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Merge pull request #196 from FredHutch/latex-template-cleanup
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latex template cleanup
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@kelliemac
kelliemac authored Jul 23, 2024
2 parents b9c6275 + ab7d4eb commit 72087ad
Showing 1 changed file with 94 additions and 84 deletions.
178 changes: 94 additions & 84 deletions inst/rmarkdown/templates/visc_report/resources/template.tex
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% general document layout
\documentclass[11pt]{article}
%\usepackage{etex}
%\reserveinserts{28}
\usepackage{lastpage}
\usepackage[hmargin=2cm, top=2.7cm, bottom=3.5cm, footskip=0.5cm]{geometry}
\usepackage{url}
\usepackage[maxfloats=50]{morefloats}
\usepackage{parskip}
%\usepackage[citestyle=authoryear-comp,natbib=true]{biblatex}
\usepackage{pdflscape}
\usepackage[absolute]{textpos}
\usepackage{rotating} %for xtable sideways
\usepackage{verbatim}
\usepackage{fancyhdr} % Extensive control of page headers and footers
\usepackage[dvipsnames, table]{xcolor} % Driver-independent color extensions for LATEX and pdfLATEX
\usepackage{lscape} % Modifies the margins and rotates the page contents but not the page number. Useful, for example, with large multipage tables, as it is compatible with longtable
\usepackage{pdflscape} % adds PDF support to the landscape environment of package lscape
\usepackage{lastpage} % for referencing last page in footers as "page N of M"
\usepackage{setspace} % Provides support for setting the spacing between lines in a document
\usepackage{float} % Improves the interface for defining floating objects such as figures and tables
\usepackage[maxfloats=50]{morefloats} % Increase the number of simultaneous LATEX floats (default can only cope with 18)

% table formatting
\usepackage{multirow} % for creating tabular cells spanning multiple rows
\usepackage{makecell} % Tabular column heads and multilined cells
\usepackage{longtable}
\usepackage{multirow}
\usepackage{lipsum}
%\usepackage[acronym,nomain]{glossaries}
\usepackage{fancyhdr, graphicx, lastpage, ifthen, lscape}
\usepackage[dvipsnames, table]{xcolor}
\usepackage{soul}
\usepackage{booktabs}
\usepackage{setspace}
\usepackage{relsize}
\usepackage{tabularx}
\usepackage{makecell}
\usepackage{threeparttable}
\usepackage{threeparttablex}
\usepackage{hyperref}
\usepackage{float}
\usepackage{tabularx} % defines an environment tabularx, an extension of tabular which has an additional column designator, X, which creates a paragraph-like column whose width automatically expands so that the declared width of the environment is filled
\usepackage{rotating} % for xtable sideways
\usepackage{threeparttable} % provides a scheme for tables that have a structured (foot)note section, after the caption
\usepackage{threeparttablex} % provides the functionality of the threeparttable package to tables created using the longtable package

% being able to set emphasis for entire table row
\newcommand\setrow[1]{\gdef\rowmac{#1}#1\ignorespaces}
\newcommand\clearrow{\global\let\rowmac\relax}
\clearrow

% for links and cross-referencing
\usepackage{url} % for email addresses, hypertext links, directories/paths, etc.
\usepackage{hyperref} % for cross-referencing commands to produce hypertext links in the document
\hypersetup{
colorlinks = true, % color links instead of covering them w/red boxes
urlcolor = blue, % color for external hyperlinks
linkcolor = cyan, % color of internal links
citecolor = gray % color of citations
}

\bibliography{$bibliography$}
% other utilities
\usepackage{graphicx} % Enhanced support for graphics
\usepackage{ifthen} % Conditional commands such as \ifthenelse andn \whiledo
\usepackage{verbatim} % Reimplementation of and extensions to LATEX verbatim
\usepackage{parskip} % alleviate untidiness from changing \parskip and \parindent
\usepackage{lipsum} % Easy access to the Lorem Ipsum and other dummy texts
\usepackage{soul} % Hyphenation for letterspacing, underlining, and more
\usepackage{relsize} % Set the font size relative to the current font size

% Add unicode checkmark for DataPackageR support. The green checkmark
% that DataPackageR prints to the console during package_build() causes
% an error with latex. This changes the unicode checkmark to a latex one.
\DeclareUnicodeCharacter{2714}{\checkmark}

% page settings
\setlength{\footskip}{56pt}
\pagestyle{fancy}
\setlength{\parindent}{0pt}

% For knitr
\usepackage{lmodern}
Expand Down Expand Up @@ -106,20 +127,10 @@
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
% End For knitr

\renewcommand{\abstractname}{Overview}
% ------------------------------------------------------------------------------
% settings for bibliography/references section

% Add unicode checkmark for DataPackageR support. The green checkmark
% that DataPackageR prints to the console during package_build() causes
% an error with latex. This changes the unicode checkmark to a latex one.
\DeclareUnicodeCharacter{2714}{\checkmark}

% Configure hyperref formatting bookmarks and references
\hypersetup{
colorlinks = true, % color links instead of covering them w/red boxes
urlcolor = blue, % color for external hyperlinks
linkcolor = cyan, % color of internal links
citecolor = gray % color of citations
}
\bibliography{$bibliography$}

% pandoc requires the CSLReferences environment to be defined for bibliographies
% and a breaking change was introduced in pandoc version 3.1.7
Expand All @@ -142,7 +153,7 @@
\ifnum #2 > 0
\setlength{\parskip}{#2\baselineskip}
\fi
}%
}%
{}
\usepackage{calc}
\newcommand{\CSLBlock}[1]{#1\hfill\break}
Expand Down Expand Up @@ -190,7 +201,7 @@
$endif$


