prospectr provides miscellaneous functions to preprocess spectroscopic data and conduct representative sample selection, or calibration sampling.

This package estimates conditional Akaike information in mixed-effect models. These models are fitted using (g)lmer() from lme4, lme() from nlme, and gamm() from mgcv. The provided functions facilitate the computation of the conditional Akaike information for model evaluation.

R/qtl is an extension library for the R statistics system. It is used to analyze experimental crosses for identifying genes contributing to variation in quantitative traits (so-called quantitative trait loci, QTLs).

Using a hidden Markov model, R/qtl estimates genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.

This package provides support for rendering of formatted text using Grid graphics. Text can be formatted via a minimal subset of Markdown, HTML, and inline CSS directives, and it can be rendered both with and without word wrap.

The lpSolveAPI package provides an R interface to lp_solve, a MILP, solver with support for pure linear, (mixed) integer/binary, semi-continuous and SOS models.

This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory.

This package provides a set of functions to run R code in an environment in which global state has been temporarily modified. Many of these functions were originally a part of the r-devtools package.

This package performs estimation of physical activity and sedentary behavior variables from activPAL events files.

This package provides a re-implementation of the gWidgets API. The API is defined in this package. A second, toolkit-specific package is required to use it.

This package abbreviates strings to a specified minimum number of characters, such that the strings remain unique (if they originally were).

This package lets you compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 100 classes of statistical and machine learning models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference. Details can be found in Arel-Bundock, Greifer, and Heiss (2024) <doi:10.18637/jss.v111.i09>.

This package contains extensions to ggplot2.

1. Geomas: geom_table, geom_plot and geom_grob add insets to plots using native data coordinates, while geom_table_npc, geom_plot_npc and geom_grob_npc do the same using npc coordinates through new aesthetics npcx and npcy.

2. Statistics: select observations based on 2D density.

3. Positions: radial nudging away from a center point and nudging away from a line or curve.

This package provides functions that read and solve linear inverse problems (food web problems, linear programming problems).

This package provides a set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) doi:10.1007/s11336-011-9207-7 and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) doi:10.1111/bmsp.12070 for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre doi:10.1177/0146621613479818 for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.

This package provides a toolkit of functions for nonlinear regression and repeated measurements. It was designated to be imported by other packages such as gnlm, stable, growth, repeated, and event.

This package implements multiple imputation for multivariate panel or clustered data.

This package provides a comprehensive toolbox for analysing Spatial Point Patterns. It is focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. It also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. It supports spatial covariate data such as pixel images and contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.

This package provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.

This package tracks reading and writing within R scripts that are organized into a directed acyclic graph. It contains an interactive Shiny application adaprApp(). It uses Git and file hashes to track version histories of inputs and outputs.

This package provides an implementation of the Harmony algorithm for single cell integration. This package includes a standalone Harmony function and interfaces to external frameworks.

Building modeling packages is hard. A large amount of effort generally goes into providing an implementation for a new method that is efficient, fast, and correct, but often less emphasis is put on the user interface. A good interface requires specialized knowledge about S3 methods and formulas, which the average package developer might not have. The goal of hardhat is to reduce the burden around building new modeling packages by providing functionality for preprocessing, predicting, and validating input.

This package contains supporting data sets that are used in other packages maintained by Torsten Hothorn.

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 functions for easily manipulating colors, creating color scales and calculating color distances.