issues by pull back the end-year by one year in 3.30

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T17:49:45Z

Yes, they SHOULD work with the high reporting option, although subtle differences may exist.

If you have problems with this branch of r4ss working with your existing scripts, feel free to report them at https://github.com/r4ss/r4ss/issues/9 if you have a github account, or just email me directly.

-Ian

On Wed, Jun 17, 2020 at 9:48 AM Dan Fu <VLab.Notifications@noaa.gov> wrote:

Thanks Ian, I will try. One more question on the new version - If I keep the output option in the starter file as 1. high instead of using the new custom options, I suppose all my existing r4ss calling scripts should still work ? .

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Dan Fu Stock Synthesis Virtual Lab Forum https://vlab.noaa.gov/web/stock-synthesis/public-forums/-/message_boards/view_message/10495342 VLab.Notifications@noaa.gov

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T16:48:49Z

Thanks Ian, I will try. One more question on the new version - If I keep the output option in the starter file as 1. high instead of using the new custom options, I suppose all my existing r4ss calling scripts should still work ? .

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T16:36:45Z

Hi Dan,

I just got the in-progress branch of r4ss working with your model when run using the development 3.30.15.07 version of SS.

You can install it via

remotes::install_github('r4ss/r4ss@use_blank_lines')

These changes will be merged into the master branch by the time SS version 3.30.16 gets released.

Let us know if you have problems with this.

-Ian

On Wed, Jun 17, 2020 at 9:35 AM Richard Methot <VLab.Notifications@noaa.gov> wrote:

The excel sheet with the change log has just been uploaded to its folder in the document library.

Rick

--
Richard Methot Stock Synthesis Virtual Lab Forum https://vlab.noaa.gov/web/stock-synthesis/public-forums/-/message_boards/view_message/10495241 VLab.Notifications@noaa.gov

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T16:35:49Z

The excel sheet with the change log has just been uploaded to its folder in the document library.

Rick

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T16:33:31Z

Hi Dan,

Yes, it does.

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T16:28:43Z

Thanks, noted. Does this version include the fix for the projection problem caused by the settlement time in a multi-season configuration?

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T16:13:45Z

You'll need to update your r4ss also. This version of SS implements an option for custom selection among the ~60 numbered report elements. Look at a starter.ss_new to see how to use it. We will of course get it documented more completely.

3 # detailed output (0=minimal for data-limited, 1=high (w/ wtatage.ss_new), 2=brief, 3=custom)
# custom report options: -100 to start with minimal; -101 to start with all; -number to remove, +number to add, -999 to end

-100 # start with a brief list

43 # add report 43

-31 # remove report 31

-999 # end customizing report list

The list of the report elements is found at top of the report.sso file.

Richard D. Methot Jr. Ph.D.
NOAA Fisheries Senior Scientist for Stock Assessments

Mobile: 301-787-0241

On Wed, Jun 17, 2020 at 9:02 AM Dan Fu <VLab.Notifications@noaa.gov> wrote:

Hi Kathryn, the windows version will do for me for now.

Thanks again for the timely response and help.

--
Dan Fu Stock Synthesis Virtual Lab Forum https://vlab.noaa.gov/web/stock-synthesis/public-forums/-/message_boards/view_message/10494876 VLab.Notifications@noaa.gov

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T16:01:55Z

Hi Kathryn, the windows version will do for me for now.

Thanks again for the timely response and help.

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T15:20:04Z

Hi Dan,

A development version (3.30.15.07) is available in the fixes folder. Just the Windows versions are there, so please let us know if you need the Mac or Linux versions (we can easily and quickly build them). Note we are still performing tests on this version, so please use with caution.

Thanks,

Kathryn

RE: issues by pull back the end-year by one year in 3.30

2020-06-17T05:51:12Z

Thanks Rick for the quick diagnostics. I did notice the retro feature works fine in the other example I reported a few days ago for the projection issue which is a single area model.

Looking forward to 3.30.16. In the meantime Is there a development version of 3.30 for download in case of a delay of the formal release ?

RE: issues by pull back the end-year by one year in 3.30

2020-06-16T23:32:41Z

Dan,

Thanks for testing a new situation for SS. Here's what happened.

When you reducing endyr by 1, this placed an observation in the forecast era. That should be OK and we now intentionally allow that so MSE and other procedures can know to generate expected values for these forecast observations.

The problem was that we never tested a forecast observation in a multi-area model. The call to get_expected_values() in forecast was within a loop of areas. But get_expected_values() function has an area loop within it and chaos results because the code is not sufficiently modular.

It was easy to move the call to get_expected_values outside of the area loop and all is working fine now.

Also I found that the forecast file input for benchmark range of years was not robust to years > endyr, so that code is now more robust also.

We will be releasing 3.30.16.00 with changes and a few other fixes within a couple of weeks. It will have one largish change in which we introduce custom selection of report modules so requires an upgrade of r4ss also.

RE: issues by pull back the end-year by one year in 3.30

2020-06-16T20:30:00Z

Hi Dan,

Thanks for the extra details. We will check it out and report back.

Cheers,

Kathryn

RE: issues by pull back the end-year by one year in 3.30

2020-06-16T19:50:27Z

I am using 3.30.15.

I checked more detail - the problem appears to be related to that the CPUE indices in 2015 is still retained in the file when the end year was reset to 2014. Once I removed the 2015 CPUE index for all fleets, the problem goes aways. The other data (catch, size) in 2015 could still be kept.

But this is not an issue in 3.24 .

Dan

RE: issues by pull back the end-year by one year in 3.30

2020-06-16T19:12:45Z

Dan,

We'll take a look. Which version of 3.30 are you using? We have found a couple of issues with 3.30.15.00 and also have introduced some augmentations, so we will be releasing 3.30.16 soon.

Rick

Richard D. Methot Jr. Ph.D.
NOAA Fisheries Senior Scientist for Stock Assessments

Mobile: 301-787-0241

On Tue, Jun 16, 2020 at 11:41 AM Dan Fu <VLab.Notifications@noaa.gov> wrote:

Dear SS3 team,

I'd like to report another issue I encountered with 3.30.

As part of a retrospective analysis, I am running the model by simply pulling back the end year of the model by one year, i..e, only changing in the data file:

2015 #_EndYr

to

2014 #_EndYr

Running ss.exe in the command line will hang up at the end of the estimation - it appears to generating endless warning messages to the warning file.

Performing the same operation to the original 3.24 files works fine.

Is this something you could help taking a look at? I have attached the original 3.30 files (you could reproduce the error by setting EndYr to 2014)

Thanks for your help

Dan

--
Dan Fu Stock Synthesis Virtual Lab Forum https://vlab.noaa.gov/web/stock-synthesis/public-forums/-/message_boards/view_message/10481005 VLab.Notifications@noaa.gov

RE: issues by pull back the end-year by one year in 3.30

2020-06-16T18:45:22Z

Hi Dan,

Thanks for reporting this - could you specify which version of SS 3.30 you are using that gives this issue?

Thanks,

Kathryn

issues by pull back the end-year by one year in 3.30

2020-06-16T18:41:29Z

Dear SS3 team,

I'd like to report another issue I encountered with 3.30.

As part of a retrospective analysis, I am running the model by simply pulling back the end year of the model by one year, i..e, only changing in the data file:

2015 #_EndYr

2014 #_EndYr

Running ss.exe in the command line will hang up at the end of the estimation - it appears to generating endless warning messages to the warning file.

Performing the same operation to the original 3.24 files works fine.

Is this something you could help taking a look at? I have attached the original 3.30 files (you could reproduce the error by setting EndYr to 2014)

Thanks for your help

Dan