scipy 1.16.2__cp313-cp313t-win_arm64.whl

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Files changed (1530) hide show
  1. scipy/__config__.py +161 -0
  2. scipy/__init__.py +150 -0
  3. scipy/_cyutility.cp313t-win_arm64.lib +0 -0
  4. scipy/_cyutility.cp313t-win_arm64.pyd +0 -0
  5. scipy/_distributor_init.py +18 -0
  6. scipy/_lib/__init__.py +14 -0
  7. scipy/_lib/_array_api.py +931 -0
  8. scipy/_lib/_array_api_compat_vendor.py +9 -0
  9. scipy/_lib/_array_api_no_0d.py +103 -0
  10. scipy/_lib/_bunch.py +229 -0
  11. scipy/_lib/_ccallback.py +251 -0
  12. scipy/_lib/_ccallback_c.cp313t-win_arm64.lib +0 -0
  13. scipy/_lib/_ccallback_c.cp313t-win_arm64.pyd +0 -0
  14. scipy/_lib/_disjoint_set.py +254 -0
  15. scipy/_lib/_docscrape.py +761 -0
  16. scipy/_lib/_elementwise_iterative_method.py +346 -0
  17. scipy/_lib/_fpumode.cp313t-win_arm64.lib +0 -0
  18. scipy/_lib/_fpumode.cp313t-win_arm64.pyd +0 -0
  19. scipy/_lib/_gcutils.py +105 -0
  20. scipy/_lib/_pep440.py +487 -0
  21. scipy/_lib/_sparse.py +41 -0
  22. scipy/_lib/_test_ccallback.cp313t-win_arm64.lib +0 -0
  23. scipy/_lib/_test_ccallback.cp313t-win_arm64.pyd +0 -0
  24. scipy/_lib/_test_deprecation_call.cp313t-win_arm64.lib +0 -0
  25. scipy/_lib/_test_deprecation_call.cp313t-win_arm64.pyd +0 -0
  26. scipy/_lib/_test_deprecation_def.cp313t-win_arm64.lib +0 -0
  27. scipy/_lib/_test_deprecation_def.cp313t-win_arm64.pyd +0 -0
  28. scipy/_lib/_testutils.py +373 -0
  29. scipy/_lib/_threadsafety.py +58 -0
  30. scipy/_lib/_tmpdirs.py +86 -0
  31. scipy/_lib/_uarray/LICENSE +29 -0
  32. scipy/_lib/_uarray/__init__.py +116 -0
  33. scipy/_lib/_uarray/_backend.py +707 -0
  34. scipy/_lib/_uarray/_uarray.cp313t-win_arm64.lib +0 -0
  35. scipy/_lib/_uarray/_uarray.cp313t-win_arm64.pyd +0 -0
  36. scipy/_lib/_util.py +1283 -0
  37. scipy/_lib/array_api_compat/__init__.py +22 -0
  38. scipy/_lib/array_api_compat/_internal.py +59 -0
  39. scipy/_lib/array_api_compat/common/__init__.py +1 -0
  40. scipy/_lib/array_api_compat/common/_aliases.py +727 -0
  41. scipy/_lib/array_api_compat/common/_fft.py +213 -0
  42. scipy/_lib/array_api_compat/common/_helpers.py +1058 -0
  43. scipy/_lib/array_api_compat/common/_linalg.py +232 -0
  44. scipy/_lib/array_api_compat/common/_typing.py +192 -0
  45. scipy/_lib/array_api_compat/cupy/__init__.py +13 -0
  46. scipy/_lib/array_api_compat/cupy/_aliases.py +156 -0
  47. scipy/_lib/array_api_compat/cupy/_info.py +336 -0
  48. scipy/_lib/array_api_compat/cupy/_typing.py +31 -0
  49. scipy/_lib/array_api_compat/cupy/fft.py +36 -0
  50. scipy/_lib/array_api_compat/cupy/linalg.py +49 -0
  51. scipy/_lib/array_api_compat/dask/__init__.py +0 -0
  52. scipy/_lib/array_api_compat/dask/array/__init__.py +12 -0
  53. scipy/_lib/array_api_compat/dask/array/_aliases.py +376 -0
  54. scipy/_lib/array_api_compat/dask/array/_info.py +416 -0
  55. scipy/_lib/array_api_compat/dask/array/fft.py +21 -0
  56. scipy/_lib/array_api_compat/dask/array/linalg.py +72 -0
  57. scipy/_lib/array_api_compat/numpy/__init__.py +28 -0
  58. scipy/_lib/array_api_compat/numpy/_aliases.py +190 -0
  59. scipy/_lib/array_api_compat/numpy/_info.py +366 -0
  60. scipy/_lib/array_api_compat/numpy/_typing.py +30 -0
  61. scipy/_lib/array_api_compat/numpy/fft.py +35 -0
  62. scipy/_lib/array_api_compat/numpy/linalg.py +143 -0
  63. scipy/_lib/array_api_compat/torch/__init__.py +22 -0
  64. scipy/_lib/array_api_compat/torch/_aliases.py +855 -0
  65. scipy/_lib/array_api_compat/torch/_info.py +369 -0
  66. scipy/_lib/array_api_compat/torch/_typing.py +3 -0
  67. scipy/_lib/array_api_compat/torch/fft.py +85 -0
  68. scipy/_lib/array_api_compat/torch/linalg.py +121 -0
  69. scipy/_lib/array_api_extra/__init__.py +38 -0
  70. scipy/_lib/array_api_extra/_delegation.py +171 -0
  71. scipy/_lib/array_api_extra/_lib/__init__.py +1 -0
  72. scipy/_lib/array_api_extra/_lib/_at.py +463 -0
  73. scipy/_lib/array_api_extra/_lib/_backends.py +46 -0
  74. scipy/_lib/array_api_extra/_lib/_funcs.py +937 -0
  75. scipy/_lib/array_api_extra/_lib/_lazy.py +357 -0
  76. scipy/_lib/array_api_extra/_lib/_testing.py +278 -0
  77. scipy/_lib/array_api_extra/_lib/_utils/__init__.py +1 -0
  78. scipy/_lib/array_api_extra/_lib/_utils/_compat.py +74 -0
  79. scipy/_lib/array_api_extra/_lib/_utils/_compat.pyi +45 -0
  80. scipy/_lib/array_api_extra/_lib/_utils/_helpers.py +559 -0
  81. scipy/_lib/array_api_extra/_lib/_utils/_typing.py +10 -0
  82. scipy/_lib/array_api_extra/_lib/_utils/_typing.pyi +105 -0
  83. scipy/_lib/array_api_extra/testing.py +359 -0
  84. scipy/_lib/cobyqa/__init__.py +20 -0
  85. scipy/_lib/cobyqa/framework.py +1240 -0
  86. scipy/_lib/cobyqa/main.py +1506 -0
  87. scipy/_lib/cobyqa/models.py +1529 -0
  88. scipy/_lib/cobyqa/problem.py +1296 -0
  89. scipy/_lib/cobyqa/settings.py +132 -0
  90. scipy/_lib/cobyqa/subsolvers/__init__.py +14 -0
  91. scipy/_lib/cobyqa/subsolvers/geometry.py +387 -0
  92. scipy/_lib/cobyqa/subsolvers/optim.py +1203 -0
  93. scipy/_lib/cobyqa/utils/__init__.py +18 -0
  94. scipy/_lib/cobyqa/utils/exceptions.py +22 -0
  95. scipy/_lib/cobyqa/utils/math.py +77 -0
  96. scipy/_lib/cobyqa/utils/versions.py +67 -0
  97. scipy/_lib/decorator.py +399 -0
  98. scipy/_lib/deprecation.py +274 -0
  99. scipy/_lib/doccer.py +366 -0
  100. scipy/_lib/messagestream.cp313t-win_arm64.lib +0 -0
  101. scipy/_lib/messagestream.cp313t-win_arm64.pyd +0 -0
  102. scipy/_lib/pyprima/__init__.py +212 -0
  103. scipy/_lib/pyprima/cobyla/__init__.py +0 -0
  104. scipy/_lib/pyprima/cobyla/cobyla.py +559 -0
  105. scipy/_lib/pyprima/cobyla/cobylb.py +714 -0
  106. scipy/_lib/pyprima/cobyla/geometry.py +226 -0
  107. scipy/_lib/pyprima/cobyla/initialize.py +215 -0
  108. scipy/_lib/pyprima/cobyla/trustregion.py +492 -0
  109. scipy/_lib/pyprima/cobyla/update.py +289 -0
  110. scipy/_lib/pyprima/common/__init__.py +0 -0
  111. scipy/_lib/pyprima/common/_bounds.py +34 -0
  112. scipy/_lib/pyprima/common/_linear_constraints.py +46 -0
  113. scipy/_lib/pyprima/common/_nonlinear_constraints.py +54 -0
  114. scipy/_lib/pyprima/common/_project.py +173 -0
  115. scipy/_lib/pyprima/common/checkbreak.py +93 -0
  116. scipy/_lib/pyprima/common/consts.py +47 -0
  117. scipy/_lib/pyprima/common/evaluate.py +99 -0
  118. scipy/_lib/pyprima/common/history.py +38 -0
  119. scipy/_lib/pyprima/common/infos.py +30 -0
  120. scipy/_lib/pyprima/common/linalg.py +435 -0
  121. scipy/_lib/pyprima/common/message.py +290 -0
  122. scipy/_lib/pyprima/common/powalg.py +131 -0
  123. scipy/_lib/pyprima/common/preproc.py +277 -0
  124. scipy/_lib/pyprima/common/present.py +5 -0
  125. scipy/_lib/pyprima/common/ratio.py +54 -0
  126. scipy/_lib/pyprima/common/redrho.py +47 -0
  127. scipy/_lib/pyprima/common/selectx.py +296 -0
  128. scipy/_lib/tests/__init__.py +0 -0
  129. scipy/_lib/tests/test__gcutils.py +110 -0
  130. scipy/_lib/tests/test__pep440.py +67 -0
  131. scipy/_lib/tests/test__testutils.py +32 -0
  132. scipy/_lib/tests/test__threadsafety.py +51 -0
  133. scipy/_lib/tests/test__util.py +641 -0
  134. scipy/_lib/tests/test_array_api.py +322 -0
  135. scipy/_lib/tests/test_bunch.py +169 -0
  136. scipy/_lib/tests/test_ccallback.py +196 -0
  137. scipy/_lib/tests/test_config.py +45 -0
  138. scipy/_lib/tests/test_deprecation.py +10 -0
  139. scipy/_lib/tests/test_doccer.py +143 -0
