calcRate {GenEst}

Estimate the number of fatalities in each search interval throughout the monitoring period.

Description

A carcass that is observed in a given search may have arrived at any time prior to that search, so carcass discovery time is often not a reliable estimate of carcass arrival time. For each observed carcass, calcRate takes into account the estimated probability of arrival in each possible arrival interval, adjusts by detection probability, and sums to estimate the estimated number of carcass arrivals in every search interval.

Usage

calcRate(M, Aj, days = NULL, searches_carcass = NULL, data_SS = NULL)

Arguments

M

Numeric array (ncarc x nsim) of estimated number of fatalities by observed carcass and simulation rep

Aj

Integer array (ncarc x nsim) of simulated arrival intervals for each observed carcass. Arrival intervals are given as integers j, indicating that the given carcass (indexed by row) arrived in the jth search interval in the given simulation rep (indexed by column). Arrival interval indices (j) are relative to indexed carcasses' search schedules.

days

Vector of all dates that at least one unit was searched. Format is the number of days since the first search. For example, days = c(0, 7, 14, 28, 35) for a simple 7-day search schedule in which searches were conducted every once per week on the same day for 5 weeks. Not all units need be searched on every search date.

searches_carcass

An ncarc x length(days) array of 0s and 1s to indicate searches in which the indexed carcass could have been found. For example, row i = c(1, 0, 1, 0, 1) indicates that the search schedule for the location (unit) where carcass i was found would be days[c(1, 3, 5)].

data_SS

prepSS object that contains formatted data for calculating splits. Optional argument. Alternatively, user may provide days and searches_carcass.

Value

Numeric array (nsim x nsearch) of estimated fatalities in each search interval. NOTE: The search at time t = 0 does not correspond to an interval, and all carcasses found at that time are assumed to have arrived prior to the monitoring period and are not included in mortality estimates so nsearch = length(days) - 1.