nLTTstat: Calculate the difference between two normalized...
In nLTT: Calculate the NLTT Statistic

nLTTstat

R Documentation

Calculate the difference between two normalized Lineage-Through-Time curves, given two phylogenetic trees.

Description

This function takes two ultrametric phylogenetic trees, calculates the normalized Lineage-Through-Time statistic for both trees and then calculates the difference between the two statistics.

Usage

nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE,
               log_transform = FALSE)

Arguments

`tree1`	an object of class `"phylo"`
`tree2`	an object of class `"phylo"`
`distance_method`	Chosen measurement of distance between the two nLTT curves, options are (case sensitive): - "abs": use the absolute distance - "squ": use the squared distance;
`ignore_stem`	a boolean whether to ignore the stem length
`log_transform`	a boolean wether to log-transform the number of lineages before normalization

Value

The difference between the two nLTT statistics

Author(s)

Thijs Janzen

Examples

  data(exampleTrees)
  nltt_plot(exampleTrees[[1]])
  nltt_lines(exampleTrees[[2]], lty=2)
  nLTTstat(
    exampleTrees[[1]], exampleTrees[[2]],
    distance_method = "abs", ignore_stem = TRUE)

nLTT documentation built on Aug. 21, 2023, 5:13 p.m.