R/add.env.R

In ENMTools: Analysis of Niche Evolution using Niche and Distribution Models

#' Takes an enmtools.species object and a set of environment layers, and adds the environmental predictor values to the occurrence data.  Typically not called by the user directly.
#' Code modified from Elith and Hijmans SDM with R tutorial
#'
#' @param species An enmtools.species or enmtools.clade object
#' @param env A raster stack of environmental variables
#' @param verbose Controls printing of progress messages
#'
#' @return An enmtools.species object with environmental data attached to it.


add.env <- function(species, env, verbose = TRUE){

  if(!"SpatRaster" %in% class(env)){
    stop("Argument env must be a SpatRaster object!")
  }

  if("enmtools.species" %in% class(species)){

    # Adding env data to a single species
    if(verbose == TRUE){
      message(paste("Adding environmental data to species", species$species.name, "\n"))
    }

    if(class(species$presence.points) %in% c("SpatVector")){
      if(verbose == TRUE){
        message("\tProcessing presence points...\n")
      }

      # Have to assign names manually because otherwise it fails when there's only one env layer

      #names <- c(colnames(species$presence.points), names(env))
      species$presence.points <- cbind(species$presence.points, terra::extract(env, species$presence.points, ID = FALSE))
      #colnames(species$presence.points) <- names
      species$presence.points <- species$presence.points[complete.cases(terra::values(species$presence.points)),]

    } else {
      message("No presence points, skipping...\n")
    }

    if(class(species$background.points) %in% c("SpatVector")){
      if(verbose == TRUE){
        message("\tProcessing background points...\n")
      }

      #names <- c(colnames(species$background.points), names(env))
      species$background.points <- cbind(species$background.points, terra::extract(env, species$background.points, ID = FALSE))
      #colnames(species$background.points) <- names
      species$background.points <- species$background.points[complete.cases(terra::values(species$background.points)),]
    } else {
      message("No background points, skipping...\n")
    }

  } else if("enmtools.clade" %in% class(species)){

    # Adding env data to an entire clade
    # All we need to do for this is call add.env for each species individually
    for(i in 1:length(species$species)){
      species$species[[i]] <- add.env(species$species[[i]], env)
    }

  } else {

    # Not a species or clade
    stop("Argument species is not an enmtools.species or enmtools.clade object!")

  }

  return(species)

}