| clean_ott_chronogram {datelife} | R Documentation |
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 |
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