Gabor Csardi
65 packages on CRAN
10 packages on GitHub
2 packages on Bioconductor
Run an R function in the background, possibly after a delay. The current version uses the Tcl event loop and was ported from the 'tcltk2' package.
It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.
Wrapper of .Call() that runs exit handlers to clean up C resources. Helps managing C (non-R) resources while using the R API.
A suite of tools designed to build attractive command line interfaces ('CLIs'). Includes tools for drawing rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives.
Create rich command line applications, with colors, headings, lists, alerts, progress bars, etc. It uses CSS for custom themes.
A small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode. Many symbols were taken from the 'figures' 'npm' package (see <https://github.com/sindresorhus/figures>).
'API' to the database of 'CRAN' package downloads from the 'RStudio' 'CRAN mirror'. The database itself is at <http://cranlogs.r-pkg.org>, see <https://github.com/r-hub/cranlogs.app> for the raw 'API'.
Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.
Specify debug messages as special string constants, and control debugging of packages via environment variables.
Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.
Create disposable R packages for testing. You can create, install and load multiple R packages with a single function call, and then unload, uninstall and destroy them with another function call. This is handy when testing how some R code or an R package behaves with respect to other packages.
Load configuration from a '.env' file, that is in the current working directory, into environment variables.
Place an exclusive or shared lock on a file. It uses 'LockFile' on Windows and 'fcntl' locks on Unix-like systems.
With no external dependencies and support for 335 languages; all languages spoken by more than one million speakers. 'Franc' is a port of the 'JavaScript' project of the same name, see <https://github.com/wooorm/franc>.
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
A small collection of various network data sets, to use with the 'igraph' package: the Enron email network, various food webs, interactions in the immunoglobulin protein, the karate club network, Koenigsberg's bridges, visuotactile brain areas of the macaque monkey, UK faculty friendship network, domestic US flights network, etc.
The ISA is a biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.
Wait for a single key press at the 'R' prompt. This works in terminals, but does not currently work in the 'Windows' 'GUI', the 'OS X' 'GUI' ('R.app'), in 'Emacs' 'ESS', in an 'Emacs' shell buffer or in 'R Studio'. In these cases 'keypress' stops with an error message.
Platform independent 'API' to access the operating system's credential store. Currently supports: 'Keychain' on 'macOS', Credential Store on 'Windows', the Secret Service 'API' on 'Linux', and a simple, platform independent store implemented with environment variables. Additional storage back-ends can be added easily.
Temporary and permanent message queues for R. Built on top of 'SQLite' databases. 'SQLite' provides locking, and makes it possible to detect crashed consumers. Crashed jobs can be automatically marked as "failed", or put in the queue again, potentially a limited number of times.
The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. The ISA is capable of finding overlapping modules and it is resilient to noise. This package provides a convenient interface to the ISA, using standard BioConductor data structures; and also contains various visualization tools that can be used with other biclustering algorithms.
ExpressionView visualizes possibly overlapping biclusters in a gene expression matrix. It can use the result of the ISA method (eisa package) or the algorithms in the biclust package or others. The viewer itself was developed using Adobe Flex and runs in a flash-enabled web browser.
Declare your functions with argument checks, and 'argufy' will generate and add the checking code for you.
The 'async' package brings asynchronous ('async') computation and 'I/O' to 'R'. It uses an event loop to schedule asynchronous functions that report their results via deferred values. Deferred values can be chained together for complex async computation, and they are evaluated lazily, at synchronisation points.
Create full-featured R packages, interactively, based on a couple of questions. They will have the appropriate directory structure, a testing framework, a README file with badges, GitHub integration, etc. Mason has a simple templating system, each template is provided in a separate package. The 'mason.rpkg' package contains a generic R package and it is a good place to start.
The goal of 'pak' is to make package installation faster and more reliable. In particular, it performs all HTTP operations in parallel, so metadata resolution and package downloads are fast. Metadata and package files are cached on the local disk as well. 'pak' has a dependency solver, so it finds version conflicts before performing the installation. This version of 'pak' supports CRAN, 'Bioconductor' and 'GitHub' packages as well.
Parse dates automatically, without the need of specifying a format. Currently it includes the git date parser. It can also recognize and parse all ISO 8601 formats.
Metadata and package cache for CRAN-like repositories. This is a utility package to be used by package management tools that want to take advantage of caching.
Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.
Build friendly R packages that praise their users if they have done something good, or they just need it to feel better.
Replace the standard print method for functions with one that performs syntax highlighting, using ANSI colors, if the terminal supports them.
Pretty, human readable formatting of quantities. Time intervals: 1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 1337 -> 1.34 kB.
Tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes. It can read the standard output and error of the processes, using non-blocking connections. 'processx' can poll a process for standard output or error, with a timeout. It can also poll several processes at once.
Configurable Progress bars, they may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. The package also provides a 'C++' 'API', that works with or without 'Rcpp'.
Run 'R CMD check' from 'R' and capture the results of the individual checks. Supports running checks in the background, timeouts, pretty printing and comparing check results.
