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 |
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 |