statsample 1.4.0 → 1.4.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.gitignore +14 -0
- data/Gemfile +1 -16
- data/History.txt +51 -46
- data/LICENSE.txt +7 -82
- data/README.md +145 -150
- data/Rakefile +20 -102
- data/lib/spss.rb +17 -14
- data/lib/statsample/crosstab.rb +2 -2
- data/lib/statsample/dataset.rb +82 -81
- data/lib/statsample/matrix.rb +43 -43
- data/lib/statsample/reliability.rb +1 -2
- data/lib/statsample/vector.rb +157 -124
- data/lib/statsample/version.rb +1 -1
- data/lib/statsample.rb +91 -91
- data/references.txt +2 -1
- data/statsample.gemspec +89 -0
- data/test/test_awesome_print_bug.rb +16 -0
- data/test/test_crosstab.rb +8 -0
- data/test/test_histogram.rb +7 -0
- data/test/test_vector.rb +62 -48
- metadata +109 -120
- data/.gemtest +0 -0
- data/Gemfile.lock +0 -78
- data/Manifest.txt +0 -157
- data/setup.rb +0 -1585
data/README.md
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# Statsample
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[](https://travis-ci.org/SciRuby/statsample)
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[](https://codeclimate.com/github/SciRuby/statsample)
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[](http://badge.fury.io/rb/statsample)
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Homepage :: https://github.com/sciruby/statsample
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# Installation
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You should have a recent version of GSL and R (with the `irr` and `Rserve` libraries) installed. In Ubuntu:
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```bash
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$ sudo apt-get install libgs10-dev r-base r-base-dev
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$ sudo Rscript -e "install.packages(c('Rserve', 'irr'))"
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```
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With these libraries in place, just install from rubygems:
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```bash
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$ [sudo] gem install statsample
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```
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On *nix, you should install statsample-optimization to retrieve gems gsl, statistics2 and a C extension to speed some methods.
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```bash
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$ [sudo] gem install statsample-optimization
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```
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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
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```bash
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$ [sudo] gem install statsample-sem
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```
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# Description
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A suite for basic and advanced statistics on Ruby. Tested on CRuby 1.9.3, 2.0.0 and 2.1.1. See `.travis.yml` for more information.
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Include:
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- Descriptive statistics: frequencies, median, mean, standard error, skew, kurtosis (and many others).
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- Imports and exports datasets from and to Excel, CSV and plain text files.
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- Correlations: Pearson's r, Spearman's rank correlation (rho), point biserial, tau a, tau b and gamma. Tetrachoric and Polychoric correlation provides by +statsample-bivariate-extension+ gem.
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- Intra-class correlation
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- Anova: generic and vector-based One-way ANOVA and Two-way ANOVA, with contrasts for One-way ANOVA.
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- Tests: F, T, Levene, U-Mannwhitney.
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- Regression: Simple, Multiple (OLS), Probit and Logit
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- Factorial Analysis: Extraction (PCA and Principal Axis), Rotation (Varimax, Equimax, Quartimax) and Parallel Analysis and Velicer's MAP test, for estimation of number of factors.
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- Reliability analysis for simple scale and a DSL to easily analyze multiple scales using factor analysis and correlations, if you want it.
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- Basic time series support
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- Dominance Analysis, with multivariate dependent and bootstrap (Azen & Budescu)
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- Sample calculation related formulas
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- Structural Equation Modeling (SEM), using R libraries +sem+ and +OpenMx+
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- Creates reports on text, html and rtf, using ReportBuilder gem
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- Graphics: Histogram, Boxplot and Scatterplot
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## Principles
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- Software Design:
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- One module/class for each type of analysis
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- Options can be set as hash on initialize() or as setters methods
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- Clean API for interactive sessions
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- summary() returns all necessary informacion for interactive sessions
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- All statistical data available though methods on objects
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- All (important) methods should be tested. Better with random data.
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- Statistical Design
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- Results are tested against text results, SPSS and R outputs.
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- Go beyond Null Hiphotesis Testing, using confidence intervals and effect sizes when possible
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- (When possible) All references for methods are documented, providing sensible information on documentation
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# Features
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- Classes for manipulation and storage of data:
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- Statsample::Vector: An extension of an array, with statistical methods like sum, mean and standard deviation
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- Statsample::Dataset: a group of Statsample::Vector, analog to a excel spreadsheet or a dataframe on R. The base of almost all operations on statsample.
