Two model input settings that aren't supported

[iantaylor-NOAA]

I finally took some time to work on issues identified by @JuanMatiasBraccini while testing the changes in PR #234 (now merged to the main branch).

I found 2 issues that caused problems (but informative error messages weren't being reported so it took some digging).

1. the month (formerly seas) column in the CPUE input gets converted from 1 to 7 between the input data file and the data_echo.ss_new file and this mismatch causes problems in the check_avail_dat() function. Changing the input file to use month = 7 fixed it but a better error would be helpful.
2. there are time-varying CPUE parameters with AUTOGEN = 0 in the control file. The AUTOGEN setting gets changed but the required parameter lines don't get added, causing an error. Copying the time-varying parameters from control.ss_new into the original input fixed the issue but a better solution would be helpful.

@JuanMatiasBraccini, let me know if you have any problems with these work-arounds or if they don't get the revised SSMSE working for you.

[JuanMatiasBraccini]

OFFICIAL Hi Ian, Thanks a lot for that. 1. I've updated my SSMSE version thru remotes::install_github("nmfs-ost/SSMSE") 2. In data.dat, I changed Month =1 to Month = 7 in '#_CPUE_and_surveyabundance_and_index_observations' 3. In control.ctl, I changed autogen to all 1s and copy across the 'timevary Q parameters' values from 'control.ss_new' When I execute run_SSMSE() for just 1 scenario and 1 iteration, I can get the OM folder with all required files, but then I get the 'Iteration 1 failed in directory...' message and the EM_init folder only contains these files: ***@***.*** I have attached my updated input files with the changes, but could you send me your version of all the input files, including the ss3.par file, that you managed to get run_SSMSE() to run properly so I can debug mine? Cheers Matias Dr Matias Braccini | Principal Research Scientist Aquatic Science and Assessment Fisheries and Sustainability Department of Primary Industries and Regional Development 39 Northside Drive | Hillarys WA 6025 t +61 (0)8 9203 0211 | w dpird.wa.gov.au Adjunct Research Fellow School of Molecular and Life Sciences Curtin University From: Ian Taylor ***@***.***> Sent: Saturday, 1 August 2026 8:20 AM To: nmfs-ost/SSMSE ***@***.***> Cc: Matias Braccini ***@***.***>; Mention ***@***.***> Subject: [EXT] - [nmfs-ost/SSMSE] Two model input settings that aren't supported (Issue #236) CAUTION: This email originated from outside of DPIRD. Do not click links or open attachments unless you recognise the sender and know the content is safe. [https://avatars.githubusercontent.com/u/4992918?s=20&v=4]iantaylor-NOAA created an issue (nmfs-ost/SSMSE#236)<#236> I finally took some time to work on issues identified by @JuanMatiasBraccini<https://github.com/JuanMatiasBraccini> while testing the changes in PR #234<#234> (now merged to the main branch). I found 2 issues that caused problems (but informative error messages weren't being reported so it took some digging). 1. the month (formerly seas) column in the CPUE input gets converted from 1 to 7 between the input data file and the data_echo.ss_new file and this mismatch causes problems in the check_avail_dat() function. Changing the input file to use month = 7 fixed it but a better error would be helpful. 2. there are time-varying CPUE parameters with AUTOGEN = 0 in the control file. The AUTOGEN setting gets changed but the required parameter lines don't get added, causing an error. Copying the time-varying parameters from control.ss_new into the original input fixed the issue but a better solution would be helpful. @JuanMatiasBraccini<https://github.com/JuanMatiasBraccini>, let me know if you have any problems with these work-arounds or if they don't get the revised SSMSE working for you. - Reply to this email directly, view it on GitHub<#236?email_source=notifications&email_token=AEAKRGWPHPL2KWLPBIUL4DT5HUZTRA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NJQGM2DGMJSGM4TJJTSMVQXG33OU5WWK3TUNFXW5JLFOZSW45FMMZXW65DFOJPWG3DJMNVQ>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEAKRGVRQPQVLUSB2AFYZE35HUZTRAVCNFSNUABFKJSXA33TNF2G64TZHMYTSNZQGY4TQMBRHNEXG43VMU5TKMBTGQZTCMRTHE2KC5QC>. 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You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>> [Facebook]<https://www.facebook.com/DPIRDWA> [x] <https://x.com/dpirdbroadacre> [Linkedin] <https://www.linkedin.com/company/dpirdwa> [Instagram] <https://www.instagram.com/dpirdwa/> [Dept of Primary Industries and Regional Development] [Protect, Grow, Innovate] [Artwork: "Kangaroos going to the Waterhole" by Willarra Barker.] DPIRD acknowledges the Traditional Custodians of Country, the Aboriginal people of the many lands that we work on and their language groups throughout Western Australia and recognise their continuing connection to the land and waters. We respect their continuing culture and the contribution they make to the life of our regions and we pay our respects to their Elders past, present and emerging. Artwork: "Kangaroos going to the Waterhole" by Willarra Barker. DISCLAIMER: The information contained in this email (including attachments) is intended only for the use of the person(s) to whom it is addressed as it may be confidential and contain legally privileged information. If you are not the intended recipient you are hereby notified that any perusal, use, distribution, copying or disclosure is strictly prohibited. If you have received this email in error, please immediately advise us by return email and delete the email document. This email and any attachments to it are also subject to copyright and any unauthorised reproduction, adaptation or transmission is prohibited. This notice should not be removed.

