RNeXML: A package for reading and writing richly annotated phylogenetic, character and trait data in R
Abstract
NeXML is a powerful and extensible exchange standard recently proposed to better meet
the expanding needs for phylogenetic data and metadata sharing. Here we present the
RNeXML package, which provides users of the r programming language with easy-to-use
tools for reading and writing NeXML documents, including rich metadata, in a way that
interfaces seamlessly with the extensive library of phylogenetic tools already available
in the r ecosystem. Wherever possible, we designed RNeXML to map NeXML document contents,
whose arrangement is influenced by the format's XML Schema definition, to their most
intuitive or useful representation in r. To make NeXML's powerful facility for recording
semantically rich machine-readable metadata accessible to r users, we designed a functional
programming interface to it that hides the semantic web standards leveraged by NeXML
from r users who are unfamiliar with them. RNeXML can read any NeXML document that
validates, and it generates valid NeXML documents from phylogeny and character data
in various r representations in use. The metadata programming interface at a basic
level aids fulfilling data documentation best practices, and at an advanced level
preserves NeXML's nearly limitless extensibility, for which we provide a fully working
demonstration. Furthermore, to lower the barriers to sharing well-documented phylogenetic
data, RNeXML has started to integrate with taxonomic metadata augmentation services
on the web, and with online repositories for data archiving. RNeXML allows r's rich
ecosystem to read and write data in the NeXML format through an interface that is
no more involved than reading or writing data from other, less powerful data formats.
It also provides an interface designed to feel familiar to r programmers and to be
consistent with recommended practices for r package development, yet that retains
the full power for users to add their own custom data and metadata to the phylogenies
they work with, without introducing potentially incompatible changes to the exchange
standard.
Type
Journal articlePermalink
https://hdl.handle.net/10161/15669Published Version (Please cite this version)
10.1111/2041-210X.12469Publication Info
Boettiger, C; Chamberlain, S; Vos, R; & 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(3). pp. 352-357. 10.1111/2041-210X.12469. Retrieved from https://hdl.handle.net/10161/15669.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Hilmar Lapp
Dir, IT

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