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.

• A Brief Introduction to RNeXML
• RNeXML: A Package for Reading and Writing Richly Annotated Phylogenetic, Character, and Trait Data in R (published in MEE).
• Handling Metadata in RNeXML
• The nexml S4 Object
• Semantic data & SPARQL with RNeXML
• Extending NeXML: an example based on simmap