[JuanMatiasBraccini]

OFFICIAL Forgot to check, could my 'sample_struct_list' or 'future_om_list' be the culprits? Never asked before because they worked fine the way I set them up before... This is the head of my samp_struct_list ***@***.*** ***@***.*** ***@***.*** ***@***.*** This is my future_OM ***@***.*** Cheers Matias Dr Matias Braccini | Principal Research Scientist Aquatic Science and Assessment Fisheries and Sustainability Department of Primary Industries and Regional Development 39 Northside Drive | Hillarys WA 6025 t +61 (0)8 9203 0211 | w dpird.wa.gov.au Adjunct Research Fellow School of Molecular and Life Sciences Curtin University From: Matias Braccini Sent: Monday, 3 August 2026 12:17 PM To: 'nmfs-ost/SSMSE' ***@***.***>; nmfs-ost/SSMSE ***@***.***> Cc: Mention ***@***.***> Subject: RE: [EXT] - [nmfs-ost/SSMSE] Two model input settings that aren't supported (Issue #236) Hi Ian, Thanks a lot for that. 1. I've updated my SSMSE version thru remotes::install_github("nmfs-ost/SSMSE") 2. In data.dat, I changed Month =1 to Month = 7 in '#_CPUE_and_surveyabundance_and_index_observations' 3. In control.ctl, I changed autogen to all 1s and copy across the 'timevary Q parameters' values from 'control.ss_new' When I execute run_SSMSE() for just 1 scenario and 1 iteration, I can get the OM folder with all required files, but then I get the 'Iteration 1 failed in directory...' message and the EM_init folder only contains these files: ***@***.*** I have attached my updated input files with the changes, but could you send me your version of all the input files, including the ss3.par file, that you managed to get run_SSMSE() to run properly so I can debug mine? Cheers Matias Dr Matias Braccini | Principal Research Scientist Aquatic Science and Assessment Fisheries and Sustainability Department of Primary Industries and Regional Development 39 Northside Drive | Hillarys WA 6025 t +61 (0)8 9203 0211 | w dpird.wa.gov.au Adjunct Research Fellow School of Molecular and Life Sciences Curtin University From: Ian Taylor ***@***.******@***.***>> Sent: Saturday, 1 August 2026 8:20 AM To: nmfs-ost/SSMSE ***@***.******@***.***>> Cc: Matias Braccini ***@***.******@***.***>>; Mention ***@***.******@***.***>> Subject: [EXT] - [nmfs-ost/SSMSE] Two model input settings that aren't supported (Issue #236) CAUTION: This email originated from outside of DPIRD. Do not click links or open attachments unless you recognise the sender and know the content is safe. [https://avatars.githubusercontent.com/u/4992918?s=20&v=4]iantaylor-NOAA created an issue (nmfs-ost/SSMSE#236)<#236> I finally took some time to work on issues identified by @JuanMatiasBraccini<https://github.com/JuanMatiasBraccini> while testing the changes in PR #234<#234> (now merged to the main branch). I found 2 issues that caused problems (but informative error messages weren't being reported so it took some digging). 1. the month (formerly seas) column in the CPUE input gets converted from 1 to 7 between the input data file and the data_echo.ss_new file and this mismatch causes problems in the check_avail_dat() function. Changing the input file to use month = 7 fixed it but a better error would be helpful. 