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- Statsample::Multiset: multiple datasets with same fields and type of vectors
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- Anova module provides generic Statsample::Anova::OneWay and vector based Statsample::Anova::OneWayWithVectors. Also you can create contrast using Statsample::Anova::Contrast
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- Module Statsample::Bivariate provides covariance and pearson, spearman, point biserial, tau a, tau b, gamma, tetrachoric (see Bivariate::Tetrachoric) and polychoric (see Bivariate::Polychoric) correlations. Include methods to create correlation and covariance matrices
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- Multiple types of regression.
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- Simple Regression : Statsample::Regression::Simple
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- Multiple Regression: Statsample::Regression::Multiple
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- Logit Regression: Statsample::Regression::Binomial::Logit
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- Probit Regression: Statsample::Regression::Binomial::Probit
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- Factorial Analysis algorithms on Statsample::Factor module.
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- Classes for Extraction of factors:
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- Statsample::Factor::PCA
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- Statsample::Factor::PrincipalAxis
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- Classes for Rotation of factors:
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- Statsample::Factor::Varimax
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- Statsample::Factor::Equimax
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- Statsample::Factor::Quartimax
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- Classes for calculation of factors to retain
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- Statsample::Factor::ParallelAnalysis performs Horn's 'parallel analysis' to a principal components analysis to adjust for sample bias in the retention of components.
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- Statsample::Factor::MAP performs Velicer's Minimum Average Partial (MAP) test, which retain components as long as the variance in the correlation matrix represents systematic variance.
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- Dominance Analysis. Based on Budescu and Azen papers, dominance analysis is a method to analyze the relative importance of one predictor relative to another on multiple regression
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- Statsample::DominanceAnalysis class can report dominance analysis for a sample, using uni or multivariate dependent variables
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- Statsample::DominanceAnalysis::Bootstrap can execute bootstrap analysis to determine dominance stability, as recomended by Azen & Budescu (2003) link[http://psycnet.apa.org/journals/met/8/2/129/].
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- Module Statsample::Codification, to help to codify open questions
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- Converters to import and export data:
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- Statsample::Database : Can create sql to create tables, read and insert data
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- Statsample::CSV : Read and write CSV files
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- Statsample::Excel : Read and write Excel files
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- Statsample::Mx : Write Mx Files
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- Statsample::GGobi : Write Ggobi files
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- Module Statsample::Crosstab provides function to create crosstab for categorical data
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- Module Statsample::Reliability provides functions to analyze scales with psychometric methods.
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- Class Statsample::Reliability::ScaleAnalysis provides statistics like mean, standard deviation for a scale, Cronbach's alpha and standarized Cronbach's alpha, and for each item: mean, correlation with total scale, mean if deleted, Cronbach's alpha is deleted.
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- Class Statsample::Reliability::MultiScaleAnalysis provides a DSL to easily analyze reliability of multiple scales and retrieve correlation matrix and factor analysis of them.
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- Class Statsample::Reliability::ICC provides intra-class correlation, using Shrout & Fleiss(1979) and McGraw & Wong (1996) formulations.
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- Module Statsample::SRS (Simple Random Sampling) provides a lot of functions to estimate standard error for several type of samples
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- Module Statsample::Test provides several methods and classes to perform inferencial statistics
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- Statsample::Test::BartlettSphericity
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- Statsample::Test::ChiSquare
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- Statsample::Test::F
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- Statsample::Test::KolmogorovSmirnov (only D value)
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- Statsample::Test::Levene
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- Statsample::Test::UMannWhitney
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- Statsample::Test::T
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- Statsample::Test::WilcoxonSignedRank
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- Module Graph provides several classes to create beautiful graphs using rubyvis
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- Statsample::Graph::Boxplot
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- Statsample::Graph::Histogram
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- Statsample::Graph::Scatterplot
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- Gem <tt>bio-statsample-timeseries</tt> provides module Statsample::TimeSeries with support for time series, including ARIMA estimation using Kalman-Filter.
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- Gem <tt>statsample-sem</tt> provides a DSL to R libraries +sem+ and +OpenMx+
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- Gem <tt>statsample-glm</tt> provides you with GML method, to work with Logistic, Poisson and Gaussian regression ,using ML or IRWLS.
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- Close integration with gem <tt>reportbuilder</tt>, to easily create reports on text, html and rtf formats.
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# Usage
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See the [examples folder](https://github.com/clbustos/statsample/tree/master/examples/) too.
