Francis Meets Stan

About a year ago I was introduced to Stan.  Stan is a free and open-source probabilistic programming language and Bayesian inference engine.  After watching the webinar I wanted to try it out but lacked the free time.  I finally got to it this past weekend.  Here’s my tale.

I wanted to do a regression on a well-known data set.  I decided to use the data set compiled by Francis Galton on the relationship between the height of a child and their parents.  Galton observed “regression towards mediocrity” or what would be referred to today as regression to the mean.

I analysed the Galton data published in the R HistData package.  I was going to use the pystan interface so I exported the data from R into a CSV.  I did not make any adjustments to the data.

OLS Regression Model

I ran an ordinary least squares (OLS) regression using the StatsModel library as a sort of baseline.  Here are the results of that regression:

                            OLS Regression Results                            
Dep. Variable:                  child   R-squared:                       0.210
Model:                            OLS   Adj. R-squared:                  0.210
Method:                 Least Squares   F-statistic:                     246.8
Date:                Mon, 27 Mar 2017   Prob (F-statistic):           1.73e-49
Time:                        11:09:52   Log-Likelihood:                -2063.6
No. Observations:                 928   AIC:                             4131.
Df Residuals:                     926   BIC:                             4141.
Df Model:                           1                                         
Covariance Type:            nonrobust                                         
                 coef    std err          t      P>|t|      [0.025      0.975]
Intercept     23.9415      2.811      8.517      0.000      18.425      29.458
parent         0.6463      0.041     15.711      0.000       0.566       0.727
Omnibus:                       11.057   Durbin-Watson:                   0.046
Prob(Omnibus):                  0.004   Jarque-Bera (JB):               10.944
Skew:                          -0.241   Prob(JB):                      0.00420
Kurtosis:                       2.775   Cond. No.                     2.61e+03

[1] Standard Errors assume that the covariance matrix of the errors is correctly specified.
[2] The condition number is large, 2.61e+03. This might indicate that there are
strong multicollinearity or other numerical problems.

Stan Model

Then I tried out the same process with Stan.  It took a couple of hours of the read the documentation, try, fail, pull my hair out cycle before I was successful.  Here was my Stan code:

stan_model_code = """
data {
    int<lower=0> N; // number of cases
    vector[N] x; // predictor (covariate)
    vector[N] y; // outcome (variate)
parameters {
    real alpha; // intercept
    real beta; // slope
    real<lower=0> sigma; // outcome noise
model {
    y ~ normal(x * beta + alpha, sigma);

stan_data = {
        'N': len(df['child'].values),
        'x': df['parent'].values,
        'y': df['child'].values

stan_model = pystan.stan(model_name='galton', model_code=stan_model_code, data=stan_data, iter=1000, chains=4)

I got hung up on the data section.  I didn’t use the vector type which was throwing errors.  Here’s the output from Stan:

Inference for Stan model: galton_2a77bd156aec196d5a464494a175b11a.
4 chains, each with iter=1000; warmup=500; thin=1; 
post-warmup draws per chain=500, total post-warmup draws=2000.

        mean se_mean     sd   2.5%    25%    50%    75%  97.5%  n_eff   Rhat
alpha  24.24    0.11   2.67   18.9  22.45   24.2  26.17  29.37    607   1.01
beta    0.64  1.6e-3   0.04   0.57   0.61   0.64   0.67   0.72    606   1.01
sigma   2.24  1.9e-3   0.05   2.14   2.21   2.24   2.27   2.35    732    1.0
lp__   -1211    0.05   1.19  -1214  -1212  -1211  -1210  -1210    643    1.0

Samples were drawn using NUTS at Mon Mar 27 11:11:15 2017.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at 
convergence, Rhat=1).

Comparison of Results

I’ve pulled out all the results and put them in a side by side comparison.  The results are very similar (as one would expect).  The intercept is around 24 (18-29) with the coefficient for the parent variable at about 0.6 (0.5-0.7).

OLS Stan
Mean 2.5% 97.5% Mean 2.5% 97.5%
Intercept (Alpha) 23.9415 18.425 29.458 24.24 18.9 29.37
Parent (Beta) 0.6463 0.566 0.727 0.64 0.57 0.72

Now that I’ve use Stan I am confident I will be using this Bayesian modeling tool in the future.  As always my source code is available on my GitHub repository.


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