scitex 2.1.3__py3-none-any.whl → 2.4.0__py3-none-any.whl

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 (1388) hide show
  1. scitex/__init__.py +90 -10
  2. scitex/__main__.py +0 -110
  3. scitex/__version__.py +1 -1
  4. scitex/_optional_deps.py +0 -0
  5. scitex/ai/_gen_ai/_BaseGenAI.py +1 -1
  6. scitex/ai/classification/examples/timeseries_cv_demo.py +0 -0
  7. scitex/ai/classification/reporters/_ClassificationReporter.py +1 -1
  8. scitex/ai/classification/reporters/__init__.py +0 -0
  9. scitex/ai/classification/reporters/reporter_utils/_Plotter.py +1 -1
  10. scitex/ai/classification/reporters/reporter_utils/__init__.py +0 -0
  11. scitex/ai/classification/reporters/reporter_utils/aggregation.py +0 -0
  12. scitex/ai/classification/reporters/reporter_utils/data_models.py +0 -0
  13. scitex/ai/classification/reporters/reporter_utils/reporting.py +0 -0
  14. scitex/ai/classification/reporters/reporter_utils/validation.py +0 -0
  15. scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +2 -2
  16. scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +2 -2
  17. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +6 -6
  18. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +6 -6
  19. scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +2 -2
  20. scitex/ai/classification/timeseries/_normalize_timestamp.py +1 -1
  21. scitex/ai/feature_extraction/vit.py +1 -1
  22. scitex/ai/feature_selection/__init__.py +0 -0
  23. scitex/ai/feature_selection/feature_selection.py +0 -0
  24. scitex/ai/loss/multi_task_loss.py +1 -1
  25. scitex/ai/metrics/_calc_bacc.py +0 -0
  26. scitex/ai/metrics/_calc_bacc_from_conf_mat.py +0 -0
  27. scitex/ai/metrics/_calc_clf_report.py +0 -0
  28. scitex/ai/metrics/_calc_conf_mat.py +0 -0
  29. scitex/ai/metrics/_calc_feature_importance.py +0 -0
  30. scitex/ai/metrics/_calc_mcc.py +0 -0
  31. scitex/ai/metrics/_calc_pre_rec_auc.py +0 -0
  32. scitex/ai/metrics/_calc_roc_auc.py +0 -0
  33. scitex/ai/metrics/_calc_seizure_prediction_metrics.py +1 -1
  34. scitex/ai/metrics/_normalize_labels.py +0 -0
  35. scitex/ai/plt/__init__.py +2 -2
  36. scitex/ai/plt/_plot_feature_importance.py +1 -1
  37. scitex/ai/plt/_plot_learning_curve.py +1 -1
  38. scitex/ai/plt/_plot_optuna_study.py +1 -1
  39. scitex/ai/plt/_plot_pre_rec_curve.py +1 -1
  40. scitex/ai/plt/_plot_roc_curve.py +1 -1
  41. scitex/ai/plt/{_plot_conf_mat.py → _stx_conf_mat.py} +4 -4
  42. scitex/ai/sampling/undersample.py +1 -1
  43. scitex/ai/training/_LearningCurveLogger.py +1 -1
  44. scitex/benchmark/__init__.py +3 -3
  45. scitex/benchmark/benchmark.py +0 -0
  46. scitex/benchmark/monitor.py +0 -0
  47. scitex/benchmark/profiler.py +0 -0
  48. scitex/browser/__init__.py +0 -0
  49. scitex/browser/automation/CookieHandler.py +1 -1
  50. scitex/browser/automation/__init__.py +0 -0
  51. scitex/browser/collaboration/__init__.py +0 -0
  52. scitex/browser/collaboration/auth_helpers.py +0 -0
  53. scitex/browser/collaboration/collaborative_agent.py +0 -0
  54. scitex/browser/collaboration/credential_manager.py +0 -0
  55. scitex/browser/collaboration/interactive_panel.py +0 -0
  56. scitex/browser/collaboration/persistent_browser.py +0 -0
  57. scitex/browser/collaboration/shared_session.py +0 -0
  58. scitex/browser/collaboration/standard_interactions.py +0 -0
  59. scitex/browser/collaboration/visual_feedback.py +0 -0
  60. scitex/browser/core/BrowserMixin.py +1 -1
  61. scitex/browser/core/ChromeProfileManager.py +1 -1
  62. scitex/browser/core/__init__.py +0 -0
  63. scitex/browser/debugging/_browser_logger.py +1 -1
  64. scitex/browser/debugging/_highlight_element.py +1 -1
  65. scitex/browser/debugging/_show_grid.py +1 -1
  66. scitex/browser/interaction/click_center.py +1 -1
  67. scitex/browser/interaction/click_with_fallbacks.py +1 -1
  68. scitex/browser/interaction/close_popups.py +1 -1
  69. scitex/browser/interaction/fill_with_fallbacks.py +1 -1
  70. scitex/browser/pdf/__init__.py +0 -0
  71. scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +1 -1
  72. scitex/browser/pdf/detect_chrome_pdf_viewer.py +1 -1
  73. scitex/browser/remote/CaptchaHandler.py +0 -0
  74. scitex/browser/remote/ZenRowsAPIClient.py +0 -0
  75. scitex/browser/remote/__init__.py +0 -0
  76. scitex/browser/stealth/HumanBehavior.py +1 -1
  77. scitex/browser/stealth/StealthManager.py +1 -1
  78. scitex/browser/stealth/__init__.py +0 -0
  79. scitex/cli/__init__.py +0 -0
  80. scitex/cli/cloud.py +200 -9
  81. scitex/cli/main.py +139 -10
  82. scitex/cli/scholar.py +0 -0
  83. scitex/cli/security.py +109 -0
  84. scitex/cli/web.py +409 -0
  85. scitex/cli/writer.py +270 -0
  86. scitex/cloud/__init__.py +131 -0
  87. scitex/cloud/_matplotlib_hook.py +146 -0
  88. scitex/config/PriorityConfig.py +195 -0
  89. scitex/config/__init__.py +24 -0
  90. scitex/db/_delete_duplicates.py +1 -1
  91. scitex/db/_inspect_optimized.py +0 -0
  92. scitex/db/_postgresql/_PostgreSQL.py +1 -1
  93. scitex/db/_sqlite3/_SQLite3.py +1 -1
  94. scitex/decorators/__init__.py +9 -0
  95. scitex/dict/_DotDict.py +65 -138
  96. scitex/dict/__init__.py +1 -0
  97. scitex/dict/_flatten.py +2 -10
  98. scitex/dict/_listed_dict.py +2 -3
  99. scitex/dict/_pop_keys.py +2 -3
  100. scitex/dict/_replace.py +1 -3
  101. scitex/dict/_safe_merge.py +6 -16
  102. scitex/dict/_to_str.py +6 -3
  103. scitex/dsp/_demo_sig.py +1 -1
  104. scitex/dsp/_detect_ripples.py +1 -1
  105. scitex/dsp/_ensure_3d.py +1 -1
  106. scitex/dsp/_hilbert.py +2 -2
  107. scitex/dsp/_misc.py +1 -1
  108. scitex/dsp/_modulation_index.py +2 -2
  109. scitex/dsp/_pac.py +3 -3
  110. scitex/dsp/_psd.py +2 -2
  111. scitex/dsp/_resample.py +1 -1
  112. scitex/dsp/_transform.py +1 -1
