colext {unmarked} | R Documentation |
Estimate parameters of the colonization-extinction model, including covariate-dependent rates and detection process.
colext(psiformula= ~1, gammaformula = ~ 1, epsilonformula = ~ 1, pformula = ~ 1, data, starts, B=0, method="BFGS", control=list(), se=TRUE)
psiformula |
Right-hand sided formula for the initial probability of occupancy at each site. |
gammaformula |
Right-hand sided formula for colonization probability. |
epsilonformula |
Right-hand sided formula for extinction probability. |
pformula |
Right-hand sided formula for detection probability. |
data |
unmarkedMultFrame object that supplies the data (see unmarkedMultFrame ). |
starts |
optionally, initial values for parameters in the optimization. |
B |
number of bootstrap interations (the default 0 indicates no bootstrapping). |
method |
Optimization method used by optim . |
control |
Other arguments passed to optim . |
se |
logical specifying whether or not to compute standard errors. |
This function fits the colonization-extinction model of MacKenzie et al (2003). The colonization and extinction rates
can be modeled with covariates that vary yearly at each site using a logit link. These covariates
are supplied by special unmarkedMultFrame yearlySiteCovs
slot.
These parameters are specified using the gammaformula
and epsilonformula
arguments. The initial probability of occupancy is modeled by
covariates specified in the psiformula
.
The conditional detection rate can also be modeled as a function of covariates that vary at the secondary sampling
period (ie., repeat visits). These covariates are specified by the first part of the formula
argument and
the data is supplied via the usual obsCovs
slot.
See unmarkedMultFrame
and formatMult
for more information on supplying the data.
unmarkedFitColExt object describing model fit.
MacKenzie, D.I. et al. (2002) Estimating Site Occupancy Rates When Detection Probabilities Are Less Than One. Ecology, 83(8), 2248-2255.
MacKenzie, D. I. et al. (2006) Occupancy Estimation and Modeling. Amsterdam: Academic Press. Royle, J. A. and R. Dorazio. (2008).
data(frogs) umf <- formatMult(masspcru) obsCovs(umf) <- scale(obsCovs(umf)) ## constant transition rates (fm <- colext(psiformula = ~ 1, gammaformula = ~ 1, epsilonformula = ~ 1, pformula = ~ JulianDate + I(JulianDate^2), umf, control = list(trace=1, maxit=1e4))) ## Not run: ## try yearly transition rates yearlySiteCovs(umf) <- data.frame(year = factor(rep(1:7, numSites(umf)))) (fm.yearly <- colext(psiformula = ~ 1, gammaformula = ~ year, epsilonformula = ~ year, pformula = ~ JulianDate + I(JulianDate^2), umf, control = list(trace=1, maxit=1e4))) ## End(Not run)