R/NCovered.ds.R

In mrds: Mark-Recapture Distance Sampling

# Compute abundance in covered region for ds model object
#
#  par parameter values (used when computing derivatives wrt parameter
#  uncertainty)
#  model ddf model object
#  group if TRUE computes group abundance and if FALSE individual abundance
#
# return abundance estimate
NCovered.ds <- function(par=NULL, model, group=TRUE, ...){
  if(!is.null(par) | is.null(model$fitted)){
    model$par <- par
    fitted <- predict(model, esw=FALSE, compute=TRUE)$fitted
  }else{
    fitted <- model$fitted
  }

  if(!group){
    size <- model$data$size[model$data$object %in%
                            as.numeric(names(model$fitted))]
    Nhat <- sum(compute.Nht(fitted, FALSE, size))
  }else{
    Nhat <- sum(compute.Nht(fitted, TRUE, size=NULL))
  }
  return(Nhat)
}