This package implements the algorithm of Christensen (2024) <doi:10.1214/22-BA1353> for estimating marginal likelihoods via permutation counting.

An R interface to pikchr (<https://pikchr.org>, pronounced "picture"), a PIC'-like markup language for creating diagrams within technical documentation. Originally developed by Brian Kernighan, PIC has been adapted into pikchr by D. Richard Hipp, the creator of SQLite'. pikchr is designed to be embedded in fenced code blocks of Markdown or other documentation markup languages, making it ideal for generating diagrams in text-based formats. This package allows R users to seamlessly integrate the descriptive syntax of pikchr for diagram creation directly within the R environment.

Identifies the entries with patterned responses for psychometric scales. The patterns included in the package are identical (a, a, a), ascending (a, b, c), descending (c, b, a), alternative (a, b, a, b / a, b, c, a, b, c).

This package provides methods for fitting point processes with parameters of generalised additive model (GAM) form are provided. For an introduction to point processes see Cox, D.R & Isham, V. (Point Processes, 1980, CRC Press), GAMs see Wood, S.N. (2017) <doi:10.1201/9781315370279>, and the fitting approach see Wood, S.N., Pya, N. & Safken, B. (2016) <doi:10.1080/01621459.2016.1180986>.

This package provides tools for downloading, reading and analyzing the National Survey of Health - PNS, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package survey'.

This package performs the explicit calculation -- not estimation! -- of the Rasch item parameters for dichotomous and polytomous item responses, using a pairwise comparison approach. Person parameters (WLE) are calculated according to Warm's weighted likelihood approach.

This package provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria <doi:10.48550/arXiv.1810.01005>. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.

Receiver Operating Characteristic (ROC) analysis is performed assuming samples are from the Power Lindley distribution. Specificity, sensitivity, area under the curve and ROC curve are provided.

Bland (2009) <doi:10.1136/bmj.b3985> recommended to base study sizes on the width of the confidence interval rather the power of a statistical test. The goal of presize is to provide functions for such precision based sample size calculations. For a given sample size, the functions will return the precision (width of the confidence interval), and vice versa.

Weighted Deming regression, also known as errors-in-variable regression, is applied with suitable weights. Weights are modeled via a precision profile; thus the methods implemented here are referred to as precision profile weighted Deming (PWD) regression. The package covers two settings â one where the precision profiles are known either from external studies or from adequate replication of the X and Y readings, and one in which there is a plausible functional form for the precision profiles but the exact (unknown) function must be estimated from the (generally singlicate) readings. The function set includes tools for: estimated standard errors (via jackknifing); standardized-residual analysis function with regression diagnostic tools for normality, linearity and constant variance; and an outlier analysis identifying significant outliers for closer investigation. The following reference provides further information on mathematical derivations and applications. Hawkins, D.M., and J.J. Kraker (2026). Precision Profile Weighted Deming Regression for Methods Comparison'. The Journal of Applied Laboratory Medicine 11, 379-392 <doi:10.1093/jalm/jfaf183>. Weighted Deming regression is also now implemented for multiple instruments , as set out in Hawkins, D.M., and J.J. Kraker (2026). Multiple Instrument Methods Comparison by Precision weighted Deming Regression', on Arxiv <doi:10.48550/arXiv.2607.11776>. The â multiâ functions refer to the multiple instrument analysis, and the "PWD" functions refer to the two-instrument.

Analyze spatial phylogenetic diversity patterns. Use your data on an evolutionary tree and geographic distributions of the terminal taxa to compute diversity and endemism metrics, test significance with null model randomization, analyze community turnover and biotic regionalization, and perform spatial conservation prioritizations. All functions support quantitative community data in addition to binary data.

Dates sediment cores from lead-210 (Pb-210) activity profiles measured by alpha or gamma spectrometry, following the unified formulation and nomenclature of Sanchez-Cabeza and Ruiz-Fernandez (2012) <doi:10.1016/j.gca.2010.12.024>. Implements the Constant Flux (CF) and Constant Flux Constant Sedimentation (CFCS) dating models, together with supporting tools for data input, decay correction, missing inventory estimation, calculation of sediment and mass accumulation rates, and Monte Carlo propagation of dating uncertainties as described in Sanchez-Cabeza et al. (2014) <doi:10.1016/j.quageo.2014.06.002>. Also provides functions to visualize activity profiles and resulting age models.

