rotl

Interface to Open Tree of Life API

https://github.com/ropensci/rotl

Science Score: 23.0%

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Keywords

peer-reviewed phylogeny r r-package rstats taxonomy

Keywords from Contributors

genome biodiversity taxize darwincore biology nomenclature phylogenetics geocode vertnet specimen

Last synced: 9 months ago · JSON representation

Repository

Interface to Open Tree of Life API

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/rotl
Size: 1.74 MB

Statistics

Stars: 45
Watchers: 9
Forks: 17
Open Issues: 21
Releases: 16

Topics

peer-reviewed phylogeny r r-package rstats taxonomy

Created over 11 years ago · Last pushed almost 3 years ago

Metadata Files

Readme License

README.Rmd

---
output: github_document
---

```{r setup, eval=TRUE, echo=FALSE}
library(knitr)
# opts_knit$set(upload.fun = image_uri)
opts_knit$set(upload.fun = imgur_upload)
```


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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.

[![](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org/)

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

GitHub Events

Total

Watch event: 5

Last Year

Watch event: 5

Committers

Last synced: 10 months ago

All Time

Total Commits: 833
Total Committers: 12
Avg Commits per committer: 69.417
Development Distribution Score (DDS): 0.268

Past Year

Commits: 15
Committers: 1
Avg Commits per committer: 15.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Francois Michonneau	f**u@g**m	610
David Winter	d**r@g**m	115
josephwb	p**b@g**m	95
Emily Jane McTavish	e**h@g**m	3
Daijiang Li	d**1@u**u	2
Jeroen Van Goey	j**y@g**m	2
rOpenSci Bot	m**t@g**m	1
Brian O'Meara	o**n@g**m	1
Karthik Ram	k**m@g**m	1
Maëlle Salmon	m**n@y**e	1
Patrick Hausmann	p**n@c**e	1
Scott Chamberlain	m**s@g**m	1

Committer Domains (Top 20 + Academic)

covimo.de: 1 ufl.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 83
Total pull requests: 23
Average time to close issues: 3 months
Average time to close pull requests: 13 days
Total issue authors: 29
Total pull request authors: 11
Average comments per issue: 2.6
Average comments per pull request: 1.65
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: 5 days
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 5.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

fmichonneau (38)
dwinter (6)
bomeara (5)
LunaSare (4)
rossmounce (3)
sckott (3)
marknovak (2)
jenna-tb-ekwealor (1)
jhpoelen (1)
FlukeAndFeather (1)
TarekHattab (1)
ajrominger (1)
ddenney1 (1)
noor-albader (1)
lhgergo (1)

Pull Request Authors

fmichonneau (7)
dwinter (3)
josephwb (2)
snacktavish (2)
LunaSare (2)
BioGeek (2)
maelle (1)
daijiang (1)
bomeara (1)
karthik (1)
patperu (1)

Top Labels

Issue Labels

wait for OTL (5) enhancement (2)

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- cran 7,187 last-month
Total docker downloads: 200,502

Total dependent packages: 5
(may contain duplicates)
Total dependent repositories: 16
(may contain duplicates)
Total versions: 39
Total maintainers: 1

proxy.golang.org: github.com/ropensci/rotl

Documentation: https://pkg.go.dev/github.com/ropensci/rotl#section-documentation
License: other
Latest release: v3.1.0+incompatible
published almost 3 years ago

Versions: 14
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.7%

Dependent repos count: 5.9%

Last synced: 9 months ago

cran.r-project.org: rotl

Interface to the 'Open Tree of Life' API

Homepage: https://docs.ropensci.org/rotl/
Documentation: http://cran.r-project.org/web/packages/rotl/rotl.pdf
License: BSD_2_clause + file LICENSE
Latest release: 3.1.0
published almost 3 years ago

Versions: 15
Dependent Packages: 4
Dependent Repositories: 15
Downloads: 7,187 Last month
Docker Downloads: 200,502

Rankings

Forks count: 4.1%

Downloads: 6.7%

Dependent repos count: 7.4%

Stargazers count: 8.6%

Average: 10.3%

Dependent packages count: 10.9%

Docker downloads count: 24.2%

Maintainers (1)

francois.michonneau@gmail.com

Last synced: 9 months ago

conda-forge.org: r-rotl

Homepage: https://github.com/ropensci/rotl
License: BSD-2-Clause
Latest release: 3.0.14
published over 3 years ago

Versions: 10
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 24.4%

Dependent packages count: 29.0%

Average: 34.0%

Forks count: 38.0%

Stargazers count: 44.7%

Last synced: 9 months ago

Dependencies

DESCRIPTION cran

R >= 3.1.1 depends
ape * imports
assertthat >= 0.1 imports
httr * imports
jsonlite * imports
rentrez * imports
rncl >= 0.6.0 imports
MCMCglmm * suggests
RNeXML * suggests
knitr >= 1.12 suggests
phylobase * suggests
readxl * suggests
rmarkdown >= 0.7 suggests
testthat * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite