💬 ramblings of a madman at this point

docs/_tex/index.tex

@@ -212,7 +212,7 @@
 1%
 }%
 }
-\date{2024-07-01}
+\date{2024-07-02}
 
 \usepackage{setspace}
 \usepackage[left]{lineno}
@@ -456,7 +456,7 @@ \section{Understanding the drivers of species
 environment imposes on a species\ldots{} Maybe we can also think of it
 more in terms of metabolic rate?
 
-\begin{tcolorbox}[enhanced jigsaw, toprule=.15mm, colback=white, colframe=quarto-callout-note-color-frame, coltitle=black, bottomrule=.15mm, opacitybacktitle=0.6, left=2mm, breakable, bottomtitle=1mm, toptitle=1mm, rightrule=.15mm, colbacktitle=quarto-callout-note-color!10!white, titlerule=0mm, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Box 1 -The anatomy of a food web}, leftrule=.75mm, opacityback=0, arc=.35mm]
+\begin{tcolorbox}[enhanced jigsaw, coltitle=black, toprule=.15mm, breakable, leftrule=.75mm, opacitybacktitle=0.6, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Box 1 -The anatomy of a food web}, opacityback=0, bottomrule=.15mm, colbacktitle=quarto-callout-note-color!10!white, left=2mm, titlerule=0mm, colback=white, toptitle=1mm, arc=.35mm, bottomtitle=1mm, colframe=quarto-callout-note-color-frame, rightrule=.15mm]
 
 \begin{quote}
 Important goal of this box is to highlight the different terminology
@@ -816,7 +816,7 @@ \section{How do we use networks?}\label{how-do-we-use-networks}
 \begin{quote}
 In this section I want to highlight that we don't actually have any
 clear guidelines as to how we can `use' networks - which probably stems
-from both the fact that when I am talking about a networks and when
+from both the fact that when I am talking about a network and when
 someone else is talking about a network we may actually be talking about
 two very different conceptualisations of `a network' (this should
 actually be a selling point in the intro - may have just found my
@@ -827,7 +827,18 @@ \section{How do we use networks?}\label{how-do-we-use-networks}
 Petchy dilemma space and clearly tied to the ideas we discuss in the ms.
 This includes: understanding the limits of how a network is defined and
 how the underlying theory impacts the use as well as data?? IDK we need
-to shoehorn data in here somehow\ldots{}
+to shoehorn data in here somehow\ldots{} We can also use this as a gap
+identifying space and I think the framing can still rest under the
+limits concept particularly time, space, and boundaries - which will all
+probably fall under some aspect of biological scale\ldots{} We can also
+raise the idea of trust - as in which methods have more support/trust
+than others. Also what even a `real' network entails (and this links
+again back to Tim's stuff) as well as a subtle jab at Pringles notion
+that the most critical issue in the world of food webs is being able to
+identify every. single. link. even though there is no real discussion as
+to what is an `opportunistic' link vs a link that represents a
+sustainable energy source for a population (or would it be an
+individual)\ldots{}
 \end{quote}
 
 \section{Concluding remarks}\label{concluding-remarks}

docs/index.html

@@ -10,7 +10,7 @@
 <meta name="author" content="Jennifer A. Dunne">
 <meta name="author" content="Timothée Poisot">
 <meta name="author" content="Andrew P. Beckerman">
-<meta name="dcterms.date" content="2024-07-01">
+<meta name="dcterms.date" content="2024-07-02">
 <meta name="keywords" content="food web, network construction, scientific ignorance">
 
