Greedy optimal subset selection for transformation models (Hothorn et al., 2018, <doi:10.1111/sjos.12291> ) based on the abess algorithm (Zhu et al., 2020, <doi:10.1073/pnas.2014241117> ). Applicable to models from packages tram and cotram'. Application to shift-scale transformation models are described in Siegfried et al. (2024, <doi:10.1080/00031305.2023.2203177>).

It proposes a novel variable selection approach in classification problem that takes into account the correlations that may exist between the predictors of the design matrix in a high-dimensional logistic model. Our approach consists in rewriting the initial high-dimensional logistic model to remove the correlation between the predictors and in applying the generalized Lasso criterion.

r128gain is a multi platform command line tool to scan your audio files and tag them with loudness metadata (ReplayGain v2 or Opus R128 gain format), to allow playback of several tracks or albums at a similar loudness level. r128gain can also be used as a Python module from other Python projects to scan and/or tag audio files.

This R package lets you estimate signatures of mutational processes and their activities on mutation count data. Starting from a set of single-nucleotide variants (SNVs), it allows both estimation of the exposure of samples to predefined mutational signatures (including whether the signatures are present at all), and identification of signatures de novo from the mutation counts.

This package provides tools for data importation, recoding, and inspection. There are functions to create new project folders, R code templates, create uniquely named output directories, and to quickly obtain a visual summary for each variable in a data frame. The main feature here is the systematic implementation of the "variable key" framework for data importation and recoding.

Nucleotide conversion sequencing experiments have been developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such experiments require specialized tools for primary processing such as GRAND-SLAM, and specialized tools for downstream analyses. grandR provides a comprehensive toolbox for quality control, kinetic modeling, differential gene expression analysis and visualization of such data.

Redshift adjusts the color temperature according to the position of the sun. A different color temperature is set during night and daytime. During twilight and early morning, the color temperature transitions smoothly from night to daytime temperature to allow your eyes to slowly adapt. At night the color temperature should be set to match the lamps in your room.

Analysis of DNA mixtures involving relatives by computation of likelihood ratios that account for dropout and drop-in, mutations, silent alleles and population substructure. This is useful in kinship cases, like non-invasive prenatal paternity testing, where deductions about individuals relationships rely on DNA mixtures, and in criminal cases where the contributors to a mixed DNA stain may be related. Relationships are represented by pedigrees and can include kinship between more than two individuals. The main function is relMix() and its graphical user interface relMixGUI(). The implementation and method is described in Dorum et al. (2017) <doi:10.1007/s00414-016-1526-x>, Hernandis et al. (2019) <doi:10.1016/j.fsigss.2019.09.085> and Kaur et al. (2016) <doi:10.1007/s00414-015-1276-1>.

Helps users in quickly visualizing risk-of-bias assessments performed as part of a systematic review. It allows users to create weighted bar-plots of the distribution of risk-of-bias judgments within each bias domain, in addition to traffic-light plots of the specific domain-level judgments for each study. The resulting figures are of publication quality and are formatted according the risk-of-bias assessment tool use to perform the assessments. Currently, the supported tools are ROB2.0 (for randomized controlled trials; Sterne et al (2019) <doi:10.1136/bmj.l4898>), ROBINS-I (for non-randomised studies of interventions; Sterne et al (2016) <doi:10.1136/bmj.i4919>), and QUADAS-2 (for diagnostic accuracy studies; Whiting et al (2011) <doi:10.7326/0003-4819-155-8-201110180-00009>).

Implementation of the technique of Lleonart et al. (2000) <doi:10.1006/jtbi.2000.2043> to scale body measurements that exhibit an allometric growth. This procedure is a theoretical generalization of the technique used by Thorpe (1975) <doi:10.1111/j.1095-8312.1975.tb00732.x> and Thorpe (1976) <doi:10.1111/j.1469-185X.1976.tb01063.x>.

Typically, models in R exist in memory and can be saved via regular R serialization. However, some models store information in locations that cannot be saved using R serialization alone. The goal of bundle is to provide a common interface to capture this information, situate it within a portable object, and restore it for use in new settings.