The goal of planets is to provide of very simple and accessible data containing basic information from all known planets.

This package implements a phylogeny-aware Bayesian graphical modeling framework for microbial network inference using a shrinkage precision estimator guided by a phylogenetic kernel, with optional hyperparameter-ensemble edge reliability analysis.

This uses a mixed integer mathematical programming (MIP) approach for building and solving multi-action planning problems, where the goal is to find an optimal combination of management actions that abate threats, in an efficient way while accounting for spatial aspects. Thus, optimizing the connectivity and conservation effectiveness of the prioritized units and of the deployed actions. The package is capable of handling different commercial (gurobi, CPLEX) and non-commercial (symphony, CBC) MIP solvers. Gurobi optimization solver can be installed using comprehensive instructions in the gurobi installation vignette of the prioritizr package (available in <https://prioritizr.net/articles/gurobi_installation_guide.html>). Instead, CPLEX optimization solver can be obtain from IBM CPLEX web page (available here <https://www.ibm.com/es-es/products/ilog-cplex-optimization-studio>). Additionally, the rcbc R package (available at <https://github.com/dirkschumacher/rcbc>) can be used to obtain solutions using the CBC optimization software (<https://github.com/coin-or/Cbc>). Methods used in the package refers to Salgado-Rojas et al. (2020) <doi:10.1016/j.ecolmodel.2019.108901>, Beyer et al. (2016) <doi:10.1016/j.ecolmodel.2016.02.005>, Cattarino et al. (2015) <doi:10.1371/journal.pone.0128027> and Watts et al. (2009) <doi:10.1016/j.envsoft.2009.06.005>. See the prioriactions website for more information, documentations and examples.

Statistical power simulation for testing the Rasch Model based on a three-way analysis of variance design with mixed classification.

Retrieve and analyze biomedical literature from PubMed and the wider NIH'/'NLM data stack through a single, PMID-centered interface. A PubMed search resolves to a set of PMIDs, which can be used to retrieve article metadata and abstracts, author affiliations, iCite citation data and links, PubTator3 entity and relation annotations, and open-access full text from PMC'. A local analysis layer operates on the retrieved tables, supporting corpus expansion through citation links, citation network construction, sentence-level entity co-occurrence, inspection of relation evidence, and MeSH descriptor keyness.

This package creates PRISMA <http://prisma-statement.org/> diagram from a minimal dataset of included and excluded studies and allows for more custom diagrams. PRISMA diagrams are used to track the identification, screening, eligibility, and inclusion of studies in a systematic review.

Fits multivariate pseudo-Voigt mixture models for model-based clustering and outlier detection. The model combines multivariate Gaussian and Cauchy distributions within each cluster to accommodate heavy-tailed observations and decompose the data into a high-density region and a low-density remainder, with outliers more likely to arise from the latter.

This package provides permutation methods for testing in high-dimensional linear models. The tests are often robust against heteroscedasticity and non-normality and usually perform well under anti-sparsity. See Hemerik, Thoresen and Finos (2021) <doi:10.1080/00949655.2020.1836183>.

Allows the user to convert PDF tables to formats more amenable to analysis ('.csv', .xml', or .xlsx') by wrapping the PDFTables API. In order to use the package, the user needs to sign up for an API account on the PDFTables website (<https://pdftables.com/pdf-to-excel-api>). The package works by taking a PDF file as input, uploading it to PDFTables, and returning a file with the extracted data.

Spectral emission data for some frequently used light emitting diodes available as electronic components. Part of the r4photobiology suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

This package provides tools to interact with the Pangaea Database (<https://www.pangaea.de>), including functions for searching for data, fetching datasets by dataset ID', and working with the Pangaea OAI-PMH service.

This package provides a focused implementation of the Public Suffix List (PSL). Bundles a reproducible, pinned PSL snapshot and implements the official prevailing-rule algorithm to answer public-suffix (eTLD) and registrable-domain (eTLD+1) queries. Distinguishes ICANN and PRIVATE rule sections, accepts Unicode and ASCII hostnames via punycoder canonicalization, and supports an explicit, validated offline refresh path. The matcher is compiled with cpp11 and requires no external system library. Used as the PSL engine by the rurl package.