  140. scipy/_lib/tests/test_import_cycles.py +18 -0
  141. scipy/_lib/tests/test_public_api.py +482 -0
  142. scipy/_lib/tests/test_scipy_version.py +28 -0
  143. scipy/_lib/tests/test_tmpdirs.py +48 -0
  144. scipy/_lib/tests/test_warnings.py +137 -0
  145. scipy/_lib/uarray.py +31 -0
  146. scipy/cluster/__init__.py +31 -0
  147. scipy/cluster/_hierarchy.cp313t-win_arm64.lib +0 -0
  148. scipy/cluster/_hierarchy.cp313t-win_arm64.pyd +0 -0
  149. scipy/cluster/_optimal_leaf_ordering.cp313t-win_arm64.lib +0 -0
  150. scipy/cluster/_optimal_leaf_ordering.cp313t-win_arm64.pyd +0 -0
  151. scipy/cluster/_vq.cp313t-win_arm64.lib +0 -0
  152. scipy/cluster/_vq.cp313t-win_arm64.pyd +0 -0
  153. scipy/cluster/hierarchy.py +4348 -0
  154. scipy/cluster/tests/__init__.py +0 -0
  155. scipy/cluster/tests/hierarchy_test_data.py +145 -0
  156. scipy/cluster/tests/test_disjoint_set.py +202 -0
  157. scipy/cluster/tests/test_hierarchy.py +1238 -0
  158. scipy/cluster/tests/test_vq.py +434 -0
  159. scipy/cluster/vq.py +832 -0
  160. scipy/conftest.py +683 -0
  161. scipy/constants/__init__.py +358 -0
  162. scipy/constants/_codata.py +2266 -0
  163. scipy/constants/_constants.py +369 -0
  164. scipy/constants/codata.py +21 -0
  165. scipy/constants/constants.py +53 -0
  166. scipy/constants/tests/__init__.py +0 -0
  167. scipy/constants/tests/test_codata.py +78 -0
  168. scipy/constants/tests/test_constants.py +83 -0
  169. scipy/datasets/__init__.py +90 -0
  170. scipy/datasets/_download_all.py +71 -0
  171. scipy/datasets/_fetchers.py +225 -0
  172. scipy/datasets/_registry.py +26 -0
  173. scipy/datasets/_utils.py +81 -0
  174. scipy/datasets/tests/__init__.py +0 -0
  175. scipy/datasets/tests/test_data.py +128 -0
  176. scipy/differentiate/__init__.py +27 -0
  177. scipy/differentiate/_differentiate.py +1129 -0
  178. scipy/differentiate/tests/__init__.py +0 -0
  179. scipy/differentiate/tests/test_differentiate.py +694 -0
  180. scipy/fft/__init__.py +114 -0
  181. scipy/fft/_backend.py +196 -0
  182. scipy/fft/_basic.py +1650 -0
  183. scipy/fft/_basic_backend.py +197 -0
  184. scipy/fft/_debug_backends.py +22 -0
  185. scipy/fft/_fftlog.py +223 -0
  186. scipy/fft/_fftlog_backend.py +200 -0
  187. scipy/fft/_helper.py +348 -0
  188. scipy/fft/_pocketfft/LICENSE.md +25 -0
  189. scipy/fft/_pocketfft/__init__.py +9 -0
  190. scipy/fft/_pocketfft/basic.py +251 -0
  191. scipy/fft/_pocketfft/helper.py +249 -0
  192. scipy/fft/_pocketfft/pypocketfft.cp313t-win_arm64.lib +0 -0
  193. scipy/fft/_pocketfft/pypocketfft.cp313t-win_arm64.pyd +0 -0
  194. scipy/fft/_pocketfft/realtransforms.py +109 -0
  195. scipy/fft/_pocketfft/tests/__init__.py +0 -0
  196. scipy/fft/_pocketfft/tests/test_basic.py +1011 -0
  197. scipy/fft/_pocketfft/tests/test_real_transforms.py +505 -0
  198. scipy/fft/_realtransforms.py +706 -0
  199. scipy/fft/_realtransforms_backend.py +63 -0
  200. scipy/fft/tests/__init__.py +0 -0
  201. scipy/fft/tests/mock_backend.py +96 -0
  202. scipy/fft/tests/test_backend.py +98 -0
  203. scipy/fft/tests/test_basic.py +504 -0
  204. scipy/fft/tests/test_fftlog.py +215 -0
  205. scipy/fft/tests/test_helper.py +558 -0
  206. scipy/fft/tests/test_multithreading.py +84 -0
  207. scipy/fft/tests/test_real_transforms.py +247 -0
  208. scipy/fftpack/__init__.py +103 -0
  209. scipy/fftpack/_basic.py +428 -0
  210. scipy/fftpack/_helper.py +115 -0
  211. scipy/fftpack/_pseudo_diffs.py +554 -0
  212. scipy/fftpack/_realtransforms.py +598 -0
  213. scipy/fftpack/basic.py +20 -0
  214. scipy/fftpack/convolve.cp313t-win_arm64.lib +0 -0
  215. scipy/fftpack/convolve.cp313t-win_arm64.pyd +0 -0
  216. scipy/fftpack/helper.py +19 -0
  217. scipy/fftpack/pseudo_diffs.py +22 -0
  218. scipy/fftpack/realtransforms.py +19 -0
  219. scipy/fftpack/tests/__init__.py +0 -0
  220. scipy/fftpack/tests/fftw_double_ref.npz +0 -0
  221. scipy/fftpack/tests/fftw_longdouble_ref.npz +0 -0
  222. scipy/fftpack/tests/fftw_single_ref.npz +0 -0
  223. scipy/fftpack/tests/test.npz +0 -0
  224. scipy/fftpack/tests/test_basic.py +877 -0
  225. scipy/fftpack/tests/test_helper.py +54 -0
  226. scipy/fftpack/tests/test_import.py +33 -0
  227. scipy/fftpack/tests/test_pseudo_diffs.py +388 -0
  228. scipy/fftpack/tests/test_real_transforms.py +836 -0
  229. scipy/integrate/__init__.py +122 -0
  230. scipy/integrate/_bvp.py +1160 -0
  231. scipy/integrate/_cubature.py +729 -0
  232. scipy/integrate/_dop.cp313t-win_arm64.lib +0 -0
  233. scipy/integrate/_dop.cp313t-win_arm64.pyd +0 -0
  234. scipy/integrate/_ivp/__init__.py +8 -0
  235. scipy/integrate/_ivp/base.py +290 -0
  236. scipy/integrate/_ivp/bdf.py +478 -0
  237. scipy/integrate/_ivp/common.py +451 -0
  238. scipy/integrate/_ivp/dop853_coefficients.py +193 -0
  239. scipy/integrate/_ivp/ivp.py +755 -0
  240. scipy/integrate/_ivp/lsoda.py +224 -0
  241. scipy/integrate/_ivp/radau.py +572 -0
  242. scipy/integrate/_ivp/rk.py +601 -0
  243. scipy/integrate/_ivp/tests/__init__.py +0 -0
  244. scipy/integrate/_ivp/tests/test_ivp.py +1287 -0
  245. scipy/integrate/_ivp/tests/test_rk.py +37 -0
  246. scipy/integrate/_lebedev.py +5450 -0
  247. scipy/integrate/_lsoda.cp313t-win_arm64.lib +0 -0
  248. scipy/integrate/_lsoda.cp313t-win_arm64.pyd +0 -0
  249. scipy/integrate/_ode.py +1395 -0
  250. scipy/integrate/_odepack.cp313t-win_arm64.lib +0 -0
  251. scipy/integrate/_odepack.cp313t-win_arm64.pyd +0 -0
  252. scipy/integrate/_odepack_py.py +273 -0
  253. scipy/integrate/_quad_vec.py +674 -0
  254. scipy/integrate/_quadpack.cp313t-win_arm64.lib +0 -0
  255. scipy/integrate/_quadpack.cp313t-win_arm64.pyd +0 -0
  256. scipy/integrate/_quadpack_py.py +1283 -0
  257. scipy/integrate/_quadrature.py +1336 -0
  258. scipy/integrate/_rules/__init__.py +12 -0
  259. scipy/integrate/_rules/_base.py +518 -0
  260. scipy/integrate/_rules/_gauss_kronrod.py +202 -0
  261. scipy/integrate/_rules/_gauss_legendre.py +62 -0
  262. scipy/integrate/_rules/_genz_malik.py +210 -0
  263. scipy/integrate/_tanhsinh.py +1385 -0
  264. scipy/integrate/_test_multivariate.cp313t-win_arm64.lib +0 -0
  265. scipy/integrate/_test_multivariate.cp313t-win_arm64.pyd +0 -0
  266. scipy/integrate/_test_odeint_banded.cp313t-win_arm64.lib +0 -0
  267. scipy/integrate/_test_odeint_banded.cp313t-win_arm64.pyd +0 -0
  268. scipy/integrate/_vode.cp313t-win_arm64.lib +0 -0
  269. scipy/integrate/_vode.cp313t-win_arm64.pyd +0 -0
  270. scipy/integrate/dop.py +15 -0
  271. scipy/integrate/lsoda.py +15 -0
  272. scipy/integrate/odepack.py +17 -0
  273. scipy/integrate/quadpack.py +23 -0
  274. scipy/integrate/tests/__init__.py +0 -0
  275. scipy/integrate/tests/test__quad_vec.py +211 -0
  276. scipy/integrate/tests/test_banded_ode_solvers.py +305 -0
  277. scipy/integrate/tests/test_bvp.py +714 -0
  278. scipy/integrate/tests/test_cubature.py +1375 -0
  279. scipy/integrate/tests/test_integrate.py +840 -0
  280. scipy/integrate/tests/test_odeint_jac.py +74 -0
  281. scipy/integrate/tests/test_quadpack.py +680 -0
  282. scipy/integrate/tests/test_quadrature.py +730 -0
  283. scipy/integrate/tests/test_tanhsinh.py +1171 -0
  284. scipy/integrate/vode.py +15 -0
  285. scipy/interpolate/__init__.py +228 -0
  286. scipy/interpolate/_bary_rational.py +715 -0
  287. scipy/interpolate/_bsplines.py +2469 -0
