.. _gamma_smc_demo:

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Demo: Running Gamma-SMC on Simulated Data
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   *Running mini_gamma_smc on simulated genomic data.*

.. figure:: /_static/figures/fig_demo_gamma_smc.png
   :width: 100%
   :align: center

   **Gamma-SMC demo on msprime-simulated data.** Panel A: True TMRCA vs Gamma-SMC posterior mean along the genome -- the conjugate Bayesian filter tracks coalescence time changes. Panel B: Input heterozygosity track from a diploid genome simulated under a bottleneck. Panel C: Posterior precision (shape parameter) along the genome, with inset showing the relationship to coefficient of variation. Panel D: True vs inferred TMRCA scatter plot.

This figure was generated by running the ``mini_gamma_smc`` implementation
on data simulated with ``msprime``. The script is at
``figures/fig_demo_gamma_smc.py``.
