Today a *phytools* user asked
on my GitHub page if there was any way to permit `make.simmap`

run in parallel.

Note that the issue motivating this report likely stems from a replacement of the method to do
matrix exponentiation in the latest CRAN
version of *phytools*. This has already been
fixed -
although, of course, if we are using `make.simmap`

with large trees, complex models,
or generating many samples, it will still be slow!

`make.simmap`

does not have a parallelization option; however, for the basic method
we are just estimating the transition matrix, ** Q**, via Maximum Likelihood, and then
sampling histories for the discrete character conditioned on this fitted model. Consequently,
we ought to be able to first compute

**once and then run our sampler on multiple cores. In theory, this can be done using**

*Q*`parallel::mclapply`

.Unfortunately, parallelization is not supported in R for Windows. Nonetheless, it is possible to
run `mclapply`

which pseudo-parallelizes our analysis. This is so that functions &
packages using parallelization don't break on Windows - but it will not run any faster!

Here is what that might look like. I have assumed we have 4 cores to play with.

```
library(phytools)
## our data:
cols<-setNames(colorRampPalette(c("blue","red"))(3),
c("a","b","c"))
dotTree(tree,x,fsize=0.7,ftype="i",colors=cols)
```

```
## first fit our model
fit<-fitMk(tree,x,model="ARD")
fit
```

```
## Object of class "fitMk".
##
## Fitted (or set) value of Q:
## a b c
## a -0.667821 0.667821 0.000000
## b 0.337475 -0.715334 0.377859
## c 0.989418 0.070697 -1.060115
##
## Fitted (or set) value of pi:
## a b c
## 0.3333333 0.3333333 0.3333333
##
## Log-likelihood: -51.296883
##
## Optimization method used was "nlminb"
```

```
## extracted the fitted transition matrix:
fittedQ<-matrix(NA,length(fit$states),length(fit$states))
fittedQ[]<-c(0,fit$rates)[fit$index.matrix+1]
diag(fittedQ)<-0
diag(fittedQ)<--rowSums(fittedQ)
colnames(fittedQ)<-rownames(fittedQ)<-fit$states
## ready to run our analysis
library(parallel)
trees<-mclapply(1:4,function(n,tree,x,fixedQ) make.simmap(tree,x,Q=fixedQ,nsim=100),
tree=tree,x=x,fixedQ=fittedQ,mc.cores=if(.Platform$OS.type=="windows") 1L else 4L)
```

```
## make.simmap is sampling character histories conditioned on the transition matrix
##
## Q =
## a b c
## a -0.6678208 0.66782077 0.0000000
## b 0.3374750 -0.71533391 0.3778589
## c 0.9894179 0.07069738 -1.0601152
## (specified by the user);
## and (mean) root node prior probabilities
## pi =
## a b c
## 0.3333333 0.3333333 0.3333333
```

```
## Done.
```

```
## make.simmap is sampling character histories conditioned on the transition matrix
##
## Q =
## a b c
## a -0.6678208 0.66782077 0.0000000
## b 0.3374750 -0.71533391 0.3778589
## c 0.9894179 0.07069738 -1.0601152
## (specified by the user);
## and (mean) root node prior probabilities
## pi =
## a b c
## 0.3333333 0.3333333 0.3333333
```

```
## Done.
```

```
## make.simmap is sampling character histories conditioned on the transition matrix
##
## Q =
## a b c
## a -0.6678208 0.66782077 0.0000000
## b 0.3374750 -0.71533391 0.3778589
## c 0.9894179 0.07069738 -1.0601152
## (specified by the user);
## and (mean) root node prior probabilities
## pi =
## a b c
## 0.3333333 0.3333333 0.3333333
```

```
## Done.
```

```
## make.simmap is sampling character histories conditioned on the transition matrix
##
## Q =
## a b c
## a -0.6678208 0.66782077 0.0000000
## b 0.3374750 -0.71533391 0.3778589
## c 0.9894179 0.07069738 -1.0601152
## (specified by the user);
## and (mean) root node prior probabilities
## pi =
## a b c
## 0.3333333 0.3333333 0.3333333
```

```
## Done.
```

```
trees
```

```
## [[1]]
## 100 phylogenetic trees with mapped discrete characters
##
## [[2]]
## 100 phylogenetic trees with mapped discrete characters
##
## [[3]]
## 100 phylogenetic trees with mapped discrete characters
##
## [[4]]
## 100 phylogenetic trees with mapped discrete characters
```

At the end, though, instead of one `"multiSimmap"`

object, we have a list of
4! Fortunately, we can combine these in a fairly easy way as follows:

```
trees<-do.call(c,trees)
if(!("multiSimmap"%in%class(trees))) class(trees)<-c("multiSimmap",class(trees))
trees
```

```
## 400 phylogenetic trees with mapped discrete characters
```

Neat.

Now, let's compute a summary & visualize the results:

```
obj<-summary(trees)
obj
```

```
## 400 trees with a mapped discrete character with states:
## a, b, c
##
## trees have 43.7325 changes between states on average
##
## changes are of the following types:
## a,b a,c b,a b,c c,a c,b
## x->y 18.29 0 7.945 8.745 8.1425 0.61
##
## mean total time spent in each state is:
## a b c total
## raw 27.2549076 23.1011251 8.2695555 58.62559
## prop 0.4648978 0.3940451 0.1410571 1.00000
```

```
plot(obj,colors=cols,ftype="i",fsize=0.7)
add.simmap.legend(colors=cols,prompt=FALSE,vertical=FALSE,
x=0,y=2)
```

The tree & data for this example were simulated as follows:

```
tree<-pbtree(n=60)
Q<-matrix(c(-1,1,0,
1,-2,1,
0,1,-1),3,3)
rownames(Q)<-colnames(Q)<-letters[1:3]
x<-as.factor(sim.history(tree,Q)$states)
```

I would love to hear a report from someone working on a Unix-alike system (e.g., Mac OS) who can report if this indeed works on their machine!

Thank you very much for the blog post. I have long wondered if it could be done in parallel. I tried this approach using my own dataset and it worked well on my Mac OS. - Kenji Fukushima

ReplyDeleteThis comment has been removed by the author.

ReplyDeleteTried it on my machine (running OSX) with a larger tree and it worked great! Thank you!

ReplyDeleteBefore have a

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