 <title>Navigating food web prediction; assumptions, rationale, and methods</title>
@@ -107,10 +107,10 @@
 <meta name="citation_author" content="Jennifer A. Dunne">
 <meta name="citation_author" content="Timothée Poisot">
 <meta name="citation_author" content="Andrew P. Beckerman">
-<meta name="citation_publication_date" content="2024-07-01">
-<meta name="citation_cover_date" content="2024-07-01">
+<meta name="citation_publication_date" content="2024-07-02">
+<meta name="citation_cover_date" content="2024-07-02">
 <meta name="citation_year" content="2024">
-<meta name="citation_online_date" content="2024-07-01">
+<meta name="citation_online_date" content="2024-07-02">
 <meta name="citation_language" content="en">
 <meta name="citation_journal_title" content="TREE (one can dream...)">
 <meta name="citation_reference" content="citation_title=A novel method for predicting ecological interactions with an unsupervised machine learning algorithm;,citation_abstract=This gap in knowledge regarding ecological interactions has prompted the development of various predictive approaches. Traditionally, ecological interactions have been inferred using traits. However, the lack of trait information for numerous organisms necessitates using phylogenetic data and statistical insights from interaction matrices for prediction. Previous studies have overlooked the validation of model-predicted interactions. This study used a novel method in predicting ecological interactions using a self-organizing map (SOM), an unsupervised machine learning algorithm. The SOM learns from the input interaction matrix by grouping the nodes into output layers based on their interactions. Subsequently, the trained model predicts the interactions as scores. To distinguish between interactions and non-interactions, we employed F1 score maximization, setting scores above a specific threshold as interactions and the remainder as non-interactions. We applied this method to three unipartite metawebs and one bipartite metaweb and subsequently validated the predicted interactions using two innovative approaches: taxonomic and interaction recovery validation. Our method exhibited outstanding predictive performance, particularly for large networks. Various binary classification performance indicators, including F1 score (0.84–0.97) and accuracy (0.97–0.99), indicated high performance. Moreover, the method generated minimal predicted interactions, signifying low noise in the predictions, particularly for large networks. Taxonomic validation excels in metawebs with a connectance &amp;amp;amp;gt;0.1 but performs poorly in metawebs with very low connectance. In contrast, interaction recovery was most effective in larger metawebs. Our proposed method excels at making highly accurate predictions of ecological interactions with minimal noise, solely utilizing input interaction data without relying on traits or phylogenetic information regarding interacting nodes. These predictions are particularly precise for large networks, underscoring their potential to address knowledge gaps in emerging extensive metawebs. Notably, taxonomic validation and interaction recovery methods are sensitive to connectance and network size, respectively, suggesting prospects for developing robust interaction validation methods.;,citation_author=Sagar Adhurya;,citation_author=Young-Seuk Park;,citation_publication_date=2024;,citation_cover_date=2024;,citation_year=2024;,citation_issue=n/a;,citation_doi=10.1111/2041-210X.14358;,citation_issn=2041-210X;,citation_volume=n/a;,citation_language=en-US;,citation_journal_title=Methods in Ecology and Evolution;">
@@ -306,7 +306,7 @@ <h1 class="title">Navigating food web prediction; assumptions, rationale, and me
                 <div>
             <div class="quarto-title-meta-heading">Published</div>
             <div class="quarto-title-meta-contents">
-              <p class="date">July 1, 2024</p>
+              <p class="date">July 2, 2024</p>
             </div>
           </div>
 
@@ -592,7 +592,7 @@ <h2 data-number="2.2" class="anchored" data-anchor-id="model-families"><span cla
 <section id="how-do-we-use-networks" class="level1" data-number="3">
 <h1 data-number="3"><span class="header-section-number">3</span> How do we use networks?</h1>
 <blockquote class="blockquote">
-<p>In this section I want to highlight that we don’t actually have any clear guidelines as to how we can ‘use’ networks - which probably stems from both the fact that when I am talking about a networks and when someone else is talking about a network we may actually be talking about two very different conceptualisations of ‘a network’ (this should actually be a selling point in the intro - may have just found my <em>raison d’etre</em>) as well as that a lot of the ideas that we have about networks are not really tied to any sort of tangible function (i.e.&nbsp;Tim’s GeoBon ms thing-y). However we can maybe at least try to present some guidelines - but I think specifically within the sort of Petchy dilemma space and clearly tied to the ideas we discuss in the ms. This includes: understanding the limits of how a network is defined and how the underlying theory impacts the use as well as data?? IDK we need to shoehorn data in here somehow…</p>
+<p>In this section I want to highlight that we don’t actually have any clear guidelines as to how we can ‘use’ networks - which probably stems from both the fact that when I am talking about a network and when someone else is talking about a network we may actually be talking about two very different conceptualisations of ‘a network’ (this should actually be a selling point in the intro - may have just found my <em>raison d’etre</em>) as well as that a lot of the ideas that we have about networks are not really tied to any sort of tangible function (i.e.&nbsp;Tim’s GeoBon ms thing-y). However we can maybe at least try to present some guidelines - but I think specifically within the sort of Petchy dilemma space and clearly tied to the ideas we discuss in the ms. This includes: understanding the limits of how a network is defined and how the underlying theory impacts the use as well as data?? IDK we need to shoehorn data in here somehow… We can also use this as a gap identifying space and I think the framing can still rest under the limits concept particularly time, space, and boundaries - which will all probably fall under some aspect of biological scale… We can also raise the idea of trust - as in which methods have more support/trust than others. Also what even a ‘real’ network entails (and this links again back to Tim’s stuff) as well as a subtle jab at Pringles notion that the most critical issue in the world of food webs is being able to identify every. single. link. even though there is no real discussion as to what is an ‘opportunistic’ link vs a link that represents a sustainable energy source for a population (or would it be an individual)…</p>
 </blockquote>
 </section>
 <section id="concluding-remarks" class="level1" data-number="4">
@@ -880,14 +880,14 @@ <h1 class="unnumbered">References</h1>
     and P. Beckerman, Andrew},
   title = {Navigating Food Web Prediction; Assumptions, Rationale, and
     Methods},
-  date = {2024-07-01},
+  date = {2024-07-02},
   langid = {en},
   abstract = {TODO}
 }
 </code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre><div class="quarto-appendix-secondary-label">For attribution, please cite this work as:</div><div id="ref-strydom2024" class="csl-entry quarto-appendix-citeas" role="listitem">
 Strydom, Tanya, Jennifer A. Dunne, Timothée Poisot, and Andrew P.
 Beckerman. 2024. <span>“Navigating Food Web Prediction; Assumptions,
-Rationale, and Methods.”</span> TREE (One Can Dream...). July 1, 2024.
+Rationale, and Methods.”</span> TREE (One Can Dream...). July 2, 2024.
 </div></div></section></div></main>
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index.qmd

@@ -163,7 +163,7 @@ As there are many food web models to choose from it is perhaps useful to think a
 
 # How do we use networks?
 
-> In this section I want to highlight that we don't actually have any clear guidelines as to how we can 'use' networks - which probably stems from both the fact that when I am talking about a networks and when someone else is talking about a network we may actually be talking about two very different conceptualisations of 'a network' (this should actually be a selling point in the intro - may have just found my *raison d'etre*) as well as that a lot of the ideas that we have about networks are not really tied to any sort of tangible function (i.e. Tim's GeoBon ms thing-y). However we can maybe at least try to present some guidelines - but I think specifically within the sort of Petchy dilemma space and clearly tied to the ideas we discuss in the ms. This includes: understanding the limits of how a network is defined and how the underlying theory impacts the use as well as data?? IDK we need to shoehorn data in here somehow...
+> In this section I want to highlight that we don't actually have any clear guidelines as to how we can 'use' networks - which probably stems from both the fact that when I am talking about a network and when someone else is talking about a network we may actually be talking about two very different conceptualisations of 'a network' (this should actually be a selling point in the intro - may have just found my *raison d'etre*) as well as that a lot of the ideas that we have about networks are not really tied to any sort of tangible function (i.e. Tim's GeoBon ms thing-y). However we can maybe at least try to present some guidelines - but I think specifically within the sort of Petchy dilemma space and clearly tied to the ideas we discuss in the ms. This includes: understanding the limits of how a network is defined and how the underlying theory impacts the use as well as data?? IDK we need to shoehorn data in here somehow... We can also use this as a gap identifying space and I think the framing can still rest under the limits concept particularly time, space, and boundaries - which will all probably fall under some aspect of biological scale... We can also raise the idea of trust - as in which methods have more support/trust than others. Also what even a 'real' network entails (and this links again back to Tim's stuff) as well as a subtle jab at Pringles notion that the most critical issue in the world of food webs is being able to identify every. single. link. even though there is no real discussion as to what is an 'opportunistic' link vs a link that represents a sustainable energy source for a population (or would it be an individual)...
 
 # Concluding remarks