Sounds like a problem with your initial tree. Are you sure it has valid
branch lengths?
Simon.
On Fri, 2009-03-13 at 17:33 +0100, Sebastien Lavergne wrote:
> Dear all,
>
> I am getting a puzzling error message, trying to compute Blomberg's K on
> tree with about 1200 species, and this problem disappears with a simple
> branch length transformation.
> I attach the two R objects (just load them into a R workspace).
>
> Here is the code:
>
> > load('mytree')
> > load('mytrait')
> > Kcalc(mytrait, mytree)
> Erreur dans Initialize.corSymm(X[[1L]], ...) :
> Initial values for corSymm must be between -1 and 1
>
>
> And it is working well when all branch lengths are set to 1:
>
> > mynewtree <- compute.brlen(mytree,1)
> > Kcalc(mytrait, mynewtree)
> [,1]
> [1,] 0.1138656
>
> What is wrong (singular) with this tree that Initialize.corSymm (or the
> associated gls call) doe snot handle ???!!!
>
> Any help or insight appreciated
> Cheers
> SebL
>
>
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--
Simon Blomberg, BSc (Hons), PhD, MAppStat.
Lecturer and Consultant Statistician
School of Biological Sciences
The University of Queensland
St. Lucia Queensland 4072
Australia
Room 320 Goddard Building (8)
T: +61 7 3365 2506
http://www.uq.edu.au/~uqsblomb
email: S.Blomberg1_at_uq.edu.au
Policies:
1. I will NOT analyse your data for you.
2. Your deadline is your problem.
The combination of some data and an aching desire for
an answer does not ensure that a reasonable answer can
be extracted from a given body of data. - John Tukey.
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