Various Group Calibration

jcaracappa1 commented 2 years ago

General recruitment and growth tuning to get all species within 0.5x to 10x initial conditions in prep for reasonability calibration.

Major changes include:

-- mum/c rescaling for all high priority groups -- changed growth curve for high priority groups -- alpha/beta calibrations for high priority groups -- fixed FDF diets

New functions

plot_prey_prevalence.R : Quick visual of dominant prey groups per species
reshape_mumC.R : Function to apply reshaping vector to growth and clearance rates

Changes

make_atlantis_diagnostic_tables.R : Updated for atlantisdiagnostics package changes
make_recruitment_diagnostics: Added mean recruitment metric

jcaracappa1 commented 2 years ago

@andybeet @gambler1650 Large number of group changes. Everything persisting with this version except QHG. Still needs minor refinement after merging Rob's changes too.

RGamble1 commented 2 years ago

@jcaracappa1 @andybeet This looks good to me.

NEFSC / READ-EDAB-neusAtlantis