R: Ancestral character reconstruction.

ancestral.pml {phangorn} | R Documentation

## Ancestral character reconstruction.

### Description

Marginal reconstruction of the ancestral character states.

### Usage

    ancestral.pml(object, type = "marginal", return = "prob")

    ancestral.pars(tree, data, type = c("MPR", "ACCTRAN"), cost = NULL,
      return = "prob")

    pace(tree, data, type = c("MPR", "ACCTRAN"), cost = NULL, return = "prob")

    plotAnc(tree, data, i = 1, site.pattern = TRUE, col = NULL,
      cex.pie = par("cex"), pos = "bottomright", ...)

### Arguments

`object` | an object of class pml
`type` | method used to assign characters to internal nodes, see details.
`return` | return a `phyDat` object or matrix of probabilities.
`tree` | a tree, i.e. an object of class pml
`data` | an object of class phyDat
`cost` | A cost matrix for the transitions between two states.
`i` | plots the i-th site pattern of the `data`.
`site.pattern` | logical, plot i-th site pattern or i-th site
`col` | a vector containing the colors for all possible states.
`cex.pie` | a numeric defining the size of the pie graphs
`pos` | a character string defining the position of the legend
`...` | Further arguments passed to or from other methods.

### Details

The argument "type" defines the criterion to assign the internal nodes. For `ancestral.pml` so far "ml" and (empirical) "bayes" and for `ancestral.pars` "MPR" and "ACCTRAN" are possible.

With parsimony reconstruction one has to keep in mind that there will be often no unique solution.

For further details see vignette("Ancestral").

### Value

of class "phyDat", containing the ancestral states of all nodes.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### References

Felsenstein, J. (2004). Inferring Phylogenies. Sinauer Associates, Sunderland.

Swofford, D.L., Maddison, W.P. (1987) Reconstructing ancestral character states under Wagner parsimony. Math. Biosci. 87: 199–229

Yang, Z. (2006). Computational Molecular evolution. Oxford University Press, Oxford.

### See Also

`pml`, `parsimony`, `ace`, `root`

### Examples

    example(NJ)
    fit <- pml(tree, Laurasiatherian)
    anc.ml <- ancestral.pml(fit, type = "ml")
    anc.p <- ancestral.pars(tree, Laurasiatherian)
    ## Not run:
    require(seqLogo)
    seqLogo( t(subset(anc.ml, 48, 1:20)[[1]]), ic.scale=FALSE)
    seqLogo( t(subset(anc.p, 48, 1:20)[[1]]), ic.scale=FALSE)

    ## End(Not run)
    # plot the first site pattern
    plotAnc(tree, anc.ml, 1)
    # plot the third character
    plotAnc(tree, anc.ml, attr(anc.ml, "index")[3])

[Package phangorn version 2.3.1 Index]