🥗 some more word salad

docs/index.html

@@ -1342,7 +1342,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
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docs/notebooks/model_descriptions.out.ipynb

@@ -187,7 +187,7 @@
     "\n",
     "Yeakel, Justin D., Mathias M. Pires, Lars Rudolf, Nathaniel J. Dominy, Paul L. Koch, Paulo R. Guimarães, and Thilo Gross. 2014. “Collapse of an Ecological Network in Ancient Egypt.” *PNAS* 111 (40): 14472–77. <https://doi.org/10.1073/pnas.1408471111>."
    ],
-   "id": "e0ee8fc5-f4a3-4f38-ba9d-c17a597b5b0a"
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docs/notebooks/model_qualitative-preview.html

@@ -2149,7 +2149,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
     }
   }
 });
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docs/notebooks/model_qualitative.out.ipynb

@@ -11,7 +11,7 @@
     "\n",
     "Basically the important thing here is that we want to take what is currently table 1 in the manuscript and turn that into a more elaborate ‘traits table’."
    ],
-   "id": "c082d18a-bd57-43fd-b18f-924375ce0853"
+   "id": "1c47e93a-0d1d-4b20-a86a-03b159821e43"
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   {
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@@ -38,7 +38,7 @@
    "source": [
     "library(tidyverse)\n"
    ],
-   "id": "2655a69b-9016-4a78-a032-a2f20e846c0c"
+   "id": "3ea64e9c-3a5c-461a-8e5f-9fb702e1f8e3"
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    "cell_type": "code",
@@ -1818,15 +1818,15 @@
     "    columns = everything()) %>% \n",
     "  opt_row_striping(row_striping = FALSE)\n"
    ],
-   "id": "00c4edf0-d691-49fc-92c7-35ce44fa1ed2"
+   "id": "60473868-d096-41b2-8695-0eb9e8e98037"
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   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Maybe we try some ordination based on this traits table?"
    ],
-   "id": "017ca3eb-0faa-4947-8e35-7ef313897239"
+   "id": "b2140a01-80a7-4c1d-acab-96681b6c9da9"
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   {
    "cell_type": "code",
@@ -1851,15 +1851,15 @@
     "hc <- hclust(dist(df), method = \"ave\")\n",
     "hcdata <- dendro_data(hc, type = \"rectangle\")\n"
    ],
-   "id": "9e02898b-79fc-41ad-9941-8b65ddc992ef"
+   "id": "ae1db0bd-93c2-488f-ac77-d5796896c40d"
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   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "new cell code for plotting because"
    ],
-   "id": "fcac9358-5067-401c-8e61-8c47bcf2782e"
+   "id": "05071935-6181-4790-bdde-83dab7f86247"
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@@ -1939,7 +1939,7 @@
    "source": [
     "## References"
    ],
-   "id": "e00dada6-bc00-45b6-8ed2-0117df56705c"
+   "id": "f7c8a566-512f-4c97-84bb-40d67b0f8829"
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docs/notebooks/model_quantitative-preview.html

@@ -333,7 +333,7 @@ <h2 id="toc-title">Table of contents</h2>
 <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" class="">
-<a href="model_quantitative_files/figure-html/fig-boxplot-1.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="model_quantitative_files/figure-html/fig-boxplot-1.png" class="img-fluid figure-img" width="672"></a>
+<a href="model_quantitative_files/figure-html/fig-boxplot-1.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1"><img src="model_quantitative_files/figure-html/fig-boxplot-1.png" class="img-fluid figure-img" width="672"></a>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-boxplot-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Boxplot looking at raw values for each measurement for each model. The horizontal line represents the true overall mean for each measurement
@@ -371,7 +371,7 @@ <h2 id="toc-title">Table of contents</h2>
 <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" class="">
-<a href="model_quantitative_files/figure-html/fig-topology-1.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" data-glightbox="description: .lightbox-desc-2"><img src="model_quantitative_files/figure-html/fig-topology-1.png" class="img-fluid figure-img" width="672"></a>
+<a href="model_quantitative_files/figure-html/fig-topology-1.png" class="lightbox" data-glightbox="description: .lightbox-desc-2" data-gallery="quarto-lightbox-gallery-2"><img src="model_quantitative_files/figure-html/fig-topology-1.png" class="img-fluid figure-img" width="672"></a>
 </div>
 <figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-topology-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Difference between real and model network property. S1 - S5 represent the different motif structures identified in <span class="citation" data-cites="stoufferEvidenceExistenceRobust2007">Stouffer et al. (<a href="#ref-stoufferEvidenceExistenceRobust2007" role="doc-biblioref">2007</a>)</span>.
@@ -785,7 +785,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
     }
   }
 });
-</script>  </div> <!-- /content -->  <script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","descPosition":"bottom","openEffect":"zoom","loop":false});
+</script>  </div> <!-- /content -->  <script>var lightboxQuarto = GLightbox({"openEffect":"zoom","loop":false,"selector":".lightbox","descPosition":"bottom","closeEffect":"zoom"});
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docs/notebooks/model_quantitative.out.ipynb

@@ -15,7 +15,7 @@
     "\n",
     "As well as the ‘New Zealand’ dataset from Pomeranz et al. ([2019](#ref-pomeranzInferringPredatorPrey2019))"
    ],
-   "id": "7df9282c-178b-4d31-b9f2-a1ea2c4afb75"
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   {
    "cell_type": "code",
@@ -49,7 +49,7 @@
    "source": [
     "library(tidyverse)\n"
    ],
-   "id": "4a6c5ab1-9f16-4e0c-b59b-1821c1dcabc2"
+   "id": "5c36e29a-9bad-4934-a4a0-22292742bf2d"
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    "cell_type": "markdown",
@@ -59,7 +59,7 @@
     "\n",
     "Lets start by summarising the ‘raw’ data as box plots just to see what it looks like before we calculate the Z scores"
    ],
-   "id": "14b8348c-fb89-41ac-87e4-2d3b1218b449"
+   "id": "0aa04c20-cc78-4752-8631-c891d24f7b99"
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    "cell_type": "code",
@@ -111,7 +111,7 @@
    "source": [
     "Now we can look at the difference between the mean of the real network property and the simulated one. I had originally considered using the $Z$-score but it doesn’t work well for the more ‘deterministic’ models (neutral and ADBM) because they effectively have a $\\sigma$ of zero…"
    ],
-   "id": "cbd20631-1f4c-4d57-868e-b18722be24ae"
+   "id": "593df294-f96e-46c5-8920-d14b611bafe7"
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    "cell_type": "code",
@@ -167,7 +167,7 @@
     "\n",
     "Pomeranz, Justin P. F., Ross M. Thompson, Timothée Poisot, and Jon S. Harding. 2019. “Inferring Predator–Prey Interactions in Food Webs.” *Methods in Ecology and Evolution* 10 (3): 356–67. <https://doi.org/10.1111/2041-210X.13125>."
    ],
-   "id": "e9668e50-a149-44fe-9ff6-8da78d71396b"
+   "id": "26c4ef07-7118-433b-902b-132ab57d5c88"
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