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birth-death sampling model seems to not work smoothly #637

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi Walter,

as indicated in the previous email, the birth-death sampling model seems to not 
work smoothly in Beast 1, several people reported a problem to me.
A issue I realized when looking into the code carefully right now:

if (!hasFinalSample && n != 1) {
            throw new RuntimeException(
                    "For sampling-through-time model there must be exactly one tip at time zero.");
        }

The equations are all fine for n>1 and hasFinalSample=FALSE.
We should only allow hasFinalSample=FALSE and fix p=0 (and allow n=1 or n>1, it 
doesn't matter).
hasFinalSample=TRUE might be useful for phylogenies with fossils, but we didn't 
test it properly.

Did we ever compare Denise's birth-death skyline model in Beast 2 (for 0 rate 
shifts) to the birth-death model in beast 1? they *should* be the same...

Cheers Tanja

Original issue reported on code.google.com by dong.w.xie@gmail.com on 25 Jun 2012 at 2:12

GoogleCodeExporter commented 9 years ago 
Hi Walter,
there seems to be some problem in Beast 1, see below?
Could you doublecheck and get back?
Thanks a lot, Tanja

Begin forwarded message:

From: Emmanuelle MULLER 
<emmanuelle.muller@cirad.fr<mailto:emmanuelle.muller@cirad.fr>>
Date: June 18, 2012 2:15:01 PM GMT+02:00
To: <tanja.stadler@env.ethz.ch<mailto:tanja.stadler@env.ethz.ch>>
Subject: a question about your model in BEAST

Dear Tanja,
I was at your seminar at Montpellier University last friday and was very 
interested by the models you have implemented in BEAST.
I am working on epidemiological data concerning Cacao swollen shoot virus.
Last friday, I have tested your model with my sequences (the joined file 
containig sequences from 4 genetic groups collected from 1993 to 2010) but it 
doesn't work.
I used  your "epidemiological birth and death" model implemented in BEAST and I 
obtain a message I also joined to you  because it is  not enough clear for me.
Could you help me?
Thank you in advance,
Emmanuelle Muller

Sequence data is in email.

Original comment by dong.w.xie@gmail.com on 25 Jun 2012 at 2:14

Attachments:

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 1 Aug 2012 at 4:16

GoogleCodeExporter commented 9 years ago 
change to:

        if (!hasFinalSample && n < 1) {
            throw new RuntimeException(
                    "For sampling-through-time model there must be at least one tip at time zero.");
        }

Original comment by dong.w.xie@gmail.com on 10 Aug 2012 at 12:54