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Update examples #78

Description

@antagomir

Replicating the 3 case studies with TreeSE is laborious and the code base is not organized ideally for that.

Instead of replicating the case studies exactly with TreeSE, add more examples on how similar kind of things can be done.

The examples could be added as new "articles" or in the Getting started page, implemented in vignettes/miaSim.Rmd

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