R/mpl_morphy_objects.R
GapHandler.RdGaps 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).
GapHandler(morphyObj)Object of class morphy, perhaps created with
PhyDat2Morphy().
GapHandler() returns a character string stating how
gaps are handled by morphyObj.
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()
morphyObj <- SingleCharMorphy("-0-0", "Extra")
GapHandler(morphyObj)
#> [1] "Extra state"
morphyObj <- UnloadMorphy(morphyObj)