diff --git a/_extensions/aagi/PDF/AAGI_template.tex b/_extensions/aagi/PDF/AAGI_template.tex
new file mode 100644
index 0000000..503a919
--- /dev/null
+++ b/_extensions/aagi/PDF/AAGI_template.tex
@@ -0,0 +1,145 @@
+\documentclass{scrartcl}
+
+%% Configuration %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\usepackage{lmodern}
+\usepackage{microtype}
+\usepackage[title]{appendix}
+\usepackage{parskip}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{ragged2e}
+
+% AAGI colours
+\usepackage[dvipsnames]{xcolor}
+\usepackage{graphicx}
+\definecolor{aagiteal}{HTML}{00808b}
+\definecolor{aagigreen}{HTML}{b6d438}
+\definecolor{aagiblack}{HTML}{414042}
+\definecolor{aagiblue}{HTML}{648FD2}
+\definecolor{pagenum}{HTML}{7F7F7F}
+
+% Colour tables + long tables
+\usepackage{colortbl}
+
+\usepackage{longtable}
+\setlength{\LTcapwidth}{\textwidth}
+
+% Figures configuration
+\usepackage{caption}
+\captionsetup{font={sf}}
+\setlength{\fboxsep}{0pt}
+
+% URL styling
+\usepackage{url}
+\let\harvardurl\url
+
+% Tikzpictures/PGFplots (if desired)
+%\usepackage{tikz}
+%\usepackage{pgfplots}
+%\pgfplotsset{compat=newest}
+
+% Listings for code (if desired)
+%\usepackage{inconsolata}
+%\usepackage{listings}
+%\lstset{%
+% basicstyle=\footnotesize\ttfamily,
+% keywordstyle=\footnotesize\ttfamily,
+% language=R}
+
+% A fancy coloured box for notes/warnings
+\usepackage[most]{tcolorbox}
+\newtcolorbox{note}[1][]{%
+ colback=aagiteal!7, colframe=aagiteal!7, notitle, sharp corners,
+ borderline west={2pt}{0pt}{aagiblue}, borderline east={2pt}{0pt}{aagiteal},
+ enhanced, breakable}
+
+% Hyperref for links/cross-referencing
+\def\sectionautorefname{Section}
+\def\subsectionautorefname{Subsection}
+\def\appendixautorefname{Appendix}
+\def\figureautorefname{Figure}
+\def\tableautorefname{Table}
+
+% Formating the headings
+\setkomafont{section}{\color{aagiteal}\huge\bfseries}
+\setkomafont{subsection}{\large\bfseries}
+\setkomafont{subsubsection}{\normalfont}
+\setkomafont{pageheadfoot}{\normalfont}
+\setkomafont{title}{\color{aagiteal}\RaggedRight\huge\bfseries}
+\addtokomafont{disposition}{\rmfamily}
+
+% Header and footer
+\usepackage[automark]{scrlayer-scrpage}
+\clearpairofpagestyles
+\ohead{\includegraphics[width=1.8cm, height=0.94cm]{AAGI_logo.pdf}}
+\cfoot{\includegraphics{Partners.pdf}\\
+ \begin{FlushRight}
+ \textbf{\pagemark} \textbf{|} \textcolor{pagenum}{Page}
+ \end{FlushRight}
+}
+
+\newpairofpagestyles[scrheadings]{Title_page}{
+ \clearpairofpagestyles
+ \cfoot{\includegraphics[width=\linewidth]{Partners.pdf}}
+}
+
+%Set the font
+\usepackage{fontspec}
+\setmainfont{Proxima Nova}
+
+
+%TOC entry formating
+\RedeclareSectionCommand[toclinefill=\TOCLineLeaderFill]{section}
+\setcounter{secnumdepth}{0}
+
+$pandoc.tex()$
+
+\begin{document}
+
+ \begin{titlepage}
+
+ \thispagestyle{Title_page}
+
+ \vspace*{-2cm}
+
+ \begin{center}
+ \includegraphics[height=3cm]{AAGI_logo.pdf}
+ \end{center}
+
+ \vfill
+
+ \rule{\textwidth}{0.5pt}
+
+ \begin{FlushRight}
+
+ \huge
+ \textcolor{aagiteal}{\textbf{$title$}}\\[6mm]
+
+ \large
+ {\textbf{$subtitle$}}\\[5mm]
+ \vspace{2mm}
+
+ \normalsize
+ \textbf{$for(author)$
+ $author$
+ $sep$ \\[8mm]
+ $endfor$}\\[8mm]
+
+ \today
+ \end{FlushRight}
+
+ \rule{\textwidth}{0.5pt}
+
+ \vfill
+
+ \end{titlepage}
+
+ \newpage
+
+ \tableofcontents
+
+ \newpage
+
+ $body$
+
+\end{document}
\ No newline at end of file
diff --git a/_extensions/aagi/Revealjs/_extension.yml b/_extensions/aagi/Revealjs/_extension.yml
new file mode 100644
index 0000000..5f10170
--- /dev/null
+++ b/_extensions/aagi/Revealjs/_extension.yml
@@ -0,0 +1,17 @@
+title: AAGIQuarto
+author: Adam H. Sparks
+version: 1.0.0
+quarto-required: ">=1.4.0"
+contributes:
+ formats:
+ revealjs:
+ theme: [default, aagi.scss]
+ date-format: long
+ slide-number: true
+ footer: " "
+ logo: aagi-logo.svg
+ title-slide-attributes:
+ data-background-image: title-slide-main.png
+ data-background-size: 1050px auto
+ data-background-position: 50% 85%
+ highlight-style: breeze
diff --git a/_extensions/aagi/aagi-logo.svg b/_extensions/aagi/Revealjs/aagi-logo.svg
old mode 100755
new mode 100644
similarity index 100%
rename from _extensions/aagi/aagi-logo.svg
rename to _extensions/aagi/Revealjs/aagi-logo.svg
diff --git a/_extensions/aagi/aagi.scss b/_extensions/aagi/Revealjs/aagi.scss
similarity index 100%
rename from _extensions/aagi/aagi.scss
rename to _extensions/aagi/Revealjs/aagi.scss
diff --git a/_extensions/aagi/title-slide-main.png b/_extensions/aagi/Revealjs/title-slide-main.png
similarity index 100%
rename from _extensions/aagi/title-slide-main.png
rename to _extensions/aagi/Revealjs/title-slide-main.png
diff --git a/_extensions/aagi/Word/AAGI_Word_Style_Template.docx b/_extensions/aagi/Word/AAGI_Word_Style_Template.docx
new file mode 100644
index 0000000..761b89e
Binary files /dev/null and b/_extensions/aagi/Word/AAGI_Word_Style_Template.docx differ
diff --git a/_extensions/aagi/_extension.yml b/_extensions/aagi/_extension.yml
index 5f10170..a414500 100644
--- a/_extensions/aagi/_extension.yml
+++ b/_extensions/aagi/_extension.yml
@@ -1,17 +1,34 @@
title: AAGIQuarto
-author: Adam H. Sparks
+author: Adam H. Sparks and Vinh Thiem Ma
version: 1.0.0
quarto-required: ">=1.4.0"
contributes:
formats:
revealjs:
- theme: [default, aagi.scss]
+ theme: [default, Revealjs/aagi.scss]
date-format: long
slide-number: true
footer: " "
- logo: aagi-logo.svg
- title-slide-attributes:
- data-background-image: title-slide-main.png
+ logo: Revealjs/aagi-logo.svg
+ title-slide-attributes:
+ data-background-image: Revealjs/title-slide-main.png
data-background-size: 1050px auto
data-background-position: 50% 85%
highlight-style: breeze
+ pdf:
+ template: pdf/AAGI_template.tex
