Using the Open Tree of Life for your Research -- with R!: Instructor Notes

1.1.

Note: Going from a common name to a scientific name

TNRS only deals with scientific names. If you want to work with common names, you will have to use a service that can get the scientific name of a list of common names. There are no functions in rotl to deal with this. We know of at least two places that have implemented this otherwise. The OneZoom project has developed a service that provides all scientific names associated to common names in the Encyclopedia of Life database. The phylotastic project has implemented a common name to scientific name service that is also available in the r package rphylotastic.

6.1 Getting source trees with branch lengths

Note

chronograms <- rotl::studies_find_trees(property = "ot:branchLengthMode", value = "ot:time", verbose = TRUE, detailed = TRUE)

class(chronograms)
names(chronograms)

We should be able to use list_trees() to get all trees matching our criteria.

rotl:::list_trees(chronograms)

Except, it does not really work.