Compute biomass estimates

[kstierhoff]

• [x] Set stock break at Bodega Bay for NS sardine transects
• [ ] Create ECDF plots of biomass relative to time since the nearest trawl cluster, similar to what's done for distance in the core region.
• [ ] Create ECDF plots of biomass relative to distance from the nearest trawl cluster, similar to what's done in the core region.
• [x] Include Saildrone transect data and re-compute biomass.
• [x] Trim nearshore backscatter intervals using a polygon surrounding the planned nearshore transects.
• [x] Remove offshore purse seine sets from LM data set. Use polygon surrounding planned nearshore transects to exclude sets.
• [x] Examine calibration results/ECS files for Saildrone and Shimada in S Oregon where sardine biomass is greatest @jrenfree
• [x] Compare s_V within fish schools between SH and SD off Oregon
• [x] Add positive seine clusters (blue numbers) to nearshore biomass density plots for each species
• [ ] Generate purse seine plots using plotSeine_2307RL (or generic version)

[jrenfree]

Will focus on Transect 118, sampled by SD-1060:

We conducted a pre- and post-survey calibration, which resulted in the following for 38 kHz

Parameter	PRE	POST
Gain	19.04	19.10
BW_along	17.8	17.9
BW_athwt	17.8	17.9
Offset_along	0.2	0.2
Offset_athwt	-0.6	-0.9
EBA	-12.6	-12.6
Sa_corr	-0.04	0.03
RMS	0.16	0.13

So both were very similar, and we applied the Pre-survey results for the data processing. The template ECS file appears to have the correct environment and calibration parameters entered:

The CTD cast used to process this transect was cast 158 from the Shimada hake survey, which appeared to have a harmonic sound speed of 1495.67 m/s, which matches with what's in the ECS file used to process this transect:

The calibration parameters in the ECS value are from the template file but compensated by change in sound speeds. With a calibration (template) sound speed of 1501.37 and transect sound speed of 1495.67, my calculations are:

Parameter	Template	Transect
Gain	19.04	19.073
EBA	-12.6	-12.633
BW_along	17.8	17.7324
BW_athwt	17.8	17.7324

This matches what's in the transect ECS file, so looks like it's being compensated correctly.

So unless both calibrations were way off for this echosounder, I think this checks out just fine. Suppose the question then becomes if the scatterers near the seabed are indeed CPS.

[kstierhoff]

Compelling and thorough analysis. I think we can consider that item completed and debunked.

[kstierhoff]

Final biomass estimates computed for all species/stocks, after accounting for deep backscatter from CSNA in the nearshore region of the SCB. Results incorporated into biomass report.