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xavierdidelot / BactDating

Bayesian inference of ancestral dates on bacterial phylogenetic trees
https://xavierdidelot.github.io/BactDating
MIT License
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#Acquire the estimated time for each node and add time axis when plotting the result tree #55

Closed QianGuoPKU closed 2 years ago

QianGuoPKU commented 2 years ago

Hi,

Thanks for providing such excellent tool! My question is, how to acquire the estimated time for each node? As i understand, BactDating can output the CI intervals. But I also need the estimation in addition to the CI intervals. And, do you have some idea to add the time axis when plotting the res$tree?

I would appreciate if you could reply!

Best, Qian

xavierdidelot commented 2 years ago

The res$tree contains the point estimate of each node date. If you use plot(res) instead of plot(res$tree) the tree will be shown with the time axis. You can also use plot(res,'treeCI') to show the credible intervals.