The SaTScan'(TM) <https://www.satscan.org> software uses spatial and space-time scan statistics to detect and evaluate spatial and space-time clusters. With the rsatscan package, you can run the external SaTScan software from within R using R data formats. To successfully select appropriate parameter settings within rsatscan', you must first learn SaTScan'.

Read Statistical Data and Metadata Exchange (SDMX) XML data. This the main transmission format used in official statistics. Data can be imported from local SDMX-ML files or a SDMX web-service and will be read in as is into a dataframe object. The RapidXML C++ library <https://rapidxml.sourceforge.net/> is used to parse the XML data.

This package provides a solution path for Reinforced Angle-based Multicategory Support Vector Machines, with linear learning, polynomial learning, and Gaussian kernel learning. C. Zhang, Y. Liu, J. Wang and H. Zhu. (2016) <doi:10.1080/10618600.2015.1043010>.

Direct insertion of over 1000 symbols (e.g. currencies, letters, emojis, arrows, mathematical symbols and so on) into Rmarkdown documents and Shiny applications by incorporating HTML hex codes.

Implementation of a Principal Component Analysis (PCA) in the torus via density ridge estimation. The main function, ridge_pca(), obtains the relevant density ridge for bivariate sine von Mises and bivariate wrapped Cauchy distribution models and provides the associated scores and variance decomposition. Auxiliary functions for evaluating, fitting, and sampling these models are also provided. The package provides replicability to Garcà a-Portugués and Prieto-Tirado (2023) <doi:10.1007/s11222-023-10273-9>.

This package provides a task-oriented R interface to the RDKit <https://www.rdkit.org> library through its Python API via reticulate'. The package offers high-level cheminformatics functionality, including molecule parsing, descriptor calculation, and fingerprint generation without replicating the native structure of RDKit'.

Scans manuscripts, bibliographies, and reference lists for citations to retracted publications so that authors can avoid citing retracted work. retraction reads bibliographic formats (BibTeX, BibLaTeX, CSL-JSON, RIS, EndNote XML) and document formats (R Markdown, Quarto, LaTeX', Markdown, HTML, JATS XML, Word, and PDF), extracts and normalizes identifiers, and checks them against retraction data. The default data source is the Retraction Watch database served through the XeraRetractionTracker API; Crossref', OpenAlex', Europe PMC', PubMed', DataCite', and a preprint source ('arXiv and bioRxiv withdrawals) are available as additional sources ('OpenAlex retraction data is itself derived from Retraction Watch). Within each source, matching proceeds from exact Digital Object Identifier (DOI) and PubMed identifier lookups to fuzzy title matching, and results are returned as a tidy table with a match-quality score and an optional self-contained HTML report.

Clusters functionally related biological terms from gene set enrichment results. Terms are compared by the overlap of their gene sets using Cohen's kappa, the Jaccard index, or the Dice coefficient, and the resulting similarity matrix is grouped either by agglomerative hierarchical clustering with single, complete, average, or Ward linkage, or by the seed-and-merge procedure of the DAVID functional classification tool. The distance and clustering routines are written in C++ for speed. The methods are described in Huang et al. (2007) <doi:10.1186/gb-2007-8-9-r183>, Ward (1963) <doi:10.1080/01621459.1963.10500845>, Cohen (1960) <doi:10.1177/001316446002000104>, and Jaccard (1912) <doi:10.1111/j.1469-8137.1912.tb05611.x>.

Compute time-dependent Incident/dynamic accuracy measures (ROC curve, AUC, integrated AUC )from censored survival data under proportional or non-proportional hazard assumption of Heagerty & Zheng (Biometrics, Vol 61 No 1, 2005, PP 92-105).

This package provides an infrastructure for handling multiple R Markdown reports, including automated curation and time-stamping of outputs, parameterisation and provision of helper functions to manage dependencies.

Automates the download and processing of historical weather data from the Brazilian National Institute of Meteorology (INMET). It provides a cached catalogue of automatic stations, resumable and validated downloads, and parsers for formatting inconsistencies in raw CSV files across different years. It removes structural artifacts, standardizes column names, parses timestamps, and returns data frames ready for analysis. Data are retrieved from <https://portal.inmet.gov.br/dadoshistoricos> and <https://apitempo.inmet.gov.br/estacoes/T>.

