Create, Modify and Analyse Phylogenetic Trees
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Documentation for package ‘TreeTools’ version 1.12.0
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A B C D E F G H I J K L M N P R S T U V W X Y Z misc
-- A --
| AddTip | Add a tip to a phylogenetic tree |
| AddTipEverywhere | Add a tip to a phylogenetic tree |
| AddUnconstrained | Force a tree to match a constraint |
| AllAncestors | List ancestors |
| AllDescendantEdges | Identify descendant edges |
| AllTipLabels | Extract tip labels |
| AllTipLabels.list | Extract tip labels |
| AllTipLabels.matrix | Extract tip labels |
| AllTipLabels.multiPhylo | Extract tip labels |
| AllTipLabels.phylo | Extract tip labels |
| AllTipLabels.Splits | Extract tip labels |
| AllTipLabels.TreeNumber | Extract tip labels |
| ApeTime | Read modification time from "ape" Nexus file |
| ArtEx | Artificial Extinction |
| ArtificialExtinction | Artificial Extinction |
| ArtificialExtinction.matrix | Artificial Extinction |
| ArtificialExtinction.phyDat | Artificial Extinction |
| as.ClusterTable | Convert phylogenetic tree to 'ClusterTable' |
| as.ClusterTable.list | Convert phylogenetic tree to 'ClusterTable' |
| as.ClusterTable.multiPhylo | Convert phylogenetic tree to 'ClusterTable' |
| as.ClusterTable.phylo | Convert phylogenetic tree to 'ClusterTable' |
| as.logical.Splits | Convert object to 'Splits' |
| as.matrix.ClusterTable | S3 methods for 'ClusterTable' objects |
| as.MixedBase | Unique integer indices for bifurcating tree topologies |
| as.MixedBase.integer64 | Unique integer indices for bifurcating tree topologies |
| as.MixedBase.MixedBase | Unique integer indices for bifurcating tree topologies |
| as.MixedBase.multiPhylo | Unique integer indices for bifurcating tree topologies |
| as.MixedBase.numeric | Unique integer indices for bifurcating tree topologies |
| as.MixedBase.phylo | Unique integer indices for bifurcating tree topologies |
| as.MixedBase.TreeNumber | Unique integer indices for bifurcating tree topologies |
| as.multiPhylo | Convert object to 'multiPhylo' class |
| as.multiPhylo.list | Convert object to 'multiPhylo' class |
| as.multiPhylo.phyDat | Convert object to 'multiPhylo' class |
| as.multiPhylo.phylo | Convert object to 'multiPhylo' class |
| as.multiPhylo.Splits | Convert object to 'multiPhylo' class |
| as.Newick | Write a phylogenetic tree in Newick format |
| as.Newick.list | Write a phylogenetic tree in Newick format |
| as.Newick.multiPhylo | Write a phylogenetic tree in Newick format |
| as.Newick.phylo | Write a phylogenetic tree in Newick format |
| as.phylo.MixedBase | Unique integer indices for bifurcating tree topologies |
| as.phylo.numeric | Unique integer indices for bifurcating tree topologies |
| as.phylo.TreeNumber | Unique integer indices for bifurcating tree topologies |
| as.Splits | Convert object to 'Splits' |
| as.Splits.character | Convert object to 'Splits' |
| as.Splits.list | Convert object to 'Splits' |
| as.Splits.logical | Convert object to 'Splits' |
| as.Splits.matrix | Convert object to 'Splits' |
| as.Splits.multiPhylo | Convert object to 'Splits' |
| as.Splits.phylo | Convert object to 'Splits' |
| as.Splits.Splits | Convert object to 'Splits' |
| as.TreeNumber | Unique integer indices for bifurcating tree topologies |
| as.TreeNumber.character | Unique integer indices for bifurcating tree topologies |
| as.TreeNumber.MixedBase | Unique integer indices for bifurcating tree topologies |
