🚑 ref fix

docs/_tex/index.tex

@@ -502,13 +502,12 @@ \subsection{The processes that determine species
 species can further aid us in refining metawebs by allowing us to
 downsample the network based on the species found in a specific
 location, or even add additional uncertainty based in how likely species
-are to co-occur (\textbf{dansereauSpatiallyExplicitPredictions2023?}).
-Additionally the interplay between the interaction between a species
-pair and their co-occurrence is meaningful when one is operating in the
-space of trying to determine the distribution of a species (Higino et
-al., 2023), and forms a key component of some of the next generation
-species distribution models \emph{e.g.,} joint SDMs (Pollock et al.,
-2014).
+are to co-occur (Dansereau et al., 2024). Additionally the interplay
+between the interaction between a species pair and their co-occurrence
+is meaningful when one is operating in the space of trying to determine
+the distribution of a species (Higino et al., 2023), and forms a key
+component of some of the next generation species distribution models
+\emph{e.g.,} joint SDMs (Pollock et al., 2014).
 
 \textbf{Abundance}
 
@@ -601,8 +600,8 @@ \section{Network construction is
 network representation in the context of trying to understand the
 feeding dynamics of a seasonal community.
 
-\begin{tcolorbox}[enhanced jigsaw, rightrule=.15mm, breakable, colframe=quarto-callout-note-color-frame, opacitybacktitle=0.6, toprule=.15mm, colbacktitle=quarto-callout-note-color!10!white, titlerule=0mm, left=2mm, opacityback=0, bottomtitle=1mm, arc=.35mm, coltitle=black, toptitle=1mm, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Box 1 - Why we need to aggregate networks at different scales: A
-hypothetical case study}, bottomrule=.15mm, leftrule=.75mm, colback=white]
+\begin{tcolorbox}[enhanced jigsaw, coltitle=black, colbacktitle=quarto-callout-note-color!10!white, leftrule=.75mm, colback=white, rightrule=.15mm, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Box 1 - Why we need to aggregate networks at different scales: A
+hypothetical case study}, left=2mm, toprule=.15mm, bottomtitle=1mm, opacitybacktitle=0.6, opacityback=0, breakable, titlerule=0mm, toptitle=1mm, bottomrule=.15mm, colframe=quarto-callout-note-color-frame, arc=.35mm]
 
 Although it might seem most prudent to be predicting, constructing, and
 defining networks that are the closest representation of reality there
@@ -1006,6 +1005,13 @@ \section*{References}\label{references}
 signature of food webs' backbones using functional traits. \emph{Oikos},
 \emph{125}(4), 446--456. \url{https://doi.org/10.1111/oik.02305}
 
+\bibitem[\citeproctext]{ref-dansereauSpatiallyExplicitPredictions2024}
+Dansereau, G., Barros, C., \& Poisot, T. (2024). Spatially explicit
+predictions of food web structure from regional-level data.
+\emph{Philosophical Transactions of the Royal Society B: Biological
+Sciences}, \emph{379}(1909).
+\url{https://doi.org/10.1098/rstb.2023.0166}
+
 \bibitem[\citeproctext]{ref-delmasAnalysingEcologicalNetworks2019}
 Delmas, E., Besson, M., Brice, M.-H., Burkle, L. A., Riva, G. V. D.,
 Fortin, M.-J., Gravel, D., Guimarães, P. R., Hembry, D. H., Newman, E.

