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I have produced a dynamic document using knitr. The document makes extensive use of the package's knit_expand() function for templates. This is illustrated by the MWE (based on Yihui Xie's own example for the function).

  • Main document knit-expand-MWE.Rnw

    \documentclass{article}

\title{How to extract code when using\\
knit\_expand() for templates?}%
\author{Knitr User}

\begin{document}

\maketitle
\tableofcontents

\newpage
\section{Write one row of data}

Only the first two sections are evaluated.

<<run-all, include=FALSE>>=
library(knitr)
src = NULL
for (i in 1:3) src = c(src, knit_expand('template.Rnw'))
@

\Sexpr{paste(knit(text = src), collapse = '\n')}

\end{document}

  • Template template.Rnw called by main document

    \subsection{Now i is {{i}}}

This chunk is {{if (i > 2) 'not '}}evaluated.
<<row-{{i}}, eval={{i <= 2}}>>=
# row number {{i}}
iris[{{i}}, ]
@

I now need to extract the corresponding R code. Running purl("knit-expand-MWE.Rnw") outputs knit-expand-MWE.R, which includes the code in the chunk with a reference to the template:

## ----run-all, include=FALSE----------------------------------------------
library(knitr)
src = NULL
for (i in 1:3) src = c(src, knit_expand('template.Rnw'))

What I would like instead is the corresponding "expanded" code (for the benefit of colleagues who do not use knitr), for example:

## ----row-1, eval=TRUE----------------------------------------------
## row number 1
iris[1, ]

## ----row-2, eval=TRUE----------------------------------------------
## row number 2
iris[2, ]

## ----row-3, eval=FALSE----------------------------------------------
## row number 3
iris[3, ]

How can I achieve this?

Laura Fortunato
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  • 7

1 Answers1

2

You can run purl() on src, e. g.

purl(text = src, output = 'knit-expand.R')
Yihui Xie
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  • In the MWE, putting that line of code at the bottom of the `run-all` chunk does the trick. But if the chunk is instead in a child document called by the main document, then the compilation chokes with this error: `## Error in parse block(g[-1], g[1], params.src): duplicate label ’row-1’`. Is there a way around this? – Laura Fortunato Aug 24 '17 at 20:55
  • 1
    I'm not quite sure if the error makes sense in this case, but you can suppress it by setting `options(knitr.duplicate.label = 'allow')`. – Yihui Xie Aug 25 '17 at 04:00
  • I **believe** the issue is that both `knit_child()` and `purl()` effectively call `knit()` on `src`, which leads to the duplicate labels (there are no duplicate labels otherwise). So the option you suggest above resolves the issue. Thanks Yihui! – Laura Fortunato Aug 28 '17 at 17:58
  • You are right that `purl()` essentially calls `knit()`, which caused the issue of duplicated labels. – Yihui Xie Aug 28 '17 at 19:27