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
get.nexus.comments      Get comments from nexus text
get.nodenames           Read node names from newick text
get.tree.weights        Get tree weights
getEmptyDataFrame       Get empty data.frame
getSubNodeData          Return subnode data
getSubNodeEdgeInds      Return subnode edge indices
getSubNodePosish        Return the subnode position
has.block               Check for nexus block
has.characters2         Check for CHARACTERS2 block
has.weights             Check for tree weights
hasData-methods         Methods for Function hasData in Package
                        'RBrownie'
hasDataColumn-methods   Does a tree object contain a specific data
                        column
hasSubNodes-methods     Does an object contain subnodes?
is.simmap               Check SIMMAP v1.0
match.order             Matching orders
nSubNodes               Get number of subnodes
newlabels.v15           Generate simmap v1.5 labels
newlabels.v1x           Generate simmap v1.0 or v1.1 labels
phyext-methods          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-methods          rmdata from a tree object
showSubNodes            Display subnodes
strip                   Strip whitespace
tipdate.ci              Get coalescent intervals for a tip-dated tree
treeHeight-methods      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
