CommT (version 0.1.1)

CommT-package: Comparative phylogeographic analysis using the community tree framework

Description

CommT Provides functions to measure the difference between constrained and unconstrained gene tree distributions using various tree distance metrics. Constraints are enforced prior to this analysis via the estimation of a tree under the community tree model.

References

Gruenstaeudl, M., Reid, N.M., Wheeler, G.R. and Carstens, B.C., 2015. Posterior Predictive Checks of Coalescent Models: P2C2M, an R package. Molecular Ecology Resources, in press.

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)

  # Generate ANOVA legend
    legend_text = CommT.anova(in_data)

  # Generate coordinates for plot
    legend_pos = CommT.legendpos(in_data)

  # Visualize KF distances
    my_plot = CommT.viz(in_data, "my_project", alpha=0.05, legend_text, legend_pos)

  # Display plot
    my_plot