scicom 0.3.0-java → 0.4.0-java

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  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/file_list.html ADDED
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+ <div id="nav">
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+ Classes
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+ Methods
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+ </a></span>
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+ Files
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+ </a></span>
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+ </div>
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+ <div id="search">Search: <input type="text" /></div>
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+ <ul id="full_list" class="file">
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+
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+
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+ <li class="r1"><span class="object_link"><a href="index.html" title="README">README</a></a></li>
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+
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+
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+ </ul>
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+ </div>
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+ </body>
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+ &mdash; Documentation by YARD 0.8.7.6
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+ </title>
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ <a class="full_list_link" id="method_list_link"
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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"><div id='filecontents'>
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+ <h1 id="label-Announcement">Announcement</h1>
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+
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+ <p>SciCom (Scientific Computing) for Ruby brings the power of R to the Ruby
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+ community. SciCom is based on Renjin, a JVM-based interpreter for the R
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+ language for statistical computing.</p>
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+
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+ <h2 id="label-R+on+the+JVM">R on the JVM</h2>
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+
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+ <p>Over the past two decades, the R language for statistical computing has
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+ emerged as the de facto standard for analysts, statisticians, and
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+ scientists. Today, a wide range of enterprises – from pharmaceuticals to
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+ insurance – depend on R for key business uses. Renjin is a new
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+ implementation of the R language and environment for the Java Virtual
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+ Machine (JVM), whose goal is to enable transparent analysis of big data
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+ sets and seamless integration with other enterprise systems such as
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+ databases and application servers.</p>
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+
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+ <p>Renjin is still under development, but it is already being used in
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+ production for a number of client projects, and supports most CRAN
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+ packages, including some with C/Fortran dependencies.</p>
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+
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+ <h2 id="label-SciCom+and+Renjin">SciCom and Renjin</h2>
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+
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+ <p>SciCom integrates with Renjin and allows the use of R inside a Ruby script.
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+ In a sense, SciCom is similar to other solutions such as RinRuby, Rpy2,
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+ PipeR, etc. However, since SciCom and Renjin both target the JVM there is
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+ no need to integrate both solutions and there is no need to send data
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+ between Ruby and R, as it all resides in the same JVM. Further,
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+ installation of SciCom does not require the installation of GNU R; Renjin
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+ is the interpreter and comes with SciCom. Finally, although SciCom provides
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+ a basic interface to Renjin similar to RinRuby, a much tighter integration
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+ is also possible.</p>
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+
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+ <h2 id="label-SciCom+and+Renjin+Limitations">SciCom and Renjin Limitations</h2>