2. there are time-varying CPUE parameters with AUTOGEN = 0 in the control file. The AUTOGEN setting gets changed but the required parameter lines don't get added, causing an error. Copying the time-varying parameters from control.ss_new into the original input fixed the issue but a better solution would be helpful. @JuanMatiasBraccini<https://github.com/JuanMatiasBraccini>, let me know if you have any problems with these work-arounds or if they don't get the revised SSMSE working for you. - Reply to this email directly, view it on GitHub<#236?email_source=notifications&email_token=AEAKRGWPHPL2KWLPBIUL4DT5HUZTRA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NJQGM2DGMJSGM4TJJTSMVQXG33OU5WWK3TUNFXW5JLFOZSW45FMMZXW65DFOJPWG3DJMNVQ>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEAKRGVRQPQVLUSB2AFYZE35HUZTRAVCNFSNUABFKJSXA33TNF2G64TZHMYTSNZQGY4TQMBRHNEXG43VMU5TKMBTGQZTCMRTHE2KC5QC>. Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS<https://github.com/notifications/mobile/ios/AEAKRGUTQJV5C3ZDYW3GNAL5HUZTRA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NJQGM2DGMJSGM4TJJTSMVQXG33OU5WWK3TUNFXW5JLFOZSW45FKMZXW65DFOJPWS33T> and Android<https://github.com/notifications/mobile/android/AEAKRGSHG4L4IUESKACL4XL5HUZTRA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NJQGM2DGMJSGM4TJJTSMVQXG33OU5WWK3TUNFXW5JLFOZSW45FOMZXW65DFOJPWC3TEOJXWSZA>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>> [Facebook]<https://www.facebook.com/DPIRDWA> [x] <https://x.com/dpirdbroadacre> [Linkedin] <https://www.linkedin.com/company/dpirdwa> [Instagram] <https://www.instagram.com/dpirdwa/> [Dept of Primary Industries and Regional Development] [Protect, Grow, Innovate] [Artwork: "Kangaroos going to the Waterhole" by Willarra Barker.] DPIRD acknowledges the Traditional Custodians of Country, the Aboriginal people of the many lands that we work on and their language groups throughout Western Australia and recognise their continuing connection to the land and waters. We respect their continuing culture and the contribution they make to the life of our regions and we pay our respects to their Elders past, present and emerging. Artwork: "Kangaroos going to the Waterhole" by Willarra Barker. DISCLAIMER: The information contained in this email (including attachments) is intended only for the use of the person(s) to whom it is addressed as it may be confidential and contain legally privileged information. If you are not the intended recipient you are hereby notified that any perusal, use, distribution, copying or disclosure is strictly prohibited. If you have received this email in error, please immediately advise us by return email and delete the email document. This email and any attachments to it are also subject to copyright and any unauthorised reproduction, adaptation or transmission is prohibited. This notice should not be removed.

[iantaylor-NOAA]

@JuanMatiasBraccini, sorry for the continued frustrations. I had changed the directories around a little bit in the dummy.R file that you shared and have further refined them in the attached file. This may just be related to my confusion about where files should be located for SSMSE. I will email you the revised script as well as the modified input files rather than posting to github.

@nathanvaughan-NOAA, when you're back from vacation next week and have time to take a look at any of this, here's an additional change that github copilot suggested to help debug the errors I was getting related to folders being in the wrong places or something: iantaylor-NOAA@aae0551.