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```ruby
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require 'statsample'
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ss_analysis(Statsample::Graph::Boxplot) do
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n=30
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a=rnorm(n-1,50,10)
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b=rnorm(n, 30,5)
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c=rnorm(n,5,1)
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ss_analysis(Statsample::Graph::Boxplot) do
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a = rnorm(n-1, 50, 10)
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a.push(2)
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boxplot(:
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boxplot(vectors: [a, b, c],
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width: 300,
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height: 300,
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groups: %w{first first second},
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minimum: 0)
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end
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Statsample::Analysis.run # Open svg file on *nix application defined
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```
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## Correlation matrix
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```ruby
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require 'statsample'
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# and correlation matrix
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ss_analysis("Statsample::Bivariate.correlation_matrix") do
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ds=data_frame(
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'a'=>rnorm(samples),
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'b'=>rnorm(samples),
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'c'=>rnorm(samples),
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'd'=>rnorm(samples))
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cm=cor(ds)
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ds = data_frame(
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'a' => rnorm(samples),
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'b' => rnorm(samples),
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'c' => rnorm(samples),
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'd' => rnorm(samples))
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cm = cor(ds)
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summary(cm)
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end
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Statsample::Analysis.run_batch # Echo output to console
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```
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* Plotting: gnuplot and rbgnuplot, SVG::Graph
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* 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>.
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*Note*: Use gsl 1.12.109 or later.
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## Resources
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* Source code on github :: http://github.com/clbustos/statsample
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* Docs :: http://rubydoc.info/gems/statsample/
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* Bug report and feature request :: http://github.com/clbustos/statsample/issues
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* E-mailing list :: http://groups.google.com/group/statsample
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# Installation
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```bash
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```
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On *nix, you should install statsample-optimization to retrieve gems gsl, statistics2 and a C extension to speed some methods.
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There are available precompiled version for Ruby 1.9 on x86, x86_64 and mingw32 archs.
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```
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# Resources
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- Source code on github :: http://github.com/sciruby/statsample
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- Bug report and feature request :: http://github.com/sciruby/statsample/issues
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- E-mailing list :: https://groups.google.com/forum/#!forum/sciruby-dev
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$ sudo gem install statsample-optimization --platform ruby
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```
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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
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177
|
-
|
|
178
|
-
```bash
|
|
179
|
-
$ sudo gem install statsample-sem
|
|
180
|
-
```
|
|
181
|
-
|
|
182
|
-
Available setup.rb file
|
|
183
|
-
|
|
184
|
-
```bash
|
|
185
|
-
sudo gem ruby setup.rb
|
|
186
|
-
```
|
|
181
|
+
# License
|
|
187
182
|
|
|
188
|
-
|
|
183
|
+
BSD-3 (See LICENSE.txt)
|
|
189
184
|
|
|
190
|
-
|
|
185
|
+
Could change between version, without previous warning. If you want a specific license, just choose the version that you need.
|
data/Rakefile
CHANGED
|
@@ -1,32 +1,30 @@
|
|
|
1
|
-
|
|
2
|
-
# -*- ruby -*-
|
|
3
|
-
# -*- coding: utf-8 -*-
|
|
4
|
-
$:.unshift(File.dirname(__FILE__)+'/lib/')
|
|
1
|
+
$:.unshift File.expand_path("../lib/", __FILE__)
|
|
5
2
|
|
|
6
|
-
require '
|
|
7
|
-
require '
|
|
8
|
-
require '
|
|
9
|
-
require 'rdoc'
|
|
3
|
+
require 'statsample/version'
|
|
4
|
+
require 'rake'
|
|
5
|
+
require 'rake/testtask'
|
|
6
|
+
require 'rdoc/task'
|
|
7
|
+
require 'bundler/gem_tasks'
|
|
10
8
|
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
end
|
|
20
|
-
}
|
|
9
|
+
# Setup the necessary gems, specified in the gemspec.
|
|
10
|
+
require 'bundler'
|
|
11
|
+
begin
|
|
12
|
+
Bundler.setup(:default, :development)
|
|
13
|
+
rescue Bundler::BundlerError => e
|
|
14
|
+
$stderr.puts e.message
|
|
15
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
|
16
|
+
exit e.status_code
|
|
21
17
|
end
|
|
22
18
|
|
|
23
|
-
|
|
24
|
-
|
|
19
|
+
Rake::TestTask.new do |t|
|
|
20
|
+
t.pattern = "test/test_*.rb"
|
|
25
21
|
end
|
|
26
22
|
|
|
27
|
-
|
|
28
|
-
|
|
23
|
+
RDoc::Task.new do |rdoc|
|
|
24
|
+
rdoc.main = "README.md"
|
|
25
|
+
rdoc.rdoc_files.include("README.md", "lib", "History.txt", "LICENSE.txt", "references.txt")
|
|
29
26
|
end
|
|
27
|
+
|
|
30
28
|
desc "Update pot/po files."
