I have looked all over and haven’t found any information on the topic. I am trying to extract the number and timing of introductions from one discrete state to another from the time-resolved tree output from treetime. Essentially getting the data would allow me to recreate and extract the information that is present in the exploded tree on auspice.
You’ve found the right place to ask! Apologies for the delay.
It is possible to programatically analyze the auspice.json, e.g. in Python. It sounds like all the information you’d need is in there: timing of internal nodes, inferred discrete states etc.
I’m not sure why you mention ‘exploded’ here “getting the data would allow me to recreate and extract the information that is present in the exploded tree on auspice.” I don’t see why you’d need to explode the tree to get what you want.
When you’re saying “from the time-resolved tree output from treetime” it appears that you’re doing the timetree inference using a direct call to
treetime as opposed to via
augur refine. Is that correct? In that case, I’d recommend you run things through
augur refine, get the auspice json from
augur export and then analyse the resulting
auspice.json in a custom Python or R script or whatever you’re comfortable with.
Does that make sense?