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 |
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