An implementation of Horn's technique for numerically and graphically evaluating the components or factors retained in a principle components analysis (PCA) or common factor analysis (FA). Horn's method contrasts eigenvalues produced through a PCA or FA on a number of random data sets of uncorrelated variables with the same number of variables and observations as the experimental or observational data set to produce eigenvalues for components or factors that are adjusted for the sample error-induced inflation. Components with adjusted eigenvalues greater than one are retained. paran may also be used to conduct parallel analysis following Glorfeld's (1995) suggestions to reduce the likelihood of over-retention.

This package provides a clinical decision support system for sub-symptom threshold aerobic exercise (SSTAE) prescription in adolescents with persistent post-concussion symptoms (PPCS). Implements an evidence-based protocol derived from a systematic review of seven studies (Li, 2026; <doi:10.17605/osf.io/kvuf6>), encoding safety screening, Buffalo Concussion Treadmill Test (BCTT)-guided heart rate prescription, session-level progress tracking, and evidence disclosure using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) framework into an open-source tool for athletic trainers and clinicians. Designed to support implementation in resource-limited settings where BCTT equipment may be unavailable. GRADE certainty of evidence: LOW. For clinician use only; not a substitute for clinical judgement.

An integrative toolbox of word embedding research that provides: (1) a collection of pre-trained static word vectors in the .RData compressed format <https://psychbruce.github.io/WordVector_RData.pdf>; (2) a group of functions to process, analyze, and visualize word vectors; (3) a range of tests to examine conceptual associations, including the Word Embedding Association Test <doi:10.1126/science.aal4230> and the Relative Norm Distance <doi:10.1073/pnas.1720347115>, with permutation test of significance; and (4) a set of training methods to locally train (static) word vectors from text corpora, including Word2Vec <doi:10.48550/arXiv.1301.3781>, GloVe <doi:10.3115/v1/D14-1162>, and FastText <doi:10.48550/arXiv.1607.04606>.

This package provides a Shiny application for calculating phytosanitary inspection plans based on risks. It generates a diagram of pallets in a lot, highlights the units to be sampled, and documents them based on the selected sampling method (simple random or systematic sampling).

Uses provenance collected by rdtLite package or comparable tool to display information about input files, output files, and exchanged files for a single R script or a series of R scripts.

Create PX-files from scratch or read and modify existing ones. Includes a function for every PX keyword, making metadata manipulation simple and human-readable.

Compilation and digitalization of the official registry of victims of state terrorism in Argentina during the last military coup. The original data comes from RUVTE-ILID (2019) <https://www.argentina.gob.ar/sitiosdememoria/ruvte/informe> and <http://basededatos.parquedelamemoria.org.ar/registros/>. The title, presentes, comes from present in spanish.

This package provides a tidyverse'-style interface to the Brazilian Central Bank (<https://www.bcb.gov.br>) PIX Open Data API <https://olinda.bcb.gov.br/olinda/servico/Pix_DadosAbertos/versao/v1/aplicacao#!/recursos>. Retrieve statistics on PIX keys, transactions by municipality, and monthly transaction summaries. All functions return tibbles and support OData query parameters for filtering, selecting, and ordering data.

Generates chronological and ordered p-plots for data vectors or vectors of p-values. The p-plot visualizes the evolution of the p-value of a significance test across the sampled data. It allows for assessing the consistency of the observed effects, for detecting the presence of potential moderator variables, and for estimating the influence of outlier values on the observed results. For non-significant findings, it can diagnose patterns indicative of underpowered study designs. The p-plot can thus either back the binary accept-vs-reject decision of common null-hypothesis significance tests, or it can qualify this decision and stimulate additional empirical work to arrive at more robust and replicable statistical inferences.

Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. pathfindR is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. pathfindR also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in pathfindR are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR': An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.

Fornece acesso eficiente à malha espacial de precariedade viária brasileira. O pacote realiza o download em cache e a leitura otimizada (via Apache Arrow) de arquivos Parquet particionados, contendo o cruzamento de variáveis de infraestrutura do Entorno do Censo Demográfico 2022 (IBGE) com a malha viária aberta do Overture Maps. [English] Provides efficient access to the spatial network of road precariousness in Brazil. The package performs cached downloads and optimized reading (via Apache Arrow) of partitioned Parquet files. These files contain the intersection of infrastructure variables from the 2022 Demographic Census (IBGE) with the open street network from Overture Maps. Methodology and datasets are detailed in Passos (2026) <doi:10.5281/zenodo.19711448>.

This package implements a procedure for forecasting time series data based on an additive model where non-linear trends are fit with yearly, weekly, and daily seasonality, plus holiday effects. It works best with time series that have strong seasonal effects and several seasons of historical data. Prophet is robust to missing data and shifts in the trend, and typically handles outliers well.

Transforms datetime data into a format ready for analysis. It offers two core functionalities; aggregating data to a higher level interval (thicken) and imputing records where observations were absent (pad).

This package performs demographic, bifurcation and evolutionary analysis of physiologically structured population models, which is a class of models that consistently translates continuous-time models of individual life history to the population level. A model of individual life history has to be implemented specifying the individual-level functions that determine the life history, such as development and mortality rates and fecundity. M.A. Kirkilionis, O. Diekmann, B. Lisser, M. Nool, B. Sommeijer & A.M. de Roos (2001) <doi:10.1142/S0218202501001264>. O.Diekmann, M.Gyllenberg & J.A.J.Metz (2003) <doi:10.1016/S0040-5809(02)00058-8>. A.M. de Roos (2008) <doi:10.1111/j.1461-0248.2007.01121.x>.

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.

Carrying out inferences about any linear combination of proportions and the ratio of two proportions.

The rgl implementation of plot3D functions.

This package provides a coding assistant using Perplexity's Large Language Models <https://www.perplexity.ai/> API. A set of functions and RStudio add-ins that aim to help R developers.

In each odd dimension is a convex body - the polar zonoid - whose generating functions are trigonometric polynomials. The polar zonoid is a straightforward generalization of the polar zonohedron in dimension 3, as defined by Chilton and Coxeter (1963) <doi:10.2307/2313051>. The package has some applications of the polar zonoid, including the properties of configuration spaces of arcs on the circle and 3x3 rotation matrices. There is also a root solver for trigonometric polynomials.

Drawing population pyramid using (1) data.frame or (2) vectors. The former is named as pyramid() and the latter pyramids(), as wrapper function of pyramid(). pyramidf() is the function to draw population pyramid within the specified frame.

Computes the Physiological and Operative Severity Score for the enUmeration of Mortality and morbidity (POSSUM), its Portsmouth modification (P-POSSUM), and the colorectal (CR-POSSUM), vascular (V-POSSUM) and ruptured aortic aneurysm (RAAA-POSSUM) variants, risk-adjustment systems used in surgical audit. Functions map physiological and operative variables to their component scores and return the predicted probabilities of morbidity and mortality from the published logistic equations. The coefficients follow Copeland and others (1991) <doi:10.1002/bjs.1800780327> for POSSUM, Prytherch and others (1998) <doi:10.1046/j.1365-2168.1998.00840.x> for P-POSSUM, Tekkis and others (2004) <doi:10.1002/bjs.4430> for the colorectal variant (CR-POSSUM), and Neary and others (2003) <doi:10.1002/bjs.4041> for the vascular variant (V-POSSUM). The package is intended for audit and research; it is not a validated medical device and must not be used as the sole basis for clinical decisions.

This package provides functions to simplify the PatentsView API (<https://search.patentsview.org/docs/docs/Search%20API/SearchAPIReference/#api-query-language>) query language, send GET and POST requests to the API's twenty seven endpoints, and parse the data that comes back.

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.

This package creates a non-negative low-rank approximate factorization of a sparse counts matrix by maximizing Poisson likelihood with L1/L2 regularization (e.g. for implicit-feedback recommender systems or bag-of-words-based topic modeling) (Cortes, (2018) <arXiv:1811.01908>), which usually leads to very sparse user and item factors (over 90% zero-valued). Similar to hierarchical Poisson factorization (HPF), but follows an optimization-based approach with regularization instead of a hierarchical prior, and is fit through gradient-based methods instead of variational inference.