@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (830) hide show
  1. package/bin/skills/adaptyv/SKILL.md +114 -0
  2. package/bin/skills/adaptyv/reference/api_reference.md +308 -0
  3. package/bin/skills/adaptyv/reference/examples.md +913 -0
  4. package/bin/skills/adaptyv/reference/experiments.md +360 -0
  5. package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
  6. package/bin/skills/aeon/SKILL.md +374 -0
  7. package/bin/skills/aeon/references/anomaly_detection.md +154 -0
  8. package/bin/skills/aeon/references/classification.md +144 -0
  9. package/bin/skills/aeon/references/clustering.md +123 -0
  10. package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
  11. package/bin/skills/aeon/references/distances.md +256 -0
  12. package/bin/skills/aeon/references/forecasting.md +140 -0
  13. package/bin/skills/aeon/references/networks.md +289 -0
  14. package/bin/skills/aeon/references/regression.md +118 -0
  15. package/bin/skills/aeon/references/segmentation.md +163 -0
  16. package/bin/skills/aeon/references/similarity_search.md +187 -0
  17. package/bin/skills/aeon/references/transformations.md +246 -0
  18. package/bin/skills/alphafold-database/SKILL.md +513 -0
  19. package/bin/skills/alphafold-database/references/api_reference.md +423 -0
  20. package/bin/skills/anndata/SKILL.md +400 -0
  21. package/bin/skills/anndata/references/best_practices.md +525 -0
  22. package/bin/skills/anndata/references/concatenation.md +396 -0
  23. package/bin/skills/anndata/references/data_structure.md +314 -0
  24. package/bin/skills/anndata/references/io_operations.md +404 -0
  25. package/bin/skills/anndata/references/manipulation.md +516 -0
  26. package/bin/skills/arboreto/SKILL.md +243 -0
  27. package/bin/skills/arboreto/references/algorithms.md +138 -0
  28. package/bin/skills/arboreto/references/basic_inference.md +151 -0
  29. package/bin/skills/arboreto/references/distributed_computing.md +242 -0
  30. package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
  31. package/bin/skills/astropy/SKILL.md +331 -0
  32. package/bin/skills/astropy/references/coordinates.md +273 -0
  33. package/bin/skills/astropy/references/cosmology.md +307 -0
  34. package/bin/skills/astropy/references/fits.md +396 -0
  35. package/bin/skills/astropy/references/tables.md +489 -0
  36. package/bin/skills/astropy/references/time.md +404 -0
  37. package/bin/skills/astropy/references/units.md +178 -0
  38. package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
  39. package/bin/skills/benchling-integration/SKILL.md +480 -0
  40. package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
  41. package/bin/skills/benchling-integration/references/authentication.md +379 -0
  42. package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
  43. package/bin/skills/biopython/SKILL.md +443 -0
  44. package/bin/skills/biopython/references/advanced.md +577 -0
  45. package/bin/skills/biopython/references/alignment.md +362 -0
  46. package/bin/skills/biopython/references/blast.md +455 -0
  47. package/bin/skills/biopython/references/databases.md +484 -0
  48. package/bin/skills/biopython/references/phylogenetics.md +566 -0
  49. package/bin/skills/biopython/references/sequence_io.md +285 -0
  50. package/bin/skills/biopython/references/structure.md +564 -0
  51. package/bin/skills/biorxiv-database/SKILL.md +483 -0
  52. package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
  53. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
  54. package/bin/skills/bioservices/SKILL.md +361 -0
  55. package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
  56. package/bin/skills/bioservices/references/services_reference.md +636 -0
  57. package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
  58. package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
  59. package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
  60. package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
  61. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
  62. package/bin/skills/brenda-database/SKILL.md +719 -0
  63. package/bin/skills/brenda-database/references/api_reference.md +537 -0
  64. package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
  65. package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
  66. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
  67. package/bin/skills/cellxgene-census/SKILL.md +511 -0
  68. package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
  69. package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
  70. package/bin/skills/chembl-database/SKILL.md +389 -0
  71. package/bin/skills/chembl-database/references/api_reference.md +272 -0
  72. package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
  73. package/bin/skills/cirq/SKILL.md +346 -0
  74. package/bin/skills/cirq/references/building.md +307 -0
  75. package/bin/skills/cirq/references/experiments.md +572 -0
  76. package/bin/skills/cirq/references/hardware.md +515 -0
  77. package/bin/skills/cirq/references/noise.md +515 -0
  78. package/bin/skills/cirq/references/simulation.md +350 -0
  79. package/bin/skills/cirq/references/transformation.md +416 -0
  80. package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
  81. package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
  82. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
  83. package/bin/skills/clinpgx-database/SKILL.md +638 -0
  84. package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
  85. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
  86. package/bin/skills/clinvar-database/SKILL.md +362 -0
