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| addSubNode | Add subnode to phylo4d_ext object |
| as | Class "phylo4d_ext" |
| as-method | Class "phylo4d_ext" |
| coerce-method | Class "phylo4d_ext" |
| coerce-methods | Class "phylo4d_ext" |
| 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 for Function hasData in Package 'RBrownie' |
| hasData-method | Methods for Function hasData in Package 'RBrownie' |
| hasData-methods | Methods for Function hasData in Package 'RBrownie' |
| hasDataColumn | Does a tree object contain a specific data column |
| hasDataColumn-method | Does a tree object contain a specific data column |
| hasDataColumn-methods | Does a tree object contain a specific data column |
| hasSubNodes | Does an object contain subnodes? |
| hasSubNodes-method | Does an object contain subnodes? |
| hasSubNodes-methods | Does an object contain subnodes? |
| hasWeight | Class "phylo4d_ext" |
| hasWeight-method | Class "phylo4d_ext" |
| 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 |
| phyext-method | A function which returns a phylo4d_ext object |
| phyext-methods | A function which returns a phylo4d_ext object |
| phyextPlot | Plot phylo4d_ext object |
| phylo4d_ext-class | Class "phylo4d_ext" |
| plot-method | 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 |
| rmdata-method | rmdata from a tree object |
| rmdata-methods | rmdata from a tree object |
| show-method | Class "phylo4d_ext" |
| showSubNodes | Display subnodes |
| snbranch | Class "phylo4d_ext" |
| snbranch-method | Class "phylo4d_ext" |
| sndata | Class "phylo4d_ext" |
| sndata-method | Class "phylo4d_ext" |
| sndata<- | Class "phylo4d_ext" |
| sndata<--method | Class "phylo4d_ext" |
| snid | Class "phylo4d_ext" |
| snid-method | Class "phylo4d_ext" |
| snposition | Class "phylo4d_ext" |
| snposition-method | Class "phylo4d_ext" |
| strip | Strip whitespace |
| tipdate.ci | Get coalescent intervals for a tip-dated tree |
| treeHeight | Get the height (depth) of a tree |
| treeHeight-method | Get the height (depth) of a tree |
| treeHeight-methods | Get the height (depth) of a tree |
| validPhylo4d_ext | Validate a phylo4d_ext object |
| weight | Class "phylo4d_ext" |
| weight-method | Class "phylo4d_ext" |
| weight<- | Class "phylo4d_ext" |
| weight<--method | Class "phylo4d_ext" |
| 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 |