phyext2: An Extension (for Package 'SigTree') of Some of the Classes in Package 'phylobase'
Version 0.0.4

Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.

AuthorJ. Conrad Stack
Date of publication2015-07-27 23:38:32
MaintainerJohn R. Stevens <>
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:

Popular man pages

phyext2: Misc. functions from phyext package
phyext2class: Misc. functions from phyext package (class definitions)
phyext2methods: Misc. functions from phyext package (methods definitions)
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All man pages Function index File listing

Man pages

phyext2: Misc. functions from phyext package
phyext2class: Misc. functions from phyext package (class definitions)
phyext2methods: Misc. functions from phyext package (methods definitions)


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 Man page Source code
contData Man page Source code
deep.phy.copy Man page Source code
discData Man page Source code
edge.index Source code Man page Source code Source code 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 Man page 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 Man page 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 Man page Source code Man page Source code
read.simmap Man page Source code 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 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 Man page Source code Man page Source code
write.simmap Man page Source code Man page Source code
write.simmap.old Man page Source code


phyext2 documentation built on May 19, 2017, 1:16 p.m.

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