phylo4d_ext-class: Class "phylo4d_ext"

In phyext: An extension of some of the classes in phylobase. Tree objects now support subnodes on branches

Description

This class extends phylo4d in adding support for subnodes (not singletons) and tree weights.

Objects from the Class

Objects can be created by calls of the form new("phylo4d_ext", ...).

Slots

subnode.id:

Object of class "integer". The subnode identifier. Not currently being used.

subnode.data:

Object of class "data.frame". The subnode data frame. This data frame should extend the parent phylo4d class data frame - it extends the parent data frame in the same way the phylo4d_ext extends phylo4d.

subnode.branch:

Object of class "matrix". This is a two-column matrix. The first column contains the ancestor node Id and the descendant node Id for the two nodes spanning a branch. This copies data directly from the edge slot. It uses the node ids instead of the edge row index because the edge slot is often reordered.

subnode.pos:

Object of class "matrix". This is the position of the subnode on the branch as a fraction of the branch length. It is the fraction of the branch length starting from the descendant node.

So for the hypothetical branch: ANC <——–subnode–> DEC, the subnode position might be 0.25.

This is currently a two column matrix, but the columns should contain the same data. Eventually, these two columns will represent a confidence interval that the subnode might exist within.

weight:

Object of class "numeric". This is the weight for this tree. The weight is gleaned from nexus comments in a nexus file or set manually.

This is the only piece of data that is not replicated across every member of a phylo4d_ext list. Each tree can have a unique weight.

data:

Object of class "data.frame". Inherited from phylo4d

metadata:

Object of class "list". Inherited from phylo4d

edge:

Object of class "matrix". Inherited from phylo4

edge.length:

Object of class "numeric". Inherited from phylo4

label:

Object of class "character". Inherited from phylo4

edge.label:

Object of class "character". Inherited from phylo4

order:

Object of class "character". Inherited from phylo4

annote:

Object of class "list". Inherited from phylo4

Extends

Class "phylo4d", directly. Class "phylo4", by class "phylo4d", distance 2.

Methods

hasWeight

signature(x = "phylo4d_ext"): Checks whether or not a phylo4d_ext object or list of these objects contain weights.

plot

signature(x = "phylo4d_ext", y = "missing"): Calls phyextPlot with no extra arguments

snbranch

signature(x = "phylo4d_ext"): Return the subnode.branch matrix

sndata

signature(x = "phylo4d_ext"): Return the subnode.data data.frame

sndata<-

signature(x = "phylo4d_ext"): This adds column to the subnode data.frame. Pass the datnames option which will be the column name(s) of the new data columns.

snid

signature(x = "phylo4d_ext"): Return the subnode.id vector

snposition

signature(x = "phylo4d_ext"): Return the subnode.pos matrix

weight

signature(x = "phylo4d_ext"): Return the weight for a phylo4d_ext object or a vector of weights for a list of phylo4d_ext objects.

weight<-

signature(x = "phylo4d_ext"): Replaces the weight vector.

Author(s)

J. Conrad Stack

References

~put references to the literature/web site here ~

See Also

phylo4d

phyext documentation built on May 2, 2019, 5:19 p.m.