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Data Preparation
In order to be understood by the tool box your data should be organized in one .xlsx file, using your favorite prefix instead of '' (Example file is given in the repository: Cases/HAMMOND/Data_HAMMOND.xls). The .xlsx file should contain four sheets named and organized as the following.
This sheet contains profiles for sliced cores, both solid and solute phases. It should contain at least the following column.
| Station | Campaign | UpperDepth | LowerDepth | 'VAR1' | 'VAR1'_ERR | 'VAR2' | 'VAR2'_ERR... |
|---|
UpperDepth and LowerDepth define each slice (cm, positive below the interface).
It is considered that VAR1 is an average value between UpperDepth and LowerDepth.
Any additional column is understood as a profile variable. If this variable does not directly coincide (in name, definition and units) to a model variable, then the user should add a model diagnostic function at the end of the UserDefinitions file, where corresponding diagnostics should be defined in terms of model variables (see examples).
Variables obtained for different vertical slicing schemes can be included in additional rows, the system accepts empty cells.
In addition, it is possible to include here vertical profiles of Porosity, using the variable name 'Porosity'. There are also other means to characterize porosity.
This sheet is intended for sediment-water interface fluxes.
| Station | Campaign | F'VAR1' | F'VAR1'_ERR | ... |
|---|
FVAR1 should correspond to model variables VAR1 or have an equivalent diagnostic function defined.
Basically it is considered that those fluxes are obtained from incubation chambers, ie. they combine diffusive and bio-irrigation fluxes.
| Station | Campaign | Date | Lon | Lat | ... |
|---|
In addition this sheet includes parameters values that are specific for each station : eg. upper porosity, accumulation rate, bottom water concentration (given as bw_VAR1), ...
This sheet incorporates observed microprofiling data of O2 to the calibration procedure.
| Station | Campaign | Depth | O2 |
|---|