docs/index.html

@@ -447,7 +447,7 @@ <h1 data-number="2"><span class="header-section-number">2</span> From Nodes and
 <div id="fig-process" class="quarto-figure quarto-figure-center quarto-float anchored">
 <figure class="quarto-float quarto-float-fig figure">
 <div aria-describedby="fig-process-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="images/concept_v2.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1"><img src="images/concept_v2.png" class="img-fluid figure-img"></a>
+<a href="images/concept_v2.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="images/concept_v2.png" class="img-fluid figure-img"></a>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-process-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Figure&nbsp;1: TODO.
@@ -459,7 +459,7 @@ <h2 data-number="2.1" class="anchored" data-anchor-id="the-processes-that-determ
 <p><strong>Evolutionary compatibility</strong></p>
 <p>There is compelling evidence that the possibility of an interaction occurring between two species is the result of their shared (co)evolutionary history <span class="citation" data-cites="segarRoleEvolutionShaping2020 gomezEcologicalInteractionsAre2010 dallarivaExploringEvolutionarySignature2016">(<a href="#ref-segarRoleEvolutionShaping2020" role="doc-biblioref">Segar et al. 2020</a>; <a href="#ref-gomezEcologicalInteractionsAre2010" role="doc-biblioref">Gómez, Verdú, and Perfectti 2010</a>; <a href="#ref-dallarivaExploringEvolutionarySignature2016" role="doc-biblioref">Dalla Riva and Stouffer 2016</a>)</span>. In the more proximal sense this is manifested as the ‘trait complementarity’ between two species, whereby one species (the predator) has the ‘correct’ set of traits that allow it to chase, capture, kill, and consume the other species (the prey). For species pairs where this condition is not met the link is deemed to be forbidden <span class="citation" data-cites="jordanoSamplingNetworksEcological2016">(<a href="#ref-jordanoSamplingNetworksEcological2016" role="doc-biblioref">Jordano 2016b</a>)</span>; <em>i.e.,</em> not physically possible and will always be absent within the network. In the context of trying to determine the feasibility (<em>i.e.,</em> the <em>possibility</em>) of an interaction, phylogeny is an excellent predictor <span class="citation" data-cites="strydomFoodWebReconstruction2022 frickeCollapseTerrestrialMammal2022">(<a href="#ref-strydomFoodWebReconstruction2022" role="doc-biblioref">Strydom et al. 2022</a>; <a href="#ref-frickeCollapseTerrestrialMammal2022" role="doc-biblioref">Fricke et al. 2022</a>)</span> and allows one to construct what can be considered to be a metaweb. In terms of thinking about the anatomy of an ‘feasibility network’ one should be aware that it is possible to represent interactions as either binary (feasible/forbidden; <em>i.e.,</em> the traditional definition of a metaweb <span class="citation" data-cites="dunneNetworkStructureFood2006">Jennifer A. Dunne (<a href="#ref-dunneNetworkStructureFood2006" role="doc-biblioref">2006</a>)</span>) or as a probability <span class="citation" data-cites="banvilleDecipheringProbabilisticSpecies2024">(<a href="#ref-banvilleDecipheringProbabilisticSpecies2024" role="doc-biblioref">Banville et al. 2024</a>)</span>, where the probability represents how likely that the interaction between to species is feasible (what is the possibility of this interaction occurring?).</p>
 <p><strong>(Co)occurrence</strong></p>
-<p>Although the outright assumption that because two species are co-occurring it must mean that they are interacting is inherently flawed <span class="citation" data-cites="blanchetCooccurrenceNotEvidence2020">(<a href="#ref-blanchetCooccurrenceNotEvidence2020" role="doc-biblioref">Blanchet, Cazelles, and Gravel 2020</a>)</span>, it is of course impossible for two species to interact (at least in terms of feeding links) if they are not co-occurring in time and space. Thus co-occurrence data alone is insufficient to build an accurate and ecologically meaningful representation of a food web having information on the co-occurrence of species can further aid us in refining metawebs by allowing us to downsample the network based on the species found in a specific location, or even add additional uncertainty based in how likely species are to co-occur <span class="citation" data-cites="dansereauSpatiallyExplicitPredictions2023">(<a href="#ref-dansereauSpatiallyExplicitPredictions2023" role="doc-biblioref"><strong>dansereauSpatiallyExplicitPredictions2023?</strong></a>)</span>. Additionally the interplay between the interaction between a species pair and their co-occurrence is meaningful when one is operating in the space of trying to determine the distribution of a species <span class="citation" data-cites="higinoMismatchIUCNRange2023">(<a href="#ref-higinoMismatchIUCNRange2023" role="doc-biblioref">Higino et al. 2023</a>)</span>, and forms a key component of some of the next generation species distribution models <em>e.g.,</em> joint SDMs <span class="citation" data-cites="pollockUnderstandingCooccurrenceModelling2014">(<a href="#ref-pollockUnderstandingCooccurrenceModelling2014" role="doc-biblioref">Pollock et al. 2014</a>)</span>.</p>
