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\name{unmarkedFrame-class}
\Rdversion{1.1}
\docType{class}
\alias{unmarkedFrame-class}
\alias{coordinates,unmarkedFrame-method}
\alias{coordinates}
\alias{coords}
\alias{getY}
\alias{getY,unmarkedFrame-method}
\alias{head,unmarkedFrame-method}
\alias{hist,unmarkedFrameDS-method}
\alias{mapInfo}
\alias{numSites}
\alias{numSites,unmarkedFrame-method}
\alias{numY}
\alias{numY,unmarkedFrame-method}
\alias{obsCovs,unmarkedFrame-method}
\alias{obsCovs<-,unmarkedFrame-method}
\alias{obsCovs}
\alias{obsCovs<-}
\alias{obsNum,unmarkedFrame-method}
\alias{obsNum}
\alias{obsToY,unmarkedFrame-method}
\alias{obsToY<-,unmarkedFrame-method}
\alias{obsToY}
\alias{obsToY<-}
\alias{plot,unmarkedFrame,missing-method}
\alias{plot,unmarkedFrameOccuMulti,missing-method}
\alias{plot,unmarkedFrameOccuTTD,missing-method}
\alias{projection,unmarkedFrame-method}
\alias{projection}
\alias{siteCovs,unmarkedFrame-method}
\alias{siteCovs<-,unmarkedFrame-method}
\alias{siteCovs}
\alias{siteCovs<-}
\alias{unmarkedFrameOccu-class}
\alias{unmarkedFrameOccuMulti-class}
\alias{unmarkedFrameOccuMS-class}
\alias{unmarkedFrameOccuTTD-class}
\alias{unmarkedFrameMPois-class}
\alias{unmarkedFramePCount-class}
\alias{unmarkedFrameDS-class}
\alias{unmarkedMultFrame-class}
\alias{unmarkedFramePCO-class}
\alias{unmarkedFrameGMM-class}
\alias{unmarkedFrameGDS-class}
\alias{unmarkedFrameGPC-class}
\alias{unmarkedFrameDSO-class}
\alias{unmarkedFrameMMO-class}
\alias{show,unmarkedFrame-method}
\alias{show,unmarkedFrameOccuMulti-method}
\alias{show,unmarkedFrameOccuTTD-method}
\alias{show,unmarkedMultFrame-method}
\alias{show,unmarkedFrameOccuCOP-method}
\alias{summary,unmarkedFrame-method}
\alias{summary,unmarkedFrameDS-method}
\alias{summary,unmarkedMultFrame-method}
\alias{summary,unmarkedFrameOccuMulti-method}
\alias{summary,unmarkedFrameOccuTTD-method}
\alias{summary,unmarkedFrameOccuCOP-method}
\alias{[,unmarkedFrameOccuMulti,missing,numeric,missing-method}
\alias{[,unmarkedFrameOccuTTD,missing,numeric,missing-method}
\alias{[,unmarkedFrameGDR,missing,numeric,missing-method}
\alias{[,unmarkedFrameOccuMS,numeric,missing,missing-method}
\alias{[,unmarkedFrameOccuTTD,numeric,missing,missing-method}
\alias{[,unmarkedFrameOccuMulti,numeric,missing,missing-method}
\alias{[,unmarkedFrameDSO,numeric,missing,missing-method}
\alias{[,unmarkedFrameGDR,numeric,missing,missing-method}
\alias{[,unmarkedFrameGDR,logical,missing,missing-method}
\alias{[,unmarkedFrameOccuCOP,missing,numeric,missing-method}
\alias{[,unmarkedFrameOccuCOP,numeric,missing,missing-method}
\alias{[,unmarkedFrameOccuCOP,numeric,numeric,missing-method}
\title{Class "unmarkedFrame" }
\description{Methods for manipulating, summarizing and viewing
unmarkedFrames}
\section{Objects from the Class}{
Objects can be created by calls to the constructor function
\code{\link{unmarkedFrame}}. These objects are passed to the data
argument of the fitting functions.
}
\section{Slots}{
\describe{
\item{\code{y}:}{Object of class \code{"matrix"}}
\item{\code{obsCovs}:}{Object of class \code{"optionalDataFrame"}}
\item{\code{siteCovs}:}{Object of class \code{"optionalDataFrame"}}
\item{\code{mapInfo}:}{Object of class \code{"optionalMapInfo"}}
\item{\code{obsToY}:}{Object of class \code{"optionalMatrix"}}
}
}
\section{Methods}{
\describe{
\item{[}{\code{signature(x = "unmarkedFrame", i = "numeric", j =
"missing", drop = "missing")}: ... }
\item{[}{\code{signature(x = "unmarkedFrame", i = "numeric", j =
"numeric", drop = "missing")}: ... }
\item{[}{\code{signature(x = "unmarkedFrame", i = "missing", j =
"numeric", drop = "missing")}: ... }
\item{coordinates}{\code{signature(object = "unmarkedFrame")}: extract
coordinates }
\item{getY}{\code{signature(object = "unmarkedFrame")}: extract y
matrix }
\item{numSites}{\code{signature(object = "unmarkedFrame")}: extract M }
\item{numY}{\code{signature(object = "unmarkedFrame")}: extract
ncol(y) }
\item{obsCovs}{\code{signature(object = "unmarkedFrame")}: extract
observation-level covariates }
\item{obsCovs<-}{\code{signature(object = "unmarkedFrame")}: add or
modify observation-level covariates }
\item{obsNum}{\code{signature(object = "unmarkedFrame")}: extract
number of observations }
\item{obsToY}{\code{signature(object = "unmarkedFrame")}: }
\item{obsToY<-}{\code{signature(object = "unmarkedFrame")}: ... }
\item{plot}{\code{signature(x = "unmarkedFrame", y = "missing")}:
visualize response variable.
Takes additional argument \code{panels} which specifies how many
panels data should be split over.}
\item{projection}{\code{signature(object = "unmarkedFrame")}: extract
projection information }
\item{show}{\code{signature(object = "unmarkedFrame")}: view data as
data.frame }
\item{siteCovs}{\code{signature(object = "unmarkedFrame")}: extract
site-level covariates }
\item{siteCovs<-}{\code{signature(object = "unmarkedFrame")}: add or
modify site-level covariates }
\item{summary}{\code{signature(object = "unmarkedFrame")}: summarize
data }
\item{getL}{\code{signature(object = "unmarkedFrameOccuCOP")}: extract L }
}
}
\note{ This is a superclass with child classes for each fitting function.}
\seealso{\code{\link{unmarkedFrame}}, \code{\linkS4class{unmarkedFit}},
\code{\link{unmarked-package}}
}
\examples{
# List all the child classes of unmarkedFrame
showClass("unmarkedFrame")
# Organize data for pcount()
data(mallard)
mallardUMF <- unmarkedFramePCount(mallard.y, siteCovs = mallard.site,
obsCovs = mallard.obs)
# Vizualize it
plot(mallardUMF)
mallardUMF
# Summarize it
summary(mallardUMF)
str(mallardUMF)
numSites(mallardUMF)
numY(mallardUMF)
obsNum(mallardUMF)
# Extract components of data
getY(mallardUMF)
obsCovs(mallardUMF)
obsCovs(mallardUMF, matrices = TRUE)
siteCovs(mallardUMF)
mallardUMF[1:5,] # First 5 rows in wide format
mallardUMF[,1:2] # First 2 observations
}
\keyword{classes}
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