  288. scipy/interpolate/_cubic.py +973 -0
  289. scipy/interpolate/_dfitpack.cp313t-win_arm64.lib +0 -0
  290. scipy/interpolate/_dfitpack.cp313t-win_arm64.pyd +0 -0
  291. scipy/interpolate/_dierckx.cp313t-win_arm64.lib +0 -0
  292. scipy/interpolate/_dierckx.cp313t-win_arm64.pyd +0 -0
  293. scipy/interpolate/_fitpack.cp313t-win_arm64.lib +0 -0
  294. scipy/interpolate/_fitpack.cp313t-win_arm64.pyd +0 -0
  295. scipy/interpolate/_fitpack2.py +2397 -0
  296. scipy/interpolate/_fitpack_impl.py +811 -0
  297. scipy/interpolate/_fitpack_py.py +898 -0
  298. scipy/interpolate/_fitpack_repro.py +996 -0
  299. scipy/interpolate/_interpnd.cp313t-win_arm64.lib +0 -0
  300. scipy/interpolate/_interpnd.cp313t-win_arm64.pyd +0 -0
  301. scipy/interpolate/_interpolate.py +2266 -0
  302. scipy/interpolate/_ndbspline.py +415 -0
  303. scipy/interpolate/_ndgriddata.py +329 -0
  304. scipy/interpolate/_pade.py +67 -0
  305. scipy/interpolate/_polyint.py +1025 -0
  306. scipy/interpolate/_ppoly.cp313t-win_arm64.lib +0 -0
  307. scipy/interpolate/_ppoly.cp313t-win_arm64.pyd +0 -0
  308. scipy/interpolate/_rbf.py +290 -0
  309. scipy/interpolate/_rbfinterp.py +550 -0
  310. scipy/interpolate/_rbfinterp_pythran.cp313t-win_arm64.lib +0 -0
  311. scipy/interpolate/_rbfinterp_pythran.cp313t-win_arm64.pyd +0 -0
  312. scipy/interpolate/_rgi.py +764 -0
  313. scipy/interpolate/_rgi_cython.cp313t-win_arm64.lib +0 -0
  314. scipy/interpolate/_rgi_cython.cp313t-win_arm64.pyd +0 -0
  315. scipy/interpolate/dfitpack.py +24 -0
  316. scipy/interpolate/fitpack.py +31 -0
  317. scipy/interpolate/fitpack2.py +29 -0
  318. scipy/interpolate/interpnd.py +24 -0
  319. scipy/interpolate/interpolate.py +30 -0
  320. scipy/interpolate/ndgriddata.py +23 -0
  321. scipy/interpolate/polyint.py +24 -0
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  1511. scipy/stats/tests/test_odds_ratio.py +148 -0
  1512. scipy/stats/tests/test_qmc.py +1492 -0
  1513. scipy/stats/tests/test_quantile.py +199 -0
  1514. scipy/stats/tests/test_rank.py +345 -0
  1515. scipy/stats/tests/test_relative_risk.py +95 -0
  1516. scipy/stats/tests/test_resampling.py +2000 -0
  1517. scipy/stats/tests/test_sampling.py +1450 -0
  1518. scipy/stats/tests/test_sensitivity_analysis.py +310 -0
  1519. scipy/stats/tests/test_stats.py +9707 -0
  1520. scipy/stats/tests/test_survival.py +466 -0
  1521. scipy/stats/tests/test_tukeylambda_stats.py +85 -0
  1522. scipy/stats/tests/test_variation.py +216 -0
  1523. scipy/version.py +12 -0
  1524. scipy-1.16.2.dist-info/DELVEWHEEL +2 -0
  1525. scipy-1.16.2.dist-info/LICENSE.txt +912 -0
  1526. scipy-1.16.2.dist-info/METADATA +1061 -0
  1527. scipy-1.16.2.dist-info/RECORD +1530 -0
  1528. scipy-1.16.2.dist-info/WHEEL +4 -0
  1529. scipy.libs/msvcp140-5f1c5dd31916990d94181e07bc3afb32.dll +0 -0
  1530. scipy.libs/scipy_openblas-f3ac85b1f412f7e86514c923dc4058d1.dll +0 -0
@@ -0,0 +1,1090 @@
1
+ import os
2
+ import numpy as np
3
+ import numpy.testing as npt
4
+ from numpy.testing import assert_allclose, assert_equal
5
+ import pytest
6
+ from scipy import stats
7
+ from scipy.optimize import differential_evolution
8
+
9
+ from .test_continuous_basic import distcont
10
+ from scipy.stats._distn_infrastructure import FitError
11
+ from scipy.stats._distr_params import distdiscrete
12
+ from scipy.stats import goodness_of_fit
13
+
14
+
15
+ # this is not a proper statistical test for convergence, but only
16
+ # verifies that the estimate and true values don't differ by too much
17
+
18
+ fit_sizes = [1000, 5000, 10000] # sample sizes to try
19
+
20
+ thresh_percent = 0.25 # percent of true parameters for fail cut-off
21
+ thresh_min = 0.75 # minimum difference estimate - true to fail test
22
+
23
+ mle_failing_fits = [
24
+ 'dpareto_lognorm',
25
+ 'gausshyper',
26
+ 'genexpon',
27
+ 'gengamma',
28
+ 'irwinhall',
29
+ 'kappa4',
30
+ 'ksone',
31
+ 'kstwo',
32
+ 'ncf',
33
+ 'ncx2',
34
+ 'truncexpon',
35
+ 'tukeylambda',
36
+ 'vonmises',
37
+ 'levy_stable',
38
+ 'trapezoid',
39
+ 'truncweibull_min',
40
+ 'studentized_range',
41
+ ]
42
+
43
+ # these pass but are XSLOW (>1s)
44
+ mle_Xslow_fits = ['betaprime', 'crystalball', 'exponweib', 'f', 'geninvgauss',
45
+ 'jf_skew_t', 'nct', 'recipinvgauss', 'rel_breitwigner',
46
+ 'vonmises_line']
47
+
48
+ # The MLE fit method of these distributions doesn't perform well when all
49
+ # parameters are fit, so test them with the location fixed at 0.
50
+ mle_use_floc0 = [
51
+ 'burr',
52
+ 'chi',
53
+ 'chi2',
54
+ 'mielke',
55
+ 'pearson3',
56
+ 'genhalflogistic',
57
+ 'rdist',
58
+ 'pareto',
59
+ 'powerlaw', # distfn.nnlf(est2, rvs) > distfn.nnlf(est1, rvs) otherwise
60
+ 'powerlognorm',
61
+ 'wrapcauchy',
62
+ 'rel_breitwigner',
63
+ ]
64
+
65
+ mm_failing_fits = ['alpha', 'betaprime', 'burr', 'burr12', 'cauchy', 'chi',
66
+ 'chi2', 'crystalball', 'dgamma', 'dpareto_lognorm', 'dweibull',
67
+ 'f', 'fatiguelife', 'fisk', 'foldcauchy', 'genextreme',
68
+ 'gengamma', 'genhyperbolic', 'gennorm', 'genpareto',
69
+ 'halfcauchy', 'invgamma', 'invweibull', 'irwinhall', 'jf_skew_t',
70
+ 'johnsonsu', 'kappa3', 'ksone', 'kstwo', 'landau', 'levy', 'levy_l',
71
+ 'levy_stable', 'loglaplace', 'lomax', 'mielke', 'nakagami',
72
+ 'ncf', 'nct', 'ncx2', 'pareto', 'powerlognorm', 'powernorm',
73
+ 'rel_breitwigner', 'skewcauchy', 't', 'trapezoid', 'triang',
74
+ 'truncpareto', 'truncweibull_min', 'tukeylambda',
75
+ 'studentized_range']
76
+
77
+ # not sure if these fail, but they caused my patience to fail
78
+ mm_XXslow_fits = ['argus', 'exponpow', 'exponweib', 'gausshyper', 'genexpon',
79
+ 'genhalflogistic', 'halfgennorm', 'gompertz', 'johnsonsb',
80
+ 'kappa4', 'kstwobign', 'recipinvgauss',
81
+ 'truncexpon', 'vonmises', 'vonmises_line']
82
+
83
+ # these pass but are XSLOW (>1s)
84
+ mm_Xslow_fits = ['wrapcauchy']
85
+
86
+ failing_fits = {"MM": mm_failing_fits + mm_XXslow_fits, "MLE": mle_failing_fits}
87
+ xslow_fits = {"MM": mm_Xslow_fits, "MLE": mle_Xslow_fits}
88
+ fail_interval_censored = {"truncpareto"}
89
+
90
+ # Don't run the fit test on these:
91
+ skip_fit = [
92
+ 'erlang', # Subclass of gamma, generates a warning.
93
+ 'genhyperbolic', 'norminvgauss', # too slow
94
+ ]
95
+
96
+
97
+ def cases_test_cont_fit():
98
+ # this tests the closeness of the estimated parameters to the true
99
+ # parameters with fit method of continuous distributions
100
+ # Note: is slow, some distributions don't converge with sample
101
+ # size <= 10000
102
+ for distname, arg in distcont:
103
+ if distname not in skip_fit:
104
+ yield distname, arg
105
+
106
+
107
+ @pytest.mark.slow
108
+ @pytest.mark.parametrize('distname,arg', cases_test_cont_fit())
109
+ @pytest.mark.parametrize('method', ["MLE", "MM"])
110
+ def test_cont_fit(distname, arg, method):
111
+ run_xfail = int(os.getenv('SCIPY_XFAIL', default=False))
112
+ run_xslow = int(os.getenv('SCIPY_XSLOW', default=False))
113
+
114
+ if distname in failing_fits[method] and not run_xfail:
115
+ # The generic `fit` method can't be expected to work perfectly for all
116
+ # distributions, data, and guesses. Some failures are expected.
117
+ msg = "Failure expected; set environment variable SCIPY_XFAIL=1 to run."
118
+ pytest.xfail(msg)
119
+
120
+ if distname in xslow_fits[method] and not run_xslow:
121
+ msg = "Very slow; set environment variable SCIPY_XSLOW=1 to run."
