Much as roxygen2 allows one to document functions in the same file as the function itself, roxut allows one to write the unit tests in the same file as the function. Once processed, the unit tests are moved to the appropriate directory. Currently supports testthat and tinytest frameworks. The roxygen2 package provides much of the infrastructure.

This package provides an R interface to the Data Retriever <https://retriever.readthedocs.io/en/latest/> via the Data Retriever's command line interface. The Data Retriever automates the tasks of finding, downloading, and cleaning public datasets, and then stores them in a local database.

Interface to the ChEA3 transcription factor enrichment API. ChEA3 integrates evidence from ChIP-seq, co-expression, and literature resources to prioritize transcription factors regulating a given set of genes. This package provides convenient R functions to query the API, retrieve ranked results across collections (including integrated scores), and standardize output for downstream analysis in R/Bioconductor workflows. See <https://maayanlab.cloud/chea3/> or Keenan (2019) <doi:10.1093/nar/gkz446> for further details.

This package provides a collection of small text corpora of interesting data. It contains all data sets from dariusk/corpora'. Some examples: names of animals: birds, dinosaurs, dogs; foods: beer categories, pizza toppings; geography: English towns, rivers, oceans; humans: authors, US presidents, occupations; science: elements, planets; words: adjectives, verbs, proverbs, US president quotes.

Implementation of the algorithms (with minor modifications) to correct bias in quantitative DNA methylation analyses as described by Moskalev et al. (2011) <doi:10.1093/nar/gkr213>. Publication: Kapsner et al. (2021) <doi:10.1002/ijc.33681>.

Allows to get weather data from Automated Surface Observing System (ASOS) stations (airports) in the whole world thanks to the Iowa Environment Mesonet website.

Transfer REDCap (Research Electronic Data Capture) data to a database, specifically optimized for DuckDB'. Processes data in chunks to handle large datasets without exceeding available memory. Features include data labeling, coded value conversion, and hearing a "quack" sound on success.

Utility functions to download data from the RESOURCECODE hindcast database of sea-states, time series of sea-state parameters and time series of 1D and 2D wave spectra. See <https://resourcecode.ifremer.fr> for more details about the available data. Also provides facilities to plot and analyse downloaded data, such as computing the sea-state parameters from both the 1D and 2D surface elevation variance spectral density.

Computes attributable effects based confidence interval, permutation test confidence interval, or asymptotic confidence interval for the average treatment effect on a binary outcome. Methods outlined in further detail in Rigdon and Hudgens (2015) <doi:10.1002/sim.6384>.

Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.

Use trend filtering, a type of regularized nonparametric regression, to estimate the instantaneous reproduction number, also called Rt. This value roughly says how many new infections will result from each new infection today. Values larger than 1 indicate that an epidemic is growing while those less than 1 indicate decline. For more details about this methodology, see Liu, Cai, Gustafson, and McDonald (2024) <doi:10.1371/journal.pcbi.1012324>.

Compute an exact CI for the population mean under a random effects model. The routines implement the algorithm described in Michael, Thronton, Xie, and Tian (2017) <https://haben-michael.github.io/research/Exact_Inference_Meta.pdf>.

Show physics, math and engineering students how an ODE solver is made and how effective R classes can be for the construction of the equations that describe natural phenomena. Inspiration for this work comes from the book on "Computer Simulations in Physics" by Harvey Gould, Jan Tobochnik, and Wolfgang Christian. Book link: <http://www.compadre.org/osp/items/detail.cfm?ID=7375>.

This package provides R functions to selectively rasterize components of grid output.

Base S4-classes and functions for robust asymptotic statistics.

An interactive data visualization and exploration toolkit that implements Breiman and Cutler's original random forest Java based visualization tools in R, for supervised and unsupervised classification and regression within the algorithm random forest.

Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.

This package provides a straightforward, easy-to-use and robust parsing package which aims to digest history files from the popular messenger service WhatsApp in all locales and from all devices.

This package performs RNA emulation and active learning proposed by Heo and Sung (2025) <doi:10.1080/00401706.2024.2376173> for multi-fidelity computer experiments. The RNA emulator is particularly useful when the simulations with different fidelity level are nonlinearly correlated. The hyperparameters in the model are estimated by maximum likelihood estimation.

This project is a tool for words edit similarity joins (a.k.a. all-pairs similarity search) under small (< 3) edit distance constraints. It works for Levenshtein/Hamming distances and words from any alphabet. The software was originally developed for joining amino-acid/nucleotide sequences from Adaptive Immune Repertoires, where the number of words is relatively large (10^5-10^6) and the average length of words is relatively small (10-100).

The graphical approach is proposed as a general framework for clinical trial designs involving multiple hypotheses, where decisions are made only based on the observed marginal p-values. A reverse graphical approach starts from a set of singleton graphs, and gradually add vertices into graphs until rejection of a set of hypotheses is made. See Gou, J. (2020). Reverse graphical approaches for multiple test procedures. Technical Report.

Perform derivative-free optimization algorithms in R using C++. A wrapper interface is provided to call C function of the bobyqa implementation (See <https://github.com/emmt/Algorithms/tree/master/bobyqa>).

This package provides a platform-independent browser-based interface for business analytics in R, based on the shiny package. The application combines the functionality of radiant.data', radiant.design', radiant.basics', radiant.model', and radiant.multivariate'.

This package provides functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).