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intro to knitr with RStudio


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intro to knitr with RStudio

  1. 1. Introduction Details Reproducible research with RStudio and knitr Ben Bolker McMaster University, Mathematics & Statistics and Biology 25 February 2014 Ben Bolker RStudio and knitr
  2. 2. Introduction Details Reproducible research Science requires reproducibility 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. 3. Introduction Details Literate programming Knuth (1984) ancestor of 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. 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. 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. 6. Introduction Details Sweave/knitr Leisch / Xie A literate programming 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. 7. Introduction Details RStudio Allaire et al. front-end for 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. 8. Introduction Details Getting started bookmark the knitr 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. 9. Introduction Details Troubleshooting load the knitr package 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. 10. Introduction Details Code options Set per chunk, e.g. <<mychunk,echo=TRUE,eval=FALSE>> or globally via opts chunk$set(...) eval: evaluate? echo: show code? warning/message/error: show/stop? (knitr does not stop on errors by default!) results: "markup" is default, I sometimes use "hide" tidy: reformat code? cache: cache results? Ben Bolker RStudio and knitr
  11. 11. Introduction Details More stuff about code if you’re using beamer, need to use begin{frame}[fragile] if you’re going to show code (i.e., echo=TRUE) code in chunks must be complete/syntactically correct: no fragments allowed; can’t (e.g.) separate parts of a for loop, even if eval=FALSE in-line expressions via Sexpr{} (don’t forget to round numeric values) Ben Bolker RStudio and knitr
  12. 12. Introduction Code example library(nlme) ## comments get formatted nicely too fm1 <- lme(distance ~ age, data = Orthodont) Ben Bolker RStudio and knitr Details
  13. 13. Introduction Details Graphics Graphics automatically run (stored in figures directory) fig.width, fig.height control the size/aspect ratio of the plot window (in inches!) out.width controls the size of the printed plot A (in LTEX units, e.g. "0.7textwidth") (note double backslashes) dev controls device: default is ”pdf”, may want ”png” for A huge figures or ”tikz” for LTEX fonts and symbols (not for big figures!) fig.cap generates a figure caption and puts the plot in a figure environment (need math mode where appropriate, and double backslashes!) Ben Bolker RStudio and knitr
  14. 14. Introduction Details 0 −2 −1 rnorm(100) 1 2 Graphics example: basic −2 Ben Bolker RStudio and knitr −1 0 rnorm(100) 1 2
  15. 15. Introduction Details 2 0 −2 rnorm(100) Graphics example: fig.width=3,fig.height=3 −3 −1 0 1 rnorm(100) Ben Bolker RStudio and knitr 2
  16. 16. Introduction Details Graphics example: dev="png" 0 −2 rnorm(10000) 2 4 plot(rnorm(10000), rnorm(10000)) −4 −2 0 rnorm(10000) Ben Bolker RStudio and knitr 2 4
  17. 17. Introduction Details Graphics example: dev="tikz" 0 -2 -1 √ ξα 1 2 plot(rnorm(100),rnorm(100), xlab="${cal R}_0$",ylab="$sqrt{xi^alpha}$") -3 -2 -1 0 R0 Ben Bolker RStudio and knitr 1 2 3
  18. 18. Introduction Details Other stuff other input formats: 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. 19. Introduction Details Further resources knitr web page, including the demos and showcase . . . StackOverflow my examples on Rpubs knitr book on Amazon Ben Bolker RStudio and knitr