R/island_colonist-accessors.R

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

#' @include island_colonist-class.R
NULL

#' Accessor functions for the data (slots) in objects of the
#' \code{\linkS4class{Island_colonist}} class
#'
#' @inheritParams default_params_doc
#' @author Joshua W. Lambert
#' @rdname Island_colonist-accessors
#' @return Getter functions (get_*) return a variable from the Island_colonist
#' class, the setter functions (set_*) return the modified Island_colonist
#' class.
#' @export
#' @examples
#'   colonist <- island_colonist()
#'   get_clade_name(colonist)
#'   set_clade_name(colonist) <- "abc"
#'   get_status(colonist)
#'   set_status(colonist) <- "abc"
#'   get_missing_species(colonist)
#'   set_missing_species(colonist) <- 0
#'   get_col_time(colonist)
#'   set_col_time(colonist) <- 1
#'   get_col_max_age(colonist)
#'   set_col_max_age(colonist) <- FALSE
#'   get_branching_times(colonist)
#'   set_branching_times(colonist) <- 0
#'   get_min_age(colonist)
#'   set_min_age(colonist) <- 0.1
#'   get_species(colonist)
#'   set_species(colonist) <- "abc_a"
#'   get_clade_type(colonist)
#'   set_clade_type(colonist) <- 1
setGeneric("get_clade_name", function(x) standardGeneric("get_clade_name"))

#' @rdname Island_colonist-accessors
#' @aliases get_clade_name,Island_colonist-method
#' @export
setMethod("get_clade_name", "Island_colonist", function(x) methods::slot(x, "clade_name"))

#' @rdname Island_colonist-accessors
setGeneric("set_clade_name<-", function(x, value) standardGeneric("set_clade_name<-"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("set_clade_name<-", "Island_colonist", function(x, value) {
  methods::slot(x, "clade_name") <- value
  x
})

#' @rdname Island_colonist-accessors
setGeneric("get_status", function(x) standardGeneric("get_status"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("get_status", "Island_colonist", function(x) x@status)

#' @rdname Island_colonist-accessors
setGeneric("set_status<-", function(x, value) standardGeneric("set_status<-"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("set_status<-", "Island_colonist", function(x, value) {
  methods::slot(x, "status") <- value
  x
})

#' @rdname Island_colonist-accessors
setGeneric("get_missing_species", function(x) standardGeneric("get_missing_species"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("get_missing_species", "Island_colonist", function(x) x@missing_species)

#' @rdname Island_colonist-accessors
setGeneric("set_missing_species<-", function(x, value) standardGeneric("set_missing_species<-"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("set_missing_species<-", "Island_colonist", function(x, value) {
  x@missing_species <- value
  x
})

#' @rdname Island_colonist-accessors
setGeneric("get_col_time", function(x) standardGeneric("get_col_time"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("get_col_time", "Island_colonist", function(x) x@col_time)

#' @rdname Island_colonist-accessors
setGeneric("set_col_time<-", function(x, value) standardGeneric("set_col_time<-"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("set_col_time<-", "Island_colonist", function(x, value) {
  x@col_time <- value
  x
})

#' @rdname Island_colonist-accessors
setGeneric("get_col_max_age", function(x) standardGeneric("get_col_max_age"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("get_col_max_age", "Island_colonist", function(x) x@col_max_age)

#' @rdname Island_colonist-accessors
setGeneric("set_col_max_age<-", function(x, value) standardGeneric("set_col_max_age<-"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("set_col_max_age<-", "Island_colonist", function(x, value) {
  x@col_max_age <- value
  x
})

#' @rdname Island_colonist-accessors
setGeneric("get_branching_times", function(x) standardGeneric("get_branching_times"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("get_branching_times", "Island_colonist", function(x) x@branching_times)

#' @rdname Island_colonist-accessors
setGeneric("set_branching_times<-", function(x, value) standardGeneric("set_branching_times<-"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("set_branching_times<-", "Island_colonist", function(x, value) {
  x@branching_times <- value
  x
})

#' @rdname Island_colonist-accessors
setGeneric("get_min_age", function(x) standardGeneric("get_min_age"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("get_min_age", "Island_colonist", function(x) x@min_age)

#' @rdname Island_colonist-accessors
setGeneric("set_min_age<-", function(x, value) standardGeneric("set_min_age<-"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("set_min_age<-", "Island_colonist", function(x, value) {
  x@min_age <- value
  x
})

#' @rdname Island_colonist-accessors
setGeneric("get_species", function(x) standardGeneric("get_species"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("get_species", "Island_colonist", function(x) x@species)

#' @rdname Island_colonist-accessors
setGeneric("set_species<-", function(x, value) standardGeneric("set_species<-"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("set_species<-", "Island_colonist", function(x, value) {
  x@species <- value
  x
})

#' @rdname Island_colonist-accessors
setGeneric("get_clade_type", function(x) standardGeneric("get_clade_type"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("get_clade_type", "Island_colonist", function(x) x@clade_type)

#' @rdname Island_colonist-accessors
setGeneric("set_clade_type<-", function(x, value) standardGeneric("set_clade_type<-"))

#' @rdname Island_colonist-accessors
#' @export
setMethod("set_clade_type<-", "Island_colonist", function(x, value) {
  x@clade_type <- value
  x
})