[beast-mcmc] r6747 committed - Increased accuracy for log-transformed KDE estimation close to zero.
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beast...@googlecode.com
Apr 23, 2015, 2:25:12 PM4/23/15
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Revision: 6747
Author: bael...@gmail.com
Date: Thu Apr 23 18:24:52 2015 UTC
Log: Increased accuracy for log-transformed KDE estimation close to
zero.
https://code.google.com/p/beast-mcmc/source/detail?r=6747
Modified:
/trunk/src/dr/math/distributions/LogTransformedNormalKDEDistribution.java
=======================================
---
/trunk/src/dr/math/distributions/LogTransformedNormalKDEDistribution.java
Tue Apr 14 09:33:53 2015 UTC
+++
/trunk/src/dr/math/distributions/LogTransformedNormalKDEDistribution.java
Thu Apr 23 18:24:52 2015 UTC
@@ -237,6 +237,8 @@
to = DiscreteStatistics.max(this.sample) + this.cut *
this.bandWidth;
if (DEBUG) {
+ System.out.println("min: " +
DiscreteStatistics.min(this.sample));
+ System.out.println("max: " +
DiscreteStatistics.max(this.sample));
System.out.println("bandWidth = " + this.bandWidth);
System.out.println("cut = " + this.cut);
System.out.println("from = " + from);
@@ -250,51 +252,40 @@
System.out.println("lo = " + lo);
System.out.println("up = " + up);
}
-
- /*if (from < 0.0) {
- from = 0.0;
+
+ if (lo < 0.0) {
+ //small hack, but our asymmetric kernel estimators are
terribly slow
+ lo = DiscreteStatistics.min(this.sample);
}
- if (lo < 0.0) {
- lo = 0.0;
- }*/
//make new ordinates for the transformation back to normal space
//need a backup of the xPoints for the log scale KDE
this.backupXPoints = new double[xPoints.length];
System.arraycopy(xPoints, 0, backupXPoints, 0, xPoints.length);
makeOrdinates();
-
- int numberOfNegatives = 0;
- if (DEBUG) {
- System.out.println("\nxPoints length = " + xPoints.length);
- }
- for (int i = 0; i < xPoints.length; i++) {
- if (xPoints[i] < 0.0) {
- numberOfNegatives++;
- }
- //System.out.println(xPoints[i]);
- }
- if (DEBUG) {
- System.out.println("number of negative xPoints = " +
numberOfNegatives);
- }
//the KDE on log scale is contained in the xPoints and
densityPoints arrays
//copy them to finalXPoints and finalDensityPoints
- this.finalXPoints = new double[xPoints.length - numberOfNegatives];
- System.arraycopy(xPoints, numberOfNegatives, finalXPoints, 0,
xPoints.length - numberOfNegatives);
+
+ //this.finalXPoints = new double[xPoints.length - numberOfNegatives];
+ //this.finalXPoints = new double[xPoints.length];
+
+ //System.arraycopy(xPoints, numberOfNegatives, finalXPoints, 0,
xPoints.length - numberOfNegatives);
+ //System.arraycopy(xPoints, numberOfNegatives, finalXPoints, 0,
xPoints.length);
if (DEBUG) {
for (int i = 0; i < xPoints.length; i++) {
- System.out.println(backupXPoints[i] + " : " +
densityPoints[i]);
+ System.out.println(xPoints[i] + " " + backupXPoints[i]
+ " : " + densityPoints[i]);
}
- System.out.println("\nfinalXPoints length = " +
finalXPoints.length);
+ //System.out.println("\nfinalXPoints length = " +
finalXPoints.length);
}
- this.finalDensityPoints = new double[densityPoints.length -
numberOfNegatives];
+ //this.finalDensityPoints = new double[densityPoints.length -
numberOfNegatives];
+ this.finalDensityPoints = new double[densityPoints.length];
- for (int i = 0; i < finalXPoints.length; i++) {
- finalDensityPoints[i] = linearApproximate(backupXPoints,
densityPoints, Math.log(finalXPoints[i]), 0.0, 0.0)*(1.0/finalXPoints[i]);
+ for (int i = 0; i < xPoints.length; i++) {
+ finalDensityPoints[i] = linearApproximate(backupXPoints,
densityPoints, Math.log(xPoints[i]), 0.0, 0.0)*(1.0/xPoints[i]);
if (DEBUG) {
- System.out.println(finalXPoints[i] + "\t" +
finalDensityPoints[i]);
+ System.out.println(xPoints[i] + "\t" +
finalDensityPoints[i]);
}
}
@@ -343,13 +334,16 @@
xPoints = new double[gridSize];
double x = lo;
double delta = (up - lo) / (gridSize - 1);
- //System.out.println("X");
+ if (DEBUG) {
+ System.out.println("X");
+ }
for (int i = 0; i < gridSize; i++) {
xPoints[i] = x;
x += delta;
- //System.out.println(xPoints[i]);
+ if (DEBUG) {
+ System.out.println(xPoints[i]);
+ }
}
- //System.out.println();
}
@Override
@@ -359,7 +353,7 @@
computeDensity();
}
//xPoints and densityPoints are now back in normal space
- return linearApproximate(finalXPoints, finalDensityPoints, x, 0.0,
0.0);
+ return linearApproximate(xPoints, finalDensityPoints, x, 0.0, 0.0);
}
@Override
@@ -393,7 +387,7 @@
}
private ComplexArray kOrdinates;
- private double[] xPoints, finalXPoints, backupXPoints;
+ private double[] xPoints, backupXPoints;
private double[] densityPoints, finalDensityPoints;
private double[] backupSample, logSample;
@@ -408,6 +402,38 @@
