Data Management for Biologists

Surveying the hidden parts of the data life cycle

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APIs & supplemental data

Get weather


Weather is one of the most frequently desired covariates for any environmental analysis. The National Oceanic and Atmospheric Administration has a history of high quality, high frequency, high resolution datasets that are available to the public.

The National Climatic Data Center provides an API connection to historical weather.

The rOpenSci team has created an R package that queries this API directly, called rnoaa.

  1. Get a key from NOAA NCDC - this is necessary to use the API package.
  2. Install and load the package, and paste your token into an object
install.packages('rnoaa')
library(rnoaa)
?rnoaa

mytoken <- 'QrKTCPmNwJWXxFhpLHijBfXPIRShBAiv'
# this is EL's token

This part takes a while, so the identifier for the weather station is provided for you. But if you want to explore available stations, you can download the whole set (~600K stations, takes a few minutes).

#library(data.table)
#station_data <- ghcnd_stations()
#setDT(station_data)
#station_data[latitude > 44.9 & latitude < 45 & longitude > -93.2 & longitude < -93,
             .N, name]
#station_data[name == 'UNIV OF MINN ST PAUL']

Once the weather station is identified, you can pull observations:

# the weather station USC00218450 is on the St Paul Campus
out <- ncdc(datasetid='GHCND',
 stationid='GHCND:USC00218450',
 datatypeid='TMAX',
 startdate = '2017-03-01',
 enddate = '2017-03-31',
 limit=500, token = mytoken)

out # examine results 
ncdc_plot(out) # built-in plot function (limited but quick)

Challenge problem:

  1. Connect to the Bee Lab database (your local copy, or the remote hosted one)

  2. Get the “collection_events” table from the database into an R data frame.

  3. Using the St. Paul campus weather station (ID above), download the precipitation data for the dates inclusive of all the collection events.

    HINT: use datatypeid = 'PRCP'

  4. What was the rainiest date during the study period? How much rain fell (in mm)?

[click here for output]