Release notifications

SS3.30.23 Release Oct 31, 2024

2024-10-31T19:17:02Z

Greetings SS3 Users,

Here's your Halloween treat - the next release of SS3. Read the attached release notes and download it from our github site: https://github.com/nmfs-ost/ss3-source-code/releases/tag/v3.30.23

Rick and the SS3 Team

New Stock Synthesis (SS3) Forum

2024-06-12T22:10:06Z

We have created a new space for SS3 Q&A and discussions. It is a Google Group called the SS3 Forum . We hope this can be a vibrant discussion space. For technical code issues, we still recommend using the GitHub Discussions. The SS3 team encourages other SS3 users to answer each other's questions, with Rick or other team members providing occasional supplemental comments. You will need to visit the SS3 Forum once to register by stating your reason for joining, then a team member will let you in. After that, there is no recurring login and you can follow discussions via your email. Please don’t be shy about responding to a post as we genuinely want this to be a user-supported community that builds good practices together!

All the best,

Rick and the SS3 Team

ss3diags new release

2024-02-20T18:08:59Z

Aloha Stock Synthesis users,

Version 2.2.0 of the ss3diags R package is now available! The main feature of this release improves our documentation. Vignettes describe how to implement and interpret common diagnostic tests using the r4ss and ss3diags functions and include detailed instructions for customizing plots to make it easier for them to fit your needs. We have noted all changes in this release in the change log.

As always, please do not hesitate to reach out to the ss3diags team to ask a question, report a bug, or request a feature. You can contact us by opening an issue or emailing megumi.oshima@noaa.gov.

Best,
ss3diags team

SS3.30.22.01 Release Jan 31, 2024

2024-01-31T17:20:30Z

Greetings SS3 users. Here is a small release that fixes a couple of bugs and adds two small features. See the attached pdf for more info and links to download the new exes.

Rick and the SS3 Team

SS3 github repos renaming on Dec 4

2023-11-29T17:30:25Z

On December 4, 2023, we will be moving the nmfs-stock-synthesis organization over to the NOAA Fisheries GitHub Enterprise Cloud (GHEC) account under the nmfs-ost organization. The nmfs-stock-synthesis repositories and the documentation github.io site will be down on December 4th as we migrate over to GHEC.

Additionally, the repository names will add ss3 to the beginning of each name (e.x. ss3-source-code, ss3-test-models, etc.) so that the repos belonging to stock synthesis will be easily identifiable under the nmfs-ost org. It will likely take us a few days to ensure that all links are updated with the new org and repo names, so we appreciate your patience during this time. Come December 15th, if you find a link that isn't working, please submit an issue and we will promptly fix it.

We ask that you go ahead and update any bookmarks that you have saved to the new github org/repo link and to the new github.io site. GitHub does provide an automatic redirect when the names of repositories change so you should initially still be taken to the new url even using the previous url. We will be creating a redirect for the github.io site to allow a similar thing to happen with that (though this only persists only for however long we retain the old github.io org/repo name).

Please feel free to email nmfs.stock.synthesis@noaa.gov if you have any further questions or concerns about the upcoming move to GHEC.

SS3.30.22 Release Oct 31, 2023

2023-10-31T20:31:28Z

Greetings Stock Synthesis users. Release 3.30.22 is now available. You will find a summary and relevant links in the attached pdf. The executables can be downloaded from github.

SS3.30.21 Release Feb 10, 2023

2023-02-10T20:23:06Z

Release notes for Stock Synthesis 3.30.21

Feb 10, 2023

Greetings Stock Synthesis Users,

A new release of Stock Synthesis is now available. The most notable changes in 3.30.21 are:

Introduction of the capability to have a different Dirichlet-multinomial parameter for discard length comp rather than sharing the same parameter as retained catch length comp. We did not extend this split capability to age composition or generalized size composition as it seemed unlikely that differential weighting of comps would be needed in those cases. This change comes with a new input structure only if you are using the new feature. With the new input approach we did not keep a way to share the same parameter for both discard and retained and combined comps. While that would have given more backward compatibility, it is illogical to think that discard and retained catch would have the same sampling characteristics.
SS3 is now compiled with ADMB 13.1. Note that SS3.30.20 used ADMB 13.0 which made several helpful revisions to the console output and we made corresponding revisions to the SS3 specific console output. We highly recommend that you study the new features of ADMB (listed here) so you can use its advanced command line features. In particular, the -hess_step command lets ADMB use the inverse Hessian to make additional iterations to achieve exact convergence, and the -nuts command enables more efficient MCMC sampling.
Our development team continues to advance our use of GitHub features. Notably, you can now view the change log as a GitHub project board incorporating links to the list of issues worked for this release. Find more information at the GitHub SS3 readme.
New Team Member: Elizabeth Gugliotti has joined the SS3 team. She brings great skills in R and Git to continue our enhancement of the SS3 ecosystem of tools.
Unfortunately, we did not get to making Multivariate Tweedie composition weighting operational, but it is close.
Upcoming: Following the CAPAM workshop on good practices, I’ve begun thinking that the SS3 philosophy of great flexibility in options needs to be tempered with a good practices approach. The old options won’t disappear, but more suggestions will appear.

There are no mandatory input changes. As always, we recommend that you update to the latest version of Stock Synthesis to take advantage of augmentations and bug fixes. Updating to the newest version even if no new features pertain to your model ensures that the *.ss_new files created whenever you do a run contain updated notes on what we consider to be good practices with respect to SS3.

Change Log: Now directly linked to the included issues on GitHub.

VLAB updates: No updates at VLAB as we are migrating more resources to GitHub. See the Stock Synthesis homepage for the latest links. The message forum at VLAB is still a good way to post inquiries.

GUI - Stock Synthesis Interface (SSI) updates: The GUI has been updated to accommodate changes for this release of Stock Synthesis.

ss3sim updates: See the ss3sim vignettes for information on getting started.

r4ss updates: r4ss has been updated to maintain compatibility with Stock Synthesis 3.30.21.

SS3 User Manual: Most documentation for Stock Synthesis can be viewed at https://nmfs-stock-synthesis.github.io/doc/. In particular, there is now an html version of the user manual.

Contact us: Please do not hesitate to report bugs, ask a question about SS3, or request a feature. Contact the SS3 development team by opening an issue (for those with GitHub accounts), posting on the forums, or emailing nmfs.stock.synthesis@noaa.gov.

SS3.30.20 re-released Sept 30, 2022

2022-09-30T22:20:14Z

Here is a small tweak so that the model output headers refer to ADMB 13.0.

https://github.com/nmfs-stock-synthesis/stock-synthesis/releases/tag/v3.30.20

SS3.30.20 released Sept 29, 2022

2022-09-29T22:50:02Z

Greetings SS3 users.

We have released version 3.30.20 with ADMB 13.0. Please see the attached release notes.

Rick and the SS3 Team

SS3.30.19.01 Fixes released on Apr 15, 2022

2022-04-15T19:01:28Z

Hello Stock Synthesis Users,

Two issues were discovered within hours of the release of 3.30.19. Both were fixed and are released as the 3.30.19.01 fix. Changes are:

#283 (fixed by #284) Fix two errors in reporting of results. One caused doubled reporting of recruitment in the time_series table in a model with multiple seasons and only one recruitment event. The other caused incorrect fecundity-at-age to be used in the SPR/YPR profile if empirical wt-at-age was used.
#288 (fixed by #290) Fix reporting of catch at age in equilibrium and initial year report

SS3.30.19 released April 4, 2022

2022-04-04T18:58:10Z

Release notes for Stock Synthesis 3.30.19

April 4, 2022

Greetings Stock Synthesis Users,

The release of Stock Synthesis (3.30.19.00) is now available. There are no mandatory input changes. We recommend that all users update to the latest version of Stock Synthesis to take advantage of augmentations and bug fixes. Recently, our team did a thorough review of all accumulated requests and prioritized them for development, so look forward to more advancements with 3.30.20 in about 6 months. We’ll certainly be looking to integrate the newest capabilities of ADMB.

The most notable changes in 3.30.19 are:

The data.ss_new file is now deprecated. Instead, data_echo.ss_new, which echoes inputs to the data file with SS3 standardized comments, is generated. If requested, the expected values will be output into the file data_expval.ss, while each bootstrap file will be output into a separate file called data_boot_XXX.ss, where XXX is the number bootstrap. This change was made because dividing up the files will make examining the output files less error-prone. See the output files section of the user manual for more information.
Optional output to sub-folders. If the user creates a sub-folder named ssnew, then all .ss_new files will go there (with their new names). If the user creates a sub-folder named sso, then all .sso output files will go there. We hope this new option will ease management of output files.
A new bioeconomic option created in collaboration with Andre Punt has been added to benchmarks. This option allows the MSY search to be in terms of value or retained catch, rather than dead catch. It is still a beta feature. See the features section of these release notes for how to invoke this option.
Added a sub-option for cubic spline to control performance at tails.
Improved predator M2.
Fixed and improved output for hermaphroditic populations, in particular for multi-season models and for male-to-female transitions.
Added option to help work with tag-recapture data having small number of returns
Deprecated the helper spreadsheets. See the Selectivity Web App and the User Manual instead.