| as.TreeNumber.multiPhylo | Unique integer indices for bifurcating tree topologies |
| as.TreeNumber.phylo | Unique integer indices for bifurcating tree topologies |
| as.TreeNumber.TreeNumber | Unique integer indices for bifurcating tree topologies |
-- B --
| BalancedTree | Generate pectinate, balanced or random trees |
| brewer | Brewer palettes |
-- C --
| CharacterInformation | Character information content |
| CladeSizes | Clade sizes |
| CladisticInfo | Cladistic information content of a tree |
| CladisticInfo.list | Cladistic information content of a tree |
| CladisticInfo.multiPhylo | Cladistic information content of a tree |
| CladisticInfo.phylo | Cladistic information content of a tree |
| CladisticInfo.Splits | Cladistic information content of a tree |
| CladisticInformation | Cladistic information content of a tree |
| ClusterTable | Convert phylogenetic tree to 'ClusterTable' |
| ClusterTable-methods | S3 methods for 'ClusterTable' objects |
| CollapseEdge | Collapse nodes on a phylogenetic tree |
| CollapseNode | Collapse nodes on a phylogenetic tree |
| CollapseNode.phylo | Collapse nodes on a phylogenetic tree |
| Consensus | Construct consensus trees |
| ConsensusWithout | Reduced consensus, omitting specified taxa |
| ConsensusWithout.list | Reduced consensus, omitting specified taxa |
| ConsensusWithout.multiPhylo | Reduced consensus, omitting specified taxa |
| ConsensusWithout.phylo | Reduced consensus, omitting specified taxa |
| ConstrainedNJ | Constrained neighbour-joining tree |
-- D --
| DescendantEdges | Identify descendant edges |
| DescendantTips | Identify descendant edges |
| DoubleFactorial | Double factorial |
| DoubleFactorial64 | Double factorial |
| doubleFactorials | Double factorials |
| DropTip | Drop leaves from tree |
| DropTip.list | Drop leaves from tree |
| DropTip.multiPhylo | Drop leaves from tree |
| DropTip.NULL | Drop leaves from tree |
| DropTip.phylo | Drop leaves from tree |
| DropTip.Splits | Drop leaves from tree |
| DropTipPhylo | Drop leaves from tree |
-- E --
| EdgeAncestry | Ancestors of an edge |
| EdgeDistances | Distance between edges |
| edge_to_splits | Efficiently convert edge matrix to splits |
| EndSentence | Add full stop to end of a sentence |
| EnforceOutgroup | Generate a tree with a specified outgroup |
| EnforceOutgroup.character | Generate a tree with a specified outgroup |
| EnforceOutgroup.phylo | Generate a tree with a specified outgroup |
-- F --
| ForestSplits | Frequency of splits |
-- G --
| GenerateTree | Generate pectinate, balanced or random trees |
-- H --
| Hamming | Hamming distance between taxa in a phylogenetic dataset |
-- I --
| IC1Spr | Number of trees one SPR step away |
| ImposeConstraint | Force a tree to match a constraint |
| in.Splits | Split matching |
| is.TreeNumber | Is an object a 'TreeNumber' object? |
-- J --
| J1Index | Robust universal tree balance index |
| JQIndex | Robust universal tree balance index |
-- K --
| KeepTip | Drop leaves from tree |
| KeepTipPostorder | Drop leaves from tree |
| KeepTipPreorder | Drop leaves from tree |
| KeptPaths | Paths present in reduced tree |
| KeptPaths.data.frame | Paths present in reduced tree |
| KeptPaths.matrix | Paths present in reduced tree |
| KeptVerts | Identify vertices retained when leaves are dropped |
| KeptVerts.numeric | Identify vertices retained when leaves are dropped |
| KeptVerts.phylo | Identify vertices retained when leaves are dropped |
-- L --
| LabelSplits | Label splits |
