Dear Miguel.
One way to do something like would be by using the phytools function
treeSlice.
treeSlice cuts the tree at a particular point. Depending on the argument
orientation, it returns either the rootward tree or the descendant
subtrees. So, say you want to simulate under Brownian motion from time 0
to time t, and then just draw random values from a distribution centered
on the ancestral value of each subtree descended from time t, you would
just need to do two sets of simulations. First on the rootward tree, and
then on each descendant subtree.
This could look something like the following:
## get hidden lambdaTree function (this is just to simulate random
## values for the subtrees from time t
lt<-phytools:::lambdaTree
## set t (here I'm imagining the tree has a total length of 100 and
## I want to slice it at time = 70 units above the root
t<-70
## slice the tree rootward of time = t -- this generates an object
## of class "multiPhylo"
rootward<-treeSlice(tree,orientation="rootwards",slice=t)
## now slice the tree tipward of time t -- this generates an object
## of class "multiPhylo" with a length equal to the number of tips
## in rootward
tipward<-treeSlice(tree,orientation="tipwards",trivial=TRUE,
slice=t)
## convert each subtree in tipward to a "phylo" object with an
## unbranching (singleton) root node. This is for simulation.
tipward<-lapply(tipward,rootedge.to.singleton)
## simulate the ancestral states for each subtree in tipward under
## pure Brownian motion
aa<-fastBM(rootward)
## create a vector of values
xx<-vector()
## simulate on each subtree to populate it. a is the ancestral state
## for each simulation
for(i in 1:length(tipward))
xx<-c(xx,fastBM(lt(tipward[[i]],0),a=aa[i]))
All the best, Liam
Liam J. Revell
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católica de la Ssma Concepción [Adj. Res.]
Web & phytools:
http://faculty.umb.edu/liam.revell/, http://www.phytools.org,
http://blog.phytools.org
Academic Director UMass Boston Chile Abroad:
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On 11/4/2021 1:29 PM, Miguel Verdú del Campo wrote:
EXTERNAL SENDER
Dear list
Is there any way to simulate the evolution of a trait with a given significant
signal (say K=1) from the tree root to time x and no signal (K=0) from time X
to the present?
Thanks
Miguel Verdú
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