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Missing documentation for 'Population structure'

Hello and thanks for this amazing software!

I find myself having some issues understanding each and every parameter of your software. The documentation of the .json used to configure the model is missing description of fields of 'Population structure' (data type, description).

In addition, I have some questions regarding other parameters:

  • Is the mutation_rate parameter expressed per base per generation, or only per base? (same goes for recombination_rate)
  • I saw that the parameter generation_time was the duration in years for a single generation, but I don't see any parameter to set the simulation duration – or maybe it is linked to population dynamics described in 'Population structure' ?
  • Does the selection of a distribution model (for variants types for instance) implies that they are being differently positioned along the ancestral genome, or that they occur differently in-between coalescent trees, or that MSpangepop get to pick one value at the start and stick with it? (I would guess the third one based on the documentation but i'm not 100% sure)

Thanks by advance! Siegfried