public static void main(String[] args) {
+ /*Double[] testfivehundred =
{9.169378e-06,9.169378e-06,9.169378e-06,9.169378e-06,4.116020e-06,4.116020e-06,4.116020e-06,4.161038e-07,3.644982e-07,2.195354e-07,2.195354e-07,2.195354e-07,2.195354e-07,7.462043e-08,7.462043e-08,8.368972e-08,9.283378e-08,9.283378e-08,2.866075e-08,6.532907e-09,6.532907e-09,3.936993e-08,3.936993e-08,2.257473e-08,2.257473e-08,1.525075e-08,1.525075e-08,1.525075e-08,1.525075e-08,1.525075e-08,2.370723e-08,2.370723e-08,1.961463e-08,7.642434e-08,8.838916e-08,8.838916e-08,8.838916e-08,8.838916e-08,1.149915e-07,1.149915e-07,7.226055e-08,7.226055e-08,6.276125e-08,5.330820e-08,5.330820e-08,4.626315e-08,4.626315e-08,4.709987e-08,1.011533e-07,1.011533e-07,1.011533e-07,1.011533e-07,9.176941e-08,1.876641e-08,1.876641e-08,1.582991e-08,1.582991e-08,6.121650e-08,5.823668e-08,5.823668e-08,5.823668e-08,5.823668e-08,5.823668e-08,1.138725e-08,1.327368e-08,1.327368e-08,1.327368e-08,5.123223e-08,5.123223e-08,5.123223e-08,3.812422e-08,2.592858e-08,1.584334e-07,1.584334e-07,1.584334e-07,4.091027e-07,4.091027e-07,4.091027e-07,3.180726e-07,5.671995e-07,5.671995e-07,5.671995e-07,5.671995e-07,3.718532e-07,2.140636e-07,1.141818e-07,9.974324e-08,8.885531e-08,8.885531e-08,1.336255e-08,1.336255e-08,1.336255e-08,2.066815e-09,1.359399e-09,2.433474e-09,2.433474e-09,2.621958e-09,2.621958e-09,2.621958e-09,2.621958e-09,1.760426e-09,5.016878e-09,1.297173e-09,1.297173e-09,2.729714e-09,2.729714e-09,4.096775e-09,4.066638e-09,4.938423e-09,2.279718e-09,2.279718e-09,2.279718e-09,2.279718e-09,7.927200e-09,7.927200e-09,5.882404e-09,3.039284e-09,3.039284e-09,7.933658e-09,1.577847e-08,1.577847e-08,1.577847e-08,1.577847e-08,7.421679e-09,9.966059e-09,9.966059e-09,2.978775e-08,2.978775e-08,2.978775e-08,2.037757e-08,2.037757e-08,3.838478e-08,6.434436e-09,6.434436e-09,6.434436e-09,1.330451e-09,1.330451e-09,1.330451e-09,1.330451e-09,1.330451e-09,1.821259e-09,1.821259e-09,1.821259e-09,1.821259e-09,1.136283e-09,1.136283e-09,1.136283e-09,8.538424e-09,1.115792e-08,1.115792e-08,1.115792e-08,6.708989e-09,6.708989e-09,6.708989e-09,6.708989e-09,6.708989e-09,6.171120e-09,6.171120e-09,6.171120e-09,4.324598e-09,4.324598e-09,4.086923e-09,1.018727e-08,1.076947e-08,7.300160e-09,1.882574e-08,7.825507e-09,5.768726e-09,5.768726e-09,5.768726e-09,3.647371e-09,5.801127e-09,5.801127e-09,5.801127e-09,1.061525e-08,1.232341e-08,1.232341e-08,1.232341e-08,1.232341e-08,3.058357e-09,3.058357e-09,3.058357e-09,4.222149e-09,4.222149e-09,4.222149e-09,9.101976e-09,9.101976e-09,9.101976e-09,9.101976e-09,1.272342e-08,5.057809e-08,8.124001e-08,2.988208e-07,2.988208e-07,2.208343e-06,2.208343e-06,2.563228e-06,7.319180e-06,5.100615e-06,5.100615e-06,3.908437e-05,9.561673e-06,9.561673e-06,4.051668e-07,1.165789e-06,1.165789e-06,6.355679e-07,1.267624e-06,1.267624e-06,1.269425e-06,1.269425e-06,6.906194e-07,3.027074e-06,4.954935e-06,4.954935e-06,3.069373e-06,3.516738e-05,3.516738e-05,1.337480e-04,2.621304e-04,2.621304e-04,2.621304e-04,2.621304e-04,2.621304e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,3.789225e-03,2.911953e-03,2.911953e-03,2.911953e-03,2.911953e-03,2.911953e-03,2.911953e-03,2.889193e-03,2.741145e-03,2.741145e-03,2.741145e-03,2.741145e-03,1.039219e-03,1.039219e-03,1.039219e-03,4.519776e-04,5.756779e-04,5.756779e-04,1.608451e-04,2.319337e-04,1.004998e-04,1.004998e-04,1.004998e-04,2.479749e-04,2.479749e-04,2.479749e-04,2.290535e-04,2.290535e-04,2.290535e-04,5.562921e-05,5.562921e-05,5.562921e-05,2.263067e-05,2.924862e-05,1.625127e-05,1.625127e-05,1.625127e-05,5.130025e-06,5.130025e-06,5.130025e-06,2.601581e-06,3.884423e-05,3.884423e-05,3.884423e-05,1.899082e-05,1.128966e-05,1.128966e-05,1.128966e-05,1.457212e-05,8.006272e-06,8.006272e-06,1.007007e-05,1.007007e-05,1.007007e-05,1.007007e-05,8.494570e-06,8.494570e-06,8.494570e-06,1.394617e-05,1.394617e-05,1.394617e-05,7.943013e-06,1.523964e-05,1.523964e-05,2.775473e-05,2.775473e-05,2.775473e-05,2.775473e-05,2.775473e-05,3.772894e-05,3.637147e-05,7.268067e-06,3.481332e-06,3.481332e-06,2.401154e-06,2.401154e-06,8.197940e-06,8.197940e-06,3.997811e-06,3.997811e-06,3.997811e-06,3.997811e-06,1.207494e-05,1.207494e-05,1.963691e-05,2.055311e-05,2.178261e-06,3.398210e-06,3.398210e-06,3.175174e-06,3.175174e-06,1.975710e-05,5.860156e-05,5.860156e-05,5.860156e-05,7.028432e-05,7.028432e-05,7.028432e-05,7.028432e-05,7.028432e-05,7.028432e-05,8.770771e-05,8.770771e-05,3.941266e-04,3.941266e-04,1.002434e-04,4.501147e-04,9.140456e-05,9.140456e-05,9.140456e-05,1.216764e-04,1.216764e-04,1.216764e-04,1.216764e-04,1.216764e-04,1.358293e-04,1.358293e-04,1.358293e-04,1.358293e-04,2.433390e-04,2.128913e-04,6.047829e-05,6.047829e-05,6.047829e-05,6.047829e-05,6.047829e-05,6.047829e-05,1.559