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mpm_methods.R
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mpm_methods.R
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#' Extract stage-class information from CompadreMat or CompadreDB objects
#'
#' @description
#' Methods for extracting stage-class information from CompadreMat or CompadreDB
#' objects, including whether the matrix population model includes one or more
#' propagule stages (\code{mpm_has_prop}), dormant stages (\code{mpm_has_dorm}),
#' or active stages (\code{mpm_has_active}), and the integer index of the first
#' active stage class (\code{mpm_first_active}).
#'
#' These methods will return a single value if passed a CompadreMat object, or a
#' vector of values if passed a CompadreDB object (one value for every
#' CompadreMat object within the column 'mat').
#'
#' @return No return value, called for side effects
#'
#' @name mpm_methods
#'
#' @author Patrick Barks <patrick.barks@@gmail.com>
#'
#' @family data checking
#'
#' @examples
#' # with CompadreMat object
#' mpm_has_prop(Compadre$mat[[1]])
#' mpm_has_active(Compadre$mat[[1]])
#' mpm_has_dorm(Compadre$mat[[1]])
#' mpm_first_active(Compadre$mat[[1]])
#'
#' # with CompadreDB object
#' mpm_has_prop(Compadre)
#' mpm_has_active(Compadre)
#' mpm_has_dorm(Compadre)
#' mpm_first_active(Compadre)
#'
NULL
#' @rdname mpm_methods
#' @param object A CompadreMat or CompadreDB object
#' @export
setGeneric(
"mpm_has_prop",
function(object) {
standardGeneric("mpm_has_prop")
}
)
#' @rdname mpm_methods
#' @export
setMethod("mpm_has_prop",
signature = "CompadreMat",
function(object) {
"prop" %in% object@matrixClass$MatrixClassOrganized
}
)
#' @rdname mpm_methods
#' @export
setMethod("mpm_has_prop",
signature = "CompadreDB",
function(object) {
vapply(
object@data$mat,
function(m) "prop" %in% m@matrixClass$MatrixClassOrganized,
logical(1)
)
}
)
#' @rdname mpm_methods
#' @export
setGeneric(
"mpm_has_active",
function(object) {
standardGeneric("mpm_has_active")
}
)
#' @rdname mpm_methods
#' @export
setMethod("mpm_has_active",
signature = "CompadreMat",
function(object) {
"active" %in% object@matrixClass$MatrixClassOrganized
}
)
#' @rdname mpm_methods
#' @export
setMethod("mpm_has_active",
signature = "CompadreDB",
function(object) {
vapply(
object@data$mat,
function(m) "active" %in% m@matrixClass$MatrixClassOrganized,
logical(1)
)
}
)
#' @rdname mpm_methods
#' @export
setGeneric(
"mpm_has_dorm",
function(object) {
standardGeneric("mpm_has_dorm")
}
)
#' @rdname mpm_methods
#' @export
setMethod("mpm_has_dorm",
signature = "CompadreMat",
function(object) {
"dorm" %in% object@matrixClass$MatrixClassOrganized
}
)
#' @rdname mpm_methods
#' @export
setMethod("mpm_has_dorm",
signature = "CompadreDB",
function(object) {
vapply(
object@data$mat,
function(m) "dorm" %in% m@matrixClass$MatrixClassOrganized,
logical(1)
)
}
)
#' @rdname mpm_methods
#' @export
setGeneric(
"mpm_first_active",
function(object) {
standardGeneric("mpm_first_active")
}
)
#' @rdname mpm_methods
#' @export
setMethod("mpm_first_active",
signature = "CompadreMat",
function(object) {
mclass <- object@matrixClass$MatrixClassOrganized
ifelse(!"active" %in% mclass,
NA_integer_,
min(which(mclass == "active"))
)
}
)
#' @rdname mpm_methods
#' @export
setMethod("mpm_first_active",
signature = "CompadreDB",
function(object) {
vapply(
object@data$mat,
function(m) {
mclass <- m@matrixClass$MatrixClassOrganized
ifelse(!"active" %in% mclass,
NA_integer_,
min(which(mclass == "active"))
)
},
integer(1)
)
}
)