├── .Rbuildignore ├── .circleci └── config.yml ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── .travis.yml ├── CONTRIBUTING.md ├── CRAN-RELEASE ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── S4-utils.R ├── add_basic_meta.R ├── add_characters.R ├── add_meta.R ├── add_namespaces.R ├── add_trees.R ├── character_classes.R ├── 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 ├── nexmlTree.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 ├── README.Rmd ├── README.md ├── RNeXML.Rproj ├── _pkgdown.yml ├── appveyor.yml ├── codecov.yml ├── codemeta.json ├── cran-comments.md ├── docs ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── link.svg └── logo.svg ├── inst ├── CITATION ├── WORDLIST ├── examples │ ├── RDFa2RDFXML.xsl │ ├── biophylo.xml │ ├── characters.xml │ ├── coal.xml │ ├── comp_analysis.xml │ ├── gardiner_1984.xml │ ├── geospiza.xml │ ├── jsonld-ex.R │ ├── mbank_X962_11-22-2013_1534.nex │ ├── merge_data.Rmd │ ├── merge_data.md │ ├── meta_example.xml │ ├── meta_taxa.xml │ ├── missing_some_branchlengths.xml │ ├── multitrees.xml │ ├── ncbii.xml │ ├── no-base-ns.xml │ ├── ontotrace-result.xml │ ├── phenex.xml │ ├── phenoscape.xml │ ├── primates.xml │ ├── primates_from_R.xml │ ├── primates_meta.xml │ ├── primates_meta_xslt.xml │ ├── simmap.nex │ ├── simmap.xml │ ├── simmap_ex.xml │ ├── some_missing_branchlengths.xml │ ├── sparql.newick │ ├── taxa.xml │ ├── treebase-record.xml │ └── trees.xml ├── simmap.md └── xsd │ ├── .htaccess │ ├── LICENSE │ ├── README.txt │ ├── abstract.xsd │ ├── characters │ ├── README.txt │ ├── abstractcharacters.xsd │ ├── characters.xsd │ ├── continuous.xsd │ ├── dna.xsd │ ├── protein.xsd │ ├── restriction.xsd │ ├── rna.xsd │ └── standard.xsd │ ├── external │ ├── sawsdl.xsd │ ├── xhtml-datatypes-1.xsd │ ├── xlink.xsd │ └── xml.xsd │ ├── meta │ ├── README.txt │ ├── annotations.xsd │ └── sets.xsd │ ├── nexml.xsd │ ├── taxa │ ├── README.txt │ └── taxa.xsd │ └── trees │ ├── README.txt │ ├── abstracttrees.xsd │ ├── network.xsd │ ├── tree.xsd │ └── trees.xsd ├── man ├── Annotated-class.Rd ├── New.Rd ├── add_basic_meta.Rd ├── add_characters.Rd ├── add_meta.Rd ├── add_namespaces.Rd ├── add_trees.Rd ├── c-meta.Rd ├── c-nexml-method.Rd ├── charzero_as_empty.Rd ├── coalesce_.Rd ├── constructors.Rd ├── dot-cacheNextMethod.Rd ├── dot-callGeneric.Rd ├── dot-methodWithNext.Rd ├── dot-sigLabel.Rd ├── expand_prefix.Rd ├── figures │ ├── Figure1-1.png │ ├── logo.svg │ ├── unnamed-chunk-5-1.png │ └── unnamed-chunk-8-1.png ├── findNextMethod.Rd ├── flatten_multiphylo.Rd ├── get_all_meta.Rd ├── get_characters.Rd ├── get_characters_list.Rd ├── get_citation.Rd ├── get_flat_trees.Rd ├── get_level.Rd ├── get_license.Rd ├── get_meta.Rd ├── get_metadata.Rd ├── get_metadata_values.Rd ├── get_namespaces.Rd ├── get_rdf.Rd ├── get_taxa.Rd ├── get_taxa_list.Rd ├── get_taxa_meta.Rd ├── get_taxa_meta_list.Rd ├── get_trees.Rd ├── get_trees_list.Rd ├── lcapply.Rd ├── meta.Rd ├── nexml-class.Rd ├── nexml_add.Rd ├── nexml_figshare.Rd ├── nexml_get.Rd ├── nexml_publish.Rd ├── nexml_read.Rd ├── nexml_validate.Rd ├── nexml_write.Rd ├── reset_id_counter.Rd ├── simmap_to_nexml.Rd ├── slot-ResourceMeta-method.Rd ├── summary-nexml-method.Rd ├── taxize_nexml.Rd └── toPhylo.Rd ├── manuscripts ├── .gitignore ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── components │ ├── comp_analysis.xml │ ├── elsarticle.cls │ ├── elsarticle.latex │ ├── methods-in-ecology-and-evolution.csl │ ├── references.bib │ ├── restore-cache.R │ ├── sup-references.bib │ └── trees.xml ├── manuscript.Rmd ├── manuscript.pdf ├── manuscript.tex └── public-domain-versions.txt ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── spelling.R ├── test-all.R └── testthat │ ├── conversions.R │ ├── geiger_test.R │ ├── helper-RNeXML.R │ ├── test_01_exported_util.R │ ├── test_01_utils.R │ ├── test_02_summary.R │ ├── test_ape.R │ ├── test_characters.R │ ├── test_comp_analysis.R │ ├── test_concatenate.R │ ├── test_get_characters.R │ ├── test_get_level.R │ ├── test_global_ids.R │ ├── test_inheritance.R │ ├── 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