For lectures, I am using knitr to produce LaTeX beamer slides as a PDF. For a given lecture, I want to produce also (a) 1-up handout (using the handout option, and (b) the same handout formatted 4-up.
I find I have to run knitr 3 times to do this as shown below. Is there a way to simplify this work flow?
A lecture stub:
\documentclass[10pt,table]{beamer}
\input{inputs/beamer-setup}
\input{inputs/defs}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
...
\end{document}
And I run knitr as
knit2pdf("Lecture1.Rnw")
To get the 1-up handout (which suppresses the separate pages when you use transitions), I edit the first line to:
\documentclass[10pt,table,handout]{beamer}
and run
knit2pdf("Lecture1.Rnw" output="Lecture1-1up.tex")
Finally, to get the 2 x 2 version, I use the LaTeX pgfpages package,
\documentclass[10pt,table,handout]{beamer}
\input{inputs/beamer-setup}
\input{inputs/defs}
\usepackage{pgfpages}
\pgfpagesuselayout{4 on 1}[letterpaper,landscape]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
And run:
knit2pdf("Lecture1.Rnw" output="Lecture1-4up.tex")
(I found that with beamer, I could not simply print the PDF 4-up using Adobe Acrobat -- it generated a corrupt PDF file. I was forced to use pgfpages)
Then, of course I have to revert my .Rnw file to the original if I need re-do the slides. Very tedious. There must be a better way.
I have foo.Rnw file which uses the extrafont package for generating figures with text elements that use non-standard font families. After knitr calls pdflatex on my document, I want to run extrafont::embed_fonts on the resulting foo.pdf file.
I can do this manually, but is there a way to do this from within knitr? (e.g., some knitr package option I can set to automatically call extrafont::embed_fonts after it knits my file and runs it through pdflatex)
As explained in this answer, it is possible to modify the behavior of the "Compile PDF" button in RStudio by setting the YAML option knit. This allows to run arbitrary code when hitting the "Knit" button. Note that the code must be formatted as a one-liner and you need to use single quotes for character data (double quotes won't work).
I don't know the extrafont package, so here an example that crops the generated PDF. Calling extrafont::embed_fonts should work analogously:
---
knit: (function(inputFile, encoding) { rmarkdown::render(input = inputFile, encoding = encoding); knitr::plot_crop(paste0(basename(tools::file_path_sans_ext(inputFile)), '.pdf')) } )
output: pdf_document
---
```{r}
print("Hello world!")
```
It's actually pretty simple; the most complicated part is composing the output file name: (paste0(basename(tools::file_path_sans_ext(inputFile)), '.pdf') (see here).
I can't seem to hack my way through all the possibilities and have a full bibliography inserted in the PDF output of RStudio, knitr, an .Rnw script, and the "Compile PDF" button. The desired text in the PDF would be the details of the cited works.
Here is a Lilliputian bibtex file, called jabrefbibtest.bib, saved in the working directory.
#Book{GreentargetEngagement2012,
Title = {"2012 - In - House Counsel New Media Engagement Survey"},
Author = {"Inside Counsel "},
Publisher = {"Greentarget"},
Year = {"2012"},
Pages = {"20"},
Plots = {"9"},
Tables = {"0"},
Url = {"http://www.greentarget.com/wp-content/uploads/2012/01/2012GTZGICSurveyReportFinal-WebsiteVersion.pdf"}
}
#Book{CitiprivateBank,
Title = {"Intellectual Leadership with Law Watch"},
Author = {""},
Publisher = {""},
Year = {"2008"},
Pages = {"2"},
Plots = {"1"},
Tables = {"4"},
Url = {"http://www.citigroup.com/privatebank/lawassociates/pdfs/lawwatch/slipsheet.pdf"}
}
The .Rnw script, stripped down, is
\documentclass[11pt]{article}
\usepackage[backend=bibtex]{biblatex}
% \addbibresource{} # not sure if this is needed
\begin{document}
<<bibbackground, echo=FALSE, include=FALSE>>=
setwd("~/R/knitr docs/")
Sys.setenv(TEXINPUTS=getwd(),
BIBINPUTS=getwd(),
BSTINPUTS=getwd())
#
\bibliographystyle{plain}
\bibliography{jabrefbibtest}
Here is one citation \cite{GreentargetEngagement2012} and here is a second \cite{CitiprivateBank}.