573e-04,6.756065e-04,6.756065e-04,1.252698e-03,1.252698e-03,1.252698e-03,1.722452e-03,2.974541e-03,2.788099e-03,2.788099e-03,2.788099e-03,2.788099e-03,2.788099e-03,2.788099e-03,9.704677e-04,6.524029e-04,6.524029e-04,6.524029e-04,6.524029e-04,1.986166e-04,5.148064e-04,3.935172e-05,3.935172e-05,3.935172e-05,3.596480e-05,3.596480e-05,3.840476e-04,3.265822e-04,3.265822e-04,1.699738e-03,3.382742e-04,3.382742e-04,4.291126e-04,4.291126e-04,4.291126e-04,4.291126e-04,3.012033e-04,7.874703e-05,4.009423e-04,4.009423e-04,4.009423e-04,4.009423e-04,7.015827e-04,7.015827e-04,8.998811e-04,3.750951e-04,8.001801e-05,8.001801e-05,8.001801e-05,8.001801e-05,8.769844e-05,8.769844e-05,2.336436e-05,8.662544e-05,4.360443e-05,4.360443e-05,4.360443e-05,4.360443e-05,4.360443e-05,4.360443e-05,3.684793e-05,1.296607e-05,2.434277e-06,4.454218e-06,4.454218e-06,5.346013e-06,5.346013e-06,5.346013e-06,9.166112e-07,9.166112e-07,9.166112e-07,2.914328e-07,4.793011e-08,4.793011e-08,2.518825e-08,2.518825e-08,2.559798e-08,2.559798e-08,2.559798e-08,2.559798e-08,1.786016e-08,1.786016e-08,1.786016e-08,1.786016e-08,1.786016e-08,2.581946e-08,2.581946e-08,7.651924e-09,7.651924e-09,7.651924e-09,2.654439e-09,2.654439e-09,1.160599e-08,1.089639e-08,4.441808e-09,2.993354e-08,2.993354e-08,6.597157e-09,1.756244e-08,3.663998e-08,3.663998e-08,3.663998e-08,3.663998e-08,2.087983e-08,7.219497e-09,7.219497e-09,7.219497e-09,8.681694e-09,8.681694e-09,8.681694e-09,8.681694e-09,8.681694e-09,2.434356e-10,5.152142e-10,1.627307e-10,1.627307e-10,1.627307e-10,3.166602e-10,3.166602e-10,3.166602e-10,3.166602e-10,1.984753e-10,1.984753e-10,6.607674e-10,6.607674e-10,7.945952e-10,7.945952e-10,1.049938e-09,1.049938e-09,1.049938e-09,1.049938e-09,1.049938e-09,1.049938e-09,1.049938e-09,7.585986e-10,7.585986e-10,7.585986e-10,8.310453e-10,3.369425e-10,3.369425e-10,3.369425e-10,3.369425e-10};
+ LogTransformedNormalKDEDistribution five = new
LogTransformedNormalKDEDistribution(testfivehundred);
+
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E7) + " : " +
five.evaluateKernel((double)i/1E7));
+ }
+
+ System.exit(0);*/
+
+
+ /*Double[] testvpu =
{3.264474e-10,3.264474e-10,2.270974e-10,4.053443e-10,1.440543e-10,1.948030e-11,2.160727e-11,2.160727e-11,2.160727e-11,2.798423e-11,1.220722e-10,1.220722e-10,6.669941e-11,6.669941e-11,4.142276e-11,5.325259e-11,5.325259e-11,5.325259e-11,9.190992e-11,1.165668e-10,4.202000e-11,4.202000e-11,4.202000e-11,7.824317e-12,7.824317e-12,7.824317e-12,7.824317e-12,7.824317e-12,7.824317e-12,1.245222e-12,5.797409e-14,5.797409e-14,5.797409e-14,5.797409e-14,5.797409e-14,5.797409e-14,6.524378e-14,3.446118e-14,3.446118e-14,3.446118e-14,1.406773e-14,3.089455e-14,3.089455e-14,3.089455e-14,4.719081e-14,2.636496e-14,2.854360e-14,2.854360e-14,3.201851e-14,3.201851e-14,5.526584e-14,5.526584e-14,5.526584e-14,5.526584e-14,2.943399e-13,4.180499e-13,4.180499e-13,4.180499e-13,3.678937e-13,3.678937e-13,2.121552e-13,8.475159e-13,3.201119e-13,2.478820e-13,2.478820e-13,2.927839e-13,2.927839e-13,1.586398e-13,1.586398e-13,8.238769e-14,1.329486e-13,9.046881e-13,9.046881e-13,9.046881e-13,9.046881e-13,1.075469e-13,7.662459e-14,9.494873e-14,9.494873e-14,1.415190e-13,1.415190e-13,1.415190e-13,1.415190e-13,1.180839e-13,1.180839e-13,1.180839e-13,1.180839e-13,7.610445e-14,7.150592e-14,3.058209e-14,2.428279e-14,2.428279e-14,2.428279e-14,2.428279e-14,2.428279e-14,3.412281e-14,1.005870e-13,1.005870e-13,3.600161e-14,5.032761e-14,4.792479e-14,3.137045e-14,3.137045e-14,7.775396e-15,9.260730e-15,2.632486e-14,1.542887e-14,1.542887e-14,1.542887e-14,3.920010e-16,2.705095e-16,2.705095e-16,2.705095e-16,1.611363e-16,1.611363e-16,1.611363e-16,1.611363e-16,1.611363e-16,1.611363e-16,1.611363e-16,5.833794e-17,9.684154e-18,9.684154e-18,2.140219e-17,2.140219e-17,2.140219e-17,2.131286e-17,1.997783e-18,1.003044e-18,1.003044e-18,1.003044e-18,1.003044e-18,1.252530e-18,1.252530e-18,1.252530e-18,5.360969e-19,4.049063e-20,8.391021e-20,8.391021e-20,8.391021e-20,8.391021e-20,8.391021e-20,1.656486e-20,1.656486e-20,2.592875e-20,2.592875e-20,2.592875e-20,6.944018e-20,6.944018e-20,9.193503e-21,3.153529e-20,2.002192e-21,9.662736e-22,9.662736e-22,2.366541e-21,2.366541e-21,9.746925e-22,5.145195e-22,5.145195e-22,2.040818e-21,9.600368e-22,9.600368e-22,9.600368e-22,9.600368e-22,9.600368e-22,6.477488e-22,8.845651e-23,8.845651e-23,8.612247e-23,4.819019e-23,5.332775e-23,5.332775e-23,1.612997e-23,3.568781e-24,4.478014e-25,4.478014e-25,4.608863e-25,2.532690e-25,2.532690e-25,4.184380e-26,4.184380e-26,4.833258e-26,1.996298e-26,7.691123e-27,7.691123e-27,7.577914e-27,7.506433e-27,7.506433e-27,7.506433e-27,4.145722e-28,2.791080e-28,1.087618e-27,1.087618e-27,1.152689e-27,1.152689e-27,1.152689e-27,1.152689e-27,9.221644e-28,8.193