PhyDat2Morphy: Initialize a Morphy object from a 'phyDat' object

In ms609/TreeSearch: Phylogenetic Analysis with Discrete Character Data

Initialize a Morphy object from a phyDat object

Description

Creates a new Morphy object with the same size and characters as the phyDat object. Once finished with the object, it should be destroyed using UnloadMorphy() to free the allocated memory.

Usage

PhyDat2Morphy(phy, gap = "inapplicable")

Arguments

phy	An object of phangorn class phyDat.
gap	An unambiguous abbreviation of inapplicable, ambiguous (= missing), or ⁠extra state⁠, specifying how gaps will be handled.

Value

PhyDat2Morphy() returns a pointer to an initialized Morphy object.

Author(s)

Martin R. Smith ([e-mail])

See Also

Other Morphy API functions: GapHandler(), MorphyErrorCheck(), MorphyWeights(), 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

data("Lobo", package="TreeTools")
morphyObj <- PhyDat2Morphy(Lobo.phy)
# Set object to be destroyed at end of session or closure of function
# on.exit(morphyObj <- UnloadMorphy(morphyObj), add = TRUE)

# Do something with pointer
# ....

# Or, instead of on.exit, manually destroy morphy object and free memory:
morphyObj <- UnloadMorphy(morphyObj)

ms609/TreeSearch documentation built on April 7, 2024, 7:06 p.m.