Tuesday, June 23, 2015

Update to rerootingMethod for ancestral state reconstruction to permit polytomies

A phytools user recently reported that the ancestral character estimation method for discrete traits in phytools, rerootingMethod, does not work for trees with polytomies. This is in fact correct - although I had long forgotten that this was the case.

The function rerootingMethod uses the approach of Yang et al. (1995) to compute the marginal ancestral states by re-rooting the tree at all internal nodes. For instances in which some states at the tips are uncertain, it can also re-root at the tip to compute empirical Bayesian posterior probabilities for the leaves as well. The function is less relevant now that ace in the ape package also can compute the marginal ancestral states. (Although, as far as I know, ace can also not handle polytomies.) rerootingMethod stays somewhat relevant only by virtue of being able to compute posterior probabilities at tips, and for handling uncertainty at tip states (two sides of the same coin, I guess).

It was fairly straightforward to update rerootingMethod to handle polytomies, and the code is posted here. The way that this current version works is pretty simple. It just first takes the input tree, checks for polytomies using is.binary.tree in the ape package, resolves polytomies randomly with branches of zero length using multi2di, estimates ancestral states for all internal nodes (& tips, if tips=TRUE), and the uses the phytools function matchNodes to back-translate the reconstructed nodes in the resolved tree to the original, input tree. Note that although it is doing something here that ace does not do - the code internally uses (modified code from) ace.

Here - we can check it out by simulating a tree with some polytomies, generating trait data for tips & nodes, and then reconstructing ancestral states on the tree:

library(phytools)
dt<-rtree(n=26)
dt$tip.label<-LETTERS
## set some of the internal branches
ii<-which(dt$edge[,2]>Ntip(dt))
dt$edge.length[sample(ii,4)]<-0
mt<-di2multi(dt)
plotTree(mt)

plot of chunk unnamed-chunk-1

Next let's simulate a character up the tree:

Q<-matrix(c(-1,0.5,0.5,
    0.5,-1,0.5,0.5,0.5,-1),3,3,
    dimnames=list(letters[1:3],letters[1:3]))
st<-sim.history(mt,Q)
## Done simulation(s).
x<-st$states
y<-getStates(st,"nodes")

Now, we can reconstruct & plot ancestral states using ace on the bifurcating tree; and rerootingMethod on the bi- and on the multifurcating trees. If the methods are working properly then the reconstructions will be the same - although in the bifurcating node there will be additional nodes with states identical to other nodes from which they are separated by branches of zero length.

## first ace
fit1<-ace(x,mt,type="discrete",model="ER") ## doesn't work
## Error in ace(x, mt, type = "discrete", model = "ER"): "phy" is not rooted AND fully dichotomous.
fit2<-ace(x,dt,type="discrete",model="ER") ## doesn't work
## Error in ace(x, dt, type = "discrete", model = "ER"): some branches have length zero or negative
## set zero-length branches to be 1/1000000 total tree length
dst<-dt
dst$edge.length[dst$edge.length==0]<-max(nodeHeights(dt))*1e-6
fit3<-ace(x,dst,type="discrete",model="ER")
fit3
## 
##     Ancestral Character Estimation
## 
## Call: ace(x = x, phy = dst, type = "discrete", model = "ER")
## 
##     Log-likelihood: -25.3342 
## 
## Rate index matrix:
##   a b c
## a . 1 1
## b 1 . 1
## c 1 1 .
## 
## Parameter estimates:
##  rate index estimate std-err
##           1   0.3278  0.1042
## 
## Scaled likelihoods at the root (type '...$lik.anc' to get them for all nodes):
##          a          b          c 
## 0.82837257 0.09781827 0.07380916

Now with the new version of rerootingMethod:

packageVersion("phytools")
## [1] '0.4.57'
fit4<-rerootingMethod(mt,x,model="ER")
fit4
## $loglik
## [1] -25.33421
## 
## $Q
##            a          b          c
## a -0.6556595  0.3278298  0.3278298
## b  0.3278298 -0.6556595  0.3278298
## c  0.3278298  0.3278298 -0.6556595
## 
## $marginal.anc
##               a          b            c
## 27 0.8283833959 0.09781145 0.0738051507
## 28 0.2121485528 0.69489845 0.0929529991
## 29 0.0532939602 0.91028552 0.0364205221
## 30 0.0627113681 0.88952034 0.0477682947
## 31 0.0132238730 0.97569370 0.0110824277
## 32 0.3870898035 0.30541903 0.3074911711
## 33 0.4035347684 0.15548939 0.4409758369
## 34 0.5865138808 0.07266794 0.3408181834
## 35 0.3530969369 0.06523786 0.5816652004
## 36 0.7045263050 0.13922658 0.1562471186
## 37 0.1288634178 0.06087131 0.8102652730
## 38 0.3401006710 0.49952777 0.1603715570
## 39 0.4129576403 0.32707964 0.2599627226
## 40 0.1266883464 0.35550347 0.5178081798
## 41 0.0553700550 0.21371716 0.7309127832
## 42 0.8088376946 0.10680265 0.0843596595
## 43 0.8570510600 0.08945954 0.0534894017
## 44 0.6274100032 0.30199393 0.0705960682
## 45 0.0836944308 0.86315981 0.0531457619
## 46 0.0119373448 0.97893201 0.0091306462
## 47 0.0006664523 0.99874487 0.0005886784

If we plot both of these on our trees in turn, we should see that the marginal reconstructions (excepting the small deviation that was required to give our tree non-zero branch lengths throughout) should be equal:

## first ace
plotTree(dt,offset=0.5)
nodelabels(pie=fit3$lik.anc)
tiplabels(pie=to.matrix(x,seq=letters[1:3]),cex=0.5)

plot of chunk unnamed-chunk-5

## now phytools
plotTree(mt,offset=0.5)
nodelabels(pie=fit4$marginal.anc)
tiplabels(pie=to.matrix(x,seq=letters[1:3]),cex=0.5)

plot of chunk unnamed-chunk-5

Finally, for fun let's overlay the true, known states to see how close (or off) we were:

plotSimmap(st,colors=setNames(c("red","green","blue"),letters[1:3]),
    offset=0.5)
nodelabels(pie=fit4$marginal.anc)
tiplabels(pie=to.matrix(x,seq=letters[1:3]),cex=0.5)

plot of chunk unnamed-chunk-6

That's it.

3 comments:

  1. I am unable to run the rerootingMethod, despite it having the same format input of 'x':

    Error in `colnames<-`(`*tmp*`, value = c("a", "c")) :
    attempt to set 'colnames' on an object with less than two dimensions

    Any suggestions? Thanks

    ReplyDelete
    Replies
    1. Hi Alex. What is your object x? It should be a vector of type character (or a factor) with names corresponding to the species names in the tree.

      Delete
  2. Hi Liam,
    I’m working on adding evolution of a discrete character to a phylogeny. First I am attempting to model ER, SYM, and ARD using rerootingMethod. ER and ARD seem to work properly, with ARD being a better fit. SYM, however, produces the error “In log(comp[1:M + N]) : NaNs produced”. I suspect from your post here (http://blog.phytools.org/2016/05/more-on-plot-method-for-object-class.html) it has to do with parameters versus tips, but in that case, why does ARD seem to work? Furthermore, when I move onto using make.simmap to see the (code: SYMtrees <- make.simmap(tree,character,model="SYM",nsim=1000,q="mcmc"), the resulting sectors in the node piecharts are all equal, and the same process for ARD produces NaNs but with a sensible output. Does this suggest that the character and phylogeny will only support the simpler ER model? Is there something else I am missing? Thank you!
    -Bob

    ReplyDelete