Hello All,
Great discussion, I'm learning a lot about the inner workings of some of these
packages.
So for starters, all my taxa are fossil taxa, no extant, and in terms of branch
lengths the shortest branches seem to be internal edges, which can be as short
as 0.15 Ma (whole tree spans over 1
I think it's convenient to think about how fitContinuous actually works here,
or at least to think about the impact of the EB parameter on a transformed
tree's branch lengths. Using simulations, try this:
require(TreeSim);
require(geiger);
phy <- sim.bd.taxa(50, 1, 0.1, 0.05, 1)[[1]][[1]]; ## si
Yeah, my simulations with paleotree agrees with Frank's, except no values
below a=0 will work at all without using addTermBranchLength; apparently
the terminal ZLBs are having some effect on it. When I use
addTermBranchLength, then I can get down to -0.4, at which point I get a
slightly new warning
Just as a followup to my example (which contains numerous extinct taxa).
Using these values for alpha fails:
fitContinuous(tree,data,model="EB",bounds=list(alpha=c(-1,0)))
Fitting EB model:
Error in solve.default(phyvcv) :
Lapack routine dgesv: system is exactly singular
Above the lower boun
Good point. They should all work with these data though.
This mobile message may have
typos. Sorry...
On Nov 4, 2012, at 3:10 PM, wrote:
> Just to add one point, if you do run this:
>
> fitContinuous(trueTree,trait,model="EB",bounds=list(alpha=c(0,1)))
>
> you're actually not fitting an e
Just to add one point, if you do run this:
fitContinuous(trueTree,trait,model="EB",bounds=list(alpha=c(0,1)))
you're actually not fitting an early burst at all - bounding the
optimization of alpha with 0 at the lower end restricts you to an
accelerating, or late burst model of evolution. To
Yeah, I was concerned it might have been related to a zero-branch-length
problem, but some simulation shows that only Graham's fix will let
fitContinuous run with a simulated paleo-tree.
-Dave
library(paleotree)
library(geiger)
taxa<-simFossilTaxa_SRCond(avgtaxa=30,p=0.1,q=0.1,r=0.1)
rangesCont<-
Just to confirm that Graham's fix works.
Using the following libraries (and their dependencies) I conducted the
simulations:
library(TreeSim)
library(phytools)
sim.bd.taxa(30,1,lambda=0.1,mu=0.05)[[1]][[1]]->tree
fastBM(tree)->data
fitContinuous(tree,data,model="EB")
Fitting EB model:
Error in
Nicolas,
Not certain how you are time-scaling your tree, but I often get warnings of
singularity from various comparative analysis functions due to the presence
of very short terminal branches. I have found that such warnings of
singularity when dealing with paleo-trees can often be avoided by addi
Oops...sorry about that Nicolas. I just ran a quick sim and Graham is right on
the money...ultrametricity doesn't matter and setting the lower bound on the
exp change param is the way to go. I must be getting senile...
This mobile message may have
typos. Sorry...
On Nov 4, 2012, at 1:07 PM
Hi Nic,
It's not a problem with the branch lengths, at least not the non-ultrametricity
of the tree. It's probably that the lower bound on the exponential change
parameter is too low, resulting in a singular phylogenetic variance covariance
matrix. Try changing the lower bound as follows:
eb.f
Dear R Phylo List,
I'm trying to test an Early Burst model of evolution against a tree using the
'fitContinuous' function in 'geiger'. However, I get the following error
message, and am unsure as to what I can do to fix this:
> fitContinuous(tree,trait,model="EB")
Fitting EB model:
Error in s
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