scicom 0.2.3.1-java → 0.3.0-java

data/lib/JRubyR/renjin.rb

@@ -25,6 +25,7 @@ require 'java'
 require 'securerandom'
 
 require_relative 'rbsexp'
+require_relative 'package'
 # require_relative 'index'
 
 
@@ -97,7 +98,8 @@ class Renjin
 
     factory = Java::JavaxScript.ScriptEngineManager.new()
     @engine = factory.getEngineByName("Renjin")
-    
+    super
+
   end
 
   #----------------------------------------------------------------------------------------
@@ -394,6 +396,31 @@ class Renjin
 
   end
 
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def install__package(name)
+
+    pm = PackageManager.new
+    pm.load_package(name)
+
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def library(package)
+
+    Dir.chdir(SciCom.cran_dir)
+    filename = SciCom.cran_dir + "/#{package}.jar"
+
+    require filename
+    eval("library(#{package})")
+
+  end
+
   #----------------------------------------------------------------------------------------
   # Builds a Renjin vector from an MDArray. Should be private, but public for testing.
   #----------------------------------------------------------------------------------------

data/test/test_dataframe.rb

@@ -163,7 +163,7 @@ class SciComTest < Test::Unit::TestCase
       # engine, ..., etc.
       mtcars[24, nil].pp
 
-      # To retrieve more than one rows, we use a numeric index vector.
+      # To retrieve more than one row, we use a numeric index vector.
       mtcars[R.c(3, 24), nil].pp 
 
       # Name Indexing
@@ -213,7 +213,6 @@ class SciComTest < Test::Unit::TestCase
       df.colnames.pp
       df.colnames(prefix: "sc").pp
 
-
       # Renjin allows changes to variable properties
       R.eval("colnames(#{df.r}) = c('name', 'age', 'height', 'weigth', 'race', 'SAT')")
       R.eval("print(colnames(#{df.r}))")

data/test/test_linear_model.rb

@@ -46,6 +46,9 @@ class SciComTest < Test::Unit::TestCase
 
         # This dataset comes from Baseball-Reference.com.
         baseball = R.read__csv("baseball.csv")
+        # convert the second column of dataframe 'baseball' to a Ruby vector
+        # arr = baseball[[2]].get
+        # arr.print
         # Lets look at the data available for Momeyball.
         # (baseball.Year < R.d(2002)).pp
         moneyball = baseball.subset(baseball.Year < 2002)

data/test/test_list.rb

@@ -54,7 +54,7 @@ class SciComTest < Test::Unit::TestCase
     #
     #--------------------------------------------------------------------------------------
 
-    should "access lists elements with indexing [] and [[]]" do
+    should "access list elements with indexing [] and [[]]" do
       
       # get the first element of the list, usign indexing.  
       # Both [] and [[]] indexing can be used with the same R rules. 

data/test/test_package.rb

@@ -0,0 +1,66 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'rubygems'
+require "test/unit"
+require 'shoulda'
+
+require 'env'
+require 'scicom'
+
+class SciComTest < Test::Unit::TestCase
+
+  context "R environment" do
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    setup do 
+      
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    should "download the proper package" do
+
+      R.install__package("AssetPricing")
+      R.library("AssetPricing")
+
+      R.install__package("AppliedPredictiveModeling")
+      R.library("AppliedPredictiveModeling")
+      
+      ### Section 3.1 Case Study: Cell Segmentation in High-Content Screening
+      
+      R.data('segmentationOriginal')
+      seg = R.segmentationOriginal
+      segTrain = seg.subset(Case: "Train")
+      segTrainX = segTrain[true, -(1..3)]
+      segTrainClass = segTrain.Class
+      segTrainClass.pp
+
+    end
+
+  end
+
+end

data/test/test_tmp.rb

@@ -55,11 +55,11 @@ class SciComTest < Test::Unit::TestCase
     #--------------------------------------------------------------------------------------
 
     should "assign to a character vector" do
-
-      h = {f: :colnames, index: [[1]]}
-      p h[:f]
-      p h[:index]
-
+      
+      R.eval("r.i = 10L")
+      R.eval("print(r.i)")  # will print the R int vector
+      p r.i                 # results in an error in the Ruby script
+      
     end
 
   end

data/test/test_vector.rb

@@ -65,6 +65,9 @@ class SciComTest < Test::Unit::TestCase
       assert_equal(4, log_var.length)
       assert_equal(true, log_var.logical?)
 
