Hi John,
It looks like that the constraints on the dates with the 4 calibrations
are such that the penalized likelihood cannot be calculated. There are
several occasions when a value of -1e100 is returned (non finite value,
negative branch lenghts, ...) so it's hard to see what is the problem
here. Maybe it's better we discuss about this off-list.
Best,
Emmanuel
Le 13/12/2018 à 04:05, John S Denton a écrit :
As an update to my question--when I try to calibrate the tree itself
using the default single root calibration and default 1/1 min/max ages,
the function appears to run fine. When I add in my calibration table,
the function exits with the -Inf LL.
The tree is rooted. There are no duplicated nodes with conflicting
ages, and R does not give errors about the formatting of the calibration
table.
~John
________________________________
From: R-sig-phylo <r-sig-phylo-boun...@r-project.org> on behalf of John S Denton
<jden...@amnh.org>
Sent: Wednesday, December 12, 2018 1:20:20 PM
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] ape chronos function returning pLL of -1E100
I'm trying to use chronos (ape version 5.2) to scale a tree of ~800 tips, with
branch lengths derived from a RAxML analysis. I'm using 4 outgroup
calibrations. When I run the analysis using
t.og <- chronos(tree, lambda = 1, model = "relaxed", quiet = FALSE,
calibration = dd.out)
I get the following returned, in almost 5 seconds:
Setting initial dates...
Fitting in progress... get a first set of estimates
Penalised log-lik = -1e+100
Optimising rates... dates... -1e+100
Done.
a look at attributes (attr(t.og, "message")) gives a "relative convergence
(4)." The pLL, however, is -Inf. I have tried setting chronos.control to different values,
with no success. It looks like it may be an issue with the optimization function inside chronos.
Are there additional constraints/code I can apply to make it optimize without
(apparently) simply running to the boundary?
Thanks,
~John
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