Dynamic report generation using knitr package

Kate Ren

ScHARR, University of Sheffield

May 19, 2015

Introduction

I knitr is a package writen by Yihui Xie

I generate dynamic documents

I save you time

I reproducible research

What are dynamic documents

I mix source code and documentation together

I computing languages + authoring languages

Here is the plot of the fitted model.

‘‘‘r, ,fig.height=3,fig.width=3, echo=T, results=’hide’

x<-c(1:10)

y<-x+rnorm(10)

par(mar=c(4,4,1,1))

plot(x,y,pch=16)

(lm1<-lm(y x))

abline(lm1)

‘‘‘

Tools in R

I Sweave packageI R+LaTeX

I knitr packageI R+LaTexI R+MarkdownI other computing language (e.g. Python, C++, SAS, etc.)

Note:

LaTeX: “a high-quality typesetting system; it includes featuresdesigned for the production of technical and scientificdocumentation.”

Markdown: “a text-to-HTML conversion tool for web writers; itallows to write using an easy-to-read, easy-to-write plain textformat, then convert it to structurally valid XHTML (or HTML).”

knitr

I install.packages(‘‘knitr")

I editors: RStuodio, LyX, etc.

knitr

I in RStudio, change weave Rnw files using Sweave to knitr

knitrI *.Rnw file: LaTeX document with embedded R code (R

Sweave document in RStudio)I *.Rmd file: Markdown document (R Markdown document in

RStudio)I no space in the file names for *.Rnw files, e.g.

Intro-to-knitr.Rnw

An example in LaTeXI � �=: mark the beginning of code chunksI @: terminate a code chunkI \Sexpr { }: embed inline R code

An example in LaTeX

An example in MarkdownI “‘{}: mark the beginning of code chunksI “‘: terminate a code chunkI ‘ ‘: embed inline R codeI ‘: a backtick

An example in Markdown

Chunk options

I syntax almost exactly the same as the syntax for functionaruments in R: option=value

I e.g. echo=TRUEI fig.height=5I results=‘markup’

I can have arbitrary valid R codeI e.g. � foo, eval = if(bar < 5)TRUE else FALSE �=

I chunk label does not have to follow the syntax ruleI e.g. � foo�=I � “foo”�=I � ‘foo′ �=I � label = “foo”�=

I chunk label should have unique id

Chunk options

I echo: TRUE, FALSE

I results: markup, hide, hold, asis

Tables: a LaTeX exampleI Use xtable package

Tables: a Markdown example

Beamer

I Using knitr in beamer slides is similar to LaTeX documnets

I Need to specify fragile option on beamer frames withverbatim output

Other features

I Cache: not re-execute a chunk if it has not been modified

I cross reference: for both code chunks and child documents

I hooks: user-defined R function to fulfill tasks beyond thedefult settings in knitr

Resources

I book by Yihui Xie: Dynamic Documents with R and knitr,Second Edition

I articles about knitr from r-bloggers.com:http://www.r-bloggers.com/search/knitr

I overview of knitr by Yihui Xie from his blog:http://yihui.name/knitr/