Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
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.
RNeXML has been published in the following article:
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.
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:
See the vignettes below for both a general quick start and an overview of more specialized features.
For more fine-grained list of changes or to report a bug, consult
This release addresses several aspects improving the handling of metadata:
add_meta()now works for trees and characters (#213, PR #217)
rootEdge(#207, PR #218)
taxadbmethod. (#224, PR #226). This remains only a suggested package and has much lighter dependencies as well.
taxizeas Suggests only
rrdfin favor of
Sxsltin favor of
get_taxa()now return much richer
data.framesinstead of named vectors. This is potentially a non-backwards compatible change if scripts use the output of these functions as lists (#129). See updated metadata vignette. This introduces new dependencies
nexml_read()method for URLs, (#123)
nexfor nexml elements (#51, #124, #126). Includes a fix server-side on the NeXML validator as well.
nexml_validate()points to the new validator. (#126)
install.packages()compatible repository for
rrdf, as per request from the CRAN team.
add URL and BugReports to Description. #103
for consistency with other
add_ methods, the
nexml object is now the last, not the first,
add_basic_meta. As this changes the function API, it could break code that does not
explicitly name the arguments, so we release this as 2.0.0
Less aggressive unit-tests