Package fork.lib.math.applied.stat

Examples of fork.lib.math.applied.stat.Distribution.standartDeviation()

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public static void subtractBackground(Distribution dis, File f, File outSub, double rat)throws Exception {
    Distribution dislow= dis.subsetLowerThan(dis.quantileBoundaries(100).get(99));
    double med= dislow.median();
    double sd= dislow.standartDeviation();
    double thr= med+ sd* rat;
    System.out.println("med: "+ med+"   sd: "+ sd+"     trh:"+ thr);
   
   

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        }
    }
    out= out.substring(0, out.length()-1);
    out+=")";
    out+="\nmu:"+dis.mean()+"   zero:"+ (double)dis.subsetLowerOrEqualTo(0).size()/dis.size()
            +"  me:"+dis.median()+"   s:"+dis.standartDeviation();
    return out;
}
   
   
   
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    Distribution dis= dis0.subsetHigherThan(1);
    dis= dis.subsetLowerOrEqualTo(dis.quantileBoundaries(10).get(5));
   
   
    double mean= dis.mean();
    double sd= dis.standartDeviation();
    double rat= mean+ 1.2 *sd;
   
    System.out.println("m: "+ mean+"   sd: "+sd+"  rat: "+rat);
   
    //double rat= 2.5;
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public void subtract2()throws Exception {
    Distribution dis= new BedGraphBuffer(outSub).getDistributionNonZero();
    dis= dis.subsetLowerThan(dis.quantileBoundaries(10).get(7));
    double med= dis.median();
    double sd= dis.standartDeviation();
    double thr= med+ sd* 2;
    System.out.println("med: "+ med+"   sd: "+ sd+"     "+ thr);

    BufferedWriter bw= new BufferedWriter(new FileWriter(outSub2));
    BedGraphExporter.writeTitle(bw, FileName.getBaseName(outSub2));
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    ArrayList<Double> qs= d.quantileBoundaries(100);
    double m=0 ,sd=0;
    for( int i=0; i<50; i++ ){
        Distribution df= d.subset(qs.get(i), qs.get(qs.size()-1-i), true, true);
        m= df.mean();
        sd= df.standartDeviation();
        double z= sd/m;
        //System.out.println(i+"   mean: "+m+"   med: "+med+"   sd: "+ sd+"  z:"+z);
        if(z<0.2){
            break;
        }
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    double m=0 ,sd=0;
    for( int i=0; i<50; i++ ){
        Distribution df= d.subset(qs.get(i), qs.get(qs.size()-1-i), true, true);
        m= df.mean();
        double med= df.median();
        sd= df.standartDeviation();
        double z= sd/m;
        //System.out.println(i+"   mean: "+m+"   med: "+med+"   sd: "+ sd+"  z:"+z);
        if(z<0.2){
            break;
        }
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protected void init() throws Exception{
    Distribution d= new Distribution();
    d.add(lbf.getDistribution());
    d.add(lbr.getDistribution());
    double med= Math.ceil( d.median() *1.7 );
    double sd= d.standartDeviation();
    System.out.println("med:  "+med +"    sd:  "+sd);
    //d.print(); System.exit(1);
    new LandscapeTransformer(lbf).subtract(med);
    new LandscapeTransformer(lbr).subtract(med);
   
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