occuRN: Fit the Occupancy model of Royle and Nichols...

In ianfiske/unmarked: Models for Data from Unmarked Animals

Description

Fit the Occupancy model of Royle and Nichols

Usage

occuRN(formula, data, K=25, starts, method="BFGS", control=list(),
    se=TRUE)

Arguments

formula	double right-hand side formula describing covariates of detection and occupancy in that order.
data	unmarkedFrameOccu supplying data to the model.
K	the upper summation index used to numerically integrate out the latent abundance.
starts	initial values for the optimization.
method	Optimization method used by optim.
control	Other arguments passed to optim.
se	logical specifying whether or not to compute standard errors.

Details

See unmarked for detailed descriptions of passing data y, covdata.site, and covdata.obs, and specifying covariates with stateformula and detformula.

This function fits the latent abundance mixture model described in Royle and Nichols (2003).

The latent abundance of site i is modelled as Poisson:

N_i ~ Poisson(lambda_i)

The detection of a single individual in site i during sample j is modelled as Bernoulli:

w_ij ~ Bernoulli(r_ij)

.

Thus, the detection probability for a single site is linked to the detection probability for an individual by

p_ij = 1 - (1 - r_ij) ^ N_i

Covariates of lambda_i are modelled with the log link and covariates of r_ij are modelled with the logit link.

Value

unmarkedFit object describing the model fit.

Author(s)

Ian Fiske

References

Royle, J. A. and Nichols, J. D. (2003) Estimating Abundance from Repeated Presence-Absence Data or Point Counts. Ecology, 84(3) pp. 777–790.

Examples

data(birds)
woodthrushUMF <- unmarkedFrameOccu(woodthrush.bin)
(fm.wood.rn <- occuRN(~ obs ~ 1, woodthrushUMF))

ianfiske/unmarked documentation built on May 18, 2019, 1:28 a.m.