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A C D E F G H I L M N P R S T misc
| phylobase-package | Utilities and Tools for Phylogenetics |
| addData | Adding data to a phylo4 or a phylo4d object |
| addData-method | Adding data to a phylo4 or a phylo4d object |
| addData-methods | Adding data to a phylo4 or a phylo4d object |
| ancestor | tree traversal and utility functions |
| ancestors | tree traversal and utility functions |
| as | Converting between phylo4/phylo4d and other phylogenetic tree formats |
| as-method | Converting between phylo4/phylo4d and other phylogenetic tree formats |
| as_phylo4vcov | matrix classes for phylobase |
| checkPhylo4 | Validity checking for phylo4 objects |
| checkPhylo4Data | Validity checking for phylo4 objects |
| checkTree | Validity checking for phylo4 objects |
| check_pdata | Constructor for pdata (phylogenetic data) class |
| children | tree traversal and utility functions |
| coerce-method | Converting between phylo4/phylo4d and other phylogenetic tree formats |
| coerce-method | Class "phylog" |
| coerce-methods | Converting between phylo4/phylo4d and other phylogenetic tree formats |
| descendants | tree traversal and utility functions |
| edgeId | node and edge look-up functions |
| edgeId-method | node and edge look-up functions |
| edgeLabels | Labels for phylo4/phylo4d objects |
| edgeLabels-method | Labels for phylo4/phylo4d objects |
| edgeLabels-methods | Labels for phylo4/phylo4d objects |
| edgeLabels<- | Labels for phylo4/phylo4d objects |
| edgeLabels<--method | Labels for phylo4/phylo4d objects |
| edgeLength | Methods for S4 phylogeny classes |
| edgeLength-method | Methods for S4 phylogeny classes |
| edgeLength-methods | Methods for S4 phylogeny classes |
| edgeLength<- | Methods for S4 phylogeny classes |
| edgeLength<--method | Methods for S4 phylogeny classes |
| edgeOrder | Methods for S4 phylogeny classes |
| edgeOrder-method | Methods for S4 phylogeny classes |
| edges | Methods for S4 phylogeny classes |
| edges-method | Methods for S4 phylogeny classes |
| edges-methods | Methods for S4 phylogeny classes |
| extractTree | Get tree from tree+data object |
| formatData | Format data for use in phylo4d objects |
| geospiza | Data from Darwin's finches |
| geospiza_raw | Data from Darwin's finches |
| getEdge | node and edge look-up functions |
| getNode | node and edge look-up functions |
| hasEdgeLabels | Labels for phylo4/phylo4d objects |
| hasEdgeLabels-method | Labels for phylo4/phylo4d objects |
| hasEdgeLabels-methods | Labels for phylo4/phylo4d objects |
| hasEdgeLength | Methods for S4 phylogeny classes |
| hasEdgeLength-method | Methods for S4 phylogeny classes |
| hasEdgeLength-methods | Methods for S4 phylogeny classes |
| hasNodeData | Tests for presence of data associated with trees stored as phylo4d objects |
| hasNodeData-method | Tests for presence of data associated with trees stored as phylo4d objects |
| hasNodeData-methods | Tests for presence of data associated with trees stored as phylo4d objects |
| hasNodeLabels | Labels for phylo4/phylo4d objects |
| hasNodeLabels-method | Labels for phylo4/phylo4d objects |
| hasNodeLabels-methods | Labels for phylo4/phylo4d objects |
| hasPoly | Test trees for polytomies, inline nodes, or reticulation |
| hasRetic | Test trees for polytomies, inline nodes, or reticulation |
| hasSingle | Test trees for polytomies, inline nodes, or reticulation |
| hasTipData | Tests for presence of data associated with trees stored as phylo4d objects |
| hasTipData-method | Tests for presence of data associated with trees stored as phylo4d objects |
| hasTipData-methods | Tests for presence of data associated with trees stored as phylo4d objects |
| head-method | Displaying phylo4 object |
| head-method | Display methods for phylo4d objects |
| isRooted | Methods for S4 phylogeny classes |
| isRooted-method | Methods for S4 phylogeny classes |
| isRooted-methods | Methods for S4 phylogeny classes |
| labels-method | Labels for phylo4/phylo4d objects |
| labels<- | Labels for phylo4/phylo4d objects |
| labels<--method | Labels for phylo4/phylo4d objects |
| MRCA | tree traversal and utility functions |
| multiPhylo-class | multiPhylo4 and extended classes |
| multiPhylo4-class | multiPhylo4 and extended classes |
| multiPhylo4d-class | multiPhylo4 and extended classes |
| na.omit-method | Methods for creating subsets of phylogenies |
| names-method | Displaying phylo4 object |
| names-method | Display methods for phylo4d objects |
| nEdges | Methods for S4 phylogeny classes |
| nEdges-method | Methods for S4 phylogeny classes |
| nEdges-methods | Methods for S4 phylogeny classes |
| nNodes | Methods for S4 phylogeny classes |
| nNodes-method | Methods for S4 phylogeny classes |
| nNodes-methods | Methods for S4 phylogeny classes |
