Monday, March 3, 2014

New version of rateshift; new version of phytools submitted to CRAN

Some comments on earlier version of the function rateshift for identifying one or multiple shifts in the Brownian rate of evolution on the tree suggested that there were some difficulties in converging to the ML solution. Indeed, this is not too surprising. I have now posted a new version of rateshift that has more robust optimization. Here's a quick demo:

> require(phytools)
Loading required package: phytools
Loading required package: ape
Loading required package: maps
Loading required package: rgl
> packageVersion("phytools")
[1] ‘0.3.93’
> ## simulate tree & data
> tree<-pbtree(n=100,scale=1)
> tree<-make.era.map(tree,c(0,.5))
> x<-sim.rates(tree,c(10,1),internal=TRUE)
names absent from sig2: assuming same order as $mapped.edge
> ## here's a visual of our simulation
> phenogram(tree,x,ftype="off")
> ## peel off ancestral states
> x<-x[tree$tip.label]
> ## fit one-rate model:
> fit1<-rateshift(tree,x,nrates=1)
Optimization progress:
|..........|
Done.

> ## fit two-rate model:
> fit2<-rateshift(tree,x,nrates=2)
Optimization progress:
|..........|
Done.

> fit1
ML 1-rate model:
        s^2(1)  se(1)   k       logL  
value   1.5419  0.2179  2       -89.379
This is a one-rate model.

R thinks it has found the ML solution.

> fit2
ML 2-rate model:
        s^2(1)  se(1)   s^2(2)  se(2)   k       logL  
value   7.3925  4.0858  1.2412  0.1903  4       -85.911

Shift point(s) between regimes (height above root):
        1|2     se(1|2)
value   0.5274  0.01

R thinks it has found the ML solution.

In addition, I was recently informed that the package extrafonts has been removed from CRAN. phytools depends on extrafonts for the plotting functions xkcdTree and fancyTree. To address this dependency issue I have now removed xkcdTree from phytools (source code is still available from the phytools page) and modified fancyTree so that it no longer uses extrafonts. This new version has now been submitted to CRAN. It is already available on phytools.org.

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