clean_ott_chronogram: Clean up some issues with Open Tree of Life chronograms For...

In datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Clean up some issues with Open Tree of Life chronograms For now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted

Description

Clean up some issues with Open Tree of Life chronograms For now it 1) checks unmapped taxa and maps them with tnrs_match.phylo, 2) roots the chronogram if unrooted

Usage

clean_ott_chronogram(phy)

Arguments

phy	A phylo object.

Details

There is no limit to the number of names that can be queried and matched.

The output will preserve all elements from original input phylo object and will add

phy$mapped

A character vector indicating the state of mapping of phy$tip.labels:

original

Tnrs matching was not attempted. Original labeling is preserved.

ott

Matching was manually made by a curator in Open Tree of Life.

tnrs

Tnrs matching was attempted and successful with no approximate matching. Original label is replaced by the matched name.

approximated

Tnrs matching was attempted and successful but with approximate matching. Original labeling is preserved.

unmatched

Tnrs matching was attempted and unsuccessful. Original labeling is preserved.

phy$original.tip.label

A character vector preserving all original labels.

phy$ott_ids

A numeric vector with ott id numbers of matched tips. Unmatched and original tips will be NaN.

if tips are duplicated, tnrs will only be run once (avoiding increases in function running time) but the result will be applied to all duplicated tip labels

Value

An object of class data frame or phylo, with the added class match_names.

NULL

NULL

datelife documentation built on July 10, 2023, 2:02 a.m.