treestats (version 1.70.5)

nLTT: Normalized LTT statistic

Description

The nLTT statistic calculates the sum of absolute differences in the number of lineages over time, where both the number of lineages and the time are normalized. The number of lineages is normalized by the number of extant tips, whereas the time is normalized by the crown age. The nLTT can only be calculated for reconstructed trees. Only use the treestats version if you are very certain about the input data, and are certain that performing nLTT is valid (e.g. your tree is ultrametric etc). If you are less certain, use the nLTT function from the nLTT package.

Usage

nLTT(phy, ref_tree)

Value

number of lineages

Arguments

phy

phylo object or ltable

ref_tree

reference tree to compare with (should be same type as phy)

References

Janzen, T., Höhna, S. and Etienne, R.S. (2015), Approximate Bayesian Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT. Methods Ecol Evol, 6: 566-575. https://doi.org/10.1111/2041-210X.12350

Examples

simulated_tree <- ape::rphylo(n = 10, birth = 1, death = 0)
reference_tree <- ape::rphylo(n = 10, birth = 0.2, death = 0)
nLTT(simulated_tree, reference_tree)
nLTT(simulated_tree, simulated_tree) # should be zero.