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richelbilderbeek / razzo

Research project by Giovanni Laudanno and Richel J.C. Bilderbeek
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Decide: do run with Yule generative and twin tree for zero extinction rate? #316

Closed richelbilderbeek closed 4 years ago

richelbilderbeek commented 5 years ago

I quote from razzo_article:

For the MBD model without extinction, [...] we could have picked the Yule tree prior [...]

I wonder, shouldn't we pick the Yule tree prior as a generative tree prior and/or as the twin tree?

richelbilderbeek commented 4 years ago

Sent email to @Giappo:

razzo approve/suggest: use Yule as the generative tree prior for settings with zero extinction rate

9 January 2020 07:43 3 KB From: Richel Bilderbeek To: Giovanni Laudanno

[...]

I need your approval/suggestion of using the Yule tree model as a prior in the razzo settings with zero extinction rate.

Currently, in razzo, we always use a BD tree model as the generative tree prior. This is then compared with some candidate models, some of which with a Yule tree prior.

I'd say, this is correct for non-zero extinction rate, but incorrect for an extinction rate of zero. For settings without extinction, I suggest to use a Yule tree model as a generative prior and use a BD tree model in the candidate models.

So, do you approve?

    1. Yes, I approve
    1. No, I need more information/options: we'll discuss this on Friday

[...]

Giappo commented 4 years ago

Keep it as it is :+1: