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

addSubNodeAdd subnode to phylo4d_ext object
collapse.singletonsCollapse singleton nodes
collapse.subnodesCollapse subnodes into singletons zero-length branches
deep.phy.copyCopy a tree object slot by slot
expand.singlesExpand singletons
getEmptyDataFrameGet empty data.frame comments from nexus text
get.nodenamesRead node names from newick text
getSubNodeDataReturn subnode data
getSubNodeEdgeIndsReturn subnode edge indices
getSubNodePosishReturn the subnode position
get.tree.weightsGet tree weights
has.blockCheck for nexus block
has.characters2Check for CHARACTERS2 block
hasDataMethods for Function hasData in Package 'RBrownie'
hasDataColumnDoes a tree object contain a specific data column
hasSubNodesDoes an object contain subnodes?
has.weightsCheck for tree weights
is.simmapCheck SIMMAP v1.0
match.orderMatching orders
newlabels.v15Generate simmap v1.5 labels
newlabels.v1xGenerate simmap v1.0 or v1.1 labels
nSubNodesGet number of subnodes
phyextA function which returns a phylo4d_ext object
phyextPlotPlot phylo4d_ext object
phylo4d_ext-classClass "phylo4d_ext"
read.characters2Read CHARACTERS2 block a block in a nexus file a nexus file with SIMMAP-formatted trees (v1.0)
read.simmapRead simmap-formatted newick strings (version 1.0)
read.simmap.newRead simmap-formatted newick strings (version 1.5)
rmdatarmdata from a tree object
showSubNodesDisplay subnodes
stripStrip whitespace
tipdate.ciGet coalescent intervals for a tip-dated tree
treeHeightGet the height (depth) of a tree
validPhylo4d_extValidate a phylo4d_ext object phylo4d_ext object or list to a nexus file
write.simmapWrite phylo4d_ext tree to newick string
write.simmap.newWrapper for write.simmap
write.simmap.oldWrapper for write.simmap
phyext documentation built on May 2, 2019, 5:19 p.m.