statsample-ekatena 2.0.2
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- checksums.yaml +7 -0
- data/.gitignore +15 -0
- data/.travis.yml +23 -0
- data/CONTRIBUTING.md +17 -0
- data/Gemfile +2 -0
- data/History.txt +457 -0
- data/LICENSE.txt +12 -0
- data/README.md +175 -0
- data/Rakefile +44 -0
- data/benchmarks/correlation_matrix_15_variables.rb +32 -0
- data/benchmarks/correlation_matrix_5_variables.rb +33 -0
- data/benchmarks/correlation_matrix_methods/correlation_matrix.ds +0 -0
- data/benchmarks/correlation_matrix_methods/correlation_matrix.html +93 -0
- data/benchmarks/correlation_matrix_methods/correlation_matrix.rb +71 -0
- data/benchmarks/correlation_matrix_methods/correlation_matrix.xls +0 -0
- data/benchmarks/correlation_matrix_methods/correlation_matrix_gsl_ruby.ods +0 -0
- data/benchmarks/correlation_matrix_methods/correlation_matrix_with_graphics.ods +0 -0
- data/benchmarks/correlation_matrix_methods/results.ds +0 -0
- data/benchmarks/factor_map.rb +37 -0
- data/benchmarks/helpers_benchmark.rb +5 -0
- data/data/locale/es/LC_MESSAGES/statsample.mo +0 -0
- data/doc_latex/manual/equations.tex +78 -0
- data/examples/boxplot.rb +28 -0
- data/examples/chisquare_test.rb +23 -0
- data/examples/correlation_matrix.rb +32 -0
- data/examples/dataset.rb +30 -0
- data/examples/dominance_analysis.rb +33 -0
- data/examples/dominance_analysis_bootstrap.rb +32 -0
- data/examples/histogram.rb +26 -0
- data/examples/icc.rb +24 -0
- data/examples/levene.rb +29 -0
- data/examples/multiple_regression.rb +20 -0
- data/examples/multivariate_correlation.rb +33 -0
- data/examples/parallel_analysis.rb +40 -0
- data/examples/polychoric.rb +40 -0
- data/examples/principal_axis.rb +26 -0
- data/examples/reliability.rb +31 -0
- data/examples/scatterplot.rb +25 -0
- data/examples/t_test.rb +27 -0
- data/examples/tetrachoric.rb +17 -0
- data/examples/u_test.rb +24 -0
- data/examples/vector.rb +20 -0
- data/examples/velicer_map_test.rb +46 -0
- data/grab_references.rb +29 -0
- data/lib/spss.rb +134 -0
- data/lib/statsample-ekatena/analysis.rb +100 -0
- data/lib/statsample-ekatena/analysis/suite.rb +89 -0
- data/lib/statsample-ekatena/analysis/suitereportbuilder.rb +44 -0
- data/lib/statsample-ekatena/anova.rb +24 -0
- data/lib/statsample-ekatena/anova/contrast.rb +79 -0
- data/lib/statsample-ekatena/anova/oneway.rb +187 -0
- data/lib/statsample-ekatena/anova/twoway.rb +207 -0
- data/lib/statsample-ekatena/bivariate.rb +406 -0
- data/lib/statsample-ekatena/bivariate/pearson.rb +54 -0
- data/lib/statsample-ekatena/codification.rb +182 -0
- data/lib/statsample-ekatena/converter/csv.rb +28 -0
- data/lib/statsample-ekatena/converter/spss.rb +48 -0
- data/lib/statsample-ekatena/converters.rb +211 -0
- data/lib/statsample-ekatena/crosstab.rb +188 -0
- data/lib/statsample-ekatena/daru.rb +115 -0
- data/lib/statsample-ekatena/dataset.rb +10 -0
- data/lib/statsample-ekatena/dominanceanalysis.rb +425 -0
- data/lib/statsample-ekatena/dominanceanalysis/bootstrap.rb +232 -0
- data/lib/statsample-ekatena/factor.rb +104 -0
- data/lib/statsample-ekatena/factor/map.rb +124 -0
- data/lib/statsample-ekatena/factor/parallelanalysis.rb +166 -0
- data/lib/statsample-ekatena/factor/pca.rb +242 -0
- data/lib/statsample-ekatena/factor/principalaxis.rb +243 -0
- data/lib/statsample-ekatena/factor/rotation.rb +198 -0
- data/lib/statsample-ekatena/formula/fit_model.rb +46 -0
- data/lib/statsample-ekatena/formula/formula.rb +306 -0
- data/lib/statsample-ekatena/graph.rb +11 -0
- data/lib/statsample-ekatena/graph/boxplot.rb +236 -0
- data/lib/statsample-ekatena/graph/histogram.rb +198 -0
- data/lib/statsample-ekatena/graph/scatterplot.rb +213 -0
- data/lib/statsample-ekatena/histogram.rb +180 -0
- data/lib/statsample-ekatena/matrix.rb +329 -0
- data/lib/statsample-ekatena/multiset.rb +310 -0
- data/lib/statsample-ekatena/regression.rb +65 -0
- data/lib/statsample-ekatena/regression/multiple.rb +89 -0
- data/lib/statsample-ekatena/regression/multiple/alglibengine.rb +128 -0
- data/lib/statsample-ekatena/regression/multiple/baseengine.rb +251 -0
- data/lib/statsample-ekatena/regression/multiple/gslengine.rb +129 -0
- data/lib/statsample-ekatena/regression/multiple/matrixengine.rb +205 -0
- data/lib/statsample-ekatena/regression/multiple/rubyengine.rb +86 -0
- data/lib/statsample-ekatena/regression/simple.rb +121 -0
- data/lib/statsample-ekatena/reliability.rb +150 -0
- data/lib/statsample-ekatena/reliability/icc.rb +415 -0
- data/lib/statsample-ekatena/reliability/multiscaleanalysis.rb +181 -0
- data/lib/statsample-ekatena/reliability/scaleanalysis.rb +233 -0
- data/lib/statsample-ekatena/reliability/skillscaleanalysis.rb +114 -0
- data/lib/statsample-ekatena/resample.rb +15 -0