  87. package/bin/skills/clinvar-database/references/api_reference.md +227 -0
  88. package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
  89. package/bin/skills/clinvar-database/references/data_formats.md +358 -0
  90. package/bin/skills/cobrapy/SKILL.md +463 -0
  91. package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
  92. package/bin/skills/cobrapy/references/workflows.md +593 -0
  93. package/bin/skills/cosmic-database/SKILL.md +336 -0
  94. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
  95. package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
  96. package/bin/skills/dask/SKILL.md +456 -0
  97. package/bin/skills/dask/references/arrays.md +497 -0
  98. package/bin/skills/dask/references/bags.md +468 -0
  99. package/bin/skills/dask/references/best-practices.md +277 -0
  100. package/bin/skills/dask/references/dataframes.md +368 -0
  101. package/bin/skills/dask/references/futures.md +541 -0
  102. package/bin/skills/dask/references/schedulers.md +504 -0
  103. package/bin/skills/datacommons-client/SKILL.md +255 -0
  104. package/bin/skills/datacommons-client/references/getting_started.md +417 -0
  105. package/bin/skills/datacommons-client/references/node.md +250 -0
  106. package/bin/skills/datacommons-client/references/observation.md +185 -0
  107. package/bin/skills/datacommons-client/references/resolve.md +246 -0
  108. package/bin/skills/datamol/SKILL.md +706 -0
  109. package/bin/skills/datamol/references/conformers_module.md +131 -0
  110. package/bin/skills/datamol/references/core_api.md +130 -0
  111. package/bin/skills/datamol/references/descriptors_viz.md +195 -0
  112. package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
  113. package/bin/skills/datamol/references/io_module.md +109 -0
  114. package/bin/skills/datamol/references/reactions_data.md +218 -0
  115. package/bin/skills/deepchem/SKILL.md +597 -0
  116. package/bin/skills/deepchem/references/api_reference.md +303 -0
  117. package/bin/skills/deepchem/references/workflows.md +491 -0
  118. package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
  119. package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
  120. package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
  121. package/bin/skills/deeptools/SKILL.md +531 -0
  122. package/bin/skills/deeptools/assets/quick_reference.md +58 -0
  123. package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
  124. package/bin/skills/deeptools/references/normalization_methods.md +410 -0
  125. package/bin/skills/deeptools/references/tools_reference.md +533 -0
  126. package/bin/skills/deeptools/references/workflows.md +474 -0
  127. package/bin/skills/deeptools/scripts/validate_files.py +195 -0
  128. package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
  129. package/bin/skills/denario/SKILL.md +215 -0
  130. package/bin/skills/denario/references/examples.md +494 -0
  131. package/bin/skills/denario/references/installation.md +213 -0
  132. package/bin/skills/denario/references/llm_configuration.md +265 -0
  133. package/bin/skills/denario/references/research_pipeline.md +471 -0
  134. package/bin/skills/diffdock/SKILL.md +483 -0
  135. package/bin/skills/diffdock/assets/batch_template.csv +4 -0
  136. package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
  137. package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
  138. package/bin/skills/diffdock/references/parameters_reference.md +163 -0
  139. package/bin/skills/diffdock/references/workflows_examples.md +392 -0
  140. package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
  141. package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
  142. package/bin/skills/diffdock/scripts/setup_check.py +278 -0
  143. package/bin/skills/dnanexus-integration/SKILL.md +383 -0
  144. package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
  145. package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
  146. package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
  147. package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
  148. package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
  149. package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
  150. package/bin/skills/document-skills/docx/SKILL.md +233 -0
  151. package/bin/skills/document-skills/docx/docx-js.md +350 -0
  152. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  153. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  154. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  155. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  156. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  157. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  158. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
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  160. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  161. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  162. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
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  193. package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  194. package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
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  825. package/bin/skills/zarr-python/SKILL.md +779 -0
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  827. package/bin/skills/zinc-database/SKILL.md +404 -0
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@@ -0,0 +1,859 @@
1
+ # Statistical Tests and Diagnostics Reference
2
+
3
+ This document provides comprehensive guidance on statistical tests, diagnostics, and tools available in statsmodels.
