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Anna Störikoaseyboldt
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Fix quickstart with pymc
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doc/source/quickstart_pymc3.rst

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@@ -53,6 +53,7 @@ We'll use some time artificial data:::
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hare_data = np.array([
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30.0, 47.2, 70.2, 77.4, 36.3, 20.6, 18.1, 21.4, 22.0, 25.4,
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27.1, 40.3, 57.0, 76.6, 52.3, 19.5, 11.2, 7.6, 14.6, 16.2, 24.7
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])
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We also define a function for the right-hand-side of the ODE:::
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@@ -138,12 +139,12 @@ We are only missing the likelihood now::
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with model:
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# We can access the individual variables of the solution using the
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# variable names.
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pm.Deterministic('hares_mu', y_hat['hares'])
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pm.Deterministic('lynx_mu', y_hat['lynx'])
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pm.Deterministic('hares_mu', solution['hares'])
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pm.Deterministic('lynxes_mu', solution['lynxes'])
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sd = pm.HalfNormal('sd')
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pm.Lognormal('hares', mu=y_hat['hares'], sd=sd, observed=hare_data)
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pm.Lognormal('lynx', mu=y_hat['lynx'], sd=sd, observed=lynx_data)
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pm.Lognormal('hares', mu=solution['hares'], sd=sd, observed=hare_data)
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pm.Lognormal('lynxes', mu=solution['lynxes'], sd=sd, observed=lynx_data)
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We can sample from the posterior with the gradient-based PyMC3 samplers:::
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