- data/lib/statsample-ekatena/shorthand.rb +125 -0
- data/lib/statsample-ekatena/srs.rb +169 -0
- data/lib/statsample-ekatena/test.rb +82 -0
- data/lib/statsample-ekatena/test/bartlettsphericity.rb +45 -0
- data/lib/statsample-ekatena/test/chisquare.rb +73 -0
- data/lib/statsample-ekatena/test/f.rb +52 -0
- data/lib/statsample-ekatena/test/kolmogorovsmirnov.rb +63 -0
- data/lib/statsample-ekatena/test/levene.rb +88 -0
- data/lib/statsample-ekatena/test/t.rb +309 -0
- data/lib/statsample-ekatena/test/umannwhitney.rb +208 -0
- data/lib/statsample-ekatena/test/wilcoxonsignedrank.rb +90 -0
- data/lib/statsample-ekatena/vector.rb +19 -0
- data/lib/statsample-ekatena/version.rb +3 -0
- data/lib/statsample.rb +282 -0
- data/po/es/statsample.mo +0 -0
- data/po/es/statsample.po +959 -0
- data/po/statsample.pot +947 -0
- data/references.txt +24 -0
- data/statsample-ekatena.gemspec +49 -0
- data/test/fixtures/bank2.dat +200 -0
- data/test/fixtures/correlation_matrix.rb +17 -0
- data/test/fixtures/df.csv +15 -0
- data/test/fixtures/hartman_23.matrix +9 -0
- data/test/fixtures/stock_data.csv +500 -0
- data/test/fixtures/tetmat_matrix.txt +5 -0
- data/test/fixtures/tetmat_test.txt +1001 -0
- data/test/helpers_tests.rb +83 -0
- data/test/test_analysis.rb +176 -0
- data/test/test_anova_contrast.rb +36 -0
- data/test/test_anovaoneway.rb +26 -0
- data/test/test_anovatwoway.rb +37 -0
- data/test/test_anovatwowaywithdataset.rb +47 -0
- data/test/test_anovawithvectors.rb +102 -0
- data/test/test_awesome_print_bug.rb +16 -0
- data/test/test_bartlettsphericity.rb +25 -0
- data/test/test_bivariate.rb +164 -0
- data/test/test_codification.rb +78 -0
- data/test/test_crosstab.rb +67 -0
- data/test/test_dominance_analysis.rb +39 -0
- data/test/test_factor.rb +228 -0
- data/test/test_factor_map.rb +38 -0
- data/test/test_factor_pa.rb +56 -0
- data/test/test_fit_model.rb +88 -0
- data/test/test_ggobi.rb +35 -0
- data/test/test_gsl.rb +15 -0
- data/test/test_histogram.rb +109 -0
- data/test/test_matrix.rb +48 -0
- data/test/test_multiset.rb +176 -0
- data/test/test_regression.rb +231 -0
- data/test/test_reliability.rb +223 -0
- data/test/test_reliability_icc.rb +198 -0
- data/test/test_reliability_skillscale.rb +57 -0
- data/test/test_resample.rb +24 -0
- data/test/test_srs.rb +9 -0
- data/test/test_statistics.rb +69 -0
- data/test/test_stest.rb +69 -0
- data/test/test_stratified.rb +17 -0
- data/test/test_test_f.rb +33 -0
- data/test/test_test_kolmogorovsmirnov.rb +34 -0
- data/test/test_test_t.rb +62 -0
- data/test/test_umannwhitney.rb +27 -0
- data/test/test_vector.rb +12 -0
- data/test/test_wilcoxonsignedrank.rb +64 -0
- metadata +570 -0
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module Statsample
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module Reliability
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# = Intra-class correlation
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# According to Shrout & Fleiss (1979, p.422): "ICC is the correlation
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# between one measurement (either a single rating or a mean of
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# several ratings) on a target and another measurement obtained on that target"
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# == Usage
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# require 'statsample'
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# size = 1000
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# a = Daru::Vector.new(size.times.map {rand(10)})
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# b = a.recode{|i|i+rand(4)-2}
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# c = a.recode{|i|i+rand(4)-2}
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# d = a.recode{|i|i+rand(4)-2}
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# ds = Daru::DataFrame.new({:a => a,:b => b,:c => c,:d => d})
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# # Use :type attribute to set type to summarize
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# icc=Statsample::Reliability::ICC.new(ds, :type=>:icc_1_k)
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# puts icc.summary
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#
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# == Reference
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# * Shrout,P. & Fleiss, J. (1979). Intraclass Correlation: Uses in assessing rater reliability. Psychological Bulletin, 86(2), 420-428
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# * McGraw, K. & Wong, S.P. (1996). Forming Inferences About Some Intraclass Correlation Coefficients. Psychological methods, 1(1), 30-46.
