Improve stratum polygon creation

[kstierhoff]

Presently, there are oddly-shaped stratum polygons that cause issues with area calculations, and also gaps between nearshore and core area stratum polygons. To address both of these issues, we should update the method for drawing both core and nearshore area stratum polygons.

The rationale for the decisions below are based on the idea that, when nearshore sampling is conducted, the acoustic data collected from the nearshore vessels provide better measures of CPS backscatter in the areas where FSV and fishing vessels overlap, and that there should be no gaps between the nearshore and core area stratum polygons.

In estimateBiomass.Rmd:

• If nearshore sampling is conducted (i.e., estimate.ns = TRUE), use planned nearshore transects to define the nearshore survey area (a continuous strip along the coast); remove overlap with land mask, if possible (but could be done later). Requires new code. Subset nearshore transects to only include transects that were actually sampled, to make more robust to changes between the survey plan and execution.
• Define the core area stratum polygons using the inshore endpoints of the core area transects sampled during the survey. See create-pseudo-transects (~Line 4813).
• If the core area transects overlap the nearshore area, the nearshore area is used to remove acoustic intervals from the core area transects, and the core area stratum polygons are trimmed to remove overlap with the nearshore strata. See create-final-strata-polygons (~Line 5079; clip.poly.j).
• Compute the area of the core area stratum polygons.

In estimateNearshore.R (details about how to do this must be refined, but in brief):

• Create pseudo-polygons that include the first and last transect of each stratum (plus one transect with zero backscatter) extend beyond the inshore and offshore extent of the nearshore survey area polygon (created in step one above) (~Line 1424).
• Intersect pseudo-polygons with nearshore area polygon to create nearshore stratum polygons.
• Compute the are of the nearshore area stratum polygons.

Other to-do items:

• Remove code that clips core area polygons using na_buffer.