| LeafLabelInterchange | Leaf label interchange |
| ListAncestors | List ancestors |
| LnDoubleFactorial | Double factorial |
| LnDoubleFactorial.int | Double factorial |
| LnRooted | Number of trees |
| LnRooted.int | Number of trees |
| LnSplitMatchProbability | Probability of matching this well |
| LnTreesMatchingSplit | Number of trees matching a bipartition split |
| LnTreesMatchingTree | Number of trees containing a tree |
| LnUnrooted | Number of trees |
| LnUnrooted.int | Number of trees |
| LnUnrootedMult | Number of trees |
| LnUnrootedSplits | Number of trees |
| LnUnrootedTreesMatchingSplit | Number of trees consistent with split |
| Lobo.data | Data from Zhang et al. 2016 |
| Lobo.phy | Data from Zhang et al. 2016 |
| Log2DoubleFactorial | Double factorial |
| Log2Rooted | Number of trees |
| Log2Rooted.int | Number of trees |
| Log2TreesMatchingSplit | Number of trees matching a bipartition split |
| Log2TreesMatchingTree | Number of trees containing a tree |
| Log2Unrooted | Number of trees |
| Log2Unrooted.int | Number of trees |
| Log2UnrootedMult | Number of trees |
| Log2UnrootedSplits | Number of trees |
| Log2UnrootedTreesMatchingSplit | Number of trees consistent with split |
| LogDoubleFactorial | Double factorial |
| LogDoubleFactorial.int | Double factorial |
| logDoubleFactorials | Natural logarithms of double factorials |
-- M --
| MakeTreeBinary | Generate binary tree by collapsing polytomies |
| MarkMissing | Reduced consensus, omitting specified taxa |
| match | Split matching |
| match-method | Split matching |
| match.Splits | Split matching |
| MatchEdges | Match nodes and edges between trees |
| MatchNodes | Match nodes and edges between trees |
| MatrixToPhyDat | Convert between matrices and 'phyDat' objects |
| MorphoBankDecode | Decode MorphoBank text |
| MrBayesTrees | Read posterior tree sample produced by MrBayes |
| MRCA | Most recent common ancestor |
| MSTEdges | Minimum spanning tree |
| MSTLength | Minimum spanning tree |
| MultiSplitInformation | Phylogenetic information content of splitting leaves into two partitions |
-- N --
| N1Spr | Number of trees one SPR step away |
| NDescendants | Count descendants for each node in a tree |
| NewickTree | Write Newick Tree |
| NJTree | Generate a neighbour joining tree |
| NodeDepth | Distance of each node from tree exterior |
| NodeNumbers | Numeric index of each node in a tree 'NodeNumbers()' returns a sequence corresponding to the nodes in a tree |
| NodeOrder | Number of edges incident to each node in a tree |
| NPartitionPairs | Distributions of tips consistent with a partition pair |
| NPartitions | Number of distinct splits |
| NRooted | Number of trees |
| NRooted64 | Number of trees |
| nRootedShapes | Number of rooted / unrooted tree shapes |
| NSplits | Number of distinct splits |
| NSplits.character | Number of distinct splits |
| NSplits.ClusterTable | Number of distinct splits |
| NSplits.list | Number of distinct splits |
| NSplits.multiPhylo | Number of distinct splits |
| NSplits.NULL | Number of distinct splits |
| NSplits.numeric | Number of distinct splits |
| NSplits.phylo | Number of distinct splits |
| NSplits.Splits | Number of distinct splits |
| NTip | Number of leaves in a phylogenetic tree |
| NTip.default | Number of leaves in a phylogenetic tree |
| NTip.list | Number of leaves in a phylogenetic tree |
| NTip.matrix | Number of leaves in a phylogenetic tree |
| NTip.multiPhylo | Number of leaves in a phylogenetic tree |
| NTip.phyDat | Number of leaves in a phylogenetic tree |
