Fix seasonal recruitment

[Rick-Methot-NOAA]

What issue(s) does this PR address? Describe and add issue numbers, if applicable.

• [errors in seasonal recruitment and empirical wtatage #283 ] Link issue on pull request

What tests have been done? Upload any model input files created for testing in a zip file, if possible.

compare output between tables for the anchovy assessment files

What tests/review still need to be done? Who can do it, and by when is it needed (ideally)?

another sharp set of eyes

Check which is true. This PR requires:

• Changes in r4ss
• Changes to SS3 manual
• Changes to SSI (the SS3 GUI)
• An entry in the stock synthesis change log (new features, bug reports)

Describe any changes in r4ss/SS3 manual/SSI/change log that are needed (if checked):

Additional information (optional):

[Rick-Methot-NOAA]

This second issue was detected while diagnosing the same set of input files that use empirical wtatage (wtatage==1) . The problem was that fecundity, as calculated from growth parameters, was erroneously overwriting the fec(g) array. This occurred when save_for_report was turned on. This problem showed up in the biology used for SPR/YPR profile differing from the biology used for benchmark. The fix was to add a conditional statement in get_mat_fec()
if(WTage_rd==1){
fec(g)=Wt_Age_t(t,-2,g);
}
else{ // make fecundity from biology

[Rick-Methot-NOAA]

r4ss problems probably due to some extra output lines that are not finalized.

[k-doering-NOAA]

r4ss problems probably due to some extra output lines that are not finalized.

Yes, that makes sense. We should probably get those sorted out before merging into main, right?

Here is the error: https://github.com/nmfs-stock-synthesis/stock-synthesis/runs/5841949938?check_suite_focus=true#step:12:72

<simpleError in order(yielddat[["Depletion"]], decreasing = FALSE): argument 1 is not a vector>

[k-doering-NOAA]

This second issue was detected while diagnosing the same set of input files. It is due to the non-modularity of the growth&biology parameters vs. the input of all biology from wtatage.ss The problem was that fecundity, as calculated from growth parameters, was erroneously overwriting the fec(g) array. Really should have been a separate issue with separate fix.

Thanks for explaining!

[Rick-Methot-NOAA]

with nearly every check passed, I will let this issue sit until I return to office on 4/11,