est_node_density: Test for the node-density artifact

In suryakevin/drugcandy: Detecting Punctuated Evolution in Dinosaurs and Viruses

Test for the node-density artifact

Description

This function checks for the node-density artifact, where branches in parts of a phylogenetic tree with few tips are shorter than their actual lengths. This artifact can bias the regression model towards detecting punctuated evolution even if this is not the case. A symptom of this artifact would be a positive curvilinear relationship between the node count and phylogenetic path length (δ > 1).

Usage

est_node_density(data, vcv_parts)

Arguments

data	A data frame with path length in the 1st column and node count in the 2nd
vcv_parts	A list outputted from the break_vcv function

Value

This function returns a list of the fitted model and node-density parameter estimates.

Author(s)

Kevin Surya

References

Webster et al. (2003); Venditti et al. (2006)

suryakevin/drugcandy documentation built on May 6, 2022, 6:37 p.m.