occMS: occMS

In dslramsey/eradicate: Functions to support the "eradication tools" shiny app

occMS

Description

occMS fits the dynamic multi-season occupancy model of MacKenzie et al. (2003). This is a port of the colext function in unmarked.

Usage

occMS(lamformula, gamformula, epsformula, detformula,
data, starts, method="BFGS", se=TRUE, ...)

Arguments

lamformula	formula for the latent (initial) occupancy component.
gamformula	formula for the latent colonisation component. If season specific colonisation/extinction parameters are desired, then use the reserved keyword .season, (i.e. ~.season).
epsformula	formula for the latent survival component.
detformula	formula for the detection component. Only site- or .season-level covariates are allowed for the detection component. This differs from the similar model in unmarked.
data	A eFrameMS object containing the detection/non-detection data (0/1) and site-level covariates. see eFrameMS for how to format the required data. count data will get trunctated to (0/1) by occMS().
starts	Initial values for parameters
method	Optimisation method
se	flag to return the standard error (hessian).

Value

a efit model object.

Examples

 counts<- san_nic_open$index
 emf <- eFrameMS(df=counts)
 mod <- occMS(~1, ~1, ~.season, ~1, data=emf)
 Nhat<- calcN(mod)

dslramsey/eradicate documentation built on March 16, 2024, 1:40 p.m.