Hi everybody,
I am now trying to explain the principles of phylogenetics to the students
using R and went into a very simple problem that I cannot solve. Probably a
very simple and basic thing, sorry for a stupid questions:
When checking the details of models selected for my data by modelTest() in
phangorn, the rate matrix always includes number around 1 or even mich
higher (for example this is the matrix for Laurasiatherian data with
GTR+I+G model:
Rate matrix:
a c g t
a 0.000000 3.0009884 11.8735854 2.608831
c 3.000988 0.0000000 0.5162325 21.771813
g 11.873585 0.5162325 0.0000000 1.000000
t 2.608831 21.7718125 1.0000000 0.000000
For some simple models it gives just 0 or 1 as for example this for JC:
Rate matrix:
a c g t
a 0 1 1 1
c 1 0 1 1
g 1 1 0 1
t 1 1 1 0
I would normally expect the rate matric to have values lower than 1, and to
sum up to 0. Then it would make sense to use it also for calculating the
probability matrix using e^(Q*t). I wanted to illustrate the meaning of the
rate matrix estimated for real data to the students in this way, which is
why I realized that the output by phangorn is different and I fail to find
out why.
Thanks for any hint!
Martin
--
*Martin Fikáček (費卡契) MSc. PhD.*
*Department of Biological Sciences*
*National Sun Yat-sen University*
*No. 70, Lienhai Rd., Kaohsiung 80424, Taiwan*
*E-mail: *mfika...@gmail.com, mfika...@mail.nsysu.edu.tw
*Phone: *(+886) 75252000 # 3622
*Website: *www.cercyon.eu
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
