R/lampop.r

In openfields/Ambcitsci: Package for analyzing the effect of road crossing brigades on amphibian populations

lampop <- function(dat,qe){
  # calculate lambda from time series: divide 2nd through last element by 1st through 2nd to last element
  # sum across time steps to get total population
  dat <- apply(dat,1,sum)
  # set quasi-ext threshold
  dat[which(dat<qe)] <- 0
  which(dat==0) -> extind
  
  # print(extind)
  
  tmp1 <- dat[1:length(dat)-1]
  tmp2 <- dat[2:length(dat)]
  tmp2/tmp1 -> lam
  if(length(which(dat==0))>=1) {
    lam <- lam[1:(extind[1]-1)]
  }
  
  # print(lam)
  return(list(lam=lam, vlam=var(lam)))
}