I want demonstrate a sample piece of R code WITH the knitr <<..>>= preamble in a LaTeX document. Here is an example of the output I desire:
It's got to be simple - but I'm missing something. I checked the documentation and scanned stack overflow - but without luck. Here is a MWE:
\documentclass{article}
\begin{document}
<<mychunk, cache=TRUE, eval=FALSE, dpi=100>>=
"hello world"
#
\end{document}
Suggestions? I tried indenting the code in LaTex and wrapping in a verbatim block, but only got errors.
I just checked the manual of knitr. This is how the package author solved the problem:
<<use-ext-chunk, echo=FALSE, comment=NA>>=
cat('<<Q1, echo=TRUE, tidy=TRUE>>=','#',sep='\n')
#
which produces the output as shown on page 9 of the knitr manual
Here is a minimal example:
\documentclass[a4paper]{article}
\begin{document}
<<use-ext-chunk, echo=FALSE, comment=NA>>=
cat('<<Q1, echo=TRUE, tidy=TRUE>>=','#',sep='\n')
#
\end{document}
which produces the attached output.
I had the same question on tex.stackexchange.com a year ago and got a few nice responses: https://tex.stackexchange.com/q/35485/3419. This is for Sweave but I think it will work the same in knitr.
I think I ended up just using \Sexpr{"<<>>="} and \Sexpr{"#"} in verbatim environment. e.g.:
\documentclass{article}
\begin{document}
\begin{verbatim}
\Sexpr{"<<mychunk, cache=TRUE, eval=FALSE, dpi=100>>="}
"hello world"
\Sexpr{"#"}
\end{verbatim}
\end{document}
Just a quick follow-up: this feature has been implemented in knitr (devel version >= 0.8.15); see examples for both Rnw and Rmd. An alternative solution is in knitr FAQ.
Related
I would like to know how to display the result of a variable that is in the environment
\documentclass{article}
\begin{document}
\SweaveOpts{concordance=TRUE}
Hello,
\input{test2.Rnw}
\end{document}
test2.Rnw
\section{test}
<<eval=TRUE, echo=F>>=
paste0("my variable v is worth: ", v)
#
When I compile I get this
You can use the knitr package inside your Rmarkdown code. Check https://riptutorial.com/r/topic/4334/r-in-latex-with-knitr and also this SO Q&A : knitr chunk option eval=TRUE, echo=TRUE, include=FALSE
I'm trying to output the source of a knitr chunk onto a beamer slide.
For example, I would like the following code chunk to be displayed as is in the .Rnw:
<<code-chunk, echo=TRUE, tidy=TRUE>>=
#
I've attempted to recreate this behavior using:
<<out-first-code-chunk, echo=FALSE, comment=NA>>=
cat(paste("<<example-code-chunk, echo=TRUE, tidy=TRUE>>=","#",sep="\n"))
#
This code is legitimate since the cat command in R's console gives:
> cat('<<example-code-chunk, echo=TRUE, tidy=TRUE>>=','#',sep='\n')
<<code-chunk, echo=TRUE, tidy=TRUE>>=
#
However, the resulting latex:
\begin{frame}
\frametitle{Code Chunk}
To incorporate R code into your knitr documents
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{verbatim}
<<example-code-chunk, echo=TRUE, tidy=TRUE>>=
#
\end{verbatim}
\end{kframe}
\end{knitrout}
Throws errors:
<<example-code-chunk, echo=TRUE, tidy=TRUE>>= # \end {verbatim} \end
\ETC. ! Paragraph ended before \#xverbatim was complete. <to be read
again> \par l.198 \end{frame} I suspect you've forgotten a `}',
causing me to apply this control sequence to too much text. How can we
recover? My plan is to forget the whole thing and hope for the best. !
LaTeX Error: \begin{verbatim} on input line 198 ended by
\end{beamer#framepau ses}. See the LaTeX manual or LaTeX Companion for
explanation. Type H <return> for immediate help. ... l.198 \end{frame}
Your command was ignored. Type I <command> <return> to replace it with
another command, or <return> to continue without it. ! LaTeX Error:
\begin{kframe} on input line 198 ended by \end{beamer#frameslide }.
