mapr tutorial

for v0.2.0

Utilities for 'vizualizing' species occurrence data. Includes functions to 'vizualize' occurrence data from 'spocc', 'rgbif', and other packages. Mapping options included for base R plots, 'ggplot2', and various interactive maps.

Installation

Stable version from CRAN

install.packages("mapr")

Development version from GitHub

if (!require("devtools")) install.packages("devtools")
devtools::install_github("ropensci/mapr")
library("mapr")
library("spocc")

Usage

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)

leaflet

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"))

gist

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, cex = 1, pch = 10)

plot of chunk unnamed-chunk-7

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")

plot of chunk unnamed-chunk-8

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

Citing

Scott Chamberlain (2016). mapr: 'Visualize' Species Occurrence Data. R package version 0.2.0. https://cran.rstudio.com/package=mapr

License and bugs

Back to top

comments powered by Disqus