taxa_to_highertaxa: Change taxa to higher taxa level

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

Description

This function modifies the taxa names in the @commdf@counts slot of epd.entity.df-class objects. More specifically, this function compares the taxa name with the taxonomy of the EPD to use the higher taxa names. If these changes result in duplicated columns of the same taxa their values are unified by summing them.

Usage

taxa_to_highertaxa(x, epd.taxonomy, rm_null_mhvar = FALSE)

## S4 method for signature 'epd.entity.df,data.frame'
taxa_to_highertaxa(x, epd.taxonomy,
  rm_null_mhvar = FALSE)

## S4 method for signature 'epd.entity,data.frame'
taxa_to_highertaxa(x, epd.taxonomy,
  rm_null_mhvar = FALSE)

Arguments

x	epd.entity epd.entity.df-class object.
epd.taxonomy	data.frame Data frame with the taxonomy from the EPD as from the get_taxonomy_epd function.
rm_null_mhvar	logical Logical value indicating whether to remove or not those taxa that has no value for higher level taxa.

Value

Object of class epd.entity.df-class with new taxa names.

Examples

## Not run: 
epd.connection <- connect_to_epd(host="localhost", database="epd",
                                 user="epdr", password="epdrpw")
epd.1 <- get_entity(1, epd.connection)
epd.1 <- entity_to_matrices(epd.1)
epd.1@commdf@taxanames
colnames(epd.1@commdf@counts)
epd.1.hn <- taxa_to_highertaxa(epd.1, get_taxonomy_epd(epd.connection))
epd.1.hn@commdf@taxanames
colnames(epd.1.hn@commdf@counts)

## End(Not run)

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