SSMSE

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Progress bar

1

Suggested by Quang in JOSS review: Due to long runtime, I recommend progress bars for run_SSMSE to inform users of elapsed and projected time. See the pbapply R package.

k-doering-NOAA

add more parallel options

1

Suggestion On Iago's SSMSE JOSS review: Packages 'foreach' and 'doParallel' are only 'Suggests' in DESCRIPTION, but `foreach()` is used in package code, although its presence is checked. If option 'parallel=TRUE'...

k-doering-NOAA

Need to confirm that the manual/example documentation makes it clear that all NA's in the future_OM_list object need to be replaced with real values or removed by making them NULL....

nathanvaughan-NOAA

Implementation error parameters when stddev=0

1

Old versions of SS3 included implementation error parameters in the forecast for almost all scenarios. In the new versions of SS, implementation parameters are not included unless stddev is >0...

nathanvaughan-NOAA

add more data types for sampling

3

Currently, can sample catch, indices, age/length comps. Add the other data types to SSMSE to allow users to sample gen comps, mean size, and mean age at size, tagging data....

k-doering-NOAA

Need to add ability to specify more than one custom_MS_source?

1

In #144 @rwildermuth noted the following: >[...]I need to call run_SSMSE() separately for our project in order to use multiple different custom HCR functions and [run_SSMSE()] won't allow you to...

k-doering-NOAA

"replicate" option in future_om_list does not replicate rec_devs when scenarios run in tandem

3

After some digging, I figured out that running multiple scenarios in a single run_SSMSE() call with scen = c("replicate", "all") in the future_om_list doesn't actually make the recruitment deviations in...

rwildermuth

The r4ss issue https://github.com/r4ss/r4ss/issues/460 "create a single function for running SS models for use in r4ss, SSMSE, and ss3sim" has been resolved thanks to PR https://github.com/r4ss/r4ss/pull/722 so the modified functions...

iantaylor-NOAA

Try out changing R0 in the future_om_list

1

Thanks @rwildermuth for trying out some different specifications for changing recruitment regimes. Trying to make R0 time varying did not work, and I think this is a bug. Works: ```r...

k-doering-NOAA

ALK tolerance mismatch between OM and EM can cause a large bias in SSB

2

Thanks to the sardine team for pointing this out! In the OM, the ALK tolerance setting is reset to 0, as Rick Methot has recommended turning off tail compression in...

k-doering-NOAA