Model a realistic system of costs and benefits

[rosemckeon]

Is it possible to find reasonable parameter values for all the costs and benefits in the model based on the literature?

• ploidy_growth_benefit look at biomass comparisons.
• inbreeding_cost look at inbreeding depression.
• selfing_polyploid_prob
• uneven_matching_prob
• triploid_mum_prob look at seed number and size comparisons.

I've set simulations going that test all of these individually at different levels while I try and find realistic values.

[rosemckeon]

ploidy_growth_benefit

Size should increase by roughly 1.7 times as ploidy doubles.
ref: https://medium.com/plant-cell-extracts/up-sizing-the-tale-of-the-polyploid-giants-508f9f7db

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Not sure quite how to put that in the parameters.

@bradduthie If I made max_growth_rate = 1.7 (as we have the system capped at tetraploidy) then put ploidy_growth_rate = 1, would that work? diploids would get their mean x 2 converted to a rate between 1 and 1.7 and tetraploids would get their mean x 4 converted.

[bradduthie]

That sounds reasonable to me @rozeykex -- the article you link to lists two peer-reviewed sources. Perhaps they give a range? It might be that 1.5 or 2 are entirely reasonable as well.

[rosemckeon]

@bradduthie thanks, I'll check the proper papers for a range and do some mini tests I think, to see if these parameter values give the correct kind of size difference.

I have the max rate set to 4 at the moment. I don't suppose that matters for the other tests.

[rosemckeon]

triploid_mum_prob

I remember reading somewhere that seeds were reduced by 75%. I'll find clarification and a source for that asap.

[rosemckeon]

selfing_polyploid_prob

I'm thinking it would be fair just to set this equal to the standard fertilisation_prob so it's simply on for polyploids.