unmarkedRanef-class: Class '"unmarkedRanef"'
In unmarked: Models for Data from Unmarked Animals

unmarkedRanef-class

R Documentation

Class `"unmarkedRanef"`

Description

Stores the estimated posterior distributions of the latent abundance or occurrence variables.

Objects from the Class

Objects can be created by calls of the form ranef.

Slots

post:: An array with nSites rows and Nmax (K+1) columns and nPrimaryPeriod slices

Methods

bup: signature(object = "unmarkedRanef"): Extract the Best Unbiased Predictors (BUPs) of the latent variables (abundance or occurrence state). Either the posterior mean or median can be requested using the stat argument.
confint: signature(object = "unmarkedRanef"): Compute confidence intervals.
plot: signature(x = "unmarkedRanef", y = "missing"): Plot the posteriors using xyplot
show: signature(object = "unmarkedRanef"): Display the modes and confidence intervals

Warnings

Empirical Bayes methods can underestimate the variance of the posterior distribution because they do not account for uncertainty in the hyperparameters (lambda or psi). Simulation studies indicate that the posterior mode can exhibit (3-5 percent) negatively bias as a point estimator of site-specific abundance. It appears to be safer to use the posterior mean even though this will not be an integer in general.

References

Laird, N.M. and T.A. Louis. 1987. Empirical Bayes confidence intervals based on bootstrap samples. Journal of the American Statistical Association 82:739–750.

Carlin, B.P and T.A Louis. 1996. Bayes and Empirical Bayes Methods for Data Analysis. Chapman and Hall/CRC.

Royle, J.A and R.M. Dorazio. 2008. Hierarchical Modeling and Inference in Ecology. Academic Press.