---
name: rotl-paper-published
layout: post
title: "rotl paper published"
date: 2016-18-02
authors:
- name: Francois Michonneau
url: http://francoismichonneau.net/
- name: Joseph Brown
url: http://www-personal.umich.edu/~josephwb/
- name: David Winter
url: http://david-winter.info
tags:
- R
- rotl
- open-tree
- publication
---
We are excited to say a paper describing rotl, our package for the Open Tree
of Life data, has been published
at Methods and Ecology and Evolution. The paper, which is freely available,
describes the package and the data it wraps in detail. Rather than rehash the
information here, we will use this post to briefly introduce the goals of the
package and thank some of the people that helped it come to be.
The Open Tree of Life combines knowledge from
thousands of scientific studies to produce a single source of information about
the relationships among all species on earth. In addition to storing the
trees and taxonomies that go into this project, the Open Tree provides a
"synthesis tree" that represents this combined knowledge. The Open Tree data can
be accessed via the web page linked above, and through an API.rotl takes
advantage of this API to give R users the ability to search for phylogenetic
information and import the results into their R sessions. The imported data can
then be used with the growing ecosystem of packages for phylogenetic and
comparative biology in R.
Using rotl to get a tree for a set of names is usually two step process. You
need to start by matching the set of names you have to records in the Open Tree
database, and obtain unique IDs for each one. The function tnrs_match_names
handles this task:
library(rotl)
apes <- c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo")
resolved_names <- tnrs_match_names(apes)
resolved_names ## search_string unique_name approximate_match ott_id is_synonym flags
## 1 pongo Pongo FALSE 417949 FALSE
## 2 pan Pan FALSE 417957 FALSE
## 3 gorilla Gorilla FALSE 417969 FALSE
## 4 hoolock Hoolock FALSE 712902 FALSE
## 5 homo Homo FALSE 770309 FALSE
## number_matches
## 1 1
## 2 1
## 3 1
## 4 1
## 5 1
Once you have a good set of unique IDs, you will want to fetch a tree. You can
use ott_id to extract just the IDs from the table returned by
tnrs_match_names and pass those to tol_induced_subtree to fetch a
tree with theses species in the tips
tr <- tol_induced_subtree(ott_ids=ott_id(resolved_names))
plot(tr)
The tree is an object of the ape class phylo, which is used by most other
phylogeny packages in R. There are two vignettes describing how the fetched
trees can be paired with other data
and used to reproduce a comparative analysis.
Another vignette
provides and introduction to the package and includes an FAQ.
We'd like to thank the Open Tree project for providing such an amazing resource
and produce and powerful and well-documented API. rotl was initially developed
as part of the Open Tree's hackathon in Ann Arbor in 2014.
We'd like to thank the Open Tree project for inviting us to the meeting and all
participants of that meeting for discussions and their feedback on rotl. The
package was reviewed as part of the ROpenSci onboarding process, and we'd like to
thank Scott Chamberlain for the time and
expertise that went into this review and improved the package.