Implementation of the Stochastic Multi-Criteria Acceptability Analysis (SMAA) family of Multiple Criteria Decision Analysis (MCDA) methods. Tervonen, T. and Figueira, J. R. (2008) <doi:10.1002/mcda.407>.

St implements a simple and lightweight terminal emulator. It implements 256 colors, most VT10X escape sequences, utf8, X11 copy/paste, antialiased fonts (using fontconfig), fallback fonts, resizing, and line drawing.

This package performs joint selection in Generalized Linear Mixed Models (GLMMs) using penalized likelihood methods. Specifically, the Penalized Quasi-Likelihood (PQL) is used as a loss function, and penalties are then augmented to perform simultaneous fixed and random effects selection. Regularized PQL avoids the need for integration (or approximations such as the Laplace's method) during the estimation process, and so the full solution path for model selection can be constructed relatively quickly.

This package provides a set of functions to analyze and print the development of a commodity using the Point and Figure (P&F) approach. A P&F processor can be used to calculate daily statistics for the time series. These statistics can be used for deeper investigations as well as to create plots. Plots can be generated as well known X/O Plots in plain text format, and additionally in a more graphical format.

This package provides tools for molecule-oriented and reaction-centred analysis of root exudate datasets. It supports structural matching based on PubChem', calculation of molecular descriptors, and inference of candidate microbe-associated metabolic reactions using Kyoto Encyclopedia of Genes and Genomes ('KEGG') identifiers and Enzyme Commission ('EC') numbers. For background on these databases, see Kanehisa et al. (2023) <doi:10.1093/nar/gkac963> and Kim et al. (2023) <doi:10.1093/nar/gkac956>.

This package lets you fit beta regression and zero-or-one inflated beta regression and obtain Bayesian inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.

Uniform manifold approximation and projection is a technique for dimension reduction. This package provides an interface to the UMAP algorithm in R, including a translation of the original algorithm into R.

This package provides functions to handle basic input output. These functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.

This package provides a way to read, write and display bitmap images stored in the JPEG format with R. It can read and write both files and in-memory raw vectors.

This package provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.

Client for the Archaeology Knowledge Graph of Chile (ArKG, <https://arkg.cl>), providing access to Chilean archaeological dates (radiocarbon and thermoluminescence) via its SPARQL endpoint powered by MillenniumDB'.

Estimate diagnosis performance (Sensitivity, Specificity, Positive predictive value, Negative predicted value) of a diagnostic test where can not measure the golden standard but can estimate it using the attributable fraction.

This package provides the source and examples for James P. Howard, II, "Computational Methods for Numerical Analysis with R," <https://jameshoward.us/cmna/>, a book on numerical methods in R.

This package contains data sets, examples and software from the Second Edition of "Design of Observational Studies"; see Rosenbaum, P.R. (2010) <doi:10.1007/978-1-4419-1213-8>.

Bayesian networks with continuous and/or discrete variables can be learned and compared from data. The method is described in Boettcher and Dethlefsen (2003), <doi:10.18637/jss.v008.i20>.

Background correction of spectral like data. Handles variations in scaling, polynomial baselines, interferents, constituents and replicate variation. Parameters for corrections are stored for further analysis, and spectra are corrected accordingly.

Estimates extinction risk from population time series under a drifted Wiener process using MLE and observation-error-and-autocovariance-robust estimators, with confidence intervals based on the w-z method.

This package implements common geostatistical methods in a clean, straightforward, efficient manner. The methods are discussed in Schabenberger and Gotway (2004, <ISBN:9781584883227>) and Waller and Gotway (2004, <ISBN:9780471387718>).

This package implements assessment of benefit-risk balance using Bayesian Discrete Choice Experiment. For more details see the article by Mukhopadhyay et al. (2019) <DOI:10.1080/19466315.2018.1527248>.

This package provides a component-based reactive UI framework for Shiny that binds reactive values directly to DOM attributes, enabling fine-grained updates without re-rendering or update*Input callbacks.

Analyzing data under multivariate mixed effects model using multivariate REML and multivariate Henderson3 methods. See Meyer (1985) <doi:10.2307/2530651> and Wesolowska Janczarek (1984) <doi:10.1002/bimj.4710260613>.

Generates multivariate subgaussian stable probabilities using the QRSVN algorithm as detailed in Genz and Bretz (2002) <DOI:10.1198/106186002394> but by sampling positive stable variates not chi/sqrt(nu).