RNeXML

Implementing semantically rich NeXML I/O in R

https://github.com/ropensci/rnexml

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: arxiv.org, zenodo.org
✓
Committers with academic emails
1 of 15 committers (6.7%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (19.9%) to scientific vocabulary

Keywords

nexml phylogenetics r r-package rstats

Keywords from Contributors

taxonomy climate biodiversity genome noaa-data mock noaa fish fishbase dbi

Last synced: 6 months ago · JSON representation

Repository

Implementing semantically rich NeXML I/O in R

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/RNeXML
Size: 8.54 MB

Statistics

Stars: 13
Watchers: 8
Forks: 9
Open Issues: 12
Releases: 8

Topics

nexml phylogenetics r r-package rstats

Created over 12 years ago · Last pushed almost 2 years ago

Metadata Files

Readme Changelog Contributing License Codemeta

README.Rmd

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "tools/README-"
)
```


# RNeXML  

[![DOI](https://zenodo.org/badge/11856817.svg)](https://zenodo.org/badge/latestdoi/11856817)
[![Build Status](https://api.travis-ci.org/ropensci/RNeXML.png)](https://travis-ci.org/ropensci/RNeXML)
[![Windows build status](https://ci.appveyor.com/api/projects/status/dhiwp5blx2ns2yba/branch/master?svg=true)](https://ci.appveyor.com/project/cboettig/rnexml/branch/master)
[![CRAN status](https://www.r-pkg.org/badges/version/RNeXML)](https://cran.r-project.org/package=RNeXML)
[![codecov.io](https://codecov.io/github/ropensci/RNeXML/coverage.svg?branch=master)](https://codecov.io/github/ropensci/RNeXML?branch=master)
![downloads](http://cranlogs.r-pkg.org/badges/grand-total/RNeXML)



* 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)
 



-----

[![ropensci footer](https://ropensci.org//public_images/github_footer.png)](https://ropensci.org/)

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

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GitHub Events

Total

Last Year

Committers

Last synced: 7 months ago

All Time

Total Commits: 910
Total Committers: 15
Avg Commits per committer: 60.667
Development Distribution Score (DDS): 0.351

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Carl Boettiger	c**g@g**m	591
Hilmar Lapp	h**p@d**t	135
rvosa	r**o@g**m	69
rstudio	r**o@e**m	39
Scott Chamberlain	m**s@g**m	37
Kseniia Shumelchyk	s**k@g**m	12
Carl Boettiger	c**l@r**g	7
Jeroen Ooms	j**s@g**m	5
Craig Citro	c**o@g**m	4
Carl Boettiger	c**g@g**m	4
Hadley Wickham	h**m@g**m	2
steven2249	s**w@b**u	2
Bryce Mecum	p**h@g**m	1
Edmund Hart	e**t@g**m	1
Francois Michonneau	f**u@g**m	1

Committer Domains (Top 20 + Academic)

berkeley.edu: 1 google.com: 1 ropensci.org: 1 drycafe.net: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 53
Total pull requests: 49
Average time to close issues: about 1 year
Average time to close pull requests: 1 day
Total issue authors: 9
Total pull request authors: 4
Average comments per issue: 3.85
Average comments per pull request: 1.88
Merged pull requests: 46
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 0
Average comments per issue: 3.5
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

hlapp (30)
cboettig (13)
sckott (3)
lionel- (2)
laurajackson (1)
fmichonneau (1)
krlmlr (1)
wdahdul (1)
gvegayon (1)

Pull Request Authors

hlapp (36)
cboettig (11)
hadley (1)
jeroen (1)

Top Labels

Issue Labels

bug (13) question (9) use-case (4) documentation (1) metadata (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 4,865 last-month
Total docker downloads: 132,196

Total dependent packages: 2
Total dependent repositories: 7
Total versions: 28
Total maintainers: 1

cran.r-project.org: RNeXML

Semantically Rich I/O for the 'NeXML' Format

Homepage: https://docs.ropensci.org/RNeXML/
Documentation: http://cran.r-project.org/web/packages/RNeXML/RNeXML.pdf
License: BSD_3_clause + file LICENSE
Latest release: 2.4.11
published about 3 years ago

Versions: 28
Dependent Packages: 2
Dependent Repositories: 7
Downloads: 4,865 Last month
Docker Downloads: 132,196

Rankings

Downloads: 7.2%

Forks count: 7.3%

Dependent repos count: 11.1%

Average: 13.2%

Dependent packages count: 13.7%

Stargazers count: 15.1%

Docker downloads count: 24.7%

Maintainers (1)

cboettig@gmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.0.0 depends
ape >= 3.1 depends
methods >= 3.0.0 depends
XML >= 3.95 imports
dplyr >= 0.5.0 imports
httr >= 0.3 imports
lazyeval >= 0.1.0 imports
plyr >= 1.8 imports
reshape2 >= 1.2.2 imports
rlang * imports
stringi * imports
stringr >= 1.0 imports
tidyr >= 0.3.1 imports
uuid >= 0.1 imports
xml2 * imports
covr * suggests
geiger >= 2.0 suggests
knitcitations >= 1.0.1 suggests
knitr >= 1.5 suggests
phytools >= 0.3.93 suggests
rdflib * suggests
rfigshare >= 0.3.0 suggests
rmarkdown >= 0.3.3 suggests
spelling * suggests
taxalight * suggests
testthat >= 0.10.0 suggests
xslt * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

manuscripts/Dockerfile docker

rocker/ropensci latest build