Data.md

@@ -8,7 +8,38 @@ _Under construction_
 # Introduction
 The model makes use of several type of data
 
-# Water Quality
+# Water quality and temperature
+Data on water quality is derived from [Rijkswaterstaat](https://waterinfo.rws.nl). From the category nutrients and eutrophication: all parameters are selected and from the category veldparameters-OW the concentration of Chl-a is selected. For the locations, all stations in Oosterschelde are selected and the stations Walcheren 2 on North Sea and Steenbergen and Oesterdam in Volkerak Zoommeer. For the water temperature, the measurements from Rijkswaterstaat for the location Marollegat is used.
+
+
+![WQstations_28Comp](uploads/87b614de9cb20a31213260180c77eb04/WQstations_28Comp.png)
+*Overview of the locations where water quality data is available. The locations LODSGT, ZIJPE, WISSKKE, HAMMOT, STEENBGN and OESTDM are measured by Rijkswaterstaat.The locations NIOZ_1 to NIOZ_8 are measured by NIOZ*
+
+Data are downloaded (all nutrient and eutrophication parameters and chlorophyll-a) for all locations within the Oosterschelde, the location Walcheren 2 km, Steenbergen and Oesterdam and stored as *.csv file in the directory “./rawdata/WQData/Waterinfo/”. 
+Parameters included in the files are included in the file:
+- Chla: chlorofyll-a concentration [µg l<sup>-1</sup>];
+- NH4: ammonium concentration in the water [mg-N l<sup>-1</sup>];
+- NO2: nitrite concentration in the water [mg-N l<sup>-1</sup>]; 
+- NO3: nitrate concentration in the water [mg-N l<sup>-1</sup>]; 
+- NO2NO3: sum of nitrate and nitrite concentration in the water [mg-N l<sup>-1</sup>]; 
+- Ntot: total nitrogen in the water, dissolved, particulate or total [mg-N l<sup>-1</sup>];  
+- KjN: sum of organic N and NH3 in the water [mg-N l<sup>-1</sup>];
+- Ptot: total nitrogen in the water, dissolved, particulate or total [mg-P l<sup>-1</sup>]; 
+- PO4: total ortho-phosphate concentration in the water [mg-P l<sup>-1</sup>];
+- SO4: total sulphate concentration in the water [mg-S l<sup>-1</sup>].
+
+The data are read and processed with the R-script “WQData_RWS.R” that is located in the subdirectory “./Preprocessing/”.
+Not all components are measured at all stations over the whole period. The nitrogen components and chlorophyll-a concentration are used to calculate dissolved inorganic nitrogen (DIN), particulate organic nitrogen (PON) and Chla.
+- Missing data in NO2NO3 are supplemented from the sum of NO2 and NO3;
+- Missing are supplemented by calculation from based on location-specific linear regression functions;
+- Missing values particulate organic nitrogen (PON) are supplemented by the difference between Kjeldahl N (KjN) and NH4;
+- Dissolved inorganic nitrogen (DIN) is calculated from the sum of NO2NO3 and NH4
+
+Dissolved inorganic nitrogen (DIN) and particulate organic nitrogen (PON) are expressed in mmol-N m<sup>-3</sup> by dividing by the molecular weight of nitrogen (14 g mole-1) and multiplying by 1000 (l m<sup>-3</sup>).
+Additionally, NIOZ measured nutrients (NO3 and particulate organic nitrogen) and chlorophyll-a at 8 locations ((NIOZ_1 to NIOZ_8)) in the Oosterschelde from 1995 to 2013. The data are combined with the data from Rijkswaterstaat. Finally, negative values for PON are set to 0 and for the stations in the Oosterschelde, the concentration of particulate organic nitrogen is set to a maximum of 30 mmol-N m<sup>-3</sup>. 
+The data are stored as R data file (*.rds) in the subdrirectory “./DataOS/WQData/”.
+The concentrations of WALCRN2 and STEENBGN are used for the boundary concentrations at the North Sea and Krammersluizen, respectively (function “Boundary_NPZ()”). The data in the Oosterschelde is used to compare the model results with the observation with the visualisation app.
+Water temperature
 
 # KNMI
 Data on irradiation are derived from the [KNMI](https://www.knmi.nl/nederland-nu/klimatologie/daggegevens). Since the location Wilhelminadorp has a gap in the data, data from the location Westdorpe (319) is used. The variable Q contains data on Global radiation [J cm<sup>-2</sup>]. The irradiation is converted into units of W d<sup>-1</sup>. The data are stored as an R-data file in the directory "/DataOS/KNMI/"