A collection of small text corpora of interesting data. It contains all data sets from https://github.com/dariusk/corpora. Some examples: names of animals: birds, dinosaurs, dogs; foods: beer categories, pizza toppings; geography: English towns, rivers, oceans; humans: authors, US presidents, occupations; science: elements, planets; words: adjectives, verbs, proverbs, US president quotes.
Query the main 'R' 'SVN' repository to find the versions 'r-release' and 'r-oldrel' refer to, and also all previous 'R' versions and their release dates.
Allow sharing sensitive information, for example passwords, 'API' keys, etc., in R packages, using public key cryptography.
Query and print information about the current R session. It is similar to 'utils::sessionInfo()', but includes more information about packages, and where they were installed from.
Sometimes it is handy to be able to view an image file on an 'R' graphics device. This package just does that. Currently it supports 'PNG' files.
Decide which server to connect to, based on previous response times, and configuration.
A 'sparkline' is a line chart, without axes and labels. Its goal is to show the general shape of changes over time, or another quantity. This package is an 'R' implementation of the original shell project: <http://zachholman.com/spark/>.
The goal of 'pkg' is to make package installation faster and more reliable. In particular, it performs all HTTP operations in parallel, so metadata resolution and package downloads are fast. Metadata and package files are cached on the local disk as well. 'pkg' has a dependency solver, so it finds version conflicts before performing the installation. This version of 'pkg' supports CRAN, 'BioConductor' and 'GitHub' packages as well.
Create a snapshot of your installed CRAN packages with 'snap', and then use 'restore' on another system to recreate exactly the same environment.
One difficulty of 'magrittr' pipes is that they make debugging harder. If you don't always write correct code, and you use pipes, then you'll find tamper very useful. It is the 'magrittr' specific alternative of the 'recover' function: when used with 'options(error=tamper)', after an error, it displays the whole pipeline, marks the place of the error, and helps saving the temporary results.
A client for the 'WebDriver' 'API'. It allows driving a (probably headless) web browser, and can be used to test web applications, including 'Shiny' apps. In theory it works with any 'WebDriver' implementation, but it was only tested with 'PhantomJS'.
Look up the username and full name of the current user, the current user's email address and 'GitHub' username, using various sources of system and configuration information.
Convert the output of 'utils::getParseData()' to an 'XML' tree, that one can search via 'XPath', and easier to manipulate in general.
Cross platform solution to open files, directories or 'URLs' with their associated programs.
Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.
Check if a given package name is available to use. It checks the name's validity. Checks if it is used on 'GitHub', 'CRAN' and 'Bioconductor'. Checks for unintended meanings by querying Urban Dictionary, 'Wiktionary' and Wikipedia.
Cyclomatic complexity is a software metric (measurement), used to indicate the complexity of a program. It is a quantitative measure of the number of linearly independent paths through a program's source code. It was developed by Thomas J. McCabe, Sr. in 1976.
A micro-package for reading "passwords", i.e. reading user input with masking, so that the input is not displayed as it is typed. Currently we have support for 'RStudio', the command line (every OS), and any platform where 'tcltk' is present.
Give advice about good practices when building R packages. Advice includes functions and syntax to avoid, package structure, code complexity, code formatting, etc.
Functions to fit log-multiplicative models using 'gnm', with support for convenient printing, plots, and jackknife/bootstrap standard errors. For complex survey data, models can be fitted from design objects from the 'survey' package. Currently supported models include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative layer effect model (Xie), and several association models: Goodman's row-column association models of the RC(M) and RC(M)-L families with one or several dimensions; two skew-symmetric association models proposed by Yamaguchi and by van der Heijden & Mooijaart. Functions allow computing the intrinsic association coefficient (and therefore the Altham index), including via the Bayes shrinkage estimator proposed by Zhou; and the RAS/IPF/Deming-Stephan algorithm.
Extract all function calls from an R package, or a set of R scripts. Create a network of functions that can be then visualized. Can also extract the places of the function definitions and function calls and export them in a 'JSON' file.
Provides a simple interface to lookup and print R function definitions, including C and C++ compiled code from .Call, .C, .Internal and .External calls. Also lookup of S3 and S4 generics, including a simple dialog to print any or all of the loaded methods for the generic.
An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's 'Appdirs' (\url{https://github.com/ActiveState/appdirs}) to R.
A small wrapper on 'regexpr' to extract the matches and captured groups from the match of a regular expression to a character vector.
Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Installs shiny apps packaged as stand-alone Electron apps using Inno Setup, an open source software that builds installers for Windows programs <http://www.jrsoftware.org/ishelp/>.
'R' 'Markdown' format for 'shower' presentations, see <https://github.com/shower/shower>.
An extremely simple stack data type, implemented with 'R6' classes. The size of the stack increases as needed, and the amortized time complexity is O(1). The stack may contain arbitrary objects.
Browser notifications in 'Shiny' apps, using 'toastr': <https://github.com/CodeSeven/toastr#readme>.
Simple classic graph algorithms for simple graph classes. Graphs may possess vertex and edge attributes. 'simplegraph' has so dependencies and it is written entirely in R, so it is easy to install.
Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales.