Updates to help navigation from html files.

1_prep_consumption_data.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Sagar Shah, Rethink Priorities">
-<meta name="dcterms.date" content="2024-02-08">
+<meta name="dcterms.date" content="2024-02-16">
 
 <title>EU Farm Fish CEA - 1. Consumption Prep File</title>
 <style>
@@ -3025,7 +3025,9 @@
     <h2 id="toc-title">Table of contents</h2>
 
   <ul>
-  <li><a href="#preparation" id="toc-preparation" class="nav-link active" data-scroll-target="#preparation">Preparation</a>
+  <li><a href="#navigation" id="toc-navigation" class="nav-link active" data-scroll-target="#navigation">Navigation</a></li>
+  <li><a href="#about-this-file" id="toc-about-this-file" class="nav-link" data-scroll-target="#about-this-file">About this file</a></li>
+  <li><a href="#preparation" id="toc-preparation" class="nav-link" data-scroll-target="#preparation">Preparation</a>
   <ul class="collapse">
   <li><a href="#clear-environment" id="toc-clear-environment" class="nav-link" data-scroll-target="#clear-environment">Clear environment</a></li>
   <li><a href="#load-packages" id="toc-load-packages" class="nav-link" data-scroll-target="#load-packages">Load packages</a></li>
@@ -3061,7 +3063,7 @@ <h1 class="title">EU Farm Fish CEA - 1. Consumption Prep File</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">February 8, 2024</p>
+      <p class="date">February 16, 2024</p>
     </div>
   </div>
 
@@ -3071,7 +3073,14 @@ <h1 class="title">EU Farm Fish CEA - 1. Consumption Prep File</h1>
 
 </header>
 
+<section id="navigation" class="level1">
+<h1>Navigation</h1>
+<p>Return to the full <a href="https://github.com/rethinkpriorities/farmfish_stunning_cea">Github repository</a> for this project, or the <a href="https://rethinkpriorities.github.io/farmfish_stunning_cea/">html version of the readme file</a>.</p>
+</section>
+<section id="about-this-file" class="level1">
+<h1>About this file</h1>
 <p>This file brings together estimates of per country EU consumption of Sea bream, Sea bass, Carp, Salmon and Rainbow Trout into a single dataset in long format.</p>
+</section>
 <section id="preparation" class="level1">
 <h1>Preparation</h1>
 <section id="clear-environment" class="level2">

2_code/1_prep_consumption_data.qmd

@@ -1,12 +1,14 @@
-
-Return to the full [Github repository](https://github.com/rethinkpriorities/farmfish_stunning_cea) for this project, or the [html version of the readme file](https://rethinkpriorities.github.io/farmfish_stunning_cea/).
-
 ---
 title: "EU Farm Fish CEA - 1. Consumption Prep File"
 author: "Sagar Shah, Rethink Priorities"
 date: "`r Sys.Date()`"
 ---
 
+# Navigation
+
+Return to the full [Github repository](https://github.com/rethinkpriorities/farmfish_stunning_cea) for this project, or the [html version of the readme file](https://rethinkpriorities.github.io/farmfish_stunning_cea/).
+
+# About this file
 
 This file brings together estimates of per country EU consumption of Sea bream, Sea bass, Carp, Salmon and Rainbow Trout into a single dataset in long format.
 

2_code/2_intro_charts.qmd

@@ -4,6 +4,14 @@ author: "Sagar Shah, Rethink Priorities"
 date: "`r Sys.Date()`"
 ---
 
+# Navigation
+
+Return to the full [Github repository](https://github.com/rethinkpriorities/farmfish_stunning_cea) for this project, or the [html version of the readme file](https://rethinkpriorities.github.io/farmfish_stunning_cea/).
+
+# About this file
+
+This file prepares the charts used in the introduction section of the report.
+
 # Prep
 
 Clear memory, load packages and run functions script.

2_code/3_main_results.qmd

@@ -3,6 +3,13 @@ title: "3. Main results - stunning intervention"
 author: "Sagar Shah, Rethink Priorities"
 date: "`r Sys.Date()`"
 ---
+# Navigation
+
+Return to the full [Github repository](https://github.com/rethinkpriorities/farmfish_stunning_cea) for this project, or the [html version of the readme file](https://rethinkpriorities.github.io/farmfish_stunning_cea/).
+
+# About this file
+
+This conducts cost-effectiveness analysis and produces the main results tables charts used in the Results section of the report.
 
 # Generic prep
 

2_code/4_annex_results.qmd

@@ -4,6 +4,14 @@ author: "Sagar Shah, Rethink Priorities"
 date: "`r Sys.Date()`"
 ---
 
+# Navigation
+
+Return to the full [Github repository](https://github.com/rethinkpriorities/farmfish_stunning_cea) for this project, or the [html version of the readme file](https://rethinkpriorities.github.io/farmfish_stunning_cea/).
+
+# About this file
+
+This file contains cost-effectiveness analysis of non-slaughter intervention contained within Annex 2 of the report.
+
 # Generic prep
 
 ```{r}

2_code/5_time_pain_exploration.qmd

@@ -4,9 +4,21 @@ author: "Sagar Shah, Rethink Priorities"
 date: "`r Sys.Date()`"
 ---
 
+# Navigation
+
+Return to the full [Github repository](https://github.com/rethinkpriorities/farmfish_stunning_cea) for this project, or the [html version of the readme file](https://rethinkpriorities.github.io/farmfish_stunning_cea/).
+
+# About this file
+
 This file explores the extent to which the fish stunning intervention in the scale scenario might avert more time in various pain intensities than historic estimates for chicken campaigns, using the results of this project for fish stunning, and Šimčikas (2019) and Welfare Footprint Project data.
 
-Conclusion is that it is unlikely that the fish stunning intervention can have an impact that comes close to the impact (in terms of duration affected) of chicken campaigns for annoying, hurtful or disabling pain. For these pain intensities, whether or not fish stunning appears to avert more time in pain appears to be entirely driven by uncertainty of whether the chicken intervention increases or decreases time in pain.
+# Caveats
+
+Note that this analysis was not subject to review and should come with health warnings. Another caveat is that I only used the I only used welfare footprint data for time in pain at the farm level for broiler reform, and not the impact of alternative poultry slaughter and stunning systems.  I'd be surprised if taking this into account changes the emerging conclusions - but this is definitely something that should be looked into.
+
+# Emerging findigns
+
+Emerging findings seem to be that it is unlikely that the fish stunning intervention can have an impact that comes close to the impact (in terms of duration affected) of chicken campaigns for annoying, hurtful or disabling pain. For these pain intensities, whether or not fish stunning appears to avert more time in pain appears to be entirely driven by uncertainty of whether the chicken intervention increases or decreases time in pain.
 
 But for excruciating pain, its plausible that the fish stunning intervention could reduce more time in pain if at least 10-15% of the duration of conventional fish slaughter for affected species is excruciating pain, and most of this is mitigated through stunning.
 
@@ -32,6 +44,7 @@ library(forcats)
 
