cristin to Zotero ('c2z') aims at obtaining total dominion over Cristin ('Current Research Information SysTem in Norway') and Zotero'. The package enables manipulating Zotero libraries using R'. Import references from Cristin', Regjeringen', CRAN', ISBN ('Alma', LoC'), and DOI ('CrossRef', DataCite') to a Zotero library. Add, edit, copy, or delete items, including attachments and collections, and export references to BibLaTeX (and other formats).

Client for the Open Citations Corpus (<http://opencitations.net/>). Includes a set of functions for getting one identifier type from another, as well as getting references and citations for a given identifier.

This package provides a collection of functions that make it easier to understand crime (or other) data, and assist others in understanding it. The package helps you read data from various sources, clean it, fix column names, and graph the data.

Estimation of quantile regression models for survival data.

Computer algebra via the SymPy library (<https://www.sympy.org/>). This makes it possible to solve equations symbolically, find symbolic integrals, symbolic sums and other important quantities.