File contents
# 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