Phylogenetic Analysis with Discrete Character Data
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Documentation for package ‘TreeSearch’ version 1.6.1
Help Pages
| AdditionTree | Addition tree |
| AllSPR | All SPR trees |
| Carter1 | Number of trees with _m_ steps |
| CharacterLength | Character length |
| ClusteringConcordance | Calculate site concordance factor |
| ClusterStrings | Cluster similar strings |
| cNNI | Nearest neighbour interchange (NNI) |
| ConcordantInfo | Evaluate the concordance of information between a tree and a dataset |
| ConcordantInformation | Evaluate the concordance of information between a tree and a dataset |
| congreveLamsdellMatrices | 100 simulated data matrices |
| Consistency | Consistency / retention "indices" |
| cSPR | 'cSPR()' expects a tree rooted on a single tip. |
| EasyTrees | Find most parsimonious trees |
| EasyTreesy | Find most parsimonious trees |
| Evaluate | Evaluate the concordance of information between a tree and a dataset |
| FastCharacterLength | Character length |
| Fitch | Calculate the parsimony score of a tree given a dataset |
| FitchSteps | Character length |
| GapHandler | Read how a Morphy Object handles the inapplicable token |
| inapplicable.citations | Thirty datasets with inapplicable data |
| inapplicable.datasets | Thirty datasets with inapplicable data |
| inapplicable.phyData | Thirty datasets with inapplicable data |
| inapplicable.trees | Thirty datasets with inapplicable data |
| is.morphyPtr | Is an object a valid Morphy object? |
| IWScore | Calculate the parsimony score of a tree given a dataset |
| Jackknife | Jackknife resampling |
| JackLabels | Label nodes with jackknife support values |
| LengthAdded | Contribution of character to leaf instability |
| Log2Carter1 | Number of trees with _m_ steps |
| LogCarter1 | Number of trees with _m_ steps |
| MaximizeParsimony | Find most parsimonious trees |
| MaximumLength | Minimum and Maximum lengths possible for a character |
| MaximumLength.character | Minimum and Maximum lengths possible for a character |
| MaximumLength.numeric | Minimum and Maximum lengths possible for a character |
| MinimumLength | Minimum and Maximum lengths possible for a character |
| MinimumLength.character | Minimum and Maximum lengths possible for a character |
| MinimumLength.numeric | Minimum and Maximum lengths possible for a character |
| MinimumLength.phyDat | Minimum and Maximum lengths possible for a character |
| MinimumSteps | Minimum and Maximum lengths possible for a character |
| MorphyBootstrap | Parsimony Ratchet |
| MorphyWeights | Set and get the character weightings associated with a Morphy object. |
| MultiRatchet | Parsimony Ratchet |
| MutualClusteringConcordance | Calculate site concordance factor |
| NNI | Nearest neighbour interchange (NNI) |
| NNISwap | Nearest neighbour interchange (NNI) |
| PhyDat2Morphy | Initialize a Morphy object from a 'phyDat' object |
| PhylogeneticConcordance | Calculate site concordance factor |
| PlotCharacter | Plot the distribution of a character on a tree |
| PlotCharacter.list | Plot the distribution of a character on a tree |
| PlotCharacter.multiPhylo | Plot the distribution of a character on a tree |
| PlotCharacter.phylo | Plot the distribution of a character on a tree |
| PolEscapa | Contribution of character to leaf instability |
| PrepareDataIW | Prepare data for Profile Parsimony |
| PrepareDataProfile | Prepare data for Profile Parsimony |
| profiles | Empirically counted profiles for small trees |
| QuartetConcordance | Calculate site concordance factor |
| QuartetResolution | Relationship between four taxa |
| RandomMorphyTree | Random postorder tree |
| RandomTreeScore | Parsimony score of random postorder tree |
| Ratchet | Parsimony Ratchet |
| RatchetConsensus | Parsimony Ratchet |
| RearrangeEdges | Rearrange edges of a phylogenetic tree |
| referenceTree | Tree topology for matrix simulation |
| Resample | Find most parsimonious trees |
| RootedNNI | Nearest neighbour interchange (NNI) |
| RootedNNISwap | Nearest neighbour interchange (NNI) |
| RootedSPR | Subtree pruning and rearrangement (SPR) |
| RootedSPRSwap | Subtree pruning and rearrangement (SPR) |
| RootedTBR | Tree bisection and reconnection (TBR) |
| RootedTBRSwap | Tree bisection and reconnection (TBR) |
| SetMorphyWeights | Set and get the character weightings associated with a Morphy object. |
| SharedPhylogeneticConcordance | Calculate site concordance factor |
| SingleCharMorphy | Morphy object from single character |
| SiteConcordance | Calculate site concordance factor |
| SPR | Subtree pruning and rearrangement (SPR) |
| SPRMoves | Subtree pruning and rearrangement (SPR) |
| SPRMoves.matrix | Subtree pruning and rearrangement (SPR) |
| SPRMoves.phylo | Subtree pruning and rearrangement (SPR) |
| SPRSwap | Subtree pruning and rearrangement (SPR) |
| StepInformation | Information content of a character known to contain _e_ steps |
| summary.morphyPtr | Details the attributes of a morphy object |
| TaxonInfluence | Rank taxa by their influence on phylogenetic results |
| TBR | Tree bisection and reconnection (TBR) |
| TBRMoves | Tree bisection and reconnection (TBR) |
| TBRMoves.matrix | Tree bisection and reconnection (TBR) |
| TBRMoves.phylo | Tree bisection and reconnection (TBR) |
| TBRSwap | Tree bisection and reconnection (TBR) |
| TreeLength | Calculate the parsimony score of a tree given a dataset |
| TreeLength.list | Calculate the parsimony score of a tree given a dataset |
| TreeLength.multiPhylo | Calculate the parsimony score of a tree given a dataset |
| TreeLength.numeric | Calculate the parsimony score of a tree given a dataset |
| TreeLength.phylo | Calculate the parsimony score of a tree given a dataset |
| UnloadMorphy | Destroy a Morphy object |
| WhenFirstHit | When was a tree topology first hit? |
| WithOneExtraStep | Number of trees with one extra step |