AllSPR | All SPR trees |
AllTBR | Tree bisection and reconnection (TBR) |
AsBinary | Convert a number to binary |
CharacterLength | Character length |
congreveLamsdellMatrices | 100 simulated data matrices |
Evaluate | Evaluate tree |
FastCharacterLength | Character length |
Fitch | Calculate parsimony score with inapplicable data |
FitchSteps | Character length |
ICSteps | Information Content Steps |
inapplicable.citations | Thirty Datasets with Inapplicable data |
inapplicable.datasets | Thirty Datasets with Inapplicable data |
inapplicable.phyData | Thirty Datasets with Inapplicable data |
InfoAmounts | Amount of information in each character |
IWBootstrap | Ratchet bootstrapper |
IWDestroyMorphy | Implied weights parsimony Score |
IWInitMorphy | Implied weights parsimony Score |
IWMultiRatchet | Parsimony Ratchet |
IWRatchet | Parsimony Ratchet |
IWRatchetConsensus | Parsimony Ratchet |
IWScore | Implied weights parsimony Score |
IWScoreMorphy | Profile Parsimony Score |
Jackknife | Parsimony Ratchet |
JackLabels | Label nodes with jackknife support values |
LogisticPoints | Logistic Points Extract points from a fitted model |
MinimumLength | Minimum length |
MinimumSteps | Minimum length |
MorphyBootstrap | Ratchet bootstrapper |
MorphyWeights | Report the character weightings associated with a Morphy object |
MultiRatchet | Parsimony Ratchet |
NNI | Nearest Neighbour Interchange (NNI) |
NNISwap | Nearest Neighbour Interchange (NNI) |
PhyDat2Morphy | Initialize a Morphy Object from a 'phyDat' object |
PrepareDataIW | Prepare data for Profile Parsimony |
PrepareDataProfile | Prepare data for Profile Parsimony |
ProfileBootstrap | Ratchet bootstrapper |
ProfileDestroyMorphy | Profile Parsimony Score |
ProfileInitMorphy | Profile Parsimony Score |
ProfileRatchet | Parsimony Ratchet |
ProfileScore | Profile Parsimony Score |
ProfileScoreMorphy | Profile Parsimony Score |
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 |
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 the character weightings associated with a Morphy object |
SingleCharMorphy | Morphy object from single character |
SPR | Subtree Pruning and Rearrangement (SPR) |
SPRSwap | Subtree Pruning and Rearrangement (SPR) |
SuccessiveApproximations | Tree Search using Successive Approximations |
summary.morphyPtr | Details the attributes of a morphy object |
TBR | Tree bisection and reconnection (TBR) |
TBRMoves | Tree bisection and reconnection (TBR) |
TBRSwap | Tree bisection and reconnection (TBR) |
UnloadMorphy | Destroy a Morphy Object |
WithOneExtraStep | Number of trees with one extra step |