CompletelyProcess: CompletelyProcess

Description Usage Arguments Details Value Author(s)

Description

Do all the processing required to ready a tree for deposition in OpenTree

Usage

1
KillAllDuplicates(phy, verbose=TRUE, autoroot=TRUE, monophy=TRUE)

Arguments

phy

a phylo object

verbose

If TRUE, outputs the status for the slowest step, TNRS with OpenTree

autoroot

If TRUE, sticks a root on the implied root of the tree

monophy

If TRUE, uses MonoPhy and taxize to download a taxonomy and prune off taxa that disagree with the taxonomy

Details

This will remove duplicate taxa (using ape), convert taxon names to those used by OpenTree using its TNRS service and rotl, and then delete taxa that are duplicates after this process. If verbose=TRUE, gives progress reports every 25 taxa. If autoroot=TRUE, it'll add a root if needed to the tree. If monophy=TRUE, it will download an NCBI taxonomy for the tree using taxize and find taxa that are "invaders" or "outliers" and delete them. The thinking is that those taxa may have been poorly TNRSed.

Value

returns a pruned phylo object

Author(s)

Brian O'Meara


bomeara/prepotol documentation built on May 12, 2019, 11:36 p.m.