2

I have a document that looks exactly like I want but the bookmarks link to the wrong spot. This MWE is long because if I hacked it down too much I couldn't replicate the issue. Unfortunately, I couldn't isolate the issue either. In the following code, when I run PDFTexify, in the PDF, it links the Acknowledgement bookmark to the table of contents and the Abstract bookmark to the title page.

I had read (click here) that \cleardoublepage and \phantomsection could set things right (this works for the List of Figures/Tables pages), calling hyperref first (before bookmark), or ordering package calls correctly could help. These suggestions, as I understood and tried them, do not seem to fix the problem.

How can I...

  1. Link Acknowledgement bookmark to the correct page (not toc)
  2. Link Abstract bookmark to the correct page (not title page)

While keeping the layout/look of the actual document the same?

My Bib File (Seems that addbibresource{biblatex-examples.bib} no longer works)

@INCOLLECTION{Adams2002,
  author = {Peter Adams},
  title = {Technology in Publishing: {A} Century of Progress},
  booktitle = {Scholarly Publishing: {B}ooks, Journals, Publishers, and Libraries
    in the Twentieth Century},
  publisher = {Wiley},
  year = {2002},
  editor = {Abel, R. and Newlin, L. W.},
  address = {New York}
}

MWE

\documentclass[12pt]{report}

\usepackage[american]{babel}
\usepackage[T1]{fontenc}
\usepackage[style=apa, backend=biber]{biblatex}
\addbibresource{mybib.bib}
\DeclareLanguageMapping{american}{american-apa}

\usepackage{outlines}
\usepackage{enumitem}
\usepackage[autostyle]{csquotes}
\usepackage{url}

\usepackage{hyperref}
\hypersetup{
    colorlinks=true,
    linkcolor=blue,
    filecolor=magenta,
    urlcolor=blue,
    citecolor=blue,
}

\usepackage{booktabs}
\newcommand{\ra}[1]{\renewcommand{\arraystretch}{#1}}

\newcommand{\specialcell}[2][c]{%
  \begin{tabular}[#1]{@{}c@{}}#2\end{tabular}}

\urlstyle{same}
\usepackage{filecontents}

%% figures and table numbered continuosly
\usepackage{chngcntr}
\counterwithout{figure}{chapter}
\counterwithout{table}{chapter}

%% increase space between bib entries
\setlength\bibitemsep{2\itemsep}

%% change Bibliography name to REFERENCES
\renewcommand{\bibname}{REFERENCES}

\usepackage{setspace}
\usepackage{graphicx}
\usepackage{color,soul}

\addto\captionsamerican{
  \renewcommand{\contentsname}%
    {\large Table of Contents}%
}


\usepackage{etoolbox}
\makeatletter
\patchcmd{\l@section}
  {\hfil}
  {\leaders\hbox{\normalfont$\m@th\mkern \@dotsep mu\hbox{.}\mkern \@dotsep mu$}\hfill}
  {}{}
\makeatother



\usepackage{titlesec}
\makeatletter
\def\@makechapterhead#1{%
  \vspace*{10\p@}%
  {\parindent \z@ \centering \reset@font
        \par\nobreak
        \vspace*{2\p@}%
        {\large \bfseries \thechapter\quad #1\par\nobreak}
        \par\nobreak
        \vspace*{2\p@}%
    %\vskip 40\p@
    \vskip 100\p@
  }}
\def\@makeschapterhead#1{%
  \vspace*{10\p@}%
  {\parindent \z@ \centering \reset@font
        \par\nobreak
        \vspace*{2\p@}%
        {\large \bfseries #1\par\nobreak}
        \par\nobreak
        \vspace*{2\p@}%
    \vskip 100\p@
  }}
\makeatother



%% possessive citation
\newcommand\posscite[1]{\citeauthor{#1}'s (\citeyear{#1})}
\newcommand\poscite[1]{\citeauthor{#1}' (\citeyear{#1})}

\usepackage{bookmark}

%% All headers 12pt
\usepackage{sectsty,textcase}
\allsectionsfont{\large\MakeUppercase}
\chapterfont{\large\MakeUppercase}

