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Trouble with multiple growth morphs

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Thom D. Teears, modified 2 Years ago.

Trouble with multiple growth morphs

Youngling Posts: 23 Join Date: 8/13/18 Recent Posts

Hello all,

      I was wondering if someone could help explain the multiple growth morph option. I specified 2 growth patterns with a recruitment settlement assignment for each one. The model runs and provides estimates for M and growth params for each of the growth patterns for the two sexes (a total of 4 morphs, 2 for each sex) but the numbers at age and biomass at age in the report file don't have any values for the males. Does it calculate numbers and biomass differently when multiple growth patterns are used?

Many thanks,

Thom

 

2  #_N_Growth_Patterns (Growth Patterns, Morphs, Bio Patterns, GP are terms used interchangeably in SS)
1 #_N_platoons_Within_GrowthPattern 
#_Cond 1 #_Platoon_between/within_stdev_ratio (no read if N_platoons=1)
#_Cond  1 #vector_platoon_dist_(-1_in_first_val_gives_normal_approx)
#
4 # recr_dist_method for parameters:  2=main effects for GP, Area, Settle timing; 3=each Settle entity; 4=none (only when N_GP*Nsettle*pop==1)
1 # not yet implemented; Future usage: Spawner-Recruitment: 1=global; 2=by area
2 #  number of recruitment settlement assignments 
0 # unused option
#GPattern month  area  age (for each settlement assignment)
1 1 1 0
2 1 1 0

 

 

Richard Methot, modified 2 Years ago.

RE: Trouble with multiple growth morphs

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

Hi Thom,

One logical inconsistency I see is that you should use recr_dist_method = 3 because with two morphs N_GP*Nsettle*pop > 1.

I do get full output of all morphs in a test model.

TT
Thom D. Teears, modified 2 Years ago.

RE: Trouble with multiple growth morphs

Youngling Posts: 23 Join Date: 8/13/18 Recent Posts

Thanks Rick. That change gave me the full output. I appreciate it.

TT
Thom D. Teears, modified 2 Years ago.

RE: Trouble with multiple growth morphs

Youngling Posts: 23 Join Date: 8/13/18 Recent Posts

Hello all,

      Based on a previous thread, I am aware that the cohort growth deviation function has been used in several previous assessments but I was wondering if the multiple growth pattern (morphs) function has been used in an assessment? Chris Francis discusses this briefly in his growth paper but I just wanted to know if it hasn't been used yet if anyone has any thoughts on why?

 

Many thanks,

Thom

IT
Ian Taylor, modified 2 Years ago.

RE: Trouble with multiple growth morphs

Youngling Posts: 117 Join Date: 12/8/14 Recent Posts
Hi Thom,
Carey McGilliard <carey.mcgilliard@noaa.gov> used growth morphs in Stock Synthesis for a Rex Sole assessment in the Gulf of Alaska. 
The report is available here: https://apps-afsc.fisheries.noaa.gov/REFM/Docs/2017/GOArex.pdf and figure shoing differences in growth is below.

I'm not aware of other production assessments which used growth morphs for the base model.
-Ian 
image.png

On Thu, Nov 18, 2021 at 7:05 PM Thom D. Teears <VLab.Notifications@noaa.gov> wrote:

Hello all,

      Based on a previous thread, I am aware that the cohort growth deviation function has been used in several previous assessments but I was wondering if the multiple growth pattern (morphs) function has been used in an assessment? Chris Francis discusses this briefly in his growth paper but I just wanted to know if it hasn't been used yet if anyone has any thoughts on why?

 

Many thanks,

Thom


--
Thom D. Teears Stock Synthesis Virtual Lab Forum https://vlab.noaa.gov/web/stock-synthesis/public-forums/-/message_boards/view_message/19072132VLab.Notifications@noaa.gov

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Richard Methot, modified 2 Years ago.

Underutilized growth features in Stock Synthesis

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

Glad to hear of your interest Thom.  I've renamed this thread to align more closely with your question. I'll expand my response to address some related issues.

Time-varying growth parameters, including cohort specific growth have definitely been used. We have no way of recording how SS3 is used in practice, but I certainly am aware of such uses.

Multiple growth patterns have also been used; mostly in context of a multi-area model that needed different growth pattern for a northern vs southern morph.

I am not aware of anyone using the platoon feature in an assessment. Platoons subdivide each sex x morph into multiple platoons, not with different growth parameters, rather by simply breaking the overall length-at-age distribution at birth into a range of growth trajectories such that the larger platoons experience more cumulative effect of length-dependent fishing mortality and causing the average length-at-age of older fish to decline because of this differential mortality.

Another available feature is seasonal settlement. The total recruitment can be distributed into multiple settlement events, each with a unique date on which they enter the population and begin growing. Even though all of these settlement events may have the same growth parameters, early born fish have a head start so at a particular time of year, they are larger than late born siblings. So, this settlement phenomenon, which must happen in nature for any species with an extended spawning/recruitment season, can produce an effect just like that of platoons.

