scicom 0.3.0-java → 0.4.0-java

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Files changed (155) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +239 -55
  3. data/Rakefile +58 -5
  4. data/config.rb +34 -2
  5. data/doc/Array.html +153 -0
  6. data/doc/Java/OrgRenjinSexp/LogicalArrayVector.html +120 -0
  7. data/doc/Java/OrgRenjinSexp/StringArrayVector.html +133 -0
  8. data/doc/Java/RbScicom/MDDoubleVector.html +133 -0
  9. data/doc/MDArray.html +153 -0
  10. data/doc/MergeObservable.html +347 -0
  11. data/doc/NegRange.html +166 -0
  12. data/doc/PackageManager.html +823 -0
  13. data/doc/PackageManager/ParseXML.html +595 -0
  14. data/doc/Range.html +243 -0
  15. data/doc/Renjin.html +2210 -0
  16. data/doc/Renjin/Attributes.html +401 -0
  17. data/doc/Renjin/Closure.html +181 -0
  18. data/doc/Renjin/ComplexVector.html +557 -0
  19. data/doc/Renjin/DataFrame.html +258 -0
  20. data/doc/Renjin/Environment.html +279 -0
  21. data/doc/Renjin/Function.html +243 -0
  22. data/doc/Renjin/Index.html +628 -0
  23. data/doc/Renjin/List.html +398 -0
  24. data/doc/Renjin/Logical.html +352 -0
  25. data/doc/Renjin/Primitive.html +181 -0
  26. data/doc/Renjin/RBSexp.html +1151 -0
  27. data/doc/Renjin/RubySexp.html +498 -0
  28. data/doc/Renjin/Vector.html +3163 -0
  29. data/doc/RinRuby.html +2079 -0
  30. data/doc/_index.html +365 -0
  31. data/doc/class_list.html +58 -0
  32. data/doc/css/common.css +1 -0
  33. data/doc/css/full_list.css +57 -0
  34. data/doc/css/style.css +339 -0
  35. data/doc/file.README.html +159 -0
  36. data/doc/file_list.html +60 -0
  37. data/doc/frames.html +26 -0
  38. data/doc/index.html +159 -0
  39. data/doc/js/app.js +219 -0
  40. data/doc/js/full_list.js +181 -0
  41. data/doc/js/jquery.js +4 -0
  42. data/doc/method_list.html +939 -0
  43. data/doc/top-level-namespace.html +679 -0
  44. data/lib/JRubyR/attributes.rb +5 -2
  45. data/lib/JRubyR/callback.rb +115 -0
  46. data/lib/JRubyR/environment.rb +0 -1
  47. data/lib/JRubyR/indexed.rb +139 -0
  48. data/lib/JRubyR/list.rb +0 -16
  49. data/lib/JRubyR/logical_value.rb +0 -1
  50. data/lib/JRubyR/rbsexp.rb +20 -131
  51. data/lib/JRubyR/renjin.rb +201 -71
  52. data/lib/JRubyR/vector.rb +16 -15
  53. data/lib/scicom.rb +1 -3
  54. data/target/helper.jar +0 -0
  55. data/test/test_R_interface.rb +1 -1
  56. data/test/test_array.rb +1 -1
  57. data/test/test_assign_mdarray.rb +1 -1
  58. data/test/test_assign_mdarray_2d.rb +1 -1
  59. data/test/test_assign_mdarray_3d.rb +1 -1
  60. data/test/test_attributes.rb +1 -1
  61. data/test/test_basic.rb +7 -5
  62. data/test/test_callback.rb +176 -0
  63. data/test/test_complete.rb +1 -1
  64. data/test/test_creation.rb +29 -5
  65. data/test/test_dataframe.rb +1 -1
  66. data/test/test_factor.rb +1 -1
  67. data/test/test_functions.rb +13 -10
  68. data/test/test_linear_model.rb +1 -1
  69. data/test/test_list.rb +49 -10
  70. data/test/test_matrix.rb +6 -6
  71. data/test/test_operators.rb +1 -1
  72. data/test/test_package.rb +5 -5
  73. data/test/test_vector.rb +13 -7
  74. data/vendor/aether-api-1.0.2.v20150114.jar +0 -0
  75. data/vendor/aether-connector-basic-1.0.2.v20150114.jar +0 -0
  76. data/vendor/aether-impl-1.0.2.v20150114.jar +0 -0
  77. data/vendor/aether-spi-1.0.2.v20150114.jar +0 -0
  78. data/vendor/aether-transport-file-1.0.2.v20150114.jar +0 -0
  79. data/vendor/aether-transport-http-1.0.2.v20150114.jar +0 -0
  80. data/vendor/aether-util-1.0.2.v20150114.jar +0 -0
  81. data/vendor/aopalliance-1.0.jar +0 -0
  82. data/vendor/asm-3.3.1.jar +0 -0
  83. data/vendor/asm-5.0.4.jar +0 -0
  84. data/vendor/asm-commons-5.0.4.jar +0 -0
  85. data/vendor/asm-tree-5.0.4.jar +0 -0
  86. data/vendor/asm-util-5.0.4.jar +0 -0
  87. data/vendor/blas-0.8.jar +0 -0
  88. data/vendor/cdi-api-1.0.jar +0 -0
  89. data/vendor/codemodel-2.6.jar +0 -0
  90. data/vendor/collections-generic-4.01.jar +0 -0
  91. data/vendor/commons-codec-1.6.jar +0 -0
  92. data/vendor/commons-compress-1.4.1.jar +0 -0
  93. data/vendor/commons-logging-1.1.1.jar +0 -0
  94. data/vendor/commons-math-2.2.jar +0 -0
  95. data/vendor/commons-vfs2-2.0.jar +0 -0
  96. data/vendor/datasets-0.8.1891.jar +0 -0
  97. data/vendor/f2jutil-0.8.jar +0 -0
  98. data/vendor/gcc-runtime-0.8.1891.jar +0 -0
  99. data/vendor/grDevices-0.8.1891.jar +0 -0
  100. data/vendor/graphics-0.8.1891.jar +0 -0
  101. data/vendor/guava-17.0.jar +0 -0
  102. data/vendor/httpclient-4.2.6.jar +0 -0
