phyext: An extension of some of the classes in phylobase. Tree objects now support subnodes on branches
Version 0.0.1

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
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("phyext", repos="http://R-Forge.R-project.org")

Popular man pages

collapse.singletons: Collapse singleton nodes
getSubNodeEdgeInds: Return subnode edge indices
hasSubNodes: Does an object contain subnodes?
is.simmap: Check SIMMAP v1.0
rmdata: rmdata from a tree object
showSubNodes: Display subnodes
write.simmap: Write phylo4d_ext tree to newick string
See all...

All man pages Function index File listing

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

Functions

addSubNode Man page Source code
as Man page
as,phylo,phylo4d_ext-method Man page
as,phylo4,phylo4d_ext-method Man page
as,phylo4d,phylo4d_ext-method Man page
as-method Man page
coerce,phylo,phylo4d_ext-method Man page
coerce,phylo4,phylo4d_ext-method Man page
coerce,phylo4d,phylo4d_ext-method Man page
coerce-methods Man page
collapse.singletons Man page Source code
collapse.subnodes Man page Source code
collapse.to.singles Man page Source code
contData Source code
deep.phy.copy Man page Source code
discData Source code
edge.index Source code
expand.singles Man page Source code
get.nexus.block.inds Source code
get.nexus.comments Man page Source code
get.nodenames Man page Source code
get.tree.weights Man page Source code
getEmptyDataFrame Man page Source code
getSubNodeData Man page Source code
getSubNodeEdgeInds Man page Source code
getSubNodePosish Man page Source code
guess.datatype Source code
has.block Man page Source code
has.characters2 Man page Source code
has.weights Man page Source code
hasData Man page
hasData,list-method Man page
hasData,phylo-method Man page
hasData,phylo4-method Man page
hasData,phylo4d-method Man page
hasData-methods Man page
hasDataColumn Man page
hasDataColumn,phylo,ANY-method Man page
hasDataColumn,phylo4,ANY-method Man page
hasDataColumn,phylo4d,character-method Man page
hasDataColumn,phylo4d,numeric-method Man page
hasDataColumn-methods Man page
hasSubNodes Man page
hasSubNodes,list-method Man page
hasSubNodes,phylo-method Man page
hasSubNodes,phylo4-method Man page
hasSubNodes,phylo4d_ext-method Man page
hasSubNodes-methods Man page
hasWeight Man page
hasWeight,list-method Man page
hasWeight,phylo4d_ext-method Man page
is.simmap Man page Source code
match.order Man page Source code
nSubNodes Man page Source code
newlabels.v15 Man page Source code
newlabels.v1x Man page Source code
noneData Source code
onLoad Source code
phyext Man page
phyext,character-method Man page
phyext,list-method Man page
phyext,phylo-method Man page
phyext,phylo4-method Man page
phyext,phylo4d-method Man page
phyext,phylo4d_ext-method Man page
phyext-methods Man page
phyextPlot Man page Source code
phylo4d_ext-class Man page
plot,phylo4d_ext,missing-method Man page
read.characters2 Man page Source code
read.nexus.block Man page Source code
read.nexus.simmap Man page Source code
read.simmap Man page Source code
read.simmap.new Man page Source code
rmdata Man page
rmdata,brownie,character,missing-method Man page
rmdata,brownie,numeric,ANY-method Man page
rmdata,brownie,numeric,missing-method Man page
rmdata,brownie,numeric,numeric-method Man page
rmdata,list,ANY,missing-method Man page
rmdata,phylo4d,character,missing-method Man page
rmdata,phylo4d,numeric,missing-method Man page
rmdata,phylo4d_ext,character,missing-method Man page
rmdata,phylo4d_ext,numeric,missing-method Man page
rmdata,phylo4d_ext,numeric,numeric-method Man page
rmdata-methods Man page
show,phylo4d_ext-method Man page
showSubNodes Man page Source code
snbranch Man page
snbranch,list-method Man page
snbranch,phylo4d_ext-method Man page
sndata Man page
sndata,list-method Man page
sndata,phylo4d_ext-method Man page
sndata<- Man page
sndata<-,list-method Man page
sndata<-,phylo4d_ext-method Man page
snid Man page
snid,list-method Man page
snid,phylo4d_ext-method Man page
snposition Man page
snposition,list-method Man page
snposition,phylo4d_ext-method Man page
split.tokens Source code
strip Man page Source code
strip.tree.comments Source code
tipdate.ci Man page Source code
treeHeight Man page
treeHeight,phylo4-method Man page
treeHeight,phylo4d-method Man page
treeHeight,phylo4d_ext-method Man page
treeHeight-methods Man page
validPhylo4d_ext Man page Source code
weight Man page
weight,list-method Man page
weight,phylo4d_ext-method Man page
weight<- Man page
weight<-,list-method Man page
weight<-,phylo4d_ext-method Man page
write.characters2 Source code
write.nexus.simmap Man page Source code
write.simmap Man page Source code
write.simmap.new Man page Source code
write.simmap.old Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/ci.R
R/class-phylo4d_ext.R
R/methods-phylo4d_ext.R
R/phyextPlots.R
R/processNexus.R
R/setAs-phyext.R
R/zzz.R
man
man/addSubNode.Rd
man/collapse.singletons.Rd
man/collapse.subnodes.Rd
man/collapse.to.singles.Rd
man/deep.phy.copy.Rd
man/expand.singles.Rd
man/get.nexus.comments.Rd
man/get.nodenames.Rd
man/get.tree.weights.Rd
man/getEmptyDataFrame.Rd
man/getSubNodeData.Rd
man/getSubNodeEdgeInds.Rd
man/getSubNodePosish.Rd
man/has.block.Rd
man/has.characters2.Rd
man/has.weights.Rd
man/hasData.Rd
man/hasDataColumn.Rd
man/hasSubNodes.Rd
man/is.simmap.Rd
man/match.order.Rd
man/nSubNodes.Rd
man/newlabels.v15.Rd
man/newlabels.v1x.Rd
man/phyext.Rd
man/phyextPlot.Rd
man/phylo4d_ext-class.Rd
man/read.characters2.Rd
man/read.nexus.block.Rd
man/read.nexus.simmap.Rd
man/read.simmap.Rd
man/read.simmap.new.Rd
man/rmdata.Rd
man/showSubNodes.Rd
man/strip.Rd
man/tipdate.ci.Rd
man/treeHeight.Rd
man/validPhylo4d_ext.Rd
man/write.nexus.simmap.Rd
man/write.simmap.Rd
man/write.simmap.new.Rd
man/write.simmap.old.Rd
phyext documentation built on May 21, 2017, 1:13 a.m.

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