Avoid code-chunks from breaking in Knitr? ( preferably using a chunk option ) - r

Using knitr to create a pdf, codechunks break according to page breaks. Usually this is exactly what I want, but in some cases I would like to be able to avoid this. E.g. by making a code-chunk jump to the next page if it does not fit the current page. I would prefer if this could be done in a chunk option, I.E not using eg. \newpage etc.
The following is an example of a code-chunk that breaks. How do I avoid this?
\documentclass{article}
\usepackage[english]{babel}
\usepackage{lipsum}
\begin{document}
\lipsum[1-3] \textbf{The following chunk will break. How do I avoid this breaking? }
<<echo=TRUE>>=
(iris)[1:20,]
#
\end{document}

I left an empty environment knitrout in the knitr design for such purposes. You can redefine this environment to achieve what you want. There are many LaTeX environments that are non-breakable, such as a figure environment. Below I use the minipage environment as an example:
\documentclass{article}
\renewenvironment{knitrout}{\begin{minipage}{\columnwidth}}{\end{minipage}}
% alternatively, you can use `figure`
% \renewenvironment{knitrout}{\begin{figure}}{\end{figure}}
\begin{document}
\begin{figure}
\caption{One figure.}
\end{figure}
% placeholder
\framebox{\begin{minipage}[t][0.3\paperheight]{1\columnwidth}%
nothing
\end{minipage}}
<<echo=TRUE>>=
(iris)[1:20,]
#
\begin{figure}
\caption{Another one.}
\end{figure}
\end{document}

Related

Is it possible to give a figure/plot a label in Sweave? [duplicate]

I can't get R/KnitR to create the LaTeX \label{} statement for a figure. The manual seems to indicate that a \label{} statement will be created by concatenating the string in fig.lp ("fig:" by default) with the label for the R-code chunk. I haven't been able to get this to work, however. No \label{} statement is created for the first figure created by knitting the MWE below. The second figure has it's label added with a workaround that I just discovered, putting the R chunk in a figure environment, and putting the \label tag after or inside the \caption tag.
\documentclass[12pt, english, oneside]{amsart}
\begin{document}
Figure \ref{fig:plot} doesn't have it's label.
<<plot>>=
plot(x=0, y=0)
#
Figure \ref{fig:plot2} has its label.
\begin{figure}
\caption{\label{fig:plot2}}
<<>>=
plot(x=1,y=1)
#
\end{figure}
\end{document}
Okay, I've found a workaround by putting the R chunk in a \begin{figure} . . .\end{figure} environment in LaTeX. I can create the label in that same environment. Still, I'd like to understand how Yihui intends for this to be handled with KnitR.
You need to set fig.cap = '' (or whatever you wish) to ensure that a figure environment is used in the latex document. (you may have noticed that the \begin{figure} ... \end{figure} is missing along with the \label{} component
eg
\documentclass[12pt, english, oneside]{amsart}
\begin{document}
See Figure \ref{fig:plot}.
<<plot, fig.lp="fig:", fig.cap = ''>>=
plot(x=0, y=0)
#
\end{document}
I would agree that the description from the website is less than clear as to this being necessary.
fig.env: ('figure') the LaTeX environment for figures, e.g. set fig.env='marginfigure' to get \begin{marginfigure}
fig.cap: (NULL; character) figure caption to be used in a figure environment in LaTeX (in \caption{}); if NULL or NA, it will be
ignored, otherwise a figure environment will be used for the plots in
the chunk (output in \begin{figure} and \end{figure})
Although the graphics manual is clear, and the reasoning makes sense
Figure Caption
If the chunk option fig.cap is not NULL or NA, the
plots will be put in a figure environment when the output format is
LATEX, and this option is used to write a caption in this environment
using \caption{}. The other two related options are fig.scap and
fig.lp which set the short caption and a prefix string for the figure
label. The default short caption is extracted from the caption by
truncating it at the first period or colon or semi-colon. The label is
a combination of fig.lp and the chunk label. Because figure is a float
environment, it can float away from the chunk output to other places
such as the top or bottom of a page when the TEX document is compiled.
If you were wishing to replicate a R session output, you wouldn't want the figures to float away from the line of code which defines how they were created.

