db2taxlist: Import relational databases into taxlist objects

In kamapu/vegtables2: Handling Vegetation Data Sets (Advanced Features)

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,
  taxon_names,
  taxon_relations,
  taxon_traits,
  taxon_levels,
  taxon_views,
  names2concepts,
  subset_levels = TRUE,
  as_list = FALSE,
  ...
)

swea_tax(
  conn,
  taxon_names = c("tax_commons", "taxonNames"),
  taxon_relations = c("swea_dataveg", "taxonRelations"),
  taxon_traits = c("swea_dataveg", "taxonTraits"),
  taxon_views = c("bib_references", "main_table"),
  taxon_levels = c("tax_commons", "taxonLevels"),
  names2concepts = c("swea_dataveg", "names2concepts"),
  ...
)

sam_tax(
  conn,
  taxon_names = c("tax_commons", "taxonNames"),
  taxon_relations = c("sudamerica", "taxonRelations"),
  taxon_traits = c("sudamerica", "taxonTraits"),
  taxon_views = c("bib_references", "main_table"),
  taxon_levels = c("tax_commons", "taxonLevels"),
  names2concepts = c("sudamerica", "names2concepts"),
  ...
)

Arguments

conn	A database connection provided by dbConnect().
...	Further arguments passed among methods. In the two wrappers the arguments are passed to db2taxlist.
taxon_names, taxon_relations, taxon_traits, taxon_views	Character vectors indicating the name of the schema and the table containing the information for the respective slots.
taxon_levels, names2concepts	Character vectors indicating the name of schema and table indicating the taxonomic ranks and the correspondence of names to taxonomic concepts.
subset_levels	Logical value indicating whether taxonomic ranks should be restricted to the used ones or all ranks available in the database.
as_list	Logical value indicating whether the output should be a list or a taxlist object.

kamapu/vegtables2 documentation built on July 8, 2021, 7:57 a.m.