The nLTT statistic is a likelihood free summary statistic to compare the similarity between two phylogenetic trees. It calculates the distance between the lineage through time curves of the two trees, after normalizing the lineage through time curves with respect to the maximum number of lineages obtained in each tree, and with respect to the total time between the root and the tips of the tree.

To get a feeling of how the nLTT statistic package work, we provide some worked examples:

###Worked Examples

And we provide some more background information, which can also be found (including intermediary output) in the vignette:

###How to get the average nLTT plot

###How to stretch a nLTT timepoints matrix

###Trees with a root edge

Furthermore, we provide some background information on the MCMC and ABC-SMC techniques used in the original paper describing the nLTT statistic:

###MCMC & ABC-SMC examples