Dear Emmanuel,
Thank you very much for the explanation and example! This works just as I
expected. When I divide the divergence rate by 2 (i.e., .0221 / 2 =
0.01105) and use it as "mu", like you showed, I get a tree that has node
dates pretty close to what I get when using BEAST with a strict
What about this (after reading 'tree' using your code):
n <- Ntip(tree)
dates <- estimate.dates(tree, rep(0, n), .0221)
plot(compute.brtime(tree, -dates[-(1:n)]))
axisPhylo()
?
E.
- Le 6 Mar 24, à 2:50, Vincenzo Ellis vael...@udel.edu a écrit :
> Dear Klaus,
>
> Thank you for your
Hi Vincenzo,
"node.dating" is a help topic that points to two functions which seem to do
what you are looking for. As a simple example:
R> n <- 3
R> tr <- rcoal(n)
R> estimate.dates(tr, rep(0, n), .01)
[1] 0.0 0.0 0.0 -144.32183 -43.67435
R> estimate.dates(tr, rep(0, n), .1)
Dear Klaus,
Thank you for your response. I was wondering if you could expand on how to
do this with phangorn::pml_bb(). Here's a small tree I made in Raxml with
the cytochrome b gene of a few species of birds:
library(ape)
tree <- read.tree(text =
Dear Vincenzo,
For ML estimates the edge length are the expected number of substitutions per
site, which depends on the product of rate and time. So you need either a rate
estimate or calibration points to estimate the time. If you divide the edge
length by the rate the edges should be
Dear Liam,
Thank you for your answer. Yes, I have a hypothesized average clock rate
and no explicit calibration points.
If I use ape::chronos() with default values it gives me a depth of 1 at the
root. So I suppose to rescale the branch lengths I just need to multiply
all of the branch lengths
Dear Vincenzo.
If I understand your problem problem, you do not have any explicit
calibration points -- but you have a hypothesized average clock rate?
If so, then you can obtain an ultrametric tree from/ape::chronos/ for
any value of the smoothing parameter (/lambda/) and then simply re-scale
Dear Emmanuel,
Thank you very much for your response. I cannot see how to provide the
substitution rate to the phangorn::pml_bb() function, but I was looking at
the ape::node.dating() function and it appears that I could provide the
substitution rate to the "mu" argument and then set the
Hi Vincenzo,
There's no direct way to do this with ape::chronos(). You may have a look at
the function phangorn::pml_bb() but I'm not sure it can estimate the dates if
the rate is provided in a model object given as main argument(?)
That said, I expect that estimating so many dates to be very
