Standard survey specifications list

[sgaichas]

create_survey works, but a standardized survey or two for testing across systems is helpful:
Work is in progress to create a "test_survey_census" for comparison to BiomIndx.txt with specifications:

• whole time series
• all vertebrates
• all boxes
• efficiency=1 all species
• selectivity=1 all species all ages

Work is in progress to create a "basic_trawl_survey" with specifications (please comment on these):

• once per year at mid year
• all fish
• 75% of boxes (leave off deeper boxes?)
• mixed efficiency
  • 0.01 for large pelagics, reef dwellers, others not in trawlable habitat
  • 0.1 for pelagics
  • 0.7 for demersals
  • 1.1 for selected flatfish
• mixed selectivity (using 10 agecl for all species)
  • flat=1 for large pelagics, reef dwellers, others not in trawlable habitat
  • sigmoid 0 to 1 with 0.5 inflection at agecl 3 for pelagics, reaching 1 at agecl 5, flat top
  • sigmoid 0 to 1 with 0.5 inflection at agecl 5 for most demersals and flatfish, reaching 1 at agecl 7, flat top
  • dome shaped 0 to 1 at agecl 6&7 for selected demersals, falling off to 0.7 by agecl 10

[sgaichas]

initial helper functions to create a census and to map actual survey stations to Atlantis polygons have been added in https://docker.pkg.github.com/r4atlantis/atlantisom/commit/cfecad95ff867190b1c3e6910a7a41dfc4a2bf9c:
config/census_spec.R
config/Map_Polygons_Surveys.R
both may need further generalization but they are a start