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aezarebski / timtam2

This repository is an implementation of the TimTam likelihood as a BEAST2 package.
https://aezarebski.github.io/timtam/
MIT License
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Tutorial 3: prevalence curve #42

Closed xieruopeng closed 2 years ago

xieruopeng commented 2 years ago

Dear Alex,

In tutorial 3, the log file just shows prevalence at the time of the last observation. Is it possible to show prevalence curve over time like birthRate?

Many thanks in advance!

Cheers, Ruopeng

aezarebski commented 2 years ago

Hi Ruopeng,

The current method does not have a way to estimate the prevalence through time. There are a couple of approaches that could work, but they all require non-trivial changes to the package.

If you are in a rush for any estimate, you could generate a rough estimate of the prevalence at time T by only using the data from before then, and then do this for a couple of different times.

I hope the tutorials have been helpful, please let me know if you have any feedback/suggestions.

Cheers, Alex

xieruopeng commented 2 years ago

Thanks Alex!

aezarebski commented 2 years ago

Hey @xieruopeng

Just wanted to let you know that historical prevalence estimation is now implemented on the dev branch so will hopefully appear in v.0.3.0. It appears to work on a simple example (included in examples/ex4.xml) but BEAUti support is pretty rubbish and there isn't any proper documentation on it yet, so it might be a while.

Cheers, Alex

aezarebski commented 2 years ago

There is now a pre-release with this implemented so I'll close the issue :)