entropy 0.0.2
Sign up to get free protection for your applications and to get access to all the features.
- data/.gitignore +4 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +674 -0
- data/README.txt +48 -0
- data/Rakefile +22 -0
- data/doc/rdocs/Entropy.html +234 -0
- data/doc/rdocs/Entropy/Dict.html +311 -0
- data/doc/rdocs/Entropy/ProbabilityMetricSpace.html +544 -0
- data/doc/rdocs/Entropy/ProbabilitySpace.html +473 -0
- data/doc/rdocs/Entropy/Stream.html +281 -0
- data/doc/rdocs/LICENSE_txt.html +834 -0
- data/doc/rdocs/README_txt.html +138 -0
- data/doc/rdocs/created.rid +9 -0
- data/doc/rdocs/images/brick.png +0 -0
- data/doc/rdocs/images/brick_link.png +0 -0
- data/doc/rdocs/images/bug.png +0 -0
- data/doc/rdocs/images/bullet_black.png +0 -0
- data/doc/rdocs/images/bullet_toggle_minus.png +0 -0
- data/doc/rdocs/images/bullet_toggle_plus.png +0 -0
- data/doc/rdocs/images/date.png +0 -0
- data/doc/rdocs/images/find.png +0 -0
- data/doc/rdocs/images/loadingAnimation.gif +0 -0
- data/doc/rdocs/images/macFFBgHack.png +0 -0
- data/doc/rdocs/images/package.png +0 -0
- data/doc/rdocs/images/page_green.png +0 -0
- data/doc/rdocs/images/page_white_text.png +0 -0
- data/doc/rdocs/images/page_white_width.png +0 -0
- data/doc/rdocs/images/plugin.png +0 -0
- data/doc/rdocs/images/ruby.png +0 -0
- data/doc/rdocs/images/tag_green.png +0 -0
- data/doc/rdocs/images/wrench.png +0 -0
- data/doc/rdocs/images/wrench_orange.png +0 -0
- data/doc/rdocs/images/zoom.png +0 -0
- data/doc/rdocs/index.html +155 -0
- data/doc/rdocs/js/darkfish.js +116 -0
- data/doc/rdocs/js/jquery.js +32 -0
- data/doc/rdocs/js/quicksearch.js +114 -0
- data/doc/rdocs/js/thickbox-compressed.js +10 -0
- data/doc/rdocs/lib/entropy/dict_rb.html +56 -0
- data/doc/rdocs/lib/entropy/metric_space_rb.html +54 -0
- data/doc/rdocs/lib/entropy/probability_space_rb.html +52 -0
- data/doc/rdocs/lib/entropy/stream_rb.html +52 -0
- data/doc/rdocs/lib/entropy/version_rb.html +52 -0
- data/doc/rdocs/lib/entropy_rb.html +62 -0
- data/doc/rdocs/rdoc.css +763 -0
- data/entropy.gemspec +24 -0
- data/example/metric_prob_space.rb +42 -0
- data/example/prob_space.rb +31 -0
- data/lib/entropy.rb +13 -0
- data/lib/entropy/dict.rb +30 -0
- data/lib/entropy/metric_space.rb +116 -0
- data/lib/entropy/probability_space.rb +91 -0
- data/lib/entropy/stream.rb +37 -0
- data/lib/entropy/version.rb +3 -0
- data/test/stream0.txt +1 -0
- data/test/stream1.txt +1 -0
- data/test/stream2.txt +1 -0
- data/test/stream_random.bin +2 -0
- data/test/test_entropy_def.rb +10 -0
- data/test/test_entropy_metr.rb +36 -0
- data/test/test_entropy_prob.rb +64 -0
- data/test/test_entropy_stream.rb +29 -0
- metadata +127 -0
|
@@ -0,0 +1,544 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="UTF-8"?>
|
|
2
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
|
|
3
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
|
4
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
5
|
+
<head>
|
|
6
|
+
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
|
|
7
|
+
|
|
8
|
+
<title>Class: Entropy::ProbabilityMetricSpace</title>
|
|
9
|
+
|
|
10
|
+
<link rel="stylesheet" href="../rdoc.css" type="text/css" media="screen" />
|
|
11
|
+
|
|
12
|
+
<script src="../js/jquery.js" type="text/javascript" charset="utf-8"></script>
|
|
13
|
+
<script src="../js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
|
|
14
|
+
<script src="../js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
|
|
15
|
+
<script src="../js/darkfish.js" type="text/javascript" charset="utf-8"></script>
|
|
16
|
+
|
|
17
|
+
</head>
|
|
18
|
+
<body id="top" class="class">
|
|
19
|
+
|
|
20
|
+
<div id="metadata">
|
|
21
|
+
<div id="home-metadata">
|
|
22
|
+
<div id="home-section" class="section">
|
|
23
|
+
<h3 class="section-header">
|
|
24
|
+
<a href="../index.html">Home</a>
|
|
25
|
+
<a href="../index.html#classes">Classes</a>
|
|
26
|
+
<a href="../index.html#methods">Methods</a>
|
|
27
|
+
</h3>
|
|
28
|
+
</div>
|
|
29
|
+
</div>
|
|
30
|
+
|
|
31
|
+
<div id="file-metadata">
|
|
32
|
+
<div id="file-list-section" class="section">
|
|
33
|
+
<h3 class="section-header">In Files</h3>
|
|
34
|
+
<div class="section-body">
|
|
35
|
+
<ul>
|
|
36
|
+
|
|
37
|
+
<li><a href="../lib/entropy/metric_space_rb.html?TB_iframe=true&height=550&width=785"
|
|
38
|
+
class="thickbox" title="lib/entropy/metric_space.rb">lib/entropy/metric_space.rb</a></li>
|
|
39
|
+
|
|
40
|
+
</ul>
|
|
41
|
+
</div>
|
|
42
|
+
</div>
|
|
43
|
+
|
|
44
|
+
|
|
45
|
+
</div>
|
|
46
|
+
|
|
47
|
+
<div id="class-metadata">
|
|
48
|
+
|
|
49
|
+
<!-- Parent Class -->
|
|
50
|
+
<div id="parent-class-section" class="section">
|
|
51
|
+
<h3 class="section-header">Parent</h3>
|
|
52
|
+
|
|
53
|
+
<p class="link"><a href="ProbabilitySpace.html">Entropy::ProbabilitySpace</a></p>
|
|
54
|
+
|
|
55
|
+
</div>
|
|
56
|
+
|
|
57
|
+
|
|
58
|
+
|
|
59
|
+
|
|
60
|
+
|
|
61
|
+
|
|
62
|
+
|
|
63
|
+
<!-- Method Quickref -->
|
|
64
|
+
<div id="method-list-section" class="section">
|
|
65
|
+
<h3 class="section-header">Methods</h3>
|
|
66
|
+
<ul class="link-list">
|
|
67
|
+
|
|
68
|
+
<li><a href="#method-c-new">::new</a></li>
|
|
69
|
+
|
|
70
|
+
<li><a href="#method-i-add_stream">#add_stream</a></li>
|
|
71
|
+
|
|
72
|
+
<li><a href="#method-i-cardinality">#cardinality</a></li>
|
|
73
|
+
|
|
74
|
+
<li><a href="#method-i-define_distance">#define_distance</a></li>
|
|
75
|
+
|
|
76
|
+
<li><a href="#method-i-diversity">#diversity</a></li>
|
|
77
|
+
|
|
78
|
+
<li><a href="#method-i-rao_entropy">#rao_entropy</a></li>
|
|
79
|
+
|
|
80
|
+
<li><a href="#method-i-renyi_entropy">#renyi_entropy</a></li>
|
|
81
|
+
|
|
82
|
+
<li><a href="#method-i-shannon_entropy">#shannon_entropy</a></li>
|
|
83
|
+
|
|
84
|
+
</ul>
|
|
85
|
+
</div>
|
|
86
|
+
|
|
87
|
+
|
|
88
|
+
|
|
89
|
+
</div>
|
|
90
|
+
|
|
91
|
+
<div id="project-metadata">
|
|
92
|
+
|
|
93
|
+
|
|
94
|
+
<div id="fileindex-section" class="section project-section">
|
|
95
|
+
<h3 class="section-header">Files</h3>
|
|
96
|
+
<ul>
|
|
97
|
+
|
|
98
|
+
<li class="file"><a href="../LICENSE_txt.html">LICENSE.txt</a></li>
|
|
99
|
+
|
|
100
|
+
<li class="file"><a href="../README_txt.html">README.txt</a></li>
|
|
101
|
+
|
|
102
|
+
</ul>
|
|
103
|
+
</div>
|
|
104
|
+
|
|
105
|
+
|
|
106
|
+
<div id="classindex-section" class="section project-section">
|
|
107
|
+
<h3 class="section-header">Class/Module Index
|
|
108
|
+
<span class="search-toggle"><img src="../images/find.png"
|
|
109
|
+
height="16" width="16" alt="[+]"
|
|
110
|
+
title="show/hide quicksearch" /></span></h3>
|
|
111
|
+
<form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
|
|
112
|
+
<fieldset>
|
|
113
|
+
<legend>Quicksearch</legend>
|
|
114
|
+
<input type="text" name="quicksearch" value=""
|
|
115
|
+
class="quicksearch-field" />
|
|
116
|
+
</fieldset>
|
|
117
|
+
</form>
|
|
118
|
+
|
|
119
|
+
<ul class="link-list">
|
|
120
|
+
|
|
121
|
+
<li><a href="../Entropy.html">Entropy</a></li>
|
|
122
|
+
|
|
123
|
+
<li><a href="../Entropy/Dict.html">Entropy::Dict</a></li>
|
|
124
|
+
|
|
125
|
+
<li><a href="../Entropy/ProbabilityMetricSpace.html">Entropy::ProbabilityMetricSpace</a></li>
|
|
126
|
+
|
|
127
|
+
<li><a href="../Entropy/ProbabilitySpace.html">Entropy::ProbabilitySpace</a></li>
|
|
128
|
+
|
|
129
|
+
<li><a href="../Entropy/Stream.html">Entropy::Stream</a></li>
|
|
130
|
+
|
|
131
|
+
</ul>
|
|
132
|
+
<div id="no-class-search-results" style="display: none;">No matching classes.</div>
|
|
133
|
+
</div>
|
|
134
|
+
|
|
135
|
+
|
|
136
|
+
</div>
|
|
137
|
+
</div>
|
|
138
|
+
|
|
139
|
+
<div id="documentation">
|
|
140
|
+
<h1 class="class">Entropy::ProbabilityMetricSpace</h1>
|
|
141
|
+
|
|
142
|
+
<div id="description" class="description">
|
|
143
|
+
|
|
144
|
+
<p><a href="ProbabilityMetricSpace.html">Entropy::ProbabilityMetricSpace</a>
|
|
145
|
+
defines a finite probability metric space</p>
|
|
146
|
+
|
|
147
|
+
</div><!-- description -->
|
|
148
|
+
|
|
149
|
+
|
|
150
|
+
|
|
151
|
+
|
|
152
|
+
<div id="5Buntitled-5D" class="documentation-section">
|
|
153
|
+
|
|
154
|
+
|
|
155
|
+
|
|
156
|
+
|
|
157
|
+
|
|
158
|
+
|
|
159
|
+
|
|
160
|
+
<!-- Attributes -->
|
|
161
|
+
<div id="attribute-method-details" class="method-section section">
|
|
162
|
+
<h3 class="section-header">Attributes</h3>
|
|
163
|
+
|
|
164
|
+
|
|
165
|
+
<div id="distance_function-attribute-method" class="method-detail">
|
|
166
|
+
<a name="distance_function"></a>
|
|
167
|
+
|
|
168
|
+
<div class="method-heading attribute-method-heading">
|
|
169
|
+
<span class="method-name">distance_function</span><span
|
|
170
|
+
class="attribute-access-type">[R]</span>
|
|
171
|
+
</div>
|
|
172
|
+
|
|
173
|
+
<div class="method-description">
|
|
174
|
+
|
|
175
|
+
|
|
176
|
+
|
|
177
|
+
</div>
|
|
178
|
+
</div>
|
|
179
|
+
|
|
180
|
+
<div id="distance_matrix-attribute-method" class="method-detail">
|
|
181
|
+
<a name="distance_matrix"></a>
|
|
182
|
+
|
|
183
|
+
<div class="method-heading attribute-method-heading">
|
|
184
|
+
<span class="method-name">distance_matrix</span><span
|
|
185
|
+
class="attribute-access-type">[R]</span>
|
|
186
|
+
</div>
|
|
187
|
+
|
|
188
|
+
<div class="method-description">
|
|
189
|
+
|
|
190
|
+
|
|
191
|
+
|
|
192
|
+
</div>
|
|
193
|
+
</div>
|
|
194
|
+
|
|
195
|
+
</div><!-- attribute-method-details -->
|
|
196
|
+
|
|
197
|
+
|
|
198
|
+
<!-- Methods -->
|
|
199
|
+
|
|
200
|
+
<div id="public-class-method-details" class="method-section section">
|
|
201
|
+
<h3 class="section-header">Public Class Methods</h3>
|
|
202
|
+
|
|
203
|
+
|
|
204
|
+
<div id="new-method" class="method-detail ">
|
|
205
|
+
<a name="method-c-new"></a>
|
|
206
|
+
|
|
207
|
+
|
|
208
|
+
<div class="method-heading">
|
|
209
|
+
<span class="method-name">new</span><span
|
|
210
|
+
class="method-args">()</span>
|
|
211
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
212
|
+
</div>
|
|
213
|
+
|
|
214
|
+
|
|
215
|
+
<div class="method-description">
|
|
216
|
+
|
|
217
|
+
|
|
218
|
+
|
|
219
|
+
|
|
220
|
+
|
|
221
|
+
<div class="method-source-code" id="new-source">
|
|
222
|
+
<pre>
|
|
223
|
+
<span class="ruby-comment"># File lib/entropy/metric_space.rb, line 10</span>
|
|
224
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>
|
|
225
|
+
<span class="ruby-ivar">@distance_matrix</span> = <span class="ruby-keyword">nil</span>
|
|
226
|
+
<span class="ruby-ivar">@density</span> = <span class="ruby-keyword">nil</span>
|
|
227
|
+
<span class="ruby-keyword">super</span>
|
|
228
|
+
<span class="ruby-keyword">end</span></pre>
|
|
229
|
+
</div><!-- new-source -->
|
|
230
|
+
|
|
231
|
+
</div>
|
|
232
|
+
|
|
233
|
+
|
|
234
|
+
|
|
235
|
+
|
|
236
|
+
</div><!-- new-method -->
|
|
237
|
+
|
|
238
|
+
|
|
239
|
+
</div><!-- public-class-method-details -->
|
|
240
|
+
|
|
241
|
+
<div id="public-instance-method-details" class="method-section section">
|
|
242
|
+
<h3 class="section-header">Public Instance Methods</h3>
|
|
243
|
+
|
|
244
|
+
|
|
245
|
+
<div id="add_stream-method" class="method-detail ">
|
|
246
|
+
<a name="method-i-add_stream"></a>
|
|
247
|
+
|
|
248
|
+
|
|
249
|
+
<div class="method-heading">
|
|
250
|
+
<span class="method-name">add_stream</span><span
|
|
251
|
+
class="method-args">(stream)</span>
|
|
252
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
253
|
+
</div>
|
|
254
|
+
|
|
255
|
+
|
|
256
|
+
<div class="method-description">
|
|
257
|
+
|
|
258
|
+
<p>Adds a set of elements (char, bit) to the space</p>
|
|
259
|
+
|
|
260
|
+
|
|
261
|
+
|
|
262
|
+
<div class="method-source-code" id="add_stream-source">
|
|
263
|
+
<pre>
|
|
264
|
+
<span class="ruby-comment"># File lib/entropy/metric_space.rb, line 17</span>
|
|
265
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">add_stream</span>(<span class="ruby-identifier">stream</span>)
|
|
266
|
+
<span class="ruby-keyword">super</span>(<span class="ruby-identifier">stream</span>)
|
|
267
|
+
<span class="ruby-keyword">end</span></pre>
|
|
268
|
+
</div><!-- add_stream-source -->
|
|
269
|
+
|
|
270
|
+
</div>
|
|
271
|
+
|
|
272
|
+
|
|
273
|
+
|
|
274
|
+
|
|
275
|
+
</div><!-- add_stream-method -->
|
|
276
|
+
|
|
277
|
+
|
|
278
|
+
<div id="cardinality-method" class="method-detail ">
|
|
279
|
+
<a name="method-i-cardinality"></a>
|
|
280
|
+
|
|
281
|
+
|
|
282
|
+
<div class="method-heading">
|
|
283
|
+
<span class="method-name">cardinality</span><span
|
|
284
|
+
class="method-args">(alpha)</span>
|
|
285
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
286
|
+
</div>
|
|
287
|
+
|
|
288
|
+
|
|
289
|
+
<div class="method-description">
|
|
290
|
+
|
|
291
|
+
<p>Computes the α-Cardinality of the space</p>
|
|
292
|
+
|
|
293
|
+
|
|
294
|
+
|
|
295
|
+
<div class="method-source-code" id="cardinality-source">
|
|
296
|
+
<pre>
|
|
297
|
+
<span class="ruby-comment"># File lib/entropy/metric_space.rb, line 87</span>
|
|
298
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">cardinality</span>(<span class="ruby-identifier">alpha</span>)
|
|
299
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-string">"Warning: distance metric not defined..."</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@distance_matrix</span>.<span class="ruby-identifier">nil?</span>
|
|
300
|
+
<span class="ruby-identifier">card</span> = <span class="ruby-value">0</span>
|
|
301
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">alpha</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span>
|
|
302
|
+
<span class="ruby-identifier">card</span> = <span class="ruby-value">1</span>
|
|
303
|
+
<span class="ruby-ivar">@prob_space</span>.<span class="ruby-identifier">each_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
304
|
+
<span class="ruby-identifier">card</span> = <span class="ruby-identifier">card</span> * (<span class="ruby-ivar">@density</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">**</span> (<span class="ruby-operator">-</span><span class="ruby-ivar">@prob_space</span>[<span class="ruby-identifier">i</span>]))
|
|
305
|
+
<span class="ruby-keyword">end</span>
|
|
306
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">alpha</span> <span class="ruby-operator">==</span> <span class="ruby-value">:infinite</span>
|
|
307
|
+
<span class="ruby-identifier">card</span> = <span class="ruby-value">1.0</span><span class="ruby-operator">/</span><span class="ruby-ivar">@density</span>.<span class="ruby-identifier">max</span>
|
|
308
|
+
<span class="ruby-keyword">else</span>
|
|
309
|
+
<span class="ruby-ivar">@prob_space</span>.<span class="ruby-identifier">each_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
310
|
+
<span class="ruby-identifier">card</span> <span class="ruby-operator">+=</span> <span class="ruby-ivar">@prob_space</span>[<span class="ruby-identifier">i</span>] * (<span class="ruby-ivar">@density</span>[<span class="ruby-identifier">i</span>]<span class="ruby-operator">**</span>(<span class="ruby-identifier">alpha</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>))
|
|
311
|
+
<span class="ruby-keyword">end</span>
|
|
312
|
+
<span class="ruby-identifier">card</span> = <span class="ruby-identifier">card</span> <span class="ruby-operator">**</span> (<span class="ruby-value">1.0</span> <span class="ruby-operator">/</span> (<span class="ruby-value">1</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">alpha</span>))
|
|
313
|
+
<span class="ruby-keyword">end</span>
|
|
314
|
+
<span class="ruby-identifier">card</span>
|
|
315
|
+
<span class="ruby-keyword">end</span></pre>
|
|
316
|
+
</div><!-- cardinality-source -->
|
|
317
|
+
|
|
318
|
+
</div>
|
|
319
|
+
|
|
320
|
+
|
|
321
|
+
|
|
322
|
+
|
|
323
|
+
</div><!-- cardinality-method -->
|
|
324
|
+
|
|
325
|
+
|
|
326
|
+
<div id="define_distance-method" class="method-detail ">
|
|
327
|
+
<a name="method-i-define_distance"></a>
|
|
328
|
+
|
|
329
|
+
|
|
330
|
+
<div class="method-heading">
|
|
331
|
+
<span class="method-name">define_distance</span><span
|
|
332
|
+
class="method-args">(*args, &blk)</span>
|
|
333
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
334
|
+
</div>
|
|
335
|
+
|
|
336
|
+
|
|
337
|
+
<div class="method-description">
|
|
338
|
+
|
|
339
|
+
<p>Defines the distance among the elements of the set. The method accepts a
|
|
340
|
+
block, so you can use your function to calculate the distance. The function
|
|
341
|
+
should accept two parameters, viz. the ordinals i,j of the elements and
|
|
342
|
+
should return a decimal number, the distance between element i and j. In
|
|
343
|
+
alternative you could pass a matrix of numbers defining the distances among
|
|
344
|
+
i’s and j’s.</p>
|
|
345
|
+
|
|
346
|
+
|
|
347
|
+
|
|
348
|
+
<div class="method-source-code" id="define_distance-source">
|
|
349
|
+
<pre>
|
|
350
|
+
<span class="ruby-comment"># File lib/entropy/metric_space.rb, line 29</span>
|
|
351
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">define_distance</span>(*<span class="ruby-identifier">args</span>, &<span class="ruby-identifier">blk</span>)
|
|
352
|
+
<span class="ruby-keyword">if</span> <span class="ruby-operator">!</span><span class="ruby-identifier">blk</span>.<span class="ruby-identifier">nil?</span>
|
|
353
|
+
<span class="ruby-ivar">@distance_function</span> = <span class="ruby-identifier">blk</span>
|
|
354
|
+
<span class="ruby-identifier">update_distance_matrix</span>
|
|
355
|
+
<span class="ruby-keyword">else</span>
|
|
356
|
+
<span class="ruby-identifier">mat</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">0</span>]
|
|
357
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-string">"distance matrix is not a matrix object"</span> <span class="ruby-keyword">if</span> <span class="ruby-operator">!</span><span class="ruby-identifier">mat</span>.<span class="ruby-identifier">respond_to</span>(<span class="ruby-string">"square?"</span>)
|
|
358
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-string">"distance matrix is not square"</span> <span class="ruby-keyword">if</span> <span class="ruby-operator">!</span><span class="ruby-identifier">mat</span>.<span class="ruby-identifier">square?</span>
|
|
359
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-string">"distance matrix has wrong dimensions"</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">mat</span>.<span class="ruby-identifier">to_a</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-ivar">@prob_space</span>.<span class="ruby-identifier">size</span>
|
|
360
|
+
<span class="ruby-ivar">@distance_matrix</span> = <span class="ruby-identifier">mat</span>
|
|
361
|
+
<span class="ruby-keyword">end</span>
|
|
362
|
+
<span class="ruby-identifier">z</span> = <span class="ruby-ivar">@distance_matrix</span>.<span class="ruby-identifier">map</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">d</span><span class="ruby-operator">|</span> <span class="ruby-constant">Math</span>.<span class="ruby-identifier">exp</span>(<span class="ruby-operator">-</span><span class="ruby-identifier">d</span>) }
|
|
363
|
+
<span class="ruby-ivar">@density</span> = <span class="ruby-identifier">z</span> * <span class="ruby-constant">Matrix</span>.<span class="ruby-identifier">column_vector</span>(<span class="ruby-ivar">@prob_space</span>)
|
|
364
|
+
<span class="ruby-ivar">@density</span> = <span class="ruby-ivar">@density</span>.<span class="ruby-identifier">column</span>(<span class="ruby-value">0</span>).<span class="ruby-identifier">to_a</span>
|
|
365
|
+
<span class="ruby-keyword">end</span></pre>
|
|
366
|
+
</div><!-- define_distance-source -->
|
|
367
|
+
|
|
368
|
+
</div>
|
|
369
|
+
|
|
370
|
+
|
|
371
|
+
|
|
372
|
+
|
|
373
|
+
</div><!-- define_distance-method -->
|
|
374
|
+
|
|
375
|
+
|
|
376
|
+
<div id="diversity-method" class="method-detail ">
|
|
377
|
+
<a name="method-i-diversity"></a>
|
|
378
|
+
|
|
379
|
+
|
|
380
|
+
<div class="method-heading">
|
|
381
|
+
<span class="method-name">diversity</span><span
|
|
382
|
+
class="method-args">(alpha)</span>
|
|
383
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
384
|
+
</div>
|
|
385
|
+
|
|
386
|
+
|
|
387
|
+
<div class="method-description">
|
|
388
|
+
|
|
389
|
+
<p>Computes the α-Diversity of the space</p>
|
|
390
|
+
|
|
391
|
+
|
|
392
|
+
|
|
393
|
+
<div class="method-source-code" id="diversity-source">
|
|
394
|
+
<pre>
|
|
395
|
+
<span class="ruby-comment"># File lib/entropy/metric_space.rb, line 76</span>
|
|
396
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">diversity</span>(<span class="ruby-identifier">alpha</span>)
|
|
397
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-string">"Warning: distance metric not defined..."</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@distance_matrix</span>.<span class="ruby-identifier">nil?</span>
|
|
398
|
+
<span class="ruby-identifier">div</span> = []
|
|
399
|
+
<span class="ruby-ivar">@prob_space</span>.<span class="ruby-identifier">each_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
400
|
+
<span class="ruby-identifier">p</span> = <span class="ruby-ivar">@prob_space</span>[<span class="ruby-identifier">i</span>]
|
|
401
|
+
