Hi all,
I am new to this forum and also new to phylogenetic analysis.
I am trying to study phylogenetic signal on traits from plant
communities following an environmental gradient.
Part of my traits are continuous and for them I have used Blomberg's K.
However for the multistate discrete traits I was not able yet to run an
adequate methodology.
When exploring data, I have tried fitDiscrete {geiger} to fit a
Jukes-Cantor model to each trait (i.e. first trait :DEN1) but I always
obtain the following error:
Finding the maximum likelihood solution
[0 50 100]
[....................]
Error in fitDiscrete(treeDNNnexus, DEN1) :
ERROR: No solution found. Does your tree contain zero-length tip
branches?
Although I don't have zero-length tip branches in my phylo tree, there
are 3 pairs of species which display very small length tip branches.
Is there any alternative to run this function keeping or modifying the
characteristics of my tree?
Or, if this function couldn't be applied in my case, Does anybody
recommend an alternative methodology that could be implemented in R or
Matlab?
Thank you in advance for your help
Patricia
-------------------------------
Patricia Rodríguez González
Post Doc at Centro de Estudos Florestais
Instituto Superior de Agronomia
Universidade Técnica de Lisboa
Tapada da Ajuda
1349-017 Lisboa
PORTUGAL
http://www.isa.utl.pt/cef/ForEcoGen/
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