| nodeData | Retrieving or updating tip and node data in phylo4d objects |
| nodeData-method | Retrieving or updating tip and node data in phylo4d objects |
| nodeData<- | Retrieving or updating tip and node data in phylo4d objects |
| nodeData<--method | Retrieving or updating tip and node data in phylo4d objects |
| nodeId | node and edge look-up functions |
| nodeId-method | node and edge look-up functions |
| nodeLabels | Labels for phylo4/phylo4d objects |
| nodeLabels-method | Labels for phylo4/phylo4d objects |
| nodeLabels-methods | Labels for phylo4/phylo4d objects |
| nodeLabels<- | Labels for phylo4/phylo4d objects |
| nodeLabels<--method | Labels for phylo4/phylo4d objects |
| nodeType | Methods for S4 phylogeny classes |
| nodeType-method | Methods for S4 phylogeny classes |
| nTips | Methods for S4 phylogeny classes |
| nTips-method | Methods for S4 phylogeny classes |
| nTips-methods | Methods for S4 phylogeny classes |
| pdata | Constructor for pdata (phylogenetic data) class |
| pdata-class | Class "pdata" |
| phylo-class | The phylo4 class |
| phylo4 | Create a phylogenetic tree |
| phylo4-class | The phylo4 class |
| phylo4-method | Create a phylogenetic tree |
| phylo4-methods | Create a phylogenetic tree |
| phylo4d | Combine a phylogenetic tree with data |
| phylo4d-class | phylo4d class |
| phylo4d-method | Combine a phylogenetic tree with data |
| phylo4d-methods | Combine a phylogenetic tree with data |
| phylo4vcov-class | matrix classes for phylobase |
| phylo4_orderings | The phylo4 class |
| phylobase | Utilities and Tools for Phylogenetics |
| phylobubbles | Bubble plots for phylo4d objects |
| phylog-class | Class "phylog" |
| phyloXXYY | Calculate node x and y coordinates |
| plot-method | Phylogeny plotting |
| plotOneTree | Plot a phylo4 object |
| print-method | Displaying phylo4 object |
| print-method | Display methods for phylo4d objects |
| printphylo4 | print a phylogeny |
| prune | Methods for creating subsets of phylogenies |
| prune-method | Methods for creating subsets of phylogenies |
| prune-methods | Methods for creating subsets of phylogenies |
| ptypes | Class "pdata" |
| read.nexustreestring | Read Nexus tree string |
| readNexus | Create a phylo4 or a phylo4d object from a Nexus file |
| reorder-method | reordering trees within phylobase objects |
| reorder-methods | reordering trees within phylobase objects |
| rootEdge | Methods for S4 phylogeny classes |
| rootEdge-method | Methods for S4 phylogeny classes |
| rootEdge-methods | Methods for S4 phylogeny classes |
| rootNode | Methods for S4 phylogeny classes |
| rootNode-method | Methods for S4 phylogeny classes |
| rootNode-methods | Methods for S4 phylogeny classes |
| rootNode<- | Methods for S4 phylogeny classes |
| rootNode<--method | Methods for S4 phylogeny classes |
| shortestPath | tree traversal and utility functions |
| show-method | Displaying phylo4 object |
| show-method | Display methods for phylo4d objects |
| siblings | tree traversal and utility functions |
| subset-method | Methods for creating subsets of phylogenies |
| subset-methods | Methods for creating subsets of phylogenies |
| sumEdgeLength | tree traversal and utility functions |
| sumEdgeLength-method | tree traversal and utility functions |
| summary-method | Displaying phylo4 object |
| summary-method | Display methods for phylo4d objects |
| tail-method | Displaying phylo4 object |
| tail-method | Display methods for phylo4d objects |
| tbind | multiPhylo4 and extended classes |
| tdata | Retrieving or updating tip and node data in phylo4d objects |
| tdata-method | Retrieving or updating tip and node data in phylo4d objects |
| tdata<- | Retrieving or updating tip and node data in phylo4d objects |
| tdata<--method | Retrieving or updating tip and node data in phylo4d objects |
| tip.data.plot | Plotting trees and associated data |
| tipData | Retrieving or updating tip and node data in phylo4d objects |
| tipData-method | Retrieving or updating tip and node data in phylo4d objects |
| tipData<- | Retrieving or updating tip and node data in phylo4d objects |
| tipData<--method | Retrieving or updating tip and node data in phylo4d objects |
| tipLabels | Labels for phylo4/phylo4d objects |
| tipLabels-method | Labels for phylo4/phylo4d objects |
| tipLabels-methods | Labels for phylo4/phylo4d objects |
| tipLabels<- | Labels for phylo4/phylo4d objects |
| tipLabels<--method | Labels for phylo4/phylo4d objects |
| treePlot | Phylogeny plotting |
| treePlot-method | Phylogeny plotting |
| [-method | Class "pdata" |
| [-method | Methods for creating subsets of phylogenies |
| [-methods | Methods for creating subsets of phylogenies |
| [<--method | Class "pdata" |
| [[-method | Class "pdata" |
| [[<--method | Class "pdata" |