first commit for #182; Bmsy_for_H4010_top by Rick-Methot-NOAA · Pull Request #322 · nmfs-ost/ss3-source-code

Rick-Methot-NOAA · 2022-05-23T20:45:20Z

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

Link issue(s) here: #182

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

verified with simple example

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

none, but checking variance would be good idea

Check which is true. This PR requires:

no further changes to r4ss
no further changes to the manual
no further changes to SSI (the SS3 GUI)
no further changes to the stock synthesis change log (new features, bug reports)

Describe any changes in r4ss/SS3 manual/SSI/change log that are needed (if not checked):

Additional information (optional):

kellijohnson-NOAA

I was able to compile this branch locally and I too ran the simple example as practice of running through the process. After running simple and looking at some of the comments and warning messages I think with just a little bit more effort we could increase consistency to help future users. For example "control rule bottom" should be "control rule cutoff" in all instances.

I am not sure what is standard practice here? Does the review commit the proposed changes in this branch or a fork or would @Rick-Methot-NOAA be responsible for making changes if he agrees with the comments?

Also, who is responsible for making issues in nmfs-stock-synthesis/doc, nmfs-stock-synthesis/ssi, and r4ss/r4ss?

kellijohnson-NOAA · 2022-05-24T02:09:05Z

SS_write_ssnew.tpl

  NuFore << HarvestPolicy << " # Control rule method (0: none; 1: ramp does catch=f(SSB), buffer on F; 2: ramp does F=f(SSB), buffer on F; 3: ramp does catch=f(SSB), buffer on catch; 4: ramp does F=f(SSB), buffer on catch) " << endl;
  NuFore << "# values for top, bottom and buffer exist, but not used when Policy=0" << endl;
-  NuFore << H4010_top << " # Control rule Biomass level for constant F (as frac of Bzero, e.g. 0.40); (Must be > the no F level below) " << endl;
+  NuFore << H4010_top_rd << " # Control rule Biomass level for constant F (as frac of Bzero, e.g. 0.40); must be > the no F level below, or set to -1 to use Bmsy/SSB_unf " << endl;


I think that we should change this to

" # Control rule inflection, level for constant F (as frac of Bzero, e.g. 0.40); must be > level for no F, or set to -1 to use Bmsy/SSB_unf

and change line 1485 to

" # Control rule cutoff, level for no F (as frac of Bzero, e.g., 0.10) "

to increase consistency and allow users to search for "level for no F", which, with this change, they would find on two lines. We could add the word Biomass back into the line after control rule, where I propose removing it to match the wording used in echoinput.sso and warnings.sso.

kellijohnson-NOAA · 2022-05-24T02:31:19Z

SS_readdata_330.tpl

    H4010_scale=H4010_scale_rd;
  echoinput<<H4010_scale<<"   # echoed harvest policy scalar "<<endl;
-  if(H4010_top<=H4010_bot) {N_warn++; cout<<" EXIT - see warning "<<endl;  warning<<N_warn<<" control rule inflection: "<<H4010_top<<" must be > control rule bottom "<<H4010_bot<<endl; exit(1);}
+  if(H4010_top_rd > 0.0 && H4010_top_rd<=H4010_bot) {N_warn++; cout<<" EXIT - see warning "<<endl;  warning<<N_warn<<" control rule inflection: "<<H4010_top_rd<<" must be > control rule bottom "<<H4010_bot<<endl; exit(1);}


Change "control rule bottom" to "control rule cutoff" to increase consistency

kellijohnson-NOAA · 2022-05-24T02:35:12Z

SS_readdata_330.tpl

-  *(ad_comm::global_datafile) >> H4010_top;
-  echoinput<<H4010_top<<"   # echoed harvest policy inflection "<<endl;
+  *(ad_comm::global_datafile) >> H4010_top_rd;  //  use -1 to set H4010_top to Bmsy/SSB_unf
+  echoinput<<H4010_top_rd<<"   # echoed harvest policy inflection (-1 for H4010_top set to Bmsy/SSB_unf)"<<endl;


I think that we should change lines 3227, 3229, and 3232 to use "control rule" rather than "harvest policy".

