Re: [simuPOP-list] RandomParentChooser in HomoMating

[Zhian K. <ka...@sc...>]

Hi Bo,

I realize I left a few details out:

The population I'm trying to simulate is an Oomycete population, where either "sex" (in reality mating types) can produce clonal offspring. In this situation, only one mating type is producing offspring. 

In the documentation of the CloneGenoTransmitter(), it states that if two parents are supplied, the maternal genotype will be copied. Since I want a mixture of both male and female clones, I tried to use RandomParentChooser(), which I assume randomly selects a single individual. Am I wrong thinking that RandomParentChooser() selects a single individual?

Thanks,
Zhian


> On Jun 30, 2016, at 18:34 , Bo Peng <be...@gm...> wrote:
> 
> Hi, Zhian,
> 
> I am not sure what is the problem here because your mating scheme works as expected when I run a test simulation. When I set numOffspring=1, the mother_id and father_id of the population are
> 
> (90.0, 7.0, 79.0, 14.0, 68.0, 24.0, 79.0, 80.0, 60.0, 71.0, 100.0, 28.0, 97.0, 13.0, 64.0, 85.0, 43.0, 98.0, 59.0, 46.0, 2.0, 42.0, 46.0, 15.0, 79.0, 38.0, 16.0, 32.0, 75.0, 61.0, 4.0, 71.0, 7.0, 71.0, 84.0, 94.0, 16.0, 62.0, 31.0, 24.0, 36.0, 83.0, 75.0, 10.0, 27.0, 27.0, 6.0, 42.0, 41.0, 74.0, 31.0, 12.0, 16.0, 22.0, 58.0, 25.0, 43.0, 15.0, 12.0, 3.0, 52.0, 64.0, 81.0, 22.0, 5.0, 18.0, 51.0, 47.0, 57.0, 33.0, 19.0, 4.0, 41.0, 60.0, 55.0, 9.0, 71.0, 19.0, 18.0, 91.0, 62.0, 18.0, 64.0, 44.0, 78.0, 49.0, 49.0, 83.0, 49.0, 53.0, 93.0, 97.0, 82.0, 8.0, 9.0, 12.0, 99.0, 99.0, 39.0, 95.0)
> 
> (0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
> 
> So only mothers are chosen. If you have numOffspring as specified, several consecutive offspring will share a mother.
> 
> Cheers,
> 
> Bo
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Thu, Jun 30, 2016 at 6:09 PM, Zhian Kamvar <ka...@sc... <mailto:ka...@sc...>> wrote:
> Hello,
> 
> I'm wondering if I can construct a scenario of diploid clonal reproduction by utilizing RandomParentChooser in HomoMating:
> 
> 
> sim.HomoMating(
>     chooser = sim.RandomParentChooser(),
>     generator = sim.OffspringGenerator(
>         ops = [
>             sim.CloneGenoTransmitter(),
>             sim.PedigreeTagger(infoFields=['mother_id', 'father_id']),
>             ],
>         numOffspring=(sim.UNIFORM_DISTRIBUTION, 1, 3)
>         )
>     )
> 
> I expect that the chooser would select a single parent, but when I run the simulation, it appears that two parents are chosen since I only have females left in the population ( as documented in the CloneGenoTransmitter ). Is there a way to address this?
> 
> Thanks,
> Zhian
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