4
+
5
+ ## Overview
6
+
7
+ Statsmodels provides extensive statistical testing capabilities:
8
+ - Residual diagnostics and specification tests
9
+ - Hypothesis testing (parametric and non-parametric)
10
+ - Goodness-of-fit tests
11
+ - Multiple comparisons and post-hoc tests
12
+ - Power and sample size calculations
13
+ - Robust covariance matrices
14
+ - Influence and outlier detection
15
+
16
+ ## Residual Diagnostics
17
+
18
+ ### Autocorrelation Tests
19
+
20
+ **Ljung-Box Test**: Tests for autocorrelation in residuals
21
+
22
+ ```python
23
+ from statsmodels.stats.diagnostic import acorr_ljungbox
24
+
25
+ # Test residuals for autocorrelation
26
+ lb_test = acorr_ljungbox(residuals, lags=10, return_df=True)
27
+ print(lb_test)
28
+
29
+ # H0: No autocorrelation up to lag k
30
+ # If p-value < 0.05, reject H0 (autocorrelation present)
31
+ ```
32
+
33
+ **Durbin-Watson Test**: Tests for first-order autocorrelation
34
+
35
+ ```python
36
+ from statsmodels.stats.stattools import durbin_watson
37
+
38
+ dw_stat = durbin_watson(residuals)
39
+ print(f"Durbin-Watson: {dw_stat:.4f}")
40
+
41
+ # DW ≈ 2: no autocorrelation
42
+ # DW < 2: positive autocorrelation
43
+ # DW > 2: negative autocorrelation
44
+ # Exact critical values depend on n and k
45
+ ```
46
+
47
+ **Breusch-Godfrey Test**: More general test for autocorrelation
48
+
49
+ ```python
50
+ from statsmodels.stats.diagnostic import acorr_breusch_godfrey
51
+
52
+ bg_test = acorr_breusch_godfrey(results, nlags=5)
53
+ lm_stat, lm_pval, f_stat, f_pval = bg_test
54
+
55
+ print(f"LM statistic: {lm_stat:.4f}, p-value: {lm_pval:.4f}")
56
+ # H0: No autocorrelation up to lag k
57
+ ```
58
+
59
+ ### Heteroskedasticity Tests
60
+
61
+ **Breusch-Pagan Test**: Tests for heteroskedasticity
62
+
63
+ ```python
64
+ from statsmodels.stats.diagnostic import het_breuschpagan
65
+
66
+ bp_test = het_breuschpagan(residuals, exog)
67
+ lm_stat, lm_pval, f_stat, f_pval = bp_test
68
+
69
+ print(f"Breusch-Pagan test p-value: {lm_pval:.4f}")
70
+ # H0: Homoskedasticity (constant variance)
71
+ # If p-value < 0.05, reject H0 (heteroskedasticity present)
72
+ ```
73
+
74
+ **White Test**: More general test for heteroskedasticity
75
+
76
+ ```python
77
+ from statsmodels.stats.diagnostic import het_white
78
+
79
+ white_test = het_white(residuals, exog)
80
+ lm_stat, lm_pval, f_stat, f_pval = white_test
81
+
82
+ print(f"White test p-value: {lm_pval:.4f}")
83
+ # H0: Homoskedasticity
84
+ ```
85
+
86
+ **ARCH Test**: Tests for autoregressive conditional heteroskedasticity
87
+
88
+ ```python
89
+ from statsmodels.stats.diagnostic import het_arch
90
+
91
+ arch_test = het_arch(residuals, nlags=5)
92
+ lm_stat, lm_pval, f_stat, f_pval = arch_test
93
+
94
+ print(f"ARCH test p-value: {lm_pval:.4f}")
95
+ # H0: No ARCH effects
96
+ # If significant, consider GARCH model
97
+ ```
98
+
99
+ ### Normality Tests
100
+
101
+ **Jarque-Bera Test**: Tests for normality using skewness and kurtosis
102
+
103
+ ```python
104
+ from statsmodels.stats.stattools import jarque_bera
105
+
106
+ jb_stat, jb_pval, skew, kurtosis = jarque_bera(residuals)
107
+
108
+ print(f"Jarque-Bera statistic: {jb_stat:.4f}")
109
+ print(f"p-value: {jb_pval:.4f}")
110
+ print(f"Skewness: {skew:.4f}")
111
+ print(f"Kurtosis: {kurtosis:.4f}")
112
+
113
+ # H0: Residuals are normally distributed
114
+ # Normal: skewness ≈ 0, kurtosis ≈ 3
115
+ ```
116
+
117
+ **Omnibus Test**: Another normality test (also based on skewness/kurtosis)
118
+
119
+ ```python
120
+ from statsmodels.stats.stattools import omni_normtest
121
+
122
+ omni_stat, omni_pval = omni_normtest(residuals)
123
+ print(f"Omnibus test p-value: {omni_pval:.4f}")
124
+ # H0: Normality
125
+ ```
126
+
127
+ **Anderson-Darling Test**: Distribution fit test
128
+
129
+ ```python
130
+ from statsmodels.stats.diagnostic import normal_ad
131
+
132
+ ad_stat, ad_pval = normal_ad(residuals)
133
+ print(f"Anderson-Darling test p-value: {ad_pval:.4f}")
134
+ ```
135
+
136
+ **Lilliefors Test**: Modified Kolmogorov-Smirnov test
137
+
138
+ ```python
139
+ from statsmodels.stats.diagnostic import lilliefors
140
+
141
+ lf_stat, lf_pval = lilliefors(residuals, dist='norm')
142
+ print(f"Lilliefors test p-value: {lf_pval:.4f}")
143
+ ```
144
+
145
+ ### Linearity and Specification Tests
146
+
147
+ **Ramsey RESET Test**: Tests for functional form misspecification
148
+
149
+ ```python
150
+ from statsmodels.stats.diagnostic import linear_reset
151
+
152
+ reset_test = linear_reset(results, power=2)
153
+ f_stat, f_pval = reset_test
154
+
155
+ print(f"RESET test p-value: {f_pval:.4f}")
156
+ # H0: Model is correctly specified (linear)
157
+ # If rejected, may need polynomial terms or transformations
158
+ ```
159
+
160
+ **Harvey-Collier Test**: Tests for linearity
161
+
162
+ ```python
163
+ from statsmodels.stats.diagnostic import linear_harvey_collier
164
+
165
+ hc_stat, hc_pval = linear_harvey_collier(results)
166
+ print(f"Harvey-Collier test p-value: {hc_pval:.4f}")
167
+ # H0: Linear specification is correct
168
+ ```
169
+
170
+ ## Multicollinearity Detection
171
+
172
+ **Variance Inflation Factor (VIF)**:
173
+
174
+ ```python
175
+ from statsmodels.stats.outliers_influence import variance_inflation_factor
176
+ import pandas as pd
177
+
178
+ # Calculate VIF for each variable
179
+ vif_data = pd.DataFrame()
180
+ vif_data["Variable"] = X.columns
181
+ vif_data["VIF"] = [variance_inflation_factor(X.values, i)
182
+ for i in range(X.shape[1])]
183
+
184
+ print(vif_data.sort_values('VIF', ascending=False))
185
+
186
+ # Interpretation:
187
+ # VIF = 1: No correlation with other predictors
188
+ # VIF > 5: Moderate multicollinearity
189
+ # VIF > 10: Serious multicollinearity problem
190
+ # VIF > 20: Severe multicollinearity (consider removing variable)
191
+ ```
192
+
193
+ **Condition Number**: From regression results
194
+
195
+ ```python
196
+ print(f"Condition number: {results.condition_number:.2f}")
197
+
198
+ # Interpretation:
199
+ # < 10: No multicollinearity concern
200
+ # 10-30: Moderate multicollinearity
201
+ # > 30: Strong multicollinearity
202
+ # > 100: Severe multicollinearity
203
+ ```
204
+
205
+ ## Influence and Outlier Detection
206
+
207
+ ### Leverage
208
+
209
+ High leverage points have extreme predictor values.
210
+
211
+ ```python
212
+ from statsmodels.stats.outliers_influence import OLSInfluence
213
+
214
+ influence = results.get_influence()
215
+
216
+ # Hat values (leverage)
217
+ leverage = influence.hat_matrix_diag
218
+
219
+ # Rule of thumb: leverage > 2*p/n or 3*p/n is high
220
+ # p = number of parameters, n = sample size
221
+ threshold = 2 * len(results.params) / len(y)
222
+ high_leverage = np.where(leverage > threshold)[0]
223
+
224
+ print(f"High leverage observations: {high_leverage}")
225
+ ```
226
+
227
+ ### Cook's Distance
228
+
229
+ Measures overall influence of each observation.
230
+
231
+ ```python
232
+ # Cook's distance
233
+ cooks_d = influence.cooks_distance[0]
234
+
235
+ # Rule of thumb: Cook's D > 4/n is influential
236
+ threshold = 4 / len(y)
237
+ influential = np.where(cooks_d > threshold)[0]
238
+
239
+ print(f"Influential observations (Cook's D): {influential}")
240
+
241
+ # Plot
242
+ import matplotlib.pyplot as plt
243
+ plt.stem(range(len(cooks_d)), cooks_d)
244
+ plt.axhline(y=threshold, color='r', linestyle='--', label=f'Threshold (4/n)')
245
+ plt.xlabel('Observation')
246
+ plt.ylabel("Cook's Distance")
247
+ plt.legend()
248
+ plt.show()
249
+ ```
250
+
251
+ ### DFFITS
252
+
253
+ Measures influence on fitted value.
254
+
255
+ ```python
256
+ # DFFITS
257
+ dffits = influence.dffits[0]
258
+
259
+ # Rule of thumb: |DFFITS| > 2*sqrt(p/n) is influential
260
+ p = len(results.params)
261
+ n = len(y)
262
+ threshold = 2 * np.sqrt(p / n)
263
+
264
+ influential_dffits = np.where(np.abs(dffits) > threshold)[0]
265
+ print(f"Influential observations (DFFITS): {influential_dffits}")
266
+ ```
267
+
268
+ ### DFBETAs
269
+
270
+ Measures influence on each coefficient.
271
+
272
+ ```python
273
+ # DFBETAs (one for each parameter)
274
+ dfbetas = influence.dfbetas
275
+
276
+ # Rule of thumb: |DFBETA| > 2/sqrt(n)
277
+ threshold = 2 / np.sqrt(n)
278
+
279
+ for i, param_name in enumerate(results.params.index):
280
+ influential = np.where(np.abs(dfbetas[:, i]) > threshold)[0]
281
+ if len(influential) > 0:
282
+ print(f"Influential for {param_name}: {influential}")
283
+ ```
284
+
285
+ ### Influence Plot
286
+
287
+ ```python
288
+ from statsmodels.graphics.regressionplots import influence_plot
289
+
290
+ fig, ax = plt.subplots(figsize=(12, 8))
291
+ influence_plot(results, ax=ax, criterion='cooks')
292
+ plt.show()
293
+
294
+ # Combines leverage, residuals, and Cook's distance
295
+ # Large bubbles = high Cook's distance
296
+ # Far from x=0 = high leverage
297
+ # Far from y=0 = large residual
298
+ ```
299
+
300
+ ### Studentized Residuals
301
+
302
+ ```python
303
+ # Studentized residuals (outliers)
304
+ student_resid = influence.resid_studentized_internal
305
+
306
+ # External studentized residuals (more conservative)
307
+ student_resid_external = influence.resid_studentized_external
308
+
309
+ # Outliers: |studentized residual| > 3 (or > 2.5)
310
+ outliers = np.where(np.abs(student_resid_external) > 3)[0]
311
+ print(f"Outliers: {outliers}")
312
+ ```
313
+
314
+ ## Hypothesis Testing
315
+
316
+ ### t-tests
317
+
318
+ **One-sample t-test**: Test if mean equals specific value
319
+
320
+ ```python
321
+ from scipy import stats
322
+
323
+ # H0: population mean = mu_0
324
+ t_stat, p_value = stats.ttest_1samp(data, popmean=mu_0)
325
+
326
+ print(f"t-statistic: {t_stat:.4f}")
327
+ print(f"p-value: {p_value:.4f}")
328
+ ```
329
+
330
+ **Two-sample t-test**: Compare means of two groups
331
+
332
+ ```python
333
+ # H0: mean1 = mean2 (equal variances)
334
+ t_stat, p_value = stats.ttest_ind(group1, group2)
335
+
336
+ # Welch's t-test (unequal variances)
337
+ t_stat, p_value = stats.ttest_ind(group1, group2, equal_var=False)
338
+
339
+ print(f"t-statistic: {t_stat:.4f}")
340
+ print(f"p-value: {p_value:.4f}")
341
+ ```
342
+
343
+ **Paired t-test**: Compare paired observations
344
+
345
+ ```python
346
+ # H0: mean difference = 0
347
+ t_stat, p_value = stats.ttest_rel(before, after)
348
+
349
+ print(f"t-statistic: {t_stat:.4f}")
350
+ print(f"p-value: {p_value:.4f}")
351
+ ```
352
+
353
+ ### Proportion Tests
354
+
355
+ **One-proportion test**:
356
+
357
+ ```python
358
+ from statsmodels.stats.proportion import proportions_ztest
359
+
360
+ # H0: proportion = p0
361
+ count = 45 # successes
362
+ nobs = 100 # total observations
363
+ p0 = 0.5 # hypothesized proportion
364
+
365
+ z_stat, p_value = proportions_ztest(count, nobs, value=p0)
366
+
367
+ print(f"z-statistic: {z_stat:.4f}")
368
+ print(f"p-value: {p_value:.4f}")
369
+ ```
370
+
371
+ **Two-proportion test**:
372
+
373
+ ```python
374
+ # H0: proportion1 = proportion2
375
+ counts = [45, 60]
376
+ nobs = [100, 120]
377
+
378
+ z_stat, p_value = proportions_ztest(counts, nobs)
379
+ print(f"z-statistic: {z_stat:.4f}")
380
+ print(f"p-value: {p_value:.4f}")
381
+ ```
382
+
383
+ ### Chi-square Tests
384
+
385
+ **Chi-square test of independence**:
386
+
387
+ ```python
388
+ from scipy.stats import chi2_contingency
389
+
390
+ # Contingency table
391
+ contingency_table = pd.crosstab(variable1, variable2)
392
+
393
+ chi2, p_value, dof, expected = chi2_contingency(contingency_table)
394
+
395
+ print(f"Chi-square statistic: {chi2:.4f}")
396
+ print(f"p-value: {p_value:.4f}")
397
+ print(f"Degrees of freedom: {dof}")
398
+
399
+ # H0: Variables are independent
400
+ ```
401
+
402
+ **Chi-square goodness-of-fit**:
403
+
404
+ ```python
405
+ from scipy.stats import chisquare
406
+
407
+ # Observed frequencies
408
+ observed = [20, 30, 25, 25]
409
+
410
+ # Expected frequencies (equal by default)
411
+ expected = [25, 25, 25, 25]
412
+
413
+ chi2, p_value = chisquare(observed, expected)
414
+
415
+ print(f"Chi-square statistic: {chi2:.4f}")
416
+ print(f"p-value: {p_value:.4f}")
417
+
418
+ # H0: Data follow the expected distribution
419
+ ```
420
+
421
+ ### Non-parametric Tests
422
+
423
+ **Mann-Whitney U test** (independent samples):
424
+
425
+ ```python
426
+ from scipy.stats import mannwhitneyu
427
+
428
+ # H0: Distributions are equal
429
+ u_stat, p_value = mannwhitneyu(group1, group2, alternative='two-sided')
430
+
431
+ print(f"U statistic: {u_stat:.4f}")
432
+ print(f"p-value: {p_value:.4f}")
433
+ ```
434
+
435
+ **Wilcoxon signed-rank test** (paired samples):
436
+
437
+ ```python
438
+ from scipy.stats import wilcoxon
439
+
440
+ # H0: Median difference = 0
441
+ w_stat, p_value = wilcoxon(before, after)
442
+
443
+ print(f"W statistic: {w_stat:.4f}")
444
+ print(f"p-value: {p_value:.4f}")
445
+ ```
446
+
447
+ **Kruskal-Wallis H test** (>2 groups):
448
+
449
+ ```python
450
+ from scipy.stats import kruskal
451
+
452
+ # H0: All groups have same distribution
453
+ h_stat, p_value = kruskal(group1, group2, group3)
454
+
455
+ print(f"H statistic: {h_stat:.4f}")
456
+ print(f"p-value: {p_value:.4f}")
457
+ ```
458
+
459
+ **Sign test**:
460
+
461
+ ```python
462
+ from statsmodels.stats.descriptivestats import sign_test
463
+
464
+ # H0: Median = m0
465
+ result = sign_test(data, m0=0)
466
+ print(result)
467
+ ```
468
+
469
+ ### ANOVA
470
+
471
+ **One-way ANOVA**:
472
+
473
+ ```python
474
+ from scipy.stats import f_oneway
475
+
476
+ # H0: All group means are equal
477
+ f_stat, p_value = f_oneway(group1, group2, group3)
478
+
479
+ print(f"F-statistic: {f_stat:.4f}")
480
+ print(f"p-value: {p_value:.4f}")
481
+ ```
482
+
483
+ **Two-way ANOVA** (with statsmodels):
484
+
485
+ ```python
486
+ from statsmodels.formula.api import ols
487
+ from statsmodels.stats.anova import anova_lm
488
+
489
+ # Fit model
490
+ model = ols('response ~ C(factor1) + C(factor2) + C(factor1):C(factor2)',
491
+ data=df).fit()
492
+
493
+ # ANOVA table
494
+ anova_table = anova_lm(model, typ=2)
495
+ print(anova_table)
496
+ ```
497
+
498
+ **Repeated measures ANOVA**:
499
+
500
+ ```python
501
+ from statsmodels.stats.anova import AnovaRM
502
+
503
+ # Requires long-format data
504
+ aovrm = AnovaRM(df, depvar='score', subject='subject_id', within=['time'])
505
+ results = aovrm.fit()
506
+
507
+ print(results.summary())
508
+ ```
509
+
510
+ ## Multiple Comparisons
511
+
512
+ ### Post-hoc Tests
513
+
514
+ **Tukey's HSD** (Honest Significant Difference):
515
+
516
+ ```python
517
+ from statsmodels.stats.multicomp import pairwise_tukeyhsd
518
+
519
+ # Perform Tukey HSD test
520
+ tukey = pairwise_tukeyhsd(data, groups, alpha=0.05)
521
+
522
+ print(tukey.summary())
523
+
524
+ # Plot confidence intervals
525
+ tukey.plot_simultaneous()
526
+ plt.show()
527
+ ```
528
+
529
+ **Bonferroni correction**:
530
+
531
+ ```python
532
+ from statsmodels.stats.multitest import multipletests
533
+
534
+ # P-values from multiple tests
535
+ p_values = [0.01, 0.03, 0.04, 0.15, 0.001]
536
+
537
+ # Apply correction
538
+ reject, pvals_corrected, alphac_sidak, alphac_bonf = multipletests(
539
+ p_values,
540
+ alpha=0.05,
541
+ method='bonferroni'
542
+ )
543
+
544
+ print("Rejected:", reject)
545
+ print("Corrected p-values:", pvals_corrected)
546
+ ```
547
+
548
+ **False Discovery Rate (FDR)**:
549
+
550
+ ```python
551
+ # FDR correction (less conservative than Bonferroni)
552
+ reject, pvals_corrected, alphac_sidak, alphac_bonf = multipletests(
553
+ p_values,
554
+ alpha=0.05,
555
+ method='fdr_bh' # Benjamini-Hochberg
556
+ )
557
+
558
+ print("Rejected:", reject)
559
+ print("Corrected p-values:", pvals_corrected)
560
+ ```
561
+
562
+ ## Robust Covariance Matrices
563
+
564
+ ### Heteroskedasticity-Consistent (HC) Standard Errors
565
+
566
+ ```python
567
+ # After fitting OLS
568
+ results = sm.OLS(y, X).fit()
569
+
570
+ # HC0 (White's heteroskedasticity-consistent SEs)
571
+ results_hc0 = results.get_robustcov_results(cov_type='HC0')
572
+
573
+ # HC1 (degrees of freedom adjustment)
574
+ results_hc1 = results.get_robustcov_results(cov_type='HC1')
575
+
576
+ # HC2 (leverage adjustment)
577
+ results_hc2 = results.get_robustcov_results(cov_type='HC2')
578
+
579
+ # HC3 (most conservative, recommended for small samples)
580
+ results_hc3 = results.get_robustcov_results(cov_type='HC3')
