Multi-species co-occurrence occupancy family

Joint occupancy of S species where the occupancy state z in {0,1}^S follows a log-linear model with first-order (per species) and second-order (per species pair) natural parameters (Rota et al. 2016; unmarked occuMulti). The second-order parameters are the species interactions (positive = co-occur more than independent; negative = avoid). The state formula is the shared occupancy covariate design (each natural parameter carries its own coefficients); detection the shared site-level per-species detection design. The latent state integrates out by enumerating the 2^S states, so the exact marginal is maximised with an observed-information vcov.

Usage

occu_multi()

Value

A tobs_family object for tobs().

Details

y is a length-S list of N x J 0/1/NA detection matrices (or a 3D [sites x visits x species] array); species names the arms.

Examples

# \donttest{
sim <- simulate_occu_multi(S = 2, N = 300, seed = 1)
fit <- tobs(~ scov1, data = sim$data, family = occu_multi(),
            detection = ~ 1, y = sim$y, species = sim$species,
            control = list(verbose = FALSE))
coef(fit)
# }