Confirmation on what went into the likelihood function (table 2) and the estimated parameters

[iantaylor-NOAA]

Item (b2) from Andre's to-do list was "Confirmation on what went intro the likelihood function (table 2) and the estimated parameters" which Rick suggested should be the focus for @k-doering-NOAA and @iantaylor-NOAA.

Here's Table 2 with some draft edits in bold:

The estimable parameters of the two models.

Parameter	Treatment in SS3	Treatment in Slice
Unfished recruitment	Estimated	N/A
Von Bert. growth parameters	Estimated	?
Recruitment	Age-0; penalty of deviations from the mean	Age-2; estimated independently
Fishing mortality	Estimated from the catch	Related to fishing effort
Selectivity	L50 and L95 estimated	L50 and L95 estimated
Likelihood components
Index	Log-normal	N/A
Length moments (by cohort)	N/A [Ian: I'm not totally sure what this means]
Length-at-age	excluded from likelihood but expected values computed for comparison with observed
Age-composition	excluded from likelihood but expected values calculated for comparison with observed
Length-composition	multinomial*
Conditional age-at-length	multinomial*	N/A

* the multinomial likelihoods in Stock Synthesis included a value of 0.0001 added to expected and observed values in each bin

@k-doering-NOAA, can you check on which parameters are estimated in the most recent model files and add some rows if needed? Feel free to modify my proposed additions above as well.

[Rick-Methot-NOAA]

Length moments would include mean length as output in the Fit_Len table and used for the Francis weighting

[iantaylor-NOAA]

@Rick-Methot-NOAA, thank you for chiming in on that. I'm guessing that N/A is still the best answer with regard to likelihood contribution, right?

[k-doering-NOAA]

Thanks @iantaylor-NOAA for getting started on this. Here's a table of all the model parameters used in the Stock Synthesis EMs and whether they were estimated or not. (created using code committed in ca381b1):

name	estimated_or_fixed	init
NatM_p_1_Fem_GP_1	fixed	0.1500000
L_at_Amin_Fem_GP_1	estimated	20.0000000
L_at_Amax_Fem_GP_1	estimated	100.0000000
VonBert_K_Fem_GP_1	estimated	0.1000000
CV_young_Fem_GP_1	estimated	0.1000000
CV_old_Fem_GP_1	estimated	0.2500000
Wtlen_1_Fem_GP_1	fixed	0.0000217
Wtlen_2_Fem_GP_1	fixed	2.8600000
Mat50%_Fem_GP_1	fixed	55.0000000
Mat_slope_Fem_GP_1	fixed	-0.2500000
Eggs/kg_inter_Fem_GP_1	fixed	1.0000000
Eggs/kg_slope_wt_Fem_GP_1	fixed	0.0000000
CohortGrowDev	fixed	1.0000000
FracFemale_GP_1	fixed	0.5000000
SR_LN(R0)	estimated	10.0000000
SR_BH_steep	fixed	1.0000000
SR_sigmaR	fixed	0.5000000
SR_regime	fixed	0.0000000
SR_autocorr	fixed	0.0000000
LnQ_base_fishery(1)	fixed	-6.9798000
SizeSel_P_1_fishery(1)	estimated	40.0000000
SizeSel_P_2_fishery(1)	estimated	1.0000000

[k-doering-NOAA]

Also, the ctl file that can be looked at for settings is: ctl template. It was used for the one way trip runs. This initF template was used for the baseline runs, but only differs in that it has 2 initF parameters and a different Platoon_between/within_stdev_ratio (which hopefully this setting makes sense?)