knitr

knitr
Name	knitr
Author	Yihui Xie
Latest release version	1.40
Operating system	Cross-platform
License	MIT

knitr is a literate programming engine for R that combines code, prose, and output to produce reproducible documents. It enables researchers, analysts, and authors to interleave R code with narrative, generating reports in multiple formats while integrating with tools and institutions across data science and scientific publishing. knitr is widely used in academic, government, and industry contexts for reproducible workflows.

Overview

knitr was created to facilitate reproducible research practices by merging R code execution with document production. It connects R with publishing systems and platforms used by figures such as Hadley Wickham, RStudio, CRAN, Bioconductor, Nature Publishing Group, PLOS, The New England Journal of Medicine, United Nations, World Health Organization, European Space Agency, NASA, MIT Press, Oxford University Press, Cambridge University Press, Stanford University Press, Harvard University Press, IEEE, ACM, American Statistical Association, Royal Statistical Society, National Institutes of Health, National Science Foundation, Wellcome Trust, Gates Foundation, Microsoft Research, Google Research, Amazon Web Services, IBM Research, Facebook AI Research, OpenAI, DeepMind, Toyota Research Institute, Siemens, Boeing, Lockheed Martin, Goldman Sachs, Morgan Stanley, JP Morgan Chase, UBS, Deutsche Bank, Barclays, Bank of America.

Features and Functionality

knitr supports chunked execution, caching, figure generation, and conditional evaluation to produce reproducible outputs used by Yihui Xie, Hadley Wickham, RStudio, Jeroen Ooms, Stefan Milton Bache, Dirk Eddelbuettel, Winston Chang, Jenny Bryan, Roger D. Peng, Jeff Leek, Hilary Parker, David Robinson, Claudia Perlich, Cade Metz, Nate Silver, Tim Harford, Hans Rosling, Edward Tufte, John Tukey, Florence Nightingale, Ada Lovelace, Alan Turing, Grace Hopper, Katherine Johnson, Srinivasa Ramanujan, Carl Friedrich Gauss, Isaac Newton, Albert Einstein, Marie Curie, Charles Darwin, Gregor Mendel, Louis Pasteur, Robert Koch, Alexander Fleming, Jonas Salk.

Usage and Workflow

Typical workflows interleave R code with narrative to produce vignettes, slides, and reports that circulate among groups such as Harvard University, Stanford University, Massachusetts Institute of Technology, Princeton University, Yale University, University of Oxford, University of Cambridge, University of California, Berkeley, California Institute of Technology, University of Washington, University of Toronto, ETH Zurich, Imperial College London, Peking University, Tsinghua University, National University of Singapore, University of Melbourne, University of Tokyo, Seoul National University, McGill University, Karolinska Institutet, UCL, Sorbonne University, University of Chicago, Columbia University, New York University, University of Michigan, University of California, Los Angeles, Johns Hopkins University.

Integration with R and RStudio

knitr integrates closely with the R language and the RStudio IDE, alongside package ecosystems like tidyverse, data.table, ggplot2, shiny, plotly, leaflet, rmarkdown, bookdown, blogdown, xaringan, pagedown, pkgdown, devtools, roxygen2, testthat, covr, drake, targets, Bioconductor, caret, mlr3, sparklyr, keras, tensorflow, torch, Stan, JAGS, BUGS, rstan.

Output Formats and Engines

knitr can produce output in HTML, PDF, Word, Markdown, and presentation formats by leveraging engines and backends used by Pandoc, LaTeX Project, Beamer, Reveal.js, Slidy, PowerPoint, Microsoft Office, LibreOffice, Sphinx, Jupyter Notebook, IPython, Binder, GitHub Pages, Netlify, Travis CI, GitHub Actions, CircleCI, AppVeyor, Zenodo, Figshare, Dryad, OSF, Docker, Kubernetes, Apache Spark, Hadoop, Amazon S3, Google Cloud Platform, Microsoft Azure.

Development History and Versions

knitr was developed and maintained through contributions from an ecosystem including Yihui Xie, contributors from RStudio, and community participants affiliated with CRAN, Bioconductor, GitHub, Stack Overflow, GitLab, Bitbucket, SourceForge, OpenAI, Mozilla Foundation, Linux Foundation, Apache Software Foundation, Eclipse Foundation, Free Software Foundation, Creative Commons, Open Data Institute, DataCamp, Coursera, edX, Udacity, Kaggle, ArXiv, bioRxiv, medRxiv, SSRN.

Adoption and Community Extensions

knitr’s adoption spans academia, industry, and government, with community extensions and integrations developed by people at RStudio, Posit, Microsoft Research, Google Research, IBM Research, Facebook, Twitter, GitHub, LinkedIn, Uber Technologies, Airbnb, Netflix, Spotify, Adobe, Oracle, SAP, Siemens Healthineers, GE Healthcare, Johnson & Johnson, Pfizer, Moderna, AstraZeneca, Merck & Co., Bayer, Novartis, Roche, Eli Lilly and Company, Sanofi, GlaxoSmithKline, Boehringer Ingelheim, Takeda, Bristol-Myers Squibb.

Category:Software