<span class="ruby-identifier">div</span>[<span class="ruby-identifier">i</span>] = <span class="ruby-identifier">p</span> * <span class="ruby-identifier">surprise</span>(<span class="ruby-identifier">alpha</span>, <span class="ruby-ivar">@density</span>[<span class="ruby-identifier">i</span>])
|
|
402
|
+
<span class="ruby-keyword">end</span>
|
|
403
|
+
<span class="ruby-identifier">div</span>.<span class="ruby-identifier">inject</span>(<span class="ruby-value">:+</span>)
|
|
404
|
+
<span class="ruby-keyword">end</span></pre>
|
|
405
|
+
</div><!-- diversity-source -->
|
|
406
|
+
|
|
407
|
+
</div>
|
|
408
|
+
|
|
409
|
+
|
|
410
|
+
|
|
411
|
+
|
|
412
|
+
</div><!-- diversity-method -->
|
|
413
|
+
|
|
414
|
+
|
|
415
|
+
<div id="rao_entropy-method" class="method-detail ">
|
|
416
|
+
<a name="method-i-rao_entropy"></a>
|
|
417
|
+
|
|
418
|
+
|
|
419
|
+
<div class="method-heading">
|
|
420
|
+
<span class="method-name">rao_entropy</span><span
|
|
421
|
+
class="method-args">()</span>
|
|
422
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
423
|
+
</div>
|
|
424
|
+
|
|
425
|
+
|
|
426
|
+
<div class="method-description">
|
|
427
|
+
|
|
428
|
+
<p>Computes the Rao <a href="../Entropy.html">Entropy</a> of the space</p>
|
|
429
|
+
|
|
430
|
+
|
|
431
|
+
|
|
432
|
+
<div class="method-source-code" id="rao_entropy-source">
|
|
433
|
+
<pre>
|
|
434
|
+
<span class="ruby-comment"># File lib/entropy/metric_space.rb, line 51</span>
|
|
435
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">rao_entropy</span>
|
|
436
|
+
<span class="ruby-identifier">diversity</span>(<span class="ruby-value">2</span>)
|
|
437
|
+
<span class="ruby-keyword">end</span></pre>
|
|
438
|
+
</div><!-- rao_entropy-source -->
|
|
439
|
+
|
|
440
|
+
</div>
|
|
441
|
+
|
|
442
|
+
|
|
443
|
+
|
|
444
|
+
|
|
445
|
+
</div><!-- rao_entropy-method -->
|
|
446
|
+
|
|
447
|
+
|
|
448
|
+
<div id="renyi_entropy-method" class="method-detail ">
|
|
449
|
+
<a name="method-i-renyi_entropy"></a>
|
|
450
|
+
|
|
451
|
+
|
|
452
|
+
<div class="method-heading">
|
|
453
|
+
<span class="method-name">renyi_entropy</span><span
|
|
454
|
+
class="method-args">(alpha)</span>
|
|
455
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
456
|
+
</div>
|
|
457
|
+
|
|
458
|
+
|
|
459
|
+
<div class="method-description">
|
|
460
|
+
|
|
461
|
+
<p>Computes the Renyi <a href="../Entropy.html">Entropy</a> (α-<a
|
|
462
|
+
href="../Entropy.html">Entropy</a>) of the space</p>
|
|
463
|
+
|
|
464
|
+
|
|
465
|
+
|
|
466
|
+
<div class="method-source-code" id="renyi_entropy-source">
|
|
467
|
+
<pre>
|
|
468
|
+
<span class="ruby-comment"># File lib/entropy/metric_space.rb, line 57</span>
|
|
469
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">renyi_entropy</span>(<span class="ruby-identifier">alpha</span>)
|
|
470
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-string">"Warning: distance metric not defined..."</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@distance_matrix</span>.<span class="ruby-identifier">nil?</span>
|
|
471
|
+
<span class="ruby-identifier">h</span> = <span class="ruby-value">0</span>
|
|
472
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">alpha</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span>
|
|
473
|
+
<span class="ruby-ivar">@prob_space</span>.<span class="ruby-identifier">each_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
474
|
+
<span class="ruby-identifier">h</span> <span class="ruby-operator">+=</span> <span class="ruby-operator">-</span><span class="ruby-ivar">@prob_space</span>[<span class="ruby-identifier">i</span>] * <span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-ivar">@density</span>[<span class="ruby-identifier">i</span>], <span class="ruby-value">2</span>)
