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_tex/index.tex

@@ -367,19 +367,19 @@ \subsection{What is captured by an
 feeding links between species (be that realised or potential (Dunne,
 2006; Pringle, 2020), or fluxes within a system \emph{e.g.,} energy
 transfer or material flow as the result of the feeding links between
-species (Lindeman, 1942). These correspond to different `currencies'
-(the feasibility of links or the energy that is moving between nodes).
-There are also a myriad of ways in which the links themselves can be
-specified. Links between species can be treated present or absent
-(\emph{i.e.,} binary), may be defined as probabilities (Banville et al.,
-2024; Poisot, Cirtwill, et al., 2016) or by continuous functions which
-further quantify the strength of an interaction (Berlow et al., 2004).
-How links are specified will influence the structure of the network. For
-example, taking a food web that consists of links representing all
-\emph{potential} feeding links in a collection of species will be
-meaningless if one is interested in understanding the flow of energy
-through the network as the links are not environmentally/energetically
-constrained.
+species (Lindeman, 1942; Proulx et al., 2005). These correspond to
+different `currencies' (the feasibility of links or the energy that is
+moving between nodes). There are also a myriad of ways in which the
+links themselves can be specified. Links between species can be treated
+present or absent (\emph{i.e.,} binary), may be defined as probabilities
+(Banville et al., 2024; Poisot, Cirtwill, et al., 2016) or by continuous
+functions which further quantify the strength of an interaction (Berlow
+et al., 2004). How links are specified will influence the structure of
+the network. For example, taking a food web that consists of links
+representing all \emph{potential} feeding links in a collection of
+species will be meaningless if one is interested in understanding the
+flow of energy through the network as the links are not
+environmentally/energetically constrained.
 
 \subsection{Network representations}\label{sec-representation}
 
@@ -530,7 +530,7 @@ \subsection{Processes that modify the behaviour (preference) of
 `truly realised' network is the product of different facets of both the
 properties of the community (\textbf{abundance} and \textbf{non-trophic
 interactions}) as well as the individual (\textbf{profitability}). This
-represents a contextual shift where the presence (realisation) of an
+represents a conceptual shift where the presence (realisation) of an
 interaction is no longer constrained to evaluating the viability between
 a \emph{pair} of species but rather takes into consideration information
 about the community and the individual (Quintero et al., 2024), and as
@@ -544,15 +544,14 @@ \subsection{Processes that modify the behaviour (preference) of
 proportion to their abundance (Stephens \& Krebs, 1986), and
 interactions are not necessarily contingent on there being any
 compatibility between them (E. Canard et al., 2012; Momal et al., 2020;
-Pomeranz et al., 2019). However, a more ecologically sound assumption
-would be that the abundance of different prey species will influence the
-distribution of links in a network (Vázquez et al., 2009), by
-influencing which prey are targeted or preferred by the predator, as
-abundance influences factors such as the likelihood of two species
-(individuals) meeting (Banville et al., 2024; Poisot et al., 2015).
-Thus, if abundance data are combined with a derived metaweb, there is a
-basic ruleset that can define the distribution (\emph{e.g.,} structure)
-and potentially the strength of links.
+Pomeranz et al., 2019). Alternatively the abundance of different prey
+species will influence the distribution of links in a network (Vázquez
+et al., 2009), by influencing which prey are targeted or preferred by
+the predator, as abundance influences factors such as the likelihood of
+two species (individuals) meeting (Banville et al., 2024; Poisot et al.,
+2015). Thus, if abundance data are combined with a derived metaweb,
+there is a basic ruleset that can define the distribution (\emph{e.g.,}
+structure) and potentially the strength of links.