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class ICC
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include Summarizable
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# Create a ICC analysis for a given dataset
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# Each vector is a different measurement. Only uses complete data
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# (listwise deletion).
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#
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attr_reader :df_bt
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attr_reader :df_wt
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attr_reader :df_bj
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attr_reader :df_residual
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attr_reader :ms_bt
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attr_reader :ms_wt
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attr_reader :ms_bj
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attr_reader :ms_residual
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alias :bms :ms_bt
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alias :wms :ms_wt
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alias :jms :ms_bj
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alias :ems :ms_residual
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alias :msr :ms_bt
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alias :msw :ms_wt
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alias :msc :ms_bj
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alias :mse :ms_residual
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# :section: Shrout and Fleiss ICC denominations
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attr_reader :icc_1_1
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attr_reader :icc_2_1
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attr_reader :icc_3_1
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attr_reader :icc_1_k
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attr_reader :icc_2_k
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attr_reader :icc_3_k
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# :section: McGraw and Wong ICC denominations
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attr_reader :icc_1
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attr_reader :icc_c_1
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attr_reader :icc_a_1
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attr_reader :icc_k
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attr_reader :icc_c_k
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attr_reader :icc_a_k
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attr_reader :n, :k
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attr_reader :total_mean
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# Type of analysis, for easy summarization
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# By default, set to :icc_1
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# * Shrout & Fleiss(1979) denominations
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# * :icc_1_1
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# * :icc_2_1
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# * :icc_3_1
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# * :icc_1_k
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# * :icc_2_k
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# * :icc_3_k
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# * McGraw & Wong (1996) denominations
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# * :icc_1
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# * :icc_k
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# * :icc_c_1
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# * :icc_c_k
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# * :icc_a_1
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# * :icc_a_k
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attr_reader :type
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# ICC value, set with :type
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attr_reader :r
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attr_reader :f
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attr_reader :lbound
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attr_reader :ubound
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attr_accessor :g_rho
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attr_accessor :alpha
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attr_accessor :name
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def initialize(ds, opts=Hash.new)
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@ds=ds.reject_values(*Daru::MISSING_VALUES)
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@vectors=@ds.map { |e| e }
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@n=@ds.nrows
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@k=@ds.ncols
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compute
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@g_rho=0
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@alpha=0.05
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@icc_name=nil
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opts_default={:name=>"Intra-class correlation", :type=>:icc_1}
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@opts=opts_default.merge(opts)
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@opts.each{|k,v| self.send("#{k}=",v) if self.respond_to? k }
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end
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def type=(v)
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case v
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when :icc_1_1
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@icc_name=_("Shrout & Fleiss ICC(1,1)")
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@r=@icc_1_1
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@f=icc_1_f
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@lbound, @ubound=icc_1_1_ci(@alpha)
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when :icc_2_1
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@icc_name=_("Shrout & Fleiss ICC(2,1)")
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@r=@icc_2_1
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@f=icc_2_f
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@lbound, @ubound=icc_2_1_ci(@alpha)
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when :icc_3_1
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@icc_name=_("Shrout & Fleiss ICC(3,1)")
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@r=@icc_3_1
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@f=icc_3_f
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@lbound, @ubound=icc_3_1_ci(@alpha)
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when :icc_1_k
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@icc_name=_("Shrout & Fleiss ICC(1,k)")
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@r=@icc_1_k
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@f=icc_1_k_f
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@lbound, @ubound=icc_1_k_ci(@alpha)
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when :icc_2_k
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@icc_name=_("Shrout & Fleiss ICC(2,k)")
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@r=@icc_2_k
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@f=icc_2_k_f
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@lbound, @ubound=icc_2_k_ci(@alpha)
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when :icc_3_k
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@icc_name=_("Shrout & Fleiss ICC(3,k)")
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@r=@icc_3_k
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@f=icc_3_k_f
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@lbound, @ubound=icc_3_k_ci(@alpha)
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when :icc_1
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@icc_name=_("McGraw & Wong ICC(1)")
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@r=@icc_1_1
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@f=icc_1_f(@g_rho)
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@lbound, @ubound=icc_1_1_ci(@alpha)
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when :icc_k
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@icc_name=_("McGraw & Wong ICC(K)")
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@r=@icc_1_k
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@f=icc_1_k_f(@g_rho)
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@lbound, @ubound=icc_1_k_ci(@alpha)
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when :icc_c_1
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@icc_name=_("McGraw & Wong ICC(C,1)")
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@r=@icc_3_1
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@f=icc_c_1_f(@g_rho)