Bayesian analysis of luminescence data and C-14 age estimates. Bayesian models are based on the following publications: Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003> and Combes et al. (2015) <doi:10.1016/j.quageo.2015.04.001>. This includes, amongst others, data import, export, application of age models and palaeodose model.

The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.

Convert text into synthesized speech and get a list of supported voices for a region. Microsoft's Cognitive Services Text to Speech REST API <https://learn.microsoft.com/en-us/azure/cognitive-services/speech-service/rest-text-to-speech?tabs=streaming> supports neural text to speech voices, which support specific languages and dialects that are identified by locale.

Create and customize interactive collapsible D3 trees using the D3 JavaScript library and the htmlwidgets package. These trees can be used directly from the R console, from RStudio', in Shiny apps and R Markdown documents. When in Shiny the tree layout is observed by the server and can be used as a reactive filter of structured data.

Allows humanitarian community, academia, media, government, and non-governmental organizations to utilize the data collected by the Displacement Tracking Matrix (<https://dtm.iom.int>), a unit in the International Organization for Migration. This also provides non-sensitive Internally Displaced Person figures, aggregated at the country, Admin 1 (states, provinces, or equivalent), and Admin 2 (smaller administrative areas) levels.

Allows to perform the dynamic mixture estimation with state-space components and normal regression components, and clustering with normal mixture. Quasi-Bayesian estimation, as well as, that based on the Kerridge inaccuracy approximation are implemented. Main references: Nagy and Suzdaleva (2013) <doi:10.1016/j.apm.2013.05.038>; Nagy et al. (2011) <doi:10.1002/acs.1239>.

Tool to print out the value of R objects/expressions while running an R script. Outputs can be made dependent on user-defined conditions/criteria. Debug messages only appear when a global option for debugging is set. This way, debugr code can even remain in the debugged code for later use without any negative effects during normal runtime.

This package provides utility functions for standardizing economic entity (economy, aggregate, institution, etc.) name and id in economic datasets such as those published by the International Monetary Fund and World Bank. Aims to facilitate consistent data analysis, reporting, and joining across datasets. Used as a foundational building block in the econdataverse family of packages (<https://www.econdataverse.org>).

This package performs test procedures for general hypothesis testing problems for four multivariate coefficients of variation (Ditzhaus and Smaga, 2023 <arXiv:2301.12009>). We can verify the global hypothesis about equality as well as the particular hypotheses defined by contrasts, e.g., we can conduct post hoc tests. We also provide the simultaneous confidence intervals for contrasts.

This package provides a suite of routines for the hyperdirichlet distribution and reified Bradley-Terry; supersedes the hyperdirichlet package; uses disordR discipline <doi:10.48550/ARXIV.2210.03856>. To cite in publications please use Hankin 2017 <doi:10.32614/rj-2017-061>, and for Generalized Plackett-Luce likelihoods use Hankin 2024 <doi:10.18637/jss.v109.i08>.

This package provides functions for genome-wide association studies (GWAS)/gene-environment-wide interaction studies (GEWIS) with longitudinal outcomes and exposures. He et al. (2017) "Set-Based Tests for Gene-Environment Interaction in Longitudinal Studies" and He et al. (2017) "Rare-variant association tests in longitudinal studies, with an application to the Multi-Ethnic Study of Atherosclerosis (MESA)".

Simulation, analysis and sampling of spatial biodiversity data (May, Gerstner, McGlinn, Xiao & Chase 2017) <doi:10.1111/2041-210x.12986>. In the simulation tools user define the numbers of species and individuals, the species abundance distribution and species aggregation. Functions for analysis include species rarefaction and accumulation curves, species-area relationships and the distance decay of similarity.

Fits community site occupancy models to environmental DNA metabarcoding data collected using spatially-replicated survey design. Model fitting results can be used to evaluate and compare the effectiveness of species detection to find an efficient survey design. Reference: Fukaya et al. (2022) <doi:10.1111/2041-210X.13732>, Fukaya and Hasebe (2025) <doi:10.1002/1438-390X.12219>.