As a refinement of this question, does anyone know how to tell Sweave (or better the driver) to put all the graphics in a specific directory when using the RweaveHTML driver from the R2HTML package? I can't find any option for that :(
Sweave responds to the prefix.string option for figures. E.g. in one recent document I use
\SweaveOpts{engine=R,eps=FALSE,echo=TRUE,prefix.string=figures/chart}
which leads to files figures/chart-chunkname.pdf where I use chunkname as the identifier in the Sweave code snippet. I suspect the same may help for R2HTML but I have not tried that driver.
Related
I am new to the R/exams package and I try to produce a pdf document from one of the templates provided by the developers. (http://www.R-exams.org/templates/confint3/)
I am able to compile a Rnw file into a HTML document using the commands
library("exams")
exams2html("confint3.Rnw")
When calling the function
exams2pdf("confint3.Rnw")
it gives the error message
! LaTeX Error: File `Sweave.sty' not found.
I have Latex installed and there are no problems using it in general. I do not understand:
Do I need to tell exams2pdf() the location of the latex installation?
Do I need to define a template (as plain.tex) first? How should it look like?
What is it that I do not understand?
I looked at the documentation of the exams package, I also tried exams2pdf() after installing and calling library("tinytex").
Any help where to look at or what to do is highly appreciated. Thank you!
Minimal example:
install.packages("exams")
install.packages("tth")
library("exams")
set.seed(1090)
exams2html("confint3.Rnw")
set.seed(1090)
exams2pdf("confint3.Rnw")
It is hard to diagnose what exactly goes wrong with the information provided. In any case, when running pdfLaTeX either through utils::texi2dvi() (the default when the R package tinytex is not installed) or through tinytex::latexmk() (the default when the R package tinytex is installed) does not find the Sweave.sty file provided by the R base system. What is not clear to me which LaTeX engine is running in the background: MikTeX on Windows?
There are several strategies that could resolve this issue:
Tell your LaTeX installation about the texmf directory provided by the R base system so that it is found no matter where on your system you call pdfLaTeX.
Use a different LaTeX installation, e.g., by installing TinyTeX (the LaTeX distribution) through tinytex (the R package): tinytex::install_tinytex(). This might be particularly attractive if you are not actually a LaTeX user and just need it to compile PDF exams.
Avoid using the Sweave.sty file in a custom template file, say myplain.tex. A suggestion for such a file is included at the end of this post.
Further details are discussed in this thread: https://tex.stackexchange.com/questions/153193/latex-error-sweave-sty-not-found
As for your three questions:
As already explained above: exams2pdf() leverages either utils::texi2dvi() or tinytex::latexmk(). So these need to know about the LaTeX installation - but this seems to be the case. They just don't find the texmf provided by base R.
You should not have to do this but it is certainly an option that you can use. As a starting point, run exams_skeleton(markup = "latex", writer = "exams2pdf"). Among other things this creates a templates folder where you could put the myplain.tex template below.
As I said above, it's hard to answer that with the information provided. Hopefully, one of the clues provided here gets you a couple of steps forward.
Content of myplain.tex:
\documentclass[a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage{a4wide,graphicx,color,verbatim,url,fancyvrb,ae,amsmath,amssymb,booktabs,longtable,eurosym}
\newenvironment{question}{\item \textbf{Problem}\newline}{}
\newenvironment{solution}{\textbf{Solution}\newline}{}
\newenvironment{answerlist}{\renewcommand{\labelenumi}{(\alph{enumi})}\begin{enumerate}}{\end{enumerate}}
\providecommand{\tightlist}{\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setkeys{Gin}{keepaspectratio}
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
\newenvironment{Schunk}{}{}
\begin{document}
\begin{enumerate}
%% \exinput{exercises}
\end{enumerate}
\end{document}
When working on a reproducible research project, I would like to know the name of the Rnw file that is being run to use as an R variable.
This would be analogous to inserting an MSExcel filename in a footer
I am using RStudio Server on Ubuntu.
Thank you.
knitr now has a method for this: current_input()
https://github.com/yihui/knitr/issues/701
You can use the following two idioms to fetch the directory and name of the current file in knitr:
knitr:::.knitEnv$input.dir
knitr:::knit_concord$get("infile")
This is independent of RStudio, the knitr package is entirely responsible for this. These are private functions and variables that can change at any time without notice, so if you need something reliable, you might want to file an issue on GitHub.
I would like to use knitr to create presentations that embed R objects and code.
For IT reasons I am restricted to vim, so i have found the available Rstudio+knitr examples fairly unhelpful. The vim section of the knitr documents is also very skinny, and therefore unhelpful.
