statsample 0.11.0 → 0.11.1

data.tar.gz.sig

@@ -1 +1,2 @@
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+
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data/History.txt

@@ -1,3 +1,6 @@
+=== 0.11.1 / 2010-05-04
+* Removed Matrix almost all Matrix extensions and replaced by dependency on 'extendmatrix' gem
+* Added dependency to gsl >=1.12.109. Polychoric with joint method fails without this explicit dependency
 === 0.11.0 / 2010-04-16
 <b>New features:</b>
 * Added Statsample::Anova::TwoWay and Statsample::Anova::TwoWayWithVectors

data/Rakefile

@@ -37,7 +37,7 @@ h=Hoe.spec('statsample') do
   #self.testlib=:minitest
 	self.rubyforge_name = "ruby-statsample"
 	self.developer('Claudio Bustos', 'clbustos@gmail.com')
-	self.extra_deps << ["spreadsheet","~>0.6.0"] << ["svg-graph", "~>1.0"] << ["reportbuilder", "~>1.0"] << ["minimization", "~>0.2.0"] << ["fastercsv"] << ["dirty-memoize", "~>0.0"] << ["statistics2", "~>0.54"]
+	self.extra_deps << ["spreadsheet","~>0.6.0"] << ["svg-graph", "~>1.0"] << ["reportbuilder", "~>1.0"] << ["minimization", "~>0.2.0"] << ["fastercsv"] << ["dirty-memoize", "~>0.0"] << ["statistics2", "~>0.54"] << ["extendmatrix","~>0.1"] << ["gsl", "~>1.12.109"]
 	self.clean_globs << "test/images/*" << "demo/item_analysis/*" << "demo/Regression"
 	self.need_rdoc=false
 end

data/lib/statsample.rb

@@ -111,7 +111,7 @@ module Statsample
       false
     end
   end
-  VERSION = '0.11.0'
+  VERSION = '0.11.1'
   SPLIT_TOKEN = ","
   autoload(:Database, 'statsample/converters')
   autoload(:Anova, 'statsample/anova')

data/lib/statsample/bivariate/polychoric.rb

@@ -438,8 +438,7 @@ module Statsample
           message+=sprintf("f() = %7.3f size = %.3f\n", minimizer.fval, minimizer.size)+"\n";
         end while status == GSL::CONTINUE and iter < @max_iterations
         @iteration=iter
-        @log+=message
-        puts message if @debug
+        @log+=message        
         @r=minimizer.x[0]
         @alpha=minimizer.x[1,@nr-1].to_a
         @beta=minimizer.x[@nr,@nc-1].to_a

data/lib/statsample/matrix.rb

@@ -1,19 +1,4 @@
-require 'matrix'
-
-class ::Vector
-  if RUBY_VERSION<="1.9.0"
-    alias_method :old_coerce, :coerce
-    def coerce(other)
-      case other
-      when Numeric
-        return Matrix::Scalar.new(other), self
-      else
-        raise TypeError, "#{self.class} can't be coerced into #{other.class}"
-      end
-    end
-    
-  end
-end
+require 'extendmatrix'
 
 
 class ::Matrix
@@ -24,63 +9,6 @@ class ::Matrix
     }
     GSL::Matrix[*out]
   end
-  # Calculate marginal of rows
-  def row_sum
-  (0...row_size).collect {|i|
-    row(i).to_a.inject(0) {|a,v| a+v}
-  }
-  end
-  # Calculate marginal of columns
-  def column_sum
-  (0...column_size).collect {|i|
-    column(i).to_a.inject(0) {|a,v| a+v}
-  }
-  end
-
-  
-  alias :old_par :[]
-  
-  # Select elements and submatrixes
-  # Implement row, column and minor in one method
-  # 
-  # * [i,j]:: Element i,j
-  # * [i,:*]:: Row i
-  # * [:*,j]:: Column j
-  # * [i1..i2,j]:: Row i1 to i2, column j
-  
-  def [](*args)
-    raise ArgumentError if args.size!=2
-    x=args[0]
-    y=args[1]
-    if x.is_a? Integer and y.is_a? Integer
-      @rows[args[0]][args[1]]
-    else
-      # set ranges according to arguments
-      
-      rx=case x
-        when Numeric
-          x..x
-        when :*
-          0..(row_size-1)
-        when Range
-          x
-      end
-      ry=case y
-        when Numeric
-          y..y
-        when :*
-          0..(column_size-1)
-        when Range
-          y
-      end
-      Matrix.rows(rx.collect {|i| ry.collect {|j| @rows[i][j]}})
-    end
-  end
-  # Calculate sum of cells
-  def total_sum
-    row_sum.inject(0){|a,v| a+v}
-  end
-
 end
 
