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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-b8d9590b
+93deffdf
diff --git a/_tex/index.tex b/_tex/index.tex
@@ -75,6 +75,39 @@
 \makeatletter
 \def\fps@figure{htbp}
 \makeatother
+% definitions for citeproc citations
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+\makeatletter
+ % allow citations to break across lines
+ \let\@cite@ofmt\@firstofone
+ % 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}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
+ {\begin{list}{}{%
+  \setlength{\itemindent}{0pt}
+  \setlength{\leftmargin}{0pt}
+  \setlength{\parsep}{0pt}
+  % turn on hanging indent if param 1 is 1
+  \ifodd #1
+   \setlength{\leftmargin}{\cslhangindent}
+   \setlength{\itemindent}{-1\cslhangindent}
+  \fi
+  % set entry spacing
+  \setlength{\itemsep}{#2\baselineskip}}}
+ {\end{list}}
+\usepackage{calc}
+\newcommand{\CSLBlock}[1]{\hfill\break\parbox[t]{\linewidth}{\strut\ignorespaces#1\strut}}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{\strut#1\strut}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{\strut#1\strut}}
+\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
 
 \usepackage{url} %this package should fix any errors with URLs in refs.
 \usepackage{lineno}
@@ -173,9 +206,8 @@ \section{Data \& Methods}\label{sec-data-methods}
 
 \subsection{Metacommunity model}\label{metacommunity-model}
 
-The metacommunity model developed by
-(\textbf{thompsonDispersalGovernsReorganization2017a?}) is a good
-starting point to use for this `case study' as it allows us some
+The metacommunity model developed by Thompson \& Gonzalez (2017) is a
+good starting point to use for this `case study' as it allows us some
 flexibility with how we want to parameterise the system. The model
 (Equation~\ref{eq-metacomm}) itself is based on a tritrophic community
 (`plants', `herbivores', and `carnivores') and is a collection of
@@ -297,9 +329,9 @@ \subsection{Spatial wombling}\label{spatial-wombling}
 }\end{equation}
 
 The spatial wombling analyses were done using
-\texttt{SpatialBoundaries.jl}
-(\textbf{strydomSpatialBoundariesJlEdge2023?}). The docuemntation
-provides a more detailed breakdown of the underlying methodology.
+\texttt{SpatialBoundaries.jl} (Strydom \& Poisot, 2023). The
+docuemntation provides a more detailed breakdown of the underlying
+methodology.
 
 \section{Conclusion}\label{conclusion}
 
@@ -312,6 +344,21 @@ \section*{References}\label{references}
 \href{https://PoisotLab.github.io/ms_womble_ya_net/index.qmd.html}{Article
 Notebook}}
 
+\phantomsection\label{refs}
+\begin{CSLReferences}{1}{0}
+\bibitem[\citeproctext]{ref-Strydom2023Spatialboundariesa}
+Strydom, T., \& Poisot, T. (2023). {SpatialBoundaries}.jl: Edge
+detection using spatial wombling. \emph{Ecography}, \emph{2023}(5),
+e06609. \url{https://doi.org/10.1111/ecog.06609}
+
+\bibitem[\citeproctext]{ref-Thompson2017Dispersala}
+Thompson, P. L., \& Gonzalez, A. (2017). Dispersal governs the
+reorganization of ecological networks under environmental change.
+\emph{Nature Ecology \& Evolution}, \emph{1}(6).
+\url{https://doi.org/10.1038/s41559-017-0162}
+
+\end{CSLReferences}
+
 
