Pnd_reparam: Probability density of node depths reparametrised.

In sophia-lambert/UDivEvo: A package for Unknown Diversity Diversification Analysis in Evolution

Probability density of node depths reparametrised.

Description

Calculating the probability density of node depths of a phylogenetic tree parametrised on y*λ and r.

Usage

Pnd_reparam(t, yl, r)

Arguments

t	Numeric vector. A vector specifying the node depths of a phylogeny in millions of years.
yl	Numeric. The sampling probability times the speciation rate: y*λ.
r	Numeric. The net diversification rate: λ - μ. The units are in events/lineages/millions years.

Value

The probability density of node depths equivalent to f\_y(t) in Lambert 2018 and to λ*p1 in Stadler 2010 and Lambert et al. 2022 but parametrised on y*λ and r see also Stadler 2009.

Author(s)

Sophia Lambert

References

Lambert, A. (2018). The coalescent of a sample from a binary branching process. Theoretical population biology, 122, 30-35. Stadler, T. (2010). Sampling-through-time in birth–death trees. Journal of theoretical biology, 267(3), 396-404. Stadler, T. (2009). On incomplete sampling under birth–death models and connections to the sampling-based coalescent. Journal of theoretical biology, 261(1), 58-66.

See Also

likelihood_bdRho, fitMCMC_bdRho

sophia-lambert/UDivEvo documentation built on Sept. 27, 2022, 11:05 p.m.