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chapters/health.qmd

@@ -45,9 +45,9 @@ colnames(prev_ablation_dist)<-prev_ablation_stat$FarmType
 prev_ablation_unadjusted<-as.data.frame(prev_ablation_dist)
 ```
 
-We also need to adjust for the fact that only female broodstock are subjected to eyestalk ablation, not their offspring who are actually raised for food. We calculate the number of broodstock by using the total number of shrimp that die on farms *from the postlarval stage onward* (from [Waldhorn & Autric's 2023](http://doi.org/10.31219/osf.io/b8n3t) Guesstimate model), divided by the number of eggs different species lay per spawn, and assuming only half the eggs hatch.
+We also need to adjust for the fact that only female broodstock are subjected to eyestalk ablation, not their offspring who are actually raised for food. We calculate the number of broodstock by using the total number of shrimp that die on farms (from [Waldhorn & Autric's 2023](http://doi.org/10.31219/osf.io/b8n3t) Guesstimate model), divided by the number of eggs different species lay per spawn, and assuming only half the eggs hatch. The denominator in this equation represents how many shrimp that die on farms each broodstock is responsible for hatching. We will then represent the number of female broodstock as a proportion of the number of shrimp that die on farms *from the postlarval stage onward* (as this is the ongrowing stage). We do so because other threats are evaluated for the harms they cause in the ongrowing stage only, so we must weight the eyestalk ablation prevalence by the proportion of shrimp that are broodstock from only this population.
 
-See [set up chapter](set-up.qmd) for how the variables used here were calculated. First, we must calculate the number of shrimp that die on farms from the postlarval stage onward. We do so because other threats are evaluated for the harms they cause in the ongrowing stage only, so we must calculate the proportion of shrimp that are broodstock against only this population. We do so handling the data in the same way as the Set-up chapter, using the `kde1d` function to generate 100,000 samples.
+See [set up chapter](set-up.qmd) for how the variables used here were calculated. First, we calculate the number of shrimp that die on farms from the postlarval stage onward. We do so handling the data in the same way as the Set-up chapter, using the `kde1d` function to generate 100,000 samples.
 
 ```{r}
 library(kde1d) # load the required package

docs/chapters/health.html

@@ -315,8 +315,8 @@ <h2 class="anchored" data-anchor-id="prevalence">Prevalence</h2>
 <span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a>prev_ablation_unadjusted<span class="ot">&lt;-</span><span class="fu">as.data.frame</span>(prev_ablation_dist)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
-<p>We also need to adjust for the fact that only female broodstock are subjected to eyestalk ablation, not their offspring who are actually raised for food. We calculate the number of broodstock by using the total number of shrimp that die on farms <em>from the postlarval stage onward</em> (from <a href="http://doi.org/10.31219/osf.io/b8n3t">Waldhorn &amp; Autric’s 2023</a> Guesstimate model), divided by the number of eggs different species lay per spawn, and assuming only half the eggs hatch.</p>
-<p>See <a href="../chapters/set-up.html">set up chapter</a> for how the variables used here were calculated. First, we must calculate the number of shrimp that die on farms from the postlarval stage onward. We do so because other threats are evaluated for the harms they cause in the ongrowing stage only, so we must calculate the proportion of shrimp that are broodstock against only this population. We do so handling the data in the same way as the Set-up chapter, using the <code>kde1d</code> function to generate 100,000 samples.</p>
+<p>We also need to adjust for the fact that only female broodstock are subjected to eyestalk ablation, not their offspring who are actually raised for food. We calculate the number of broodstock by using the total number of shrimp that die on farms (from <a href="http://doi.org/10.31219/osf.io/b8n3t">Waldhorn &amp; Autric’s 2023</a> Guesstimate model), divided by the number of eggs different species lay per spawn, and assuming only half the eggs hatch. The denominator in this equation represents how many shrimp that die on farms each broodstock is responsible for hatching. We will then represent the number of female broodstock as a proportion of the number of shrimp that die on farms <em>from the postlarval stage onward</em> (as this is the ongrowing stage). We do so because other threats are evaluated for the harms they cause in the ongrowing stage only, so we must weight the eyestalk ablation prevalence by the proportion of shrimp that are broodstock from only this population.</p>
+<p>See <a href="../chapters/set-up.html">set up chapter</a> for how the variables used here were calculated. First, we calculate the number of shrimp that die on farms from the postlarval stage onward. We do so handling the data in the same way as the Set-up chapter, using the <code>kde1d</code> function to generate 100,000 samples.</p>
 <div 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">library</span>(kde1d) <span class="co"># load the required package</span></span>
 <span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a></span>

docs/index.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Hannah McKay and William McAuliffe">
-<meta name="dcterms.date" content="2024-07-15">
+<meta name="dcterms.date" content="2024-07-16">
 
 <title>Methods for quantifying and prioritizing shrimp welfare threats</title>
 <style>
@@ -210,7 +210,7 @@ <h1 class="title">Methods for quantifying and prioritizing shrimp welfare threat
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">July 15, 2024</p>
+      <p class="date">July 16, 2024</p>
     </div>
   </div>