optim.pml error

[Neutrino1234]

Hello!

When I'm trying to use optim.pml for certain datasets using the following code segment

dm_h <- dist.hamming(data)
starting_tree <- NJ(dm_h)
starting_tree <- root(starting_tree, outgroup = "outgroup",resolve.root = TRUE)
Lf <- pml(starting_tree, data)
Lf_JC <- optim.pml(Lf,optNni = TRUE, optEdge = TRUE, model = "JC")

I get the error message

Error in if (!any(betahat < 0)) { : missing value where TRUE/FALSE needed.

I've tried to reinstall R and phangorn but the same problem appears again.

R version 3.5.2
phangorn 2.4.0
ape 5.3

[KlausVigo]

Hi @Neutrino1234 ,
a few comments, optim.pml usually ignores the position of the root. I recently updated phangorn on CRAN (the windows, OS X binaries should be available soon), can you please check if the problem is still persists with the new version (2.5.3). If you still get this error can you send me your data?
Regards,
Klaus

[Neutrino1234]

Hello!

Sorry for the late reply @KlausVigo. I still have the same problem with the updated version.

traceback() gives:
4: nnls.tree(dm, x, rooted, trace = trace, ...)
3: nnls.phylo(tree, dist.ml(data))
2: optim.pml(Lf, model = "JC") at #6
1: ml_tree(EM_phyDat, root)

Best Regards