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

This package enhancements to phylobase classes. It provides classes and methods which help uses manipulate branch-annotated trees and provides supports for a few other extra features.

AuthorJ. Conrad Stack <conrad.stack@gmail.com>
Date of publication2014-01-05 19:13:04
MaintainerJ. Conrad Stack <conrad.stack@gmail.com>
LicenseGPL-3
Version0.0.1

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Man pages

addSubNode: Add subnode to phylo4d_ext object

collapse.singletons: Collapse singleton nodes

collapse.subnodes: Collapse subnodes into singletons

collapse.to.singles: Collapse zero-length branches

deep.phy.copy: Copy a tree object slot by slot

expand.singles: Expand singletons

getEmptyDataFrame: Get empty data.frame

get.nexus.comments: Get comments from nexus text

get.nodenames: Read node names from newick text

getSubNodeData: Return subnode data

getSubNodeEdgeInds: Return subnode edge indices

getSubNodePosish: Return the subnode position

get.tree.weights: Get tree weights

has.block: Check for nexus block

has.characters2: Check for CHARACTERS2 block

hasData: Methods for Function hasData in Package 'RBrownie'

hasDataColumn: Does a tree object contain a specific data column

hasSubNodes: Does an object contain subnodes?

has.weights: Check for tree weights

is.simmap: Check SIMMAP v1.0

match.order: Matching orders

newlabels.v15: Generate simmap v1.5 labels

newlabels.v1x: Generate simmap v1.0 or v1.1 labels

nSubNodes: Get number of subnodes

phyext: A function which returns a phylo4d_ext object

phyextPlot: Plot phylo4d_ext object

phylo4d_ext-class: Class "phylo4d_ext"

read.characters2: Read CHARACTERS2 block

read.nexus.block: Find a block in a nexus file

read.nexus.simmap: Read a nexus file with SIMMAP-formatted trees (v1.0)

read.simmap: Read simmap-formatted newick strings (version 1.0)

read.simmap.new: Read simmap-formatted newick strings (version 1.5)

rmdata: rmdata from a tree object

showSubNodes: Display subnodes

strip: Strip whitespace

tipdate.ci: Get coalescent intervals for a tip-dated tree

treeHeight: Get the height (depth) of a tree

validPhylo4d_ext: Validate a phylo4d_ext object

write.nexus.simmap: Write phylo4d_ext object or list to a nexus file

write.simmap: Write phylo4d_ext tree to newick string

write.simmap.new: Wrapper for write.simmap

write.simmap.old: Wrapper for write.simmap

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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