R/MP_1_Observation.R

In ElsevierSoftwareX/SOFTX-D-15-00067: Bio-Economic Impact Assessment of Management strategies using FLR

#-------------------------------------------------------------------------------
#                           Observation models
#   - observation.mp 
#
# Dorleta GarcYYYa
# Created: 21/12/2010 14:34:47
# Changed: 27/04/2011 09:23:01
# Changes: 2012-06-15 12:51:01  Sonia Sánchez - for allowing assessment in different seasons and multiannual advice
#-------------------------------------------------------------------------------

observation.mp <- function(biols, fleets, covars, indices, advice, obs.ctrl, year, season, stknm){

    indices.upd    <- indices #vector('list', length(stnms))
    
# 1 stock per biol
# 1 FLIndices per stock
# 1 FLFleets from fleets the number of fleets/metiers do not need to be equal, 
# for the time being not fleets observation implemented.
     
    st <- stknm
    
    # Generete the FLStock
    stock <- eval(call(obs.ctrl[[st]][['stkObs']][['stkObs.model']], biol = biols[[st]], fleets = fleets,  advice = advice,
                    covars = covars, obs.ctrl = obs.ctrl[[st]][['stkObs']], year = year, season=season, stknm = st))
    
    # Update the FLIndices [year-1]
    #indices observation (stock by stock)
    nind     <- length(indices[[st]])
    indSt    <- indices[[st]]
    indStnms <- names(indSt)
   # indices.upd[[st]] <- FLIndices()
    
    # Year  => Character, because the year dimension in indices does not coincide with year dimension in biol. 
  #  yrnm.1 <- dimnames(biols[[1]]@n)[[2]][year-1] 
                                                                                           
    for(id in indStnms){
   #     indX <- trim(indices[[st]][[id]], year = dimnames(indices[[st]][[id]]@index)[[2]][1]:yrnm.1)
        obs.model <- obs.ctrl[[st]][['indObs']][[id]][['indObs.model']]
        obs.model <- ifelse(obs.model == 'NoObservation','NoObsIndex', obs.model)
        indices.upd[[st]][[id]] <- eval(call(obs.model, biol = biols[[st]], index = indices[[st]][[id]],
                                        fleets = fleets, covars = covars, obs.ctrl = obs.ctrl[[st]][['indObs']][[id]], year = year))
        
    }
    
    names(indices.upd[[st]]) <- indStnms 
        
    # TO DO: 
    # fleet observaction.
    fleets.obs <- NULL    
    
    return(list(stock = stock, fleets.obs = fleets.obs, indices = indices.upd))
}  


NoObsStock <- function(...) return(NULL)

NoObsIndex <- function(...) return(FLIndex())