This package provides a robust implementation of Topolow algorithm. It embeds objects into a low-dimensional Euclidean space from a matrix of pairwise dissimilarities, even when the data do not satisfy metric or Euclidean axioms. The package is particularly well-suited for sparse, incomplete, and censored (thresholded) datasets such as antigenic relationships. The core is a physics-inspired, gradient-free optimization framework that models objects as particles in a physical system, where observed dissimilarities define spring rest lengths and unobserved pairs exert repulsive forces. The package also provides functions specific to antigenic mapping to transform cross-reactivity and binding affinity measurements into accurate spatial representations in a phenotype space. Key features include: * Robust Embedding from Sparse Data: Effectively creates complete and consistent maps (in optimal dimensions) even with high proportions of missing data (e.g., >95%). * Physics-Inspired Optimization: Models objects (e.g., antigens, landmarks) as particles connected by springs (for measured dissimilarities) and subject to repulsive forces (for missing dissimilarities), and simulates the physical system using laws of mechanics, reducing the need for complex gradient computations. * Automatic Dimensionality Detection: Employs a likelihood-based approach to determine the optimal number of dimensions for the embedding/map, avoiding distortions common in methods with fixed low dimensions. * Noise and Bias Reduction: Naturally mitigates experimental noise and bias through its network-based, error-dampening mechanism. * Antigenic Velocity Calculation (for antigenic data): Introduces and quantifies "antigenic velocity," a vector that describes the rate and direction of antigenic drift for each pathogen isolate. This can help identify cluster transitions and potential lineage replacements. * Broad Applicability: Analyzes data from various objects that their dissimilarity may be of interest, ranging from complex biological measurements such as continuous and relational phenotypes, antibody-antigen interactions, and protein folding to abstract concepts, such as customer perception of different brands. Methods are described in the context of bioinformatics applications in Arhami and Rohani (2025a) <doi:10.1093/bioinformatics/btaf372>, and mathematical proofs and Euclidean embedding details are in Arhami and Rohani (2025b) <doi:10.48550/arXiv.2508.01733>.

Census and administrative data in South Korea are a basic source of quantitative and mixed-methods research for social and urban scientists. This package provides a sf (Pebesma et al., 2024 <doi:10.32614/CRAN.package.sf>) based standardized workflow based on direct open API access to the major census and administrative data sources and pre-generated files in South Korea.

Programs for Martinussen and Scheike (2006), `Dynamic Regression Models for Survival Data', Springer Verlag. Plus more recent developments. Additive survival model, semiparametric proportional odds model, fast cumulative residuals, excess risk models and more. Flexible competing risks regression including GOF-tests. Two-stage frailty modelling. PLS for the additive risk model. Lasso in the ahaz package.

This package provides triangulations of regular height fields, based on the methods described in "Fast Polygonal Approximation of Terrains and Height Fields" Michael Garland and Paul S. Heckbert (1995) <https://www.mgarland.org/files/papers/scape.pdf> using code from the hmm library written by Michael Fogleman <https://github.com/fogleman/hmm>.

Helper functions for processing REDCap data in R. REDCap is a web-enabled application for building and managing surveys and databases developed at Vanderbilt University.

Each sequence is predicted by expanding the distance matrix. The compact set of hyper-parameters is tuned through random search.

Estimation of transition probabilities for the illness-death model and or the three-state progressive model.

An extension of ExPosition for two table analyses, specifically, discriminant analyses.

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.

This package provides a wrapper for the TexTra API <https://mt-auto-minhon-mlt.ucri.jgn-x.jp/>, a web service for translating texts between different languages. TexTra API account is required to use the service.

Find the optimal decision rules (AKA progression criteria) and sample size for clinical trials with three (stop/pause/go) outcomes. Both binary and continuous endpoints can be accommodated, as can cases where an adjustment is planned following a pause outcome. For more details see Wilson et al. (2024) <doi:10.1186/s12874-024-02351-x>.

Theme ggplot2', lattice', and base graphics based on a few choices, including foreground color, background color, accent color, and font family. Fonts that aren't available on the system, but are available via download on Google Fonts', can be automatically downloaded, cached, and registered for use with the showtext and ragg packages.

The Cancer Genome Atlas (TCGA) is a program aimed at improving our understanding of Cancer Biology. Several TCGA Datasets are available online. TCGAretriever helps accessing and downloading TCGA data hosted on cBioPortal via its Web Interface (see <https://www.cbioportal.org/> for more information).

Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. Details can be found in Leifeld (2013), JStatSoft <doi:10.18637/jss.v055.i08>.).

This package provides a compilation of fish stock assessment methods for the analysis of length-frequency data in the context of data-poor fisheries. Includes methods and examples included in the FAO Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish stock assessment" (<https://openknowledge.fao.org/server/api/core/bitstreams/bc7c37b6-30df-49c0-b5b4-8367a872c97e/content>), as well as other more recent methods.

Enables the acquisition of Korean financial market data, designed to integrate seamlessly with the tidyquant package.

This package provides a pipeline for short tandem repeat instability analysis from fragment analysis data. Inputs of fsa files or peak tables, and a user supplied metadata data-frame. The package identifies ladders, calls peaks, identifies the modal peaks, calls repeats, then calculates repeat instability metrics (e.g. expansion index from Lee et al. (2010) <doi:10.1186/1752-0509-4-29>).

The Taylor Russell model is a widely used method for assessing test validity in personnel selection tasks. The three functions in this package extend this model in a number of notable ways. TR() estimates test validity for a single selection test via the original Taylor Russell model. It extends this model by allowing users greater flexibility in argument choice. For example, users can specify any three of the four parameters (base rate, selection ratio, criterion validity, and positive predictive value) of the Taylor Russell model and estimate the remaining parameter (see the help file for examples). The TaylorRussell() function generalizes the original Taylor Russell model to allow for multiple selection tests (predictors). To our knowledge, this is the first generalization of the Taylor Russell model to allow for three or more selection tests (it is also the first to correctly handle models with two selection tests). TRDemo() is a shiny program for illustrating the underlying logic of the Taylor Russell model. Taylor, HC and Russell, JT (1939) "The relationship of validity coefficients to the practical effectiveness of tests in selection: Discussion and tables" <doi:10.1037/h0057079>.

Simulation, estimation and inference for univariate and multivariate TV(s)-GARCH(p,q,r)-X models, where s indicates the number and shape of the transition functions, p is the ARCH order, q is the GARCH order, r is the asymmetry order, and X indicates that covariates can be included; see Campos-Martins and Sucarrat (2024) <doi:10.18637/jss.v108.i09>. In the multivariate case, variances are estimated equation by equation and dynamic conditional correlations are allowed. The TV long-term component of the variance as in the multiplicative TV-GARCH model of Amado and Terasvirta (2013) <doi:10.1016/j.jeconom.2013.03.006> introduces non-stationarity whereas the GARCH-X short-term component describes conditional heteroscedasticity. Maximisation by parts leads to consistent and asymptotically normal estimates.

Allows users to quickly load multiple patients electrocardiographic (ECG) data at once and conduct relevant time analysis of heart rate variability (HRV) without manual edits from a physician or data cleaning specialist. The package provides the unique ability to iteratively filter, plot, and store time analysis results in a data frame while writing plots to a predefined folder. This streamlines the workflow for HRV analysis across multiple datasets. Methods are based on Rodrà guez-Liñares et al. (2011) <doi:10.1016/j.cmpb.2010.05.012>. Examples of applications using this package include Kwon et al. (2022) <doi:10.1007/s10286-022-00865-2> and Lawrence et al. (2023) <doi:10.1016/j.autneu.2022.103056>.

Parse XML documents from the Open Access subset of Europe PubMed Central <https://europepmc.org> including section paragraphs, tables, captions and references.

This package provides a system for personalized exercise plan recommendations for T2D (Type 2 Diabetes) patients based on the primary outcome of HbA1c (Glycated Hemoglobin). You provide the individual's information, and T2DFitTailor details the exercise plan and predicts the intervention's effectiveness.

The goal of trainR is to provide a simple interface to the National Rail Enquiries (NRE) systems. There are few data feeds available, the simplest of them is Darwin, which provides real-time arrival and departure predictions, platform numbers, delay estimates, schedule changes and cancellations. Other data feeds provide historical data, Historic Service Performance (HSP), and much more. trainR simplifies the data retrieval, so that the users can focus on their analyses. For more details visit <https://www.nationalrail.co.uk/46391.aspx>.

Helps the user to build and register schema descriptions of disorganised (messy) tables. Disorganised tables are tables that are not in a topologically coherent form, where packages such as tidyr could be used for reshaping. The schema description documents the arrangement of input tables and is used to reshape them into a standardised (tidy) output format.