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Post-MCMC analysis

graph LR
    g0[Project loading];
    g1[Prior elicitation];
    g2[Posterior inference];
    g3[Post-MCMC analysis];
    g0 --> g1;
    g1 --> g2;
    g2 --> g3;

    classDef selected-mermaid-node fill:#33658a60,stroke:#cc5f00,stroke-width:4px
    class g3 selected-mermaid-node

After posterior inference is complete and MCMC results are available for a model, the Dating Results tab can be used for post-MCMC analysis.

The Dating Results view includes the chronological DAG which can be used to select contexts and group boundary nodes for subsequent analysis, by right-clicking on the context/group boundary shape.

A screenshot of the PolyChron Dating Results view for the examples 'thesis' model after calibration has completed

Posterior Densities

Posterior densities for a selection of contexts or group boundary nodes can plotted by selecting nodes from the chronological graph.

Contexts or group boundaries can be selected by right-clicking on the node and selecting "Add to results list".

On clicking the "Posterior densities" button, posterior probability density plots for the selected nodes will be displayed.

A screenshot of the Dating REsults view for the 'thesis' example after posterior densities have been plotted for contexts 1210, 358, 1235, 493 & 925

The plots are interactive, and can be exported to file using the toolbar at the bottom of the plot area.

The exported posterior densities for contexts 1210, 358, 1235, 493 & 925 from the 'thesis' example

HPD Intervals

Marginal HPD intervals for a selection of contexts or group boundary nodes can be displayed in the "Calendar date range estimates" table.

Contexts or group boundaries can be selected by right-clicking on the node and selecting "Add to results list".

On clicking the "HPD intervals" button, you will be prompted for the HPD interval percentage (95% is used as standard). On submission, HPD intervals will be computed and displayed in the "Calendar date range estimates" table.

Time elapsed between contexts or group boundaries

The time elapsed between any two contexts or group boundaries can be examined by:

  1. Right click on the first node, selecting "Get time elapsed"
  2. Right click on the second node, selecting "Get time elapsed between X and another context"

The "Calendar date range estimates" table will have been updated to include the HPD interval between the two nodes, and the "Posterior densities" area will include a plot of the posterior density probability density plot, which can be exported if required.

A screenshot of the Dating Results tab showing the updated table and posterior densities plot between contexts 1210 and 1235 in the example 'thesis' model

Clearing selected contexts, HPD Intervals and Posterior Densities

The "Clear list" button can be used to clear the selected nodes, HPD Intervals table and posterior densities plots.