read.phyloxml

read.phyloxml(file)

Arguments

file

phyloxml file

Value

treedata class or treedataList class

Examples

xmlfile1 <- system.file("extdata/phyloxml", "test_x2.xml", package="treeio")
px1 <- read.phyloxml(xmlfile1)
px1
#> 'treedata' S4 object that stored information
#> of
#> 	'/usr/local/lib/R/site-library/treeio/extdata/phyloxml/test_x2.xml'.
#> 
#> [email protected] phylo:
#> 
#> Phylogenetic tree with 10 tips and 9 internal nodes.
#> 
#> Tip labels:
#>   t7, t2, t3, t8, t1, t5, ...
#> 
#> Rooted; includes branch lengths.
#> 
#> with the following features available:
#>   ''.
#> 
#> # The associated data tibble abstraction: 19 × 3
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#>     node label isTip
#>    <int> <chr> <lgl>
#>  1     1 t7    TRUE 
#>  2     2 t2    TRUE 
#>  3     3 t3    TRUE 
#>  4     4 t8    TRUE 
#>  5     5 t1    TRUE 
#>  6     6 t5    TRUE 
#>  7     7 t6    TRUE 
#>  8     8 t9    TRUE 
#>  9     9 t10   TRUE 
#> 10    10 t4    TRUE 
#> 11    11 NA    FALSE
#> 12    12 NA    FALSE
#> 13    13 NA    FALSE
#> 14    14 NA    FALSE
#> 15    15 NA    FALSE
#> 16    16 NA    FALSE
#> 17    17 NA    FALSE
#> 18    18 NA    FALSE
#> 19    19 NA    FALSE
xmlfile2 <- system.file("extdata/phyloxml", "phyloxml_examples.xml", package="treeio")
px2 <- read.phyloxml(xmlfile2)
px2
#> 13 phylogenetic trees