+      str_var = R.c("hello there")
+      str_var.pp
+
       # string vector: create string (character) vectors
       chr_var = R.c("these are", "some strings")
       assert_equal("character", chr_var.typeof.gz)

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "scicom"
-$version="0.2.3.1"
+$version="0.3.0"

metadata

@@ -1,52 +1,84 @@
 --- !ruby/object:Gem::Specification
 name: scicom
 version: !ruby/object:Gem::Version
-  version: 0.2.3.1
+  version: 0.3.0
 platform: java
 authors:
 - Rodrigo Botafogo
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2015-01-02 00:00:00.000000000 Z
+date: 2015-03-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '3.5'
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '3.5'
   prerelease: false
   type: :runtime
 - !ruby/object:Gem::Dependency
   name: mdarray
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.5'
     - - '>='
       - !ruby/object:Gem::Version
         version: 0.5.5.2
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.5'
     - - '>='
       - !ruby/object:Gem::Version
         version: 0.5.5.2
   prerelease: false
   type: :runtime
+- !ruby/object:Gem::Dependency
+  name: state_machine
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+  prerelease: false
+  type: :runtime
 - !ruby/object:Gem::Dependency
   name: simplecov
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.7'
     - - '>='
       - !ruby/object:Gem::Version
         version: 0.7.1
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.7'
     - - '>='
       - !ruby/object:Gem::Version
         version: 0.7.1
@@ -56,11 +88,17 @@ dependencies:
   name: yard
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.8'
     - - '>='
       - !ruby/object:Gem::Version
         version: 0.8.5.2
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.8'
     - - '>='
       - !ruby/object:Gem::Version
         version: 0.8.5.2
@@ -70,11 +108,17 @@ dependencies:
   name: kramdown
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
     - - '>='
       - !ruby/object:Gem::Version
         version: 1.0.1
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
     - - '>='
       - !ruby/object:Gem::Version
         version: 1.0.1
@@ -118,7 +162,9 @@ files:
 - lib/JRubyR/logical_value.rb
 - lib/JRubyR/environment.rb
 - lib/JRubyR/ruby_classes.rb
+- lib/JRubyR/package.rb
 - lib/JRubyR/function.rb
+- lib/JRubyR/download_url_to_file.rb
 - lib/JRubyR/dataframe.rb
 - test/env.rb
 - test/test_tmp.rb
@@ -146,15 +192,27 @@ files:
 - test/test_assign_mdarray_2d.rb
 - test/test_assign_mdarray_3d.rb
 - test/test_assign_mdarray_4d.rb
+- test/test_package.rb
 - test/test_list.rb
 - test/baseball.csv
 - doc/PypeR.pdf
 - doc/The R interface.docx
 - doc/Stat 133 Class Notes (Phil Spector).pdf
-- vendor/renjin-script-engine-0.7.0-RC7-SNAPSHOT-jar-with-dependencies.jar
+- doc/SciCom.tex~
+- doc/hearder.tex~
+- doc/hearder.tex
+- doc/hearder.log
+- doc/hearder.aux
+- doc/hearder.pdf
+- doc/SciCom.tex
+- doc/hearder.synctex.gz
 - vendor/Renjin.pdf
+- vendor/renjin-script-engine-0.7.0-RC7-SNAPSHOT-jar-with-dependencies.jar
 - target/helper.jar
-- README.md~
+- cran/AssetPricing.xml
+- cran/AssetPricing.jar
+- cran/AppliedPredictiveModeling.xml
+- cran/AppliedPredictiveModeling.jar
 - README.md
 - LICENSE.txt
 homepage: http://github.com/rbotafogo/scicom/wiki
@@ -208,4 +266,5 @@ test_files:
 - test/test_assign_mdarray_2d.rb
 - test/test_assign_mdarray_3d.rb
 - test/test_assign_mdarray_4d.rb
+- test/test_package.rb
 - test/test_list.rb