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+
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+ <p>Renjin is in development and still has some limitations</p>
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+ <ul><li>
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+ <p>Renjin does not allow dynamic loading of libaries. My understanding is that
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+ Renjin developers are actually working on a new version on which loading
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+ of libraries will be possible.</p>
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+ </li><li>
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+ <p>Renjin does not implement any of the graphical libaries such as plot or
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+ ggplot. We hope that this limitation will be solved not by implementing
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+ those libraries but by the use of Ruby libraries from SciRuby such as
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+ NyaPlot (<a
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+ href="https://github.com/domitry/nyaplot">github.com/domitry/nyaplot</a>)
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+ or daru (<a
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+ href="https://github.com/v0dro/daru">github.com/v0dro/daru</a>).</p>
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+ </li></ul>
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+
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+ <h1 id="label-What%C2%B4s+new%3A">What´s new:</h1>
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+
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+ <p>This version includes integration of MDArray and SciCom.</p>
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+
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+ <h1 id="label-SciCom+installation+and+download%3A">SciCom installation and download:</h1>
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+ <ul><li>
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+ <p>Install Jruby</p>
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+ </li><li>
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+ <p>jruby –S gem install scicom</p>
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+ </li></ul>
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+
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+ <h1 id="label-SciCom+Homepages%3A">SciCom Homepages:</h1>
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+ <ul><li>
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+ <p><a href="http://rubygems.org/gems/scicom">rubygems.org/gems/scicom</a></p>
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+ </li><li>
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+ <p><a
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+ href="https://github.com/rbotafogo/scicom/wiki">github.com/rbotafogo/scicom/wiki</a></p>
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+ </li></ul>
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+
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+ <h1 id="label-Contributors%3A">Contributors:</h1>
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+
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+ <p>Contributors are welcome.</p>
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+
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+ <h1 id="label-SciCom+History%3A">SciCom History:</h1>
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+ <ul><li>
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+ <p>30/Dec/2014: Version 0.2.3 - Integration with MDArray</p>
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+ </li><li>
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+ <p>19/Nov/2014: Version 0.2.2 - Printing in Jirb</p>
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+ </li><li>
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+ <p>17/Nov/2014: Version 0.2.1 - Added MDArray dependency</p>
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+ </li><li>
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+ <p>17/Nov/2014: Version 0.2.0 - Most R functionality available to SciCom</p>
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+ </li><li>
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+ <p>21/Jul/2014: Version 0.0.1 - Initial release</p>
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+ </li></ul>
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+ </div></div>
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+
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+ <div id="footer">
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+ Generated on Tue Jul 14 18:12:21 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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+
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+ </body>
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+ </html>
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+ return false;
55
+ });
56
+ }
57
+
58
+ function toggleSearchFrame(id, link) {
59
+ var frame = $('#search_frame');
60
+ $('#search a').removeClass('active').addClass('inactive');
61
+ if (frame.attr('src') == link && frame.css('display') != "none") {