For Linux users, we have changed to compiling the Linux binary on CentOS to Ubuntu. This is because we have easier access to Ubuntu machines and the version of CentOS Linux we were using has reached end-of-life. However, this may cause issues for some Linux users. Please let us know through the forums or email if you are running into difficulties due to this change in compiling. If necessary, Stock Synthesis can be built from source.

VLAB updates: We are providing more resources on Github rather than on the website. See the Stock Synthesis homepage for the latest links.

GUI - Stock Synthesis Interface (SSI) updates: The GUI has been updated to accommodate changes for this release of Stock Synthesis.

ss3sim updates: See the ss3sim vignettes for information on getting started.

r4ss updates: r4ss has been updated to maintain compatibility with Stock Synthesis 3.30.19.

Additional tools for SS updates:

The helper spreadsheets have been deprecated, the information they provided is available in other resources. Please see the user manual for input file specifications and the SS3 helper shiny app or SSI for visualizations of the double normal and logistic selectivity functions. Thanks to Allan Hicks and Andrea Havron for developing the shiny app!
The ss3diags R package contains additional diagnostic routines for SS3 models.

SS3 User Manual updates: Most documentation for Stock Synthesis can be viewed at https://nmfs-stock-synthesis.github.io/doc/. In particular, there is now an html version of the user manual.

Contact us: Please do not hesitate to report bugs, ask a question about SS, or request a feature by posting on the forums, opening an issue (for those with github accounts), or emailing the SS3 team at nmfs.stock.synthesis@noaa.gov.

Change log since last release:

See Change_log_for_SS_3.30.xlsx for more details.

Features

Revise lines needed for West Coast rebuilder (new option 2 in forecast file). Issue #276
Bioecon benchmark beta feature - Benchmark options and output in economic units. Issues #222, #251

To use this feature, use the following options in the forecast file:

# MSY Method (FMEY)

COND: MSY Method = 5

Maximum economic yield (MEY) units

1 = dead biomass;

2 = dead biomass without excluded bycatch fleet;

3 = retained biomass; and

4 = profits using price and costs.

1 0 0 1

-9999 0 0 0

MEY options - Fleet, Cost/F, Price/F, and Include FMEY in Optimization

To calculate the FMEY enter fleet number, the cost per fishing mortality, price per mt, and whether optimization should adjust the fleet’s F or keep it at the mean from the benchmark years (0 = no, 1= yes). Care should be taken when scaling the values used for cost/F and price/mt. Units in the example show cost=0 and price = 1, so will be identical to MSY in weight. Note, if a fleet’s catch is excluded from the FMEY search, its catch or profits are still included in the MSY value using historical F levels from benchmark years

Add option for constant/0 selectivity below the first knot in cubic spline. Issue #86. See setup in the cubic spline selectivity description of the User Manual.
Add option to get a report file for each MCEVAL sample. Issue #70. Evoke this by using this line in the starter file: 2 # MCMC output detail
Allow subfolders for .sso and .ssnew output; new filenames for ss_new output. Issue #226. Details available in the optional output subfolders and the output files sections of the user manual.
Augment reporting of overall comps (table in Report.sso with the header OVERALL_COMPS report:30) to inclue breakdown by season and sex. Issue #215. New output has these fields after adding area and season:

area seas Fleet N_obs len_bins 10 14 18 22 etc.

New rows include rows for season = 0 to report combined seasons when the number of seasons is more than 1 and separate rows for males and females in a two sex model.

Corrections and Revisions

Fix summary biomass sd so will work. Issue #271
Remove deprecated selectivity patterns. Issue #272
Fix length comp super-periods so that they work with retrospectives. Issue #265
Fix mirroring dispersion tag parameters. Issue #268
Fix output for hermaphroditic populations. Issue #246
Improve weight at age storage efficiency. Issue #136
Revise F method 4 to allow constant F. Issue #243
Fix multi-season forecast catch output. Issue #205
Fixes for predator M2. Issue #45
Add option for dealing with tag-recapture data having low N recaptures #280
convert catchfleet IF statements to a lookup table. Issue #192

SS3.30.19 Pre-release Feb 25, 2022

2022-02-25T19:03:33Z

Greetings SS3 colleagues,

Here we provide information about and access to a pre-release version of SS3.30.19. Thanks to the several of you who worked with us to develop some of these changes. We will keep this as a pre-release for a few weeks to see if any of you encounter problems with this version of the code and the new features. Please send a separate forum message as replies to this message will go to all users.

Rick and the SS3 Team

********

Pre-Release notes for Stock Synthesis 3.30.19

February 2022

Greetings Stock Synthesis Users,

The release of Stock Synthesis (3.30.19.00) is planned for March 2022. Here we provide a pre-release version with notes on the included changes. There are no mandatory input changes with version 3.30.19.00. We recommend that all users update to the latest version of Stock Synthesis to take advantage of augmentations and bug fixes. The most notable changes in 3.30.19 are:

The data.ss_new file is now deprecated. Instead, data_echo.ss_new, which echoes inputs to the data file with SS3 standardized comments, is generated. If requested, the expected values will be output into the file data_expval.ss, while each bootstrap file will be output into a separate file called data_boot_XXX.ss, where XXX is the number bootstrap. This change was made because dividing up the files will make examining the output files less error-prone. See the output files section of the user manual for more information.
Optional outputting to sub-folders. If the user creates a sub-folder named ssnew, then all .ss_new files will go there. If the user creates a sub-folder named sso, then all .sso output files will go there. We hope this new option will ease management of output files.
A new bioeconomic option created in collaboration with Andre Punt has been added to benchmarks. This option allows the MSY search to be in terms of value rather than dead catch. It is still a beta feature. See the features section of these release notes for how to invoke this option.
Added a sub-option for cubic spline to control performance at tails.
Improved predator M2.
Fixed and improved output for hermaphroditic populations, in particular for multi-season models and for male-to-female transitions.
Deprecated the helper spreadsheets. See the Selectivity Web App and the User Manual instead.

VLAB updates: We are providing more resources on Github rather than on the website. See the Stock Synthesis homepage for the latest links.

GUI - Stock Synthesis Interface (SSI) updates: The GUI has been updated to accommodate changes for this release of Stock Synthesis.

ss3sim updates: See the ss3sim vignettes for information on getting started.

r4ss updates: r4ss has been updated to maintain compatibility with Stock Synthesis 3.30.19.

Additional tools for SS updates:

The helper spreadsheets have been deprecated, the information they provided is available in other resources. Please see the user manual for input file specifications and the SS3 helper shiny app or SSI for visualizations of the double normal and logistic selectivity functions. Thanks to Allan Hicks and Andrea Havron for developing the shiny app!
The ss3diags R package contains additional diagnostic routines for SS3 models.

SS3 User Manual updates: Most documentation for Stock Synthesis can be viewed at https://nmfs-stock-synthesis.github.io/doc/. In particular, there is now an html version of the user manual.

Change log since last release:

See Change_log_for_SS_3.30.xlsx for more details.

Features

Bioecon benchmark beta feature - Benchmark options and output in economic units. Issues #222, #251

To use this feature, use the following options in the forecast file:

# MSY Method (FMEY)

COND: MSY Method = 5

Maximum economic yield (MEY) units

1 = dead biomass;

2 = dead biomass without excluded bycatch fleet;

3 = retained biomass; and

4 = profits using price and costs.

1 0 0 1

-9999 0 0 0

MEY options - Fleet, Cost/F, Price/F, and Include FMEY in Optimization

Add option for constant/0 selectivity below the first knot in cubic spline. Issue #86. See setup in the cubic spline selectivity description of the User Manual.
Add option to get a report file for each MCEVAL sample. Issue #70. Evoke this by using this line in the starter file: 2 # MCMC output detail
Allow subfolders for .sso and .ssnew output; new filenames for ss_new output. Issue #226. Details available in the optional output subfolders and the output files sections of the user manual.
Augment reporting of overall comps (table in Report.sso with the header OVERALL_COMPS report:30) to inclue breakdown by season and sex. Issue #215. New output has these fields after adding area and season:

area seas Fleet N_obs len_bins 10 14 18 22 etc.

New rows include rows for season = 0 to report combined seasons when the number of seasons is more than 1 and separate rows for males and females in a two sex model.

