Pigot's rho

Calculates the change in rate between the first half and the second half of the extant phylogeny. Rho = (r2 - r1) / (r1 + r2), where r reflects the rate in either the first or second half. The rate within a half is given by (log(n2) - log(n1) / t, where n2 is the number of lineages at the end of the half, and n1 the number of lineages at the start of the half. Rho varies between -1 and 1, with a 0 indicating a constant rate across the phylogeny, a rho < 0 indicating a slow down and a rho > 0 indicating a speed up of speciation. In contrast to the Gamma statistic, Pigot's rho is not sensitive to tree size.

Usage

pigot_rho(phy)

Arguments

phy

phylo object

Value

rho

References

Alex L. Pigot, Albert B. Phillimore, Ian P. F. Owens, C. David L. Orme, The Shape and Temporal Dynamics of Phylogenetic Trees Arising from Geographic Speciation, Systematic Biology, Volume 59, Issue 6, December 2010, Pages 660–673, https://doi.org/10.1093/sysbio/syq058

Examples

simulated_tree <- ape::rphylo(n = 10, birth = 1, death = 0)
pigot_rho(simulated_tree) # should be around 0.
#> [1] -0.3652124
ddd_tree <- DDD::dd_sim(pars = c(1, 0, 10), age = 7)$tes
pigot_rho(ddd_tree) # because of diversity dependence, should be < 0
#> [1] -1