Hello Tristan,
Does the code below work for your purpose? I don't know of a function
off the top of my head that does this in a current package on CRAN
(and although I might have missed such, I try to keep myself aware of
time-scaling functions in R, given my interests). However, its not too
difficult of an issue to come up with a solution for.
Cheers,
-Dave
PS: I appear to have done this with 16 minutes of getting your email...
###################################################################
library(ape)
nodeDates2branchLengths<-function(nodeDates, tree, allTipsModern){
if(!allTipsModern){
stop("nodeDates2branchLengths doesn't handle non-ultrametric
trees or trees where not all tips are at the modern day... yet")}
if(length(nodeDates)!=Nnode(tree)){
stop("nodeDates must be same length as number of nodes on input tree")}
if(!is.null(tree$edge.lengths)){
message("Warning: input tree has $edge.lengths present, these
will be replaced")}
#add zero ages for tips
allAges<-c(rep(0,Ntip(tree)),nodeDates)
# get mother node age for each edge
momAges<-allAges[tree$edge[,1]]
# get node ages for child nodes of each edge
childAges<-allAges[tree$edge[,2]]
#edge lengths = mom - child
edgeLengths<-momAges-childAges
tree$edge.length<-edgeLengths
return(tree)
}
chrono<-rcoal(10)
tr <- chrono
tr$edge.length <- NULL
bt <- branching.times(chrono)
chrono2 <- nodeDates2branchLengths(bt, tr, allTipsModern=TRUE)
layout(1:2)
plot(chrono);axisPhylo()
plot(chrono);axisPhylo()
On Wed, Oct 28, 2015 at 8:31 AM, Tristan Lefebure
<tristan.lefeb...@gmail.com> wrote:
> Greetings all,
>
> Does anyone know a way to transform branching times into branch length of a
> chronogram. Like the inverse function of ape::branching.time() ?
>
> say you have a chronogram named chrono:
>
> tr <- chrono
> tr$edge.length <- NULL
> bt <- branching.times(chrono)
> chrono2 <- magical.function.here(bt, tr)
>
> here I want :
>
> all(chrono2$edge.length == chrono$edge.length)
>
> This would be helpful in situations such as parsing the mcmctree output
> (mcmc.txt) that are made of sampled branching times by the MCMC (a big
> table with row=iteration and col=node age) and then, say, run the same
> diversification analysis on the MCMC trees to get some credibility
> intervals on the diversification parameters.
>
> Thanks !
>
> --
> Tristan
>
> [[alternative HTML version deleted]]
>
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--
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701
http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html
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