| NTip.phylo | Number of leaves in a phylogenetic tree |
| NTip.Splits | Number of leaves in a phylogenetic tree |
| NUnrooted | Number of trees |
| NUnrooted64 | Number of trees |
| NUnrootedMult | Number of trees |
| nUnrootedShapes | Number of rooted / unrooted tree shapes |
| NUnrootedSplits | Number of trees |
-- P --
| PairwiseDistances | Distances between each pair of trees |
| PathLengths | Calculate length of paths between each pair of vertices within tree |
| PectinateTree | Generate pectinate, balanced or random trees |
| PhyDat | Read phylogenetic characters from file |
| PhyDatToMatrix | Convert between matrices and 'phyDat' objects |
| PhyDatToString | Convert between strings and 'phyDat' objects |
| PhydatToString | Convert between strings and 'phyDat' objects |
| PhylogeneticInfo | Cladistic information content of a tree |
| PhylogeneticInformation | Cladistic information content of a tree |
| PhyToString | Convert between strings and 'phyDat' objects |
| PolarizeSplits | Polarize splits on a single taxon |
| print.ClusterTable | S3 methods for 'ClusterTable' objects |
| print.TreeNumber | Print 'TreeNumber' object |
-- R --
| RandomTree | Generate pectinate, balanced or random trees |
| ReadAsPhyDat | Read phylogenetic characters from file |
| ReadCharacters | Read phylogenetic characters from file |
| ReadMrBayes | Read posterior tree sample produced by MrBayes |
| ReadMrBayesTrees | Read posterior tree sample produced by MrBayes |
| ReadNotes | Read phylogenetic characters from file |
| ReadTntAsPhyDat | Read phylogenetic characters from file |
| ReadTntCharacters | Read phylogenetic characters from file |
| ReadTntTree | Parse TNT Tree |
| Renumber | Renumber a tree's nodes and tips |
| RenumberTips | Renumber a tree's tips |
| RenumberTips.list | Renumber a tree's tips |
| RenumberTips.multiPhylo | Renumber a tree's tips |
| RenumberTips.NULL | Renumber a tree's tips |
| RenumberTips.phylo | Renumber a tree's tips |
| replicate64 | Apply a function that returns 64-bit integers over a list or vector |
| RightmostCharacter | Rightmost character of string |
| RoguePlot | Visualize position of rogue taxa |
| RootNode | Which node is a tree's root? |
| RootNodeDist | "Stemwardness" of a leaf |
| RootNodeDistance | "Stemwardness" of a leaf |
| RootNodeDistance.character | "Stemwardness" of a leaf |
| RootNodeDistance.numeric | "Stemwardness" of a leaf |
| RootOnNode | Root or unroot a phylogenetic tree |
| RootTree | Root or unroot a phylogenetic tree |
-- S --
| sapply64 | Apply a function that returns 64-bit integers over a list or vector |
| SingleTaxonTree | Generate trivial trees |
| SisterSize | "Stemwardness" of a leaf |
| SisterSize.character | "Stemwardness" of a leaf |
| SisterSize.numeric | "Stemwardness" of a leaf |
| sort.multiPhylo | Sort a list of phylogenetic trees |
| SortTree | Sort tree |
| SortTree.list | Sort tree |
| SortTree.multiPhylo | Sort tree |
| SortTree.phylo | Sort tree |
| SplitFrequency | Frequency of splits |
| SplitImbalance | Tips contained within splits |
| SplitImbalance.phylo | Tips contained within splits |
| SplitImbalance.Splits | Tips contained within splits |
| SplitInformation | Phylogenetic information content of splitting leaves into two partitions |
| SplitMatchProbability | Probability of matching this well |
| SplitNumber | Frequency of splits |
| Splits | Convert object to 'Splits' |
| SplitsInBinaryTree | Maximum splits in an _n_-leaf tree |
