clean_ott_chronogram: Clean up some issues with OToL chronograms For now it 1)...

Description Usage Arguments Details Value

View source: R/opentree_chronograms.R

Description

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

Usage

1

Arguments

phy

A phylo object

Details

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 succesful with no approximate matching. Original label is replaced by the matched name.

approximated

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

unmatched

Tnrs matching was attempted and unsuccesful. 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 phylo and match_names. See details.


phylotastic/datelife documentation built on Jan. 22, 2019, 12:29 a.m.