Harrell Miscellaneous

Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to Typst, LaTeX, and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.

Lightning Fast Serialization of Data Frames

Multithreaded serialization of compressed data frames using the 'fst' format. The 'fst' format allows for full random access of stored data and a wide range of compression settings using the LZ4 and ZSTD compressors.

Export Tables to LaTeX or HTML

Coerce data to LaTeX and HTML tables.

Presentation-Ready Data Summary and Analytic Result Tables

Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.

Manipulate and Visualize VCF Data

Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.

TH's Data Archive

Contains data sets used in other packages Torsten Hothorn maintains.

Bayesian Latent Gaussian Modelling using INLA and Extensions

Facilitates spatial and general latent Gaussian modelling using integrated nested Laplace approximation via the INLA package (< https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modelling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) .

Extract and Visualize the Results of Multivariate Data Analyses

Provides easy-to-use functions to extract and visualize the output of multivariate data analyses, including 'PCA' (Principal Component Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis), and 'HMFA' (Hierarchical Multiple Factor Analysis) from different R packages. It standardizes coordinates, squared cosines, contributions, and eigenvalues from several analysis backends and produces 'ggplot2'-based factor maps, scree plots, contribution plots, clustering diagnostics, dendrograms, and silhouette plots. It also visualizes two-dimensional 'UMAP' and t-SNE embeddings and adapts precomputed or 'tidymodels' principal-component results for the same plotting interface.

An R Interface for Downloading, Reading, and Handling IPUMS Data

An easy way to work with census, survey, and geographic data provided by IPUMS in R. Generate and download data through the IPUMS API and load IPUMS files into R with their associated metadata to make analysis easier. IPUMS data describing 1.4 billion individuals drawn from over 750 censuses and surveys is available free of charge from the IPUMS website < https://www.ipums.org>.

Tidy Verbs for Fast Data Manipulation

A toolkit of tidy data manipulation verbs with 'data.table' as the backend. Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table', 'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain. This package is an extension of 'data.table'. While enjoying a tidy syntax, it also wraps combinations of efficient functions to facilitate frequently-used data operations.