statsample 1.2.0 → 1.3.0

data/Gemfile

@@ -0,0 +1,9 @@
+source :rubygems
+
+gem 'minitest'
+gem 'rdoc'
+gem 'mocha', '0.10.5' #:require=>'mocha/setup'
+gem 'shoulda','2.11.3'
+gem 'shoulda-matchers','1.1.0'
+gem 'hoe'
+gem 'bio-statsample-timeseries'

data/Gemfile.lock

@@ -0,0 +1,32 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    activesupport (3.2.10)
+      i18n (~> 0.6)
+      multi_json (~> 1.0)
+    hoe (3.4.0)
+      rake (>= 0.8, < 11.0)
+    i18n (0.6.1)
+    json (1.7.6)
+    metaclass (0.0.1)
+    minitest (4.3.3)
+    mocha (0.10.5)
+      metaclass (~> 0.0.1)
+    multi_json (1.5.0)
+    rake (10.0.3)
+    rdoc (3.12)
+      json (~> 1.4)
+    shoulda (2.11.3)
+    shoulda-matchers (1.1.0)
+      activesupport (>= 3.0.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  hoe
+  minitest
+  mocha (= 0.10.5)
+  rdoc
+  shoulda (= 2.11.3)
+  shoulda-matchers (= 1.1.0)

data/History.txt

@@ -1,3 +1,13 @@
+=== 1.3.0 / 2013-09-19
+
+  * Merge remote-tracking branch 'vpereira/master' into vpereira
+  * New Wilcoxon Signed Rank test
+  * Remove TimeSeries class. Now is available on gem "bio-statsample-timeseries" [GSOC 2013 project :) ]
+  * Update shoulda support
+  * added Bundle depds
+  * improved the csv read method (requires tests)
+  * open svg on mac osx
+
 === 1.2.0 / 2011-12-15
   
   * Added support for time series (TimeSeries object): MA, EMA, MACD, acf, lag and delta. [Rob Britton]

data/Manifest.txt

@@ -1,3 +1,5 @@
+Gemfile
+Gemfile.lock
 History.txt
 LICENSE.txt
 Manifest.txt
@@ -102,7 +104,7 @@ lib/statsample/test/kolmogorovsmirnov.rb
 lib/statsample/test/levene.rb
 lib/statsample/test/t.rb
 lib/statsample/test/umannwhitney.rb
-lib/statsample/timeseries.rb
+lib/statsample/test/wilcoxonsignedrank.rb
 lib/statsample/vector.rb
 lib/statsample/vector/gsl.rb
 po/es/statsample.mo
@@ -161,5 +163,6 @@ test/test_test_t.rb
 test/test_tseries.rb
 test/test_umannwhitney.rb
 test/test_vector.rb
+test/test_wilcoxonsignedrank.rb
 test/test_xls.rb
 web/Rakefile

data/Rakefile

@@ -43,11 +43,11 @@ end
 h=Hoe.spec('statsample') do 
   self.version=Statsample::VERSION
   #self.testlib=:minitest
-	self.rubyforge_name = "ruby-statsample"
-	self.developer('Claudio Bustos', 'clbustos@gmail.com')
-	self.extra_deps << ["spreadsheet","~>0.6.5"] <<  ["reportbuilder", "~>1.4"] << ["minimization", "~>0.2.0"] << ["fastercsv", ">0"] << ["dirty-memoize", "~>0.0"] << ["extendmatrix","~>0.3.1"] << ["statsample-bivariate-extension", ">0"] << ["rserve-client", "~>0.2.5"] << ["rubyvis", "~>0.5"] << ["distribution", "~>0.6"]
+  self.rubyforge_name = "ruby-statsample"
+  self.developer('Claudio Bustos', 'clbustos@gmail.com')
+  self.extra_deps << ["spreadsheet","~>0.6.5"] <<  ["reportbuilder", "~>1.4"] << ["minimization", "~>0.2.0"] << ["fastercsv", ">0"] << ["dirty-memoize", "~>0.0"] << ["extendmatrix","~>0.3.1"] << ["statsample-bivariate-extension", ">0"] << ["rserve-client", "~>0.2.5"] << ["rubyvis", "~>0.5"] << ["distribution", "~>0.6"]
   
