Jeroen Ooms

A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of 'RJSONIO', but has been completely rewritten in recent versions. The package offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.

The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), 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. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package which builds on this package with http specific tools and logic.

Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.

The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.

Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package.

Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.

Utilities based on 'libpoppler' for extracting text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.

Spell checking common document formats including latex, markdown, manual pages, and description files. Includes utilities to automate checking of documentation and vignettes as a unit test during 'R CMD check'. Both British and American English are supported out of the box and other languages can be added. In addition, packages may define a 'wordlist' to allow custom terminology without having to abuse punctuation.

Low level spell checker and morphological analyzer based on the famous 'hunspell' library <https://hunspell.github.io>. The package can analyze or check individual words as well as parse text, latex, html or xml documents. For a more user-friendly interface use the 'spelling' package which builds on this package to automate checking of files, documentation and vignettes in all common formats.

An R interface to Google's open source JavaScript engine. V8 is written in C++ and implements ECMAScript as specified in ECMA-262, 5th edition. In addition, this package implements typed arrays as specified in ECMA 6 used for high-performance computing and libraries compiled with 'emscripten'.

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. On Unix platforms the package also provides functions for evaluating expressions inside a temporary fork. Such evaluations have no side effects on the main R process, and support reliable interrupts and timeouts. This provides the basis for a sandboxing mechanism.

Wraps the 'AntiWord' utility to extract text from Microsoft Word documents. The utility only supports the old 'doc' format, not the new xml based 'docx' format. Use the 'xml2' package to read the latter.

Zero-dependency data frame to xlsx exporter based on 'libxlsxwriter'. Fast and no Java or Excel required.

Multi-threaded GIF encoder written in Rust: <https://gif.ski/>. Converts images to GIF animations using pngquant's efficient cross-frame palettes and temporal dithering with thousands of colors per frame.

Renders vector-based svg images into high-quality custom-size bitmap arrays using 'librsvg2'. The resulting bitmap can be written to e.g. png, jpeg or webp format. In addition, the package can convert images directly to various formats such as pdf or postscript.

Bindings to 'Tesseract' <https://opensource.google.com/projects/tesseract>: a powerful optical character recognition (OCR) engine that supports over 100 languages. The engine is highly configurable in order to tune the detection algorithms and obtain the best possible results.

Optimized C++ implementations for reading and writing protocol-buffers. Currently supports 'rexp.proto' for serializing R objects and 'geobuf.proto' for geojson data. This lightweight package is complementary to the much larger 'RProtoBuf' package which provides a full featured toolkit for working with protocol-buffers in R.

Compatibility wrapper to replace the orphaned package by Romain Francois. New applications should use the 'openssl' or 'base64enc' package instead.

High performance in-memory http request parser for application/json, multipart/form-data, and application/x-www-form-urlencoded. Includes live demo of hosting and parsing multipart forms with either 'httpuv' or 'Rhttpd'.

Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with audio and video in R. Generate high quality videos files by capturing images from the R graphics device combined with custom audio stream. This package interfaces directly to the C API and does not require any command line utilities.

High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication, and GridFS. The online user manual provides an overview of the available methods in the package: <https://jeroen.github.io/mongolite/>.

Lossless webp images are 26% smaller in size compared to PNG. Lossy webp images are 25-34% smaller in size compared to JPEG. This package reads and writes webp images into a 3 (rgb) or 4 (rgba) channel bitmap array using conventions from the 'jpeg' and 'png' packages.

A system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user Linux stack based on Apache2. The entire system is fully open source and permissively licensed. The OpenCPU website has detailed documentation and example apps.

Bindings to 'libsodium': a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a state-of-the-art Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.

Read and write JSON Web Keys (JWK, rfc7517), generate and verify JSON Web Signatures (JWS, rfc7515) and encode/decode JSON Web Tokens (JWT, rfc7519). These standards provide modern signing and encryption formats that are the basis for services like OAuth 2.0 or LetsEncrypt and are natively supported by browsers via the JavaScript WebCryptoAPI.

An extension for the 'xml2' package to transform XML documents by applying an 'xslt' style-sheet.

JSON-LD is a light-weight syntax for expressing linked data. It is primarily intended for web-based programming environments, interoperable web services and for storing linked data in JSON-based databases. This package provides bindings to the JavaScript library for converting, expanding and compacting JSON-LD documents.

Interface to the 'ZeroMQ' lightweight messaging kernel (see <http://www.zeromq.org/> for more information).

Connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client.

Google's Compact Language Detector 3 is a neural network model for language identification and the successor of 'cld2' (available from CRAN). The algorithm is still experimental and takes a novel approach to language detection with different properties and outcomes. It can be useful to combine this with the Bayesian classifier results from 'cld2'. See <https://github.com/google/cld3#readme> for more information.

A lossless compressed data format that uses a combination of the LZ77 algorithm and Huffman coding. Brotli is similar in speed to deflate (gzip) but offers more dense compression.

