Downloaded 84 times
![Introduction
Details
More stuff about code
if you’re using beamer, need to use
begin{frame}[fragile] if you’re going to show code (i.e.,
echo=TRUE)
code in chunks must be complete/syntactically correct: no
fragments allowed;
can’t (e.g.) separate parts of a for loop, even if eval=FALSE
in-line expressions via Sexpr{} (don’t forget to round
numeric values)
Ben Bolker
RStudio and knitr](https://image.slidesharecdn.com/rstudiobeamer-140225085224-phpapp01/85/intro-to-knitr-with-RStudio-11-320.jpg)
More Related Content
Similar to intro to knitr with RStudio
intro to knitr with RStudio
- 1. Introduction Details Reproducible research withRStudio and knitr Ben Bolker McMaster University, Mathematics & Statistics and Biology 25 February 2014 Ben Bolker RStudio and knitr
- 2. Introduction Details Reproducible research Science requiresreproducibility Computational methods: harder to reproduce than math/analytic methods (but easier than non-computational science) Maintain integrity Disseminate knowledge Maintain personal sanity Ben Bolker RStudio and knitr
- 3. Introduction Details Literate programming Knuth (1984) ancestorof RR similar tools (WEB/weave/tangle), but different scope targets code as a document with interwoven discussion some notes on the LP-RR ecosystem Ben Bolker RStudio and knitr
- 4. Introduction Details A TEX/LTEX Knuth (1978)/Lamport (1980s) mathematical(and general-purpose) typesetting system pro: beautiful, widely used, cross-platform, customizable, stable con: old-fashioned, arcane Ben Bolker RStudio and knitr
- 5. Introduction Details R Gentleman and Ihaka,1990s statistical programming language/data analysis environment pro: powerful, widely used (3000+ packages), cross-platform, customizable con: slower than low-level languages; organic/inconsistent Ben Bolker RStudio and knitr
- 6. Introduction Details Sweave/knitr Leisch / Xie A literateprogramming tool, allowing LTEX chunks in R highlighted code chunks (echo=TRUE) automatically generated figures, optionally in a figure environment pro: super-convenient, once you get used to it con: one more software layer; not suited for big projects/code Ben Bolker RStudio and knitr
- 7. Introduction Details RStudio Allaire et al. front-endfor R one-button front end for knitr (“Compile PDF”) pro: beginner-friendly; cross-platform; zoomable graphics, code highlighting, tab completion, environment listing, etc. con: R-centric; restriction to built-in editor; one more software layer Ben Bolker RStudio and knitr
- 8. Introduction Details Getting started bookmark theknitr web page and especially the options page switch RStudio to compile documents with knitr (Tools/Global options/Sweave/Weave Rnw files using ...) A make sure LTEX is installed/working and the knitr package is installed (install.packages("knitr")); also install tikzDevice package build this document, or use (File/New File/R Sweave) to generate an empty template (need to add something to it); RStudio recognizes .Rnw extension code chunks start with <<>>= and end with @ Ben Bolker RStudio and knitr
- 9. Introduction Details Troubleshooting load the knitrpackage in the R console: library("knitr") R code failing? Try running it interactively in the console, or purl() to pull the code into a separate file in the console: knit2pdf("myfile.Rnw") = pushing the button step by step: knit("myfile.Rnw") + externally pdflatex myfile always name your code chunks! RStudio always compiles PDF in a clean environment Ben Bolker RStudio and knitr
- 10. Introduction Details Code options Set perchunk, e.g. <<mychunk,echo=TRUE,eval=FALSE>> or globally via opts chunk$set(...) eval: evaluate? echo: show code? warning/message/error: show/stop? (knitr does not stop on errors by default!) results: "markup" is default, I sometimes use "hide" tidy: reformat code? cache: cache results? Ben Bolker RStudio and knitr
- 11. Introduction Details More stuff aboutcode if you’re using beamer, need to use begin{frame}[fragile] if you’re going to show code (i.e., echo=TRUE) code in chunks must be complete/syntactically correct: no fragments allowed; can’t (e.g.) separate parts of a for loop, even if eval=FALSE in-line expressions via Sexpr{} (don’t forget to round numeric values) Ben Bolker RStudio and knitr
- 12. Introduction Code example library(nlme) ## commentsget formatted nicely too fm1 <- lme(distance ~ age, data = Orthodont) Ben Bolker RStudio and knitr Details
- 13. Introduction Details Graphics Graphics automatically run(stored in figures directory) fig.width, fig.height control the size/aspect ratio of the plot window (in inches!) out.width controls the size of the printed plot A (in LTEX units, e.g. "0.7textwidth") (note double backslashes) dev controls device: default is ”pdf”, may want ”png” for A huge figures or ”tikz” for LTEX fonts and symbols (not for big figures!) fig.cap generates a figure caption and puts the plot in a figure environment (need math mode where appropriate, and double backslashes!) Ben Bolker RStudio and knitr
- 14. Introduction Details 0 −2 −1 rnorm(100) 1 2 Graphics example: basic −2 BenBolker RStudio and knitr −1 0 rnorm(100) 1 2
- 15. Introduction Details 2 0 −2 rnorm(100) Graphics example: fig.width=3,fig.height=3 −3 −10 1 rnorm(100) Ben Bolker RStudio and knitr 2
- 16. Introduction Details Graphics example: dev="png" 0 −2 rnorm(10000) 2 4 plot(rnorm(10000),rnorm(10000)) −4 −2 0 rnorm(10000) Ben Bolker RStudio and knitr 2 4
- 17. Introduction Details Graphics example: dev="tikz" 0 -2 -1 √ ξα 1 2 plot(rnorm(100),rnorm(100), xlab="${calR}_0$",ylab="$sqrt{xi^alpha}$") -3 -2 -1 0 R0 Ben Bolker RStudio and knitr 1 2 3
- 18. Introduction Details Other stuff other inputformats: R markdown chunks in other languages output to other formats: HTML, docx other ways of documenting/disseminating results: commented R code (spin()); R packages/vignettes; roxygen2 package large/batch jobs: caching gets tricky, use Makefiles instead? figure tricks: 3D (rgl) plots, animation . . . Ben Bolker RStudio and knitr
- 19. Introduction Details Further resources knitr webpage, including the demos and showcase . . . StackOverflow my examples on Rpubs knitr book on Amazon Ben Bolker RStudio and knitr