MorphyDat: PhyDat to MorphyDat

In ms609/inapplicable: Inapplicable data in parsimony analysis

Description

Converts a PhyDat object to allow processing by MorphyDat

Usage

MorphyDat(phydat)

Arguments

phydat

A phyDat object

Value

This function returns a matrix of class *phyDat.

• Each row of the matrix corresponds to an operational taxonomic unit;

• Each column of the matrix represents a transformation series, with all transformation series containing three or more inapplicable tokens (and thus requiring the use of the modified Fitch algorithm) listed first;

• Each cell in the matrix contains an integer that denotes the possible tokens. This integer is the decimal representation of the binary figure represented by a row in the contrast matrix (in reverse order), after phangorn:::prepareFitchData.

In addition to the standard phyDat attributes, the returned object bears an attribute inapp.level, specifying the level that corresponds to the inapplicable token, inapp.chars, specifying the number of transformation series in which three or more inapplicable tokens are present (thus requiring the use of the modified Fitch algorithm), and [#TODO] min.steps, specifying the minimum number of steps necessary to obtain the observed distribution of tokens (necessary when calculating implied weights).

Author(s)

Martin R. Smith

See Also

phyDat

Examples

data(inapplicable.datasets)
morphy <- MorphyDat(inapplicable.phyData[[1]])

ms609/inapplicable documentation built on May 23, 2019, 7:49 a.m.