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docs/_tex/index.tex

@@ -444,7 +444,7 @@ \subsection{Putting the parts together; what does it
 research programmes (or even practical needs) that have been driving the
 construction of them.
 
-\begin{tcolorbox}[enhanced jigsaw, bottomtitle=1mm, leftrule=.75mm, breakable, opacitybacktitle=0.6, arc=.35mm, coltitle=black, colbacktitle=quarto-callout-note-color!10!white, toprule=.15mm, left=2mm, titlerule=0mm, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Box 1 - Moving between the feasibility and reality of interactions}, opacityback=0, rightrule=.15mm, bottomrule=.15mm, colframe=quarto-callout-note-color-frame, toptitle=1mm, colback=white]
+\begin{tcolorbox}[enhanced jigsaw, toptitle=1mm, toprule=.15mm, coltitle=black, opacityback=0, left=2mm, leftrule=.75mm, colback=white, breakable, colframe=quarto-callout-note-color-frame, titlerule=0mm, opacitybacktitle=0.6, bottomrule=.15mm, bottomtitle=1mm, rightrule=.15mm, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Box 1 - Moving between the feasibility and reality of interactions}, colbacktitle=quarto-callout-note-color!10!white, arc=.35mm]
 
 Before thinking about the ways in which we can predict networks it is
 perhaps meaningful to take a step back and think about the different
@@ -570,14 +570,13 @@ \subsection*{`Mechanisms'}\label{mechanisms}
 of how prey choice as informed by energetic cost (not just purely based
 on \emph{e.g.,} the most abundant species). If we think about ways that
 people have approached this there are the diet models of (Beckerman et
-al., 2006) and (Petchey et al., 2008) that tike a high-level (imo)
-approach to accounting for energy acquisition, then you get the `trait'
-framework developed by K. L. Wootton et al. (2023) that moves the
-`energy' into different `modules' related to the process of the consumer
-acquiring energy from the resource (however there is a disregard for the
-`Rule 1' requirement of forbidden links, again not bad just pointing it
-out). The idea of the consumer search space developed by Pawar et al.
-(2012) is also an interesting consideration.
+al., 2006) and (Petchey et al., 2008) as well as the `trait' framework
+developed by K. L. Wootton et al. (2023) that moves the `energy' into
+different `modules' related to the process of the consumer acquiring
+energy from the resource (however there is a disregard for the `Rule 1'
+requirement of forbidden links, again not bad just pointing it out). The
+idea of the consumer search space developed by Pawar et al. (2012) is
+also an interesting consideration.
 
 \textbf{5. Consumer--environment (energetic) interactions}
 
@@ -836,7 +835,7 @@ \subsection{Model families}\label{model-families}
 
 \end{figure}%
 
-\begin{tcolorbox}[enhanced jigsaw, bottomtitle=1mm, leftrule=.75mm, breakable, opacitybacktitle=0.6, arc=.35mm, coltitle=black, colbacktitle=quarto-callout-note-color!10!white, toprule=.15mm, left=2mm, titlerule=0mm, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Box 2 - Assessing model outputs}, opacityback=0, rightrule=.15mm, bottomrule=.15mm, colframe=quarto-callout-note-color-frame, toptitle=1mm, colback=white]
+\begin{tcolorbox}[enhanced jigsaw, toptitle=1mm, toprule=.15mm, coltitle=black, opacityback=0, left=2mm, leftrule=.75mm, colback=white, breakable, colframe=quarto-callout-note-color-frame, titlerule=0mm, opacitybacktitle=0.6, bottomrule=.15mm, bottomtitle=1mm, rightrule=.15mm, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Box 2 - Assessing model outputs}, colbacktitle=quarto-callout-note-color!10!white, arc=.35mm]
 
