Description Usage Arguments Author(s) References Examples
Function to calculate a selected tree distance metric between posterior gene tree distributions.
1 2 | CommT.kfdist(post_gt_distrs_BEAST, post_gt_distrs_starBEAST,
outlier_num = 1, treedist_select = 2)
|
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 |
treedist_select |
an integer specifying the type of tree distance metric. The selection hereby follows the output order employed in function |
Michael Gruenstaeudl
Maintainer: Michael Gruenstaeudl mi.gruenstaeudl@gmail.com
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.
1 2 3 4 5 6 7 8 9 | # 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)
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