+ format-resources:
+ - assets/AAGI_logo.pdf
+ - assets/Partners.pdf
+ pdf-enginge: xelatex
+ fig-width: 7
+ fig-height: 7
+ fontsize: 11pt
+ geometry:
+ - top=2.54cm
+ - bottom=3cm
+ - right=1.91cm
+ - includefoot
+ linkcolor: aagiblue
+ docx:
+ reference-doc: Word/AAGI_Word_Style_Template.docx
diff --git a/_extensions/aagi/assets/AAGI.sty b/_extensions/aagi/assets/AAGI.sty
new file mode 100644
index 0000000..5954a02
--- /dev/null
+++ b/_extensions/aagi/assets/AAGI.sty
@@ -0,0 +1,218 @@
+\RequirePackage{ifpdf}
+\newcommand{\pdfgraphics}{\ifpdf\DeclareGraphicsExtensions{.pdf,.jpg,.png}\else\fi}
+
+\newcommand{\PDFPackage}[1]{
+ \ifpdf
+ \RequirePackage[pdftex]{#1}
+ \else
+ \RequirePackage{#1}
+ \fi
+}
+
+%% knitr inclusion
+
+\RequirePackage{ifthen}
+\newboolean{AAGI@knit}
+\setboolean{AAGI@knit}{true}
+
+\DeclareOption{knit}{\setboolean{AAGI@knit}{false}}
+\ProcessOptions
+
+\ifthenelse{\boolean{AAGI@knit}}{
+ \PDFPackage{graphicx}
+ \PDFPackage{color}
+}{}
+
+\usepackage{graphicx}
+\usepackage{color}
+
+% \def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+% \def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+% \makeatother
+% % Scale images if necessary, so that they will not overflow the page
+% % margins by default, and it is still possible to overwrite the defaults
+% % using explicit options in \includegraphics[width, height, ...]{}
+% \setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+
+\usepackage{natbib}
+\usepackage{fancyhdr}
+\usepackage{fancyvrb}
+\usepackage{amssymb, amsmath}
+\usepackage{longtable}
+\usepackage{rotating}
+\usepackage{titlesec}
+\usepackage{tocloft}
+\usepackage{parskip}
+\usepackage{setspace}
+
+%% hyperlnk highlighting and geometry
+
+\PDFPackage{hyperref}
+\hypersetup{colorlinks,linkcolor=blue,citecolor=blue,urlcolor=blue}
+\usepackage[paper=a4paper,top=35mm,left=25mm,right=25mm,bottom=30mm]{geometry}
+\setlength{\parindent}{0cm}
+\setlength{\headheight}{15pt}
+\setlength{\parskip}{3ex}
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+
+%% font declarations and definitions
+
+\let\proglang=\textsf
+\let\pkg=\textbf
+\DeclareOldFontCommand{\sbf}{\normalfont\bfseries\sffamily}{\mathsf}
+\DeclareOldFontCommand{\tbf}{\normalfont\bfseries\ttfamily}{\mathtt}
+\newcommand{\HRule}{\hspace{-25mm}\rule{160mm}{0.5mm}}
+\newcommand\Trule{\rule{0pt}{2.6ex}}
+\newcommand\Brule{\rule[-2.5ex]{0pt}{0pt}}
+\renewcommand{\bibname}{References}
+
+\def\mbf#1{{% \mbf{X} makes X a math bold letter
+\mathchoice% selects with respect to current style
+{\hbox{\boldmath$\displaystyle{#1}$}}% case 1 is displaystyle
+{\hbox{\boldmath$\textstyle{#1}$}}% case 2 is textstyle
+{\hbox{\boldmath$\scriptstyle{#1}$}}% case 3 is scriptstyle
+{\hbox{\boldmath$\scriptscriptstyle{#1}$}}% case 4 is scriptscriptstyle
+}}
+\def\vec{\mbf}
+
+%% chapter and section head changes
+
+% \titlespacing*{\section}{0pt}{0pt}{-0.20ex}
+% \titlespacing*{\subsection}{0pt}{0pt}{-0.20ex}
+% \titlespacing*{\subsubsection}{0pt}{0pt}{-0.20ex}
+
+\titleformat*{\section}{\sbf\large}
+\titleformat*{\subsection}{\sbf\normalsize}
+\titleformat*{\subsubsection}{\sbf\normalsize}
+
+%% set up fancy headings
+
+\pagestyle{fancy}
+\renewcommand{\sectionmark}[1]{\markboth{\thesection\hspace{2.5mm} #1}{}}
+\fancyhf{}
+\fancyhead[L]{\sffamily\bfseries\leftmark}
+\fancyfoot[C]{\sffamily \thepage}
+
+\@ifclassloaded{book}{
+
+\pagestyle{fancy}
+\pagenumbering{roman}
+\renewcommand{\chaptermark}[1]{\markboth{\thechapter\hspace{2.5mm} #1}{}}
+\fancyhf{}
+\fancyhead[L]{\sffamily\bfseries\leftmark}
+\fancyfoot[C]{\sffamily \thepage}
+
+\renewcommand{\chaptername}{}
+
+\renewcommand{\@makechapterhead}[1]{%
+ \vspace*{50\p@}%
+ {\parindent \z@ \normalfont \raggedright
+ \Huge \sbf \thechapter \hspace*{0.5cm} \Huge \sbf #1\par
+ \nobreak}
+ \vskip 40\p@
+ }
+
+\renewcommand{\@makeschapterhead}[1]{%
+ \vspace*{50\p@}%
+ {\parindent \z@ \normalfont \raggedright
+ \Huge \sbf #1\par
+ \nobreak}
+ \vskip 40\p@
+ }
+
+%% table of contents font changes (book)
+\renewcommand{\cfttoctitlefont}{\sbf\Huge}
+\renewcommand{\cftchapfont}{\sbf}
+\renewcommand{\cftsecfont}{\normalfont\sffamily}
+\renewcommand{\cftsubsecfont}{\normalfont\sffamily}
+\renewcommand{\cftsubsubsecfont}{\normalfont\sffamily}
+\setlength\cftbeforechapskip{1ex}
+\setlength\cftbeforesecskip{1ex}
+\setlength\cftbeforesubsecskip{1ex}
+\setlength\cftbeforesubsubsecskip{1ex}
+}{
+\let\mainmatter=\,
+\let\frontmatter=\,
+
+%% table of contents font changes (article)
+\renewcommand{\cfttoctitlefont}{\sbf\large}
+\renewcommand{\cftsecfont}{\sbf}
+\renewcommand{\cftsubsecfont}{\normalfont\sffamily}
+\renewcommand{\cftsubsubsecfont}{\normalfont\sffamily}
+
+}
+
+%% figure and table font changes
+
+\newcommand{\captionfonts}{\sf}
+
+\long\def\@makecaption#1#2{%
+ \vskip\abovecaptionskip
+ \sbox\@tempboxa{{\captionfonts #1: #2}}%
+ \ifdim \wd\@tempboxa >\hsize
+ {\captionfonts #1: #2\par}
+ \else
+ \hbox to\hsize{\hfil\box\@tempboxa\hfil}%
+ \fi
+ \vskip\belowcaptionskip}
+
+%% Alter some LaTeX defaults for better treatment of figures:
+
+\renewcommand{\topfraction}{0.9} % max fraction of floats at top
+\renewcommand{\bottomfraction}{0.8} % max fraction of floats at bottom
+% Parameters for TEXT pages (not float pages):
+\setcounter{topnumber}{2}
+\setcounter{bottomnumber}{2}
+\setcounter{totalnumber}{4} % 2 may work better
+\setcounter{dbltopnumber}{2} % for 2-column pages
+\renewcommand{\dbltopfraction}{0.9} % fit big float above 2-col. text
+\renewcommand{\textfraction}{0.07} % allow minimal text w. figs
+% Parameters for FLOAT pages (not text pages):
+\renewcommand{\floatpagefraction}{0.7} % require fuller float pages
+% N.B.: floatpagefraction MUST be less than topfraction !!