 Although understanding the underlying philosophy of the different model
 families is beneficial it is also important to understand in what

docs/index.html

@@ -431,7 +431,7 @@ <h3 class="unnumbered anchored" data-anchor-id="mechanisms">‘Mechanisms’</h3
 <p>Not sure if there are models that ‘only’ consider abundance (barring the neutral model) and that it is rather more of a building block in some of the models that are more relevant to the next steps. Maybe there is an argument that this ‘rule’ is ‘irrelevant’ in the context of how I am presenting network prediction and more so a data parameter one needs… maybe…</p>
 <p>This is probably the point where we start to shift from a <em>potential</em> (presence/absence) way of defining interactions and start moving into the ‘qualitative’/weighted interaction space - we are not ‘determining’ if the interaction is feasible but rather making an assumption on prey selection based on the species’ likelihood of ‘meeting’, although Banville (in prep) presents a compelling case that this could still be considered something that falls under the ‘feasibility’ and not ‘reality’ side of the spectrum… (well at least past Tanya seemed to think so)</p>
 <p><strong>4. Consumer–resource (energetic) interactions</strong></p>
-<p>This is where we begin to move into the foraging ecology space - specifically consumption rate and how that pertains to energy acquisition <em>i.e.,</em> optimal foraging theory. In the loosest sense I think this is the ‘prey choice’ space - but specifically in the context of how prey choice as informed by energetic cost (not just purely based on <em>e.g.,</em> the most abundant species). If we think about ways that people have approached this there are the diet models of <span class="citation" data-cites="beckermanForagingBiologyPredicts2006">(<a href="#ref-beckermanForagingBiologyPredicts2006" role="doc-biblioref">Beckerman, Petchey, and Warren 2006</a>)</span> and <span class="citation" data-cites="petcheySizeForagingFood2008">(<a href="#ref-petcheySizeForagingFood2008" role="doc-biblioref">Petchey et al. 2008</a>)</span> that tike a high-level (imo) approach to accounting for energy acquisition, then you get the ‘trait’ framework developed by <span class="citation" data-cites="woottonModularTheoryTrophic2023">K. L. Wootton et al. (<a href="#ref-woottonModularTheoryTrophic2023" role="doc-biblioref">2023</a>)</span> that moves the ‘energy’ into different ‘modules’ related to the process of the consumer acquiring energy from the resource (however there is a disregard for the ‘Rule 1’ requirement of forbidden links, again not bad just pointing it out). The idea of the consumer search space developed by <span class="citation" data-cites="pawarDimensionalityConsumerSearch2012">Pawar, Dell, and Savage (<a href="#ref-pawarDimensionalityConsumerSearch2012" role="doc-biblioref">2012</a>)</span> is also an interesting consideration.</p>
+<p>This is where we begin to move into the foraging ecology space - specifically consumption rate and how that pertains to energy acquisition <em>i.e.,</em> optimal foraging theory. In the loosest sense I think this is the ‘prey choice’ space - but specifically in the context of how prey choice as informed by energetic cost (not just purely based on <em>e.g.,</em> the most abundant species). If we think about ways that people have approached this there are the diet models of <span class="citation" data-cites="beckermanForagingBiologyPredicts2006">(<a href="#ref-beckermanForagingBiologyPredicts2006" role="doc-biblioref">Beckerman, Petchey, and Warren 2006</a>)</span> and <span class="citation" data-cites="petcheySizeForagingFood2008">(<a href="#ref-petcheySizeForagingFood2008" role="doc-biblioref">Petchey et al. 2008</a>)</span> as well as the ‘trait’ framework developed by <span class="citation" data-cites="woottonModularTheoryTrophic2023">K. L. Wootton et al. (<a href="#ref-woottonModularTheoryTrophic2023" role="doc-biblioref">2023</a>)</span> that moves the ‘energy’ into different ‘modules’ related to the process of the consumer acquiring energy from the resource (however there is a disregard for the ‘Rule 1’ requirement of forbidden links, again not bad just pointing it out). The idea of the consumer search space developed by <span class="citation" data-cites="pawarDimensionalityConsumerSearch2012">Pawar, Dell, and Savage (<a href="#ref-pawarDimensionalityConsumerSearch2012" role="doc-biblioref">2012</a>)</span> is also an interesting consideration.</p>
 <p><strong>5. Consumer–environment (energetic) interactions</strong></p>
 <p>I think this should be it’s own rule since its really more about the idea of how the environment is imposing energy costs on the predator as opposed the energetic costs (and gain) of consuming the prey. Basically the ideas presented in <span class="citation" data-cites="cherifEnvironmentRescueCan2024">Cherif et al. (<a href="#ref-cherifEnvironmentRescueCan2024" role="doc-biblioref">2024</a>)</span>, which is essentially a take on movement ecology? What it boils down to is being able to quantify the cost of movement <em>i.e.,</em> the physical constraints that the environment imposes on a species… Maybe we can also think of it more in terms of metabolic rate?</p>
 <blockquote class="blockquote">
@@ -1343,7 +1343,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
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docs/notebooks/model_qualitative-preview.html

