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

View on R-Forge

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.