Merge pull request #750 from pymc-devs/rsv

add RSV example

Author: twiecki

pymc3/examples/rsv.py

@@ -0,0 +1,46 @@
+'''
+This model estimates the population prevalence of respiratory syncytial virus (RSV) among children in Amman, Jordan, based on 3 years of admissions diagnosed with RSV to Al Bashir hospital. 
+
+To estimate this parameter from raw counts of diagnoses, we need to establish the population of  1-year-old children from which the diagnosed individuals were sampled. This involved correcting census data (national estimate of 1-year-olds) for the proportion of the population in the city, as well as for the market share of the hospital. The latter is based on expert esimate, and hence encoded as a prior.
+'''
+
+import pymc3 as pm
+import numpy as np
+
+# 1-year-old children in Jordan
+kids = np.array([180489, 191817, 190830])
+# Proportion of population in Amman
+amman_prop = 0.35
+# infant RSV cases in Al Bashir hostpital
+rsv_cases = np.array([40, 59, 65])
+
+with pm.Model() as model:
+
+    # Al Bashir hospital market share
+    market_share = pm.Uniform('market_share', 0.5, 0.6)
+
+    # Number of 1 y.o. in Amman
+    n_amman = pm.Binomial('n_amman', kids, amman_prop, shape=3)
+
+    # Prior probability
+    prev_rsv = pm.Beta('prev_rsv', 1, 5, shape=3)
+
+    # RSV in Amman
+    y_amman = pm.Binomial('y_amman', n_amman, prev_rsv, shape=3, testval=100)
+
+    # Likelihood for number with RSV in hospital (assumes Pr(hosp | RSV) = 1)
+    y_hosp = pm.Binomial('y_hosp', y_amman, market_share, observed=rsv_cases)
+
+
+    
+
+def run(n=1000): 
+    if n == "short":
+        n = 50
+    with model:
+        trace = pm.sample(10000, step=[pm.NUTS(), pm.Metropolis()]) 
+
+if __name__ == '__main__':
+    run()
+
+