Have students install Python (if using Data Retriever)

Types of data access

• Variety of ways in which data is made publicly available
• We’ve seen many of these and will talk about more today

Direct Downloads

• Website that lets you download data
  • Dataset specific
  • General data archive
  • Aggregator for specific kinds of data
• Ideally an unchanging url
• Sometimes requires point and click interface to get data
• Examples
  • Data paper: https://www.nature.com/articles/sdata2018165
  • NEON website: http://data.neonscience.org/static/browse.html

APIs

• Programmatically access data over the web
• Typically allows choosing subsets of data
• Specially structured urls
• Mostly used through packages that “wrap” the APIs
• E.g., used spocc which include multiple API wrappers for occurrence data
• One of those sources is the GBIF with the rgbif API wrapper

install.packages('rgbif')
library('rgbif')
rgbif::occ_search(scientificName = "Ursus americanus", limit = 50)
rgbif::occ_search(scientificName = "Ursus americanus", limit = 50,
                  fields=c('name','decimalLatitude','decimalLongitude'))

Data Packages

• An R package that contains data

install.packages('gapminder')
library('gapminder')
gapminder

• Also some non-R specific versions
  • datapackage-r

Data Retrievers

• Software that acquires data from other sources
• Sometimes cleans and restructures that data as well

• retriever

• Go to https://www.python.org/downloads
• Click the yellow Download Python button
• Start the installer

• Click “Add Python 3.7 to PATH” then “Install Now”

• In RStudio
  • Terminal: pip install retriever
  • Console: install.packages('rdataretriever')

library(rdataretriever)
get_updates()
install('breed-bird-survey', 'csv')
counts <- read.csv("breed_bird_survey_counts")
mammal_masses <- fetch("mammal-masses")
mammal_masses$

Licenses

• What can you do with the data
• Creative Commons
  • CC0: Anything at all
  • CC-BY: Anything you want, but you must cite the source
  • CC-BY-SA: If you build on it you must redistribute with the same license
  • CC-BY-NC: Only available for non-commercial use (but this is tricky)
• Roll your own licenses
• Data may not even be copyrightable
• Important express of how folks would like their public data used

Citing data

• Many datasets specificy how to cite them
• If published as data papers cite the paper
• If published on an archiving site there will be a link for how to cite
• Often request acknowledgements as well