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Get the desired element from the nexml object

Source: R/nexml_get.R
nexml_get.Rd

Get the desired element from the nexml object

Usage

nexml_get(
  nexml,
  element = c("trees", "trees_list", "flat_trees", "metadata", "otu", "taxa",
    "characters", "characters_list", "namespaces"),
  ...
)

Arguments

nexml

a nexml object (from read_nexml)

element

the kind of object desired, see details.

...

additional arguments, if applicable to certain elements

Value

return type depends on the element requested. See details.

Details

  • "tree" an ape::phylo tree, if only one tree is represented. Otherwise returns a list of lists of multiphylo trees. To consistently receive the list of lists format (preserving the hierarchical nature of the nexml), use trees instead.

  • "trees" returns a list of lists of multiphylo trees, even if all trees are in the same trees node (and hence the outer list will be of length 1) or if there is only a single tree (and hence the inner list will also be of length 1. This ensures a consistent return type regardless of the number of trees present in the nexml file, and also preserves any hierarchy/grouping of trees.

  • "flat_trees" a multiPhylo object (list of ape::phylo objects) Note that this method collapses any hierarchical structure that may have been present as multiple trees nodes in the original nexml (though such a feature is rarely used). To preserve that structure, use trees instead.

  • "metadata"Get metadata from the specified level (default is top/nexml level)

  • "otu" returns a named character vector containing all available metadata. names indicate property (or rel in the case of links/resourceMeta), while values indicate the content (or href for links).

  • "taxa" alias for otu

For a slightly cleaner interface, each of these elements is also defined as an S4 method for a nexml object. So in place of get_item(nexml, "tree"), one could use get_tree(nexml), and so forth for each element type.

See also

get_trees

Examples

comp_analysis <- system.file("examples", "comp_analysis.xml", package="RNeXML")
nex <- nexml_read(comp_analysis)
nexml_get(nex, "trees")
#> 
#> Phylogenetic tree with 10 tips and 9 internal nodes.
#> 
#> Tip labels:
#>   taxon_8, taxon_9, taxon_10, taxon_1, taxon_2, taxon_3, ...
#> 
#> Rooted; includes branch length(s).
nexml_get(nex, "characters_list")
#> $cs15
#>          <NA> log snout-vent length
#> taxon_8  ou10            -3.2777799
#> taxon_9  ou11             2.0959433
#> taxon_10 ou12             3.1373971
#> taxon_1   ou3             4.7532824
#> taxon_2   ou4            -2.7624146
#> taxon_3   ou5             2.1049413
#> taxon_4   ou6            -4.9504770
#> taxon_5   ou7             1.2714718
#> taxon_6   ou8             6.2593966
#> taxon_7   ou9             0.9099634
#> 
#> $cs31
#>          reef-dwelling
#> taxon_8              0
#> taxon_9              1
#> taxon_10             0
#> taxon_1              1
#> taxon_2              0
#> taxon_3              0
#> taxon_4              0
#> taxon_5              1
#> taxon_6              1
#> taxon_7              1
#>