MorphyWeights: Set and get the character weightings associated with a Morphy...

In TreeSearch: Phylogenetic Analysis with Discrete Character Data

Set and get the character weightings associated with a Morphy object.

Description

MorphyWeights() details the approximate and exact weights associated with characters in a Morphy object; SetMorphyWeights() edits them.

Usage

MorphyWeights(morphyObj)

SetMorphyWeights(weight, morphyObj, checkInput = TRUE)

Arguments

morphyObj	Object of class morphy, perhaps created with PhyDat2Morphy().
weight	A vector listing the new weights to be applied to each character
checkInput	Whether to sanity-check input data before applying. Defaults to TRUE to protect the user from crashes.

Value

MorphyWeights() returns a data frame with two named rows and one column per character pattern: row 1, approx, is a list of integers specifying the approximate (integral) weights used by MorphyLib; row 2, exact, is a list of numerics specifying the exact weights specified by the user.

SetMorphyWeights() returns the Morphy error code generated when applying weight.

Author(s)

Martin R. Smith ([e-mail])

See Also

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

tokens <- matrix(c(
  0, 0, 0, 1, 1, 2,
  0, 0, 0, 0, 0, 0), byrow = TRUE, nrow = 2L,
  dimnames = list(letters[1:2], NULL))
pd <- TreeTools::MatrixToPhyDat(tokens)
morphyObj <- PhyDat2Morphy(pd)
MorphyWeights(morphyObj)
if (SetMorphyWeights(c(1, 1.5, 2/3), morphyObj) != 0L) message("Errored")
MorphyWeights(morphyObj)
morphyObj <- UnloadMorphy(morphyObj)

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