With knitr and .Rnw for LaTeX, how do you print th

Question

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?

Answer 1

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

Answer 2

I always just place \bibliography{jabrefbibtest} at the end of the script where I want the references to occur.

Answer 3

As the error messages told you:

1. Don't use \bibliographystyle{plain} (this does not work for biblatex); use the style option in \usepackage[]{biblatex} instead;
2. \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.

Answer 4

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.