Fix BGC includes

jjohnston-aims · Sep 27, 2023 · 8b780ce · 8b780ce
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diff --git a/gbr1/temp-wind-salt-current/index.qmd b/gbr1/temp-wind-salt-current/index.qmd
@@ -59,7 +59,7 @@ Many marine organisms (such as Crown-of-Thorns Starfish and corals) are disperse
 
 ### Interesting events
 
-- Cyclones: [Nathan (March 2015)](#year=2015;month=3), [Debbi (March 2017)](#year=2017;month=3),
+- Cyclones: [**Nathan** (March 2015)](#year=2015;month=3), [**Debbi** (March 2017)](#year=2017;month=3),
 - Coral bleaching from high temperature ([March 2016](#year=2016;month=3), [March 2017](#year=2017;month=3)),
 - Flood plumes with low salinity ([Feb 2019](#region=townsville-3;year=2019;month=2))
 - Strong East Australian Current ([Nov 2015, monthly average current](#frame=Monthly;year=2015;month=11))

diff --git a/gbr4/bgc/baseline/alk_ph_omega-ar/index.qmd b/gbr4/bgc/baseline/alk_ph_omega-ar/index.qmd
@@ -154,6 +154,6 @@ Zheng, M. & Cao, L. (2015) Simulation of global ocean acidification and
 chemical habitats of shallow- and cold-water coral reefs,
 https://doi.org/10.1016/j.accre.2015.05.002
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/chl-a-sum_din_efi/index.qmd b/gbr4/bgc/baseline/chl-a-sum_din_efi/index.qmd
@@ -23,6 +23,6 @@ Concentration of dissolved inorganic nitrogen (DIN). DIN = \[NH4] + \[NO3].
 
 This is the sum of the suspended sediments in the water column. It is \[Fine sediment] + \[Mud] + \[Mud carbonate] + \[Mud mineral] + \[Dust]
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/cs-n_cs-chl_ch-n/index.qmd b/gbr4/bgc/baseline/cs-n_cs-chl_ch-n/index.qmd
@@ -90,6 +90,6 @@ sum of the biomass of all symbiotic filter-feeding organisms such as
 corals, sponges, clams etc. C:N:P is 106:16:1. Light is accessed in the
 following order: Macroalgae, Seagrass, Coral.
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/din_dip_dic/index.qmd b/gbr4/bgc/baseline/din_dip_dic/index.qmd
@@ -23,6 +23,6 @@ Concentration of dissolved inorganic phosphorus, also referred to as orthophosph
 
 Concentration of dissolved inorganic carbon, composed chiefly at seawater pH of HCO3-, with a small percentage present as CO32-.
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/din_no3_nh4/index.qmd b/gbr4/bgc/baseline/din_no3_nh4/index.qmd
@@ -61,6 +61,6 @@ nitrate represents [NO3-] + [NO2-].
 
 Concentration of ammonia ions [NH4+].
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/dor-c_dor-n_dor-p/index.qmd b/gbr4/bgc/baseline/dor-c_dor-n_dor-p/index.qmd
@@ -23,6 +23,6 @@ The concentration of nitrogen in dissolved organic compounds.
 
 The concentration of phosphorus in dissolved organic compounds.
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/efi_dust_mud-carbonate_mud-mineral/index.qmd b/gbr4/bgc/baseline/efi_dust_mud-carbonate_mud-mineral/index.qmd
@@ -52,6 +52,6 @@ Mud mineral
 Small sized (nominal size 30 µm), re-suspending particles with a sinking
 velocity of 17 m d^-1^. This sediment is brown in colour.
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/ma-n_sg-n_sgh-n_sgd-n/index.qmd b/gbr4/bgc/baseline/ma-n_sg-n_sgh-n_sgd-n/index.qmd
@@ -103,6 +103,6 @@ Environmental Modelling Suite (EMS): Scientific description of the
 optical and biogeochemical models (vB3p0). Geosci. Model Dev. Discuss.
 <https://doi.org/10.5194/gmd-2019-115>
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/oxygen_oxy-sat/index.qmd b/gbr4/bgc/baseline/oxygen_oxy-sat/index.qmd
@@ -23,14 +23,14 @@ More detail on how oxygen levels were modelled can be found in Baird et al. (202
 
 ### Oxygen saturation percentage
 
-The saturation state of oxygen [O2]sat is determined as a function of temperature and salinity following Weiss (1970). It represents the maximum amount of the dissolved oxygen that the water can hold. It is used to calculate the amount of oxygen exchange in the sea-air boundary. If the oxygen saturation percentage is below 100% then oxygen will be absorbed from the atmosphere. If it is above 100% then oxygen will be out gased from the sea into the atmosphere.
+The saturation state of oxygen \[O2\]~sat~ is determined as a function of temperature and salinity following Weiss (1970). It represents the maximum amount of the dissolved oxygen that the water can hold. It is used to calculate the amount of oxygen exchange in the sea-air boundary. If the oxygen saturation percentage is below 100% then oxygen will be absorbed from the atmosphere. If it is above 100% then oxygen will be out gased from the sea into the atmosphere.
 
