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:
If you want to test the development version, you first need to install ghit (
ghit is a more lightweight version of devtools if your sole purpose is to install packages that are hosted on GitHub).
Then you can install
library(ghit) # or library(devtools) install_github("ropensci/rotl")
There are three vignettes:
Start by checking out the “How to use
rotl?” by typing:
vignette("how-to-use-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:
The vignette “Using the Open Tree Synthesis in a comparative analsysis” demonstrates how you can reproduce an analysis of a published paper by downloading the tree they used, and data from the supplementary material:
The vignettes are also available from CRAN: How to use
rotl?, 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
library(rotl) apes <- c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo") (resolved_names <- tnrs_match_names(apes))
## 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 2 ## 2 2 ## 3 1 ## 4 1 ## 5 1
Now we can get the tree with just those tips:
tr <- tol_induced_subtree(ott_ids=ott_id(resolved_names)) 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
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.