def test_make_summary_stat_df_no_warning(self):
df = pd.DataFrame({'A': [1, 2, np.nan], 'B': [np.nan, 2, 3]})
with warnings.catch_warnings():
warnings.simplefilter('error')
Comparer.make_summary_stat_df(df)
def test_make_summary_stat_df_no_warning(self):
df = pd.DataFrame({'A': [1, 2, np.nan],
'B': [np.nan, 2, 3]})
with warnings.catch_warnings():
warnings.simplefilter('error')
Comparer.make_summary_stat_df(df)
def test_compute_correlations_between_versions_no_matching_feature(self):
df_old = pd.DataFrame({'id': ['a', 'b', 'c'],
'feature1': [1.3, 1.5, 2.1],
'feature2': [1.1, 6.2, 2.1],
'r1': [2, 3, 4]})
df_new = pd.DataFrame({'id': ['a', 'b', 'c'],
'feature3': [-1.3, -1.5, -2.1],
'feature4': [1.1, 6.2, 2.1],
'r1': [2, 3, 4]})
Comparer.compute_correlations_between_versions(df_old, df_new,
human_score='r1',
id_column='id')
def test_compute_correlations_between_versions_no_matching_feature(self):
df_old = pd.DataFrame({
'id': ['a', 'b', 'c'],
'feature1': [1.3, 1.5, 2.1],
'feature2': [1.1, 6.2, 2.1],
'r1': [2, 3, 4]
})
df_new = pd.DataFrame({
'id': ['a', 'b', 'c'],
'feature3': [-1.3, -1.5, -2.1],
'feature4': [1.1, 6.2, 2.1],
'r1': [2, 3, 4]
})
Comparer.compute_correlations_between_versions(df_old,
df_new,
human_score='r1',
id_column='id')
def test_load_rsmtool_output(self):
source = 'lr-subgroups-with-h2'
experiment_id = 'lr_subgroups_with_h2'
test_dir = dirname(__file__)
config_file = join(test_dir, 'data', 'experiments', source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
output_dir = join('test_outputs', source, 'output')
figure_dir = join('test_outputs', source, 'figure')
comparer = Comparer()
csvs, figs, file_format = comparer.load_rsmtool_output(
output_dir, figure_dir, experiment_id, 'scale', ['QUESTION', 'L1'])
expected_csv_keys = [
'df_coef', 'df_confmatrix', 'df_consistency', 'df_degradation',
'df_descriptives', 'df_disattenuated_correlations',
'df_disattenuated_correlations_by_L1',
'df_disattenuated_correlations_by_L1_overview',
'df_disattenuated_correlations_by_QUESTION',
'df_disattenuated_correlations_by_QUESTION_overview', 'df_eval',
'df_eval_by_L1', 'df_eval_by_L1_m_sd', 'df_eval_by_L1_overview',
'df_eval_by_QUESTION', 'df_eval_by_QUESTION_m_sd',
'df_eval_by_QUESTION_overview', 'df_eval_for_degradation',
'df_feature_cors', 'df_mcor_sc1', 'df_mcor_sc1_L1_overview',
'df_mcor_sc1_QUESTION_overview', 'df_mcor_sc1_by_L1',
'df_mcor_sc1_by_QUESTION', 'df_mcor_sc1_overview', 'df_model_fit',
'df_outliers', 'df_pca', 'df_pcavar', 'df_pcor_sc1',
'df_pcor_sc1_L1_overview', 'df_pcor_sc1_QUESTION_overview',
'df_pcor_sc1_by_L1', 'df_pcor_sc1_by_QUESTION',
'df_pcor_sc1_overview', 'df_percentiles', 'df_score_dist',
'df_scores', 'df_train_features'
]
expected_fig_keys = [
'betas', 'eval_barplot_by_L1', 'eval_barplot_by_QUESTION',
'feature_boxplots_by_L1_svg', 'feature_boxplots_by_QUESTION_svg',
'feature_distplots', 'pca_scree_plot'
]
assert_equal(file_format, 'csv')
assert_equal(expected_csv_keys, sorted(csvs.keys()))
assert_equal(expected_fig_keys, sorted(figs.keys()))
def test_make_summary_stat_df(self):
array = np.random.multivariate_normal([100, 25], [[25, .5], [.5, 1]],
5000)
df = pd.DataFrame(array, columns=['A', 'B'])
summary = Comparer.make_summary_stat_df(df)
assert np.isclose(summary.loc['A', 'SD'], 5, rtol=0.1)
assert np.isclose(summary.loc['B', 'SD'], 1, rtol=0.1)
assert np.isclose(summary.loc['A', 'MEAN'], 100, rtol=0.1)
assert np.isclose(summary.loc['B', 'MEAN'], 25, rtol=0.1)
def test_process_confusion_matrix(self):
in_cm = pd.DataFrame({1: [2, 3, 5],
2: [2, 5, 7],
3: [1, 3, 6]},
index=[1, 2, 3])
expected_out_cm = pd.DataFrame({'human 1': [2, 3, 5],
'human 2': [2, 5, 7],
'human 3': [1, 3, 6]},
index=['machine 1', 'machine 2', 'machine 3'])
out_cm = Comparer.process_confusion_matrix(in_cm)
assert_frame_equal(out_cm, expected_out_cm)
def test_process_confusion_matrix_with_zero(self):
in_cm = pd.DataFrame({0: [2, 3, 5],
1: [2, 5, 7],
2: [1, 3, 6]},
index=[0, 1, 2])
expected_out_cm = pd.DataFrame({'human 0': [2, 3, 5],
'human 1': [2, 5, 7],
'human 2': [1, 3, 6]},
index=['machine 0', 'machine 1', 'machine 2'])
out_cm = Comparer.process_confusion_matrix(in_cm)
assert_frame_equal(out_cm, expected_out_cm)
def test_make_summary_stat_df(self):
array = np.random.multivariate_normal([100, 25],
[[25, .5],
[.5, 1]],
5000)
df = pd.DataFrame(array, columns=['A', 'B'])
summary = Comparer.make_summary_stat_df(df)
assert np.isclose(summary.loc['A', 'SD'], 5, rtol=0.1)
assert np.isclose(summary.loc['B', 'SD'], 1, rtol=0.1)
assert np.isclose(summary.loc['A', 'MEAN'], 100, rtol=0.1)
assert np.isclose(summary.loc['B', 'MEAN'], 25, rtol=0.1)
def test_compute_correlations_between_versions_default_columns(self):
df_old = pd.DataFrame({'spkitemid': ['a', 'b', 'c'],
'feature1': [1.3, 1.5, 2.1],
'feature2': [1.1, 6.2, 2.1],
'sc1': [2, 3, 4]})
df_new = pd.DataFrame({'spkitemid': ['a', 'b', 'c'],
'feature1': [-1.3, -1.5, -2.1],
'feature2': [1.1, 6.2, 2.1],
'sc1': [2, 3, 4]})
df_cors = Comparer.compute_correlations_between_versions(df_old, df_new)
assert_equal(df_cors.at['feature1', 'old_new'], -1.0)
assert_equal(df_cors.at['feature2', 'old_new'], 1.0)
assert_equal(df_cors.at['feature1', 'human_old'], pearsonr(df_old['feature1'],
df_old['sc1'])[0])
assert_equal(df_cors.at['feature1', 'human_new'], pearsonr(df_new['feature1'],
df_new['sc1'])[0])
assert_equal(df_cors.at['feature1', "N"], 3)
def test_compute_correlations_between_versions_extra_data(self):
df_old = pd.DataFrame({'spkitemid': ['a', 'b', 'c', 'd'],
'feature1': [1.3, 1.5, 2.1, 5],
'feature2': [1.1, 6.2, 2.1, 1],
'feature3': [3, 5, 6, 7],
'sc1': [2, 3, 4, 3]})
df_new = pd.DataFrame({'spkitemid': ['a', 'b', 'c', 'e'],
'feature1': [-1.3, -1.5, -2.1, 2],
'feature2': [1.1, 6.2, 2.1, 8],
'feature4': [1, 3, 6, 7],
'sc1': [2, 3, 4, 3]})
with warnings.catch_warnings():
warnings.filterwarnings('ignore')
df_cors = Comparer.compute_correlations_between_versions(df_old, df_new)
assert_equal(df_cors.at['feature1', 'old_new'], -1.0)
assert_equal(df_cors.at['feature2', 'old_new'], 1.0)
assert_equal(df_cors.at['feature1', "N"], 3)
assert_equal(len(df_cors), 2)
def test_process_confusion_matrix_with_zero(self):
in_cm = pd.DataFrame({
0: [2, 3, 5],
1: [2, 5, 7],
2: [1, 3, 6]
},
index=[0, 1, 2])
expected_out_cm = pd.DataFrame(
{
'human 0': [2, 3, 5],
'human 1': [2, 5, 7],
'human 2': [1, 3, 6]
},
index=['machine 0', 'machine 1', 'machine 2'])
out_cm = Comparer.process_confusion_matrix(in_cm)
assert_frame_equal(out_cm, expected_out_cm)
def test_process_confusion_matrix(self):
in_cm = pd.DataFrame({
1: [2, 3, 5],
2: [2, 5, 7],
3: [1, 3, 6]
},
index=[1, 2, 3])
expected_out_cm = pd.DataFrame(
{
'human 1': [2, 3, 5],
'human 2': [2, 5, 7],
'human 3': [1, 3, 6]
},
index=['machine 1', 'machine 2', 'machine 3'])
out_cm = Comparer.process_confusion_matrix(in_cm)
assert_frame_equal(out_cm, expected_out_cm)
def test_compute_correlations_between_versions_default_columns(self):
df_old = pd.DataFrame({
'spkitemid': ['a', 'b', 'c'],
'feature1': [1.3, 1.5, 2.1],
'feature2': [1.1, 6.2, 2.1],
'sc1': [2, 3, 4]
})
df_new = pd.DataFrame({
'spkitemid': ['a', 'b', 'c'],
'feature1': [-1.3, -1.5, -2.1],
'feature2': [1.1, 6.2, 2.1],
'sc1': [2, 3, 4]
})
df_cors = Comparer.compute_correlations_between_versions(
df_old, df_new)
assert_equal(df_cors.at['feature1', 'old_new'], -1.0)
assert_equal(df_cors.at['feature2', 'old_new'], 1.0)
assert_equal(df_cors.at['feature1', 'human_old'],
pearsonr(df_old['feature1'], df_old['sc1'])[0])
assert_equal(df_cors.at['feature1', 'human_new'],
pearsonr(df_new['feature1'], df_new['sc1'])[0])
assert_equal(df_cors.at['feature1', "N"], 3)
def test_compute_correlations_between_versions_extra_data(self):
df_old = pd.DataFrame({
'spkitemid': ['a', 'b', 'c', 'd'],
'feature1': [1.3, 1.5, 2.1, 5],
'feature2': [1.1, 6.2, 2.1, 1],
'feature3': [3, 5, 6, 7],
'sc1': [2, 3, 4, 3]
})
df_new = pd.DataFrame({
'spkitemid': ['a', 'b', 'c', 'e'],
'feature1': [-1.3, -1.5, -2.1, 2],
'feature2': [1.1, 6.2, 2.1, 8],
'feature4': [1, 3, 6, 7],
'sc1': [2, 3, 4, 3]
})
with warnings.catch_warnings():
warnings.filterwarnings('ignore')
df_cors = Comparer.compute_correlations_between_versions(
df_old, df_new)
assert_equal(df_cors.at['feature1', 'old_new'], -1.0)
assert_equal(df_cors.at['feature2', 'old_new'], 1.0)
assert_equal(df_cors.at['feature1', "N"], 3)
assert_equal(len(df_cors), 2)
def test_compute_correlations_between_versions_custom_columns(self):
df_old = pd.DataFrame({
'id': ['a', 'b', 'c'],
'feature1': [1.3, 1.5, 2.1],
'feature2': [1.1, 6.2, 2.1],
'r1': [2, 3, 4]
})
df_new = pd.DataFrame({
'id': ['a', 'b', 'c'],
'feature1': [-1.3, -1.5, -2.1],
'feature2': [1.1, 6.2, 2.1],
'r1': [2, 3, 4]
})
df_cors = Comparer.compute_correlations_between_versions(
df_old, df_new, human_score='r1', id_column='id')
assert_almost_equal(df_cors.at['feature1', 'old_new'], -1.0)
assert_almost_equal(df_cors.at['feature2', 'old_new'], 1.0)
assert_equal(df_cors.at['feature1', 'human_old'],
pearsonr(df_old['feature1'], df_old['r1'])[0])
assert_equal(df_cors.at['feature1', 'human_new'],
pearsonr(df_new['feature1'], df_new['r1'])[0])
assert_equal(df_cors.at['feature1', "N"], 3)
def test_load_rsmtool_output(self):
source = 'lr-subgroups-with-h2'
experiment_id = 'lr_subgroups_with_h2'
test_dir = dirname(__file__)
config_file = join(test_dir,
'data',
'experiments',
source,
'{}.json'.format(experiment_id))
do_run_experiment(source, experiment_id, config_file)
output_dir = join('test_outputs', source, 'output')
figure_dir = join('test_outputs', source, 'figure')
comparer = Comparer()
csvs, figs, file_format = comparer.load_rsmtool_output(output_dir,
figure_dir,
experiment_id,
'scale',
['QUESTION', 'L1'])
expected_csv_keys = ['df_coef',
'df_confmatrix',
'df_consistency',
'df_degradation',
'df_descriptives',
'df_disattenuated_correlations',
'df_disattenuated_correlations_by_L1',
'df_disattenuated_correlations_by_L1_overview',
'df_disattenuated_correlations_by_QUESTION',
'df_disattenuated_correlations_by_QUESTION_overview',
'df_eval',
'df_eval_by_L1',
'df_eval_by_L1_m_sd',
'df_eval_by_L1_overview',
'df_eval_by_QUESTION',
'df_eval_by_QUESTION_m_sd',
'df_eval_by_QUESTION_overview',
'df_eval_for_degradation',
'df_feature_cors',
'df_mcor_sc1',
'df_mcor_sc1_L1_overview',
'df_mcor_sc1_QUESTION_overview',
'df_mcor_sc1_by_L1',
'df_mcor_sc1_by_QUESTION',
'df_mcor_sc1_overview',
'df_model_fit',
'df_outliers',
'df_pca',
'df_pcavar',
'df_pcor_sc1',
'df_pcor_sc1_L1_overview',
'df_pcor_sc1_QUESTION_overview',
'df_pcor_sc1_by_L1',
'df_pcor_sc1_by_QUESTION',
'df_pcor_sc1_overview',
'df_percentiles',
'df_score_dist',
'df_scores',
'df_train_features']
expected_fig_keys = ['betas',
'eval_barplot_by_L1',
'eval_barplot_by_QUESTION',
'feature_boxplots_by_L1_svg',
'feature_boxplots_by_QUESTION_svg',
'feature_distplots',
'pca_scree_plot']
assert_equal(file_format, 'csv')
assert_equal(expected_csv_keys, sorted(csvs.keys()))
assert_equal(expected_fig_keys, sorted(figs.keys()))
