alexanderdank
commented
3 years ago When citing, I use the basic @citation format, not the latex commands
Closed alexanderdank closed 3 years ago
alexanderdank
commented
3 years ago When citing, I use the basic @citation format, not the latex commands
alexanderdank
commented
3 years ago I found out that if another chapter is included, the references from the previous chapter are also converted to bold text when knitting index.rmd, so it seems only the bibliography of the last chapter is recognised
alexanderdank
commented
3 years ago When including all references in one .bib file and specifying this file in each chapter at the bibliography section the error has gone. However, now when trying to print the references per chapter the entire reference list is displayed, instead of the chapter references
ulyngs
commented
3 years ago This might be because you are pointing to different .bib files in index.Rmd and in the YAML headers for the individual chapters.
I don't think I've documented this anywhere, but if there is a bibliography: some-file.bib line in the YAML header of your individual chapters, then that may override the bibliography line in index.Rmd.
First thing to try, then:
alexanderdank
commented
3 years ago Commenting out all the bibliographies and specifying the bibliography in index.rmd worked! The Entire reference list was caused by an incorrect set-up template.tex file
For anyone else with the same issue for separate libraries please find the template.tex setup for chapter bibliographies below:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% OXFORD THESIS TEMPLATE
% Use this template to produce a standard thesis that meets the Oxford University requirements for DPhil submission
%
% Originally by Keith A. Gillow (gillow@maths.ox.ac.uk), 1997
% Modified by Sam Evans (sam@samuelevansresearch.org), 2007
% Modified by John McManigle (john@oxfordechoes.com), 2015
% Modified by Ulrik Lyngs (ulrik.lyngs@cs.ox.ac.uk), 2018-, for use with R Markdown
%
% Ulrik Lyngs, 25 Nov 2018: Following John McManigle, broad permissions are granted to use, modify, and distribute this software
% as specified in the MIT License included in this distribution's LICENSE file.
%
% John commented this file extensively, so read through to see how to use the various options. Remember that in LaTeX,
% any line starting with a % is NOT executed. Several places below, you have a choice of which line to use
% out of multiple options (eg draft vs final, for PDF vs for binding, etc.) When you pick one, add a % to the beginning of
% the lines you don't want.
%%%%% PAGE LAYOUT
% The most common choices should be below. You can also do other things, like replacing "a4paper" with "letterpaper", etc.
% This one formats for two-sided binding (ie left and right pages have mirror margins; blank pages inserted where needed):
%\documentclass[a4paper,twoside]{templates/ociamthesis}
% This one formats for one-sided binding (ie left margin > right margin; no extra blank pages):
%\documentclass[a4paper]{ociamthesis}
% This one formats for PDF output (ie equal margins, no extra blank pages):
%\documentclass[a4paper,nobind]{templates/ociamthesis}
% As you can see from the uncommented line below, oxforddown template uses the a4paper size,
% and passes in the binding option from the YAML header in index.Rmd:
\documentclass[a4paper, $if(page-layout)$$page-layout$$endif$]{templates/ociamthesis}
%%%%% ADDING LATEX PACKAGES
% add hyperref package with options from YAML %
\usepackage[pdfpagelabels]{hyperref}
% change the default coloring of links to something sensible
\usepackage{xcolor}
$if(linkcolor-rgb)$
\definecolor{mylinkcolor}{RGB}{$linkcolor-rgb$}
$endif$
$if(urlcolor-rgb)$
\definecolor{myurlcolor}{RGB}{$urlcolor-rgb$}
$endif$
$if(citecolor-rgb)$
\definecolor{mycitecolor}{RGB}{$citecolor-rgb$}
$endif$
$if(colored-not-bordered-links)$
\hypersetup{
hidelinks,
colorlinks,
linkcolor=$if(linkcolor-rgb)$mylinkcolor$else$.$endif$,
urlcolor=$if(urlcolor-rgb)$myurlcolor$else$.$endif$,
citecolor=$if(citecolor-rgb)$mycitecolor$else$.$endif$
}
$else$
\hypersetup{
colorlinks=false,
