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******************************
Coalescent class documentation
******************************
.. Note::
Using the coalescent model is optional. When running via the command line this class will only be initialized when
the flag
.. code-block:: bash
--coalescent <arg>
is used.
The argument is either ``‘const’`` (have TreeTime estimate a constant coalescence rate), or ``‘skyline’`` (estimate a piece-wise linear merger rate trajectory)
or a floating point number giving the time scale of coalescence in units of divergence (``Tc``). This is also
called the effective population size.
.. autoclass:: treetime.Coalescent
:members: __init__
Parameters of the Kingsman coalescence model
--------------------------------------------
.. automethod:: treetime.Coalescent.branch_merger_rate
.. automethod:: treetime.Coalescent.total_merger_rate
.. automethod:: treetime.Coalescent.cost
Skyline Methods
---------------------
.. automethod:: treetime.Coalescent.optimize_skyline
.. automethod:: treetime.Coalescent.skyline_empirical
.. automethod:: treetime.Coalescent.skyline_inferred
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