Rev Language Reference

dnCoalescent(RealPos theta, Taxon[] taxa, Clade[] constraints)

theta :	RealPos (pass by const reference)
	The constant population size.
taxa :	Taxon[] (pass by value)
	The taxa used when drawing a random tree.
constraints :	Clade[] (pass by value)
	The topological constraints strictly enforced.
	Default : [ ]

TimeTree

The underlying theory of the constant population size Coalescent implemented here is Kingman's Coalescent. The implementation here assumes haploid individuals, so for diploid study systems one needs to multiply the effective population size by 2 and the true effective population size in units of individuals needs to be divided by 2 afterwards. The Coalescent process is parameterized with theta, which here stands for the effective population size (not 4 * Ne * mu). For detailed examples see https://revbayes.github.io/tutorials/coalescent/

# specify a prior distribution on the constant population size
pop_size ~ dnUniform(0,1E6)
moves.append( mvScale(pop_size, lambda=0.1, tune=true, weight=2.0) )

# specify the coalescent process.
# note that you need to have a vector of taxa
psi ~ dnCoalescent(theta=pop_size, taxa=taxa)

# for monitoring purposes, you may want the root age
root_height := psi.rootAge()

# continue as usual to either clamp the genealogy or infer the genealogy based on sequence data

• dnCoalescentSkyline
• dnCoalescentDemography