This package provides functions to compute Shannon entropy, Renyi entropy, Tsallis entropy, and related extropy measures for discrete probability distributions. Includes joint and conditional entropy, KL divergence, Jensen-Shannon divergence, cross-entropy, normalized entropy, and Renyi extropy (including the conditional and maximum forms). All measures use the natural logarithm (nats). Useful for information theory, statistics, and machine learning applications.

As an advanced approach to computerized adaptive testing (CAT), shadow testing (van der Linden(2005) <doi:10.1007/0-387-29054-0>) dynamically assembles entire shadow tests as a part of selecting items throughout the testing process. Selecting items from shadow tests guarantees the compliance of all content constraints defined by the blueprint. RSCAT is an R package for the shadow-test approach to CAT. The objective of RSCAT is twofold: 1) Enhancing the effectiveness of shadow-test CAT simulation; 2) Contributing to the academic and scientific community for CAT research. RSCAT is currently designed for dichotomous items based on the three-parameter logistic (3PL) model.

Allows the user to implement a dark/light toggle mode in shiny using the Nightly JavaScript library. The default mode is dark/light however the user can also specify other colours.

This package provides functions for reconstructing individual-level data (time, status, arm) from Kaplan-MEIER curves published in academic journals (e.g. NEJM, JCO, JAMA). The individual-level data can be used for re-analysis, meta-analysis, methodology development, etc. This package was used to generate the data for commentary such as Sun, Rich, & Wei (2018) <doi:10.1056/NEJMc1808567>. Please see the vignette for a quickstart guide.

Radioactive doses estimation using individual chromosomal aberrations information. See Higueras M, Puig P, Ainsbury E, Rothkamm K. (2015) <doi:10.1088/0952-4746/35/3/557>.

This package provides a common framework for calculating distance matrices.

Detects copy number alteration events in targeted exon sequencing data for tumor samples without matched normal controls. The advantage of this method is that it can be applied to smaller sequencing panels including evaluations of exon, transcript, gene, or even user specified genetic regions of interest. Functions in the package include steps for GC-content correction, calculation of quantile based normal karyotype ranges, and calculation of feature score. Cutoffs for "normal" quantile and score are user-adjustable.

This package provides an interface to Mapzen'-based APIs (including geocode.earth, Nextzen, and NYC GeoSearch) for geographic search and geocoding, isochrone calculation, and vector data to draw map tiles. See <https://www.mapzen.com/documentation/> for more information. The original Mapzen has gone out of business, but rmapzen can be set up to work with any provider who implements the Mapzen API.

An implementation of functions for the analysis of crime incident or records management system data. The package implements analysis algorithms scaled for city or regional crime analysis units. The package provides functions for kernel density estimation for crime heat maps, geocoding using the Google Maps API, identification of repeat crime incidents, spatio-temporal map comparison across time intervals, time series analysis (forecasting and decomposition), detection of optimal parameters for the identification of near repeat incidents, and near repeat analysis with crime network linkage.

Enhances the R Optimization Infrastructure ('ROI') package with the quadratic solver OSQP'. More information about OSQP can be found at <https://osqp.org>.

Convert a string of text characters to Elder Futhark Runes <https://en.wikipedia.org/wiki/Elder_Futhark>.

The Rcpp package contains a C++ library that facilitates the integration of R and C++ in various ways via a rich API. This API was preceded by an earlier version which has been deprecated since 2010 (but is still supported to provide backwards compatibility in the package RcppClassic'). This package RcppClassicExamples provides usage examples for the older, deprecated API. There is also a corresponding package RcppExamples with examples for the newer, current API which we strongly recommend as the basis for all new development.

Implementation of Taylor Regression Estimator (TRE), Tulip Extreme Finding Estimator (TEFE), Bell Extreme Finding Estimator (BEFE), Integration Extreme Finding Estimator (IEFE) and Integration Root Finding Estimator (IRFE) for roots, extrema and inflections of a curve . Christopoulos, DT (2019) <doi:10.13140/RG.2.2.17158.32324> . Christopoulos, DT (2016) <doi:10.2139/ssrn.3043076> . Christopoulos, DT (2016) <https://demovtu.veltech.edu.in/wp-content/uploads/2016/04/Paper-04-2016.pdf> . Christopoulos, DT (2014) <doi:10.48550/arXiv.1206.5478> .