581
+
582
+ print("Standard OLS SEs:", results.bse)
583
+ print("Robust HC3 SEs:", results_hc3.bse)
584
+ ```
585
+
586
+ ### HAC (Heteroskedasticity and Autocorrelation Consistent)
587
+
588
+ **Newey-West standard errors**:
589
+
590
+ ```python
591
+ # For time series with autocorrelation and heteroskedasticity
592
+ results_hac = results.get_robustcov_results(cov_type='HAC', maxlags=4)
593
+
594
+ print("HAC (Newey-West) SEs:", results_hac.bse)
595
+ print(results_hac.summary())
596
+ ```
597
+
598
+ ### Cluster-Robust Standard Errors
599
+
600
+ ```python
601
+ # For clustered/grouped data
602
+ results_cluster = results.get_robustcov_results(
603
+ cov_type='cluster',
604
+ groups=cluster_ids
605
+ )
606
+
607
+ print("Cluster-robust SEs:", results_cluster.bse)
608
+ ```
609
+
610
+ ## Descriptive Statistics
611
+
612
+ **Basic descriptive statistics**:
613
+
614
+ ```python
615
+ from statsmodels.stats.api import DescrStatsW
616
+
617
+ # Comprehensive descriptive stats
618
+ desc = DescrStatsW(data)
619
+
620
+ print("Mean:", desc.mean)
621
+ print("Std Dev:", desc.std)
622
+ print("Variance:", desc.var)
623
+ print("Confidence interval:", desc.tconfint_mean())
624
+
625
+ # Quantiles
626
+ print("Median:", desc.quantile(0.5))
627
+ print("IQR:", desc.quantile([0.25, 0.75]))
628
+ ```
629
+
630
+ **Weighted statistics**:
631
+
632
+ ```python
633
+ # With weights
634
+ desc_weighted = DescrStatsW(data, weights=weights)
635
+
636
+ print("Weighted mean:", desc_weighted.mean)
637
+ print("Weighted std:", desc_weighted.std)
638
+ ```
639
+
640
+ **Compare two groups**:
641
+
642
+ ```python
643
+ from statsmodels.stats.weightstats import CompareMeans
644
+
645
+ # Create comparison object
646
+ cm = CompareMeans(DescrStatsW(group1), DescrStatsW(group2))
647
+
648
+ # t-test
649
+ print("t-test:", cm.ttest_ind())
650
+
651
+ # Confidence interval for difference
652
+ print("CI for difference:", cm.tconfint_diff())
653
+
654
+ # Test for equal variances
655
+ print("Equal variance test:", cm.test_equal_var())
656
+ ```
657
+
658
+ ## Power Analysis and Sample Size
659
+
660
+ **Power for t-test**:
661
+
662
+ ```python
663
+ from statsmodels.stats.power import tt_ind_solve_power
664
+
665
+ # Solve for sample size
666
+ effect_size = 0.5 # Cohen's d
667
+ alpha = 0.05
668
+ power = 0.8
669
+
670
+ n = tt_ind_solve_power(effect_size=effect_size,
671
+ alpha=alpha,
672
+ power=power,
673
+ alternative='two-sided')
674
+
675
+ print(f"Required sample size per group: {n:.0f}")
676
+
677
+ # Solve for power given n
678
+ power = tt_ind_solve_power(effect_size=0.5,
679
+ nobs1=50,
680
+ alpha=0.05,
681
+ alternative='two-sided')
682
+
683
+ print(f"Power: {power:.4f}")
684
+ ```
685
+
686
+ **Power for proportion test**:
687
+
688
+ ```python
689
+ from statsmodels.stats.power import zt_ind_solve_power
690
+
691
+ # For proportion tests (z-test)
692
+ effect_size = 0.3 # Difference in proportions
693
+ alpha = 0.05
694
+ power = 0.8
695
+
696
+ n = zt_ind_solve_power(effect_size=effect_size,
697
+ alpha=alpha,
698
+ power=power,
699
+ alternative='two-sided')
700
+
701
+ print(f"Required sample size per group: {n:.0f}")
702
+ ```
703
+
704
+ **Power curves**:
705
+
706
+ ```python
707
+ from statsmodels.stats.power import TTestIndPower
708
+ import matplotlib.pyplot as plt
709
+
710
+ # Create power analysis object
711
+ analysis = TTestIndPower()
712
+
713
+ # Plot power curves for different sample sizes
714
+ sample_sizes = range(10, 200, 10)
715
+ effect_sizes = [0.2, 0.5, 0.8] # Small, medium, large
716
+
717
+ fig, ax = plt.subplots(figsize=(10, 6))
718
+
719
+ for es in effect_sizes:
720
+ power = [analysis.solve_power(effect_size=es, nobs1=n, alpha=0.05)
721
+ for n in sample_sizes]
722
+ ax.plot(sample_sizes, power, label=f'Effect size = {es}')
723
+
724
+ ax.axhline(y=0.8, color='r', linestyle='--', label='Power = 0.8')
725
+ ax.set_xlabel('Sample size per group')
726
+ ax.set_ylabel('Power')
727
+ ax.set_title('Power Curves for Two-Sample t-test')
728
+ ax.legend()
729
+ ax.grid(True, alpha=0.3)
730
+ plt.show()
731
+ ```
732
+
733
+ ## Effect Sizes
734
+
735
+ **Cohen's d** (standardized mean difference):
