Adjusting recruitment for yearly time step projections #5
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I believe it would be useful to cross-check this idea.
We want to be able to use the estimated parameters of the Beverton-Holt
stock-recruitment relationship.
The SR curve produces numbers of age-0 recruits on July 1st of year Y based
on spawning biomass
in year Y and the recruitment deviation.
R(Y,0) = f( SB(Y), Recdev )
The value of predicted numbers at age-1 in year Y+1 (N) would be the same
as the predicted recruitment (R)
at age-0 in year Y if adjusted by one-half of the total annual mortality
rate (Z) experienced at age-0 as
N(Y+1, 1) = R(Y, 0) * exp(-Z0/2)
If the fishing mortality rate on age-(1/4) and age-(2/4) fish is zero, then
N(Y+1, 1) = R(Y, 0) * exp(-M0/2)
should hold, given age-0 natural mortality rate M0. The question is how
much mortality occurs due to
fishery removals at age-0 (Q1 and Q2)? If F0 is very small then there will
not be much difference between
recruitment at age-0 adjusted for M0 on Jan 1st year Y+1 and the numbers at
age-1 on Jan-1st of
year Y+1, N(Y+1,1)
…On Thu, Nov 30, 2023 at 9:49 AM Michelle Sculley ***@***.***> wrote:
Just thinking about how we need to adjust the recruitment of age 0 fish to
account for the fact that they are born in July of the previous year, could
we just use the number of age-1 fish in Jan of the following year? In SS3
all fish turn 1 at the start of the next calendar year which would make all
the age one fish in Jan actually 6 months old. @fecor21
<https://github.com/fecor21> can correct me if I'm wrong, but in that
case, we should be able to use those age-1 fish as the recruitment from the
previous year and we won't have to correct for the half-year of mortality.
To clarify, I'm suggesting that we could use the numbers at age 1 in Jan-1
1990 for the recruitment that occurred in July 1989. What do you think
@JonBrodziak <https://github.com/JonBrodziak>? Those values can be easily
pulled using the SS_to_agepro function we walked through yesterday.
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Jon Brodziak, Ph.D.
NOAA Inouye Regional Center
Pacific Islands Fisheries Science Center
1845 Wasp Boulevard, Building 176, NMFS/PIFSC/FRMD Mail Room 2247
Honolulu, Hawaii 96818 USA
PIFSC Stock Asessment Program <https://pifscstockassessments.github.io/>
Phone: 808-725-5617 Email: ***@***.***
“Wherever my travels may lead, paradise is where I am.” ~ Voltaire
The views expressed in this message are my own
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In SS3 there is no Fishing mortality in Q1 and Q2 on age zero fish as there are no age-0 fish in the population, the model estimates an F for those quarters but they are all less than 0.8E-6, so essentially zero. All the age-0 fish born in Q3 then become the age 1 fish in Q1 of the following year, reduced by M/2 and F on age-0 fish in Q3 and Q4. The F on age-0 fish estimated from SS is also relatively small, between 0.02 and 0.8E-4 for all years/quarters in the model. I believe if you were to adjust the age-0 fish by just M/2 and compare it to the output of age-1 fish in the year following the recruitment, they should be almost identical, likely within rounding errors. |
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I agree.
And the question below was intended to refer to Q1 and Q2 of an age-0
fish's lifetime.
*"The question is how much mortality occurs due to fishery removals at
age-0 (Q1 and Q2)?"*
The intended question was for the age-(1/4 year) in quarter 3 when they are
one quarter
of a year old, and for age-(2/4 year) fish in quarter 4 when they are two
quarters
of a year old. I denoted the ages of age-(1/4) fish by Q1 and age-(2/4)
fish by Q2.
If the fishing mortality rate on age-(1/4) and age-(2/4) fish is nearly zero
in quarters 3 and 4, then effectively one can say that the number of age-1
fish in year Y+1 is
N(Y+1, 1) = R(Y, 0) * exp(-M0/2)
which is what you point out in your reply.
Apologies for the confusing notation.
It would be informative to make the comparison as this
would support adjusting the BH stock-recruitment model parameters
to represent age-1 recruits.
Thanks,
Jon
…On Thu, Nov 30, 2023 at 2:01 PM Michelle Sculley ***@***.***> wrote:
In SS3 there is no Fishing mortality in Q1 and Q2 on age zero fish as
there are no age-0 fish in the population, the model estimates an F for
those quarters but they are all less than 0.8E-6, so essentially zero. All
the age-0 fish born in Q3 then become the age 1 fish in Q1 of the following
year, reduced by M/2 and F on age-0 fish in Q3 and Q4. The F on age-0 fish
estimated from SS is also relatively small, between 0.02 and 0.8E-4 for all
years/quarters in the model. I believe if you were to adjust the age-0 fish
by just M/2 and compare it to the output of age-1 fish in the year
following the recruitment, they should be almost identical, likely within
rounding errors.
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You are receiving this because you were mentioned.Message ID:
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Jon Brodziak, Ph.D.
NOAA Inouye Regional Center
Pacific Islands Fisheries Science Center
1845 Wasp Boulevard, Building 176, NMFS/PIFSC/FRMD Mail Room 2247
Honolulu, Hawaii 96818 USA
PIFSC Stock Asessment Program <https://pifscstockassessments.github.io/>
Phone: 808-725-5617 Email: ***@***.***
“Wherever my travels may lead, paradise is where I am.” ~ Voltaire
The views expressed in this message are my own
and do not necessarily reflect any position of NOAA.
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The age-0.5 adjustment has been added to the Build_Input_File code for recruitment models 2, 3, 5, and 14. |
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Just thinking about how we need to adjust the recruitment of age 0 fish to account for the fact that they are born in July of the previous year, could we just use the number of age-1 fish in Jan of the following year? In SS3 all fish turn 1 at the start of the next calendar year which would make all the age one fish in Jan actually 6 months old. @fecor21 can correct me if I'm wrong, but in that case, we should be able to use those age-1 fish as the recruitment from the previous year and we won't have to correct for the half-year of mortality.
To clarify, I'm suggesting that we could use the numbers at age 1 in Jan-1 1990 for the recruitment that occurred in July 1989. What do you think @JonBrodziak? Those values can be easily pulled using the SS_to_agepro function we walked through yesterday.
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