212e-29,8.193212e-29,8.193212e-29,2.450405e-29,2.591711e-29,2.591711e-29,2.591711e-29,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,4.053158e-30,3.491727e-29,1.156184e-28,1.156184e-28,1.379535e-28,9.951936e-28,9.951936e-28,9.951936e-28,9.951936e-28,9.951936e-28,9.951936e-28,1.452129e-27,6.233493e-27,6.233493e-27,1.890821e-27,1.890821e-27,4.573558e-27,4.573558e-27,1.852501e-26,1.852501e-26,3.534462e-26,6.457303e-26,6.457303e-26,6.457303e-26,9.789591e-26,1.722045e-26,2.146792e-27,2.146792e-27,2.146792e-27,2.146792e-27,2.146792e-27,2.163014e-27,2.163014e-27,4.770303e-28,4.770303e-28,4.770303e-28,9.266854e-28,9.266854e-28,9.266854e-28,7.038816e-28,2.887066e-28,2.887066e-28,2.887066e-28,3.215952e-28,1.694957e-28,1.787078e-28,1.787078e-28,1.533689e-28,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.202488e-29,8.202488e-29,2.341551e-28,2.341551e-28,3.304727e-29,3.127826e-29,3.127826e-29,5.295062e-30,5.295062e-30,5.295062e-30,9.226137e-30,9.226137e-30,9.226137e-30,5.203193e-30,1.288022e-29,1.288022e-29,2.330187e-29,9.787334e-29,9.787334e-29,1.559790e-29,1.559790e-29,2.492078e-30,2.492078e-30,2.492078e-30,4.966093e-30,4.966093e-30,4.966093e-30,4.966093e-30,1.350492e-29,2.104433e-29,8.483873e-29,5.165878e-29,3.600579e-29,3.600579e-29,3.600579e-29,2.624000e-28,3.463846e-28,3.463846e-28,1.481569e-28,1.481569e-28,3.577404e-28,3.914783e-28,4.493977e-28,4.493977e-28,4.493977e-28,4.493977e-28,4.493977e-28,4.493977e-28,3.432940e-28,3.432940e-28,3.432940e-28,3.432940e-28,3.432940e-28,4.480180e-28,4.390359e-28,5.724157e-28,5.724157e-28,8.549744e-28,8.549744e-28,4.305970e-28,4.305970e-28,1.393338e-27,8.152519e-28,4.189267e-27,5.074637e-26,5.074637e-26,5.074637e-26,7.426017e-26,6.834243e-26,3.218294e-26,3.218294e-26,4.572465e-26,4.572465e-26,4.572465e-26,2.120649e-25,2.120649e-25,2.120649e-25,2.120649e-25,8.192616e-25,1.464765e-25,1.464765e-25,1.464765e-25,1.464765e-25,1.464765e-25,3.165377e-25,3.165377e-25,3.165377e-25,3.165377e-25,2.657489e-25,2.657489e-25,2.657489e-25,3.619027e-25,2.767848e-25,1.162370e-24,1.162370e-24,3.354422e-24,3.967748e-24,3.967748e-24,3.967748e-24,3.967748e-24,3.967748e-24,2.275277e-24,4.737946e-24,4.737946e-24,3.155432e-24,3.155432e-24,3.155432e-24,3.155432e-24,3.155432e-24,5.108613e-24,2.534356e-23,9.638765e-23,9.638765e-23,1.082050e-22,3.284043e-22,2.544953e-22,2.561433e-22,2.561433e-22,2.561433e-22,1.788474e-22,1.788474e-22,3.070120e-22,6.679008e-22,4.254458e-23,4.254458e-23,6.737668e-24,9.744693e-24,6.508964e-24,3.432448e-23,3.432448e-23,3.997224e-23,3.997224e-23,3.997224e-23,3.997224e-23,3.997224e-23,3.997224e-23,3.380456e-23,1.697625e-23,1.697625e-23,3.928130e-24,9.920672e-25,9.920672e-25,9.920672e-25,6.972963e-25,6.972963e-25,6.972963e-25,6.972963e-25,1.245301e-24,4.815021e-25,2.025882e-24,2.025882e-24,2.025882e-24,2.025882e-24,3.271768e-24,3.271768e-24,7.527654e-24,7.527654e-24,4.701377e-24,2.168193e-24,2.168193e-24,3.201564e-24,3.201564e-24,3.201564e-24,3.320860e-25,3.320860e-25,3.320860e-25,3.320860e-25,4.065828e-25,3.251797e-25,3.251797e-25,3.251797e-25,3.251797e-25,3.251797e-25,3.251797e-25,4.751037e-25,4.751037e-25,4.751037e-25,4.751037e-25,2.470807e-25,2.470807e-25,1.533374e-25,1.533374e-25,8.054821e-26,5.435195e-25,1.292397e-24,1.270255e-24,1.270255e-24,1.270255e-24,1.270255e-24,1.013316e-24,1.242894e-24,2.091064e-24,2.091064e-24,2.729537e-24,9.825103e-25,9.825103e-25,9.825103e-25,9.825103e-25,9.825103e-25,2.213826e-25,9.499452e-25,1.038643e-24,1.038643e-24,3.891512e-24,2.886182e-24,9.920124e-25,9.920124e-25,9.920124e-25,2.813333e-24,1.258997e-23,8.722277e-24,8.722277e-24,8.722277e-24,2.575166e-24,1.972378e-24,1.972378e-24,1.972378e-24,1.925702e-24,5.637562e-24,5.637562e-24,5.637562e-24,1.047603e-23,1.245956e-23,1.245956e-23,1.034809e-23,1.034809e-23,1.034809e-23,1.034809e-23,1.218613e-23};
+ LogTransformedNormalKDEDistribution five = new
LogTransformedNormalKDEDistribution(testvpu);
+
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E12) + " : " +
five.evaluateKernel((double)i/1E12));
+ }
+ System.out.println();
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E14) + " : " +
five.evaluateKernel((double)i/1E14));
+ }
+ System.out.println();
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E16) + " : " +
five.evaluateKernel((double)i/1E16));
+ }
+ System.out.println();
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E26) + " : " +
five.evaluateKernel((double)i/1E26));
+ }
+
+ System.exit(0);*/
+
+
//Normal distribution
Double[] samples = new Double[10000];
NormalDistribution dist = new NormalDistribution(0.5, 0.10);
Author: bael...@gmail.com
Date: Thu Apr 23 18:24:52 2015 UTC
Log: Increased accuracy for log-transformed KDE estimation close to
zero.
https://code.google.com/p/beast-mcmc/source/detail?r=6747
Modified:
/trunk/src/dr/math/distributions/LogTransformedNormalKDEDistribution.java
=======================================
---
/trunk/src/dr/math/distributions/LogTransformedNormalKDEDistribution.java
Tue Apr 14 09:33:53 2015 UTC
+++
/trunk/src/dr/math/distributions/LogTransformedNormalKDEDistribution.java
Thu Apr 23 18:24:52 2015 UTC
@@ -237,6 +237,8 @@
to = DiscreteStatistics.max(this.sample) + this.cut *
this.bandWidth;
if (DEBUG) {
+ System.out.println("min: " +
DiscreteStatistics.min(this.sample));
+ System.out.println("max: " +
DiscreteStatistics.max(this.sample));
System.out.println("bandWidth = " + this.bandWidth);
System.out.println("cut = " + this.cut);
System.out.println("from = " + from);
@@ -250,51 +252,40 @@
System.out.println("lo = " + lo);
System.out.println("up = " + up);
}
-
- /*if (from < 0.0) {
- from = 0.0;
+
+ if (lo < 0.0) {
+ //small hack, but our asymmetric kernel estimators are
terribly slow
+ lo = DiscreteStatistics.min(this.sample);
}
- if (lo < 0.0) {
- lo = 0.0;
- }*/
//make new ordinates for the transformation back to normal space
//need a backup of the xPoints for the log scale KDE
this.backupXPoints = new double[xPoints.length];
System.arraycopy(xPoints, 0, backupXPoints, 0, xPoints.length);
makeOrdinates();
-
- int numberOfNegatives = 0;
- if (DEBUG) {
- System.out.println("\nxPoints length = " + xPoints.length);
- }
- for (int i = 0; i < xPoints.length; i++) {
- if (xPoints[i] < 0.0) {
- numberOfNegatives++;
- }
- //System.out.println(xPoints[i]);
- }
- if (DEBUG) {
- System.out.println("number of negative xPoints = " +
numberOfNegatives);
- }
//the KDE on log scale is contained in the xPoints and
densityPoints arrays
//copy them to finalXPoints and finalDensityPoints
- this.finalXPoints = new double[xPoints.length - numberOfNegatives];
- System.arraycopy(xPoints, numberOfNegatives, finalXPoints, 0,
xPoints.length - numberOfNegatives);
+
+ //this.finalXPoints = new double[xPoints.length - numberOfNegatives];
+ //this.finalXPoints = new double[xPoints.length];
+
+ //System.arraycopy(xPoints, numberOfNegatives, finalXPoints, 0,
xPoints.length - numberOfNegatives);
+ //System.arraycopy(xPoints, numberOfNegatives, finalXPoints, 0,
xPoints.length);
if (DEBUG) {
for (int i = 0; i < xPoints.length; i++) {
- System.out.println(backupXPoints[i] + " : " +
densityPoints[i]);
+ System.out.println(xPoints[i] + " " + backupXPoints[i]
+ " : " + densityPoints[i]);
}
- System.out.println("\nfinalXPoints length = " +
finalXPoints.length);
+ //System.out.println("\nfinalXPoints length = " +
finalXPoints.length);
}
- this.finalDensityPoints = new double[densityPoints.length -
numberOfNegatives];
+ //this.finalDensityPoints = new double[densityPoints.length -
numberOfNegatives];
+ this.finalDensityPoints = new double[densityPoints.length];
- for (int i = 0; i < finalXPoints.length; i++) {
- finalDensityPoints[i] = linearApproximate(backupXPoints,
densityPoints, Math.log(finalXPoints[i]), 0.0, 0.0)*(1.0/finalXPoints[i]);
+ for (int i = 0; i < xPoints.length; i++) {
+ finalDensityPoints[i] = linearApproximate(backupXPoints,
densityPoints, Math.log(xPoints[i]), 0.0, 0.0)*(1.0/xPoints[i]);
if (DEBUG) {
- System.out.println(finalXPoints[i] + "\t" +
finalDensityPoints[i]);
+ System.out.println(xPoints[i] + "\t" +
finalDensityPoints[i]);
}
}
@@ -343,13 +334,16 @@
xPoints = new double[gridSize];
double x = lo;
double delta = (up - lo) / (gridSize - 1);
- //System.out.println("X");
+ if (DEBUG) {
+ System.out.println("X");
+ }
for (int i = 0; i < gridSize; i++) {
xPoints[i] = x;
x += delta;
- //System.out.println(xPoints[i]);
+ if (DEBUG) {
+ System.out.println(xPoints[i]);
+ }
}
- //System.out.println();
}
@Override
@@ -359,7 +353,7 @@
computeDensity();
}
//xPoints and densityPoints are now back in normal space
- return linearApproximate(finalXPoints, finalDensityPoints, x, 0.0,
0.0);
+ return linearApproximate(xPoints, finalDensityPoints, x, 0.0, 0.0);
}
@Override
@@ -393,7 +387,7 @@
}
private ComplexArray kOrdinates;
- private double[] xPoints, finalXPoints, backupXPoints;
+ private double[] xPoints, backupXPoints;
private double[] densityPoints, finalDensityPoints;
private double[] backupSample, logSample;
@@ -408,6 +402,38 @@
public static void main(String[] args) {
+ /*Double[] testfivehundred =