%% refs to toc
%\usepackage[nottoc,numbib]{tocbibind}

\usepackage{titlesec}
\titleformat{\chapter}[display]
{\normalfont\large\bfseries}{\chaptertitlename\ \thechapter}{12pt}{\large\MakeUppercase}
\titlespacing*{\chapter}{0pt}{-50pt}{40pt}

%% appendices
\usepackage[title,titletoc]{appendix}

%% dot fill chapters
\usepackage{tocloft}

\renewcommand\cftchapdotsep{\cftdotsep}
\renewcommand\cftchapleader{\large\cftdotfill{\cftchapdotsep}}
\renewcommand\cftloftitlefont{\large\textbf}
\renewcommand\cftlottitlefont{\large\textbf}

%% Set margins to 1 inch
\usepackage[margin=1in]{geometry}
\setlength\cftbeforetoctitleskip{-1cm}  %toc
\setlength\cftbeforeloftitleskip{-1cm}  % list of figs
\setlength\cftbeforelottitleskip{-1cm}  % lsit of tables

\singlespace

\author{\vspace{0cm} \large by Me}
\title{\vspace{-5cm} \large The Title}

\setcounter{secnumdepth}{0}


\begin{document}

\maketitle
\pagenumbering{roman}
\thispagestyle{empty}

\newpage
\section*{}
\doublespacing
\vspace{14cm}
\begin{center}
Copyright by  \\
2014 \\
\end{center}

\newpage
\cleardoublepage
\phantomsection
\addcontentsline{toc}{section}{Acknowledgement}
%\section{Acknowledgment}

\newpage
\pdfbookmark[section]{\contentsname}{toc}
\tableofcontents

\newpage
\cleardoublepage
\phantomsection
\addcontentsline{toc}{section}{List of Tables}
\listoftables

\newpage
\cleardoublepage
\phantomsection
\addcontentsline{toc}{section}{List of Figures}
\listoffigures

\newpage

%https://tex.stackexchange.com/questions/30122/generate-table-of-contents-when-section-sections-without-numbering-has-been
\section{Abstract}

Some Info

\newpage
\pagenumbering{arabic}

\setcounter{secnumdepth}{2}

\part{Fox and Cat}

\chapter{Dog}

\section{Food}
\chapter{Run}

\part{Chicken and Hen}

\chapter{Introduction}

\part{Discussion}

\chapter{Discussion}

\clearpage

\section*{Tables}
\addtocounter{section}{3}

\begin{table}[!ht]
    \parbox{7.5cm}{\caption{Yepper}}
      \centering
\begin{singlespace}
\begin{tabular}{lrrrr}
\hline \\
%\multicolumn{5}{c}{\textbf{Average Student Engagement Level}} \\
\multicolumn{5}{c}{} \\
\multicolumn{1}{c}{} & \multicolumn{2}{c}{Special Ed.} & \multicolumn{2}{c}{Reg. Ed.} \\
\cmidrule(lr){2-3}
\cmidrule(l ){4-5}
Gender & Charter & Public & Charter & Public \\
\midrule
Male & 643 & 793 & 590 & 724 \\
Female & 735 & 928 & 863 & 662 \\
\end{tabular}
\end{singlespace}
\end{table}

\clearpage

\section*{Visuals}
hello

\begin{appendices}
\renewcommand{\appendixname}{APPENDIX}

\bookmarksetup{startatroot}
\chapter{Foo}
some text

\bookmarksetup{startatroot}
\chapter{Bar}
some more text
\end{appendices}

\addcontentsline{toc}{chapter}{REFERENCES}

\nocite{*}
\renewcommand{\bibname}{\vspace{1cm} REFERENCES}

\newpage
\singlespacing
\bookmarksetup{startatroot}
\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{REFERENCES}
\printbibliography

\end{document}

Link to output file
Link to PDF

1

I have changed your given MWE a little bit, for example I changes the order of package calls, and added some missing commands to correct your bookmarks.

Please compare the new MWE with your own. Then you will see were I had to change your code to get the result you wanted.

BTW: I changed all \newpage to \clearpage.

MWE:

\RequirePackage{filecontents}
\begin{filecontents*}{\jobname.bib}
@article{JoeDoe2012,
  Author  = {Joe Doe},
  Title   = {My article's title},
  Journal = {My journal's title},
  Editor  = {Ben Editor},
  URL     = {http://webpage.com},
}
@INCOLLECTION{Adams2002,
  author    = {Peter Adams},
  title     = {Technology in Publishing: {A} Century of Progress},
  booktitle = {Scholarly Publishing: {B}ooks, Journals, Publishers, and Libraries
    in the Twentieth Century},
  publisher = {Wiley},
  year      = {2002},
  editor    = {Abel, R. and Newlin, L. W.},
  address   = {New York},
}
@article{Agarwal2011,
  author   = {Agarwal, Gautam and Isacoff, Ehud},
  doi      = {10.1152/jn.00591.2010},
  issn     = {1522-1598},
  journal  = {Journal of neurophysiology},
  keywords = {Animals,Behavior, Animal,Behavior, Animal: physiology,Calcium,Calcium: metabolism,Drosophila,Drosophila: physiology,Electric Stimulation,Female,Male,Odors,Olfactory Pathways,Olfactory Pathways: physiology,Sex Attractants,Sex Attractants: physiology},
  month    = apr,
  number   = {4},
  pages    = {1711--21},
  pmid     = {21289134},
  title    = {{Specializations of a pheromonal glomerulus in the Drosophila olfactory system.}},
  url      = {http://jn.physiology.org/cgi/content/abstract/105/4/1711},
  volume   = {105},
  year     = {2011},
}
\end{filecontents*}


\documentclass[12pt]{report}

\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage[american]{babel}

\usepackage[style=apa, backend=biber]{biblatex}
\addbibresource{\jobname.bib}
\DeclareLanguageMapping{american}{american-apa}

\usepackage{outlines}
\usepackage{enumitem}
\usepackage[autostyle]{csquotes}

\usepackage{booktabs}
\newcommand{\ra}[1]{\renewcommand{\arraystretch}{#1}}

\newcommand{\specialcell}[2][c]{%
  \begin{tabular}[#1]{@{}c@{}}#2\end{tabular}}


%% figures and table numbered continuosly
\usepackage{chngcntr}
\counterwithout{figure}{chapter}
\counterwithout{table}{chapter}

%% increase space between bib entries
\setlength\bibitemsep{2\itemsep}

%% change Bibliography name to REFERENCES
\renewcommand{\bibname}{REFERENCES}

\usepackage{setspace}
\usepackage{graphicx}
\usepackage{color,soul}

\addto\captionsamerican{
  \renewcommand{\contentsname}%
    {\large Table of Contents}%
}

\usepackage{etoolbox}
\makeatletter
\patchcmd{\l@section}
  {\hfil}
  {\leaders\hbox{\normalfont$\m@th\mkern \@dotsep mu\hbox{.}\mkern \@dotsep mu$}\hfill}
  {}{}
\makeatother

\usepackage{titlesec}
\makeatletter
\def\@makechapterhead#1{%
  \vspace*{10\p@}%
  {\parindent \z@ \centering \reset@font
        \par\nobreak
        \vspace*{2\p@}%
        {\large \bfseries \thechapter\quad #1\par\nobreak}
        \par\nobreak
        \vspace*{2\p@}%
    %\vskip 40\p@
    \vskip 100\p@
  }}
\def\@makeschapterhead#1{%
  \vspace*{10\p@}%
  {\parindent \z@ \centering \reset@font
        \par\nobreak
        \vspace*{2\p@}%
        {\large \bfseries #1\par\nobreak}
        \par\nobreak
        \vspace*{2\p@}%
    \vskip 100\p@
  }}
\makeatother

%% possessive citation
\newcommand\posscite[1]{\citeauthor{#1}'s (\citeyear{#1})}
\newcommand\poscite[1]{\citeauthor{#1}' (\citeyear{#1})}

%% All headers 12pt
\usepackage{sectsty,textcase}
\allsectionsfont{\large\MakeUppercase}
\chapterfont{\large\MakeUppercase}

