Hi,
I’m interested in using the OUCH package to estimate BM and OU parameters for a
specific trait among many different trees.
My goal is to determined which model is the most suitable for each tree,
applying likelihood ratio test.
As I’m a new user in R when it comes to phylogenetic analysis, I started by
running the documentation example (Hansen, documentation page 11) and was
surprised to see that the loglikelihood was a positive number
BM:
$call
brown(data = otd[c("tarsusL", "beakD")], tree = ot)
$sigma.squared
[,1] [,2]
[1,] 0.02878091 0.08897504
[2,] 0.08897504 0.43711838
$theta
$theta$tarsusL
[1] 3.020419
$theta$beakD
[1] 1.826695
$loglik
[1] 9.90115
As this number is crucial for further analysis - Is this a transformation of
the resulting log likelihood? (e.g. -2 * log(L) as described in the paper) or
am I missing something here..?
In addition I have another issue, I have a tree constructed of ~400 viral
genomes and their corresponding trait values. When I’m running the
documentation script with my own data (in the same format)
I get the following error:
Error in solve.default(v, e) :
system is computationally singular: reciprocal condition number = 1.59061e-17
I guess it says that my variance covariance matrix is not inversable, hence I
manually tried to adjust the retol parameter in the Hansen function in order to
make it work (however I’ll need to second guess my results?), but I still get
the same error.
Code example:
h1 <- hansen(
+ tree=ot,
+ data=otd[c("k5")],
+ regimes=otd["regimes"],
+ fit=TRUE,
+ sqrt.alpha=1,
+ sigma=1,
+ maxit=500000,
+ reltol=1e-20,
+ method="Nelder-Mead"
+ )
I’ll be thankful for any advice or answer,
Danielle
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