simulateIndTree: Simulate randomised "individuals" tree

In treespace: Statistical Exploration of Landscapes of Phylogenetic Trees

Simulate randomised "individuals" tree

Description

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

Usage

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.

See Also

treeConcordance makeCollapsedTree

Examples

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

treespace documentation built on Sept. 8, 2023, 6:04 p.m.