occRNS: occuRNS

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

occuRNS

Description

occuRNS fits the occupancy/abundance model of Royle & Nichols (2003) to 'stacked' data from M sites over T primary periods (sessions) with each primary period consisting of J secondary periods. Currently supported model for the abundance process is the Poisson

Usage

occuRNS(lamformula, detformula, data, K, starts, method="BFGS", se=TRUE, ...)

Arguments

lamformula	formula for the latent abundance component.
detformula	formula for the detection component. Only site-level covariates are allowed for the detection component. This differs from the similar model in unmarked.
data	A eFrameS object containing the response for each site, indexed by primary period (sessions) and site-level covariates.see eFrameS for how to format the required data. count data will get trunctated to (0/1) by occuRNS().
K	Integer upper index of integration for abundance. This should be set high enough so that it does not affect the parameter estimates. Note that computation time will increase with K
starts	Initial values for parameters
method	Optimisation method
se	flag to return the standard error (hessian).

Value

a efitS model object.

Examples

 counts<- san_nic_open$index
 emf <- eFrameS(counts)
 mod <- occuRNS(~.season, ~1, data=emf)  # counts truncated to (0/1)
 Nhat<- calcN(mod)

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