Built site for gh-pages

.nojekyll

@@ -1 +1 @@
-2d00e43d
+e67d1e19

_tex/index.tex

@@ -341,6 +341,7 @@ \subsection{Overview of topology
 Trait-based & Caron et al. (2022) & mechanistic & Caron et al. (2023) &
 & metaweb & traits determine interactions & feeding mechanisms are trait
 correlated \\
+Random & & & & & & & chaos and anarchy \\
 \end{longtable}
 
 \begin{quote}

index.html

@@ -354,6 +354,16 @@ <h3 data-number="2.1" class="anchored" data-anchor-id="overview-of-topology-gene
 <td>traits determine interactions</td>
 <td>feeding mechanisms are trait correlated</td>
 </tr>
+<tr class="even">
+<td>Random</td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td>chaos and anarchy</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -942,7 +952,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
 });
 </script>
 </div> <!-- /content -->
-<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","openEffect":"zoom","selector":".lightbox","loop":false,"closeEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":false,"descPosition":"bottom","openEffect":"zoom","closeEffect":"zoom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

index.xml

@@ -321,6 +321,16 @@ work. Well they did I just haven’t done the</funding-statement>
               <td>traits determine interactions</td>
               <td>feeding mechanisms are trait correlated</td>
             </tr>
+            <tr>
+              <td>Random</td>
+              <td></td>
+              <td></td>
+              <td></td>
+              <td></td>
+              <td></td>
+              <td></td>
+              <td>chaos and anarchy</td>
+            </tr>
           </tbody>
         </table>
       </table-wrap>
@@ -1253,28 +1263,36 @@ The following object is masked from 'package:tidyr':
     unite</preformat>
 </sec>
 </sec>
-<p>First we need to create the</p>
+<p>First we need to create the df with the relevant ‘traits’ for each
+model</p>
 <sec id="nb-code-cell-2-nb-1" specific-use="notebook-code">
-<code language="r script">genes &lt;- paste(&quot;gene&quot;,1:1000,sep=&quot;&quot;)
-set.seed(20231214)
-x &lt;- list(A=sample(genes,300),
-          B=sample(genes,525),
-          C=sample(genes,440),
-          D=sample(genes,350))
+<code language="r script">x &lt;- list(Niche=c(&quot;species agnostic&quot;, &quot;structural&quot;, &quot;synthetic network&quot;),
+          ADBM=c(&quot;node-level&quot;, &quot;mechanistic&quot;),
+          `Transfer`=c(&quot;node-level&quot;, &quot;embedding&quot;, &quot;metaweb&quot;),
+          PFIM=c(&quot;node-level&quot;, &quot;mechanistic&quot;, &quot;metaweb&quot;),
+          Cascade=c(&quot;species agnostic&quot;, &quot;structural&quot;, &quot;synthetic network&quot;))
+
+venn &lt;- Venn(x)
+data &lt;- process_data(venn)
 </code>
 </sec>
-<p>Create spatial plot:</p>
+<p>Create venn diagram:</p>
 <sec id="cell-fig-venn-nb-1" specific-use="notebook-code">
-<code language="r script">ggVennDiagram(x) + 
-  scale_fill_gradient(low=&quot;grey90&quot;,
-                      high = &quot;red&quot;)
+<code language="r script">ggVennDiagram(x, 
+              label = &quot;none&quot;) +
+  theme_void() +
+  theme(legend.position = 'none')
 </code>
 <fig id="fig-venn-nb-1">
   <caption><p>Venn diagram for qualitative analysis/overview of the
   fancy maths things</p></caption>
   <graphic mimetype="image" mime-subtype="png" xlink:href="model_qualitative_files/figure-jats/fig-venn-1.png" />
 </fig>
 </sec>
+<p>Looking at it now I don’t think this is the wayTM and trying to sort
+of ‘ordinate’ modelling space might actually be more meaningful…
+Specifically thinking here that I need to also actually just read about
+model comparison (but without the performance aspect)</p>
 <sec id="references-nb-1">
   <title>References</title>
 </sec>

notebooks/model_qualitative-preview.html

@@ -266,20 +266,23 @@ <h2 id="toc-title">Table of contents</h2>
     unite</code></pre>
 </div>
 </div></div>
-<p>First we need to create the</p>
+<p>First we need to create the df with the relevant ‘traits’ for each model</p>
 <div class="cell-container"><div class="cell-decorator"><pre>In [2]:</pre></div><div class="cell">
-<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>genes <span class="ot">&lt;-</span> <span class="fu">paste</span>(<span class="st">"gene"</span>,<span class="dv">1</span><span class="sc">:</span><span class="dv">1000</span>,<span class="at">sep=</span><span class="st">""</span>)</span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">20231214</span>)</span>
-<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>x <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">A=</span><span class="fu">sample</span>(genes,<span class="dv">300</span>),</span>
-<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>          <span class="at">B=</span><span class="fu">sample</span>(genes,<span class="dv">525</span>),</span>
-<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>          <span class="at">C=</span><span class="fu">sample</span>(genes,<span class="dv">440</span>),</span>
-<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>          <span class="at">D=</span><span class="fu">sample</span>(genes,<span class="dv">350</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>x <span class="ot">&lt;-</span> <span class="fu">list</span>(<span class="at">Niche=</span><span class="fu">c</span>(<span class="st">"species agnostic"</span>, <span class="st">"structural"</span>, <span class="st">"synthetic network"</span>),</span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>          <span class="at">ADBM=</span><span class="fu">c</span>(<span class="st">"node-level"</span>, <span class="st">"mechanistic"</span>),</span>
+<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>          <span class="st">`</span><span class="at">Transfer</span><span class="st">`</span><span class="ot">=</span><span class="fu">c</span>(<span class="st">"node-level"</span>, <span class="st">"embedding"</span>, <span class="st">"metaweb"</span>),</span>
+<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>          <span class="at">PFIM=</span><span class="fu">c</span>(<span class="st">"node-level"</span>, <span class="st">"mechanistic"</span>, <span class="st">"metaweb"</span>),</span>
+<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>          <span class="at">Cascade=</span><span class="fu">c</span>(<span class="st">"species agnostic"</span>, <span class="st">"structural"</span>, <span class="st">"synthetic network"</span>))</span>
+<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a>venn <span class="ot">&lt;-</span> <span class="fu">Venn</span>(x)</span>
+<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a>data <span class="ot">&lt;-</span> <span class="fu">process_data</span>(venn)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div></div>
-<p>Create spatial plot:</p>
+<p>Create venn diagram:</p>
 <div class="cell-container"><div class="cell-decorator"><pre>In [3]:</pre></div><div id="cell-fig-venn" class="cell">
-<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ggVennDiagram</span>(x) <span class="sc">+</span> </span>
-<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>  <span class="fu">scale_fill_gradient</span>(<span class="at">low=</span><span class="st">"grey90"</span>,</span>
-<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>                      <span class="at">high =</span> <span class="st">"red"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ggVennDiagram</span>(x, </span>
+<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>              <span class="at">label =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
+<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme_void</span>() <span class="sc">+</span></span>
+<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">'none'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output-display">
 <div id="fig-venn" class="quarto-figure quarto-figure-center quarto-float anchored" alt="TODO">
 <figure class="quarto-float quarto-float-fig figure">
@@ -293,6 +296,7 @@ <h2 id="toc-title">Table of contents</h2>
 </div>
 </div>
 </div></div>
+<p>Looking at it now I don’t think this is the wayTM and trying to sort of ‘ordinate’ modelling space might actually be more meaningful… Specifically thinking here that I need to also actually just read about model comparison (but without the performance aspect)</p>
 <section id="references" class="level2 unnumbered">
 <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
 <div id="refs" role="list">
@@ -686,7 +690,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
     }
   }
 });
-</script>  </div> <!-- /content -->  <script>var lightboxQuarto = GLightbox({"loop":false,"closeEffect":"zoom","selector":".lightbox","descPosition":"bottom","openEffect":"zoom"});
+</script>  </div> <!-- /content -->  <script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":false,"descPosition":"bottom","closeEffect":"zoom","openEffect":"zoom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

notebooks/model_qualitative.qmd

@@ -11,28 +11,34 @@ library(ggVennDiagram)
 ```
 
 
-First we need to create the 
+First we need to create the df with the relevant 'traits' for each model
 
 ```{r}
-genes <- paste("gene",1:1000,sep="")
-set.seed(20231214)
-x <- list(A=sample(genes,300),
-          B=sample(genes,525),
-          C=sample(genes,440),
-          D=sample(genes,350))
+
+x <- list(Niche=c("species agnostic", "structural", "synthetic network"),
+          ADBM=c("node-level", "mechanistic"),
+          `Transfer`=c("node-level", "embedding", "metaweb"),
+          PFIM=c("node-level", "mechanistic", "metaweb"),
+          Cascade=c("species agnostic", "structural", "synthetic network"))
+
+venn <- Venn(x)
+data <- process_data(venn)
 ```
 
-Create spatial plot:
+Create venn diagram:
 
 ```{r}
 #| label: fig-venn
 #| fig-cap: "Venn diagram for qualitative analysis/overview of the fancy maths things"
 #| fig-alt: "TODO"
-ggVennDiagram(x) + 
-  scale_fill_gradient(low="grey90",
-                      high = "red")
+ggVennDiagram(x, 
+              label = "none") +
+  theme_void() +
+  theme(legend.position = 'none')
 ```
 
+Looking at it now I don't think this is the wayTM and trying to sort of 'ordinate' modelling space might actually be more meaningful... Specifically thinking here that I need to also actually just read about model comparison (but without the performance aspect)
+
 ## References {.unnumbered}
 
 ::: {#refs}