... | @@ -4,7 +4,7 @@ Created by Alexander Zarebski |
... | @@ -4,7 +4,7 @@ Created by Alexander Zarebski |
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Edited by [[https://github.com/BernardoGG][Bernardo Gutierrez]] on 12/08/2022
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Edited by [[https://github.com/BernardoGG][Bernardo Gutierrez]] on 12/08/2022
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Last edited using version =v0.3.0=.
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Last edited using =BEAST v2.6.7= and =timtam v0.3.1=.
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This tutorial demonstrates how to use TimTam to estimate the reproduction number
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This tutorial demonstrates how to use TimTam to estimate the reproduction number
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and prevalence of infection using a sequence alignment and a time series of
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and prevalence of infection using a sequence alignment and a time series of
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... | @@ -82,7 +82,8 @@ expected for an RNA virus. The origin time for our simulated epidemic took place |
... | @@ -82,7 +82,8 @@ expected for an RNA virus. The origin time for our simulated epidemic took place |
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- Remove operators relating to the clock rate, as we are working with a known
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- Remove operators relating to the clock rate, as we are working with a known
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(from the simulation parameters) evolutionary rate. There should be two of
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(from the simulation parameters) evolutionary rate. There should be two of
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these clock operators, you can identify them because they begin with
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these clock operators, you can identify them because they begin with
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~<operator id="clock.rate"~
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~<operator id="clock.rate"~.
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- Ensure the =originTime= is set to \(70.0\).
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- Remove all references to =historySizes= and =historyChecks=, these are used
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- Remove all references to =historySizes= and =historyChecks=, these are used
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to estimate historical prevalence and are not needed for this example.
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to estimate historical prevalence and are not needed for this example.
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- Copy and paste the two number series from the R script output as the values
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- Copy and paste the two number series from the R script output as the values
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