Filename,Expected_subdir,Description,Comments
physical_parameters_NORTH_SEA.csv,Param,Physical parameters (areas thickness and sediments),North Sea model data
physics_NORTH_SEA_2003-2013.csv,Driving,Physics drivers (ocean inflows temperature etc),North Sea 2003-2013 data from NEMO-ERSEM and elsewhere
chemistry_NORTH_SEA_2003-2013.csv,Driving,Chemistry drivers (boundary nutrients etc),North Sea 2003-2013 data from NEMO-ERSEM World Ocean Atlas and elsewhere
initial_values_NORTH_SEA_2003-2013.csv,Param,Initial state of each state variable,Data exported from end of run for stationary state North Sea 2003-2013 model
event_timing_NORTH_SEA_2003-2013.csv,Param,Biological event timing parameters,North Sea spawning recruitment and mackerel migrations in the 2003-2013 period
fixed_consumers_NORTH_SEA_2003-2013.csv,Param,Fixed parameters for consumer guilds,Mostly generic parameters for European temperate waters with minor variation in harvestable fraction for carniv zoo for 2003-2013
fixed_miscellaneous.csv,Param,Fixed miscellaneous parameters (Q10s etc),Miscellaneous fixed parameters for European temperate waters
fitted_preference_matrix_NORTH_SEA.csv,Param,Fitted prey preference matrix,North Sea preference matrix generic for both 1970-1999 and 2003-2013 periods 
fitted_uptake_mort_rates_NORTH_SEA.csv,Param,Fitted uptake and mortality parameters,North Sea parameters generic for both 1970-1999 and 2003-2013 periods 
fitted_microbiology_others_NORTH_SEA.csv,Param,Fitted microibiology and other parameters,North Sea parameters generic for both 1970-1999 and 2003-2013 periods 
fishing_fleet_NORTH_SEA_2003-2013.csv,Param,Fishing fleet basic parameters,North Sea fleet parameters for the 2003-2013 period (uses demersal discard rates from csv file)
fishing_activity_NORTH_SEA_2003-2013.csv,Param,Fishing activity and seabed abrasion rates for each gear,North Sea gear activity rates from STECF and Norway for the 2003-2013 period
fishing_power_NORTH_SEA_2003-2013.csv,Param,Fishing power parameters for each gear and guild,North Sea power parameters derived from 2003-2013 STECF data - used generically for both 1970-1999 and 2003-2013 periods
fishing_discards_NORTH_SEA.csv,Param,Discard rates for each gear and guild,North Sea discard rates from 2003-2013 STECF data - used generically for both 1970-1999 and 2003-2013 - EXCEPT for demersal fish rates need to be set to internally derived in 1970-1999
fishing_processing_NORTH_SEA.csv,Param,Processing at sea ratyes for each gear and guild,North Sea processing-at-sea rates generic for both 1970-1999 and 2003-2013 periods
fishing_distribution_NORTH_SEA.csv,Param,Spatial distribution of activity rates across habitats,North Sea gear activity distributions from 2003-2013 STECF data - used generically for both the 1970-1999 and 2003-2013 periods
fishing_gear_multiplier.csv,Param,Gear activity multipiers,Multipliers to be applied to activity rates of gears used in the North Sea (values >=0)
harvest_ratio_multiplier.csv,Param,Harvest ratio multipliers,Multipliers to be applied to guild harvest ratios (values >=0)
food_web_flow_matrix_template.csv,Param,Food web flow matrix template,Template file for the creation of a mass flow matrix for the final year of the model run
fishing_gear_linkages.csv,Param,Relationships between gear activity rates over time,North Sea estimates _ only required by fitting function to seek activity rates generating given patterns of harvest ratios
annual_observed_NORTH_SEA_2003-2013.csv,Target,Annual target data,Compilation of annual observational data on the mean state of the North Sea during 2003-2013
monthly_observed_NORTH_SEA_2003-2013.csv,Target,Monthly target data,Compilation of monthly observational data on the mean state of the North Sea during 2003-2013
region_harvest_r_NORTH_SEA_2003-2013.csv,Target,Independently estimates guild harvest ratios,North Sea 2003-2013 guild HRs from ICES stock assessments and survey data and regional ecosystem review _  only required by utility function to calculate HRscale parameters given known regional harvest ratios
zonal_harvest_r_NORTH_SEA_2003-2013.csv,Target,Inshore and offshore harvest ratios,North Sea 2003-2013 inshore and offshore harvest ratios genertaed by a prior run of the model  _ only required by fitting function to seek activity rates generating given patterns of harvest ratios
