Interface to Open Tree of Life API
rotl is an R package to interact with the Open Tree of Life data APIs.
It was initially developed as part of the NESCENT/OpenTree/Arbor
hackathon.
Client libraries to interact with the Open Tree of Life API also exists
for Python and
Ruby.
The current stable version is available from CRAN, and can be installed
by typing the following at the prompt in R:
install.packages("rotl")
If you want to test the development version, you first need to install
the remotes package.
install.packages("remotes")
Then you can install rotl using:
remotes::install_github("ropensci/rotl")
There are three vignettes:
Start by checking out the “How to use rotl?” by typing:vignette("rotl", package="rotl") after installing the package.
Then explore how you can use rotl with other packages to combine
your data with trees from the Open Tree of Life project by typing:vignette("data_mashups", package="rotl").
The vignette “Using the Open Tree Synthesis in a comparative
analysis” demonstrates how you can reproduce an analysis of a
published paper by downloading the tree they used, and data from the
supplementary material: vignette("meta-analysis", package="rotl").
The vignettes are also available from CRAN: How to userotl?,
Data
mashups,
and Using the Open Tree synthesis in a comparative
analysis.
Taxonomic names are represented in the Open Tree by numeric identifiers,
the ott_ids (Open Tree Taxonomy identifiers). To extract a portion of
a tree from the Open Tree, you first need to find ott_ids for a set of
names using the tnrs_match_names function:
library(rotl)apes <- c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo")(resolved_names <- tnrs_match_names(apes))
## search_string unique_name approximate_match score ott_id is_synonym## 1 pongo Pongo FALSE 1 417949 FALSE## 2 pan Pan FALSE 1 417957 FALSE## 3 gorilla Gorilla FALSE 1 417969 FALSE## 4 hoolock Hoolock FALSE 1 712902 FALSE## 5 homo Homo FALSE 1 770309 FALSE## flags number_matches## 1 2## 2 sibling_higher 2## 3 sibling_higher 1## 4 1## 5 sibling_higher 1
Now we can get the tree with just those tips:
tr <- tol_induced_subtree(ott_ids = ott_id(resolved_names))
## Warning in collapse_singles(tr, show_progress): Dropping singleton nodes with## labels: mrcaott83926ott6145147, mrcaott83926ott3607728, mrcaott83926ott3607876,## mrcaott83926ott3607873, mrcaott83926ott3607687, mrcaott83926ott3607716,## mrcaott83926ott3607689, mrcaott83926ott3607732, mrcaott770295ott3607719,## mrcaott770295ott3607692, Ponginae ott1082538, Hylobatidae ott166544
plot(tr)
The code above can be summarized in a single pipe:
library(magrittr)## or expressed as a pipe:c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo") %>%tnrs_match_names() %>%ott_id() %>%tol_induced_subtree() %>%plot()
## Warning in collapse_singles(tr, show_progress): Dropping singleton nodes with## labels: mrcaott83926ott6145147, mrcaott83926ott3607728, mrcaott83926ott3607876,## mrcaott83926ott3607873, mrcaott83926ott3607687, mrcaott83926ott3607716,## mrcaott83926ott3607689, mrcaott83926ott3607732, mrcaott770295ott3607719,## mrcaott770295ott3607692, Ponginae ott1082538, Hylobatidae ott166544
To cite rotl in publications pleases use:
Michonneau, F., Brown, J. W. and Winter, D. J. (2016), rotl: an R
package to interact with the Open Tree of Life data. Methods in
Ecology and Evolution. 7(12):1476-1481. doi:
10.1111/2041-210X.12593
You may also want to cite the paper for the Open Tree of Life
Hinchliff, C. E., et al. (2015). Synthesis of phylogeny and taxonomy
into a comprehensive tree of life. Proceedings of the National Academy
of Sciences 112.41 (2015): 12764-12769 doi:
10.1073/pnas.1423041112
The manuscript in Methods in Ecology and Evolution includes additional
examples on how to use the package. The manuscript and the code it
contains are also hosted on GitHub at:
https://github.com/fmichonneau/rotl-ms
Starting with v3.0.0 of the package, the major and minor version numbers
(the first 2 digits of the version number) will be matched to those of
the API. The patch number (the 3rd digit of the version number) will be
used to reflect bug fixes and other changes that are independent from
changes to the API.
rotl can be used to access other versions of the API (if they are
available) but most likely the high level functions will not work.
Instead, you will need to parse the output yourself using the “raw”
returns from the unexported low-level functions (all prefixed with a.). For instance to use the tnrs/match_names endpoint for v2 of
the API:
rotl:::.tnrs_match_names(c("pan", "pango", "gorilla", "hoolock", "homo"), otl_v = "v2")
Please note that this project is released with a Contributor Code of
Conduct. By
participating in this project you agree to abide by its terms.
