Fit Bayesian generalized (non-)linear multivariate multilevel models using Stan for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation.

The Munsell package contains functions for exploring and using the Munsell colour system.

The tidyverse is a set of packages that work in harmony because they share common data representations and API design. This package is designed to make it easy to install and load multiple tidyverse packages in a single step.

This package provides tools to get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily OCR images, barcodes, forms, documents with machine readable zones, e.g. passports and get the results in a variety of formats including plain text and XML. To learn more about the Abbyy OCR API, see http://ocrsdk.com/.

This package lets you use syntax inspired by the package glue to extract matched substrings in a more intuitive and compact way than by using standard regular expressions.

This package provides pure C++ implementations for reading and writing several common data formats based on Google protocol-buffers. It currently supports rexp.proto for serialized R objects, geobuf.proto for binary geojson, and mvt.proto for vector tiles. This package uses the auto-generated C++ code by protobuf-compiler, hence the entire serialization is optimized at compile time. The RProtoBuf package on the other hand uses the protobuf runtime library to provide a general-purpose toolkit for reading and writing arbitrary protocol-buffer data in R.

This package computes Hartigan's dip test statistic for unimodality, multimodality and provides a test with simulation based p-values, where the original public code has been corrected.

This package provides a color picker that can be used as an input in Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, custom color palettes, and many more options. A plot color helper tool is available as an RStudio Addin, which helps you pick colors to use in your plots. A more generic color picker RStudio Addin is also provided to let you select colors to use in your R code.

Common utilities used in other Mosaic family packages are collected here.

Obtain any major version of jQuery and use it in any webpage generated by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't need to use this package directly, but other R packages (e.g. shiny, rmarkdown, etc.) depend on this package to avoid bundling redundant copies of jQuery.

This package provides methods for cluster analysis. It is a much extended version of the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".

This package provides basic infrastructure and some algorithms for the traveling salesperson problem(TSP) (also known as the traveling salesman problem).

The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.

This package provides different approaches for selecting the threshold in generalized Pareto distributions. Most of them are based on minimizing the AMSE-criterion or at least by reducing the bias of the assumed GPD-model. Others are heuristically motivated by searching for stable sample paths, i.e. a nearly constant region of the tail index estimator with respect to k, which is the number of data in the tail. The third class is motivated by graphical inspection. In addition, a sequential testing procedure for GPD-GoF-tests is also implemented here.

This package provides a toolkit for working with Biological Observation Matrix (BIOM) files. Features include reading/writing all BIOM formats, rarefaction, alpha diversity, beta diversity (including UniFrac), summarizing counts by taxonomic level, and sample subsetting. Standalone functions for reading, writing, and subsetting phylogenetic trees are also provided.

This package provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline.

This package provides an R interface to the Tabler HTML template. tablerDash is a light Bootstrap 4 dashboard template. There are different layouts available such as a one page dashboard or a multi-page template, where the navigation menu is contained in the navigation bar.

This package provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. It is designed to work with FlowSOM and flow-cytometry use-cases.

This package provides S3 classes and methods for one-dimensional normal mixture models, for, e.g., density estimation or clustering algorithms research and teaching; it provides the widely used Marron-Wand densities. It also provides tools for efficient random number generation and graphics.

This package provides an easy to use library to setup, apply and make inference with discrete time and discrete space hidden Markov models.

This package provides an interface to the Nexus class library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's phylo or phylobase's phylo4(d). This functionality is demonstrated with read_newick_phylo() and read_nexus_phylo().

Recipes is an extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis "steps". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.

This package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. It provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.

This is an R package for spell checking common document formats including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes utilities to automate checking of documentation and vignettes as a unit test during R CMD check. Both British and American English are supported out of the box and other languages can be added. In addition, packages may define a wordlist to allow custom terminology without having to abuse punctuation.