NPZ-model/State-Variables.md

@@ -22,7 +22,7 @@ graph TD;
   Shellfish-- DINprod--> DIN;
 ```
 
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 ## Phytoplankton (Phy)
 Phytoplankton is composed of microalgae in the water column that are transported by tidal currents. The unit of phytoplankton is mmol-N m<sup>-3</sup>. Phytoplankton increases by primary production (DINuptake). Phytoplankton is consumed by zooplankton (ZooGrazing) and shellfish (GrazingPhy). Also phytoplankton can sink to the bottom (SinkPhy), where it becomes part of the bottom detritus (Bot_Det).
 
@@ -33,7 +33,7 @@ graph TD;
   Phy-- GrazingPhy--> Shellfish;
   Phy-- SinkPhy--> Bot_Det;
 ```
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 ## Zooplankton (Zoo)
 Zooplankton (Zoo) are small animals (e.g. crustaceans, shellfish larvae) that live in the water column and are transported by the tidal currents. The unit is mmol-N m<sup>-3</sup>. Zooplankton consumes phytoplankton (ZooGrazing). A fraction of the nitrogen that is grazed is lost as feaces (ZooFaeces) and the rest will result in an increase of the zooplankton biomass. Zooplankton can also be consumed by shellfish (GrazingZoo). When the zooplankton dies (ZooMortality) it will become detritus (Det). Finally, zooplankton also produces dissolved inorganic nitrogen by respiration (ZooExcretion).
 
@@ -45,7 +45,7 @@ graph TD;
   Zoo-- ZooMortality--> Det;
   Zoo-- ZooExcretion--> DIN;
 ```
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 ## Detritus (Det)
 Detritus (Det) is the dead organic carbon. The unit is mmol-N m<sup>-3</sup>. Detritus is produced by mortality of zooplankton (ZooMortality) and the production of faeces by zooplankton (ZooFaeces). Detritus is mineralized in the watercolum (Mineralisation). Shellfish can also filter detritus from the water column (GrazingDet). Finally detritus can sink to the seafloor (SinkDet) where it becomes Bot_Det .
 
@@ -59,7 +59,7 @@ graph TD;
   Det-- SinkDet--> Bot_Det;
 ```
 
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 # State variables in the bottom
 ## Microphytobenthos (MPB)
 Microphytobenthos (MPD) are microalgae that live on sea floor. The unit is mmol-N m<sup>-2</sup>. MPB only occurs on the intertidal areas. The biomass of MPB increases through primary production (DINuptMPB). When the MPB dies (MortMPB) the nitrogen goes to the bottom detritus (Bot_Det). 
@@ -70,7 +70,7 @@ graph TD;
   MPB-- MortMPB--> Bot_Det;
 ```
 
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+[top](NPZ model/State Variables)
 ## Detritus in the bottom (Bot_Det)
 Detritus in the bottom (Bot_Det, mmol-N m<sup>-2</sup>) increases by the sinking of detritus and phytoplankton (SinkDet and SinkPhy, respectively). When the microphytobenthos  and shellfish (Mus, Oys and Coc) die, the nitrogen also goes to the pool of Bot_Det (MortMPB and MortShellfish, respectively). Finally, the faeces and pseudo faeces that is produced by the shellfish is also a source for the Bot_Det (PseudoFaeces). Nitrogen is released to the water column through mineralization of the Bot_Det (BotMin) where it becomes part of the DIN. A fraction of the nitrogen is lost as N<sub>2</sub> due to denitrification (not included in the scheme below).
 
@@ -85,7 +85,7 @@ graph TD;
   Bot_Det-- BotMin--> DIN;
 ```
 
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+[top](NPZ model/State Variables)
 ## Shellfish (Mus, Oys and Coc)
 Three shellfish species are included in the model, mussels (Mus), Pacific oysters (Oys) and cockles (Coc). The units are in mmol-N m<sup>-2</sup>. The mussels are only present at the mussel culture plots in the Oosterschelde, oysters are present at the oyster culture plots and at the wild oyster beds. Cockles are only present at the intertidal flats. The physiology of the shellfish is described by the function “SFG()”. This function calculates clearance rate (Clearance), filtration rate of phytoplankton, zooplankton and detritus (GrazingPhy, GrazingZoo and GrazingDet, respectively), respiration rate (DINprod), the production of faeces and pseudo faeces (PseudoFaeces) and the growth of the shellfish (dFF).
 The shellfish populations are controlled by a variable mortality (MortShellfish) which is a function of the total stock and the carrying capacity. 
@@ -100,6 +100,5 @@ graph TD;
   Shellfish-- Faeces--> Bot_Det;
   Shellfish-- PseudoFaeces--> Bot_Det;
 ```
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+[top](NPZ model/State Variables)
 [^2956]: Carrasco de la Cruz, P. M. (2018) An ecosystem model of the Oosterschelde estuary (EMOES), Ghent University.
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