data/README.md~

@@ -1,290 +0,0 @@
-Announcement
-============
-
-MDArray version 0.5.5 has Just been released. MDArray is a multi dimensional array implemented 
-for JRuby inspired by NumPy (www.numpy.org) and Masahiro Tanaka´s Narray (narray.rubyforge.org).  
-MDArray stands on the shoulders of Java-NetCDF and Parallel Colt.  At this point MDArray has 
-libraries for linear algebra, mathematical, trigonometric and descriptive statistics methods.
-
-NetCDF-Java Library is a Java interface to NetCDF files, as well as to many other types of 
-scientific data formats.  It is developed and distributed by Unidata (http://www.unidata.ucar.edu).
- 
-Parallel Colt (https://sites.google.com/site/piotrwendykier/software/parallelcolt is a
- multithreaded version of Colt (http://acs.lbl.gov/software/colt/).  Colt provides a set of 
-Open Source Libraries for High Performance Scientific and Technical Computing in Java. 
-Scientific and technical computing is characterized by demanding problem sizes and a need for 
-high performance at reasonably small memory footprint.
-
-
-What´s new:
-===========
-
-Class MDMatrix and Linear Algebra Methods
------------------------------------------
-
-This version of MDArray introduces class MDMatrix.  MDMatrix is a matrix class wrapping many 
-linear algebra methods from Parallel Colt (see below).  MDMatrix support only the following 
-types: i) int; ii) long; iii) float and iv) double.
-
-Differently from other libraries, in which matrix is a subclass of array, MDMatrix is a 
-twin class of MDArray.  MDMatrix is a twin class of MDArray as every time an MDMatrix is 
-instantiated, an MDArray class is also instantiated.  In reality, there is only one backing 
-store that can be viewed by either MDMatrix or MDArray. 
- 
-Creation of MDMatrix follows the same API as MDArray API.  For instance, creating a double 
-square matrix of size 5 x 5 can be done by:
- 
-    matrix = MDMatrix.double([5, 5], [2.0, 0.0, 8.0, 6.0, 0.0,\
-                                      1.0, 6.0, 0.0, 1.0, 7.0,\
-                                      5.0, 0.0, 7.0, 4.0, 0.0,\
-                                      7.0, 0.0, 8.0, 5.0, 0.0,\
-                                      0.0, 10.0, 0.0, 0.0, 7.0])
-
-Creating an int matrix filled with zero can be done by:
-
-    matrix = MDMatrix.int([4, 3])
-
-MDMatrix also supports creation based on methods such as fromfunction, linspace, init_with, 
-arange, typed_arange and ones:
-
-
-    array = MDArray.typed_arange("double", 0, 15)
-    array = MDMatrix.fromfunction("double", [4, 4]) { |x, y| x + y }
-
-An MDMatrix can also be created from an MDArray as follows:
-
-    d2 = MDArray.typed_arange("double", 0, 15)
-    double_matrix = MDMatrix.from_mdarray(d2)
-
-An MDMatrix can only be created from MDArrays of one, two or three dimensions.  However, 
-one can take a view from an MDArray to create an MDMatrix, as long as the view is at most 
-three dimensional:
-
-    # Instantiate an MDArray and shape it with 4 dimensions
-    > d1 = MDArray.typed_arange("double", 0, 420)
-    > d1.reshape!([5, 4, 3, 7])
-    # slice the array, getting a three dimensional array and from that, make a matrix
-    > matrix = MDMatrix.from_mdarray(d1.slice(0, 0))
-    # get a region from the array, with the first two dimensions of size 0, reduce it to a
-    # size two array and then build a two dimensional matrix
-    > matrix = MDMatrix.from_mdarray(d1.region(:spec => "0:0, 0:0, 0:2, 0:6").reduce)
-
-printing the above two dimensional matrix gives us:
-
-    > matrix.print
-    3 x 7 matrix
-    0,00000 1,00000 2,00000 3,00000 4,00000 5,00000 6,00000
-    7,00000 8,00000 9,00000 10,0000 11,0000 12,0000 13,0000
-    14,0000 15,0000 16,0000 17,0000 18,0000 19,0000 20,0000
-
-Every MDMatrix instance has a twin MDArray instance that uses the same backing store.  This 
-allows the user to treat the data as either a matrix or an array and use methods either from 
