https://github.com/cran/unmarked
Tip revision: 0e9915b1bbee346e4c283f39772af69032684e39 authored by Ken Kellner on 09 January 2024, 10:20:02 UTC
version 1.4.1
version 1.4.1
Tip revision: 0e9915b
unmarkedFrameOccu.Rd
\name{unmarkedFrameOccu}
\title{Organize data for the single season occupancy models fit by occu and
occuRN}
\alias{unmarkedFrameOccu}
\usage{unmarkedFrameOccu(y, siteCovs=NULL, obsCovs=NULL, mapInfo)}
\description{Organizes detection, non-detection data along with the covariates.
This S4 class is required by the data argument of \code{\link{occu}} and
\code{\link{occuRN}}}
\arguments{
\item{y}{An RxJ matrix of the detection, non-detection data, where R is the
number of sites, J is the maximum number of sampling periods per site.}
\item{siteCovs}{A \code{\link{data.frame}} of covariates that vary at the
site level. This should have M rows and one column per covariate}
\item{obsCovs}{Either a named list of \code{\link{data.frame}}s of
covariates that vary within sites, or a \code{\link{data.frame}} with
RxJ rows in site-major order.}
\item{mapInfo}{Currently ignored}
}
\details{
unmarkedFrameOccu is the S4 class that holds data to be passed
to the \code{\link{occu}} and \code{\link{occuRN}} model-fitting function.
}
\value{an object of class unmarkedFrameOccu}
\seealso{\code{\link{unmarkedFrame-class}}, \code{\link{unmarkedFrame}},
\code{\link{occu}}, \code{\link{occuRN}}}
\examples{
# Fake data
R <- 4 # number of sites
J <- 3 # number of visits
y <- matrix(c(
1,1,0,
0,0,0,
1,1,1,
1,0,1), nrow=R, ncol=J, byrow=TRUE)
y
site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
site.covs
obs.covs <- list(
x3 = matrix(c(
-1,0,1,
-2,0,0,
-3,1,0,
0,0,0), nrow=R, ncol=J, byrow=TRUE),
x4 = matrix(c(
'a','b','c',
'd','b','a',
'a','a','c',
'a','b','a'), nrow=R, ncol=J, byrow=TRUE))
obs.covs
umf <- unmarkedFrameOccu(y=y, siteCovs=site.covs,
obsCovs=obs.covs) # organize data
umf # look at data
summary(umf) # summarize
fm <- occu(~1 ~1, umf) # fit a model
}