R/calcREF.R

In szuwalski/GeMS: Generic Management Strategy Evaluation

#' Calculates... STUFF for use in Cody's brain. Probably related to \code{\link{StockRecCheck}}
#' 
#' @param SRouts List of something or other.
#'
#' @return STUFF
#' 
#' @examples
#' \dontrun{
#' calcREF(DERP)
#' }

calcREF<-function(SRouts)
{
if(SRouts[[1]][1]!="Average")
{
 testExp	<-seq(0.001,1,0.01)
 recYield	<-rep(0,length(testExp))
 projYrs	<-100
 tempN	<-matrix(nrow=projYrs,ncol=maxAge)
 tempN[1,]	<-virInit
 tempYield	<-rep(0,length(testExp))
for(f in seq_along(testF))
{
 tempExp<-testExp[f]
 for(j in 2:projYrs)
 {
  for (i in 2:(maxAge-1))
   tempN[j,i]		<-tempN[j-1,i-1]*(1-tempExp*vuln[i-1])*survival
   tempN[j,maxAge]	<-(tempN[j-1,(maxAge-1)])*(1-tempExp*vuln[maxAge])*survival + tempN[j-1,maxAge]*(1-tempExp*vuln[maxAge])*survival
   spbioIn			<-sum(tempN[j-1,]*mature*weight)
   if(SRouts[[1]][1]=="BevH")
    tempN[j,1]		<-calcBHrec(SRouts,spbioIn) 
   if(SRouts[[1]][1]=="Rick")
    tempN[j,1]		<-calcRICKrec(SRouts,spbioIn) 
  }
   tempYield[f]		<-sum(tempN[j,]*tempExp*vuln*weight)
 }
}
calcRICKrec(SRouts,virBio)
if(SRouts[[1]][1]=="Average")
{
#STUFF
}

}