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rwildermuth / atlantisom

Forked from Atlantis operating model 10/20/2020. Generates data sets from Atlantis scenarios. Modifications for functionality with old (pre-Dec 2015) Atlantis code base.
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Survey efficiency and selectivities #3

Open rwildermuth opened 3 years ago

rwildermuth commented 3 years ago

Hi @sgaichas,

I'm looking into using the create_survey() code for my application of measurement error for the Bayesian network data. Do you have a reasonable example of the survey efficiency and selectivity matrices to use for the NEUS model?

My understanding is that output from run_truth() is fed to create_survey(), which is then sent through sample_survey_biomass(). Is this correct?

Thank you, Robert

sgaichas commented 3 years ago

Hi @rwildermuth, yes, your understanding is correct. There is an example script here that defines some basic survey attributes, but this was just a test (outputs are here). For actual survey q values by species I would ask @slucey; the survdat package does take q as a user input but does not appear to include the values.

rwildermuth commented 3 years ago

Thank you @sgaichas. Do you think it's find to simply use the values you specify for my ch 4 simulations? Or should I get some more realistic estimates from Sean?

Also, will these functions work for the invertebrate/biomass pool groups that I need for some of the lower trophic indicators?

sgaichas commented 3 years ago

To avoid hassles with future reviewers, I'd start with Sean's; he has a survey q for GB species listed in this RData file.

To be honest, I have not tested the functions with biomass pool groups. they don't have age classes so the age selectivity won't work (and may break) so you could just comment that out of the function. I think you could apply q to them though.