Bindings to Google's C++ library Compact Language Detector 2 (see <https://github.com/cld2owners/cld2#readme> for more information). Probabilistically detects over 80 languages in plain text or HTML. For mixed-language input it returns the top three detected languages and their approximate proportion of the total classified text bytes (e.g. 80% English and 20% French out of 1000 bytes). There is also a 'cld3' package on CRAN which uses a neural network model instead.

Bindings to the 'libgraphqlparser' C++ library. Parses GraphQL syntax and exports the AST in JSON format.

Bindings to the 'blowfish' password hashing algorithm derived from the 'OpenBSD' implementation.

A set of utilities for working with JavaScript syntax in R. Includes tools to parse, tokenize, compile, validate, reformat, optimize and analyze JavaScript code.

Some canned plots and functions designed for the mobilize project. Designed to be called remotely.

A binding to the minimist JavaScript library. This module implements the guts of optimist's argument parser without all the fanciful decoration.

R Client for Ohmage 2 server. Implements basic R functions to retrieve and process data.

Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods. Includes utilities for public key encryption, creating and verifying digital signatures, and managing your local keyring. Note that some functionality depends on the version of GnuPG that is installed on the system. On Windows this package can be used together with 'GPG4Win' which provides a GUI for managing keys and entering passphrases.

Jade is a high performance template engine heavily influenced by Haml and implemented with JavaScript for node and browsers.

Wraps the 'unrtf' utility to extract text from RTF files. Supports document conversion to HTML, LaTeX or plain text. Output in HTML is recommended because 'unrtf' has limited support for converting between character encodings.

Bindings to system utilities found in most Unix systems such as POSIX functions which are not part of the Standard C Library.

Bindings to various methods in the kernel for enforcing security restrictions. AppArmor can apply mandatory access control (MAC) policies on a given task (process) via security profiles with detailed ACL definitions. In addition the package has kernel bindings for setting the process hardware resource limits (rlimit), uid, gid, affinity and priority. The high level R function 'eval.secure' builds on these methods to do dynamic sandboxing: it evaluates a single R expression within a temporary fork which acts as a sandbox by enforcing fine grained restrictions without affecting the main R process. Recent versions on this package can also be installed on systems without libapparmor, in which case some features are automatically disabled.

Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no 'tcltk' is required. Password entry can be invoked in two different ways: directly from R via the askpass() function, or indirectly as password-entry back-end for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.

Convenience functions for reading and writing datasets following the 'data packagist' format.

Some R code for the OpenCPU framework.

Programmatic interface to the Dat system for data versioning and replication.

Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)

Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.

Provides R bindings to the 'Sundown' 'Markdown' rendering library (<https://github.com/vmg/sundown>). 'Markdown' is a plain-text formatting syntax that can be converted to 'XHTML' or other formats. See <http://en.wikipedia.org/wiki/Markdown> for more information about 'Markdown'.

Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.

Support for simple features, a standardized way to encode spatial vector data. Binds to 'GDAL' for reading and writing data, to 'GEOS' for geometrical operations, and to 'PROJ' for projection conversions and datum transformations.

Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.

Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <http://codecov.io> or 'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.

Useful tools for writing vector graphics devices.

Fully 'DBI'-compliant 'Rcpp'-backed interface to 'PostgreSQL' <https://www.postgresql.org/>, an open-source relational database.

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.

Implements a 'DBI'-compliant interface to 'MariaDB' (<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>) databases.

Classes for 'GeoJSON' to make working with 'GeoJSON' easier. Includes S3 classes for 'GeoJSON' classes with brief summary output, and a few methods such as extracting and adding bounding boxes, properties, and coordinate reference systems; working with newline delimited 'GeoJSON'; linting through the 'geojsonlint' package; and serializing to/from 'Geobuf' binary 'GeoJSON' format.

Client for 'jq', a 'JSON' processor (<https://stedolan.github.io/jq/>), written in C. 'jq' allows the following with 'JSON' data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.

Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal 'RPC' protocols and file formats. Additional documentation is available in two included vignettes one of which corresponds to our 'JSS' paper (2016, <doi:10.18637/jss.v071.i02>. Either version 2 or 3 of the 'Protocol Buffers' 'API' is supported.

Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <http://www.w3.org/TR/rdf-primer>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <http://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.

Interface to 'Phylocom' (<http://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.

Allows using some services of Monkeylearn <http://monkeylearn.com/> which is a Machine Learning platform on the cloud for text analysis (classification and extraction).

The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.

General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.nih.gov/ij/>. Also supports text image I/O.

Simplified document database manipulation and analysis, including support for many 'NoSQL' databases, including document databases ('Elasticsearch', 'CouchDB', 'MongoDB'), 'key-value' databases ('Redis'), and other 'NoSQL' types ('etcd').

Client for accessing data journalism APIs from ProPublica <http://www.propublica.org/>.

R bindings for Google's s2 library for geometric calculations on the sphere.

Signing and verification of R packages.

Provides a way to describe common build and deployment workflows for R-based projects: packages, websites (e.g. blogdown, pkgdown), or data processing (e.g. research compendia). The recipe is described independent of the continuous integration tool used for processing the workflow (e.g. 'Travis CI' or 'AppVeyor').