François Michonneau

Joseph Brown

David Winter

We are excited to announce a paper describing `rotl`, our package for
the[Open Tree of Life](http://www.opentreeoflife.org/) data, has
been[published](https://doi.org/10.1111/2041-210X.12593). The
fullcitation is:

Michonneau, F., Brown, J. W. and Winter, D. J. (2016), rotl: an Rpackage
to interact with the Open Tree of Life data. *Methods EcolEvol.* doi:
<https://doi.org/10.1111/2041-210X.12593>

The paper, which is freely available, describes the package and the
datait wraps in detail. Rather than rehash the information here, we will
usethis post to briefly introduce the goals of the package and thank
someof the people that helped it come to be.

### What data does Open Tree have and how can `rotl` help you get it?

The [Open Tree of Life](http://www.opentreeoflife.org/)
combinesknowledge from thousands of scientific studies to produce a
singlesource of information about the relationships among all species
onearth. In addition to storing the trees and taxonomies that go into
thisproject, the Open Tree provides a "synthesis tree" that represents
thiscombined knowledge. The Open Tree data can be accessed via the web
pagelinked above, and through an API.`rotl` takes advantage of this API
togive R users the ability to search for phylogenetic information
andimport the results into their R sessions. The imported data can then
beused with the growing ecosystem of packages for phylogenetic
andcomparative biology in R.

### A small example

Using `rotl` to get a tree for a set of names is usually a two
stepprocess. You need to start by matching the set of names you have
torecords 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 atree with theses species in the tips

    tr <- tol_induced_subtree(ott_ids=ott_id(resolved_names))plot(tr)

![img](/assets/blog-images/rotl_pub/ape_tree.png)

The tree is an object of the `ape` class `phylo`, which is used by
mostother phylogeny packages in R. There are two vignettes describing
howthe fetched trees can be [paired with
otherdata](https://cran.rstudio.com/web/packages/rotl/vignettes/data_mashups.html)and
used to [reproduce a
comparativeanalysis](https://cran.rstudio.com/web/packages/rotl/vignettes/meta-analysis.html).[Anothervignette](https://cran.rstudio.com/web/packages/rotl/vignettes/rotl.html)provides
and introduction to the package and includes an FAQ.

### Thanks

We'd like to thank the Open Tree project for providing such an
amazingresource, and for producing a powerful and well-documented API.
`rotl` wasinitially developed as part of the [Open Tree's hackathon in
Ann Arborin2014](/blog/2014/08/15/open-tree-of-life-hackathon/).We'd
like to thank the Open Tree project for inviting us to the meetingand
all participants of that meeting for discussions and their feedbackon
`rotl`. The package was reviewed as part of the rOpenSci
onboardingprocess, and we'd like to thank
[ScottChamberlain](https://scottchamberlain.info/) for the time and
expertisethat went into this review and improved the package.


We are excited to announce a paper describing rotl, our package for theOpen Tree of Life data, has beenpublished. The fullcitation is: Michonneau, F., Brown, J. W. and Winter, D. J. (2016), rotl: an Rpackage to interact with the Open Tree of Life data.
<em>
 Methods EcolEvol.
</em>
doi: https://doi.org/10.1111/2041-210X.12593 The paper, which is freely available, describes the package and the datait wraps in detail.

Rogue Scholar Beiträge

rotl paper published