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Export pml objects

Source: R/pml_generics.R
write.pml.Rd

write.pml writes out the ML tree and the model parameters.

Usage

write.pml(x, file = "pml", save_rds = TRUE, digits = 10, ...)

Arguments

x

an object of class pml.

file

a file name. File endings are added.

save_rds

logical, if TRUE saves the pml object as a rds file, otherwise the alignment is saved as a fasta file.

digits

default is 10, i.e. edge length for the bootstrap trees are exported. For digits larger smaller than zero no edge length are exported.

...

Further arguments passed to or from other methods.

Value

write.pml returns the input x invisibly.

Details

write.pml creates several files. It exports the alignment as fasta file. It writes out the ML tree in a newick file and the estimates parameters in a txt file. It should be possible to (re-)create the pml object up to numerical inaccuracies and this is possible with the *.rds file. If bootstrap trees exist these are additionally exported in a compressed nexus file. Additionally several plots are returned. The maximum likelihood tree, with support values, if these are available. If an bootstrapped trees exist, a consensus tree, a consensus network (< 200 tips) and terrace plot. And last but not least the distribution of the rates. It might be better to adopt these on the dataset.

See also

ancestral.pml, plotAnc

Examples

data(woodmouse)
fit <- pml_bb(woodmouse, "JC", rearrangement = "none")
#> optimize edge weights:  -1864.042 --> -1857.165 
#> optimize edge weights:  -1857.165 --> -1857.165 
#> optimize edge weights:  -1857.165 --> -1857.165 
write.pml(fit, "woodmouse")
unlink(c("woodmouse.txt", "woodmouse_tree.nwk", "woodmouse_align.fasta",
       "woodmouse_tree.pdf", "woodmouse.rds", "woodmouse_rates.pdf"))