Calculate initial values of the scaling parameters for the fishing fleet model which link effort to harvest ratios.

The scaling parameters convert the effort applied by each gear to each living resource guild in the model, into a harvest ratio (proportion of mass captured per day). Effort is the product of activity and the relative power of each gear with respect to each guild.

Usage

e2e_calculate_hrscale(model)

Arguments

model: R-list object generated by the e2e_read() function which defined the model configuration

Value

Dataframe of the effort-harvest ratio scaling parameter values for each guild

Details

In order to estimate these scaling parameters, data are needed for a 'calibration' time period when activity, catch and harvest ratio are all known.

The function assumes that the relevant model configuration has already been loaded using the e2e_read() function. It is expected that this has loaded the array of power parameters (catch per unit activity by gear and guild during the calibration period) given in the file /Param/fishing_power_*.csv, the corresponding activity in the file /Param/fishing_activity_*.csv, and the known harvest ratios of each guild in the file /Target/region_harvest_r_*.csv

The function returns rough estimates of the scaling parameters. These are only rough because they assume that the effort and resource biomass are distributed uniformly over the model domain. Hence they should be used as initial estimates to be refined by optimization.

The scaling parameters are dispayed on the screen and saved in a dataframe. The values then need to be manually edited into rows 12-21 (excluding the header row) of the file /Param/fishing_fleet_*.csv

Examples

# Load the 2003-2013 version of the North Sea model supplied with the package and calculate
# scaling parameter values:
    model <- e2e_read("North_Sea", "2003-2013", quiet=FALSE)
#> Current working directory is... 
#> 'C:/Users/jackl/OneDrive - University of Strathclyde/Documents/Research/Packages/StrathE2E/strathe2e2/docs/reference'
#> No 'results.path' specified so any csv data requested
#> will be directed to/from the temporary directory...
#> 'C:\Users\jackl\AppData\Local\Temp\RtmpYdRhoX'
#> 
#> Loading model   : C:/Users/jackl/AppData/Local/Temp/Rtmp0GrtpA/temp_libpath850c45470c/StrathE2E2/extdata/Models/North_Sea/2003-2013
#>  Reading CSV file: MODEL_SETUP.csv
#>  Reading CSV file: physical_parameters_NORTH_SEA.csv
#>  Reading CSV file: fixed_miscellaneous.csv
#>  Reading CSV file: fixed_consumers_NORTH_SEA_2003-2013.csv
#>  Reading CSV file: physics_NORTH_SEA_2003-2013.csv
#>  Reading CSV file: chemistry_NORTH_SEA_2003-2013.csv
#>  Reading CSV file: event_timing_NORTH_SEA_2003-2013.csv
#>  Reading CSV file: fitted_preference_matrix_NORTH_SEA.csv
#>  Reading CSV file: fitted_uptake_mort_rates_NORTH_SEA.csv
#>  Reading CSV file: fitted_microbiology_others_NORTH_SEA.csv
#>  Reading CSV file: initial_values_NORTH_SEA_2003-2013.csv
#>  Reading CSV file: fishing_activity_NORTH_SEA_2003-2013.csv
#>  Reading CSV file: fishing_power_NORTH_SEA_2003-2013.csv
#>  Reading CSV file: fishing_discards_NORTH_SEA.csv
#>  Reading CSV file: fishing_distribution_NORTH_SEA.csv
#>  Reading CSV file: fishing_fleet_NORTH_SEA_2003-2013.csv
#>  Reading CSV file: fishing_processing_NORTH_SEA.csv
#>  Reading CSV file: fishing_gear_multiplier.csv
#>  Reading CSV file: harvest_ratio_multiplier.csv
#>  Reading CSV file: additional_mortality.csv
#>  Reading CSV file: uptake_multiplier.csv
#> Model setup and parameters gathered from ...
#> StrathE2E2 package folder
#> Model results will be directed to/from ...
#> 'C:\Users\jackl\AppData\Local\Temp\RtmpYdRhoX/North_Sea/2003-2013/'
    scale_values <- e2e_calculate_hrscale(model)
#>  Reading CSV file: region_harvest_r_NORTH_SEA_2003-2013.csv
#> Manually edit these values into the 'fishing_fleet_*.csv' file, rows 12-21, in the 'Param' folder
    scale_values
#>                 Guild     HRscale
#> 1  Planktivorous_fish  0.03102313
#> 2       Demersal_fish  0.10674489
#> 3      Migratory_fish  0.05912854
#> 4    Benthos_susp-dep  5.86628271
#> 5   Benthos_carn-scav  0.78986760
#> 6    Zooplankton_carn 14.22221473
#> 7               Birds  2.71513873
#> 8           Pinnipeds  4.38631271
#> 9           Cetaceans  3.21801138
#> 10        Macrophytes  0.00000000