Read NeXML files into various R formats
Usage
nexml_read(x, ...)
# S3 method for character
nexml_read(x, ...)
# S3 method for XMLInternalDocument
nexml_read(x, ...)
# S3 method for XMLInternalNode
nexml_read(x, ...)Arguments
- x
Path to the file to be read in. An
XML::XMLDocument-classorXMLNode-class- ...
Further arguments passed on to
xmlTreeParse
Examples
# file
f <- system.file("examples", "trees.xml", package="RNeXML")
nexml_read(f)
#> A nexml object representing:
#> 1 phylogenetic tree block(s), where:
#> block 1 contains 2 phylogenetic tree(s)
#> 0 character block(s),
#> 5 taxonomic units in 1 block(s)
#> Taxa: species 1, species 2, species 3, species 4, species 5 ...
#> Metadata annotations:
#> 0 at top level
#> 0 in block 1 at otu level
#>
#> NeXML generated by RNeXML using schema version: 0.9
#> Size: 139.1 Kb
if (FALSE) # may take > 5 s
# url
url <- "https://raw.githubusercontent.com/ropensci/RNeXML/master/inst/examples/trees.xml"
nexml_read(url)
#> Error in UseMethod("nexml_read"): no applicable method for 'nexml_read' applied to an object of class "function"
# character string of XML
str <- paste0(readLines(f), collapse = "")
nexml_read(str)
#> A nexml object representing:
#> 1 phylogenetic tree block(s), where:
#> block 1 contains 2 phylogenetic tree(s)
#> 0 character block(s),
#> 5 taxonomic units in 1 block(s)
#> Taxa: species 1, species 2, species 3, species 4, species 5 ...
#> Metadata annotations:
#> 0 at top level
#> 0 in block 1 at otu level
#>
#> NeXML generated by RNeXML using schema version: 0.9
#> Size: 139.1 Kb
# XMLInternalDocument
library("httr")
library("XML")
x <- xmlParse(content(GET(url)))
#> Error in as.character(url): cannot coerce type 'closure' to vector of type 'character'
nexml_read(x)
#> Error in eval(expr, envir, enclos): object 'x' not found
# XMLInternalNode
nexml_read(xmlRoot(x))
#> Error in eval(expr, envir, enclos): object 'x' not found