LikDD: LikDD: Calculates the likelihood of speciation and extinction...
In tanja819/TreePar: Estimating Birth and Death Rates Based on Phylogenies

Description Usage Arguments Value Note Author(s) References Examples

LikDD calculates the likelihood of speciation and extinction rates for a phylogeny under a density-dependent speciation model. Speciation rate is a function of the number of species N, lambda(N) = max(0,lambda(1-N/K)), where K is the carying capacity and lambda the speciation rate when N<<K. Extinction rate is mu (constant). For a computationally much faster implementation, please use function runExpoTree in R package expoTree. In contrast to LikDD, runExpoTree can handle trees with tips sampled sequentially through time.

1	LikDD(par,model=-1,x,Ndec=-1,minN=0,psi=0,sampling=1,root=0,ki=0,muset=0,vec=0)

`par`	Parameters (lambda,mu,K) for which to calculate the likelihood: lambda is speciation rate, mu is extinction rate, and K is carrying capacity.
`model`	model = -1: speciation rate is lambda(N) = max(0,lambda(1-N/K)). model = 0: speciation rate is lambda(N) = lambda for N <= K, und lambda(N) = 0 for N>K.
`x`	Vector of speciation times and ancient lineage sampling times in the phylogeny. Time is measured increasing going into the past with the present being time 0. x can be obtained from a phylogenetic tree using getx(TREE).
`Ndec`	Help variable when optimizing.
`minN`	Help variable when optimizing.
`psi`	Rate for sampling lineages through time.
`sampling`	Probabiliy to sample a present day lineage.
`root`	If root = 1 then max(x) is the mrca (crown age), if root = 0 then max(x) is the age of a branch ancestral to the mrca (stem age).
`ki`	Help variable when optimizing.
`muset`	Help variable when optimizing.
`vec`	vec=0 returns likelihood of model parameters for a tree given 1 lineage at beginning. vec=1 returns vector of likelihoods given i lineages at beginning.

res

-log likelihood of the parameters given the tree.

A faster version is now implemented in R package expoTree by Gabriel Leventhal. It is equivalent to the method here, see examples in LikShifts() manual. Further, expoTree can handle trees with sequentially sampled tips.

Tanja Stadler, Gabriel Leventhal

R.S. Etienne, B. Haegeman, T. Stadler, T. Aze, P.N. Pearson, A. Purvis, A.B. Phillimore. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc. Roy. Soc. B, 279: 1300-1309, 2012.

G. Leventhal, H. Guenthard, S. Bonhoeffer, T. Stadler. Using an epidemiological model for phylogenetic inference reveals density-dependence in HIV transmission. Mol. Biol. Evol., 31(1): 6-17, 2014.