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@lbound, @ubound=icc_3_1_ci(@alpha)
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when :icc_c_k
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@icc_name=_("McGraw & Wong ICC(C,K)")
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@r=@icc_3_k
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@f=icc_c_k_f(@g_rho)
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@lbound, @ubound=icc_c_k_ci(@alpha)
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when :icc_a_1
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@icc_name=_("McGraw & Wong ICC(A,1)")
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@r=@icc_2_1
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@f=icc_a_1_f(@g_rho)
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@lbound,@ubound = icc_2_1_ci(@alpha)
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when :icc_a_k
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@icc_name=_("McGraw & Wong ICC(A,K)")
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@r=@icc_2_k
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@f=icc_a_k_f(@g_rho)
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@lbound,@ubound=icc_2_k_ci(@alpha)
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else
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raise "Type #{v} doesn't exists"
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end
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end
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def compute
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@df_bt=n-1
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@df_wt=n*(k-1)
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@df_bj=k-1
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@df_residual=(n-1)*(k-1)
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@total_mean=@vectors.inject(0){|ac,v| ac+v.sum}.quo(n*k)
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vm=@ds.vector_mean
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@ss_bt=k*vm.ss(@total_mean)
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@ms_bt=@ss_bt.quo(@df_bt)
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@ss_bj=n*@vectors.inject(0){|ac,v| ac+(v.mean-@total_mean).square}
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@ms_bj=@ss_bj.quo(@df_bj)
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@ss_wt=@vectors.inject(0){|ac,v| ac+(v-vm).ss(0)}
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@ms_wt=@ss_wt.quo(@df_wt)
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@ss_residual=@ss_wt-@ss_bj
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@ms_residual=@ss_residual.quo(@df_residual)
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###
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# Shrout and Fleiss denomination
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###
|
218
|
+
# ICC(1,1) / ICC(1)
|
219
|
+
@icc_1_1=(bms-wms).quo(bms+(k-1)*wms)
|
220
|
+
# ICC(2,1) / ICC(A,1)
|
221
|
+
@icc_2_1=(bms-ems).quo(bms+(k-1)*ems+k*(jms - ems).quo(n))
|
222
|
+
# ICC(3,1) / ICC(C,1)
|
223
|
+
@icc_3_1=(bms-ems).quo(bms+(k-1)*ems)
|
224
|
+
|
225
|
+
|
226
|
+
|
227
|
+
# ICC(1,K) / ICC(K)
|
228
|
+
@icc_1_k=(bms-wms).quo(bms)
|
229
|
+
# ICC(2,K) / ICC(A,k)
|
230
|
+
@icc_2_k=(bms-ems).quo(bms+(jms-ems).quo(n))
|
231
|
+
# ICC(3,K) / ICC(C,k) = Cronbach's alpha
|
232
|
+
@icc_3_k=(bms-ems).quo(bms)
|
233
|
+
|
234
|
+
###
|
235
|
+
# McGraw and Wong
|
236
|
+
###
|
237
|
+
|
238
|
+
end
|
239
|
+
|
240
|
+
def icc_1_f(rho=0.0)
|
241
|
+
num=msr*(1-rho)
|
242
|
+
den=msw*(1+(k-1)*rho)
|
243
|
+
Statsample::Test::F.new(num, den, @df_bt, @df_wt)
|
244
|
+
end
|
245
|
+
# One way random F, type k
|
246
|
+
def icc_1_k_f(rho=0)
|
247
|
+
num=msr*(1-rho)
|
248
|
+
den=msw
|
249
|
+
Statsample::Test::F.new(num, den, @df_bt, @df_wt)
|
250
|
+
end
|
251
|
+
|
252
|
+
def icc_c_1_f(rho=0)
|
253
|
+
num=msr*(1-rho)
|
254
|
+
den=mse*(1+(k-1)*rho)
|
255
|
+
Statsample::Test::F.new(num, den, @df_bt, @df_residual)
|
256
|
+
end
|
257
|
+
def icc_c_k_f(rho=0)
|
258
|
+
num=(1-rho)
|
259
|
+
den=1-@icc_3_k
|
260
|
+
Statsample::Test::F.new(num, den, @df_bt, @df_residual)
|
261
|
+
end
|
262
|
+
|
263
|
+
def v(a,b)
|
264
|
+
((a*msc+b*mse)**2).quo(((a*msc)**2.quo(k-1))+((b*mse)**2.quo( (n-1) * (k-1))))
|
265
|
+
end
|
266
|
+
def a(rho)
|
267
|
+
(k*rho).quo(n*(1-rho))
|
268
|
+
end
|
269
|
+
def b(rho)
|
270
|
+
1+((k*rho*(n-1)).quo(n*(1-rho)))
|
