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green-striped-gecko / PopGenReport

a simple way to analyse population genetic data using R
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Is there a way to extract the spatial location of individuals that have been simulated in run.popgensim()? #9

Closed michaelschwob closed 1 year ago

michaelschwob commented 1 year ago

I have locations of the initial populations for the simulation. However, I'm wondering if there's a way to have the simulation report locations of the simulated individuals. I'd assume that this is possible because we can pass a cost matrix to the function. Perhaps I'm overlooking something simple.

michaelschwob commented 1 year ago

At the moment, it seems that the location for simulated individuals is the same location as the population initially was. Is there a way to have populations migrate and branch off?

green-striped-gecko commented 1 year ago

Hi.

Yes it is not really individual based in terms of location (the individuals have the coordinates of the population).

In terms of branching off there is no mechanism either, but you could simply try to build it per hand and use the genind object that is returned at the end of the simulation and split of the population by hand and restart the population(s) again.

Not 100% sure if that makes sense for what you want to do, but should be fairly straight forward.

[maybe you could even set the migration matrix in such a way that migration is zero between this the branching populations and the others and restart with the new migration matrix]

Cheers,Bernd Currently there is no mechanism build in to

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From: M. R. @.> Sent: Thursday, 19 January 2023 1:05 PM To: @.> Cc: @.***> Subject: Re: [green-striped-gecko/PopGenReport] Is there a way to extract the spatial location of individuals that have been simulated in run.popgensim()? (Issue #9)

At the moment, it seems that the location for simulated individuals is the same location as the population initially was. Is there a way to have populations migrate and branch off?

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michaelschwob commented 1 year ago

Thank you for the response and clarification. Love the package!