122
+ pytest.skip(msg)
123
+
124
+ distfn = getattr(stats, distname)
125
+
126
+ truearg = np.hstack([arg, [0.0, 1.0]])
127
+ diffthreshold = np.max(np.vstack([truearg*thresh_percent,
128
+ np.full(distfn.numargs+2, thresh_min)]),
129
+ 0)
130
+
131
+ for fit_size in fit_sizes:
132
+ # Note that if a fit succeeds, the other fit_sizes are skipped
133
+ rng = np.random.default_rng(1234)
134
+
135
+ with np.errstate(all='ignore'):
136
+ rvs = distfn.rvs(size=fit_size, *arg, random_state=rng)
137
+ if method == 'MLE' and distfn.name in mle_use_floc0:
138
+ kwds = {'floc': 0}
139
+ else:
140
+ kwds = {}
141
+ # start with default values
142
+ est = distfn.fit(rvs, method=method, **kwds)
143
+ if method == 'MLE':
144
+ # Trivial test of the use of CensoredData. The fit() method
145
+ # will check that data contains no actual censored data, and
146
+ # do a regular uncensored fit.
147
+ data1 = stats.CensoredData(rvs)
148
+ est1 = distfn.fit(data1, **kwds)
149
+ msg = ('Different results fitting uncensored data wrapped as'
150
+ f' CensoredData: {distfn.name}: est={est} est1={est1}')
151
+ assert_allclose(est1, est, rtol=1e-10, err_msg=msg)
152
+ if method == 'MLE' and distname not in fail_interval_censored:
153
+ # Convert the first `nic` values in rvs to interval-censored
154
+ # values. The interval is small, so est2 should be close to
155
+ # est.
156
+ nic = 15
157
+ interval = np.column_stack((rvs, rvs))
158
+ interval[:nic, 0] *= 0.99
159
+ interval[:nic, 1] *= 1.01
160
+ interval.sort(axis=1)
161
+ data2 = stats.CensoredData(interval=interval)
162
+ est2 = distfn.fit(data2, **kwds)
163
+ msg = ('Different results fitting interval-censored'
164
+ f' data: {distfn.name}: est={est} est2={est2}')
165
+ assert_allclose(est2, est, rtol=0.05, err_msg=msg)
166
+
167
+ diff = est - truearg
168
+
169
+ # threshold for location
170
+ diffthreshold[-2] = np.max([np.abs(rvs.mean())*thresh_percent,
171
+ thresh_min])
172
+
173
+ if np.any(np.isnan(est)):
174
+ raise AssertionError('nan returned in fit')
175
+ else:
176
+ if np.all(np.abs(diff) <= diffthreshold):
177
+ break
178
+ else:
179
+ txt = f'parameter: {str(truearg)}\n'
180
+ txt += f'estimated: {str(est)}\n'
181
+ txt += f'diff : {str(diff)}\n'
182
+ raise AssertionError(f'fit not very good in {distfn.name}\n' + txt)
183
+
184
+
185
+ def _check_loc_scale_mle_fit(name, data, desired, atol=None):
186
+ d = getattr(stats, name)
187
+ actual = d.fit(data)[-2:]
188
+ assert_allclose(actual, desired, atol=atol,
189
+ err_msg=f'poor mle fit of (loc, scale) in {name}')
190
+
191
+
192
+ def test_non_default_loc_scale_mle_fit():
193
+ data = np.array([1.01, 1.78, 1.78, 1.78, 1.88, 1.88, 1.88, 2.00])
194
+ _check_loc_scale_mle_fit('uniform', data, [1.01, 0.99], 1e-3)
195
+ _check_loc_scale_mle_fit('expon', data, [1.01, 0.73875], 1e-3)
196
+
197
+
198
+ def test_expon_fit():
199
+ """gh-6167"""
200
+ data = [0, 0, 0, 0, 2, 2, 2, 2]
201
+ phat = stats.expon.fit(data, floc=0)
202
+ assert_allclose(phat, [0, 1.0], atol=1e-3)
203
+
204
+
205
+ def test_fit_error():
206
+ data = np.concatenate([np.zeros(29), np.ones(21)])
207
+ message = "Optimization converged to parameters that are..."
208
+ with pytest.raises(FitError, match=message), \
209
+ pytest.warns(RuntimeWarning):
210
+ stats.beta.fit(data)
211
+
212
+
213
+ @pytest.mark.parametrize("dist, params",
214
+ [(stats.norm, (0.5, 2.5)), # type: ignore[attr-defined]
215
+ (stats.binom, (10, 0.3, 2))]) # type: ignore[attr-defined]
216
+ def test_nnlf_and_related_methods(dist, params):
217
+ rng = np.random.default_rng(983459824)
218
+
219
+ if hasattr(dist, 'pdf'):
220
+ logpxf = dist.logpdf
221
+ else:
222
+ logpxf = dist.logpmf
223
+
224
+ x = dist.rvs(*params, size=100, random_state=rng)
225
+ ref = -logpxf(x, *params).sum()
226
+ res1 = dist.nnlf(params, x)
227
+ res2 = dist._penalized_nnlf(params, x)
228
+ assert_allclose(res1, ref)
229
+ assert_allclose(res2, ref)
230
+
231
+
232
+ def cases_test_fit_mle():
233
+ # These fail default test or hang
234
+ skip_basic_fit = {'argus', 'irwinhall', 'foldnorm', 'truncpareto',
235
+ 'truncweibull_min', 'ksone', 'levy_stable',
236
+ 'studentized_range', 'kstwo',
237
+ 'beta', 'nakagami', 'truncnorm', # don't meet tolerance
238
+ 'poisson_binom'} # vector-valued shape parameter
239
+
240
+ # Please keep this list in alphabetical order...
241
+ slow_basic_fit = {'alpha', 'arcsine', 'betaprime', 'binom', 'bradford', 'burr12',
242
+ 'chi', 'crystalball', 'dweibull', 'erlang', 'exponnorm',
243
+ 'exponpow', 'f', 'fatiguelife', 'fisk', 'foldcauchy', 'gamma',
244
+ 'genexpon', 'genextreme', 'gennorm', 'genpareto',
245
+ 'gompertz', 'halfgennorm', 'invgamma', 'invgauss', 'invweibull',
246
+ 'jf_skew_t', 'johnsonsb', 'johnsonsu', 'kappa3',
247
+ 'kstwobign', 'loglaplace', 'lognorm', 'lomax', 'mielke',
248
+ 'nbinom', 'norminvgauss',
249
+ 'pareto', 'pearson3', 'powerlaw', 'powernorm',
250
+ 'randint', 'rdist', 'recipinvgauss', 'rice', 'skewnorm',
251
+ 't', 'uniform', 'weibull_max', 'weibull_min', 'wrapcauchy'}
252
+
253
+ # Please keep this list in alphabetical order...
254
+ xslow_basic_fit = {'betabinom', 'betanbinom', 'burr', 'dpareto_lognorm',
255
+ 'exponweib', 'gausshyper', 'gengamma', 'genhalflogistic',
256
+ 'genhyperbolic', 'geninvgauss',
257
+ 'hypergeom', 'kappa4', 'loguniform',
258
+ 'ncf', 'nchypergeom_fisher', 'nchypergeom_wallenius',
259
+ 'nct', 'ncx2', 'nhypergeom',
260
+ 'powerlognorm', 'reciprocal', 'rel_breitwigner',
261
+ 'skellam', 'trapezoid', 'triang',
262
+ 'tukeylambda', 'vonmises', 'zipfian'}
263
+
264
+ for dist in dict(distdiscrete + distcont):
265
+ if dist in skip_basic_fit or not isinstance(dist, str):
266
+ reason = "tested separately"
267
+ yield pytest.param(dist, marks=pytest.mark.skip(reason=reason))
268
+ elif dist in slow_basic_fit:
269
+ reason = "too slow (>= 0.25s)"
270
+ yield pytest.param(dist, marks=pytest.mark.slow(reason=reason))
271
+ elif dist in xslow_basic_fit:
272
+ reason = "too slow (>= 1.0s)"
273
+ yield pytest.param(dist, marks=pytest.mark.xslow(reason=reason))
274
+ else:
275
+ yield dist
276
+
277
+
278
+ def cases_test_fit_mse():
279
+ # the first four are so slow that I'm not sure whether they would pass
280
+ skip_basic_fit = {'levy_stable', 'studentized_range', 'ksone', 'skewnorm',
281
+ 'irwinhall', # hangs
282
+ 'norminvgauss', # super slow (~1 hr) but passes
283
+ 'kstwo', # very slow (~25 min) but passes
284
+ 'geninvgauss', # quite slow (~4 minutes) but passes
285
+ 'gausshyper', 'genhyperbolic', # integration warnings
286
+ 'tukeylambda', # close, but doesn't meet tolerance
287
+ 'vonmises', # can have negative CDF; doesn't play nice
288
+ 'arcsine', 'argus', 'powerlaw', 'rdist', # don't meet tolerance
289
+ 'poisson_binom', # vector-valued shape parameter
290
+ }
291
+
292
+ # Please keep this list in alphabetical order...
293
+ slow_basic_fit = {'alpha', 'anglit', 'betabinom', 'bradford',
294
+ 'chi', 'chi2', 'crystalball', 'dweibull',
295
+ 'erlang', 'exponnorm', 'exponpow', 'exponweib',
296
+ 'fatiguelife', 'fisk', 'foldcauchy', 'foldnorm',
297
+ 'gamma', 'genexpon', 'genextreme', 'genhalflogistic',
298
+ 'genlogistic', 'genpareto', 'gompertz',
299
+ 'hypergeom', 'invweibull',
300
+ 'johnsonsu', 'kappa3', 'kstwobign',
301
+ 'laplace_asymmetric', 'loggamma', 'loglaplace',
302
+ 'lognorm', 'lomax',
303
+ 'maxwell', 'nhypergeom',
304
+ 'pareto', 'powernorm', 'randint', 'recipinvgauss',
305
+ 'semicircular',
306
+ 't', 'triang', 'truncexpon', 'truncpareto',
307
+ 'uniform',
308
+ 'wald', 'weibull_max', 'weibull_min', 'wrapcauchy'}
309
+
310
+ # Please keep this list in alphabetical order...
311
+ xslow_basic_fit = {'argus', 'beta', 'betaprime', 'burr', 'burr12',
312
+ 'dgamma', 'dpareto_lognorm', 'f', 'gengamma', 'gennorm',
313
+ 'halfgennorm', 'invgamma', 'invgauss', 'jf_skew_t',
314
+ 'johnsonsb', 'kappa4', 'loguniform', 'mielke',
315
+ 'nakagami', 'ncf', 'nchypergeom_fisher',
316
+ 'nchypergeom_wallenius', 'nct', 'ncx2',
317
+ 'pearson3', 'powerlognorm',
318
+ 'reciprocal', 'rel_breitwigner', 'rice',
319
+ 'trapezoid', 'truncnorm', 'truncweibull_min',
320
+ 'vonmises_line', 'zipfian'}
321
+
322
+ warns_basic_fit = {'skellam'} # can remove mark after gh-14901 is resolved
323
+
324
+ for dist in dict(distdiscrete + distcont):
325
+ if dist in skip_basic_fit or not isinstance(dist, str):
326
+ reason = "Fails. Oh well."