271
|
+
end
|
272
|
+
def c(rho)
|
273
|
+
rho.quo(n*(1-rho))
|
274
|
+
end
|
275
|
+
def d(rho)
|
276
|
+
1+((rho*(n-1)).quo(n*(1-rho)))
|
277
|
+
end
|
278
|
+
private :v, :a, :b, :c, :d
|
279
|
+
def icc_a_1_f(rho=0)
|
280
|
+
fj=jms.quo(ems)
|
281
|
+
num=msr
|
282
|
+
den=a(rho)*msc+b(rho)*mse
|
283
|
+
pp = @icc_2_1
|
284
|
+
vn=(k-1)*(n-1)*((k*pp*fj+n*(1+(k-1)*pp)-k*pp)**2)
|
285
|
+
vd=(n-1)*(k**2)*(pp**2)*(fj**2)+((n*(1+(k-1)*pp)-k*pp)**2)
|
286
|
+
v=vn.quo(vd)
|
287
|
+
Statsample::Test::F.new(num, den, @df_bt, v)
|
288
|
+
end
|
289
|
+
|
290
|
+
def icc_a_k_f(rho=0)
|
291
|
+
num=msr
|
292
|
+
den=c(rho)*msc+d(rho)*mse
|
293
|
+
|
294
|
+
fj=jms.quo(ems)
|
295
|
+
|
296
|
+
pp = @icc_2_k
|
297
|
+
vn=(k-1)*(n-1)*((k*pp*fj+n*(1+(k-1)*pp)-k*pp)**2)
|
298
|
+
vd=(n-1)*(k**2)*(pp**2)*(fj**2)+((n*(1+(k-1)*pp)-k*pp)**2)
|
299
|
+
v=vn.quo(vd)
|
300
|
+
|
301
|
+
|
302
|
+
Statsample::Test::F.new(num, den, @df_bt,v)
|
303
|
+
|
304
|
+
end
|
305
|
+
|
306
|
+
# F test for ICC Case 1. Shrout and Fleiss
|
307
|
+
def icc_1_f_shrout
|
308
|
+
Statsample::Test::F.new(bms, wms, @df_bt, @df_wt)
|
309
|
+
end
|
310
|
+
|
311
|
+
# Intervale of confidence for ICC (1,1)
|
312
|
+
def icc_1_1_ci(alpha=0.05)
|
313
|
+
per=1-(0.5*alpha)
|
314
|
+
|
315
|
+
fu=icc_1_f.f*Distribution::F.p_value(per, @df_wt, @df_bt)
|
316
|
+
fl=icc_1_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_wt))
|
317
|
+
|
318
|
+
[(fl-1).quo(fl+k-1), (fu-1).quo(fu+k-1)]
|
319
|
+
end
|
320
|
+
|
321
|
+
# Intervale of confidence for ICC (1,k)
|
322
|
+
def icc_1_k_ci(alpha=0.05)
|
323
|
+
per=1-(0.5*alpha)
|
324
|
+
fu=icc_1_f.f*Distribution::F.p_value(per, @df_wt, @df_bt)
|
325
|
+
fl=icc_1_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_wt))
|
326
|
+
[1-1.quo(fl), 1-1.quo(fu)]
|
327
|
+
end
|
328
|
+
|
329
|
+
# F test for ICC Case 2
|
330
|
+
def icc_2_f
|
331
|
+
Statsample::Test::F.new(bms, ems, @df_bt, @df_residual)
|
332
|
+
end
|
333
|
+
|
334
|
+
|
335
|
+
#
|
336
|
+
# F* for ICC(2,1) and ICC(2,k)
|
337
|
+
#
|
338
|
+
def icc_2_1_fs(pp,alpha=0.05)
|
339
|
+
fj=jms.quo(ems)
|
340
|
+
per=1-(0.5*alpha)
|
341
|
+
vn=(k-1)*(n-1)*((k*pp*fj+n*(1+(k-1)*pp)-k*pp)**2)
|
342
|
+
vd=(n-1)*(k**2)*(pp**2)*(fj**2)+((n*(1+(k-1)*pp)-k*pp)**2)
|
343
|
+
v=vn.quo(vd)
|
344
|
+
f1=Distribution::F.p_value(per, n-1,v)
|
345
|
+
f2=Distribution::F.p_value(per, v, n-1)
|
346
|
+
[f1,f2]
|
347
|
+
end
|
348
|
+
|
349
|
+
|
350
|
+
def icc_2_1_ci(alpha=0.05)
|
351
|
+
icc_2_1_ci_mcgraw
|
352
|
+
end
|
353
|
+
|
354
|
+
# Confidence interval ICC(A,1), McGawn
|
355
|
+
|
356
|
+
def icc_2_1_ci_mcgraw(alpha=0.05)
|
357
|
+
fd,fu=icc_2_1_fs(icc_2_1,alpha)
|
358
|
+
cl=(n*(msr-fd*mse)).quo(fd*(k*msc+(k*n-k-n)*mse)+n*msr)
|
359
|
+
cu=(n*(fu*msr-mse)).quo(k*msc+(k*n-k-n)*mse+n*fu*msr)
|
360
|
+
[cl,cu]
|
361
|
+
end
|
362
|
+
|
363
|
+
def icc_2_k_ci(alpha=0.05)
|
364
|
+
icc_2_k_ci_mcgraw(alpha)
|
365
|
+
end
|
366
|
+
|
367
|
+
def icc_2_k_ci_mcgraw(alpha=0.05)
|
368
|
+
f1,f2=icc_2_1_fs(icc_2_k,alpha)
|
369
|
+
[
|
370
|
+
(n*(msr-f1*mse)).quo(f1*(msc-mse)+n*msr),
|
371
|
+
(n*(f2*msr-mse)).quo(msc-mse+n*f2*msr)
|
372
|
+
]
|
373
|
+
|
374
|
+
end
|
375
|
+
def icc_2_k_ci_shrout(alpha=0.05)
|
376
|
+
ci=icc_2_1_ci(alpha)
|
377
|
+
[(ci[0]*k).quo(1+(k-1)*ci[0]), (ci[1]*k).quo(1+(k-1)*ci[1])]
|
378
|
+
end
|
379
|
+
|
380
|
+
|
381
|
+
def icc_3_f
|
382
|
+
Statsample::Test::F.new(bms, ems, @df_bt, @df_residual)
|
383
|
+
end
|
384
|
+
|
385
|
+
def icc_3_1_ci(alpha=0.05)
|
386
|
+
per=1-(0.5*alpha)
|
387
|
+
fl=icc_3_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_residual))
|
388
|
+
fu=icc_3_f.f*Distribution::F.p_value(per, @df_residual, @df_bt)
|
389
|
+
[(fl-1).quo(fl+k-1), (fu-1).quo(fu+k-1)]
|
390
|
+
end
|
391
|
+
|
392
|
+
def icc_3_k_ci(alpha=0.05)
|
393
|
+
per=1-(0.5*alpha)
|
394
|
+
fl=icc_3_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_residual))
|
395
|
+
fu=icc_3_f.f*Distribution::F.p_value(per, @df_residual, @df_bt)
|
396
|
+
[1-1.quo(fl),1-1.quo(fu)]
|
397
|
+
end
|
398
|
+
|
399
|
+
def icc_c_k_ci(alpha=0.05)
|
400
|
+
per=1-(0.5*alpha)
|
401
|
+
fl=icc_c_k_f.f.quo(Distribution::F.p_value(per, @df_bt, @df_residual))
|
402
|
+
fu=icc_c_k_f.f*Distribution::F.p_value(per, @df_residual, @df_bt)
|
403
|
+
[1-1.quo(fl),1-1.quo(fu)]
|
404
|
+
end
|
405
|
+
def report_building(b)
|
406
|
+
b.section(:name=>name) do |s|
|
407
|
+
s.text @icc_name
|
408
|
+
s.text _("ICC: %0.4f") % @r
|
409
|
+
s.parse_element(@f)
|
410
|
+
s.text _("CI (%0.2f): [%0.4f - %0.4f]") % [(1-@alpha)*100, @lbound, @ubound]