  113. scitex/dsp/_wavelet.py +2 -2
  114. scitex/dsp/add_noise.py +1 -1
  115. scitex/dsp/filt.py +6 -6
  116. scitex/dsp/norm.py +1 -1
  117. scitex/dsp/reference.py +1 -1
  118. scitex/dsp/utils/_differential_bandpass_filters.py +3 -3
  119. scitex/dsp/utils/_ensure_3d.py +1 -1
  120. scitex/dsp/utils/_zero_pad.py +1 -1
  121. scitex/dsp/utils/filter.py +2 -2
  122. scitex/dt/_normalize_timestamp.py +1 -1
  123. scitex/gen/_check_host.py +1 -1
  124. scitex/gen/_deprecated_close.py +3 -3
  125. scitex/gen/_deprecated_start.py +1 -1
  126. scitex/gen/_norm.py +2 -2
  127. scitex/gen/_norm_cache.py +1 -1
  128. scitex/gen/_symlink.py +1 -1
  129. scitex/gen/_to_rank.py +1 -1
  130. scitex/gen/_transpose.py +1 -1
  131. scitex/git/__init__.py +0 -0
  132. scitex/git/_branch.py +5 -3
  133. scitex/git/_clone.py +35 -6
  134. scitex/git/_commit.py +3 -2
  135. scitex/git/_constants.py +0 -0
  136. scitex/git/_init.py +0 -0
  137. scitex/git/_remote.py +1 -1
  138. scitex/git/_result.py +0 -0
  139. scitex/git/_retry.py +0 -0
  140. scitex/git/_session.py +1 -1
  141. scitex/git/_types.py +0 -0
  142. scitex/git/_utils.py +0 -0
  143. scitex/git/_validation.py +0 -0
  144. scitex/git/_workflow.py +1 -1
  145. scitex/io/README.md +65 -1
  146. scitex/io/__init__.py +12 -0
  147. scitex/io/_glob.py +1 -1
  148. scitex/io/_load.py +59 -9
  149. scitex/io/_load_cache.py +0 -0
  150. scitex/io/_load_configs.py +9 -4
  151. scitex/io/_load_modules/_image.py +48 -4
  152. scitex/io/_load_modules/_pdf.py +95 -32
  153. scitex/io/_load_modules/_sqlite3.py +1 -1
  154. scitex/io/_metadata.py +298 -0
  155. scitex/io/_path.py +2 -2
  156. scitex/io/_qr_utils.py +75 -0
  157. scitex/io/_save.py +324 -45
  158. scitex/io/_save_modules/_image.py +92 -23
  159. scitex/io/_save_modules/_tex.py +1 -1
  160. scitex/io/memo.md +2827 -0
  161. scitex/io/utils/h5_to_zarr.py +1 -1
  162. scitex/linalg/_distance.py +2 -2
  163. scitex/linalg/_geometric_median.py +1 -1
  164. scitex/logging/README.md +1 -1
  165. scitex/logging/_Tee.py +2 -2
  166. scitex/logging/_context.py +0 -0
  167. scitex/logging/_formatters.py +9 -2
  168. scitex/logging/_handlers.py +0 -0
  169. scitex/logging/_levels.py +0 -0
  170. scitex/logging/_logger.py +59 -20
  171. scitex/logging/_print_capture.py +0 -0
  172. scitex/ml/__init__.py +1 -1
  173. scitex/nn/_Filters.py +6 -6
  174. scitex/nn/_Spectrogram.py +1 -1
  175. scitex/nn/_Wavelet.py +2 -2
  176. scitex/pd/_force_df.py +1 -1
  177. scitex/plt/README.md +26 -1
  178. scitex/plt/__init__.py +559 -8
  179. scitex/plt/_subplots/_AxesWrapper.py +2 -1
  180. scitex/plt/_subplots/_AxisWrapper.py +98 -50
  181. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +93 -4
  182. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +267 -127
  183. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +49 -8
  184. scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +2 -2
  185. scitex/plt/_subplots/_FigWrapper.py +104 -10
  186. scitex/plt/_subplots/_SubplotsWrapper.py +471 -26
  187. scitex/plt/_subplots/_export_as_csv.py +193 -57
  188. scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +26 -16
  189. scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +0 -0
  190. scitex/plt/_subplots/_export_as_csv_formatters/_format_contourf.py +54 -0
  191. scitex/plt/_subplots/_export_as_csv_formatters/_format_hexbin.py +41 -0
  192. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist2d.py +41 -0
  193. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +59 -47
  194. scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +42 -0
  195. scitex/plt/_subplots/_export_as_csv_formatters/_format_pie.py +42 -0
  196. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +72 -35
  197. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +1 -1
  198. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_imshow.py +40 -0
  199. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +2 -2
  200. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +0 -0
  201. scitex/plt/_subplots/_export_as_csv_formatters/_format_quiver.py +53 -0
  202. scitex/plt/_subplots/_export_as_csv_formatters/_format_stem.py +42 -0
  203. scitex/plt/_subplots/_export_as_csv_formatters/_format_step.py +42 -0
  204. scitex/plt/_subplots/_export_as_csv_formatters/_format_streamplot.py +48 -0
  205. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_conf_mat.py → _format_stx_conf_mat.py} +2 -2
  206. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_ecdf.py → _format_stx_ecdf.py} +2 -2
  207. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_fillv.py → _format_stx_fillv.py} +2 -2
  208. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_heatmap.py → _format_stx_heatmap.py} +2 -2
  209. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_image.py → _format_stx_image.py} +2 -2
  210. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_joyplot.py → _format_stx_joyplot.py} +2 -2
  211. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_line.py → _format_stx_line.py} +3 -3
  212. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_mean_ci.py → _format_stx_mean_ci.py} +2 -2
  213. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_mean_std.py → _format_stx_mean_std.py} +2 -2
  214. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_median_iqr.py → _format_stx_median_iqr.py} +2 -2
  215. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_raster.py → _format_stx_raster.py} +2 -2
  216. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_rectangle.py → _format_stx_rectangle.py} +1 -1
  217. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_scatter_hist.py → _format_stx_scatter_hist.py} +2 -2
  218. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_shaded_line.py → _format_stx_shaded_line.py} +2 -2
