Inference plots - Pairwise scatterplots

This example builds on adaptive covariance MCMC, and shows you how to plot the parameter distributions.

Inference plots:

Setting up an MCMC routine

See the adaptive covariance MCMC example for details.



In [1]:

    
from __future__ import print_function
import pints
import pints.toy as toy
import numpy as np
import matplotlib.pyplot as plt

# Load a forward model
model = toy.LogisticModel()

# Create some toy data
real_parameters = [0.015, 500]
times = np.linspace(0, 1000, 100)
org_values = model.simulate(real_parameters, times)

# Add noise
noise = 50
values = org_values + np.random.normal(0, noise, org_values.shape)
real_parameters = np.array(real_parameters + [noise])

# Get properties of the noise sample
noise_sample_mean = np.mean(values - org_values)
noise_sample_std = np.std(values - org_values)

# Create an object with links to the model and time series
problem = pints.SingleOutputProblem(model, times, values)

# Create a log-likelihood function (adds an extra parameter!)
log_likelihood = pints.GaussianLogLikelihood(problem)

# Create a uniform prior over both the parameters and the new noise variable
log_prior = pints.UniformLogPrior(
    [0.01, 400, noise*0.1],
    [0.02, 600, noise*100]
    )

# Create a posterior log-likelihood (log(likelihood * prior))
log_posterior = pints.LogPosterior(log_likelihood, log_prior)

# Perform sampling using MCMC, with a single chain
x0 = real_parameters * 1.1
mcmc = pints.MCMCController(log_posterior, 1, [x0])
mcmc.set_max_iterations(6000)
mcmc.set_log_to_screen(False)

Plotting 1d histograms

We can now run the MCMC routine and plot the histograms of the inferred parameters.



In [2]:

    
print('Running...')
chains = mcmc.run()
print('Done!')









    



Running...
Done!



In [3]:

    
# Select chain 0 and discard warm-up
chain = chains[0]
chain = chain[3000:]



In [4]:

    
import pints.plot

# Plot the 1d histogram of each parameter
pints.plot.histogram([chain])
plt.show()

Plotting 2d histograms and a matrix of parameter distribution plots

Plotting the histograms of two variables (showing their correlation) can be performed using pints.plot.pairwise with the parameter heatmap set to True. Additionally, by supplying the known real parameters, we see the locations of the true values appear as dotted lines in each plot.



In [5]:

    
pints.plot.pairwise(chain, heatmap=True, ref_parameters=real_parameters)
plt.show()

Matrix of parameter distribution plots with KDE

It is also possible to use kernel density estimation (KDE) to visualize the probability distributions of each parameter. Using the pints.plot.pairwise function, this time with the parameter kde set to True, we can create a matrix of scatterplots with KDE.



In [6]:

    
pints.plot.pairwise(chain, kde=True, ref_parameters=real_parameters)
plt.show()