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

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 <john.r.stevens@usu.edu>
LicenseGPL-3
Version0.0.4

View on CRAN

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
contData Man page
deep.phy.copy Man page
discData 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
guess.datatype 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
noneData 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.characters2 Man page
write.nexus.simmap Man page
write.simmap Man page
write.simmap.new Man page
write.simmap.old Man page

Files

phyext2
phyext2/NAMESPACE
phyext2/NEWS
phyext2/R
phyext2/R/phyext2.R
phyext2/MD5
phyext2/DESCRIPTION
phyext2/man
phyext2/man/phyext2class.Rd phyext2/man/phyext2methods.Rd phyext2/man/phyext2.Rd

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