Questions about General IPM vignette

[Aariq]

https://github.com/levisc8/ipmr/blob/ad143c10e68bd40a2cac605bbd0f599314a1329d/vignettes/general-ipms.Rmd#L47

I don't see f_G or f_{r_d} in the previous list of equations. Do you mean G(z, z') and f_d(z') ?

I'm also not sure I understand why germination is part of the go_discrete kernel. Shouldn't that be part of leave_discrete for a seed bank? The current formulation seems more like a seedling bank to me.

[levisc8]

Ah, so the f_G and f_{r_d} refer to functions in the list below that line (see equations for the growth model (2) and recruit size (5)). reckon I should move that line to be closer to them?

re: 2 - that's a way of saying "only viable seeds in the seedbank". We provide a bit more detail in the full model description in the data paper the model appears in. It's worth noting that you could move the g_i term to the leave_discrete kernel and get almost exactly the same values (difference is ~ 3e-12).

[Aariq]

Ohh, I see them now! Thanks, this makes sense now. And it makes sense to think of the g_i term as seed viability. It's the probability that it can become a seedling, but not describing it becoming a seedling of size z', which goes in the leave_discrete kernel.