stan_occuTTD {ubms} | R Documentation |
Fit Time-to-detection Occupancy Models
Description
Fit time-to-detection occupancy models of Garrard et al. (2008, 2013). Time-to-detection can be modeled with either an exponential or Weibull distribution.
Usage
stan_occuTTD(
psiformula = ~1,
gammaformula = ~1,
epsilonformula = ~1,
detformula = ~1,
data,
ttdDist = c("exp", "weibull"),
linkPsi = c("logit"),
prior_intercept_state = logistic(0, 1),
prior_coef_state = logistic(0, 1),
prior_intercept_det = normal(0, 5),
prior_coef_det = normal(0, 2.5),
prior_intercept_shape = normal(0, 2.5),
prior_sigma = gamma(1, 1),
log_lik = TRUE,
...
)
Arguments
psiformula |
Right-hand sided formula for the initial probability of occupancy at each site. |
gammaformula |
Right-hand sided formula for colonization probability. Currently ignored as dynamic models are not yet supported. |
epsilonformula |
Right-hand sided formula for extinction probability. Currently ignored as dynamic models are not yet supported. |
detformula |
Right-hand sided formula for mean time-to-detection. |
data |
|
ttdDist |
Distribution to use for time-to-detection; either
|
linkPsi |
Link function for the occupancy model. Only option is
|
prior_intercept_state |
Prior distribution for the intercept of the
state (occupancy probability) model; see |
prior_coef_state |
Prior distribution for the regression coefficients of the state model |
prior_intercept_det |
Prior distribution for the intercept of the time-to-detection model |
prior_coef_det |
Prior distribution for the regression coefficients of the time-to-detection model |
prior_intercept_shape |
Prior distribution for the intercept of the shape parameter (i.e., log(shape)) for Weibull TTD models |
prior_sigma |
Prior distribution on random effect standard deviations |
log_lik |
If |
... |
Arguments passed to the |
Value
ubmsFitOccuTTD
object describing the model fit.
References
Garrard, G.E., Bekessy, S.A., McCarthy, M.A. and Wintle, B.A. 2008. When have we looked hard enough? A novel method for setting minimum survey effort protocols for flora surveys. Austral Ecology 33: 986-998.
Garrard, G.E., McCarthy, M.A., Williams, N.S., Bekessy, S.A. and Wintle, B.A. 2013. A general model of detectability using species traits. Methods in Ecology and Evolution 4: 45-52.
Kery, Marc, and J. Andrew Royle. 2016. Applied Hierarchical Modeling in Ecology, Volume 1. Academic Press.
See Also
Examples
#Simulate data
N <- 500; J <- 1
scovs <- data.frame(elev=c(scale(runif(N, 0,100))),
forest=runif(N,0,1),
wind=runif(N,0,1))
beta_psi <- c(-0.69, 0.71, -0.5)
psi <- plogis(cbind(1, scovs$elev, scovs$forest) %*% beta_psi)
z <- rbinom(N, 1, psi)
Tmax <- 10 #Same survey length for all observations
beta_lam <- c(-2, -0.2, 0.7)
rate <- exp(cbind(1, scovs$elev, scovs$wind) %*% beta_lam)
ttd <- rexp(N, rate)
ttd[z==0] <- Tmax #Censor at unoccupied sites
ttd[ttd>Tmax] <- Tmax #Censor when ttd was greater than survey length
#Build unmarkedFrame
umf <- unmarkedFrameOccuTTD(y=ttd, surveyLength=Tmax, siteCovs=scovs)
#Fit model
(fit <- stan_occuTTD(psiformula=~elev+forest, detformula=~elev+wind,
data=umf, chains=3, iter=300))