+<p>Although the outright assumption that because two species are co-occurring it must mean that they are interacting is inherently flawed <span class="citation" data-cites="blanchetCooccurrenceNotEvidence2020">(<a href="#ref-blanchetCooccurrenceNotEvidence2020" role="doc-biblioref">Blanchet, Cazelles, and Gravel 2020</a>)</span>, it is of course impossible for two species to interact (at least in terms of feeding links) if they are not co-occurring in time and space. Thus co-occurrence data alone is insufficient to build an accurate and ecologically meaningful representation of a food web having information on the co-occurrence of species can further aid us in refining metawebs by allowing us to downsample the network based on the species found in a specific location, or even add additional uncertainty based in how likely species are to co-occur <span class="citation" data-cites="dansereauSpatiallyExplicitPredictions2024">(<a href="#ref-dansereauSpatiallyExplicitPredictions2024" role="doc-biblioref">Dansereau, Barros, and Poisot 2024</a>)</span>. Additionally the interplay between the interaction between a species pair and their co-occurrence is meaningful when one is operating in the space of trying to determine the distribution of a species <span class="citation" data-cites="higinoMismatchIUCNRange2023">(<a href="#ref-higinoMismatchIUCNRange2023" role="doc-biblioref">Higino et al. 2023</a>)</span>, and forms a key component of some of the next generation species distribution models <em>e.g.,</em> joint SDMs <span class="citation" data-cites="pollockUnderstandingCooccurrenceModelling2014">(<a href="#ref-pollockUnderstandingCooccurrenceModelling2014" role="doc-biblioref">Pollock et al. 2014</a>)</span>.</p>
 <p><strong>Abundance</strong></p>
 <p>The abundance of the different species within the community can influence the likelihood of an interaction occurring in a myriad of ways. There is the argument that networks (and the interactions that make them up) are driven by only the abundance of the different species and not the characteristics (traits), <em>sensu</em> neutral processes and have been formalised with the neutral model <span class="citation" data-cites="canardEmergenceStructuralPatterns2012">(<a href="#ref-canardEmergenceStructuralPatterns2012" role="doc-biblioref">Canard et al. 2012</a>)</span>, as well as statistical tools <span class="citation" data-cites="momalTreebasedInferenceSpecies2020">(<a href="#ref-momalTreebasedInferenceSpecies2020" role="doc-biblioref">Momal, Robin, and Ambroise 2020</a>)</span>. Alternatively the abundance of species in a community can influence which interactions are ultimately realised <span class="citation" data-cites="poisotSpeciesWhyEcological2015 banvilleDecipheringProbabilisticSpecies2024">(<a href="#ref-poisotSpeciesWhyEcological2015" role="doc-biblioref">Poisot, Stouffer, and Gravel 2015</a>; <a href="#ref-banvilleDecipheringProbabilisticSpecies2024" role="doc-biblioref">Banville et al. 2024</a>)</span>.</p>
 <p><strong>Predator choice (energetic cost)</strong></p>
@@ -607,6 +607,9 @@ <h1 class="unnumbered">References</h1>
 <div id="ref-dallarivaExploringEvolutionarySignature2016" class="csl-entry" role="listitem">
 Dalla Riva, Giulio V, and Daniel B. Stouffer. 2016. <span>“Exploring the Evolutionary Signature of Food Webs’ Backbones Using Functional Traits.”</span> <em>Oikos</em> 125 (4): 446–56. <a href="https://doi.org/10.1111/oik.02305">https://doi.org/10.1111/oik.02305</a>.
 </div>
+<div id="ref-dansereauSpatiallyExplicitPredictions2024" class="csl-entry" role="listitem">
+Dansereau, Gabriel, Ceres Barros, and Timothée Poisot. 2024. <span>“Spatially Explicit Predictions of Food Web Structure from Regional-Level Data.”</span> <em>Philosophical Transactions of the Royal Society B: Biological Sciences</em> 379 (1909). <a href="https://doi.org/10.1098/rstb.2023.0166">https://doi.org/10.1098/rstb.2023.0166</a>.
+</div>
 <div id="ref-delmasAnalysingEcologicalNetworks2019" class="csl-entry" role="listitem">
 Delmas, Eva, Mathilde Besson, Marie-Hélène Brice, Laura A. Burkle, Giulio V. Dalla Riva, Marie-Josée Fortin, Dominique Gravel, et al. 2019. <span>“Analysing Ecological Networks of Species Interactions.”</span> <em>Biological Reviews</em> 94 (1): 16–36. <a href="https://doi.org/10.1111/brv.12433">https://doi.org/10.1111/brv.12433</a>.
 </div>
@@ -1218,7 +1221,7 @@ <h1 class="unnumbered">References</h1>
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@@ -2092,7 +2092,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
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@@ -501,7 +501,7 @@ <h2 class="anchored" data-anchor-id="visualising-results">Visualising results</h
 <div id="fig-boxplot" class="quarto-figure quarto-figure-center quarto-float anchored">
 <figure class="quarto-float quarto-float-fig figure">
 <div aria-describedby="fig-boxplot-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="../images/boxplot.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1"><img src="../images/boxplot.png" class="img-fluid figure-img"></a>
+<a href="../images/boxplot.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="../images/boxplot.png" class="img-fluid figure-img"></a>
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 Boxplot
@@ -512,7 +512,7 @@ <h2 class="anchored" data-anchor-id="visualising-results">Visualising results</h
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+<a href="../images/topology.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" data-glightbox="description: .lightbox-desc-2"><img src="../images/topology.png" class="img-fluid figure-img"></a>
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 Differences
@@ -952,7 +952,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
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index.qmd

