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