NPZ-model/State-Variables.md

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+# Introduction
 The NPZ (Nutrients, Phytoplankton, Zooplankton) model is based on the model that is developed by Carrasco de la Cruz (2018). The model consists of 9 state variables of which 4 in the water column (DIN, Phyto, Zoo, Det) and 5 in the bottom (MUS, COC, OYS, MPB and Bot_Det). All state variables are expressed in terms of nitrogen (N). The state variables in the water column have the unit of mmol N m<sup>-3</sup> and the state variables in the bottom have a unit of mmol N m<sup>-2</sup>. The state variables in the water column can be transported between the compartments and the North Sea by tidal currents. Also they can be introduced into the Oosterschelde through the Krammersluizen. The state variables in the bottom are not exchanged between the compartments.
 
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-# State variables
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+# State variables in the water column
 ## Dissolved inorganic nitrogen (DIN)
 Dissolved inorganic nutrients (DIN) is the sum of NO<sub>2</sub>, NO<sub>3</sub> and NH<sub>4</sub>. The unit is mmol N m<sup>-3</sup>. DIN is used by phytoplankton and microphytobenthos for primary production (DINuptake and DINupMPB, respectively). DIN is released by mineralization of detritus in the water column (Mineralization) and in the bottom (BotMin) and respiration by zooplankton (ZooExcretion) and shellfish (DINprod). 
 
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 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 .
 
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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). 
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 ## 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 (MUSS, COC and OYSS) 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.
 
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 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. 
 
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