statsample 1.3.1 → 1.4.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.travis.yml

@@ -0,0 +1,15 @@
+language:
+  ruby
+
+rvm:
+  - '1.9.3'
+  - '2.0.0'
+  - '2.1.1'
+
+script:
+  bundle exec rake test
+  
+before_install:
+  - sudo apt-get update -qq
+  - sudo apt-get install -y libgsl0-dev r-base r-base-dev
+  - sudo Rscript -e "install.packages(c('Rserve','irr'),,'http://cran.us.r-project.org')"

data/Gemfile

@@ -5,5 +5,13 @@ gem 'mocha', '0.14.0' #:require=>'mocha/setup'
 gem 'shoulda','3.5.0'
 gem 'shoulda-matchers','2.2.0'
 gem 'hoe'
-gem 'bio-statsample-timeseries'
+#gem 'bio-statsample-timeseries'
 gem 'reportbuilder'
+gem 'dirty-memoize'
+gem 'distribution'
+gem 'extendmatrix'
+gem 'minimization'
+gem 'rserve-client'
+gem 'rubyvis'
+gem 'spreadsheet'
+gem 'rb-gsl'

data/Gemfile.lock

@@ -1,28 +1,27 @@
 GEM
   remote: https://www.rubygems.org/
   specs:
-    activesupport (3.2.10)
-      i18n (~> 0.6)
-      multi_json (~> 1.0)
-    bio-statsample-timeseries (0.2.1)
-      activesupport (= 3.2.10)
-      statsample (= 1.2.0)
+    activesupport (4.1.1)
+      i18n (~> 0.6, >= 0.6.9)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
+      thread_safe (~> 0.1)
+      tzinfo (~> 1.1)
     clbustos-rtf (0.4.2)
     dirty-memoize (0.0.4)
     distribution (0.7.0)
     extendmatrix (0.3.1)
-    fastercsv (1.5.5)
-    hoe (3.4.0)
+    hoe (3.12.0)
       rake (>= 0.8, < 11.0)
-    i18n (0.6.5)
-    json (1.7.6)
-    metaclass (0.0.1)
+    i18n (0.6.9)
+    json (1.8.1)
+    metaclass (0.0.4)
     minimization (0.2.1)
       text-table (~> 1.2)
-    minitest (4.3.3)
+    minitest (5.3.5)
     mocha (0.14.0)
       metaclass (~> 0.0.1)
-    multi_json (1.8.0)
+    narray (0.6.0.9)
     prawn (0.8.4)
       prawn-core (>= 0.8.4, < 0.9)
       prawn-layout (>= 0.8.4, < 0.9)
@@ -32,49 +31,48 @@ GEM
     prawn-security (0.8.4)
     prawn-svg (0.9.1.11)
       prawn (>= 0.8.4)
-    rake (10.0.3)
-    rdoc (3.12)
+    rake (10.3.2)
+    rb-gsl (1.16.0.1)
+      narray (>= 0.5.9)
+    rdoc (4.1.1)
       json (~> 1.4)
     reportbuilder (1.4.2)
       clbustos-rtf (~> 0.4.0)
       prawn (~> 0.8.4)
       prawn-svg (~> 0.9.1)
       text-table (~> 1.2)
-    rserve-client (0.2.5)
+    rserve-client (0.3.1)
     ruby-ole (1.2.11.7)
     rubyvis (0.6.0)
     shoulda (3.5.0)
       shoulda-context (~> 1.0, >= 1.0.1)
       shoulda-matchers (>= 1.4.1, < 3.0)
-    shoulda-context (1.1.5)
+    shoulda-context (1.2.1)
     shoulda-matchers (2.2.0)
       activesupport (>= 3.0.0)
-    spreadsheet (0.6.9)
+    spreadsheet (0.9.7)
       ruby-ole (>= 1.0)
-    statsample (1.2.0)
-      dirty-memoize (~> 0.0)
-      distribution (~> 0.6)
-      extendmatrix (~> 0.3.1)
-      fastercsv (> 0)
-      minimization (~> 0.2.0)
-      reportbuilder (~> 1.4)
-      rserve-client (~> 0.2.5)
-      rubyvis (~> 0.5)
-      spreadsheet (~> 0.6.5)
-      statsample-bivariate-extension (> 0)
-    statsample-bivariate-extension (1.1.0)
-      distribution (~> 0.6)
     text-table (1.2.3)
+    thread_safe (0.3.4)
+    tzinfo (1.2.1)
+      thread_safe (~> 0.1)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bio-statsample-timeseries
+  dirty-memoize
+  distribution
+  extendmatrix
   hoe
+  minimization
   minitest
   mocha (= 0.14.0)
+  rb-gsl
   rdoc
   reportbuilder
+  rserve-client
+  rubyvis
   shoulda (= 3.5.0)
   shoulda-matchers (= 2.2.0)
+  spreadsheet

