[beast-mcmc] r6733 committed - Finished test script for log transformed KDE distribution.

[beast...@googlecode.com]

Revision: 6733
Author: bael...@gmail.com
Date: Mon Apr 13 12:47:30 2015 UTC
Log: Finished test script for log transformed KDE distribution.
https://code.google.com/p/beast-mcmc/source/detail?r=6733

Modified:
/trunk/src/dr/math/distributions/LogTransformedNormalKDEDistribution.java

=======================================
---
/trunk/src/dr/math/distributions/LogTransformedNormalKDEDistribution.java
Fri Apr 10 12:37:38 2015 UTC
+++
/trunk/src/dr/math/distributions/LogTransformedNormalKDEDistribution.java
Mon Apr 13 12:47:30 2015 UTC
@@ -408,27 +408,79 @@

public static void main(String[] args) {

+ //Normal distribution
Double[] samples = new Double[10000];
NormalDistribution dist = new NormalDistribution(0.5, 0.10);
for (int i = 0; i < samples.length; i++) {
samples[i] = (Double)dist.nextRandom();
- if (samples[i] < 0.0) {
+ if (samples[i] < 0.0 && DEBUG) {
System.err.println("Negative value generated!");
}
}
Arrays.sort(samples);
- System.out.println("min: " + samples[0]);
- System.out.println("max: " + samples[samples.length-1] + "\n");
+ if (DEBUG) {
+ System.out.println("min: " + samples[0]);
+ System.out.println("max: " + samples[samples.length - 1]
+ "\n");
+ }

LogTransformedNormalKDEDistribution ltn = new
LogTransformedNormalKDEDistribution(samples);
NormalKDEDistribution nKDE = new NormalKDEDistribution(samples);

- for (int i = 0; i < 50; i++) {
- Double test = (Double)dist.nextRandom();
- System.out.println("random draw: " + test);
- System.out.println("normal KDE: " + nKDE.evaluateKernel(test));
- System.out.println("log transformed normal KDE: " +
ltn.evaluateKernel(test) + "\n");
+ if (DEBUG) {
+ for (int i = 0; i < 50; i++) {
+ Double test = (Double) dist.nextRandom();
+ System.out.println("random draw: " + test);
+ System.out.println("normal KDE: " +
nKDE.evaluateKernel(test));
+ System.out.println("log transformed normal KDE: " +
ltn.evaluateKernel(test) + "\n");
+ }
}
+
+
+ //LogNormal distribution
+ samples = new Double[2000];
+ dist = new NormalDistribution(0.0, 1.0);
+ for (int i = 0; i < samples.length; i++) {
+ samples[i] = (Double)dist.nextRandom();
+ while (samples[i] < 0.0) {
+ samples[i] = (Double)dist.nextRandom();
+ }
+ samples[i] = Math.exp(samples[i]-Math.exp(1.0));
+ }
+
+ //Generate R code for visualisation
+ System.out.print("par(mfrow=c(2,2))\n\nsamples <- c(");
+ for (int i = 0; i < samples.length-1; i++) {
+ System.out.print(samples[i] + ",");
+ }
+ System.out.println(samples[samples.length-1] + ")\n\n");
+ System.out.println("hist(samples,
200)\nminimum=min(samples)\nabline(v=minimum,col=2,lty=2)\n");
+
System.out.println("plot(density(samples))\nabline(v=minimum,col=2,lty=2)\n");
+
+ Arrays.sort(samples);
+ if (DEBUG) {
+ System.out.println("min: " + samples[0]);
+ System.out.println("max: " + samples[samples.length - 1]
+ "\n");
+ }
+
+ ltn = new LogTransformedNormalKDEDistribution(samples);
+ nKDE = new NormalKDEDistribution(samples);
+
+ System.out.print("normalKDE <- c(");
+ for (int i = 0; i < 1999; i++) {
+ Double test = 0.0 + ((double)i)/((double)1000);
+ System.out.print(nKDE.evaluateKernel(test) + ",");
+ }
+
System.out.println(nKDE.evaluateKernel(((double)1999)/((double)1000))
+ ")\n");
+ System.out.println("index <- seq(0.0,1.999,by=0.001)");
+
System.out.println("plot(index,normalKDE,type=\"l\")\nabline(v=minimum,col=2,lty=2)\n");
+
+ System.out.print("TransKDE <- c(");
+ for (int i = 0; i < 1999; i++) {
+ Double test = 0.0 + ((double)i)/((double)1000);
+ System.out.print(ltn.evaluateKernel(test) + ",");
+ }
+
System.out.println(ltn.evaluateKernel(((double)1999)/((double)1000))
+ ")\n");
+
System.out.println("plot(index,TransKDE,type=\"l\")\nabline(v=minimum,col=2,lty=2)");

}