/*
GeoGebra - Dynamic Mathematics for Everyone
http://www.geogebra.org
This file is part of GeoGebra.
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by
the Free Software Foundation.
*/
package org.geogebra.common.kernel.statistics;
import java.util.Arrays;
import org.apache.commons.math3.distribution.NormalDistribution;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.geogebra.common.kernel.Construction;
import org.geogebra.common.kernel.algos.AlgoElement;
import org.geogebra.common.kernel.arithmetic.NumberValue;
import org.geogebra.common.kernel.commands.Commands;
import org.geogebra.common.kernel.geos.GeoElement;
import org.geogebra.common.kernel.geos.GeoList;
import org.geogebra.common.kernel.geos.GeoPoint;
import org.geogebra.common.kernel.geos.GeoSegment;
/**
* Creates a Normal Quantile Plot.
*
* Input: list of unsorted raw numeric data Output: list containing (1) points
* forming a normal quantile plot for the raw data and (2) a linear function for
* the qq line.
*
* Point ordering: x-coords = data values y-coords = expected z-scores
*
*
* The algorithm follows the description given by:
* http://en.wikipedia.org/wiki/Normal_probability_plot
* http://www.itl.nist.gov/div898/handbook/eda/section3/normprpl.htm
*
* @author G.Sturr
*/
public class AlgoNormalQuantilePlot extends AlgoElement {
private GeoList inputList; // input
private GeoList outputList; // output
private int size;
private double[] zValues;
private double[] sortedData;
public AlgoNormalQuantilePlot(Construction cons, String label,
GeoList inputList) {
this(cons, inputList);
outputList.setLabel(label);
}
public AlgoNormalQuantilePlot(Construction cons, GeoList inputList) {
super(cons);
this.inputList = inputList;
outputList = new GeoList(cons);
setInputOutput();
compute();
}
@Override
public Commands getClassName() {
return Commands.NormalQuantilePlot;
}
@Override
protected void setInputOutput() {
input = new GeoElement[1];
input[0] = inputList;
setOutputLength(1);
setOutput(0, outputList);
setDependencies(); // done by AlgoElement
}
public GeoList getResult() {
return outputList;
}
private void calculateZValues(int n) {
zValues = new double[n];
NormalDistribution normalDist = new NormalDistribution(0, 1);
double x;
try {
x = 1 - Math.pow(0.5, 1.0 / n);
zValues[0] = normalDist.inverseCumulativeProbability(x);
for (int i = 2; i < n; i++) {
x = (i - 0.3175) / (n + 0.365);
zValues[i - 1] = normalDist.inverseCumulativeProbability(x);
}
x = Math.pow(0.5, 1.0 / n);
zValues[n - 1] = normalDist.inverseCumulativeProbability(x);
} catch (RuntimeException e) {
// catches ArithmeticException, IllegalStateException and
// ArithmeticException
e.printStackTrace();
}
}
private GeoSegment getQQLineSegment() {
SummaryStatistics stats = new SummaryStatistics();
for (int i = 0; i < sortedData.length; i++) {
stats.addValue(sortedData[i]);
}
double sd = stats.getStandardDeviation();
double mean = stats.getMean();
double min = stats.getMin();
double max = stats.getMax();
// qq line: y = (1/sd)x - mean/sd
GeoPoint startPoint = new GeoPoint(cons);
startPoint.setCoords(min, (min / sd) - mean / sd, 1.0);
GeoPoint endPoint = new GeoPoint(cons);
endPoint.setCoords(max, (max / sd) - mean / sd, 1.0);
GeoSegment seg = new GeoSegment(cons, startPoint, endPoint);
seg.calcLength();
return seg;
}
@Override
public final void compute() {
// validate
size = inputList.size();
if (!inputList.isDefined() || size == 0) {
outputList.setUndefined();
return;
}
// convert geoList to sorted array of double
sortedData = new double[size];
for (int i = 0; i < size; i++) {
GeoElement geo = inputList.get(i);
if (geo instanceof NumberValue) {
NumberValue num = (NumberValue) geo;
sortedData[i] = num.getDouble();
} else {
outputList.setUndefined();
return;
}
}
Arrays.sort(sortedData);
// create the z values
calculateZValues(size);
// prepare output list. Pre-existing geos will be recycled,
// but extra geos are removed when outputList is too long
outputList.setDefined(true);
for (int i = outputList.size() - 1; i >= size; i--) {
GeoElement extraGeo = outputList.get(i);
extraGeo.remove();
outputList.remove(extraGeo);
}
int oldListSize = outputList.size();
// iterate through the sorted data and create the normal quantile points
boolean suppressLabelCreation = cons.isSuppressLabelsActive();
cons.setSuppressLabelCreation(true);
for (int i = 0; i < sortedData.length; i++) {
if (i < oldListSize) {
((GeoPoint) outputList.get(i)).setCoords(sortedData[i],
zValues[i], 1.0);
} else {
outputList.add(new GeoPoint(cons, null, sortedData[i],
zValues[i], 1.0));
}
}
// create qq line segment and add it to the list
outputList.add(getQQLineSegment());
cons.setSuppressLabelCreation(suppressLabelCreation);
}
}