betydb
Search for traits from BETYdb
Search for traits from BETYdb
Usage
betydb_search(query = "Maple SLA", fmt = "json", key = NULL,
user = NULL, pwd = NULL, ...)betydb_trait(id, genus = NULL, species = NULL, fmt = "json", key = NULL,
user = NULL, pwd = NULL, ...)
betydb_specie(id, genus = NULL, species = NULL, fmt = "json",
key = NULL, user = NULL, pwd = NULL, ...)
betydb_citation(id, genus = NULL, species = NULL, fmt = "json",
key = NULL, user = NULL, pwd = NULL, ...)
betydb_site(id, fmt = "json", key = NULL, user = NULL, pwd = NULL, ...)
Arguments
- query
- Query terms
- fmt
- (character) Format to return data in, one of json, xml, csv. Only json currently supported.
- key
- (character) An API key. Use this or user/pwd combo. Save in your
.Rprofile
file asbetydb_key
. Optional - user,pwd
- (character) A user name and password. Use a user/pwd combo or an API key.
Save in your
.Rprofile
file asbetydb_user
andbetydb_pwd
. Optional - ...
- Curl options passed on to
GET
. Optional - id
- (integer) One or more ids for a species, site, variable, etc.
- genus
- (character) A genus name. Optional
- species
- (character) A specific epithet. Optional
Details
Details:
Authentication
Defers to use API key first since it's simpler, but if you don't have an API key, you can supply a username and password.
Functions
Singular functions like betydb_trait
accept an id and additional parameters,
and return a list of variable outputs depending on the inputs.
However, plural functions like betydb_traits
accept query parameters, but not
ids, and always return a single data.frame.
References
API documentation
Examples
# General Search
out <- betydb_search(query = "Switchgrass Yield")
library("dplyr")
out %>%
group_by(id) %>%
summarise(mean_result = mean(as.numeric(mean), na.rm = TRUE)) %>%
arrange(desc(mean_result))
# Get by ID
## Traits
betydb_trait(id = 10)
## Species
betydb_specie(id = 1)
## Citations
betydb_citation(id = 1)
## Citations
betydb_site(id = 795)