A General-Purpose Package for Dynamic Report Generation in R

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.


Build Status Coverage Status Downloads from the RStudio CRAN mirror

The R package knitr is a general-purpose literate programming engine, with lightweight API's designed to give users full control of the output without heavy coding work. It combines many features into one package with slight tweaks motivated from my everyday use of Sweave. See the package homepage for details and examples. See FAQ's for a list of frequently asked questions (including where to ask questions).

Installation

You can install the stable version on CRAN:

install.packages('knitr', dependencies = TRUE)

You can also install the development version from XRAN, which provides daily build of knitr:

# update all existing packages first
update.packages(ask = FALSE, repos = 'https://cran.rstudio.org')
install.packages('knitr', repos = c('https://xran.yihui.name', 'https://cran.rstudio.org'))

Note that if you want to build the source package via R CMD INSTALL without a previously installed version of knitr, you must either pre-install knitr from CRAN, or run R CMD INSTALL on this source repo, otherwise R CMD build will fail (which is probably a bug of base R).

Motivation

While Sweave and related add-on packages like cacheSweave and pgfSweave are fairly good engines for literate programming in R, but I often feel my hands are tied, for example:

  • I stared at the source code of Sweave and wished for hundreds of times that if only I could easily insert [width=.8\textwidth] between \includegraphics and {my-plot.pdf} (the official way in Sweave is \setkeys{Gin} but it is setting a global width, which is unrealistic since we often have to set widths individually; yes, you can use \setkeys{Gin} for many times, but why not just provide an option for each chunk?)
  • I wished for many times that if only I could use graphics devices other than PDF and postscript; now the dream has come true in the official R, but what I was hoping for was an option as simple as dev = 'png' or dev = 'CairoJPEG'
  • I wished multiple plots in a code chunk could be recorded instead of only the last one
  • I wished there was a way to round the numbers in \Sexpr{} other than writing expressions like \Sexpr{round(x, 3)} for each single \Sexpr{}
  • I wished I did not have to print() plots from ggplot2 and a simple qplot(x, y) would just give me a plot in Sweave
  • I wished users would never need instructions on Sweave.sty or run into troubles due to the fact that LaTeX cannot find Sweave.sty
  • I wished cacheSweave could print the results of a code chunk even if it was cached
  • I wished brew could support graphics
  • I wished R2HTML could support R code syntax highlighting
  • ...

The book Dynamic Documents with R and knitr

The package knitr was designed to give the user access to every part of the process of dealing with a literate programming document, so there is no need to hack at any core components if you want more freedom. I have gone through the source code of pgfSweave and cacheSweave for a couple of times, and I often feel uncomfortable with the large amount of code copied from official R, especially when R has a new version released (I will begin to worry if the add-on packages are still up-to-date with the official Sweave).

Usage

library(knitr)
?knit
knit(input)

If options are not explicitly specified, knitr will try to guess reasonable default settings. A few manuals are available such as the main manual, and the graphics manual. For a more organized reference, see the knitr book.

License

This package is free and open source software, licensed under GPL.

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("knitr")