|
411
|
+
end
|
412
|
+
end
|
413
|
+
end
|
414
|
+
end
|
415
|
+
end
|
@@ -0,0 +1,181 @@
|
|
1
|
+
module Statsample
|
2
|
+
module Reliability
|
3
|
+
# DSL for analysis of multiple scales analysis.
|
4
|
+
# Retrieves reliability analysis for each scale and
|
5
|
+
# provides fast accessors to correlations matrix,
|
6
|
+
# PCA and Factor Analysis.
|
7
|
+
#
|
8
|
+
# == Usage
|
9
|
+
# @x1 = Daru::Vector.new([1,1,1,1,2,2,2,2,3,3,3,30])
|
10
|
+
# @x2 = Daru::Vector.new([1,1,1,2,2,3,3,3,3,4,4,50])
|
11
|
+
# @x3 = Daru::Vector.new([2,2,1,1,1,2,2,2,3,4,5,40])
|
12
|
+
# @x4 = Daru::Vector.new([1,2,3,4,4,4,4,3,4,4,5,30])
|
13
|
+
# ds = Daru::DataFrame.new({:x1 => @x1,:x2 => @x2,:x3 => @x3,:x4 => @x4})
|
14
|
+
# opts={:name=>"Scales", # Name of analysis
|
15
|
+
# :summary_correlation_matrix=>true, # Add correlation matrix
|
16
|
+
# :summary_pca } # Add PCA between scales
|
17
|
+
# msa=Statsample::Reliability::MultiScaleAnalysis.new(opts) do |m|
|
18
|
+
# m.scale :s1, ds.clone([:x1, :x2])
|
19
|
+
# m.scale :s2, ds.clone([:x3, :x4]), {:name=>"Scale 2"}
|
20
|
+
# end
|
21
|
+
# # Retrieve summary
|
22
|
+
# puts msa.summary
|
23
|
+
class MultiScaleAnalysis
|
24
|
+
include Statsample::Summarizable
|
25
|
+
# Hash with scales
|
26
|
+
attr_reader :scales
|
27
|
+
# Name of analysis
|
28
|
+
attr_accessor :name
|
29
|
+
# Add a correlation matrix on summary
|
30
|
+
attr_accessor :summary_correlation_matrix
|
31
|
+
# Add PCA to summary
|
32
|
+
attr_accessor :summary_pca
|
33
|
+
# Add Principal Axis to summary
|
34
|
+
attr_accessor :summary_principal_axis
|
35
|
+
# Options for Factor::PCA object
|
36
|
+
attr_accessor :pca_options
|
37
|
+
# Options for Factor::PrincipalAxis
|
38
|
+
attr_accessor :principal_axis_options
|
39
|
+
|
40
|
+
# Add Parallel Analysis to summary
|
41
|
+
attr_accessor :summary_parallel_analysis
|
42
|
+
# Options for Parallel Analysis
|
43
|
+
attr_accessor :parallel_analysis_options
|
44
|
+
|
45
|
+
# Add MPA to summary
|
46
|
+
attr_accessor :summary_map
|
47
|
+
# Options for MAP
|
48
|
+
attr_accessor :map_options
|
49
|
+
|
50
|
+
|
51
|
+
# Generates a new MultiScaleAnalysis
|
52
|
+
# Opts could be any accessor of the class
|
53
|
+
# * :name,
|
54
|
+
# * :summary_correlation_matrix
|
55
|
+
# * :summary_pca
|
56
|
+
# * :summary_principal_axis
|
57
|
+
# * :summary_map
|
58
|
+
# * :pca_options
|
59
|
+
# * :factor_analysis_options
|
60
|
+
# * :map_options
|
61
|
+
# If block given, all methods should be called
|
62
|
+
# inside object environment.
|
63
|
+
#
|
64
|
+
def initialize(opts=Hash.new, &block)
|
65
|
+
@scales=Hash.new
|
66
|
+
@scales_keys=Array.new
|
67
|
+
opts_default={ :name=>_("Multiple Scale analysis"),
|
68
|
+
:summary_correlation_matrix=>false,
|
69
|
+
:summary_pca=>false,
|
70
|
+
:summary_principal_axis=>false,
|
71
|
+
:summary_parallel_analysis=>false,
|
72
|
+
:summary_map=>false,
|
73
|
+
:pca_options=>Hash.new,
|
74
|
+
:principal_axis_options=>Hash.new,
|
75
|
+
:parallel_analysis_options=>Hash.new,
|
76
|
+
:map_options=>Hash.new
|
77
|
+
}
|
78
|
+
@opts=opts_default.merge(opts)
|
79
|
+
@opts.each{|k,v|
|
80
|
+
self.send("#{k}=",v) if self.respond_to? k
|
81
|
+
}
|
82
|
+
|
83
|
+
if block
|
84
|
+
block.arity<1 ? instance_eval(&block) : block.call(self)
|
85
|
+
end
|
86
|
+
end
|
87
|
+
# Add or retrieve a scale to analysis.
|
88
|
+
# If second parameters is a dataset, generates a ScaleAnalysis
|
89
|
+
# for <tt>ds</tt>, named <tt>code</tt> with options <tt>opts</tt>.
|
90
|
+
#
|
91
|
+
# If second parameters is empty, returns the ScaleAnalysis
|
92
|
+
# <tt>code</tt>.
|
93
|
+
def scale(code, ds=nil, opts=nil)
|
94
|
+
if ds.nil?