+\renewcommand{\dblfloatpagefraction}{0.7} % require fuller float pages
+
+%% ripped from jss.cls; does nice printing of R commands for input and output
+
+\ifthenelse{\boolean{AAGI@knit}}{%
+\DefineVerbatimEnvironment{Rinput}{Verbatim}{fontshape=sl,fontsize =\small}
+\DefineVerbatimEnvironment{Routput}{Verbatim}{fontsize=\small}
+\DefineVerbatimEnvironment{Rcode}{Verbatim}{fontshape=sl,fontsize=\small}
+\newenvironment{Rchunk}{}{}
+\DefineVerbatimEnvironment{Code}{Verbatim}{fontsize=\small}
+\DefineVerbatimEnvironment{CodeInput}{Verbatim}{fontshape=sl,fontsize=\small}
+\DefineVerbatimEnvironment{CodeOutput}{Verbatim}{fontsize=\small}
+\newenvironment{CodeChunk}{}{}
+}{
+\DefineVerbatimEnvironment{Rinput}{Verbatim}{fontshape=sl}
+\DefineVerbatimEnvironment{Routput}{Verbatim}{}
+\DefineVerbatimEnvironment{Rcode}{Verbatim}{fontshape=sl}
+\newenvironment{Rchunk}{}{}
+\DefineVerbatimEnvironment{Code}{Verbatim}{}
+\DefineVerbatimEnvironment{CodeInput}{Verbatim}{fontshape=sl}
+\DefineVerbatimEnvironment{CodeOutput}{Verbatim}{}
+\newenvironment{CodeChunk}{}{}
+}
+
+% \let\knitrout\Rchunk
+% \let\endknitrout\endRchunk
+
+% \let\kframe\Rchunk
+% \let\endkframe\endRchunk
+
+% \renewenvironment{kframe}{\vspace{-0.3cm}}{\vspace{-0.3cm}}
+
+%% ripped from Rd.sty for use of \code in text
+
+{\catcode`\-=\active%
+ \global\def\code{\bgroup%
+ \catcode`\-=\active \let-\codedash%
+ \Rd@code}}
+\def\codedash{-\discretionary{}{}{}}
+\def\Rd@code#1{\normalfont\texttt{#1}\egroup}
+
+\def\AsIs{\bgroup\let\do\@makeother\Rd@AsIs@dospecials\@noligs\@vobeyspaces\Rd@AsIsX}
+\def\Rd@AsIs@dospecials{\do\$\do\&\do\#\do\^\do\_\do\%\do\~}
+\def\Rd@AsIsX#1{\normalfont #1\egroup}
+\let\command=\code
+\let\env=\code
diff --git a/_extensions/aagi/assets/AAGI_logo.pdf b/_extensions/aagi/assets/AAGI_logo.pdf
new file mode 100644
index 0000000..79205b5
Binary files /dev/null and b/_extensions/aagi/assets/AAGI_logo.pdf differ
diff --git a/_extensions/aagi/assets/AAGI_markdown.tex b/_extensions/aagi/assets/AAGI_markdown.tex
new file mode 100644
index 0000000..8995028
--- /dev/null
+++ b/_extensions/aagi/assets/AAGI_markdown.tex
@@ -0,0 +1,207 @@
+\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$lang$,$endif$$if(papersize)$$papersize$,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}
+$if(knit)$
+\usepackage[knit]{assets/AAGI}
+$endif$
+$if(fontfamily)$
+\usepackage{$fontfamily$}
+$else$
+\usepackage[T1]{fontenc}
+\usepackage{lmodern}
+$endif$
+$if(linestretch)$
+\setstretch{$linestretch$}
+$endif$
+
+% Define the AAGI colour
+\usepackage{xcolor}
+\definecolor{AAGI}{HTML}{00808b}
+
+\usepackage{hyperref}
+\hypersetup{
+ colorlinks=true,
+ linkcolor=AAGI,
+ urlcolor=AAGI
+ }
+
+\usepackage{graphicx}
+
+% Enable shading if it's set, otherwise disable
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+
+% Set up tightlist because Rmarkdown is crashing on it
+\providecommand{\tightlist}{%
+ \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+% use microtype if available
+\IfFileExists{microtype.sty}{%
+\usepackage{microtype}
+\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+ \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+\makeatletter
+% avoid brackets around text for \cite:
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newenvironment{CSLReferences}%
+{\setlength{\parindent}{0pt}%
+\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces}%
+{\par}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslentryspacing}
+\setlength{\cslentryspacing}{0em}
+\usepackage{enumitem}
+\newlist{biblist}{itemize}{1}
+\setlist[biblist]{label={},leftmargin=\cslhangindent,itemindent=-1\cslhangindent,itemsep=\cslentryspacing}
+\usepackage{calc}
+\newcommand{\CSLBlock}[1]{#1\hfill\break}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
+\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+
+$if(links-as-notes)$
+% Make links footnotes instead of hotlinks:
+\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
+$endif$
+$if(strikeout)$
+\usepackage[normalem]{ulem}
+% avoid problems with \sout in headers with hyperref:
+\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
+$endif$
+$if(number-sections)$
+\setcounter{secnumdepth}{2}
+$else$
+\setcounter{secnumdepth}{0}
+$endif$
+$if(verbatim-in-note)$
+\VerbatimFootnotes % allows verbatim text in footnotes
+$endif$
+
+%%% Use protect on footnotes to avoid problems with footnotes in titles
+\let\rmarkdownfootnote\footnote%
+\def\footnote{\protect\rmarkdownfootnote}
+
+$for(header-includes)$
+$header-includes$
+$endfor$
+
+\begin{document}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% start titlepage
+
+\thispagestyle{empty}
+\vspace*{-30mm}
+
+\begin{center}
+\includegraphics[height = 3cm]{assets/AAGI_logo}
+\end{center}
+
+
+\vfill
+
+\begin{flushright}
+\HRule\\[5mm]
+
+
+\huge
+$if(report-number)$
+\textcolor{AAGI}{\sbf $report-series$ \\Technical Report Series: $report-number$}\\[6mm]
+$else$
+\textcolor{AAGI}{\sbf $report-series$}\\[6mm]
+$endif$
+
+{\sbf $title$}\\
+\Large
+$if(subtitle)$
+\vspace{2mm}{\sbf $subtitle$}\\[5mm]
+$else$
+\vspace{2mm}
+$endif$
+
+\sf\normalsize
+$if(author)$
+$for(author)$$author$\\ $endfor$
+$endif$
+$if(job-title)$
+$job-title$\\
+$endif$
+$if(address)$
+$address$\\
+$endif$
+\vspace*{0.4cm}
+$if(email)$
+email:\;$email$\\[8mm]
+$endif$
+
+
+$if(date)$
+$date$\\
+$else$
+\today\\
+$endif$
+\HRule
+\end{flushright}
+
+
+
+%%% logos go here ...
