Updates to the OM (#2)

[allanhicks]

FROM Cole in ss3sim_hake:

A few thoughts from my first round of testing. I just had a quick look so feel free to reject any of these suggestions if they don't make sense.

Control file
(1) We should set the years of the model to be 1-100. (I'm going to change the other models to be like this too)
(2) What do the advanced recruitment options do in an OM? I would guess we want to turn those off.
(3) We might want to up the max F, in case we have a scenario with F larger than what it is now we might not notice that it is being truncated (I assume that is what SS does)
(4) We probably want to have parametric selectivity so that it's more general and we can add time-varying process to those parameters. I believe the other models have asymptotic but that is something we should discuss further.
(5) It looks like the lambda for the age comps is not 1, we should probably set it at that for clarity, although obviously it doesn't matter for the OM.

Data file
(1) Again, set the years.
(2) Delete the months? Per on conversation and Ian's recommendation.
(3) Change so catches and indices match new years (we need expected values for all years available to our sampling functions).
(4) Verify that the length bins cover the entire plausible range of the length distribution. Again, we need lots of information in the expected values for sampling functions. We might want to set all models to have a finer resolution (1cm?) since we're examining binning strategies.
(5) Add length observations for all years. This contribution can be turned off if desired, but should be available for the other groups.
(6) Turn aging error off. Not sure what exactly that does in the context of an OM, but probably more clear if it's off. We'll be adding aging error to the EM this time around.
(7) Add age comps for each year and fleet.

[allanhicks]

Also (from 7/17/14 meeting)

Data

1. we need months/season (set to 12 or 1)
2. Put in data for all years (how do we do age-at-length)
3. We should input mean length-at-age also

#Ctl

1. We should keep advanced recruitment devs on, b ut we need to remember why (ask Kotaro)
2. Selectivity: one parameterization that can be asymptotic or dome-shaped
3. Selectivity length or age-based (maybe a part of exptl design)
4. Set up growth parameters for hake (OM will not use wtatage.ss)

[kellijohnson-NOAA]

You need to set advanced recruitment deviations so that you can supply
rec devs.
On 7/17/2014 02:58 PM, allanhicks wrote:

Also (from 7/17/14 meeting)

Data

1. we need months/season (set to 12 or 1)
2. Put in data for all years (how do we do age-at-length)
3. We should input mean length-at-age also

#Ctl

1. We should keep advanced recruitment devs on, b ut we need to
   remember why (ask Kotaro)
2. Selectivity: one parameterization that can be asymptotic or dome-shaped
3. Selectivity length or age-based (maybe a part of exptl design)
4. Set up growth parameters for hake (OM will not use wtatage.ss)

—
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#2 (comment).

[kellijohnson-NOAA]

Max F was set to 4 in other models (at least according to my old notes).
On 7/14/2014 10:56 PM, allanhicks wrote:

FROM Cole in ss3sim_hake:

A few thoughts from my first round of testing. I just had a quick look
so feel free to reject any of these suggestions if they don't make sense.

Control file
(1) We should set the years of the model to be 1-100. (I'm going to
change the other models to be like this too)
(2) What do the advanced recruitment options do in an OM? I would
guess we want to turn those off.
(3) We might want to up the max F, in case we have a scenario with F
larger than what it is now we might not notice that it is being
truncated (I assume that is what SS does)
(4) We probably want to have parametric selectivity so that it's more
general and we can add time-varying process to those parameters. I
believe the other models have asymptotic but that is something we
should discuss further.
(5) It looks like the lambda for the age comps is not 1, we should
probably set it at that for clarity, although obviously it doesn't
matter for the OM.

Data file
(1) Again, set the years.
(2) Delete the months? Per on conversation and Ian's recommendation.
(3) Change so catches and indices match new years (we need expected
values for all years available to our sampling functions).
(4) Verify that the length bins cover the entire plausible range of
the length distribution. Again, we need lots of information in the
expected values for sampling functions. We might want to set all
models to have a finer resolution (1cm?) since we're examining binning
strategies.
(5) Add length observations for all years. This contribution can be
turned off if desired, but should be available for the other groups.
(6) Turn aging error off. Not sure what exactly that does in the
context of an OM, but probably more clear if it's off. We'll be adding
aging error to the EM this time around.
(7) Add age comps for each year and fleet.

—
Reply to this email directly or view it on GitHub
#2.

[peterkuriyama]

Allan, I saw that you reverted a couple of commits to the dat file. So should we keep the years at 1966 and 2013 and adjust the other parts of the data file accordingly?

[allanhicks]

Sorry about that. I was learning about reverting to older versions, and got a little confused. I think that we should keep the years at 1-100.

[peterkuriyama]

Ok and just so I'm clear there should be 100 years of dummy data for:
Catch
Acoustic Survey Observations
Ageing Error Keys
Acoustic Survey Age Comps
Marginal Fishery Age Comps

Is that it for the dat file?

[allanhicks]

And length comps. That should be it for the dat file. Do not put in age-at-length comps (yet).

The ctl file will need the wtatage file turned off (maturity option), then verify growth is set up properly. Check recruitment. Put in the double normal for length based selectivity (I think #24) and make it asymptotic (see SS manual).

Let me know when you have finished the dat file and I'll have a look through it.
Thanks!

[iantaylor-NOAA]

Peter,
You mention ageing error keys.
For now, I would change from 41 definitions to 2, uncomment the first 2:
"# No ageing error"
"# Baseline ageing error"
and then delete all of the currently active lines below. For the model to
run, the AgeErr values in the age composition table would need to be
changed to 1 or 2 (either is fine for now).
-Ian

On Tue, Jul 22, 2014 at 2:22 PM, allanhicks [email protected]
wrote:

And length comps. That should be it for the dat file. Do not put in
age-at-length comps (yet).

The ctl file will need the wtatage file turned off (maturity option), then
verify growth is set up properly. Check recruitment. Put in the double
normal for length based selectivity (I think #24) and make it asymptotic
(see SS manual).

Let me know when you have finished the dat file and I'll have a look
through it.
Thanks!

—
Reply to this email directly or view it on GitHub
#2 (comment).

[peterkuriyama]

Ok I think I finished the .dat file and am going through the ctl file now

[peterkuriyama]

I'm not sure how to incorporate double normal for length based asymptotic selectivity. I think option 1 is asymptotic selectivity but 24 is double normal. Can asymptotic selectivity come in by specifying parameters that lead to an asymptotic curve?

[allanhicks]

That is exactly right. Check out page 75 of the SS manual. Fix FINAL at 1, and DESC-WIDTH at a large value (like 5 maybe). There is a xls file that allows you to play with parameters, but I use an r4ss function called selfit to play around with the parameters. However, I'm not sure if the tcl/tk package is working on a Mac.

[allanhicks]

Great job Peter. It looked good except that there was only one fleet in each comp set of data. I also made the change of putting population length bins, data length bins to 1 cm intervals and to be the same. And, i changed the age data to be from 0 to 20. Note that the fishery fleets are always numbered first and the surveys after all fishery fleets (may change in new SS). That means that the fishery is fleet 1 and the survey is fleet 2 in this model. It runs through the data file now.