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Add metadata to a nexml file

Source: R/add_meta.R
add_meta.Rd

Add metadata to a nexml file

Usage

add_meta(
  meta,
  nexml = new("nexml"),
  level = c("nexml", "otus", "trees", "characters"),
  namespaces = NULL,
  i = 1,
  at_id = NULL
)

Arguments

meta

a meta S4 object, e.g. ouput of the function meta, or a list of these meta objects

nexml

(S4) object

level

the level at which the metadata annotation should be added.

namespaces

named character string for any additional namespaces that should be defined.

i

for otus, trees, characters: if there are multiple such blocks, which one should be annotated? Default is first/only block.

at_id

the id of the element to be annotated. Optional, advanced use only.

Value

the updated nexml object

See also

meta add_trees add_characters add_basic_meta

Examples

## Create a new nexml object with a single metadata element: 
modified <- meta(property = "prism:modificationDate", content = "2013-10-04")
nex <- add_meta(modified) # Note: 'prism' is defined in nexml_namespaces by default.  

## Write multiple metadata elements, including a new namespace:  
website <- meta(href = "http://carlboettiger.info", 
                rel = "foaf:homepage")              # meta can be link-style metadata
nex <- add_meta(list(modified,  website), 
                namespaces = c(foaf = "http://xmlns.com/foaf/0.1/"))

## Append more metadata, and specify a level: 
history <- meta(property = "skos:historyNote",
                 content = "Mapped from the bird.orders data in the ape package using RNeXML")
data(bird.orders)
nex <- add_trees(bird.orders) # need to have created a trees block first
nex <- add_meta(history, 
                nexml = nex,
                level = "trees",
                namespaces = c(skos = "http://www.w3.org/2004/02/skos/core#"))