+$if(colspace)$
+\setlength{\tabcolsep}{$colspace$}
+$else$
+\setlength{\tabcolsep}{12pt}
+$endif$
+
+\vfill
+
+$if(partner-logo)$
+\begin{tabular}{cl}
+\noindent\makebox[\textwidth]{\includegraphics[width=\paperwidth, height=3cm]{assets/Project_partner}}
+\makebox[0pt][r]{% Similar to \llap
+ \raisebox{1.8em}{%
+ \includegraphics[width=3cm]{$partner-logo$}
+ }\hspace*{-2.5em}
+ }
+\end{tabular}
+$else$
+\noindent\makebox[\textwidth]{\includegraphics[width=\paperwidth]{assets/Partners}}
+$endif$
+\vspace*{-30mm}
+
+\setlength{\tabcolsep}{6pt}
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% end titlepage
+
+\clearpage
+$if(book-class)$
+\frontmatter
+$endif$
+$if(toc)$
+\pagestyle{plain}
+\setcounter{page}{1}
+\setcounter{tocdepth}{2}
+\tableofcontents
+\clearpage
+$endif$
+$if(lot)$
+\listoftables
+$endif$
+$if(lof)$
+\listoffigures
+$endif$
+$body$
+$for(include-after)$
+$include-after$
+$endfor$
+\end{document}
diff --git a/_extensions/aagi/assets/Partners.pdf b/_extensions/aagi/assets/Partners.pdf
new file mode 100644
index 0000000..0190e9e
Binary files /dev/null and b/_extensions/aagi/assets/Partners.pdf differ
diff --git a/_extensions/aagi/assets/Project_partner.pdf b/_extensions/aagi/assets/Project_partner.pdf
new file mode 100644
index 0000000..36d5a51
Binary files /dev/null and b/_extensions/aagi/assets/Project_partner.pdf differ
diff --git a/_extensions/aagi/assets/biometrics.csl b/_extensions/aagi/assets/biometrics.csl
new file mode 100644
index 0000000..88d20e8
--- /dev/null
+++ b/_extensions/aagi/assets/biometrics.csl
@@ -0,0 +1,170 @@
+
+
+
diff --git a/_quarto.yml b/docs/_quarto.yml
similarity index 100%
rename from _quarto.yml
rename to docs/_quarto.yml
diff --git a/docs/demos/assets/AAGI.sty b/docs/demos/assets/AAGI.sty
new file mode 100644
index 0000000..5954a02
--- /dev/null
+++ b/docs/demos/assets/AAGI.sty
@@ -0,0 +1,218 @@
+\RequirePackage{ifpdf}
+\newcommand{\pdfgraphics}{\ifpdf\DeclareGraphicsExtensions{.pdf,.jpg,.png}\else\fi}
+
+\newcommand{\PDFPackage}[1]{
+ \ifpdf
+ \RequirePackage[pdftex]{#1}
+ \else
+ \RequirePackage{#1}
+ \fi
+}
+
+%% knitr inclusion
+
+\RequirePackage{ifthen}
+\newboolean{AAGI@knit}
+\setboolean{AAGI@knit}{true}
+
+\DeclareOption{knit}{\setboolean{AAGI@knit}{false}}
+\ProcessOptions
+
+\ifthenelse{\boolean{AAGI@knit}}{
+ \PDFPackage{graphicx}
+ \PDFPackage{color}
+}{}
+
+\usepackage{graphicx}
+\usepackage{color}
+
+% \def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+% \def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+% \makeatother
+% % Scale images if necessary, so that they will not overflow the page
+% % margins by default, and it is still possible to overwrite the defaults
+% % using explicit options in \includegraphics[width, height, ...]{}
+% \setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+
+\usepackage{natbib}
+\usepackage{fancyhdr}
+\usepackage{fancyvrb}
+\usepackage{amssymb, amsmath}
+\usepackage{longtable}
+\usepackage{rotating}
+\usepackage{titlesec}
+\usepackage{tocloft}
+\usepackage{parskip}
+\usepackage{setspace}
+
+%% hyperlnk highlighting and geometry
+
+\PDFPackage{hyperref}
+\hypersetup{colorlinks,linkcolor=blue,citecolor=blue,urlcolor=blue}
+\usepackage[paper=a4paper,top=35mm,left=25mm,right=25mm,bottom=30mm]{geometry}
+\setlength{\parindent}{0cm}
+\setlength{\headheight}{15pt}
+\setlength{\parskip}{3ex}
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+
+%% font declarations and definitions
+
+\let\proglang=\textsf
+\let\pkg=\textbf
+\DeclareOldFontCommand{\sbf}{\normalfont\bfseries\sffamily}{\mathsf}
+\DeclareOldFontCommand{\tbf}{\normalfont\bfseries\ttfamily}{\mathtt}
+\newcommand{\HRule}{\hspace{-25mm}\rule{160mm}{0.5mm}}
+\newcommand\Trule{\rule{0pt}{2.6ex}}
+\newcommand\Brule{\rule[-2.5ex]{0pt}{0pt}}
+\renewcommand{\bibname}{References}
+
+\def\mbf#1{{% \mbf{X} makes X a math bold letter
+\mathchoice% selects with respect to current style
+{\hbox{\boldmath$\displaystyle{#1}$}}% case 1 is displaystyle
+{\hbox{\boldmath$\textstyle{#1}$}}% case 2 is textstyle
+{\hbox{\boldmath$\scriptstyle{#1}$}}% case 3 is scriptstyle
+{\hbox{\boldmath$\scriptscriptstyle{#1}$}}% case 4 is scriptscriptstyle
+}}
+\def\vec{\mbf}
+
+%% chapter and section head changes
+
+% \titlespacing*{\section}{0pt}{0pt}{-0.20ex}
+% \titlespacing*{\subsection}{0pt}{0pt}{-0.20ex}
+% \titlespacing*{\subsubsection}{0pt}{0pt}{-0.20ex}
+
+\titleformat*{\section}{\sbf\large}
+\titleformat*{\subsection}{\sbf\normalsize}
+\titleformat*{\subsubsection}{\sbf\normalsize}
+
+%% set up fancy headings
+
+\pagestyle{fancy}
+\renewcommand{\sectionmark}[1]{\markboth{\thesection\hspace{2.5mm} #1}{}}
+\fancyhf{}
+\fancyhead[L]{\sffamily\bfseries\leftmark}
+\fancyfoot[C]{\sffamily \thepage}
+
+\@ifclassloaded{book}{
+
+\pagestyle{fancy}
+\pagenumbering{roman}
+\renewcommand{\chaptermark}[1]{\markboth{\thechapter\hspace{2.5mm} #1}{}}
+\fancyhf{}
+\fancyhead[L]{\sffamily\bfseries\leftmark}
+\fancyfoot[C]{\sffamily \thepage}
+
+\renewcommand{\chaptername}{}
+
+\renewcommand{\@makechapterhead}[1]{%
+ \vspace*{50\p@}%
+ {\parindent \z@ \normalfont \raggedright
+ \Huge \sbf \thechapter \hspace*{0.5cm} \Huge \sbf #1\par
+ \nobreak}
+ \vskip 40\p@
+ }
+
+\renewcommand{\@makeschapterhead}[1]{%
+ \vspace*{50\p@}%
+ {\parindent \z@ \normalfont \raggedright
