This package provides an interface to the NetCDF file formats designed by Unidata for efficient storage of array-oriented scientific data and descriptions. Most capabilities of NetCDF version 4 are supported. Optional conversions of time units are enabled by UDUNITS version 2, also from Unidata.

This package provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.

This package provides a scripting and command-line front-end is provided by r (aka littler) as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both shebang-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard pipelines. In other words, r provides the R language without the environment.

This package provides a collection of templates to author preregistration documents for scientific studies in PDF format.

Easily and flexibly insert Font Awesome icons into R Markdown documents and Shiny apps. These icons can be inserted into HTML content through inline SVG tags or i tags. There is also a utility function for exporting Font Awesome icons as PNG images for those situations where raster graphics are needed.

This package provides tools to convert the output of utils::getParseData() to an XML tree, that one can search via XPath, and is easier to manipulate in general.

This package allows for the imputation of the last largest censored observantions. This method brings less bias and more efficient estimates for AFT models.

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 tools to convert R Markdown documents into a variety of formats.

The wordspace package turns R into an interactive laboratory for empirical research on distributional semantic models (DSM). It consists of a small set of carefully designed functions, most of which

• encapsulate non-trivial R operations in a user-friendly manner or

• provide efficient and memory-lean C implementations of key operations.

This package provides a dataset with an uneven number of cases in each class is said to be unbalanced. Many models produce a subpar performance on unbalanced datasets.

The vctrs package provides a concept of vector prototype that can be especially useful when deploying models and code. Serialize these object prototypes to JSON so they can be used to check and coerce data in production systems, and deserialize JSON back to the correct object prototypes.

This package provides a toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.

This package provides a bunch of convenience functions that transform the results of some basic statistical analyses into table format nearly ready for publication. This includes descriptive tables, tables of logistic regression and Cox regression results as well as forest plots.

This package provides utility functions for easy parallelism in R. This includes some reexports from other packages, utility functions for splitting and parallelizing over blocks, and choosing and setting the number of cores used.

This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies.

Users may want to align plots with associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. This package provides utilities to align associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.

This package performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. It includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 <doi:10.1093/molbev/MSR262>; Leblois et al., 2014 <doi:10.1093/molbev/msu212>; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.

This package uses both ridge and lasso penalties (and extensions) to penalize specific parameters in structural equation models. The package offers additional cost functions, cross validation, and other extensions beyond traditional structural equation models. It also contains a function to perform exploratory mediation (XMed).

This package implements the Subplex optimization algorithm. It solves unconstrained optimization problems using a simplex method on subspaces. The method is well suited for optimizing objective functions that are noisy or are discontinuous at the solution.

The grammar of graphics as shown in ggplot2 has provided an expressive API for users to build plots. This package ggside extends ggplot2 by allowing users to add graphical information about one of the main panel's axis using a familiar ggplot2 style API with tidy data. This package is particularly useful for visualizing metadata on a discrete axis, or summary graphics on a continuous axis such as a boxplot or a density distribution.

This package provides a comprehensive collection for structural multivariate function estimation using smoothing splines.

This package provides utilities to work with indices of effect size and standardized parameters for a wide variety of models, allowing computation and conversion of indices such as Cohen's d, r, odds, etc.

This r-rbenchmark package is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.