#' Estimate abundance from STE
#'
#' A function to estimate abundance from an STE encounter history
#'
#' @param eh STE encounter history. A dataframe formulated by ste_build_eh
#' @param study_area the size of the study area (same units as camera viewshed)
#' @return A data.frame with the estimated abundance with its standard error and confidence intervals.
#' @export
#'
#' @examples
#' df <- data.frame(
#' cam = c(1,1,2,2,2),
#' datetime = as.POSIXct(c("2016-01-02 12:00:00",
#' "2016-01-03 13:12:00",
#' "2016-01-02 12:00:00",
#' "2016-01-02 14:00:00",
#' "2016-01-03 16:53:42"),
#' tz = "GMT"),
#' count = c(1, 0, 2, 1, 2)
#' )
#' deploy <- data.frame(
#' cam = c(1, 2, 2, 2),
#' start = as.POSIXct(c("2015-12-01 15:00:00",
#' "2015-12-08 00:00:00",
#' "2016-01-01 00:00:00",
#' "2016-01-02 00:00:00"),
#' tz = "GMT"),
#' end = as.POSIXct(c("2016-01-05 00:00:00",
#' "2015-12-19 03:30:00",
#' "2016-01-01 05:00:00",
#' "2016-01-05 00:00:00"),
#' tz = "GMT"),
#' area = c(300, 200, 200, 450)
#' )
#'study_dates <- as.POSIXct(c("2016-01-01 00:00:00", "2016-01-04 23:59:59"), tz = "GMT")
#'occ <- build_occ(samp_freq = 3600,
#' samp_length = 10,
#' study_start = study_dates[1],
#' study_end = study_dates[2])
#' dat_ste <- ste_build_eh(df, deploy, occ)
#' ste_estN_fn(dat_ste, study_area = 1e6)
ste_estN_fn <- function(eh, study_area){
dat <- list(toevent = matrix(eh$STE, nrow = 1),
censor = eh$censor)
opt <- suppressWarnings(
stats::optim(log(1/mean(dat$toevent, na.rm = T)),
exp_logl_fn,
x = dat,
control = list(fnscale = -1),
hessian = T)
)
# Estimate of lambda
estlam <- exp(opt$par)
# estlam is average density per m2
estN <- estlam * study_area
# Delta method for variance
varB <- -1 * MASS::ginv(opt$hessian)
form <- sprintf("~ %f * exp(x1)", study_area)
SE_N <- msm::deltamethod(g = stats::as.formula(form),
mean = opt$par,
cov = varB,
ses = T)
CI <- logCI(estN, SE_N)
out <- data.frame(
N = estN,
SE = SE_N
) %>%
bind_cols(CI)
return(out)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.