-	self.extra_dev_deps << ["hoe","~>0"] << ["shoulda","~>0"] << ["minitest", "~>2.0"] << ["rserve-client", "~>0"] << ["gettext", "~>0"] << ["mocha", "~>0"] << ["hoe-git", "~>0"]
+  self.extra_dev_deps << ["hoe","~>0"] << ["shoulda","~>3.1.1"] << ["minitest", "~>2.0"] << ["rserve-client", "~>0"] << ["gettext", "~>0"] << ["mocha", "~>0"] << ["hoe-git", "~>0"]
   
   self.clean_globs << "test/images/*" << "demo/item_analysis/*" << "demo/Regression"
   self.post_install_message = <<-EOF
@@ -69,7 +69,7 @@ source code first.
 
 *****************************************************
   EOF
-	self.need_rdoc=false
+  self.need_rdoc=false
 end
 
 if Rake.const_defined?(:RDocTask)

data/lib/statsample.rb

@@ -26,7 +26,6 @@ require 'dirty-memoize'
 require 'reportbuilder'
 
 
-
 class Numeric
   def square ; self * self ; end
 end
@@ -134,7 +133,7 @@ module Statsample
   
   create_has_library :gsl
   
-  VERSION = '1.2.0'
+  VERSION = '1.3.0'
   SPLIT_TOKEN = ","
   autoload(:Analysis, 'statsample/analysis')
   autoload(:Database, 'statsample/converters')
@@ -161,7 +160,6 @@ module Statsample
   autoload(:Test, 'statsample/test')
   autoload(:Factor, 'statsample/factor')
   autoload(:Graph, 'statsample/graph')
-  autoload(:TimeSeries, 'statsample/timeseries')
   
   
   class << self

data/lib/statsample/analysis/suite.rb

@@ -62,7 +62,11 @@ module Statsample
         require 'tmpdir'
         fn=Dir.tmpdir+"/image_#{Time.now.to_f}.svg"
         File.open(fn,"w") {|fp| fp.write svg}
-        `xdg-open '#{fn}'`
+	if RUBY_PLATFORM =~/darwin/
+	  %x(open -a safari #{fn})
+	else
+	  %x(xdg-open #{fn})
+	end
       end
       def boxplot(*args)
         show_svg(old_boxplot(*args).to_svg)

data/lib/statsample/converter/csv.rb

@@ -8,6 +8,25 @@ module Statsample
       CSV_klass=::CSV  
     end    
     class << self
+
+      def read19(filename,ignore_lines=0,csv_opts=Hash.new)
+        #default first line is header
+        csv_opts.merge!(:headers=>true, :header_converters => :symbol)
+        csv = CSV_klass::Table.new(CSV_klass::read(filename,'r',csv_opts))
+        csv_headers = if csv_opts[:headers]
+          csv.headers
+        else
+          #as in R, if no header we name the headers as V1,V2,V3,V4,..
+          1.upto(csv.first.length).collect { |i| "V#{i}" }
+        end
+        #we invert row -> column. It means csv[0] is the first column and not row. Similar to R
+        csv.by_col!
+        thash = {}
+        csv_headers.each_with_index do |header,idx|
+          thash[header] = Statsample::Vector.new(csv[idx].drop(ignore_lines))
+        end
+        ds=Statsample::Dataset.new(thash)
+      end
       # Returns a Dataset  based on a csv file
       #
       # USE:

data/lib/statsample/dataset.rb

@@ -705,7 +705,7 @@ module Statsample
     
     # Return a correlation matrix for fields included as parameters.
     # By default, uses all fields of dataset
-		def correlation_matrix(fields=nil)
+	def correlation_matrix(fields=nil)
       if fields
         ds=clone(fields)
       else
@@ -715,7 +715,7 @@ module Statsample
     end
    # Return a correlation matrix for fields included as parameters.
     # By default, uses all fields of dataset
-		def covariance_matrix(fields=nil)
+	def covariance_matrix(fields=nil)
       if fields
         ds=clone(fields)
       else

data/lib/statsample/test.rb

@@ -9,6 +9,8 @@ module Statsample
     autoload(:ChiSquare, 'statsample/test/chisquare')
     autoload(:BartlettSphericity, 'statsample/test/bartlettsphericity')
     autoload(:KolmogorovSmirnov, 'statsample/test/kolmogorovsmirnov')
+    autoload(:WilcoxonSignedRank, 'statsample/test/wilcoxonsignedrank')
+    
     
