´create.fleets.data´ does not distinguish fixed biomass stock

[marchtaylor]

I have several stocks which are without age structure, (1 year class), but which will be fixed populations (i.e. no biomass dynamics). In the create.fleets.data conditioning function, I get an error at lines 464-466 (https://github.com/flr/FLBEIA/blob/master/R/Conditioning_create.fleets.data.R) because I am not providing a biomass growth value in the list stks.data:

if(length(stk.age.min:stk.age.max)==1){
     largs$stk.gB <- get(grep(stks.data[[ nmfl.met.stk]],pattern=paste(nmfl.met.stk,'_gB.flq',sep=''), value = TRUE)) 
}else{ largs <- NULL}

Should I just provide a dummy value (e.g. 1.0), or is there a change that should be made to the conditioning function?

[ssanchezAZTI]

Dear Marc, When you have an stock aggregated in biomass and fixed population, then you have to set the gB parameter to 0. We have already added this information in the new FLBEIA manual: fixedPopulation: Fixed population function In this function all the parameters are given as input, because there is not any population dynamics simulated. For the stocks for which we select its dynamics as fixed population, natural mortality (i.e. biols[[stock.name]]@m) has to be set equal to 0 and additionally, if the population is aggregated in biomass, biomass growth (i.e. BDs[[stock.name]]@gb) has also to be set equal to 0. You can find the last version of this manual in GitHub (FLR/FLBEIA/inst/doc/). Regards, Sonia De: Marc Taylor [mailto:[email protected]] Enviado el: miércoles, 31 de mayo de 2017 17:38 Para: flr/FLBEIA <[email protected]> CC: Subscribed <[email protected]> Asunto: [flr/FLBEIA] ´create.fleets.data´ does not distinguish fixed biomass stock (#17) I have several stocks which are without age structure, (1 year class), but which will be fixed populations (i.e. no biomass dynamics). In the create.fleets.data conditioning function, I get an error at lines 464-466 (https://github.com/flr/FLBEIA/blob/master/R/Conditioning_create.fleets.data.R) because I am not providing a biomass growth value in the list stks.data: if(length(stk.age.min:stk.age.max)==1){ largs$stk.gB <- get(grep(stks.data[[ nmfl.met.stk]],pattern=paste(nmfl.met.stk,'_gB.flq',sep=''), value = TRUE)) }else{ largs <- NULL} Should I just provide a dummy value (e.g. 1.0), or is there a change that should be made to the conditioning function? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#17>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AEz9kvzAjd-GWzLgLkGEVUjoRpA44SzRks5r_YlsgaJpZM4Nr0Jx>.

[marchtaylor]

Hi Sonia,
Great, thanks for this information and the notice of the new manual.
Cheers, Marc