A different approach is to use CartoDB, a freemium service with sql interface to your data tables that provides a map to visualize data in those tables. They released an R interace to their sql API on Github here – which we can use to make an interactive map from R.
We'll first get some data from GBIF, ~500 occurrences of Puma concolor in the US, then push that data to a CartoDB table. There are a couple more non-programmatic steps in this workflow than with pushing geojson file to Github as outlined in the previous linked above (i.e., going to the CartoDB site and making a visualization, and making it public).
install.packages("devtools") library(devtools) install_github("rgbif", "ropensci", ref = "newapi") install_github("cartodb-r", "Vizzuality", subdir = "CartoDB")
Get some data from GBIF
Here, we'll get data for Puma concolor, the hello, world for biodiversity data.
key <- gbif_lookup(name = "Puma concolor", kingdom = "animals")$speciesKey data <- occ_search(taxonKey = key, limit = 500, georeferenced = TRUE, country = "US", return = "data") head(data) ## name longitude latitude ## 1 Puma concolor (Linnaeus, 1771) -108.9 32.70 ## 2 Puma concolor (Linnaeus, 1771) -108.0 32.88 ## 3 Puma concolor (Linnaeus, 1771) -105.5 32.95 ## 4 Puma concolor (Linnaeus, 1771) -107.8 33.61 ## 5 Puma concolor (Linnaeus, 1771) -107.5 33.00 ## 6 Puma concolor (Linnaeus, 1771) -106.5 36.69 str(data) ## 'data.frame': 500 obs. of 3 variables: ## $ name : Factor w/ 7 levels "Animalia","Carnivora",..: 7 7 7 7 7 7 7 7 7 7 ... ## $ longitude: num -109 -108 -105 -108 -107 ... ## $ latitude : num 32.7 32.9 33 33.6 33 ...
Great, we have some data. Now let's make a map.
Push data up to CartoDB
I frist crated a table in my CartoDB account named
pumamap. Then, I need to initialize the connection with CartoDB with my account name and API key. Note that I am pulling up my key from my .Rprofile file on my machine for ease and so it's not revealed to you 🙂
key = getOption("mycartodbkey") cartodb("recology", api.key = key)
Now we need to push data to our
pumamap table using the function
cartodb.row.insert. It accepts one row of data, so we'll pass each row of data with an
rows <- apply(data, 1, as.list) lapply(rows, function(x) cartodb.row.insert(name = "pumamap", columns = list("name", "longitude", "latitude"), values = x))
After the upload is finished, I had to make sure the table was georeferenced, and played with settings to suit my style. And then I made a visualization from the
pumamap dataset and made it public. And that's it! You can find the map here, and it can be embedded:
And we can examine a row from the table in our CartoDB account with a single line of code
cartodb.row.get(name = "pumamap", cartodb_id = 10) ## cartodb_id name description ## 1 1 Puma concolor (Linnaeus, 1771) NULL ## created_at updated_at ## 1 2013-11-03T06:40:12+0100 2013-11-03T06:46:55+0100 ## the_geom the_geom_webmercator ## 1 0101000020E610000089247A19C5365BC08C15359886594040 NULL ## latitude longitude ## 1 32.7 -108.9