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https://github.com/ropensci/rotl

Interface to Open Tree of Life API
https://github.com/ropensci/rotl

peer-reviewed phylogeny r r-package rstats taxonomy

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Interface to Open Tree of Life API

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output: github_document

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```{r setup, eval=TRUE, echo=FALSE}

library(knitr)

# opts_knit$set(upload.fun = image_uri)

opts_knit$set(upload.fun = imgur_upload)

```



[![R-CMD-check](https://github.com/ropensci/rotl/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/rotl/actions/workflows/R-CMD-check.yaml)

[![codecov.io](https://app.codecov.io/github/ropensci/rotl?branch=master)](https://app.codecov.io/github/ropensci/rotl?branch=master)

[![](https://www.r-pkg.org/badges/version/rotl)](https://www.r-pkg.org/pkg/rotl)

[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/rotl)](https://www.r-pkg.org/pkg/rotl)

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# rotl: An R interface to Open Tree 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](https://github.com/OpenTreeOfLife/pyopentree)

and [Ruby](https://github.com/SpeciesFileGroup/bark).



## Installation



The current stable version is available from CRAN, and can be installed by

typing the following at the prompt in R:



```{r, eval=FALSE}

install.packages("rotl")

```



If you want to test the development version, you first need to install

the `remotes` package.



```{r, eval=FALSE}

install.packages("remotes")

```



Then you can install `rotl` using:



```{r, eval=FALSE}

remotes::install_github("ropensci/rotl")

```



## Vignettes



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 use `rotl`?](https://cran.r-project.org/package=rotl/vignettes/rotl.html),

[Data mashups](https://cran.r-project.org/package=rotl/vignettes/data_mashups.html),

and

[Using the Open Tree synthesis in a comparative analysis](https://cran.r-project.org/package=rotl/vignettes/meta-analysis.html).



## Quick start



### Get a little bit of the big Open Tree tree



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:



```{r resolve}

library(rotl)

apes <- c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo")

(resolved_names <- tnrs_match_names(apes))

```



Now we can get the tree with just those tips:



```{r get_tr}

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

plot(tr)

```



The code above can be summarized in a single pipe:



```{r pipe, plot=FALSE}

library(magrittr)

## or expressed as a pipe:

c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo") %>%

  tnrs_match_names() %>%

  ott_id() %>%

  tol_induced_subtree() %>%

  plot()

```



## Citation and Manuscript



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](https://doi.org/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](https://doi.org/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



## Versioning



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:



```{r versioning, eval=FALSE}

rotl:::.tnrs_match_names(c("pan", "pango", "gorilla", "hoolock", "homo"), otl_v = "v2")

```



### Code of Conduct



Please note that this project is released with a

[Contributor Code of Conduct](https://github.com/ropensci/rotl/blob/master/CONDUCT.md). By participating in this project you

agree to abide by its terms.



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