GapHandler {TreeSearch} | R Documentation |
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 |
Value
GapHandler()
returns a character string stating how
gaps are handled by morphyObj
.
Author(s)
Martin R. Smith (martin.smith@durham.ac.uk)
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)