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I want to determine birth and death rate of a given phylogenetic tree using birthdeath of the ape package, and I get the following error:

birthdeath(phy)

Error in solve.default(out$hessian) : 
  Lapack routine dgesv: system is exactly singular: U[1,1] = 0
In addition: Warning messages:
1: In nlm(function(p) dev(p[1], p[2]), c(0.1, 0.2), hessian = TRUE) :
  NA/Inf replaced by maximum positive value
2. etc...

The tree phy is ultrametric and appears to be fine, checkValidPhylo is true (in particular all edges have positive lengths). It plots just fine and looks normal...

I can upload the tree if need be.

C_Z_
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Robert
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  • Posting the tree would probably be necessary to fix this problem – C_Z_ Feb 12 '16 at 16:26
  • You now find the full three in the edit. – Robert Feb 12 '16 at 16:40
  • The problem seems to be the length of the branches (scaling the branch lengths back by a factor of 1000 causes the function to run without error). I would recommend posting to the r-sig phylo mailing group about what to do. – C_Z_ Feb 12 '16 at 17:13
  • interesting.... i'll do that! thank you very much – Robert Feb 12 '16 at 17:22

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