Package: RNeXML 2.4.11

Carl Boettiger

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.

Authors:Carl Boettiger [cre, aut], Scott Chamberlain [aut], Hilmar Lapp [aut], Kseniia Shumelchyk [aut], Rutger Vos [aut]

RNeXML_2.4.11.tar.gz
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RNeXML.pdf |RNeXML.html✨
RNeXML/json (API)
NEWS

# Install 'RNeXML' in R:
install.packages('RNeXML', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/rnexml/issues

On CRAN:

metadatanexmlphylogeneticslinked-data

9.82 score 13 stars 18 packages 100 scripts 3.5k downloads 62 exports 38 dependencies

Last updated 7 months agofrom:f94903a248. Checks:OK: 3 NOTE: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-winNOTENov 02 2024
R-4.5-linuxNOTENov 02 2024
R-4.4-winNOTENov 02 2024
R-4.4-macNOTENov 02 2024
R-4.3-winOKNov 02 2024
R-4.3-macOKNov 02 2024

Exports:add_basic_metaadd_charactersadd_metaadd_namespacesadd_treesexpand_prefixflatten_multiphyloget_all_metaget_charactersget_characters_listget_citationget_flat_treesget_levelget_licenseget_metaget_metadataget_metadata_valuesget_namespacesget_otuget_otus_listget_rdfget_taxaget_taxa_listget_treesget_trees_listmetanexmlnexml_addnexml_figsharenexml_getnexml_publishnexml_readnexml_to_simmapnexml_validatenexml_writenexml.cellnexml.charnexml.charactersnexml.edgenexml.formatnexml.matrixnexml.membernexml.nodenexml.otunexml.otusnexml.polymorphic_statesnexml.rownexml.seqnexml.statenexml.statesnexml.treenexml.treesnexml.uncertain_statenexml.uncertain_statesread.nexmlreset_id_countersimmap_to_nexmlslotslot<-summarytaxize_nexmlwrite.nexml

Dependencies:apeaskpassclicpp11curldigestdplyrfansigenericsgluehttrjsonlitelatticelifecyclemagrittrmimenlmeopensslpillarpkgconfigplyrpurrrR6Rcppreshape2rlangstringistringrsystibbletidyrtidyselectutf8uuidvctrswithrXMLxml2

A Brief Introduction to RNeXML

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered fromintro.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2020-01-28
Started: 2018-12-08

Extending NeXML: an example based on simmap

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered fromsimmap.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2020-01-28
Started: 2015-01-08

Handling Metadata in RNeXML

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered frommetadata.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2020-01-28
Started: 2015-01-08

SPARQL with RNeXML

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered fromsparql.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2020-01-28
Started: 2015-01-08

The nexml S4 Object

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered fromS4.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2020-01-28
Started: 2015-01-08

Readme and manuals

Help Manual

Help pageTopics
Calls the given generic with the given arguments.callGeneric
Saves the next method in the method meta data.methodWithNext
Create a label for a method signature.sigLabel
Add basic metadataadd_basic_meta
Add character data to a nexml objectadd_characters
Add metadata to a nexml fileadd_meta
Add namespacesadd_namespaces
add_treesadd_trees
Class of objects that have metadata as lists of meta elementsAnnotated-class
Concatenate meta elements into a ListOfmetac,ListOfmeta-method c,meta-method c-ListOfmeta c-meta
Concatenate nexml filesc,nexml-method
Treats zero-length character vectors as empty stringscharzero_as_empty
Front-end to dplyr::coalesce to deal with NULL vectorscoalesce_
Expand namespace-prefixed stringexpand_prefix
Finds the method that callNextMethod() should chain tofindNextMethod
Flatten a multiphylo objectflatten_multiphylo
Get flattened list of meta annotationsget_all_meta
Get character data.frame from nexmlget_characters
Extract the character matrixget_characters_list
Get citation from metadataget_citation
get_flat_treesget_flat_trees
get_levelget_level
Get license from metadataget_license
Extracts meta objects matching propertiesget_meta
get_metadataget_metadata
Get the value(s) for metadataget_metadata_values
get namespacesget_namespaces
Extract rdf-xml from a NeXML fileget_rdf
get_taxaget_otu get_taxa
get_taxa_listget_otus_list get_taxa_list
extract a phylogenetic tree from the nexmlget_trees
extract all phylogenetic trees in ape formatget_trees_list
Compact list then lapplylcapply
Constructor function for metadata nodesmeta nexml.meta
new with namespaced class nameNew
add elements to a new or existing nexml objectnexml_add
publish nexml to figsharenexml_figshare
Get the desired element from the nexml objectget_item nexml_get
publish nexml files to the web and receive a DOInexml_publish
Read NeXML files into various R formatsnexml_read nexml_read.character nexml_read.XMLInternalDocument nexml_read.XMLInternalNode read.nexml
validate nexml using the online validator toolnexml_validate
Write nexml filesnexml_write write.nexml
Class representing a NeXML documentnexml nexml-class
Constructor for the respective classnexml.cell nexml.char nexml.characters nexml.edge nexml.format nexml.matrix nexml.member nexml.meta_ nexml.node nexml.otu nexml.otus nexml.polymorphic_states nexml.row nexml.seq nexml.state nexml.states nexml.tree nexml.trees nexml.uncertain_state nexml.uncertain_states
reset id counterreset_id_counter
Convert phylo with attached simmap to nexml objectnexml_to_simmap simmap_to_nexml
Access or set slot of S4 objectslot,ResourceMeta-method slot-ResourceMeta slot<-,ResourceMeta-method
Summary method for nexml objectssummary,nexml-method summary.nexml
taxize nexmltaxize_nexml
nexml to phylotoPhylo