data/History.txt

@@ -1,3 +1,9 @@
+=== 1.4.0 / 2014-10-11
+  * Replaced README.txt for README.md
+  * Replace File.exists? for File.exist?
+  + New Dataset.join to join two dataset based on some fields
+  * Deleted MLE based regression (Probit and logistic). Now all GML methods are on statsample-glm
+  
 === 1.3.1 / 2014-06-26
 
   * Example referred to a SimpleRegression class which doesn't exist. Updated to working example.

data/Manifest.txt

@@ -1,9 +1,10 @@
+.travis.yml
 Gemfile
 Gemfile.lock
 History.txt
 LICENSE.txt
 Manifest.txt
-README.txt
+README.md
 Rakefile
 benchmarks/correlation_matrix_15_variables.rb
 benchmarks/correlation_matrix_5_variables.rb
@@ -16,7 +17,6 @@ benchmarks/correlation_matrix_methods/correlation_matrix_with_graphics.ods
 benchmarks/correlation_matrix_methods/results.ds
 benchmarks/factor_map.rb
 benchmarks/helpers_benchmark.rb
-bin/statsample
 data/locale/es/LC_MESSAGES/statsample.mo
 doc_latex/manual/equations.tex
 examples/boxplot.rb
@@ -71,15 +71,8 @@ lib/statsample/graph/histogram.rb
 lib/statsample/graph/scatterplot.rb
 lib/statsample/histogram.rb
 lib/statsample/matrix.rb
-lib/statsample/mle.rb
-lib/statsample/mle/logit.rb
-lib/statsample/mle/normal.rb
-lib/statsample/mle/probit.rb
 lib/statsample/multiset.rb
 lib/statsample/regression.rb
-lib/statsample/regression/binomial.rb
-lib/statsample/regression/binomial/logit.rb
-lib/statsample/regression/binomial/probit.rb
 lib/statsample/regression/multiple.rb
 lib/statsample/regression/multiple/alglibengine.rb
 lib/statsample/regression/multiple/baseengine.rb
@@ -107,6 +100,7 @@ lib/statsample/test/umannwhitney.rb
 lib/statsample/test/wilcoxonsignedrank.rb
 lib/statsample/vector.rb
 lib/statsample/vector/gsl.rb
+lib/statsample/version.rb
 po/es/statsample.mo
 po/es/statsample.po
 po/statsample.pot
@@ -114,11 +108,9 @@ references.txt
 setup.rb
 test/fixtures/bank2.dat
 test/fixtures/correlation_matrix.rb
-test/fixtures/crime.txt
 test/fixtures/hartman_23.matrix
 test/fixtures/repeated_fields.csv
 test/fixtures/stock_data.csv
-test/fixtures/test_binomial.csv
 test/fixtures/test_csv.csv
 test/fixtures/test_xls.xls
 test/fixtures/tetmat_matrix.txt
@@ -143,9 +135,7 @@ test/test_factor_pa.rb
 test/test_ggobi.rb
 test/test_gsl.rb
 test/test_histogram.rb
-test/test_logit.rb
 test/test_matrix.rb
-test/test_mle.rb
 test/test_multiset.rb
 test/test_regression.rb
 test/test_reliability.rb

data/{README.txt → README.md}

@@ -1,9 +1,10 @@
-= Statsample
+# Statsample
 
-http://ruby-statsample.rubyforge.org/
+Homepage :: https://github.com/clbustos/statsample
 
+[![Build Status](https://travis-ci.org/clbustos/statsample.svg?branch=master)](https://travis-ci.org/clbustos/statsample)
 
-== DESCRIPTION:
+## DESCRIPTION
 
 A suite for basic and advanced statistics on Ruby. Tested on Ruby 2.1.1p76 (June 2014), 1.8.7, 1.9.1, 1.9.2 (April, 2010), ruby-head(June, 2011) and JRuby 1.4 (Ruby 1.8.7 compatible).
 
