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rotl

Interface to the 'Open Tree of Life' API

An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.

output: github_document

Build Status Build status codecov.io CRAN RStudio mirror downloads Research software impact Project Status: Active – The project has reached a stable, usable state and is being actively developed.

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.

Installation

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")

Vignettes

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: vignette("data_mashups", package="rotl").

  • 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: vignette("meta-analysis", package="rotl").

The vignettes are also available from CRAN: How to use rotl?, Data mashups, and Using the Open Tree synthesis in a comparative analysis.

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:

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)

plot of chunk get_tr

The code above can be summarized in a single pipe:

library(magrittr)
## 
## Attaching package: 'magrittr'

## The following objects are masked from 'package:testthat':
## 
##     equals, is_less_than, not

## or expressed as a pipe:
c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo") %>%
    tnrs_match_names %>%
    ott_id %>%
    tol_induced_subtree %>%
    plot

plot of chunk pipe

Citation and Manuscript

To cite rotl in publications pleases use:

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

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:

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. By participating in this project you agree to abide by its terms.

News

rotl 3.0.7

  • Minor update to vignette to address change to TNRS endpoint (underscores can't be included in the taxon names anymore).

rotl 3.0.6

  • Minor update to address warnings seen on CRAN.

rotl 3.0.5

New features

  • The data types in the data frame returned by tnrs_match_names are consistent, and remain the same even after using update().

Other changes

  • Small internal changes that reflect changes in the data structures returned by the API.

rotl 3.0.4

New features

  • To improve stability of results across releases of the Open Tree Taxonomy, the TNRS match with the lowest OTT id is returned instead of the first one in case a name is shared across multiple domains (related to #88)
  • A warning is issued when users attempt to use TNRS on duplicated names.

Other changes

  • Fix typos and workaround broken API to retrieve supplementary materials in vignette.

rotl 3.0.3

New features

  • The function get_study_subtree gains the argument tip_label to control the formatting of the tip labels, #90, reported by @bomeara
  • The new function is_in_tree takes a list of OTT ids (i.e., the output of ott_id()), and returns a vector of logical indiicating whether they are included in the synthetic tree (workaround #31).

Bug fixes

  • The function get_study_subtree ignored the argument subtree_id, #89 reported by @bomeara

Other chaanges

  • citation("rotl") now includes the reference to the Open Tree of Life publication.
  • The "How to use rotl?" vignette was updated to document the behavior of v3 of the OTL API which returns an HTTP error code 400 when the request for induced subtree includes taxa that are not in the synthetic tree (fix #84)

rotl 3.0.1

  • Fix tests and vignette to reflect changes accompanying release 6.1 of the synthetic tree

  • Add section in vignette "How to use rotl?" about how to get the higher taxonomy from a given taxon.

  • Add CITATION file with MEE manuscript information (#82)

rotl 3.0.0

  • rotl now interacts with v3.0 of the Open Tree of Life APIs. The documentation has been updated to reflect the associated changes. More information about the v3.0 of the Open Tree of Life APIs can be found on their wiki.

New features

  • New methods: tax_sources, is_suppressed, tax_rank, unique_name, name, ott_id, for objects returned by tnrs_match_names(), taxonomy_taxon_info(), taxonomy_taxon_mrca(), tol_node_info(), tol_about(), and tol_mrca(). Each of these methods have their own class.

  • New method tax_lineage() to extract the higher taxonomy from an object returned by taxonomy_taxon_info() (initally suggested by Matt Pennell, #57).

  • New method tol_lineage() to extract the nodes towards the root of the tree.

  • New print methods for tol_node_info() and tol_mrca().

  • New functions study_external_IDs() and taxon_external_IDs() that return the external identifiers for a study and associated trees (e.g., DOI, TreeBase ID); and the identifiers of taxon names in taxonomic databases. The vignette "Data mashup" includes an example on how to use it.

  • The function strip_ott_id() gains the argument remove_underscores to remove underscores from tips in trees returned by OTL.

Changes

  • Rename method ott_taxon_name() to tax_name() for consistency.

  • Rename method synth_sources() and study_list() to source_list().

  • Refactor how result of query is checked and parsed (invisible to the user).

Bug fixes

  • Fix bug in studies_find_studies(), the arguments verbose and exact were ignored.

  • The argument only_current has been dropped for the methods associated with objects returned by tnrs_match_names()

  • The print method for tnrs_context() duplicated some names.

  • inspect(), update() and synonyms() methods for tnrs_match_names() did not work if the query included unmatched taxa.

rotl 0.5.0

  • New vignette: meta-analysis

  • Added arguments include_lineage and list_terminal_descendants to taxonomy_taxon()

  • Improve warning and format of the result if one of the taxa requested doesn't match anything tnrs_match_names.

  • In the data frame returned by tnrs_match_names, the columns approximate_match, is_synonym and is_deprecated are now logical (instead of character) [issue #54]

  • New utility function strip_ott_ids removes OTT id information from a character vector, making it easier to match tip labels in trees returned by tol_induced_subtree to taxonomic names in other data sources. This function can also remove underscores from the taxon names.

  • New method list_trees returns a list of tree ids associated with studies. The function takes the output of studies_find_studies or studies_find_trees.

  • studies_find_studies and studies_find_trees gain argument detailed (default set to TRUE), that produces a data frame summarizing information (title of the study, year of publication, DOI, ids of associated trees, ...) about the studies matching the search criteria.

  • get_study_tree gains argument deduplicate. When TRUE, if the tree returned for a given study contains duplicated tip labels, they will be made unique before being parsed by NCL by appending a suffix (_1, _2, _3, etc.). (#46, reported by @bomeara)

  • New method get_study_year for objects of class study_meta that returns the year of publication of the study.

  • A more robust approach is used by get_tree_ids to identify the tree ids in the metadata returned by the API

rotl 0.4.1

  • Initial CRAN release on July, 24th 2015

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.
install.packages("rotl")

3.0.7 by Francois Michonneau, 4 months ago

https://github.com/ropensci/rotl

Report a bug at https://github.com/ropensci/rotl/issues

Browse source code at https://github.com/cran/rotl

Authors: Francois Michonneau [aut, cre] , Joseph Brown [aut] , David Winter [aut] , Scott Chamberlain [rev]

Documentation:   PDF Manual  

Task views: Phylogenetics, Especially Comparative Methods

BSD_2_clause + file LICENSE license

Imports httr, jsonlite, assertthat, rncl, ape, rentrez

Suggests knitr, rmarkdown, testthat, RNeXML, phylobase, MCMCglmm, fulltext, readxl

Imported by taxize.

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