Evaluate tree
Calculate parsimony score with inapplicable data
Prepare data for Profile Parsimony
Initialize a Morphy Object from a phyDat object
Rearrange edges of a phylogenetic tree
Check for error whilst modifying Morphy object
Subtree Pruning and Rearrangement (SPR)
Tree Search using Successive Approximations
Successive Weights
All SPR trees
Calculate parsimony score with inapplicable data
Check that all nodes in a tree are bifurcating.
Thirty Datasets with Inapplicable data
Deletes the caller-input data.
Morphy object from single character
Nearest Neighbour Interchange (NNI)
Destroys an instance of a Morphy object.
Information Content Steps
Character length
Tree bisection and reconnection (TBR)
Finalises the ancestral state reconstructions for characters with
inapplicable values.
Tree suboptimality
Convert a number to binary
Ratchet bootstrapper
Set the character weightings associated with a Morphy object
Initial update of tip values following uppass reconstruction.
TBR Warning
Print a warning and return given tree
Attach raw character state data (i.e. tip data).
Creates a new instance of a Morphy object
Commits parameters prior to nodal set calculations.
Minimum length
Double NNI
Report the character weightings associated with a Morphy object
Extract character data from dataset
Set the weight of a character in the dataset
Tree topology for matrix simulation
Parsimony score of random postorder tree
Performs the second nodal reconstructions for characters with
inapplicability.
Updates the nodal sets for a lower ('dummy') root node
Converts a numeric error code to human-readable format
Label nodes with jackknife support values
Information content per step
Number of trees with one extra step
Search for most parsimonious trees
Retrieve the number of character (columns) in the dataset.
Parsimony Ratchet
Profile Parsimony Score
Attach a caller-specified list of symbols.
Retrieves the current list of symbols.
Reconstructs the first (downpass) nodal reconstructions
Sets up the dimensions of the dataset.
Unique trees (ignoring 'hits' attribute)
100 simulated data matrices
Logistic Points
Extract points from a fitted model
Random postorder tree
Reconstructs the second (uppass) nodal reconstructions.
Destroy a Morphy Object
Retrieve the weight of a character in the dataset
Retrieve the number of taxa (rows) in the dataset.
Thirty Datasets with Inapplicable data
mpl_set_num_internal_nodes
Sets the number of internal nodes in the dataset
mpl_get_num_internal_nodes
Gets the number of internal nodal reconstruction sets being used by
MorphyLib.
Thirty Datasets with Inapplicable data
Details the attributes of a morphy object
Sets a character's parsimony function type
Implied weights parsimony Score
Amount of information in each character