R/island_colonist-class.R

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

#' Checks the validity of the Island_colonist class
#'
#' @param object Instance of the island_colonist class
#'
#' @return Boolean or errors
#' @export
#'
#' @examples
#' island_colonist <- island_colonist()
#' check_island_colonist(island_colonist)
check_island_colonist <- function(object) {
  errors <- character()
  length_clade_name <- length(object@clade_name)
  if (length_clade_name != 1) {
    msg <- paste("clade_name is length ", length_clade_name, ". Should be 1",
                 sep = "")
    errors <- c(errors, msg)
  }

  length_status <- length(object@status)
  if (length_status != 1) {
    msg <- paste("status is length ", length_status, ". Should be 1", sep = "")
    errors <- c(errors, msg)
  }

  length_missing_species <- length(object@missing_species)
  if (length_missing_species != 1) {
    msg <- paste(
      "missing_species is length ", length_missing_species, ". Should be 1",
      sep = ""
    )
    errors <- c(errors, msg)
  }

  length_col_time <- length(object@col_time)
  if (length_col_time != 1) {
    msg <- paste(
      "col_time is length ", length_col_time, ". Should be 1",
      sep = ""
    )
    errors <- c(errors, msg)
  }

  length_col_max_age <- length(object@col_max_age)
  if (length_col_max_age != 1) {
    msg <- paste(
      "col_max_age is length ", length_col_max_age, ". Should be 1",
      sep = ""
    )
    errors <- c(errors, msg)
  }

  length_min_age <- length(object@min_age)
  if (length_min_age != 1) {
    msg <- paste(
      "min_age is length ", length_min_age, ". Should be 1",
      sep = ""
    )
    errors <- c(errors, msg)
  }

  length_clade_type <- length(object@clade_type)
  if (length_clade_type != 1) {
    msg <- paste(
      "clade_type is length ", length_clade_type, ". Should be 1",
      sep = ""
    )
    errors <- c(errors, msg)
  }

  if (length(errors) == 0) {
    TRUE
  } else {
    errors
  }
}

#' Defines the `island_tbl` class which is used when extracting information
#' from the phylogenetic and island data to be used for constructing a
#' `daisie_data_tbl`
#'
#' @slot clade_name character.
#' @slot status character.
#' @slot missing_species character.
#' @slot col_time numeric.
#' @slot col_max_age logical.
#' @slot branching_times numeric.
#' @slot min_age numeric.
#' @slot species character.
#' @slot clade_type numeric.
#'
#' @export
setClass(
  # name of the class
  Class = "Island_colonist",

  # define the types of the class
  slots = c(
    clade_name = "character",
    status = "character",
    missing_species = "numeric",
    col_time = "numeric",
    col_max_age = "logical",
    branching_times = "numeric",
    min_age = "numeric",
    species = "character",
    clade_type = "numeric"
  ),

  # define the default values of the slots
  prototype = list(
    clade_name = NA_character_,
    status = NA_character_,
    missing_species = NA_real_,
    col_time = NA_real_,
    col_max_age = NA,
    branching_times = NA_real_,
    min_age = NA_real_,
    species = NA_character_,
    clade_type = NA_integer_
  ),

  # check validity of class
  validity = check_island_colonist
)

#' Constructor for Island_colonist
#'
#' @inheritParams default_params_doc
#'
#' @return Object of `Island_colonist` class.
#' @export
#'
#' @examples
#' # Without initial values
#' colonist <- island_colonist()
#'
#' # With initial values
#' colonist <- island_colonist(
#'   clade_name = "bird",
#'   status = "endemic",
#'   missing_species = 0,
#'   col_time = 0.5,
#'   col_max_age = FALSE,
#'   branching_times = 0.5,
#'   min_age = NA_real_,
#'   species = "bird_a",
#'   clade_type = 1
#')
island_colonist <- function(clade_name = NA_character_,
                            status = NA_character_,
                            missing_species = NA_real_,
                            col_time = NA_real_,
                            col_max_age = NA,
                            branching_times = NA_real_,
                            min_age = NA_real_,
                            species = NA_character_,
                            clade_type = NA_integer_) {

  methods::new(
    "Island_colonist",
    clade_name = clade_name,
    status = status,
    missing_species = missing_species,
    col_time = col_time,
    col_max_age = col_max_age,
    branching_times = branching_times,
    min_age = min_age,
    species = species,
    clade_type = clade_type
  )
}