     # Returns probability of getting a value lower or higher
     # than sample, using cdf and number of tails.
@@ -66,7 +68,10 @@ module Statsample
       def t_two_samples_independent(v1,v2, opts=Hash.new)
         Statsample::Test::T::TwoSamplesIndependent.new(v1,v2,opts)
       end
-
+      # Shorthand for Statsample::Test::WilcoxonSignedRank.new
+	  def wilcoxon_signed_rank(v1,v2,opts=Hash.new)
+		Statsample::Test::WilcoxonSignedRank.new(v1,v2,opts)
+	  end
       # Shorthand for Statsample::Test::Levene.new
       def levene(input, opts=Hash.new)
         Statsample::Test::Levene.new(input,opts)

data/lib/statsample/test/wilcoxonsignedrank.rb

@@ -0,0 +1,88 @@
+module Statsample
+  module Test
+    # From Wikipedia:
+    # The Wilcoxon signed-rank test is a non-parametric statistical hypothesis test used when comparing two related samples, matched samples, or repeated measurements on a single sample to assess whether their population mean ranks differ (i.e. it is a paired difference test). It can be used as an alternative to the paired Student's t-test, t-test for matched pairs, or the t-test for dependent samples when the population cannot be assumed to be normally distributed.
+    class WilcoxonSignedRank
+      include Statsample::Test
+      include Summarizable
+      
+      # Name of F analysis
+      attr_accessor :name
+	  attr_reader :w
+	  attr_reader :nr
+	  attr_writer :tails
+      # Parameters:
+      def initialize(v1,v2, opts=Hash.new)
+		@v1=v1
+		@v2=v2
+        opts_default={:name=>_("Wilcoxon Signed Rank Test"),:tails=>:both}
+        @opts=opts_default.merge(opts)
+        opts_default.keys.each {|k|
+          send("#{k}=", @opts[k])
+        }
+        calculate
+      end
+      def calculate
+		df=Statsample::Dataset.new({'v1'=>@v1,'v2'=>@v2})
+		df["abs"]=df.collect {|row| 
+			r=(row["v2"]-row["v1"]).abs
+		}
+		df["sgn"]=df.collect {|row| 
+			r=row["v2"]-row["v1"]
+			r==0 ? 0 : r/r.abs
+		}
+		df=df.filter {|row| row["sgn"]!=0}
+		df["rank"]=df["abs"].ranked
+		@nr=df.cases
+		@w=df.collect {|row|
+			row["sgn"]*row["rank"]
+			#p row["sgn"]*row["rank"]
+		}.sum
+      end
+      def report_building(generator) # :nodoc:
+        generator.section(:name=>@name) do |s|
+          s.table(:name=>_("%s results") % @name) do |t|
+            t.row([_("W Value"), "%0.3f" % @w])
+            t.row([_("Z"), "%0.3f (p: %0.3f)" % [z, probability_z]])
+            if(nr<=10) 
+				t.row([_("Exact probability"), "p-exact: %0.3f" % [probability_exact]])
+            end
+          end
+        end
+      end
+      def z
+		sigma=Math.sqrt((nr*(nr+1)*(2*nr+1))/6)
+		(w-0.5)/sigma
+      end
+      # Assuming normal distribution of W, this calculate
+      # the probability of samples with Z equal or higher than
+      # obtained on sample
+      def probability_z
+		(1-Distribution::Normal.cdf(z))*(@tails==:both ? 2:1)
+      end
+      # Calculate exact probability.
+      # Don't calculate for large Nr, please!
+      def probability_exact
+		str_format="%0#{nr}b"
+		combinations=2**nr
+		#p str_format
+		total_w=combinations.times.map {|i|
+			comb=sprintf(str_format,i)
+			w_local=comb.length.times.inject(0) {|ac,j|
+				sgn=comb[j]=="0" ? -1 : 1
+				ac+(j+1)*sgn
+			}
+		}.sort
+		total_w.find_all {|v| 
+			if @tails==:both
+				v<=-w.abs or v>=w.abs
+			elsif @tails==:left
+				v<=w
+			elsif @tails==:right
+				v>=w
+			end
+		}.count/(combinations.to_f)
+      end
+    end
+  end
+end

data/test/helpers_tests.rb

@@ -2,10 +2,11 @@ $:.unshift(File.expand_path(File.dirname(__FILE__)+'/../lib/'))
 $:.unshift(File.expand_path(File.dirname(__FILE__)+'/'))
 
 require 'minitest/unit'
-require 'mocha'
+require 'mocha/setup'
 require 'tempfile'
 require 'tmpdir'
 require 'shoulda'
+require 'shoulda-context'
 require 'fixtures/correlation_matrix'
 
 require 'statsample'
@@ -14,10 +15,9 @@ require 'statsample'
 module MiniTest
   class Unit
     class TestCase
-      include Shoulda::InstanceMethods
-      extend Shoulda::ClassMethods
-      include Shoulda::Assertions
-      
+    include Shoulda::Context::Assertions
+    include Shoulda::Context::InstanceMethods
+    extend Shoulda::Context::ClassMethods
       def self.should_with_gsl(name,&block)
         should(name) do
           if Statsample.has_gsl?

data/test/test_csv.rb

@@ -38,3 +38,43 @@ class StatsampleCSVTestCase < MiniTest::Unit::TestCase
     }
   end
 end
+
+class StatsampleCSVTestCase2 < MiniTest::Unit::TestCase
+  def setup
+    @ds=Statsample::CSV.read19(File.dirname(__FILE__)+"/fixtures/test_csv.csv")
+  end
+  def test_read
+    assert_equal(6,@ds.cases)
+    assert_equal(%w{id name age city a1}, @ds.fields)
+    id=[1,2,3,4,5,6].to_vector(:scale)
+    name=["Alex","Claude","Peter","Franz","George","Fernand"].to_vector(:nominal)
+    age=[20,23,25,27,5.5,nil].to_vector(:scale)
+    city=["New York","London","London","Paris","Tome",nil].to_vector(:nominal)
+    a1=["a,b","b,c","a",nil,"a,b,c",nil].to_vector(:nominal)
+    ds_exp=Statsample::Dataset.new({'id'=>id,'name'=>name,'age'=>age,'city'=>city,'a1'=>a1}, %w{id name age city a1})
+    ds_exp.fields.each{|f|
+      assert_equal(ds_exp[f],@ds[f])
+    }
+    assert_equal(ds_exp,@ds)
+  end
+  def test_nil
+    assert_equal(nil,@ds['age'][5])
+  end
+  def test_repeated
+    ds=Statsample::CSV.read19(File.dirname(__FILE__)+"/fixtures/repeated_fields.csv")
+    assert_equal(%w{id name_1 age_1 city a1 name_2 age_2},ds.fields)
+    age=[3,4,5,6,nil,8].to_vector(:scale)
+    assert_equal(age,ds['age_2'])
+  end
+  def test_write
+    filename=Tempfile.new("afile")
+    #  filename=Dir::tmpdir+"/test_write.csv"
+    Statsample::CSV.write(@ds, filename.path)
+    ds2=Statsample::CSV.read19(filename.path)
+    i=0
+    ds2.each_array{|row|
+      assert_equal(@ds.case_as_array(i),row)
+      i+=1
+    }
+  end
+end

