Rcmd::Normality - Interfaces to tests of normality of R language.

    This class is a part of G-language Genome Analysis Environment, 
    collecting interfaces to tests of normality of R language.

    my $rcmd = shift;
    $rcmd->set_mode('tmp');

    opt_default(method=>"ks", sampledata=>0);
    my @args = opt_get(@_);
    my $sampledata = opt_val("sampledata");
    my $method = opt_val("method");
    
    if($sampledata){
	$rcmd->sample_data_for_normality();
    }else{
	$rcmd->array('rnormality', @args);
	
	if(scalar(@args) > 5000 && $method eq 'sw'){
	    carp("Shapiro-Wilk test cannot handle samples >5000.\nUsing Kolmogorov-Smirnov Lilliefors instead.\n");
	    $method = "ks";
	}
    }
    
    unless($method eq 'sw'){
	my $message = $rcmd->exec(
				  'require(nortest)'
				  );
	
	croak(
	      "\n\nPackage nortest not installed.\nrun\n\tinstall.packages(\'nortest\')\n" . 
	      "in R as root.\n\n"
	      ) if ($message =~ /FALSE/);
    }	
    
    my @result;

    if($method eq 'sw'){
	@result = $rcmd->exec(
			      'result = shapiro.test(rnormality)',
			      'c(as.vector(result$statistic), result$p.value)'
			      );
    }elsif($method eq 'ad'){
	@result = $rcmd->exec(
			      'result = ad.test(rnormality)',
			      'c(as.vector(result$statistic), result$p.value)'
			      );
    }else{
	unless($method eq 'ks'){
	    carp("Unknown method specified.\nUsing Kolmogorov-Smirnov Lillifors instead.\n");
	}

	@result = $rcmd->exec(
			      'result = lillie.test(rnormality)',
			      'c(as.vector(result$statistic), result$p.value)'
			      );
    }

    $rcmd->set_mode();
    return @result;

    my $rcmd = shift;

    $rcmd->exec(
		'rnormality<-rnorm(100,mean=5,sd=3)'
		);

  Name: $rcmd->normtest()   -   performs test for normality

  Description:
    Performs test for normality of the given vector, using
    Anderson-Darling test, Kolmogorov-Smirnov Lilliefors test,
    or Shapiro-Wilk test.
    
    Anderson-Darling test gives more weight to the tails
    of the distribution than Kolmogorov-Smirnov Lilliefors test
    or Shapiro-Wilk test.

    Kolmogorov-Smirnov Lilliefors test is one of the most widely 
    used methods for the test of normality, but is known to 
    perform worse than Anderson-Darling test or Shapiro-Wilk test.

    Shapiro-Wilk test is limited to samples less than 5000.

    Installation of nortest library for R language is required.
        run R as a super user - sudo R - and type the following:
        install.packages('nortest')) 
    
  Usage:
    $rcmd = new Rcmd();
    ($statistic, $pvalue) = $rcmd->normtest(@data);
      or
    ($statistic, $pvalue) = $rcmd->normtest(-sampledata=>1);

  Options:
   -method       name of the test
                 "ad" for Anderson-Darling 
                 "ks" for Kolmogorov-Smirnov Lilliefors (default)
                 "sw" for Shapiro-Wilk
   -sampledata   use sample data (default: 0)

  References:
   Thode Jr., H.C. (2002) Testing for Normality, Marcel Dekker, NewYork

  Author: 
    Kazuharu Arakawa (gaou@sfc.keio.ac.jp)

  History:
   20070613-01 initial posting