# aspminit.r 
 #
 # Set up initial values for age-structured dynamic stock-production models
 #
 # Set up data
 # 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)

 # Number of ages and years
 g<-4                           # Number of true age groups
 totyrs<-19                     # Number of years

 # Initialize values of all parameters 
 # Some will later be estimated - others simply fixed at assumed values
 Ninit<-c(100,50,25,10,5)       # Initial values for initial stock size
 Rvec<-rep(100,totyrs)          # Initial values of annual recruitment
 selpat<-c(0.1,0.333,0.667,1,1) # Selection pattern-Might estimate
 w<-c(100,250,325,375,400)      # Weight at age
 M<-rep(0.3,(g+1))              # Natural mortality
 q<-1                           # Initial value of catchability
 Fvec<-rep(0.5,totyrs)          # Annual fishing mortality

# Beverton-Holt parameters:
alpha<-0.006
K<-5000
 # Put the initial values of parameters to be estimated into a vector

parameters<-log(c(Fvec,Rvec,q,alpha,K))     # Initial values of all parameters