|
|
475
|
+
<span class="ruby-keyword">end</span>
|
|
476
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">alpha</span> <span class="ruby-operator">==</span> <span class="ruby-value">:infinite</span>
|
|
477
|
+
<span class="ruby-identifier">h</span> = <span class="ruby-operator">-</span><span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-ivar">@density</span>.<span class="ruby-identifier">max</span>, <span class="ruby-value">2</span>)
|
|
478
|
+
<span class="ruby-keyword">else</span>
|
|
479
|
+
<span class="ruby-ivar">@prob_space</span>.<span class="ruby-identifier">each_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
480
|
+
<span class="ruby-identifier">h</span> <span class="ruby-operator">+=</span> <span class="ruby-ivar">@prob_space</span>[<span class="ruby-identifier">i</span>] * (<span class="ruby-ivar">@density</span>[<span class="ruby-identifier">i</span>]<span class="ruby-operator">**</span>(<span class="ruby-identifier">alpha</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>))
|
|
481
|
+
<span class="ruby-keyword">end</span>
|
|
482
|
+
<span class="ruby-identifier">h</span> = <span class="ruby-value">1.0</span> <span class="ruby-operator">/</span> (<span class="ruby-value">1</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">alpha</span>) * <span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-identifier">h</span>, <span class="ruby-value">2</span>)
|
|
483
|
+
<span class="ruby-keyword">end</span>
|
|
484
|
+
<span class="ruby-identifier">h</span>
|
|
485
|
+
<span class="ruby-keyword">end</span></pre>
|
|
486
|
+
</div><!-- renyi_entropy-source -->
|
|
487
|
+
|
|
488
|
+
</div>
|
|
489
|
+
|
|
490
|
+
|
|
491
|
+
|
|
492
|
+
|
|
493
|
+
</div><!-- renyi_entropy-method -->
|
|
494
|
+
|
|
495
|
+
|
|
496
|
+
<div id="shannon_entropy-method" class="method-detail ">
|
|
497
|
+
<a name="method-i-shannon_entropy"></a>
|
|
498
|
+
|
|
499
|
+
|
|
500
|
+
<div class="method-heading">
|
|
501
|
+
<span class="method-name">shannon_entropy</span><span
|
|
502
|
+
class="method-args">()</span>
|
|
503
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
504
|
+
</div>
|
|
505
|
+
|
|
506
|
+
|
|
507
|
+
<div class="method-description">
|
|
508
|
+
|
|
509
|
+
<p>Computes the Shannon <a href="../Entropy.html">Entropy</a> of the space</p>
|
|
510
|
+
|
|
511
|
+
|
|
512
|
+
|
|
513
|
+
<div class="method-source-code" id="shannon_entropy-source">
|
|
514
|
+
<pre>
|
|
515
|
+
<span class="ruby-comment"># File lib/entropy/metric_space.rb, line 46</span>
|
|
516
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">shannon_entropy</span>
|
|
517
|
+
<span class="ruby-identifier">diversity</span>(<span class="ruby-value">1</span>)
|
|
518
|
+
<span class="ruby-keyword">end</span></pre>
|
|
519
|
+
</div><!-- shannon_entropy-source -->
|
|
520
|
+
|
|
521
|
+
</div>
|
|
522
|
+
|
|
523
|
+
|
|
524
|
+
|
|
525
|
+
|
|
526
|
+
</div><!-- shannon_entropy-method -->
|
|
527
|
+
|
|
528
|
+
|
|
529
|
+
</div><!-- public-instance-method-details -->
|
|
530
|
+
|
|
531
|
+
</div><!-- 5Buntitled-5D -->
|
|
532
|
+
|
|
533
|
+
|
|
534
|
+
</div><!-- documentation -->
|
|
535
|
+
|
|
536
|
+
<div id="validator-badges">
|
|
537
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
538
|
+
<p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
|
|
539
|
+
Rdoc Generator</a> 2</small>.</p>
|
|
540
|
+
</div>
|
|
541
|
+
|
|
542
|
+
</body>
|
|
543
|
+
</html>
|
|
544
|
+
|