This package provides a methodology to analyze how species occurrences change over time, particularly in relation to spatial and thermal factors. It facilitates the development of explanatory hypotheses about the impact of environmental shifts on species by analyzing historical presence data that includes temporal and geographic information. Approach described in Lobo et al., 2023 <doi:10.1002/ece3.10674>.

Utils for basic statistical experiments, that can be used for teaching introductory statistics. Each experiment generates a tibble. Dice rolls and coin flips are simulated using sample(). The properties of the dice can be changed, like the number of sides. A coin flip is simulated using a two sided dice. Experiments can be combined with the pipe-operator.

This is a collection of tools for conducting both basic and advanced statistical power analysis including correlation, proportion, t-test, one-way ANOVA, two-way ANOVA, linear regression, logistic regression, Poisson regression, mediation analysis, longitudinal data analysis, structural equation modeling and multilevel modeling. It also serves as the engine for conducting power analysis online at <https://webpower.psychstat.org>.

Use behavioural variables to compute period, rhythmicity and other circadian parameters. Methods include computation of chi square periodograms (Sokolove and Bushell (1978) <DOI:10.1016/0022-5193(78)90022-X>), Lomb-Scargle periodograms (Lomb (1976) <DOI:10.1007/BF00648343>, Scargle (1982) <DOI:10.1086/160554>, Ruf (1999) <DOI:10.1076/brhm.30.2.178.1422>), and autocorrelation-based periodograms.

This package provides a cross-platform Perl-based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX) files from one or more data frames. Each data frame will be written to a separate named worksheet in the Excel spreadsheet. The worksheet name will be the name of the data frame it contains or can be specified by the user.

This package lets you create a web app that makes it easier to test web clients without using the internet. It includes a web app framework with path matching, parameters and templates. It can parse various HTTP request bodies. It can send JSON data or files from the disk. It includes a web app that implements the httpbin.org web service.

Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data could be used as an example supporting BloodGen3Module R package.

The process of resolving and updating taxon names is necessary when working with biodiversity data. APCalign uses the Australian Plant Census (APC) and the Australian Plant Name Index (APNI) to align and update plant taxon names to current, accepted standards. APCalign also supplies information about the establishment status (i.e. native or introduced) of plant taxa across different states/territories.

This package provides statistical tools for Bayesian estimation of mixture distributions, mainly a mixture of Gamma, Normal, and t-distributions. The package is implemented based on the Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.

This package provides functions that allow users to quantify the relative contributions of geographic and ecological distances to empirical patterns of genetic differentiation on a landscape. Specifically, we use a custom Markov chain Monte Carlo (MCMC) algorithm, which is used to estimate the parameters of the inference model, as well as functions for performing MCMC diagnosis and assessing model adequacy.

Bayesian Network Structure Learning from Data with Missing Values. The package implements the Silander-Myllymaki complete search, the Max-Min Parents-and-Children, the Hill-Climbing, the Max-Min Hill-climbing heuristic searches, and the Structural Expectation-Maximization algorithm. Available scoring functions are BDeu, AIC, BIC. The package also implements methods for generating and using bootstrap samples, imputed data, inference.

Chromosome files in the Fasta format usually contain large sequences like human genome. Sometimes users have to split these chromosomes into different files according to their chromosome number. The chromseq can help to handle this. So the selected chromosome sequence can be used for downstream analysis like motif finding. Howard Y. Chang(2019) <doi:10.1038/s41587-019-0206-z>.

Many correlation coefficient related functions are offered, such as correlations, partial correlations and hypothesis testing using asymptotic tests and computer intensive methods (bootstrap and permutation). References include Mardia K.V., Kent J.T. and Bibby J.M. (1979). "Multivariate Analysis". ISBN: 978-0124712522. London: Academic Press and Owen A. B. (2001). "Empirical likelihood". Chapman and Hall/CRC Press. ISBN: 9781584880714.

Uses optimal transport distances to find probabilistic matching estimators for causal inference. These methods are described in Dunipace, Eric (2021) <doi:10.48550/arXiv.2109.01991>. The package will build the weights, estimate treatment effects, and calculate confidence intervals via the methods described in the paper. The package also supports several other methods as described in the help files.

Hospital data analysis workflow tools, modeling, and automations. This library provides many useful tools to review common administrative hospital data. Some of these include average length of stay, readmission rates, average net pay amounts by service lines just to name a few. The aim is to provide a simple and consistent verb framework that takes the guesswork out of everything.

This package provides features that allow users to download weather data published by the Japan Meteorological Agency (JMA) website (<https://www.jma.go.jp/jma/index.html>). The data includes information dating back to 1976 and aligns with the categories available on the website. Additionally, users can process the best track data of typhoons and easily handle earthquake record files.

Stability based methods for model order selection in clustering problems (Valentini, G (2007), <doi:10.1093/bioinformatics/btl600>). Using multiple perturbations of the data the stability of clustering solutions is assessed. Different perturbations may be used: resampling techniques, random projections and noise injection. Stability measures for the estimate of clustering solutions and statistical tests to assess their significance are provided.

Calculate various functions needed for design and monitoring clinical trials with negative binomial endpoint with variable follow-up. This version has a few changes compared to the previous version 1.0.0, including (1) correct a typo in Type 1 censoring, mtbnull=bnull and (2) restructure the code to account for shape parameter equal to zero, i.e. Poisson scenario.

Distance based bipartite matching using minimum cost flow, oriented to matching of treatment and control groups in observational studies ('Hansen and Klopfer 2006 <doi:10.1198/106186006X137047>). Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination.

Analysis of features by phi delta diagrams. In particular, functions for reading data and calculating phi and delta as well as the functionality to plot it. Moreover it is possible to do further analysis on the data by generating rankings. For more information on phi delta diagrams, see also Giuliano Armano (2015) <doi:10.1016/j.ins.2015.07.028>.

This package provides a suite of empirical Bayes methods to use in pharmacovigilance. Contains various model fitting and post-processing functions. For more details see Tan et al. (2025) <doi:10.48550/arXiv.2502.09816>, <doi:10.48550/arXiv.2512.01057>; Koenker and Mizera (2014) <doi:10.1080/01621459.2013.869224>; Efron (2016) <doi:10.1093/biomet/asv068>.

This package provides a shiny interface for a simpler use of the sbm R package. It also contains useful functions to easily explore the sbm package results. With this package you should be able to use the stochastic block model without any knowledge in R, get automatic reports and nice visuals, as well as learning the basic functions of sbm'.

Srt file is a common subtitle format for videos, it contains subtitle and when the subtitle showed. This package is for align time of srt file, and also change color, style and position of subtitle in videos, the srt file will be read as a vector into R, and can be write into srt file after modified using this package.

Simulates data sets in order to explore modeling techniques or better understand data generating processes. The user specifies a set of relationships between covariates, and generates data based on these specifications. The final data sets can represent data from randomized control trials, repeated measure (longitudinal) designs, and cluster randomized trials. Missingness can be generated using various mechanisms (MCAR, MAR, NMAR).