Calculate the NLTT Statistic

[Up] [Top]

Documentation for package ‘nLTT’ version 1.4.9

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.
check_input_event_times Checks that event times are correct
check_phylogenies Check if the input is a valid collection of one or more phylogenies
check_step_type Check if the step type is valid
check_time_unit Check if the time unit is valid
default_params_doc This function does nothing. It is intended to inherit is parameters' documentation.
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 Get the nLTT values in time
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 function, using a Monte Carlo Markov Chain
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_calc_extinct Calculates the exact difference between the nLTT curves of the event times. This includes extinction events.
nltt_diff_exact_extinct Calculates the exact difference between the nLTT curves of the event times. This includes extinction events.
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'.