Examples of org.apache.commons.math.stat.Frequency

org.apache.commons.math.stat.Frequency
Maintains a frequency distribution.
Accepts int, long, char or Comparable values. New values added must be comparable to those that have been added, otherwise the add method will throw an IllegalArgumentException.

Integer values (int, long, Integer, Long) are not distinguished by type -- i.e. addValue(Long.valueOf(2)), addValue(2), addValue(2l) all have the same effect (similarly for arguments to getCount, etc.).

char values are converted by addValue to Character instances. As such, these values are not comparable to integral values, so attempts to combine integral types with chars in a frequency distribution will fail.

The values are ordered using the default (natural order), unless a Comparator is supplied in the constructor.
@version $Revision: 1054186 $ $Date: 2011-01-01 03:28:46 +0100 (sam. 01 janv. 2011) $

            ;
        }
        if (hexString.length() != 1) {
                fail("incorrect length for generated string");
        }      
        Frequency f = new Frequency();
        for (int i = 0; i < smallSampleSize; i++) {
            hexString = randomData.nextSecureHexString(100);
            if (hexString.length() != 100) {
                fail("incorrect length for generated string");
            }
            for (int j = 0; j < hexString.length(); j++) {
                f.addValue(hexString.substring(j,j+1));
            }
        }
        double[] expected = new double[16];
        long[] observed = new long[16];
        for (int i = 0; i < 16; i++) {
            expected[i] = (double)smallSampleSize*100/(double)16;
            observed[i] = f.getCount(hex[i]);
        }
        /* Use ChiSquare dist with df = 16-1 = 15, alpha = .001
         * Change to 30.58 for alpha = .01
         */
        assertTrue("chi-square test -- will fail about 1 in 1000 times",

View Full Code Here

            int x = randomData.nextInt(4,3);
            fail("IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            ;
        }
        Frequency freq = new Frequency();
        int value = 0;
        for (int i=0;i<smallSampleSize;i++) {
            value = randomData.nextInt(0,3);
            assertTrue("nextInt range",(value >= 0) && (value <= 3));
            freq.addValue(value);  
        }
        double[] observed = new double[4];
        for (int i=0; i<4; i++) {
            String iString = new Integer(i).toString();
            observed[i] = freq.getCount(iString);
        } 
        
        /* Use ChiSquare dist with df = 4-1 = 3, alpha = .001
         * Change to 11.34 for alpha = .01
         */

View Full Code Here

            long x = randomData.nextLong(4,3);
            fail("IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            ;
        }
       Frequency freq = new Frequency();
       long value = 0;
        for (int i=0;i<smallSampleSize;i++) {
            value = randomData.nextLong(0,3);
            assertTrue("nextInt range",(value >= 0) && (value <= 3));
            freq.addValue(value);  
        }
        double[] observed = new double[4];
        for (int i=0; i<4; i++) {
            String iString = new Integer(i).toString();
            observed[i] = freq.getCount(iString);
        } 
        
        /* Use ChiSquare dist with df = 4-1 = 3, alpha = .001
         * Change to 11.34 for alpha = .01
         */

View Full Code Here

            long x = randomData.nextSecureLong(4,3);
            fail("IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            ;
        }
        Frequency freq = new Frequency();
        long value = 0;
        for (int i=0;i<smallSampleSize;i++) {
            value = randomData.nextSecureLong(0,3);
            assertTrue("nextInt range",(value >= 0) && (value <= 3));
            freq.addValue(value);  
        }
        double[] observed = new double[4];
        for (int i=0; i<4; i++) {
            String iString = new Integer(i).toString();
            observed[i] = freq.getCount(iString);
        } 
        
        /* Use ChiSquare dist with df = 4-1 = 3, alpha = .001
         * Change to 11.34 for alpha = .01
         */

View Full Code Here

            long x = randomData.nextSecureInt(4,3);
            fail("IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            ;
        }
        Frequency freq = new Frequency();
        int value = 0;
        for (int i=0;i<smallSampleSize;i++) {
            value = randomData.nextSecureInt(0,3);
            assertTrue("nextInt range",(value >= 0) && (value <= 3));
            freq.addValue(value);  
        }
        double[] observed = new double[4];
        for (int i=0; i<4; i++) {
            String iString = new Integer(i).toString();
            observed[i] = freq.getCount(iString);
        } 
        
