R/SDMmodel2MaxEnt.R

In SDMtune: Species Distribution Model Selection

#' SDMmodel2MaxEnt
#'
#' Converts an \linkS4class{SDMmodel} object containing a \linkS4class{Maxent}
#' model into a dismo \linkS4class{MaxEnt} object.
#'
#' @param model \linkS4class{SDMmodel} object to be converted.
#'
#' @return The converted dismo \linkS4class{MaxEnt} object.
#' @export
#' @importFrom dismo maxent
#'
#' @author Sergio Vignali
#'
#' @examples
#' \donttest{# Acquire environmental variables
#' files <- list.files(path = file.path(system.file(package = "dismo"), "ex"),
#'                     pattern = "grd",
#'                     full.names = TRUE)
#'
#' predictors <- terra::rast(files)
#'
#' # Prepare presence and background locations
#' p_coords <- virtualSp$presence
#' bg_coords <- virtualSp$background
#'
#' # Create SWD object
#' data <- prepareSWD(species = "Virtual species",
#'                    p = p_coords,
#'                    a = bg_coords,
#'                    env = predictors,
#'                    categorical = "biome")
#'
#' # Train a Maxent model
#' model <- train(method = "Maxent",
#'                data = data,
#'                fc = "l")
#'
#' dismo_model <- SDMmodel2MaxEnt(model)
#' dismo_model}
SDMmodel2MaxEnt <- function(model) {

  if (!inherits(model@model, "Maxent"))
    cli::cli_abort(c(
      "!" = "Function available only for {.cls Maxent} models",
      "x" = "You have supplied a {.cls {class(model@model)}} instead."))

  maxent_model <- new("MaxEnt")
  maxent_model@presence <- .get_presence(model@data)
  maxent_model@absence <- .get_absence(model@data)
  maxent_model@lambdas <- model@model@lambdas
  maxent_model@hasabsence <- TRUE

  maxent_model
}