Map biodiversity records with rgbif and ggmap packages in R

23 Jul

When I attended usrR! 2012 last month, there was an interesting presentation by Dr. David Kahle about the package ggmap. It is a package built over ggmap2 and helps us map spatial data over online maps like Google maps or Open Street Maps. I decided to give ggmap package a try with biodiversity data.

So first let us create a map for the Plain Tiger or the African Monarch Butterfly (Danaus chrysippus). We use occurrencelist from rgbif package again like previous post.

We use qmap function from ggmap package to quickly pull up the base map from Google Maps. So in essence the qmap function eliminates two step process of getting map data using map_data function and then setting up map display using ggplot function into one step. We use geom_jitter function to plot the occurrence points in the specified size(size = 4) and color(color = “red”).

library(rgbif)
Dan_chr=occurrencelist(sciname = 'Danaus chrysippus',
                       coordinatestatus = TRUE,
                       maxresults = 1000,
                       latlongdf = TRUE, removeZeros = TRUE)
library(ggmap)
library(ggplot2)
wmap1 = qmap('India',zoom=2)
wmap1 +
      geom_jitter(data = Dan_chr,
                  aes(decimalLongitude, decimalLatitude),
                  alpha=0.6, size = 4, color = "red") +
                    opts(title = "Danaus chrysippus")

Here is the opuput map of the code snippet:

Though in earlier code we have used geom_jitter, high density of the points in some regions are not clearly seen. If we want to get better idea about the number of points we can try two dimensional density maps using the stat_density2d function. It just adds density lines on the map showing higher density with darker circles.

library(rgbif)
Dan_chr=occurrencelist(sciname = 'Danaus chrysippus',
                       coordinatestatus = TRUE,
                       maxresults = 1000,
                       latlongdf = TRUE, removeZeros = TRUE)
library(ggmap)
library(ggplot2)
wmap1 = qmap('India',zoom=2)
wmap1 +
  stat_density2d(aes(x = decimalLongitude, y = decimalLatitude,
                     fill = ..level.., alpha = ..level..),
                 size = 4, bins = 6,
                 data = Dan_chr, geom = 'line') +
      geom_jitter(data = Dan_chr,
                  aes(decimalLongitude, decimalLatitude),
                  alpha=0.6, size = 4, color = "red") +
                    opts(title = "Danaus chrysippus :: Density Plot")

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