+ \Huge \sbf #1\par
+ \nobreak}
+ \vskip 40\p@
+ }
+
+%% table of contents font changes (book)
+\renewcommand{\cfttoctitlefont}{\sbf\Huge}
+\renewcommand{\cftchapfont}{\sbf}
+\renewcommand{\cftsecfont}{\normalfont\sffamily}
+\renewcommand{\cftsubsecfont}{\normalfont\sffamily}
+\renewcommand{\cftsubsubsecfont}{\normalfont\sffamily}
+\setlength\cftbeforechapskip{1ex}
+\setlength\cftbeforesecskip{1ex}
+\setlength\cftbeforesubsecskip{1ex}
+\setlength\cftbeforesubsubsecskip{1ex}
+}{
+\let\mainmatter=\,
+\let\frontmatter=\,
+
+%% table of contents font changes (article)
+\renewcommand{\cfttoctitlefont}{\sbf\large}
+\renewcommand{\cftsecfont}{\sbf}
+\renewcommand{\cftsubsecfont}{\normalfont\sffamily}
+\renewcommand{\cftsubsubsecfont}{\normalfont\sffamily}
+
+}
+
+%% figure and table font changes
+
+\newcommand{\captionfonts}{\sf}
+
+\long\def\@makecaption#1#2{%
+ \vskip\abovecaptionskip
+ \sbox\@tempboxa{{\captionfonts #1: #2}}%
+ \ifdim \wd\@tempboxa >\hsize
+ {\captionfonts #1: #2\par}
+ \else
+ \hbox to\hsize{\hfil\box\@tempboxa\hfil}%
+ \fi
+ \vskip\belowcaptionskip}
+
+%% Alter some LaTeX defaults for better treatment of figures:
+
+\renewcommand{\topfraction}{0.9} % max fraction of floats at top
+\renewcommand{\bottomfraction}{0.8} % max fraction of floats at bottom
+% Parameters for TEXT pages (not float pages):
+\setcounter{topnumber}{2}
+\setcounter{bottomnumber}{2}
+\setcounter{totalnumber}{4} % 2 may work better
+\setcounter{dbltopnumber}{2} % for 2-column pages
+\renewcommand{\dbltopfraction}{0.9} % fit big float above 2-col. text
+\renewcommand{\textfraction}{0.07} % allow minimal text w. figs
+% Parameters for FLOAT pages (not text pages):
+\renewcommand{\floatpagefraction}{0.7} % require fuller float pages
+% N.B.: floatpagefraction MUST be less than topfraction !!
+\renewcommand{\dblfloatpagefraction}{0.7} % require fuller float pages
+
+%% ripped from jss.cls; does nice printing of R commands for input and output
+
+\ifthenelse{\boolean{AAGI@knit}}{%
+\DefineVerbatimEnvironment{Rinput}{Verbatim}{fontshape=sl,fontsize =\small}
+\DefineVerbatimEnvironment{Routput}{Verbatim}{fontsize=\small}
+\DefineVerbatimEnvironment{Rcode}{Verbatim}{fontshape=sl,fontsize=\small}
+\newenvironment{Rchunk}{}{}
+\DefineVerbatimEnvironment{Code}{Verbatim}{fontsize=\small}
+\DefineVerbatimEnvironment{CodeInput}{Verbatim}{fontshape=sl,fontsize=\small}
+\DefineVerbatimEnvironment{CodeOutput}{Verbatim}{fontsize=\small}
+\newenvironment{CodeChunk}{}{}
+}{
+\DefineVerbatimEnvironment{Rinput}{Verbatim}{fontshape=sl}
+\DefineVerbatimEnvironment{Routput}{Verbatim}{}
+\DefineVerbatimEnvironment{Rcode}{Verbatim}{fontshape=sl}
+\newenvironment{Rchunk}{}{}
+\DefineVerbatimEnvironment{Code}{Verbatim}{}
+\DefineVerbatimEnvironment{CodeInput}{Verbatim}{fontshape=sl}
+\DefineVerbatimEnvironment{CodeOutput}{Verbatim}{}
+\newenvironment{CodeChunk}{}{}
+}
+
+% \let\knitrout\Rchunk
+% \let\endknitrout\endRchunk
+
+% \let\kframe\Rchunk
+% \let\endkframe\endRchunk
+
+% \renewenvironment{kframe}{\vspace{-0.3cm}}{\vspace{-0.3cm}}
+
+%% ripped from Rd.sty for use of \code in text
+
+{\catcode`\-=\active%
+ \global\def\code{\bgroup%
+ \catcode`\-=\active \let-\codedash%
+ \Rd@code}}
+\def\codedash{-\discretionary{}{}{}}
+\def\Rd@code#1{\normalfont\texttt{#1}\egroup}
+
+\def\AsIs{\bgroup\let\do\@makeother\Rd@AsIs@dospecials\@noligs\@vobeyspaces\Rd@AsIsX}
+\def\Rd@AsIs@dospecials{\do\$\do\&\do\#\do\^\do\_\do\%\do\~}
+\def\Rd@AsIsX#1{\normalfont #1\egroup}
+\let\command=\code
+\let\env=\code
diff --git a/docs/demos/assets/AAGI_logo.pdf b/docs/demos/assets/AAGI_logo.pdf
new file mode 100644
index 0000000..79205b5
Binary files /dev/null and b/docs/demos/assets/AAGI_logo.pdf differ
diff --git a/docs/demos/assets/AAGI_markdown.tex b/docs/demos/assets/AAGI_markdown.tex
new file mode 100644
index 0000000..8995028
--- /dev/null
+++ b/docs/demos/assets/AAGI_markdown.tex
@@ -0,0 +1,207 @@
+\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$lang$,$endif$$if(papersize)$$papersize$,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}
+$if(knit)$
+\usepackage[knit]{assets/AAGI}
+$endif$
+$if(fontfamily)$
+\usepackage{$fontfamily$}
+$else$
+\usepackage[T1]{fontenc}
+\usepackage{lmodern}
+$endif$
+$if(linestretch)$
+\setstretch{$linestretch$}
+$endif$
+
+% Define the AAGI colour
+\usepackage{xcolor}
+\definecolor{AAGI}{HTML}{00808b}
+
+\usepackage{hyperref}
+\hypersetup{
+ colorlinks=true,
+ linkcolor=AAGI,
+ urlcolor=AAGI
+ }
+
+\usepackage{graphicx}
+
+% Enable shading if it's set, otherwise disable
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+
+% Set up tightlist because Rmarkdown is crashing on it
+\providecommand{\tightlist}{%
+ \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+% use microtype if available
+\IfFileExists{microtype.sty}{%
+\usepackage{microtype}
+\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+ \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+\makeatletter
+% avoid brackets around text for \cite:
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newenvironment{CSLReferences}%
+{\setlength{\parindent}{0pt}%
+\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces}%
+{\par}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslentryspacing}
+\setlength{\cslentryspacing}{0em}
+\usepackage{enumitem}
