calc_partialr2: Calculate partial R^2

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

Calculate partial R²

Description

This function calculates the partial R² of a phylogenetic regression model. In the context of models for detecting punctuated evolution, this value represents the proportion of the deviation from the strict molecular (or morphological) clock that is attributable to net speciation or gene duplication events. Specifically, the partial R² roughly represents how much the sum of squared errors (SSE) decreases after including node count in the model. So, the more complex model has node count as the only additional parameter (e.g., path ~ node or path ~ time + node) compared to the simpler model (e.g., path ~ 1 or path ~ time).

Usage

calc_partialr2(output_simple, output_complex)

Arguments

output_simple	A list outputted from the fit_punc_model function (the simpler model)
output_complex	A list outputted from the fit_punc_model function (the more complex model)

Value

This function returns the partial R² value.

Author(s)

Kevin Surya

References

Anderson-Sprecher (1994)

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