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16 | 16 | with pm.Model() as model:
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17 | 17 |
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18 | 18 | # Impute missing values
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19 |
| - sib_mean = pm.Exponential('sib_mean', 1) |
| 19 | + sib_mean = pm.Exponential('sib_mean', 1.) |
20 | 20 | siblings_imp = pm.Poisson('siblings_imp', sib_mean,
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21 | 21 | observed=masked_values(siblings, value=-999))
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22 | 22 |
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23 |
| - p_disab = pm.Beta('p_disab', 1, 1) |
| 23 | + p_disab = pm.Beta('p_disab', 1., 1.) |
24 | 24 | disability_imp = pm.Bernoulli(
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25 | 25 | 'disability_imp', p_disab, observed=masked_values(disability, value=-999))
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26 | 26 |
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27 |
| - p_mother = pm.Beta('p_mother', 1, 1) |
| 27 | + p_mother = pm.Beta('p_mother', 1., 1.) |
28 | 28 | mother_imp = pm.Bernoulli('mother_imp', p_mother,
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29 | 29 | observed=masked_values(mother_hs, value=-999))
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30 | 30 |
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31 |
| - s = pm.HalfCauchy('s', 5, testval=5) |
32 |
| - beta = pm.Laplace('beta', 0, 100, shape=7, testval=.1) |
| 31 | + s = pm.HalfCauchy('s', 5., testval=5) |
| 32 | + beta = pm.Laplace('beta', 0., 100., shape=7, testval=.1) |
33 | 33 |
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34 | 34 | expected_score = (beta[0] + beta[1] * male + beta[2] * siblings_imp + beta[3] * disability_imp +
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35 | 35 | beta[4] * age + beta[5] * mother_imp + beta[6] * early_ident)
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36 | 36 |
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37 | 37 | observed_score = pm.Normal(
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38 |
| - 'observed_score', expected_score, s, observed=score) |
| 38 | + 'observed_score', expected_score, tau=s, observed=score) |
39 | 39 |
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40 | 40 |
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41 | 41 | with model:
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42 | 42 | start = pm.find_MAP()
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43 | 43 | step1 = pm.NUTS([beta, s, p_disab, p_mother, sib_mean], scaling=start)
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44 |
| - |
45 | 44 | step2 = pm.Metropolis([mother_imp.missing_values,
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46 | 45 | disability_imp.missing_values,
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47 | 46 | siblings_imp.missing_values])
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