Bayesian model using KDE

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Filippo Rizzitano

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Oct 18, 2024, 5:33:08 AMOct 18
to OxCal

Hi everyone,

I’m trying to create a Bayesian model using KDE for five phases. In this case, I have intricate relationships (based on stratigraphic data) between the phases, where: Phase 1 overlaps all the other four phases; Phases 2 and 3 overlap each other; Phases 3, 4, and 5 are contiguous.

To address this, I created the following code:


 Plot()
 {
  Phase(Overlap 1)
  {
   Sequence()
   {
    Boundary("Start 1");
    Phase("1")
    {
     KDE_Model("1")
     {
     };
    };
    Boundary("End 1");
   };
   Phase("Overlap 2")
   {
    Sequence()
    {
     Boundary("Start 2");
     Phase("2")
     {
      KDE_Model("2")
      {
      };
     };
     Boundary("End 2");
    };
    Sequence()
    {
     Boundary("Start 3");
     Phase("3")
     {
      KDE_Model("3")
      {
      };
     };
     Boundary("Transition 3/4");
     Phase("4")
     {
      KDE_Model("4")
      {
      };
     };
     Boundary("Transition 4/5");
     Phase("5")
     {
      KDE_Model("5")
      {
      };
     };
     Boundary("End 5");
    };
   };
  };
 };

However, after running this model, OxCal gives me the following warning:
Warning! Model not supported in this context - KDE_Model.”

I’m wondering if it would be better to use the KDE_Plot command instead, or if perhaps KDE in general isn’t well suited for this type of model with overlapping and contiguous phases?

Thanks in advance for any advice!

Filippo

Christopher Ramsey

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Oct 18, 2024, 5:35:52 AMOct 18
to OxCal group
Yes - if you are using a Bayesian phase model you should use KDE_Plot to show the distribution of events within the phase. This is not part of the model but will generate a KDE distribution of the marginal posteriors within each phase which is I think what you want.

The KDE_Model is used as a standalone model where there is no clear phase structure.

Best wishes

Christopher
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Filippo Rizzitano

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Oct 18, 2024, 5:59:04 AMOct 18
to ox...@googlegroups.com

Hi Christopher,

Thank you for the clarification! That makes perfect sense now. I’ve switched to using KDE_Plot as you suggested, and it works well without any warnings. It seems to capture the relationships between the phases exactly as I intended.

I appreciate your help in understanding the correct usage of these functions!

Best regards,

Filippo


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