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xavierdidelot / BactDating

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

Consider STAN as an MCMC engine #2

Closed andersgs closed 5 years ago

andersgs commented 6 years ago

Hello.

I have not tried BactDating yet, but I am keen.

From a quick glance at the code, and from my reading of the paper, I am wondering why you did not consider using STAN to run the MCMC?

It is fast, there is a considerable amount of development that has gone into it, there are associated libraries to help with model selection and assessment (e.g., loo), useful libraries for visualisation (e.g., bayesplot and ShinyStan), and they provide tools to help package precompiled binaries of the models with R (package rstantools).

More information here: http://mc-stan.org/users/interfaces/rstan and here http://mc-stan.org/users/interfaces/

Best. A.

tseemann commented 5 years ago

@xavierdidelot any reason for closing this without a response?

xavierdidelot commented 5 years ago

I have plans for extensions of BactDating and don't want to be tied down to a specific MCMC engine.

tseemann commented 5 years ago

Thank you.