stan_occu: Fit the MacKenzie et al. (2002) Occupancy Model

In kenkellner/ubms: Bayesian Models for Data from Unmarked Animals using 'Stan'

Fit the MacKenzie et al. (2002) Occupancy Model

Description

This function fits the single season occupancy model of MacKenzie et al. (2002).

Usage

stan_occu(
  formula,
  data,
  prior_intercept_state = logistic(0, 1),
  prior_coef_state = logistic(0, 1),
  prior_intercept_det = logistic(0, 1),
  prior_coef_det = logistic(0, 1),
  prior_sigma = gamma(1, 1),
  log_lik = TRUE,
  ...
)

Arguments

formula	Double right-hand side formula describing covariates of detection and occupancy in that order
data	A unmarkedFrameOccu object
prior_intercept_state	Prior distribution for the intercept of the state (occupancy probability) model; see ?priors for options
prior_coef_state	Prior distribution for the regression coefficients of the state model
prior_intercept_det	Prior distribution for the intercept of the detection probability model
prior_coef_det	Prior distribution for the regression coefficients of the detection model
prior_sigma	Prior distribution on random effect standard deviations
log_lik	If TRUE, Stan will save pointwise log-likelihood values in the output. This can greatly increase the size of the model. If FALSE, the values are calculated post-hoc from the posteriors
...	Arguments passed to the stan call, such as number of chains chains or iterations iter

Value

ubmsFitOccu object describing the model fit.

References

MacKenzie DI, Nichols JD, Lachman GB, Droege S, Royle JA, Langtimm CA. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83: 2248-2255.

See Also

occu, unmarkedFrameOccu

Examples

data(frogs)
pferUMF <- unmarkedFrameOccu(pfer.bin)

#Add some covariates
siteCovs(pferUMF) <- data.frame(cov1=rnorm(numSites(pferUMF)))

#Fit model
(fm <- stan_occu(~1~cov1, pferUMF, chains=3, iter=300))

kenkellner/ubms documentation built on March 1, 2025, 7:02 a.m.