|
|
31
29
|
task "gettext:updatepo" do
|
|
32
30
|
require 'gettext/tools'
|
|
@@ -37,84 +35,4 @@ desc "Create mo-files"
|
|
|
37
35
|
task "gettext:makemo" do
|
|
38
36
|
require 'gettext/tools'
|
|
39
37
|
GetText.create_mofiles()
|
|
40
|
-
# GetText.create_mofiles(true, "po", "locale") # This is for "Ruby on Rails".
|
|
41
|
-
end
|
|
42
|
-
|
|
43
|
-
h=Hoe.spec('statsample') do
|
|
44
|
-
self.version=Statsample::VERSION
|
|
45
|
-
self.urls=["https://github.com/clbustos/statsample"]
|
|
46
|
-
#self.testlib=:minitest
|
|
47
|
-
self.readme_file = 'README.md'
|
|
48
|
-
self.urls = ['https://github.com/clbustos/statsample']
|
|
49
|
-
self.developer('Claudio Bustos', 'clbustos@gmail.com')
|
|
50
|
-
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"]
|
|
51
|
-
|
|
52
|
-
self.extra_dev_deps << ["hoe","~>0"] << ["shoulda","~>3"] << ["minitest", "~>2"] << ["gettext", "~>0"] << ["mocha", "~>0"] << ["hoe-git", "~>0"]
|
|
53
|
-
|
|
54
|
-
self.clean_globs << "test/images/*" << "demo/item_analysis/*" << "demo/Regression"
|
|
55
|
-
self.post_install_message = <<-EOF
|
|
56
|
-
***************************************************
|
|
57
|
-
Thanks for installing statsample.
|
|
58
|
-
|
|
59
|
-
On *nix, you could install statsample-optimization
|
|
60
|
-
to retrieve gems gsl, statistics2 and a C extension
|
|
61
|
-
to speed some methods.
|
|
62
|
-
|
|
63
|
-
$ sudo gem install statsample-optimization
|
|
64
|
-
|
|
65
|
-
On Ubuntu, install build-essential and libgsl0-dev
|
|
66
|
-
using apt-get. Compile ruby 1.8 or 1.9 from
|
|
67
|
-
source code first.
|
|
68
|
-
|
|
69
|
-
$ sudo apt-get install build-essential libgsl0-dev
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
*****************************************************
|
|
73
|
-
EOF
|
|
74
|
-
self.need_rdoc=false
|
|
75
|
-
end
|
|
76
|
-
|
|
77
|
-
if Rake.const_defined?(:RDocTask)
|
|
78
|
-
Rake::RDocTask.new(:docs) do |rd|
|
|
79
|
-
rd.main = h.readme_file
|
|
80
|
-
rd.options << '-d' if (`which dot` =~ /\/dot/) unless
|
|
81
|
-
ENV['NODOT'] || Hoe::WINDOZE
|
|
82
|
-
rd.rdoc_dir = 'doc'
|
|
83
|
-
|
|
84
|
-
rd.rdoc_files.include("lib/**/*.rb")
|
|
85
|
-
rd.rdoc_files += h.spec.extra_rdoc_files
|
|
86
|
-
rd.rdoc_files.reject! {|f| f=="Manifest.txt"}
|
|
87
|
-
title = h.spec.rdoc_options.grep(/^(-t|--title)=?$/).first
|
|
88
|
-
if title then
|
|
89
|
-
rd.options << title
|
|
90
|
-
|
|
91
|
-
unless title =~ /\=/ then # for ['-t', 'title here']
|
|
92
|
-
title_index = spec.rdoc_options.index(title)
|
|
93
|
-
rd.options << spec.rdoc_options[title_index + 1]
|
|
94
|
-
end
|
|
95
|
-
else
|
|
96
|
-
title = "#{h.name}-#{h.version} Documentation"
|
|
97
|
-
title = "#{h.rubyforge_name}'s " + title if h.rubyforge_name != h.name
|
|
98
|
-
rd.options << '--title' << title
|
|
99
|
-
end
|
|
100
|
-
end
|
|
101
|
-
|
|
102
|
-
end
|
|
103
|
-
|
|
104
|
-
desc 'Publish rdocs with analytics support'
|
|
105
|
-
task :publicar_docs => [:clean, :docs] do
|
|
106
|
-
ruby %{agregar_adsense_a_doc.rb}
|
|
107
|
-
path = File.expand_path("~/.rubyforge/user-config.yml")
|
|
108
|
-
config = YAML.load(File.read(path))
|
|
109
|
-
host = "#{config["username"]}@rubyforge.org"
