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.