initial

.gitignore

@@ -0,0 +1,6 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+
+/.quarto/

LV-19-050-189-ABM.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: XeLaTeX

README.md

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+# EON Summer School 2023

_extensions/EmilHvitfeldt/roughnotation/_extension.yml

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+title: RoughNotations
+author: Emil Hvitfeldt
+version: 1.0.0
+contributes:
+ filters:
+ - rough.lua

_extensions/EmilHvitfeldt/roughnotation/rough.js

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+document.addEventListener("DOMContentLoaded", function () {
+ var rn_counter = 0;
+
+ Reveal.on("slidechanged", (event) => {
+ rn_counter = 0;
+ });
+
+ function strictly_false(x) {
+ var out = true;
+ if (x === "false") {
+ out = false;
+ }
+ return out;
+ }
+
+ Reveal.addKeyBinding(
+ { keyCode: 82, key: "R", description: "Trigger RoughNotation" },
+ function () {
+ rn_counter = rn_counter + 1;
+
+ const slide = Reveal.getCurrentSlide();
+ const divs = Array.from(slide.querySelectorAll(".rn"));
+ const new_divs = divs
+ .filter(function (rn) {
+ if (rn_counter == 1) {
+ if (rn.dataset.rnIndex > 1) {
+ return false;
+ }
+ } else {
+ if (typeof rn.dataset.rnIndex == "undefined") {
+ return false;
+ }
+ if (rn.dataset.rnIndex != rn_counter) {
+ return false;
+ }
+ }
+ return true;
+ })
+ .map(function (rn) {
+ return RoughNotation.annotate(rn, {
+ type: rn.dataset.rnType || "highlight",
+ animate: strictly_false(rn.dataset.rnAnimate),
+ animationDuration: parseInt(rn.dataset.rnAnimationduration) || 800,
+ color: rn.dataset.rnColor || "#fff17680",
+ strokeWidth: parseInt(rn.dataset.rnStrokewidth) || 1,
+ multiline: strictly_false(rn.dataset.rnMultiline),
+ iterations: parseInt(rn.dataset.rnIterations) || 2,
+ rtl: !strictly_false(rn.dataset.rnRtl),
+ });
+ });
+
+ new_divs.map(function (rn) {
+ rn.show();
+ });
+ }
+ );
+})

_extensions/EmilHvitfeldt/roughnotation/rough.lua

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+function Meta(m)
+ quarto.doc.addHtmlDependency({
+ name = "roughnotation",
+ version = "0.5.1",
+ scripts = {"assets/rough-notation.iife.js"}
+ })
+ quarto.doc.addHtmlDependency({
+ name = "roughnotation-init",
+ version = "1.0.0",
+ scripts = {"rough.js"}
+ })
+end

_extensions/andrewheiss/hikmah-manuscript/_extension.yml

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+title: Hikma Manuscript
+author: Andrew Heiss
+version: 0.0.1
+contributes:
+ formats:
+ common:
+ date-format: full
+ docx:
+ reference-doc: "styles/reference.docx"
+ knitr:
+ opts_chunk:
+ dev: "png"
+ dev-args:
+ - "cairo-png"
+ dpi: 300
+ out.width: "80%"
+ odt:
+ template: "templates/odt-manuscript.odt"
+ reference-doc: "styles/reference.odt"
+ knitr:
+ opts_chunk:
+ dev: "png"
+ dev-args:
+ - "cairo-png"
+ dpi: 300
+ out.width: "80%"
+ pdf:
+ documentclass: article
+ papersize: letter
+ fontsize: 12pt
+ linestretch: 2
+
+ # Template pieces
+ template-partials:
+ - "partials/title.tex"
+ - "partials/before-body.tex"
+ include-in-header:
+ - "include-in-header.tex"
+
+ # Document styling
+ geometry:
+ - top=1in
+ - bottom=1in
+ - left=1in
+ - right=1in
+
+ # Citations and links
+ colorlinks: true
+ linkcolor: DarkSlateBlue
+ urlcolor: DarkSlateBlue
+ citecolor: DarkSlateBlue
+ link-citations: true
+
+ biblio-title: "References"
+ biblio-config: false # Don't use the default template's biblatex commands
+ cite-method: biblatex
+ biblatex-chicago: false # Custom flag for enabling biblatex-chicago
+ biblio-style: apa
+ biblatexoptions:
+ - backend=biber
+
+ # The titlesec package provides its own mechanism for dealing with 
+ # inline/block headings, so we need to disable pandoc's support for it
+ # (see https://stackoverflow.com/q/42916124/120898)
+ block-headings: false
+ # Indent paragraphs instead of adding space between them
+ indent: true
+ html:
+ theme: styles/pretty.scss