@@ -96,7 +96,7 @@ There is compelling evidence that the possibility of an interaction occurring be
 
 **(Co)occurrence**
 
-Although the outright assumption that because two species are co-occurring it must mean that they are interacting is inherently flawed [@blanchetCooccurrenceNotEvidence2020], it is of course impossible for two species to interact (at least in terms of feeding links) if they are not co-occurring in time and space. Thus co-occurrence data alone is insufficient to build an accurate and ecologically meaningful representation of a food web having information on the co-occurrence of species can further aid us in refining metawebs by allowing us to downsample the network based on the species found in a specific location, or even add additional uncertainty based in how likely species are to co-occur [@dansereauSpatiallyExplicitPredictions2023]. Additionally the interplay between the interaction between a species pair and their co-occurrence is meaningful when one is operating in the space of trying to determine the distribution of a species [@higinoMismatchIUCNRange2023], and forms a key component of some of the next generation species distribution models *e.g.,* joint SDMs [@pollockUnderstandingCooccurrenceModelling2014].
+Although the outright assumption that because two species are co-occurring it must mean that they are interacting is inherently flawed [@blanchetCooccurrenceNotEvidence2020], it is of course impossible for two species to interact (at least in terms of feeding links) if they are not co-occurring in time and space. Thus co-occurrence data alone is insufficient to build an accurate and ecologically meaningful representation of a food web having information on the co-occurrence of species can further aid us in refining metawebs by allowing us to downsample the network based on the species found in a specific location, or even add additional uncertainty based in how likely species are to co-occur [@dansereauSpatiallyExplicitPredictions2024]. Additionally the interplay between the interaction between a species pair and their co-occurrence is meaningful when one is operating in the space of trying to determine the distribution of a species [@higinoMismatchIUCNRange2023], and forms a key component of some of the next generation species distribution models *e.g.,* joint SDMs [@pollockUnderstandingCooccurrenceModelling2014].
 
 **Abundance**