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.
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)
#> [1] 0.1506625
nLTT(simulated_tree, simulated_tree) # should be zero.
#> [1] 0