  219. scitex/plt/_subplots/_export_as_csv_formatters/{_format_plot_violin.py → _format_stx_violin.py} +2 -2
  220. scitex/plt/_subplots/_export_as_csv_formatters/verify_formatters.py +23 -23
  221. scitex/plt/ax/__init__.py +25 -16
  222. scitex/plt/ax/_plot/__init__.py +32 -30
  223. scitex/plt/ax/_plot/_add_fitted_line.py +151 -0
  224. scitex/plt/ax/_plot/_plot_statistical_shaded_line.py +104 -76
  225. scitex/plt/ax/_plot/{_plot_conf_mat.py → _stx_conf_mat.py} +12 -12
  226. scitex/plt/ax/_plot/_stx_ecdf.py +109 -0
  227. scitex/plt/ax/_plot/{_plot_fillv.py → _stx_fillv.py} +7 -7
  228. scitex/plt/ax/_plot/_stx_heatmap.py +366 -0
  229. scitex/plt/ax/_plot/{_plot_image.py → _stx_image.py} +1 -1
  230. scitex/plt/ax/_plot/_stx_joyplot.py +113 -0
  231. scitex/plt/ax/_plot/{_plot_raster.py → _stx_raster.py} +37 -25
  232. scitex/plt/ax/_plot/{_plot_rectangle.py → _stx_rectangle.py} +10 -9
  233. scitex/plt/ax/_plot/{_plot_scatter_hist.py → _stx_scatter_hist.py} +1 -1
  234. scitex/plt/ax/_plot/_stx_shaded_line.py +215 -0
  235. scitex/plt/ax/_plot/{_plot_violin.py → _stx_violin.py} +13 -6
  236. scitex/plt/ax/_style/__init__.py +4 -0
  237. scitex/plt/ax/_style/_auto_scale_axis.py +195 -0
  238. scitex/plt/ax/_style/_format_units.py +103 -0
  239. scitex/plt/ax/_style/_set_ticks.py +2 -2
  240. scitex/plt/ax/_style/_style_barplot.py +69 -0
  241. scitex/plt/ax/_style/_style_boxplot.py +144 -0
  242. scitex/plt/ax/_style/_style_errorbar.py +82 -0
  243. scitex/plt/ax/_style/_style_scatter.py +82 -0
  244. scitex/plt/ax/_style/_style_suptitles.py +76 -0
  245. scitex/plt/ax/_style/_style_violinplot.py +109 -0
  246. scitex/plt/color/_PARAMS.py +2 -2
  247. scitex/plt/color/_colors.py +1 -1
  248. scitex/plt/color/_vizualize_colors.py +3 -3
  249. scitex/plt/styles/SCITEX_STYLE.yaml +104 -0
  250. scitex/plt/styles/__init__.py +57 -0
  251. scitex/plt/styles/_plot_defaults.py +209 -0
  252. scitex/plt/styles/_plot_postprocess.py +518 -0
  253. scitex/plt/styles/_style_loader.py +268 -0
  254. scitex/plt/styles/presets.py +208 -0
  255. scitex/plt/utils/__init__.py +21 -0
  256. scitex/plt/utils/_calc_bacc_from_conf_mat.py +1 -1
  257. scitex/plt/utils/_collect_figure_metadata.py +620 -0
  258. scitex/plt/utils/_colorbar.py +72 -10
  259. scitex/plt/utils/_configure_mpl.py +194 -68
  260. scitex/plt/utils/_crop.py +246 -0
  261. scitex/plt/utils/_dimension_viewer.py +437 -0
  262. scitex/plt/utils/_figure_from_axes_mm.py +353 -0
  263. scitex/plt/utils/_figure_mm.py +356 -0
  264. scitex/plt/utils/_get_actual_font.py +56 -0
  265. scitex/plt/utils/_units.py +123 -0
  266. scitex/{rng/README.md → repro/README_RandomStateManager.md} +2 -2
  267. scitex/{rng → repro}/_RandomStateManager.py +99 -10
  268. scitex/repro/__init__.py +32 -50
  269. scitex/repro/_gen_ID.py +84 -0
  270. scitex/repro/_gen_timestamp.py +78 -0
  271. scitex/repro/_hash_array.py +143 -0
  272. scitex/reproduce/__init__.py +2 -2
  273. scitex/resource/_get_specs.py +1 -1
  274. scitex/resource/_log_processor_usages.py +4 -4
  275. scitex/rng/__init__.py +20 -27
  276. scitex/scholar/auth/core/__init__.py +0 -0
  277. scitex/scholar/auth/gateway/__init__.py +0 -0
  278. scitex/scholar/auth/providers/OpenAthensAuthenticator.py +3 -3
  279. scitex/scholar/auth/providers/__init__.py +0 -0
  280. scitex/scholar/auth/session/__init__.py +0 -0
  281. scitex/scholar/auth/sso/BaseSSOAutomator.py +1 -1
  282. scitex/scholar/auth/sso/__init__.py +0 -0
  283. scitex/scholar/browser/utils/__init__.py +0 -0
  284. scitex/scholar/cli/_CentralArgumentParser.py +0 -0
  285. scitex/scholar/cli/_argument_groups.py +0 -0
  286. scitex/scholar/cli/_doi_operations.py +0 -0
  287. scitex/scholar/cli/_url_utils.py +0 -0
  288. scitex/scholar/cli/handlers/__init__.py +0 -0
  289. scitex/scholar/cli/handlers/bibtex_handler.py +0 -0
  290. scitex/scholar/cli/handlers/doi_handler.py +0 -0
  291. scitex/scholar/cli/handlers/project_handler.py +0 -0
  292. scitex/scholar/cli/open_browser.py +0 -0
  293. scitex/scholar/cli/open_browser_auto.py +0 -0
  294. scitex/scholar/cli/open_browser_monitored.py +0 -0
  295. scitex/scholar/config/PublisherRules.py +0 -0
  296. scitex/scholar/config/core/_PathManager.py +42 -0
  297. scitex/scholar/core/__init__.py +0 -0
  298. scitex/scholar/docs/template.py +1 -1
  299. scitex/scholar/docs/to_claude/guidelines/python/env.md +1 -1
  300. scitex/scholar/docs/to_claude/guidelines/python/general.md +1 -1
  301. scitex/scholar/examples/07_storage_integration.py +1 -1
  302. scitex/scholar/examples/zotero_integration.py +0 -0
  303. scitex/scholar/impact_factor/estimation/ImpactFactorEstimationEngine.py +0 -0
  304. scitex/scholar/impact_factor/estimation/__init__.py +0 -0
  305. scitex/scholar/impact_factor/estimation/build_database.py +0 -0
  306. scitex/scholar/impact_factor/estimation/core/__init__.py +0 -0
  307. scitex/scholar/impact_factor/estimation/core/cache_manager.py +0 -0
  308. scitex/scholar/impact_factor/estimation/core/calculator.py +0 -0
  309. scitex/scholar/impact_factor/estimation/core/journal_matcher.py +0 -0
  310. scitex/scholar/impact_factor/jcr/ImpactFactorJCREngine.py +1 -1
  311. scitex/scholar/impact_factor/jcr/build_database.py +1 -1
  312. scitex/scholar/integration/__init__.py +0 -0
  313. scitex/scholar/integration/base.py +0 -0
  314. scitex/scholar/integration/mendeley/__init__.py +0 -0
  315. scitex/scholar/integration/mendeley/exporter.py +0 -0
  316. scitex/scholar/integration/mendeley/importer.py +0 -0
  317. scitex/scholar/integration/mendeley/linker.py +0 -0
  318. scitex/scholar/integration/mendeley/mapper.py +0 -0
  319. scitex/scholar/integration/zotero/__init__.py +0 -0
