Read phyloXML files

Read phyloXML files

read_phyloxml(x)

# S3 method for character
read_phyloxml(x)

# S3 method for default
read_phyloxml(x)

Arguments

x	Character scalar. Path to a phyloXML file.

Value

A list of class phyloxml in which each element represents a tree: A data.frame with the following elements:

id

Integer, the id of the node.

name

Character, the name of the node (can be NA).

branch_length

Numeric, the length of the branch (can be NA).

iselaf

Logical, whether it is leaf (tip) or not.

parent

Integer, the id of the parent node.

Details

phyloxml objects can be coerced as ape::multiphylo using the phyloxml2phylo function.

Examples

library(ape)
set.seed(1)

x <- rtree(10)
x2 <- write_phyloxml(x)
read_phyloxml(x2)
#> $`A phylogenetic tree`
#> $`A phylogenetic tree`$.Data
#>    id name branch_length isleaf parent confidence width taxonomy sequence
#> 11 11 <NA>            NA  FALSE     NA         NA    NA       NA       NA
#> 12 12 <NA>    0.71761851  FALSE     11         NA    NA       NA       NA
#> 1   1  t10    0.99190609   TRUE     12         NA    NA       NA       NA
#> 13 13 <NA>    0.38003518  FALSE     12         NA    NA       NA       NA
#> 2   2   t6    0.77744522   TRUE     13         NA    NA       NA       NA
#> 3   3   t9    0.93470523   TRUE     13         NA    NA       NA       NA
#> 14 14 <NA>    0.21214252  FALSE     11         NA    NA       NA       NA
#> 15 15 <NA>    0.65167377  FALSE     14         NA    NA       NA       NA
#> 16 16 <NA>    0.12555510  FALSE     15         NA    NA       NA       NA
#> 4   4   t1    0.26722067   TRUE     16         NA    NA       NA       NA
#> 17 17 <NA>    0.38611409  FALSE     16         NA    NA       NA       NA
#> 5   5   t2    0.01339033   TRUE     17         NA    NA       NA       NA
#> 6   6   t7    0.38238796   TRUE     17         NA    NA       NA       NA
#> 7   7   t3    0.86969085   TRUE     15         NA    NA       NA       NA
#> 18 18 <NA>    0.34034900  FALSE     14         NA    NA       NA       NA
#> 19 19 <NA>    0.48208012  FALSE     18         NA    NA       NA       NA
#> 8   8   t8    0.59956583   TRUE     19         NA    NA       NA       NA
#> 9   9   t4    0.49354131   TRUE     19         NA    NA       NA       NA
#> 10 10   t5    0.18621760   TRUE     18         NA    NA       NA       NA
#>    events
#> 11     NA
#> 12     NA
#> 1      NA
#> 13     NA
#> 2      NA
#> 3      NA
#> 14     NA
#> 15     NA
#> 16     NA
#> 4      NA
#> 17     NA
#> 5      NA
#> 6      NA
#> 7      NA
#> 18     NA
#> 19     NA
#> 8      NA
#> 9      NA
#> 10     NA
#> 
#> $`A phylogenetic tree`$rooted
#> [1] "true"
#> 
#> 
#> attr(,"class")
#> [1] "phyloxml"