This package lets you compute the median ranking according to Kemeny's axiomatic approach. Rankings can or cannot contain ties, rankings can be both complete or incomplete. The package contains both branch-and-bound algorithms and heuristic solutions recently proposed. The searching space of the solution can either be restricted to the universe of the permutations or unrestricted to all possible ties. The package also provides some useful utilities for deal with preference rankings, including both element-weight Kemeny distance and correlation coefficient.

This is a subset of the spatstat package, containing its functionality for spatial data on a linear network.

This package provides a fast implementation of hierarchical clustering.

Quantile Regression Forests is a tree-based ensemble method for estimation of conditional quantiles. It is particularly well suited for high-dimensional data. Predictor variables of mixed classes can be handled.

The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption, gzip compression, authentication, and other libcurl goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces.

This package provides a set of predicates and assertions for checking the properties of US-specific complex data types. This is mainly for use by other package developers who want to include run-time testing features in their own packages.

This package provides common base and stats methods for rle objects, aiming to make it possible to treat them transparently as vectors.

This package provides a drop-in replacement for rasterize from the raster package that takes sf-type objects, and is much faster. There is support for the main options provided by the rasterize function, including setting the field used and background value, and options for aggregating multi-layer rasters.

This package provides fast algorithms for the Theil-Sen estimator, Siegel's repeated median slope estimator, and Passing-Bablok regression. The implementation is based on algorithms by Dillencourt et al. (1992) <doi:10.1142/S0218195992000020> and Matousek et al. (1998) <doi:10.1007/PL00009190>. The implementations are detailed in Raymaekers (2023) <doi:10.32614/RJ-2023-012> and Raymaekers J., Dufey F. (2022) <arXiv:2202.08060>. All algorithms run in quasilinear time.

This package provides an object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided.

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 an all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).

In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match scores. TFMPvalue provides the accurate calculation of a p-value with a score threshold for position weight matrices, or the score with a given p-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).

The empirical transition matrix (etm) package estimates the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator.

This package is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted.

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.

This package provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

Structural equation modeling (SEM) has a long history of representing models graphically as path diagrams. The semPlot package for R fills the gap between advanced, but time-consuming, graphical software and the limited graphics produced automatically by SEM software. In addition, semPlot offers more functionality than drawing path diagrams: it can act as a common ground for importing SEM results into R. Any result usable as input to semPlot can also be represented in any of the three popular SEM frame-works, as well as translated to input syntax for the R packages sem and lavaan.

This package provides a package for quantifying, profiling and removing cell free mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments.

There are three main goals to the vctrs package:

1. To propose vec_size() and vec_type() as alternatives to length() and class(). These definitions are paired with a framework for type-coercion and size-recycling.

2. To define type- and size-stability as desirable function properties, use them to analyse existing base function, and to propose better alternatives. This work has been particularly motivated by thinking about the ideal properties of c(), ifelse(), and rbind().

3. To provide a new vctr base class that makes it easy to create new S3 vectors. vctrs provides methods for many base generics in terms of a few new vctrs generics, making implementation considerably simpler and more robust.

The brew package implements a templating framework for mixing text and R code for report generation. The template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.

This package creates scatterpie plots, especially useful for plotting pies on a map.

This package provides tools and functions for managing the download of binary files. Binary repositories are defined in the YAML format. Defining new pre-download, download and post-download templates allow additional repositories to be added.

This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting.