distclassipy 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

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Files changed (8) hide show
  1. distclassipy/classifier.py +141 -58
  2. distclassipy/distances.py +389 -226
  3. {distclassipy-0.1.0.dist-info → distclassipy-0.1.2.dist-info}/METADATA +64 -13
  4. distclassipy-0.1.2.dist-info/RECORD +9 -0
  5. {distclassipy-0.1.0.dist-info → distclassipy-0.1.2.dist-info}/WHEEL +1 -1
  6. distclassipy-0.1.0.dist-info/RECORD +0 -9
  7. {distclassipy-0.1.0.dist-info → distclassipy-0.1.2.dist-info}/LICENSE +0 -0
  8. {distclassipy-0.1.0.dist-info → distclassipy-0.1.2.dist-info}/top_level.txt +0 -0
distclassipy/distances.py CHANGED
@@ -4,38 +4,26 @@ A module providing a variety of distance metrics to calculate the distance betwe
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4
  This module includes implementations of various distance metrics, including both common and less
5
5
  common measures. It allows for the calculation of distances between data points in a vectorized
6
6
  manner using numpy arrays.
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- This code is based on the work of Andrzej Zielezinski, originally retrieved on 20 November 2022 from
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- https://github.com/aziele/statistical-distances/blob/04412b3155c59fc7238b3d8ecf6f3723ac5befff/distance.py
9
-
10
- It has been modified by Siddharth Chaini on 27 November 2022.
11
-
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- Licensed GNU General Public License v3.0;
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- you may not use this file except in compliance with the License.
14
- You may obtain a copy of the License at
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-
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- https://www.gnu.org/licenses/gpl-3.0.en.html
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-
18
- Unless required by applicable law or agreed to in writing, software
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- distributed under the License is distributed on an "AS IS" BASIS,
20
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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- See the License for the specific language governing permissions and
22
- limitations under the License.
23
-
24
- Modifications by Siddharth Chaini include the addition of the following distance measures:
25
- 1. Meehl distance
26
- 2. Sorensen distance
27
- 3. Ruzicka distance
28
- 4. Inner product distance
29
- 5. Harmonic mean distance
30
- 6. Fidelity
31
- 7. Minimimum Symmetric Chi Squared
32
- 8. Probabilistic Symmetric Chi Squared
33
-
34
- In addition, the following code was added to all functions for array conversion:
35
- u,v = np.asarray(u), np.asarray(v)
36
-
37
- Todos:
38
- ALSO COMPARE RUNTIME OF THIS v/s custom v/s Tschopp
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+ A part of this code is based on the work of Andrzej Zielezinski, originally retrieved on 20 November 2022 from
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+ https://github.com/aziele/statistical-distances/blob/04412b3155c59fc7238b3d8ecf6f3723ac5befff/distance.py, which was released via the GNU General Public License v3.0.
9
+
10
+ It was originally modified by Siddharth Chaini on 27 November 2022.
11
+
12
+ Notes
13
+ -----
14
+
15
+ Modifications by Siddharth Chaini include the addition of the following distance measures:
16
+ 1. Meehl distance
17
+ 2. Sorensen distance
18
+ 3. Ruzicka distance
19
+ 4. Inner product distance
20
+ 5. Harmonic mean distance
21
+ 6. Fidelity
22
+ 7. Minimimum Symmetric Chi Squared
23
+ 8. Probabilistic Symmetric Chi Squared
24
+
25
+ In addition, the following code was added to all functions for array conversion:
26
+ u,v = np.asarray(u), np.asarray(v)
39
27
  """
40
28
 
41
29
  import numpy as np
@@ -47,7 +35,8 @@ class Distance:
47
35
  """
48
36
  Initialize the Distance class with an optional epsilon value.
49
37
 
50
- Parameters:
38
+ Parameters
39
+ ----------
51
40
  - epsilon: A small value to avoid division by zero errors.
52
41
  """
53
42
  self.epsilon = np.finfo(float).eps if not epsilon else epsilon
@@ -55,41 +44,45 @@ class Distance:
55
44
  def acc(self, u, v):
56
45
  """
57
46
  Calculate the average of Cityblock/Manhattan and Chebyshev distances.
58
-
59
47
  This function computes the ACC distance, also known as the Average distance, between two
60
48
  vectors u and v. It is the average of the Cityblock (or Manhattan) and Chebyshev distances.
61
49
 
62
- Parameters:
50
+ Parameters
51
+ ----------
63
52
  - u, v: Input vectors between which the distance is to be calculated.
64
53
 
65
- Returns:
54
+ Returns
55
+ -------
66
56
  - The ACC distance between the two vectors.
67
57
 
68
- References:
69
- 1. Krause EF (2012) Taxicab Geometry An Adventure in Non-Euclidean Geometry. Dover Publications.
70
- 2. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity Measures between Probability
71
- Density Functions. International Journal of Mathematical Models and Methods in Applied Sciences.
72
- vol. 1(4), pp. 300-307.
58
+ References
59
+ ----------
60
+ 1. Krause EF (2012) Taxicab Geometry An Adventure in Non-Euclidean Geometry. Dover Publications.
61
+ 2. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity Measures between Probability
62
+ Density Functions. International Journal of Mathematical Models and Methods in Applied Sciences.
63
+ vol. 1(4), pp. 300-307.
73
64
  """
74
65
  return (self.cityblock(u, v) + self.chebyshev(u, v)) / 2
75
66
 
76
67
  def add_chisq(self, u, v):
77
68
  """
78
69
  Compute the Additive Symmetric Chi-square distance between two vectors.
79
-
80
70
  The Additive Symmetric Chi-square distance is a measure that can be used to compare two vectors.
81
71
  This function calculates it based on the input vectors u and v.
82
72
 
83
- Parameters:
73
+ Parameters
74
+ ----------
84
75
  - u, v: Input vectors between which the distance is to be calculated.
85
76
 
86
- Returns:
77
+ Returns
78
+ -------
87
79
  - The Additive Symmetric Chi-square distance between the two vectors.
88
80
 
89
- References:
90
- 1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity Measures between Probability
91
- Density Functions. International Journal of Mathematical Models and Methods in Applied Sciences.
92
- vol. 1(4), pp. 300-307.
81
+ References
82
+ ----------
83
+ 1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity Measures between Probability
84
+ Density Functions. International Journal of Mathematical Models and Methods in Applied Sciences.
85
+ vol. 1(4), pp. 300-307.
93
86
  """
94
87
  u, v = np.asarray(u), np.asarray(v)
95
88
  uvmult = u * v
@@ -102,21 +95,24 @@ class Distance:
102
95
 
103
96
  Returns a distance value between 0 and 1.
104
97
 
105
- Parameters:
98
+ Parameters
99
+ ----------
106
100
  - u, v: Input vectors between which the distance is to be calculated.
107
101
 
108
- Returns:
102
+ Returns
103
+ -------
109
104
  - The Bhattacharyya distance between the two vectors.
110
105
 
111
- References:
112
- 1. Bhattacharyya A (1947) On a measure of divergence between two
113
- statistical populations defined by probability distributions,
114
- Bull. Calcutta Math. Soc., 35, 99–109.
115
- 2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
116
- Measures between Probability Density Functions. International
117
- Journal of Mathematical Models and Methods in Applied Sciences.
118
- 1(4), 300-307.
119
- 3. https://en.wikipedia.org/wiki/Bhattacharyya_distance
106
+ References
107
+ ----------
108
+ 1. Bhattacharyya A (1947) On a measure of divergence between two
109
+ statistical populations defined by probability distributions,
110
+ Bull. Calcutta Math. Soc., 35, 99–109.
111
+ 2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
112
+ Measures between Probability Density Functions. International
113
+ Journal of Mathematical Models and Methods in Applied Sciences.
114
+ 1(4), 300-307.
115
+ 3. https://en.wikipedia.org/wiki/Bhattacharyya_distance
120
116
  """
121
117
  u, v = np.asarray(u), np.asarray(v)
122
118
  return -np.log(np.sum(np.sqrt(u * v)))
@@ -130,17 +126,21 @@ class Distance:
130
126
  of species at both sites. It is closely related to the Sørensen distance and is also known as
131
127
  Bray-Curtis dissimilarity.
132
128
 
133
- Notes:
129
+ Notes
130
+ -----
134
131
  When used for comparing two probability density functions (pdfs),
135
132
  the Bray-Curtis distance equals the Cityblock distance divided by 2.
136
133
 
137
- Parameters:
134
+ Parameters
135
+ ----------
138
136
  - u, v: Input vectors between which the distance is to be calculated.
139
137
 
140
- Returns:
138
+ Returns
139
+ -------
141
140
  - The Bray-Curtis distance between the two vectors.
142
141
 
143
- References:
142
+ References
143
+ ----------
144
144
  1. Bray JR, Curtis JT (1957) An ordination of the upland forest of
145
145
  southern Wisconsin. Ecological Monographs, 27, 325-349.
146
146
  2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
@@ -158,17 +158,21 @@ class Distance:
158
158
 
159
159
  The Canberra distance is a weighted version of the Manhattan distance, used in numerical analysis.
160
160
 
161
- Notes:
161
+ Notes
162
+ -----
162
163
  When `u[i]` and `v[i]` are 0 for given i, then the fraction 0/0 = 0
163
164
  is used in the calculation.
164
165
 
165
- Parameters:
166
+ Parameters
167
+ ----------
166
168
  - u, v: Input vectors between which the distance is to be calculated.
167
169
 
168
- Returns:
170
+ Returns
171
+ -------
169
172
  - The Canberra distance between the two vectors.
170
173
 
171
- References:
174
+ References
175
+ ----------
172
176
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
173
177
  Measures between Probability Density Functions. International
174
178
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -191,13 +195,16 @@ class Distance:
191
195
  Maximum value distance
192
196
  Minimax approximation
193
197
 
194
- Parameters:
198
+ Parameters
199
+ ----------
195
200
  - u, v: Input vectors between which the distance is to be calculated.
196
201
 
197
- Returns:
202
+ Returns
203
+ -------
198
204
  - The Chebyshev distance between the two vectors.
199
205
 
200
- References:
206
+ References
207
+ ----------
201
208
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
202
209
  Measures between Probability Density Functions. International
203
210
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -212,10 +219,12 @@ class Distance:
212
219
 
213
220
  This measure represents a custom approach by Zielezinski to distance measurement, focusing on the minimum absolute difference.
214
221
 
215
- Parameters:
222
+ Parameters
223
+ ----------
216
224
  - u, v: Input vectors between which the distance is to be calculated.
217
225
 
218
- Returns:
226
+ Returns
227
+ -------
219
228
  - The minimum value distance between the two vectors.
220
229
  """
221
230
  u, v = np.asarray(u), np.asarray(v)
@@ -227,17 +236,21 @@ class Distance:
227
236
 
228
237
  The Clark distance equals the square root of half of the divergence.
229
238
 
230
- Notes:
239
+ Notes
240
+ -----
231
241
  When `u[i]` and `v[i]` are 0 for given i, then the fraction 0/0 = 0
232
242
  is used in the calculation.
233
243
 
234
- Parameters:
244
+ Parameters
245
+ ----------
235
246
  - u, v: Input vectors between which the distance is to be calculated.
236
247
 
237
- Returns:
248
+ Returns
249
+ -------
238
250
  - The Clark distance between the two vectors.
239
251
 
240
- References:
252
+ References
253
+ ----------
241
254
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
242
255
  Measures between Probability Density Functions. International
243
256
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -251,13 +264,16 @@ class Distance:
251
264
  """
252
265
  Calculate the cosine distance between two vectors.
253
266
 
254
- Parameters:
267
+ Parameters
268
+ ----------
255
269
  - u, v: Input vectors between which the distance is to be calculated.
256
270
 
257
- Returns:
271
+ Returns
272
+ -------
258
273
  - The cosine distance between the two vectors.
259
274
 
260
- References:
275
+ References
276
+ ----------
261
277
  1. SciPy.
262
278
  """
263
279
  u, v = np.asarray(u), np.asarray(v)
@@ -269,10 +285,12 @@ class Distance:
269
285
 
270
286
  Returns a distance value between 0 and 2.
271
287
 
272
- Parameters:
288
+ Parameters
289
+ ----------
273
290
  - u, v: Input vectors between which the distance is to be calculated.
274
291
 
275
- Returns:
292
+ Returns
293
+ -------
276
294
  - The Pearson correlation distance between the two vectors.
277
295
  """
278
296
 
@@ -284,13 +302,16 @@ class Distance:
284
302
  """
285
303
  Calculate the Czekanowski distance between two vectors.
286
304
 
287
- Parameters:
305
+ Parameters
306
+ ----------
288
307
  - u, v: Input vectors between which the distance is to be calculated.
289
308
 
290
- Returns:
309
+ Returns
310
+ -------
291
311
  - The Czekanowski distance between the two vectors.
292
312
 
293
- References:
313
+ References
314
+ ----------
294
315
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
295
316
  Measures between Probability Density Functions. International
296
317
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -306,13 +327,16 @@ class Distance:
306
327
  Synonyms:
307
328
  Sorensen distance
308
329
 
309
- Parameters:
330
+ Parameters
331
+ ----------
310
332
  - u, v: Input vectors between which the distance is to be calculated.
311
333
 
312
- Returns:
334
+ Returns
335
+ -------
313
336
  - The Dice dissimilarity between the two vectors.
314
337
 
315
- References:
338
+ References
339
+ ----------
316
340
  1. Dice LR (1945) Measures of the amount of ecologic association
317
341
  between species. Ecology. 26, 297-302.
318
342
  2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
@@ -330,13 +354,16 @@ class Distance:
330
354
 
331
355
  Divergence equals squared Clark distance multiplied by 2.
332
356
 
333
- Parameters:
357
+ Parameters
358
+ ----------
334
359
  - u, v: Input vectors between which the distance is to be calculated.
335
360
 
336
- Returns:
361
+ Returns
362
+ -------
337
363
  - The divergence between the two vectors.
338
364
 
339
- References:
365
+ References
366
+ ----------
340
367
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
341
368
  Measures between Probability Density Functions. International
342
369
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -352,13 +379,16 @@ class Distance:
352
379
 
353
380
  The Euclidean distance is the "ordinary" straight-line distance between two points in Euclidean space.
354
381
 
355
- Parameters:
382
+ Parameters
383
+ ----------
356
384
  - u, v: Input vectors between which the distance is to be calculated.
357
385
 
358
- Returns:
386
+ Returns
387
+ -------
359
388
  - The Euclidean distance between the two vectors.
360
389
 
361
- References:
390
+ References
391
+ ----------
362
392
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
363
393
  Measures between Probability Density Functions. International
364
394
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -373,13 +403,16 @@ class Distance:
373
403
 
374
404
  The fidelity distance measures the similarity between two probability distributions.
375
405
 
376
- Parameters:
406
+ Parameters
407
+ ----------
377
408
  - u, v: Input vectors between which the distance is to be calculated.
378
409
 
379
- Returns:
410
+ Returns
411
+ -------
380
412
  - The fidelity distance between the two vectors.
381
413
 
382
- Notes:
414
+ Notes
415
+ -----
383
416
  Added by SC.
384
417
  """
385
418
  u, v = np.asarray(u), np.asarray(v)
@@ -391,17 +424,21 @@ class Distance:
391
424
 
392
425
  NGD is a measure of similarity derived from the number of hits returned by the Google search engine for a given set of keywords.
393
426
 
394
- Parameters:
427
+ Parameters
428
+ ----------
395
429
  - u, v: Input vectors between which the distance is to be calculated.
396
430
 
397
- Returns:
431
+ Returns
432
+ -------
398
433
  - The Normalized Google Distance between the two vectors.
399
434
 
400
- Notes:
435
+ Notes
436
+ -----
401
437
  When used for comparing two probability density functions (pdfs),
402
438
  Google distance equals half of Cityblock distance.
403
439
 
404
- References:
440
+ References
441
+ ----------
405
442
  1. Lee & Rashid (2008) Information Technology, ITSim 2008.
406
443
  doi:10.1109/ITSIM.2008.4631601.
407
444
  """
@@ -417,13 +454,16 @@ class Distance:
417
454
 
418
455
  The Gower distance equals the Cityblock distance divided by the vector length.
419
456
 
420
- Parameters:
457
+ Parameters
458
+ ----------
421
459
  - u, v: Input vectors between which the distance is to be calculated.
422
460
 
423
- Returns:
461
+ Returns
462
+ -------
424
463
  - The Gower distance between the two vectors.
425
464
 
426
- References:
465
+ References
466
+ ----------
427
467
  1. Gower JC. (1971) General Coefficient of Similarity
428
468
  and Some of Its Properties, Biometrics 27, 857-874.
429
469
  2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
@@ -451,18 +491,22 @@ class Distance:
451
491
 
452
492
  The Hellinger distance is a measure of similarity between two probability distributions.
453
493
 
454
- Parameters:
494
+ Parameters
495
+ ----------
455
496
  - u, v: Input vectors between which the distance is to be calculated.
456
497
 
457
- Returns:
498
+ Returns
499
+ -------
458
500
  - The Hellinger distance between the two vectors.
459
501
 
460
- Notes:
502
+ Notes
503
+ -----
461
504
  This implementation produces values two times larger than values
462
505
  obtained by Hellinger distance described in Wikipedia and also
463
506
  in https://gist.github.com/larsmans/3116927.
464
507
 
465
- References:
508
+ References
509
+ ----------
466
510
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
467
511
  Measures between Probability Density Functions. International
468
512
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -477,13 +521,16 @@ class Distance:
477
521
 
478
522
  The inner product distance is a measure of similarity between two vectors, based on their inner product.
479
523
 
480
- Parameters:
524
+ Parameters
525
+ ----------
481
526
  - u, v: Input vectors between which the distance is to be calculated.
482
527
 
483
- Returns:
528
+ Returns
529
+ -------
484
530
  - The inner product distance between the two vectors.
485
531
 
486
- Notes:
532
+ Notes
533
+ -----
487
534
  Added by SC.
488
535
  """
489
536
  u, v = np.asarray(u), np.asarray(v)
@@ -495,13 +542,16 @@ class Distance:
495
542
 
496
543
  The Jaccard distance measures dissimilarity between sample sets.
497
544
 
498
- Parameters:
545
+ Parameters
546
+ ----------
499
547
  - u, v: Input vectors between which the distance is to be calculated.
500
548
 
501
- Returns:
549
+ Returns
550
+ -------
502
551
  - The Jaccard distance between the two vectors.
503
552
 
504
- References:
553
+ References
554
+ ----------
505
555
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
506
556
  Measures between Probability Density Functions. International
507
557
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -517,13 +567,16 @@ class Distance:
517
567
 
518
568
  The Jeffreys divergence is a symmetric version of the Kullback-Leibler divergence.
519
569
 
520
- Parameters:
570
+ Parameters
571
+ ----------
521
572
  - u, v: Input vectors between which the divergence is to be calculated.
522
573
 
523
- Returns:
574
+ Returns
575
+ -------
524
576
  - The Jeffreys divergence between the two vectors.
525
577
 
526
- References:
578
+ References
579
+ ----------
527
580
  1. Jeffreys H (1946) An Invariant Form for the Prior Probability
528
581
  in Estimation Problems. Proc.Roy.Soc.Lon., Ser. A 186, 453-461.
529
582
  2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
@@ -547,13 +600,16 @@ class Distance:
547
600
 
548
601
  The Jensen-Shannon divergence is a symmetric and finite measure of similarity between two probability distributions.
549
602
 
550
- Parameters:
603
+ Parameters
604
+ ----------
551
605
  - u, v: Input vectors between which the divergence is to be calculated.
552
606
 
553
- Returns:
607
+ Returns
608
+ -------
554
609
  - The Jensen-Shannon divergence between the two vectors.
555
610
 
556
- References:
611
+ References
612
+ ----------
557
613
  1. Lin J. (1991) Divergence measures based on the Shannon entropy.
558
614
  IEEE Transactions on Information Theory, 37(1):145–151.
559
615
  2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
@@ -582,18 +638,22 @@ class Distance:
582
638
 
583
639
  The Jensen difference is considered similar to the Jensen-Shannon divergence.
584
640
 
585
- Parameters:
641
+ Parameters
642
+ ----------
586
643
  - u, v: Input vectors between which the distance is to be calculated.
587
644
 
588
- Returns:
645
+ Returns
646
+ -------
589
647
  - The Jensen difference between the two vectors.
590
648
 
591
- Notes:
649
+ Notes
650
+ -----
592
651
  1. Equals half of Topsøe distance
593
652
  2. Equals squared jensenshannon_distance.
594
653
 
595
654
 
596
- References:
655
+ References
656
+ ----------
597
657
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
598
658
  Measures between Probability Density Functions. International
599
659
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -610,13 +670,16 @@ class Distance:
610
670
  """
611
671
  Calculate the K divergence between two vectors.
612
672
 
613
- Parameters:
673
+ Parameters
674
+ ----------
614
675
  - u, v: Input vectors between which the divergence is to be calculated.
615
676
 
616
- Returns:
677
+ Returns
678
+ -------
617
679
  - The K divergence between the two vectors.
618
680
 
619
- References:
681
+ References
682
+ ----------
620
683
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
621
684
  Measures between Probability Density Functions. International
622
685
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -633,13 +696,16 @@ class Distance:
633
696
 
634
697
  The Kullback-Leibler divergence measures the difference between two probability distributions.
635
698
 
636
- Parameters:
699
+ Parameters
700
+ ----------
637
701
  - u, v: Input vectors between which the divergence is to be calculated.
638
702
 
639
- Returns:
703
+ Returns
704
+ -------
640
705
  - The Kullback-Leibler divergence between the two vectors.
641
706
 
642
- References:
707
+ References
708
+ ----------
643
709
  1. Kullback S, Leibler RA (1951) On information and sufficiency.
644
710
  Ann. Math. Statist. 22:79–86
645
711
  2. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
@@ -656,13 +722,16 @@ class Distance:
656
722
  """
657
723
  Calculate the Kulczynski distance between two vectors.
658
724
 
659
- Parameters:
725
+ Parameters
726
+ ----------
660
727
  - u, v: Input vectors between which the distance is to be calculated.
661
728
 
662
- Returns:
729
+ Returns
730
+ -------
663
731
  - The Kulczynski distance between the two vectors.
664
732
 
665
- References:
733
+ References
734
+ ----------
666
735
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
667
736
  Measures between Probability Density Functions. International
668
737
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -675,13 +744,16 @@ class Distance:
675
744
  """
676
745
  Calculate the Kumar-Johnson distance between two vectors.
677
746
 
678
- Parameters:
747
+ Parameters
748
+ ----------
679
749
  - u, v: Input vectors between which the distance is to be calculated.
680
750
 
681
- Returns:
751
+ Returns
752
+ -------
682
753
  - The Kumar-Johnson distance between the two vectors.
683
754
 
684
- References:
755
+ References
756
+ ----------
685
757
  1. Kumar P, Johnson A. (2005) On a symmetric divergence measure
686
758
  and information inequalities, Journal of Inequalities in pure
687
759
  and applied Mathematics. 6(3).
@@ -701,19 +773,23 @@ class Distance:
701
773
  """
702
774
  Calculate the Lorentzian distance between two vectors.
703
775
 
704
- Parameters:
776
+ Parameters
777
+ ----------
705
778
  - u, v: Input vectors between which the distance is to be calculated.
706
779
 
707
- Returns:
780
+ Returns
781
+ -------
708
782
  - The Lorentzian distance between the two vectors.
709
783
 
710
- References:
784
+ References
785
+ ----------
711
786
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
712
787
  Measures between Probability Density Functions. International
713
788
  Journal of Mathematical Models and Methods in Applied Sciences.
714
789
  1(4):300-307.
715
790
 
716
- Notes:
791
+ Notes
792
+ -----
717
793
  One (1) is added to guarantee the non-negativity property and to
718
794
  eschew the log of zero.
719
795
  """
@@ -724,13 +800,16 @@ class Distance:
724
800
  """
725
801
  Calculate the Cityblock (Manhattan) distance between two vectors.
726
802
 
727
- Parameters:
803
+ Parameters
804
+ ----------
728
805
  - u, v: Input vectors between which the distance is to be calculated.
729
806
 
730
- Returns:
807
+ Returns
808
+ -------
731
809
  - The Cityblock distance between the two vectors.
732
810
 
733
- References:
811
+ References
812
+ ----------
734
813
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
735
814
  Measures between Probability Density Functions. International
736
815
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -742,7 +821,8 @@ class Distance:
742
821
  Rectilinear distance
743
822
  Taxicab norm
744
823
 
745
- Notes:
824
+ Notes
825
+ -----
746
826
  Cityblock distance between two probability density functions
747
827
  (pdfs) equals:
748
828
  1. Non-intersection distance multiplied by 2.
@@ -757,13 +837,16 @@ class Distance:
757
837
  """
758
838
  Calculate the Maryland Bridge distance between two vectors.
759
839
 
760
- Parameters:
840
+ Parameters
841
+ ----------
761
842
  - u, v: Input vectors between which the distance is to be calculated.
762
843
 
763
- Returns:
844
+ Returns
845
+ -------
764
846
  - The Maryland Bridge distance between the two vectors.
765
847
 
766
- References:
848
+ References
849
+ ----------
767
850
  1. Deza M, Deza E (2009) Encyclopedia of Distances.
768
851
  Springer-Verlag Berlin Heidelberg. 1-590.
769
852
  """
@@ -775,19 +858,23 @@ class Distance:
775
858
  """
776
859
  Calculate the Matusita distance between two vectors.
777
860
 
778
- Parameters:
861
+ Parameters
862
+ ----------
779
863
  - u, v: Input vectors between which the distance is to be calculated.
780
864
 
781
- Returns:
865
+ Returns
866
+ -------
782
867
  - The Matusita distance between the two vectors.
783
868
 
784
- References:
869
+ References
870
+ ----------
785
871
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
786
872
  Measures between Probability Density Functions. International
787
873
  Journal of Mathematical Models and Methods in Applied Sciences.
788
874
  1(4):300-307.
789
875
 
790
- Notes:
876
+ Notes
877
+ -----
791
878
  Equals square root of Squared-chord distance.
792
879
  """
793
880
  u, v = np.asarray(u), np.asarray(v)
@@ -797,13 +884,16 @@ class Distance:
797
884
  """
798
885
  Calculate the maximum symmetric chi-square distance between two vectors.
799
886
 
800
- Parameters:
887
+ Parameters
888
+ ----------
801
889
  - u, v: Input vectors between which the distance is to be calculated.
802
890
 
803
- Returns:
891
+ Returns
892
+ -------
804
893
  - The maximum symmetric chi-square distance between the two vectors.
805
894
 
806
- References:
895
+ References
896
+ ----------
807
897
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
808
898
  Measures between Probability Density Functions. International
809
899
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -816,13 +906,16 @@ class Distance:
816
906
  """
817
907
  Calculate the minimum symmetric chi-square distance between two vectors.
818
908
 
819
- Parameters:
909
+ Parameters
910
+ ----------
820
911
  - u, v: Input vectors between which the distance is to be calculated.
821
912
 
822
- Returns:
913
+ Returns
914
+ -------
823
915
  - The minimum symmetric chi-square distance between the two vectors.
824
916
 
825
- Notes:
917
+ Notes
918
+ -----
826
919
  Added by SC.
827
920
  """
828
921
  u, v = np.asarray(u), np.asarray(v)
@@ -832,16 +925,20 @@ class Distance:
832
925
  """
833
926
  Calculate the Meehl distance between two vectors.
834
927
 
835
- Parameters:
928
+ Parameters
929
+ ----------
836
930
  - u, v: Input vectors between which the distance is to be calculated.
837
931
 
838
- Returns:
932
+ Returns
933
+ -------
839
934
  - The Meehl distance between the two vectors.
840
935
 
841
- Notes:
936
+ Notes
937
+ -----
842
938
  Added by SC.
843
939
 
844
- References:
940
+ References
941
+ ----------
845
942
  1. Deza M. and Deza E. (2013) Encyclopedia of Distances.
846
943
  Berlin, Heidelberg: Springer Berlin Heidelberg.
847
944
  https://doi.org/10.1007/978-3-642-30958-8.
@@ -860,17 +957,21 @@ class Distance:
860
957
  """
861
958
  Calculate the Minkowski distance between two vectors.
862
959
 
863
- Parameters:
960
+ Parameters
961
+ ----------
864
962
  - u, v: Input vectors between which the distance is to be calculated.
865
963
  - p: The order of the norm of the difference.
866
964
 
867
- Returns:
965
+ Returns
966
+ -------
868
967
  - The Minkowski distance between the two vectors.
869
968
 
870
- Notes:
969
+ Notes
970
+ -----
871
971
  When p goes to infinite, the Chebyshev distance is derived.
872
972
 
873
- References:
973
+ References
974
+ ----------
874
975
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
875
976
  Measures between Probability Density Functions. International
876
977
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -883,16 +984,20 @@ class Distance:
883
984
  """
884
985
  Calculate the Motyka distance between two vectors.
885
986
 
886
- Parameters:
987
+ Parameters
988
+ ----------
887
989
  - u, v: Input vectors between which the distance is to be calculated.
888
990
 
889
- Returns:
991
+ Returns
992
+ -------
890
993
  - The Motyka distance between the two vectors.
891
994
 
892
- Notes:
995
+ Notes
996
+ -----
893
997
  The distance between identical vectors is not equal to 0 but 0.5.
894
998
 
895
- References:
999
+ References
1000
+ ----------
896
1001
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
897
1002
  Measures between Probability Density Functions. International
898
1003
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -905,13 +1010,16 @@ class Distance:
905
1010
  """
906
1011
  Calculate the Neyman chi-square distance between two vectors.
907
1012
 
908
- Parameters:
1013
+ Parameters
1014
+ ----------
909
1015
  - u, v: Input vectors between which the distance is to be calculated.
910
1016
 
911
- Returns:
1017
+ Returns
1018
+ -------
912
1019
  - The Neyman chi-square distance between the two vectors.
913
1020
 
914
- References:
1021
+ References
1022
+ ----------
915
1023
  1. Neyman J (1949) Contributions to the theory of the chi^2 test.
916
1024
  In Proceedings of the First Berkley Symposium on Mathematical
917
1025
  Statistics and Probability.
@@ -928,19 +1036,23 @@ class Distance:
928
1036
  """
929
1037
  Calculate the Nonintersection distance between two vectors.
930
1038
 
931
- Parameters:
1039
+ Parameters
1040
+ ----------
932
1041
  - u, v: Input vectors between which the distance is to be calculated.
933
1042
 
934
- Returns:
1043
+ Returns
1044
+ -------
935
1045
  - The Nonintersection distance between the two vectors.
936
1046
 
937
- References:
1047
+ References
1048
+ ----------
938
1049
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
939
1050
  Measures between Probability Density Functions. International
940
1051
  Journal of Mathematical Models and Methods in Applied Sciences.
941
1052
  1(4), 300-307.
942
1053
 
943
- Notes:
1054
+ Notes
1055
+ -----
944
1056
  When used for comparing two probability density functions (pdfs),
945
1057
  Nonintersection distance equals half of Cityblock distance.
946
1058
  """
@@ -951,13 +1063,16 @@ class Distance:
951
1063
  """
952
1064
  Calculate the Pearson chi-square divergence between two vectors.
953
1065
 
954
- Parameters:
1066
+ Parameters
1067
+ ----------
955
1068
  - u, v: Input vectors between which the divergence is to be calculated.
956
1069
 
957
- Returns:
1070
+ Returns
1071
+ -------
958
1072
  - The Pearson chi-square divergence between the two vectors.
959
1073
 
960
- References:
1074
+ References
1075
+ ----------
961
1076
  1. Pearson K. (1900) On the Criterion that a given system of
962
1077
  deviations from the probable in the case of correlated system
963
1078
  of variables is such that it can be reasonable supposed to have
@@ -967,7 +1082,8 @@ class Distance:
967
1082
  Journal of Mathematical Models and Methods in Applied Sciences.
968
1083
  1(4), 300-307.
969
1084
 
970
- Notes:
1085
+ Notes
1086
+ -----
971
1087
  Pearson chi-square divergence is asymmetric.
972
1088
  """
973
1089
  u, v = np.asarray(u), np.asarray(v)
@@ -978,13 +1094,16 @@ class Distance:
978
1094
  """
979
1095
  Calculate the Penrose shape distance between two vectors.
980
1096
 
981
- Parameters:
1097
+ Parameters
1098
+ ----------
982
1099
  - u, v: Input vectors between which the distance is to be calculated.
983
1100
 
984
- Returns:
1101
+ Returns
1102
+ -------
985
1103
  - The Penrose shape distance between the two vectors.
986
1104
 
987
- References:
1105
+ References
1106
+ ----------
988
1107
  1. Deza M, Deza E (2009) Encyclopedia of Distances.
989
1108
  Springer-Verlag Berlin Heidelberg. 1-590.
990
1109
  """
@@ -997,13 +1116,16 @@ class Distance:
997
1116
  """
998
1117
  Calculate the Probabilistic chi-square distance between two vectors.
999
1118
 
1000
- Parameters:
1119
+ Parameters
1120
+ ----------
1001
1121
  - u, v: Input vectors between which the distance is to be calculated.
1002
1122
 
1003
- Returns:
1123
+ Returns
1124
+ -------
1004
1125
  - The Probabilistic chi-square distance between the two vectors.
1005
1126
 
1006
- Notes:
1127
+ Notes
1128
+ -----
1007
1129
  Added by SC.
1008
1130
  """
1009
1131
  u, v = np.asarray(u), np.asarray(v)
@@ -1015,13 +1137,16 @@ class Distance:
1015
1137
  """
1016
1138
  Calculate the Ruzicka distance between two vectors.
1017
1139
 
1018
- Parameters:
1140
+ Parameters
1141
+ ----------
1019
1142
  - u, v: Input vectors between which the distance is to be calculated.
1020
1143
 
1021
- Returns:
1144
+ Returns
1145
+ -------
1022
1146
  - The Ruzicka distance between the two vectors.
1023
1147
 
1024
- Notes:
1148
+ Notes
1149
+ -----
1025
1150
  Added by SC.
1026
1151
  """
1027
1152
  u, v = np.asarray(u), np.asarray(v)
@@ -1033,13 +1158,16 @@ class Distance:
1033
1158
  """
1034
1159
  Calculate the Sorensen distance between two vectors.
1035
1160
 
1036
- Parameters:
1161
+ Parameters
1162
+ ----------
1037
1163
  - u, v: Input vectors between which the distance is to be calculated.
1038
1164
 
1039
- Returns:
1165
+ Returns
1166
+ -------
1040
1167
  - The Sorensen distance between the two vectors.
1041
1168
 
1042
- Notes:
1169
+ Notes
1170
+ -----
1043
1171
  The Sorensen distance equals the Manhattan distance divided by the sum of the two vectors.
1044
1172
 
1045
1173
  Added by SC.
@@ -1051,16 +1179,20 @@ class Distance:
1051
1179
  """
1052
1180
  Calculate the Soergel distance between two vectors.
1053
1181
 
1054
- Parameters:
1182
+ Parameters
1183
+ ----------
1055
1184
  - u, v: Input vectors between which the distance is to be calculated.
1056
1185
 
1057
- Returns:
1186
+ Returns
1187
+ -------
1058
1188
  - The Soergel distance between the two vectors.
1059
1189
 
1060
- Notes:
1190
+ Notes
1191
+ -----
1061
1192
  Equals Tanimoto distance.
1062
1193
 
1063
- References:
1194
+ References
1195
+ ----------
1064
1196
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
1065
1197
  Measures between Probability Density Functions. International
1066
1198
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -1073,13 +1205,16 @@ class Distance:
1073
1205
  """
1074
1206
  Calculate the Squared chi-square distance between two vectors.
1075
1207
 
1076
- Parameters:
1208
+ Parameters
1209
+ ----------
1077
1210
  - u, v: Input vectors between which the distance is to be calculated.
1078
1211
 
1079
- Returns:
1212
+ Returns
1213
+ -------
1080
1214
  - The Squared chi-square distance between the two vectors.
1081
1215
 
1082
- References:
1216
+ References
1217
+ ----------
1083
1218
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
1084
1219
  Measures between Probability Density Functions. International
1085
1220
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -1094,13 +1229,16 @@ class Distance:
1094
1229
  """
1095
1230
  Calculate the Squared-chord distance between two vectors.
1096
1231
 
1097
- Parameters:
1232
+ Parameters
1233
+ ----------
1098
1234
  - u, v: Input vectors between which the distance is to be calculated.
1099
1235
 
1100
- Returns:
1236
+ Returns
1237
+ -------
1101
1238
  - The Squared-chord distance between the two vectors.
1102
1239
 
1103
- References:
1240
+ References
1241
+ ----------
1104
1242
  1. Gavin DG et al. (2003) A statistical approach to evaluating
1105
1243
  distance metrics and analog assignments for pollen records.
1106
1244
  Quaternary Research 60:356–367.
@@ -1109,7 +1247,8 @@ class Distance:
1109
1247
  Journal of Mathematical Models and Methods in Applied Sciences.
1110
1248
  1(4), 300-307.
1111
1249
 
1112
- Notes:
1250
+ Notes
1251
+ -----
1113
1252
  Equals to squared Matusita distance.
1114
1253
  """
1115
1254
  u, v = np.asarray(u), np.asarray(v)
@@ -1119,13 +1258,16 @@ class Distance:
1119
1258
  """
1120
1259
  Calculate the Squared Euclidean distance between two vectors.
1121
1260
 
1122
- Parameters:
1261
+ Parameters
1262
+ ----------
1123
1263
  - u, v: Input vectors between which the distance is to be calculated.
1124
1264
 
1125
- Returns:
1265
+ Returns
1266
+ -------
1126
1267
  - The Squared Euclidean distance between the two vectors.
1127
1268
 
