Goal: import data using API directly into R
rOpenSci
- group building R package wrappers to science APIs
- lots of useful wrappers
Do Exercise 3: Get weather
Exploring other weather APIs
There are an abundance of other options for exploring weather observations, both raw weather station reports, and modeled and forecasted weather.
# some weather packages I have used...
install.packages('darksky', 'RNCEP', 'GhcnDaily', 'rwunderground')
Taxonomy APIs
Taxonomy can be a moving target, yet biodiversity conservation depends in part on being able to name and identify species in a consistent way.
This has been controversial recently:
- Taxonomy anarchy hampers conservation
- Taxonomy based on science is necessary for global conservation
Because taxonomy changes (though maybe not as frequently as the weather), it helps to be able to check your species list against a standard list.
The Plant List is an example for true plants (including ferns and allies). It is a web API that compiles the latest up-to-date taxonomic thinking of the major herbaria and the specialists in certain clades.
Do Exercise 4: Check taxonomy
Taxize
Another, more broad API wrapper for taxonomy is taxize from rOpenSci.
It connects to multiple data sources including animal taxonomy.
library(taxize)
###
new.dat$gs <- paste(new.dat$plant_genus,new.dat$plant_species)
# We can do an entire vector
plants2<-as.vector(unique(new.dat[["gs"]]))
classification(plants2, db="itis", row = 1)
# Or simply 1 species at a time
classification("Sander vitreus", db="itis")
#Maybe we just want family
tax_name(query = "Helianthus annuus", get = "family", db = "itis", rows=1)[[3]]
# Get Downstream Data. How many genera are in the perch family?
downstream("Percidae", downto = "Genus", db = "col")
downstream("Percidae", downto = "Species", db = "col", intermediate = TRUE)