B Related tools

B.1 rtol: An R interface to Open Tree API

rtol (Michonneau, Brown, and Winter 2016) is an R package to interact with the Open Tree of Life data APIs.

## example from: https://github.com/ropensci/rotl
library(rotl)
apes <- c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo")
(resolved_names <- tnrs_match_names(apes))

##   search_string unique_name approximate_match ott_id
## 1         pongo       Pongo             FALSE 417949
## 2           pan         Pan             FALSE 417957
## 3       gorilla     Gorilla             FALSE 417969
## 4       hoolock     Hoolock             FALSE 712902
## 5          homo        Homo             FALSE 770309
##   is_synonym          flags number_matches
## 1      FALSE                             2
## 2      FALSE sibling_higher              1
## 3      FALSE sibling_higher              1
## 4      FALSE                             1
## 5      FALSE sibling_higher              1

tr <- tol_induced_subtree(ott_ids = ott_id(resolved_names))
ggtree(tr) + geom_tiplab() + xlim(NA, 5)

Figure B.1: Get an induced subtree from the big Open Tree.

References

Michonneau, François, Joseph W. Brown, and David J. Winter. 2016. “Rotl: An R Package to Interact with the Open Tree of Life Data.” Methods in Ecology and Evolution 7 (12): 1476–81. https://doi.org/10.1111/2041-210X.12593.