RNeXML: 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.

AuthorCarl Boettiger [cre, aut], Scott Chamberlain [aut], Hilmar Lapp [aut], Kseniia Shumelchyk [aut], Rutger Vos [aut]
Date of publication2016-06-28 23:36:34
MaintainerCarl Boettiger <cboettig@gmail.com>
LicenseBSD_3_clause + file LICENSE
Version2.0.7
https://github.com/ropensci/RNeXML

View on CRAN

Man pages

add_basic_meta: Add basic metadata

add_characters: Add character data to a nexml object

add_meta: Add metadata to a nexml file

add_namespaces: add namespaces

add_trees: add_trees

c-ListOfmeta-method: Concatenate ListOfmeta elements into a ListOfmeta

c-meta-method: Concatenate meta elements into a ListOfmeta

c-nexml-method: Concatenate nexml files

flatten_multiphylo: Flatten a multiphylo object

get_characters: Get character data.frame from nexml

get_characters_list: Extract the character matrix

get_citation: get_citation

get_flat_trees: get_flat_trees

get_level: get_level

get_license: get_license

get_metadata: get_metadata

get_namespaces: get namespaces

get_rdf: Extract rdf-xml from a NeXML file

get_taxa: get_taxa

get_taxa_list: get_taxa_list

get_taxa_meta: get_taxa_meta

get_taxa_meta_list: get_taxa_meta_list

get_trees: extract a phylogenetic tree from the nexml

get_trees_list: extract all phylogenetic trees in ape format

meta: Constructor function for metadata nodes

nexml_add: add elements to a new or existing nexml object

nexml_figshare: publish nexml to figshare

nexml_get: Get the desired element from the nexml object

nexml_publish: publish nexml files to the web and receive a DOI

nexml_read: Read NeXML files into various R formats

nexml_to_simmap: nexml_to_simmap

nexml_validate: validate nexml using the online validator tool

nexml_write: Write nexml files

reset_id_counter: reset id counter

simmap_ex: A nexml class R object that includes simmap annotations

simmap_to_nexml: simmap_to_nexml

taxize_nexml: taxize nexml

toPhylo: nexml to phylo

Files in this package

RNeXML
RNeXML/inst
RNeXML/inst/examples
RNeXML/inst/examples/ontotrace-result.xml
RNeXML/inst/examples/meta_taxa.xml
RNeXML/inst/examples/mbank_X962_11-22-2013_1534.nex
RNeXML/inst/examples/taxa.xml
RNeXML/inst/examples/trees.xml
RNeXML/inst/examples/gardiner_1984.xml
RNeXML/inst/examples/missing_some_branchlengths.xml
RNeXML/inst/examples/characters.xml
RNeXML/inst/examples/treebase-record.xml
RNeXML/inst/examples/comp_analysis.xml
RNeXML/inst/examples/simmap.xml
RNeXML/inst/examples/primates_meta_xslt.xml
RNeXML/inst/examples/meta_example.xml
RNeXML/inst/examples/RDFa2RDFXML.xsl
RNeXML/inst/examples/primates_meta.xml
RNeXML/inst/examples/geospiza.xml
RNeXML/inst/examples/biophylo.xml
RNeXML/inst/examples/ncbii.xml
RNeXML/inst/examples/merge_data.md
RNeXML/inst/examples/multitrees.xml
RNeXML/inst/examples/merge_data.Rmd
RNeXML/inst/examples/primates_from_R.xml
RNeXML/inst/examples/some_missing_branchlengths.xml
RNeXML/inst/examples/phenoscape.xml
RNeXML/inst/examples/sparql.newick
RNeXML/inst/examples/simmap.nex
RNeXML/inst/examples/primates.xml
RNeXML/inst/CITATION
RNeXML/inst/simmap.md
RNeXML/inst/doc
RNeXML/inst/doc/metadata.Rmd
RNeXML/inst/doc/simmap.R
RNeXML/inst/doc/simmap.Rmd
RNeXML/inst/doc/sparql.R
RNeXML/inst/doc/sparql.html
RNeXML/inst/doc/S4.Rmd
RNeXML/inst/doc/sparql.Rmd
RNeXML/inst/doc/S4.html
