Thinning (skeletonization) algorithms for binary raster images. Provides seven algorithms behind a single dispatching function: Zhang-Suen (Zhang and Suen 1984) <doi:10.1145/357994.358023>, Guo-Hall (Guo and Hall 1989) <doi:10.1145/62065.62074>, a 2-D adaptation of Lee (Lee, Kashyap, and Chu 1994) <doi:10.1006/cgip.1994.1042>, K3M (Saeed, Tabedzki, Rybnik, and Adamski 2010) <doi:10.2478/v10006-010-0024-4>, the parallel form commonly attributed to Hilditch (1969, in Machine Intelligence 4'), OPTA / SPTA (Naccache and Shinghal 1984), and Holt and colleagues (1987) <doi:10.1145/12527.12531>. Also provides the medial axis transform (Blum 1967) and a distance transform implementation following Felzenszwalb and Huttenlocher (2012) <doi:10.4086/toc.2012.v008a019>. The thin() API selects the algorithm by name, defaulting to Zhang-Suen. Complements the morphology in the EBImage package, which does not provide a thinning operator.

Treatment and visualization of membrane (selective) transport data. Transport profiles involving up to three species are produced as publication-ready plots and several membrane performance parameters (e.g. separation factors as defined in Koros et al. (1996) <doi:10.1351/pac199668071479> and non-linear regression parameters for the equations described in Rodriguez de San Miguel et al. (2014) <doi:10.1016/j.jhazmat.2014.03.052>) can be obtained. Many widely used experimental setups (e.g. membrane physical aging) can be easily studied through the package's graphical representations.

Carries out analyses of two-way tables with one observation per cell, together with graphical displays for an additive fit and a diagnostic plot for removable non-additivity via a power transformation of the response. It implements methods from Tukey's Exploratory Data Analysis (1973) <ISBN: 978-0201076165>, including a 1-degree-of-freedom test for row*column non-additivity', linear in the row and column effects.

Plot official statistics time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. tstools comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, tstools provides a super fast, data.table backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.

Checks LaTeX documents and .bib files for typing errors, such as spelling errors, incorrect quotation marks. Also provides useful functions for parsing and linting bibliography files.

This package provides a variety of tools for assessing dose response curves, with an emphasis on toxicity test data. The main feature of this package are modular functions which can be combined through the namesake pipeline, runtoxdrc', to automate the analysis for large and complex datasets. This includes optional data preprocessing steps, like outlier detection, solvent effects, blank correction, averaging technical replicates, and much more. Additionally, this pipeline is adaptable to any long form dataset, and does not require specific column or group naming to work.

This package provides functions for visualizing networks with tmap'. It supports sfnetworks objects natively but is not limited to them. Useful for adding network layers such as edges and nodes to tmap maps. More features may be added in future versions.

This package provides a toolkit for web scraping, modular NLP pipelines, and text preparation for large language models. Organized around four core actions: fetching, reading, processing, and searching. Covers the full pipeline from raw web data acquisition to structural text processing and BM25 indexing. Supports multiple retrieval strategies including regex, dictionary matching, and ranked keyword search. Pipe-friendly with no heavy dependencies; all outputs are plain data frames or data.tables.

TEMPoral TEnsor Decomposition (TEMPTED), is a dimension reduction method for multivariate longitudinal data with varying temporal sampling. It formats the data into a temporal tensor and decomposes it into a summation of low-dimensional components, each consisting of a subject loading vector, a feature loading vector, and a continuous temporal loading function. These loadings provide a low-dimensional representation of subjects or samples and can be used to identify features associated with clusters of subjects or samples. TEMPTED provides the flexibility of allowing subjects to have different temporal sampling, so time points do not need to be binned, and missing time points do not need to be imputed.

This package provides a type system for R. It supports setting variable types in a script or the body of a function, so variables can't be assigned illegal values. Moreover it supports setting argument and return types for functions.

Implementation of two transportation problem algorithms. 1. North West Corner Method 2. Minimum Cost Method or Least cost method. For more technical details about the algorithms please refer below URLs. <http://www.universalteacherpublications.com/univ/ebooks/or/Ch5/nw.htm>. <http://personal.maths.surrey.ac.uk/st/J.F/chapter7.pdf>.

Generate constrained Delaunay triangulation meshes for use with stochastic partial differential equation (SPDE) spatial models (Lindgren, Rue and Lindstroem 2011 <doi:10.1111/j.1467-9868.2011.00777.x>). Provides automatic mesh generation from point coordinates with boundary constraints, Ruppert refinement for mesh quality, finite element method (FEM) matrix assembly (mass, stiffness, projection), barrier models, spherical meshes via icosahedral subdivision, and metric graph meshes for network geometries. Built on the CDT header-only C++ library (Amirkhanov 2024 <https://github.com/artem-ogre/CDT>). Designed as the mesh backend for the tulpa Bayesian hierarchical modelling engine but usable standalone for any spatial triangulation task.

This package provides access to the complete Pali Canon, or Tipitaka, the canonical scripture for Theravadin Buddhists worldwide. Based on the Chattha Sangayana Tipitaka version 4 (Vipassana Research Institute, 1990). Includes word frequency data and tools for Pali string sorting. For a lemmatized critical edition with sutta-level granularity, see the companion package tipitaka.critical'.

Perform two types of analysis: 1) checking the goodness-of-fit of tree models to your single-cell gene expression data; and 2) deciding which tree best fits your data.

BEAST2 (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. Tracer (<https://github.com/beast-dev/tracer/>) is a GUI tool to parse and analyze the files generated by BEAST2'. This package provides a way to parse and analyze BEAST2 input files without active user input, but using R function calls instead.

To facilitate the analysis of positron emission tomography (PET) time activity curve (TAC) data, and to encourage open science and replicability, this package supports data loading and analysis of multiple TAC file formats. Functions are available to analyze loaded TAC data for individual participants or in batches. Major functionality includes weighted TAC merging by region of interest (ROI), calculating models including standardized uptake value ratio (SUVR) and distribution volume ratio (DVR, Logan et al. 1996 <doi:10.1097/00004647-199609000-00008>), basic plotting functions and calculation of cut-off values (Aizenstein et al. 2008 <doi:10.1001/archneur.65.11.1509>). Please see the walkthrough vignette for a detailed overview of tacmagic functions.

UpSet.js is a re-implementation of UpSetR to create interactive set visualizations for more than three sets. This is a htmlwidget wrapper around the JavaScript library UpSet.js'.

Generates reproducible random samples from any user-specified univariate distribution under a comprehensive suite of censoring and truncation schemes. Users supply the probability density function (PDF), cumulative distribution function (CDF), survival function, support bounds, and parameters; the same seed and inputs yield identical samples across sessions. Supported schemes include right and left truncation, random, right, left, interval, and middle censoring, block random censoring, balanced joint progressive Type-II (BJPT-II), progressive first failure, joint Type-I, Type-I, Type-II, progressive Type-II, Type-II progressively hybrid, joint Type-II, hybrid, hybrid Type-I, doubly Type-II, Type-I hybrid, and hybrid Type-II censoring. Diagnostic histogram, dot plot, and autocorrelation plots are provided for each scheme to verify distributional behaviour. Methods are described in Nagar, Kumar, and Krishna (2026) <doi:10.59467/IJASS.2026.22.1>, Goel, Kumar, and Krishna (2026, "Estimation in power Lindley distributions using balanced joint progressively Type-II censored data"), Wu and Kus (2009) <doi:10.1016/j.csda.2009.03.010>, Goel and Krishna (2026) <doi:10.1007/s13198-026-03208-w>, Balakrishnan and Aggarwala (2000, ISBN:978-1-4612-1334-5), Mondal and Kundu (2020) <doi:10.1080/03610926.2018.1554128>, Ding and Gui (2023) <doi:10.3390/math11092003>, Prajapati, Mitra, and Kundu (2019) <doi:10.1007/s13571-018-0167-0>, Yadav, Jaiswal, and Yadav (2026) <doi:10.1007/s11135-026-02647-8>, Iyer, Jammalamadaka, and Kundu (2008) <doi:10.1016/j.jspi.2007.03.062>, Banerjee and Kundu (2008) <doi:10.1109/TR.2008.916890>, and Kundu and Joarder (2006) <doi:10.1016/j.csda.2005.05.002>.

The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with links to associated outcomes. See Zhang and Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the ability to simulate realistic mixed-typed clinical data.

Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <doi:10.1016/j.jprot.2019.103613>.

This package provides an algorithm to detect and characterize disturbances (start, end dates, intensity) that can occur at different hierarchical levels by studying the dynamics of longitudinal observations at the unit level and group level based on Nadaraya-Watson's smoothing curves, but also a shiny app which allows to visualize the observations and the detected disturbances. Finally the package provides a dataframe mimicking a pig farming system subsected to disturbances simulated according to Le et al.(2022) <doi:10.1016/j.animal.2022.100496>.

Elasticsearch is an open-source, distributed, document-based datastore (<https://www.elastic.co/products/elasticsearch>). It provides an HTTP API for querying the database and extracting datasets, but that API was not designed for common data science workflows like pulling large batches of records and normalizing those documents into a data frame that can be used as a training dataset for statistical models. uptasticsearch provides an interface for Elasticsearch that is explicitly designed to make these data science workflows easy and fun.

The framework proposed in Jenul et al., (2022) <doi:10.1007/s10994-022-06221-9>, together with an interactive Shiny dashboard. UBayFS is an ensemble feature selection technique embedded in a Bayesian statistical framework. The method combines data and user knowledge, where the first is extracted via data-driven ensemble feature selection. The user can control the feature selection by assigning prior weights to features and penalizing specific feature combinations. UBayFS can be used for common feature selection as well as block feature selection.

Implement a shrinkage estimation for the univariate normal mean based on a preliminary test (pretest) estimator. This package also provides the confidence interval based on pivoting the cumulative density function. The methodologies are published in Taketomi et al.(2024) <doi:10.1007/s42081-023-00221-2> and Taketomi et al.(2024-)(under review).