aphylo-class function

Annotated Phylogenetic Tree

The aphylo class tree holds both the tree structure represented as a partially ordered phylogenetic tree, and node annotations. While annotations are included for both leafs and inner nodes, the algorithms included in this package only uses the leaf annotations.

new_aphylo(tree, tip.annotation, ...)

## S3 method for class 'phylo'
new_aphylo(
  tree,
  tip.annotation,
  node.annotation = NULL,
  tip.type = NULL,
  node.type = NULL,
  ...
)

Arguments

• tree: An object of class phylo
• tip.annotation, node.annotation: Annotation data. See aphylo .
• ...: Further argmuents passed to the method.
• tip.type, node.type: Integer vectors with values 0 or 1. 0 denotes duplication node and 1 speciation node. This is used in LogLike .

Returns

A list of class aphylo with the following elements: - tree: An object of class phylo .

• tip.annotation: An integer matrix. Tip (leaf) nodes annotations.

• node.annotation: An integer matrix (optional). Internal nodes annotations.

• offspring: A list. List of offspring of each node.

• pseq: Integer vector. The pruning sequence (postorder).

• reduced_pseq: Integer vector. The reduced version of pseq.

• Ntips.annotated: Integer. Number of tips with annotations.

• tip.type: Binary of length ape::Ntip(). 0 means duplication and 1 speciation.

• tip.type: Binary of length ape::Nnode(). 0 means duplication and 1 speciation.

Examples

# A simple example ----------------------------------------------------------

data(fakeexperiment)
data(faketree)
ans <- new_aphylo(fakeexperiment[,2:3], tree = as.phylo(faketree))
 
# We can visualize it
plot(ans)

See Also

Other Data management functions: aphylo_from_data_frame()

Other aphylo methods: aphylo-methods