How to design correct epoch matrices as input in the R package rmetasim?

08 August 2019 2 4K Report

Hi,

I settled on rmetasim to forward-simulate genetic data. The study system comprises a species with three stages (juvenile, female and male adults) and four habitats with differing migration of male and female adults in between those.

Can you help me how to create the correct input epoch matrices for the specific command landscape.new.epoch?

I specifically wonder (a) where and how to inlcude migration rates, (b) if the diagonal of the matrices should have the same information as in the single local-demography-matrices or if it should be blank and (c) if the rest of the matrices gives transition and reproduction rates during migration.

Also, does someone know if I can incorporate maximum age of an individual in any way, to avoid potential immortal (or biologically impossible old) individuals that still contribute to reproduction?

Any information on how to get this matrices right is very much appreciated.

Thanks in advance, Florian

Mohamed-Mourad Lafifi

Dear Florian,

I suggest you to see links and attached file on topic.

rmetasim source: R/create_landscape.R - Rdrr.io

https://rdrr.io › CRAN › rmetasim

Setting up simulations in rmetasim

https://cran.r-project.org/web/packages/rmetasim/.../Simulating.htm...

How to create a sequential model in Keras for R - Towards Data Science

https://towardsdatascience.com/how-to-create-a-sequential-model-i...

Best regards

Florian Kunz

Hi Mohamed-Mourad Lafifi,

thank you for your answer.

I am still struggeling with the specific design of the matrices, as they are not explained in detail in the supplied information.

If you have experience with it, could you help me and explain shortly what exact inputs should be given in those epoch matrices?

E.g.: R, M matrices describe "number of offspring per individual that migrate"?

S matrix returns "survival rate of migrating individuals"?

Because this results in errorous landscpae objects.

Also, do you happen to know how the command landscape.mig.matrix is supposed to be incorporated into the landscape/simulation?

Thanks again,

Florian

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