pdf - How to create R-markdown sections inside a R code chunk? With proper code display

Question

I am currently writing on a report with rmarkdown and therefore I want to create sections inside a r code chunk. I figured out that this is possible with the help of cat() and results="asis". My problem with this solution is, that my R code results and code isn't properly displayed as usual.

For example

---
title: "test"
output: pdf_document
---

```{r, results='asis'}
for (i in 1:10) {
  cat("\section{Part:", i, "}")
  print(summary(lm(data=X, X1~X2))
  $alpha = `r X[1,i]`$  
}
```

pretty much does the trick, but here there are still two problems:

• the R output for summary() is displayed very strange because I guess it`s interpreted as LaTeX code
• I can't use LaTeX formulas in this enviroment, so if I want every section to end with a equation, which also might use a R variable, this is not possible

Does somebody know a solution for this, or is there even a workaround to create sections within a loop and to have R code, R output and LaTeX formulas in this section?

I am very thankful for every kind of advice :)

Answer 1

Using markdown and the verbatim environment

You could surround R output with verbatim environment, escape code with four in chunks.

```{r, results='asis'}
for (i in 1:10) {
  cat("\section{Part:", i, "}")
  cat("\begin{verbatim}")
  print(summary(lm(data=mtcars, mtcars[,1]~ mtcars[,i])))
  cat("\end{verbatim}")
  cat(paste0("$\\alpha$ = ", mtcars[1,i]))  
}
```

Something more fancy using the listings package

At some point, when running latex, I tend to quit markdown (.Rmd) and use sweave (.Rnw), I find it much more easy, you can check what's happening in .tex files and figure out what's wrong.

documentclass[a4paper]{article}
usepackage{listings}
usepackage[usename,dvipsnames]{xcolor}
% create a set of colors
definecolor{mygreen}{rgb}{0,0.6,0} 
definecolor{mygray}{rgb}{0.5,0.5,0.5}
definecolor{mymauve}{rgb}{0.58,0,0.82}
% create a listings environment suitable for R code
lstset{ %
  backgroundcolor=color{white},   % choose the background color; you must add usepackage{color} or usepackage{xcolor}
  basicstyle=footnotesizetfamily, % the size of the fonts that are used for the
  % code
  breakatwhitespace=false,         % sets if automatic breaks should only happen at whitespace
  breaklines=true,                 % sets automatic line breaking
  captionpos=b,                    % sets the caption-position to bottom
  commentstyle=color{mygreen},      % comment style
  deletekeywords={...},            % if you want to delete keywords from the given language
  escapeinside={\%*}{*)},          % if you want to add LaTeX within your code
  extendedchars=true,              % lets you use non-ASCII characters; for 8-bits encodings only, does not work with UTF-8
  frame=single,                    % adds a frame around the code
  keepspaces=true,                 % keeps spaces in text, useful for keeping indentation of code (possibly needs columns=flexible)
  keywordstyle=color{blue},       % keyword style
  language=R,                       % the language of the code
  morekeywords={*,...},            % if you want to add more keywords to the set
  numbers=left,                    % where to put the line-numbers; possible values are (none, left, right)
  numbersep=5pt,                   % how far the line-numbers are from the code
  numberstyle=inycolor{mygray},   % the style that is used for the line-numbers
  rulecolor=color{black},         % if not set, the frame-color may be changed on line-breaks within not-black text (e.g. comments (green here))
  showspaces=false,                % show spaces everywhere adding particular underscores; it overrides 'showstringspaces'
  showstringspaces=false,          % underline spaces within strings only
  showtabs=false,                  % show tabs within strings adding particular underscores
  stepnumber=2,                    % the step between two line-numbers. If it is 1, each line will be numbered
  stringstyle=color{mymauve},      % string literal style
  tabsize=2,                       % sets default tabsize to 2 spaces
  title=lstname                   % show the filename of files included with lstinputlisting; also try caption instead of title
}
itle{test}
egin{document}
maketitle

<<r, results='asis'>>=
for (i in 1:10) {
  cat("\section{Part:", i, "}")
  cat("\begin{lstlisting}")
  print(summary(lm(data=mtcars, mtcars[,1]~ mtcars[,i])))
  cat("\end{lstlisting}")
  cat(paste0("$\\alpha$ = ", mtcars[1,i]))  
}
@

end{document}