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 (N*log(s) is
corrected to be N*log(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 | |
|
