R: Write a tree to file with ancestral states and (optionally)...

writeAncestors {phytools}

R Documentation

Write a tree to file with ancestral states and (optionally) CIs at nodes

This function writes a tree to file with ancestral character states and (optionally) 95% confidence intervals stored as node value.

writeAncestors(tree, Anc=NULL, file="", digits=6, format=c("phylip","nexus"), 
   ...)

`tree`	a phylogenetic tree or set of trees as an object of class `"phylo"` or `"multiPhylo"`.
`Anc`	a vector of ancestral states, a list containing the ancestral states and 95% confidence intervals (as from `fastAnc` or `ace`, or a list of such results.
`file`	an optional string with the filename for output.
`digits`	an integer indicating the number of digits to print for branch lengths and ancestral character values.
`format`	a string indicating whether to output the result in simple Newick (i.e., `"phylip"`) or Nexus format.
`...`	additional arguments including `x`: a vector of character values, in which case ancestral states are estimated internally using `fastAnc`; and `CI`: a logical value indicating whether or not to estimate 95% confidence intervals.

A file, string, or vector of strings.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.