327
+ yield pytest.param(dist, marks=pytest.mark.skip(reason=reason))
328
+ elif dist in slow_basic_fit:
329
+ reason = "too slow (>= 0.25s)"
330
+ yield pytest.param(dist, marks=pytest.mark.slow(reason=reason))
331
+ elif dist in xslow_basic_fit:
332
+ reason = "too slow (>= 1.0s)"
333
+ yield pytest.param(dist, marks=pytest.mark.xslow(reason=reason))
334
+ elif dist in warns_basic_fit:
335
+ mark = pytest.mark.filterwarnings('ignore::RuntimeWarning')
336
+ yield pytest.param(dist, marks=mark)
337
+ else:
338
+ yield dist
339
+
340
+
341
+ def cases_test_fitstart():
342
+ for distname, shapes in dict(distcont).items():
343
+ if (not isinstance(distname, str) or
344
+ distname in {'studentized_range', 'recipinvgauss'}): # slow
345
+ continue
346
+ yield distname, shapes
347
+
348
+
349
+ @pytest.mark.parametrize('distname, shapes', cases_test_fitstart())
350
+ def test_fitstart(distname, shapes):
351
+ dist = getattr(stats, distname)
352
+ rng = np.random.default_rng(216342614)
353
+ data = rng.random(10)
354
+
355
+ with np.errstate(invalid='ignore', divide='ignore'): # irrelevant to test
356
+ guess = dist._fitstart(data)
357
+
358
+ assert dist._argcheck(*guess[:-2])
359
+
360
+
361
+ def assert_nlff_less_or_close(dist, data, params1, params0, rtol=1e-7, atol=0,
362
+ nlff_name='nnlf'):
363
+ nlff = getattr(dist, nlff_name)
364
+ nlff1 = nlff(params1, data)
365
+ nlff0 = nlff(params0, data)
366
+ if not (nlff1 < nlff0):
367
+ np.testing.assert_allclose(nlff1, nlff0, rtol=rtol, atol=atol)
368
+
369
+
370
+ class TestFit:
371
+ dist = stats.binom # type: ignore[attr-defined]
372
+ seed = 654634816187
373
+ rng = np.random.default_rng(seed)
374
+ data = stats.binom.rvs(5, 0.5, size=100, random_state=rng) # type: ignore[attr-defined] # noqa: E501
375
+ shape_bounds_a = [(1, 10), (0, 1)]
376
+ shape_bounds_d = {'n': (1, 10), 'p': (0, 1)}
377
+ atol = 5e-2
378
+ rtol = 1e-2
379
+ tols = {'atol': atol, 'rtol': rtol}
380
+
381
+ def opt(self, *args, rng=1, **kwds):
382
+ return differential_evolution(*args, rng=rng, **kwds)
383
+
384
+ def test_dist_iv(self):
385
+ message = "`dist` must be an instance of..."
386
+ with pytest.raises(ValueError, match=message):
387
+ stats.fit(10, self.data, self.shape_bounds_a)
388
+
389
+ def test_data_iv(self):
390
+ message = "`data` must be exactly one-dimensional."
391
+ with pytest.raises(ValueError, match=message):
392
+ stats.fit(self.dist, [[1, 2, 3]], self.shape_bounds_a)
393
+
394
+ message = "All elements of `data` must be finite numbers."
395
+ with pytest.raises(ValueError, match=message):
396
+ stats.fit(self.dist, [1, 2, 3, np.nan], self.shape_bounds_a)
397
+ with pytest.raises(ValueError, match=message):
398
+ stats.fit(self.dist, [1, 2, 3, np.inf], self.shape_bounds_a)
399
+ with pytest.raises(ValueError, match=message):
400
+ stats.fit(self.dist, ['1', '2', '3'], self.shape_bounds_a)
401
+
402
+ def test_bounds_iv(self):
403
+ message = "Bounds provided for the following unrecognized..."
404
+ shape_bounds = {'n': (1, 10), 'p': (0, 1), '1': (0, 10)}
405
+ with pytest.warns(RuntimeWarning, match=message):
406
+ stats.fit(self.dist, self.data, shape_bounds)
407
+
408
+ message = "Each element of a `bounds` sequence must be a tuple..."
409
+ shape_bounds = [(1, 10, 3), (0, 1)]
410
+ with pytest.raises(ValueError, match=message):
411
+ stats.fit(self.dist, self.data, shape_bounds)
412
+
413
+ message = "Each element of `bounds` must be a tuple specifying..."
414
+ shape_bounds = [(1, 10, 3), (0, 1, 0.5)]
415
+ with pytest.raises(ValueError, match=message):
416
+ stats.fit(self.dist, self.data, shape_bounds)
417
+ shape_bounds = [1, 0]
418
+ with pytest.raises(ValueError, match=message):
419
+ stats.fit(self.dist, self.data, shape_bounds)
420
+
421
+ message = "A `bounds` sequence must contain at least 2 elements..."
422
+ shape_bounds = [(1, 10)]
423
+ with pytest.raises(ValueError, match=message):
424
+ stats.fit(self.dist, self.data, shape_bounds)
425
+
426
+ message = "A `bounds` sequence may not contain more than 3 elements..."
427
+ bounds = [(1, 10), (1, 10), (1, 10), (1, 10)]
428
+ with pytest.raises(ValueError, match=message):
429
+ stats.fit(self.dist, self.data, bounds)
430
+
431
+ message = "There are no values for `p` on the interval..."
432
+ shape_bounds = {'n': (1, 10), 'p': (1, 0)}
433
+ with pytest.raises(ValueError, match=message):
434
+ stats.fit(self.dist, self.data, shape_bounds)
435
+
436
+ message = "There are no values for `n` on the interval..."
437
+ shape_bounds = [(10, 1), (0, 1)]
438
+ with pytest.raises(ValueError, match=message):
439
+ stats.fit(self.dist, self.data, shape_bounds)
440
+
441
+ message = "There are no integer values for `n` on the interval..."
442
+ shape_bounds = [(1.4, 1.6), (0, 1)]
443
+ with pytest.raises(ValueError, match=message):
444
+ stats.fit(self.dist, self.data, shape_bounds)
445
+
446
+ message = "The intersection of user-provided bounds for `n`"
447
+ with pytest.raises(ValueError, match=message):
448
+ stats.fit(self.dist, self.data)
449
+ shape_bounds = [(-np.inf, np.inf), (0, 1)]
450
+ with pytest.raises(ValueError, match=message):
451
+ stats.fit(self.dist, self.data, shape_bounds)
452
+
453
+ def test_guess_iv(self):
454
+ message = "Guesses provided for the following unrecognized..."
455
+ guess = {'n': 1, 'p': 0.5, '1': 255}
456
+ with pytest.warns(RuntimeWarning, match=message):
457
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
458
+
459
+ message = "Each element of `guess` must be a scalar..."
460
+ guess = {'n': 1, 'p': 'hi'}
461
+ with pytest.raises(ValueError, match=message):
462
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
463
+ guess = [1, 'f']
464
+ with pytest.raises(ValueError, match=message):
465
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
466
+ guess = [[1, 2]]
467
+ with pytest.raises(ValueError, match=message):
468
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
469
+
470
+ message = "A `guess` sequence must contain at least 2..."
471
+ guess = [1]
472
+ with pytest.raises(ValueError, match=message):
473
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
474
+
475
+ message = "A `guess` sequence may not contain more than 3..."
476
+ guess = [1, 2, 3, 4]
477
+ with pytest.raises(ValueError, match=message):
478
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
479
+
480
+ message = "Guess for parameter `n` rounded.*|Guess for parameter `p` clipped.*"
481
+ guess = {'n': 4.5, 'p': -0.5}
482
+ with pytest.warns(RuntimeWarning, match=message):
483
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
484
+
485
+ message = "Guess for parameter `loc` rounded..."
486
+ guess = [5, 0.5, 0.5]
487
+ with pytest.warns(RuntimeWarning, match=message):
488
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
489
+
490
+ message = "Guess for parameter `p` clipped..."
491
+ guess = {'n': 5, 'p': -0.5}
492
+ with pytest.warns(RuntimeWarning, match=message):
493
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
494
+
495
+ message = "Guess for parameter `loc` clipped..."
496
+ guess = [5, 0.5, 1]
497
+ with pytest.warns(RuntimeWarning, match=message):
498
+ stats.fit(self.dist, self.data, self.shape_bounds_d, guess=guess)
499
+
500
+ def basic_fit_test(self, dist_name, method, rng=1):
501
+
502
+ N = 5000
503
+ dist_data = dict(distcont + distdiscrete)
504
+ rng = np.random.default_rng(self.seed)
505
+ dist = getattr(stats, dist_name)
506
+ shapes = np.array(dist_data[dist_name])
507
+ bounds = np.empty((len(shapes) + 2, 2), dtype=np.float64)
508
+ bounds[:-2, 0] = shapes/10.**np.sign(shapes)
509
+ bounds[:-2, 1] = shapes*10.**np.sign(shapes)
510
+ bounds[-2] = (0, 10)
511
+ bounds[-1] = (1e-16, 10)
512
+ loc = rng.uniform(*bounds[-2])
513
+ scale = rng.uniform(*bounds[-1])
514
+ ref = list(dist_data[dist_name]) + [loc, scale]
515
+
516
+ if getattr(dist, 'pmf', False):
517
+ ref = ref[:-1]
518
+ ref[-1] = np.floor(loc)
519
+ data = dist.rvs(*ref, size=N, random_state=rng)
520
+ bounds = bounds[:-1]
521
+ if getattr(dist, 'pdf', False):
522
+ data = dist.rvs(*ref, size=N, random_state=rng)
523
+
524
+ with npt.suppress_warnings() as sup:
525
+ sup.filter(RuntimeWarning, "overflow encountered")
526
+ res = stats.fit(dist, data, bounds, method=method,
527
+ optimizer=self.opt)
528
+
529
+ nlff_names = {'mle': 'nnlf', 'mse': '_penalized_nlpsf'}
530
+ nlff_name = nlff_names[method]
531
+ assert_nlff_less_or_close(dist, data, res.params, ref, **self.tols,
532
+ nlff_name=nlff_name)
533
+
534
+ @pytest.mark.parametrize("dist_name", cases_test_fit_mle())
535
+ def test_basic_fit_mle(self, dist_name):
536
+ self.basic_fit_test(dist_name, "mle", rng=5)
537
+
538
+ @pytest.mark.parametrize("dist_name", cases_test_fit_mse())
539
+ def test_basic_fit_mse(self, dist_name):
540
+ self.basic_fit_test(dist_name, "mse", rng=2)
541
+
542
+ @pytest.mark.slow
543
+ def test_arcsine(self):
544
+ # Can't guarantee that all distributions will fit all data with
545
+ # arbitrary bounds. This distribution just happens to fail above.