\usepackage{titlesec}
\titleformat{\chapter}[display]
{\normalfont\large\bfseries}{\chaptertitlename\ \thechapter}{12pt}{\large\MakeUppercase}
\titlespacing*{\chapter}{0pt}{-50pt}{40pt}

%% appendices
\usepackage[title,titletoc]{appendix}

%% dot fill chapters
\usepackage{tocloft}

\renewcommand\cftchapdotsep{\cftdotsep}
\renewcommand\cftchapleader{\large\cftdotfill{\cftchapdotsep}}
\renewcommand\cftloftitlefont{\large\textbf}
\renewcommand\cftlottitlefont{\large\textbf}

%% Set margins to 1 inch
\usepackage[margin=1in]{geometry}
\setlength\cftbeforetoctitleskip{-1cm}  %toc
\setlength\cftbeforeloftitleskip{-1cm}  % list of figs
\setlength\cftbeforelottitleskip{-1cm}  % lsit of tables

\singlespace

\author{\vspace{0cm} \large by Me}
\title{\vspace{-5cm} \large The Title}

\usepackage{url}
\urlstyle{same}

\usepackage{hyperref}
\hypersetup{
    colorlinks=true,
    linkcolor=blue,
    filecolor=magenta,
    urlcolor=blue,
    citecolor=blue,
}
\usepackage{bookmark}

\begin{document}

\pagenumbering{roman}    % starts numbering with: i
%\thispagestyle{empty}
\maketitle


\clearpage
\section*{~}
\doublespacing
\vspace{14cm}
\begin{center}
Copyright by  \\
2014 \\
\end{center}

\cleardoublepage
\phantomsection
\addcontentsline{toc}{section}{Acknowledgement}
\section*{Acknowledgment}

\clearpage
\pdfbookmark[section]{\contentsname}{toc}
\tableofcontents

\cleardoublepage
\phantomsection
\addcontentsline{toc}{section}{List of Tables}
\listoftables

\cleardoublepage
\phantomsection
\addcontentsline{toc}{section}{List of Figures}
\listoffigures


%http://tex.stackexchange.com/questions/30122/generate-table-of-contents-when-section-sections-without-numbering-has-been
\clearpage
\phantomsection
\addcontentsline{toc}{section}{Abstract}
\section*{Abstract}

Some Info

\clearpage
\pagenumbering{arabic}

\part{Fox and Cat}

\chapter{Dog}

\section{Food}
\chapter{Run}

\part{Chicken and Hen}

\chapter{Introduction}

\part{Discussion}

\chapter{Discussion}

\clearpage
\section*{Tables}
\addtocounter{section}{3}

\begin{table}[!ht]
    \parbox{7.5cm}{\caption{Yepper}}
      \centering
\begin{singlespace}
\begin{tabular}{lrrrr}
\hline \\
\multicolumn{5}{c}{} \\ 
\multicolumn{1}{c}{} & \multicolumn{2}{c}{Special Ed.} & \multicolumn{2}{c}{Reg. Ed.} \\
\cmidrule(lr){2-3}
\cmidrule(l ){4-5}
Gender & Charter & Public & Charter & Public \\
\midrule
Male   & 643     & 793    & 590     & 724 \\
Female & 735     & 928    & 863     & 662 \\
\end{tabular}
\end{singlespace}
\end{table}

\clearpage

\section*{Visuals}
hello

\begin{appendices}
\renewcommand{\appendixname}{APPENDIX}

\bookmarksetup{startatroot}
\chapter{Foo}
some text

\bookmarksetup{startatroot}
\chapter{Bar}
some more text
\end{appendices}

\nocite{*}
\renewcommand{\bibname}{\vspace{1cm} REFERENCES}

\cleardoublepage
\singlespacing
\bookmarksetup{startatroot}
\phantomsection
\addcontentsline{toc}{chapter}{REFERENCES}
\printbibliography

\end{document}
  • Perfect. Thank you for your response. I think I get it now. – Tyler Rinker Sep 28 '14 at 13:47

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