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[Bug]: "inf" value in bootstrap of mean size-at-age data for ages with sample size 0 #598

@iantaylor-NOAA

Description

@iantaylor-NOAA

Describe the bug

@e-perl-NOAA reported "inf" values in the bootstraps of the mean size-at-age data for the BigSkate_2019 test model.
I was able to replicate the issue in the attached files.

There is a single vector of observations where the last three bins (for males age 13-15) have 0 sample size. The bootstrap observations are reported as inf 0.0001 inf in data_boot_001.ss and as 0.0001 inf inf in data_boot_002.ss in the attached files:
boot.zip.

It looks like the code here may be randomly generating a mix of inf and -inf and then replacing the -inf with 0.0001.
https://github.com/nmfs-ost/ss3-source-code/blob/main/SS_write_ssnew.tpl#L1271-L1275

I think the following steps should be taken:

  • decide on a placeholder value for the observation. SS3 doesn't like NA (or inf) as an input value here. I used 99.9 in the original Big Skate model, perhaps because it was closer to the range of observed non-placeholder values whereas 999 would have messed up scaling in any rudimentary plot of the results before filtering those observations).
  • add a test for obs_ms_n(f, i, a) == 0 and use the placeholder value instead of generating a bootstrap value

Note that these data are excluded from the likelihood with a lambda = 0 setting, but I think that doesn't matter for any of this.

To Reproduce

Run the attached input files (which is just the BigSkate_2019 in ss3-test-models with the starter file changed to produce bootstrap files).

Expected behavior

A model without inf output that can be used as an SS3 input file.

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Which OS are you seeing the problem on?

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Which version of SS3 are you seeing the problem on?

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Additional Context

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bugSomething isn't working; don't remove label after fixingmisc. outputquickfew hours work

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