546
+ # Try something slightly different.
547
+ N = 1000
548
+ rng = np.random.default_rng(self.seed)
549
+ dist = stats.arcsine
550
+ shapes = (1., 2.)
551
+ data = dist.rvs(*shapes, size=N, random_state=rng)
552
+ shape_bounds = {'loc': (0.1, 10), 'scale': (0.1, 10)}
553
+ res = stats.fit(dist, data, shape_bounds, method='mse', optimizer=self.opt)
554
+ assert_nlff_less_or_close(dist, data, res.params, shapes,
555
+ nlff_name='_penalized_nlpsf', **self.tols)
556
+
557
+ @pytest.mark.parametrize("method", ('mle', 'mse'))
558
+ def test_argus(self, method):
559
+ # Can't guarantee that all distributions will fit all data with
560
+ # arbitrary bounds. This distribution just happens to fail above.
561
+ # Try something slightly different.
562
+ N = 1000
563
+ rng = np.random.default_rng(self.seed)
564
+ dist = stats.argus
565
+ shapes = (1., 2., 3.)
566
+ data = dist.rvs(*shapes, size=N, random_state=rng)
567
+ shape_bounds = {'chi': (0.1, 10), 'loc': (0.1, 10), 'scale': (0.1, 10)}
568
+ res = stats.fit(dist, data, shape_bounds, optimizer=self.opt, method=method)
569
+ nlff_name = {'mle': 'nnlf', 'mse': '_penalized_nlpsf'}[method]
570
+ assert_nlff_less_or_close(dist, data, res.params, shapes, **self.tols,
571
+ nlff_name=nlff_name)
572
+
573
+ @pytest.mark.xslow
574
+ def test_beta(self):
575
+ # Can't guarantee that all distributions will fit all data with
576
+ # arbitrary bounds. This distribution just happens to fail above.
577
+ # Try something slightly different.
578
+ N = 1000
579
+ rng = np.random.default_rng(self.seed)
580
+ dist = stats.beta
581
+ shapes = (2.3098496451481823, 0.62687954300963677, 1., 2.)
582
+ data = dist.rvs(*shapes, size=N, random_state=rng)
583
+ shape_bounds = {'a': (0.1, 10), 'b':(0.1, 10),
584
+ 'loc': (0.1, 10), 'scale': (0.1, 10)}
585
+ res = stats.fit(dist, data, shape_bounds, method='mle', optimizer=self.opt)
586
+ assert_nlff_less_or_close(dist, data, res.params, shapes,
587
+ nlff_name='nnlf', **self.tols)
588
+
589
+ def test_foldnorm(self):
590
+ # Can't guarantee that all distributions will fit all data with
591
+ # arbitrary bounds. This distribution just happens to fail above.
592
+ # Try something slightly different.
593
+ N = 1000
594
+ rng = np.random.default_rng(self.seed)
595
+ dist = stats.foldnorm
596
+ shapes = (1.952125337355587, 2., 3.)
597
+ data = dist.rvs(*shapes, size=N, random_state=rng)
598
+ shape_bounds = {'c': (0.1, 10), 'loc': (0.1, 10), 'scale': (0.1, 10)}
599
+ res = stats.fit(dist, data, shape_bounds, optimizer=self.opt)
600
+
601
+ assert_nlff_less_or_close(dist, data, res.params, shapes, **self.tols)
602
+
603
+ def test_nakagami(self):
604
+ # Can't guarantee that all distributions will fit all data with
605
+ # arbitrary bounds. This distribution just happens to fail above.
606
+ # Try something slightly different.
607
+ N = 1000
608
+ rng = np.random.default_rng(self.seed)
609
+ dist = stats.nakagami
610
+ shapes = (4.9673794866666237, 1., 2.)
611
+ data = dist.rvs(*shapes, size=N, random_state=rng)
612
+ shape_bounds = {'nu':(0.1, 10), 'loc': (0.1, 10), 'scale': (0.1, 10)}
613
+ res = stats.fit(dist, data, shape_bounds, method='mle', optimizer=self.opt)
614
+ assert_nlff_less_or_close(dist, data, res.params, shapes,
615
+ nlff_name='nnlf', **self.tols)
616
+
617
+ @pytest.mark.slow
618
+ def test_powerlaw(self):
619
+ # Can't guarantee that all distributions will fit all data with
620
+ # arbitrary bounds. This distribution just happens to fail above.
621
+ # Try something slightly different.
622
+ N = 1000
623
+ rng = np.random.default_rng(self.seed)
624
+ dist = stats.powerlaw
625
+ shapes = (1.6591133289905851, 1., 2.)
626
+ data = dist.rvs(*shapes, size=N, random_state=rng)
627
+ shape_bounds = {'a': (0.1, 10), 'loc': (0.1, 10), 'scale': (0.1, 10)}
628
+ res = stats.fit(dist, data, shape_bounds, method='mse', optimizer=self.opt)
629
+ assert_nlff_less_or_close(dist, data, res.params, shapes,
630
+ nlff_name='_penalized_nlpsf', **self.tols)
631
+
632
+ def test_truncpareto(self):
633
+ # Can't guarantee that all distributions will fit all data with
634
+ # arbitrary bounds. This distribution just happens to fail above.
635
+ # Try something slightly different.
636
+ N = 1000
637
+ rng = np.random.default_rng(self.seed)
638
+ dist = stats.truncpareto
639
+ shapes = (1.8, 5.3, 2.3, 4.1)
640
+ data = dist.rvs(*shapes, size=N, random_state=rng)
641
+ shape_bounds = [(0.1, 10)]*4
642
+ res = stats.fit(dist, data, shape_bounds, optimizer=self.opt)
643
+
644
+ assert_nlff_less_or_close(dist, data, res.params, shapes, **self.tols)
645
+
646
+ @pytest.mark.slow
647
+ def test_truncweibull_min(self):
648
+ # Can't guarantee that all distributions will fit all data with
649
+ # arbitrary bounds. This distribution just happens to fail above.
650
+ # Try something slightly different.
651
+ N = 1000
652
+ rng = np.random.default_rng(self.seed)
653
+ dist = stats.truncweibull_min
654
+ shapes = (2.5, 0.25, 1.75, 2., 3.)
655
+ data = dist.rvs(*shapes, size=N, random_state=rng)
656
+ shape_bounds = [(0.1, 10)]*5
657
+ res = stats.fit(dist, data, shape_bounds, optimizer=self.opt)
658
+
659
+ assert_nlff_less_or_close(dist, data, res.params, shapes, **self.tols)
660
+
661
+ def test_missing_shape_bounds(self):
662
+ # some distributions have a small domain w.r.t. a parameter, e.g.
