Generate Global Biotic Interaction Distribution Maps

createDistributionMap.R

# see Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and 
# analyze species-interaction datasets. Ecological Informatics. http://dx.doi.org/10.1016/j.ecoinf.2014.08.005

# rasterize locations, retrieve stats for bounding boxes, plot graphs
if (!'package:raster' %in% search()) {
	install.packages(c('raster','maps'), repos='http://cran.us.r-project.org')
	library('raster')
	library('maps')
}

url.prefix <- 'http://api.globalbioticinteractions.org/'

retrieveLocations <- function() {
  url.locations <- paste(url.prefix, 'locations?type=csv', sep='')
  cat('locations retrieving from [')
  cat(url.locations)
  cat(']...')
  locations <- read.csv(url.locations)
  cat('done.\n')
  locations
}

locations <- retrieveLocations()

# create raster with cells 5' x 5'
r <- raster()
nrow(r) <- 36
ncol(r) <- 72

xy <- cbind(locations$loc.longitude,locations$loc.latitude)

rWithData <- rasterize(xy, r, fun='count')

world <- map(interior=FALSE)
plot(rWithData)
lines(world, col=rgb(0.8,0.8,1,1.0))

pointsWithLocations <- rasterToPoints(rWithData)

getLocationInfo <- function(points) {
	longitudes <- points[,1]
	latitudes <- points[,2]
	bboxes <- cbind(longitudes-5, latitudes-5, longitudes+5, latitudes+5)
	colnames(bboxes) <- c('west', 'south', 'east', 'north')

	bbox <- paste(bboxes[,'west'],bboxes[,'south'], bboxes[,'east'], bboxes[,'north'], sep=",")

	request <- paste(url.prefix, 'spatialInfo?type=csv&bbox=', bbox, sep='')

	location.info <- t(sapply(request, function(url) { 
			cat(paste('retrieving [', url, ']...', sep=''))  
			data <- read.csv(url)
			cat(' done.\n')
			data
		}
	))
}

points <- pointsWithLocations[,1:2]
info <- getLocationInfo(points)

logScale <- function(x, ...) { log10(x) }

rasterizeWithInfo = function(points, info, r, colname, fun = logScale) {
	rasterize(points[,1:2], r, as.numeric(info[,colname]), fun=fun)
}

SetFilename <- function(n) {
  filename <- paste('distribution_', gsub('\\.','_', n), '.png', sep='')
  png(file=filename, width=640, height=320)
  filename
}

DrawMap <- function(variable.name) {
  rWithInteractions <- rasterizeWithInfo(points, info, r, variable.name)
  filename <- SetFilename(variable.name)
  par(bty='n')
  par(mar=rep(0,4))
  par(col.axis='yellow')
  plot(rWithInteractions, axes=FALSE, xlim=c(-180,180), ylim=c(-90,90),bty='n')
  lines(world, col=rgb(0,0,1,1.0))
  dev.off()
  cat(paste('wrote distribution graph to', filename, '\n'))
  filename
}

DrawMaps <- function() {
  variables <- list('number.of.interactions', 
    'number.of.interactions.with.timestamp',
    'number.of.distinct.interactions',
    'number.of.distinct.studies',
    'number.of.distinct.study.sources',
    'number.of.distinct.locations')
  filenames <- lapply(variables, DrawMap)
}

DrawMaps()