R/covered.region.dht.R

In mrds: Mark-Recapture Distance Sampling

#' Covered region estimate of abundance from Horvitz-Thompson-like estimator
#'
#' Computes H-T abundance within covered region by sample.
#'
#'
#' @param obs observations table
#' @param samples samples table
#' @param group if TRUE compute abundance of group otherwise abundance of
#'   individuals
#' @return Nhat.by.sample - dataframe of abundance by sample
#' @note Internal function called by \code{\link{dht}} and related functions
#' @author Jeff Laake
#' @keywords utility
covered.region.dht <- function(obs, samples, group){

  # Compute abundance in covered region depending on value of
  # group = TRUE (do group abundance); F(do individual abundance)
  # if there are observations of this species
  if(nrow(obs) > 0){
    Nhats <- compute.Nht(obs$pdot, group, obs$size)

    # Sum abundances by sample within region
    Nhats <- by(Nhats, obs$Label, sum)

    # Sum observations by sample within region
    if(group){
      sum.obs <- by(obs$object, obs$Label, length)
    }else{
      sum.obs <- by(obs$size, obs$Label, sum)
    }

    # Merge with samples
    num.obs <- data.frame(Label = names(sum.obs), n = as.vector(sum.obs))
    Nhats <- data.frame(Label = names(Nhats), Nhat = as.vector(Nhats))
    Nhat.by.sample <- merge(samples, Nhats,by.x = "Label", by.y = "Label",
                            all.x = TRUE)
    Nhat.by.sample <- merge(Nhat.by.sample, num.obs, by.x = "Label",
                            by.y = "Label", all.x = TRUE)
    Nhat.by.sample$Nhat[is.na(Nhat.by.sample$Nhat)] <- 0
    Nhat.by.sample$n[is.na(Nhat.by.sample$n)] <- 0

  # Create Nhat.by.sample in the case where there were no sightings
  }else{
    Nhat.by.sample <- cbind(samples,
                            Nhat = rep(0,nrow(samples)),
                            n = rep(0,nrow(samples)))
  }
  return(Nhat.by.sample)
}