lynchD {paleoTS}R Documentation

Compute rate metric from Lynch (1990)

Description

This function computes D, the rate metric proposed by Lynch (1990). This metric derives from the random walk model, with D = Vstep/Vp, where Vstep is the step variance of the unbiased random walk, and Vp is the within sample variance, pooled among samples. Under mutation - drift equilibrium, D is expected to range approximately between 5e-5 and 5e-3.

Usage

lynchD(y, gen.per.t = 1e+06, pool = TRUE, ...)

Arguments

y a paleoTS object
gen.per.t the number of generations per unit time
pool logical, if the variance should be pooled across samples in estimating Vstep
... further arguments, passed to opt.URW

Details

The gen.per.t argument indicates the number of organismal generations for each unit of time with which the time-series y was measured. For example, is y$tt is measured in millions of years, and the species has annual generations, gen.per.t would be 1e6.
Estimation of Vstep is done on the original time scale of y, and then the values are converted to generational time scales using gen.per.t. This is for numerical reasons, as it avoids computations on possible very low numbers.

Value

D value of rate metric
pooled.var value of pooled within-sample variance
gen.per.t number of generations per unit time
vstep
computed Vstep, at the original time scale of y
drift.range exepcted minimum and maximum values of D consistent with neutral evoltuion
result conclusion reached about the plausibility of neutral evolution

Author(s)

Gene Hunt

References

Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. The American Naturalist 136:727–741.

See Also

opt.URW

Examples

 y<- sim.GRW(ns=20, ms=0, vs=1e-4, tt=seq(0,1e6, length.out=20))  # per-year simulation
 lynchD(y, gen.per.t=1)		# 1 generation per year

[Package paleoTS version 0.3-1 Index]