Yesterday I posted
about implementing Pybus & Harvey's (2000) MCCR
test. This used to be in Dan Rabosky's *laser*, which is no longer available (except in archived
versions) on CRAN. The method is quite simple as it merely uses Monte Carlo simulation to generate a
null distribution of the γ-statistic for incompletely sampled phylogenies. I have now
added
this function (and a couple of associated methods) to *phytools*. This update can be obtained by
installing the latest version of *phytools* from GitHub using *devtools*.

Here's a quick demo of how the function works:

```
library(phytools)
packageVersion("phytools")
```

```
## [1] '0.6.66'
```

```
tree<-pbtree(n=600,scale=100)
ltt(tree,show.tree=TRUE,lwd=3)
```

```
## Object of class "ltt" containing:
##
## (1) A phylogenetic tree with 600 tips and 599 internal nodes.
##
## (2) Vectors containing the number of lineages (ltt) and branching times (times) on the tree.
##
## (3) A value for Pybus & Harvey's "gamma" statistic of -0.1158, p-value = 0.9078.
```

```
## subsample the tree to introduce a downward bias in gamma:
incomplete<-drop.tip(tree,sample(tree$tip.label,400))
ltt(incomplete,show.tree=TRUE,lwd=3)
```

```
## Object of class "ltt" containing:
##
## (1) A phylogenetic tree with 200 tips and 199 internal nodes.
##
## (2) Vectors containing the number of lineages (ltt) and branching times (times) on the tree.
##
## (3) A value for Pybus & Harvey's "gamma" statistic of -4.4687, p-value = 0.
```

```
## MCCR test to take into account incomplete sampling:
object<-ltt(incomplete,plot=FALSE)
mccr.result<-mccr(object,rho=200/600,nsim=500)
mccr.result
```

```
## Object of class "mccr" consisting of:
##
## (1) A value for Pybus & Harvey's "gamma" statistic of -4.4687.
##
## (2) A two-tailed p-value from the MCCR test of 0.92.
##
## (3) A simulated null-distribution of gamma from 500 simulations.
```

```
plot(mccr.result)
```

We can also do a small experiment to show that the MCCR test has the correct type I error rate. Here I'm going to simulate five hundred 150 taxon trees, each of which I proceed to randomly subsample to include only 100 taxa. I'll then compute γ & a P-value for the null hypothesis test of γ equal to zero on the original tree; the same things on the subsampled tree; and finally a P-value based on the MCCR method:

```
foo<-function(){
full<-pbtree(n=150)
full.ltt<-ltt(full,plot=FALSE)
incomplete<-drop.tip(full,sample(full$tip.label,50))
incomplete.ltt<-ltt(incomplete,plot=FALSE)
setNames(c(full.ltt$gamma,full.ltt$p,
incomplete.ltt$gamma,incomplete.ltt$p,
mccr(incomplete.ltt,rho=100/150,nsim=200)$'P(two-tailed)'),
c("full-gamma","full-P(gamma)","inc-gamma",
"inc-P(gamma)","P(mccr)"))
}
sim.Result<-t(replicate(500,foo()))
bb<-seq(0,1,by=0.05)
par(mfrow=c(3,1))
obj<-hist(sim.Result[,2],bb,plot=FALSE)
obj$counts<-obj$counts/nrow(sim.Result)
plot(obj,ylab="relative frequency",col="grey",ylim=c(0,0.4),xlab="P-value",main="")
lines(c(0,1),rep(0.05,2),col="blue",lty="dotted")
mtext(text="a) P-value distribution on complete trees",adj=0,line=1,
cex=1)
obj<-hist(sim.Result[,4],bb,plot=FALSE)
obj$counts<-obj$counts/nrow(sim.Result)
plot(obj,ylab="relative frequency",col="grey",ylim=c(0,0.4),xlab="P-value",main="")
lines(c(0,1),rep(0.05,2),col="blue",lty="dotted")
mtext(text="b) P-value distribution on incompletely sampled trees",adj=0,line=1,
cex=1)
obj<-hist(sim.Result[,5],bb,plot=FALSE)
obj$counts<-obj$counts/nrow(sim.Result)
plot(obj,ylab="relative frequency",col="grey",ylim=c(0,0.4),xlab="P-value",main="")
lines(c(0,1),rep(0.05,2),col="blue",lty="dotted")
mtext(text="c) P-value distribution on incompletely sampled trees using MCCR test",
adj=0,line=1,cex=1)
```

We can see that the parametric test has good type I error on completely sampled tree, but elevated error on incompletely sampled trees. The MCCR test recovers this good type I error of the parametric test when our taxon sampling is incomplete. We can also compute the type I errors directly as follows:

```
typeI<-setNames(c(mean(sim.Result[,2]<=0.05),
mean(sim.Result[,4]<=0.05),mean(sim.Result[,5]<=0.05)),
c("complete","incomplete","MCCR"))
typeI
```

```
## complete incomplete MCCR
## 0.044 0.190 0.052
```

Neat.

Hi Liam,

ReplyDeleteis there any chance to include the results of the MCCR test in the LTT plot as seen here (https://link.springer.com/article/10.1186/s12862-015-0435-9/figures/2)?

Cheers Josef