GapHandler: Read how a Morphy Object handles the inapplicable token

In TreeSearch: Phylogenetic Analysis with Discrete Character Data

Read how a Morphy Object handles the inapplicable token

Description

Gaps represented by the inapplicable token can be treated as "missing data", i.e. as equivalent to the ambiguous token ⁠?⁠; as an extra state, equivalent to other states such as 0 or 1; or as "inapplicable data" using the algorithm of Brazeau, Guillerme and Smith (2019).

Usage

GapHandler(morphyObj)

Arguments

morphyObj

Object of class morphy, perhaps created with PhyDat2Morphy().

Value

GapHandler() returns a character string stating how gaps are handled by morphyObj.

Author(s)

Martin R. Smith ([e-mail])

See Also

Other Morphy API functions: 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_second_up_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()

Examples

morphyObj <- SingleCharMorphy("-0-0", "Extra")
GapHandler(morphyObj)
morphyObj <- UnloadMorphy(morphyObj)

TreeSearch documentation built on Aug. 26, 2023, 9:06 a.m.