list_taxa: List taxa in the EPD

In dinilu/EPDr: Interact with the European Pollen Database (EPD)

Description

This function looks into the database and returns combined information in the P_VARS and P_GROUP tables (see documentation of the EPD: http://www.europeanpollendatabase.net/data/downloads/image/pollen-database-manual-20071011.doc). The function allows to restrict the list to taxa in an specific group, using parameter group_id along with a valid connection to the database.

Usage

list_taxa(connection, group_id = NULL)

Arguments

connection	PostgreSQLConnection. Object of class PostgreSQLConnection as returned by function connect_to_epd.
group_id	character. Character vector with group ids (four character strings; see list_taxagroups to check correspondence between groups and group ids). The user can specify as many groups as desired in a single call of the function.

Value

data.frame The function returns a data frame with five columns: var_, varname, varcode, mhvar, and groupid.

• "var_ is" the taxa identification number in the database.

• "varname" is the taxa name.

• "varcode" is the short taxa name.

• "mhvar" is the identification number of the higher taxonomical level.

• "groupid" is the identification number of the group that the taxa belongs to.

Examples

## Not run: 
epd.connection <- connect_to_epd(host = "localhost", database = "epd",
                                 user = "epdr", password = "epdrpw")
list_taxa(epd.connection, "HERB")
list_taxa(epd.connection, c("HERB", "TRSH"))

## End(Not run)

dinilu/EPDr documentation built on Aug. 22, 2019, 1:03 p.m.