R/PresenceAbsence-class.R

#'@title PresenceAbsence Class
#'
#'@description The \code{PresenceAbsence} is a new S3 object class created and
#'  used inside the \code{\link{letsR}} package. This object class is used to
#'  store information on species distribution within a geographic domain in the
#'  form of a presence-absence matrix. In addition, the \code{PresenceAbsence}
#'  object also contains other essential information (e.g. user-defined grid
#'  cell system, including resolution, projection, datum, and extent) necessary
#'  for other analysis performed with the package's functions.
#'
#'@details \strong{Creating a PresenceAbsence object}\cr A
#'  \code{PresenceAbsence} object can be generated using the following
#'  functions:\cr
#' - \code{\link{lets.presab}}\cr
#' - \code{\link{lets.presab.birds}}\cr
#' - \code{\link{lets.presab.points}}\cr\cr
#'
#' \strong{The PresenceAbsence information}\cr The result is a \code{list}
#' object of class \code{PresenceAbsence} that includes the following
#' objects:\cr
#' - Presence_and_Absence_Matrix: A matrix of species' presence(1) and absence(0)
#' information. The first two columns contain the longitude (x) and latitude (y)
#' of the cells' centroid (from the gridded domain used);\cr
#' - Richness_Raster: A raster containing species richness information across 
#' the geographic domain, which can be used to map the observed geographic 
#' gradient in species richness;\cr
#' - Species_name: A character vector with species' names contained in
#' the matrix.\cr\cr Each of the objects can be obtained usign the standard
#' subsetting operators that are commonly applied to a \code{list} object (i.e.
#' '[[' and '$').\cr\cr
#'
#'\strong{letsR functions applied to a PresenceAbsence object}\cr The following
#'functions from the letsR package can be directly applied to a
#'\code{PresenceAbsence}:\cr
#' - \code{\link{lets.addpoly}}\cr
#' - \code{\link{lets.addvar}}\cr
#' - \code{\link{lets.distmat}}\cr
#' - \code{\link{lets.field}}\cr
#' - \code{\link{lets.gridirizer}}\cr
#' - \code{\link{lets.iucn}}\cr
#' - \code{\link{lets.iucn.ha}}\cr
#' - \code{\link{lets.iucn.his}}\cr
#' - \code{\link{lets.maplizer}}\cr
#' - \code{\link{lets.midpoint}}\cr
#' - \code{\link{lets.overlap}}\cr
#' - \code{\link{lets.pamcrop}}\cr
#' - \code{\link{lets.rangesize}}\cr
#'
#'\strong{Generic functions applied to a PresenceAbsence object}\cr The
#'following generic functions can be directly applied to the
#'\code{PresenceAbsence} object.\cr
#' - \code{print} (\code{\link{print.PresenceAbsence}})\cr
#' - \code{summary} (\code{\link{summary.PresenceAbsence}})\cr
#' - \code{plot} (\code{\link{plot.PresenceAbsence}})\cr\cr
#'
#'@name PresenceAbsence
#'@aliases PresenceAbsence-class


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letsR documentation built on Nov. 23, 2023, 9:07 a.m.