 ### Reference
 
 Baird, M. E., Wild-Allen, K. A., Parslow, J., Mongin, M., Robson, B., Skerratt, J., Rizwi, F., Soja-Woźniak, M., Jones, E., Herzfeld, M., Margvelashvili, N., Andrewartha, J., Langlais, C., Adams, M. P., Cherukuru, N., Gustafsson, M., Hadley, S., Ralph, P. J., Rosebrock, U., … Steven, A. D. L. (2020). CSIRO Environmental Modelling Suite (EMS): scientific description of the optical and biogeochemical models (vB3p0). Geoscientific Model Development, 13(9), 4503–4553. https://doi.org/10.5194/gmd-13-4503-2020
 
 Weiss, R.: The solubility of nitrogen, oxygen and argon in water and seawater, Deep Sea Res., 17, 721–735, 1970.
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/pip_pip-sed/index.qmd b/gbr4/bgc/baseline/pip_pip-sed/index.qmd
@@ -21,6 +21,6 @@ Phosphorus ions that are absorbed onto particles. It is considered a particulate
 
 Phosphorus that is permanently removed from the system through burial of Particulate Inorganic Phosphorus in the sediment.
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/secchi_kd-490_epipar-sg/index.qmd b/gbr4/bgc/baseline/secchi_kd-490_epipar-sg/index.qmd
@@ -69,6 +69,6 @@ condition for the Great Barrier Reef: a case study for seagrass meadows
 in the Burdekin region*) is currently investigating the possibility of
 using this model to derive and test ecologically relevant targets.
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/gbr4/bgc/baseline/true-colour/index.qmd b/gbr4/bgc/baseline/true-colour/index.qmd
@@ -25,6 +25,6 @@ MODIS satellite, except with no clouds. While we don't create a direct
 comparison with the MODIS imagery here on this site, you can view the MODIS
 imagery via the [NASA WorldView browser](https://worldview.earthdata.nasa.gov/?v=128.54593584758447,-31.75702092134829,171.2501420451839,-8.125135981270493&l=Reference_Labels(hidden),Reference_Features(hidden),Coastlines,MODIS_Aqua_CorrectedReflectance_TrueColor(hidden),MODIS_Terra_CorrectedReflectance_TrueColor).
 
-{{< include ../../../../includes/_source_data_gbr4.qmd >}}
+{{< include ../../../../includes/_source_data_bgc.qmd >}}
 
-{{< include ../../../../includes/_recent_data.qmd >}}
+{{< include ../../../../includes/_data_span.qmd >}}
diff --git a/includes/_data_span.qmd b/includes/_data_span.qmd
@@ -0,0 +1,5 @@
+## Data span
+
+These results are based on a fixed time period (Dec 2010 - Apr 2019) hind-cast analysis developed 
+for comparing changes in land practices. The river run off used to drive the BGC model were 
+provided by the [SOURCE Catchments modelling](https://www.reefplan.qld.gov.au/tracking-progress/paddock-to-reef/modelling-and-monitoring).
diff --git a/includes/_source_data_bgc.qmd b/includes/_source_data_bgc.qmd
@@ -0,0 +1,8 @@
+## Source data
+
+The videos/images on this page are based on the [4km eReefs BioGeoChemical model (v3.1) (GBR4_H2p0_B3p1_Cq3b_Dhnd)](https://research.csiro.au/ereefs/models/) 
+run with SOURCE Catchments using Baseline catchment conditions. Detailed information about the model can be found 
+in the paper: [CSIRO Environmental Modelling Suite (EMS): Scientific description of the optical and biogeochemical 
+models (vB3p0)](https://doi.org/10.5194/gmd-2019-115). The raw model data is available from the [NCI THREDDS server](https://dapds00.nci.org.au/thredds/catalog/fx3/gbr4_bgc_GBR4_H2p0_B3p1_Cq3b_Dhnd/catalog.html) (daily, in curvilinear NetCDF format) 
+and the aggregate data from the [AIMS eAtlas THREDDS server](https://thredds.ereefs.aims.gov.au/thredds/s3catalogue/aims-ereefs-public-prod/derived/ncaggregate/ereefs/GBR4_H2p0_B3p1_Cq3b_Dhnd/catalog.html?_gl=1*140ovqw*_ga*MTg3NjQyODQyNS4xNjk1MTY5ODcw*_ga_6SSTNBNHXG*MTY5NTc3MDQwNC4xMy4xLjE2OTU3NzA4MzEuMC4wLjA.) (daily, monthly, yearly, in in regular rectangular 
+grid NetCDF format).