data/test/test_wilcoxonsignedrank.rb

@@ -0,0 +1,67 @@
+require(File.expand_path(File.dirname(__FILE__)+'/helpers_tests.rb'))
+
+class StatsampleUMannWhitneyTestCase < MiniTest::Unit::TestCase
+  include Statsample::Test
+  context Statsample::Test::WilcoxonSignedRank do
+	context "Example 1" do
+		setup do
+		  @v1=[110,122,125,120,140,124,123,137,135,145].to_scale
+		  @v2=[125,115,130,140,140,115,140,125,140,135].to_scale
+		  @u=Statsample::Test::WilcoxonSignedRank.new(@v1,@v2)
+		end
+		should "have same result using class or Test#u_mannwhitney" do 
+		  assert_equal(Statsample::Test.wilcoxon_signed_rank(@v1,@v2).w, @u.w) 
+		end
+		should "have correct W values" do
+		  assert_equal(9,@u.w)
+		end
+		should "have correct nr values" do
+			assert_equal(9,@u.nr)
+		end
+		should "have correct value for z" do
+		  assert_in_delta(0.503,@u.z,0.001)
+		end
+		should "have correct value for probability_z" do
+		  assert_in_delta(0.614,@u.probability_z,0.001)
+		end
+		should "have correct value for probability_exact" do
+		  assert_in_delta(0.652,@u.probability_exact,0.001)
+		end    
+		should "have summary" do
+		  assert(@u.summary!="")
+		end 
+	  end
+	  
+	  context "Example 2" do
+		setup do
+		  @v2=[78,24,64,45,64,52,30,50,64,50,78,22,84,40,90,72].to_scale
+		  @v1=[78,24,62,48,68,56,25,44,56,40,68,36,68,20,58,32].to_scale
+		  @u=Statsample::Test::WilcoxonSignedRank.new(@v1,@v2)
+		end
+		should "have same result using class or Test#u_mannwhitney" do 
+		  assert_equal(Statsample::Test.wilcoxon_signed_rank(@v1,@v2).w, @u.w) 
+		end
+		should "have correct W values" do
+		  assert_equal(67,@u.w)
+		end
+		should "have correct nr values" do
+			assert_equal(14,@u.nr)
+		end
+		should "have correct value for z" do
+		  assert_in_delta(2.087,@u.z,0.001)
+		end
+		should "have correct value for probability_z" do
+		  assert_in_delta(0.036,@u.probability_z,0.001)
+		end
+		should "have correct value for probability_exact" do
+		  assert_in_delta(0.036,@u.probability_exact,0.001)
+		end    
+		should "have summary" do
+		  assert(@u.summary!="")
+		end 
+	  end
+	
+	
+	end
+	  
+end

metadata

@@ -1,46 +1,19 @@
 --- !ruby/object:Gem::Specification
 name: statsample
 version: !ruby/object:Gem::Version
-  version: 1.2.0
+  version: 1.3.0
   prerelease: 
 platform: ruby
 authors:
 - Claudio Bustos
 autorequire: 
 bindir: bin
-cert_chain:
-- !binary |-
-  LS0tLS1CRUdJTiBDRVJUSUZJQ0FURS0tLS0tCk1JSURNakNDQWhxZ0F3SUJB
-  Z0lCQURBTkJna3Foa2lHOXcwQkFRVUZBREEvTVJFd0R3WURWUVFEREFoamJH
-  SjEKYzNSdmN6RVZNQk1HQ2dtU0pvbVQ4aXhrQVJrV0JXZHRZV2xzTVJNd0VR
-  WUtDWkltaVpQeUxHUUJHUllEWTI5dApNQjRYRFRFd01ETXlPVEl4TXpnMU5W
-  b1hEVEV4TURNeU9USXhNemcxTlZvd1B6RVJNQThHQTFVRUF3d0lZMnhpCmRY
-  TjBiM014RlRBVEJnb0praWFKay9Jc1pBRVpGZ1ZuYldGcGJERVRNQkVHQ2dt
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-  RGdnRVBBRENDQVFvQ2dnRUJBTGY4SlZNR3FFN201a1liK1BOTgpuZVp2MnBj
-  WFY1ZlFDaTZ4a3lHOGJpMi9TSUZ5L0x5eHV2THpFZU94QmVhejFCZTkzYmF5
-  SVVxdU9JcXczZHl3Ci9LWFdhMzFGeHVOdXZBbTZDTjhmeWVSWVgvb3U0Y3cz
-  T0lVVW5JdkI3Uk1OSXU0d2JnZU02aHRWL1FFc05McnYKYXQxL21oOUpwcWF3
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-  dTVNQTBHQ1NxR1NJYjNEUUVCQlFVQUE0SUJBUUNWMFVua2E1aXNyaFprCkdq
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-  b2FudWFoSExaRXRrLytaODg1bEZlbmUrbkhhZGtlbTFuOWlBQgpjczk2Sk85
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-  cnBwUnJaYXlFMkZWc3BzNFg2V3dCZHJLVE1aMENLU1hUUmN0YkVqMUJBWjY3
-  ZW9UdkJCdApycFAwampzMAotLS0tLUVORCBDRVJUSUZJQ0FURS0tLS0tCg==
-date: 2011-12-15 00:00:00.000000000 Z
+cert_chain: []
+date: 2013-09-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: spreadsheet
-  requirement: &16328900 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -48,10 +21,15 @@ dependencies:
         version: 0.6.5
   type: :runtime
   prerelease: false
-  version_requirements: *16328900
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.6.5
 - !ruby/object:Gem::Dependency
   name: reportbuilder
-  requirement: &16340700 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -59,10 +37,15 @@ dependencies:
         version: '1.4'
   type: :runtime
   prerelease: false
-  version_requirements: *16340700
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.4'
 - !ruby/object:Gem::Dependency
   name: minimization
-  requirement: &16366980 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -70,10 +53,15 @@ dependencies:
         version: 0.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *16366980
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.2.0
 - !ruby/object:Gem::Dependency
   name: fastercsv
-  requirement: &16365020 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -81,10 +69,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *16365020
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: dirty-memoize
-  requirement: &16362640 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -92,10 +85,15 @@ dependencies:
         version: '0.0'
   type: :runtime
   prerelease: false
-  version_requirements: *16362640
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.0'
 - !ruby/object:Gem::Dependency
   name: extendmatrix
-  requirement: &16360700 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -103,10 +101,15 @@ dependencies:
         version: 0.3.1
   type: :runtime
   prerelease: false
-  version_requirements: *16360700
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.3.1
 - !ruby/object:Gem::Dependency
   name: statsample-bivariate-extension
-  requirement: &16385380 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -114,10 +117,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *16385380
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rserve-client
-  requirement: &16383940 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -125,10 +133,15 @@ dependencies:
         version: 0.2.5
   type: :runtime
   prerelease: false
-  version_requirements: *16383940
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.2.5
 - !ruby/object:Gem::Dependency
   name: rubyvis
-  requirement: &16381840 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -136,10 +149,15 @@ dependencies:
         version: '0.5'
   type: :runtime
   prerelease: false
-  version_requirements: *16381840
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.5'
 - !ruby/object:Gem::Dependency
   name: distribution
-  requirement: &16379020 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -147,10 +165,31 @@ dependencies:
         version: '0.6'
   type: :runtime
   prerelease: false
-  version_requirements: *16379020
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.6'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
 - !ruby/object:Gem::Dependency
   name: hoe
-  requirement: &16402020 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -158,21 +197,31 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *16402020
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &16418560 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 3.1.1