linkbordercolor=$if(linkcolor-rgb)$mylinkcolor$else$.$endif$,
urlbordercolor=$if(urlcolor-rgb)$myurlcolor$else$.$endif$,
citebordercolor=$if(citecolor-rgb)$mycitecolor$else$.$endif$
}
$endif$
% add float package to allow manual control of figure positioning %
\usepackage{float}
% enable strikethrough
\usepackage[normalem]{ulem}
% use soul package for correction highlighting
\usepackage{color, soul}
\definecolor{correctioncolor}{HTML}{CCCCFF}
\sethlcolor{correctioncolor}
\newcommand{\ctext}[3][RGB]{%
\begingroup
\definecolor{hlcolor}{#1}{#2}\sethlcolor{hlcolor}%
\hl{#3}%
\endgroup
}
\soulregister\ref7
\soulregister\cite7
\soulregister\autocite7
\soulregister\textcite7
\soulregister\pageref7
%%%%% FIXING / ADDING THINGS THAT'S SPECIAL TO R MARKDOWN'S USE OF LATEX TEMPLATES
% pandoc puts lists in 'tightlist' command when no space between bullet points in Rmd file,
% so we add this command to the template
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
% UL 1 Dec 2018, fix to include code in shaded environments
$if(highlighting-macros)$
$highlighting-macros$
%UL set white space before and after code blocks
\renewenvironment{Shaded}
{
\vspace{$space-before-code-block$}%
\begin{snugshade}%
}{%
\end{snugshade}%
\vspace{$space-after-code-block$}%
}
$endif$
% User-included things with header_includes or in_header will appear here
% kableExtra packages will appear here if you use library(kableExtra)
$for(header-includes)$
$header-includes$
$endfor$
%UL set section header spacing
\usepackage{titlesec}
%
\titlespacing\subsubsection{0pt}{24pt plus 4pt minus 2pt}{0pt plus 2pt minus 2pt}
%UL set whitespace around verbatim environments
\usepackage{etoolbox}
\makeatletter
\preto{\@verbatim}{\topsep=0pt \partopsep=0pt }
\makeatother
%%%%%%% PAGE HEADERS AND FOOTERS %%%%%%%%%
\usepackage{fancyhdr}
\setlength{\headheight}{15pt}
\fancyhf{} % clear the header and footers
\pagestyle{fancy}
\renewcommand{\chaptermark}[1]{\markboth{\thechapter. #1}{\thechapter. #1}}
\renewcommand{\sectionmark}[1]{\markright{\thesection. #1}}
\renewcommand{\headrulewidth}{0pt}
$if(running-header)$
\fancy$running-header-foot-or-head$[$running-header-position-leftmark$]{\emph{\leftmark}}
\fancy$running-header-foot-or-head$[$running-header-position-rightmark$]{\emph{\rightmark}}
$endif$
% UL page number position
\fancy$ordinary-page-number-foot-or-head$[$ordinary-page-number-position$]{\emph{\thepage}} %regular pages
\fancypagestyle{plain}{\fancyhf{}\fancy$chapter-page-number-foot-or-head$[$chapter-page-number-position$]{\emph{\thepage}}} %chapter pages
% JEM fix header on cleared pages for openright
\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
\hbox{}
\fancy$ordinary-page-number-foot-or-head$[$ordinary-page-number-position$]{}
\newpage
\if@twocolumn\hbox{}\newpage
\fi
\fancy$running-header-foot-or-head$[$running-header-position-leftmark$]{\emph{\leftmark}}
\fancy$running-header-foot-or-head$[$running-header-position-rightmark$]{\emph{\rightmark}}
\fi\fi}
%%%%% SELECT YOUR DRAFT OPTIONS
% This adds a "DRAFT" footer to every normal page. (The first page of each chapter is not a "normal" page.)
$if(draft-mark)$
\fancy$draft-mark-foot-or-head$[$draft-mark-position$]{\emph{DRAFT Printed on \today}}
$endif$
% IP feb 2021: option to include line numbers in PDF
$if(includeline-num)$
\usepackage{lineno}
\linenumbers
$endif$
% This highlights (in blue) corrections marked with (for words) \mccorrect{blah} or (for whole
% paragraphs) \begin{mccorrection} . . . \end{mccorrection}. This can be useful for sending a PDF of
% your corrected thesis to your examiners for review. Turn it off, and the blue disappears.
$if(corrections)$
\correctionstrue
$endif$
%%%%% BIBLIOGRAPHY SETUP
% Note that your bibliography will require some tweaking depending on your department, preferred format, etc.
% If you've not used LaTeX before, I recommend reading a little about biblatex/biber and getting started with it.
% If you're already a LaTeX pro and are used to natbib or something, modify as necessary.
% Either way, you'll have to choose and configure an appropriate bibliography format...