Corrections and Revisions

Fix output for hermaphroditic populations. Issue #246
Improve weight at age storage efficiency. Issue #136
Revise F method 4 to allow constant F. Issue #243
Fix multi-season forecast catch output. Issue t#205
Fixes for predator M2. Issue #45
convert catchfleet IF statements to a lookup table. Issue #192

SS3.30.18.00 released Sept 30, 2021

2021-09-30T17:20:00Z

Greetings Stock Synthesis users,

Today we are releasing the newest version of Stock Synthesis. The release notes are attached.

This version contains three significant new features that are fully described in the release notes:

A new fleet type (4) provides the capability to define an entity as a predator that adds the predation mortality to the base natural mortality.
A new Fleet-specific F method = 4. With this approach, some fleets can stay in hybrid F mode while others transition to parameters. Method 4 is now a recommended superset of methods 2 and 3.
An option to produce output for F at Blimit, where Blimit is a fraction of Bmsy.

If you try out any of these new features, we would like to hear from you about your experience. Suggestions for further augmentation and new issues are always welcome.

You will notice that the development work is now principally at our NOAA github site: https://github.com/nmfs-stock-synthesis and some of our VLAB links will take you there for details.

Rick and the SS Team

RE: SS3.36.17.00 released June 11, 2021 - SSI updated

2021-07-07T22:57:01Z

The graphical Stock Synthesis Interface has been updated to more fully implement features available in SS and be more robust. It's object-oriented approach is a great logical improvement over the many inconsistencies in the order of text-oriented inputs in the data and control files. It also allows you to preview the shapes of selectivity curves and other aspects dependent on the input values. Give it a try and send us your input. Find it in the latest executables folder.

Rick and Neal

SS3.36.17.00 released June 11, 2021

2021-06-11T19:37:22Z

June 11, 2021

Greetings Stock Synthesis (SS) Users,

This release of SS (3.30.17.00) includes both augmentations and bug fixes. The latest 3.30.17.00 executables can be found on vlab or through github releases. Please note that between releases, fixes are available in the latest executables folder at VLAB. The most notable changes are:

SS is now compiled with ADMB 12.3, which was released in January 2021. This upgrade enables improved MCMC performance using ADNUTS with an experimental diagnostic, -hess_step. ADMB 12.3 also resolves a speed degradation we noticed when SS was compiled with ADMB 12.2.
A new natural mortality function has been contributed by Mark Maunder and his team.
Capabilities of the hermaphroditism function have been augmented to meet the needs of assessments by the NMFS Southeast Fisheries Science Center.
The number of parameters in the par file has changed for many models. In 3.30.16, some models included an implementation error parameter that wasn’t used; now implementation error parameters are only included in models that use implementation error. To use an older par file as the starting values with 3.30.17, try manually removing the implementation error parameters from the par file if implementation error is not used.
We continue to improve tools to help users get the most out of SS. This includes more situations that get reported to warnings.sso as suggestions. We also have added more information in data.ss_new and control.ss_new about usage options. Even if your input control file has a long history of your own custom comments, it is advisable to occasionally look at the control.ss_new for tips on improving your setup.

We advise all users to update to this version of SS to take advantage of augmentations and bug fixes. Remember to update your copy of r4ss, SSI and the User Manual also as these work closely together.

There are no mandatory input changes with SS3.30.17.00, except for

users of option 2 for extra standard deviation reporting in the control file (see details in the “Controls for Variance of Derived Quantities” section of the user manual. Two additional values are now required in 3.30.17 so that variance can be reported for dynamic B0 and Summary Bio.
SS now has stricter checks on parameter bounds

The full list of changes is in the change log, and an abbreviated list of changes since the last SS release is posted at the end of this message. Thank you to all users who reported bugs or requested features - your suggestions help us improve SS for everyone.

The translation version of the executable (ss_trans) will no longer be updated after the 3.30.17 release. This decision was made because of the necessary maintenance time of the translation executable as new features of SS are added, which would be better spent on maintaining and developing new features. Users who wish to convert models from 3.24 to 3.30 in the future will be able to convert using the 3.30.17 version of ss_trans(.exe), and then can convert to newer versions of SS from there.

Stock Synthesis goes github: The Stock Synthesis source code is now publicly available on github! Users can now more easily clone and browse the source code, report bugs and request features, or contribute to Stock Synthesis through a pull request. The nmfs-stock-synthesis organization also contains other repositories related to Stock Synthesis. For example, a repository containing example Stock Synthesis models for users is now available; we invite users to contribute their own models to this repository, to provide the SS user community with a greater diversity of Stock Synthesis model examples.

In addition to increasing transparency, we continue to improve automation in our development processes. For instance, Stock Synthesis is now tested using Github Actions on every new addition to the repository. We hope these improvements increase the stability and reliability of Stock Synthesis.

Vlab updates: The address for the Stock Synthesis website has been changed from https://vlab.ncep.noaa.gov/web/stock-synthesis/home to https://vlab.noaa.gov/web/stock-synthesis/home. For approximately 2 months, the old site will redirect to the new site, after which the old address will cease to work. VLAB is now in the cloud where system uptime is expected to be more reliable.

GUI - Stock Synthesis Interface (SSI) updates: The GUI is being updated to accommodate changes for this release of Stock Synthesis; a new version will be posted within the next few weeks.

ss3sim updates: The codebase was refactored to allow users to specify the season and partition in sampling. See the ss3sim vignettes for more information on using ss3sim. A new version of ss3sim is expected to be tested with SS v. 3.30.17 and submitted to CRAN later this summer.

r4ss updates: r4ss has been updated to maintain compatibility with SS 3.30.17 and is back compatible to 3.24. Example plots (Big Skate and Simple) and a rendered version of the introduction vignette are now available. A new version of r4ss is expected to be submitted to CRAN later this summer. In the meantime, the github main branch is considered the most reliable and up-to-date version.

r4ss can now be cited as:

Ian G. Taylor, Kathryn L. Doering, Kelli F. Johnson, Chantel R. Wetzel, Ian J. Stewart, 2021. Beyond visualizing catch-at-age models: Lessons learned from the r4ss package about software to support stock assessments, Fisheries Research, 239:105924. https://doi.org/10.1016/j.fishres.2021.105924.

Additional tools for SS updates:

Data limited tools - Options included Simple Stock Synthesis (SSS) and Extended Simple Stock Synthesis (XSSS), as well as SS-DL-tool, a shiny app that includes XSSS and SSS in its functionality.
SSMSE remains under active development, with a preliminary version expected this fall.

SS User Manual updates: The latest version of the user manual includes documentation of new features in the release and a thorough update of information on time-varying parameters. A citable version of the manual is available and can be cited as:

Methot, R. D., Jr., C. R. Wetzel, I. G. Taylor, and K. Doering. 2020. Stock Synthesis User Manual Version 3.30.15. U.S. Department of Commerce, NOAA Processed Report NMFS-NWFSC-PR-2020-05. https://doi.org/10.25923/5wpn-qt71

Contact us: Please do not hesitate to report bugs, ask a question about SS, or request a feature by posting on the forums, opening an issue, or emailing the SS team at nmfs.stock.synthesis@noaa.gov. Please contact VLAB administrators at vlab.admin@noaa.gov to change your username or password or for other VLAB related questions.

Change log since last release:

See Change_log_for_SS_3.30.xlsx for more details and references to github issue number.

Features

output: provide std.err. for time series of summary biomass, see Extra_Std input options
biology: new age and maturity linked natural mortality option; thanks Mark Maunder
output: reduce output of derived quantities if there is no recruitment deviations used, and/or if implementation error is 0.0
biology: modify hermaphroditism to allow entry of age-at-first-transition, and fraction of males contributing to SSB options; thanks SEFSC
selectivity: create len selex pattern No. 2 as a modification of pattern No. 24 to provide better control in sex-specific selex situations
output: report empirical autocorrelation of dev vectors, including recdevs
output: improve reporting of Hessian status in report.sso
forecast: improve forecast performance when forecast F approaches the max F constraint in control file; add warning when constraint is hit
output: add output table with Z and F by area and platoon
forecast: create control rule option 0: this ignores ramp and intercept values, which are still read
output: add component specific logL to parmtrace.sso; can allow component-specific gradients to be calculated from parmtrace entries during Hessian creation
output: provide log-scale option for depletion and F_std; and provide multi-yr averaging
output: calculate and report autocorrelation for parameter and recruitment deviations

Corrections and Revisions

output: fix reporting of total biomass in ss_summary.sso (also see #155 regarding small fix to time-varying growth)
likelihood: change logL for D-M composition; will cause a change in reported logL if used
timevary: improve control of the time-varying recruitment distribution (among areas) feature during forecast years (git #101) and provide report.sso output of time-series of recruitment distribution results (git #96); fixes in #153 for transition to forecast years
checks: Improve error checking for parameter min-max bounds
selectivity: Fix error in age-based retention calculations (git #100)
timevary: Fix error in environmental link option 4 (logistic link)
output: deprecate SIS_table.sso; use r4ss::get_SIS_info instead
build: begin using ADMB 12.3 instead of 12.2
biology: fix updating of empirical wt-at-age vector at beginning of year as used for smrybio
forecast: negative year inputs for Bmark_years in forecast file working again after breaking in 3.30.16.
likelihood: fix error in recommended var_adjustment for age comp sample size
likelihood: Fix problem with D-M indexing for length when no age data
timevary: fix, and augment control of, the continue last dev feature
input: fix read error for mean weight-at-age data
forecast: fix error in control rule for Fmethod 1 in forecast
likelihood: correction to use of the init_equil catch lambda, it was mixed up with catch lambda
biology: fix output of mean size-at-age when N platoons > 1
forecast: fix problem with N forecast years > 50

RE: SS3.36.16.00 released Sept 3, 2020

2020-09-03T18:07:59Z

Well that didn't take long. A user found that forecasts > 50 years ran into an array problem. I've already fixed it and we will get it out to everyone soon, so look for it in the fixes folder.

