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We need to define the scope of the spec somehow. We know that demes is not a "universal specification format" for population genetic simulations and inference methods. It is for describing demographic models that people estimate and simulate. But, how do we concisely say what that actually means, and avoid feature creep in the future?
One way we might do this is to say that Demes is concerned with population-level processes only, and any parameters that are about the individual genomes are out of scope. So, this means that things like mutation rates, recombination rates, selection coefficients are out of scope, but things like migration and dispersal rates are in scope.There's probably a grey area somewhere, but this is biology, so there's never going to be a perfectly crisp definition of anything.
We need to define the scope of the spec somehow. We know that demes is not a "universal specification format" for population genetic simulations and inference methods. It is for describing demographic models that people estimate and simulate. But, how do we concisely say what that actually means, and avoid feature creep in the future?
One way we might do this is to say that Demes is concerned with population-level processes only, and any parameters that are about the individual genomes are out of scope. So, this means that things like mutation rates, recombination rates, selection coefficients are out of scope, but things like migration and dispersal rates are in scope.There's probably a grey area somewhere, but this is biology, so there's never going to be a perfectly crisp definition of anything.
This is something we'd need to deal with in the paper too, but the specification needs to prominently define what it's about. See also https://github.com/apragsdale/demes-paper/issues/4 and https://github.com/apragsdale/demes-paper/issues/5
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