This package provides functions for phylocom integration, community analyses, null-models, traits and evolution. It implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010).

This package provides an implementation of multiscale bootstrap resampling for assessing the uncertainty in hierarchical cluster analysis. It provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability) value for each cluster in a dendrogram.

This package is intended to make it easy to create D3 JavaScript network, tree, dendrogram, and Sankey graphs from R using data frames.

This package provides a language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.

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 extendable, performant and multithreaded alt-string implementation backed by C++ vectors and strings.

This is a package for computation and visualization of the empirical attainment function (EAF) for the analysis of random sets in multi-criterion optimization.

This package supports multiple precision arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the GNU Multiple Precision library.

This is a package for simplified document database access and manipulation, providing a common API across supported NoSQL databases Elasticsearch, CouchDB, MongoDB as well as SQLite/JSON1, PostgreSQL, and DuckDB.

This package parses a fitted R model object, and returns a formula in Tidy Eval code that calculates the predictions. It works with several database backends because it leverages dplyr and dbplyr for the final SQL translation of the algorithm. It currently supports lm(), glm(), randomForest(), ranger(), earth(), xgb.Booster.complete(), cubist(), and ctree() models.

Download and install R packages stored in GitHub, BitBucket, or plain subversion or git repositories. This package is a lightweight replacement of the install_* functions in the devtools package. Indeed most of the code was copied over from devtools.

This package lets you take formulas including random-effects components (formatted as in lme4, glmmTMB, etc.) and process them. It includes various helper functions.

This package provides a cross between a 2D density plot and a scatter plot, implemented as a ggplot2 geom. Points in the scatter plot are colored by the number of neighboring points. This is useful to visualize the 2D-distribution of points in case of overplotting.

This package solves convex cone programs via operator splitting. It can solve: linear programs, second-order cone programs, semidefinite programs, exponential cone programs, and power cone programs, or problems with any combination of those cones. SCS uses AMD (a set of routines for permuting sparse matrices prior to factorization) and LDL (a sparse LDL factorization and solve package) from SuiteSparse.

This package contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library. All models return coda mcmc objects that can then be summarized using the coda package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.

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.

Extracts sentiment and sentiment-derived plot arcs from text using a variety of sentiment dictionaries conveniently packaged for consumption by R users. Implemented dictionaries include syuzhet (default) developed in the Nebraska Literary Lab, afinn developed by Finn Arup Nielsen, bing developed by Minqing Hu and Bing Liu, and nrc developed by Mohammad, Saif M. and Turney, Peter D. Applicable references are available in README.md and in the documentation for the get_sentiment function. The package also provides a hack for implementing Stanford's coreNLP sentiment parser. The package provides several methods for plot arc normalization.

This package provides a parallel estimation of the mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for the reconstruction of gene regulatory networks.

This package provides an extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for the special data format used for quantitative language comparison (QLC).

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 implements various procedures for finding multiple change-points. Two methods make use of dynamic programming and pruning, with no distributional assumptions other than the existence of certain absolute moments in one method. Hierarchical and exact search methods are included. All methods return the set of estimated change-points as well as other summary information.

This tool generates high number of both single- and multi-objective test functions. These functions are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.

This package provides tools for calculating the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. It plots triangulations and tessellations in various ways, clips tessellations to sub-windows, calculates perimeters of tessellations, and summarizes information about the tiles of the tessellation.

Hnswlib is a C++ library for approximate nearest neighbors. This package provides a minimal R interface by relying on the Rcpp package.