Derived from the work of Kruschke (2015, <ISBN:9780124058880>), the present package aims to provide a framework for conducting Bayesian analysis using Markov chain Monte Carlo (MCMC) sampling utilizing the Just Another Gibbs Sampler ('JAGS', Plummer, 2003, <https://mcmc-jags.sourceforge.io>). The initial version includes several modules for conducting Bayesian equivalents of chi-squared tests, analysis of variance (ANOVA), multiple (hierarchical) regression, softmax regression, and for fitting data (e.g., structural equation modeling).

This package provides memory-efficient biweight midcorrelation and exact bicor-based k-nearest-neighbor graph construction for dense and sparse numeric matrices. Dense, sparse, and mixed-input paths avoid materializing full dense similarity matrices for tidy and k-nearest-neighbor workflows where possible. The implementation supports pairwise finite-overlap handling and robust correlation-based graph construction for biological expression matrices and other high-dimensional numeric data.

This package provides Brazilian municipality population estimates from official and research sources, with functions to aggregate the data by state, health region, sex, and age group.

This package provides functions for downloading data from the Bank for International Settlements (BIS; <https://www.bis.org/>) in Basel. Supported are only full datasets in (typically) CSV format. The package is lightweight and without dependencies; suggested packages are used only if data is to be transformed into particular data structures, for instance into zoo objects. Downloaded data can optionally be cached, to avoid repeated downloads of the same files.

This package provides functions for blind source separation over multivariate spatial data, and useful statistics for evaluating performance of estimation on mixing matrix. BSSoverSpace is based on an eigen analysis of a positive definite matrix defined in terms of multiple normalized spatial local covariance matrices, and thus can handle moderately high-dimensional random fields. This package is an implementation of the method described in Zhang, Hao and Yao (2022)<arXiv:2201.02023>.

This package provides methods to estimate optimal dynamic treatment regimes using Bayesian likelihood-based regression approach as described in Yu, W., & Bondell, H. D. (2023) <doi:10.1093/jrsssb/qkad016> Uses backward induction and dynamic programming theory for computing expected values. Offers options for future parallel computing.

This package implements the Butterworth-Induced Autoregressive ('BTWAR') model, where autoregressive coefficients are obtained from analog Butterworth filter prototypes mapped into the discrete-time domain using the Matched Z-Transform. The framework establishes a structured connection between frequency-domain filter design and time-domain autoregressive modeling. Model order selection is performed via nested rolling-origin cross-validation. Method described in Bras-Geraldes, Rocha and Martins (2026) <doi:10.3390/math14030479>.

Propose a parametric fit for censored linear regression models based on SMSN distributions, from a Bayesian perspective. Also, generates SMSN random variables.

This package provides a Bayesian tool to test for population trends and changes in trends under arbitrary designs, including before-after (BA), control-intervention (CI) and before-after-control-intervention (BACI) designs commonly used to assess conservation impact. It infers changes in trends jointly from data obtained with multiple survey methods, as well as from limited and noisy data not necessarily collected in standardized ecological surveys. Observed counts can be modeled as following either a Poisson or a negative binomial model, and both deterministic and stochastic trend models are available. For more details on the model see Singer et al. (2025) <doi:10.1101/2025.01.08.631844>, and the file AUTHORS for a list of copyright holders and contributors.

This package provides a set of functions to apply HC3 (FIRORES) and HC2 (ROOT) sandwich estimators to make small-sample adjustments to standard errors of Generalized Linear Model statistics used to analyze cluster randomized trial data. The functions in the ClusterRandSSAdj package make small-sample adjustments to Generalized Linear Model parameter estimates, least squares means and pair-wise comparison of least squares means, Type III tests, and estimates from linear combinations of Generalized Linear Model parameters. For more details see Ford (2017) <doi:10.1002/bimj.201600182> and Westgate (2022) <doi:10.1177/17407745211063479>.

Analyzes data from a Conconi et al. (1996) <doi:10.1055/s-2007-972887> treadmill fitness test where speed is augmented by a constant amount every set number of seconds to estimate the anaerobic (lactate) threshold speed and heart rate. It reads a TCX file, allows optional removal observations from before and after the actual test, fits a change-point linear model where the change-point is the estimate of the lactate threshold, and plots the data points and fit model. Details of administering the fitness test are provided in the package vignette. Functions work by default for Garmin Connect TCX exports but may require additional data preparation for heart rate, time, and speed data from other sources.

Encode and decode c-squares, from and to simple feature (sf) or spatiotemporal arrays (stars) objects. Use c-squares codes to quickly join or query spatial data.

This package provides a collection of functions for modeling fissile material operations in nuclear facilities, based on Zywiec et al (2021) <doi:10.1016/j.ress.2020.107322>.

This package provides methods for interpreting CoDa (Compositional Data) regression models along the lines of "Pairwise share ratio interpretations of compositional regression models" (Dargel and Thomas-Agnan 2024) <doi:10.1016/j.csda.2024.107945>. The new methods include variation scenarios, elasticities, elasticity differences and share ratio elasticities. These tools are independent of log-ratio transformations and allow an interpretation in the original space of shares. CoDaImpact is designed to be used with the compositions package and its ecosystem.

This package provides automated small-cell suppression for one- and two-way frequency tables. Cells falling below a user-defined frequency threshold are masked, with suppression propagated to secondary cells to prevent indirect disclosure. Designed for clinical and health administrative data, the package supports a range of tabular structures and fits into reproducible reporting pipelines, reducing manual review while applying consistent suppression rules across data sharing workflows.

This package provides equations commonly used in clinical pharmacokinetics and clinical pharmacology, such as equations for dose individualization, compartmental pharmacokinetics, drug exposure, anthropomorphic calculations, clinical chemistry, and conversion of common clinical parameters. Where possible and relevant, it provides multiple published and peer-reviewed equations within the respective R function.

Features tools for exploring congruent phylogenetic birth-death models. It can construct the pulled speciation- and net-diversification rates from a reference model. Given alternative speciation- or extinction rates, it can construct new models that are congruent with the reference model. Functionality is included to sample new rate functions, and to visualize the distribution of one congruence class. See also Louca & Pennell (2020) <doi:10.1038/s41586-020-2176-1>.

Estimates the parameters of models with a single change-point in the hazard rate for time-to-event data. Supported models include the exponential (Gijbels & Gürler (2003) <doi:10.1023/B:LIDA.0000012424.71723.9d>, Matthews & Farewell (1982) <doi:10.2307/2530460>), Exponential-Lindley (Joshi & Rattihalli (2020) <doi:10.1007/978-981-15-5414-8_29>), Lindley (Joshi, Jose, & Bhati (2016) <doi:10.1080/03610918.2015.1096381>), log-logistic (Nadar, Upadhyay, & Joshi (2025) <doi:10.3390/math13091457>), and Weibull (Williams & Kim (2013) <doi:10.1080/03610926.2011.600505>) hazard change-point models. Provides functions for generating random variates and evaluating the probability density function (PDF) and the cumulative distribution function (CDF) of the fitted change-point models. Includes Kaplan-Meier and Nelson-Aalen diagnostic plots, together with goodness-of-fit measures such as the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC), distance metrics such as the L1-norm and L2-norm, and the Kolmogorov-Smirnov (K-S) statistic for model evaluation.

An educational package providing intuitive functions for calculating confidence intervals (CI) for various statistical parameters. Designed primarily for teaching and learning about statistical inference (particularly confidence intervals). Offers user-friendly wrappers around established methods for proportions, means, and bootstrap-based intervals. Integrates seamlessly with Tidyverse workflows, making it ideal for classroom demonstrations and student exercises.

Extension of cmprsk to Stratified and Clustered data. A goodness of fit test for Fine-Gray model is also provided. Methods are detailed in the following articles: Zhou et al. (2011) <doi:10.1111/j.1541-0420.2010.01493.x>, Zhou et al. (2012) <doi:10.1093/biostatistics/kxr032>, Zhou et al. (2013) <doi: 10.1002/sim.5815>.

An interactive document on the topic of classification tree analysis using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://kartikeyab.shinyapps.io/CTShiny/>.

This package provides a collection of clinical trial example datasets from multiple sources including the CDISC Pilot 01 study (CDISC <https://www.cdisc.org/>). All datasets are provided in Parquet format for efficient storage and can be accessed using the connector package. Designed for training, testing, prototyping, and demonstrating clinical data analysis workflows.

The cmgnd implements the constrained mixture of generalized normal distributions model, a flexible statistical framework for modelling univariate data exhibiting non-normal features such as skewness, multi-modality, and heavy tails. By imposing constraints on model parameters, the cmgnd reduces estimation complexity while maintaining high descriptive power, offering an efficient solution in the presence of distributional irregularities. For more details see Duttilo and Gattone (2025) <doi:10.1007/s00180-025-01638-x> and Duttilo et al (2025) <doi:10.48550/arXiv.2506.03285>.

This package provides a unified toolkit for cointegration testing including Fourier-based cointegration tests (FADL, FEG, FEG2, Tsong) that accommodate smooth structural breaks via flexible Fourier terms, and panel CADF cointegration tests with structural breaks using the Common Correlated Effects (CCE) estimator following Banerjee, Arcabic and Lee (2017) <doi:10.1016/j.econmod.2016.11.004>, Tsong, Lee, Tsai and Hu (2016) <doi:10.1007/s00181-015-1028-6>, and Banerjee and Carrion-i-Silvestre (2025) <doi:10.1080/07350015.2024.2327844>.