 
 \textbf{Profitability}
 

index.html

@@ -471,7 +471,7 @@ <h2 data-number="1.1" class="anchored" data-anchor-id="how-do-we-define-a-node">
 </section>
 <section id="what-is-captured-by-an-edge" class="level2" data-number="1.2">
 <h2 data-number="1.2" class="anchored" data-anchor-id="what-is-captured-by-an-edge"><span class="header-section-number">1.2</span> What is captured by an edge?</h2>
-<p>Links within food webs can be thought of as a representation of either feeding links between species (be that realised or potential <span class="citation" data-cites="dunneNetworkStructureFood2006 pringleUntanglingFoodWebs2020">(<a href="#ref-dunneNetworkStructureFood2006" role="doc-biblioref">Dunne 2006</a>; <a href="#ref-pringleUntanglingFoodWebs2020" role="doc-biblioref">Pringle 2020</a>)</span>, or fluxes within a system <em>e.g.,</em> energy transfer or material flow as the result of the feeding links between species <span class="citation" data-cites="lindemanTrophicDynamicAspectEcology1942">(<a href="#ref-lindemanTrophicDynamicAspectEcology1942" role="doc-biblioref">Lindeman 1942</a>)</span>. These correspond to different ‘currencies’ (the feasibility of links or the energy that is moving between nodes). There are also a myriad of ways in which the links themselves can be specified. Links between species can be treated present or absent (<em>i.e.,</em> binary), may be defined as probabilities <span class="citation" data-cites="banvilleDecipheringProbabilisticSpecies2024 poisotStructureProbabilisticNetworks2016">(<a href="#ref-banvilleDecipheringProbabilisticSpecies2024" role="doc-biblioref">Banville et al. 2024</a>; <a href="#ref-poisotStructureProbabilisticNetworks2016" role="doc-biblioref">Poisot et al. 2016</a>)</span> or by continuous functions which further quantify the strength of an interaction <span class="citation" data-cites="berlowInteractionStrengthsFood2004">(<a href="#ref-berlowInteractionStrengthsFood2004" role="doc-biblioref">Berlow et al. 2004</a>)</span>. How links are specified will influence the structure of the network. For example, taking a food web that consists of links representing all <em>potential</em> feeding links in a collection of species will be meaningless if one is interested in understanding the flow of energy through the network as the links are not environmentally/energetically constrained.</p>
+<p>Links within food webs can be thought of as a representation of either feeding links between species (be that realised or potential <span class="citation" data-cites="dunneNetworkStructureFood2006 pringleUntanglingFoodWebs2020">(<a href="#ref-dunneNetworkStructureFood2006" role="doc-biblioref">Dunne 2006</a>; <a href="#ref-pringleUntanglingFoodWebs2020" role="doc-biblioref">Pringle 2020</a>)</span>, or fluxes within a system <em>e.g.,</em> energy transfer or material flow as the result of the feeding links between species <span class="citation" data-cites="lindemanTrophicDynamicAspectEcology1942 proulxNetworkThinkingEcology2005">(<a href="#ref-lindemanTrophicDynamicAspectEcology1942" role="doc-biblioref">Lindeman 1942</a>; <a href="#ref-proulxNetworkThinkingEcology2005" role="doc-biblioref">Proulx, Promislow, and Phillips 2005</a>)</span>. These correspond to different ‘currencies’ (the feasibility of links or the energy that is moving between nodes). There are also a myriad of ways in which the links themselves can be specified. Links between species can be treated present or absent (<em>i.e.,</em> binary), may be defined as probabilities <span class="citation" data-cites="banvilleDecipheringProbabilisticSpecies2024 poisotStructureProbabilisticNetworks2016">(<a href="#ref-banvilleDecipheringProbabilisticSpecies2024" role="doc-biblioref">Banville et al. 2024</a>; <a href="#ref-poisotStructureProbabilisticNetworks2016" role="doc-biblioref">Poisot et al. 2016</a>)</span> or by continuous functions which further quantify the strength of an interaction <span class="citation" data-cites="berlowInteractionStrengthsFood2004">(<a href="#ref-berlowInteractionStrengthsFood2004" role="doc-biblioref">Berlow et al. 2004</a>)</span>. How links are specified will influence the structure of the network. For example, taking a food web that consists of links representing all <em>potential</em> feeding links in a collection of species will be meaningless if one is interested in understanding the flow of energy through the network as the links are not environmentally/energetically constrained.</p>
