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improve text about lambdas in the User Manual #168

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iantaylor-NOAA opened this issue Jun 14, 2023 · 2 comments
Open

improve text about lambdas in the User Manual #168

iantaylor-NOAA opened this issue Jun 14, 2023 · 2 comments
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documentation Improvements or additions to documentation help wanted Extra attention is needed Manual Priority: Low

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@iantaylor-NOAA
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I've come across two unrelated issues with the lambdas that could use more documentation:

  1. The "Lambdas" section in the User Manual doesn't explain what the "SizeFreq Method" column is used for.
    When asked about it by @brianlangseth-NOAA, my response was "That is just a placeholder if you are using generalized size frequency data, where you can have multiple size frequency methods per fleet and thus need to indicate which one(s) gets the lambda." I'm assuming that any value could go here. @Rick-Methot-NOAA, I've never used lambdas in a model with generalized size frequency data, so if there's more nuance to this, please add it here.

  2. I tried applying a lambda to the recruitment deviations where I put "99" in the fleet column since recruitment is independent of fleet, but the lambda didn't get applied. Changing to fleet 1 had it working. This should probably be documented and perhaps an additional warning added if the fleet input is outside the range of fleets in the model (if that's indeed the requirement).

@iantaylor-NOAA iantaylor-NOAA added documentation Improvements or additions to documentation help wanted Extra attention is needed Manual Priority: Low labels Jun 14, 2023
@e-perl-NOAA
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@iantaylor-NOAA for (2), so with the lambda for recruitment deviations, would you suggest adding a sentence or so specifying that when using lambdas for recruitment deviation, the values in the matrix should be applied to each fleet (and maybe including it in the example table in the manual? Such as:

Likelihood component Fleet Phase Lambda Value SizeFreq Method
1 2 2 1.5 1
4 2 2 10 1
4 2 3 0.2 1
10 1 ? ? 1
10 2 ? ? 1
-9999 1 1 1 1

@Rick-Methot-NOAA
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Rick-Methot-NOAA commented Jun 15, 2023

@e-gugliotti-NOAA
@iantaylor-NOAA

For recruitment, and anything else that is not fleet-specific, the value read for fleet is ignored. I will fix the problem in the SS code, which is not immediately obvious.

For sizefreq, and only sizefreq, the fifth element is used to identify the sizefreq method, which is in addition to the standard designation of fleet. This is useful because a fleet's composition data can utilize more than one sizefreq method.

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Labels
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