tester

Author: matthipsey

02-ocean-climatology.Rmd

@@ -6,6 +6,7 @@ rmd_files: ["index.Rmd",
             "csiem_overview.Rmd",
             "csiem_data.Rmd",
             "csiem_integration.Rmd",
+            "02-ocean-climatology.Rmd",
           # "csiem_resuspension_and_turbidity.Rmd",
           # "csiem_water_biogeochemistry.Rmd",
           # "csiem_macroalgae.Rmd",

_bookdown.yml

@@ -72,7 +72,8 @@ <h1>
 <li><a class="" href="csiem-model-overview.html"><span class="header-section-number">2</span> CSIEM Model Overview</a></li>
 <li><a class="" href="cockburn-environmental-data.html"><span class="header-section-number">3</span> Cockburn Environmental Data</a></li>
 <li><a class="" href="model-data-organisation.html"><span class="header-section-number">4</span> Model-Data Organisation</a></li>
-<li><a class="" href="integrated-assessment.html"><span class="header-section-number">5</span> Integrated Assessment</a></li>
+<li><a class="" href="ocean-climatology.html"><span class="header-section-number">5</span> Resolving Perth Waters Monthly Ocean Climatology</a></li>
+<li><a class="" href="integrated-assessment.html"><span class="header-section-number">6</span> Integrated Assessment</a></li>
 <li><a class="" href="references.html">References</a></li>
 <li><a class="" href="appendix-a-data-catalogue.html">Appendix A : Data Catalogue</a></li>
 <li><a class="" href="appendix-b-results-archive.html">Appendix B : Results Archive</a></li>
@@ -110,7 +111,7 @@ <h1>Page not found<a class="anchor" aria-label="anchor" href="#page-not-found"><
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 29-September-2025.</p>
+    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 07-October-2025.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

docs/404.html

@@ -72,7 +72,8 @@ <h1>
 <li><a class="" href="csiem-model-overview.html"><span class="header-section-number">2</span> CSIEM Model Overview</a></li>
 <li><a class="" href="cockburn-environmental-data.html"><span class="header-section-number">3</span> Cockburn Environmental Data</a></li>
 <li><a class="" href="model-data-organisation.html"><span class="header-section-number">4</span> Model-Data Organisation</a></li>
-<li><a class="" href="integrated-assessment.html"><span class="header-section-number">5</span> Integrated Assessment</a></li>
+<li><a class="" href="ocean-climatology.html"><span class="header-section-number">5</span> Resolving Perth Waters Monthly Ocean Climatology</a></li>
+<li><a class="" href="integrated-assessment.html"><span class="header-section-number">6</span> Integrated Assessment</a></li>
 <li><a class="" href="references.html">References</a></li>
 <li><a class="active" href="appendix-a-data-catalogue.html">Appendix A : Data Catalogue</a></li>
 <li><a class="" href="appendix-b-results-archive.html">Appendix B : Results Archive</a></li>
@@ -101,7 +102,7 @@ <h3>V1.6 Dataset Overview<a class="anchor" aria-label="anchor" href="#v1.6-datas
 <div style="border: 1px solid #ddd; padding: 5px; ">
 <div class="inline-table"><table class="table" style="font-size: 10px; margin-left: auto; margin-right: auto;">
 <caption style="font-size: initial !important;">
-<span id="tab:A-datasummary16">Table 5.1: </span>Data summary in CSIEM V1.6 (ingested) data-set. Please note that other data-sets are included in the CSIEM data-lake that may not appear on these images. Please refer to the data snapshot link above for the current data summary list.
+<span id="tab:A-datasummary16">Table 6.1: </span>Data summary in CSIEM V1.6 (ingested) data-set. Please note that other data-sets are included in the CSIEM data-lake that may not appear on these images. Please refer to the data snapshot link above for the current data summary list.
 </caption>
 <thead><tr>
 <th style="text-align:left;font-weight: bold;color: white !important;background-color: #14759e !important;">
@@ -312,7 +313,7 @@ <h3>V2.0 Dataset Overview<a class="anchor" aria-label="anchor" href="#v2.0-datas
 <div style="border: 1px solid #ddd; padding: 5px; ">
 <div class="inline-table"><table class="table" style="font-size: 10px; margin-left: auto; margin-right: auto;">
 <caption style="font-size: initial !important;">
-<span id="tab:A-datasummary15">Table 5.2: </span>Pending.)
+<span id="tab:A-datasummary15">Table 6.2: </span>Pending.)
 </caption>
 <thead><tr>
 <th style="text-align:left;font-weight: bold;color: white !important;background-color: #14759e !important;">
@@ -374,7 +375,7 @@ <h3>V2.0 Dataset Overview<a class="anchor" aria-label="anchor" href="#v2.0-datas
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 29-September-2025.</p>
+    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 07-October-2025.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

docs/appendix-a-data-catalogue.html

@@ -72,7 +72,8 @@ <h1>
 <li><a class="" href="csiem-model-overview.html"><span class="header-section-number">2</span> CSIEM Model Overview</a></li>
 <li><a class="" href="cockburn-environmental-data.html"><span class="header-section-number">3</span> Cockburn Environmental Data</a></li>
 <li><a class="" href="model-data-organisation.html"><span class="header-section-number">4</span> Model-Data Organisation</a></li>
-<li><a class="" href="integrated-assessment.html"><span class="header-section-number">5</span> Integrated Assessment</a></li>
+<li><a class="" href="ocean-climatology.html"><span class="header-section-number">5</span> Resolving Perth Waters Monthly Ocean Climatology</a></li>
+<li><a class="" href="integrated-assessment.html"><span class="header-section-number">6</span> Integrated Assessment</a></li>
 <li><a class="" href="references.html">References</a></li>
 <li><a class="" href="appendix-a-data-catalogue.html">Appendix A : Data Catalogue</a></li>
 <li><a class="active" href="appendix-b-results-archive.html">Appendix B : Results Archive</a></li>
@@ -88,9 +89,9 @@ <h1>Appendix B : Results Archive<a class="anchor" aria-label="anchor" href="#app
 </h1>
 <p>The aim of this section is to compare the modelling results against historical data collected within Cockbrun Sound and surrounding waters (where available), with outputs of various generations of the CSIEM. The model performance in predicting a range of relevant variables such as salinity, temperature, nitrogen, phosphorus and total chlorophyll-a, are assessed with a set of statistical metrics, and other supporting analyses.</p>
 <p>This appendix is in progres during the active development of the model and being updated with the CSIEM modelling as it evolves.</p>
-<div id="synoptic-scale-validation" class="section level2" number="5.4">
+<div id="synoptic-scale-validation" class="section level2" number="6.4">
 <h2>
-<span class="header-section-number">5.4</span> Synoptic-scale validation<a class="anchor" aria-label="anchor" href="#synoptic-scale-validation"><i class="fas fa-link"></i></a>
+<span class="header-section-number">6.4</span> Synoptic-scale validation<a class="anchor" aria-label="anchor" href="#synoptic-scale-validation"><i class="fas fa-link"></i></a>
 </h2>
 <p>A “high-level” annual-scale analysis of the model is undertaken for each model version during development. This is to provide a synoptic scale assessment of how key variables are preodcited with different model configurations.</p>
 <p>Time-series validation plots including the statistics for each site are available via the links in the below table (Table <a href="#tab:A-testing"><strong>??</strong></a>). The tables are organised based on model generation, in addition to a comparison of the performance of the model generations (termed ‘multi’).</p>
@@ -103,7 +104,7 @@ <h3>GEN 2.0 alpha<a class="anchor" aria-label="anchor" href="#gen-2.0-alpha"><i
 <div style="border: 1px solid #ddd; padding: 5px; ">
 <div class="inline-table"><table class="table" style="font-size: 10px; margin-left: auto; margin-right: auto;">
 <caption style="font-size: initial !important;">
-<span id="tab:A-testing4">Table 5.3: </span>Model results for GEN 2.1 nWV nSDG simulation (Generation 2.1 model without wave or dynamic sediment modules engaged.)
+<span id="tab:A-testing4">Table 6.3: </span>Model results for GEN 2.1 nWV nSDG simulation (Generation 2.1 model without wave or dynamic sediment modules engaged.)
 </caption>
 <thead><tr>
 <th style="text-align:left;font-weight: bold;color: white !important;background-color: #14759e !important;">
@@ -130,7 +131,7 @@ <h3>GEN 1.6<a class="anchor" aria-label="anchor" href="#gen-1.6"><i class="fas f
 <div style="border: 1px solid #ddd; padding: 5px; ">
 <div class="inline-table"><table class="table" style="font-size: 10px; margin-left: auto; margin-right: auto;">
 <caption style="font-size: initial !important;">
-<span id="tab:A-testing3">Table 5.4: </span>Model results for GEN 2 nWV nSDG simulation (Generation 2 model without wave or dynamic sediment modules engaged.)
+<span id="tab:A-testing3">Table 6.4: </span>Model results for GEN 2 nWV nSDG simulation (Generation 2 model without wave or dynamic sediment modules engaged.)
 </caption>
 <thead><tr>
 <th style="text-align:left;font-weight: bold;color: white !important;background-color: #14759e !important;">
@@ -157,7 +158,7 @@ <h3>GEN 1.5<a class="anchor" aria-label="anchor" href="#gen-1.5"><i class="fas f
 <div style="border: 1px solid #ddd; padding: 5px; ">
 <div class="inline-table"><table class="table" style="font-size: 10px; margin-left: auto; margin-right: auto;">
 <caption style="font-size: initial !important;">
-<span id="tab:A-testing2">Table 5.5: </span>Model results for Generation 1.5
+<span id="tab:A-testing2">Table 6.5: </span>Model results for Generation 1.5
 </caption>
 <thead><tr>
 <th style="text-align:left;font-weight: bold;color: white !important;background-color: #14759e !important;">
@@ -184,7 +185,7 @@ <h3>GEN 1.1<a class="anchor" aria-label="anchor" href="#gen-1.1"><i class="fas f
 <div style="border: 1px solid #ddd; padding: 5px; ">
 <div class="inline-table"><table class="table" style="font-size: 10px; margin-left: auto; margin-right: auto;">
 <caption style="font-size: initial !important;">
-<span id="tab:A-testing1">Table 5.6: </span>Model results for Generation 1
+<span id="tab:A-testing1">Table 6.6: </span>Model results for Generation 1
 </caption>
 <thead><tr>
 <th style="text-align:left;font-weight: bold;color: white !important;background-color: #14759e !important;">
@@ -206,7 +207,7 @@ <h3>MULTI<a class="anchor" aria-label="anchor" href="#multi"><i class="fas fa-li
 <div style="border: 1px solid #ddd; padding: 5px; ">
 <div class="inline-table"><table class="table" style="font-size: 10px; margin-left: auto; margin-right: auto;">
 <caption style="font-size: initial !important;">
-<span id="tab:A-testing5">Table 5.7: </span>Comparison of Model Generations 1, 1.5 &amp; 2
+<span id="tab:A-testing5">Table 6.7: </span>Comparison of Model Generations 1, 1.5 &amp; 2
 </caption>
 <thead><tr>
 <th style="text-align:left;font-weight: bold;color: white !important;background-color: #14759e !important;">
@@ -222,9 +223,9 @@ <h3>MULTI<a class="anchor" aria-label="anchor" href="#multi"><i class="fas fa-li
 </div>
 </div>
 </div>
-<div id="context-specific-validation" class="section level2" number="5.5">
+<div id="context-specific-validation" class="section level2" number="6.5">
 <h2>
-<span class="header-section-number">5.5</span> Context-specific validation<a class="anchor" aria-label="anchor" href="#context-specific-validation"><i class="fas fa-link"></i></a>
+<span class="header-section-number">6.5</span> Context-specific validation<a class="anchor" aria-label="anchor" href="#context-specific-validation"><i class="fas fa-link"></i></a>
 </h2>
 
