gdistremoval: Fit the combined distance and removal model of Amundson et...

In rbchan/unmarked: Models for Data from Unmarked Animals

Fit the combined distance and removal model of Amundson et al. (2014).

Description

Fit the model of Amundson et al. (2014) to point count datasets containing both distance and time of observation data. The Amundson et al. (2014) model is extended to account for temporary emigration by estimating an additional availability probability if multiple counts at a site are available. Abundance can be modeled as a Poisson, negative binomial, or Zero-inflated Poisson. Multiple distance sampling key functions are also available.

Usage

gdistremoval(lambdaformula=~1, phiformula=~1, removalformula=~1,
  distanceformula=~1, data, keyfun=c("halfnorm", "exp", "hazard", "uniform"),
  output=c("abund", "density"), unitsOut=c("ha", "kmsq"), mixture=c('P', 'NB', 'ZIP'), 
  K, starts, method = "BFGS", se = TRUE, engine=c("C","TMB"), threads=1, ...)

Arguments

lambdaformula	A right-hand side formula describing the abundance covariates
phiformula	A right-hand side formula describing the availability covariates
removalformula	A right-hand side formula describing removal probability covariates
distanceformula	A right-hand side formula describing the detection function covariates
data	An object of class unmarkedFrameGDR
keyfun	One of the following detection functions: "halfnorm", "hazard", "exp", or "uniform"
output	Model either "abund" or "density"
unitsOut	Units of density. Either "ha" or "kmsq" for hectares and square kilometers, respectively
mixture	Either "P", "NB", or "ZIP" for the Poisson, negative binomial, and Zero-inflated Poisson models of abundance
K	An integer value specifying the upper bound used in the integration
starts	A numeric vector of starting values for the model parameters
method	Optimization method used by optim
se	logical specifying whether or not to compute standard errors
engine	Either "C" to use C++ code or "TMB" to use TMB for optimization
threads	Set the number of threads to use for optimization in C++, if OpenMP is available on your system. Increasing the number of threads may speed up optimization in some cases by running the likelihood calculation in parallel. If threads=1 (the default), OpenMP is disabled
...	Additional arguments to optim, such as lower and upper bounds

Value

An object of class unmarkedFitGDR

Author(s)

Ken Kellner [e-mail]

References

Amundson, C.L., Royle, J.A. and Handel, C.M., 2014. A hierarchical model combining distance sampling and time removal to estimate detection probability during avian point counts. The Auk 131: 476-494.

See Also

unmarkedFrameGDR, gdistsamp, gmultmix

rbchan/unmarked documentation built on April 3, 2024, 10:11 p.m.