Presentation given by Kate Ren at the Sheffield R Users Group May meeting - introduction to knitr for dynamic report generation

1. Dynamic report generation using knitr package
Kate Ren
ScHARR, University of Sheffield
May 19, 2015

2. Introduction
knitr is a package writen by Yihui Xie
generate dynamic documents
save you time
reproducible research

3. What are dynamic documents
mix source code and documentation together
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)
‘‘‘

4. Tools in R
Sweave package
R+LaTeX
knitr package
R+LaTex
R+Markdown
other computing language (e.g. Python, C++, SAS, etc.)
Note:
LaTeX: “a high-quality typesetting system; it includes features
designed for the production of technical and scientific
documentation.”
Markdown: “a text-to-HTML conversion tool for web writers; it
allows to write using an easy-to-read, easy-to-write plain text
format, then convert it to structurally valid XHTML (or HTML).”

5. knitr
install.packages(‘‘knitr")
editors: RStuodio, LyX, etc.

6. knitr
in RStudio, change weave Rnw files using Sweave to knitr

7. knitr
*.Rnw file: LaTeX document with embedded R code (R
Sweave document in RStudio)
*.Rmd file: Markdown document (R Markdown document in
RStudio)
no space in the file names for *.Rnw files, e.g.
Intro-to-knitr.Rnw

8. An example in LaTeX
=: mark the beginning of code chunks
@: terminate a code chunk
Sexpr { }: embed inline R code

9. An example in LaTeX

10. An example in Markdown
“‘{}: mark the beginning of code chunks
“‘: terminate a code chunk
‘ ‘: embed inline R code
‘: a backtick

11. An example in Markdown

12. Chunk options
syntax almost exactly the same as the syntax for function
aruments in R: option=value
e.g. echo=TRUE
fig.height=5
results=‘markup’
can have arbitrary valid R code
e.g. foo, eval = if(bar < 5)TRUE else FALSE =
chunk label does not have to follow the syntax rule
e.g. foo =
“foo” =
‘foo =
label = “foo” =
chunk label should have unique id

13. Chunk options
echo: TRUE, FALSE
results: markup, hide, hold, asis

14. Tables: a LaTeX example
Use xtable package

15. Tables: a Markdown example

16. Beamer
Using knitr in beamer slides is similar to LaTeX documnets
Need to specify fragile option on beamer frames with
verbatim output

17. Other features
Cache: not re-execute a chunk if it has not been modified
cross reference: for both code chunks and child documents
hooks: user-defined R function to fulfill tasks beyond the
defult settings in knitr

18. Resources
book by Yihui Xie: Dynamic Documents with R and knitr,
Second Edition
articles about knitr from r-bloggers.com:
http://www.r-bloggers.com/search/knitr
overview of knitr by Yihui Xie from his blog:
http://yihui.name/knitr/