@@ -24,7 +25,7 @@ Include:
 * Creates reports on text, html and rtf, using ReportBuilder gem
 * Graphics: Histogram, Boxplot and Scatterplot
 
-== PRINCIPLES
+## Principles
 
 * Software Design: 
   * One module/class for each type of analysis
@@ -38,7 +39,7 @@ Include:
   * Go beyond Null Hiphotesis Testing, using confidence intervals and effect sizes when possible
   * (When possible) All references for methods are documented, providing sensible information on documentation 
 
-== FEATURES:
+## Features
 
 * Classes for manipulation and storage of data:
   * Statsample::Vector: An extension of an array, with statistical methods like sum, mean and standard deviation
@@ -81,7 +82,7 @@ Include:
 * Module Statsample::Test provides several methods and classes to perform inferencial statistics
   * Statsample::Test::BartlettSphericity
   * Statsample::Test::ChiSquare
-  * Statsample::Test::F  
+  * Statsample::Test::F
   * Statsample::Test::KolmogorovSmirnov (only D value)
   * Statsample::Test::Levene
   * Statsample::Test::UMannWhitney
@@ -95,81 +96,95 @@ Include:
 * Gem +statsample-sem+ provides a DSL to R libraries +sem+ and +OpenMx+
 * Close integration with gem <tt>reportbuilder</tt>, to easily create reports on text, html and rtf formats.
 
-== Examples of use:
-
-See multiples examples of use on [http://github.com/clbustos/statsample/tree/master/examples/]
-
-=== Boxplot
-
-    require 'statsample'
-    ss_analysis(Statsample::Graph::Boxplot) do 
-      n=30
-      a=rnorm(n-1,50,10)
-      b=rnorm(n, 30,5)
-      c=rnorm(n,5,1)
-      a.push(2)
-      boxplot(:vectors=>[a,b,c], :width=>300, :height=>300, :groups=>%w{first first second}, :minimum=>0)
-    end    
-    Statsample::Analysis.run # Open svg file on *nix application defined
-
-=== Correlation matrix
-
-    require 'statsample'
-    # Note R like generation of random gaussian variable
-    # and correlation matrix
-    
-    ss_analysis("Statsample::Bivariate.correlation_matrix") do
-      samples=1000
-      ds=data_frame(
-        'a'=>rnorm(samples), 
-        'b'=>rnorm(samples),
-        'c'=>rnorm(samples),
-        'd'=>rnorm(samples))
-      cm=cor(ds) 
-      summary(cm)
-    end
-    
-    Statsample::Analysis.run_batch # Echo output to console
-
-
-== REQUIREMENTS:
+# Examples of use:
+
+See the [examples folder](https://github.com/clbustos/statsample/tree/master/examples/) too.
+
+## Boxplot
+
+```ruby
+require 'statsample'
+
+ss_analysis(Statsample::Graph::Boxplot) do 
+  n=30
+  a=rnorm(n-1,50,10)
+  b=rnorm(n, 30,5)
+  c=rnorm(n,5,1)
+  a.push(2)
+  boxplot(:vectors=>[a,b,c], :width=>300, :height=>300, :groups=>%w{first first second}, :minimum=>0)
+end
+Statsample::Analysis.run # Open svg file on *nix application defined
+```
+
+### Correlation matrix
+
+```ruby
+require 'statsample'
+# Note R like generation of random gaussian variable
+# and correlation matrix
+
+ss_analysis("Statsample::Bivariate.correlation_matrix") do
+  samples=1000
+  ds=data_frame(
+    'a'=>rnorm(samples), 
+    'b'=>rnorm(samples),
+    'c'=>rnorm(samples),
+    'd'=>rnorm(samples))
+  cm=cor(ds) 
+  summary(cm)
+end
+
+Statsample::Analysis.run_batch # Echo output to console
+```
+
+## Requirements
 
 Optional: 
 
 * Plotting: gnuplot and rbgnuplot, SVG::Graph
-* Factorial analysis and polychorical correlation(joint estimate and polychoric series): gsl library and rb-gsl (http://rb-gsl.rubyforge.org/). You should install it using <tt>gem install gsl</tt>. 
+* Factorial analysis and polychorical correlation(joint estimate and polychoric series): gsl library and rb-gsl (https://rubygems.org/gems/rb-gsl/). You should install it using <tt>gem install rb-gsl</tt>. 
 
