R/enmtools.clade.R

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

#' Defining a class for enmtools.clade.  Each clade gets:
#' @param species A list of enmtools.species objects
#' @param tree A tree showing the relationships between the species
#'
#' @return An enmtools.clade object, either empty or containing a formatted version of the data that was passed into the function.



enmtools.clade <- function(species = NA, tree = NA){

   # Checking classes of input args.  The isTRUE stuff is needed because R doesn't
   # know how to do is.na on raster data, so it was barfing and error when a raster
   # was passed in.

   if(!isTRUE(is.na(species))){

      # Checking to see if species is a list
      if(!"list" %in% class(species)){
         stop("Argument species requires a list of enmtools.species objects")
      }

      # This if statement is asking whether any of the list elements don't have
      # enmtools.species in their class definitions
      if(any(unlist(lapply(species, function(x) !"enmtools.species" %in% class(x))))){
         warning("The following objects in the species list do not appear to be enmtools.species objects:\n",
         names(which(unlist(lapply(species, function(x) !"enmtools.species" %in% class(x))))))
      }

   }

   if(!isTRUE(is.na(tree))){
      # Checking to see if species is a list
      if(!"phylo" %in% class(tree)){
         stop("Argument tree requires a phylo object")
      }
   }

   output <- list(species = species,
                  tree = tree)

   class(output) <- c("list", "enmtools.clade")

   return(output)
}

summary.enmtools.clade <- function(object, ...){

  object <- check.clade(object)

  cat(paste("\n\nAn enmtools.clade object with", length(object$species), "species\n"))

  cat("\nSpecies names: \n")
  cat(paste("\t", lapply(object$species, function(object) object$species.name)))

  cat("\n\nTree: \n")
  print(object$tree)

  cat("\n\nData Summary: \n")
  print(kable(object$summary))

  cat("\n")
}

plot.enmtools.clade <- function(x, ...){

  # Figure out how many plots you need.  We'll do one for each species (up to 15)
  # and one for the tree.
  n.plot <- min(16, length(x$species))

  # We'll use this to keep track of how many plots we've made
  plotted <- 0

  # Figure out how many rows and columns we need, declare a new plot
  n.rows <- ceiling(sqrt(n.plot))
  n.cols <- ceiling(n.plot/n.rows)

  # Storing and resetting par on exit as required by CRAN
  opar <- par(no.readonly =TRUE)
  on.exit(par(opar))

  plot.new()
  par(mfrow = c(n.rows, n.cols))

  for(i in 1:n.plot){
    plot(x$species[[i]])
  }

  par(mfrow = c(1,1))

}

print.enmtools.clade <- function(x, ...){
  summary(x)
}

#' @describeIn enmtools.clade Save an ENMTools clade object
#' @param x An enmtools.clade object to be saved
#' @param ... Other arguments passed to R's save function (eg., filename)
save.enmtools.clade <- function(x, ...){
  x <- rapply(x, terra::wrap, classes = c("SpatVector", "SpatRaster"), how = "replace")
  save(x, ...)
}

#' @describeIn enmtools.clade Load an ENMTools clade object
#' @param x Path to an enmtools.species file
#' @param ... Other arguments passed to R's load function
load.enmtools.clade<- function(x, ...) {
  load(x, ...)
  x <- rapply(x, terra::unwrap, classes = c("PackedSpatVector", "PackedSpatRaster"), how = "replace")
  return(x)
}