As mentioned in my prior post, I intend to do some walk-throughs and take some notes on some fisheries analysis processes. Right now, I’m going to add some notes on where I’m at, which is not the beginning! Ideally, more tutorials to come, and more content to be presented in order 🙂

Currently, we’re working through the age-structured assessment program (ASAP). The leader of our subcommittee was kind enough to provide us a tutorial and commentary, so this is me transcribing some notes for myself (and hopefully that someone else might find helpful)…though plenty will be specific to me and this exercise/session/assessment.

Inputs

Any

• For tog in our region, dead releases are lumped in with total catch (i.e. not handled separately in the “discards” tab)
• provided to us: time series of data for MRIP index and CAA
• The scale of what’s entered on the catch-at-age tab doesn’t matter (e.g. if a prior year used 1000s of fish, you can use raw numbers because ASAP converts it to proportions immediately)
• “scan …results” under “Run” allows you to read results back in
• can set option to keep terminal open to see more output
• for final run: adjust effective sample sizes based on output

Retrospective

for me: your last block starts 2018 so set there to not “overrun” the next block

Note to self — 1:13:30 gets to running the model (below)

Interpreting results

Diagnostic Results

• stage 2 multipliers is where you find the ESS you can re-run with
• you can try to optimize RMSE…(you don’t have to)
  • increase CV where RMSE > 1, decrease where it’s < 1
  • if CV is too big, it won’t fit to the index
  • ideal: indices and catch RMSE = 1

ASAP Model Results

• SSB: roughly 4321 is ok
• MSY: roughly 933 is ok

Retrospective results (1:24:40)

R plots (1:30:12)