R/plotRPD.r

In iSDM: Invasive Species Distribution Modelling

#' R function to plot the realized versus the potential distribution using a RGB colour space  
#'@description R function to plot the realized versus the potential distribution using a RGB colour space  
#'@usage plotRPD(x=x,y=y,cex,xlab=xlab,ylab=ylab)
#'@param x Either a SpatialPixelsDataFrame, or a SpatialGridDataFrame as defined in package sp or a RasterLayer as defined in package raster
#'@param y An object belonging to the same class as x
#'@param cex A numerical value giving the amount by which plotting symbols should be magnified relative to the default
#'@param xlab A title for the x axis
#'@param ylab A title for the y axis
#'@export
#'@references Tarek Hattab, Carol Ximena Garzon Lopez, Michael Ewald, Sandra Skowronek, Raf Aerts, Helene Horen, Boris Brasseur, Emilie Gallet-Moron, Fabien Spicher, Guillaume Decocq, Hannes Feilhauer, Olivier Honnay, Pieter Kempeneers, Sebastian Schmidtlein, Ben Somers, Ruben Van De Kerchove, Duccio Rocchini and Jonathan Lenoir (2017). A unified framework to model the potential and realized distributions of invasive species within the invaded range. Diversity and Distributions. DOI: 10.1111/ddi.12566
#'@examples
#'\dontrun{
#'library(raster)
#'library(sp)
#'library(virtualspecies)
#'library(colorRamps)
#'
#'envData<-getData('worldclim', var='bio', res=10)
#'envData<-crop(envData,extent(-8,15,38,55))
#'
#' # Generate virtual species responses with formatfunctions
#'my.parameters <- formatFunctions(bio1 = c(fun = "dnorm", mean = 140, sd = 40), 
#'bio5 = c(fun = "dnorm",mean = 230, sd = 70),
#'bio6 = c(fun = "dnorm",mean = 10, sd = 40))
#' # Generate a virtual species potential distributions with responses to environmental variables
#'potential.dist <- generateSpFromFun(envData[[c(1,5,6)]], my.parameters)$suitab.raster
#'
#' #Limit the distribution 
#'realized.dist<-potential.dist
#'cell.id<-which(coordinates(realized.dist)[,2]>48)
#'dis.lim<-sample(seq(0,1,by=0.01),length(cell.id),replace=TRUE)
#'values(realized.dist)[cell.id]<-ifelse(values(realized.dist)[cell.id]>dis.lim,
#'values(realized.dist)[cell.id]-dis.lim,0)

#'plotRPD(x=potential.dist,y=realized.dist,cex=0.8,xlab="Potential distribution"
#',ylab="Realized distribution")
#'}


plotRPD<-function(x=x,y=y,cex=0.5,xlab=xlab,ylab=ylab) {
  if(class(x)!=class(y)) {stop("x and Y  must belong to the same class")}
  if(!any(dim(x)==dim(y))) {stop("x and y must have the same dimensions")}
  if(class(x) %in% c("SpatialPixelsDataFrame","SpatialGridDataFrame")){x<-raster::raster(x)
                                                                       y<-raster::raster(y)}
  if(class(x)!="RasterLayer"){stop("the class of the object x does not correspond to the classes handled by this function")}
  XY<-sp::coordinates(x)                         
  x<-raster::values(x)
  y<-raster::values(y)
  names(x)<-seq(1:length(x))
  names(y)<-seq(1:length(y))
  rownames(XY)<-names(x)
  x<-stats::na.omit(x)
  y<-y[names(x)]
  XY<-XY[names(x),]
  RGB<-matrix(NA,ncol=3,nrow=length(x))
  RGB[,1]<-(x-min(x)/(max(x)-min(x)))*255
  RGB[,2]<-(y-min(y)/(max(y)-min(y)))*255
  RGB[,3]<-c(255-RGB[,1])
  col<-grDevices::rgb(RGB[,1],RGB[,2],RGB[,3],maxColorValue =255)
  graphics::layout(mat=matrix(c(2,1),ncol=2,nrow=1),widths=c(0.8,0.8))
  graphics::par(mar=c(2,2,1,1))
  graphics::plot(XY,col=col,cex=cex,pch=15,xlab="Longitude",ylab="Latitude")
  graphics::par(mar=c(4,4,4,4))
  graphics::plot(x,y,xlab=xlab,ylab=ylab,cex=cex,col=col,pch=15)
} # end of function plotRPD