 
 \end{document}
diff --git a/index-meca.zip b/index-meca.zip
diff --git a/index.docx b/index.docx
diff --git a/index.html b/index.html
@@ -28,6 +28,7 @@
 div.csl-bib-body { }
 div.csl-entry {
   clear: both;
+  margin-bottom: 0em;
 }
 .hanging-indent div.csl-entry {
   margin-left:2em;
@@ -216,7 +217,7 @@ <h2 data-number="1" class="anchored" data-anchor-id="introduction"><span class="
 <h2 data-number="2" class="anchored" data-anchor-id="sec-data-methods"><span class="header-section-number">2</span> Data &amp; Methods</h2>
 <section id="metacommunity-model" class="level3" data-number="2.1">
 <h3 data-number="2.1" class="anchored" data-anchor-id="metacommunity-model"><span class="header-section-number">2.1</span> Metacommunity model</h3>
-<p>The metacommunity model developed by <span class="citation" data-cites="thompsonDispersalGovernsReorganization2017a">(<a href="#ref-thompsonDispersalGovernsReorganization2017a" role="doc-biblioref"><strong>thompsonDispersalGovernsReorganization2017a?</strong></a>)</span> is a good starting point to use for this ‘case study’ as it allows us some flexibility with how we want to parameterise the system. The model (<a href="#eq-metacomm" class="quarto-xref">Equation&nbsp;1</a>) itself is based on a tritrophic community (‘plants’, ‘herbivores’, and ‘carnivores’) and is a collection of modified Lotka–Volterra equations and (broadly) models species abundance as a function of interaction strength, environmental effect, immigration, and emigration. The metacommunity consists of <span class="math inline">\(S\)</span> species with <span class="math inline">\(M\)</span> environmental patches and looks as follows:</p>
+<p>The metacommunity model developed by <span class="citation" data-cites="Thompson2017Dispersala">Thompson and Gonzalez (<a href="#ref-Thompson2017Dispersala" role="doc-biblioref">2017</a>)</span> is a good starting point to use for this ‘case study’ as it allows us some flexibility with how we want to parameterise the system. The model (<a href="#eq-metacomm" class="quarto-xref">Equation&nbsp;1</a>) itself is based on a tritrophic community (‘plants’, ‘herbivores’, and ‘carnivores’) and is a collection of modified Lotka–Volterra equations and (broadly) models species abundance as a function of interaction strength, environmental effect, immigration, and emigration. The metacommunity consists of <span class="math inline">\(S\)</span> species with <span class="math inline">\(M\)</span> environmental patches and looks as follows:</p>
 <p><span id="eq-metacomm"><span class="math display">\[
 X_{ij}(t+1)=X_{ij}(t)exp\left[C_{i} + \sum_{k=1}^{S}B_{ik}X_{kj}(t)+A_{ij}(t)\right]+I_{ij}(t)-X_{ij}(t)a_{i}
 \tag{1}\]</span></span></p>
@@ -332,16 +333,21 @@ <h3 data-number="2.3" class="anchored" data-anchor-id="spatial-wombling"><span c
 <p><span id="eq-womble"><span class="math display">\[
 m = \sqrt{\frac{\partial f(x,y)}{\partial x}^2 + \frac{\partial f(x,y)}{\partial y}^2}
 \tag{4}\]</span></span></p>
-<p>The spatial wombling analyses were done using <code>SpatialBoundaries.jl</code> <span class="citation" data-cites="strydomSpatialBoundariesJlEdge2023">(<a href="#ref-strydomSpatialBoundariesJlEdge2023" role="doc-biblioref"><strong>strydomSpatialBoundariesJlEdge2023?</strong></a>)</span>. The docuemntation provides a more detailed breakdown of the underlying methodology.</p>
+<p>The spatial wombling analyses were done using <code>SpatialBoundaries.jl</code> <span class="citation" data-cites="Strydom2023Spatialboundariesa">(<a href="#ref-Strydom2023Spatialboundariesa" role="doc-biblioref">Strydom and Poisot 2023</a>)</span>. The docuemntation provides a more detailed breakdown of the underlying methodology.</p>
 </section>
 </section>
 <section id="conclusion" class="level2" data-number="3">
 <h2 data-number="3" class="anchored" data-anchor-id="conclusion"><span class="header-section-number">3</span> Conclusion</h2>
 </section>
 <section id="references" class="level2 unnumbered">
 <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
-<div id="refs" role="list">
-
+<div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list">
+<div id="ref-Strydom2023Spatialboundariesa" class="csl-entry" role="listitem">
+Strydom, Tanya, and Timothée Poisot. 2023. <span>“<span>SpatialBoundaries</span>.jl: Edge Detection Using Spatial Wombling.”</span> <em>Ecography</em> 2023 (5): e06609. <a href="https://doi.org/10.1111/ecog.06609">https://doi.org/10.1111/ecog.06609</a>.
+</div>
+<div id="ref-Thompson2017Dispersala" class="csl-entry" role="listitem">
+Thompson, Patrick L., and Andrew Gonzalez. 2017. <span>“Dispersal Governs the Reorganization of Ecological Networks Under Environmental Change.”</span> <em>Nature Ecology &amp; Evolution</em> 1 (6). <a href="https://doi.org/10.1038/s41559-017-0162">https://doi.org/10.1038/s41559-017-0162</a>.
+</div>
 </div>
 </section>
 

