Simulate randomised "individuals" tree

Source: R/simulateIndTree.R

This function takes in a "category" tree and outputs a simulated corresponding "individuals" tree, for testing the concordance measure.

simulateIndTree(
  catTree,
  itips = 5,
  permuteCat = FALSE,
  permuteTips = TRUE,
  tipPercent = 100
)

Arguments

catTree

object of class phylo, the category-level tree

itips

number of individual tips to assign per category

permuteCat

logical specifying whether to permute the category labels on the category tree before grafting on individual tips. Defaults to FALSE.

permuteTips

logical specifying whether to permute the individual tip labels after building the individual level tree based on the category tree. Defaults to TRUE.

tipPercent

number specifying the percentage of tips to be permuted. Defaults to 100, ignored if permuteTips=FALSE.

Examples

tree <- simulateIndTree(rtree(3))
plot(tree)