-<b>Note</b>: Use gsl 1.12.109 or later.
+*Note*: Use gsl 1.12.109 or later.
 
-== RESOURCES
+## Resources
 
-* Source code on github: http://github.com/clbustos/statsample
-* API: http://ruby-statsample.rubyforge.org/statsample/
-* Bug report and feature request: http://github.com/clbustos/statsample/issues
-* E-mailing list: http://groups.google.com/group/statsample
+* Source code on github :: http://github.com/clbustos/statsample
+* Docs :: http://rubydoc.info/gems/statsample/
+* Bug report and feature request :: http://github.com/clbustos/statsample/issues
+* E-mailing list :: http://groups.google.com/group/statsample
 
-== INSTALL:
+# Installation
 
-  $ sudo gem install statsample
+```bash
+$ sudo gem install statsample
+```
 
 On *nix, you should install statsample-optimization to retrieve gems gsl, statistics2 and a C extension to speed some methods. 
 
 There are available precompiled version for Ruby 1.9 on x86, x86_64 and mingw32 archs.
 
-  $ sudo gem install statsample-optimization
+```bash
+$ sudo gem install statsample-optimization
+```
 
 If you use Ruby 1.8, you should compile statsample-optimization, usign parameter <tt>--platform ruby</tt>
 
-  $ sudo gem install statsample-optimization --platform ruby
+```bash
+$ sudo gem install statsample-optimization --platform ruby
+```
 
 If you need to work on Structural Equation Modeling, you could see +statsample-sem+. You need R with +sem+ or +OpenMx+ [http://openmx.psyc.virginia.edu/] libraries installed
 
-  $ sudo gem install statsample-sem
+```bash
+$ sudo gem install statsample-sem
+```
 
 Available setup.rb file
 
-  sudo gem ruby setup.rb
+```bash
+sudo gem ruby setup.rb
+```
 
-== LICENSE:
+## License
 
 GPL-2 (See LICENSE.txt)

data/Rakefile

@@ -42,12 +42,14 @@ end
 
 h=Hoe.spec('statsample') do 
   self.version=Statsample::VERSION
+  self.urls=["https://github.com/clbustos/statsample"]
   #self.testlib=:minitest
-#  self.rubyforge_name = "ruby-statsample"
+  self.readme_file = 'README.md'
+  self.urls = ['https://github.com/clbustos/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_deps << ["spreadsheet","~>0.6"] <<  ["reportbuilder", "~>1.4"] << ["minimization", "~>0.2.0"] << ["fastercsv", ">0"] << ["dirty-memoize", "~>0.0"] << ["extendmatrix","~>0.3.1"] << ["statsample-bivariate-extension", ">0"] << ["rserve-client"] << ["rubyvis"] << ["distribution"]
   
-  self.extra_dev_deps << ["hoe","~>0"] << ["shoulda","~>3.1.1"] << ["minitest", "~>2.0"] << ["rserve-client", "~>0"] << ["gettext", "~>0"] << ["mocha", "~>0"] << ["hoe-git", "~>0"]
+  self.extra_dev_deps << ["hoe","~>0"] << ["shoulda","~>3"] << ["minitest", "~>2"]  << ["gettext", "~>0"] << ["mocha", "~>0"] << ["hoe-git", "~>0"]
   
   self.clean_globs << "test/images/*" << "demo/item_analysis/*" << "demo/Regression"
   self.post_install_message = <<-EOF
@@ -98,6 +100,7 @@ Rake::RDocTask.new(:docs) do |rd|
 end
 
 end
+
 desc 'Publish rdocs with analytics support'
 task :publicar_docs => [:clean, :docs] do
   ruby %{agregar_adsense_a_doc.rb}

data/lib/statsample.rb

@@ -133,7 +133,6 @@ module Statsample
   
   create_has_library :gsl
   
-  VERSION = '1.3.1'
   SPLIT_TOKEN = ","
   autoload(:Analysis, 'statsample/analysis')
   autoload(:Database, 'statsample/converters')
@@ -165,7 +164,7 @@ module Statsample
   class << self
     # Load a object saved on a file.
     def load(filename)
-      if File.exists? filename
+      if File.exist? filename
         o=false
         File.open(filename,"r") {|fp| o=Marshal.load(fp) }
         o
@@ -290,4 +289,4 @@ require 'statsample/dataset'
 require 'statsample/crosstab'
 require 'statsample/matrix'
 require 'statsample/shorthand'
-
+require 'statsample/version'