aspminit.r
aspminit.r
— 2.0 KB
File contents
# aspminit.r # # Set up initial values for age-structured dynamic stock-production models # # Set up data-nephrops specific yrs<-1980:1998 # actual data years ages<-3:6 # actual ages # Annual catch data Y<-c(2398,2520,2603,2672,2459,2385,2564, 2712,2240,1866,1692,2157,2230,2381, 2238,1027,1633,1228,1411) # Annual abundance index I<-c(45.5,51.8,51.5,47.8,45.6,56.4,61.3, 52.6,39.9,36.0,40.0,42.1,51.3, 51.4,38.0,27.0,35.2,31.3,38.9) wts<-c(8,14,23,34,46,60,75,89,104,119,131,145,159,175) # Wt ages 3-16, MRI 2011 report # Number of ages and years g<-length(ages) # Number of true age groups totyrs<-length(Y) # Number of years # Initialize values of all parameters # Some will later be estimated - others simply fixed at assumed values M<-rep(0.3,(g+1)) # Natural mortality aveRecr<-100 selpat<-c(0.1,0.333,0.667,1,1) # Selection pattern-might estimate-probably not q<-1 # Initial value of catchability Fvec<-rep(0.5,totyrs) # Annual fishing mortality # now set up an appropriate mean weight at age for age grps 1:g and plus grp Zplus<-cumsum(g:(g+9))*M[g+1] # cumZ values in the plus group Nplus<-aveRecr*exp(-Zplus) # age structure in plus group wtplus<-sum(Nplus*wts[(g+1):(g+10)])/sum(Nplus) # mean wt in plus grp w<-c(wts[1:g],wtplus) # Weight at age 3-6 from MRI 2011 report # Initial stock size: Assume equilibrium Ninit<-aveRecr*exp(-cumsum(c(0,M))[1:g]) # only true ages Ninit<-c(Ninit,aveRecr*exp(-g*M[g+1])/(1-exp(-M[g+1])))# Append the plus group # Alternatively, sum up instead of using a formula: # # Ninit<-aveRecr*exp(-cumsum(c(0,rep(0.3,100)))) # Ninit<-c(Ninit[1:g],sum(Ninit[(g+1):100])) Rvec<-rep(aveRecr,totyrs) # Initial values of annual recruitment # Put the initial values of parameters to be estimated into a vector parameters<-c(log(Fvec),log(Rvec),log(q)) # Initial values of all parameters