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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "tools/README-"
)
```
# RNeXML <img src="man/figures/logo.svg" align="right" alt="" width="120" />
[](https://zenodo.org/badge/latestdoi/11856817)
[](https://travis-ci.org/ropensci/RNeXML)
[](https://ci.appveyor.com/project/cboettig/rnexml/branch/master)
[](https://cran.r-project.org/package=RNeXML)
[](https://codecov.io/github/ropensci/RNeXML?branch=master)
* Maintainer: Carl Boettiger
* Authors: Carl Boettiger, Scott Chamberlain, Hilmar Lapp, Kseniia Shumelchyk, Rutger Vos
* License: BSD-3
* [Issues](https://github.com/ropensci/RNeXML/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](https://doi.org/10.1093/sysbio/sys025 "NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata.") 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](https://arxiv.org/abs/1506.02722).
```{r compile-settings, include=FALSE}
library(methods)
```
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:
```{r eval=FALSE}
install.packages("RNeXML", deps = TRUE)
```
The development version can be installed using:
```{r eval=FALSE}
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](https://docs.ropensci.org/RNeXML/articles/intro)
- [RNeXML: A Package for Reading and Writing Richly Annotated Phylogenetic, Character, and Trait Data in R](https://github.com/ropensci/RNeXML/tree/master/manuscripts) (published in MEE).
- [Handling Metadata in RNeXML](https://docs.ropensci.org/RNeXML/articles/metadata)
- [The `nexml` S4 Object](https://docs.ropensci.org/RNeXML/articles/S4)
- [Semantic data & SPARQL with RNeXML](https://docs.ropensci.org/RNeXML/articles/sparql)
- [Extending NeXML: an example based on simmap](https://docs.ropensci.org/RNeXML/articles/simmap)
-----
[](https://ropensci.org/)