 </div>
@@ -244,7 +245,7 @@ <h2>
     <nav id="toc" data-toggle="toc" aria-label="On this page"><h2>On this page</h2>
       <ul class="nav navbar-nav">
 <li><a class="nav-link" href="#appendix-b-results-archive">Appendix B : Results Archive</a></li>
-<li><a class="nav-link" href="#synoptic-scale-validation"><span class="header-section-number">5.4</span> Synoptic-scale validation</a></li>
+<li><a class="nav-link" href="#synoptic-scale-validation"><span class="header-section-number">6.4</span> Synoptic-scale validation</a></li>
 <li>
 <a class="nav-link" href="#section-1"></a><ul class="nav navbar-nav">
 <li><a class="nav-link" href="#gen-2.0-alpha">GEN 2.0 alpha</a></li>
@@ -254,7 +255,7 @@ <h2>
 <li><a class="nav-link" href="#multi">MULTI</a></li>
 </ul>
 </li>
-<li><a class="nav-link" href="#context-specific-validation"><span class="header-section-number">5.5</span> Context-specific validation</a></li>
+<li><a class="nav-link" href="#context-specific-validation"><span class="header-section-number">6.5</span> Context-specific validation</a></li>
 </ul>
 
       <div class="book-extra">
@@ -271,7 +272,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 29-September-2025.</p>
+    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 07-October-2025.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

docs/appendix-b-results-archive.html

@@ -72,7 +72,8 @@ <h1>
 <li><a class="" href="csiem-model-overview.html"><span class="header-section-number">2</span> CSIEM Model Overview</a></li>
 <li><a class="active" href="cockburn-environmental-data.html"><span class="header-section-number">3</span> Cockburn Environmental Data</a></li>
 <li><a class="" href="model-data-organisation.html"><span class="header-section-number">4</span> Model-Data Organisation</a></li>
-<li><a class="" href="integrated-assessment.html"><span class="header-section-number">5</span> Integrated Assessment</a></li>
+<li><a class="" href="ocean-climatology.html"><span class="header-section-number">5</span> Resolving Perth Waters Monthly Ocean Climatology</a></li>
+<li><a class="" href="integrated-assessment.html"><span class="header-section-number">6</span> Integrated Assessment</a></li>
 <li><a class="" href="references.html">References</a></li>
 <li><a class="" href="appendix-a-data-catalogue.html">Appendix A : Data Catalogue</a></li>
 <li><a class="" href="appendix-b-results-archive.html">Appendix B : Results Archive</a></li>
@@ -1459,7 +1460,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 29-September-2025.</p>
+    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 07-October-2025.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

docs/cockburn-environmental-data.html

@@ -72,7 +72,8 @@ <h1>
 <li><a class="active" href="csiem-model-overview.html"><span class="header-section-number">2</span> CSIEM Model Overview</a></li>
 <li><a class="" href="cockburn-environmental-data.html"><span class="header-section-number">3</span> Cockburn Environmental Data</a></li>
 <li><a class="" href="model-data-organisation.html"><span class="header-section-number">4</span> Model-Data Organisation</a></li>
-<li><a class="" href="integrated-assessment.html"><span class="header-section-number">5</span> Integrated Assessment</a></li>
+<li><a class="" href="ocean-climatology.html"><span class="header-section-number">5</span> Resolving Perth Waters Monthly Ocean Climatology</a></li>
+<li><a class="" href="integrated-assessment.html"><span class="header-section-number">6</span> Integrated Assessment</a></li>
 <li><a class="" href="references.html">References</a></li>
 <li><a class="" href="appendix-a-data-catalogue.html">Appendix A : Data Catalogue</a></li>
 <li><a class="" href="appendix-b-results-archive.html">Appendix B : Results Archive</a></li>
@@ -123,7 +124,7 @@ <h1>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 29-September-2025.</p>
+    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 07-October-2025.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

docs/csiem-model-overview.html

@@ -72,7 +72,8 @@ <h1>
 <li><a class="" href="csiem-model-overview.html"><span class="header-section-number">2</span> CSIEM Model Overview</a></li>
 <li><a class="" href="cockburn-environmental-data.html"><span class="header-section-number">3</span> Cockburn Environmental Data</a></li>
 <li><a class="" href="model-data-organisation.html"><span class="header-section-number">4</span> Model-Data Organisation</a></li>
-<li><a class="" href="integrated-assessment.html"><span class="header-section-number">5</span> Integrated Assessment</a></li>
+<li><a class="" href="ocean-climatology.html"><span class="header-section-number">5</span> Resolving Perth Waters Monthly Ocean Climatology</a></li>
+<li><a class="" href="integrated-assessment.html"><span class="header-section-number">6</span> Integrated Assessment</a></li>
 <li><a class="" href="references.html">References</a></li>
 <li><a class="" href="appendix-a-data-catalogue.html">Appendix A : Data Catalogue</a></li>
 <li><a class="" href="appendix-b-results-archive.html">Appendix B : Results Archive</a></li>
@@ -186,7 +187,7 @@ <h2>Citing this document<a class="anchor" aria-label="anchor" href="#citing-this
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 29-September-2025.</p>
+    <p>"<strong>The Cockburn Sound Integrated Ecosystem Model</strong>" was written by AED. It was last built on 07-October-2025.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">