Stat 506 knitR

knitr requires R 2.14.0 or better.
It is supported in the current version of Rstudio. You need to install LaTeX. to use it, and have to learn some minimal LaTeX formatting commands.

install.packages('knitr', dep=T)
require(knitr)
knit("myfile.Rnw")             ## build   myfile.tex
system("pdflatex myfile.tex")  ## process it to make the pdf
knit2pdf("myfile.Rnw")         ## in 1 step
purl("myfile.Rnw")             ## extract R code into myfile.R

Options

• To decrease font size, redefine knitrout environment in the document header.

  \ifdefined\knitrout
  \renewenvironment{knitrout}{\begin{footnotesize}}{\end{footnotesize}}
   \else
  \fi

• Set a default size for figures

  \SweaveOpts{fig.width=4, fig.height=4}

  then begin the document.

• Some options go in the first R code chunk

  <<setup, echo=F,results=hide>>=
  options(width=120)
  options(max.print="70") ## limit number of rows of output
  @

  Note: Code chunks MUST start and stop on the far left of a line!

  In this html document you see them indented, but that will not work in the Rnw file.

• Code chunk options:

  <<bwplot, fig=T, dev=pdf, fig.width=10, fig.height=4, out.height=.5\linewidth, out.width=.95\linewidth, cache =T>>=
    data(singer)
    bwplot(voice.part ~ height, data=singer, xlab="Height (inches)")
  @ 

  Do not need to put lattice and ggplot commands within a print(...) call as in Sweave.
  Choose from many devices (png or tikz, for example)
  Set fig.height and fig.width to get axis labels to be right proportional to plot window size. Smaller numbers make labels bigger.
  out.height and out.width relative to \linewidth or \textwidth to get settings on the page.
  Use cache=TRUE to avoid repeatedly computing the same values.

• Appendix: to rerun the code and show output, refer to the same label created above.

  << ref.label=bwplot,  echo=TRUE, results=markup>>=
  @

  That repeats the code, and reruns it. Use eval=FALSE to omit results.

knitR website