|
|
110
|
-
|
|
111
|
-
remote_dir = "/var/www/gforge-projects/#{h.rubyforge_name}/#{h.remote_rdoc_dir
|
|
112
|
-
}"
|
|
113
|
-
local_dir = h.local_rdoc_dir
|
|
114
|
-
Dir.glob(local_dir+"/**/*") {|file|
|
|
115
|
-
sh %{chmod 755 #{file}}
|
|
116
|
-
}
|
|
117
|
-
sh %{rsync #{h.rsync_args} #{local_dir}/ #{host}:#{remote_dir}}
|
|
118
38
|
end
|
|
119
|
-
|
|
120
|
-
# vim: syntax=Ruby
|
data/lib/spss.rb
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
# = spss.rb -
|
|
1
|
+
# = spss.rb -
|
|
2
2
|
#
|
|
3
3
|
# Provides utilites for working with spss files
|
|
4
4
|
#
|
|
@@ -12,40 +12,43 @@ module SPSS # :nodoc: all
|
|
|
12
12
|
def add(a)
|
|
13
13
|
@elements.push(a)
|
|
14
14
|
end
|
|
15
|
-
|
|
16
|
-
|
|
15
|
+
|
|
16
|
+
def parse_elements(func = :to_s)
|
|
17
|
+
@elements.collect{ |e| " "+e.send(func) }.join("\n")
|
|
17
18
|
end
|
|
19
|
+
|
|
18
20
|
def init_with config
|
|
19
|
-
config.each
|
|
20
|
-
self.send(key.to_s+"=",value) if methods.include? key.to_s
|
|
21
|
-
|
|
21
|
+
config.each do |key, value|
|
|
22
|
+
self.send(key.to_s + "=", value) if methods.include? key.to_s
|
|
23
|
+
end
|
|
22
24
|
end
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
@
|
|
25
|
+
|
|
26
|
+
def initialize(config = {})
|
|
27
|
+
@config = config
|
|
28
|
+
@elements = []
|
|
26
29
|
end
|
|
27
30
|
end
|
|
28
31
|
class Dictionary < Element
|
|
29
32
|
attr_accessor :locale, :date_time, :row_count
|
|
30
|
-
def initialize(config={})
|
|
33
|
+
def initialize(config = {})
|
|
31
34
|
super
|
|
32
35
|
init_with ({
|
|
33
|
-
:locale=>"en_US",
|
|
36
|
+
:locale=>"en_US",
|
|
34
37
|
:date_time=>Time.new().strftime("%Y-%m-%dT%H:%M:%S"),
|
|
35
38
|
:row_count=>1
|
|
36
39
|
})
|
|
37
40
|
init_with config
|
|
38
41
|
end
|
|
39
|
-
|
|
42
|
+
|
|
40
43
|
def to_xml
|
|
41
44
|
"<dictionary locale='#{@locale}' creationDateTime='#{@date_time}' rowCount='#{@row_count}' xmlns='http://xml.spss.com/spss/data'>\n"+parse_elements(:to_xml)+"\n</dictionary>"
|
|
42
|
-
|
|
45
|
+
|
|
43
46
|
end
|
|
44
47
|
def to_spss
|
|
45
48
|
parse_elements(:to_spss)
|
|
46
49
|
end
|
|
47
50
|
end
|
|
48
|
-
|
|
51
|
+
|
|
49
52
|
class MissingValue < Element
|
|
50
53
|
attr_accessor :data, :type, :from, :to
|
|
51
54
|
def initialize(data,type=nil)
|
data/lib/statsample/crosstab.rb
CHANGED
|
@@ -8,9 +8,9 @@ module Statsample
|
|
|
8
8
|
attr_reader :v_rows, :v_cols
|
|
9
9
|
attr_accessor :row_label, :column_label, :name, :percentage_row, :percentage_column, :percentage_total
|
|
10
10
|
def initialize(v1, v2, opts=Hash.new)
|
|
11
|
-
raise ArgumentError, "Both arguments should be Vectors" unless v1.is_a? Statsample::Vector and v2.is_a? Statsample::Vector
|
|
11
|
+
#raise ArgumentError, "Both arguments should be Vectors" unless v1.is_a? Statsample::Vector and v2.is_a? Statsample::Vector
|
|
12
12
|
raise ArgumentError, "Vectors should be the same size" unless v1.size==v2.size
|
|
13
|
-
@v_rows, @v_cols=Statsample.only_valid_clone(v1,v2)
|
|
13
|
+
@v_rows, @v_cols=Statsample.only_valid_clone(v1.to_vector,v2.to_vector)
|
|
14
14
|
@cases=@v_rows.size
|
|
15
15
|
@row_label=v1.name
|
|
16
16
|
@column_label=v2.name
|