-matrix or array.  The above matrix can be printed as an array:
-
-
-    > matrix.mdarray.print
-    [[0.00 1.00 2.00 3.00 4.00 5.00 6.00]
-     [7.00 8.00 9.00 10.00 11.00 12.00 13.00]
-     [14.00 15.00 16.00 17.00 18.00 19.00 20.00]]
-
-With an MDMatrix, many linear algebra methods can be easily calculated:
-
-    # basic operations on matrix can be done, such as, ‘+’, ‘-‘, ´*’, ‘/’
-    # make a 4 x 4 matrix and fill it with ´double´ 2.5
-    > a = MDMatrix.double([4, 4])
-    > a.fill(2.5)
-    > make a 4 x 4 matrix ´b´ from a given function (block)
-    > b = MDMatrix.fromfunction("double", [4, 4]) { |x, y| x + y }
-    # add both matrices
-    > c = a + b
-    # multiply by scalar
-    > c = a * 2
-    # divide two matrices.  Matrix ´b´ has to be non-singular, otherwise an exception is
-    # raised.
-    # generate a non-singular matrix from a given matrix
-    > b.generate_non_singular!
-    > c = a / b
-
-Linear algebra methods:
-
-    # create a matrix with the given data
-    > pos = MDArray.double([3, 3], [4, 12, -16, 12, 37, -43, -16, -43, 98])
-    > matrix = MDMatrix.from_mdarray(pos)
-    # Cholesky decomposition from wikipedia example
-    > chol = matrix.chol
-    > assert_equal(2, chol[0, 0])
-    > assert_equal(6, chol[1, 0])
-    > assert_equal(-8, chol[2, 0])
-    > assert_equal(5, chol[2, 1])
-    > assert_equal(3, chol[2, 2])
-
-All other linear algebra methods are called the same way.
-
-
-MDArray and SciRuby:
-====================
-
-MDArray subscribes fully to the SciRuby Manifesto (http://sciruby.com/). 
-
-“Ruby has for some time had no equivalent to the beautifully constructed NumPy, SciPy, and 
-matplotlib libraries for Python. 
-
-We believe that the time for a Ruby science and visualization package has come. Sometimes 
-when a solution of sugar and water becomes super-saturated, from it precipitates a pure, 
-delicious, and diabetes-inducing crystal of sweetness, induced by no more than the tap of a 
-finger. So is occurring now, we believe, with numeric and visualization libraries for Ruby.”
-
-MDArray main properties are:
-============================
-
- + Homogeneous multidimensional array, a table of elements (usually numbers), all of the 
-     same type, indexed by a tuple of positive integers;
- + Support for many linear algebra methods (see bellow);
- + Easy calculation for large numerical multi dimensional arrays;
- + Basic types are: boolean, byte, short, int, long, float, double, string, structure;
- + Based on JRuby, which allows importing Java libraries;
- + Operator: +,-,*,/,%,**, >, >=, etc.;
- + Functions: abs, ceil, floor, truncate, is_zero, square, cube, fourth;
- + Binary Operators: &, |, ^, ~ (binary_ones_complement), <<, >>;
- + Ruby Math functions: acos, acosh, asin, asinh, atan, atan2, atanh, cbrt, cos, erf, exp, 
-     gamma, hypot, ldexp, log, log10, log2, sin, sinh, sqrt, tan, tanh, neg;
- + Boolean operations on boolean arrays: and, or, not;
- + Fast descriptive statistics from Parallel Colt (complete list found bellow);
- + Easy manipulation of arrays: reshape, reduce dimension, permute, section, slice, etc.;
- + Support for reading and writing NetCDF-3 files;
- + Reading of two dimensional arrays from CSV files (mainly for debugging and simple testing 
-     purposes);
- + StatList: a list that can grow/shrink and that can compute Parallel Colt descriptive 
-     statistics;
- + Experimental lazy evaluation (still slower than eager evaluation).
-
-Supported linear algebra methods:
-=================================
-
-  + backwardSolve:  Solves the upper triangular system U*x=b;
-  + chol: Constructs and returns the cholesky-decomposition of the given matrix.
-  + cond: Returns the condition of matrix A, which is the ratio of largest to smallest singular value.
-  + det: Returns the determinant of matrix A.
-  + eig: Constructs and returns the Eigenvalue-decomposition of the given matrix.
