Hi Laura.
There was a bug in make.simmap for the "ARD" model in earlier versions.
Can you check to make sure that you have the most recent version of
phytools? If you do, please let me know & send the tree & data that
result in this error.
The latest CRAN version of phytools is 0.4-45. You can check your
current package version using:
packageVersion("phytools")
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/10/2015 12:57 PM, Laura Alencar wrote:
Hi,
I’m using the function “make.simmap” from Phytools to reconstruct ancestral
states in 10 trees with 248 tips obtained from a BEAST analysis. I believe
rates might be different between states (four states) and I think this
would probably be the best way to run it:
simmap.trees.bs <- make.simmap(trees.bs, x = hab.bs, nsim = 1, "ARD", Q =
"empirical", pi = "estimated")
However after a while it returns me an error:
Error in rmultinom(1, 1, y/sum(y)) : non-positive probability
Do you have any suggestions of why is this happening?.
Any help is greatly appreciated.
Laura Alencar.
R output:
simmap.trees.bs <- make.simmap(trees.bs, x = hab.bs, nsim = 1, "ARD", Q =
"empirical", pi = "estimated")
Warning: some elements of Q not numerically distinct from 0; setting to
1e-08
make.simmap is sampling character histories conditioned on the transition
matrix
Q =
1 2 3
4
1 -0.0968244043 0.06758894 0.029235453 0.0000000100
2 0.0225745893 -0.02675244 0.004024555 0.0001532927
3 0.0212390324 0.01319612 -0.053640721 0.0192055634
4 0.0003248535 0.00000001 0.006457870 -0.0067827337
(estimated using likelihood);
and (mean) root node prior probabilities
pi =
1 2 3 4
0.1141217 0.3555619 0.1363109 0.3940054
Done.
Warning: some elements of Q not numerically distinct from 0; setting to
1e-08
make.simmap is sampling character histories conditioned on the transition
matrix
Q =
1 2 3 4
1 -0.08346002 0.0724513259 0.01100869 0.000000010
2 0.01457896 -0.0317484605 0.00000001 0.017169490
3 0.01022154 0.0066068752 -0.02122808 0.004399662
4 0.01546898 0.0001664635 0.01762501 -0.033260454
(estimated using likelihood);
and (mean) root node prior probabilities
pi =
1 2 3 4
0.1391800 0.3730572 0.2607005 0.2270623
*Error in rmultinom(1, 1, y/sum(y)) : non-positive probability*
Laura Rodrigues Vieira de Alencar
PhD student
Department of Ecology
University of São Paulo
Phone 55-11-96190222
Website: alencarlaura.weebly.com
Lattes: *http://lattes.cnpq.br/3112833291166033
<http://lattes.cnpq.br/3112833291166033>*
Lab Meme: *http://ecologia.ib.usp.br/labmeme/Site/Inicio.html*
<http://ecologia.ib.usp.br/labmeme/Site/Inicio.html>
Labvert: *http://eco.ib.usp.br/labvert/* <http://eco.ib.usp.br/labvert/>
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