We have also recently reached the first milestone in RNeXML. We can now read NeXML files into R and convert to the popular phylo format from the ape package, as well as writing the ape::phylo trees out into valid NeXML. We can also add basic metadata such as author, license, title and description to the file.
Development notes
At the heart of this package is an internal S4 representation of the schema. While knowledgable users could interact with the S4 objects directly (easier and less error-prone than interacting with the XML parsing/serializing directly), we in general provide an end-user API which hides the internal complexity of S4 classes, as illustrated below. In principle this representation could be automatically generated from the schema using the XMLSchema package, but that must wait until that package is more mature. Meanwhile, we rely on hand-coded classes and hand-coded coercion functions.
The coercion functions take care of the translation into and out of the XML (parsing and serializing) without any need for xpath expressions. At the moment they are verbosely spelled out under the class definitions in classes.R file, though ideally they could be abstracted (e.g. as we do in reml). Classes are based on the inheritance structure of the schema (unlike reml), which makes additional nodes much easier to add and hence it is easier to extend this library. At this time we have only certain core elements from the schema as map naturally to ape trees, along with the essential annotation elements (meta nodes). Support for additional classes / schema elements will be added as driven by use cases.
(See the Github page for the most recent tutorial, this is just added here for my record).
Tutorial
The development version of RNeXML is available on Github. With the devtools package installed on your system, RNeXML can be installed using:
library(devtools)
install_github("RNeXML", "ropensci")
library(RNeXML)Read in a nexml file into the ape::phylo format:
f <- system.file("examples", "trees.xml", package = "RNeXML")
tr <- nexml_read(f, "phylo")Write an ape::phylo tree into the nexml format, including optional metadata:
nexml_write(bird.orders, "birds.xml", creator = "Carl Boettiger <cboettig@ropensci.org>",
title = "example NeXML file for bird orders", description = "Example phylogeny taken from the ape documentation showing the major bird orders")Next Steps
Developing use cases, soliciting input, and writing a manuscript… See issues log.