[R-sig-phylo] compar.ou in ape package - warnings and error messages on bird.orders example dataset

Anna Kostikova anna.kostikova at gmail.com
Tue Mar 2 12:07:43 CET 2010


Dear list,

When running compar.ou example from APE package documentation (v.
23-11-09), I've got couple of error messages.
What might be the reason for them:

> compar.ou(rnorm(23), bird.orders, alpha = 0.1)
$deviance
[1] 57.60627

$para
          estimate    stderr
sigma2  0.71937096 0.1500408
theta1 -0.04114436 0.1365702

$call
compar.ou(x = rnorm(23), phy = bird.orders, alpha = 0.1)

attr(,"class")
[1] "compar.ou"
Warning messages:
1: In log(2 * pi * p[2]) : NaNs produced
2: In nlm(function(p) dev(c(alpha, p)), p = c(1, rep(mean(x), ncol(Wstart))),  :
  NA/Inf replaced by maximum positive value

> y <- c(rnorm(5, 0), rnorm(18, 5))
> compar.ou(y, bird.orders, node = -2, alpha = .1)
Error in dimnames(x) <- dn :
  length of 'dimnames' [2] not equal to array extent

Thanks a lot for any clue,

Best regards,
Anna



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