This package provides a general framework for performing sparse functional clustering as originally described in Floriello and Vitelli (2017) <doi:10.1016/j.jmva.2016.10.008>, with the possibility of jointly handling data misalignment (see Vitelli, 2019, <doi:10.48550/arXiv.1912.00687>).

Bayesian regression tree ensembles for survival analysis and causal inference. Implements BART, DART, Bayesian Causal Forests (BCF), and Horseshoe Forest models. Supports right-censored and interval-censored survival outcomes via accelerated failure time (AFT) formulations. Designed for high-dimensional prediction and heterogeneous treatment effect estimation.

Offers a handful of useful wrapper functions which streamline the reading, analyzing, and visualizing of variant call format (vcf) files in R. This package was designed to facilitate an explicit pipeline for optimizing Stacks (Rochette et al., 2019) (<doi:10.1111/mec.15253>) parameters during de novo (without a reference genome) assembly and variant calling of restriction-enzyme associated DNA sequence (RADseq) data. The pipeline implemented here is based on the 2017 paper "Lost in Parameter Space" (Paris et al., 2017) (<doi:10.1111/2041-210X.12775>) which establishes clear recommendations for optimizing the parameters m', M', and n', during the process of assembling loci.

This package provides a collection of utilities that allow programming with R's operators. Routines allow classifying operators, translating to and from an operator and its underlying function, and inverting some operators (e.g. comparison operators), etc. All methods can be extended to custom infix operators.

This package provides a cross between a 2D density plot and a scatter plot, implemented as a ggplot2 geom. Points in the scatter plot are colored by the number of neighboring points. This is useful to visualize the 2D-distribution of points in case of overplotting.

The package adds a macro \rgcounts which displays the allocation status of the TeX registers. The display is written into the .log file as it is a bit verbose. An automatic call to \rgcounts is done at \begin{document} and \end{document}.

This package provides a package for typesetting scholarly critical editions, replacing the established ledmac and eledmac packages. It supports indexing by page and by line numbers, and simple tabular- and array-style environments. The package is distributed with the related reledpar package.

Bars, in the present context, are lines above and below text that abut with the text. Barred roman numerals are sometimes found in publications. The package provides a function that prints barred roman numerals (converting Arabic numerals if necessary). The package also provides a predicate \ifnumeric.

This package provides a collection of Hi-C files (pairs, (m)cool and fastq). These datasets can be read into R and further investigated and visualized with the HiContacts package. Data includes yeast Hi-C data generated by the Koszul lab from the Pasteur Institute.

This package provides a collection of helper functions and htmlwidgets to help publishers curate content collections on Posit Connect'. The components, Card, Grid, Table, Search, and Filter can be used to produce a showcase page or gallery contained within a static or interactive R Markdown page.

This package provides a greta extension for analysing transition matrices and ordinary differential equations representing dynamical systems. Provides functions for analysing transition matrices by iteration, and solving ordinary differential equations. This is an extension to the greta software, Golding (2019) <doi:10.21105/joss.01601>.

Allows to import functions and whole packages from Julia in R. Imported Julia functions can directly be called as R functions. Data structures can be translated between Julia and R. More details can also be found in the corresponding article <doi:10.18637/jss.v101.i06>.

Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk, and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in parallel).

Two functions for financial portfolio optimization by linear programming are provided. One function implements Benders decomposition algorithm and can be used for very large data sets. The other, applicable for moderate sample sizes, finds optimal portfolio which has the smallest distance to a given benchmark portfolio.

This package implements S-type ridge regression, a robust and multicollinearity-aware linear regression estimator that combines S-type robust weighting (via the Stype.est package) with ridge penalization; automatically selects the ridge parameter using the ridgregextra approach targeting a close to 1 variance inflation factor (VIF), and returns comprehensive outputs (coefficients, fitted values, residuals, mean squared error (MSE), etc.) with an easy x/y interface and optional user-supplied weights. See Sazak and Mutlu (2021) <doi:10.1080/03610918.2021.1928196>, Karadag et al. (2023) <https://CRAN.R-project.org/package=ridgregextra> and Sazak et al. (2025) <https://CRAN.R-project.org/package=Stype.est>.

Markup allows the use of HTML syntax with in Common Lisp code. This has the advantage of being able to copy HTML snippets and have them instantly be functional, less double quotes than a s-expression approach, and designers will be able to understand the embedded HTML.

File::Remove::remove removes files and directories. It acts like /bin/rm, for the most part. Although unlink can be given a list of files, it will not remove directories; this module remedies that. It also accepts wildcards, * and ?, as arguments for file names.

This package provides the \setcounterref and \addtocounterref commands which use the section (or other) number from the reference as the value to put into the counter. It also provides \setcounterpageref and \addtocounterpageref that do the corresponding thing with the page reference of the label.

This package provides a much faster analytical implementation of chromVAR, with additional features, used to infer TF activity from (bulk or single-cell) ATAC-seq data and motif annotations (or binding probabilities). The package also includes the CVnorm normalization method based on the chromVAR logic.

Provide addins for RStudio'. It currently contains 3 addins. The first to add a shortcut for the double pipe. The second is to add a shortcut for the same operator. And the third to simplify the creation of vectors from texts pasted from the computer transfer area.

Numerous indices to choose the optimal number of clusters when performing k-means. Relevant papers include: Tsagris M. and Kontemeniotis N. (2025). Lobachevskii Journal of Mathematics <doi:10.1134/S1995080225613700>. Garcia-Escudero Luis A., Gordaliza Alfonso, Matran Carlos, Mayo-Iscar Agustin. (2008) <doi:10.1214/07-AOS515>.

It contains functions to apply blockmodeling of signed (positive and negative weights are assigned to the links), one-mode and valued one-mode and two-mode (two sets of nodes are considered, e.g. employees and organizations) networks (Brusco et al. (2019) <doi:10.1111/bmsp.12192>).

Visual representations of model fit or predictive success in the form of "separation plots." See Greenhill, Brian, Michael D. Ward, and Audrey Sacks. "The separation plot: A new visual method for evaluating the fit of binary models." American Journal of Political Science 55.4 (2011): 991-1002.

The Patient Rule Induction Method (PRIM) is typically used for "bump hunting" data mining to identify regions with abnormally high concentrations of data with large or small values. This package extends this methodology so that it can be applied to binary classification problems and used for prediction.