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

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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.

Author
J. Conrad Stack <conrad.stack@gmail.com>
Date of publication
2014-01-05 19:13:04
Maintainer
J. Conrad Stack <conrad.stack@gmail.com>
License
GPL-3
Version
0.0.1

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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

Files in this package

phyext/DESCRIPTION
phyext/NAMESPACE
phyext/R
phyext/R/ci.R
phyext/R/class-phylo4d_ext.R
phyext/R/methods-phylo4d_ext.R
phyext/R/phyextPlots.R
phyext/R/processNexus.R
phyext/R/setAs-phyext.R
phyext/R/zzz.R
phyext/man
phyext/man/addSubNode.Rd
phyext/man/collapse.singletons.Rd
phyext/man/collapse.subnodes.Rd
phyext/man/collapse.to.singles.Rd
phyext/man/deep.phy.copy.Rd
phyext/man/expand.singles.Rd
phyext/man/get.nexus.comments.Rd
phyext/man/get.nodenames.Rd
phyext/man/get.tree.weights.Rd
phyext/man/getEmptyDataFrame.Rd
phyext/man/getSubNodeData.Rd
phyext/man/getSubNodeEdgeInds.Rd
phyext/man/getSubNodePosish.Rd
phyext/man/has.block.Rd
phyext/man/has.characters2.Rd
phyext/man/has.weights.Rd
phyext/man/hasData.Rd
phyext/man/hasDataColumn.Rd
phyext/man/hasSubNodes.Rd
phyext/man/is.simmap.Rd
phyext/man/match.order.Rd
phyext/man/nSubNodes.Rd
phyext/man/newlabels.v15.Rd
phyext/man/newlabels.v1x.Rd
phyext/man/phyext.Rd
phyext/man/phyextPlot.Rd
phyext/man/phylo4d_ext-class.Rd
phyext/man/read.characters2.Rd
phyext/man/read.nexus.block.Rd
phyext/man/read.nexus.simmap.Rd
phyext/man/read.simmap.Rd
phyext/man/read.simmap.new.Rd
phyext/man/rmdata.Rd
phyext/man/showSubNodes.Rd
phyext/man/strip.Rd
phyext/man/tipdate.ci.Rd
phyext/man/treeHeight.Rd
phyext/man/validPhylo4d_ext.Rd
phyext/man/write.nexus.simmap.Rd
phyext/man/write.simmap.Rd
phyext/man/write.simmap.new.Rd
phyext/man/write.simmap.old.Rd