traits (version 0.5.1)

betydb_query: Query a BETY table

Description

Query a BETY table

Usage

betydb_query(
  ...,
  table = "search",
  key = NULL,
  api_version = NULL,
  betyurl = NULL,
  user = NULL,
  pwd = NULL,
  progress = TRUE
)
betydb_search(
  query = "Maple SLA",
  ...,
  include_unchecked = NULL,
  progress = TRUE
)

Value

A data.frame with attributes containing request metadata, or NULL if the query produced no results

Arguments

...

(named character) Columns to query, as key="value" pairs. Note that betydb_query passes these along to BETY with no check whether the requested keys exist in the specified table.

table

(character) The name of the database table to query, or "search" (the default) for the traits and yields view

key

(character) An API key. Use this or user/pwd combo. Save in your .Rprofile file as options(betydb_key = "your40digitkey"). Optional

api_version

(character) Which version of the BETY API should we query? One of "v0" or "beta". Default is options("betydb_api_version") if set, otherwise "v0".

betyurl

(string) url to target instance of betydb. Default is options("betydb_url") if set, otherwise "https:/www.betydb.org/"

user, pwd

(character) A user name and password. Use a user/pwd combo or an API key. Save in your .Rprofile file as options(betydb_user = "yournamehere") and options(betydb_pwd = "yourpasswordhere"). Optional

progress

show progress bar? default: TRUE

query

(character) A string containing one or more words to be queried across all columns of the "search" table.

include_unchecked

(logical) Include results that have not been quality checked? Applies only to tables with a "checked" column: "search", "traits", "yields". Default is to exclude unchecked values.

Details

Use betydb_query to retrieve records from a table that match on all the column filters specified in '...'. If no filters are specified, retrieves the whole table. In API versions that support it (i.e. not in v0), filter strings beginning with "~" are treated as regular expressions.

Examples

if (FALSE) {
# literal vs regular expression vs anchored regular expression:
betydb_query(units = "Mg", table = "variables")
# NULL
betydb_query(units = "Mg/ha", table = "variables") %>% select(name) %>% c()
# $name
# [1] "a_biomass"                  "root_live_biomass"
# [3] "leaf_dead_biomass_in_Mg_ha" "SDM"

betydb_query(genus = "Miscanthus", table = "species") %>% nrow()
# [1] 10
(betydb_query(genus = "~misc", table = "species", api_version = "beta")
 %>% select(genus)
 %>% unique() %>% c())
# $genus
# [1] "Platymiscium" "Miscanthus"   "Dermiscellum"

(betydb_query(genus = "~^misc", table = "species", api_version = "beta")
 %>% select(genus)
 %>% unique() %>% c())
# $genus
# [1] "Miscanthus"
}