How do you fix a topology as a prior?

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Dylan Cohen

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Sep 26, 2020, 7:33:20 PM9/26/20
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I was able to get this to work a few weeks ago by adding a treefile to the command line and unbracketing the configure file topology/fixed parameters, but now it will not run. 

Should there be more in the configure file? 

begin RUN;

numRuns  2  

numGen 150000

numCoupledChains  2

burninProportion      0.25

end ;


begin PRIORS;

 TOPOLOGY: fixed

[   topoPr fixed()]

[   topoPr uniform(0,0) ]


end;

Andre Aberer

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Sep 27, 2020, 3:07:39 AM9/27/20
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Hi Dylan,

the line
> TOPOLOGY: fixed
does not work. This is just an explanatory comment in the config
file. Remove it or add the brackets to it.

Instead, activate this line by removing the brackets.
> [ topoPr fixed()]

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Best regards,
Andre

Dylan Cohen

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Sep 27, 2020, 1:05:24 PM9/27/20
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Hi Andre,

Thanks for the comment, it is working now.

Best,
Dylan

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