An interesting aspect of settlement spread is that the spread of length-at-age across the group will be greatest during the fast-growing young ages, then converge as they all grow towards the same Linfinity.  I believe this phenomenon is also observed in actual data.  Look for declining std.dev. of length-at-age as fish get older.

Finally, investigating phenomena like above takes detailed data.  I do not think a good investigation of growth can be done with annual data. I highly recommend seasonal time steps and paying close attention to exactly when during the year samples are taken.  SS3 needs to know exactly what time of year to calculate the age-length key for.  This is why survey and composition observations  are entered with a time stamp of decimal month, not season.  SS3 then assigns each month entry to the relevant season and calculates elapsed time from start of that season to the time of the observation.  There is one more step to refining the match; this is the subseas feature that you enter near top of the data file.  Normally people use just 2 subseasons and SS3 calculates the ALK at beginning of each subseason, which is beginning and middle of the season and which may be too crude to get accurate alignment between the model and the length modes in the data.  When you enter a larger value for subseasons, SS3 is prepared to calculate the ALK for each of those subseasons, but it only does so if there is an observation that is timed close to that subseason.

I suppose a final thought is that surveys, with a duration of 1-2 months, should provide more precise information on growth than fishery samples for which samples from a wide range of moths are accumulated into a simple "sample".  SS3 does not yet have a correction for this, but I am thinking about it.  Potentially you could use the "super-year" feature to cause SS3 to calculate the expected length composition for each month of a season and then combine those into an overall expected value to compare to the observation collected over the same range of months.  That would be quite a detailed model, would be big and run slowly due to all the computations, and probably much more suitable for a research project regarding fish growth, not an operational assessment.

Rick

 

 

MC
Massimiliano Cardinale, modified 2 Years ago.

RE: Trouble with multiple growth morphs

Youngling Posts: 40 Join Date: 2/23/17 Recent Posts

i have used growth morph in an 2-areas model but as empirical weigh at age instead than using growth. 

Max

TT
Thom D. Teears, modified 1 Year ago.

RE: Trouble with multiple growth morphs

Youngling Posts: 23 Join Date: 8/13/18 Recent Posts

Hello all,

     When estimating recruitment apportionment for a multiple growth morph model, how does the data inform these parameters in SS?

 

Cheers,
Thom

IT
Ian Taylor, modified 1 Year ago.

RE: Trouble with multiple growth morphs

Youngling Posts: 117 Join Date: 12/8/14 Recent Posts

Hi Thom,

Good question. I think it only makes sense to use multiple growth morphs if you have separate data on each morph.

In a case where you have two areas with separate growth, then the indices and comp data for each area could separately inform the recruitment allocation that fits the data best in the same way that they would inform R0 in a single-area/single-morph model. Time-varying recruitment allocation may be harder to estimate well but in theory could be estimated similarly to recdevs in a single area.

In a case where two growth morphs overlap in space, you would need some other measure of the ratio between them which could be entered using the morph composition data type (described here: https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#stock-morph-composition-data).

-Ian

 

TT
Thom D. Teears, modified 1 Year ago.

RE: Trouble with multiple growth morphs

Youngling Posts: 23 Join Date: 8/13/18 Recent Posts

Ian,

     Thanks for the information. I appreciate it. That seems like a valuable feature if the data exists to incorporate into the assessment.

 

Cheers,

Thom

Richard Methot, modified 1 Year ago.

RE: Trouble with multiple growth morphs

Youngling Posts: 219 Join Date: 11/24/14 Recent Posts
The morph composition feature was first developed for a 3 area model with one morph spawning in area 1 and another in area 3, then with seasonal mixing in area 2.  Otolith microchemistry was used to get proportions in area 2.  A shortcoming of SS3 is that it only allows a single global spawner biomass to be used in the spawner-recruitment relationship.

On Wed, Nov 9, 2022 at 2:29 PM Thom D. Teears <VLab.Notifications@noaa.gov> wrote:

Ian,

     Thanks for the information. I appreciate it. That seems like a valuable feature if the data exists to incorporate into the assessment.

 

Cheers,

Thom


--
Thom D. Teears Stock Synthesis Virtual Lab Forum https://vlab.noaa.gov/web/stock-synthesis/public-forums/-/message_boards/view_message/25908001VLab.Notifications@noaa.gov
TT
Thom D. Teears, modified 1 Year ago.

RE: Trouble with multiple growth morphs

Youngling Posts: 23 Join Date: 8/13/18 Recent Posts

Rick,

    So the biomass is aggregated across morphs and then recruitment gets calculated using the SRR and then is apportioned based on the apportionment parameters. Thanks for the clarification.

 

Cheers,
Thom