-  + forwardSolve:  Solves the lower triangular system L*x=b;
-  + inverse: Returns the inverse or pseudo-inverse of matrix A.
-  + kron: Computes the Kronecker product of two real matrices.
-  + lu: Constructs and returns the LU-decomposition of the given matrix.
-  + mult: Inner product of two vectors; Sum(x[i] * y[i]).
-  + mult: Linear algebraic matrix-vector multiplication; z = A * y.
-  + mult: Linear algebraic matrix-matrix multiplication; C = A x B.
-  + multOuter: Outer product of two vectors; Sets A[i,j] = x[i] * y[j].
-  + norm1: Returns the one-norm of vector x, which is Sum(abs(x[i])).
-  + norm1: Returns the one-norm of matrix A, which is the maximum absolute column sum.
-  + norm2: Returns the two-norm (aka euclidean norm) of vector x; equivalent to Sqrt(mult(x,x)).
-  + norm2: Returns the two-norm of matrix A, which is the maximum singular value; obtained from SVD.
-  + normF: Returns the Frobenius norm of matrix A, which is Sqrt(Sum(A[i]2)).
-  + normF: Returns the Frobenius norm of matrix A, which is Sqrt(Sum(A[i,j]2)).
-  + normInfinity: Returns the infinity norm of vector x, which is Max(abs(x[i])).
-  + normInfinity: Returns the infinity norm of matrix A, which is the maximum absolute row sum.
-  + pow: Linear algebraic matrix power; B = Ak <==> B = A*A*...*A.
-  + qr: Constructs and returns the QR-decomposition of the given matrix.
-  + rank: Returns the effective numerical rank of matrix A, obtained from Singular Value Decomposition.
-  + solve: Solves A*x = b.
-  + solve: Solves A*X = B.
-  + solveTranspose: Solves X*A = B, which is also A'*X' = B'.
-  + svd: Constructs and returns the SingularValue-decomposition of the given matrix.
-  + trace: Returns the sum of the diagonal elements of matrix A; Sum(A[i,i]).
-  + trapezoidalLower: Modifies the matrix to be a lower trapezoidal matrix.
-  + vectorNorm2: Returns the two-norm (aka euclidean norm) of vector X.vectorize();
-  + xmultOuter: Outer product of two vectors; Returns a matrix with A[i,j] = x[i] * y[j].
-  + xpowSlow: Linear algebraic matrix power; B = Ak <==> B = A*A*...*A.
-
-Properties´ methods tested on matrices:
-=======================================
-
-  + density: Returns the matrix's fraction of non-zero cells; A.cardinality() / A.size().
-  + generate_non_singular!: Modifies the given square matrix A such that it is diagonally dominant by row and column, hence non-singular, hence invertible.
-  + diagonal?: A matrix A is diagonal if A[i,j] == 0 whenever i != j.
-  + diagonally_dominant_by_column?: A matrix A is diagonally dominant by column if the absolute value of each diagonal element is larger than the sum of the absolute values of the off-diagonal elements in the corresponding column.
-  + diagonally_dominant_by_row?: A matrix A is diagonally dominant by row if the absolute value of each diagonal element is larger than the sum of the absolute values of the off-diagonal elements in the corresponding row.
-  + identity?: A matrix A is an identity matrix if A[i,i] == 1 and all other cells are zero.
-  + lower_bidiagonal?: A matrix A is lower bidiagonal if A[i,j]==0 unless i==j || i==j+1.
-  + lower_triangular?: A matrix A is lower triangular if A[i,j]==0 whenever i < j.
-  + nonnegative?: A matrix A is non-negative if A[i,j] >= 0 holds for all cells.
-  + orthogonal?: A square matrix A is orthogonal if A*transpose(A) = I.
-  + positive?: A matrix A is positive if A[i,j] > 0 holds for all cells.
-  + singular?: A matrix A is singular if it has no inverse, that is, iff det(A)==0.
-  + skew_symmetric?: A square matrix A is skew-symmetric if A = -transpose(A), that is A[i,j] == -A[j,i].
-  + square?: A matrix A is square if it has the same number of rows and columns.
-  + strictly_lower_triangular?: A matrix A is strictly lower triangular if A[i,j]==0 whenever i <= j.
