db2taxlist: Import relational databases into taxlist objects

In kamapu/vegtableDB: Handling Vegetation Data Sets (Advanced Features)

Import relational databases into taxlist objects

Description

Ad-hoc function for importing Postgres tables into objects of class taxlist.

This function has been modified to a new version of the database.

Usage

db2taxlist(conn, ...)

## S3 method for class 'PostgreSQLConnection'
db2taxlist(
  conn,
  taxonomy,
  concepts,
  schema = "plant_taxonomy",
  schema_refs = "bib_references",
  subset_levels = TRUE,
  keep_parents = FALSE,
  keep_children = FALSE,
  as_list = FALSE,
  ...
)

Arguments

conn	A database connection provided by dbConnect().
...	Further arguments passed among methods (not used here).
taxonomy	Character value with the name of the taxonomy in the database.
concepts	A vector with taxon concept IDs to be included in the output. If not provided the whole taxonomy will be imported. IDs belonging to a different taxonomy will cause an error message.
schema	Character value indicating the name of the schema containing taxonomic information within the database.
schema_refs	Character value indicating the name of the schema containing the electronic library with taxon views.
subset_levels	Logical value indicating whether taxonomic ranks should be restricted to the used ones or all ranks available in the database.
keep_parents	A logical value indicating whether parents of queried concepts should be included in the output or not. It works only if an argument is provided for the parameter 'concepts'.
keep_children	A logical value indicating whether children of queried concepts should be included in the output or not. It works only if an argument is provided for the parameter 'concepts'.
as_list	Logical value indicating whether the output should be a list or a taxlist object.

kamapu/vegtableDB documentation built on June 18, 2024, 1:13 a.m.