Finalises the ancestral state reconstructions for characters with inapplicable values.

Finalises the nodal sets for any characters that may have involved the inapplicable token and counts excess regions of applicability at nodes having at least two descendant subtrees that possess any applicable characters. Because this function needs to be fairly high-performance, it does not do much checking for parameter validity, thus unsafe usage of this function might not be caught. It is up to calling functions to ensure that the appropriate parameters have been set before use.

Usage

mpl_second_up_recon(node_id, left_id, right_id, anc_id, morphyobj)

Arguments

node_id

The index of the node being reconstructed.

left_id

The index of the left descendant.

right_id

The index of the right descendant.

anc_id

The index of the immediate ancestor of the node.

morphyobj

An instance of the Morphy object.

Value

The integral parsimony length (right now)

See also

Other Morphy API functions: GapHandler(), MorphyErrorCheck(), MorphyWeights(), PhyDat2Morphy(), SingleCharMorphy(), UnloadMorphy(), is.morphyPtr(), mpl_apply_tipdata(), mpl_attach_rawdata(), mpl_attach_symbols(), mpl_delete_Morphy(), mpl_delete_rawdata(), mpl_first_down_recon(), mpl_first_up_recon(), mpl_get_charac_weight(), mpl_get_gaphandl(), mpl_get_num_charac(), mpl_get_num_internal_nodes(), mpl_get_numtaxa(), mpl_get_symbols(), mpl_init_Morphy(), mpl_new_Morphy(), mpl_second_down_recon(), mpl_set_charac_weight(), mpl_set_num_internal_nodes(), mpl_set_parsim_t(), mpl_translate_error(), mpl_update_lower_root(), mpl_update_tip(), summary.morphyPtr()

Author

Thomas Guillerme