Should we shorten the comment in the brackets to "(-1 to set to Bmsy/SSB_unf)"? I don't think many users look at the source code to know what H4010_top is referring to.

SS_benchfore.tpl

kellijohnson-NOAA · 2022-05-24T02:37:05Z

SS_benchfore.tpl

+    if (H4010_top_rd < 0.0)
+      {
+        H4010_top = Bmsy / SSB_unf;
+        if(H4010_bot > 0.25) {N_warn++; warning<<N_warn<<" Beware: control rule bottom is large ("<<H4010_bot<<"); so may not be < calculated Bmsy/SSB_unf ("<<H4010_top<<")"<<endl;}


Change "bottom" to "cutoff"

Compile/Make_SS_safe.bat

Rick-Methot-NOAA · 2022-05-24T16:05:40Z

consistency is good and not my forte. I am fine with use of control rule throughout and glad if someone else can make those edits.

change to the .bat file in this commit was accidental and harmless. It need not be isolated in its own commit.

@k-doering-NOAA

Thanks to @k-doering-NOAA for guidance on formatting. PR #322

* H4010_* is called control rule in all files except where it was being read in and displayed back to echoinput. * uses `control rule cutoff` instead of `control rule bottom` * control rule* in comments instead of other verbage * removes H4010_top from comment because most people won't be looking at source code PR #322

kellijohnson-NOAA

4a19422 increases consistency in comments. I think this can be merged once checks show that they are all passing.

kellijohnson-NOAA · 2022-05-31T18:00:55Z

Info for change log

Description

Option for control rule inflection point to use Bmsy / SSB_unf
instead of user-specified value. If read in value is -1 then,
Stock Synthesis will use calculated Bmsy/SSB_unf to override input value.

Version	Date	Description	Issue	Input change	Action	Topic	Type
3.30.20	2022-05-31	#182	Option for control rule inflection point to use Bmsy / SSB_unf instead of user-specified value. If read in value is -1 then, Stock Synthesis will use calculated Bmsy/SSB_unf to override input value.	No	revise	forecast	input, calc

Rick-Methot-NOAA · 2022-06-03T16:52:10Z

Thanks Kelli for the improvements.

first commit for #182; Bmsy_for_H4010_top

0a9a676

k-doering-NOAA requested a review from kellijohnson-NOAA May 23, 2022 20:47

update a warning

bf1c8ee

kellijohnson-NOAA reviewed May 24, 2022

View reviewed changes

kellijohnson-NOAA added 2 commits May 31, 2022 07:59

Refactors to add space after if

f62b141

Thanks to @k-doering-NOAA for guidance on formatting. PR #322

kellijohnson-NOAA approved these changes May 31, 2022

View reviewed changes

k-doering-NOAA added this to the 3.30.20 milestone May 31, 2022

k-doering-NOAA mentioned this pull request May 31, 2022

improve automation of routine tasks during PRs nmfs-ost/ss3-workflows#43

Closed

Rick-Methot-NOAA merged commit 5540006 into main Jun 3, 2022

k-doering-NOAA deleted the BMSY_for_H4010_top branch August 10, 2022 20:25

Rick-Methot-NOAA linked an issue Sep 15, 2022 that may be closed by this pull request

new control rule option with inflection linked to Bmsy rather than % of Bzero #182

Closed

Rick-Methot-NOAA added forecast change log use for issues that should appear in change log labels Sep 16, 2022

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first commit for #182; Bmsy_for_H4010_top#322

first commit for #182; Bmsy_for_H4010_top#322
Rick-Methot-NOAA merged 4 commits intomainfrom
BMSY_for_H4010_top

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Rick-Methot-NOAA commented May 23, 2022

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

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

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

Check which is true. This PR requires:

Describe any changes in r4ss/SS3 manual/SSI/change log that are needed (if not checked):

Additional information (optional):

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