SSMSE

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Change column names per r4ss updates

4

Column header updates in r4ss in PR [#945](https://github.com/r4ss/r4ss/pull/945) will require updates in SSMSE functions such as those with [FltSvy](https://github.com/search?q=repo%3Anmfs-fish-tools%2FSSMSE+FltSvy&type=code). Additional changes in r4ss headers can be found in the [PR...

e-perl-NOAA

allow SSMSE to work with SS3.30.21

9

@e-perl-NOAA is working on making SSMSE compatible with SS3.30.21. This is because a user needs a feature that is only available in 3.30.21 and newer. SSMSE will continue to work...

k-doering-NOAA

Forecast File Inputs not copying?

2

I am running an MSE using sablefish stock assessment files, which have catch inputs specified at the bottom of the forecast file that cap catch at the ACLs set by...

Mkrig24

Thanks to @mkapur-noaa for reporting the following issue: As an aside, our implementation of the helper function didn't get us there at first because we actually had two separate chunks...

k-doering-NOAA

curate functions on pkgdown site to improve documentation

1

Use the user manual classifications: https://nmfs-fish-tools.github.io/SSMSE/manual/intro.html#funs Some exported functions are not useful to users (they are exported so examples can run, I believe). How to curate pkgdown reference: https://pkgdown.r-lib.org/articles/pkgdown.html#reference

k-doering-NOAA

Pass back the future_om_dat object as a return from run_SSMSE so the user can double-check their inputs are being processed as expected. From #188

k-doering-NOAA

Upon reading the [user manual custom example](https://nmfs-fish-tools.github.io/SSMSE/manual/SSMSE.html#example-using-custom-pattern-instead-of-model_change), it's not spelled out that the user should put in the actual parameter values desired From #188

k-doering-NOAA

SS3 update to .ss_new naming convention

8

SS3 v3.30.19.01 renames new data file as data_echo.ss_new (instead of previously named data.ss_new). This triggers an error in the function SSMSE:::copy_model_files(). See lines of code below. ``` if (!all(c("control.ss_new", "data.ss_new",...

CassidyPeterson-NOAA

as suggested in JOSS review - maybe add to the simple example?

k-doering-NOAA

A simple wrapper function to generate the file structure needed for the analysis (model_runs, figures, input_models) would be helpful. (Quang suggestion from JOSS review)

k-doering-NOAA