diff --git a/index.pdf b/index.pdf
diff --git a/index.xml b/index.xml
@@ -140,8 +140,8 @@ Nacional (IGN). …</p>
   <title>2 Data &amp; Methods</title>
   <sec id="metacommunity-model">
     <title>2.1 Metacommunity model</title>
-    <p>The metacommunity model developed by
-    (<xref alt="thompsonDispersalGovernsReorganization2017a?" rid="ref-thompsonDispersalGovernsReorganization2017a" ref-type="bibr"><bold>thompsonDispersalGovernsReorganization2017a?</bold></xref>)
+    <p>The metacommunity model developed by Thompson and Gonzalez
+    (<xref alt="2017" rid="ref-Thompson2017Dispersala" ref-type="bibr">2017</xref>)
     is a good starting point to use for this ‘case study’ as it allows
     us some flexibility with how we want to parameterise the system. The
     model (<xref alt="Equation 1" rid="eq-metacomm">Equation 1</xref>)
@@ -432,20 +432,53 @@ Nacional (IGN). …</p>
     <mml:math display="block" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>m</mml:mi><mml:mo>=</mml:mo><mml:msqrt><mml:mrow><mml:msup><mml:mfrac><mml:mrow><mml:mi>∂</mml:mi><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy="true" form="prefix">(</mml:mo><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>y</mml:mi><mml:mo stretchy="true" form="postfix">)</mml:mo></mml:mrow></mml:mrow><mml:mrow><mml:mi>∂</mml:mi><mml:mi>x</mml:mi></mml:mrow></mml:mfrac><mml:mn>2</mml:mn></mml:msup><mml:mo>+</mml:mo><mml:msup><mml:mfrac><mml:mrow><mml:mi>∂</mml:mi><mml:mi>f</mml:mi><mml:mrow><mml:mo stretchy="true" form="prefix">(</mml:mo><mml:mi>x</mml:mi><mml:mo>,</mml:mo><mml:mi>y</mml:mi><mml:mo stretchy="true" form="postfix">)</mml:mo></mml:mrow></mml:mrow><mml:mrow><mml:mi>∂</mml:mi><mml:mi>y</mml:mi></mml:mrow></mml:mfrac><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:msqrt><mml:mspace width="2.0em"></mml:mspace><mml:mrow><mml:mo stretchy="true" form="prefix">(</mml:mo><mml:mn>4</mml:mn><mml:mo stretchy="true" form="postfix">)</mml:mo></mml:mrow></mml:mrow></mml:math></alternatives></disp-formula></styled-content></p>
     <p>The spatial wombling analyses were done using
     <monospace>SpatialBoundaries.jl</monospace>
-    (<xref alt="strydomSpatialBoundariesJlEdge2023?" rid="ref-strydomSpatialBoundariesJlEdge2023" ref-type="bibr"><bold>strydomSpatialBoundariesJlEdge2023?</bold></xref>).
-    The docuemntation provides a more detailed breakdown of the
-    underlying methodology.</p>
+    (<xref alt="Strydom and Poisot 2023" rid="ref-Strydom2023Spatialboundariesa" ref-type="bibr">Strydom
+    and Poisot 2023</xref>). The docuemntation provides a more detailed
+    breakdown of the underlying methodology.</p>
   </sec>
 </sec>
 <sec id="conclusion">
   <title>3 Conclusion</title>
 </sec>
-<sec id="references">
-  <title>References</title>
-</sec>
 </body>
 
