write.ancestral: Export and convenience functions for ancestral...

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

Export and convenience functions for ancestral reconstructions

Description

write.ancestral allows to export ancestral reconstructions. It writes out the tree, a tab delimited text file with the probabilities and the alignment. ancestral generates an object of class ancestral.

Usage

write.ancestral(x, file = "ancestral")

as.ancestral(tree, prob, align = NULL)

## S3 method for class 'ancestral'
print(x, ...)

## S3 method for class 'ancestral'
as.phyDat(x, ...)

## S3 method for class 'ancestral'
as.data.frame(x, ...)

Arguments

x	an object of class ancestral
file	a file name. File endings are added.
tree	an object of class phylo.
prob	an data.frame containing a matrix of posterior probabilities for each state and site.
align	an object of class phyDat.
...	Further arguments passed to or from other methods.

Details

This allows also to read in reconstruction made by iqtree to use the plotting capabilities of R.

Value

write.ancestral returns the input x invisibly.

See Also

anc_pml, plotAnc

Examples

data(Laurasiatherian)
fit <- pml_bb(Laurasiatherian[,1:100], "JC", rearrangement = "none")
anc_ml <- anc_pml(fit)
write.ancestral(anc_ml)
# Can be also results from iqtree
align <- read.phyDat("ancestral_align.fasta", format="fasta")
tree <- read.tree("ancestral_tree.nwk")
df <- read.table("ancestral.state", header=TRUE)
anc_ml_disc <- as.ancestral(tree, df, align)
plotAnc(anc_ml_disc, 20)
unlink(c("ancestral_align.fasta", "ancestral_tree.nwk", "ancestral.state"))

KlausVigo/phangorn documentation built on Nov. 20, 2024, 12:47 p.m.