_extensions/andrewheiss/hikmah-manuscript/include-in-header.tex

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+% -----------------------
+% CUSTOM PREAMBLE STUFF
+% -----------------------
+
+% -----------------
+% Typography tweaks
+% -----------------
+% Indent size
+\setlength{\parindent}{0.5in}
+\setlength{\leftmargin}{0.5in}
+
+% Fix widows and orphans
+\usepackage[all,defaultlines=2]{nowidow}
+
+% List things
+\usepackage{enumitem}
+% Same document-level indentation for ordered and ordered lists
+\setlist[1]{labelindent=\parindent}
+\setlist[itemize]{leftmargin=*}
+\setlist[enumerate]{leftmargin=*}
+
+% Wrap definition list terms
+% https://tex.stackexchange.com/a/9763/11851
+\setlist[description]{style=unboxed}
+
+
+% For better TOCs
+\usepackage{tocloft}
+
+% Remove left margin in lists inside longtables
+% https://tex.stackexchange.com/a/378190/11851
+\AtBeginEnvironment{longtable}{\setlist[itemize]{nosep, wide=0pt, leftmargin=*, before=\vspace*{-\baselineskip}, after=\vspace*{-\baselineskip}}}
+
+% For fancy ORCID links
+\usepackage{orcidlink}
+
+% Indent all first paragraphs because APA wants that
+\usepackage{indentfirst}
+
+
+% -----------------
+% Title block stuff
+% -----------------
+
+% Abstract
+\usepackage{abstract}
+\renewcommand{\abstractnamefont}{\normalfont\normalsize\bfseries}
+\renewcommand{\abstracttextfont}{\normalsize}
+\setlength{\absleftindent}{\parindent}
+\setlength{\absrightindent}{\parindent}
+
+
+% Keywords
+\providecommand{\keywords}[1]{\textbf{\textit{Keywords---}}#1}
+
+% Title
+\usepackage{titling}
+\setlength{\droptitle}{2\baselineskip}
+\pretitle{\begin{center}\normalfont\normalsize\bfseries}
+\posttitle{\par\end{center}\vspace{2\baselineskip}}
+
+
+% ------------------
+% Section headings
+% ------------------
+\usepackage{titlesec}
+\titleformat*{\section}{\center\normalsize\bfseries}
+\titleformat*{\subsection}{\normalsize\bfseries}
+\titleformat*{\subsubsection}{\normalsize\bfseries\itshape}
+\titleformat{\paragraph}[runin]{\bfseries}{\theparagraph.}{3pt}{\space}[.]
+\titleformat{\subparagraph}[runin]{\bfseries\itshape}{\thesubparagraph.}{3pt}{\space}[.]
+
+% \titlespacing{<command>}{<left>}{<before-sep>}{<after-sep>}
+% Starred version removes indentation in following paragraph
+\titlespacing*{\section}{0em}{2em}{0em}
+\titlespacing*{\subsection}{0em}{1em}{0em}
+\titlespacing*{\subsubsection}{0em}{0em}{0em}
+\titlespacing*{\paragraph}{\parindent}{1ex}{1em}
+\titlespacing*{\subparagraph}{\parindent}{1ex}{1em}
+
+
+% -----------
+% Footnotes
+% -----------
+% NB: footmisc has to come after biblatex because of conflicts
+\usepackage[bottom]{footmisc}
+\renewcommand*{\footnotelayout}{\footnotesize}
+
+\addtolength{\skip\footins}{12pt} % vertical space between rule and main text
+\setlength{\footnotesep}{16pt} % vertical space between footnotes
+
+
+% ----------
+% Captions
+% ----------
+\usepackage[font=normalsize]{caption}
+
+
+% ---------------------------
+% END CUSTOM PREAMBLE STUFF
+% ---------------------------