 </section>
 <section id="sec-representation" class="level2" data-number="1.3">
 <h2 data-number="1.3" class="anchored" data-anchor-id="sec-representation"><span class="header-section-number">1.3</span> Network representations</h2>
@@ -506,9 +506,9 @@ <h2 data-number="2.1" class="anchored" data-anchor-id="sec-process-feasibility">
 </section>
 <section id="sec-process-realisation" class="level2" data-number="2.2">
 <h2 data-number="2.2" class="anchored" data-anchor-id="sec-process-realisation"><span class="header-section-number">2.2</span> Processes that modify the behaviour (preference) of species</h2>
-<p>Here we will showcase three processes that will ultimately influence the realisation of an interaction between species and form the conceptual basis for realised networks. As we show in <a href="#fig-process" class="quarto-xref">Figure&nbsp;1</a> a ‘truly realised’ network is the product of different facets of both the properties of the community (<strong>abundance</strong> and <strong>non-trophic interactions</strong>) as well as the individual (<strong>profitability</strong>). This represents a contextual shift where the presence (realisation) of an interaction is no longer constrained to evaluating the viability between a <em>pair</em> of species but rather takes into consideration information about the community and the individual <span class="citation" data-cites="quinteroDownscalingMutualisticNetworks2024">(<a href="#ref-quinteroDownscalingMutualisticNetworks2024" role="doc-biblioref">Quintero et al. 2024</a>)</span>, and as discussed in <a href="#sec-representation" class="quarto-xref">Section&nbsp;1.3</a>, links are now <em>constrained</em> by consumer choice.</p>
+<p>Here we will showcase three processes that will ultimately influence the realisation of an interaction between species and form the conceptual basis for realised networks. As we show in <a href="#fig-process" class="quarto-xref">Figure&nbsp;1</a> a ‘truly realised’ network is the product of different facets of both the properties of the community (<strong>abundance</strong> and <strong>non-trophic interactions</strong>) as well as the individual (<strong>profitability</strong>). This represents a conceptual shift where the presence (realisation) of an interaction is no longer constrained to evaluating the viability between a <em>pair</em> of species but rather takes into consideration information about the community and the individual <span class="citation" data-cites="quinteroDownscalingMutualisticNetworks2024">(<a href="#ref-quinteroDownscalingMutualisticNetworks2024" role="doc-biblioref">Quintero et al. 2024</a>)</span>, and as discussed in <a href="#sec-representation" class="quarto-xref">Section&nbsp;1.3</a>, links are now <em>constrained</em> by consumer choice.</p>
 <p><strong>Abundance</strong></p>
-<p>The most basic abundance constraint linked to foraging biology is the principle that organisms feeding randomly will consume resources in proportion to their abundance <span class="citation" data-cites="stephensForagingTheory1986">(<a href="#ref-stephensForagingTheory1986" role="doc-biblioref">Stephens and Krebs 1986</a>)</span>, and interactions are not necessarily contingent on there being any compatibility between them <span class="citation" data-cites="canardEmergenceStructuralPatterns2012 momalTreebasedInferenceSpecies2020 pomeranzInferringPredatorPrey2019">(<a href="#ref-canardEmergenceStructuralPatterns2012" role="doc-biblioref">E. Canard et al. 2012</a>; <a href="#ref-momalTreebasedInferenceSpecies2020" role="doc-biblioref">Momal, Robin, and Ambroise 2020</a>; <a href="#ref-pomeranzInferringPredatorPrey2019" role="doc-biblioref">Pomeranz et al. 2019</a>)</span>. However, a more