  103. data/vendor/httpcore-4.2.5.jar +0 -0
  104. data/vendor/javax.inject-1.jar +0 -0
  105. data/vendor/jcl-over-slf4j-1.6.2.jar +0 -0
  106. data/vendor/joda-time-2.0.jar +0 -0
  107. data/vendor/jsr250-api-1.0.jar +0 -0
  108. data/vendor/jtransforms-2.4.jar +0 -0
  109. data/vendor/jung-api-2.0.1.jar +0 -0
  110. data/vendor/jung-graph-impl-2.0.1.jar +0 -0
  111. data/vendor/lapack-0.8.jar +0 -0
  112. data/vendor/maven-aether-provider-3.1.0.jar +0 -0
  113. data/vendor/maven-model-3.1.0.jar +0 -0
  114. data/vendor/maven-model-builder-3.1.0.jar +0 -0
  115. data/vendor/maven-repository-metadata-3.1.0.jar +0 -0
  116. data/vendor/maven-scm-api-1.4.jar +0 -0
  117. data/vendor/maven-scm-provider-svn-commons-1.4.jar +0 -0
  118. data/vendor/maven-scm-provider-svnexe-1.4.jar +0 -0
  119. data/vendor/maven-settings-3.1.0.jar +0 -0
  120. data/vendor/maven-settings-builder-3.1.0.jar +0 -0
  121. data/vendor/methods-0.8.1891.jar +0 -0
  122. data/vendor/netlib-java-0.9.3-renjin-patched-2.jar +0 -0
  123. data/vendor/org.eclipse.sisu.inject-0.0.0.M2a.jar +0 -0
  124. data/vendor/org.eclipse.sisu.plexus-0.0.0.M2a.jar +0 -0
  125. data/vendor/plexus-cipher-1.4.jar +0 -0
  126. data/vendor/plexus-classworlds-2.4.jar +0 -0
  127. data/vendor/plexus-component-annotations-1.5.5.jar +0 -0
  128. data/vendor/plexus-interpolation-1.16.jar +0 -0
  129. data/vendor/plexus-sec-dispatcher-1.3.jar +0 -0
  130. data/vendor/plexus-utils-1.5.6.jar +0 -0
  131. data/vendor/plexus-utils-3.0.10.jar +0 -0
  132. data/vendor/regexp-1.3.jar +0 -0
  133. data/vendor/renjin-aether-package-loader-0.8.1891.jar +0 -0
  134. data/vendor/renjin-appl-0.8.1891.jar +0 -0
  135. data/vendor/renjin-core-0.8.1891.jar +0 -0
  136. data/vendor/renjin-gnur-runtime-0.8.1891.jar +0 -0
  137. data/vendor/renjin-script-engine-0.8.1891.jar +0 -0
  138. data/vendor/sisu-guice-3.1.0-no_aop.jar +0 -0
  139. data/vendor/slf4j-api-1.6.2.jar +0 -0
  140. data/vendor/stats-0.8.1891.jar +0 -0
  141. data/vendor/utils-0.8.1891.jar +0 -0
  142. data/vendor/xerbla-0.8.jar +0 -0
  143. data/vendor/xz-1.0.jar +0 -0
  144. data/version.rb +1 -1
  145. metadata +229 -127
  146. data/cran/AppliedPredictiveModeling.jar +0 -0
  147. data/cran/AppliedPredictiveModeling.xml +0 -25
  148. data/cran/AssetPricing.jar +0 -0
  149. data/cran/AssetPricing.xml +0 -25
  150. data/lib/env.rb +0 -12
  151. data/lib/rinruby.rb +0 -795
  152. data/test/env.rb +0 -2
  153. data/test/test_tmp.rb +0 -67
  154. data/vendor/Renjin.pdf +0 -0
  155. data/vendor/renjin-script-engine-0.7.0-RC7-SNAPSHOT-jar-with-dependencies.jar +0 -0
data/doc/_index.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ Documentation by YARD 0.8.7.6
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+ </title>
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+ <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
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+ <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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+ <script type="text/javascript" charset="utf-8">
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+ hasFrames = window.top.frames.main ? true : false;
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+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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+ <body>
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+ </div>
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+ <div id="search">
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+ <a class="full_list_link" id="class_list_link"
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+ href="class_list.html">
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+ Class List
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+ </a>
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+ <a class="full_list_link" id="method_list_link"
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+ href="method_list.html">
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+ Method List
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+ </a>
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+ <a class="full_list_link" id="file_list_link"
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+ File List
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+ </a>
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+ </div>
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+ <div class="clear"></div>
