This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network.

The pls package implements multivariate regression methods: Partial Least Squares Regression (PLSR), Principal Component Regression (PCR), and Canonical Powered Partial Least Squares (CPPLS). It supports:

• several algorithms: the traditional orthogonal scores (NIPALS) PLS algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through svd

• multi-response models (or PLS2)

• flexible cross-validation

• Jackknife variance estimates of regression coefficients

• extensive and flexible plots: scores, loadings, predictions, coefficients, (R)MSEP, R², and correlation loadings

• formula interface, modelled after lm(), with methods for predict, print, summary, plot, update, etc.

• extraction functions for coefficients, scores, and loadings

• MSEP, RMSEP, and R² estimates

• multiplicative scatter correction (MSC)

This package provides an R to C/C++ interface that runs the Leiden community detection algorithm to find a basic partition. It runs the equivalent of the leidenalg find_partition() function. This package includes the required source code files from the official leidenalg distribution and functions from the R igraph package.

This package provides functions for working with legends and axis lines of ggplot2, facets that repeat axis lines on all panels, and some knitr extensions.

This package includes size measurements, clutch observations, and blood isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins observed on islands in the Palmer Archipelago near Palmer Station, Antarctica. Data were collected and made available by Dr. Kristen Gorman and the Palmer Station Long Term Ecological Research (LTER) Program.

This package contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.

Multivariate data sets often differ in several factors or derived statistical parameters, which have to be selected for a valid interpretation. Basing this selection on traditional statistical limits leads occasionally to the perception of losing information from a data set. This package provides tools to calculate these limits on the basis of the mathematical properties of the distribution of the analyzed items.

This package provides functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).

This package creates square pie charts also known as waffle charts. These can be used to communicate parts of a whole for categorical quantities. To emulate the percentage view of a pie chart, a 10x10 grid should be used. In this way each square is representing 1% of the total. Waffle provides tools to create charts as well as stitch them together. Isotype pictograms can be made by using glyphs.

This package simulates the process of installing a package and then attaching it. This is a key part of the devtools package as it allows you to rapidly iterate while developing a package.

The r-abd package contains data sets and sample code for the Analysis of biological data by Michael Whitlock and Dolph Schluter.

Partial application is the process of reducing the arity of a function by fixing one or more arguments, thus creating a new function lacking the fixed arguments. The curry package provides three different ways of performing partial function application by fixing arguments from either end of the argument list (currying and tail currying) or by fixing multiple named arguments (partial application). This package provides this functionality through the %<%, %-<%, and %><% operators which allows for a programming style comparable to modern functional languages. Compared to other implementations such a purrr::partial() the operators in curry composes functions with named arguments, aiding in autocomplete etc.

This package provides classes and methods for spatial objects that have a registered time column, in particular for irregular spatiotemporal data. The time column can be of any type, but needs to be ordinal. Regularly laid out spatiotemporal data (vector or raster data cubes) are handled by package stars'.

R-hub uses GitHub Actions to run R CMD check and similar package checks. The rhub package helps you set up R-hub for your R package, and start running checks.

This package provides a suite of functions to help ease the use of the d3.js visualization library in R. These helpers include htmltools::htmlDependency functions, hierarchy builders, and conversion tools for partykit, igraph, table, and data.frame R objects into the JSON format that the d3.js library expects.

This package provides an implementation of heatmaps that offers more control over dimensions and appearance.

This package creates alluvial diagrams (also known as parallel sets plots) for multivariate and time series-like data.

This package provides bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods. It includes utilities for public key encryption, creating and verifying digital signatures, and managing your local keyring. Some functionality depends on the version of GnuPG that is installed on the system.

Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification.

This package provides methods for fast access to large ASCII files. Currently the following file formats are supported: comma separated format (CSV) and fixed width format. It is assumed that the files are too large to fit into memory, although the package can also be used to efficiently access files that do fit into memory. Methods are provided to access and process files blockwise. Furthermore, an opened file can be accessed as one would an ordinary data.frame. The LaF vignette gives an overview of the functionality provided.

This package provides tools for functional linear modeling and analysis of actigraphy data.

This package provides a simple, consistent interface to working with XML files in R. It is built on top of the libxml2 C library.

This package provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.

Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. This is useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.