Now do full References show below?
\printbibliography
\end{document}
The log:
! Package biblatex Error: '\bibliographystyle' invalid.
See the biblatex package documentation for explanation.
Type H <return> for immediate help.
...
l.59 \bibliographystyle{plain}
Use the package option 'style' instead.
I'm ignoring this command.
! LaTeX Error: Can be used only in preamble.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.60 \bibliography
{jabrefbibtest}
Your command was ignored.
Type I <command> <return> to replace it with another command,
or <return> to continue without it.
LaTeX Warning: Citation 'GreentargetEngagement2012' on page 1 undefined on inpu
t line 62.
[more omitted]
Along with The Latex Companion, Dynamic Documents with R and knitr, by Yihui Xie, two LaTeX primers and the 262-page manual for biblatex I have struggled through the complicated advice of these sites. Fruitlessly.
https://tex.stackexchange.com/questions/71565/knitr-and-biblatex
https://tex.stackexchange.com/questions/63852/question-mark-instead-of-citation-number
http://texblog.org/2013/08/20/rknitr-automatic-bibliography-generation-with-biblatex-in-rstudio/
http://www.inside-r.org/packages/cran/knitcitations/docs/bibliography
EDIT after COMMENTS
All the PDF file has is this:
References
Here is one citation [?] and here is a second [?].
Now do full References show below?
As the error messages told you:
Don't use \bibliographystyle{plain} (this does not work for biblatex); use the style option in \usepackage[]{biblatex} instead;
\bibliography{jabrefbibtest} must be put in the preamble instead of the body.
After you correct these issues, it should work:
\documentclass[11pt]{article}
\usepackage[backend=bibtex]{biblatex}
\bibliography{jabrefbibtest}
% or use \addbibresource{jabrefbibtest.bib}
\begin{document}
Here is one citation \cite{ABFWomenFirstChairs2015} and
here is a second \cite{ACCGCSkills2013}.
Now do full References show below?
\printbibliography
\end{document}
BTW, RStudio probably does not support the default backend biber of biblatex, so the backend=bibtex option was used.
I use exactly this setup below to get (note I'm not a fan of changing wd in knitr/rmarkdown and removed this; also your keys in the Rnw didn't match the key in the mwe):
\documentclass[11pt]{article}
\usepackage[american]{babel}
\usepackage[style=apa,backend=biber,bibencoding=latin1]{biblatex}
\DeclareLanguageMapping{american}{american-apa}
\addbibresource{jabrefbibtest.bib}
\begin{document}
<<bibbackground, echo=FALSE, include=FALSE>>=
#setwd("~/R/knitr docs/")
Sys.setenv(TEXINPUTS=getwd(),
BIBINPUTS=getwd(),
BSTINPUTS=getwd())
#
%\bibliographystyle{plain}
Here is one citation \cite{GreentargetEngagement2012} and here is a second \cite{CitiprivateBank}.
Now do full References show below?
\printbibliography
\end{document}
Also after the Rnw knits I have to run the tex file though a LaTeX compiler to render the references the first time.
I always just place \bibliography{jabrefbibtest} at the end of the script where I want the references to occur.
To include all references from your .bib file in your bibliography, i.e. even ones that you didn't end up citing, include the line
\nocite{*} right before the line \printbibliography
I'm converting a markdown document to a PDF document using Pandoc from within R. I'm trying to centre the title.
So far, I've tried:
<center># This is my title</center>
and
-># This is my title<-
but neither have worked. Is there a way to centre the title when converting from markdown to PDF using Pandoc?
pandoc has its own extended version of markdown. This includes a title block.
If the file begins with a title block
% my title
% Me; Someone else
% May 2013
This will be parsed into LaTeX and the resulting pdf as
\title{my title}
\author{Me \and Someone Else}
\date{May 2013}
and then `
\maketitle
called within the document.
This will create the standard centred title.
If you want to change how the title etc is formatted you could use the titling package.
If you want to change how the section headers are formatted, you could use the titlesec package.
To automagically have pandoc implement these you could define your own template. A simpler option is to have a file with your desired latex preamble to be included in the header. and then use the appropriate arguments when calling pandoc (eg -H FILE or --include-in-header=FILE)
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") ...