        /* Use ChiSquare dist with df = 4-1 = 3, alpha = .001
         * Change to 11.34 for alpha = .01
         */

View Full Code Here

            long x = randomData.nextPoisson(0);
            fail("zero mean -- expecting IllegalArgumentException");
        } catch (IllegalArgumentException ex) {
            ;
        }
        Frequency f = new Frequency();
        long v = 0;
        for (int i = 0; i<largeSampleSize; i++) {
            try {
                f.addValue(randomData.nextPoisson(4.0d));
            } catch (Exception ex) {
                fail(ex.getMessage());
            }
        }
        long cumFreq = f.getCount("0") + f.getCount("1") + f.getCount("2") + 
                        f.getCount("3") + f.getCount("4") + f.getCount("5");
        long sumFreq = f.getSumFreq();
        double cumPct = 
            new Double(cumFreq).doubleValue()/new Double(sumFreq).doubleValue();
        assertEquals("cum Poisson(4)",cumPct,0.7851,0.2);
        try {
            long x = randomData.nextPoisson(-1);

View Full Code Here

            ;
        }
        if (hexString.length() != 1) {
                fail("incorrect length for generated string");
        }      
        Frequency f = new Frequency();
        for (int i = 0; i < smallSampleSize; i++) {
            hexString = randomData.nextHexString(100);
            if (hexString.length() != 100) {
                fail("incorrect length for generated string");
            }
            for (int j = 0; j < hexString.length(); j++) {
                f.addValue(hexString.substring(j,j+1));
            }
        }
        double[] expected = new double[16];
        double[] observed = new double[16];
        for (int i = 0; i < 16; i++) {
            expected[i] = (double)smallSampleSize*100/(double)16;
            observed[i] = f.getCount(hex[i]);
        }
        /* Use ChiSquare dist with df = 16-1 = 15, alpha = .001
         * Change to 30.58 for alpha = .01
         */
        assertTrue("chi-square test -- will fail about 1 in 1000 times",

View Full Code Here

            ;
        }
        if (hexString.length() != 1) {
                fail("incorrect length for generated string");
        }      
        Frequency f = new Frequency();
        for (int i = 0; i < smallSampleSize; i++) {
            hexString = randomData.nextSecureHexString(100);
            if (hexString.length() != 100) {
                fail("incorrect length for generated string");
            }
            for (int j = 0; j < hexString.length(); j++) {
                f.addValue(hexString.substring(j,j+1));
            }
        }
        double[] expected = new double[16];
        double[] observed = new double[16];
        for (int i = 0; i < 16; i++) {
            expected[i] = (double)smallSampleSize*100/(double)16;
            observed[i] = f.getCount(hex[i]);
        }
        /* Use ChiSquare dist with df = 16-1 = 15, alpha = .001
         * Change to 30.58 for alpha = .01
         */
        assertTrue("chi-square test -- will fail about 1 in 1000 times",

View Full Code Here

            SpliceJunctionFeature selectedFeature =
                    (SpliceJunctionFeature) ((FeatureTrack) track).getSelectedFeature();


            // Start of Roche-Tessella modification
            if (track.getAutoScale())    {
                Frequency f = new Frequency();
                List<Integer> scores = new ArrayList<Integer>();


                for (IGVFeature feature : featureList) {
                    SpliceJunctionFeature junctionFeature = (SpliceJunctionFeature) feature;
                    f.addValue(junctionFeature.getScore());
                    scores.add((int) junctionFeature.getScore());
                }


                Collections.sort(scores);
                Collections.reverse(scores);
                for (int s: scores)  {
                    if (f.getCumPct(s) < 0.99)  {
                        maxDepth = s;
                        break;
                    }
                }

View Full Code Here

            randomData.nextInt(4,3);
            fail("IllegalArgumentException expected");
        } catch (IllegalArgumentException ex) {
            ;
        }
        Frequency freq = new Frequency();
        int value = 0;
        for (int i=0;i<smallSampleSize;i++) {
            value = randomData.nextInt(0,3);
            assertTrue("nextInt range",(value >= 0) && (value <= 3));
            freq.addValue(value);  
        }
        long[] observed = new long[4];
        for (int i=0; i<4; i++) {
            observed[i] = freq.getCount(i);
        } 
        
        /* Use ChiSquare dist with df = 4-1 = 3, alpha = .001
         * Change to 11.34 for alpha = .01
         */

View Full Code Here

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