@@ -1688,7 +1688,7 @@ <h2 class="anchored" data-anchor-id="visualisation">Visualisation</h2>
 <div id="fig-dendro" class="quarto-figure quarto-figure-center quarto-float anchored">
 <figure class="quarto-float quarto-float-fig figure">
 <div aria-describedby="fig-dendro-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="../images/dendo.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="../images/dendo.png" class="img-fluid figure-img"></a>
+<a href="../images/dendo.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1"><img src="../images/dendo.png" class="img-fluid figure-img"></a>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-dendro-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Dendrogram of the trait table using a hierarchical clustering model, This is based off of the traits table in SuppMat 2)
@@ -2092,7 +2092,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
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docs/notebooks/model_quantitative-preview.html

@@ -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-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="../images/boxplot.png" class="img-fluid figure-img"></a>
+<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>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-boxplot-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Boxplot
@@ -512,7 +512,7 @@ <h2 class="anchored" data-anchor-id="visualising-results">Visualising results</h
 <div id="fig-topology" class="quarto-figure quarto-figure-center quarto-float anchored">
 <figure class="quarto-float quarto-float-fig figure">
 <div aria-describedby="fig-topology-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<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>
+<a href="../images/topology.png" class="lightbox" data-glightbox="description: .lightbox-desc-2" data-gallery="quarto-lightbox-gallery-2"><img src="../images/topology.png" class="img-fluid figure-img"></a>
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 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-topology-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Differences
@@ -949,7 +949,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
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index.qmd

@@ -106,7 +106,7 @@ This is probably the point where we start to shift from a *potential* (presence/
 
 **4. Consumer–resource (energetic) interactions**
 
-This is where we begin to move into the foraging ecology space - specifically consumption rate and how that pertains to energy acquisition *i.e.,* optimal foraging theory. In the loosest sense I think this is the 'prey choice' space - but specifically in the context of how prey choice as informed by energetic cost (not just purely based on *e.g.,* the most abundant species). If we think about ways that people have approached this there are the diet models of [@beckermanForagingBiologyPredicts2006] and [@petcheySizeForagingFood2008] that tike a high-level (imo) approach to accounting for energy acquisition, then you get the 'trait' framework developed by @woottonModularTheoryTrophic2023 that moves the 'energy' into different 'modules' related to the process of the consumer acquiring energy from the resource (however there is a disregard for the 'Rule 1' requirement of forbidden links, again not bad just pointing it out). The idea of the consumer search space developed by @pawarDimensionalityConsumerSearch2012 is also an interesting consideration.
+This is where we begin to move into the foraging ecology space - specifically consumption rate and how that pertains to energy acquisition *i.e.,* optimal foraging theory. In the loosest sense I think this is the 'prey choice' space - but specifically in the context of how prey choice as informed by energetic cost (not just purely based on *e.g.,* the most abundant species). If we think about ways that people have approached this there are the diet models of [@beckermanForagingBiologyPredicts2006] and [@petcheySizeForagingFood2008] as well as the 'trait' framework developed by @woottonModularTheoryTrophic2023 that moves the 'energy' into different 'modules' related to the process of the consumer acquiring energy from the resource (however there is a disregard for the 'Rule 1' requirement of forbidden links, again not bad just pointing it out). The idea of the consumer search space developed by @pawarDimensionalityConsumerSearch2012 is also an interesting consideration.
 
 **5. Consumer–environment (energetic) interactions**