   type: :development
   prerelease: false
-  version_requirements: *16418560
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.1.1
 - !ruby/object:Gem::Dependency
   name: minitest
-  requirement: &16432600 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -180,21 +229,15 @@ dependencies:
         version: '2.0'
   type: :development
   prerelease: false
-  version_requirements: *16432600
-- !ruby/object:Gem::Dependency
-  name: rserve-client
-  requirement: &16443500 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: *16443500
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: gettext
-  requirement: &16438020 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -202,10 +245,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *16438020
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: mocha
-  requirement: &16469980 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -213,10 +261,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *16469980
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: hoe-git
-  requirement: &16468800 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -224,18 +277,12 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *16468800
-- !ruby/object:Gem::Dependency
-  name: hoe
-  requirement: &16466880 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '2.12'
-  type: :development
-  prerelease: false
-  version_requirements: *16466880
+        version: '0'
 description: ! 'A suite for basic and advanced statistics on Ruby. Tested on Ruby
   1.8.7, 1.9.1, 1.9.2 (April, 2010), ruby-head(June, 2011) and JRuby 1.4 (Ruby 1.8.7
   compatible).
@@ -291,6 +338,8 @@ extra_rdoc_files:
 - README.txt
 - references.txt
 files:
+- Gemfile
+- Gemfile.lock
 - History.txt
 - LICENSE.txt
 - Manifest.txt
@@ -395,7 +444,7 @@ files:
 - lib/statsample/test/levene.rb
 - lib/statsample/test/t.rb
 - lib/statsample/test/umannwhitney.rb
-- lib/statsample/timeseries.rb
+- lib/statsample/test/wilcoxonsignedrank.rb
 - lib/statsample/vector.rb
 - lib/statsample/vector/gsl.rb
 - po/es/statsample.mo
@@ -454,11 +503,13 @@ files:
 - test/test_tseries.rb
 - test/test_umannwhitney.rb
 - test/test_vector.rb
+- test/test_wilcoxonsignedrank.rb
 - test/test_xls.rb
 - web/Rakefile
 - .gemtest
 homepage: http://ruby-statsample.rubyforge.org/
-licenses: []
+licenses:
+- MIT
 post_install_message: ! "***************************************************\nThanks
   for installing statsample.\n\nOn *nix, you could install statsample-optimization\nto
   retrieve gems gsl, statistics2 and a C extension\nto speed some methods.\n\n  $
@@ -484,48 +535,49 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: ruby-statsample
-rubygems_version: 1.8.10
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: A suite for basic and advanced statistics on Ruby
 test_files:
+- test/test_regression.rb
+- test/test_reliability_skillscale.rb
+- test/test_anovatwoway.rb
+- test/test_anova_contrast.rb
+- test/test_resample.rb
+- test/test_ggobi.rb
+- test/test_reliability_icc.rb
+- test/test_logit.rb
+- test/test_stratified.rb
+- test/test_srs.rb
+- test/test_test_f.rb
+- test/test_anovawithvectors.rb
+- test/test_reliability.rb
+- test/test_csv.rb
+- test/test_codification.rb
+- test/test_multiset.rb
+- test/test_anovatwowaywithdataset.rb
+- test/test_statistics.rb
 - test/test_bivariate.rb
+- test/test_histogram.rb
 - test/test_factor_pa.rb
-- test/test_dominance_analysis.rb
+- test/test_analysis.rb
+- test/test_factor_map.rb
+- test/test_anovaoneway.rb
 - test/test_factor.rb
-- test/test_test_kolmogorovsmirnov.rb
-- test/test_codification.rb
-- test/test_anovatwowaywithdataset.rb
+- test/test_vector.rb
+- test/test_tseries.rb
+- test/test_test_t.rb
+- test/test_dataset.rb
+- test/test_dominance_analysis.rb
+- test/test_gsl.rb
 - test/test_umannwhitney.rb
-- test/test_anova_contrast.rb
-- test/test_factor_map.rb
-- test/test_anovawithvectors.rb
+- test/test_stest.rb
 - test/test_crosstab.rb
-- test/test_rserve_extension.rb
-- test/test_csv.rb
-- test/test_analysis.rb
 - test/test_matrix.rb
-- test/test_gsl.rb
-- test/test_tseries.rb
 - test/test_bartlettsphericity.rb
-- test/test_mle.rb
-- test/test_resample.rb
-- test/test_stratified.rb
-- test/test_vector.rb
-- test/test_srs.rb
-- test/test_ggobi.rb
+- test/test_wilcoxonsignedrank.rb
 - test/test_xls.rb
-- test/test_logit.rb
-- test/test_stest.rb
-- test/test_statistics.rb
-- test/test_reliability.rb
-- test/test_reliability_icc.rb
-- test/test_anovatwoway.rb
-- test/test_test_f.rb
-- test/test_test_t.rb
-- test/test_histogram.rb
-- test/test_dataset.rb
-- test/test_regression.rb
-- test/test_multiset.rb
-- test/test_reliability_skillscale.rb
-- test/test_anovaoneway.rb
+- test/test_mle.rb
+- test/test_rserve_extension.rb
+- test/test_test_kolmogorovsmirnov.rb

