sim_occ: Simulate data from the single species, single season site...

In StrattonCh/occupancy: Fit and Analyze Occupancy Models

Description

This function simulates data from the single species, single season occupancy model first developed by MacKenzie et al. (2002).

Usage

sim_occ(
  M = 20,
  max_j = 10,
  beta_psi = c(0, 1),
  beta_p = c(0, 1),
  seed = NULL,
  rand_visits = TRUE
)

Arguments

M	number of sites
max_j	maximum number of visits to each site. If rand_visits = FALSE, this value is the number of visits to each site. If rand_visits = TRUE, each site is visited a random (sample(2:max_j, size = 1)) number of times.
beta_psi	vector of regression coefficients used to generate psi
beta_p	vector of regression coefficients used to generate p
seed	optional seed for reproducibility
rand_visits	logical; should each site be visited a random number of times? See details.

Details

This function simulates data from the vanilla single season, single species occupancy model using the logit link function. If rand_visits = TRUE, each site is visited a random number of times between two and max_j. Covariates are drawn from the uniform(0, 1.5) distribution so that the effect of the direction of each regression coefficient is intuitive. Note that if covariates are not desired, beta_psi and beta_p can be set to intercepts that generate the desired derived probabilities.

Value

object of class list containing the following elements:

• beta_psi vector of regression coefficients used to generate psi

• beta_p vector of regression coefficients used to generate p

• psi_cov matrix of site level covariates

• p_cov array of detection level covariates; each slice represents a single covariate

• psi vector of derived site level occupancy probabilities

• p matrix of derived visit level detection probabilities

• z vector of latent occupancy states for each site

• Y matrix of observed Bernoulli responses

• n_visits vector of number of visits to each site

• data a data frame containing all information necessary to fit the model

Examples

sim <- sim_occ(M = 100, max_j = 20, beta_psi = c(0, 1), beta_p = c(0, 1, 1), rand_visits = TRUE)
sim$Y

StrattonCh/occupancy documentation built on Feb. 17, 2021, 6:36 a.m.