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.

Install the latest version of this package by entering the following in R:
install.packages("RNeXML")
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

Functions

add_basic_meta Man page
add_characters Man page
add_meta Man page
add_namespaces Man page
add_trees Man page
c,ListOfmeta-method Man page
c,meta-method Man page
c,nexml-method Man page
flatten_multiphylo Man page
get_characters Man page
get_characters_list Man page
get_citation Man page
get_flat_trees Man page
get_item Man page
get_level Man page
get_license Man page
get_metadata Man page
get_namespaces Man page
get_otu Man page
get_otus_list Man page
get_rdf Man page
get_taxa Man page
get_taxa_list Man page
get_taxa_meta Man page
get_taxa_meta_list Man page
get_trees Man page
get_trees_list Man page
meta Man page
nexml_add Man page
nexml_figshare Man page
nexml_get Man page
nexml_publish Man page
nexml_read Man page
nexml_read.character Man page
nexml_read.XMLInternalDocument Man page
nexml_read.XMLInternalNode Man page
nexml_to_simmap Man page
nexml_validate Man page
nexml_write Man page
read.nexml Man page
reset_id_counter Man page
simmap_ex Man page
simmap_to_nexml Man page
taxize_nexml Man page
toPhylo Man page
write.nexml Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.