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KlausVigo / phangorn

Phylogenetic analysis in R
http://klausvigo.github.io/phangorn/
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optim.pml error missing value where TRUE/FALSE neede #95

Closed Alonso-Garcia closed 4 years ago

Alonso-Garcia commented 4 years ago

Hello, I'm using phangorn (v. 2.5.5) in R studio (64-bit, R-3.6.3) to analysis my 16S data. I follow the workflow for microbiome by Callahan et al. (2017).

I have some problems to construct the phylogenetic tree with optim.pml. Here you have the code: fitGTR <- update(fit, k=4, inv=0.2) fitGTR <- optim.pml(fitGTR, model="GTR", optInv=TRUE, optGamma=TRUE, rearrangement = "stochastic", control = pml.control(trace = 0))

and this is the error: Error in if (((ll1 - ll)/ll < control$eps) && rounds > 2) opti <- FALSE : missing value where TRUE/FALSE needed

Could you suggest me something to solve it? Thank you

KlausVigo commented 4 years ago

Hello @Alonso-Garcia , that seems a bug. Is it possible to send me the alignment, e.g. using saveRDS(phangAlign, file="phangAlign.rds") , so that I can reproduce the error and hopefully fix it. Regards, Klaus

Alonso-Garcia commented 4 years ago

Hello @KlausVigo , Thank you for your quick response. Please, find attache the file (compressed into zip). Regards :) phang.aling.zip

Alonso-Garcia commented 4 years ago

Thank you very much. It works!

wanjauk commented 4 years ago

Hello @KlausVigo , The phangorn package on CRAN seems to be on version 2.5.5 and has the bug described here. You may need to bump up its version with the current version on GitHub. Thanks.