| SplitsInBinaryTree.default | Maximum splits in an _n_-leaf tree |
| SplitsInBinaryTree.list | Maximum splits in an _n_-leaf tree |
| SplitsInBinaryTree.multiPhylo | Maximum splits in an _n_-leaf tree |
| SplitsInBinaryTree.NULL | Maximum splits in an _n_-leaf tree |
| SplitsInBinaryTree.numeric | Maximum splits in an _n_-leaf tree |
| SplitsInBinaryTree.phylo | Maximum splits in an _n_-leaf tree |
| SplitsInBinaryTree.Splits | Maximum splits in an _n_-leaf tree |
| StarTree | Generate pectinate, balanced or random trees |
| Stemwardness | "Stemwardness" of a leaf |
| StringToPhyDat | Convert between strings and 'phyDat' objects |
| StringToPhydat | Convert between strings and 'phyDat' objects |
| Subsplit | Subset of a split on fewer leaves |
| Subtree | Extract a subtree |
| summary.ClusterTable | S3 methods for 'ClusterTable' objects |
| SupportColor | Colour for node support value |
| SupportColour | Colour for node support value |
-- T --
| TCIContext | Total Cophenetic Index |
| TCIContext.numeric | Total Cophenetic Index |
| TipLabels | Extract tip labels |
| TipLabels.character | Extract tip labels |
| TipLabels.default | Extract tip labels |
| TipLabels.list | Extract tip labels |
| TipLabels.logical | Extract tip labels |
| TipLabels.matrix | Extract tip labels |
| TipLabels.MixedBase | Extract tip labels |
| TipLabels.multiPhylo | Extract tip labels |
| TipLabels.numeric | Extract tip labels |
| TipLabels.phyDat | Extract tip labels |
| TipLabels.phylo | Extract tip labels |
| TipLabels.Splits | Extract tip labels |
| TipLabels.TreeNumber | Extract tip labels |
| TipsInSplits | Tips contained within splits |
| TipsInSplits.phylo | Tips contained within splits |
| TipsInSplits.Splits | Tips contained within splits |
| TipTimedTree | Display time-calibrated tree using tip information only |
| TNTText2Tree | Parse TNT Tree |
| TntText2Tree | Parse TNT Tree |
| TopologyOnly | Remove metadata from trees |
| TotalCopheneticIndex | Total Cophenetic Index |
| TreeIsRooted | Is tree rooted? |
| TreeNumber | Unique integer indices for bifurcating tree topologies |
| TreesMatchingSplit | Number of trees matching a bipartition split |
| TreesMatchingTree | Number of trees containing a tree |
| TreeSplits | Frequency of splits |
| TrivialSplits | Identify and remove trivial splits |
| TrivialTree | Generate trivial trees |
-- U --
| Unquote | Remove quotation marks from a string |
| UnrootedTreesMatchingSplit | Number of trees consistent with split |
| UnrootTree | Root or unroot a phylogenetic tree |
| UnshiftTree | Add tree to start of list |
-- V --
| vapply64 | Apply a function that returns 64-bit integers over a list or vector |
-- W --
| WithoutTrivialSplits | Identify and remove trivial splits |
| WriteTntCharacters | Write morphological character matrix to TNT file |
| WriteTntCharacters.matrix | Write morphological character matrix to TNT file |
| WriteTntCharacters.phyDat | Write morphological character matrix to TNT file |
-- X --
| xor | Exclusive OR operation |
| xor-method | Exclusive OR operation |
-- Y --
| YuleTree | Generate pectinate, balanced or random trees |
-- Z --
| ZeroTaxonTree | Generate trivial trees |
-- misc --
| %in%-method | Split matching |
| <.MixedBase | Sort a list of phylogenetic trees |
| <.phylo | Sort a list of phylogenetic trees |
| ==.MixedBase | Sort a list of phylogenetic trees |
| ==.phylo | Sort a list of phylogenetic trees |
| >.MixedBase | Sort a list of phylogenetic trees |
| >.phylo | Sort a list of phylogenetic trees |