SS 3.30.12.00 released Sept. 13, 2018

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Richard Methot, modified 4 Years ago.

SS 3.30.12.00 released Sept. 13, 2018

Youngling Posts: 219 Join Date: 11/24/14 Recent Posts

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

Richard Methot, modified 5 Years ago.

RE: SS 3.30.12.00 released Sept. 13, 2018

Youngling Posts: 219 Join Date: 11/24/14 Recent Posts

Perhaps some of you have wondered about, or been bewildered by, the large number of executables distributed for SS. Here is a brief roadmap to that collection found in the SS_latest_executables folder.

For each operating system: Linux, OSX, and Windows, we distribute three SS files: ss.exe, ss_opt.exe, and ss_trans.exe. Where ss_trans will read files in 3.24 format and run and write in 3.30 format, ss.exe is the normal version to use, and ss_opt is optimized for speed but less able to detect some kinds of errors.

For Windows, we also include versions compiled for 32bit computers. These are appropriately labelled and found in the Windows folder.

We have just started compiling with the latest version of ADMB - Version 12.0. We think everything is 100% compatible, but provide these versions in separate folders. In future, we will only provide SS with just one ADMB version. We will explore even newer releases of ADMB as they come available.

The SS Interface folder contains the executable for the graphical interface. I encourage you to try it.

Rick