$if(use-biblatex)$
\usepackage[backend=biber,
bibencoding=utf8,
refsection=chapter, % referencing by chapter
style=authoryear,
firstinits=true,
isbn=false,
doi=true,
url=false,
eprint=false,
related=false,
dashed=false,
clearlang=true,
maxcitenames=2,
mincitenames=1,
maxbibnames=10,
abbreviate=false,
minbibnames=3,
uniquelist=minyear,
sortcites=true,
date=year
]{biblatex}
\AtEveryBibitem{%
\clearlist{language}%
\clearfield{note}
}
\DeclareFieldFormat{titlecase}{\MakeTitleCase{#1}}
\newrobustcmd{\MakeTitleCase}[1]{%
\ifthenelse{\ifcurrentfield{booktitle}\OR\ifcurrentfield{booksubtitle}%
\OR\ifcurrentfield{maintitle}\OR\ifcurrentfield{mainsubtitle}%
\OR\ifcurrentfield{journaltitle}\OR\ifcurrentfield{journalsubtitle}%
\OR\ifcurrentfield{issuetitle}\OR\ifcurrentfield{issuesubtitle}%
\OR\ifentrytype{book}\OR\ifentrytype{mvbook}\OR\ifentrytype{bookinbook}%
\OR\ifentrytype{booklet}\OR\ifentrytype{suppbook}%
\OR\ifentrytype{collection}\OR\ifentrytype{mvcollection}%
\OR\ifentrytype{suppcollection}\OR\ifentrytype{manual}%
\OR\ifentrytype{periodical}\OR\ifentrytype{suppperiodical}%
\OR\ifentrytype{proceedings}\OR\ifentrytype{mvproceedings}%
\OR\ifentrytype{reference}\OR\ifentrytype{mvreference}%
\OR\ifentrytype{report}\OR\ifentrytype{thesis}}
{#1}
{\MakeSentenceCase{#1}}}
% \renewbibmacro{in:}{}
% suppress "in" for articles
%
\renewbibmacro{in:}{%
\ifentrytype{article}{}{\printtext{\bibstring{in}\intitlepunct}}}
%-- no "quotes" around titles of chapters/article titles
\DeclareFieldFormat[article, inbook, incollection, inproceedings, misc, thesis, unpublished]
{title}{#1}
%-- no punctuation after volume
\DeclareFieldFormat[article]
{volume}{{#1}}
%-- puts number/issue between brackets
\DeclareFieldFormat[article, inbook, incollection, inproceedings, misc, thesis, unpublished]
{number}{\mkbibparens{#1}}
%-- and then for articles directly the pages w/o any "pages" or "pp."
\DeclareFieldFormat[article]
{pages}{#1}
%-- for some types replace "pages" by "p."
\DeclareFieldFormat[inproceedings, incollection, inbook]
{pages}{p. #1}
%-- format 16(4):224--225 for articles
\renewbibmacro*{volume+number+eid}{
\printfield{volume}%
\printfield{number}%
\printunit{\addcolon}
}
$for(bibliography)$
\addbibresource{$bibliography$}
$endfor$
$endif$
$if(use-natbib)$
\usepackage{natbib}
\setcitestyle{$natbib-citation-style$}
\bibliographystyle{$natbib-bibliography-style$}
\addto\captionsenglish{%
\renewcommand{\bibname}{$bibliography-heading-in-pdf$}
}
$endif$
% This makes the bibliography left-aligned (not 'justified') and slightly smaller font.
\renewcommand*{\bibfont}{\raggedright\small}
% Uncomment this if you want equation numbers per section (2.3.12), instead of per chapter (2.18):
%\numberwithin{equation}{subsection}
%%%%% THESIS / TITLE PAGE INFORMATION
% Everybody needs to complete the following:
\title{$title$}
\author{$author$}
\college{$college$}
% Master's candidates who require the alternate title page (with candidate number and word count)
% must also un-comment and complete the following three lines:
$if(masters-submission)$
\masterssubmissiontrue
\candidateno{$candidate-number$}
\wordcount{$word-count$}
$endif$
% Uncomment the following line if your degree also includes exams (eg most masters):
%\renewcommand{\submittedtext}{Submitted in partial completion of the}
% Your full degree name. (But remember that DPhils aren't "in" anything. They're just DPhils.)
\degree{$degree$}
% Term and year of submission, or date if your board requires (eg most masters)
\degreedate{$degreedate$}
%%%%% YOUR OWN PERSONAL MACROS
% This is a good place to dump your own LaTeX macros as they come up.
% To make text superscripts shortcuts
\renewcommand{\th}{\textsuperscript{th}} % ex: I won 4\th place
\newcommand{\nd}{\textsuperscript{nd}}
\renewcommand{\st}{\textsuperscript{st}}
\newcommand{\rd}{\textsuperscript{rd}}
%%%%% THE ACTUAL DOCUMENT STARTS HERE
\begin{document}
%%%%% CHOOSE YOUR LINE SPACING HERE
% This is the official option. Use it for your submission copy and library copy:
\setlength{\textbaselineskip}{$linespacing$}
% This is closer spacing (about 1.5-spaced) that you might prefer for your personal copies:
%\setlength{\textbaselineskip}{18pt plus2pt minus1pt}
% You can set the spacing here for the roman-numbered pages (acknowledgements, table of contents, etc.)
