[Tex/LaTex] Embedding knitr tex files on a bigger latex file

knitr

There are already some question about about how to use Knitr's latex output within a new knitr document, using Rstudio and include or input and declaring some chunks as child.

But what if I want to use a simple knitr output (such as an R xtable) from within an external LaTeX program, such as TeXStudio to build a larger project?

For example, I could create a mytable.rnw file and generate this simple table

\documentclass{article}
\begin{document}

<<r table2, results='asis', message=T, echo=F>>=

library(xtable) 
print(
  xtable(
    head(iris),
    caption = 'Iris data'
  ),
  comment = FALSE,
  type = 'latex'
)

@

\end{document}

And now I want to grab the generated mytable.tex file and use it in a bigger document from TexStudio, in the same folder.

\documentclass{article}
\begin{document}
 First table:
 \include{mytable}
 Second table:
 \include{mytable}
\end{document}

(Maybe is better to use input)
When I try to compile it I get many errors:

Can be used only in preamble. \documentclass
Can be used only in preamble. \documentclass{article}\usepackage
Can be used only in preamble. ...ss{article}\usepackage[]{graphicx}\usepackage
Undefined control sequence. \definecolor
Can be used only in preamble. \usepackage
Undefined control sequence. \definecolor
Undefined control sequence. \definecolor
Undefined control sequence. \definecolor
Undefined control sequence. \definecolor
Can be used only in preamble. \usepackage
Can be used only in preamble. ...eExists{upquote.sty}{\usepackage{upquote}}{}
Can be used only in preamble. \begin{document}

I guess the problem arises because knitr ouput includes a lot of preamble information that can't be included within the document body, not only usepackage directives but also a lot of fie-tune information about colors, tables…

What's the proper way do it?
How to force Rstudio's knitr to output only the proper information?
Or how to force my main latex document (from TexStudio) to correct the problem?

If we have to do it many times is there any easy way to include that preamble in the main tex document without going manually one by one.
Or even worse, some genetared outputs may contain incompatible preambles.

Best Answer

The easiest way to do it, would be to make your main document also a .Rnw file, that could contain nothing but LaTeX (at first).

Within the main .Rnw document you could do something like

<<child="myTable.Rnw">>=
@

where myTable.Rnw can be any .Rnw file that does not include header information, e.g. your example document without documentclass and begin{document}/\end{document}

Of course you could just as well include the r-chunk from myTable.Rnw in to the main document (as well as other r-chunks).

Option 1: Using `knit_child()` with inline R code

Say your setup is like the following. In the same directory, you have:

`graph.R`

## ---- graph
library(ggplot2)
CarPlot <- ggplot() +
    stat_summary(data= mtcars,
                 aes(x = factor(gear),
                     y = mpg
                 ),
                 fun.y = "mean",
                 geom = "bar"
                 )
CarPlot

`chapter1.Rnw`

Hey, look, a graph (Figure~\ref{fig:graph})!

<<graph, echo=FALSE, message=FALSE, fig.lp='fig:', out.width='.5\\linewidth', fig.align='center', fig.cap="A graph", fig.pos='h!'>>=
@

`main.Rnw`

\documentclass{article}

\begin{document}

<<external-code, echo=FALSE, cache=FALSE>>=
read_chunk('./graph.R')
@

\Sexpr{knit_child('chapter1.Rnw')}

\end{document}

Then, you can knit the main.Rnw file and compile the resulting .tex file with either pdflatex or xelatex.

The output is:

enter image description here

Note that you can also read the external .R file from the child .Rnw file.

So, the following would have worked just as well.

`chapter1-mod.Rnw`

<<external-code, echo=FALSE, cache=FALSE>>=
read_chunk('./graph.R')
@

Hey, look, a graph (Figure~\ref{fig:graph})!

<<graph, echo=FALSE, message=FALSE, fig.lp='fig:', out.width='.5\\linewidth', fig.align='center', fig.cap="A graph", fig.pos='h!'>>=
@

`main-mod.Rnw`

\documentclass{article}

\begin{document}

\Sexpr{knit_child('chapter1-mod.Rnw')}

\end{document}

Option 2: Using chunk option `child`

Assuming you have graph.R and chapter1.Rnw from above in the same directory, then your main.Rnw should be:

\documentclass{article}

\begin{document}

<<external-code, echo=FALSE, cache=FALSE>>=
read_chunk('./graph.R')
@

<<child-demo, child='chapter1.Rnw'>>=
@

\end{document}

Note that you can also read the external .R file from within the child document in this case, too.

So, assuming you had graph.R and chapter1-mod.Rnw from above in the same directory, then your main-mod.Rnw file should be:

\documentclass{article}

\begin{document}

<<child-demo, child='chapter1-mod.Rnw'>>=
@

\end{document}

[Tex/LaTex] knitr in RStudio produces ‘Undefined control sequence’, alongside other issues

The compile sequence for a file using LaTeX and R code which is to be processed through knitr is as follows where * is your filename without extension. I would recommend that you run these using TeXworks (bundled with MikTeX) and R before you diagnose the problem in RStudio. RStudio in the past was very picky on setup of supporting programs (I have not used it recently)

The *.tex file is renamed with the suffix *.Rnw (this is case sensitive)
Within the now *.Rnw file you need to use R-blocks to load any needed R library's and do any computations.
When the *.Rnw file is ready for a compile (and you file is ready when renamed) you then need to start R, change the working directory to the same one as the *.Rnw file. Now you need to Load the knitr package. (If needed install it and thereafter just load it.
In the R console you issue the command knit *.Rnw and this will create a *.tex file with the R commands replaces with the output.
Now return to your LaTeX and run pdflatex twice and then run your viewer.

If you are using an IDE there are setups which allow you to do all of this from within the LaTeX IDE. However I am not familiar with current version of RStudio. In the past it was not able to run knitr from RStudio as then RStudio was hardwired for Sweave.

I would recommend you visit http://yihui.name/knitr/ as the author of knitr has provided an extensive help and demo site(examples).

Best Answer

Related Solutions

[Tex/LaTex] Building TeX file from knitr Rnw as child of larger parent TeX file to use R objects and output

Option 1: Using knit_child() with inline R code

graph.R

chapter1.Rnw

main.Rnw

chapter1-mod.Rnw

main-mod.Rnw

Option 2: Using chunk option child