%this is to adjust header and footer in landscaped pages
% this is to adjust header and footer in landscaped pages
\fancypagestyle{lscape}{%
\fancyhf{} % clear all header and footer fields
\fancyhead[R]{\begin{footnotesize}
Expand All @@ -200,61 +211,53 @@
\begin{textblock}{1}(21,1.75){\color{gray}\rotatebox{90}{Page \thepage{}~of~\pageref{LastPage}}}\end{textblock}
\end{footnotesize} }
\fancyfoot[R]{\begin{footnotesize}
% \begin{textblock}{19.8}[-0.01,{\DynLength}](1.5,23.20){\color{gray}\rotatebox{90}{\Rver}}\end{textblock}
\begin{textblock}{19.8}(1.5,23.20){\color{gray}\rotatebox{90}{\Rver}}\end{textblock}
\end{footnotesize} }
\setlength{\TPHorizModule}{1cm}
\setlength{\TPVertModule}{1cm}
\renewcommand{\headrulewidth}{0.0pt}
\renewcommand{\footrulewidth}{0.0pt}}

%set header and footer for first page
\renewcommand{\headrulewidth}{0.8pt}
\renewcommand{\footrulewidth}{0.8pt}
\fancyhead[L]{\includegraphics[height=0.8cm]{$logo_path_fh$}}
$if(dropVISClogo)$
$else$
\fancyhead[C]{\includegraphics[height=0.8cm]{$logo_path_visc$}}
$endif$
\fancyhead[R]{\includegraphics[height=0.8cm]{$logo_path_scharp$}}
\fancyfoot[C]{Page \thepage{}~of~\pageref{LastPage}}
\setlength{\headheight}{27pt}

%decrease margins for landscape pages
% decrease margins for landscape pages
\newenvironment{changemargin}[2]{%
\begin{list}{}{%
\setlength{\topsep}{0pt}%
\setlength{\leftmargin}{#1}%
\setlength{\rightmargin}{#2}%
%\setlength{\listparindent}{\parindent}%
%\setlength{\itemindent}{\parindent}%
\setlength{\parsep}{\parskip}%
}%
\item[]}{\end{list}}

% being able to set emphasis for entire table row
\newcommand\setrow[1]{\gdef\rowmac{#1}#1\ignorespaces}
\newcommand\clearrow{\global\let\rowmac\relax}
\clearrow
% workaround to use landscape environment with pandoc
\newcommand{\blandscape}{\begin{landscape}}
\newcommand{\elandscape}{\end{landscape}}

% ------------------------------------------------------------------------------
% begin first page

% set header and footer
\renewcommand{\headrulewidth}{0.8pt}
\renewcommand{\footrulewidth}{0.8pt}
\fancyhead[L]{\includegraphics[height=0.8cm]{$logo_path_scharp$}}
$if(dropVISClogo)$
$else$
\fancyhead[C]{\includegraphics[height=0.8cm]{$logo_path_visc$}}
$endif$
\fancyhead[R]{\includegraphics[height=0.8cm]{$logo_path_fh$}}
\fancyfoot[C]{Page \thepage{}~of~\pageref{LastPage}}
\setlength{\headheight}{27pt}

%page settings
\setlength{\footskip}{56pt}
\pagestyle{fancy}
\setlength{\parindent}{0pt}
%\makeglossaries
\begin{document}
\sloppy

%get current date into insertdate
% ------------------------------------------------------------------------------
% To and From Section

% get current date into insertdate
\makeatletter
\let\insertdate\@date
\makeatother

% workaround to use landscape environment with pandoc
\newcommand{\blandscape}{\begin{landscape}}
\newcommand{\elandscape}{\end{landscape}}

%begin To and From Section
\makeatletter
\newcommand\tabfill[1]{%
\dimen@\linewidth
Expand All @@ -266,6 +269,7 @@
\makeatother

\vspace{0.1cm}

\begin{flushleft}
\begin{tabbing}
this line is to\= set up the tab stop \kill
Expand All @@ -285,20 +289,13 @@

\vspace{2cm}

%begin contents section
% ------------------------------------------------------------------------------

$if(toc)$
\tableofcontents
$endif$

%change color of header and footer text to gray
\makeatletter
\patchcmd{\@fancyhead}{\rlap}{\color{gray}\rlap}{}{}
\patchcmd{\headrule}{\hrule}{\color{gray}\hrule}{}{}
\patchcmd{\@fancyfoot}{\rlap}{\color{gray}\rlap}{}{}
\patchcmd{\footrule}{\hrule}{\color{gray}\hrule}{}{}
\makeatother


\renewcommand{\abstractname}{Overview}
$if(includesummary)$
\begin{abstract}
$summary$
Expand All @@ -313,6 +310,16 @@
\listoftables
$endif$

% ------------------------------------------------------------------------------
% document body

% updating header style
\makeatletter
\patchcmd{\@fancyhead}{\rlap}{\color{gray}\rlap}{}{}
\patchcmd{\headrule}{\hrule}{\color{gray}\hrule}{}{}
\patchcmd{\@fancyfoot}{\rlap}{\color{gray}\rlap}{}{}
\patchcmd{\footrule}{\hrule}{\color{gray}\hrule}{}{}
\makeatother
\newpage
\fancyhead[R]{\em $shorttitle$}
\fancyhead[C]{}
Expand All @@ -321,9 +328,12 @@
$else$
\fancyhead[L]{\em VISC Report}
$endif$
%\printglossaries

$body$
\label{LastPageOfBackMatter}~

% ------------------------------------------------------------------------------

\label{LastPageOfBackMatter}~ % for total page count

\end{document}

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