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84 lines
3.6 KiB
R
84 lines
3.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/occ.mod.so.fp.R
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\name{occMod_SO_fp}
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\alias{occMod_SO_fp}
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\title{Fit static occupancy/single season model}
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\usage{
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occMod_SO_fp(psi = call(), psi.cov = data$unitcov, p11 = call(),
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p11.cov = cbind(data$unitcov, data$survcov), p10 = call(),
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p10.cov = cbind(data$unitcov, data$survcov), b = call(),
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b.cov = cbind(data$unitcov, data$survcov), modname = NULL,
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paoname = NULL, outfile, model = 100, 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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\item{psi.cov}{a data frame containing the unit-specific covariates to use for the occupancy
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component of the model.}
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\item{p11}{the right-hand side of the formula for the model to fit for "sure" detection probability.}
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\item{p11.cov}{a data frame containing the survey-specific covariates to use for the detection
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component of the model.}
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\item{p10}{the right-hand side of the formula for the model to fit for false-positive detection probability.}
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\item{p10.cov}{a data frame containing the survey-specific covariates to use for the detection
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component of the model.}
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\item{b}{the right-hand side of the formula for the model to fit for Pr(detection is "sure")}
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\item{b.cov}{a data frame containing the survey-specific covariates to use for the b}
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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}{level for confidence interval (may be vector valued).}
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\item{miscopts}{}
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}
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\value{
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returns a list of class \code{"occMod"} and \code{"soFp"}.
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\code{occMod$beta} contains the objects:
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\item{psi}{estimated logistic regression coefficients and standard errors for probability of occurrence.}
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\item{psi.VC}{variance-covariance matrix for logistic regression coefficients for probability of occurrence.}
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\item{p}{estimated logistic regression coefficients and standard errors for probability of detection.}
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\item{p.VC}{variance-covariance matrix for logistic regression coefficients for probability of detection.}
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\item{VC}{the full variance-covariance matrix for all logistic regression coefficients.}
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\code{occMod$real} contains the objects:
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\item{psi}{estimated probabilities of occurrence for each sampling unit, along with standard
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errors and limits of 95\% confidence interval.}
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\item{p}{estimated probabilities of detection for each survey, along with standard errors and
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limits of 95\% confidence interval.}
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\code{occMod$derived} contains the objects:
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\item{psi_c}{estimated probabilities of occurrence given the detection history for each sampling
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unit, along with standard errors and limits of 95\% confidence interval. Will be \code{=1} for
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any unit where the species was detected at least once.}
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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 be used with \code{type="so.fp"}.
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}
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\seealso{
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\code{\link{occMod}}, \code{pao}
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}
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\author{
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Darryl MacKenzie
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}
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