1128
- References:
1269
+ References
1270
+ ----------
1129
1271
  1. Gavin DG et al. (2003) A statistical approach to evaluating
1130
1272
  distance metrics and analog assignments for pollen records.
1131
1273
  Quaternary Research 60:356–367.
@@ -1134,7 +1276,8 @@ class Distance:
1134
1276
  Journal of Mathematical Models and Methods in Applied Sciences.
1135
1277
  1(4), 300-307.
1136
1278
 
1137
- Notes:
1279
+ Notes
1280
+ -----
1138
1281
  Equals to squared Euclidean distance.
1139
1282
  """
1140
1283
  u, v = np.asarray(u), np.asarray(v)
@@ -1144,13 +1287,16 @@ class Distance:
1144
1287
  """
1145
1288
  Calculate the Taneja distance between two vectors.
1146
1289
 
1147
- Parameters:
1290
+ Parameters
1291
+ ----------
1148
1292
  - u, v: Input vectors between which the distance is to be calculated.
1149
1293
 
1150
- Returns:
1294
+ Returns
1295
+ -------
1151
1296
  - The Taneja distance between the two vectors.
1152
1297
 
1153
- References:
1298
+ References
1299
+ ----------
1154
1300
  1. Taneja IJ. (1995), New Developments in Generalized Information
1155
1301
  Measures, Chapter in: Advances in Imaging and Electron Physics,
1156
1302
  Ed. P.W. Hawkes, 91, 37-135.
@@ -1169,19 +1315,23 @@ class Distance:
1169
1315
  """
1170
1316
  Calculate the Tanimoto distance between two vectors.
1171
1317
 
1172
- Parameters:
1318
+ Parameters
1319
+ ----------
1173
1320
  - u, v: Input vectors between which the distance is to be calculated.
1174
1321
 
1175
- Returns:
1322
+ Returns
1323
+ -------
1176
1324
  - The Tanimoto distance between the two vectors.
1177
1325
 
1178
- References:
1326
+ References
1327
+ ----------
1179
1328
  1. Sung-Hyuk C. (2007) Comprehensive Survey on Distance/Similarity
1180
1329
  Measures between Probability Density Functions. International
1181
1330
  Journal of Mathematical Models and Methods in Applied Sciences.
1182
1331
  1(4), 300-307.
1183
1332
 
1184
- Notes:
1333
+ Notes
1334
+ -----
1185
1335
  Equals Soergel distance.
1186
1336
  """
1187
1337
  u, v = np.asarray(u), np.asarray(v)
@@ -1195,19 +1345,23 @@ class Distance:
1195
1345
  """
1196
1346
  Calculate the Topsøe distance between two vectors.
1197
1347
 
1198
- Parameters:
1348
+ Parameters
1349
+ ----------
1199
1350
  - u, v: Input vectors between which the distance is to be calculated.
1200
1351
 
1201
- Returns:
1352
+ Returns
1353
+ -------
1202
1354
  - The Topsøe distance between the two vectors.
1203
1355
 
1204
- References:
1356
+ References
1357
+ ----------
1205
1358
  1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
1206
1359
  Measures between Probability Density Functions. International
1207
1360
  Journal of Mathematical Models and Methods in Applied Sciences.
1208
1361
  1(4), 300-307.
1209
1362
 
1210
- Notes:
1363
+ Notes
1364
+ -----
1211
1365
  Equals two times Jensen-Shannon divergence.
1212
1366
  """
1213
1367
  u, v = np.asarray(u), np.asarray(v)
@@ -1221,13 +1375,16 @@ class Distance:
1221
1375
  """
1222
1376
  Calculate the Vicis Symmetric chi-square distance between two vectors.
1223
1377
 
1224
- Parameters:
1378
+ Parameters
1379
+ ----------
1225
1380
  - u, v: Input vectors between which the distance is to be calculated.
1226
1381
 
1227
- Returns:
1382
+ Returns
1383
+ -------
1228
1384
  - The Vicis Symmetric chi-square distance between the two vectors.
1229
1385
 
1230
- References:
1386
+ References
1387
+ ----------
1231
1388
  1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
1232
1389
  Measures between Probability Density Functions. International
1233
1390
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -1243,13 +1400,16 @@ class Distance:
1243
1400
  """
1244
1401
  Calculate the Vicis-Wave Hedges distance between two vectors.
1245
1402
 
1246
- Parameters:
1403
+ Parameters
1404
+ ----------
1247
1405
  - u, v: Input vectors between which the distance is to be calculated.
1248
1406
 
1249
- Returns:
1407
+ Returns
1408
+ -------
1250
1409
  - The Vicis-Wave Hedges distance between the two vectors.
1251
1410
 
1252
- References:
1411
+ References
1412
+ ----------
1253
1413
  1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
1254
1414
  Measures between Probability Density Functions. International
1255
1415
  Journal of Mathematical Models and Methods in Applied Sciences.
@@ -1265,13 +1425,16 @@ class Distance:
1265
1425
  """
1266
1426
  Calculate the Wave Hedges distance between two vectors.
1267
1427
 
1268
- Parameters:
1428
+ Parameters
1429
+ ----------
1269
1430
  - u, v: Input vectors between which the distance is to be calculated.
1270
1431
 
1271
- Returns:
1432
+ Returns
1433
+ -------
1272
1434
  - The Wave Hedges distance between the two vectors.
1273
1435
 
1274
- References:
1436
+ References
1437
+ ----------
1275
1438
  1. Sung-Hyuk C (2007) Comprehensive Survey on Distance/Similarity
1276
1439
  Measures between Probability Density Functions. International
1277
1440
  Journal of Mathematical Models and Methods in Applied Sciences.