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.