Also apologies for the typo in the post's title. Obviously this is 3.30.16, not 3.36.16.

Finally, we forgot one item in the change log. There now is a command line alternative to the editing of maxphase (turn_off_phase) in starter.ss. Simply run ss.exe with -stopph N to have it stop after phase N. Internally, this replaces the starter file's value of maxphase with N. This works with N=-1, 0, or +integer.

SS3.36.16.00 released Sept 3, 2020

2020-09-03T00:46:17Z

Latest SS News: Sept 3, 2020

Greetings Stock Synthesis (SS) Users,

This release of SS (3.30.16.00) includes both augmentations and bug fixes. There are no mandatory input changes. The most notable augmentations are:

An option to reduce and customize the tables output in Report.sso.
A size-based selectivity option to fix selectivity to be constant over a range of size bins.
New parameter deviation and environmental linkage options to restrict the adjusted parameter within the low-high range of the base parameter (similar to a 3.24 option).
SS is now compiled with ADMB 12.2 (instead of ADMB 12.0). This allows SS to work with the NUTS (No U-Turn Sampler) algorithm for MCMC (through ADMB command line options or the adnuts R package, which has a recent release).

We advise users to update their version of SS to take advantage of augmentations and bug fixes. Remember to update your copy of r4ss and SSI also as these work closely together. The full list of changes is in the change log, and an abbreviated list of changes since the last SS release is posted at the end of this message. Thank you to all users who reported bugs or requested features - your suggestions help us improve SS for everyone.

We have been improving on our SS build and test processes since the last release. We have implemented an automated build and test routine using Jenkins on a linux server, which runs about 25 complex stock assessment models using the latest code commit for SS and checks for changes in the model results. This allows us to run tests more frequently than before and hopefully results in catching bugs more quickly.

The latest 3.30.16.00 executables can be found in the SS document library. Please note that between releases, fixes are posted in the latest executables folder. A copy of the SS source code (the ADMB tpl) for this release is available to browse.

GUI - Stock Synthesis Interface (SSI) updates: The GUI was updated to accommodate changes for this release of Stock Synthesis. For details, please see the SSI_readme.txt file that is included in the zipped GUI files. Have bug reports or feature requests for the GUI? Please send the SS team an email at nmfs.stock.synthesis@noaa.gov or post in the forums.

ss3sim updates: The process to run simulations in ss3sim was simplified from needing several text files to the use of a single data frame; check out the vignette for an example. We hope to have the changes on CRAN soon.

r4ss updates: The biggest change is a rewrite of the SS_output() function (discussed on github) to use blank lines instead of the following keyword to mark the end of each table when parsing Report.sso. This was necessary to adapt to the potential absence of individual pieces due to the new customized reporting feature in SS. More information on changes to r4ss is available by looking at recently modified issues on the r4ss GitHub issues page.

Additional tools for SS updates: An R package to use SS models in an MSE is under active development. Please visit the SSMSE repository for more information. Occasionally, we hear from users who have developed useful add-ons to SS. If you have such a tool, we’d love to hear about it. We can advertise it in SS release announcements or on the SS website if you would like and would be happy to consider whether a change to SS could make your package easier and better.

SS User Manual updates: An updated version of the user manual includes documentation of new features in the release. A citable version of the manual is available and can be cited as:

Contact us: Please do not hesitate to report bugs, ask a question about SS, or request a feature by posting on the forums or emailing the SS team at nmfs.stock.synthesis@noaa.gov. Please contact VLAB administrators at vlab.admin@noaa.gov to change your username or password or for other VLAB related questions.

Rick Methot and the SS Team (alphabetically):

Kathryn Doering

Kelli Johnson

Neal Schindler

Ian Taylor

Chantel Wetzel

*********************************************

Change log since last release:

FEATURES

Selectivity: add size selectivity option 11: sel=1.0 over a bin range
TimeVary: creates new option to Z score or mean center environmental data within SS. Use this with a new environmental link option (#3), which uses a logit transform to constrain the result to the base parameter’s min-max. Value of the envlink should be constrained to about 1.8 to prevent U-shaped distribution of adjusted parameters.
TimeVary: create new parameter deviation approach (#5) that uses logit transformation to constrain the result to the base parameter’s min-max.
I/O: change init_equ_catch logL and lambda from scalar to fleet-specific vector
I/O: custom control of 60 reporting options; use report detail option 3 in the starter.ss file to invoke custom reporting options
I/O: generate warning when accumulating catch specified more than once for the same yr, seas, and fleet
I/O: add another extra_std option to get se of dynamic Bzero
I/O: add option in starter.ss allowing multi-year average of F_std
- 11 # F_std_basis: 0=raw_annual_F; 1=F/Fspr; 2=F/Fmsy; 3=F/Fbtgt; where F means annual_F; values >=11 invoke multiyr with 10's digit

CORRECTIONS & REVISIONS

Selectivity: mirror, change length selex #5 to set selectivity = 1.0e-10 outside of range where selectivity = 1.0 to avoid gradient error; add more warnings for input of selex min-max ranges
Benchmark: now initialize 2 vectors that occasionally caused erratic benchmark calculations
Benchmark: input for the range of years to average now enforces input <= endyr
Forecast: correct array index to allow forecast observations in a multi-area model
Forecast: correct indexing error for N-at-age in forecast when settlement age > 0
Forecast: correct timevary biology parameter indexing to operate in forecast
Forecast: revise internal tracking to allow a fleet with no historical catch to operate in forecast (e.g., a forecast only fleet)
I/O: revise starter.ss_new and forecast.ss_new to display input values for year ranges in addition to the absolute years
I/O: fix output of RET and MORT in report.sso so it displays correctly for Benchmark and Forecast years; internal calcs were OK
I/O: autogeneration of time-varying parameters: change ss_trans so that autogen set to 1 in control.ss_new in case the trans process has created some time-vary parameters

SS3.30.15.00 released 2020-03-26

2020-03-26T17:24:28Z

Latest SS News: March 26, 2020

Greetings Stock Synthesis (SS) Users,

This release of SS (3.30.15.00) encompasses nine months and nearly 50 commits of augmentations and fixes. Of particular note are new capabilities to read a random seed for generating bootstrap data, allow users to skip forecasting, improve Dirichlet-multinomial compositional data weighting output, and improve the usability of the semi-parametric (2D-AR) selectivity option. Most fixes are for seldom used SS features including changes so that Lorenzen natural mortality can now be used when time-varying growth is estimated, and corrected calculations for the expected values of morph composition. It always is advisable to update your version to take advantage of improvements in outputs and to learn of new options. The full list of changes is in the change log and searchable by keyword, date, and version. An abbreviated, recent list is posted at the end of this message. Thank you to all users who reported bugs or requested features.

The latest 3.30.15.00 executables can be found in the SS document library. Please note that between releases, fixes are posted in the latest executables folder. Sometimes the Linux and OSX version are not compiled as frequently as the Windows version, so please do not hesitate to contact the SS development team (“SS team”) at nmfs.stock.synthesis@noaa.gov if you require a more up-to-date Linux or OSX version.

An essay describing how fishing mortality, F, is used and reported by SS is attached to these release notes. This essay was written to answer questions users had about the various aspects of F in SS. It is also included in the SS manual.

Website changes: The SS team has been making SS more accessible. As part of this process, a copy of the SS source code (the ADMB tpl) for this release is available to browse. In addition, the SS forums are now public, meaning that even those without an account can view and create posts. Need a refresher on creating forum posts or (for registered users) subscribing/unsubscribing to the forums? See this article on using forums in the vlab user guide.

