This package provides a minimum set of functions to perform compositional data analysis using the log-ratio approach introduced by John Aitchison (1982). Main functions have been implemented in c++ for better performance.

Compares two dataframes which have the same column structure to show the rows that have changed. Also gives a git style diff format to quickly see what has changed in addition to summary statistics.

This package provides plugins for setting up fiery apps as a reverse proxy. This allows you to use a fiery server as a front for multiple services or even work as a load-balancer.

Draws gene or genome maps and comparisons between these, in a publication-grade manner. Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.

Large language models are readily accessible via API. This package lowers the barrier to use the API inside of your development environment. For more on the API, see <https://platform.openai.com/docs/introduction>.

Create groups of ggplot2 layers that can be easily migrated from one plot to another, reducing redundant code and improving the ability to format many plots that draw from the same source ggpacket layers.

This package provides ggplot2 geoms analogous to geom_col() and geom_bar() that allow for treemaps using treemapify nested within each bar segment. Also provides geometries for subgroup bordering and text annotation.

Check if an externalptr is a null pointer. R does currently not have a native function for that purpose. This package contains a C function that returns TRUE in case of a null pointer.

This package provides tools for using the API of e-Stat (<https://www.e-stat.go.jp/>), a portal site for Japanese government statistics. Includes functions for automatic query generation, data collection and formatting.

Extends the simple k-nearest neighbors algorithm by incorporating numerous kernel functions and a variety of distance metrics. The package takes advantage of RcppArmadillo to speed up the calculation of distances between observations.

Automatically install, update, and load CRAN', GitHub', and Bioconductor packages in a single function call. By accepting bare unquoted names for packages, it's easy to add or remove packages from the list.

Aims to support all features of the system credential store, including non-portable ones. Supports Keychain on macOS', and Credential Manager on Windows'. See the keyring package if you need a portable API'.

This package provides a comprehensive and easy to use R implementation of confirmatory phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer (2012) <doi:10.1111/j.1558-5646.2012.01790.x>.

Models the nonnegative entries of a rectangular adjacency matrix using a sparse latent position model, as illustrated in Rastelli, R. (2018) "The Sparse Latent Position Model for nonnegative weighted networks" <arXiv:1808.09262>.

This package provides a scrolling chat interface with multiline input, suitable for creating chatbot apps based on Large Language Models (LLMs). Designed to work particularly well with the ellmer R package for calling LLMs.

This package provides a graphical user interface (GUI) for fitting Bayesian regression models using the package brms which in turn relies on Stan (<https://mc-stan.org/>). The shinybrms GUI is a shiny app.

Solving a system of linear equations is one of the most fundamental computational problems for many fields of mathematical studies, such as regression problems from statistics or numerical partial differential equations. This package provides basic stationary iterative solvers such as Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods. Nonstationary, also known as Krylov subspace methods are also provided. Sparse matrix computation is also supported in that solving large and sparse linear systems can be manageable using the Matrix package along with RcppArmadillo.

This package contains functions for random generation of R x C and 2 x 2 x K contingency tables. In addition to the generation of contingency tables over predetermined intraclass-correlated clusters, it is possible to generate contingency tables without intraclass correlations under product multinomial, multinomial, and Poisson sampling plans. It also consists of a function for generation of random data from a given discrete probability distribution function. See Demirhan (2016) <https://journal.r-project.org/archive/2016-1/demirhan.pdf> for more information.

This package provides a cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an executable script.

RedNotebook is a modern desktop journal. It lets you format, tag and search your entries. You can also add pictures, links and customizable templates, spell check your notes, and export to plain text, HTML, Latex or PDF.

This library allows reading and writing RPM packages. It is used by the fpm tool. It is written in pure Ruby because librpm is not available on all systems and requires many dependencies.

As everyone knows, the most complex codes were composed of a mass of different kinds of parentheses (typically: lisp). This plugin will help you read these codes by showing different levels of parentheses in different colors.

Supplies AnnotationHub with `MeSHDb` NIH MeSH annotation databases for many species. All the SQLite files and metadata.csv are generated by our Snakemake workflow [mesh-workflow](https://github.com/rikenbit/mesh-workflow).

This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.