CommT (version 0.1.1)

CommT.kfdist: Calculate the tree distance metric

Description

Function to calculate a selected tree distance metric between posterior gene tree distributions.

Usage

CommT.kfdist(post_gt_distrs_BEAST, post_gt_distrs_starBEAST, outlier_num = 1, treedist_select = 2)

Arguments

post_gt_distrs_BEAST

a multiPhylo object representing the posterior gene tree distribution estimated in the absence of a multispecies coalescent model. This object is split into individual lists of trees, whereby each list represents a posterior gene tree distribution inferred under a specific genetic locus. Each list should be named by the respective locus.

post_gt_distrs_starBEAST

a multiPhylo object representing the posterior gene tree distribution estimated in the presence of a multispecies coalescent model. This object is split into individual lists of trees, whereby each list represents a posterior gene tree distribution inferred under a specific genetic locus. Each list should be named by the respective locus.

outlier_num

an integer specifying the number of the genetic locus to be used as positive control in the ANOVA calculations employing mixed effects models. The default is 1.

treedist_select

an integer specifying the type of tree distance metric. The selection hereby follows the output order employed in function treedist of the R package phangorn. The default is 2, which represents the Kuhner-Felsenstein distance.

References

Kuhner, M.K. and Felsenstein. J., 1994. Simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11: 459-468.

Examples

  # Load libraries
  #  require(ape)

  # Load input data
    data(post_gt_distrs_BEAST)
    data(post_gt_distrs_starBEAST)
    
  # Calculate KF distances
    in_data = CommT.kfdist(post_gt_distrs_BEAST, post_gt_distrs_starBEAST)