Update on GUI - Stock Synthesis Interface (SSI): New features added to the SSI expand its capabilities and make the interface more user-friendly. These features include the ability to choose a default model to load when starting SSI, selectivity and stock recruitment relationship curves can be viewed while editing the model, reading models with tagging data, and r4ss plots can be created with a click of a button after a successful model run. There is also a new quick start guide for the SSI which documents initial setup.

ss3sim updates: ss3sim (on CRAN and github) has been updated to work with SS 3.30 models. ss3sim is an R package that facilitates flexible, rapid, and reproducible fisheries stock assessment simulation testing with SS. If you are interested in using ss3sim and wish to develop additional functionality, please open an issue in the ss3sim repository. The ss3sim team is happy to coordinate with you to make the range of options that ss3sim can handle more broad.

r4ss updates: The r4ss functions for reading and writing SS input files (see functions SS_readctl(), SS_writectl(), SS_readdat(), and SS_writedat() especially) have been expanded to work with a wider range of SS models. If you are using R as a tool to interact with SS, these functions may be of use for modifying SS files programmatically within R. The SS team is using these functions within ss3sim, to advance a decision support tool that provides a GUI for control of some forecast features, and to develop a generic MSE framework for SS. More information on changes to r4ss is available by looking at recently modified issues on the r4ss GitHub issues page.

Additional tools for SS updates: An R package to use SS models in an MSE is under active development.

SS User Manual updates: The manual has been reorganized with three new sections that focus on advanced SS configurations, detailed information on internal SS processes, and general population dynamic modeling advice. Additionally, the manual now includes a new description of the SS bootstrapping feature and an improved description of how to use conditional-age-at-length in SS. Have a suggestion for the manual or need clarification? Email the SS development team at nmfs.stock.synthesis@noaa.gov.

Contact us: Please do not hesitate to report strange SS behavior, ask a question about SS, or request a feature by posting on the forums or emailing the SS team at nmfs.stock.synthesis@noaa.gov. Please contact VLAB administrators at vlab.admin@noaa.gov to change your username or password.

Change log since last release:

Dirichlet-multinomial composition likelihood: Improve reporting of adjusted sample sizes; include adjusted sample sizes in bootstrap data generation. NOTE: still need to extend to generalized size comp.
empirical wt-at-age: Fix internal storage of annual fecundity; improve filling wtatage in forecast years; merge writing of wtatage.ss_new into other reporting rather than separate iteration
Sdreport: improve input format for extra sdreport quantities and introduce sdreport output for M-at-age
Selectivity: introduce ability to set selex = 0.0 for young age range because length selex alone can allow their selection
Bootstrap data: allow user input (starter.ss) of seed for random number generator
Morph composition data: fix major problem that affected expected values for morph composition since creation of this feature in 3.24; improve output
Forecast: add no forecast (-1) option and improve simple one year forecast option (0)
Priors: gamma prior was incorrect, had wrong sign
Priors: clarify how prior like for non-estimated parameters is used, esp. for prior on survey Q
Data Input: fix problem that converted fractional data months to integers
Forecast: make forecast F robust to high catches and pin at maxF; improve performance when used fixed F inputs
Report: output each block's age-age' key when blocks used for estimated age-age' key
Selectivity: clarify age/len terminology in parameter names and warnings for 2DAR
Warnings: improve accuracy of N warn count; add warnings for illogical data specifications for retention; improve warnings for %depletion fleet
Retention: add handling of age-retention when discard option=3; add check for correct parameter range for asymptotic selectivity
Internal calc: revise the nil expected value warning so it only adds a smaller constant
Bootstrap: can generate observations in forecast out to 50 years
Warnings: note that F0.1 search can fail if bycatch fleets' catch is included
Warnings: make code more robust to retained catch data used when fleet is bycatch only
Growth: change internal order of operations and time index tracking to allow Lorenzen M to work with time-varying growth
Report: add N observation info to logL table in report.sso
Forecast: option to set max bias adjustment to 1.0 for all years was incorrectly beingapplied in forecast
Control input: revise autogen to retain input values in control.ss_new unless used; also fix autogen of block offsets
Report: formatting fixes in .ssnew and reporting in Impl_err and F parameters in output
Report: fix output issue with recruitment in time_series for multi-season models
Report: fix Z-at-age output for N morphs>1
Input: fix the mirroring of tag recapture parameters
Forecast: correct problem with heterogeneous catch types (bio vs num) in forecast
Report: fix output of sample size in data.ss_new for mean length@age observations

SS3.30.14.00 released July 22, 2019

2020-01-21T17:29:42Z

Greetings SS users. Please see the attached file for news about SS version 3.30.14. You'll finally find more flexibility for assigning tag-recapture parameters and there several minor, special-case fixes to report. Especially see news about improved user guides.

Rick and the SS team

Fwd: [Stock Synthesis - Release updates] SS 3.30.13.00 released Mar 13, 201

2019-03-13T23:17:56Z

Sharing this with VLST: Great example of the collaboration.

---------- Forwarded message ---------
From: Richard Methot <VLab.Notifications@noaa.gov>
Date: Wed, Mar 13, 2019 at 6:51 PM
Subject: [Stock Synthesis - Release updates] SS 3.30.13.00 released Mar 13, 2019
To: VLab.Notifications@noaa.gov <VLab.Notifications@noaa.gov>

Latest SS News: March 13, 2019

Greetings Stock Synthesis (SS) Users,

In this release of Stock Synthesis 3.30.13.00 we have included some fixes, augmentations and new features. Thanks to some users who were pushing the envelope on time-varying parameters for finding some needed fixes to the code. You can find all the changes listed in the Change Log and below. The fixes were minor and mostly in the output, but there is one big fix affecting the calculation of the log likelihood for the parameter deviations. We will put out a fuller report on that later and encourage you to contact us if you need info on this change sooner.

Please remember to check the change log frequently so you are aware of anything relevant for your SS project. It also is a good idea to look over the *.ss_new files created by the newest version of SS so you can see listed all available input options. Of course, the user manual, r4ss, and graphical Stock Synthesis Interface (SSI) have been updated. The SSI now provides previews for the shape of most selectivity functions.

We have a new SS team member, Kathryn Doering. She will be involved with VLAB maintenance, creation of an example library, and developing more R-based routines to enhance SS. Welcome Kathryn.

If you have any SS usage questions or issues please post in the FORUM.

Problems using the SS VLAB site can be addressed to nmfs.stock.synthesis@noaa.gov

Please contact VLAB administrators at vlab.admin@noaa.gov to change your username or password.

ADMB 12.0

SS is now being compiled exclusively with ADMB 12.0 (except the 32 bit versions). An important new feature in ADMB 12.0 improves the MCMC algorithm. See below from the admb-project.org website:

Dr. Cole Monnahan has developed a new MCMC functionality into ADMB. The current Metropolis algorithm was updated to have more meaningful console output and not require an sdreport object. The old method remains, and the new one is accessible with argument ‘-rwm’. A new algorithm, the no-U-turn sampler (a self-tuning extension of the existing ‘hybrid’ method was also added, and available with ‘-nuts’. The functionality matches the software platform Stan closely. The user can specify whether to use the MLE covariance, an arbitrary matrix, or adapt one during the warmup phase (recommended). Both these additions work much with the R package adnuts, which streamlines workflow, including parallel chains, diagnostic checking, and inference. See adnuts package vignette for more information.

Future big features on the wish list:

Option to replace input of growth parameters with input of empirical length-at-age
Change input of tagging parameters to use a much more concise design matrix approach
Adding otolith weight as a proxy for fish age as a new data type
Area-specific spawner-recruitment
Area-specific growth in addition to morph specific growth

SS VLAB Release 3.30.13.00 changes:

Type	Category	Description	Input_Change?
fix	tag	fix formatting problem for tag output in compreport.sso
fix	survey	fix issue with float Q that may have been source of some poor convergences
fix	controls	fix implementation of seasons as pseudo-years
fix	survey	fix ss_trans to handle mirror q better
fix	output	fix reporting when using seasonal MGparms
fix	output	fix output of Dirichlet parameters
fix	input	fix reading of sizecomp obs before styr
fix	output	fix output of equilibrium F when using F_reporting=5
fix	output	fix issues with F_reporting=4 and 5 for multiseason models
fix	statistics	Important: corrected the -logL calculation for parameter deviations. This affects only a constant (Nlog(s) is corrected to be Nlog(1)) in the logL of the devs, it does not affect how the devs are used.
new	survey	create new Q option so that mirror Q uses an offset to ln(Q)	Yes, if used
new	growth	add growth cessation model per Maunder et al (2018)	Yes, if used
new	time_vary	add dev vector options so last dev can persist to end of time series (codes 21, 22, 23, 24)	Yes, if used
new	recruitment	add new recdev approach based on dev being relative to R0, not SRR; add column to spawn_recr in report.sso	Yes, if used
new	forecast	add new forecast feature: year-specific ABC buffer	Yes, if used
new	output	add table for F in report.sso
revise	input	revise warning for recrdist options
revise	tag	move tag recapture code into a separate file for ease in future updating: SS_tagrep.tpl
revise	output	re-order and organize the list of tables appearing at top of report.sso
revise	output	small fix to posteriors.sso for Q parms

--
Richard Methot Stock Synthesis Virtual Lab Forum https://vlab.noaa.gov/group/stock-synthesis/discussions-forums-/-/message_boards/view_message/6161546 VLab.Notifications@noaa.gov

SS 3.30.13.00 released Mar 13, 2019

2020-01-21T17:29:59Z

Latest SS News: March 13, 2019

Greetings Stock Synthesis (SS) Users,

We have a new SS team member, Kathryn Doering. She will be involved with VLAB maintenance, creation of an example library, and developing more R-based routines to enhance SS. Welcome Kathryn.

