As described in a couple of earlier posts (1, 2) I have been doing some work on the function pbtree which does pure-birth (i.e., Yule process) phylogeny simulations.

Well, as the title of this post would suggest, the function can now do birth-death simulation, as well as pure-birth. Remember, pbtree can now condition on total time, the number of tips, or both (by rejection sampling); and can simulate in continuous or discrete time.

Simulating with *death* (i.e., extinction) is not too hard. For continuous time simulation, whereas before we drew our waiting times from the exponential distribution with λ = *b* × *m* for birth-rate *b* & number of 'open' lineages *m*, with extinction we draw our wait times from the exponential distribution with λ = (*b* + *d*) × *m*. This is because if the wait time to an event of class *A* is exponentially distributed with rate λ_{A} & the wait time to an event of class *B* is exponentially distributed with rate λ_{B}, and *A* & *B* are independent, then the wait times to *A* *or* *B* are exponentially distributed with λ = λ_{A} + λ_{B}. The probabilities that an event is a birth or a death given that it has occurred are just *b*/(*b*+*d*) and *d*/(*b*+*d*), respectively. This means that our procedure for growing the tree should be (1) draw a random wait time; (2) pick a lineage at random; and (3) and then have it speciate or die with the probabilities given above.

For discrete time the procedure is only slightly different. Now we draw a random wait time from the geometric distribution with *p* = *b* + *d*.** (**Remember that we are actually drawing *m* independent waiting times & then using the one or more smallest times.) However, since *p* is a probability (whereas λ was a rate), we are now constrained such that *b* + *d* ≤ 1.0. This is because a given lineage can speciate, go extinct, or do nothing within a time-step - but it can't do more than one of these. (*b* + *d* = 1.0 *guarantees* that an event of some kind - speciation or extinction - occurs in every lineage in every generation.)

Code for the new version of pbtree is here. There is also a new phytools build (phytools 0.2-44) with these updates, and it can be downloaded & installed from source.

Here's a little demo of the function, using continuous time simulations:

Loading required package: phytools

> packageVersion("phytools")

[1] ‘0.2.44’

> # continuous time, taxa stop

> tree<-pbtree(d=0.2,n=50)

> plotTree(tree,fsize=0.8,ftype="i")

> tree<-pbtree(d=0.2,n=50)

> plotTree(tree,fsize=0.8,ftype="i")

> tt<-log(50)-log(2); tt

[1] 3.218876

> tree<-pbtree(b=1.2,d=0.2,t=tt)

> plotTree(tree,fsize=0.8,ftype="i")

> max(nodeHeights(tree))

[1] 3.218876

> tree<-pbtree(d=0.5,n=100,extant.only=TRUE)

> plotTree(tree,ftype="off")

> ltt(tree,plot=FALSE)$gamma # pull of the recent

[1] 2.298986

> tt # time for simulation

[1] 3.218876

> tree<-pbtree(b=1.2,d=0.2,n=50,t=tt)

simulating with both taxa-stop (n) and time-stop (t) is

performed via rejection sampling & may be slow

13 trees rejected before finding a tree

> max(nodeHeights(tree))

[1] 3.218876

> length(getExtant(tree))

[1] 50

> plotTree(tree,fsize=0.8,ftype="i")

> # function to get the number of extant tips

> ff<-function(x){

tol<-1e-12

if(max(nodeHeights(x))<(tt-tol)) 0

else length(getExtant(x))

}

> # low extinction rate

> lowD<-pbtree(b=1.1,d=0.1,t=tt,nsim=1000)

> lowD

1000 phylogenetic trees

> NlD<-sapply(lowD,ff)

> mean(NlD)

[1] 48.283

> var(NlD)

[1] 1360.986

> # high extinction rate

> highD<-pbtree(b=1.5,d=0.5,t=tt,nsim=1000)

> highD

1000 phylogenetic trees

> NhD<-sapply(highD,ff)

> mean(NhD)

[1] 48.681

> var(NhD)

[1] 2321.631

> # distribution of tree sizes

> hist(NlD,0:ceiling(max(c(NlD,NhD))/10)*10,col="grey", xlab="frequency",ylab="number of tips",main=NULL)

Pretty cool. The purpose of the final exercise was just to illustrate that although the *expected* number of lineages at time *t* can be computed as *N* = *e*^{(b-d)×t}, the *variance* among simulations goes up with increasing *b*.

That's it. I've been testing out the new pbtree extensively - but please report if you are able to break it! Thanks!

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