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#' Summary for object of class PresenceAbsence
#' @author Bruno Vilela
#'
#' @description Summary for objects of class PresenceAbsence.
#'
#' @usage
#' \method{summary}{PresenceAbsence}(object, \dots)
#'
#' @param object an object of class \code{\link{PresenceAbsence}}.
#' @param ... additional arguments affecting the summary produced.
#' @method summary PresenceAbsence
#' @export
#' @import terra
summary.PresenceAbsence <- function(object, ...) {
object <- .check_pam(object)
class <- class(object)
Numberofspecies <- ncol(object$Pre) - 2
Numberofcells <- nrow(object$Pre)
x2 <- object$Pre[, -(1:2), drop = FALSE]
if (is.vector(x2)) {
nomes <- names(x2)
x2 <- matrix(x2, ncol = length(x2))
colnames(x2) <- nomes
}
Cellswithpresence <- sum(rowSums(x2) > 0)
Cellswithoutanypresence <- sum(rowSums(x2) == 0)
Specieswithoutanypresence <- sum(colSums(x2) == 0)
SpeciesLargestRange <- names(2 + which(colSums(x2) == max(colSums(x2))))
resolution <- terra::res(object$Ri)
extention <- terra::ext(object$Ri)
coordRef <- terra::crs(object$R, proj = TRUE)
result <- list(class = class,
Numberofspecies = Numberofspecies,
Numberofcells = Numberofcells,
Cellswithpresence = Cellswithpresence,
Cellswithoutanypresence = Cellswithoutanypresence,
Specieswithoutanypresence = Specieswithoutanypresence,
SpeciesLargestRange = SpeciesLargestRange,
resolution = resolution,
extention = extention,
coordRef = coordRef)
class(result) <- "summary.PresenceAbsence"
return(result)
}
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