Is someone able to provide some guidance on how to compile a *.Rnw or *.Rmd file using knitr (or alternately point me to a decent online tutorial?) using some combination of vim, R, and the command line?
thanks in advance
Instead of going through Rstudio, you can use the functions in the knitr package directly. There are some options you can tweak, but to get started, all you have to do is call the knit() function on your .Rnw file:
library(knitr)
knit('my_input.Rnw')
If you're missing some of Rstudio's features, it's worth remembering that most of them are just making use of things that are already available in various R packages, so you can usually find a way to use them when you don't have Rstudio available.
Has anyone managed to get color syntax-highlighting working in the output of Sweave documents? I've been able to customize the output style by adding boxes, etc. in the Sweave.sty file as follows:
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontseries=bc,frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{frame=leftline}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontseries=bc}
And I can get the minted package to do syntax highlighting of verbatim-code blocks in my document like so:
\begin{minted}{perl}
use Foo::Bar;
...
\end{minted}
but I'm not sure how to combine the two for R input sections. I tried the following:
\DefineVerbatimEnvironment{Sinput}{minted}{r}
\DefineVerbatimEnvironment{Scode}{minted}{r}
Any suggestions?
Yes, look at some of the vignettes for Rcpp as for example (to pick just one) the Rcpp-FAQ pdf.
We use the highlight by Romain which itself can farm out to the hightlight binary by Andre Simon. It makes everything a little more involved---Makefiles for the vignettes etc pp---but we get colourful output from R and C/C++ code. Which makes it worth it.
I have a solution that has worked for me, I have not tried it on any other systems though so things may not work out of the box for you. I've posted some code at https://gist.github.com/797478 that is a set of modified Rweave driver functions that make use of minted blocks instead of verbatim blocks.
To use this driver just specify it when calling the Sweave function with the driver=RweaveLatexMinted() option.
Here's how I've ended up solving it, starting from #daroczig's suggestion.
\usepackage{minted}
\renewenvironment{Sinput}{\minted[frame=single]{r}}{\endminted}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{frame=leftline}
\DefineVerbatimEnvironment{Scode}{Verbatim}{}
While I was at it, I needed to get caching working because I'm using large data sets and one chunk was taking around 3 minutes to complete. So I wrote this zsh shell function to process an .Rnw file with caching:
function sweaveCache() {
Rscript -e "library(cacheSweave); setCacheDir(getwd()); Sweave('$1.Rnw', driver = cacheSweaveDriver)" &&
pdflatex --shell-escape $1.tex &&
open $1.pdf
}
Now I just do sweaveCache myFile and I get the result opened in Preview (on OS X).
This topic on tex.StackExchange might be interesting for you, as it suggest loading the SweaveListingUtils package in R for easy solution.
I've been struggling for a week now trying to figure out how to generate reports in R using either Sweave or Brew. I should say right at the beginning that I have never used Tex before but I understand the logic of it.
I have read this document several times. However, I cannot even get a simple example to parse. Brew successfully converts a simple markup file (just a title and some text) to a .tex file (no error). But it never ever converts tex to a pdf.
> library(tools)
> library(brew)
> brew("population.brew", "population.tex")
> texi2dvi("population.tex", pdf = TRUE)
The last step always fails with:
Error in texi2dvi("population.tex", pdf = TRUE) :
Running 'texi2dvi' on 'population.tex' failed.
What am I doing wrong?
The report I am trying to build is fairly simple. I have 157 different analysis to summarize. Each one has 4 plots, 1 table and a summary. I just want
output plot 1,2,3,4
output table
\pagebreak
...
that's it. Can anyone help me get further? I use osx, don't have Tex installed.
thanks
You cannot run this without texi2dvi or TeX installed.
An alternative may be html output -- the hwriter package is useful for that.
That said, if you want to produce pdf out, Sweave is the way to go. Frank Harrell's site has a lot of useful info but all this requires a bit of familiarity with LaTeX so you may need to install and learn that first.
If you are on OSX, might as well install the full tex live
http://mirror.ctan.org/systems/mac/mactex/MacTeX.mpkg.zip
It is a big download, but it will be nice to never have to install additional packages.
Another solution: the ascii package in conjonction to your favorite markup language (asciidoc, txt2tags, restructuredtext, org or textile).
http://eusebe.github.com/ascii/
It may be worthwhile spending a week or so just using LaTeX without R and going through a bunch of introductory LaTeX tutorials.
Thus, when you start producing Sweave or Brew documents and you get errors, you will be better able to identify whether the error is arising from LaTeX or Sweave / Brew.
A couple of Windows tools that make it easy to get started with LaTeX include MikTeX + TeXnicCenter or MikTeX + WinEdt.
Another solution is to try a solution of connecting R to microsoft.
It is much weaker then Sweave, but for basic reporting might be what you need.
You might want to go through the example sessions given here: Exporting R output to MS-Word with R2wd (an example session)
I've also been hearing a lot of good things about the knitr package. It seems to resemble Sweave a lot, but add some more to it. I would definitely take a look at it.