  320. scitex/scholar/integration/zotero/__main__.py +0 -0
  321. scitex/scholar/integration/zotero/exporter.py +0 -0
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  1101. scitex/scholar/url_finder/translators/individual/voxeu.py +0 -0
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  1110. scitex/scholar/url_finder/translators/individual/westlaw_uk.py +0 -0
  1111. scitex/scholar/url_finder/translators/individual/who.py +0 -0
  1112. scitex/scholar/url_finder/translators/individual/wikidata.py +0 -0
  1113. scitex/scholar/url_finder/translators/individual/wikidata_quickstatements.py +0 -0
  1114. scitex/scholar/url_finder/translators/individual/wikileaks_plusd.py +0 -0
  1115. scitex/scholar/url_finder/translators/individual/wikimedia_commons.py +0 -0
  1116. scitex/scholar/url_finder/translators/individual/wikipedia.py +0 -0
  1117. scitex/scholar/url_finder/translators/individual/wikipedia_citation_templates.py +0 -0
  1118. scitex/scholar/url_finder/translators/individual/wikisource.py +0 -0
  1119. scitex/scholar/url_finder/translators/individual/wikiwand.py +0 -0
  1120. scitex/scholar/url_finder/translators/individual/wiktionary.py +0 -0
  1121. scitex/scholar/url_finder/translators/individual/wildlife_biology_in_practice.py +0 -0
  1122. scitex/scholar/url_finder/translators/individual/wiley.py +0 -0
  1123. scitex/scholar/url_finder/translators/individual/wiley_online_library.py +0 -0
  1124. scitex/scholar/url_finder/translators/individual/wilson_center_digital_archive.py +0 -0
  1125. scitex/scholar/url_finder/translators/individual/winnipeg_free_press.py +0 -0
  1126. scitex/scholar/url_finder/translators/individual/wipo.py +0 -0
  1127. scitex/scholar/url_finder/translators/individual/wired.py +0 -0
  1128. scitex/scholar/url_finder/translators/individual/wiso.py +0 -0
  1129. scitex/scholar/url_finder/translators/individual/womennews.py +0 -0
  1130. scitex/scholar/url_finder/translators/individual/world_bank.py +0 -0
  1131. scitex/scholar/url_finder/translators/individual/world_digital_library.py +0 -0
  1132. scitex/scholar/url_finder/translators/individual/world_history_connected.py +0 -0
  1133. scitex/scholar/url_finder/translators/individual/world_shakespeare_bibliography_online.py +0 -0
  1134. scitex/scholar/url_finder/translators/individual/worldcat_discovery_service.py +0 -0
  1135. scitex/scholar/url_finder/translators/individual/xml_contextobject.py +0 -0
  1136. scitex/scholar/url_finder/translators/individual/yandex_books.py +0 -0
  1137. scitex/scholar/url_finder/translators/individual/ynet.py +0 -0
  1138. scitex/scholar/url_finder/translators/individual/youtube.py +0 -0
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  1140. scitex/scholar/url_finder/translators/individual/ypsf.py +0 -0
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  1142. scitex/scholar/url_finder/translators/individual/zenodo.py +0 -0
  1143. scitex/scholar/url_finder/translators/individual/ziponline.py +0 -0
  1144. scitex/scholar/url_finder/translators/individual/zobodat.py +0 -0
  1145. scitex/scholar/url_finder/translators/individual/zotero_org.py +0 -0
  1146. scitex/scholar/url_finder/translators/individual/zotero_rdf.py +0 -0
  1147. scitex/scholar/url_finder/translators/individual/zoterobib.py +0 -0
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  1251. scitex/writer/_compile/revision.py +81 -0
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  1260. scitex/writer/dataclasses/config/__init__.py +0 -0
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  1266. scitex/writer/dataclasses/core/_DocumentSection.py +1 -1
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  1269. scitex/writer/dataclasses/results/_LaTeXIssue.py +1 -1
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  1276. scitex/writer/dataclasses/tree/_ScriptsTree.py +5 -3
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  1285. scitex/writer/utils/_watch.py +0 -0
  1286. {scitex-2.1.3.dist-info → scitex-2.4.0.dist-info}/METADATA +362 -363
  1287. {scitex-2.1.3.dist-info → scitex-2.4.0.dist-info}/RECORD +360 -363
  1288. {scitex-2.1.3.dist-info → scitex-2.4.0.dist-info}/WHEEL +1 -1
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  1384. scitex/stats/tests/parametric/_test_anova_rm.py +0 -717
  1385. scitex/stats/tests/parametric/_test_ttest.py +0 -835
  1386. scitex/template/ANALYSIS.md +0 -202
  1387. scitex-2.1.3.dist-info/licenses/LICENSE +0 -21
  1388. {scitex-2.1.3.dist-info → scitex-2.4.0.dist-info}/entry_points.txt +0 -0
@@ -1,485 +0,0 @@
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- #!/usr/bin/env python3
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- # -*- coding: utf-8 -*-
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- # Timestamp: "2025-10-01 22:17:48 (ywatanabe)"
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- # File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/stats/tests/correlation/_test_spearman.py
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- # ----------------------------------------
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- from __future__ import annotations
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- import os
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- __FILE__ = __file__
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- __DIR__ = os.path.dirname(__FILE__)
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- # ----------------------------------------
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-
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- """
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- Spearman's rank correlation coefficient test.
