class2tree checks duplicated taxa in higher levels, resolve #934

[trvinh]

Description

class2tree can detect duplicated input taxa, which already belong to the taxonomy strings of other taxa in higher levels (e.g. genus Haliotis belongs to the taxonomy string of species H. cracherodii)

Related Issue

#934

Example

spnames <- c("Haliotis", "Haliotis cracherodii", "Haliotis rufescens", "Megabalanus californicus", "Cadlina luteomarginata", "Anthozoa", "Gastropoda")
outTaxize <- classification(spnames, db = "gbif")
tree <- class2tree(outTaxize)

The duplicated taxa will be ignored with a WARNING while creating the tree

Get all ranks and their taxIDs
Align taxonomy hierarchies...
WARNING: 2 duplicated taxa have been ignored! Including: Haliotis; Gastropoda
Taxonomy alignment done!
Calculate distance matrix
Add node labels

[zachary-foster]

Thanks! I will modify it to make it optional, since I think some may want the old behavior. In some cases it might make sense to include the coarser taxa in the tree, but this seems useful as well.