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Treat gaps as a state

Source: R/gap_as_state.R
gap_as_state.Rd

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.

See also

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

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

data(Laurasiatherian)
tmp <- gap_as_state(Laurasiatherian)
contr <- attr(tmp, "contrast")
rownames(contr) <- attr(tmp, "allLevels")
contr
#>   a c g t -
#> a 1 0 0 0 0
#> c 0 1 0 0 0
#> g 0 0 1 0 0
#> t 0 0 0 1 0
#> u 0 0 0 1 0
#> m 1 1 0 0 0
#> r 1 0 1 0 0
#> w 1 0 0 1 0
#> s 0 1 1 0 0
#> y 0 1 0 1 0
#> k 0 0 1 1 0
#> v 1 1 1 0 0
#> h 1 1 0 1 0
#> d 1 0 1 1 0
#> b 0 1 1 1 0
#> n 1 1 1 1 0
#> ? 1 1 1 1 1
#> - 0 0 0 0 1