This package provides various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.

dplyr is the next iteration of plyr. It is focused on tools for working with data frames. It has three main goals: 1) identify the most important data manipulation tools needed for data analysis and make them easy to use in R; 2) provide fast performance for in-memory data by writing key pieces of code in C++; 3) use the same code interface to work with data no matter where it is stored, whether in a data frame, a data table or database.

This package provides a replacement and extension of the optim function to call to several function minimization codes in R in a single statement. These methods handle smooth, possibly box constrained functions of several or many parameters. Note that the function optimr was prepared to simplify the incorporation of minimization codes going forward. This package also implements some utility codes and some extra solvers, including safeguarded Newton methods. Many methods previously separate are now included here.

This method identifies topological domains in genomes from Hi-C sequence data. The authors published an implementation of their method as an R script. This package originates from those original TopDom R scripts and provides help pages adopted from the original TopDom PDF documentation. It also provides a small number of bug fixes to the original code.

This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.

This package assists you in setting up and retrieving of HTTPS and SSH credentials for use with git and other services. For HTTPS remotes the package interfaces the git-credential utility which git uses to store HTTP usernames and passwords. For SSH remotes this package provides convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.

This package provides a DBI interface to MySQL / MariaDB. The RMySQL package contains an old implementation based on legacy code from S-PLUS which is being phased out. A modern MySQL client based on Rcpp is available from the RMariaDB package.

This package computes Hartigan's dip test statistic for unimodality, multimodality and provides a test with simulation based p-values, where the original public code has been corrected.

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 does local optimization using two derivatives and trust regions. Guaranteed to converge to local minimum of objective function.

The aim of httr is to provide a wrapper for RCurl customised to the demands of modern web APIs. It provides useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components.

This package Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial correlations, Chi-Squared statistics, histograms, and t-tests. Also now includes some software for quickly recoding survey data and plotting point estimates from interaction terms in regressions (and multiply imputed regressions). NOTE: Weighted partial correlation calculations pulled to address a bug.

This package provides a violin plot, which is a combination of a box plot and a kernel density plot.

Read in activity measurements from standard file formats used by circadian rhythm researchers, currently only ClockLab format, and process and plot the data. The central type of plot is the actogram, as first described in "Activity and distribution of certain wild mice in relation to biotic communities" by MS Johnson (1926) doi:10.2307/1373575.

This package checks adherence to a given style, syntax errors and possible semantic issues. It supports on the fly checking of R code edited with RStudio IDE, Emacs and Vim.

This is a package for model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).

This package provides a set of R functions for identifying and correcting HGNC human gene symbols. In addition, you can identify MGI mouse gene symbols, which have been converted to date format by Excel, withdrawn, or aliased. It also contains functions for reversibly converting between HGNC symbols and valid R names.

This package contains miscellaneous functions used to interpret and translate, factorize and negate Sum of Products expressions, for both binary and multi-value crisp sets, and to extract information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly flexible recoding routine and a more flexible alternative to the base function with().

This package contains a simple SMTP client which provides a portable solution for sending email, including attachments, from within R.

This package provides a set of simple functions that transforms longitudinal data to estimate the cosinor linear model as described in Tong (1976). Methods are given to summarize the mean, amplitude and acrophase, to predict the mean annual outcome value, and to test the coefficients.

Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation http://doi.org/10.1002/9781119942283. Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.

This package computes moments of univariate truncated T distribution. There is only one exported function, e_trunct, which should be seen for details.

This package enables variogram modelling, including: simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; and sequential Gaussian or indicator (co)simulation. It includes variogram and variogram map plotting utility functions, and supports sf and stars.

This package provides kernel smoothers for univariate and multivariate data, including density functions, density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing.