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RNeXML

  • Maintainer: Carl Boettiger
  • Authors: Carl Boettiger, Scott Chamberlain, Hilmar Lapp, Kseniia Shumelchyk, Rutger Vos
  • License: BSD-3
  • Issues: Bug reports, feature requests, and development discussion.

An extensive and rapidly growing collection of richly annotated phylogenetics data is now available in the NeXML format. NeXML relies on state-of-the-art data exchange technology to provide a format that can be both validated and extended, providing a data quality assurance and adaptability to the future that is lacking in other formats. See Vos et al 2012 for further details on the NeXML format.

How to cite

RNeXML has been published in the following article:

Boettiger C, Chamberlain S, Vos R and Lapp H (2016). “RNeXML: A Package for Reading and Writing Richly Annotated Phylogenetic, Character, and Trait Data in R.” Methods in Ecology and Evolution, 7, pp. 352-357. doi:10.1111/2041-210X.12469

Although the published version of the article is pay-walled, the source of the manuscript, and a much better rendered PDF, are included in this package (in the manuscripts folder). You can also find it freely available on arXiv.

Installation

The latest stable release of RNeXML is on CRAN, and can be installed with the usual install.packages("RNeXML") command. Some of the more specialized functionality described in the Vignettes (such as RDF manipulation) requires additional packages which can be installed using:

install.packages("RNeXML", deps = TRUE)

The development version can be installed using:

remotes::install_github("ropensci/RNeXML")

Getting Started

See the vignettes below for both a general quick start and an overview of more specialized features.


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Version

Install

install.packages('RNeXML')

Monthly Downloads

3,552

Version

2.4.11

License

BSD_3_clause + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Last Published

February 1st, 2023

Functions in RNeXML (2.4.11)

get_namespaces

get namespaces
get_characters_list

Extract the character matrix
get_metadata_values

Get the value(s) for metadata
get_metadata

get_metadata
get_trees

extract a phylogenetic tree from the nexml
get_flat_trees

get_flat_trees
get_taxa_list

get_taxa_list
get_level

get_level
get_taxa

get_taxa
get_trees_list

extract all phylogenetic trees in ape format
lcapply

Compact list then lapply
get_citation

Get citation from metadata
get_rdf

Extract rdf-xml from a NeXML file
meta

Constructor function for metadata nodes
get_taxa_meta

get_taxa_meta
slot,ResourceMeta-method

Access or set slot of S4 object
get_taxa_meta_list

get_taxa_meta_list
summary,nexml-method

Summary method for nexml objects
taxize_nexml

taxize nexml
reset_id_counter

reset id counter
simmap_to_nexml

Convert phylo with attached simmap to nexml object
nexml-class

Class representing a NeXML document
nexml_add

add elements to a new or existing nexml object
nexml_figshare

publish nexml to figshare
nexml_get

Get the desired element from the nexml object
toPhylo

nexml to phylo
nexml_publish

publish nexml files to the web and receive a DOI
nexml_read

Read NeXML files into various R formats
nexml_validate

validate nexml using the online validator tool
nexml_write

Write nexml files
get_license

Get license from metadata
get_meta

Extracts meta objects matching properties
.methodWithNext

Saves the next method in the method meta data
c,nexml-method

Concatenate nexml files
Annotated-class

Class of objects that have metadata as lists of meta elements
c,meta-method

Concatenate meta elements into a ListOfmeta
add_trees

add_trees
add_meta

Add metadata to a nexml file
charzero_as_empty

Treats zero-length character vectors as empty strings
New

new with namespaced class name
add_namespaces

Add namespaces
add_characters

Add character data to a nexml object
add_basic_meta

Add basic metadata
coalesce_

Front-end to dplyr::coalesce to deal with NULL vectors
flatten_multiphylo

Flatten a multiphylo object
findNextMethod

Finds the method that callNextMethod() should chain to
.sigLabel

Create a label for a method signature
get_characters

Get character data.frame from nexml
nexml.tree

Constructor for the respective class
get_all_meta

Get flattened list of meta annotations
expand_prefix

Expand namespace-prefixed string
.callGeneric

Calls the given generic with the given arguments