NPZ-model/State-Variables.md

@@ -14,11 +14,12 @@ Dissolved inorganic nutrients (DIN) is the sum of NO<sub>2</sub>, NO<sub>3</sub>
 
 ```mermaid
 graph TD;
-  DIN -- DINuptake --> Phy;
-  DIN -- DINupMPB --> MPB;
-  Det -- Mineralization --> DIN;
-  Shellfish -- DINprod --> DIN;
-  Zoo -- ZooExcretion --> DIN;
+  DIN-- DINuptake--> Phy;
+  DIN-- DINupMPB--> MPB;
+  Det-- Mineralization--> DIN;
+  Bot_Det-- BotMin--> DIN;
+  Zoo-- ZooExcretion--> DIN;
+  Shellfish-- DINprod--> DIN;
 ```
 
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@@ -27,10 +28,10 @@ Phytoplankton is composed of microalgae in the water column that are transported
 
 ```mermaid
 graph TD;
-  DIN -- DINuptake --> Phy;
+  DIN-- DINuptake--> Phy;
+  Phy-- ZooGrazing--> Zoo;
   Phy-- GrazingPhy--> Shellfish;
   Phy-- SinkPhy--> Bot_Det;
-  Phy-- ZooGrazing--> Zoo;
 ```
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 ## Zooplankton (Zoo)
@@ -39,21 +40,21 @@ Zooplankton (Zoo) are small animals (e.g. crustaceans, shellfish larvae) that li
 ```mermaid
 graph TD;
   Phy-- ZooGrazing--> Zoo;
+  Zoo-- Zoofaeces--> Det;
   Zoo-- GrazingZoo--> Shellfish;
-  Zoo-- ZooExcretion --> DIN;
   Zoo-- ZooMortality--> Det;
-  Zoo-- Zoofaeces--> Det;
+  Zoo-- ZooExcretion--> DIN;
 ```
 [top](NPZ model)
 ## 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). Shellfish can also filter detritus from the water column (GrazingDet). Finally detritus can sink to the seafloor (SinkDet) where it becomes Bot_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 .
 
 
 ```mermaid
 graph TD;
   Zoo-- ZooMortality--> Det;
   Zoo-- Zoofaeces--> Det;
-  Det-- Mineralization --> DIN;
+  Det-- Mineralization--> DIN;
   Det-- GrazingDet--> Shellfish;
   Det-- SinkDet--> Bot_Det;
 ```
@@ -71,11 +72,12 @@ graph TD;
 
 [top](NPZ model)
 ## 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 shellfish (Mus, Oys and Coc) die, the nitrogen also goes to the pool of Bot_Det (MortShellfish). 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).
+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).
 
 ```mermaid
 graph TD;
   Det-- SinkDet--> Bot_Det;
+  Phy-- SinkPhy--> Bot_Det;
   MPB-- MortMPB--> Bot_Det;
   Shellfish-- MortShellfish--> Bot_Det;
   Shellfish-- Faeces--> Bot_Det;
@@ -91,9 +93,9 @@ The shellfish populations are controlled by a variable mortality (MortShellfish)
 ```mermaid
 graph TD;
   Phy-- GrazingPhy--> Shellfish;
-  Det-- GrazingDet--> Shellfish;
   Zoo-- GrazingZoo--> Shellfish;
-  Shellfish -- DINprod --> DIN;
+  Det-- GrazingDet--> Shellfish;
+  Shellfish-- DINprod--> DIN;
   Shellfish-- MortShellfish--> Bot_Det;
   Shellfish-- Faeces--> Bot_Det;
   Shellfish-- PseudoFaeces--> Bot_Det;