\setlength{\frontmatterbaselineskip}{$frontmatter-linespacing$}
% UL: You can set the line and paragraph spacing here for the separate abstract page to be handed in to Examination schools
\setlength{\abstractseparatelineskip}{13pt plus1pt minus1pt}
\setlength{\abstractseparateparskip}{0pt plus 1pt}
% UL: You can set the general paragraph spacing here - I've set it to 2pt (was 0) so
% it's less claustrophobic
\setlength{\parskip}{2pt plus 1pt}
%
% Oxford University logo on title page
%
\def\crest{{\includegraphics[width=$university-logo-width$]{$university-logo$}}}
\renewcommand{\university}{$university$}
\renewcommand{\submittedtext}{$submitted-text$}
% Leave this line alone; it gets things started for the real document.
\setlength{\baselineskip}{\textbaselineskip}
%%%%% CHOOSE YOUR SECTION NUMBERING DEPTH HERE
% You have two choices. First, how far down are sections numbered? (Below that, they're named but
% don't get numbers.) Second, what level of section appears in the table of contents? These don't have
% to match: you can have numbered sections that don't show up in the ToC, or unnumbered sections that
% do. Throughout, 0 = chapter; 1 = section; 2 = subsection; 3 = subsubsection, 4 = paragraph...
% The level that gets a number:
\setcounter{secnumdepth}{$section-numbering-depth$}
% The level that shows up in the ToC:
\setcounter{tocdepth}{$toc-depth$}
%%%%% ABSTRACT SEPARATE
% This is used to create the separate, one-page abstract that you are required to hand into the Exam
% Schools. You can comment it out to generate a PDF for printing or whatnot.
$if(abstractseparate)$
\begin{abstractseparate}
$abstract$
\end{abstractseparate}
$endif$
% JEM: Pages are roman numbered from here, though page numbers are invisible until ToC. This is in
% keeping with most typesetting conventions.
\begin{romanpages}
% Title page is created here
$if(alternative-title-page)$
\input{$alternative-title-page$}
$else$
\maketitle
$endif$
%%%%% DEDICATION -- If you'd like one, un-comment the following.
$if(dedication)$
\begin{dedication}
$dedication$
\end{dedication}
$endif$
%%%%% ACKNOWLEDGEMENTS -- Nothing to do here except comment out if you don't want it.
$if(acknowledgements)$
\begin{acknowledgements}
$acknowledgements$
\end{acknowledgements}
$endif$
%%%%% ABSTRACT -- Nothing to do here except comment out if you don't want it.
\begin{abstract}
$abstract$
\end{abstract}
%%%%% MINI TABLES
% This lays the groundwork for per-chapter, mini tables of contents. Comment the following line
% (and remove \minitoc from the chapter files) if you don't want this. Un-comment either of the
% next two lines if you want a per-chapter list of figures or tables.
$if(mini-toc)$
\dominitoc % include a mini table of contents
$endif$
$if(mini-lof)$
\dominilof % include a mini list of figures
$endif$
$if(mini-lot)$
\dominilot % include a mini list of tables
$endif$
% This aligns the bottom of the text of each page. It generally makes things look better.
\flushbottom
% This is where the whole-document ToC appears:
\tableofcontents
$if(lof)$
\listoffigures
\mtcaddchapter
% \mtcaddchapter is needed when adding a non-chapter (but chapter-like) entity to avoid confusing minitoc
$endif$
% Uncomment to generate a list of tables:
$if(lot)$
\listoftables
\mtcaddchapter
$endif$
%%%%% LIST OF ABBREVIATIONS
% This example includes a list of abbreviations. Look at text/abbreviations.tex to see how that file is
% formatted. The template can handle any kind of list though, so this might be a good place for a
% glossary, etc.
$if(abbreviations)$
% First parameter can be changed eg to "Glossary" or something.
% Second parameter is the max length of bold terms.
\begin{mclistof}{$abbreviations-heading$}{$abbreviations-width$}
$abbreviations$
\end{mclistof}
$endif$
% The Roman pages, like the Roman Empire, must come to its inevitable close.
\end{romanpages}
%%%%% CHAPTERS
% Add or remove any chapters you'd like here, by file name (excluding '.tex'):
\flushbottom
% all your chapters and appendices will appear here
$body$
%%%%% REFERENCES
%$if(use-biblatex)$
%\setlength{\baselineskip}{0pt} % JEM: Single-space References
%{\renewcommand*\MakeUppercase[1]{#1}%
%\printbibliography[heading=bibintoc,title={\bibtitle}]}
%$endif$
%$if(use-natbib)$
%\bibliography{$bibliography$}
%$endif$
\end{document}In Addition I also added biblatexoptions: [refsegment=chapter] to index.rmd, although I am not sure this is required
First of all, great stuff on this package ;)
When knitting a separate document my references are correctly displayed in the text. However, when knitting the index.rmd the references are displayed as the reference-identifier in bold... Any clue on how this could be the case?