+\newlist{biblist}{itemize}{1}
+\setlist[biblist]{label={},leftmargin=\cslhangindent,itemindent=-1\cslhangindent,itemsep=\cslentryspacing}
+\usepackage{calc}
+\newcommand{\CSLBlock}[1]{#1\hfill\break}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
+\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+
+$if(links-as-notes)$
+% Make links footnotes instead of hotlinks:
+\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
+$endif$
+$if(strikeout)$
+\usepackage[normalem]{ulem}
+% avoid problems with \sout in headers with hyperref:
+\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
+$endif$
+$if(number-sections)$
+\setcounter{secnumdepth}{2}
+$else$
+\setcounter{secnumdepth}{0}
+$endif$
+$if(verbatim-in-note)$
+\VerbatimFootnotes % allows verbatim text in footnotes
+$endif$
+
+%%% Use protect on footnotes to avoid problems with footnotes in titles
+\let\rmarkdownfootnote\footnote%
+\def\footnote{\protect\rmarkdownfootnote}
+
+$for(header-includes)$
+$header-includes$
+$endfor$
+
+\begin{document}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% start titlepage
+
+\thispagestyle{empty}
+\vspace*{-30mm}
+
+\begin{center}
+\includegraphics[height = 3cm]{assets/AAGI_logo}
+\end{center}
+
+
+\vfill
+
+\begin{flushright}
+\HRule\\[5mm]
+
+
+\huge
+$if(report-number)$
+\textcolor{AAGI}{\sbf $report-series$ \\Technical Report Series: $report-number$}\\[6mm]
+$else$
+\textcolor{AAGI}{\sbf $report-series$}\\[6mm]
+$endif$
+
+{\sbf $title$}\\
+\Large
+$if(subtitle)$
+\vspace{2mm}{\sbf $subtitle$}\\[5mm]
+$else$
+\vspace{2mm}
+$endif$
+
+\sf\normalsize
+$if(author)$
+$for(author)$$author$\\ $endfor$
+$endif$
+$if(job-title)$
+$job-title$\\
+$endif$
+$if(address)$
+$address$\\
+$endif$
+\vspace*{0.4cm}
+$if(email)$
+email:\;$email$\\[8mm]
+$endif$
+
+
+$if(date)$
+$date$\\
+$else$
+\today\\
+$endif$
+\HRule
+\end{flushright}
+
+
+
+%%% logos go here ...
+$if(colspace)$
+\setlength{\tabcolsep}{$colspace$}
+$else$
+\setlength{\tabcolsep}{12pt}
+$endif$
+
+\vfill
+
+$if(partner-logo)$
+\begin{tabular}{cl}
+\noindent\makebox[\textwidth]{\includegraphics[width=\paperwidth, height=3cm]{assets/Project_partner}}
+\makebox[0pt][r]{% Similar to \llap
+ \raisebox{1.8em}{%
+ \includegraphics[width=3cm]{$partner-logo$}
+ }\hspace*{-2.5em}
+ }
+\end{tabular}
+$else$
+\noindent\makebox[\textwidth]{\includegraphics[width=\paperwidth]{assets/Partners}}
+$endif$
+\vspace*{-30mm}
+
+\setlength{\tabcolsep}{6pt}
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% end titlepage
+
+\clearpage
+$if(book-class)$
+\frontmatter
+$endif$
+$if(toc)$
+\pagestyle{plain}
+\setcounter{page}{1}
+\setcounter{tocdepth}{2}
+\tableofcontents
+\clearpage
+$endif$
+$if(lot)$
+\listoftables
+$endif$
+$if(lof)$
+\listoffigures
+$endif$
+$body$
+$for(include-after)$
+$include-after$
+$endfor$
+\end{document}
diff --git a/docs/demos/assets/Partners.pdf b/docs/demos/assets/Partners.pdf
new file mode 100644
index 0000000..0190e9e
Binary files /dev/null and b/docs/demos/assets/Partners.pdf differ
diff --git a/docs/demos/assets/Project_partner.pdf b/docs/demos/assets/Project_partner.pdf
new file mode 100644
index 0000000..36d5a51
Binary files /dev/null and b/docs/demos/assets/Project_partner.pdf differ
diff --git a/docs/demos/assets/biometrics.csl b/docs/demos/assets/biometrics.csl
new file mode 100644
index 0000000..88d20e8
--- /dev/null
+++ b/docs/demos/assets/biometrics.csl
@@ -0,0 +1,170 @@
+
+
+
diff --git a/docs/demos/figures/example-histogram-1.pdf b/docs/demos/figures/example-histogram-1.pdf
new file mode 100644
index 0000000..06ddc8d
Binary files /dev/null and b/docs/demos/figures/example-histogram-1.pdf differ
diff --git a/docs/demos/figures/example-histogram-1.png b/docs/demos/figures/example-histogram-1.png
new file mode 100644
index 0000000..cb78a60
Binary files /dev/null and b/docs/demos/figures/example-histogram-1.png differ
diff --git a/docs/demos/references.bib b/docs/demos/references.bib
new file mode 100644
index 0000000..af2364f
--- /dev/null
+++ b/docs/demos/references.bib
@@ -0,0 +1,15 @@
+@Article{Box1976,
+ author = {Box, George E. P.},
+ journal = {Journal of the American Statistical Association},
+ title = {Science and Statistics},
+ year = {1976},
+ issn = {1537-274X},
+ month = dec,
+ number = {356},
+ pages = {791--799},
+ volume = {71},
+ doi = {10.1080/01621459.1976.10480949},
+ publisher = {Informa UK Limited},
+}
+
+@Comment{jabref-meta: databaseType:bibtex;}
diff --git a/docs/demos/template-docx.qmd b/docs/demos/template-docx.qmd
new file mode 100644
index 0000000..0aa54ff
--- /dev/null
+++ b/docs/demos/template-docx.qmd
@@ -0,0 +1,155 @@
+---
+format:
+ aagi-docx: default
+execute:
+ echo: false
+knitr:
+ opts_chunk:
+ fig.path: figures/
+params:
+ uni: CU
+ pri_bio: Your.Name
+ project_num: AAA--BBB
+bibliography: references.bib
+date: "`r Sys.Date()`"
+date-format: long
+editor: visual
+---
+
+```{r}
+#| include: false
+if (params$uni == "CU") {
+ Project_Lead = "Curtin University -- Prof Mark Gibberd, Dr Julia Easton, Prof Adam Sparks"
+} else if (params$uni == "UA") {
+ Project_Lead = "University of Adelaide -- Dr Julian Taylor, Dr Olena Kravchuck"
+} else {
+ Project_Lead = "University of Queensland -- Prof Scott Chapman, Emeritus Prof Kaye Basford"
+}
+```
+
+```{r}
+#| include: false
+#| label: email for project lead