If you have any SS usage questions or issues please post in the FORUM.

Problems using the SS VLAB site can be addressed to nmfs.stock.synthesis@noaa.gov

Please contact VLAB administrators at vlab.admin@noaa.gov to change your username or password.

ADMB 12.0

SS is now being compiled exclusively with ADMB 12.0 (except the 32 bit versions). An important new feature in ADMB 12.0 improves the MCMC algorithm. See below from the admb-project.org website:

Dr. Cole Monnahan has developed a new MCMC functionality into ADMB. The current Metropolis algorithm was updated to have more meaningful console output and not require an sdreport object. The old method remains, and the new one is accessible with argument ‘-rwm’. A new algorithm, the no-U-turn sampler (a self-tuning extension of the existing ‘hybrid’ method was also added, and available with ‘-nuts’. The functionality matches the software platform Stan closely. The user can specify whether to use the MLE covariance, an arbitrary matrix, or adapt one during the warmup phase (recommended). Both these additions work much with the R package adnuts, which streamlines workflow, including parallel chains, diagnostic checking, and inference. See adnuts package vignette for more information.

Future big features on the wish list:

Option to replace input of growth parameters with input of empirical length-at-age
Change input of tagging parameters to use a much more concise design matrix approach
Adding otolith weight as a proxy for fish age as a new data type
Area-specific spawner-recruitment
Area-specific growth in addition to morph specific growth

SS VLAB Release 3.30.13.00 changes:

Type	Category	Description	Input_Change?
fix	tag	fix formatting problem for tag output in compreport.sso
fix	survey	fix issue with float Q that may have been source of some poor convergences
fix	controls	fix implementation of seasons as pseudo-years
fix	survey	fix ss_trans to handle mirror q better
fix	output	fix reporting when using seasonal MGparms
fix	output	fix output of Dirichlet parameters
fix	input	fix reading of sizecomp obs before styr
fix	output	fix output of equilibrium F when using F_reporting=5
fix	output	fix issues with F_reporting=4 and 5 for multiseason models
fix	statistics	Important: corrected the -logL calculation for parameter deviations. This affects only a constant (Nlog(s) is corrected to be Nlog(1)) in the logL of the devs, it does not affect how the devs are used.
new	survey	create new Q option so that mirror Q uses an offset to ln(Q)	Yes, if used
new	growth	add growth cessation model per Maunder et al (2018)	Yes, if used
new	time_vary	add dev vector options so last dev can persist to end of time series (codes 21, 22, 23, 24)	Yes, if used
new	recruitment	add new recdev approach based on dev being relative to R0, not SRR; add column to spawn_recr in report.sso	Yes, if used
new	forecast	add new forecast feature: year-specific ABC buffer	Yes, if used
new	output	add table for F in report.sso
revise	input	revise warning for recrdist options
revise	tag	move tag recapture code into a separate file for ease in future updating: SS_tagrep.tpl
revise	output	re-order and organize the list of tables appearing at top of report.sso
revise	output	small fix to posteriors.sso for Q parms

SS 3.30.13_beta mini-release

2020-01-21T17:30:22Z

In response to a couple of user requests, here is a mini-release of 3.30.13_beta. For now it is only available in the windows version, but let us know if you need a different compilation. Find it in the folder 3.30.13_beta in the windows folder of the latest releases folder. We will add more features and get everything documented before doing a full release of 3.30.13.

The features in this release are:

allow gender=-1 to invoke Female SSB = SSB*fracfem
Where gender=1 ignores the fracfemale parameter and creates a total, asexual population; gender=2 uses fracfemale to split into 2 sexes at time of recruitment; gender=-1 creates an asexual population then multiplies by fracfemale at the time of reporting spawning biomass.
fix formatting problem for tags output in compreport.sso
create new Q option so that mirror Q uses an offset to ln(Q)
This is created for multi-area models where the user wants fleets to mirror Q and take the relative size of the areas into account.
ln_Q2 = ln_Q1 + ln(area1/area2).
so takes an extra parameter the value of which should be ln(area1/area2), if I have my signs correct.
revise warning for recrdist options

Rick

SS 3.30.12.00 released Sept. 13, 2018

2020-01-21T17:30:57Z

Greeting Stock Synthesis (SS) Users:

With the latest release of Stock Synthesis 3.30.12.00 we have included a large number of small fixes and augmentations. Thanks to some users who were pushing the envelope on time-varying parameters for finding some needed fixes to the code. You can find all the changes listed in the Change Log and below. Please remember to check the change log frequently so you are aware of anything relevant for your SS project. It also is a good idea to look over the *.ss_new files created by the newest version of SS so you can see listed all available input options. For you Excel users, the SS-Output processors has been updated to work better with 3.30.12. Of course, the Manual, r4ss, and Stock Synthesis Interface (GUI) also have been updated.

If you have any SS usage questions or issues please post in the FORUM.

Problems using the SS VLAB site can be addressed to nmfs.stock.synthesis@noaa.gov.

Please contact VLAB administrators at vlab.admin@noaa.gov to change your username or password.

ADMB 12.0

A version of the SS executable is now available compiled with ADMB 12.0. An important new feature in ADMB 12.0 improves the MCMC algorithm. See below from the admb-project.org website:

Dr. Cole Monnahan has developed a new MCMC functionality into ADMB. The current Metropolis algorithm was updated to have more meaningful console output and not require an sdreport object. The old method remains, and the new one is accessible with argument ‘-rwm’. A new algorithm, the no-U-turn sampler (a self-tuning extension of the existing ‘hybrid’ method was also added, and available with ‘-nuts’. The functionality matches the software platform Stan closely. The user can specify whether to use the MLE covariance, an arbitrary matrix, or adapt one during the warmup phase (recommended). Both these additions work much with the R package adnuts, which streamlines workflow, including parallel chains, diagnostic checking, and inference. See adnuts package vignette for more information.

Future features and updates (somewhat in priority order):

Option to replace input of growth parameters with input of empirical length-at-age
Change input of tagging parameters to use a much more concise design matrix approach.
Adding otolith weight as a proxy for fish age as a new data type.
Area-specific Spawner-Recruitment addition.

SS VLAB Release 3.30.12.00 changes:

Type	Category	Description
fix	forecast	Time-vary SRR parms will now work in the forecast; e.g. regime shift on mean recruitment
fix	selectivity	Selectivity Patterns 42 and 43 will now be read correctly
fix	benchmark	fecundity-at-age for benchmark when growth is time-varying is no longer being overwritten
fix	growth	Time-vary growth parameters now work with Richards growth function, but there is no trap to prevent shrinkage
fix	benchmark	Benchmark selectivities now use the correct ALK when growth was time-varying
implement	time_vary	Implement time-varying ageing bias parameters
implement	time_vary	Implement density-dependent environmental effects on parameters; change specification format
improve	read	improved error checking on read of wtatage.ss
improve	fleets	Update and explain the usage of the "-1" code for fishery sample timing
improve	read	Enable transferring parameter dev phase and dev_se from 3.24 format into 3.30 format
improve	read	A fatal warning for len selectivity mirroring of higher numbered fleet
improve	statistics	only calculate selectivity softparmbounds when parameter phase is positive
improve	output	Label lines in the control.ss_new file have been added to improve readability of the parameters
improve	read	improve performance of jitter when parameter are near bounds
revise	forecast	enhance control rule options to: Control rule method (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)
revise	Mean_Size	add column for "type" in mean body size: #_yr month fleet part type obs stderr; where type=1 for mean length; type=2 for mean body weight; replaces use of the sign of partition for indicating type
new	selectivity	A new age selectivity non-parametric for sex-specific options #44 and #45
new	recruitment	Create lambda type 18 for initial equilibrium regime shift
report	output	There is now better output to Fit_Len, Fit_Age, Fit_Size for Francis weighting applications, and Durbin-Watson statistic for autocorrelation of devs
report	output	subseas info is now reported to improve ability to discern when monthly timing of samples has resulted in assignment to a different subseason
report	output	Fix and enhance reporting the full spawn_recr curve in report.sso (just after the spawn_recr output)
report	output	Bmsy/Bzero has been added to the list of derived quantities
report	output	Enabled the display of logL for ignored length and age comp observations.
report	output	Discard-at-age is now reported after catch_at_age in report.sso
revise	output	Option to report mean F without numbers weighting
revise	forecast	Changed mean forecast recruitment option to use range of years previously specified in forecast years
revise	recruitment	Allow time-vary R0 to occur in initial equilibrium year; matches 3.24
revise	growth	plus_group growth options now include: value>0 means exponential decay for growth above maxage (value should approximate initial Z; -999 replicates 3.24; -998 to not allow growth above maxage
revise		small tweak to parameter jitter and now output the jittering to echoinput.sso
		Begin compiling with ADMB 12.0

