Description

Help on authentication

What is an API?

An API is an Application Programming Interface. The term "API" can be used for lots of scenarios, but in this case we're talking about web APIs, or APIs (interfaces) to web resources. taxize interacts with remote databases on the web via their APIs. You don't need to worry about the details of how that all works; just know that some of them require authentication and some do not.

What are API keys?

For those APIs that require authentication, the way that's typically done is through API keys: alphanumeric strings of variable lengths that are supplied with a request to an API.

taxize won't get these keys for you; rather, you have to go get a key for each service, but we do provide information on how to get those keys. See key_helpers() for help on how to obtain keys for this package.

Using API keys

You can store API keys as R options in your .Rprofile file, or as environment variables in either your .Renviron file or .bash_profile file, o.zshrc file (if you use oh-my-zsh) or similar. See Startup for help on R options and environment variables.

Save your API keys with the following names:

• Tropicos: R option or env var as 'TROPICOS_KEY'

• IUCN: R option or env var as 'IUCN_REDLIST_KEY'

• ENTREZ: R option or env var as 'ENTREZ_KEY'

If you save in .Renviron it looks like: ENTREZ_KEY=somekey

If you save in a .bash_profile, .zshrc, or similar file it looks like: export ENTREZ_KEY=somekey

If you save in a .Rprofile it looks like: options(ENTREZ_KEY = "somekey")

Remember to restart your R session (and to start a new shell window/tab if you're using the shell) to take advantage of the new R options or environment variables.

We strongly recommend using environment variables (https://en.wikipedia.org/wiki/Environment_variable) over R options because environment variables are widely used across programming languages, operating systems, and computing environments; whereas R options are specific to R.

Note that NCBI Entrez doesn't require that you use an API key, but you do get a higher rate limit with a key (more requests per time period), from 3 to 10 requests per second, so do get one.

See Also

key_helpers()