{9.169378e-06,9.169378e-06,9.169378e-06,9.169378e-06,4.116020e-06,4.116020e-06,4.116020e-06,4.161038e-07,3.644982e-07,2.195354e-07,2.195354e-07,2.195354e-07,2.195354e-07,7.462043e-08,7.462043e-08,8.368972e-08,9.283378e-08,9.283378e-08,2.866075e-08,6.532907e-09,6.532907e-09,3.936993e-08,3.936993e-08,2.257473e-08,2.257473e-08,1.525075e-08,1.525075e-08,1.525075e-08,1.525075e-08,1.525075e-08,2.370723e-08,2.370723e-08,1.961463e-08,7.642434e-08,8.838916e-08,8.838916e-08,8.838916e-08,8.838916e-08,1.149915e-07,1.149915e-07,7.226055e-08,7.226055e-08,6.276125e-08,5.330820e-08,5.330820e-08,4.626315e-08,4.626315e-08,4.709987e-08,1.011533e-07,1.011533e-07,1.011533e-07,1.011533e-07,9.176941e-08,1.876641e-08,1.876641e-08,1.582991e-08,1.582991e-08,6.121650e-08,5.823668e-08,5.823668e-08,5.823668e-08,5.823668e-08,5.823668e-08,1.138725e-08,1.327368e-08,1.327368e-08,1.327368e-08,5.123223e-08,5.123223e-08,5.123223e-08,3.812422e-08,2.592858e-08,1.584334e-07,1.584334e-07,1.584334e-07,4.091027e-07,4.091027e-07,4.091027e-07,3.180726e-07,5.671995e-07,5.671995e-07,5.671995e-07,5.671995e-07,3.718532e-07,2.140636e-07,1.141818e-07,9.974324e-08,8.885531e-08,8.885531e-08,1.336255e-08,1.336255e-08,1.336255e-08,2.066815e-09,1.359399e-09,2.433474e-09,2.433474e-09,2.621958e-09,2.621958e-09,2.621958e-09,2.621958e-09,1.760426e-09,5.016878e-09,1.297173e-09,1.297173e-09,2.729714e-09,2.729714e-09,4.096775e-09,4.066638e-09,4.938423e-09,2.279718e-09,2.279718e-09,2.279718e-09,2.279718e-09,7.927200e-09,7.927200e-09,5.882404e-09,3.039284e-09,3.039284e-09,7.933658e-09,1.577847e-08,1.577847e-08,1.577847e-08,1.577847e-08,7.421679e-09,9.966059e-09,9.966059e-09,2.978775e-08,2.978775e-08,2.978775e-08,2.037757e-08,2.037757e-08,3.838478e-08,6.434436e-09,6.434436e-09,6.434436e-09,1.330451e-09,1.330451e-09,1.330451e-09,1.330451e-09,1.330451e-09,1.821259e-09,1.821259e-09,1.821259e-09,1.821259e-09,1.136283e-09,1.136283e-09,1.136283e-09,8.538424e-09,1.115792e-08,1.115792e-08,1.115792e-08,6.708989e-09,6.708989e-09,6.708989e-09,6.708989e-09,6.708989e-09,6.171120e-09,6.171120e-09,6.171120e-09,4.324598e-09,4.324598e-09,4.086923e-09,1.018727e-08,1.076947e-08,7.300160e-09,1.882574e-08,7.825507e-09,5.768726e-09,5.768726e-09,5.768726e-09,3.647371e-09,5.801127e-09,5.801127e-09,5.801127e-09,1.061525e-08,1.232341e-08,1.232341e-08,1.232341e-08,1.232341e-08,3.058357e-09,3.058357e-09,3.058357e-09,4.222149e-09,4.222149e-09,4.222149e-09,9.101976e-09,9.101976e-09,9.101976e-09,9.101976e-09,1.272342e-08,5.057809e-08,8.124001e-08,2.988208e-07,2.988208e-07,2.208343e-06,2.208343e-06,2.563228e-06,7.319180e-06,5.100615e-06,5.100615e-06,3.908437e-05,9.561673e-06,9.561673e-06,4.051668e-07,1.165789e-06,1.165789e-06,6.355679e-07,1.267624e-06,1.267624e-06,1.269425e-06,1.269425e-06,6.906194e-07,3.027074e-06,4.954935e-06,4.954935e-06,3.069373e-06,3.516738e-05,3.516738e-05,1.337480e-04,2.621304e-04,2.621304e-04,2.621304e-04,2.621304e-04,2.621304e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,8.714378e-04,3.789225e-03,2.911953e-03,2.911953e-03,2.911953e-03,2.911953e-03,2.911953e-03,2.911953e-03,2.889193e-03,2.741145e-03,2.741145e-03,2.741145e-03,2.741145e-03,1.039219e-03,1.039219e-03,1.039219e-03,4.519776e-04,5.756779e-04,5.756779e-04,1.608451e-04,2.319337e-04,1.004998e-04,1.004998e-04,1.004998e-04,2.479749e-04,2.479749e-04,2.479749e-04,2.290535e-04,2.290535e-04,2.290535e-04,5.562921e-05,5.562921e-05,5.562921e-05,2.263067e-05,2.924862e-05,1.625127e-05,1.625127e-05,1.625127e-05,5.130025e-06,5.130025e-06,5.130025e-06,2.601581e-06,3.884423e-05,3.884423e-05,3.884423e-05,1.899082e-05,1.128966e-05,1.128966e-05,1.128966e-05,1.457212e-05,8.006272e-06,8.006272e-06,1.007007e-05,1.007007e-05,1.007007e-05,1.007007e-05,8.494570e-06,8.494570e-06,8.494570e-06,1.394617e-05,1.394617e-05,1.394617e-05,7.943013e-06,1.523964e-05,1.523964e-05,2.775473e-05,2.775473e-05,2.775473e-05,2.775473e-05,2.775473e-05,3.772894e-05,3.637147e-05,7.268067e-06,3.481332e-06,3.481332e-06,2.401154e-06,2.401154e-06,8.197940e-06,8.197940e-06,3.997811e-06,3.997811e-06,3.997811e-06,3.997811e-06,1.207494e-05,1.207494e-05,1.963691e-05,2.055311e-05,2.178261e-06,3.398210e-06,3.398210e-06,3.175174e-06,3.175174e-06,1.975710e-05,5.860156e-05,5.860156e-05,5.860156e-05,7.028432e-05,7.028432e-05,7.028432e-05,7.028432e-05,7.028432e-05,7.028432e-05,8.770771e-05,8.770771e-05,3.941266e-04,3.941266e-04,1.002434e-04,4.501147e-04,9.140456e-05,9.140456e-05,9.140456e-05,1.216764e-04,1.216764e-04,1.216764e-04,1.216764e-04,1.216764e-04,1.358293e-04,1.358293e-04,1.358293e-04,1.358293e-04,2.433390e-04,2.128913e-04,6.047829e-05,6.047829e-05,6.047829e-05,6.047829e-05,6.047829e-05,6.047829e-05,1.559573e-04,6.756065e-04,6.756065e-04,1.252698e-03,1.252698e-03,1.252698e-03,1.722452e-03,2.974541e-03,2.788099e-03,2.788099e-03,2.788099e-03,2.788099e-03,2.788099e-03,2.788099e-03,