Description Author(s) References Examples
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.
Michael Gruenstaeudl
Maintainer: Michael Gruenstaeudl mi.gruenstaeudl@gmail.com
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | # 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
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