663
+ # $p \in [0, 1]$ for binomial distribution
664
+ # User does not need to provide these because the intersection of the
665
+ # user's bounds (none) and the distribution's domain is finite
666
+ N = 1000
667
+ rng = np.random.default_rng(self.seed)
668
+
669
+ dist = stats.binom
670
+ n, p, loc = 10, 0.65, 0
671
+ data = dist.rvs(n, p, loc=loc, size=N, random_state=rng)
672
+ shape_bounds = {'n': np.array([0, 20])} # check arrays are OK, too
673
+ res = stats.fit(dist, data, shape_bounds, optimizer=self.opt)
674
+ assert_allclose(res.params, (n, p, loc), **self.tols)
675
+
676
+ dist = stats.bernoulli
677
+ p, loc = 0.314159, 0
678
+ data = dist.rvs(p, loc=loc, size=N, random_state=rng)
679
+ res = stats.fit(dist, data, optimizer=self.opt)
680
+ assert_allclose(res.params, (p, loc), **self.tols)
681
+
682
+ def test_fit_only_loc_scale(self):
683
+ # fit only loc
684
+ N = 5000
685
+ rng = np.random.default_rng(self.seed)
686
+
687
+ dist = stats.norm
688
+ loc, scale = 1.5, 1
689
+ data = dist.rvs(loc=loc, size=N, random_state=rng)
690
+ loc_bounds = (0, 5)
691
+ bounds = {'loc': loc_bounds}
692
+ res = stats.fit(dist, data, bounds, optimizer=self.opt)
693
+ assert_allclose(res.params, (loc, scale), **self.tols)
694
+
695
+ # fit only scale
696
+ loc, scale = 0, 2.5
697
+ data = dist.rvs(scale=scale, size=N, random_state=rng)
698
+ scale_bounds = (0.01, 5)
699
+ bounds = {'scale': scale_bounds}
700
+ res = stats.fit(dist, data, bounds, optimizer=self.opt)
701
+ assert_allclose(res.params, (loc, scale), **self.tols)
702
+
703
+ # fit only loc and scale
704
+ dist = stats.norm
705
+ loc, scale = 1.5, 2.5
706
+ data = dist.rvs(loc=loc, scale=scale, size=N, random_state=rng)
707
+ bounds = {'loc': loc_bounds, 'scale': scale_bounds}
708
+ res = stats.fit(dist, data, bounds, optimizer=self.opt)
709
+ assert_allclose(res.params, (loc, scale), **self.tols)
710
+
711
+ def test_everything_fixed(self):
712
+ N = 5000
713
+ rng = np.random.default_rng(self.seed)
714
+
715
+ dist = stats.norm
716
+ loc, scale = 1.5, 2.5
717
+ data = dist.rvs(loc=loc, scale=scale, size=N, random_state=rng)
718
+
719
+ # loc, scale fixed to 0, 1 by default
720
+ res = stats.fit(dist, data)
721
+ assert_allclose(res.params, (0, 1), **self.tols)
722
+
723
+ # loc, scale explicitly fixed
724
+ bounds = {'loc': (loc, loc), 'scale': (scale, scale)}
725
+ res = stats.fit(dist, data, bounds)
726
+ assert_allclose(res.params, (loc, scale), **self.tols)
727
+
728
+ # `n` gets fixed during polishing
729
+ dist = stats.binom
730
+ n, p, loc = 10, 0.65, 0
731
+ data = dist.rvs(n, p, loc=loc, size=N, random_state=rng)
732
+ shape_bounds = {'n': (0, 20), 'p': (0.65, 0.65)}
733
+ res = stats.fit(dist, data, shape_bounds, optimizer=self.opt)
734
+ assert_allclose(res.params, (n, p, loc), **self.tols)
735
+
736
+ def test_failure(self):
737
+ N = 5000
738
+ rng = np.random.default_rng(self.seed)
739
+
740
+ dist = stats.nbinom
741
+ shapes = (5, 0.5)
742
+ data = dist.rvs(*shapes, size=N, random_state=rng)
743
+
744
+ assert data.min() == 0
745
+ # With lower bounds on location at 0.5, likelihood is zero
746
+ bounds = [(0, 30), (0, 1), (0.5, 10)]
747
+ res = stats.fit(dist, data, bounds)
748
+ message = "Optimization converged to parameter values that are"
749
+ assert res.message.startswith(message)
750
+ assert res.success is False
751
+
752
+ @pytest.mark.xslow
753
+ def test_guess(self):
754
+ # Test that guess helps DE find the desired solution
755
+ N = 2000
756
+ # With some seeds, `fit` doesn't need a guess
757
+ rng = np.random.default_rng(196390444561)
758
+ dist = stats.nhypergeom
759
+ params = (20, 7, 12, 0)
760
+ bounds = [(2, 200), (0.7, 70), (1.2, 120), (0, 10)]
761
+
762
+ data = dist.rvs(*params, size=N, random_state=rng)
763
+
764
+ res = stats.fit(dist, data, bounds, optimizer=self.opt)
765
+ assert not np.allclose(res.params, params, **self.tols)
766
+
767
+ res = stats.fit(dist, data, bounds, guess=params, optimizer=self.opt)
768
+ assert_allclose(res.params, params, **self.tols)
769
+
770
+ def test_mse_accuracy_1(self):
771
+ # Test maximum spacing estimation against example from Wikipedia
772
+ # https://en.wikipedia.org/wiki/Maximum_spacing_estimation#Examples
773
+ data = [2, 4]
774
+ dist = stats.expon
775
+ bounds = {'loc': (0, 0), 'scale': (1e-8, 10)}
776
+ res_mle = stats.fit(dist, data, bounds=bounds, method='mle')
777
+ assert_allclose(res_mle.params.scale, 3, atol=1e-3)
778
+ res_mse = stats.fit(dist, data, bounds=bounds, method='mse')
779
+ assert_allclose(res_mse.params.scale, 3.915, atol=1e-3)
780
+
781
+ def test_mse_accuracy_2(self):
782
+ # Test maximum spacing estimation against example from Wikipedia
783
+ # https://en.wikipedia.org/wiki/Maximum_spacing_estimation#Examples
784
+ rng = np.random.default_rng(9843212616816518964)
785
+
786
+ dist = stats.uniform
787
+ n = 10
788
+ data = dist(3, 6).rvs(size=n, random_state=rng)
789
+ bounds = {'loc': (0, 10), 'scale': (1e-8, 10)}
790
+ res = stats.fit(dist, data, bounds=bounds, method='mse')
791
+ # (loc=3.608118420015416, scale=5.509323262055043)
792
+
793
+ x = np.sort(data)
794
+ a = (n*x[0] - x[-1])/(n - 1)
795
+ b = (n*x[-1] - x[0])/(n - 1)
796
+ ref = a, b-a # (3.6081133632151503, 5.509328130317254)
797
+ assert_allclose(res.params, ref, rtol=1e-4)
798
+
799
+
800
+ # Data from Matlab: https://www.mathworks.com/help/stats/lillietest.html
801
+ examgrades = [65, 61, 81, 88, 69, 89, 55, 84, 86, 84, 71, 81, 84, 81, 78, 67,
802
+ 96, 66, 73, 75, 59, 71, 69, 63, 79, 76, 63, 85, 87, 88, 80, 71,
803
+ 65, 84, 71, 75, 81, 79, 64, 65, 84, 77, 70, 75, 84, 75, 73, 92,
804
+ 90, 79, 80, 71, 73, 71, 58, 79, 73, 64, 77, 82, 81, 59, 54, 82,
805
+ 57, 79, 79, 73, 74, 82, 63, 64, 73, 69, 87, 68, 81, 73, 83, 73,
806
+ 80, 73, 73, 71, 66, 78, 64, 74, 68, 67, 75, 75, 80, 85, 74, 76,
807
+ 80, 77, 93, 70, 86, 80, 81, 83, 68, 60, 85, 64, 74, 82, 81, 77,
808
+ 66, 85, 75, 81, 69, 60, 83, 72]
809
+
810
+
811
+ class TestGoodnessOfFit:
812
+
813
+ def test_gof_iv(self):
814
+ dist = stats.norm
815
+ x = [1, 2, 3]
816
+
817
+ message = r"`dist` must be a \(non-frozen\) instance of..."
818
+ with pytest.raises(TypeError, match=message):
819
+ goodness_of_fit(stats.norm(), x)
820
+
821
+ message = "`data` must be a one-dimensional array of numbers."
822
+ with pytest.raises(ValueError, match=message):
823
+ goodness_of_fit(dist, [[1, 2, 3]])
824
+
825
+ message = "`statistic` must be one of..."
826
+ with pytest.raises(ValueError, match=message):
827
+ goodness_of_fit(dist, x, statistic='mm')
828
+
829
+ message = "`n_mc_samples` must be an integer."
830
+ with pytest.raises(TypeError, match=message):
831
+ goodness_of_fit(dist, x, n_mc_samples=1000.5)
832
+
833
+ message = "SeedSequence expects int or sequence"
834
+ with pytest.raises(TypeError, match=message):
835
+ goodness_of_fit(dist, x, rng='herring')
836
+
837
+ def test_against_ks(self):
838
+ rng = np.random.default_rng(8517426291317196949)
839
+ x = examgrades
840
+ known_params = {'loc': np.mean(x), 'scale': np.std(x, ddof=1)}
841
+ res = goodness_of_fit(stats.norm, x, known_params=known_params,
842
+ statistic='ks', rng=rng)
843
+ ref = stats.kstest(x, stats.norm(**known_params).cdf, method='exact')
844
+ assert_allclose(res.statistic, ref.statistic) # ~0.0848
845
+ assert_allclose(res.pvalue, ref.pvalue, atol=5e-3) # ~0.335
846
+
847
+ def test_against_lilliefors(self):
848
+ rng = np.random.default_rng(2291803665717442724)
849
+ x = examgrades
850
+ # preserve use of old random_state during SPEC 7 transition
851
+ res = goodness_of_fit(stats.norm, x, statistic='ks', random_state=rng)
852
+ known_params = {'loc': np.mean(x), 'scale': np.std(x, ddof=1)}
853
+ ref = stats.kstest(x, stats.norm(**known_params).cdf, method='exact')
854
+ assert_allclose(res.statistic, ref.statistic) # ~0.0848
855
+ assert_allclose(res.pvalue, 0.0348, atol=5e-3)
856
+
857
+ def test_against_cvm(self):
858
+ rng = np.random.default_rng(8674330857509546614)
859
+ x = examgrades
860
+ known_params = {'loc': np.mean(x), 'scale': np.std(x, ddof=1)}
861
+ res = goodness_of_fit(stats.norm, x, known_params=known_params,
862
+ statistic='cvm', rng=rng)
863
+ ref = stats.cramervonmises(x, stats.norm(**known_params).cdf)
864
+ assert_allclose(res.statistic, ref.statistic) # ~0.090
865
+ assert_allclose(res.pvalue, ref.pvalue, atol=5e-3) # ~0.636
866
+
867
+ def test_against_anderson_case_0(self):
868
+ # "Case 0" is where loc and scale are known [1]
869
+ rng = np.random.default_rng(7384539336846690410)
870
+ x = np.arange(1, 101)
871
+ # loc that produced critical value of statistic found w/ root_scalar
872
+ known_params = {'loc': 45.01575354024957, 'scale': 30}
873
+ res = goodness_of_fit(stats.norm, x, known_params=known_params,
874
+ statistic='ad', rng=rng)
875
+ assert_allclose(res.statistic, 2.492) # See [1] Table 1A 1.0
876
+ assert_allclose(res.pvalue, 0.05, atol=5e-3)
877
+
878
+ def test_against_anderson_case_1(self):
879
+ # "Case 1" is where scale is known and loc is fit [1]
880
+ rng = np.random.default_rng(5040212485680146248)
881
+ x = np.arange(1, 101)
882
+ # scale that produced critical value of statistic found w/ root_scalar
883
+ known_params = {'scale': 29.957112639101933}
884
+ res = goodness_of_fit(stats.norm, x, known_params=known_params,
885
+ statistic='ad', rng=rng)
886
+ assert_allclose(res.statistic, 0.908) # See [1] Table 1B 1.1
887
+ assert_allclose(res.pvalue, 0.1, atol=5e-3)
888
+
889
+ def test_against_anderson_case_2(self):
890
+ # "Case 2" is where loc is known and scale is fit [1]
891
+ rng = np.random.default_rng(726693985720914083)
892
+ x = np.arange(1, 101)
893
+ # loc that produced critical value of statistic found w/ root_scalar
894
+ known_params = {'loc': 44.5680212261933}
895
+ res = goodness_of_fit(stats.norm, x, known_params=known_params,
896
+ statistic='ad', rng=rng)
897
+ assert_allclose(res.statistic, 2.904) # See [1] Table 1B 1.2
898
+ assert_allclose(res.pvalue, 0.025, atol=5e-3)
899
+
900
+ def test_against_anderson_case_3(self):
901
+ # "Case 3" is where both loc and scale are fit [1]
902
+ rng = np.random.default_rng(6763691329830218206)
903
+ # c that produced critical value of statistic found w/ root_scalar
904
+ x = stats.skewnorm.rvs(1.4477847789132101, loc=1, scale=2, size=100,
905
+ random_state=rng)
906
+ res = goodness_of_fit(stats.norm, x, statistic='ad', rng=rng)
907
+ assert_allclose(res.statistic, 0.559) # See [1] Table 1B 1.2
908
+ assert_allclose(res.pvalue, 0.15, atol=5e-3)
909
+
910
+ @pytest.mark.xslow
911
+ def test_against_anderson_gumbel_r(self):
912
+ rng = np.random.default_rng(7302761058217743)
913
+ # c that produced critical value of statistic found w/ root_scalar
914
+ x = stats.genextreme(0.051896837188595134, loc=0.5,
915
+ scale=1.5).rvs(size=1000, random_state=rng)
916
+ res = goodness_of_fit(stats.gumbel_r, x, statistic='ad',
917
+ rng=rng)
918
+ ref = stats.anderson(x, dist='gumbel_r')
919
+ assert_allclose(res.statistic, ref.critical_values[0])
920
+ assert_allclose(res.pvalue, ref.significance_level[0]/100, atol=5e-3)
921
+
922
+ def test_against_filliben_norm(self):
923
+ # Test against `stats.fit` ref. [7] Section 8 "Example"
924
+ rng = np.random.default_rng(8024266430745011915)
925
+ y = [6, 1, -4, 8, -2, 5, 0]
926
+ known_params = {'loc': 0, 'scale': 1}
927
+ res = stats.goodness_of_fit(stats.norm, y, known_params=known_params,
928
+ statistic="filliben", rng=rng)
929
+ # Slight discrepancy presumably due to roundoff in Filliben's
930
+ # calculation. Using exact order statistic medians instead of
931
+ # Filliben's approximation doesn't account for it.
