diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000..f17f438 --- /dev/null +++ b/.coveragerc @@ -0,0 +1,4 @@ +[run] +command_line = -m pytest +omit = + tests/*.py diff --git a/.gitignore b/.gitignore index 3e21f69..b2fd836 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ __pycache__ *.pyc +/.coverage /docs/_build diff --git a/tests/test_anova.py b/tests/test_anova.py index 4d188c4..6acabcf 100644 --- a/tests/test_anova.py +++ b/tests/test_anova.py @@ -52,3 +52,4 @@ def test_regress_ftest_ol8_2(): expected_summary = 'F(2, 21) = 29.57; p < 0.001*' assert result.summary() == expected_summary + assert result._repr_html_() == 'F(2, 21) = 29.57; p < 0.001*' diff --git a/tests/test_bayes_factors.py b/tests/test_bayes_factors.py index f099af1..37f727c 100644 --- a/tests/test_bayes_factors.py +++ b/tests/test_bayes_factors.py @@ -42,7 +42,19 @@ def test_afbf_logit_beta_zero(): assert bf.num_desc == 'Fibrinogen ≠ 0' assert bf.denom_desc == 'Fibrinogen = 0' + expected_summary = '''BF10 = 1.23, Anecdotal evidence in favour of H1 +H1: Fibrinogen ≠ 0 +H0: Fibrinogen = 0''' + assert bf.summary() == expected_summary + assert bf._repr_html_() == 'BF10 = 1.23, Anecdotal evidence in favour of H1
H1: Fibrinogen ≠ 0
H0: Fibrinogen = 0' + bf = result.bayesfactor_beta_zero('GammaGlobulin') assert bf.factor == approx(2.417, abs=0.001) assert bf.num_desc == 'GammaGlobulin = 0' assert bf.denom_desc == 'GammaGlobulin ≠ 0' + + expected_summary = '''BF01 = 2.42, Anecdotal evidence in favour of H0 +H0: GammaGlobulin = 0 +H1: GammaGlobulin ≠ 0''' + assert bf.summary() == expected_summary + assert bf._repr_html_() == 'BF01 = 2.42, Anecdotal evidence in favour of H0
H0: GammaGlobulin = 0
H1: GammaGlobulin ≠ 0' diff --git a/tests/test_chi2.py b/tests/test_chi2.py index 579e537..d4cb894 100644 --- a/tests/test_chi2.py +++ b/tests/test_chi2.py @@ -78,3 +78,4 @@ OR (95% CI) = 1.33 (1.11–1.60) RR (95% CI) = 1.11 (1.03–1.18)''' assert result.summary() == expected_summary + assert result._repr_html_() == '
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
StressFalseTrue
Response
False250400
True7501600
\n

χ2(1) = 9.82; p = 0.002*
OR (95% CI) = 1.33 (1.11–1.60)
RR (95% CI) = 1.11 (1.03–1.18)' diff --git a/tests/test_correlation.py b/tests/test_correlation.py index d3a65c0..d9fe328 100644 --- a/tests/test_correlation.py +++ b/tests/test_correlation.py @@ -1,5 +1,5 @@ # scipy-yli: Helpful SciPy utilities and recipes -# Copyright © 2022 Lee Yingtong Li (RunasSudo) +# Copyright © 2022–2023 Lee Yingtong Li (RunasSudo) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as published by @@ -35,6 +35,7 @@ def test_pearsonr_ol11_15(): expected_summary = 'r (95% CI) = 0.65 (0.11–0.89); p = 0.02*' assert result.summary() == expected_summary + assert result._repr_html_() == 'r (95% CI) = 0.65 (0.11–0.89); p = 0.02*' def test_pearsonr_ol11_16(): """Compare yli.pearsonr for Ott & Longnecker (2016) example 11.16""" @@ -64,3 +65,4 @@ def test_spearman_ol11_17(): expected_summary = 'ρ (95% CI) = 0.87 (0.60–0.96); p < 0.001*' # NB: The confidence intervals are unvalidated assert result.summary() == expected_summary + assert result._repr_html_() == 'ρ (95% CI) = 0.87 (0.60–0.96); p < 0.001*' diff --git a/tests/test_mannwhitney.py b/tests/test_mannwhitney.py index 4c87e66..99c60e3 100644 --- a/tests/test_mannwhitney.py +++ b/tests/test_mannwhitney.py @@ -1,5 +1,5 @@ # scipy-yli: Helpful SciPy utilities and recipes -# Copyright © 2022 Lee Yingtong Li (RunasSudo) +# Copyright © 2022–2023 Lee Yingtong Li (RunasSudo) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as published by @@ -42,3 +42,4 @@ U = 6.0; p < 0.001* r = 0.92, Before > After''' assert result.summary() == expected_summary + assert result._repr_html_() == '
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
SampleAfterBefore
Oxygen
Median (IQR)10.75 (10.55–10.95)11.55 (11.20–11.83)
Median (range)10.75 (11.00–12.10)11.55 (11.00–12.10)
\n

