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