# Calculate the NLTT Statistic

## Documentation for package ‘nLTT’ version 1.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

nLTT-package | Package providing functions to visualize the normalized Lineage-Through-Time statistic, and calculate the difference between two nLTT curves
abc_smc_nltt | A function to perform Approximate Bayesian Computation within a Sequential Markov Chain (ABC-SMC), for diversification analysis of phylogenetic trees.
exampleTrees | example trees to test the functionality of the package
get_average_nltt_matrix | Get the average nLTT from a collection of phylogenies
get_branching_times | Collect the branching times from the stem age
get_nltt_values | Collects the nLTT values of all phylogenies in the melted/uncast/long form
get_norm_brts | Collect the normalized branching times from the stem age
get_norm_n | Collect the normalized number of lineages from the stem age
get_n_lineages | Collect the number of lineages from the stem age
get_phylogeny_nltt_matrix | Extract the nLTT matrix from a phylogeny
mcmc_nltt | Code to perform Metropolis-Hastings MCMC for a diversification model, given a phylogenetic tree. This function was used in the MEE paper to calculate the likelihood reference estimates.
nLTT | Package providing functions to visualize the normalized Lineage-Through-Time statistic, and calculate the difference between two nLTT curves
nLTTstat | Calculate the difference between two normalized Lineage-Through-Time curves, given two phylogenetic trees.
nLTTstat_exact | Calculate the exact difference between two normalized Lineage-Through-Time curves, given two phylogenetic trees.
nltts_diff | Calculates the nLTT statistic between each phylogeny in a collection compared to a same focal/reference tree
nltts_plot | Get the average nLTT from a collection of phylogenies
nltt_diff | Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)
nltt_diff_exact | Calculates the exact, difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)
nltt_diff_exact_brts | Calculates the exact difference between the nLTT curves of the branching times
nltt_diff_exact_norm_brts | Calculates the exact difference between the nLTT curves of the branching times
nltt_lines | Normalized version of the ape function ltt.lines.
nltt_plot | Normalized version of the ape function ltt.plot
stretch_nltt_matrix | Stretch matrix 'm' with a timestep resolution of 'dt'.