Why is the latex environment thinking that verbatim was not closed? Is there a more appropriate way to display a code-chunk in its entirety?
This should do it...
1 line in the setup chunk, and 1 extra param in the chunk desired for output...
Console:
`install.packages(devtools)`
`devtools::install_github("thell/knitliteral")`
For .Rnw:
<<"knitr-setup", include=FALSE, cache=FALSE>>=
knitLiteral::kast_on()
#
<<"my_chunk", eval=FALSE, opts.label="literal-literal">>=
# Something that will not be output in the doc.
#
Output:
<<"my_chunk", eval=FALSE>>=
#
For .Rmd:
````{r knitr_setup, include=FALSE, cache=FALSE}
knitLiteral::kast_on()
````
````{r my_chunk, opts.label="literal-literal"}
# Something that will not be output in the doc.
````
Output:
````{r my_chunk}
````
** The use of 4 backticks keeps syntax highlighting as valid R (where used).
From this chunk and what you can see in the source of the example Literal Markdown doc and the rendered doc that there is no need to have a complex chunk.
The sweave example file is also available showing the same examples.
I am sorry, I am new to using knitr to make slides. I generally use the latex() function in Hmisc package to generate my tables based on R objects. I would like to produce a slide that shows the r code and then below it displays the properly formatted table. Something like:
``` {r}
latex(tabdat,file="tables/tabdat.tex",ctable=TRUE,caption="A basic table",caption.loc="bottom",label="tab:dat1",row.names=NULL,rowlabel="")
```
So that the finished slide displays the exact r code and the formatted table looking exactly as if I had run latex using \input{tabdat}
I would appreciate any advice on how to accomplish this.
Thanks!
I am a bit puzzled because you talk about PDF/LaTeX output but you are using R markdown tags.
Here are small examples for both cases, R Sweave, i.e. LaTeX output, and R markdown, i.e. HTML output. For creating the LaTeX code there are several packages available (xtable, Hmisc etc.) for HTML AFAIK only xtable.
The main point of how to include the raw output just like it appears in the console is the same for both output types and was already explained by Tyler Rinker above, i.e. by adding results="asis" to the chunk options.
PDF/LaTeX / Rnw-file
\documentclass{article}
\begin{document}
<<echo=FALSE, message=FALSE>>=
library(Hmisc)
library(xtable)
#
<<results='asis'>>=
latex(head(iris), file = '')
#
<<results='asis'>>=
xtable(head(iris))
#
\end{document}
HTML, Rmd-file
```{r echo=FALSE}
library(xtable)
```
```{r results='asis'}
tbl <- xtable(head(iris))
print(tbl, type="html")
```
Look here for more examples and options: http://www.stat.iastate.edu/centers/CCGS/slides/slides-Rtables.pdf
Can't compile the following Rnw document into pdf using knitr
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[russian]{babel}
\begin{document}
<<>>=
hist(rnorm(100),main="Гистограмма")
#
\end{document}
With labels in English everything is ok.
Edit 1:
Now i have two versions of pdf. In the first one letters are replaced by points.
In the second one all letters are overlapped. The second one is produced using addtional code chunk
<<>>=
pdf.options(encoding = "CP1251")
#
I am using Ubuntu 12.04 + R 2.14 + Texlive.
Edit 2:
For the moment i've found the following partial solution:
<<>>=
cairo_pdf("figure.pdf")
hist(rnorm(100),main="Гистограмма")
dev.off()
#
\includegraphics{figure.pdf}
Edit 3:
Using the following code:
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[russian]{babel}
\begin{document}
<<dev='cairo_pdf'>>=
hist(rnorm(100),main="Гистограмма")
#
\end{document}
I obtain a CORRECT histogram, with a lot of WARNINGS. How to avoid or at least suppress them?
Finally! Ura!
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[russian]{babel}
\begin{document}
<<dev='cairo_pdf',warning=FALSE>>=
hist(rnorm(100),main="Гистограмма")
#
\end{document}
Could i avoid warnings? Can someone explain me all that stuff with encodings and warnings?