9.704677e-04,6.524029e-04,6.524029e-04,6.524029e-04,6.524029e-04,1.986166e-04,5.148064e-04,3.935172e-05,3.935172e-05,3.935172e-05,3.596480e-05,3.596480e-05,3.840476e-04,3.265822e-04,3.265822e-04,1.699738e-03,3.382742e-04,3.382742e-04,4.291126e-04,4.291126e-04,4.291126e-04,4.291126e-04,3.012033e-04,7.874703e-05,4.009423e-04,4.009423e-04,4.009423e-04,4.009423e-04,7.015827e-04,7.015827e-04,8.998811e-04,3.750951e-04,8.001801e-05,8.001801e-05,8.001801e-05,8.001801e-05,8.769844e-05,8.769844e-05,2.336436e-05,8.662544e-05,4.360443e-05,4.360443e-05,4.360443e-05,4.360443e-05,4.360443e-05,4.360443e-05,3.684793e-05,1.296607e-05,2.434277e-06,4.454218e-06,4.454218e-06,5.346013e-06,5.346013e-06,5.346013e-06,9.166112e-07,9.166112e-07,9.166112e-07,2.914328e-07,4.793011e-08,4.793011e-08,2.518825e-08,2.518825e-08,2.559798e-08,2.559798e-08,2.559798e-08,2.559798e-08,1.786016e-08,1.786016e-08,1.786016e-08,1.786016e-08,1.786016e-08,2.581946e-08,2.581946e-08,7.651924e-09,7.651924e-09,7.651924e-09,2.654439e-09,2.654439e-09,1.160599e-08,1.089639e-08,4.441808e-09,2.993354e-08,2.993354e-08,6.597157e-09,1.756244e-08,3.663998e-08,3.663998e-08,3.663998e-08,3.663998e-08,2.087983e-08,7.219497e-09,7.219497e-09,7.219497e-09,8.681694e-09,8.681694e-09,8.681694e-09,8.681694e-09,8.681694e-09,2.434356e-10,5.152142e-10,1.627307e-10,1.627307e-10,1.627307e-10,3.166602e-10,3.166602e-10,3.166602e-10,3.166602e-10,1.984753e-10,1.984753e-10,6.607674e-10,6.607674e-10,7.945952e-10,7.945952e-10,1.049938e-09,1.049938e-09,1.049938e-09,1.049938e-09,1.049938e-09,1.049938e-09,1.049938e-09,7.585986e-10,7.585986e-10,7.585986e-10,8.310453e-10,3.369425e-10,3.369425e-10,3.369425e-10,3.369425e-10};
+ LogTransformedNormalKDEDistribution five = new
LogTransformedNormalKDEDistribution(testfivehundred);
+
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E7) + " : " +
five.evaluateKernel((double)i/1E7));
+ }
+
+ System.exit(0);*/
+
+
+ /*Double[] testvpu =
{3.264474e-10,3.264474e-10,2.270974e-10,4.053443e-10,1.440543e-10,1.948030e-11,2.160727e-11,2.160727e-11,2.160727e-11,2.798423e-11,1.220722e-10,1.220722e-10,6.669941e-11,6.669941e-11,4.142276e-11,5.325259e-11,5.325259e-11,5.325259e-11,9.190992e-11,1.165668e-10,4.202000e-11,4.202000e-11,4.202000e-11,7.824317e-12,7.824317e-12,7.824317e-12,7.824317e-12,7.824317e-12,7.824317e-12,1.245222e-12,5.797409e-14,5.797409e-14,5.797409e-14,5.797409e-14,5.797409e-14,5.797409e-14,6.524378e-14,3.446118e-14,3.446118e-14,3.446118e-14,1.406773e-14,3.089455e-14,3.089455e-14,3.089455e-14,4.719081e-14,2.636496e-14,2.854360e-14,2.854360e-14,3.201851e-14,3.201851e-14,5.526584e-14,5.526584e-14,5.526584e-14,5.526584e-14,2.943399e-13,4.180499e-13,4.180499e-13,4.180499e-13,3.678937e-13,3.678937e-13,2.121552e-13,8.475159e-13,3.201119e-13,2.478820e-13,2.478820e-13,2.927839e-13,2.927839e-13,1.586398e-13,1.586398e-13,8.238769e-14,1.329486e-13,9.046881e-13,9.046881e-13,9.046881e-13,9.046881e-13,1.075469e-13,7.662459e-14,9.494873e-14,9.494873e-14,1.415190e-13,1.415190e-13,1.415190e-13,1.415190e-13,1.180839e-13,1.180839e-13,1.180839e-13,1.180839e-13,7.610445e-14,7.150592e-14,3.058209e-14,2.428279e-14,2.428279e-14,2.428279e-14,2.428279e-14,2.428279e-14,3.412281e-14,1.005870e-13,1.005870e-13,3.600161e-14,5.032761e-14,4.792479e-14,3.137045e-14,3.137045e-14,7.775396e-15,9.260730e-15,2.632486e-14,1.542887e-14,1.542887e-14,1.542887e-14,3.920010e-16,2.705095e-16,2.705095e-16,2.705095e-16,1.611363e-16,1.611363e-16,1.611363e-16,1.611363e-16,1.611363e-16,1.611363e-16,1.611363e-16,5.833794e-17,9.684154e-18,9.684154e-18,2.140219e-17,2.140219e-17,2.140219e-17,2.131286e-17,1.997783e-18,1.003044e-18,1.003044e-18,1.003044e-18,1.003044e-18,1.252530e-18,1.252530e-18,1.252530e-18,5.360969e-19,4.049063e-20,8.391021e-20,8.391021e-20,8.391021e-20,8.391021e-20,8.391021e-20,1.656486e-20,1.656486e-20,2.592875e-20,2.592875e-20,2.592875e-20,6.944018e-20,6.944018e-20,9.193503e-21,3.153529e-20,2.002192e-21,9.662736e-22,9.662736e-22,2.366541e-21,2.366541e-21,9.746925e-22,5.145195e-22,5.145195e-22,2.040818e-21,9.600368e-22,9.600368e-22,9.600368e-22,9.600368e-22,9.600368e-22,6.477488e-22,8.845651e-23,8.845651e-23,8.612247e-23,4.819019e-23,5.332775e-23,5.332775e-23,1.612997e-23,3.568781e-24,4.478014e-25,4.478014e-25,4.608863e-25,2.532690e-25,2.532690e-25,4.184380e-26,4.184380e-26,4.833258e-26,1.996298e-26,7.691123e-27,7.691123e-27,7.577914e-27,7.506433e-27,7.506433e-27,7.506433e-27,4.145722e-28,2.791080e-28,1.087618e-27,1.087618e-27,1.152689e-27,1.152689e-27,1.152689e-27,1.152689e-27,9.221644e-28,8.193212e-29,8.193212e-29,8.193212e-29,2.450405e-29,2.591711e-29,2.591711e-