nmfs-ost
[Bug]: SPR/YPR profile and global_MSY not using correct biology vectors
Describe the bug
These calculations were using biology from the last year of forecast, not the biology associated with Benchmark specifications. This is all being worked on in the issue #191 that worked on correcting use of biology vectors for benchmark calculations.
To Reproduce
set up model with time-varying biology and set benchmark years to not be styr. Output provided by SS3.20.22 was not sufficient to see how time-varying biology was being used for these SPR/YPR
Expected behavior
correct results
Screenshots
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Which OS are you seeing the problem on?
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Which version of SS3 are you seeing the problem on?
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Additional Context
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Benchmark quantities stored in y = styr-3
- Ave_Size
- NatM (surv1 is stored by season only, but is only used by Pope's F method)
- Wt_Age_t, which includes (-2 for fecundity, -1 for beg of year, 0 for mid year wt.)
- save_sel_num (used for output only)
- sel_a
- sel_l
- sel_l_r
- migrrate
- retain
- retain_a
- discmort
- discmort2_a
- discmort2
- discmort_a
Seasonal values that yet derived from above in Make_FishSelex() sel_dead_num and 5 other sel vectors
vector created in get_mat_fec() for spawn season only fec and then gets stored in Wt_Age_t(t, -2, g)
Quantities used in equil_calcs, so all need to be available before calls to equil_calc: t_base = styr + (eq_yr - styr) * nseas - 1; recr_dist(y natM(t_base + natM(t, natM(t_base + 1 Hermaphro_val(GP4(g) migrrate(bio_yr sel_dead_bio(s and 5 similar sel_ vectors pred_M2(f1, t) using t=t_base+s Wt_Age_beg(s fec(
add temp output of bio_yr and t_base to check what equil_calc is using. Find that during forecast the bio_yr was set to endyr, not to the current forecast year.