R/mapRichness.R

In NCRN/NCRNbirds: Data analysis and visualization for NPS I&M bird monitoring.

#' @include NCRNbirds_Class_def.R birdRichness.R  mapBirds.R
#' 
#' @title mapRichness
#' 
#' @description Produces an html map of bird species richness.
#' 
#' @param object Either an object of class \code{NCRNbirds} or a list of such objects.
#' @param years Optional. A vector of numeric value(s) indicating the year of the data you wish to map. \code{NA}, the default, combines data across all
#' years.
#' @param points A character vector of point names. \code{NA}, the default, will map all points.
#' @param palette Color pallete for the colors of the points. Defaults to "BuGn" (blue green) but will accept any RColorBrewer, viridis or custom palette.
#' @param maptype The type of base map to be used. See \code{\link{mapBirds}} for options.
#' @param title  A character vector to be used as the legend title. 
#' @param ... Additional arguments passed to \code{\link{birdRichness}}. 
#' 
#' @details  This function prodcues a map showing the bird species richness of each point for one or more years. Bird species richness is calculated using the 
#' \code{\link{birdRichness}} function, and this data is then passed on to the \code{\link{mapBirds}} function. 
#' 
#' @seealso \code{\link{birdRichness}} \code{\link{mapBirds}}
#' 
#' 
#' @export

setGeneric(name="mapRichness",function(object, years=NA, points=NA, palette="BuGn",maptype="basic",
        title="Species Richness", ...){standardGeneric("mapRichness")}, signature="object")


 setMethod(f="mapRichness", signature=c(object="list"),
           function(object, years, points, palette, maptype,title,...){
             
             
             BRich<-birdRichness(object, years=years, points=points, byPoint=T, ...)
             
             mapBirds(object=object, points=BRich$Point_Name, values=BRich$Richness,  colortype = "numeric", colors=palette, 
                      maptype = maptype, title=title)     
   })



setMethod(f="mapRichness", signature=c(object="NCRNbirds"),
  function(object, years, points, palette, maptype, title,...){
      
    BRich<-birdRichness(object, years=years, points=points, byPoint=T, ...)

    mapBirds(object=object, points=BRich$Point_Name, values=BRich$Richness,  colortype = "numeric", colors=palette, 
       maptype = maptype, title=title)    
            
                           
})