SS 3.30.11.00 released Apr 26, 2018

2020-01-21T17:31:09Z

Greeting Stock Synthesis (SS) Users:

The VLAB SS website has been updated and now more content is public. The latest release of Stock Synthesis 3.30.11.00 is now available for download.

The following materials are now publicly available:

BEGIN HERE – Introduction to Stock Synthesis
Latest SS executables
Examples
Documentation
Helper Spreadsheets
Training

We are now up to 285 registered SS users. As a registered user, you also have access to the WIKI, the Archive of past executables and the FORUM. You also get this email.

If you have any SS questions or issues please post in the FORUM.

The platform VLAB is built on has been upgraded. You will see a slightly different interface and we will be using it to enhance the site.

Please contact VLAB administrators at vlab.admin@noaa.gov for technical issues and to change your username or password.

Latest SS News:

With the latest release of Stock Synthesis 3.30.11.00 we have included the following updates and changes:

Testing for future updates to ADMB 12.0.
Added a 3-parameter Ricker Power Spawner Recruitment relationship to SS. See Punt and Cope (2018) http://www.sciencedirect.com/science/article/pii/S0165783617301819
More user control of report.sso features. Now setting report_detail to 0 will omit most reporting and is great for data-limited applications.

Additional augmentations in this release include:

The standard ADMB command line option “-noest” now works with SS.
A copyright disclaimer statement has been added.
Control for transition into MCMC. When SS goes into MCMC it has always set recruitment bias adjustment to 1.0 for all years with estimated recruitment deviations. To keep the arithmetic mean recruitment approximately unchanged, ln(R0) parameter needs to be slightly increased. Now you can elect to do that adjustment using a small value now located near end of the starter.ss input file. Note that we have also detected a potential defect in the way that ADMB implements the recruitment deviation dev_vector in MCMC and are investigating it with the ADMB developers.
The ss_summary.sso output file is augmented to include: expected survey values (if requested in data file input), log(spawning biomass) for 3 years.
Find total and summary biomass time series, but with no standard error on these estimates.
Additionally, we continued to use your feedback to improve some warnings and output formatting. You’ll now see parameter-specific labels on the double normal selectivity parameters.
An issue with the Richards growth function has been resolved, but results in loss of the trap on body length shrinkage when there is time-varying growth. More on this in a future release.

Future features and updates (somewhat in priority order):

Improvements in implementation of sex-specific selectivity.
Change input of tagging parameters to use a much more concise design matrix approach.
Option to replace input of growth parameters with input of empirical length-at-age
Update to ADMB 12.0.
More testing for implementation of density-dependent parameters.
Adding otolith weight as a proxy for fish age as a new data type.
Area-specific Spawner Recruitment addition.

SS 3.30.10.00 released 2018-01-09

2020-01-21T17:31:42Z

Happy New Year.

Stock Synthesis executables, GUI, manual and change log for version 3.30.10.00 dated 2018-01-09 are now available. You will find executables for 64-bit windows, 32-bit windows, linux, and OSX.

Chantel Wetzel keeps the user manual up-to-date including all the new features above;
Ian Taylor keeps r4ss in sync with the latest version of SS;
Neal Schindler is adding new features to the GUI, now including previews of selectivity shapes;
Later this year, Kelli Johnson is looking to update ss3sim to work with 3.30.

The changes in this release include:

Additional controls for the 2D_AR selectivity; this is a mandatory change to the control file if you are using this option. This selectivity option creates a two-dimensional (age x year or length x year) matrix of deviations from an underlying parametric selectivity curve.

Controls for adjusting forecast recruitments, including recent mean, multiplier on R0 and others; this new option uses two of the “other bells&whistles” placeholders in forecast.ss
Add F0.1 as a Benchmark and Forecast option; this is either/or with the F(Btarget) benchmark option in forecast.ss;
Controls for bycatch fleets so their contribution to MSY and usage in forecasts is explicit; this is a data file input change immediately after the fleet descriptions, but only if there is at least one bycatch fleet; consider this a beta release feature so look out for anomalies and let us know;
Fix and clarify internal usage and output for SSB_virgin vs SSB_unfished (benchmark); this is tricky when there is time-varying biology or time-varying spawner-recruitment parameters; see the expanded benchmark description in the manual;
Improve and clarify the output in forecast-report.sso and in the SPR/YPR profile;
Additionally, we continued to use your feedback to improve some warnings and output formatting.

Here is another reminder about the new output file, ss_summary.sso. ss_summary.sso is designed to store key model outputs all in one concise place. It is organized as a list. At the top are some descriptors, then the likelihoods for each component, then the parameters and their standard errors, and then the derived quantities and their standard errors. We created this output to make it easier to compare results as we update the code, but we think it will find plenty of other uses also.

The major features on the to-do list include:

Update to ADMB 12.0;
change input of tagging parameters to use a much more concise design matrix approach;
3-parameter Ricker Power spawner-recruitment relationship;
new data type: otolith weight as a proxy for fish age
area-specific spawner-recruitment
more user control of report.sso features

Please post about any Stock Synthesis 3.30 issues or questions in the Stock Synthesis 3.30 forums.

We are now up to 261 registered users on this VLAB SS Forum. I'd appreciate your feedback on how we can make it more useful to you.

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password or for other VLab issues.

Rick and the SS Team

SS 3.30.08.04 released

2020-01-21T17:32:01Z

Stock Synthesis executables for version 3.30.08.04 dated 2017-11-10 are now available for 64-bit windows, 32-bit windows, linux, and OSx. The GUI has also been updated, please give it a try and give us feedback.

There is one small fix and a few small changes in this release:

fix forecast recruitment error when spawn_month>1
after bias adjustment ramp is calculated, set bias adjustment to 0.0 for years after recdev_end. This is added because r4ss can calculate a bias-adjustment ramp that extends into the future. Bias-adjustment is illogical in the forecast, so SS now hardwires ramp to go to 0.0 after the last year of the main recruitment deviations.
Adjust an array dimensions to allow very long forecasts. But note that a forecast longer than the expected interval between assessments should only be done at forecast loop 2. Forecast loop 3, that forecasts quotas for future years then calculates F to match those quotas, should only be done for a forecast of a few years, such as the expected interval between assessment updates.
In addition, I continue to use your feedback to improve some warnings.

Here is another reminder about the new output file, ss_summary.sso. ss_summary.sso is designed to put key model outputs all in one concise place. It is organized as a list. At the top are some descriptors. Then the likelihoods for each component, then the parameters and their standard errors, then the derived quantities and their standard errors. We created this output to make it easy to compare the results as we update the code, but we think it will find plenty of other uses also.

The SS 3.30 Change Log, which is available in the Document Library, has more information. We updated the user manual to reflect these changes.

(Still) at the top of the current to-do list are:

change tagging parameters to use a much more concise design matrix approach
add F0.1 to the Benchmark and Forecast code
add a constant recruitment option to forecast
add a 3-parameter Ricker Power spawner-recruitment relationship
develop controls for bycatch fleets so they can be managed better in Benchmark and Forecast

Please post about any Stock Synthesis 3.30 issues in the Stock Synthesis 3.30 forums.

We are now up to 252 registered users at this VLAB SS Forum. I'd appreciate your feedback on how we can make it more useful to you.

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password, or for other VLab issues.

Rick and the SS Team

SS 3.30.08.03 released 2017-09-29

2020-01-21T17:32:14Z

Stock Synthesis executables for version 3.30.08.03 dated 2017-09-29 are available for 64-bit Windows. Soon we will get the update for OS X and Linux uploaded.

