R/plot.phenologymap.R

In phenology: Tools to Manage a Parametric Function that Describes Phenology and More

#' plot.phenologymap plots a likelihood map with Delta and Phi varying.
#' @title Plot a likelihood map with Delta and Phi varying.
#' @author Marc Girondot
#' @return Return None
#' @param x A map generated with map_phenology.
#' @param ... not used
#' @param col Colors could be heat.colors(128) or rainbow(64) or col=gray(c(seq(0, 1, length.out=128)))
#' @param xlab Label for x axis
#' @param ylab Label for y axis
#' @description This function plots a likelihood map obtained after map_phenology.
#' @family Phenology model
#' @examples
#' \dontrun{
#' library("phenology")
#' # Read a file with data
#' data(Gratiot)
#' # Generate a formatted list nammed data_Gratiot 
#' data_Gratiot<-add_phenology(Gratiot, name="Complete", 
#' 		reference=as.Date("2001-01-01"), format="%d/%m/%Y")
#' # Generate initial points for the optimisation
#' parg<-par_init(data_Gratiot, fixed.parameters=NULL)
#' # Run the optimisation
#' result_Gratiot<-fit_phenology(data=data_Gratiot, 
#' 		fitted.parameters=parg, fixed.parameters=NULL)
#' data(result_Gratiot)
#' # Extract the fitted parameters
#' parg1<-extract_result(result_Gratiot)
#' # Add constant Alpha and Tau values 
#' # [day d amplitude=(Alpha+Nd*Beta)^Tau with Nd being the number of counts for day d]
#' pfixed<-c(parg1, Alpha=0, Tau=1)
#' pfixed<-pfixed[-which(names(pfixed)=="Theta")]
#' # The only fitted parameter will be Beta
#' parg2<-c(Beta=0.5, parg1["Theta"])
#' # Generate a likelihood map 
#' # [default Phi=seq(from=0.1, to=20, length.out=100) but it is very long]
#' # Take care, it takes 20 hours ! The data map_Gratiot has the result
#' map_Gratiot<-map_phenology(data=data_Gratiot, 
#' 		Phi=seq(from=0.1, to=20, length.out=100), 
#' 		fitted.parameters=parg2, fixed.parameters=pfixed)
#' data(map_Gratiot)
#' # Plot the map
#' plot(map_Gratiot, col=heat.colors(128))
#' }
#' @method plot phenologymap
#' @export



plot.phenologymap <- 
  
  function(x, ..., col=heat.colors(128), xlab="Phi", ylab="Delta") {

    if (!requireNamespace("fields", quietly = TRUE)) {
      stop("fields package is required for this function; Please install it first")
    }
    
    
        map <- x
    
      x <- map$Phi
      y <- map$Delta
      
      input<-map$input
            
      
     # image.plot(x, y, input, col=col, axes=TRUE, xlab=xlab, ylab=ylab, nlevel = length(col))
      getFromNamespace("image.plot", ns="fields")(x, y, input, zlim=c(min(input, na.rm=TRUE), max(input, na.rm=TRUE)), col=col, axes=TRUE, xlab="Phi", ylab="Delta", nlevel = length(col))
      

  }