Specimen records across cities


rOpenSci package: rgbif



Specimen records across cities

In this example, we collect specimen records across different cities using GBIF data from the rgbif package.

This example can be done using BISON data as well with our rbison package.

Load libraries

library("rgbif")
library("ggplot2")
library("plyr")
library("RCurl")
library("RColorBrewer")

Get bounding boxes for some cites

rawdat <- getURL("https://raw.githubusercontent.com/amyxzhang/boundingbox-cities/master/boundbox.txt")
dat <- read.table(text = rawdat, header = FALSE, sep = "\t", col.names = c("city",
    "minlat", "maxlon", "maxlat", "minlon"))
dat <- data.frame(city = dat$city, minlon = dat$minlon, minlat = dat$minlat,
    maxlon = dat$maxlon, maxlat = dat$maxlat)

getdata <- function(x) {
    coords <- as.numeric(x[c("minlon", "minlat", "maxlon", "maxlat")])
    num <- occ_search(geometry = coords)$meta$count
    data.frame(city = x["city"], richness = num, stringsAsFactors = FALSE)
}

out <- apply(dat, 1, getdata)

Merge to original table

out <- merge(dat, ldply(out), by = "city")

Add centroids from bounding boxes

out <- transform(out, lat = (minlat + maxlat)/2, lon = (minlon + maxlon)/2)

Plot data

mapp <- map_data("world")
ggplot(mapp, aes(long, lat)) + geom_polygon(aes(group = group), fill = "white",
    alpha = 0, color = "black", size = 0.4) + geom_point(data = out, aes(lon,
    lat, color = richness), size = 5, alpha = 0.8) + scale_color_continuous(low = "#60E1EE",
    high = "#0404C8") + labs(x = "", y = "") + theme_grey(base_size = 14) +
    theme(legend.position = "bottom", legend.key = element_blank()) + guides(color = guide_legend(keywidth = 2))

plot

Notes

Bounding lat/long data from here