ecologically sound assumption would be that the abundance of different prey species will influence the distribution of links in a network <span class="citation" data-cites="vazquezUnitingPatternProcess2009">(<a href="#ref-vazquezUnitingPatternProcess2009" role="doc-biblioref">Vázquez et al. 2009</a>)</span>, by influencing which prey are targeted or preferred by the predator, as abundance influences factors such as the likelihood of two species (individuals) meeting <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>. Thus, if abundance data are combined with a derived metaweb, there is a basic ruleset that can define the distribution (<em>e.g.,</em> structure) and potentially the strength of links.</p>
+<p>The most basic abundance constraint linked to foraging biology is the principle that organisms feeding randomly will consume resources in proportion to their abundance <span class="citation" data-cites="stephensForagingTheory1986">(<a href="#ref-stephensForagingTheory1986" role="doc-biblioref">Stephens and Krebs 1986</a>)</span>, and interactions are not necessarily contingent on there being any compatibility between them <span class="citation" data-cites="canardEmergenceStructuralPatterns2012 momalTreebasedInferenceSpecies2020 pomeranzInferringPredatorPrey2019">(<a href="#ref-canardEmergenceStructuralPatterns2012" role="doc-biblioref">E. Canard et al. 2012</a>; <a href="#ref-momalTreebasedInferenceSpecies2020" role="doc-biblioref">Momal, Robin, and Ambroise 2020</a>; <a href="#ref-pomeranzInferringPredatorPrey2019" role="doc-biblioref">Pomeranz et al. 2019</a>)</span>. Alternatively the abundance of different prey species will influence the distribution of links in a network <span class="citation" data-cites="vazquezUnitingPatternProcess2009">(<a href="#ref-vazquezUnitingPatternProcess2009" role="doc-biblioref">Vázquez et al. 2009</a>)</span>, by influencing which prey are targeted or preferred by the predator, as abundance influences factors such as the likelihood of two species (individuals) meeting <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>. Thus, if abundance data are combined with a derived metaweb, there is a basic ruleset that can define the distribution (<em>e.g.,</em> structure) and potentially the strength of links.</p>
 <p><strong>Profitability</strong></p>
 <p>It is well established that consumers make more active decisions than eating items in proportion to their abundance <span class="citation" data-cites="stephensForagingTheory1986">(<a href="#ref-stephensForagingTheory1986" role="doc-biblioref">Stephens and Krebs 1986</a>)</span>. Ultimately, consumer choice is underpinned by an energetic cost-benefit framework centred around profitability and defined by traits associated with finding, catching, killing, and consuming a resource <span class="citation" data-cites="woottonModularTheoryTrophic2023">(<a href="#ref-woottonModularTheoryTrophic2023" role="doc-biblioref">Wootton et al. 2023</a>)</span>. Although energetic constraints can be invoked in a myriad of ways <span class="citation" data-cites="pawarDimensionalityConsumerSearch2012 portalierMechanicsPredatorPrey2019 cherifEnvironmentRescueCan2024">(<em>e.g.,</em> <a href="#ref-pawarDimensionalityConsumerSearch2012" role="doc-biblioref">Pawar, Dell, and Savage 2012</a>; <a href="#ref-portalierMechanicsPredatorPrey2019" role="doc-biblioref">Portalier et al. 2019</a>; <a href="#ref-cherifEnvironmentRescueCan2024" role="doc-biblioref">Cherif et al. 2024</a>)</span> we select profitability as a term to capture rules linked to optimal foraging <span class="citation" data-cites="pykeOptimalForagingTheory1984">(<a href="#ref-pykeOptimalForagingTheory1984" role="doc-biblioref">Pyke 1984</a>)</span> and metabolic theory <span class="citation" data-cites="brownMetabolicTheoryEcology2004">(<a href="#ref-brownMetabolicTheoryEcology2004" role="doc-biblioref">Brown et al. 2004</a>)</span>; it is a sensible ‘umbrella concept’ for capturing the energetic constraint on of the distribution and strength of interactions.</p>
 <p><strong>Non-trophic interactions</strong></p>