Show code in appendix using knitr

Question

I have an Rnw file (a large one) and I want to show all code used in an appendix.

It is suggested in some of the knitr examples (https://github.com/yihui/knitr-examples/blob/master/073-code-appendix.Rnw, also a good MWE) that having a code block like this is the way:

<<Rcode, eval=FALSE, ref.label=all_labels()[-1],echo=TRUE, cache=FALSE>>=
@

This works fine except all the code chunks merge into each other and none are labelled.

On the other hand if I run purl(myfile.Rnw) it labels the code chunks and separates them by two lines, which makes things much easier to read.

Is there any way of automatically listing the code using the second approach in a report appendix? I know I can have a code chunk to run purl to produce myfile.R as part of my report, but how do I then show the code in myfile.R in my appendix?

Why not purl the file and then put an \include in your rnw to embed the purl output? I.e., purl first, then include the purl output? — Thomas
do you mean as in latex '\include' something like \include{myfile.R} or something else. Good if teh code were formatted too e.g. syntax highlighting — DavidC

Thomas Thomas · Accepted Answer · 2013-08-22T15:55:57

Here's an example .Rnw file (called "example.rnw"):

\documentclass{article}
\begin{document}

<<a>>=
x <- 1:10
x
@

<<b>>=
y <- 10:1
y
@

<<c>>=
z <- 1:5
z
@

\clearpage
\input{example-purl.tex}
\end{document}

If you create a file in your working directory called "template.rnw" that just contains:

<<%sCHUNK_LABEL_HERE, eval=FALSE>>=
@

Then, you run:

stitch(purl("example.rnw",output="example-purl.r"),template="template.rnw")
knit("example.rnw")

Does that make sense? Basically, you're purling, stitching the purled code, knitting the original document, and then compiling the resulting LaTeX ("example.tex") that includes the knitting and purling. Everything should be formatted nicely (and consistently).

Show code in appendix using knitr

1 Answers