/usr/lib/R/site-library/RNeXML/INDEX is in r-cran-rnexml 2.0.7-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | 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_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
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