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-
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- Non-parametric measure of rank correlation (monotonic relationship).
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- More robust to outliers than Pearson's r.
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- """
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-
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- import argparse
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- from typing import Literal, Optional, Union
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-
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- import matplotlib.axes
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- import numpy as np
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- import pandas as pd
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- import scitex as stx
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- from scipy import stats
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- from scitex.logging import getLogger
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-
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- from ...utils._formatters import p2stars
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- from ...utils._normalizers import convert_results, force_dataframe
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-
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- logger = getLogger(__name__)
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-
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-
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- def test_spearman(
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- x: Union[np.ndarray, pd.Series],
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- y: Union[np.ndarray, pd.Series],
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- var_x: str = "x",
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- var_y: str = "y",
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- alternative: Literal["two-sided", "less", "greater"] = "two-sided",
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- alpha: float = 0.05,
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- plot: bool = False,
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- ax: Optional[matplotlib.axes.Axes] = None,
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- return_as: Literal["dict", "dataframe"] = "dict",
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- decimals: int = 3,
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- verbose: bool = False,
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- ) -> Union[dict, pd.DataFrame]:
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- """
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- Spearman's rank correlation coefficient test.
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-
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- Non-parametric measure of monotonic relationship between two variables.
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- Uses rank-transformed data, more robust to outliers than Pearson.
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-
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- Parameters
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- ----------
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- x : array-like
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- First variable
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- y : array-like
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- Second variable (same length as x)
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- var_x : str, default 'x'
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- Name of first variable
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- var_y : str, default 'y'
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- Name of second variable
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- alternative : {'two-sided', 'less', 'greater'}, default 'two-sided'
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- Alternative hypothesis:
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- - 'two-sided': ρ ≠ 0
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- - 'less': ρ < 0
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- - 'greater': ρ > 0
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- alpha : float, default 0.05
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- Significance level
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- plot : bool, default False
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- If True, create visualization with scatter plot of ranks
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- return_as : {'dict', 'dataframe'}, default 'dict'
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- Return format
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- decimals : int, default 3
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- Number of decimal places for rounding
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-
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- Returns
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- -------
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- result : dict or DataFrame or (dict, Figure)
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- Test results with:
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- - test_method: Name of test
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- - statistic: Spearman's rho (ρ)
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- - pvalue: p-value
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- - alternative: Alternative hypothesis
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- - alpha: Significance level
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- - significant: Whether result is significant
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- - stars: Significance stars
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- - effect_size: Same as statistic (ρ)
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- - effect_size_metric: 'rho'
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- - effect_size_interpretation: Interpretation
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- - rho_squared: Proportion of variance explained
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- - n: Sample size
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- - var_x: First variable name
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- - var_y: Second variable name
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-
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- Notes
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- -----
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- Spearman's ρ is the Pearson correlation of rank-transformed variables.
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-
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- Assumptions:
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- - Observations are independent
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- - Variables are at least ordinal
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-
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- Interpretation (same as Pearson):
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- - |ρ| < 0.1: negligible
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- - |ρ| < 0.3: small
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- - |ρ| < 0.5: medium
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- - |ρ| ≥ 0.5: large
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-
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- References
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- ----------
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- Spearman, C. (1904). The proof and measurement of association between
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- two things. American Journal of Psychology, 15, 72-101.