29,2.591711e-29,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,7.476938e-30,4.053158e-30,3.491727e-29,1.156184e-28,1.156184e-28,1.379535e-28,9.951936e-28,9.951936e-28,9.951936e-28,9.951936e-28,9.951936e-28,9.951936e-28,1.452129e-27,6.233493e-27,6.233493e-27,1.890821e-27,1.890821e-27,4.573558e-27,4.573558e-27,1.852501e-26,1.852501e-26,3.534462e-26,6.457303e-26,6.457303e-26,6.457303e-26,9.789591e-26,1.722045e-26,2.146792e-27,2.146792e-27,2.146792e-27,2.146792e-27,2.146792e-27,2.163014e-27,2.163014e-27,4.770303e-28,4.770303e-28,4.770303e-28,9.266854e-28,9.266854e-28,9.266854e-28,7.038816e-28,2.887066e-28,2.887066e-28,2.887066e-28,3.215952e-28,1.694957e-28,1.787078e-28,1.787078e-28,1.533689e-28,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.813121e-29,8.202488e-29,8.202488e-29,2.341551e-28,2.341551e-28,3.304727e-29,3.127826e-29,3.127826e-29,5.295062e-30,5.295062e-30,5.295062e-30,9.226137e-30,9.226137e-30,9.226137e-30,5.203193e-30,1.288022e-29,1.288022e-29,2.330187e-29,9.787334e-29,9.787334e-29,1.559790e-29,1.559790e-29,2.492078e-30,2.492078e-30,2.492078e-30,4.966093e-30,4.966093e-30,4.966093e-30,4.966093e-30,1.350492e-29,2.104433e-29,8.483873e-29,5.165878e-29,3.600579e-29,3.600579e-29,3.600579e-29,2.624000e-28,3.463846e-28,3.463846e-28,1.481569e-28,1.481569e-28,3.577404e-28,3.914783e-28,4.493977e-28,4.493977e-28,4.493977e-28,4.493977e-28,4.493977e-28,4.493977e-28,3.432940e-28,3.432940e-28,3.432940e-28,3.432940e-28,3.432940e-28,4.480180e-28,4.390359e-28,5.724157e-28,5.724157e-28,8.549744e-28,8.549744e-28,4.305970e-28,4.305970e-28,1.393338e-27,8.152519e-28,4.189267e-27,5.074637e-26,5.074637e-26,5.074637e-26,7.426017e-26,6.834243e-26,3.218294e-26,3.218294e-26,4.572465e-26,4.572465e-26,4.572465e-26,2.120649e-25,2.120649e-25,2.120649e-25,2.120649e-25,8.192616e-25,1.464765e-25,1.464765e-25,1.464765e-25,1.464765e-25,1.464765e-25,3.165377e-25,3.165377e-25,3.165377e-25,3.165377e-25,2.657489e-25,2.657489e-25,2.657489e-25,3.619027e-25,2.767848e-25,1.162370e-24,1.162370e-24,3.354422e-24,3.967748e-24,3.967748e-24,3.967748e-24,3.967748e-24,3.967748e-24,2.275277e-24,4.737946e-24,4.737946e-24,3.155432e-24,3.155432e-24,3.155432e-24,3.155432e-24,3.155432e-24,5.108613e-24,2.534356e-23,9.638765e-23,9.638765e-23,1.082050e-22,3.284043e-22,2.544953e-22,2.561433e-22,2.561433e-22,2.561433e-22,1.788474e-22,1.788474e-22,3.070120e-22,6.679008e-22,4.254458e-23,4.254458e-23,6.737668e-24,9.744693e-24,6.508964e-24,3.432448e-23,3.432448e-23,3.997224e-23,3.997224e-23,3.997224e-23,3.997224e-23,3.997224e-23,3.997224e-23,3.380456e-23,1.697625e-23,1.697625e-23,3.928130e-24,9.920672e-25,9.920672e-25,9.920672e-25,6.972963e-25,6.972963e-25,6.972963e-25,6.972963e-25,1.245301e-24,4.815021e-25,2.025882e-24,2.025882e-24,2.025882e-24,2.025882e-24,3.271768e-24,3.271768e-24,7.527654e-24,7.527654e-24,4.701377e-24,2.168193e-24,2.168193e-24,3.201564e-24,3.201564e-24,3.201564e-24,3.320860e-25,3.320860e-25,3.320860e-25,3.320860e-25,4.065828e-25,3.251797e-25,3.251797e-25,3.251797e-25,3.251797e-25,3.251797e-25,3.251797e-25,4.751037e-25,4.751037e-25,4.751037e-25,4.751037e-25,2.470807e-25,2.470807e-25,1.533374e-25,1.533374e-25,8.054821e-26,5.435195e-25,1.292397e-24,1.270255e-24,1.270255e-24,1.270255e-24,1.270255e-24,1.013316e-24,1.242894e-24,2.091064e-24,2.091064e-24,2.729537e-24,9.825103e-25,9.825103e-25,9.825103e-25,9.825103e-25,9.825103e-25,2.213826e-25,9.499452e-25,1.038643e-24,1.038643e-24,3.891512e-24,2.886182e-24,9.920124e-25,9.920124e-25,9.920124e-25,2.813333e-24,1.258997e-23,8.722277e-24,8.722277e-24,8.722277e-24,2.575166e-24,1.972378e-24,1.972378e-24,1.972378e-24,1.925702e-24,5.637562e-24,5.637562e-24,5.637562e-24,1.047603e-23,1.245956e-23,1.245956e-23,1.034809e-23,1.034809e-23,1.034809e-23,1.034809e-23,1.218613e-23};
+ LogTransformedNormalKDEDistribution five = new
LogTransformedNormalKDEDistribution(testvpu);
+
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E12) + " : " +
five.evaluateKernel((double)i/1E12));
+ }
+ System.out.println();
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E14) + " : " +
five.evaluateKernel((double)i/1E14));
+ }
+ System.out.println();
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E16) + " : " +
five.evaluateKernel((double)i/1E16));
+ }
+ System.out.println();
+ for (int i = 0; i < 100; i++) {
+ System.out.println(((double) i / 1E26) + " : " +
five.evaluateKernel((double)i/1E26));
+ }
+
+ System.exit(0);*/
+
+
//Normal distribution
Double[] samples = new Double[10000];
NormalDistribution dist = new NormalDistribution(0.5, 0.10);
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