Ancestral character reconstruction.
Marginal reconstruction of the ancestral character states.
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", ...)object |
an object of class pml |
type |
method used to assign characters to internal nodes, see details. |
return |
return a |
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 |
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. |
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").
of class "phyDat", containing the ancestral states of all nodes.
Klaus Schliep klaus.schliep@gmail.com
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.
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])
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