Re: [R-sig-phylo] ape chronos function returning pLL of -1E100

[John S Denton]

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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