U = 6.0; p < 0.001*
r = 0.92, Before > After' diff --git a/tests/test_ordinallogit.py b/tests/test_ordinallogit.py index 355cac0..5b4fb83 100644 --- a/tests/test_ordinallogit.py +++ b/tests/test_ordinallogit.py @@ -62,6 +62,7 @@ somewhat likely/very likely 4.30 (2.72 - 5.88) <0.001* ------------------------------------------------------------'''.format(result.fitted_dt) assert result.summary() == expected_summary + assert result._repr_html_() == '
Ordinal Logistic Regression Results
Dep. Variable:applyNo. Observations:400
Model:Ordinal LogitDf. Model:5
Date:{0:%Y-%m-%d}Df. Residuals:395
Time:{0:%H:%M:%S}Pseudo R2:0.03
Std. Errors:Non-RobustLL-Model:-358.51
LL-Null:-370.60
p (LR):<0.001*
β(95% CI)p
pared1.05(0.53–1.57)<0.001*
public-0.06(-0.64–0.53)=0.84
gpa0.62(0.10–1.13)=0.02*
(Cutoffs)
unlikely/somewhat likely2.20(0.68–3.73)=0.005*
somewhat likely/very likely4.30(2.72–5.88)<0.001*
'.format(result.fitted_dt) def test_brant_ucla(): """Compare RegressionModel.brant with R brant library for UCLA example at https://stats.oarc.ucla.edu/r/dae/ordinal-logistic-regression/""" @@ -97,3 +98,4 @@ public 3.44 1 0.06 gpa 0.18 1 0.67 ''' assert brant_result.summary() == expected_summary + assert brant_result._repr_html_() == '
Brant Test Results
χ2dfp
Omnibus4.343=0.23
pared0.131=0.72
public3.441=0.06
gpa0.181=0.67
' diff --git a/tests/test_regress.py b/tests/test_regress.py index a9777bf..8f5200c 100644 --- a/tests/test_regress.py +++ b/tests/test_regress.py @@ -63,6 +63,7 @@ Dep. Variable: GrowthRet | No. Observations: 20 ----------------------------------------------'''.format(result.fitted_dt) assert result.summary() == expected_summary + assert result._repr_html_() == '
Ordinary Least Squares Regression Results
Dep. Variable:GrowthRetNo. Observations:20
Model:OLSDf. Model:1
Date:{0:%Y-%m-%d}Df. Residuals:18
Time:{0:%H:%M:%S}R2:0.74
Std. Errors:Non-RobustF:52.01
p (F):<0.001*
β(95% CI)p
(Intercept)47.48(38.17–56.78)<0.001*
SoilPh-7.86(-10.15–-5.57)<0.001*
'.format(result.fitted_dt) @pytest.mark.skip('Not implemented in refactored regression implementation') def test_regress_bootstrap_ols_ol11_4(): @@ -184,6 +185,7 @@ GammaGlobulin 1.17 (0.92 - 1.48) 0.19 -----------------------------------------------'''.format(result.fitted_dt) assert result.summary() == expected_summary + assert result._repr_html_() == '
Logistic Regression Results
Dep. Variable:UnhealthyNo. Observations:32
Model:LogitDf. Model:2
Date:{0:%Y-%m-%d}Df. Residuals:29
Time:{0:%H:%M:%S}Pseudo R2:0.26
Std. Errors:Non-RobustLL-Model:-11.47
LL-Null:-15.44
p (LR):0.02*
exp(β)(95% CI)p
(Intercept)0.00(0.00–0.24)=0.03*
Fibrinogen6.80(1.01–45.79)=0.049*
GammaGlobulin1.17(0.92–1.48)=0.19
'.format(result.fitted_dt) def test_regress_logit_ol10_18(): """Compare odds ratios via yli.regress for Ott & Longnecker (2016) example 10.18""" @@ -251,5 +253,4 @@ Dep. Variable: Outcome | No. Observations: 240 ---------------------------------------------'''.format(result.fitted_dt) assert result.summary() == expected_summary - -# TODO: Test for logit_then_regress + assert result._repr_html_() == '
Penalised Logistic Regression Results
Dep. Variable:OutcomeNo. Observations:240
Model:Penalised LogitDf. Model:1
Date:{0:%Y-%m-%d}Pseudo R2:0.37
Time:{0:%H:%M:%S}LL-Model:-66.43
Std. Errors:Non-RobustLL-Null:-105.91
p (LR):<0.001*
β(95% CI)p
(Intercept)-2.28(-2.77–-1.85)<0.001*
Pred5.99(3.95–10.85)<0.001*
'.format(result.fitted_dt) diff --git a/tests/test_ttest.py b/tests/test_ttest.py index 81f0f59..2c44e27 100644 --- a/tests/test_ttest.py +++ b/tests/test_ttest.py @@ -1,5 +1,5 @@ # scipy-yli: Helpful SciPy utilities and recipes -# Copyright © 2022 Lee Yingtong Li (RunasSudo) +# Copyright © 2022–2023 Lee Yingtong Li (RunasSudo) # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as published by @@ -47,3 +47,4 @@ t(18) = 4.24; p < 0.001* Δμ (95% CI) = 0.54 (0.27–0.81), Fresh > Stored''' assert result.summary() == expected_summary + assert result._repr_html_() == '
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
TypeFreshStored
Potency
μ (SD)10.37 (0.32)9.83 (0.24)
\n

t(18) = 4.24; p < 0.001*
Δμ (95% CI) = 0.54 (0.27–0.81), Fresh > Stored'