932
+ assert_allclose(res.statistic, 0.98538, atol=1e-4)
933
+ assert 0.75 < res.pvalue < 0.9
934
+
935
+ # Using R's ppcc library:
936
+ # library(ppcc)
937
+ # options(digits=16)
938
+ # x < - c(6, 1, -4, 8, -2, 5, 0)
939
+ # set.seed(100)
940
+ # ppccTest(x, "qnorm", ppos="Filliben")
941
+ # Discrepancy with
942
+ assert_allclose(res.statistic, 0.98540957187084, rtol=2e-5)
943
+ assert_allclose(res.pvalue, 0.8875, rtol=2e-3)
944
+
945
+ def test_filliben_property(self):
946
+ # Filliben's statistic should be independent of data location and scale
947
+ rng = np.random.default_rng(8535677809395478813)
948
+ x = rng.normal(loc=10, scale=0.5, size=100)
949
+ res = stats.goodness_of_fit(stats.norm, x,
950
+ statistic="filliben", rng=rng)
951
+ known_params = {'loc': 0, 'scale': 1}
952
+ ref = stats.goodness_of_fit(stats.norm, x, known_params=known_params,
953
+ statistic="filliben", rng=rng)
954
+ assert_allclose(res.statistic, ref.statistic, rtol=1e-15)
955
+
956
+ @pytest.mark.parametrize('case', [(25, [.928, .937, .950, .958, .966]),
957
+ (50, [.959, .965, .972, .977, .981]),
958
+ (95, [.977, .979, .983, .986, .989])])
959
+ def test_against_filliben_norm_table(self, case):
960
+ # Test against `stats.fit` ref. [7] Table 1
961
+ rng = np.random.default_rng(504569995557928957)
962
+ n, ref = case
963
+ x = rng.random(n)
964
+ known_params = {'loc': 0, 'scale': 1}
965
+ res = stats.goodness_of_fit(stats.norm, x, known_params=known_params,
966
+ statistic="filliben", rng=rng)
967
+ percentiles = np.array([0.005, 0.01, 0.025, 0.05, 0.1])
968
+ res = stats.scoreatpercentile(res.null_distribution, percentiles*100)
969
+ assert_allclose(res, ref, atol=2e-3)
970
+
971
+ @pytest.mark.xslow
972
+ @pytest.mark.parametrize('case', [(5, 0.95772790260469, 0.4755),
973
+ (6, 0.95398832257958, 0.3848),
974
+ (7, 0.9432692889277, 0.2328)])
975
+ def test_against_ppcc(self, case):
976
+ # Test against R ppcc, e.g.
977
+ # library(ppcc)
978
+ # options(digits=16)
979
+ # x < - c(0.52325412, 1.06907699, -0.36084066, 0.15305959, 0.99093194)
980
+ # set.seed(100)
981
+ # ppccTest(x, "qrayleigh", ppos="Filliben")
982
+ n, ref_statistic, ref_pvalue = case
983
+ rng = np.random.default_rng(7777775561439803116)
984
+ x = rng.normal(size=n)
985
+ res = stats.goodness_of_fit(stats.rayleigh, x, statistic="filliben",
986
+ rng=rng)
987
+ assert_allclose(res.statistic, ref_statistic, rtol=1e-4)
988
+ assert_allclose(res.pvalue, ref_pvalue, atol=1.5e-2)
989
+
990
+ def test_params_effects(self):
991
+ # Ensure that `guessed_params`, `fit_params`, and `known_params` have
992
+ # the intended effects.
993
+ rng = np.random.default_rng(9121950977643805391)
994
+ x = stats.skewnorm.rvs(-5.044559778383153, loc=1, scale=2, size=50,
995
+ random_state=rng)
996
+
997
+ # Show that `guessed_params` don't fit to the guess,
998
+ # but `fit_params` and `known_params` respect the provided fit
999
+ guessed_params = {'c': 13.4}
1000
+ fit_params = {'scale': 13.73}
1001
+ known_params = {'loc': -13.85}
1002
+ rng = np.random.default_rng(9121950977643805391)
1003
+ res1 = goodness_of_fit(stats.weibull_min, x, n_mc_samples=2,
1004
+ guessed_params=guessed_params,
1005
+ fit_params=fit_params,
1006
+ known_params=known_params, rng=rng)
1007
+ assert not np.allclose(res1.fit_result.params.c, 13.4)
1008
+ assert_equal(res1.fit_result.params.scale, 13.73)
1009
+ assert_equal(res1.fit_result.params.loc, -13.85)
1010
+
1011
+ # Show that changing the guess changes the parameter that gets fit,
1012
+ # and it changes the null distribution
1013
+ guessed_params = {'c': 2}
1014
+ rng = np.random.default_rng(9121950977643805391)
1015
+ res2 = goodness_of_fit(stats.weibull_min, x, n_mc_samples=2,
1016
+ guessed_params=guessed_params,
1017
+ fit_params=fit_params,
1018
+ known_params=known_params, rng=rng)
1019
+ assert not np.allclose(res2.fit_result.params.c,
1020
+ res1.fit_result.params.c, rtol=1e-8)
1021
+ assert not np.allclose(res2.null_distribution,
1022
+ res1.null_distribution, rtol=1e-8)
1023
+ assert_equal(res2.fit_result.params.scale, 13.73)
1024
+ assert_equal(res2.fit_result.params.loc, -13.85)
1025
+
1026
+ # If we set all parameters as fit_params and known_params,
1027
+ # they're all fixed to those values, but the null distribution
1028
+ # varies.
1029
+ fit_params = {'c': 13.4, 'scale': 13.73}
1030
+ rng = np.random.default_rng(9121950977643805391)
1031
+ res3 = goodness_of_fit(stats.weibull_min, x, n_mc_samples=2,
1032
+ guessed_params=guessed_params,
1033
+ fit_params=fit_params,
1034
+ known_params=known_params, rng=rng)
1035
+ assert_equal(res3.fit_result.params.c, 13.4)
1036
+ assert_equal(res3.fit_result.params.scale, 13.73)
1037
+ assert_equal(res3.fit_result.params.loc, -13.85)
1038
+ assert not np.allclose(res3.null_distribution, res1.null_distribution)
1039
+
1040
+ def test_custom_statistic(self):
1041
+ # Test support for custom statistic function.
1042
+
1043
+ # References:
1044
+ # [1] Pyke, R. (1965). "Spacings". Journal of the Royal Statistical
1045
+ # Society: Series B (Methodological), 27(3): 395-436.
1046
+ # [2] Burrows, P. M. (1979). "Selected Percentage Points of
1047
+ # Greenwood's Statistics". Journal of the Royal Statistical
1048
+ # Society. Series A (General), 142(2): 256-258.
1049
+
1050
+ # Use the Greenwood statistic for illustration; see [1, p.402].
1051
+ def greenwood(dist, data, *, axis):
1052
+ x = np.sort(data, axis=axis)
1053
+ y = dist.cdf(x)
1054
+ d = np.diff(y, axis=axis, prepend=0, append=1)
1055
+ return np.sum(d ** 2, axis=axis)
1056
+
1057
+ # Run the Monte Carlo test with sample size = 5 on a fully specified
1058
+ # null distribution, and compare the simulated quantiles to the exact
1059
+ # ones given in [2, Table 1, column (n = 5)].
1060
+ rng = np.random.default_rng(9121950977643805391)
1061
+ data = stats.expon.rvs(size=5, random_state=rng)
1062
+ result = goodness_of_fit(stats.expon, data,
1063
+ known_params={'loc': 0, 'scale': 1},
1064
+ statistic=greenwood, rng=rng)
1065
+ p = [.01, .05, .1, .2, .3, .4, .5, .6, .7, .8, .9, .95, .99]
1066
+ exact_quantiles = [
1067
+ .183863, .199403, .210088, .226040, .239947, .253677, .268422,
1068
+ .285293, .306002, .334447, .382972, .432049, .547468]
1069
+ simulated_quantiles = np.quantile(result.null_distribution, p)
1070
+ assert_allclose(simulated_quantiles, exact_quantiles, atol=0.005)
1071
+
1072
+ class TestFitResult:
1073
+ def test_plot_iv(self):
1074
+ rng = np.random.default_rng(1769658657308472721)
1075
+ data = stats.norm.rvs(0, 1, size=100, random_state=rng)
1076
+
1077
+ def optimizer(*args, **kwargs):
1078
+ return differential_evolution(*args, **kwargs, rng=rng)
1079
+
1080
+ bounds = [(0, 30), (0, 1)]
1081
+ res = stats.fit(stats.norm, data, bounds, optimizer=optimizer)
1082
+ try:
1083
+ import matplotlib # noqa: F401
1084
+ message = r"`plot_type` must be one of \{'..."
1085
+ with pytest.raises(ValueError, match=message):
1086
+ res.plot(plot_type='llama')
1087
+ except (ModuleNotFoundError, ImportError):
1088
+ message = r"matplotlib must be installed to use method `plot`."
1089
+ with pytest.raises(ModuleNotFoundError, match=message):
1090
+ res.plot(plot_type='llama')