Man pages for phylobase
Base Package for Phylogenetic Structures and Comparative Data
| addData-methods | Adding data to a phylo4 or a phylo4d object |
| ancestors | Tree traversal and utility functions |
| checkPhylo4 | Validity checking for phylo4 objects |
| edgeLength-methods | edgeLength methods |
| edges-accessors | Edges accessors |
| extractTree | Get tree from tree+data object |
| formatData | Format data for use in phylo4d objects |
| geospiza | Data from Darwin's finches |
| getNode-methods | Node and Edge look-up functions |
| labels-methods | Labels for phylo4/phylo4d objects |
| MRCA | MRCA |
| multiPhylo-class | multiPhylo4 and extended classes |
| nodeId-methods | nodeId methods |
| nTips-methods | nTips, nNodes, nEdges |
| owls4 | 'Owls' data from ape |
| pdata | Constructor for pdata (phylogenetic data) class |
| pdata-class | Class "pdata" |
| phylo4-class | The phylo4 class |
| phylo4d-accessors | Tests for presence of data associated with trees stored as... |
| phylo4d-class | phylo4d class |
| phylo4d-methods | Combine a phylogenetic tree with data |
| phylo4-methods | Create a phylogenetic tree |
| phylobase.options | Set or return options of phylobase |
| phylobase-package | Utilities and Tools for Phylogenetics |
| phylobubbles | Bubble plots for phylo4d objects |
| phylomat-class | matrix classes for phylobase |
| phyloXXYY | Calculate node x and y coordinates |
| plotOneTree | Plot a phylo4 object |
| print-methods | print a phylogeny |
| readNexus | Create a 'phylo4', 'phylo4d' or 'data.frame' object from a... |
| reorder-methods | reordering trees within phylobase objects |
| root-methods | Methods to test, access (and modify) the root of a phylo4... |
| setAs-methods | Converting between phylo4/phylo4d and other phylogenetic tree... |
| shortestPath-methods | shortestPath-methods |
| subset-methods | Methods for creating subsets of phylogenies |
| summary-methods | Summary for phylo4/phylo4d objects |
| tdata-methods | Retrieving or updating tip and node data in phylo4d objects |
| tip.data.plot | Plotting trees and associated data |
| treePlot-methods | Phylogeny plotting |
| treeStructure-methods | Test trees for polytomies, inline nodes (singletons), or... |
