SAM to SS conversion issues

[Bai-Li-NOAA]

Settings that may need to be checked

• The double normal selectivity pattern from the saconvert package is updated (see this link), but we may need to update the initial values and bounds of the parameters as well.

The updated R script to create SS input files and compare SAM and SS output can be found here

I start modifying the initial values in the control.ss directly, but the estimated selectivity curves still don't look right.
#_AgeSelex
1 13 3.0 3.0 1 0 2 0 0 0 0 0 0 0 # PEAK value
-15.0 3.0 -4.0 -4.0 1 0 3 0 0 0 0 0 0 0 # TOP logistic
-15.0 12.0 1.0 1.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-15.0 6.0 3.0 3.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-999.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # INIT logistic
-999.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # FINAL logistic
1 13 2.0 2.0 1 0 2 0 0 0 0 0 0 0 # PEAK value
-5.0 3.0 -6.0 -6.0 1 0 3 0 0 0 0 0 0 0 # TOP logistic
-4.0 12.0 -4.0 -4.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-2.0 6.0 2.0 2.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-15.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # INIT logistic
-5.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # FINAL logistic
1 13 2.0 2.0 1 0 2 0 0 0 0 0 0 0 # PEAK value
-5.0 3.0 -6.0 -6.0 1 0 3 0 0 0 0 0 0 0 # TOP logistic
-4.0 12.0 -4.0 -4.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-2.0 6.0 2.0 2.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-15.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # INIT logistic
-5.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # FINAL logistic
1 13 2.0 2.0 1 0 2 0 0 0 0 0 0 0 # PEAK value
-5.0 3.0 -6.0 -6.0 1 0 3 0 0 0 0 0 0 0 # TOP logistic
-4.0 12.0 1.0 1.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-2.0 6.0 2.0 2.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-15.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # INIT logistic
-5.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # FINAL logistic
1 13 1.0 1.0 1 0 2 0 0 0 0 0 0 0 # PEAK value
-5.0 3.0 -4.0 -4.0 1 0 3 0 0 0 0 0 0 0 # TOP logistic
-4.0 12.0 1.0 1.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-2.0 6.0 2.0 2.0 1 0 3 0 0 0 0 0 0 0 # WIDTH exp
-15.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # INIT logistic
-5.0 5.0 -999.0 -999.0 1 0 2 0 0 0 0 0 0 0 # FINAL logistic

• Fishery catch unit
• Survey time

Current saconvert uses averaged time based on starting and ending times of surveys. Maybe we can try to use starting time only?

• Use B-H model or SR option 4: SCAA?