Simulate a multi-species co-occurrence occupancy data set

Draws from the occu_multi() model: a joint occupancy state for S species from the log-linear (first + second order) occupancy model, then per-species site-level detections at the observed visit pattern.

Usage

simulate_occu_multi(
  S = 2,
  N = 300,
  J = 4,
  n_state_covs = 1,
  beta_first = NULL,
  beta_second = NULL,
  beta_p = NULL,
  seed = NULL
)

Arguments

S

Number of species (default 2).

N

Number of sites (default 300).

J

Number of replicate visits (default 4).

n_state_covs

Number of shared occupancy covariates (default 1).

beta_first

Length-S list of first-order natural-parameter coefficients c(intercept, slopes...). Default moderate occupancy.

beta_second

Length-choose(S, 2) list of second-order (interaction) coefficients (in combn(S, 2) order). Default a single positive interaction for S = 2, else 0.

beta_p

Length-S list of detection coefficients (logit). Default c(qlogis(0.5), ...).

seed

Optional random seed.

Value

A list with y (a length-S list of N x J matrices), data, species, and truth.

Examples

sim <- simulate_occu_multi(S = 2, N = 50, J = 3, seed = 1)
length(sim$y)