Sorry about the bug in the just released 3.30.08.02. Now fixed in 3.30.08.03.

The good news is that this gives me a chance to tell you about the new output file, ss_summary.sso.

ss_summary.sso is designed to put key model outputs all in one concise place. It is organized as a list. At the top are some descriptors. Then the likelihoods for each component, then the parameters and their standard errors, then the derived quantities and their standard errors. We created this output to make it easy to compare the results as we update the code, but we think it will find plenty of other uses also.

The SS 3.30 Change Log, which is available in the Document Library, has more information. We updated the user manual to reflect these changes.

At the top of the current to-do list are:

change tagging parameters to use a much more concise design matrix approach
add F0.1 to the Benchmark and Forecast code
add a constant recruitment option to forecast
develop controls for bycatch fleets so they can be managed better in Benchmark and Forecast

Please post about any Stock Synthesis 3.30 issues in the Stock Synthesis 3.30 forums

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password, or for other VLab issues

SS 3.30.08.02 released 2017-09-26

2020-01-21T17:32:25Z

Stock Synthesis executables for version 3.30.08.02 dated 2017-09-26 are available for 64-bit Windows. Soon we will get the update for OS X and Linux uploaded.

Changes in this update include:

· Add information on catchability and selectivity options to control.ss_new. The *.ss_new files are your friend as they show the full range of input options available for a SS feature.

· In forecast.ss, if the relative F input option is 2, then replace the season (row) x fleet (column) matrix of input by a list, with rows containing season, fleet, relative F. Terminate list with a row containing -9999 as the season value.

Bug fixes include

· Restore disabled age-specific K. This allows an age’s growth K to be a multiplier times the K for next youngest age. The null value is 1.0.

· Fix a growth calculation that erred if the age at settlement was not set to 0, so an uncommon problem.

· Fix some code sections that still needed fishing fleets to precede survey fleets in rank order, so an uncommon issue. This necessitated the change to a conditional forecast specification for the relative F among fleets (also uncommon). Note that if tag-recapture is used, there still is a requirement to have fishing fleets listed first. This will be addressed soon in a larger change to the tag-recapture section.

· Fix the year range of environmental data output to data-ss_new

The SS 3.30 Change Log, which is available in the Document Library, has more information. We updated the user manual to reflect these changes.

The next release will be in a couple of weeks and will address a much streamlined input format for tag-recapture parameters.

Please post about any Stock Synthesis 3.30 issues in the Stock Synthesis 3.30 forums

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password, or for other VLab issues

SS 3.30.07.01 released 8/16/2017

2020-01-21T17:32:35Z

Stock Synthesis executables for version 3.30.07.01 dated 2017-08-07 are available for 64-bit Windows, OS X, and Linux. There also is a new post in the wiki: Stock Synthesis 3.3 / Discussion Topics / Settlement Events and Growth. Rick will try to write a Discussion Topic monthly to cover various questions commonly asked by users, so check there occasionally.

Changes in 3.30.07.02 include

enhanced control of phases when using depletion fleet
improved reporting of selectivity in forecast era
reporting more info in fit_age_comps section to match what is displayed for fit_len_comps
removed the constraint that the blocks cannot end after retro_yr in order to allow changes in forecast
added a column with ABC_buffer to the time_series table in report.sso
augmentation of the SPR/YPR profile in report.sso to show mean age of catch and other information
revised detailed F input to allow filling all years with one input record

Bug fixes include

issue with overwriting averaged forecast selectivity with base selectivity when time-varying was used.
issue with reporting of dev column in INDEX_2 section of Report.sso
issue with creation of settlement timings from multiple settlement events that happen in same month

The SS 3.30 Change Log, which is available in the Document Library, has more information. We updated the user manual to reflect these changes.

The next release will be in a couple of weeks and will address a few recently detected issues:

Age-specific K was disabled.
Growth was not behaving properly with settlement age > 0.
Although fishing and survey fleets can now be in any order, some parts of the code still were expecting the fishing fleets to be first.

Please post about any Stock Synthesis 3.30 issues in the Stock Synthesis 3.30 forums

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password, or for other VLab issues

New SS 3.30 executables - 2017-07-05

2020-01-21T17:32:46Z

Stock Synthesis executables for version 3.30.05.03 are available for 64-bit Windows, OS X, and Linux. The user manual has also been updated.

New features include

new column in both the length and age comp header tables for specifying the smallest sample size allowed; the default value is 1 to match SS 3.24; these values also affect the conditional age-at-length sample sizes
new option in the forecast file for specifying the selectivity to use for forecasts (not yet implemented)

Bug fixes include

issue with wtatage.ss_new
issue with settlement timing
issue with allocation groups and no allocation fractions defined

The SS 3.30 Change Log, which is available in the Document Library, has more information.

Note: if you are using a model that is already in SS 3.30 format, the following two changes need to be made before using the latest executables:

1. In the data file, add a new column to both the length and age comp header tables for the smallest sample size (set to 1 to match SS 3.24; the minimum value is 0.001)

Change this

#_mintailcomp_addtocomp_combM+F_CompressBins_CompError_ParmSelect

-1 1e-007 5 3 0 0 #_fleet:1_Fishery

-1 1e-007 5 3 0 0 #_fleet:2_Survey

to this

#_tailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize

-1 1e-007 5 3 0 0 1 #_fleet:1_Fishery

-1 1e-007 5 3 0 0 1 #_fleet:2_Survey

2. In the forecast file, add a new value after the forecast years for the not-yet-implemented option for specifying forecast selectivity

#_Fcast_years: beg_selex, end_selex, beg_relF, end_relF, beg_recruits, end_recruits

0 0 0 0 0 0

0 # Forecast selectivity (not yet implemented)

1 # Control rule method (1=catch=f(SSB) west coast; 2=F=f(SSB) )

Please post about any Stock Synthesis 3.30 issues in the Stock Synthesis 3.30 forums

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password, or for other VLab issues

New SS 3.30 executables - 2017-06-02

2020-01-21T17:36:10Z

Stock Synthesis executables for version 3.30.04.02 are available for 64-bit Windows, OS X, and Linux. The user manual has also been updated.

Bug fixes include

issues with MG parms
issues with Q parms

The SS 3.30 Change Log, which is available in the Document Library, has more information.

Note: models with more than one growth morph will not be translated by ss_trans. Edit models with more than one growth morph to have one growth morph only before translating with ss_trans. The additional growth morphs can then be added in the SS 3.30 format input files.

Please post about any Stock Synthesis 3.30 issues in the Stock Synthesis 3.30 forums

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password, or for other VLab issues

New SS 3.30 executables - 2017-05-19

2020-01-21T17:36:45Z

Stock Synthesis executables for version 3.30.03.07 available for 64-bit Windows, OS X, and Linux

Bug fixes include

debugging issue in 3.30.03.06

Please post about any Stock Synthesis 3.30 issues in the Stock Synthesis 3.30 forums

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password, or for other VLab issues

May 2017 bug fixes

2020-01-21T17:33:14Z

Updated Stock Synthesis 3.30.03.06 executables available for 64-bit Windows, OS X, and Linux

Bug fixes include

issue with forecasts and Pope's F
issue with data starting before the model

Please post about any Stock Synthesis 3.30 issues in the Stock Synthesis 3.30 forums

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password, or for other VLab issues

May 2017; beta testing finished

2020-01-21T17:33:35Z

Over the past 5 months, we have been vigorously testing SS3.30, adding a few more features, and doing lots of fixes. Special thanks to the U.S. west coast groundfish team for being the testing grounds with over a dozen model configurations, and to the PFMC's Scientific and Statistical Committee for approving the SS3.24 to SS3.30 comparison. We are now ready to take off the beta testing label. We also have reorganized the VLAB document library where you can find the executables, manuals, change logs, examples, etc. We will continue to work on adding more examples, at this time only simple and simple with discards are up-to-date.

Note that SS3.30 comes as sstrans.exe, which can read SS3.24 format files and convert to 3.30, and ss.exe which you should use after converting. You also will find the SS GUI which makes it much easier to avoid the messy detail of the input files and it can guide you through the conversion process. Officially, this full release is labelled: SS-V3.30.03.05;_2017_05_11

Please post about any Stock Synthesis 3.30 issues in the Stock Synthesis 3.30 forums

Please contact the NOAA VLab administrators at vlab.admin@noaa.gov to change your username or password, or for other VLab issues

Rick and the SS team

Shepherd SRR Correction

2020-01-21T17:34:02Z

A new SS 3.30 User Manual was uploaded on July 15th, 2016 that contains corrections to the Shepherd Stock-Recruitment equations.

May 17 update

2020-01-21T17:34:12Z

May 17: Fix an issue in ss_write.tpl that crashed when writing fit_lencomps in a one sex model. Thanks Kevin.