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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/nexml_write.R
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\title{Write nexml files}
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nexml_write(x = new("nexml"), file = NULL, trees = NULL,
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characters = NULL, meta = NULL, ...)
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\item{x}{a nexml object, or any phylogeny object (e.g. phylo, phylo4)
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that can be coerced into one. Can also be omitted, in which case a new
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nexml object will be constructed with the additional parameters specified.}
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\item{file}{the name of the file to write out}
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\item{trees}{phylogenetic trees to add to the nexml file (if not already given in x)
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see \code{\link{add_trees}} for details.}
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\item{characters}{additional characters}
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\item{meta}{A meta element or list of meta elements, see \code{\link{add_meta}}}
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\item{...}{additional arguments to add__basic_meta, such as the title. See \code{\link{add_basic_meta}}.}
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Writes out a nexml file
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## Write an ape tree to nexml, analgous to write.nexus:
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library(ape); data(bird.orders)
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write.nexml(bird.orders, file="example.xml")
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\dontrun{ # takes > 5s
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## Assemble a nexml section by section and then write to file:
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nexml <- add_trees(geospiza$phy) # creates new nexml
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nexml <- add_characters(geospiza$dat, nexml = nexml) # pass the nexml obj to append character data
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nexml <- add_basic_meta(title="my title", creator = "Carl Boettiger", nexml = nexml)
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nexml <- add_meta(meta("prism:modificationDate", format(Sys.Date())), nexml = nexml)
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write.nexml(nexml, file="example.xml")
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## As above, but in one call (except for add_meta() call).
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write.nexml(trees = geospiza$phy,
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characters = geospiza$dat,
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creator = "Carl Boettiger",
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## Mix and match: identical to the section by section:
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nexml <- add_meta(meta("prism:modificationDate", format(Sys.Date())))
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write.nexml(x = nexml,
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characters = geospiza$dat,
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creator = "Carl Boettiger",
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\code{\link{add_trees}} \code{\link{add_characters}} \code{\link{add_meta}} \code{\link{nexml_read}}
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man/nexml_write.Rd