RNeXML/inst/doc/S4.R
RNeXML/inst/doc/metadata.R
RNeXML/inst/doc/metadata.html
RNeXML/inst/doc/simmap.html
RNeXML/tests
RNeXML/tests/testthat
RNeXML/tests/testthat/test_parsing.R
RNeXML/tests/testthat/test_taxonomy.R
RNeXML/tests/testthat/treebase_test.R
RNeXML/tests/testthat/test_serializing.R
RNeXML/tests/testthat/test_inheritance.R
RNeXML/tests/testthat/test_rdf.R
RNeXML/tests/testthat/test_ape.R
RNeXML/tests/testthat/test_get_characters.R
RNeXML/tests/testthat/test_toplevel_api.R
RNeXML/tests/testthat/test_get_level.R
RNeXML/tests/testthat/test_comp_analysis.R
RNeXML/tests/testthat/test_global_ids.R
RNeXML/tests/testthat/test_nexml_read.R
RNeXML/tests/testthat/test_meta_extract.R
RNeXML/tests/testthat/geiger_test.R
RNeXML/tests/testthat/test_publish.R
RNeXML/tests/testthat/test_validate.R
RNeXML/tests/testthat/conversions.R
RNeXML/tests/testthat/test_simmap.R
RNeXML/tests/testthat/test_meta.R
RNeXML/tests/testthat/helper-RNeXML.R
RNeXML/tests/testthat/test_characters.R
RNeXML/tests/testthat/test_concatenate.R
RNeXML/tests/test-all.R
RNeXML/NAMESPACE
RNeXML/demo
RNeXML/demo/sparql.R
RNeXML/demo/00Index
RNeXML/NEWS
RNeXML/data
RNeXML/data/simmap_ex.rda
RNeXML/R
RNeXML/R/get_level.R RNeXML/R/classes.R RNeXML/R/add_characters.R RNeXML/R/simmap.R RNeXML/R/get_characters.R RNeXML/R/nexml_methods.R RNeXML/R/nexml_publish.R RNeXML/R/get_trees.R RNeXML/R/add_meta.R RNeXML/R/get_rdf.R RNeXML/R/add_basic_meta.R RNeXML/R/meta.R RNeXML/R/get_metadata.R RNeXML/R/nexml_write.R RNeXML/R/deprecated.R RNeXML/R/add_namespaces.R RNeXML/R/internal_nexml_id.R RNeXML/R/internal_get_node_maps.R RNeXML/R/nexmlTree.R RNeXML/R/internal_name_by_id.R RNeXML/R/internal_isEmpty.R RNeXML/R/nexml_get.R RNeXML/R/get_namespaces.R RNeXML/R/get_taxa.R RNeXML/R/add_trees.R RNeXML/R/character_classes.R RNeXML/R/tbl_df.R RNeXML/R/nexml_read.R RNeXML/R/concatenate_nexml.R RNeXML/R/nexml_add.R RNeXML/R/get_basic_metadata.R RNeXML/R/taxize_nexml.R RNeXML/R/get_taxa_meta.R RNeXML/R/nexml_validate.R
RNeXML/vignettes
RNeXML/vignettes/metadata.Rmd
RNeXML/vignettes/simmap.Rmd
RNeXML/vignettes/S4.Rmd
RNeXML/vignettes/sparql.Rmd
RNeXML/vignettes/references.bib
RNeXML/README.md
RNeXML/MD5
RNeXML/build
RNeXML/build/vignette.rds
RNeXML/DESCRIPTION
RNeXML/man
RNeXML/man/flatten_multiphylo.Rd RNeXML/man/get_taxa_meta_list.Rd RNeXML/man/meta.Rd RNeXML/man/get_taxa_meta.Rd RNeXML/man/add_characters.Rd RNeXML/man/c-nexml-method.Rd RNeXML/man/reset_id_counter.Rd RNeXML/man/simmap_ex.Rd RNeXML/man/nexml_read.Rd RNeXML/man/get_characters.Rd RNeXML/man/nexml_validate.Rd RNeXML/man/taxize_nexml.Rd RNeXML/man/add_meta.Rd RNeXML/man/get_taxa.Rd RNeXML/man/get_citation.Rd RNeXML/man/get_trees_list.Rd RNeXML/man/c-meta-method.Rd RNeXML/man/get_level.Rd RNeXML/man/nexml_write.Rd RNeXML/man/nexml_figshare.Rd RNeXML/man/add_trees.Rd RNeXML/man/c-ListOfmeta-method.Rd RNeXML/man/get_characters_list.Rd RNeXML/man/add_namespaces.Rd RNeXML/man/get_trees.Rd RNeXML/man/get_flat_trees.Rd RNeXML/man/nexml_publish.Rd RNeXML/man/get_metadata.Rd RNeXML/man/get_namespaces.Rd RNeXML/man/get_rdf.Rd RNeXML/man/nexml_get.Rd RNeXML/man/nexml_add.Rd RNeXML/man/simmap_to_nexml.Rd RNeXML/man/get_taxa_list.Rd RNeXML/man/toPhylo.Rd RNeXML/man/get_license.Rd RNeXML/man/add_basic_meta.Rd RNeXML/man/nexml_to_simmap.Rd
RNeXML/LICENSE

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