In ropensci/spoccutils: Visualize Species Occurrence Data

Load spocc and mapr

library("spocc")
library("mapr")

Interactive maps

Leaflet.js

Leaflet JS is an open source mapping library that can leverage various layers from multiple sources. Using the leaflet library, we can generate a local interactive map of species occurrence data.

An example:

spp <- c('Danaus plexippus','Accipiter striatus','Pinus contorta')
dat <- occ(query = spp, from = 'gbif', has_coords = TRUE, limit = 100)
map_leaflet(dat)

Geojson map as a Github gist

You can also create interactive maps via the mapgist function. You have to have a Github account to use this function. Github accounts are free though, and great for versioning and collaborating on code or papers. When you run the map_gist function it will ask for your Github username and password. You can alternatively store those in your .Rprofile file by adding entries for username (options(github.username = 'username')) and password (options(github.password = 'password')).

spp <- c('Danaus plexippus', 'Accipiter striatus', 'Pinus contorta')
dat <- occ(query = spp, from = 'gbif', has_coords = TRUE, limit = 100)
dat <- fixnames(dat)
map_gist(dat, color = c("#976AAE", "#6B944D", "#BD5945"))

Static maps

base plots

Base plots, or the built in plotting facility in R accessed via plot(), is quite fast, but not easy or efficient to use, but are good for a quick glance at some data.

spnames <- c('Accipiter striatus', 'Setophaga caerulescens', 'Spinus tristis')
out <- occ(query = spnames, from = 'gbif', has_coords = TRUE, limit = 100)
map_plot(out, size = 1, pch = 10)

ggplot2

ggplot2 is a powerful package for making visualizations in R. Read more about it here.

dat <- occ(query = 'Lynx rufus californicus', from = 'gbif', has_coords = TRUE, limit = 200)
map_ggplot(dat, map = "usa")

via dismo

if that's your jam, though you might find rgbif easier

library("dismo")
g <- gbif('Batrachoseps', 'luciae', geo = TRUE, end = 300)
map_leaflet(g, lon = "lon", lat = "lat", name = "scientificName")

The supported inputs

All functions take the following kinds of inputs:

• An object of class occdat, from the package spocc. An object of this class is composed of many objects of class occdatind
• An object of class occdatind, from the package spocc
• An object of class gbif, from the package rgbif
• An object of class data.frame. This data.frame can have any columns, but must include a column for taxonomic names (e.g., name), and for latitude and longitude (we guess your lat/long columns, starting with the default latitude and longitude).
• An object of class SpatialPoints
• An object of class SpatialPointsDatFrame

ropensci/spoccutils documentation built on Sept. 12, 2022, 3:03 p.m.