The package aims to facilitate Russian typesetting (based on input using MicroSoft Code Page 1251). Russian hyphenation is selected, and various mathematical commands are set up in Russian style. Furthermore all Cyrillic letters catcodes are set to letter, so that commands with Cyrillic letters in their names may be defined.

The Gene Ontology (GO) Consortium <https://geneontology.org/> organizes genes into hierarchical categories based on biological process (BP), molecular function (MF) and cellular component (CC, i.e., subcellular localization). Tools such as GoMiner (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform ontological analysis of microarray and proteomics studies, typically generating a list of significant functional categories. The significance is traditionally determined by randomizing the input gene list to computing the false discovery rate (FDR) of the enrichment p-value for each category. We explore here the novel alternative of randomizing the GO database rather than the gene list.

Sequential permutation testing for statistical significance of predictors in random forests and other prediction methods. The main function of the package is rfvimptest(), which allows to test for the statistical significance of predictors in random forests using different (sequential) permutation test strategies [1]. The advantage of sequential over conventional permutation tests is that they are computationally considerably less intensive, as the sequential procedure is stopped as soon as there is sufficient evidence for either the null or the alternative hypothesis. Reference: [1] Hapfelmeier, A., Hornung, R. & Haller, B. (2023) Efficient permutation testing of variable importance measures by the example of random forests. Computational Statistics & Data Analysis 181:107689, <doi:10.1016/j.csda.2022.107689>.

Visualize results generated by Antares, a powerful open source software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions that create interactive charts to help Antares users visually explore the results of their simulations.

This package contains match results from seven European men's football leagues, namely Premier League (England), Ligue 1 (France), Bundesliga (Germany), Serie A (Italy), Primera Division (Spain), Eredivisie (The Netherlands), Super Lig (Turkey). Includes Seasons 2010/2011 until 2019/2020 and a set of interesting covariates. Can be used all purposes.

To run data analysis for enzyme-link immunosorbent assays (ELISAs). Either the five- or four-parameter logistic model will be fitted for data of single ELISA. Moreover, the batch effect correction/normalization will be carried out, when there are more than one batches of ELISAs. Feng (2018) <doi:10.1101/483800>.

Easily use Font Awesome icons as shiny favicons (the icons that appear on browser tabs). Font Awesome (<https://fontawesome.com/>) is a popular set of icons that can be used in web pages. favawesome provides a simple way to use these icons as favicons in shiny applications and other HTML pages.

Simple and integrated tool that automatically extracts and folds all hairpin sequences from raw genome-wide data. It predicts the secondary structure of several overlapped segments, with longer length than the mean length of sequences of interest for the species under processing, ensuring that no one is lost nor inappropriately cut.

This package implements transformations of p-values to the smallest possible Bayes factor within the specified class of alternative hypotheses, as described in Held & Ott (2018, <doi:10.1146/annurev-statistics-031017-100307>). Covers several common testing scenarios such as z-tests, t-tests, likelihood ratio tests and the F-test.

Installs an updated version of pomdp-solve', a program to solve Partially Observable Markov Decision Processes (POMDPs) using a variety of exact and approximate value iteration algorithms. A convenient R infrastructure is provided in the separate package pomdp. Kaelbling, Littman and Cassandra (1998) <doi:10.1016/S0004-3702(98)00023-X>.

Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness. We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.

This package provides a set of functions to interpret changes in compositional data based on a network representation of all pairwise ratio comparisons: computation of all pairwise ratio, construction of a p-value matrix of all pairwise tests of these ratios between conditions, conversion of this matrix to a network.

Improves the interpretation of the Standardized Precipitation Index under changing climate conditions. The package uses the nonstationary approach proposed in Blain et al. (2022) <doi:10.1002/joc.7550> to detect trends in rainfall quantities and to quantify the effect of such trends on the probability of a drought event occurring.

Routines for creating, manipulating, and performing Bayesian inference about Gaussian processes in one and two dimensions using the Fourier basis approximation: simulation and plotting of processes, calculation of coefficient variances, calculation of process density, coefficient proposals (for use in MCMC). It uses R environments to store GP objects as references/pointers.

Offers markdown output formats designed with various styles, allowing users to generate HTML reports tailored for scientific or machine learning showcase. The output has a contemporary appearance with vibrant visuals, providing numerous styles for effective highlighting. Created using the tufte <https://rstudio.github.io/tufte/> package code as a starting point.

Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled C++ written using the Scythe Statistical Library Version 0.3.

The maximum likelihood classifier (MLC) is one of the most common classifiers used for remote sensing imagery. This package uses RcppArmadillo to provide a fast implementation of the MLC to train and predict over tabular data (data.frame). The algorithms were based on Mather (1985) <doi:10.1080/01431168508948456> method.

This application provides exploratory and confirmatory factor analysis, classical test theory, unidimensional and multidimensional item response theory, and continuous item response model analysis, through the shiny interactive interface. In addition, it offers rich functionalities for visualizing and downloading results. Users can download figures, tables, and analysis reports via the interactive interface.

Constructs a virtual population from fertility and mortality rates for any country, calendar year and birth cohort in the Human Mortality Database <https://www.mortality.org> and the Human Fertility Database <https://www.humanfertility.org>. Fertility histories are simulated for every individual and their offspring, producing a multi-generation virtual population.

This package provides an R to C/C++ interface that runs the Leiden community detection algorithm to find a basic partition. It runs the equivalent of the leidenalg find_partition() function. This package includes the required source code files from the official leidenalg distribution and functions from the R igraph package.

This package offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can adjust a tree's graphical parameters (the color, size, type, etc of its branches, nodes and labels) and visually and statistically compare different dendrograms to one another.

Reazon is an implmentation of the miniKanren language for Emacs. It provides an interface for writing and running relational programs. That interface consists of the following macros:

* reazon-defrel * reazon-run* * reazon-run * reazon-fresh * reazon-conde * reazon-conj * reazon-disj * reazon-project

Besides these, there is a single primitive goal, reazon-==.

Simplify creating multiple, related leaflet maps across tabs for a shiny application. Users build lists of any polygons, points, and polylines needed for the project, use the map_server() function to assign built lists and other chosen aesthetics into each tab, and the package leverages modules to generate all map tabs.

This package contains the probability density function, cumulative distribution function, quantile function, and random number generator for composite and discrete composite distributions with Pareto tails. The detailed description of the methods and the applications of the methods can be found in Bowen Liu, Malwane M.A. Ananda (2023) <arXiv:2309.16443>.