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