AED manual

AquaticEcoDynamics · Jun 29, 2023 · 57dea89 · 57dea89
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diff --git a/23-sediment_biogeochemistry.Rmd b/23-sediment_biogeochemistry.Rmd
@@ -3159,21 +3159,21 @@ kable(param_UAE7 ,"html", escape = F, align = "c", caption = "Depositional thres
 
 CANDI-AED was used as part of the assessment of the Coorong Lagoon in South Australia. It was used as part of [a greater project](https://aquaticecodynamics.github.io/cdm-science/index.html), in conjunction with a fully 3D resolved Tuflow-FV model of the lagoon, that had full biogeochemistry modules and habitat assessments. In particular, the nutrient budgets and the effects of the hypersalinity were calculated. The [sediment modelling component of the project](https://aquaticecodynamics.github.io/cdm-science/sediment-biogeochemistry.html) in particular looked at the effect of hypersalinity on bioturbation and bioirrigation rates, and the resulting effects such as denitrification.
 
-```{r CoorongSVG-1, echo=FALSE, fig.cap="Test",fig.show='hold',fig.align='center', out.width = '90%'}
-knitr::include_graphics("images/23-sediment_biogeochemistry/VCW/t_D_C_6panel_oxy.svg")
-```
+<!-- ```{r CoorongSVG-1, echo=FALSE, fig.cap="Test",fig.show='hold',fig.align='center', out.width = '90%'} -->
+<!-- knitr::include_graphics("images/23-sediment_biogeochemistry/VCW/t_D_C_6panel_oxy.svg") -->
+<!-- ``` -->
 
-```{r CoorongPNG-1, echo=FALSE, fig.cap="Test",fig.show='hold',fig.align='center', out.width = '100%'}
-knitr::include_graphics("images/23-sediment_biogeochemistry/UAEFish/ThreePlots_popl_13_reso_500.png")
-```
+<!-- ```{r CoorongPNG-1, echo=FALSE, fig.cap="Test",fig.show='hold',fig.align='center', out.width = '100%'} -->
+<!-- knitr::include_graphics("images/23-sediment_biogeochemistry/UAEFish/ThreePlots_popl_13_reso_500.png") -->
+<!-- ``` -->
 
-```{r CoorongPNG-2, echo=FALSE, fig.cap="Test",fig.show='hold',fig.align='center', out.width = '100%'}
-knitr::include_graphics("images/23-sediment_biogeochemistry/UAEFish/ThreePlots_popl_13_reso_1000.png")
-```
+<!-- ```{r CoorongPNG-2, echo=FALSE, fig.cap="Test",fig.show='hold',fig.align='center', out.width = '100%'} -->
+<!-- knitr::include_graphics("images/23-sediment_biogeochemistry/UAEFish/ThreePlots_popl_13_reso_1000.png") -->
+<!-- ``` -->
 
-```{r CoorongPNG-3, echo=FALSE, fig.cap="Test",fig.show='hold',fig.align='center', out.width = '100%'}
-knitr::include_graphics("images/23-sediment_biogeochemistry/UAEFish/ThreePlots_amm_11_reso_200.png")
-```
+<!-- ```{r CoorongPNG-3, echo=FALSE, fig.cap="Test",fig.show='hold',fig.align='center', out.width = '100%'} -->
+<!-- knitr::include_graphics("images/23-sediment_biogeochemistry/UAEFish/ThreePlots_amm_11_reso_200.png") -->
+<!-- ``` -->
 
 ### Case study: Mass balance and numerical error checking
 

diff --git a/aed_science.Rmd b/aed_science.Rmd
diff --git a/docs/404.html b/docs/404.html
@@ -23,7 +23,7 @@
 <meta name="author" content="" />
 
 
-<meta name="date" content="2022-09-26" />
+<meta name="date" content="2023-06-29" />
 
  <meta name="viewport" content="width=device-width, initial-scale=1" />
  <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -426,12 +426,14 @@
 <li class="chapter" data-level="14.5.2" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#flux-of-state-variables-swi_fluxes.sed"><i class="fa fa-check"></i><b>14.5.2</b> Flux of state variables: ‘swi_fluxes.sed’</a></li>
 <li class="chapter" data-level="14.5.3" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#SedOtherVariablesExtrasSed"><i class="fa fa-check"></i><b>14.5.3</b> Other variables: ‘/Extras/ .sed’</a></li>
 <li class="chapter" data-level="14.5.4" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#depth-profile-settings-depths.sed"><i class="fa fa-check"></i><b>14.5.4</b> Depth profile settings: ‘Depths.sed’</a></li>
+<li class="chapter" data-level="14.5.5" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#mass-balance-calculation"><i class="fa fa-check"></i><b>14.5.5</b> Mass balance calculation</a></li>
 </ul></li>
 <li class="chapter" data-level="14.6" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#case-studies-examples-6"><i class="fa fa-check"></i><b>14.6</b> Case Studies &amp; Examples</a>
 <ul>
 <li class="chapter" data-level="14.6.1" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#case-study-model-benchmark-example"><i class="fa fa-check"></i><b>14.6.1</b> Case study: Model benchmark example</a></li>
-<li class="chapter" data-level="14.6.2" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#case-studyaquaculture-and-sediment-recovery"><i class="fa fa-check"></i><b>14.6.2</b> Case study:Aquaculture and sediment recovery</a></li>
+<li class="chapter" data-level="14.6.2" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#case-study-aquaculture-and-sediment-recovery"><i class="fa fa-check"></i><b>14.6.2</b> Case study: Aquaculture and sediment recovery</a></li>
 <li class="chapter" data-level="14.6.3" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#case-study-the-coorong-dynamics-model"><i class="fa fa-check"></i><b>14.6.3</b> Case study: The Coorong Dynamics Model</a></li>
+<li class="chapter" data-level="14.6.4" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#case-study-mass-balance-and-numerical-error-checking"><i class="fa fa-check"></i><b>14.6.4</b> Case study: Mass balance and numerical error checking</a></li>
 </ul></li>
 <li class="chapter" data-level="14.7" data-path="sediment-biogeochemistry.html"><a href="sediment-biogeochemistry.html#references"><i class="fa fa-check"></i><b>14.7</b> References</a></li>
 </ul></li>