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+ </div>
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+
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1 class="noborder title">Documentation by YARD 0.8.7.6</h1>
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+ <div id="listing">
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+ <h1 class="alphaindex">Alphabetic Index</h1>
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+
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+ <h2>File Listing</h2>
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+ <ul id="files" class="index_inline_list">
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+ <li class="r1"><a href="index.html" title="README">README</a></li>
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+ <div class="clear"></div>
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+ <h2>Namespace Listing A-Z</h2>
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+ <ul class="toplevel"><li><span class='object_link'><a href="top-level-namespace.html" title="Top Level Namespace (root)">Top Level Namespace</a></span></li></ul>
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+ <table>
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+ <tr>
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+ <td valign='top' width="33%">
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+ <ul id="alpha_A" class="alpha">
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+ <li class="letter">A</li>
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+ <ul>
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+ <li>
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+ <span class='object_link'><a href="Array.html" title="Array (class)">Array</a></span>
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+ </li>
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+ <li>
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+ <span class='object_link'><a href="Renjin/Attributes.html" title="Renjin::Attributes (class)">Attributes</a></span>
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+ </li>
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+ </ul>
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+ <li class="letter">C</li>
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+ <ul>
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+ <li>
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+ <span class='object_link'><a href="Renjin/Closure.html" title="Renjin::Closure (class)">Closure</a></span>
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+ <small>(Renjin)</small>
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+
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+ </li>
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+
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+ <li>
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+ <span class='object_link'><a href="Renjin/ComplexVector.html" title="Renjin::ComplexVector (class)">ComplexVector</a></span>
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+ <small>(Renjin)</small>
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+ </li>
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+ </ul>
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+ </ul>
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+ <ul id="alpha_D" class="alpha">
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+ <span class='object_link'><a href="Renjin/DataFrame.html" title="Renjin::DataFrame (class)">DataFrame</a></span>
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+ <small>(Renjin)</small>
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+ </li>
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+ </ul>
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+ <span class='object_link'><a href="Renjin/Environment.html" title="Renjin::Environment (class)">Environment</a></span>
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+ </li>
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+ <span class='object_link'><a href="Renjin/List.html" title="Renjin::List (class)">List</a></span>
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+ </li>
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+ <li>
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+ <span class='object_link'><a href="Renjin/Logical.html" title="Renjin::Logical (class)">Logical</a></span>
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+ </li>
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+ <li>
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+ <span class='object_link'><a href="Java/OrgRenjinSexp/LogicalArrayVector.html" title="Java::OrgRenjinSexp::LogicalArrayVector (class)">LogicalArrayVector</a></span>
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+ <small>(Java::OrgRenjinSexp)</small>
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+ </li>
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+ </ul>
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+ </ul>
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+ <li class="letter">M</li>
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+ <ul>
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+ <span class='object_link'><a href="MDArray.html" title="MDArray (class)">MDArray</a></span>
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+ </li>
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+ <li>
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+ <span class='object_link'><a href="Java/RbScicom/MDDoubleVector.html" title="Java::RbScicom::MDDoubleVector (class)">MDDoubleVector</a></span>
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+ <small>(Java::RbScicom)</small>
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+ </li>
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+ <span class='object_link'><a href="MergeObservable.html" title="MergeObservable (module)">MergeObservable</a></span>
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+ <span class='object_link'><a href="PackageManager/ParseXML.html" title="PackageManager::ParseXML (class)">ParseXML</a></span>
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+ </li>
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+ <li>
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+ <span class='object_link'><a href="Renjin/Primitive.html" title="Renjin::Primitive (class)">Primitive</a></span>
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+ <small>(Renjin)</small>
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+ </li>
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+ </ul>
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+ </ul>
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+ <ul id="alpha_R" class="alpha">
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+ <li class="letter">R</li>
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+ <ul>
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+ <li>
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+ <span class='object_link'><a href="Renjin/RBSexp.html" title="Renjin::RBSexp (module)">RBSexp</a></span>
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+ <small>(Renjin)</small>
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+ </li>
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+ <span class='object_link'><a href="Range.html" title="Range (class)">Range</a></span>
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+ <span class='object_link'><a href="Renjin.html" title="Renjin (class)">Renjin</a></span>
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+ <span class='object_link'><a href="RinRuby.html" title="RinRuby (class)">RinRuby</a></span>
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+ <span class='object_link'><a href="Renjin/RubySexp.html" title="Renjin::RubySexp (class)">RubySexp</a></span>
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+ <span class='object_link'><a href="Java/OrgRenjinSexp/StringArrayVector.html" title="Java::OrgRenjinSexp::StringArrayVector (class)">StringArrayVector</a></span>
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+ <small>(Java::OrgRenjinSexp)</small>
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+ <span class='object_link'><a href="Renjin/Vector.html" title="Renjin::Vector (class)">Vector</a></span>
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+ </li>
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+ </ul>
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+ </table>
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+ </div>
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+ </div>
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+ <div id="footer">
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+ Generated on Tue Jul 14 18:12:20 2015 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.8.7.6 (ruby-1.9.3).