736
+
737
+ ```python
738
+ def cohens_d(group1, group2):
739
+ \"\"\"Calculate Cohen's d for independent samples\"\"\"
740
+ n1, n2 = len(group1), len(group2)
741
+ var1, var2 = np.var(group1, ddof=1), np.var(group2, ddof=1)
742
+
743
+ # Pooled standard deviation
744
+ pooled_std = np.sqrt(((n1-1)*var1 + (n2-1)*var2) / (n1+n2-2))
745
+
746
+ # Cohen's d
747
+ d = (np.mean(group1) - np.mean(group2)) / pooled_std
748
+
749
+ return d
750
+
751
+ d = cohens_d(group1, group2)
752
+ print(f"Cohen's d: {d:.4f}")
753
+
754
+ # Interpretation:
755
+ # |d| < 0.2: negligible
756
+ # |d| ~ 0.2: small
757
+ # |d| ~ 0.5: medium
758
+ # |d| ~ 0.8: large
759
+ ```
760
+
761
+ **Eta-squared** (for ANOVA):
762
+
763
+ ```python
764
+ # From ANOVA table
765
+ # η² = SS_between / SS_total
766
+
767
+ def eta_squared(anova_table):
768
+ return anova_table['sum_sq'][0] / anova_table['sum_sq'].sum()
769
+
770
+ # After running ANOVA
771
+ eta_sq = eta_squared(anova_table)
772
+ print(f"Eta-squared: {eta_sq:.4f}")
773
+
774
+ # Interpretation:
775
+ # 0.01: small effect
776
+ # 0.06: medium effect
777
+ # 0.14: large effect
778
+ ```
779
+
780
+ ## Contingency Tables and Association
781
+
782
+ **McNemar's test** (paired binary data):
783
+
784
+ ```python
785
+ from statsmodels.stats.contingency_tables import mcnemar
786
+
787
+ # 2x2 contingency table
788
+ table = [[a, b],
789
+ [c, d]]
790
+
791
+ result = mcnemar(table, exact=True) # or exact=False for large samples
792
+ print(f"p-value: {result.pvalue:.4f}")
793
+
794
+ # H0: Marginal probabilities are equal
795
+ ```
796
+
797
+ **Cochran-Mantel-Haenszel test**:
798
+
799
+ ```python
800
+ from statsmodels.stats.contingency_tables import StratifiedTable
801
+
802
+ # For stratified 2x2 tables
803
+ strat_table = StratifiedTable(tables_list)
804
+ result = strat_table.test_null_odds()
805
+
806
+ print(f"p-value: {result.pvalue:.4f}")
807
+ ```
808
+
809
+ ## Treatment Effects and Causal Inference
810
+
811
+ **Propensity score matching**:
812
+
813
+ ```python
814
+ from statsmodels.treatment import propensity_score
815
+
816
+ # Estimate propensity scores
817
+ ps_model = sm.Logit(treatment, X).fit()
818
+ propensity_scores = ps_model.predict(X)
819
+
820
+ # Use for matching or weighting
821
+ # (manual implementation of matching needed)
822
+ ```
823
+
824
+ **Difference-in-differences**:
825
+
826
+ ```python
827
+ # Did formula: outcome ~ treatment * post
828
+ model = ols('outcome ~ treatment + post + treatment:post', data=df).fit()
829
+
830
+ # DiD estimate is the interaction coefficient
831
+ did_estimate = model.params['treatment:post']
832
+ print(f"DiD estimate: {did_estimate:.4f}")
833
+ ```
834
+
835
+ ## Best Practices
836
+
837
+ 1. **Always check assumptions**: Test before interpreting results
838
+ 2. **Report effect sizes**: Not just p-values
839
+ 3. **Use appropriate tests**: Match test to data type and distribution
840
+ 4. **Correct for multiple comparisons**: When conducting many tests
841
+ 5. **Check sample size**: Ensure adequate power
842
+ 6. **Visual inspection**: Plot data before testing
843
+ 7. **Report confidence intervals**: Along with point estimates
844
+ 8. **Consider alternatives**: Non-parametric when assumptions violated
845
+ 9. **Robust standard errors**: Use when heteroskedasticity/autocorrelation present
846
+ 10. **Document decisions**: Note which tests used and why
847
+
848
+ ## Common Pitfalls
849
+
850
+ 1. **Not checking test assumptions**: May invalidate results
851
+ 2. **Multiple testing without correction**: Inflated Type I error
852
+ 3. **Using parametric tests on non-normal data**: Consider non-parametric
853
+ 4. **Ignoring heteroskedasticity**: Use robust SEs
854
+ 5. **Confusing statistical and practical significance**: Check effect sizes
855
+ 6. **Not reporting confidence intervals**: Only p-values insufficient
856
+ 7. **Using wrong test**: Match test to research question
857
+ 8. **Insufficient power**: Risk of Type II error (false negatives)
858
+ 9. **p-hacking**: Testing many specifications until significant
859
+ 10. **Overinterpreting p-values**: Remember limitations of NHST