# Import and format growth parameters
# then define growth function
# growth parameters
Gpars=list(intcpt=rep(NA,n_spp),intcpt.yr=matrix(0,Nyrs,n_spp), intcpt.gr=matrix(0,6,n_spp),
slope=rep(NA,n_spp),slope.yr=matrix(0,Nyrs,n_spp),
nb=matrix(0,n_spp,n_spp),alpha=matrix(NA,n_spp,n_spp),
sigma2.a=rep(NA,n_spp),sigma2.b=rep(NA,n_spp))
for(i in 1:n_spp){
infile <- paste("../extdata/Growth_params_",spp_list[i],".csv",sep="")
Gdata=read.csv(infile)
Gpars$intcpt[i]=Gdata$Intercept[1]
tmp=which(names(Gdata)=="Group")
if(length(tmp)>0) Gpars$intcpt.gr[,i]=Gdata$Group[!is.na(Gdata$Group)]
Gpars$intcpt.yr[,i]=Gdata$Intercept.yr
Gpars$slope[i]=Gdata$logarea.t0[1]
# random effects on slope
tmp=which(names(Gdata)=="logarea.t0.yr")
if(length(tmp)>0) Gpars$slope.yr[,i]=Gdata[,tmp]
# get competition coefficients
tmp=paste("crowd",1:length(spp_list),sep="")
tmp=which(is.element(names(Gdata),tmp))
if(length(tmp)>0) Gpars$nb[i,]=as.numeric(Gdata[1,tmp])
Gpars$alpha[i,]=Gdata$alpha[1:length(spp_list)]
Gpars$sigma2.a[i]=Gdata$sigma.a[1]
Gpars$sigma2.b[i]=Gdata$sigma.b[1]
} # next i
rm(Gdata)
# growth function
G=function(v,u,W,Gpars,doYear,doSpp){
mu=Gpars$intcpt[doSpp]+Gpars$intcpt.yr[doYear,doSpp]+(Gpars$slope[doSpp]+Gpars$slope.yr[doYear,doSpp])*u+
W%*%(Gpars$nb[doSpp,])
sigma2=Gpars$sigma2.a[doSpp]*exp(Gpars$sigma2.b[doSpp]*mu)
out=dnorm(v,mu,sqrt(sigma2))
out
}
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