| pigot_rho {treestats} | R Documentation |
Pigot's rho
Description
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.
ddd_tree <- DDD::dd_sim(pars = c(1, 0, 10), age = 7)$tes
pigot_rho(ddd_tree) # because of diversity dependence, should be < 0