Closed Rick-Methot-NOAA closed 1 year ago
@Rick-Methot-NOAA, is there anything pertaining to this issue/addition that you think should be added to the documentation? Maybe in the output files section? SS330_User_Manual.pdf
This issue was first raised in #80 so closing that issue also.
Describe the solution you would like.
While working with a user regarding SS3 output of vulnerable biomass for fisheries (vuln_bio in Report 22 for Survey CPUE), I realized that the output of selected (vulnerable) biomass is not what users expect for fisheries.
If the index is a survey, then SS3 uses Z to get biomass at a particular time and report it as vuln_bio: tempvec_a = elem_prod(natage(t, p, g), elem_prod(mfexp(-Z_rate(t, p, g) timing), sel_a(y, f, gg))); but if a fishery, then it uses: tempvec_a = elem_prod(natage(t, p, g), elem_prod(Zrate2(p, g), sel_a(y, f, gg))); which if multiplied by F would get the catch where Zrate2 is from the baranov catch equation: Zrate2(p, g) = elem_div((1. - mfexp(-seasdur(s) Z_rate(t, p, g))), Z_rate(t, p, g));
SOLUTION:
CATCH report:15
where vuln is mid-season selected bio or numbers; sel is selected total catch; dead is catch without live discards; ret is retained catch
Fleet Fleet_Name Area Yr Seas Time Obs Exp Mult Exp*Mult se F Like vuln_bio sel_bio dead_bio ret_bio vuln_num sel_num dead_num ret_num
maximum_ASEL2
Fleet fleet_name year seas max 1 1_PS_6485 1950 2 0.422416 2 2_PS_8690 1950 1 0.298186 3 3_PS_FSC_9119 1950 1 0.557861 4 4_PS_FAD_9119 1950 1 0.178007 5 5_BBPS_Ghana 1950 1 0.106498 6 6_BB_South_Dakar 1950 4 0.308055 7 7_BB_North_Dakar_6280 1950 3 0.846796 8 8_BB_North_Dakar_8119 1950 1 0.997709 9 9_BB_North_Azores 1950 3 0.901967 10 10_Japan_LL_N 1950 2 0.86873 11 11_Japan_LL_TRO 1950 1 0.909227 12 12_Japan_LL_S 1950 1 0.914493 13 13_Other_LL_N 1950 1 0.860008 14 14_Other_LL_TRO 1950 1 0.894125 15 15_Other_LL_S 1950 1 0.936165 16 16_CTP_LL_N 1950 1 0.879249
2 # F_std_reporting_units: 0=skip; 1=exploitation(Bio); 2=exploitation(Num); 3=sum(Apical_F's); 4=true F for range of ages; 5=unweighted avg. F for range of ages
COND 10 15 #_min and max age over which mean F will be calculated with F_reporting=4 or 5
0 # F_std_scaling: 0=no scaling; 1=F/Fspr; 2=F/Fmsy; 3=F/Fbtgt; where F means annual F_std, Fmsy means F_std@msy; values >=11 invoke N multiyr (up to 9!) with 10's digit; >100 invokes log(ratio)