|
95
|
+
@scales[code]
|
96
|
+
else
|
97
|
+
opts={:name=>_("Scale %s") % code} if opts.nil?
|
98
|
+
@scales_keys.push(code)
|
99
|
+
@scales[code]=ScaleAnalysis.new(ds, opts)
|
100
|
+
end
|
101
|
+
end
|
102
|
+
# Delete ScaleAnalysis named <tt>code</tt>
|
103
|
+
def delete_scale(code)
|
104
|
+
@scales_keys.delete code
|
105
|
+
@scales.delete code
|
106
|
+
end
|
107
|
+
# Retrieves a Principal Component Analysis (Factor::PCA)
|
108
|
+
# using all scales, using <tt>opts</tt> a options.
|
109
|
+
def pca(opts=nil)
|
110
|
+
opts ||= pca_options
|
111
|
+
Statsample::Factor::PCA.new(correlation_matrix, opts)
|
112
|
+
end
|
113
|
+
# Retrieve Velicer's MAP
|
114
|
+
# using all scales.
|
115
|
+
def map(opts=nil)
|
116
|
+
opts||=map_options
|
117
|
+
Statsample::Factor::MAP.new(correlation_matrix, opts)
|
118
|
+
end
|
119
|
+
# Retrieves a PrincipalAxis Analysis (Factor::PrincipalAxis)
|
120
|
+
# using all scales, using <tt>opts</tt> a options.
|
121
|
+
def principal_axis_analysis(opts=nil)
|
122
|
+
opts||=principal_axis_options
|
123
|
+
Statsample::Factor::PrincipalAxis.new(correlation_matrix, opts)
|
124
|
+
end
|
125
|
+
def dataset_from_scales
|
126
|
+
ds = Daru::DataFrame.new({}, order: @scales_keys.map(&:to_sym))
|
127
|
+
@scales.each_pair do |code,scale|
|
128
|
+
ds[code.to_sym] = scale.ds.vector_sum
|
129
|
+
end
|
130
|
+
|
131
|
+
ds
|
132
|
+
end
|
133
|
+
|
134
|
+
def parallel_analysis(opts=nil)
|
135
|
+
opts||=parallel_analysis_options
|
136
|
+
Statsample::Factor::ParallelAnalysis.new(dataset_from_scales, opts)
|
137
|
+
end
|
138
|
+
# Retrieves a Correlation Matrix between scales.
|
139
|
+
#
|
140
|
+
def correlation_matrix
|
141
|
+
Statsample::Bivariate.correlation_matrix(dataset_from_scales)
|
142
|
+
end
|
143
|
+
|
144
|
+
def report_building(b) # :nodoc:
|
145
|
+
b.section(:name=>name) do |s|
|
146
|
+
s.section(:name=>_("Reliability analysis of scales")) do |s2|
|
147
|
+
@scales.each_pair do |k, scale|
|
148
|
+
s2.parse_element(scale)
|
149
|
+
end
|
150
|
+
end
|
151
|
+
if summary_correlation_matrix
|
152
|
+
s.section(:name=>_("Correlation matrix for %s") % name) do |s2|
|
153
|
+
s2.parse_element(correlation_matrix)
|
154
|
+
end
|
155
|
+
end
|
156
|
+
if summary_pca
|
157
|
+
s.section(:name=>_("PCA for %s") % name) do |s2|
|
158
|
+
s2.parse_element(pca)
|
159
|
+
end
|
160
|
+
end
|
161
|
+
if summary_principal_axis
|
162
|
+
s.section(:name=>_("Principal Axis for %s") % name) do |s2|
|
163
|
+
s2.parse_element(principal_axis_analysis)
|
164
|
+
end
|
165
|
+
end
|
166
|
+
|
167
|
+
if summary_parallel_analysis
|
168
|
+
s.section(:name=>_("Parallel Analysis for %s") % name) do |s2|
|
169
|
+
s2.parse_element(parallel_analysis)
|
170
|
+
end
|
171
|
+
end
|
172
|
+
if summary_map
|
173
|
+
s.section(:name=>_("MAP for %s") % name) do |s2|
|
174
|
+
s2.parse_element(map)
|
175
|
+
end
|
176
|
+
end
|
177
|
+
end
|
178
|
+
end
|
179
|
+
end
|
180
|
+
end
|
181
|
+
end
|