62
+ frame.slideUp(100);
63
+ $('#search a').removeClass('active inactive');
64
+ }
65
+ else {
66
+ $(id).addClass('active').removeClass('inactive');
67
+ frame.attr('src', link).slideDown(100);
68
+ }
69
+ }
70
+
71
+ function linkSummaries() {
72
+ $('.summary_signature').click(function() {
73
+ document.location = $(this).find('a').attr('href');
74
+ });
75
+ }
76
+
77
+ function framesInit() {
78
+ if (hasFrames) {
79
+ document.body.className = 'frames';
80
+ $('#menu .noframes a').attr('href', document.location);
81
+ try {
82
+ window.top.document.title = $('html head title').text();
83
+ } catch(error) {
84
+ // some browsers will not allow this when serving from file://
85
+ // but we don't want to stop the world.
86
+ }
87
+ }
88
+ else {
89
+ $('#menu .noframes a').text('frames').attr('href', framesUrl);
90
+ }
91
+ }
92
+
93
+ function keyboardShortcuts() {
94
+ if (window.top.frames.main) return;
95
+ $(document).keypress(function(evt) {
96
+ if (evt.altKey || evt.ctrlKey || evt.metaKey || evt.shiftKey) return;
97
+ if (typeof evt.target !== "undefined" &&
98
+ (evt.target.nodeName == "INPUT" ||
99
+ evt.target.nodeName == "TEXTAREA")) return;
100
+ switch (evt.charCode) {
101
+ case 67: case 99: $('#class_list_link').click(); break; // 'c'
102
+ case 77: case 109: $('#method_list_link').click(); break; // 'm'
103
+ case 70: case 102: $('#file_list_link').click(); break; // 'f'
104
+ default: break;
105
+ }
106
+ });
107
+ }
108
+
109
+ function summaryToggle() {
110
+ $('.summary_toggle').click(function() {
111
+ if (localStorage) {
112
+ localStorage.summaryCollapsed = $(this).text();
113
+ }
114
+ $('.summary_toggle').each(function() {
115
+ $(this).text($(this).text() == "collapse" ? "expand" : "collapse");
116
+ var next = $(this).parent().parent().nextAll('ul.summary').first();
117
+ if (next.hasClass('compact')) {
118
+ next.toggle();
119
+ next.nextAll('ul.summary').first().toggle();
120
+ }
121
+ else if (next.hasClass('summary')) {
122
+ var list = $('<ul class="summary compact" />');
123
+ list.html(next.html());
124
+ list.find('.summary_desc, .note').remove();
125
+ list.find('a').each(function() {
126
+ $(this).html($(this).find('strong').html());
127
+ $(this).parent().html($(this)[0].outerHTML);
128
+ });
129
+ next.before(list);
130
+ next.toggle();
131
+ }
132
+ });
133
+ return false;
134
+ });
135
+ if (localStorage) {
136
+ if (localStorage.summaryCollapsed == "collapse") {
137
+ $('.summary_toggle').first().click();
138
+ }
139
+ else localStorage.summaryCollapsed = "expand";
140
+ }
141
+ }
142
+
143
+ function fixOutsideWorldLinks() {
144
+ $('a').each(function() {
145
+ if (window.location.host != this.host) this.target = '_parent';
146
+ });
147
+ }
148
+
149
+ function generateTOC() {
150
+ if ($('#filecontents').length === 0) return;
151
+ var _toc = $('<ol class="top"></ol>');
152
+ var show = false;
153
+ var toc = _toc;
154
+ var counter = 0;
155
+ var tags = ['h2', 'h3', 'h4', 'h5', 'h6'];
156
+ var i;
157
+ if ($('#filecontents h1').length > 1) tags.unshift('h1');
158
+ for (i = 0; i < tags.length; i++) { tags[i] = '#filecontents ' + tags[i]; }
159
+ var lastTag = parseInt(tags[0][1], 10);
160
+ $(tags.join(', ')).each(function() {
161
+ if ($(this).parents('.method_details .docstring').length != 0) return;
162
+ if (this.id == "filecontents") return;
163
+ show = true;
164
+ var thisTag = parseInt(this.tagName[1], 10);
165
+ if (this.id.length === 0) {
166
+ var proposedId = $(this).attr('toc-id');
167
+ if (typeof(proposedId) != "undefined") this.id = proposedId;
168
+ else {
169
+ var proposedId = $(this).text().replace(/[^a-z0-9-]/ig, '_');
170
+ if ($('#' + proposedId).length > 0) { proposedId += counter; counter++; }
171
+ this.id = proposedId;
172
+ }
173
+ }
174
+ if (thisTag > lastTag) {
175
+ for (i = 0; i < thisTag - lastTag; i++) {
176
+ var tmp = $('<ol/>'); toc.append(tmp); toc = tmp;
177
+ }
178
+ }
179
+ if (thisTag < lastTag) {
180
+ for (i = 0; i < lastTag - thisTag; i++) toc = toc.parent();
181
+ }
182
+ var title = $(this).attr('toc-title');
183
+ if (typeof(title) == "undefined") title = $(this).text();
184
+ toc.append('<li><a href="#' + this.id + '">' + title + '</a></li>');
185
+ lastTag = thisTag;
186
+ });
187
+ if (!show) return;
188
+ html = '<div id="toc"><p class="title"><a class="hide_toc" href="#"><strong>Table of Contents</strong></a> <small>(<a href="#" class="float_toc">left</a>)</small></p></div>';
189
+ $('#content').prepend(html);
190
+ $('#toc').append(_toc);
191
+ $('#toc .hide_toc').toggle(function() {
192
+ $('#toc .top').slideUp('fast');
193
+ $('#toc').toggleClass('hidden');
194
+ $('#toc .title small').toggle();
195
+ }, function() {
196
+ $('#toc .top').slideDown('fast');
197
+ $('#toc').toggleClass('hidden');
198
+ $('#toc .title small').toggle();
199
+ });
200
+ $('#toc .float_toc').toggle(function() {
201
+ $(this).text('float');
202
+ $('#toc').toggleClass('nofloat');
203
+ }, function() {
204
+ $(this).text('left');
205
+ $('#toc').toggleClass('nofloat');
206
+ });
207
+ }
208
+
209
+ $(framesInit);
210
+ $(createSourceLinks);
211
+ $(createDefineLinks);
212
+ $(createFullTreeLinks);
213
+ $(fixBoxInfoHeights);
214
+ $(searchFrameLinks);
215
+ $(linkSummaries);
216
+ $(keyboardShortcuts);
217
+ $(summaryToggle);
218
+ $(fixOutsideWorldLinks);
219
+ $(generateTOC);