_extensions/andrewheiss/hikmah-manuscript/partials/before-body.tex

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+% ---------------
+% TITLE SECTION
+% ---------------
+
+\begin{titlepage}
+\center
+
+% Don't include a newpage before \maketitle
+{\let\newpage\relax\maketitle}
+
+% Needs to come after \maketitle
+\thispagestyle{title}
+
+\vspace{0.25in}
+
+$if(word-count)$
+{\center Word count: $word-count$}
+$endif$
+
+\vspace{0.5in}
+
+\begin{center}
+
+\textbf{Author note}
+
+$for(by-author)$
+\raggedright\setlength{\parindent}{0.5in}$it.name.literal$$if(it.orcid)$,~\orcidlink{$it.orcid$}~\url{https://orcid.org/$it.orcid$}$endif$$if(it.metadata.title)$, $it.metadata.title$$if(it.affiliations)$, $for(it.affiliations)$$if(it.department)$$it.department$, $endif$$it.name$$sep$; $endfor$ $endif$$endif$
+
+$endfor$
+
+\end{center}
+
+$if(correspondence-prefix)$
+\begin{center}
+
+\textbf{Correspondence}
+
+$for(by-author)$
+$if(it.attributes.corresponding)$
+\par\raggedright\setlength{\parindent}{0.5in}$correspondence-prefix$~$it.name.literal$$if(it.affiliations)$, $for(it.affiliations)$$if(it.department)$$it.department$, $endif$$it.name$, $if(it.address)$$it.address$, $endif$$if(it.city)$$it.city$, $endif$$if(it.region)$$it.region$ $endif$$if(it.postal-code)$$it.postal-code$$endif$$if(it.country)$, $it.country$$endif$$sep$; $endfor$ $endif$
+$endif$
+$endfor$
+
+\end{center}
+$endif$
+
+$if(additional-info)$
+\begin{center}
+
+\textbf{Additional information}
+
+\par\raggedright\setlength{\parindent}{0.5in}$additional-info$
+
+\end{center}
+$endif$
+
+$if(thanks)$
+\begin{center}
+
+\textbf{Acknowledgments}
+
+\par\raggedright\setlength{\parindent}{0.5in}$thanks$
+
+\end{center}
+$endif$
+
+\vfill % Fill the rest of the page with whitespace
+
+\end{titlepage}
+
+\doublespacing
+
+\begin{abstract}
+\noindent $abstract$
+\end{abstract}
+
+\vspace{\baselineskip}
+
+$if(keywords)$\indent \keywords{%
+$for(keywords)$$keywords$$sep$, $endfor$%
+}$endif$
+
+\newpage
+
+\begin{center}
+\singlespacing
+\textbf{$title$$if(subtitle)$:\\$subtitle$$endif$}
+\end{center}
+
+$if(epigraph)$
+$for(epigraph)$
+$if(epigraph.source)$
+\epigraph{$epigraph.text$}{---$epigraph.source$}
+$else$
+\epigraph{$epigraph.text$}
+$endif$
+$endfor$
+$endif$
+
+% -------------------
+% END TITLE SECTION
+% -------------------
+
+