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-
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- Examples
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- --------
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- >>> import numpy as np
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- >>> from scitex.stats.tests.correlation import test_spearman
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-
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- # Example 1: Perfect monotonic relationship
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- >>> x = np.array([1, 2, 3, 4, 5])
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- >>> y = np.array([1, 4, 9, 16, 25]) # Quadratic relationship
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- >>> result = test_spearman(x, y, var_x='x', var_y='y²', plot=True)
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- >>> print(result)
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-
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- # Example 2: Outlier-robust correlation
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- >>> x = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 100]) # Outlier
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- >>> y = np.array([2, 4, 6, 8, 10, 12, 14, 16, 18, 20])
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- >>> result = test_spearman(x, y, plot=True)
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- >>> print(f"Spearman ρ = {result['statistic']:.3f}, p = {result['pvalue']:.4f}")
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-
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- # Example 3: Compare with Pearson
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- >>> from scitex.stats.tests.correlation import test_pearson
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- >>> x = np.random.exponential(scale=2, size=50)
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- >>> y = x + np.random.normal(0, 1, size=50)
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- >>> spearman_result = test_spearman(x, y)
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- >>> pearson_result = test_pearson(x, y)
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- >>> print(f"Spearman: ρ = {spearman_result['statistic']:.3f}")
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- >>> print(f"Pearson: r = {pearson_result['statistic']:.3f}")
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-
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- # Example 4: Ordinal data
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- >>> satisfaction = np.array([1, 2, 3, 4, 5, 1, 2, 3, 4, 5])
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- >>> quality = np.array([2, 3, 4, 4, 5, 1, 2, 3, 5, 4])
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- >>> result = test_spearman(satisfaction, quality,
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- ... var_x='Satisfaction', var_y='Quality',
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- ... plot=True)
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-
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- # Example 5: One-tailed test
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- >>> x = np.arange(20)
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- >>> y = x + np.random.normal(0, 2, size=20)
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- >>> result = test_spearman(x, y, alternative='greater')
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- >>> print(f"One-tailed p-value: {result['pvalue']:.4f}")
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-
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- # Example 6: Non-linear monotonic relationship
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- >>> x = np.linspace(0, 10, 50)
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- >>> y = np.log(x + 1) + np.random.normal(0, 0.1, size=50)
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- >>> result = test_spearman(x, y, var_x='x', var_y='log(x+1)', plot=True)
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-
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- # Example 7: Export to various formats
161
- >>> result = test_spearman(x, y, return_as='dataframe')
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- >>> convert_results(result, return_as='latex', path='spearman.tex')
163
- >>> convert_results(result, return_as='csv', path='spearman.csv')
164
- """
165
- # Convert to arrays
166
- x = np.asarray(x)
167
- y = np.asarray(y)
168
-
169
- # Check lengths
170
- if len(x) != len(y):
171
- raise ValueError(
172
- f"x and y must have same length (got {len(x)} and {len(y)})"
173
- )
174
-
175
- # Remove NaN pairs
176
- mask = ~(np.isnan(x) | np.isnan(y))
177
- x = x[mask]
178
- y = y[mask]
179
- n = len(x)
180
-
181
- if n < 3:
182
- raise ValueError(f"Need at least 3 valid pairs (got {n})")
183
-
184
- # Compute Spearman correlation
185
- rho, pvalue = stats.spearmanr(x, y, alternative=alternative)
186
- rho = float(rho)
187
- pvalue = float(pvalue)
188
-
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- # Compute rho-squared (proportion of variance explained by ranks)
190
- rho_squared = rho**2
191
-
192
- # Check significance
193
- significant = pvalue < alpha
194
- stars = p2stars(pvalue)
195
-
196
- # Interpret effect size (same as Pearson)
197
- rho_abs = abs(rho)
198
- if rho_abs < 0.1:
199
- interpretation = "negligible"
200
- elif rho_abs < 0.3:
201
- interpretation = "small"
202
- elif rho_abs < 0.5:
203
- interpretation = "medium"
204
- else:
205
- interpretation = "large"
206
-
207
- # Build result
208
- result = {
209
- "test_method": "Spearman's rank correlation",
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- "statistic": round(rho, decimals),
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- "pvalue": round(pvalue, decimals),
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- "alternative": alternative,
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- "alpha": alpha,
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- "significant": significant,
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- "stars": stars,
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- "effect_size": round(rho, decimals),
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- "effect_size_metric": "rho",
218
- "effect_size_interpretation": interpretation,
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- "rho_squared": round(rho_squared, decimals),
220
- "n": n,
221
- "var_x": var_x,
222
- "var_y": var_y,
223
- }
224
-
225
- # Log results if verbose
226
- if verbose:
227
- logger.info(
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- f"Spearman: ρ = {rho:.3f}, p = {pvalue:.4f} {p2stars(pvalue)}"
229
- )
230
- logger.info(f"ρ² = {rho_squared:.3f} ({interpretation})")
231
-
232
- # Auto-enable plotting if ax is provided
233
- if ax is not None:
234
- plot = True
235
-
236
- # Generate plot if requested
237
- if plot:
238
- if ax is None:
239
- fig, ax = stx.plt.subplots()
240
- _plot_spearman(x, y, rho, pvalue, var_x, var_y, alpha, ax)
241
-
242
- # Convert to requested format
243
- if return_as == "dataframe":
244
- result = force_dataframe(result)
245
- elif return_as not in ["dict", "dataframe"]:
246
- return convert_results(result, return_as=return_as)
247
-
248
- return result
249
-
250
-
251
- def _plot_spearman(x, y, rho, pvalue, var_x, var_y, alpha, ax):
252
- """Create scatter plot with rank-based regression line on given axes."""
253
- # Convert to ranks
254
- x_ranks = stats.rankdata(x)
255
- y_ranks = stats.rankdata(y)
256
-
257
- # Scatter plot of ranks
258
- ax.scatter(
259
- x_ranks,
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- y_ranks,
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- alpha=0.6,
262
- s=50,
263
- color="C0",
264
- edgecolors="white",
265
- linewidths=0.5,
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- zorder=3,
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- )
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-
