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xavierdidelot / BactDating

Bayesian inference of ancestral dates on bacterial phylogenetic trees
https://xavierdidelot.github.io/BactDating
MIT License
80 stars 15 forks source link

Can BactDating run on R3.6.1? #34

Closed StephanieWLo closed 4 years ago

StephanieWLo commented 4 years ago

I have tried to run BactDating using R3.6.1 and got the error message. Not sure if that's due to R version. Please kindly advise. Thank you.

Error in CI[i, 1] <- s[ceiling(length(s) * 0.025)] : replacement has length zero Calls: bactdate Execution halted

xavierdidelot commented 4 years ago

Hi Stephanie,

I'm pretty sure that this error is not related to your R version. If you are still having this problem, could you please reopen this issue and paste your exact command line.

Best wishes, Xavier

StephanieWLo commented 4 years ago

Hi Xavier,

Sorry for my silly question and thank you for your reply. The error message is probably because mcmc chain length was set smaller than ceilling(10000). The error did not pop up again once set it >10000. Thank you.

Best wishes,

Steph

xavierdidelot commented 4 years ago

I think you should be able to run even for a small number of iterations (eg nbIts=1), but anyway I'm glad this problem is solved for you.