Mortality scale time series input - non-compulsory change to forcing input file
There is a new non-compulsory parameter in the forcing input prm file. This can be used to read in a time series file containing scaling to apply to linear mortality.
If the group is age structured or an age structured biomass group then a scaling value can be specified for adults and juv. If the groups is a biomass group then a single value should be specified.
The following would be added to your forcing input file:
Changes in linear mortality
LinearMort linearMortality.ts
The structure of the linearMortality.ts file is:
Changes in linear mortality test file.
COLUMNS 6
COLUMN1.name Time
COLUMN1.long_name Time
COLUMN1.units days since 2000-01-01 00:00:00 +10
COLUMN1.missing_value 0
COLUMN2.name PL
COLUMN2.long_name PL
COLUMN2.units scalar
COLUMN2.missing_value 0
COLUMN3.name juv_FMM
COLUMN3.long_name juv_FMM
COLUMN3.units scalar
COLUMN3.missing_value 0
COLUMN4.name adult_FMM
COLUMN4.long_name adult_FMM
COLUMN4.units scalar
COLUMN4.missing_value 0
COLUMN5.name juv_FMN
COLUMN5.long_name juv_FMN
COLUMN5.units scalar
COLUMN5.missing_value 0
COLUMN6.name adult_FMN
COLUMN6.long_name adult_FMN
COLUMN6.units scalar
COLUMN6.missing_value 0
1 1 1 1 1 1
1 1 1 1 1 1
2 1.5 1.5 1.5 1.5 1.5
…..
The Time should be in model time not hydro time so in the above example the model starts on the beginning of 2000 - this is the same as the time in the initial conditions netcdf file.
One thing to note is that the values are interpolated. So the mortality scalar applied at day 1 will be 1.0 for all groups listed above. Any groups that are not in the file will not be scaled.
The scalar applied at day 1.5 will be 1.25 and the scale factor at day 2 will be 1.5.
The scale factor will be applied to the linear mortality value after temperature scaling is done. See here for more information on the effect of temperature on mortality.