From occurrence data to interactive maps on the web
We have a number of packages for getting species occurrence data: rgbif and rbison. The power of R is that you can pull down this occurrence data, manipulate the data, do some analyses, and visualize the data - all in one open source framework.
However, when dealing with occurrence data on maps, it is often useful to be able to interact with the visualization. Github, a code hosting and collaboration site, now renders a particular type of map file format as an interactive map. This file format is called
.geojson. Here is an example of an interactive map hosted on Github, embedded here:
Note that you can go full screen on these maps too. Check it out here.
To demonstrate how easy it can be to do this on your own, the following is a small demo of searching for occurrence data, converting to geojson, and pushing up to Github.
Install rbison from Github
# install_github('rbison', 'ropensci') # uncomment if you haven't # installed it library(rbison)
Step 1: Seach for some occurrence data
Search for data on the bison.
dat <- bison(species = "Bison bison", count = 500)
Take a peak at the data just to make sure we have some occurrence data
id name longitude latitude 1 686467428 Bison bison -118.8 43.31 2 656975776 Bison bison -118.8 43.31 3 785794942 Bison bison -111.1 44.66 4 687029742 Bison bison -110.7 44.46 5 687027385 Bison bison -110.7 44.61 6 773434631 Bison bison -110.6 44.83 provider 1 University of Kansas Biodiversity Institute 2 Natural History Museum of Los Angeles County 3 Museum of Southwestern Biology 4 iNaturalist.org 5 iNaturalist.org 6 iNaturalist.org
Step 2: Convert the data to geojson format
Before this step I made a folder called mygeojson to write data in to, which will also be a Github repository.
In this example, we are using the option method=‘web’ in the
togeojson function, but we could also use method=‘local’ which wouldl use the
rgdal package to convert to a geojson file format locally. Specifying method=‘web’ uses the Ogre web client.
dat_df <- bison_data(dat, "data_df") write.csv(dat_df, "~/github/sac/mygeojson/bison_bison.csv") file <- "~/github/sac/mygeojson/bison_bison.csv" togeojson(file, method = "web", destpath = "~/github/sac/mygeojson/", outfilename = "bison_bison")
Step 3: Go to your terminal or git GUI and push up the new geojson file
cd ~/github/sac/mygeojson/ git init git add . git commit -a -m 'my first geojson file' git remote add origin https://github.com/sckott/mygeojson.git git push origin master
Then go to your new repo on Github and click on the
.geojson file you created, and you’ll get a map. You can share this with others, and even embed the interactive map in other web sites, as you can see below. Try clicking on the points - they give metadata associated with each point.
Check out the full screen version here.
It is as easy as that! We’ll add this functionality into our
rgbif package as well.
- I wrote earlier about this topic on my own blog here.
- Github help for geojson file https://help.github.com/articles/mapping-geojson-files-on-github#embedding-your-map-elsewhere