% preamble taken from the vignette in package strucchange
%
\documentclass[nojss,article]{jss}
\usepackage[T1]{fontenc}
%\usepackage{a4wide}
\usepackage[left=2cm,right=2cm,bottom=15mm]{geometry}
\usepackage{graphicx,color,alltt}
\usepackage[authoryear,round,longnamesfirst]{natbib}
\usepackage{hyperref}

\usepackage{amsmath, amsfonts}
% \usepackage{Sweave}
%\definecolor{Red}{rgb}{0.7,0,0}
%\definecolor{Blue}{rgb}{0,0,0.8}
%\definecolor{hellgrau}{rgb}{0.55,0.55,0.55}

%\newcommand{\E}{\mbox{$\mathsf{E}$}}
%\newcommand{\VAR}{\mbox{$\mathsf{VAR}$}}
%\newcommand{\COV}{\mbox{$\mathsf{COV}$}}
%\newcommand{\p}{\mbox{$\mathsf{P}$}}
%\newcommand{\email}[1]{\href{mailto:#1}{\normalfont\texttt{#1}}}
%\newenvironment{smallexample}{\begin{alltt}\small}{\end{alltt}}

%\setlength{\parskip}{0.5ex plus0.1ex minus0.1ex}
%\setlength{\parindent}{0em}
%
%\bibpunct{(}{)}{;}{a}{}{,}
%
%\newcommand{\ui}{\underline{i}}
%\newcommand{\oi}{\overline{\imath}}

%\RequirePackage{color}
%\definecolor{Red}{rgb}{0.5,0,0}
%\definecolor{Blue}{rgb}{0,0,0.5}
%\definecolor{hellgrau}{rgb}{0.55,0.55,0.55}
%
%\hypersetup{%
%hyperindex,%
%colorlinks,%
%linktocpage,%
%plainpages=false,%
%linkcolor=Blue,%
%citecolor=Blue,%
%urlcolor=Red,%
%pdfstartview=Fit,%
%pdfview={XYZ null null null}%
%}


% SweaveOpts{engine=R,eps=FALSE}
%\VignetteIndexEntry{Manipulate, import and export 'bibentryExtra' objects}
%\VignetteDepends{rbibutils}
%\VignetteKeyword{bibtex, bib, bibliographic references, R} % was: \VignetteKeywords
%\VignettePackage{rbibutils}


<<echo=FALSE>>=
library(rbibutils)
pd <- packageDescription("rbibutils")
@

% don't use latex commands in the title, may cause difficult to trace trouble.
\title{Manipulate, import and export "bibentryExtra" objects \\ (draft)}
\author{Georgi N. Boshnakov \\ University of Manchester }
\Plainauthor{Georgi N. Boshnakov}

\Address{
  Georgi N. Boshnakov\\
  School of Mathematics\\
  The University of Manchester\\
  Oxford Road, Manchester M13 9PL, UK\\
  URL: \url{http://www.maths.manchester.ac.uk/~gb/}
}

%\date{}
%\maketitle

 
\Abstract{

  % this paragraph is the same as the opening one below, except that t doesn't inlude the
  % citation \citep{baseR}
  Objects from class \code{"bibentryExtra"} can represent any type of bibliographic entries.
  There are functions for import, manipulation and export in different formats.  In
  comparison, class \code{"bibentry"} from base R package 'utils' has a different emphasis
  and supports only the default Bibtex types.
  
  
  This vignette is part of package \pkg{rbibutils}, version~\Sexpr{pd$Version}. %$
}

\Keywords{bibtex, bib, bibliographic references, R}
\Plainkeywords{bibtex, bib, bibliographic references, R}


\begin{document}

\section{Introduction}
\label{sec:introduction}

Objects from class \code{"bibentryExtra"} can represent any type of bibliographic entries.
There are functions for import, manipulation and export in different formats.  In comparison,
class \code{"bibentry"} from base R package 'utils'
\citep{baseR}
has a different emphasis and supports only the default Bibtex types.
 
Functions are available for import and export, as well as subsetting with index operators.
Export can be to plain text, bibtex, Latex, R code and Rd.  There is also a style,
"JSSextra", which adds a few types for exporting bibliography references to Latex.

Class \code{"bibentryExtra"} inherits from \code{"bibentry"} and is fully compatible with it
for biblography items that are handled by bibentry.

In this document we use \emph{bib file} of just \emph{bib} to refer to files or character
vectors containing bibliographic entries in Bibtex format, including Biblatex.


\section{Import to bibentryExtra}
\label{sec:import-bibentryextra}

The most common case is importing from a bib file, containing bibliographic entries (items).
<<>>=
bibdir <- system.file("bib", package = "rbibutils")
wuertzetal <- readBib(file.path(bibdir, "WuertzEtalGarch.bib"), direct = TRUE)
wuertzetal
print(wuertzetal, style = "bibtex")
@
There is a long field 'note' which we may not wish to print. We can use the assignment
version of the dollar operator, \code{$<-}, to remove it or replace it with another
value. Here we remove it:
<<>>=
wuertzetal$note <- NULL
wuertzetal
@ 
This modfied value is used velow.

There are several function for import.

There is also the function \code{bibentryExtra}, which creates objects directly in R,
similarly to \code{bibentry}.

The dollar operator extracts a field, for example
<<>>=
wuertzetal$year
@ 
If the object contains more than one bib entry the value is a list.
In this case the object contains only one bib entry, so the outer list is removed. This is
just as a matrix becomes a vector when subsetting leaves only one row.

Some fields may be \code{NULL} (absent), may have length larger than one, or have a class
other than \code{"character"}. Here we have three authors and they are contained in a single
object:
<<>>=
wuertzetal$author

class(wuertzetal$author)
@

The key used for citations is also considered a field:
<<>>=
wuertzetal$key
@ 
So is the bib type:
<<>>=
wuertzetal$bibtype
@ 
In this case the bib type is a non-standrd field for Bibtex, though it is for Biblatex.

It is important to note that the argument of the dollar operator is the name of a field, as
illustrated above. We might expect that  \code{"[["} is similar but this is not the case:

<<eval = FALSE>>=
wuertzetal[["author"]]
## Warning message:
## In `[[.bibentry`(wuertzetal, "author") : subscript out of bounds
@




<<>>=
wuertzetal[[1, "note"]]
@ 



This is because the argument of \code{"[["} is a bib entry key (a value, not the word
\emph{key}). It returns a \code{"bibentryExtra"} object:
<<>>=
<<eval = FALSE>>=
wuertzetal[["WuertzEtalGarch"]]
@ 

\section{Accessing bib items and their fields}
\label{sec:accessing-bib-items}

Currently there are \code{"bibentryExtra"} methods for \code{[}, \code{[[}, \code{[[<-}
(assignment with \code{[[}) and \code{\$<-} (assignment with \code{\$}). Also, the method for
\code{$} is inherited from that of class bibentry and there is no method for \code{[<-}
(assignment with \code{[}).


\section{Replacing bib items and fields }
\label{sec:replacing-bib-items}



% \newpage{}
\bibliography{REFERENCES}


\end{document}

%%% Local Variables:
%%% TeX-master: "rbibutils-woven"
%%% End:
