Explore likelihood parsimony surface

terraces visualizes in likelihood surface for the tree space (Sanderson et al. 2011). Usually trees are from a bootstrap or MCMC sample. There the first two axis are the principle components of distances between trees and the third axis is the likelihood value or parsimony score.

Usage

terraces(x, ...)

# S3 method for class 'pml'
terraces(x, trees = NULL, dist_fun = "RF.dist",
  di2multi = FALSE, tol = 2e-08, plot = TRUE, ...)

# S3 method for class 'phyDat'
terraces(x, trees, dist_fun = "RF.dist", di2multi = TRUE,
  tol = 2e-08, plot = TRUE, ...)

Arguments

x: an object of class pml
...: Further arguments passed to or from other methods.
trees: an object of class multiPhylo
dist_fun: a function to compute distances between trees see e.g. RF.dist
di2multi: logical, should trees multichotomies get collapsed. Useful for Robinson-Foulds distance. If edge length are used to compute the distance, e.g. Kuhner-Felsenstein distance, this is not needed.
tol: a numeric value giving the tolerance to consider a branch length significantly greater than zero.
plot: loggical if TRUE a 3D scatter is shown.

Value

terraces silently returns a matrix.

References

Sanderson, M.J., McMahon, M.M. and Steel, M. (2011). Terraces in phylogenetic tree space. Science, 333, 448–450.

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

if (FALSE) { # \dontrun{
data(woodmouse)
fit <- pml_bb(woodmouse, model="JC")
library(rgl)
open3d()
terraces(fit)
} # }