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Reword site model and nsm better #113

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richelbilderbeek opened this issue Jan 13, 2020 · 1 comment
Open

Reword site model and nsm better #113

richelbilderbeek opened this issue Jan 13, 2020 · 1 comment

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@richelbilderbeek
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As a reviewer of the pirouette manuscript pointed out, a site model has

  • a gamma site model
  • a substitution model

Therefore, create_jc69_site_model(id = NA, gamma_site_model = create_gamma_site_model()) is a minor misnomer.

Better would be: create_site_model(id = NA, gamma_site_model = create_gamma_site_model(), subst_model = create_jc69_nsm()).
@richelbilderbeek
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Check the BEAST2 source code to see Remco's achitecture.

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@richelbilderbeek