I just pushed some updates & additions
(1,
2,
3,
4)
to the *phytools* function `ltt95`

.

`ltt95`

(e.g.,
here) is a relatively
simple function for drawing (1-α) × 100% CIs around a lineage through time plot. It has two different
modes - one in which the mean or median & confidence intervals are computed in terms of the number of lineages at a given time
(`method="lineages"`

) and the other other in which the mean or median & confidence intervals are calculated for the
amount of time that has elapsed, given a certain number of lineages (`method="times"`

).

I mainly added some improved visualization - for instance, using a shaded polygon instead of simple dotted lines to
demarcate the CIs. I'll be the first to admit that the style is
unoriginal. I believe that the *paleotree*
package produces a plot that is stylistically highly similar, if not the same. Nonetheless, the function has
some potentially useful features so I thought it was worth doing. I also corrected the lower confidence bounds - previously
it was one element too low making the CIs slightly too large.

Here's a demo using some phylogenies of primates:

```
library(phytools)
primates<-read.nexus(file=
"http://www.phytools.org/TS2018/data/10kTrees_Primates.nex")
ltt95(primates,log=TRUE)
```

The weird effect where the number of accumulated lineages drops off to zero at the end of the plot is a
characteristic sign of some of the trees not being ultrametric to the precision of the machine. This is because
`phytools::ltt`

(used internally by `ltt95`

) intentionally does not assume that the trees
are ultrametric. In our case, they should be - and the small deviations that we see are merely due to
rounding of the edge lengths when our trees were written to file.

To fix that, let's use `force.ultrametric`

as follows:

```
primates<-lapply(primates,force.ultrametric)
class(primates)<-"multiPhylo"
```

Now, let's proceed to re-compute our `"ltt95"`

object, this time without plotting:

```
object<-ltt95(primates,log=TRUE,plot=FALSE)
object
```

```
## Object of class "ltt95".
## alpha: 0.05
## method: lineages
## mode: median
## N(lineages): 273
```

```
par(bty="l")
plot(object,shaded=TRUE,xaxis="flipped")
```

That's cool. Now let's switch to `mode="times"`

, just to see how it looks:

```
object<-ltt95(primates,log=TRUE,plot=FALSE,method="times")
object
```

```
## Object of class "ltt95".
## alpha: 0.05
## method: times
## mode: median
## N(lineages): 273
```

```
par(bty="l")
plot(object,shaded=TRUE,xaxis="flipped",bg=rgb(1,0,0,0.25))
```

Finally, here is what it looks like if we compute the average number of lineages at each time point, rather than the median. I'm also going to set α to 0.0 for the confidence intervals - essentially, I want my CI to include all trees in the sample:

```
object<-ltt95(primates,log=TRUE,plot=FALSE,mode="mean",alpha=0)
par(bty="l")
plot(object,shaded=TRUE,xaxis="flipped")
legend(x="topleft",c("mean number of lineages",
"total range of lineages across trees"),
lty=c(1,0),lwd=c(2,0),pch=c(NA,22),pt.cex=2.5,
pt.bg=c("black",rgb(0,0,1,0.25)),col=c("black","transparent"),
bty="n")
```

Finally, here are all the LTTs plotted for comparison:

```
object<-ltt(primates,plot=FALSE)
max.t<-max(sapply(object,function(x) max(x$times)))
for(i in 1:length(object))
object[[i]]$times<-object[[i]]$times+
diff(c(max(object[[i]]$times),max.t))
plot(object,col=rgb(0,0,1,0.5))
```

Neat.

Hi Liam, I wonder if there is an example of an LTT plot by a character's state. For instance, in fishes, two lines in a figure showing LTT for freshwater vs. marine.

ReplyDelete