def test_init_():
outcome1 = Outcome('education', 10, 10)
outcome2 = Outcome('education', 20, 20)
study = Study("hello", "Kris et al 2019", outcomes=[outcome1, outcome2])
assert study.note == 'hello'
assert study.citation == 'Kris et al 2019'
assert len(study.outcomes) == 2
def test_meta_analysis():
outcome1 = Outcome('crime', 25, 25, effect_size=0.1, variance=0.02)
outcome2 = Outcome('crime', 25, 25, effect_size=0.17, variance=0.03)
study1 = Study("hello", "Kris et al 2019", outcomes=[outcome1, outcome2])
outcome3 = Outcome('crime', 25, 25, effect_size=0.2, variance=0.01)
outcome4 = Outcome('crime', 25, 25, effect_size=0.3, variance=0.025)
outcome5 = Outcome('crime', 25, 25, effect_size=0.5, variance=0.035)
study2 = Study("hello", "Kris et al 2018", outcomes=[outcome3, outcome4, outcome5])
study_pool = StudyPool([study1, study2], outcome_label='crime')
fe_effect_size = study_pool.calculate_ivw_effect_size(method='fe')
re_effect_size = study_pool.calculate_ivw_effect_size(method='re')
fe_variance = study_pool.calculate_variance(method='fe')
re_variance = study_pool.calculate_variance(method='re')
meta_es_fe, meta_var_fe = study_pool.meta_analysis(method='fe')
meta_es_re, meta_var_re = study_pool.meta_analysis(method='re')
meta_es_auto, meta_var_auto = study_pool.meta_analysis(method='auto')
assert math.isclose(fe_effect_size, meta_es_fe)
assert math.isclose(re_effect_size, meta_es_re)
assert math.isclose(re_effect_size, meta_es_auto)
assert math.isclose(fe_variance, meta_var_fe)
assert math.isclose(re_variance, meta_var_re)
assert math.isclose(re_variance, meta_var_auto)
def test_get_outcomes_by_label():
outcome1 = Outcome('education', 30, 30)
outcome2 = Outcome('education', 25, 25)
outcome3 = Outcome('crime', 25, 25)
study = Study("hello",
"Kris et al 2019",
outcomes=[outcome1, outcome2, outcome3])
edu_outcome_list = study.get_outcomes_by_label('education')
assert len(edu_outcome_list) == 2
for outcome in edu_outcome_list:
assert outcome.label == 'education'
def test_calculate_re():
outcome1 = Outcome('crime', 25, 25, effect_size=0.1, variance=0.02)
outcome2 = Outcome('crime', 25, 25, effect_size=0.17, variance=0.03)
study1 = Study("hello", "Kris et al 2019", outcomes=[outcome1, outcome2])
outcome3 = Outcome('crime', 25, 25, effect_size=0.2, variance=0.01)
outcome4 = Outcome('crime', 25, 25, effect_size=0.3, variance=0.025)
outcome5 = Outcome('crime', 25, 25, effect_size=0.5, variance=0.035)
study2 = Study("hello", "Kris et al 2018", outcomes=[outcome3, outcome4, outcome5])
study_pool = StudyPool([study1, study2], outcome_label='crime')
tau_square = study_pool.calculate_re()
assert math.isclose(tau_square, 0.064488371103462, rel_tol=1e6)
def test_get_outcome_by_id():
outcome1 = Outcome('education', 30, 30)
outcome2 = Outcome('education', 25, 25)
outcome1_id = outcome1.id
outcome2_id = outcome2.id
study = Study("hello", "Kris et al 2019", outcomes=[outcome1, outcome2])
outcome_pull1 = study.get_outcome_by_id(outcome1_id)
assert outcome_pull1 == outcome1
outcome_pull2 = study.get_outcome_by_id(outcome2_id)
assert outcome_pull2 == outcome2
assert outcome_pull1 != outcome_pull2
def test_calculate_variance():
outcome1 = Outcome('crime', 25, 25, effect_size=0.1, variance=0.02)
outcome2 = Outcome('crime', 25, 25, effect_size=0.17, variance=0.03)
study1 = Study("hello", "Kris et al 2019", outcomes=[outcome1, outcome2])
outcome3 = Outcome('crime', 25, 25, effect_size=0.2, variance=0.01)
outcome4 = Outcome('crime', 25, 25, effect_size=0.3, variance=0.025)
outcome5 = Outcome('crime', 25, 25, effect_size=0.5, variance=0.035)
study2 = Study("hello", "Kris et al 2018", outcomes=[outcome3, outcome4, outcome5])
study_pool = StudyPool([study1, study2], outcome_label='crime')
fe_variance = study_pool.calculate_variance(method='fe')
re_variance = study_pool.calculate_variance(method='re')
assert math.isclose(fe_variance, 0.003969754253308, rel_tol=1e6)
assert math.isclose(re_variance, 0.017522267928502, rel_tol=1e6)
def test_calculate_ivw_effect_size():
outcome1 = Outcome('crime', 25, 25, effect_size=0.1, variance=0.02)
outcome2 = Outcome('crime', 25, 25, effect_size=0.17, variance=0.03)
study1 = Study("hello", "Kris et al 2019", outcomes=[outcome1, outcome2])
outcome3 = Outcome('crime', 25, 25, effect_size=0.2, variance=0.01)
outcome4 = Outcome('crime', 25, 25, effect_size=0.3, variance=0.025)
outcome5 = Outcome('crime', 25, 25, effect_size=0.5, variance=0.035)
study2 = Study("hello", "Kris et al 2018", outcomes=[outcome3, outcome4, outcome5])
study_pool = StudyPool([study1, study2], outcome_label='crime')
fe_effect_size = study_pool.calculate_ivw_effect_size(method='fe')
re_effect_size = study_pool.calculate_ivw_effect_size(method='re')
assert math.isclose(fe_effect_size, 0.226086956521739, rel_tol=1e6)
assert math.isclose(re_effect_size, 0.246115055719316, rel_tol=1e6)
def test_calculate_q():
outcome1 = Outcome('crime', 25, 25, effect_size=0.1, variance=0.02)
outcome2 = Outcome('crime', 25, 25, effect_size=0.17, variance=0.03)
study1 = Study("hello", "Kris et al 2019", outcomes=[outcome1, outcome2])
outcome3 = Outcome('crime', 25, 25, effect_size=0.2, variance=0.01)
outcome4 = Outcome('crime', 25, 25, effect_size=0.3, variance=0.025)
outcome5 = Outcome('crime', 25, 25, effect_size=0.5, variance=0.035)
study2 = Study("hello", "Kris et al 2018", outcomes=[outcome3, outcome4, outcome5])
study_pool = StudyPool([study1, study2], outcome_label='crime')
q, dof, p = study_pool.calculate_q()
assert math.isclose(q, 16.1418558826177, rel_tol=1e6)
assert dof == 4
assert math.isclose(p, 0.00283460303776, rel_tol=1e6)
def test_remove_outcome():
outcome1 = Outcome('education', 30, 30)
outcome2 = Outcome('education', 25, 25)
outcome1_id = outcome1.id
study = Study("hello", "Kris et al 2019", outcomes=[outcome1, outcome2])
exists = False
for outcome in study.outcomes:
if outcome.id == outcome1_id:
exists = True
assert exists
study = study.remove_outcome(outcome1_id)
for outcome in study.outcomes:
assert outcome.id != outcome1_id
def test_set_outcome():
outcome1 = Outcome('education', 30, 30, effect_size=0.1, variance=0.02)
outcome2 = Outcome('education', 25, 25, effect_size=0.1, variance=0.02)
outcome3 = Outcome('crime', 25, 25, effect_size=0.1, variance=0.02)
study1 = Study("hello", "Kris et al 2019", outcomes=[outcome1, outcome2, outcome3])
outcome4 = Outcome('education', 30, 30, effect_size=0.1, variance=0.02)
outcome5 = Outcome('crime', 25, 25, effect_size=0.1, variance=0.02)
outcome6 = Outcome('crime', 25, 25, effect_size=0.1, variance=0.02)
outcome7 = Outcome('crime', 25, 25, effect_size=0.1, variance=0.02)
study2 = Study("hello", "Kris et al 2018", outcomes=[outcome4, outcome5, outcome6, outcome7])
studies = StudyPool([study1, study2], outcome_label='education')
assert studies.outcome_label == 'education'
assert len(studies.effect_sizes) == 3
studies.set_outcome('crime')
assert studies.outcome_label == 'crime'
assert len(studies.effect_sizes) == 4
def test_append_outcome():
study = Study("hello", "Kris et al 2019")
study.append_outcome(Outcome('education', 10, 10))
assert len(study.outcomes) == 1
assert isinstance(study.outcomes[0], Outcome)
assert study.outcomes[0].treat_n == 10