Merge pull request #39 from hoechenberger/prior

ENH: Allow to pass a prior when instantiating `QuestPlusWeibull`

Author: hoechenberger

CHANGES.md

@@ -1,3 +1,7 @@
+v2019.3
+-------
+* Allow to pass a prior when instantiating `QuestPlusWeibull`
+
 v2019.2
 -------
 * Allow passing a random seed via `stim_selection_options` keyword

questplus/qp.py

@@ -470,6 +470,7 @@ def __init__(self, *,
                  slopes: Sequence,
                  lower_asymptotes: Sequence,
                  lapse_rates: Sequence,
+                 prior: Optional[dict] = None,
                  responses: Sequence = ('Yes', 'No'),
                  stim_scale: str = 'log10',
                  stim_selection_method: str = 'min_entropy',
@@ -481,6 +482,7 @@ def __init__(self, *,
                                            lower_asymptote=lower_asymptotes,
                                            lapse_rate=lapse_rates),
                          outcome_domain=dict(response=responses),
+                         prior=prior,
                          stim_scale=stim_scale,
                          stim_selection_method=stim_selection_method,
                          stim_selection_options=stim_selection_options,

questplus/tests/test_qp.py

@@ -658,6 +658,27 @@ def test_stim_selection_options():
     assert expected == q.stim_selection_options
 
 
+def test_weibull_prior():
+    intensities = np.linspace(-10, 0)
+    thresholds = intensities.copy()
+    slopes = [3.5]
+    lower_asymptotes = [0.01]
+    lapse_rates = [0.01]
+
+    prior_val = scipy.stats.norm.pdf(intensities, loc=-5, scale=0.2)
+    prior_val /= prior_val.sum()
+    prior = dict(threshold=prior_val)
+
+    q = QuestPlusWeibull(intensities=intensities,
+                         thresholds=thresholds,
+                         slopes=slopes,
+                         lower_asymptotes=lower_asymptotes,
+                         lapse_rates=lapse_rates,
+                         prior=prior)
+
+    assert np.allclose(q.prior.squeeze().values, prior_val)
+
+
 if __name__ == '__main__':
     test_threshold()
     test_threshold_slope()
@@ -671,3 +692,4 @@ def test_stim_selection_options():
     test_prior_for_unknown_parameter()
     test_prior_for_parameter_subset()
     test_stim_selection_options()
+    test_weibull_prior()