RNeXML: Semantically Rich I/O for the 'NeXML' Format

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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.

Author
Carl Boettiger [cre, aut], Scott Chamberlain [aut], Hilmar Lapp [aut], Kseniia Shumelchyk [aut], Rutger Vos [aut]
Date of publication
2016-06-28 23:36:34
Maintainer
Carl Boettiger <cboettig@gmail.com>
License
BSD_3_clause + file LICENSE
Version
2.0.7
URLs

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