Incremental Improvements to Misc Species

[jcaracappa1]

Summary

Incremental changes to several species to improve overall biomass and age structure before fishing sensitivity tests. Addition of several utility functions to address changes to initial conditions and catch forcing

R Scripts

• R/edit_catch_spinup.R : Function to scale the initial catch during spinup period
• edit_init_age_distribution.R : Function to manipulate the initial age distribution for groups
• edit_param_RN_init.R : Function to change the initial RN:SN ratio (i.e. body condition)
• edit_param_catch_age.R: Function to change the catch-at-age proportions in harvest.prm
• edit_param_invert_mortality.R : Added function to retrieve mL and mQ parameters
• edit_param_invert_mortality.R : Added function to retrieve mL and mQ parameters
• changed name of reshape_mumC.R to edit_param_mum_shape.R
• make_age_distribution.R : Function to generate possible age distributions with specified peak age and steepness
• make_atlantis_diagnostic_figures.R : Fixed file name/path letter case
• make_fish_condition_rescale.R deleted and split functionality into separate functions
• make_init_size_age.R : Function to generate the current size at age table from initial conditions
• make_size_age_reference.R : Converted into function
• process_atl_output.R : Improved memory management and fixed bugs related to consumed biomass
• currentVersion/CatchFiles/scale_catch_1.csv : line endings for Linux

Parameter Changes

• at_biology.prm :
  • mum/C tuning for HER, WHK, WPF, SUF, WIF, WTF, PLA, MPF, BUT, MEN, COD, POL, and YTF
  • mQ tuning for SCA, LOB, WHK, SUF, COD and STB
  • KDENR changes for SDF
  • BHalpha tuning for HER, BLF, WIF, BUT, GOO, COD, BSB, and STB

Other

Various diagnostics updated with above changes

[jcaracappa1]

Pull Request 174Model_Comparison_Biomass.pdf

[jcaracappa1]

@gambler1650

[RGamble1]

Looks good @jcaracappa1