aspmrun.r

File contents

#filename="aspmrun.r"
 source("aspminit.r")
 source("ssefcn.r")
 source("aspm.r")
 fm<-nlm(ssefcn,parameters,iterlim=500)

 parameters<-fm$estimate
 Fvec <-exp(parameters[1:totyrs])
 Rvec <-exp(parameters[(totyrs+1):(2*totyrs)])
 q    <-exp(parameters[2*totyrs+1])
 alpha<-exp(parameters[2*totyrs+2])
 K    <-exp(parameters[2*totyrs+3])

ssefcn(fm$estimate,printit=T)

fmopt<-aspm(Fvec,Rvec)
Yhat<-fmopt$Yhat
Bhat<-fmopt$Bhat
Ihat<-q*Bhat

time<-1:totyrs
par(mfrow=c(2,3))
plot(time,Y)
lines(time,Yhat)
plot(time,I)
lines(time,Ihat)
barplot(Rvec,names.arg=time,xlab="Year")
title("Annual recruitment")
plot(time,Fvec,type='b',ylim=c(0,1))
plot(time,Bhat,type='b')
Brange<-(0:160)*100
Rrange<-alpha*Brange/(1+Brange/K)
plot(Bhat,Rvec,ylim=c(0,max(Rvec)),xlim=c(0,max(Bhat)))  
lines(Brange,Rrange)