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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-class or XMLNode-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 nexml_read(x): object 'x' not found
# XMLInternalNode
nexml_read(xmlRoot(x))
#> Error in xmlRoot(x): object 'x' not found