I recently added the function `fit.bd`

to theh *phytools*
package. This function fits a birth-death model & essentially duplicates
existing function in *ape* and *diversitree*.

I discovered, however, that sometimes optimization fails even for this
simple model, and it seems to be usually due to numerical issues which
causes the log-likelihood to evaluate to a non-finite value during
optimization. This can result in some weird discrepancies between optimized
birth (λ) and death (μ) rates between *phytools* and
*ape*.

This is what I mean:

```
library(phytools)
library(TreeSim)
set.seed(1)
trees<-sim.bd.taxa.age(n=100,numbsim=200,lambda=0.059,
mu=0.020,frac=1,age=100,mrca=TRUE)
fits<-lapply(trees,fit.bd)
```

```
## There were 9 warnings (use warnings() to see them)
```

```
## birth & death rates from ape
BD.ape<-t(sapply(trees,function(x) bd(birthdeath(x))))
## birth & death rates from phytools
BD.phytools<-t(sapply(fits,function(x)
setNames(c(x$b,x$d),c("b","d"))))
plot(BD.ape[,"b"],BD.phytools[,"b"],cex=1.5,pch=21,bg="grey",
xlab=expression(paste("ape::birthdeath ",hat(lambda))),
ylab=expression(paste("phytools::fit.bd ",hat(lambda))))
text(BD.ape[,"b"],BD.phytools[,"b"],1:length(fits),cex=0.5,pos=1)
title(main=expression(paste("Estimated speciation rates, ",lambda,
", from ape & phytools")))
```

```
plot(BD.ape[,"d"],BD.phytools[,"d"],cex=1.5,pch=21,bg="grey",
xlab=expression(paste("ape::birthdeath ",hat(mu))),
ylab=expression(paste("phytools::fit.bd ",hat(mu))))
text(BD.ape[,"d"],BD.phytools[,"d"],1:length(fits),cex=0.5,pos=1)
title(main=expression(paste("Estimated extinction rates, ",mu,
", from ape & phytools")))
```

We can immediately see that three trees, #31, #147,& #161, have estimated speciation & extinction rates that are way off!

If we look at their log-likelihoods it turns out they are all non-finite:

```
sapply(fits[c(31,147,161)],logLik)
```

```
## [1] Inf Inf Inf
```

The simple fix that I have pushed so far is to simply check if the optimized log-likelihood is finite, and then, if not, to re-run the optimization routine with different starting values (or until a certain number of iterations is reached).

Let's load it & try it. (Note that the user should just update *phytools*
from GitHub).

```
source("https://raw.githubusercontent.com/liamrevell/phytools/master/R/bd.R")
qb<-phytools:::qb ## make internal function visible
fits<-lapply(trees,fit.bd)
```

```
## There were 32 warnings (use warnings() to see them)
```

```
b<-sapply(fits,function(x) x$b)
par(mar=c(5.1,5.1,4.1,2.1))
plot(BD.ape[,"b"],b,cex=1.5,pch=21,bg="grey",
xlab=expression(paste("ape::birthdeath ",hat(lambda))),
ylab=expression(paste("phytools::fit.bd ",hat(lambda))))
title(main=expression(paste("Estimated speciation rates, ",lambda,
", from ape & (fixed) phytools")))
```

Good!

## No comments:

## Post a Comment

Note: due to the very large amount of spam, all comments are now automatically submitted for moderation.