figure* environment in twocolumn knitr/Sweave document

Sounds like it should be a common problem, but I didn't find an obvious trick.
Consider the knitr Rnw file below,
\documentclass[twocolumn, 12pt]{article}
\usepackage{graphicx}
\begin{document}
%\SweaveOpts{dev=pdf, fig.align=center}
\begin{figure*}
<<aaa, fig.width=8, fig.height=5, fig.show=hold>>=
plot(1,1)
#
\end{figure*}
\end{document}
I would like this wide figure to span two columns, using a {figure*} LaTeX environment. Is there a hook for that?
EDIT: wrapping the chunk in figure* gives the following output.
Two facts:
knitr makes everything accessible for you, so LaTeX tricks are often unnecessary;
there is a chunk hook with which you can wrap your chunk results;
A simple-minded solutions is:
knit_hooks$set(chunk = function(x, options) {
sprintf('\\begin{figure*}\n%s\n\\end{figure*}', x)
})
I leave the rest of work to you to take care of more details in options (e.g. when options$fig.keep == 'none', you should not wrap the output in figure*). You may want to see how the default chunk hook for LaTeX is defined in knitr to know better how the chunk hook works.
However, in this case, I tend to write the LaTeX code by myself in the document instead of automatically creating it. After you have got figure*, you may start to think about \caption{} and \label{} (not hard, but I still want to see them in LaTeX).
Not sure about how knitr but for Sweave (and basic latex) there is in fact a trick: have the R code produce a pdf file, and then use standard \includegraphics to pull it in.
So with this:
\documentclass[twocolumn, 12pt]{article}
\usepackage{graphicx}
\begin{document}
%\SweaveOpts{dev=pdf}
<<aaa,fig=FALSE,print=FALSE,echo=FALSE>>=
pdf("mychart.pdf", width=6, height=3)
set.seed(42)
plot(cumsum(rnorm(100)), type='l', main="yet another random walk")
invisible(dev.off())
#
\begin{figure*}
\includegraphics{mychart.pdf}
\end{figure*}
\end{document}
I got the document below (which I then converted from pdf to png):
I also had a similar problem while preparing a figure that should span two columns in a IEEE two-column conference paper.
Setting the chunk hook caused some strange error in my setup.
Even this simple hook: knit_hooks$set(chunk = function(x, options) x)
But after looking into knitr::opts_chunk$get(), I realized that simply setting fig.env="figure*" solves the problem in an elegant way.
Here is how my chunk looks like in an Rnw file:
<<fig1, fig.width=18, fig.height=6, fig.env="figure*">>=
#

Getting Sweave code chunks to stay inside page margins?

Sometimes I get to make an R code chunk (in Sweave) which is longer then the margins of the page. Is there a way to force it to "go to the next line" once that happens?
Here is a simple example of that happening:
\documentclass[a4paper]{article}
\usepackage{Sweave}
\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=2em,
frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em,
frame=single}
\title{Sweave with boxes}
\begin{document}
\maketitle
<<echo=FALSE>>=
options(width=60)
#
Here is an example of a code chunk followed by an output chunk,
both enclosed in boxes.
<<>>=
print(rnorm(99))
#
<<>>=
print("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa")
#
\end{document}
This is a difficult and extreme case, because you do not have spaces among those a's, so LaTeX may not be able to wrap the words. If you do have spaces, knitr will be able to produce the output with the long lines wrapped with tidy=TRUE, highlight=TRUE (so will Sweave, I think, if you set keep.source=FALSE).

Getting Sweave code chunks inside some framed box?

I would like to make an R code chunk (in Sweave) printed inside a framed box in the resulting pdf.
Is there an easy solution for doing that?
The short answer is that yes, there is an easy way. Just add the following lines, or something like them to the preamble of your Sweave document:
\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=2em,
frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em,
frame=single}
This works because the appearance of code (and output) chunks is controlled by the definition of the Sinput and Soutput environments. These are both Verbatim environments as provided by the LaTeX package fancyvrb. (Click here for a 73 page pdf describing the numerous options that fancyvrb provides).
A quick look in the file Sweave.sty reveals the default definition of those two environments:
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
To change those definitions, just add \DefineVerbatimEnvironment statements of your own devising either: (a) at the end of the Sweave.sty file; or (b) at the start of your *.Snw document.
Finally, here's an example to show what this looks like in practice:
\documentclass[a4paper]{article}
\usepackage{Sweave}
\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=2em,
frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em,
frame=single}
\title{Sweave with boxes}
\begin{document}
\maketitle
<<echo=FALSE>>=
options(width=60)
#
Here is an example of a code chunk followed by an output chunk,
both enclosed in boxes.
<<>>=
print(rnorm(99))
#
\end{document}
knitr, a successor of Sweave, by default outputs all echoed R code in boxes, and also formats it to the margins. Other nice features include syntax coloring and PGF integration.
Sweave code of average complexity needs only minor if any adaptions to run with knitr.

Is it possible to include a Sexpr before the expression has been evaluated in Sweave / R?

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}

Resources