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nLTT (version 1.4.9)

Calculate the NLTT Statistic

Description

Provides functions to calculate the normalised Lineage-Through- Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.

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Install

install.packages('nLTT')

Monthly Downloads

566

Version

1.4.9

License

GPL-2

Issues

2

Pull Requests

0

Stars

6

Forks

4

Maintainer

Thijs Janzen

Last Published

August 21st, 2023

Functions in nLTT (1.4.9)

get_norm_brts

Collect the normalized branching times from the stem age
nltts_plot

Get the average nLTT from a collection of phylogenies
nltt_diff_exact_norm_brts

Calculates the exact difference between the nLTT curves of the branching times
nltt_diff_exact_brts

Calculates the exact difference between the nLTT curves of the branching times
nltt_diff_exact_extinct

Calculates the exact difference between the nLTT curves of the event times. This includes extinction events.
nltt_diff_exact_calc_extinct

Calculates the exact difference between the nLTT curves of the event times. This includes extinction events.
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)
stretch_nltt_matrix

Stretch matrix 'm' with a timestep resolution of 'dt'.
get_phylogeny_nltt_matrix

Extract the nLTT matrix from a phylogeny
nltts_diff

Calculates the nLTT statistic between each phylogeny in a collection compared to a same focal/reference tree
nltt_plot

Normalized version of the ape function ltt.plot
nltt_lines

Normalized version of the ape function ltt.lines.
get_n_lineages

Collect the number of lineages from the stem age
get_average_nltt_matrix

Get the average nLTT from a collection of phylogenies
check_step_type

Check if the step type is valid
abc_smc_nltt

A function to perform Approximate Bayesian Computation within a Sequential Markov Chain (ABC-SMC), for diversification analysis of phylogenetic trees.
default_params_doc

This function does nothing. It is intended to inherit is parameters' documentation.
get_branching_times

Collect the branching times from the stem age
check_time_unit

Check if the time unit is valid
check_phylogenies

Check if the input is a valid collection of one or more phylogenies
exampleTrees

example trees to test the functionality of the package
check_input_event_times

Checks that event times are correct
mcmc_nltt

function, using a Monte Carlo Markov Chain
nLTT-package

Package providing functions to visualize the normalized Lineage-Through-Time statistic, and calculate the difference between two nLTT curves
nltt_diff

Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)
get_nltt_values

Get the nLTT values in time
get_norm_n

Collect the normalized number of lineages from the stem age
nLTT-internal

Internal nLTT functions
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.