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#' Summary of distance detection function model object
#'
#' Provides a brief summary of data and fitted detection probability model
#' parameters, model selection criterion, and optionally abundance in the
#' covered (sampled) region and its standard error.
#'
#' The argument \code{N} is used to suppress computation of
#' abundance and average detection probability in calls to summarize the
#' \code{ds} and either \code{io.fi} or \code{trial.fi} for summaries of
#' \code{io} and \code{trial} objects respectively which are composed of a
#' \code{ds} model object and a mark-recapture model object. The corresponding
#' print function is called to print the summary results.
#'
#' @export
#' @param object a \code{ddf} model object
#' @param se if TRUE, computes standard errors
#' @param N if TRUE, computes abundance in covered (sampled) region
#' @param fittedmodel full fitted model when called from \code{trial} or
#' \code{io}
#' @param \dots unspecified and unused arguments for S3 consistency
#' @return list of extracted and summarized objects
#' @note This function is called by the generic function \code{summary} for any
#' \code{ddf} model object. Each function can be called directly by the
#' user, but it is typically safest to use the generic function
#' \code{summary} which calls the appropriate function based on the type of
#' \code{ddf} model.
#' @author Jeff Laake
#' @keywords utility
summary.rem.fi <- function(object,se=TRUE,N=TRUE,fittedmodel=NULL,...){
model <- object
avgp <- function(model,pdot,...) {return(pdot)}
newdat <- model$data
newdat <- newdat[newdat$distance <= model$meta.data$width &
newdat$distance >= model$meta.data$left, ]
n <- length(newdat$distance)/2
timesdetected <- newdat$detected[newdat$observer == 1] +
newdat$detected[newdat$observer == 2]
n1 <- length(newdat$distance[newdat$observer == 1 & newdat$detected == 1])
n2 <- length(newdat$distance[newdat$observer == 2 & newdat$detected == 1])
n3 <- sum(timesdetected == 2)
newdat$distance <- rep(0,length(newdat$distance))
pred.at0 <- predict(model,newdat)$fitted
if(is.null(fittedmodel)){
Nhat <- model$Nhat
pdot <- model$fitted
}else{
pdot <- fittedmodel$fitted
Nhat <- fittedmodel$Nhat
}
# Output conditional detection function values
average.p0.1 <- sum(avgp(model,pred.at0)/pdot)
ans <- list(n = n,
n1 = n1,
n2 = n2,
n3 = n3,
average.p0.1 = average.p0.1/Nhat,
cond.det.coef = coef(model),
aic = model$criterion)
# Output estimates relevant to abundance estimation. Note: that
# these estimates are for the covered region only and are not expanded
# to some larger region that was sampled.
if(N){
ans$average.p <- n1/Nhat
ans$Nhat <- Nhat
}
# Compute se for N and p's; The logical N is set when summary.trial.fi
# is being called for method="trial.fi". When method="trial" the call to
# summary.trial.fi from summary.trial sets N=FALSE. So this is used to
# determine whether the pdots are to be computed from the trial.fi model or
# the trial model results. Likewise when method="trial", fittedmodel
# contains the trial model object and is not NULL.
if(se){
if(N | is.null(fittedmodel)){
se.obj <- calc.se.Np(model, avgp, n, ans$average.p)
ans$average.p.se <- se.obj$average.p.se
ans$Nhat.se <- se.obj$Nhat.se
cvN <- se.obj$Nhat.se/Nhat
Nhatvar.list <- se.obj$Nhatvar.list
vcov <- se.obj$vcov
}
# If there is a nested model, compute the Nhat from the fitted model
# and use its variance and vector of partials.
if(!is.null(fittedmodel)){
Nhat <- fittedmodel$Nhat
vcov <- solvecov(fittedmodel$hessian)$inv
Nhatvar.list <- DeltaMethod(fittedmodel$par,NCovered,vcov,.001,
model=fittedmodel,group=TRUE)
Nhatvar <- Nhatvar.list$variance + sum((1-fittedmodel$fitted)/
fittedmodel$fitted^2)
cvN <- sqrt(Nhatvar)/Nhat
}
# Compute se of p(0)
if(is.null(fittedmodel)){
var.pbar.list <- prob.se(model,avgp,vcov,fittedmodel=NULL)
}else{
var.pbar.list <- prob.se(model,avgp,vcov,fittedmodel=fittedmodel)
}
covar <- t(Nhatvar.list$partial) %*% vcov %*% var.pbar.list$partial +
var.pbar.list$covar
var.pbar <- ans$average.p0.1^2*(cvN^2 + var.pbar.list$var/average.p0.1^2
-2*covar/(average.p0.1*Nhat))
ans$average.p0.1.se <- sqrt(var.pbar)
}
ans$mono <- model$ds$aux$mono
ans$mono.strict <- model$ds$aux$mono.strict
class(ans) <- "summary.rem.fi"
return(ans)
}
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