You may need to set pdf.options(encoding = 'your_encoding'); see https://github.com/yihui/knitr/issues/172 I'm not entirely sure what exactly the encoding should be here.
I'm writing a Sweave document, and I want to include a small section that details the R and package versions, platofrms and how long ti took to evalute the doucment, however, I want to put this in the middle of the document !
I was using a \Sexpr{elapsed} to do this (which didn't work), but thought if I put the code printing elapsed in a chunk that evaluates at the end, I could then include the chunk half way through, which also fails.
My document looks something like this
%
\documentclass[a4paper]{article}
\usepackage[OT1]{fontenc}
\usepackage{longtable}
\usepackage{geometry}
\usepackage{Sweave}
\geometry{left=1.25in, right=1.25in, top=1in, bottom=1in}
\begin{document}
<<label=start, echo=FALSE, include=FALSE>>=
startt<-proc.time()[3]
#
Text and Sweave Code in here
%
This document was created on \today, with \Sexpr{print(version$version.string)} running
on a \Sexpr{print(version$platform)} platform. It took approx sec to process.
<<>>=
<<elapsed>>
#
More text and Sweave code in here
<<label=bye, include=FALSE, echo=FALSE>>=
odbcCloseAll()
endt<-proc.time()[3]
elapsedtime<-as.numeric(endt-startt)
#
<<label=elapsed, include=FALSE, echo=FALSE>>=
print(elapsedtime)
#
\end{document}
But this doesn't seem to work (amazingly !)
Does anyone know how I could do this ?
Thanks
Paul.
This works just fine for me:
\documentclass{article}
\usepackage{Sweave}
\begin{document}
<<label=start, echo=FALSE, include=FALSE>>=
startt<-proc.time()[3]
#
Text and Sweave Code in here
This document was created on \today, with
\Sexpr{print(version$version.string)}.
<<results=hide,echo=FALSE>>=
Sys.sleep(2) # instead of real work
#
More text and Sweave code in here
<<label=bye, include=FALSE, echo=FALSE>>=
endt<-proc.time()[3]
elapsedtime<-as.numeric(endt-startt)
#
It took approx \Sexpr{elapsedtime} seconds to process.
\end{document}
I had to remove the version string inside the \Sexp{} as I get an underscore with via x86_64 which then upsets LaTeX. Otherwise just fine, and you now get the elapsed time of just over the slept amount.
You could use either R to cache the elapsed time in a temporary file for the next run, or pass it to LaTeX as some sort of variable -- but you will not be able to use 'forward references' as the R chunks gets evaluated in turn.
btw you don't usually need print to evaluate variables R
\Sexpr{version$version.string}
works fine as well
Dirk's answer is almost perfect, but still doesn't let you put the answer half way through the document. I got quite frustrated thinking it should work, but realised that the code I had was opening the time file at the start of each run (and emptying it) and writing the empty result into my document, then putting the answer in the time file at the end !
I eventually did something similar but using R to only open and write the file at the end, which worked great !;
\documentclass[a4paper]{article}
\usepackage[OT1]{fontenc}
\usepackage{longtable}
\usepackage{geometry}
\usepackage{Sweave}
\geometry{left=1.25in, right=1.25in, top=1in, bottom=1in}
\begin{document}
<<label=start, echo=FALSE, include=FALSE>>=
startt<-proc.time()[3]
#
Text and Sweave Code in here
%
This document was created on \today, with \Sexpr{print(version$version.string)} running
on a \Sexpr{print(version$platform)} platform. It took approx \input{time}
sec to process.
More text and Sweave code in here
<<label=bye, include=FALSE, echo=FALSE>>=
odbcCloseAll()
endt<-proc.time()[3]
elapsedtime<-as.numeric(endt-startt)
#
<<label=elapsed, include=FALSE, echo=FALSE>>=
fileConn<-file("time.tex", "wt")
writeLines(as.character(elapsedtime), fileConn)
close(fileConn)
#
\end{document}