New Initial Conditions and Temperature-dependent Growth

[jcaracappa1]

Summary

Adjusted size-at-age and numbers in initial conditions to match data. Turned on temperature-dependent growth for all species

Parameter files changed

• at_biology.prm : Turned on "flagTempSensitive" , Set min temperature to 0, set max temperature to 30. Other changes to facilitate future updates to v6626 (not used in current version)
• at_run.prm: Reset age-structured groups' init scalar to 1 if changed in init.nc
• neus_init.nc: Reset size-at-age and initial numbers for age-structured groups
• at_force_LINUX.prm and at_harvest.prm : Various empty flags for future updates
• neus_groups.csv: Temporarily turned on REP, since they weren't working properly

New files

• check_init_length_age.R : Script to check initial conditions length-at-age distribution compared to reference data
• edit_param_FSPB.R : Functions to edit and fetch FSPB params
• make_box_proportions.R : Script to extract proportion of biomass/numbers in each box based on initial conditions
• make_initial_numbers_rescale.R: Script to rescale initial conditions numbers (age x box)
• make_lengthage_growth_correction.R: Attempt to rescale mum/C based on discrepancy of length-at-age
• make_size_age-Reference.R: Script to get the correct size-at-age based on year not age class
• StockSmart_Conversions.csv: Converts stock smart units and metrics to get to metric tons
• LobsterBiomass.csv, MenhadenBiomass.csv, and StripedBassBiomass.csv: New data files for ASMFC data
• Various other data files as diagnostics for length/size at age

Changed Files

• process_atl_output.R : Fixed bug with RN/SN calculations for length-at-age plots

[jcaracappa1]

@gambler1650 @andybeet I didn't bother listing out all of the new data files as some of them are just checks. There's a description in the initial commit message for each though. If you think it's necessary, I can add a summary for each to the description.