gap_as_state: Treat gaps as a state

In phangorn: Phylogenetic Reconstruction and Analysis

Treat gaps as a state

Description

The function gap_as_state changes the contrast of an phyDat object to treat as its own state. Internally phyDat are stored similar to a factor objects and only the contrast matrix and some attributes change.

Usage

gap_as_state(obj, gap = "-", ambiguous = "?")

gap_as_ambiguous(obj, gap = "-")

has_gap_state(obj)

Arguments

obj	An object of class phyDat.
gap	a character which codes for the gaps (default is "-").
ambiguous	a character which codes for the ambiguous state

Value

The functions return an object of class phyDat.

Author(s)

Klaus Schliep [e-mail]

See Also

phyDat, latag2n.phyDat, latag2n, ancestral.pml, gap_as_state

Examples

data(Laurasiatherian)
tmp <- gap_as_state(Laurasiatherian)
contr <- attr(tmp, "contrast")
rownames(contr) <- attr(tmp, "allLevels")
contr

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.