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Fix incorrect usages of inclusive kwarg to Series.between #943

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merged 2 commits into from
Apr 18, 2023
+53 −34
Merged

Fix incorrect usages of inclusive kwarg to Series.between #943

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62956a5
Fix incorrect usages of inclusive kwarg to Series.between
matt-graham Apr 17, 2023
7b7aa56
Add predictor missed in refactoring
matt-graham Apr 18, 2023
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87 changes: 53 additions & 34 deletions src/tlo/methods/stunting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -213,8 +213,11 @@ def make_linear_model_stunting(intercept=1.0):
low_bound_age_in_years = agegp[0] / 12.0
high_bound_age_in_years = (1 + agegp[1]) / 12.0

mask = df.is_alive & df.age_exact_years.between(low_bound_age_in_years, high_bound_age_in_years,
inclusive='left')
mask = (
df.is_alive
& (df.age_exact_years >= low_bound_age_in_years)
& (df.age_exact_years < high_bound_age_in_years)
)

stunted = make_scaled_linear_model_stunting(target_prob=p_stunting.prob_stunting, mask=mask).predict(
df.loc[mask], self.rng, squeeze_single_row_output=False)
Expand Down Expand Up @@ -312,21 +315,23 @@ def make_lm_prob_becomes_stunted(self):
p = self.p

return LinearModel.multiplicative(
Predictor('age_exact_years',
conditions_are_exhaustive=True,
conditions_are_mutually_exclusive=True).when('< 0.5',
p['base_inc_rate_stunting_by_agegp'][0])
.when('.between(0.5, 1.0, inclusive="left")',
p['base_inc_rate_stunting_by_agegp'][1])
.when('.between(1.0, 2.0, inclusive="left")',
p['base_inc_rate_stunting_by_agegp'][2])
.when('.between(2.0, 3.0, inclusive="left")',
p['base_inc_rate_stunting_by_agegp'][3])
.when('.between(3.0, 4.0, inclusive="left")',
p['base_inc_rate_stunting_by_agegp'][4])
.when('.between(4.0, 5.0, inclusive="left")',
p['base_inc_rate_stunting_by_agegp'][5])
.when('> 5.0', 0.0),
Predictor(
conditions_are_exhaustive=True, conditions_are_mutually_exclusive=True
).when(
"age_exact_years < 0.5", p["base_inc_rate_stunting_by_agegp"][0]
).when(
"0.5 <= age_exact_years < 1", p["base_inc_rate_stunting_by_agegp"][1]
).when(
"1 <= age_exact_years < 2", p["base_inc_rate_stunting_by_agegp"][2]
).when(
"2 <= age_exact_years < 3", p["base_inc_rate_stunting_by_agegp"][3]
).when(
"3 <= age_exact_years < 4", p["base_inc_rate_stunting_by_agegp"][4]
).when(
"4 <= age_exact_years < 5", p["base_inc_rate_stunting_by_agegp"][5]
).when(
"age_exact_years >= 5", 0.0
),
Predictor('li_wealth',
conditions_are_mutually_exclusive=True).when(1, 1.0)
.otherwise(p['rr_stunting_wealth_level']),
Expand All @@ -349,8 +354,9 @@ def make_lm_prob_becomes_stunted(self):
'(nb_breastfeeding_status == "none")) & (age_exact_years < 0.5)',
p['rr_stunting_no_exclusive_breastfeeding']),
Predictor().when(
'(nb_breastfeeding_status == "none") & (age_exact_years.between(0.5, 2.0, inclusive="left"))',
p['rr_stunting_no_continued_breastfeeding']),
'(nb_breastfeeding_status == "none") & (0.5 <= age_exact_years < 2.0)',
p['rr_stunting_no_continued_breastfeeding']
),
)

def make_lm_prob_progression_to_severe_stunting(self):
Expand All @@ -359,21 +365,34 @@ def make_lm_prob_progression_to_severe_stunting(self):
p = self.p

return LinearModel.multiplicative(
Predictor('age_exact_years',
conditions_are_exhaustive=True,
conditions_are_mutually_exclusive=True).when('< 0.5',
p['r_progression_severe_stunting_by_agegp'][0])
.when('.between(0.5, 1.0, inclusive="left")',
p['r_progression_severe_stunting_by_agegp'][1])
.when('.between(1.0, 2.0, inclusive="left")',
p['r_progression_severe_stunting_by_agegp'][2])
.when('.between(2.0, 3.0, inclusive="left")',
p['r_progression_severe_stunting_by_agegp'][3])
.when('.between(3.0, 4.0, inclusive="left")',
p['r_progression_severe_stunting_by_agegp'][4])
.when('.between(4.0, 5.0, inclusive="left")',
p['r_progression_severe_stunting_by_agegp'][5])
.when('> 5.0', 1.0),
Predictor(
conditions_are_exhaustive=True, conditions_are_mutually_exclusive=True
).when(
'age_exact_years < 0.5', p['r_progression_severe_stunting_by_agegp'][0]
)
.when(
'0.5 <= age_exact_years < 1.0',
p['r_progression_severe_stunting_by_agegp'][1]
)
.when(
'1.0 <= age_exact_years < 2.0',
p['r_progression_severe_stunting_by_agegp'][2]
)
.when(
'2.0 <= age_exact_years < 3.0',
p['r_progression_severe_stunting_by_agegp'][3]
)
.when(
'3.0 <= age_exact_years < 4.0',
p['r_progression_severe_stunting_by_agegp'][4]
)
.when(
'4.0 <= age_exact_years < 5.0',
p['r_progression_severe_stunting_by_agegp'][5]
)
.when(
'age_exact_years >= 5.0', 1.0
),
Predictor('un_ever_wasted',
conditions_are_exhaustive=True,
conditions_are_mutually_exclusive=True
Expand Down