 module GSL
@@ -101,6 +29,7 @@ module Statsample
   #  matrix.extend CovariateMatrix
   # 
   module CovariateMatrix
+    include Summarizable
     # Gives a nice summary
     def summary
       rp=ReportBuilder.new()

data/test/test_bivariate_polychoric.rb

@@ -49,17 +49,22 @@ class StatsampleBivariatePolychoricTestCase < MiniTest::Unit::TestCase
       assert_in_delta(1.137, @poly.threshold_x[1],0.001)
       end
     end
-  should "compute joint" do
     if Statsample.has_gsl?
-      @poly.method=:joint
-      @poly.compute
+    context "compute joint" do
+      setup do
+        @poly.method=:joint
+        @poly.compute
+      end
+      should "have correct values" do 
+        assert_equal(:joint, @poly.method)
       assert_in_delta(0.4192, @poly.r, 0.0001)
       assert_in_delta(-0.2421, @poly.threshold_y[0],0.0001)
       assert_in_delta(-0.0297, @poly.threshold_x[0],0.0001)
       assert_in_delta(1.5938, @poly.threshold_y[1],0.0001)
       assert_in_delta(1.1331, @poly.threshold_x[1],0.0001)
     end
-  end  
+    end
+    end
   end
   
 end

data/test/test_matrix.rb

@@ -2,36 +2,6 @@ require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleMatrixTestCase < MiniTest::Unit::TestCase
-  context(Matrix) do
-    setup do 
-      @matrix=Matrix[[1,2,3],[4,5,6],[7,8,9]]
-    end
-    should "return correct value for [i,j]" do
-      assert_equal(5, @matrix[1,1])
-    end
-    should "return correct value for [i,:*]" do
-      assert_equal(Matrix[[1,2,3]], @matrix[0,:*])
-    end
-    should "return correct value for [:*,j]" do 
-      assert_equal(Matrix[[1],[4],[7]], @matrix[:*,0])
-    end
-    should "return correct value for [:*,j1..j2]" do
-      assert_equal(Matrix[[1,2],[4,5],[7,8]], @matrix[:*,0..1])
-    end
-    should "return correct value for [i1..i2,j1..j2]" do
-      assert_equal(Matrix[[1,2],[4,5]], @matrix[0..1,0..1])
-    end
-    should "return correct value for row_sum" do
-      assert_equal(6,@matrix.row_sum[0])
-    end
-    should "return correct value for column_sum" do
-      assert_equal(12,@matrix.column_sum[0])
-    end
-    should "return correct value for total_sum" do
-      assert_equal(45,@matrix.total_sum)
-    end
-  end
-  
   def test_covariate
     a=Matrix[[1.0, 0.3, 0.2], [0.3, 1.0, 0.5], [0.2, 0.5, 1.0]]
     a.extend Statsample::CovariateMatrix

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 11
-  - 0
-  version: 0.11.0
+  - 1
+  version: 0.11.1
 platform: ruby
 authors: 
 - Claudio Bustos
@@ -35,7 +35,7 @@ cert_chain:
   rpP0jjs0
   -----END CERTIFICATE-----
 
-date: 2010-05-03 00:00:00 -04:00
+date: 2010-05-04 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -131,9 +131,36 @@ dependencies:
   type: :runtime
   version_requirements: *id007
 - !ruby/object:Gem::Dependency 
-  name: rubyforge
+  name: extendmatrix
   prerelease: false
   requirement: &id008 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        - 1
+        version: "0.1"
+  type: :runtime
+  version_requirements: *id008
+- !ruby/object:Gem::Dependency 
+  name: gsl
+  prerelease: false
+  requirement: &id009 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 12
+        - 109
+        version: 1.12.109
+  type: :runtime
+  version_requirements: *id009
+- !ruby/object:Gem::Dependency 
+  name: rubyforge
+  prerelease: false
+  requirement: &id010 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -143,11 +170,11 @@ dependencies:
         - 4
         version: 2.0.4
   type: :development
-  version_requirements: *id008
+  version_requirements: *id010
 - !ruby/object:Gem::Dependency 
   name: hoe
   prerelease: false
-  requirement: &id009 !ruby/object:Gem::Requirement 
+  requirement: &id011 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -157,7 +184,7 @@ dependencies:
         - 0
         version: 2.6.0
   type: :development
-  version_requirements: *id009
+  version_requirements: *id011
 description: |-
   A suite for basic and advanced statistics on Ruby. Tested on Ruby 1.8.7, 1.9.1, 1.9.2 (April, 2010) and JRuby 1.4 (Ruby 1.8.7 compatible).