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- # Add regression line for ranks
270
- z = np.polyfit(x_ranks, y_ranks, 1)
271
- p = np.poly1d(z)
272
- x_line = np.linspace(x_ranks.min(), x_ranks.max(), 100)
273
- ax.plot(
274
- x_line, p(x_line), "r-", linewidth=2, label=f"ρ = {rho:.3f}", zorder=2
275
- )
276
-
277
- # Labels and title
278
- ax.set_xlabel(f"Rank({var_x})")
279
- ax.set_ylabel(f"Rank({var_y})")
280
- stars = p2stars(pvalue)
281
- ax.set_title(f"Spearman: ρ = {rho:.3f} {stars}")
282
- ax.legend()
283
- ax.grid(True, alpha=0.3, zorder=1)
284
-
285
-
286
- # Example usage
287
- """Main function"""
288
-
289
-
290
- def main(args):
291
- """Demonstrate Spearman correlation test functionality."""
292
- logger.info("=" * 70)
293
- logger.info("Spearman's Rank Correlation Test - Examples")
294
- logger.info("=" * 70)
295
-
296
- # Example 1: Perfect monotonic relationship
297
- logger.info("\nExample 1: Perfect monotonic (quadratic) relationship")
298
- logger.info("-" * 70)
299
- x1 = np.array([1, 2, 3, 4, 5])
300
- y1 = np.array([1, 4, 9, 16, 25])
301
- result1 = test_spearman(
302
- x1, y1, var_x="x", var_y="y²", plot=True, verbose=True
303
- )
304
- logger.info(force_dataframe(result1))
305
-
306
- # Save the figure using plt.gcf()
307
- stx.io.save(stx.plt.gcf(), "example1_perfect_monotonic.jpg")
308
- stx.plt.close()
309
-
310
- # Example 2: Outlier comparison
311
- logger.info("\nExample 2: Robustness to outliers")
312
- logger.info("-" * 70)
313
- x2 = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 100])
314
- y2 = np.array([2, 4, 6, 8, 10, 12, 14, 16, 18, 20])
315
-
316
- from ..correlation._test_pearson import test_pearson
317
-
318
- logger.info("With outlier (x=100):")
319
- logger.info("Spearman:")
320
- spearman_result = test_spearman(x2, y2, var_x="x", var_y="y", verbose=True)
321
- logger.info("Pearson:")
322
- pearson_result = test_pearson(x2, y2, var_x="x", var_y="y", verbose=True)
323
- logger.info("→ Spearman is more robust to the outlier")
324
-
325
- # Example 3: Non-linear monotonic relationship
326
- logger.info("\nExample 3: Non-linear monotonic (logarithmic) relationship")
327
- logger.info("-" * 70)
328
- np.random.seed(42)
329
- x3 = np.linspace(1, 50, 50)
330
- y3 = np.log(x3) + np.random.normal(0, 0.2, size=50)
331
- result3 = test_spearman(
332
- x3, y3, var_x="x", var_y="log(x)", plot=True, verbose=True
333
- )
334
- logger.info(force_dataframe(result3))
335
- stx.io.save(stx.plt.gcf(), "example3_logarithmic.jpg")
336
- stx.plt.close()
337
-
338
- # Example 4: Ordinal data
339
- logger.info("\nExample 4: Ordinal data (Likert scales)")
340
- logger.info("-" * 70)
341
- np.random.seed(43)
342
- satisfaction = np.random.randint(1, 6, size=30)
343
- quality = satisfaction + np.random.randint(-1, 2, size=30)
344
- quality = np.clip(quality, 1, 5)
345
- result4 = test_spearman(
346
- satisfaction,
347
- quality,
348
- var_x="Satisfaction",
349
- var_y="Quality",
350
- plot=True,
351
- verbose=True,
352
- )
353
- logger.info(force_dataframe(result4))
354
- stx.io.save(stx.plt.gcf(), "example4_ordinal.jpg")
355
- stx.plt.close()
356
-
357
- # Example 5: One-tailed test
358
- logger.info("\nExample 5: One-tailed test (expect positive correlation)")
359
- logger.info("-" * 70)
360
- np.random.seed(44)
361
- x5 = np.arange(30)
362
- y5 = x5 + np.random.normal(0, 3, size=30)
363
- logger.info("Two-tailed test:")
364
- result5_two = test_spearman(x5, y5, alternative="two-sided", verbose=True)
365
- logger.info("\nOne-tailed test (greater):")
366
- result5_greater = test_spearman(
367
- x5, y5, alternative="greater", verbose=True
368
- )
369
-
370
- # Example 6: Exponential relationship
371
- logger.info("\nExample 6: Exponential relationship")
372
- logger.info("-" * 70)
373
- np.random.seed(45)
374
- x6 = np.linspace(0, 5, 40)
375
- y6 = np.exp(x6 * 0.5) + np.random.normal(0, 2, size=40)
376
- result6 = test_spearman(
377
- x6, y6, var_x="x", var_y="exp(0.5x)", plot=True, verbose=True
378
- )
379
- logger.info(force_dataframe(result6))
380
- stx.io.save(stx.plt.gcf(), "example6_exponential.jpg")
381
- stx.plt.close()
382
-
383
- # Example 7: No correlation
384
- logger.info("\nExample 7: No correlation")
385
- logger.info("-" * 70)
386
- np.random.seed(46)
387
- x7 = np.random.normal(0, 1, size=50)
388
- y7 = np.random.normal(0, 1, size=50)
389
- result7 = test_spearman(x7, y7, var_x="x", var_y="y", verbose=True)
390
- logger.info(force_dataframe(result7))
391
-
392
- # Example 8: Compare Spearman vs Pearson on skewed data
393
- logger.info("\nExample 8: Spearman vs Pearson on skewed data")
394
- logger.info("-" * 70)
395
- np.random.seed(47)
396
- x8 = np.random.exponential(scale=2, size=60)
397
- y8 = x8**0.8 + np.random.normal(0, 1, size=60)
398
-
399
- logger.info("Exponential distribution with power relationship:")
400
- logger.info("Spearman:")
401
- spearman_res = test_spearman(x8, y8, verbose=True)
402
- logger.info("Pearson:")
403
- pearson_res = test_pearson(x8, y8, verbose=True)
404
-
405
- # Example 9: Export to multiple formats
406
- logger.info("\nExample 9: Export to multiple formats")
407
- logger.info("-" * 70)
408
- np.random.seed(48)
409
- x9 = np.arange(25)
410
- y9 = 2 * x9 + np.random.normal(0, 5, size=25)
411
- result9 = test_spearman(
412
- x9,
413
- y9,
414
- var_x="Time",
415
- var_y="Response",
416
- return_as="dataframe",
417
- verbose=True,
418
- )
419
-
420
- # Save
421
- stx.io.save(result9, "./spearman_demo.csv")
422
- stx.io.save(result9, "./spearman_demo.tex")
423
-
424
- # Example 10: Large dataset
425
- logger.info("\nExample 10: Large dataset with moderate correlation")
426
- logger.info("-" * 70)
427
- np.random.seed(49)
428
- n_large = 500
429
- x10 = np.random.normal(100, 15, size=n_large)
430
- y10 = 0.6 * x10 + np.random.normal(0, 20, size=n_large)
431
- result10 = test_spearman(
432
- x10, y10, var_x="Predictor", var_y="Outcome", plot=True, verbose=True
433
- )
434
- logger.info(force_dataframe(result10))
435
- stx.io.save(stx.plt.gcf(), "example10_large_dataset.jpg")
436
- stx.plt.close()
437
-
438
- logger.info(f"\n{'='*70}")
439
- logger.info("All examples completed")
440
- logger.info(f"{'='*70}")
441
-
442
- return 0
443
-
444
-
445
- def parse_args():
446
- """Parse command line arguments."""
447
- parser = argparse.ArgumentParser(description="")
448
- parser.add_argument(
449
- "--verbose", action="store_true", help="Enable verbose output"
450
- )
451
- return parser.parse_args()
452
-
453
-
454
- def run_main():
455
- """Initialize SciTeX framework and run main."""
456
- global CONFIG, CC, sys, plt, rng
457
-
458
- import sys
459
-
460
- import matplotlib.pyplot as plt
461
-
462
- args = parse_args()
463
-
464
- CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
465
- sys,
466
- plt,
467
- args=args,
468
- file=__FILE__,
469
- verbose=args.verbose,
470
- agg=True,
471
- )
472
-
473
- exit_status = main(args)
474
-
475
- stx.session.close(
476
- CONFIG,
477
- verbose=args.verbose,
478
- exit_status=exit_status,
479
- )
480
-
481
-
482
- if __name__ == "__main__":
483
- run_main()
484
-
485
- # EOF
@@ -1,193 +0,0 @@
1
- #!/usr/bin/env python3
2
- # -*- coding: utf-8 -*-
3
- # File: ./scitex_repo/src/scitex/stats/tests/correlation/_test_theilsen.py
4
-
5
- """
6
- Theil-Sen robust regression estimator.
7
-
8
- A non-parametric regression method that is robust to outliers.
9
- Computes the median of slopes between all pairs of points.
10
- """
11
-
12
- import warnings
13
- from typing import Union
14
-
15
- import numpy as np
16
- import pandas as pd
17
- from scipy import stats
18
-
19
-
20
- def test_theilsen(
21
- x: Union[np.ndarray, pd.Series, list],
22
- y: Union[np.ndarray, pd.Series, list],
23
- var_x: str = "x",
24
- var_y: str = "y",
25
- return_as: str = "dict",
26
- verbose: bool = True,
27
- ) -> Union[dict, pd.DataFrame]:
28
- """
29
- Theil-Sen robust regression estimator.
30
-
31
- A robust non-parametric regression method that estimates the slope as the
32
- median of all pairwise slopes. Highly resistant to outliers (up to 29.3%
33
- breakdown point).
