PyMC3 traceplot not displaying

Questions
1

Hi, I’m new here and also to PyMC3, so I hope this is an appropriate post.

I am trying to get the PyMC3 examples from Osvaldo Martin’s Bayesian Analysis with Python working. While the following code using matplotlib works fine (i.e. a chart is displayed):

import numpy as np
import matplotlib.pyplot as plt
import scipy.stats as stats


def posterior_grid(grid_points=100, heads=6, tosses=9):
    """
    A grid implementation for the coin-flip problem
    """
    grid = np.linspace(0, 1, grid_points)
    prior = 0.5 - abs(grid - 0.5)
    likelihood = stats.binom.pmf(heads, tosses, grid)
    unstd_posterior = likelihood * prior
    posterior = unstd_posterior / unstd_posterior.sum()
    return grid, posterior


if __name__ == "__main__":
    points = 100
    h, n = 1, 4
    grid, posterior = posterior_grid(points, h, n)
    plt.plot(grid, posterior, 'o-', label='heads = {}\ntosses = {}'.format(h, n))
    plt.xlabel(r'$\theta$')
    plt.legend(loc=0)
    plt.show()

…I cannot get the following - which uses PyMC3’s traceplot - to display a chart:

import pymc3 as pm
import numpy as np
import scipy.stats as stats

if __name__ == "__main__":

    np.random.seed(123)
    n_experiments = 4
    theta_real = 0.35
    data = stats.bernoulli.rvs(p=theta_real, size=n_experiments)
    print(data)

    with pm.Model() as our_first_model:
        theta = pm.Beta('theta', alpha=1, beta=1)
        y = pm.Bernoulli('y', p=theta, observed=data)
        start = pm.find_MAP()
        step = pm.Metropolis()
        trace = pm.sample(1000, step=step, start=start)

    burnin = 100
    chain = trace[burnin:]
    pm.traceplot(chain, lines={'theta':theta_real});

The code runs and exits fine, but no chart is displayed.

I have tried in IntelliJ IDEA with the Python plugin, from an Anaconda console window for my root environment, and from IPython.

In IPython, I get the following output on the console:

Out[3]:
array([[<matplotlib.axes._subplots.AxesSubplot object at 0x0000024BDD622F60>,
        <matplotlib.axes._subplots.AxesSubplot object at 0x0000024BDD667208>]], dtype=object)

…so obviously something is happening. But how can I display the results as a chart?

I have also tried the exact library versions listed in the book with Python 3.5, but still no traceplot chart:

  • Ipython 5.0
  • NumPy 1.11.1
  • SciPy 0.18.1
  • Pandas 0.18.1
  • Matplotlib 1.5.3
  • Seaborn 0.7.1
  • PyMC3 3.0
2

If you are on a console or terminal, you need to added plt.show() to display the figure. If you are on a ipython notebook, you need to add %pylab inline in code at the very beginning of the notebook.

3

Thanks for the reply. Further Googling got me to the answer during the day (UK time yesterday).

plt.show() also works with IntelliJ IDEA / PyCharm (and of course, you’ll need a import matplotlib.pyplot as plt at the top). For IPython, invoking from the command line with ipython --pylab auto also seems to work.