-  + strictly_triangular?: A matrix A is strictly triangular if it is triangular and its diagonal elements all equal 0.
-  + strictly_upper_triangular?: A matrix A is strictly upper triangular if A[i,j]==0 whenever i >= j.
-  + symmetric?: A matrix A is symmetric if A = tranpose(A), that is A[i,j] == A[j,i].
-  + triangular?: A matrix A is triangular iff it is either upper or lower triangular.
-  + tridiagonal?: A matrix A is tridiagonal if A[i,j]==0 whenever Math.abs(i-j) > 1.
-  + unit_triangular?: A matrix A is unit triangular if it is triangular and its diagonal elements all equal 1.
-  + upper_bidiagonal?: A matrix A is upper bidiagonal if A[i,j]==0 unless i==j || i==j-1.
-  + upper_triangular?: A matrix A is upper triangular if A[i,j]==0 whenever i > j.
-  + zero?: A matrix A is zero if all its cells are zero.
-  + lower_bandwidth: The lower bandwidth of a square matrix A is the maximum i-j for which A[i,j] is nonzero and i > j.
-  + semi_bandwidth: Returns the semi-bandwidth of the given square matrix A.
-  + upper_bandwidth: The upper bandwidth of a square matrix A is the maximum j-i for which A[i,j] is nonzero and j > i.
-
-Descriptive statistics methods imported from Parallel Colt:
-===========================================================
-
-  + auto_correlation, correlation, covariance, durbin_watson, frequencies, geometric_mean, 
-  + harmonic_mean, kurtosis, lag1, max, mean, mean_deviation, median, min, moment, moment3, 
-  + moment4, pooled_mean, pooled_variance, product, quantile, quantile_inverse, 
-  + rank_interpolated, rms, sample_covariance, sample_kurtosis, sample_kurtosis_standard_error, 
-  + sample_skew, sample_skew_standard_error, sample_standard_deviation, sample_variance, 
-  + sample_weighted_variance, skew, split,  standard_deviation, standard_error, sum, 
-  + sum_of_inversions, sum_of_logarithms, sum_of_powers, sum_of_power_deviations, 
-  + sum_of_squares, sum_of_squared_deviations, trimmed_mean, variance, weighted_mean, 
-  + weighted_rms, weighted_sums, winsorized_mean.
-
-Double and Float methods from Parallel Colt:
-============================================
-
-  + acos, asin, atan, atan2, ceil, cos, exp, floor, greater, IEEEremainder, inv, less, lg, 
-  + log, log2, rint, sin, sqrt, tan.
-
-Double, Float, Long and Int methods from Parallel Colt:
-=======================================================
-
-  + abs, compare, div, divNeg, equals, isEqual (is_equal), isGreater (is_greater), 
-  + isles (is_less), max, min, minus, mod, mult, multNeg (mult_neg), multSquare (mult_square), 
-  + neg, plus (add), plusAbs (plus_abs), pow (power), sign, square.
-
-Long and Int methods from Parallel Colt
-=======================================
-
-  + and, dec, factorial, inc, not, or, shiftLeft (shift_left), shiftRightSigned 
-      (shift_right_signed), shiftRightUnsigned (shift_right_unsigned), xor.
-
-MDArray installation and download:
-==================================
-
-  + Install Jruby
-  + jruby –S gem install mdarray
-
-MDArray Homepages:
-==================
-
-  + http://rubygems.org/gems/mdarray
-  + https://github.com/rbotafogo/mdarray/wiki
-
-Contributors:
-=============
-Contributors are welcome.
-
-MDArray History:
-================
-
-  + 14/11/2013: Version 0.5.5 - Support for linear algebra methods
-  + 07/08/2013: Version 0.5.4 - Support for reading and writing NetCDF-3 files
-  + 24/06/2013: Version 0.5.3 – Over 90% Performance improvements for methods imported 
-      from Parallel Colt and over 40% performance improvements for all other methods 
-      (implemented in Ruby); 
-  + 16/05/2013: Version 0.5.0 - All loops transferred to Java with over 50% performance 
-      improvements.  Descriptive statistics from Parallel Colt;
-  + 19/04/2013: Version 0.4.3 - Fixes a simple, but fatal bug in 0.4.2.  No new features;
-  + 17/04/2013: Version 0.4.2 - Adds simple statistics and boolean operators;
-  + 05/04/2013: Version 0.4.0 – Initial release.
-