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94 lines
4.2 KiB
R
94 lines
4.2 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/occ.mod.do4.R
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\name{occMod_DO4}
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\alias{occMod_DO4}
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\title{Fit dynamic (multi-season) occupancy model using the fourth parameterisation
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(random changes in occupancy, epsilon=1-gamma) in PRESENCE.}
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\usage{
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occMod_DO4(psi = call(), psi.cov = data$unitcov, p = call(),
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p.cov = cbind(data$unitcov, data$survcov), modname = NULL,
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paoname = NULL, outfile, model = 240, fixed = NULL, initvals = NULL,
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data, conf, miscopts = "")
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}
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\arguments{
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\item{psi}{the right-hand side of the formula for the model to fit for occupancy probability
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in each season.}
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\item{psi.cov}{a data frame containing the unit-specific covariates to use for the occupancy
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component of the model, with number of rows = \code{data$nunits} or \code{data$nunits*data$nseasons}.
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If the shorter version of the data frame is supplied the rows are recycled to the longer length.}
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\item{p}{the right-hand side of the formula for the model to fit for detection probability.}
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\item{p.cov}{a data frame containing the survey-specific covariates to use for the detection component
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of the model.}
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\item{modname}{(optional) a string containing the model name}
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\item{paoname}{(optional) a string containing the filename for the temporary PRESENCE data file.}
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\item{outfile}{name for output file (use outfile='modname') for outfile named via model name}
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\item{model}{The PRESENCE model code. DO NOT CHANGE.}
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\item{fixed}{a single-column matrix containing values for real parameters to be fixed at.
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\code{rownnames(fixed)} should contain the index of the real parameters to be fixed.}
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\item{initvals}{initial values for the beta parameters at which PRESENCE begins the optimisation.
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The default values in PRESENCE is 0.}
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\item{data}{the \code{pao} data object containing the detection data and other information.}
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\item{conf}{limits for confidence intervals as a proportion (defalut=0.95 for 95\% conf. interval limits)}
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\item{miscopts}{see \code{\link{occMod}}}
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}
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\value{
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list of class \code{"occMod"} and \code{"do4"}.
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\code{occMod$beta} contains the objects:
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\item{psi}{estimated logistic regression coefficients and standard errors for probabilities of occurrence in each season.}
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\item{psi.VC}{variance-covariance matrix for psi.}
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\item{p}{estimated logistic regression coefficients and standard errors for probabilities of detection in each survey.}
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\item{p.VC}{variance-covariance matrix for p.}
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\item{VC}{the full variance-covariance matrix for all logistic regression coefficients.}
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\code{occMod$real} contains the objects:
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\item{psi}{estimated probabilities of occurrence for each sampling unit, in each season,
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along with standard errors and limits of 95\% confidence interval. The season for which an
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estimate applies to can be identified from the final number of the row names
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(\code{rownames(psi)}).}
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\item{p}{estimated probabilities of detection for each survey, along with standard errors
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and limits of 95\% confidence intervals.}
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\code{occMod$derived} contains the objects:
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\item{gamma}{estimated probabilities of colonization for each sampling unit, along with
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standard errors and limits of 95\% confidence intervals. The beginning season for which an
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estimate applies to can be identified from the final number of the row names
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(\code{rownames(gamma)}).}
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\item{epsilon}{estimated probabilities of extinction for each sampling unit, along with
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standard errors and limits of 95\% confidence intervals. The beginning season for which an
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estimate applies to can be identified from the final number of the row names
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(\code{rownames(epsilon)}). Under this parameterisation, extinction probabilities have the
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same value as 1-colonization probabilties}
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Note: For this parameterization, \eqn{\gamma_t = \psi_{t+1}}{gamma(t)=psi(t+1)}, due to the
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constraint, \eqn{\epsilon=1-\gamma}{epsilon=1-gamma}
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\preformatted{
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ie., psi(t+1)=psi(t)*(1-epsilon(t))+(1-psi(t))*gamma(t)
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psi(t+1)=psi(t)*gamma(t)+(1-psi(t))*gamma(t)
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psi(t+1)=psi(t)*gamma(t)+gamma(t)-psi(t)*gamma(t)
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psi(t+1)=gamma(t)}
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}
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\description{
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This is not intended for direct use, but instead the \code{\link{occMod}} function should
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be used with \code{type="do.4"}.
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}
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\seealso{
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\code{\link{occMod}}
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}
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\author{
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Darryl MacKenzie
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}
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