Dynamic (multi-season) occupancy observed by several detection sources
(spOccupancy tIntPGOcc): the product of a dynamic
occupancy HMM (season-1 occupancy psi1, colonization gamma, extinction
eps) and integrated occupancy (a per-season emission that pools multiple
detection sources). Pooling sources across seasons is how colonization /
extinction estimates come out of individually-sparse opportunistic data. The
latent occupancy sequence integrates out by the two-state HMM forward
recursion; the exact marginal is maximised with an observed-information vcov.
Value
A tobs_family object for tobs().
Details
y is a length-S list of [sites x visits x seasons] detection arrays
(0/1/NA). The state formula models logit psi1; colonization = ~ ... and
extinction = ~ ... the site-level transitions (required, as in dyn_occu());
detection the shared per-source detection design (each source carries its own
coefficients). v1: every source covers all sites and the same season grid,
constant transitions, site-level detection.
Examples
# \donttest{
sim <- simulate_dyn_int_occu(N = 200, T_seasons = 4, S = 2, seed = 1)
fit <- tobs(~ 1, data = sim$data, family = dyn_int_occu(),
detection = ~ 1, colonization = ~ 1, extinction = ~ 1,
y = sim$y, sources = sim$sources, control = list(verbose = FALSE))
coef(fit)
# }