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#' 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)
}
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