calc_fishing_mortality - Githubissues

quantifish commented 9 years ago

Needs a good look over. Here is the header and and issue at the bottom

 * @brief Calculate fishing mortality rates for each fleet.
 * @details For each fleet estimate scaler log_fbar and deviates (f_devs).
     *
     * dmr is the discard mortality rate
 * 
 * In the event that there is effort data and catch data, then it's possible
 * to estimate a catchability coefficient and predict the catch for the
 * period of missing catch/discard data.  Best option for this would be
 * to use F = q*E, where q = F/E.  Then in the objective function, minimize
 * the variance in the estimates of q, and use the mean q to predict catch.
 * Or minimize the first difference and assume a random walk in q.
 * 
 * Note that this function calculates the fishing mortality rate including
 * deaths due to discards.  Where xi is the discard mortality rate.
 * 
 * Note also that Jie estimates F for retained fishery, f for male discards and
 * f for female discards.  Not recommended to have separate F's for retained and 
 * discard fisheries, but might be ok to have sex-specific F's.  
 * 
 * TODO 
 * -[ ] fix discard mortality rate.

wStockhausen commented 9 years ago

Darcy,

Discussing fishing mortality rates in Gmacs is somewhat problematic because we keep mixing CAPTURE rates and mortality rates. The Gmacs fishing mortality equations are based on fishery CAPTURE rates, size-specific capture selectivity functions, size-specific retention functions, and discard mortality rates. There are no "discard mortality" F's that are being estimated "separately"--these are calculated based on the estimated capture rates, etc. If Jie is estimating discard mortality rates (for males) directly as parameters somehow, then this represents a substantial difference between his model and Gmacs--and not one (in my opinion) that Gmacs should try to accomodate.

Buck

Dr. William T. Stockhausen *
Resource Ecology and Fisheries Management *
Alaska Fisheries Science Center *
National Marine Fisheries Service *
National Oceanic and Atmospheric Administration *
7600 Sand Point Way N.E. *
Seattle, Washington 98115-6349 *
email: William.Stockhausen@noaa.gov *
voice: 206-526-4241 fax: 206-526-6723 *
web : http://www.afsc.noaa.gov *

All models are wrong, some are useful.--G.E.P. Box Beware of geeks bearing equations. --W. Buffett

Disclaimer: The opinions expressed above are personal and do not necessarily reflect official NOAA policy.

On Tue, Jun 30, 2015 at 1:22 PM, Darcy Webber notifications@github.com wrote:

Needs a good look over. Here is the header and and issue at the bottom

@brief Calculate fishing mortality rates for each fleet.

@details For each fleet estimate scaler log_fbar and deviates (f_devs). *

dmr is the discard mortality rate

In the event that there is effort data and catch data, then it's possible

to estimate a catchability coefficient and predict the catch for the

period of missing catch/discard data. Best option for this would be

to use F = q*E, where q = F/E. Then in the objective function, minimize

the variance in the estimates of q, and use the mean q to predict catch.

Or minimize the first difference and assume a random walk in q. *

Note that this function calculates the fishing mortality rate including

deaths due to discards. Where xi is the discard mortality rate. *

Note also that Jie estimates F for retained fishery, f for male discards and

f for female discards. Not recommended to have separate F's for retained and

discard fisheries, but might be ok to have sex-specific F's. *

TODO

-[ ] fix discard mortality rate.

Reply to this email directly or view it on GitHub https://github.com/seacode/gmacs/issues/131.

smartell commented 9 years ago

Regarding the TODO. I neglected to X that one out. I had originally had a fixed dmr in the code and wanted to fix it such that it was a user input.

seacode / gmacs

calc_fishing_mortality #131