AdditionTree | Addition tree |
AllSPR | All SPR trees |
Carter1 | Number of trees with _m_ steps |
CharacterLength | Character length |
ClusterStrings | Cluster similar strings |
ConcordantInformation | Evaluate the concordance of information between a tree and a... |
congreveLamsdellMatrices | 100 simulated data matrices |
Consistency | Consistency / retention "indices" |
cSPR | 'cSPR()' expects a tree rooted on a single tip. |
dot-CombineResults | Combine two edge matrices |
dot-GapHandler | Translate a gap treatment into a string in the format... |
dot-NonDuplicateRoot | Non-duplicate root |
dot-UniqueExceptHits | Unique trees (ignoring "hits" attribute) |
DoubleNNI | Double NNI |
GapHandler | Read how a Morphy Object handles the inapplicable token |
inapplicable.datasets | Thirty datasets with inapplicable data |
is.morphyPtr | Is an object a valid Morphy object? |
Jackknife | Jackknife resampling |
JackLabels | Label nodes with jackknife support values |
LengthAdded | Contribution of character to leaf instability |
MaximizeParsimony | Find most parsimonious trees |
MinimumLength | Minimum and Maximum lengths possible for a character |
MorphyErrorCheck | Check for error whilst modifying Morphy object |
MorphyTreeLength | Calculate parsimony score from Morphy object |
MorphyWeights | Set and get the character weightings associated with a Morphy... |
mpl_apply_tipdata | Commits parameters prior to nodal set calculations. |
mpl_attach_rawdata | Attach raw character state data (i.e. tip data). |
mpl_attach_symbols | Attach a caller-specified list of symbols. |
mpl_delete_Morphy | Destroys an instance of a Morphy object. |
mpl_delete_rawdata | Deletes the caller-input data. |
mpl_first_down_recon | Reconstructs the first (downpass) nodal reconstructions |
mpl_first_up_recon | Reconstructs the second (uppass) nodal reconstructions. |
mpl_get_charac_weight | Retrieve the weight of a character in the dataset |
mpl_get_gaphandl | Get / set gap handler from a Morphy object. |
mpl_get_num_charac | Retrieve the number of character (columns) in the dataset. |
mpl_get_num_internal_nodes | Gets the number of internal nodal reconstruction sets being... |
mpl_get_numtaxa | Retrieve the number of taxa (rows) in the dataset. |
mpl_get_symbols | Retrieves the current list of symbols. |
mpl_init_Morphy | Sets up the dimensions of the dataset. |
mpl_new_Morphy | Creates a new instance of a Morphy object |
mpl_second_down_recon | Performs the second nodal reconstructions for characters with... |
mpl_second_up_recon | Finalises the ancestral state reconstructions for characters... |
mpl_set_charac_weight | Set the weight of a character in the dataset |
mpl_set_num_internal_nodes | Sets the number of internal nodes in the dataset |
mpl_set_parsim_t | Sets a character's parsimony function type |
mpl_translate_error | Converts a numeric error code to human-readable format |
mpl_update_lower_root | Updates the nodal sets for a lower ("dummy") root node |
mpl_update_tip | Initial update of tip values following uppass reconstruction. |
NNI | Nearest neighbour interchange (NNI) |
PhyDat2Morphy | Initialize a Morphy object from a 'phyDat' object |
PlotCharacter | Plot the distribution of a character on a tree |
PrepareDataProfile | Prepare data for Profile Parsimony |
profiles | Empirically counted profiles for small trees |
QuartetResolution | Relationship between four taxa |
RandomMorphyTree | Random postorder tree |
RandomTreeScore | Parsimony score of random postorder tree |
Ratchet | Parsimony Ratchet |
RearrangeEdges | Rearrange edges of a phylogenetic tree |
referenceTree | Tree topology for matrix simulation |
SingleCharMorphy | Morphy object from single character |
SiteConcordance | Calculate site concordance factor |
SPR | Subtree pruning and rearrangement (SPR) |
StepInformation | Information content of a character known to contain _e_ steps |
StopUnlessBifurcating | Check that all nodes in a tree are bifurcating. |
Suboptimality | Tree suboptimality |
SuccessiveApproximations | Tree search using successive approximations |
summary.morphyPtr | Details the attributes of a morphy object |
TaxonInfluence | Rank taxa by their influence on phylogenetic results |
TBR | Tree bisection and reconnection (TBR) |
TBRWarning | TBR Warning Print a warning and return given tree |
TreeLength | Calculate the parsimony score of a tree given a dataset |
TreeSearch | Search for most parsimonious trees |
UnloadMorphy | Destroy a Morphy object |
WhenFirstHit | When was a tree topology first hit? |
WithOneExtraStep | Number of trees with one extra step |
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