RNeXML v2.4.0

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Semantically Rich I/O for the 'NeXML' Format

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.

Readme

RNeXML

DOI Build
Status Windows build
status CRAN
status codecov.io downloads

  • Maintainer: Carl Boettiger
  • Authors: Carl Boettiger, Scott Chamberlain, Hilmar Lapp, Kseniia Shumelchyk, Rutger Vos
  • License: BSD-3
  • 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 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.

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:

install.packages("RNeXML", deps = TRUE)

The development version can be installed using:

remotes::install_github("ropensci/RNeXML")

Getting Started

See the vignettes below for both a general quick start and an overview of more specialized features.


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Functions in RNeXML

Name Description
get_flat_trees get_flat_trees
get_rdf Extract rdf-xml from a NeXML file
summary,nexml-method Summary method for nexml objects
.methodWithNext Saves the next method in the method meta data
slot,ResourceMeta-method Access or set slot of S4 object
get_namespaces get namespaces
.callGeneric Calls the given generic with the given arguments
.sigLabel Create a label for a method signature
expand_prefix Expand namespace-prefixed string
get_level get_level
get_metadata get_metadata
findNextMethod Finds the method that callNextMethod() should chain to
get_characters_list Extract the character matrix
get_taxa_meta get_taxa_meta
flatten_multiphylo Flatten a multiphylo object
c,meta-method Concatenate meta elements into a ListOfmeta
get_citation Get citation from metadata
get_metadata_values Get the value(s) for metadata
get_taxa_meta_list get_taxa_meta_list
nexml_publish publish nexml files to the web and receive a DOI
nexml_read Read NeXML files into various R formats
nexml-class Class representing a NeXML document
nexml_validate validate nexml using the online validator tool
nexml_add add elements to a new or existing nexml object
nexml_write Write nexml files
get_characters Get character data.frame from nexml
get_all_meta Get flattened list of meta annotations
lcapply Compact list then lapply
meta Constructor function for metadata nodes
taxize_nexml taxize nexml
toPhylo nexml to phylo
get_license Get license from metadata
get_trees extract a phylogenetic tree from the nexml
get_meta Extracts meta objects matching properties
nexml_figshare publish nexml to figshare
coalesce_ Front-end to dplyr::coalesce to deal with NULL vectors
reset_id_counter reset id counter
get_taxa get_taxa
get_trees_list extract all phylogenetic trees in ape format
nexml_get Get the desired element from the nexml object
nexml.tree Constructor for the respective class
get_taxa_list get_taxa_list
simmap_to_nexml Convert phylo with attached simmap to nexml object
Annotated-class Class of objects that have metadata as lists of meta elements
add_meta Add metadata to a nexml file
add_trees add_trees
add_namespaces Add namespaces
c,nexml-method Concatenate nexml files
New new with namespaced class name
add_basic_meta Add basic metadata
add_characters Add character data to a nexml object
charzero_as_empty Treats zero-length character vectors as empty strings
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Vignettes of RNeXML

Name
S4.Rmd
intro.Rmd
metadata.Rmd
references.bib
simmap.Rmd
sparql.Rmd
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Details

Type Package
URL https://docs.ropensci.org/RNeXML, https://github.com/ropensci/RNeXML
BugReports https://github.com/ropensci/RNeXML/issues
Additional_repositories https://cboettig.github.io/drat/
License BSD_3_clause + file LICENSE
VignetteBuilder knitr
Collate 'S4-utils.R' 'classes.R' 'add_basic_meta.R' 'add_characters.R' 'add_meta.R' 'add_namespaces.R' 'nexmlTree.R' 'add_trees.R' 'character_classes.R' 'concatenate_nexml.R' 'constructors.R' 'deprecated.R' 'get_basic_metadata.R' 'get_characters.R' 'get_level.R' 'get_metadata.R' 'get_namespaces.R' 'get_rdf.R' 'get_taxa.R' 'get_taxa_meta.R' 'get_trees.R' 'internal_get_node_maps.R' 'internal_isEmpty.R' 'internal_name_by_id.R' 'internal_nexml_id.R' 'meta.R' 'nexml_add.R' 'nexml_get.R' 'nexml_methods.R' 'nexml_publish.R' 'nexml_read.R' 'nexml_validate.R' 'nexml_write.R' 'prefixed-uris.R' 'simmap.R' 'taxize_nexml.R' 'tbl_df.R' 'utils.R'
RoxygenNote 6.1.1
X-schema.org-applicationCategory Data Publication
X-schema.org-keywords metadata, nexml, phylogenetics, linked-data
X-schema.org-isPartOf https://ropensci.org
Language en-US
Encoding UTF-8
NeedsCompilation no
Packaged 2019-11-08 16:16:27 UTC; cboettig
Repository CRAN
Date/Publication 2019-11-08 18:20:07 UTC

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