statsample-sem 0.1.0

data/lib/statsample/sem/semjfoxengine.rb

@@ -0,0 +1,197 @@
+require 'rserve'
+require 'tempfile'
+module Statsample
+  class SEM
+    # SEM using J.Fox 'sem' R library.
+    # Documentation for methods extracted from [http://davidakenny.net/cm/fit.htm]
+    #
+    class SemJFoxEngine
+      include DirtyMemoize
+      include Summarizable
+      attr_accessor :summarizable
+      attr_accessor :name
+      attr_reader :r_summary
+      def initialize(model,opts=Hash.new)
+        @model=model
+        defaults = {
+          :name=>_("SEM analysis using J.Fox sem package")
+        }
+        @opts=defaults.merge defaults
+        @name=@opts[:name]
+      end
+      def r
+        @r||=Rserve::Connection.new
+      end
+      def r_sempaths
+        @model.paths.values.map {|path|
+          sign=(path[:arrow]==1) ? " ->" : "<->"
+          label= path[:label] ? path[:label]  : "NA"  
+
+          label_and_value=(path[:free]) ? "'#{label}', NA" : "NA, #{path[:value]}"
+          "'#{path[:from]} #{sign} #{path[:to]}', #{label_and_value}"
+        }.join(",\n")
+      end
+      def r_semdata
+        type=case @model.data_type
+          when :raw
+            raise "Not implemented"
+          when :covariance
+            'cov'
+          when :correlation
+            raise "not implemented"
+        end
+      end
+def r_query
+        <<-EOF
+library(sem);
+sem.model<-matrix(c(
+#{r_sempaths}
+),
+ncol=3,byrow=TRUE)
+sem.object<-sem(sem.model,data, obs.variables=manifests, N=#{@model.cases});
+sem.summary<-summary(sem.object)
+        EOF
+      end
+      def compute
+        raise "Insuficient information" unless @model.complete?
+        r.assign 'manifests', @model.manifests
+        r.assign 'data', @model.data_type==:raw ? @model.ds : @model.matrix
+        if @model.matrix
+          r.assign 'vn', @model.variables
+          # We should assing names to fields on matrix
+          r.void_eval('dimnames(data)<-list(vn,vn)')
+        end
+        r.void_eval r_query
+        @r_summary=@r.eval('sem.summary').to_ruby
+      end
+      def graphviz
+        require 'tmpdir'
+        out=""
+        compute if @r_summary.nil?
+        Dir.mktmpdir {|dir| 
+          filename=dir+="/model_#{Time.new.to_s}"
+          r.void_eval("path.diagram(sem.object,output.type='dot',file='#{filename}')")
+          
+          file=File.open(filename+".dot","r") do |fp|
+            out=fp.read
+          end
+        }
+        out
+      end
+      # Chi-Square.
+      #
+      # For models with about 75 to 200 cases, this is a reasonable measure of fit.  But for models with more cases, the chi square is almost always statistically significant.  Chi square is also affected by the size of the correlations in the model: the larger the correlations, the poorer the fit.  
+      def chi_square
+        @r_summary["chisq"]
+      end
+      # Degrees of freedom for Chi-Square
+      def df
+        @r_summary["df"]
+      end
+      # Chi-Square for null model
+      def chi_square_null
+        @r_summary["chisqNull"]
+      end
+      def df_null
+        @r_summary["dfNull"]
+      end
+      # Lisrel measure. Don't trust!
+      def goodness_of_fit
+        @r_summary["GFI"]
+      end
+      # Lisrel measure. Don't trust!
+
+      def adjusted_goodness_of_fit
+        @r_summary["AGFI"]
+      end
+      
+      # Root Mean Square Error of Approximation (RMSEA)
+      # 
+      # This measure is based on the non-centrality parameter.  Its formula can be shown to equal:
+      # 
+      #   √[([χ2/df] - 1)/(N - 1)]
+      # 
+      # where N the sample size and df the degrees of freedom of the model.  (If χ2 is less than df, then RMSEA is set to zero.)  Good models have an RMSEA of .05 or less. Models whose RMSEA is .10 or more have poor fit. 
+      # 
+      def rmsea
+        @r_summary["RMSEA"][0]
+      end
+      def rmsea_confidence_interval
+        @r_summary["RMSEA"][1..2]
+      end
+      def rmsea_alpha
+        @r_summary["RMSEA"][3]
+      end
+      # ==Bentler-Bonett Index or Normed Fit Index (NFI).
+      # 
+      # Define the null model as a model in which all of the correlations or covariances are zero.  The null model is referred to as the "Independence Model" in AMOS.  Its formula is:
+      # 
+      #   [χ2(Null Model) - χ2(Proposed Model)]/ [χ2(Null Model)]
+      # 
+      # A value between .90 and .95 is acceptable, and above .95 is good. A disadvantage of this measure is that it cannot be smaller if more parameters are added to the model.  Thus, the more parameters added to the model, the larger the index.  It is for this reason that this measure is not recommended, but rather NNFI and CFI is used. 
+      def nfi
+        @r_summary["NFI"]
+      end
+
+      # == Tucker Lewis Index or Non-normed Fit Index (NNFI).
+      # 
+      # A problem with the Bentler-Bonett NFI index is that there is no penalty for adding parameters.  The Tucker-Lewis index does have such a penalty.  Let χ2/df be the ratio of chi square to its degrees of freedom
+      # 
+      #   [χ2/df(Null Model) - χ2/df(Proposed Model)]/[χ2/df(Null Model) - 1]
+      # 
+      # If the index is greater than one, it is set at one.  It is interpreted as the Bentler-Bonett index.  Note than for a given model, a lower chi square to df ratio (as long as it is not less than one) implies a better fitting model.   
+      def nnfi
+        @r_summary["NNFI"]
+        
+      end
+      
+      # ==Comparative Fit Index (CFI).
+      # 
+      # This measure is directly based on the non-centrality measure.  Let d = χ2 - df where df are the degrees of freedom of the model.  The Comparative Fit Index equals
+      # 
+      #   [d(Null Model) - d(Proposed Model)]/d(Null Model)
+      # 
+      # If the index is greater than one, it is set at one and if less than zero, it is set to zero. It is interpreted as the previous indexes.  If the CFI is less than one, then the CFI is always greater than the TLI.  CFI pays a penalty of one for every parameter estimated.   Note that the CFI depends on the average size of the correlations in the data.  If the average correlation between variables is not high, then the CFI will not be very high.         
+      
+      def cfi
+        @r_summary["CFI"]
+        
+      end
+      def srmr
+        @r_summary["SRMR"]
+        
+      end
+      
+      # == Bayesian Information Criterion (BIC) and Adjusted BIC
+      # 
+      # the AIC pays a penalty of 2 for each parameter estimated.  The BIC and adjusted BIC increases the penalty as sample size increases
+      # χ2 + [k(k - 1)/2 - df]ln(N)
+      # 
+      # where ln(N) is the natural logarithm of the number of cases in the sample.  The adjusted BIC replaces ln(N) with ln[(N + 2)/24].  The BIC places a high value on parsimony (perhaps too high).  The adjusted BIC, while placing a penalty for adding parameters based on sample, does not place as high a penalty as the BIC.  Like the AIC, these measures are not absolute measues and are used to compare the fit of two or more models estimated from the same data set.
+      def bic
+        @r_summary["BIC"]
+        
+      end
+      def normalized_residual
+        @r_summary["norm.res"]
+      end
+      def iterations
+        @r_summary['iterations']
+      end
+      def coefficients
+        est=Hash.new
+        coeffs=@r_summary['coeff']
+        coeffs[4].each_with_index do |v,i|
+          v=~/(.+) (<---|<-->) (.+)/
+          f1=$1
+          f2=$3
+          key=[f1,f2].sort
+          est[key]={:estimate=>coeffs[0][i], :se=>coeffs[1][i], :z=>coeffs[2][i], :p=>coeffs[3][i], :label=>@model.get_label(key)}
+        end
+        est
+      end
+      dirty_memoize :chi_square, :df, :chi_square_null, :df_null, :goodness_of_fit, :adjusted_goodness_of_fit, :rmsea, :nfi, :nnfi, :cfi, :srmr, :bic, :normalized_residual, :coefficients, :iterations
+
+    end
+  end
+end

data/spec/fixtures/demo_open_mx.csv

@@ -0,0 +1,501 @@
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