 ```
 
+
 Import data from welfare footprint and estimates of fish impact per dollar
 
 ```{r}

2_intro_charts.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Sagar Shah, Rethink Priorities">
-<meta name="dcterms.date" content="2024-02-08">
+<meta name="dcterms.date" content="2024-02-16">
 
 <title>2. Introduction section charts</title>
 <style>
@@ -3025,7 +3025,9 @@
     <h2 id="toc-title">Table of contents</h2>
 
   <ul>
-  <li><a href="#prep" id="toc-prep" class="nav-link active" data-scroll-target="#prep">Prep</a></li>
+  <li><a href="#navigation" id="toc-navigation" class="nav-link active" data-scroll-target="#navigation">Navigation</a></li>
+  <li><a href="#about-this-file" id="toc-about-this-file" class="nav-link" data-scroll-target="#about-this-file">About this file</a></li>
+  <li><a href="#prep" id="toc-prep" class="nav-link" data-scroll-target="#prep">Prep</a></li>
   <li><a href="#load-and-process-data" id="toc-load-and-process-data" class="nav-link" data-scroll-target="#load-and-process-data">Load and process data</a></li>
   <li><a href="#modify-weight-and-lifespan-data" id="toc-modify-weight-and-lifespan-data" class="nav-link" data-scroll-target="#modify-weight-and-lifespan-data">Modify weight and lifespan data</a></li>
   <li><a href="#run-calculations" id="toc-run-calculations" class="nav-link" data-scroll-target="#run-calculations">Run calculations</a></li>
@@ -3060,7 +3062,7 @@ <h1 class="title">2. Introduction section charts</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">February 8, 2024</p>
+      <p class="date">February 16, 2024</p>
     </div>
   </div>
 
@@ -3070,6 +3072,14 @@ <h1 class="title">2. Introduction section charts</h1>
 
 </header>
 
+<section id="navigation" class="level1">
+<h1>Navigation</h1>
+<p>Return to the full <a href="https://github.com/rethinkpriorities/farmfish_stunning_cea">Github repository</a> for this project, or the <a href="https://rethinkpriorities.github.io/farmfish_stunning_cea/">html version of the readme file</a>.</p>
+</section>
+<section id="about-this-file" class="level1">
+<h1>About this file</h1>
+<p>This file prepares the charts used in the introduction section of the report.</p>
+</section>
 <section id="prep" class="level1">
 <h1>Prep</h1>
 <p>Clear memory, load packages and run functions script.</p>

3_main_results.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Sagar Shah, Rethink Priorities">
-<meta name="dcterms.date" content="2024-02-08">
+<meta name="dcterms.date" content="2024-02-16">
 
 <title>3. Main results - stunning intervention</title>
 <style>
@@ -3025,7 +3025,9 @@
     <h2 id="toc-title">Table of contents</h2>
 
   <ul>
-  <li><a href="#generic-prep" id="toc-generic-prep" class="nav-link active" data-scroll-target="#generic-prep">Generic prep</a>
+  <li><a href="#navigation" id="toc-navigation" class="nav-link active" data-scroll-target="#navigation">Navigation</a></li>
+  <li><a href="#about-this-file" id="toc-about-this-file" class="nav-link" data-scroll-target="#about-this-file">About this file</a></li>
+  <li><a href="#generic-prep" id="toc-generic-prep" class="nav-link" data-scroll-target="#generic-prep">Generic prep</a>
   <ul class="collapse">
   <li><a href="#helper-functions" id="toc-helper-functions" class="nav-link" data-scroll-target="#helper-functions">Helper functions</a></li>
   </ul></li>
@@ -3109,7 +3111,7 @@ <h1 class="title">3. Main results - stunning intervention</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">February 8, 2024</p>
+      <p class="date">February 16, 2024</p>
     </div>
   </div>
 
@@ -3119,6 +3121,14 @@ <h1 class="title">3. Main results - stunning intervention</h1>
 
 </header>
 
+<section id="navigation" class="level1">
+<h1>Navigation</h1>
+<p>Return to the full <a href="https://github.com/rethinkpriorities/farmfish_stunning_cea">Github repository</a> for this project, or the <a href="https://rethinkpriorities.github.io/farmfish_stunning_cea/">html version of the readme file</a>.</p>
+</section>
+<section id="about-this-file" class="level1">
+<h1>About this file</h1>
+<p>This conducts cost-effectiveness analysis and produces the main results tables charts used in the Results section of the report.</p>
+</section>
 <section id="generic-prep" class="level1">
 <h1>Generic prep</h1>
 <p>Open libraries</p>