data/lib/statsample/timeseries.rb

@@ -1,169 +0,0 @@
-module Statsample::TimeSeriesShorthands
-  # Creates a new Statsample::TimeSeries object
-  # Argument should be equal to TimeSeries.new
-  def to_time_series(*args)
-		Statsample::TimeSeries::TimeSeries.new(self, :scale, *args)
-	end
-
-  alias :to_ts :to_time_series
-end
-
-class Array
-  include Statsample::TimeSeriesShorthands
-end
-
-module Statsample
-  module TimeSeries
-    # Collection of data indexed by time.
-    # The order goes from earliest to latest.
-    class TimeSeries < Statsample::Vector
-      # Calculates the autocorrelation coefficients of the series.
-      #
-      # The first element is always 1, since that is the correlation
-      # of the series with itself.
-      #
-      # Usage:
-      #
-      #  ts = (1..100).map { rand }.to_time_series
-      #
-      #  ts.acf   # => array with first 21 autocorrelations
-      #  ts.acf 3 # => array with first 3 autocorrelations
-      #
-      def acf maxlags = nil
-        maxlags ||= (10 * Math.log10(size)).to_i
-
-        (0..maxlags).map do |i|
-          if i == 0
-            1.0
-          else
-            m = self.mean
-
-            # can't use Pearson coefficient since the mean for the lagged series should
-            # be the same as the regular series
-            ((self - m) * (self.lag(i) - m)).sum / self.variance_sample / (self.size - 1)
-          end
-        end
-      end
-
-      # Lags the series by k periods.
-      #
-      # The convention is to set the oldest observations (the first ones
-      # in the series) to nil so that the size of the lagged series is the
-      # same as the original.
-      #
-      # Usage:
-      #
-      #  ts = (1..10).map { rand }.to_time_series
-      #           # => [0.69, 0.23, 0.44, 0.71, ...]
-      #
-      #  ts.lag   # => [nil, 0.69, 0.23, 0.44, ...]
-      #  ts.lag 2 # => [nil, nil, 0.69, 0.23, ...]
-      #
-      def lag k = 1
-        return self if k == 0
-
-        dup.tap do |lagged|
-          (lagged.size - 1).downto k do |i|
-            lagged[i] = lagged[i - k]
-          end
-
-          (0...k).each do |i|
-            lagged[i] = nil
-          end
-          lagged.set_valid_data
-        end
-      end
-
-      # Performs a first difference of the series.
-      #
-      # The convention is to set the oldest observations (the first ones
-      # in the series) to nil so that the size of the diffed series is the
-      # same as the original.
-      #
-      # Usage:
-      #
-      #  ts = (1..10).map { rand }.to_ts
-      #            # => [0.69, 0.23, 0.44, 0.71, ...]
-      #
-      #  ts.diff   # => [nil, -0.46, 0.21, 0.27, ...]
-      #  
-      def diff
-        self - self.lag
-      end
-
-      # Calculates a moving average of the series using the provided
-      # lookback argument. The lookback defaults to 10 periods.
-      #
-      # Usage:
-      #
-      #   ts = (1..100).map { rand }.to_ts
-      #            # => [0.69, 0.23, 0.44, 0.71, ...]
-      #
-      #   # first 9 observations are nil
-      #   ts.ma    # => [ ... nil, 0.484... , 0.445... , 0.513 ... , ... ]
-      def ma n = 10
-        return mean if n >= size
-
-        ([nil] * (n - 1) + (0..(size - n)).map do |i|
-          self[i...(i + n)].inject(&:+) / n
-        end).to_time_series
-      end
-
-      # Calculates an exponential moving average of the series using a
-      # specified parameter. If wilder is false (the default) then the EMA
-      # uses a smoothing value of 2 / (n + 1), if it is true then it uses the
-      # Welles Wilder smoother of 1 / n.
-      #
-      # Warning for EMA usage: EMAs are unstable for small series, as they
-      # use a lot more than n observations to calculate. The series is stable
-      # if the size of the series is >= 3.45 * (n + 1)
-      #
-      # Usage: 
-      #
-      #   ts = (1..100).map { rand }.to_ts
-      #            # => [0.69, 0.23, 0.44, 0.71, ...]
-      #
-      #   # first 9 observations are nil
-      #   ts.ema   # => [ ... nil, 0.509... , 0.433..., ... ]
-      def ema n = 10, wilder = false
-        smoother = wilder ? 1.0 / n : 2.0 / (n + 1)
-
-        # need to start everything from the first non-nil observation
-        start = self.data.index { |i| i != nil }
-
-        # first n - 1 observations are nil
-        base = [nil] * (start + n - 1)
-
-        # nth observation is just a moving average
-        base << self[start...(start + n)].inject(0.0) { |s, a| a.nil? ? s : s + a } / n
-
-        (start + n).upto size - 1 do |i|
-          base << self[i] * smoother + (1 - smoother) * base.last
-        end
-
-        base.to_time_series
-      end
-
-      # Calculates the MACD (moving average convergence-divergence) of the time
-      # series - this is a comparison of a fast EMA with a slow EMA.
-      def macd fast = 12, slow = 26, signal = 9
-        series = ema(fast) - ema(slow)
-        [series, series.ema(signal)]
-      end
-
-      # Borrow the operations from Vector, but convert to time series
-      def + series
-        super.to_a.to_ts
-      end
-
-      def - series
-        super.to_a.to_ts
-      end
-
-      def to_s
-        sprintf("Time Series(type:%s, n:%d)[%s]", @type.to_s, @data.size,
-                @data.collect{|d| d.nil? ? "nil":d}.join(","))
-      end
-    end
-  end
-end