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Data Access and Management","monthly_downloads":7515,"total_dependent_repos":16,"total_dependent_packages":5,"readme":"---\noutput: github_document\n---\n\n```{r setup, eval=TRUE, echo=FALSE}\nlibrary(knitr)\n# opts_knit$set(upload.fun = image_uri)\nopts_knit$set(upload.fun = imgur_upload)\n```\n\n\u003c!-- badges: start --\u003e\n[![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)\n[![codecov.io](https://app.codecov.io/github/ropensci/rotl?branch=master)](https://app.codecov.io/github/ropensci/rotl?branch=master)\n[![](https://www.r-pkg.org/badges/version/rotl)](https://www.r-pkg.org/pkg/rotl)\n[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/rotl)](https://www.r-pkg.org/pkg/rotl)\n[![](https://badges.ropensci.org/17_status.svg)](https://github.com/ropensci/software-review/issues/17)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n\u003c!-- badges: end --\u003e\n\n\n# rotl: An R interface to Open Tree API \u003cimg src=\"man/figures/logo.svg\" align=\"right\" /\u003e\n\n`rotl` is an R package to interact with the Open Tree of Life data APIs. It was\ninitially developed as part of the\nNESCENT/OpenTree/Arbor hackathon.\n\nClient libraries to interact with the Open Tree of Life API also exists for\n[Python](https://github.com/OpenTreeOfLife/pyopentree)\nand [Ruby](https://github.com/SpeciesFileGroup/bark).\n\n\n## Installation\n\nThe current stable version is available from CRAN, and can be installed by\ntyping the following at the prompt in R:\n\n```{r, eval=FALSE}\ninstall.packages(\"rotl\")\n```\n\nIf you want to test the development version, you first need to install\nthe `remotes` package.\n\n```{r, eval=FALSE}\ninstall.packages(\"remotes\")\n```\n\nThen you can install `rotl` using:\n\n```{r, eval=FALSE}\nremotes::install_github(\"ropensci/rotl\")\n```\n\n## Vignettes\n\nThere are three vignettes:\n\n- Start by checking out the \"How to use `rotl`?\" by typing:\n  `vignette(\"rotl\", package=\"rotl\")` after installing the\n  package.\n\n- Then explore how you can use `rotl` with other packages to combine your data\n  with trees from the Open Tree of Life project by typing:\n  `vignette(\"data_mashups\", package=\"rotl\")`.\n\n- The vignette \"Using the Open Tree Synthesis in a comparative analysis\"\n  demonstrates how you can reproduce an analysis of a published paper by\n  downloading the tree they used, and data from the supplementary material:\n  `vignette(\"meta-analysis\", package=\"rotl\")`.\n\nThe vignettes are also available from CRAN:\n[How to use `rotl`?](https://cran.r-project.org/package=rotl/vignettes/rotl.html),\n[Data mashups](https://cran.r-project.org/package=rotl/vignettes/data_mashups.html),\nand\n[Using the Open Tree synthesis in a comparative analysis](https://cran.r-project.org/package=rotl/vignettes/meta-analysis.html).\n\n## Quick start\n\n### Get a little bit of the big Open Tree tree\n\nTaxonomic names are represented in the Open Tree by numeric identifiers, the\n`ott_ids` (Open Tree Taxonomy identifiers). To extract a portion of a tree from\nthe Open Tree, you first need to find `ott_ids` for a set of names using the\n`tnrs_match_names` function:\n\n```{r resolve}\nlibrary(rotl)\napes \u003c- c(\"Pongo\", \"Pan\", \"Gorilla\", \"Hoolock\", \"Homo\")\n(resolved_names \u003c- tnrs_match_names(apes))\n```\n\nNow we can get the tree with just those tips:\n\n```{r get_tr}\ntr \u003c- tol_induced_subtree(ott_ids = ott_id(resolved_names))\nplot(tr)\n```\n\nThe code above can be summarized in a single pipe:\n\n```{r pipe, plot=FALSE}\nlibrary(magrittr)\n## or expressed as a pipe:\nc(\"Pongo\", \"Pan\", \"Gorilla\", \"Hoolock\", \"Homo\") %\u003e%\n  tnrs_match_names() %\u003e%\n  ott_id() %\u003e%\n  tol_induced_subtree() %\u003e%\n  plot()\n```\n\n## Citation and Manuscript\n\nTo cite `rotl` in publications pleases use:\n\n\u003e  Michonneau, F., Brown, J. W. and Winter, D. J. (2016), rotl: an R package to\n\u003e  interact with the Open Tree of Life data.  Methods in Ecology and\n\u003e  Evolution. 7(12):1476-1481. doi:\n\u003e  [10.1111/2041-210X.12593](https://doi.org/10.1111/2041-210X.12593)\n\nYou may also want to cite the paper for the Open Tree of Life\n\n\u003e  Hinchliff, C. E., et al. (2015). Synthesis of phylogeny and taxonomy into a\n\u003e  comprehensive tree of life. Proceedings of the National Academy of Sciences\n\u003e  112.41 (2015): 12764-12769\n\u003e  doi: [10.1073/pnas.1423041112](https://doi.org/10.1073/pnas.1423041112)\n\nThe manuscript in *Methods in Ecology and Evolution* includes additional\nexamples on how to use the package. The manuscript and the code it contains are\nalso hosted on GitHub at: https://github.com/fmichonneau/rotl-ms\n\n\n## Versioning\n\nStarting with v3.0.0 of the package, the major and minor version numbers (the\nfirst 2 digits of the version number) will be matched to those of the API. The\npatch number (the 3rd digit of the version number) will be used to reflect\nbug fixes and other changes that are independent from changes to the API.\n\n`rotl` can be used to access other versions of the API (if they are available)\nbut most likely the high level functions will not work. Instead, you will need\nto parse the output yourself using the \"raw\" returns from the unexported\nlow-level functions (all prefixed with a `.`). For instance to use the\n`tnrs/match_names` endpoint for `v2` of the API:\n\n```{r versioning, eval=FALSE}\nrotl:::.tnrs_match_names(c(\"pan\", \"pango\", \"gorilla\", \"hoolock\", \"homo\"), otl_v = \"v2\")\n```\n\n\n### Code of Conduct\n\nPlease note that this project is released with a\n[Contributor Code of Conduct](https://github.com/ropensci/rotl/blob/master/CONDUCT.md). By participating in this project you\nagree to abide by its terms.\n\n[![](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org/)\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1111/2041-210X.12593","https://doi.org/10.1073/pnas.1423041112"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["biodiversity","biology","routes","taxize","nomenclature","darwincore","cycle","ecology","spocc","climate"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/15279","html_url":"https://ost.ecosyste.ms/projects/15279"}