+
+if (params$uni == "CU") {
+ email = "cbada@curtin.edu.au"
+} else if (params$uni == "UA") {
+ email = paste(params$pri_bio, "@adelaide.edu.au", sep = "")
+} else {
+ email = paste(params$pri_bio, "@uq.edu.au")
+}
+```
+
+```{r}
+#| label: Project number
+#| include: false
+
+Pro_Num = params$project_num
+
+```
+
+```{r}
+#| label: title param
+#| include: false
+
+if (params$uni == "CU") {
+ university <- "Curtin University"
+} else if (params$uni == "UA") {
+ university <- "University of Adelaide"
+} else {
+ university <- "University of Queensland"
+}
+
+```
+
+---
+title: "Analytics for the Australian Grains Industry - `r university` (AAGI-`r params$uni`) \n Technical Report Series: 123"
+subtitle: "Descriptive title for report \n Report for `r Pro_Num`"
+author:
+ - Adam Sparks
+ - "Email: `r email`"
+ - "Project Leads: `r Project_Lead`"
+---
+
+```{r}
+#| label: load
+#| message: false
+
+library(ggplot2)
+library(AAGIThemes)
+library(flextable)
+library(dplyr)
+
+# set ggplot2 theme
+theme_set(theme_aagi())
+
+# set flextable theme
+set_flextable_defaults(
+ theme_fun = theme_ft_aagi
+)
+```
+
+\newpage
+
+# Executive summary
+
+What was provided by AAGI and the main results?
+
+# Introduction
+
+- Goals of the research project.
+
+- Background, context and rationale behind the research.
+
+# Experimental/Trial Design
+
+- Trial design type and layout.
+
+- Treatments, number of replicates.
+
+- Specific considerations for small plots, glasshouse, genetics, breeding trials, OFE projects, or bioinformatics.
+
+# Exploratory Data Analysis and Data Visualisation
+
+- Interpretation of plots and data.
+
+- Rationale behind specific methods used.
+
+# Methods
+
+- Detailed description of the procedures and methodologies used.
+
+- Include versions/commits on developed pipelines, scripts, and input/output details if applicable.
+
+# Analysis (if separate from Methods)
+
+Approach taken for data analysis.
+
+# Results and Discussion
+
+Findings and their implications.
+
+# Metadata and Datasets (Optional)
+
+- md5sums for input data and outputs (if applicable).
+
+- Git commit numbers and tags.
+
+- Location of outputs (FAIR Data).
+
+- DOI for AAGI outputs.
+
+# Map (Location, Optional)
+
+Include if relevant to the project.
+
+# References (Optional)
+
+Cited works and literature. @Box1976
+
+::: {#refs}
+:::
+
+# Appendix (Optional)
+
+Additional supporting information.
diff --git a/docs/demos/template-pdf.qmd b/docs/demos/template-pdf.qmd
new file mode 100644
index 0000000..1d25767
--- /dev/null
+++ b/docs/demos/template-pdf.qmd
@@ -0,0 +1,199 @@
+---
+format:
+ aagi-pdf: default
+execute:
+ echo: false
+knitr:
+ opts_chunk:
+ fig.path: figures/
+params:
+ uni: CU
+ pri_bio: Your.Name
+ project_num: AAA--BBB
+bibliography: references.bib
+editor: visual
+---
+
+```{r}
+#| include: false
+#| label: param_uni
+
+if (params$uni == "CU") {
+ Project_Lead = "Curtin University -- Prof Mark Gibberd, Dr Julia Easton, Prof Adam Sparks"
+} else if (params$uni == "UA") {
+ Project_Lead = "University of Adelaide -- Dr Julian Taylor, Dr Olena Kravchuck"
+} else {
+ Project_Lead = "University of Queensland -- Prof Scott Chapman, Emeritus Prof Kaye Basford"
+}
+```
+
+```{r}
+#| include: false
+#| label: email for project lead
+
+if (params$uni == "CU") {
+ email = "cbada@curtin.edu.au"
+} else if (params$uni == "UA") {
+ email = paste(params$pri_bio, "@adelaide.edu.au", sep = "")
+} else {
+ email = paste(params$pri_bio, "@uq.edu.au")
+}
+```
+
+```{r}
+#| label: title param
+#| include: false
+
+if (params$uni == "CU") {
+ university <- "Curtin University"
+} else if (params$uni == "UA") {
+ university <- "University of Adelaide"
+} else {
+ university <- "University of Queensland"
+}
+
+```
+
+```{r}
+#| label: Project number
+#| include: false
+
+Pro_Num = params$project_num
+```
+
+```{=latex}
+%\begin{titlepage}
+
+%\thispagestyle{Title_page}
+
+%\vspace*{-2cm}
+
+% \begin{center}
+% \includegraphics[height=3cm]{assets/AAGI_logo.pdf}
+% \end{center}
+
+% \vfill
+
+% \rule{\textwidth}{0.5pt}
+
+% \begin{FlushRight}
+
+% \Huge
+% \textcolor{aagiteal}{\textbf{Analytics for the Australian Grains Industry
+% -\\ `r university` (AAGI-`r params$uni`)\\
+% Technical Report Series: 123}}\\[6mm]
+
+% \Large
+% {\textbf{Informative title for report}}\\
+% \vspace{2mm}{\textbf{Report for `r Pro_Num`}}\\[5mm]
+
+% \normalsize
+% \textbf{Your Name}\\
+% \vspace*{0.4cm}
+% \textbf{Email:}\; \texttt{%
+% \href{mailto:`r email`}%
+% {`r email`}}\\[8mm]
+% \textbf{Project Leads: `r Project_Lead`}\\[8mm]
+
+% \today
+% \end{FlushRight}
+% \rule{\textwidth}{0.5pt}
+
+% \vfill
+
+%\end{titlepage}
+```
+---
+title: "Analytics for the Australian Grains Industry - `r university` (AAGI-`r params$uni`) \n Technical Report Series: 123"
+subtitle: "Descriptive title for report \n Report for `r Pro_Num`"
+author:
+ - Adam Sparks
+ - "Email: `r email`"
+ - "Project Leads: `r Project_Lead`"
+---
+
+```{r}
+#| label: load
+#| message: false
+
+library(ggplot2)
+library(AAGIThemes)
+library(flextable)
+library(dplyr)
+
+# set ggplot2 theme
+theme_set(theme_aagi())
+```
+
+\newpage
+
+```{=latex}
+\clearpage
+\setcounter{page}{1}
+```
+\tableofcontents
+
+\newpage
+
+# Executive summary
+
+What was provided by AAGI and the main results?
+
+# Introduction
+
+- Goals of the research project.
+
+- Background, context and rationale behind the research.
+
+# Experimental/Trial Design
+
+- Trial design type and layout.
+
+- Treatments, number of replicates.
+
+- Specific considerations for small plots, glasshouse, genetics, breeding trials, OFE projects, or bioinformatics.
+
+# Exploratory Data Analysis and Data Visualisation
+
+- Interpretation of plots and data.
+
+- Rationale behind specific methods used.
+
+# Methods
+
+- Detailed description of the procedures and methodologies used.
+
+- Include versions/commits on developed pipelines, scripts, and input/output details if applicable.
+
+# Analysis (if separate from Methods)
+
+Approach taken for data analysis.
+
+# Results and Discussion
+
+Findings and their implications.
+
+# Metadata and Datasets (Optional)
+
+- md5sums for input data and outputs (if applicable).
+
+- Git commit numbers and tags.
+
+- Location of outputs (FAIR Data).
+
+- DOI for AAGI outputs.
+
+# Map (Location, Optional)
+
+Include if relevant to the project.
+
+# References
+
+Cited works and literature. @Box1976
+
+::: {#refs}
+:::
+
+# Appendix (Optional)
+
+Additional supporting information.
diff --git a/aagi-template-revealjs.qmd b/docs/demos/template-revealjs.qmd
similarity index 100%
rename from aagi-template-revealjs.qmd
rename to docs/demos/template-revealjs.qmd
diff --git a/references.bib b/references.bib
new file mode 100644
index 0000000..af2364f
--- /dev/null
+++ b/references.bib
@@ -0,0 +1,15 @@
+@Article{Box1976,
+ author = {Box, George E. P.},
+ journal = {Journal of the American Statistical Association},
+ title = {Science and Statistics},
+ year = {1976},
+ issn = {1537-274X},
+ month = dec,
+ number = {356},
+ pages = {791--799},
+ volume = {71},
+ doi = {10.1080/01621459.1976.10480949},
+ publisher = {Informa UK Limited},
+}
+
+@Comment{jabref-meta: databaseType:bibtex;}
diff --git a/template.qmd b/template.qmd
new file mode 100644
index 0000000..0a94b75
--- /dev/null
+++ b/template.qmd
@@ -0,0 +1,156 @@
+---
+format:
+ aagi-docx: default
+execute:
+ echo: false
+knitr:
+ opts_chunk:
+ fig.path: figures/
+params:
+ uni: CU
+ pri_bio: Your.Name
+ project_num: AAA--BBB
+bibliography: references.bib
+date: "`r Sys.Date()`"
+date-format: long
+---
+
+```{r}
+#| include: false
+if (params$uni == "CU") {
+ Project_Lead = "Curtin University -- Prof Mark Gibberd, Dr Julia Easton, Prof Adam Sparks"
+} else if (params$uni == "UA") {
+ Project_Lead = "University of Adelaide -- Dr Julian Taylor, Dr Olena Kravchuck"
+} else {
+ Project_Lead = "University of Queensland -- Prof Scott Chapman, Emeritus Prof Kaye Basford"
+}
+```
+
+```{r}
+#| include: false
+#| label: email for project lead
+
+if (params$uni == "CU") {
+ email = "cbada@curtin.edu.au"
+} else if (params$uni == "UA") {
+ email = paste(params$pri_bio, "@adelaide.edu.au", sep = "")
+} else {
+ email = paste(params$pri_bio, "@uq.edu.au")
+}
+```
+
+```{r}
+#| label: Project number
+#| include: false
+
+Pro_Num = params$project_num
+
+```
+
+```{r}
+#| label: title param
+#| include: false
+
+if (params$uni == "CU") {
+ university <- "Curtin University"
+} else if (params$uni == "UA") {
+ university <- "University of Adelaide"
+} else {
+ university <- "University of Queensland"
+}
+
+```
+
+---
+title: "Analytics for the Australian Grains Industry - `r university` (AAGI-`r params$uni`) \n Technical Report Series: 123"
+subtitle: "Descriptive title for report \n Report for `r Pro_Num`"
+author:
+ - Adam Sparks
+ - "Email: `r email`"
+ - "Project Leads: `r Project_Lead`"
+---
+
+```{r}
+#| label: load
+#| message: false
+
+library(ggplot2)
+library(AAGIThemes)
+library(flextable)
+library(dplyr)
+
+# set ggplot2 theme
+theme_set(theme_aagi())
+
+# set flextable theme
+set_flextable_defaults(
+ theme_fun = theme_ft_aagi
+)
+```
+
+\newpage
+
+# Executive summary
+
+What was provided by AAGI and the main results?
+
+# Introduction
+
+- Goals of the research project.
+
+- Background, context and rationale behind the research.
+
+# Experimental/Trial Design
+
+- Trial design type and layout.
+
+- Treatments, number of replicates.
+
+- Specific considerations for small plots, glasshouse, genetics, breeding trials, OFE projects, or bioinformatics.
+
+# Exploratory Data Analysis and Data Visualisation
+
+- Interpretation of plots and data.
+
+- Rationale behind specific methods used.
+
+# Methods
+
+- Detailed description of the procedures and methodologies used.
+
+- Include versions/commits on developed pipelines, scripts, and input/output details if applicable.
+
+# Analysis (if separate from Methods)
+
+Approach taken for data analysis.
+
+# Results and Discussion
+
+Findings and their implications.
+
+# Metadata and Datasets (Optional)
+
+- md5sums for input data and outputs (if applicable).
+
+- Git commit numbers and tags.
+
+- Location of outputs (FAIR Data).
+
+- DOI for AAGI outputs.
+
+# Map (Location, Optional)
+
+Include if relevant to the project.
+
+# References (Optional)
+
+Cited works and literature. @Box1976
+
+::: {#refs}
+:::
+
+# Appendix (Optional)
+
+Additional supporting information.
+
+