34
-
35
- Parameters
36
- ----------
37
- x : array-like
38
- Independent variable
39
- y : array-like
40
- Dependent variable
41
- var_x : str, default="x"
42
- Name of independent variable (for reporting)
43
- var_y : str, default="y"
44
- Name of dependent variable (for reporting)
45
- return_as : str, default="dict"
46
- Format of return value: "dict" or "dataframe"
47
- verbose : bool, default=True
48
- Whether to print results
49
-
50
- Returns
51
- -------
52
- dict or pd.DataFrame
53
- Dictionary or DataFrame containing:
54
- - slope : float
55
- Theil-Sen slope estimate (median of pairwise slopes)
56
- - intercept : float
57
- Intercept of the regression line
58
- - low_slope : float
59
- Lower bound of slope confidence interval
60
- - high_slope : float
61
- Upper bound of slope confidence interval
62
- - var_x : str
63
- Name of independent variable
64
- - var_y : str
65
- Name of dependent variable
66
-
67
- Notes
68
- -----
69
- The Theil-Sen estimator:
70
- - Is robust to outliers (up to ~29% outliers)
71
- - Has no distributional assumptions
72
- - Is asymptotically normal
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- - Has ~64% efficiency compared to OLS for normal data
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- - Computational complexity: O(n²)
75
-
76
- References
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- ----------
78
- .. [1] Theil, H. (1950). "A rank-invariant method of linear and polynomial
79
- regression analysis". Indagationes Mathematicae, 12, 85-91.
80
- .. [2] Sen, P.K. (1968). "Estimates of the regression coefficient based on
81
- Kendall's tau". Journal of the American Statistical Association, 63,
82
- 1379-1389.
83
-
84
- Examples
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- --------
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- >>> import numpy as np
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- >>> from scitex.stats.tests.correlation import test_theilsen
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- >>> x = np.array([1, 2, 3, 4, 5])
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- >>> y = np.array([2, 4, 6, 8, 10])
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- >>> result = test_theilsen(x, y, verbose=False)
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- >>> print(f"Slope: {result['slope']:.3f}")
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- Slope: 2.000
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-
94
- >>> # With outlier
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- >>> y_outlier = np.array([2, 4, 6, 8, 100]) # One extreme outlier
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- >>> result = test_theilsen(x, y_outlier, verbose=False)
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- >>> print(f"Robust slope: {result['slope']:.3f}")
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- Robust slope: 2.000
99
- """
100
- # Convert inputs to numpy arrays
101
- x = np.asarray(x).flatten()
102
- y = np.asarray(y).flatten()
103
-
104
- # Remove NaN/Inf
105
- mask = np.isfinite(x) & np.isfinite(y)
106
- if not mask.all():
107
- n_removed = (~mask).sum()
108
- warnings.warn(
109
- f"Removed {n_removed} NaN/Inf values from input data",
110
- UserWarning,
111
- )
112
- x = x[mask]
113
- y = y[mask]
114
-
115
- # Check for sufficient data
116
- if len(x) < 3:
117
- raise ValueError(
118
- f"Need at least 3 valid data points, got {len(x)}"
119
- )
120
-
121
- # Check for variation
122
- if len(np.unique(x)) < 2:
123
- raise ValueError(
124
- "Independent variable has no variation (constant values)"
125
- )
126
-
127
- # Compute Theil-Sen estimator
128
- result = stats.theilslopes(y, x, alpha=0.95)
129
-
130
- # Prepare output dictionary
131
- output = {
132
- "slope": result.slope,
133
- "intercept": result.intercept,
134
- "low_slope": result.low_slope,
135
- "high_slope": result.high_slope,
136
- "var_x": var_x,
137
- "var_y": var_y,
138
- }
139
-
140
- # Print results if verbose
141
- if verbose:
142
- print("\n" + "=" * 70)
143
- print("Theil-Sen Robust Regression")
144
- print("=" * 70)
145
- print(f"Variables: {var_y} ~ {var_x}")
146
- print(f"Sample size: n = {len(x)}")
147
- print(f"\nResults:")
148
- print(f" Slope: {output['slope']:.6f}")
149
- print(f" Intercept: {output['intercept']:.6f}")
150
- print(f" 95% CI: [{output['low_slope']:.6f}, {output['high_slope']:.6f}]")
151
- print(f"\nInterpretation:")
152
- print(f" For each unit increase in {var_x},")
153
- print(f" {var_y} changes by {output['slope']:.6f} units (median slope)")
154
- print("=" * 70 + "\n")
155
-
156
- # Return as requested format
157
- if return_as == "dataframe":
158
- return pd.DataFrame([output])
159
- elif return_as == "dict":
160
- return output
161
- else:
162
- raise ValueError(
163
- f"return_as must be 'dict' or 'dataframe', got '{return_as}'"
164
- )
165
-
166
-
167
- if __name__ == "__main__":
168
- # Example usage
169
- np.random.seed(42)
170
-
171
- # Clean data
172
- print("Example 1: Clean linear data")
173
- x = np.linspace(0, 10, 50)
174
- y = 2 * x + 1 + np.random.normal(0, 1, 50)
175
- result = test_theilsen(x, y, var_x="x", var_y="y")
176
-
177
- # Data with outliers
178
- print("\n" + "=" * 70)
179
- print("Example 2: Data with outliers")
180
- x_out = np.linspace(0, 10, 50)
181
- y_out = 2 * x_out + 1 + np.random.normal(0, 1, 50)
182
- # Add outliers
183
- y_out[[10, 20, 30]] += np.array([20, -15, 25])
184
- result_out = test_theilsen(x_out, y_out, var_x="x", var_y="y")
185
-
186
- # Compare with OLS
187
- from scipy.stats import linregress
188
- ols = linregress(x_out, y_out)
189
- print(f"\nComparison:")
190
- print(f" Theil-Sen slope: {result_out['slope']:.6f}")
191
- print(f" OLS slope: {ols.slope:.6f}")
192
- print(f" True slope: 2.000000")
193
- print(f"\nTheil-Sen is more robust to the {((y_out[[10,20,30]] - (2*x_out[[10,20,30]] + 1)) != 0).sum()} outliers!")
@@ -1,23 +0,0 @@
1
- #!/usr/bin/env python3
2
- # File: ./scitex_repo/src/scitex/stats/tests/nonparametric/__init__.py
3
-
4
- """
5
- Non-parametric statistical tests.
6
-
7
- Distribution-free tests that don't assume normality.
8
- Robust to outliers and suitable for ordinal data.
9
- """
10
-
11
- from ._test_brunner_munzel import test_brunner_munzel
12
- from ._test_wilcoxon import test_wilcoxon
13
- from ._test_kruskal import test_kruskal
14
- from ._test_mannwhitneyu import test_mannwhitneyu
15
- from ._test_friedman import test_friedman
16
-
17
- __all__ = [
18
- 'test_brunner_munzel',
19
- 'test_wilcoxon',
20
- 'test_kruskal',
21
- 'test_mannwhitneyu',
22
- 'test_friedman',
23
- ]