How to have R code (R chunk) inline with my text?
Example:
Please install the package by using install.packages("ISwR")
whereby, install.packages("ISwR") is automatically highlighted as R chunk using knitr?
In other words, I would like to have R code at the same line with my text.
Following a suggestion from Yihui,
\documentclass{article}
<<setup, include=FALSE>>=
knit_hooks$set(inline = function(x) {
if (is.numeric(x)) return(knitr:::format_sci(x, 'latex'))
knitr:::hi_latex(x)
})
#
\begin{document}
Please install the package by using \Sexpr{'install.packages("ISwR")'}.
\end{document}
You can use the 3 backticks ``` if you want the encapsulated code NOT to be executed inline . E.g.
There were ```nrow(cars)``` cars studied
Related
I am working on a document about R software, which is currently stored in a Rnw file to eventually process it with Sweave. The document contains several R code chunks, of the usual form:
<<>>=
R Code
#
Next to some code lines, I would like to add specific comments, which I would like to be displayed like usual LaTeX text (so that they are easily recognizable as comments). Is there a way to display R code chunks and corresponding comments next to each other when using sweave or knitR?
Thank you for your help!
If you want the to be formatted like code (I assume that is what you mean) you can use the following code:
\begin{filecontents*}{my_r_code_test.r}
R code
#
|\includegraphics[width=0.5\textwidth]{example-image}|
\end{filecontents*}
\documentclass{article}
\usepackage{xcolor}
\usepackage{graphicx}
\usepackage{listings,mdframed}
\lstset{
language=R,
backgroundcolor=\color{black!5}, % set backgroundcolor
basicstyle=\footnotesize\ttfamily,% basic font setting
columns=fullflexible,
}
\begin{document}
\begin{mdframed}[backgroundcolor=black!5,linewidth=0pt,%
innerleftmargin=0pt,innertopmargin=0pt,innerbottommargin=0pt]
\lstinputlisting[escapeinside=||]{my_r_code_test.r}
\end{mdframed}
\end{document}
Which produces
at the top of the page.
Hope this helps!
<<newChunk,echo=FALSE,comment=NA,background=NA>>=
x <- "\\includegraphics[width=\\maxwidth]{figure/Kompetenz1.pdf}"
cat(x)
#
If I run this r code in my .Rnw file I will get the following output in my .tex file:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{1, 1, 1}\color{fgcolor}\begin{kframe}
\begin{verbatim}
\includegraphics[width=\maxwidth]{figure/Kompetenz1.pdf}
\end{verbatim}
\end{kframe}
\end{knitrout}
How can I get just the \includegraphics{...} without any environment in my .tex file?
I am not sure why you are using Knitr in the first place. It looks like your just trying to include a PDF in your latex document. To do that I would use the command:
\includepdf[pages=-]{figure/Kompetenz1.pdf}
or
\includegraphics[width=\maxwidth]{figure/Kompetenz1.pdf}
In your Rnw file. No need for a Knitr chunk here.
The answer from #baptiste was right.
Why I was using a Knitr chunk was to loop over some values. Here is my example code:
<<Ueberblick, echo = FALSE, results = 'asis'>>=
for(i in 1:nrow(Kompetenzen)){
cat(paste("\\includegraphics[width=\\maxwidth]figure/Kompetenz.pdf}",i," \\newline ",sep=""))
}
#
Thanks for the help!
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
I'd like to use a Knitr/Sweave in-line call (\Sexpr{}) in the title of a LaTeX document, after the \begin{document} command but before the \maketitle command. The in-line R code would extract one or two pieces of information from an R data-frame created early in the R script I'm embedding in LaTeX.
I have a couple of Knitr chunks that create a data.frame from which I derive the information I want to put in the Title. I've tried placing these chunks between LaTeX's \begin{document} call and the \title code, like this:
\documentclass
[LaTex Preamble]
\begin{document}
[%% Knitr chunks that initialize an R data-frame]
\title \Sexpr{--a snippet of R code that extracts an element from the data-frame --}
\maketitle
... (rest of the LaTeX document)
and I've also tried putting the Knitr chunks in the preamble to the LaTeX code before \begin{document} statement.
But in Knitr seems to ignore code (other than initialization) that is placed ahead of the \maketitle call in LaTeX, so the in-line snippets included the title look like errors to Latex and it halts output.
I can't find any information in the Knitr documentation on including in-line code in the Title of a LaTeX document.
Any ideas?
OK: Found the solution thanks to the hint from #ben-bolker below. Ben uses the formatting of R chunks before output to an RNW file (in a 2-step Knitr process: latex -> rnw -> pdf) . But I'm compiling the LaTeX file to PDF in one-step without going to an RNW file from inside TeXShop (on Mac OSX). I found that I could get Ben's example to work using the RNW delimiters (<<>>=) and one-step compiling. But I couldn't mix the usual LaTeX chunk-delimiters (%%begin.rcode and %% end.rcode) and the RNW in-line statement hook (\Sexpr{}). The latter didn't work no matter how I fiddled with it. Eventually I found that the correct in-line hook for LaTeX is \\rinline{}.
It's not very clear in the Knitr documentation that this is the required format for LaTeX and I found it eventually mainly thanks to Ben's example. Best, Peter
Update 2 ... and then there's RTFM (or the 'cheat sheet' in this case): http://cran.r-project.org/web/packages/knitr/vignettes/knitr-refcard.pdf
Hmm. The following file works for me:
\documentclass{article}
<<echo=FALSE>>=
x <- 5
#
\title{The number is \Sexpr{x^2}}
\begin{document}
\maketitle
Some stuff
\end{document}
with knitr version 0.8 on Ubuntu 10.04, via knit2pdf("knitr_title.Rnw") ...
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.