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+ </div>
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+ </body>
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+ </html>
data/doc/class_list.html ADDED
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
6
+
7
+ <link rel="stylesheet" href="css/full_list.css" type="text/css" media="screen" charset="utf-8" />
8
+
9
+ <link rel="stylesheet" href="css/common.css" type="text/css" media="screen" charset="utf-8" />
10
+
11
+
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+
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+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
14
+
15
+ <script type="text/javascript" charset="utf-8" src="js/full_list.js"></script>
16
+
17
+
18
+ <title>Class List</title>
19
+ <base id="base_target" target="_parent" />
20
+ </head>
21
+ <body>
22
+ <script type="text/javascript" charset="utf-8">
23
+ var hasFrames = false;
24
+ try {
25
+ hasFrames = window.top.frames.main ? true : false;
26
+ } catch (e) { }
27
+ if (hasFrames) {
28
+ document.getElementById('base_target').target = 'main';
29
+ document.body.className = 'frames';
30
+ }
31
+ </script>
32
+ <div id="content">
33
+ <h1 id="full_list_header">Class List</h1>
34
+ <div id="nav">
35
+
36
+ <span><a target="_self" href="class_list.html">
37
+ Classes
38
+ </a></span>
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+
40
+ <span><a target="_self" href="method_list.html">
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+ Methods
42
+ </a></span>
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+
44
+ <span><a target="_self" href="file_list.html">
45
+ Files
46
+ </a></span>
47
+
48
+ </div>
49
+ <div id="search">Search: <input type="text" /></div>
50
+
51
+ <ul id="full_list" class="class">
52
+ <li><span class='object_link'><a href="top-level-namespace.html" title="Top Level Namespace (root)">Top Level Namespace</a></span></li>
53
+ <li><span class='object_link'><a href="Array.html" title="Array (class)">Array</a></span> &lt; Object<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="Java/OrgRenjinSexp/LogicalArrayVector.html" title="Java::OrgRenjinSexp::LogicalArrayVector (class)">Java::OrgRenjinSexp::LogicalArrayVector</a></span> &lt; Object<small class='search_info'>Java::OrgRenjinSexp</small></li><li><span class='object_link'><a href="Java/OrgRenjinSexp/StringArrayVector.html" title="Java::OrgRenjinSexp::StringArrayVector (class)">Java::OrgRenjinSexp::StringArrayVector</a></span> &lt; Object<small class='search_info'>Java::OrgRenjinSexp</small></li><li><span class='object_link'><a href="Java/RbScicom/MDDoubleVector.html" title="Java::RbScicom::MDDoubleVector (class)">Java::RbScicom::MDDoubleVector</a></span> &lt; Object<small class='search_info'>Java::RbScicom</small></li><li><span class='object_link'><a href="MDArray.html" title="MDArray (class)">MDArray</a></span> &lt; Object<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="MergeObservable.html" title="MergeObservable (module)">MergeObservable</a></span><small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="NegRange.html" title="NegRange (class)">NegRange</a></span> &lt; Range<small class='search_info'>Top Level Namespace</small></li><li><a class='toggle'></a> <span class='object_link'><a href="PackageManager.html" title="PackageManager (class)">PackageManager</a></span> &lt; Object<small class='search_info'>Top Level Namespace</small></li><ul><li><span class='object_link'><a href="PackageManager/ParseXML.html" title="PackageManager::ParseXML (class)">ParseXML</a></span> &lt; Object<small class='search_info'>PackageManager</small></li></ul><li><span class='object_link'><a href="Range.html" title="Range (class)">Range</a></span> &lt; Object<small class='search_info'>Top Level Namespace</small></li><li><a class='toggle'></a> <span class='object_link'><a href="Renjin.html" title="Renjin (class)">Renjin</a></span> &lt; Object<small class='search_info'>Top Level Namespace</small></li><ul><li><span class='object_link'><a href="Renjin/Attributes.html" title="Renjin::Attributes (class)">Attributes</a></span> &lt; Object<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/Closure.html" title="Renjin::Closure (class)">Closure</a></span> &lt; Function<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/ComplexVector.html" title="Renjin::ComplexVector (class)">ComplexVector</a></span> &lt; Vector<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/DataFrame.html" title="Renjin::DataFrame (class)">DataFrame</a></span> &lt; List<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/Environment.html" title="Renjin::Environment (class)">Environment</a></span> &lt; RubySexp<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/Function.html" title="Renjin::Function (class)">Function</a></span> &lt; RubySexp<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/Index.html" title="Renjin::Index (module)">Index</a></span><small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/List.html" title="Renjin::List (class)">List</a></span> &lt; RubySexp<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/Logical.html" title="Renjin::Logical (class)">Logical</a></span> &lt; Vector<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/Primitive.html" title="Renjin::Primitive (class)">Primitive</a></span> &lt; Function<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/RBSexp.html" title="Renjin::RBSexp (module)">RBSexp</a></span><small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/RubySexp.html" title="Renjin::RubySexp (class)">RubySexp</a></span> &lt; Object<small class='search_info'>Renjin</small></li><li><span class='object_link'><a href="Renjin/Vector.html" title="Renjin::Vector (class)">Vector</a></span> &lt; RubySexp<small class='search_info'>Renjin</small></li></ul><li><span class='object_link'><a href="RinRuby.html" title="RinRuby (class)">RinRuby</a></span> &lt; Object<small class='search_info'>Top Level Namespace</small></li>
54
+
55
+ </ul>
56
+ </div>
57
+ </body>
58
+ </html>
data/doc/css/common.css ADDED
@@ -0,0 +1 @@
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+ margin: 0;
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+ height: 101%;
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+ overflow-x: hidden;
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+ #full_list ul { padding: 0; }
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+ #noresults { padding: 7px 12px; }
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+ #content.insearch #noresults { margin-left: 7px; }
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+ ul.collapsed ul, ul.collapsed li { display: none; }
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+ ul.collapsed.search_uncollapsed { display: block; }
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+ ul.collapsed.search_uncollapsed li { display: list-item; }
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+ li.clicked a.toggle { opacity: 0.5; background-position: bottom right; }
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+ li.collapsed.clicked a.toggle { background-position: top right; }
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+ #nav { margin-left: 10px; font-size: 0.9em; display: none; color: #aaa; }
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+ #nav a:link, #nav a:visited { color: #358; }
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+ #nav a:hover { background: transparent; color: #5af; }
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+ .frames #nav span:after { content: ' | '; }
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+ .frames #nav span:last-child:after { content: ''; }
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+ .frames #content h1 { margin-top: 0; }
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+ .frames li { white-space: nowrap; cursor: normal; }
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+ .frames li small:before { content: ""; }
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+ .frames li small:after { content: ""; }
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+ .frames li small.search_info { display: none; }
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+ .frames #search { width: 170px; position: static; margin: 3px; margin-left: 10px; font-size: 0.9em; color: #888; padding-left: 0; padding-right: 24px; }
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+ .frames #content.insearch #search { background-position: center right; }
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+ .frames #search input { width: 110px; }
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+ .frames #nav { display: block; }
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+
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+ #full_list.insearch li { display: none; }
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+ #full_list.insearch li.found { display: list-item; padding-left: 10px; }
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+ #full_list.insearch li a.toggle { display: none; }
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+ #full_list.insearch li small.search_info { display: block; }