 <back>
+<ref-list>
+  <title>References</title>
+  <ref id="ref-Strydom2023Spatialboundariesa">
+    <element-citation publication-type="article-journal">
+      <person-group person-group-type="author">
+        <name><surname>Strydom</surname><given-names>Tanya</given-names></name>
+        <name><surname>Poisot</surname><given-names>Timothée</given-names></name>
+      </person-group>
+      <article-title>SpatialBoundaries.jl: Edge detection using spatial wombling</article-title>
+      <source>Ecography</source>
+      <year iso-8601-date="2023">2023</year>
+      <volume>2023</volume>
+      <issue>5</issue>
+      <issn>1600-0587</issn>
+      <pub-id pub-id-type="doi">10.1111/ecog.06609</pub-id>
+      <fpage>e06609</fpage>
+      <lpage></lpage>
+    </element-citation>
+  </ref>
+  <ref id="ref-Thompson2017Dispersala">
+    <element-citation publication-type="article-journal">
+      <person-group person-group-type="author">
+        <name><surname>Thompson</surname><given-names>Patrick L.</given-names></name>
+        <name><surname>Gonzalez</surname><given-names>Andrew</given-names></name>
+      </person-group>
+      <article-title>Dispersal governs the reorganization of ecological networks under environmental change</article-title>
+      <source>Nature Ecology &amp; Evolution</source>
+      <publisher-name>Nature Publishing Group</publisher-name>
+      <publisher-loc>London, United States</publisher-loc>
+      <year iso-8601-date="2017-06">2017</year><month>06</month>
+      <volume>1</volume>
+      <issue>6</issue>
+      <pub-id pub-id-type="doi">10.1038/s41559-017-0162</pub-id>
+    </element-citation>
+  </ref>
+</ref-list>
 </back>
 
 <sub-article article-type="notebook" id="nb-4-nb-1">

diff --git a/notebooks/data-screening-preview.html b/notebooks/data-screening-preview.html
@@ -896,7 +896,7 @@ <h3 class="anchored" data-anchor-id="timeline-plot">Timeline Plot</h3>
     }
   }
 });
-</script>  </div> <!-- /content -->  <script>var lightboxQuarto = GLightbox({"loop":false,"descPosition":"bottom","selector":".lightbox","closeEffect":"zoom","openEffect":"zoom"});
+</script>  </div> <!-- /content -->  <script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","openEffect":"zoom","selector":".lightbox","loop":false,"descPosition":"bottom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

diff --git a/notebooks/data-screening.embed.ipynb b/notebooks/data-screening.embed.ipynb
@@ -9,7 +9,7 @@
     "Steve Purves [![](data:image/png;base64,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)](https://orcid.org/0000-0002-0760-5497)  \n",
     "Charlotte Wickham"
    ],
-   "id": "a531856a-9159-48d5-af35-ae87bf2d4c34"
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diff --git a/notebooks/data-screening.out.ipynb b/notebooks/data-screening.out.ipynb
@@ -9,7 +9,7 @@
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     "Charlotte Wickham"
    ],
-   "id": "cbdd7384-7f1f-411d-8f0d-96e1a887f0c6"
+   "id": "f0e1816e-bf2f-4fa8-9088-64878f2788b1"
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