1.20 by Yihui Xie, 9 months ago


https://yihui.name/knitr/


Report a bug at https://github.com/yihui/knitr/issues


Browse source code at https://github.com/cran/knitr


Authors: Yihui Xie [aut, cre] , Adam Vogt [ctb] , Alastair Andrew [ctb] , Alex Zvoleff [ctb] , Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de) , Aron Atkins [ctb] , Aaron Wolen [ctb] , Ashley Manton [ctb] , Ben Baumer [ctb] , Brian Diggs [ctb] , Cassio Pereira [ctb] , Christophe Dervieux [ctb] , David Hugh-Jones [ctb] , David Robinson [ctb] , Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty) , Doug Hemken [ctb] , Duncan Murdoch [ctb] , Elio Campitelli [ctb] , Fabian Hirschmann [ctb] , Fitch Simeon [ctb] , Forest Fang [ctb] , Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty) , Garrick Aden-Buie [ctb] , Gregoire Detrez [ctb] , Hadley Wickham [ctb] , Heewon Jeon [ctb] , Henrik Bengtsson [ctb] , Hiroaki Yutani [ctb] , Ian Lyttle [ctb] , Hodges Daniel [ctb] , Jake Burkhead [ctb] , James Manton [ctb] , Jared Lander [ctb] , Jason Punyon [ctb] , Javier Luraschi [ctb] , Jeff Arnold [ctb] , Jenny Bryan [ctb] , Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css) , Jeremy Stephens [ctb] , Jim Hester [ctb] , Joe Cheng [ctb] , Johannes Ranke [ctb] , John Honaker [ctb] , John Muschelli [ctb] , Jonathan Keane [ctb] , JJ Allaire [ctb] , Johan Toloe [ctb] , Jonathan Sidi [ctb] , Joseph Larmarange [ctb] , Julien Barnier [ctb] , Kaiyin Zhong [ctb] , Kamil Slowikowski [ctb] , Karl Forner [ctb] , Kevin K. Smith [ctb] , Kirill Mueller [ctb] , Kohske Takahashi [ctb] , Martin Modrák [ctb] , Michael Chirico [ctb] , Michael Friendly [ctb] , Michal Bojanowski [ctb] , Michel Kuhlmann [ctb] , Nacho Caballero [ctb] , Nick Salkowski [ctb] , Noam Ross [ctb] , Obada Mahdi [ctb] , Qiang Li [ctb] , Ramnath Vaidyanathan [ctb] , Richard Cotton [ctb] , Robert Krzyzanowski [ctb] , Romain Francois [ctb] , Ruaridh Williamson [ctb] , Scott Kostyshak [ctb] , Sebastian Meyer [ctb] , Sietse Brouwer [ctb] , Simon de Bernard [ctb] , Sylvain Rousseau [ctb] , Taiyun Wei [ctb] , Thibaut Assus [ctb] , Thibaut Lamadon [ctb] , Thomas Leeper [ctb] , Tom Torsney-Weir [ctb] , Trevor Davis [ctb] , Viktoras Veitas [ctb] , Weicheng Zhu [ctb] , Wush Wu [ctb] , Zachary Foster [ctb]


Documentation:   PDF Manual  


Task views: Reproducible Research


GPL license


Imports evaluate, highr, markdown, stringr, yaml, methods, tools

Suggests formatR, testit, digest, rgl, codetools, rmarkdown, htmlwidgets, webshot, tikzDevice, tinytex, xfun, reticulate, JuliaCall, png, jpeg, xml2, httr, DBI, showtext, tibble

System requirements: Package vignettes based on R Markdown v2 or reStructuredText require Pandoc (http://pandoc.org). The function rst2pdf() require rst2pdf (https://github.com/rst2pdf/rst2pdf).


Imported by ADPclust, AMR, BEQI2, BIGDAWG, BrailleR, ChocoLattes, DLMtool, DSAIDE, DSAIRM, DataPackageR, EpiReport, EpiSignalDetection, Gmisc, Greg, LPWC, MXM, MendelianRandomization, MetaLandSim, NormalizeMets, Orcs, PAFit, PSF, PTXQC, PreKnitPostHTMLRender, REPLesentR, RLumShiny, RagGrid, RcppFaddeeva, Rd2md, SASmarkdown, ShinyItemAnalysis, SpatialEpiApp, adapr, advclust, ahpsurvey, anipaths, assertive, automagic, beam, binb, blandr, blkbox, blogdown, bookdown, brainKCCA, cartools, ceterisParibus, cleanEHR, codebook, codified, compareGroups, condformat, condir, confidence, cooccurNet, crsra, cystiSim, dataCompareR, dendroTools, did, dlookr, easyformatr, epitab, ezknitr, facerec, factorMerger, febr, flexdashboard, flextable, formattable, furniture, gSEM, genogeographer, gglogo, gistr, helminthR, hpiR, hrbrthemes, htmlTable, iheatmapr, inlmisc, interAdapt, kableExtra, kdensity, kfigr, knitLatex, knitrBootstrap, lazyrmd, learnr, lemon, liftr, linguisticsdown, linl, lintr, manipulateWidget, memor, meteoland, microsamplingDesign, moderndive, modest, mosaicModel, multisensi, ncappc, netSEM, opencpu, optiRum, orloca, panelvar, pinp, pixiedust, pkgnet, polmineR, polymapR, printr, psychmeta, pubh, pysd2r, qmethod, qqplotr, quokar, qwraps2, rAmCharts, rNMF, radiant.data, radix, rcarbon, rchallenge, rgl, rleafmap, rmarkdown, rmdformats, rticles, rtimicropem, scoringRules, sdcMicro, sdcTable, sjPlot, skimr, skpr, spelling, stationery, statsr, survMisc, table1, tables, taxa, teachingApps, tidystats, tint, trelliscopejs, tufte, tutorial, ucbthesis, umx, userfriendlyscience, vote, vqtl, workflowr, xaringan.

Depended on by EasyHTMLReport, OutbreakTools, PSIMEX, PopGenReport, frequency, frequencyConnectedness, pathfindR, rmdHelpers, rrecsys, spThin, svSweave, tufterhandout.

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Enhanced by collapsibleTree, htmltools, kimisc, networkD3, patchSynctex, svgPanZoom, threejs.


See at CRAN