Google Git
Sign in
eclipse / stem / org.eclipse.stem / 1f805952242ef8c0a8ba184b86100e6d6ef24de9 / . / org.eclipse.stem.tests.diseasemodels / src / org / eclipse / stem / diseasemodels / standard / tests / DeterministicSIRScenarioTest.java
blob: e9e2f85f935f6c5aec087b05b4530d92493b01a8 [file] [log] [blame]
// DeterministicSIRScenarioTest.java
package org.eclipse.stem.diseasemodels.standard.tests;
/*******************************************************************************
* Copyright (c) 2006 IBM Corporation and others.
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
* Contributors:
* IBM Corporation - initial API and implementation
*******************************************************************************/
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.eclipse.stem.core.graph.LabelValue;
import org.eclipse.stem.core.model.NodeDecorator;
import org.eclipse.stem.diseasemodels.standard.SIRLabelValue;
import org.eclipse.stem.diseasemodels.standard.impl.SIRLabelValueImpl;
/**
* This class is a JUnit test case for a Deterministic SIR disease model
* scenario.
* <ul>
* <li>&mu; = {@link DiseaseModelTest#MORTALITY_RATE} = 0.01</li>
* <li>&beta; = {@link SITest#TRANSMISSION_RATE} = 0.1</li>
* <li>&sigma; = {@link SITest#RECOVERY_RATE} = 0.01</li>
* <li>x = {@link SITest#INFECTIOUS_MORTALITY} = 0.1 </li>
* <li>&mu;<sub>i</sub> = {@link SITest#INFECTIOUS_MORTAILY_RATE} = 0.1</li>
* <li>&gamma; = {@link SIRTest#IMMUNITY_LOSS_RATE} = 0.1</li>
* <li>Area<sub>l</sub> = 1.0</li>
* <li>Area = 1.0</li>
* <li>P = S + I = {@link DiseaseModelTestUtil#TEST_POPULATION_COUNT} = 100</li>
* </ul>
* <h2>1x1 Deterministic SIR Scenario</h2>
* <h3>Initial State</h3>
* <p>
* S= 99.0, I<sup>R</sup>=1.0, I<sup>F</sup>=0.0, R=0.0, B=0.0, D=0.0,
* DD=0.0
* </p>
* <h3>SIR 1x1 Step 0</h3>
*
* <ul>
* <li><em>TSF<sub>l</sub> = (1/P)*(Area/Area<sub>l</sub>)</em></li>
* <li><em>TSF<sub>l</sub> = (1/100)*(1/1)</em></li>
* <li><em>TSF<sub>l</sub> = 0.01</em></li>
* </ul>
* <ul>
* <li><em>&beta;<sup>*</sup> = &beta; TSF<sub>l</sub></em></li>
* <li><em>&beta;<sup>*</sup> = 0.1 * 0.01</em></li>
* <li><em>&beta;<sup>*</sup> = 0.001</em></li>
* </ul>
* <ul>
* <li><em>&Delta;B = &mu; * (S + I<sup>R</sup> + I<sup>F</sup> +R)</em></li>
* <li><em>&Delta;B = 0.01 * (99+1+0) </em> </li>
* <li><em>&Delta;B = 1.0</em> </li>
* </ul>
* <ul>
* <li><em>&Delta;DD = &mu;<sub>i</sub> I<sup>F</sup> </em> </li>
* <li><em>&Delta;DD= 0.1 * 0</em> </li>
* <li><em>&Delta;DD= 0.0</em> </li>
* </ul>
* <ul>
* <li><em>&Delta;D = &mu; S + (&mu; + &mu;<sub>i</sub> )I<sup>F</sup> + &mu; I<sup>R</sup> + &mu; R </em>
* </li>
* <li><em>&Delta;D = 0.01 * 99 + (0.01 + 0.1 ) 0 + 0.01 * 1 + 0.01 * 0</em>
* </li>
* <li><em>&Delta;D= 1</em> </li>
* </ul>
* <ul>
* <li><em>&Delta;S = &mu; (S + I + R) - &beta;<sup>*</sup> S I + &gamma;R - &mu; S</em></li>
* <li><em>&Delta;S = 0.01 (99+(1+0)+0) - 0.001 * 99 * (1+0+0) + 0.01 * 0 - 0.01 * 99</em></li>
* <li><em>&Delta;S = 1.0 - 0.099 + 0.01 - 0.99</em></li>
* <li><em>&Delta;S = -0.089</em></li>
* </ul>
* <ul>
* <li><em>&Delta;I<sup>R</sup> = (1-x)&beta;<sup>*</sup> S I - &sigma; I<sup>R</sup> - &mu; I<sup>R</sup></em></li>
* <li><em>&Delta;I<sup>R</sup> = 0.9 * 0.001 * 99 * 1 - 0.01 * 1 - 0.01 * 1</em></li>
* <li><em>&Delta;I<sup>R</sup> = 0.0891 - .01 - .01</em></li>
* <li><em>&Delta;I<sup>R</sup> = 0.0691</em></li>
* </ul>
* <ul>
* <li><em>&Delta;I<sup>F</sup> = x&beta;<sup>*</sup> S I - (&mu; + &mu;<sub>i</sub>) I<sup>F</sup></em></li>
* <li><em>&Delta;I<sup>F</sup> = 0.1 * 0.001 * 99 * 1 - (0.01 + 0.1) * 0</em></li>
* <li><em>&Delta;I<sup>F</sup> = .0099</em></li>
* </ul>
* <ul>
* <li><em>&Delta;R = &sigma; I<sup>R</sup> - &gamma;R - &mu; R</em></li>
* <li><em>&Delta;R = 0.01 * 1 - 0.01 * 0 - 0.01 * 0</em></li>
* <li><em>&Delta;R = .01</em></li>
* </ul>
* <p>
* S= 98.911, I<sup>R</sup>=1.0691, I<sup>F</sup>=0.0099, R=0.01, B=1.0,
* D=1.0, DD=0.0
* </p>
*
* <h3>SIR 1x1 Step 1</h3>
*
* <ul>
* <li><em>TSF<sub>l</sub> = (1/P)*(Area/Area<sub>l</sub>)</em></li>
* <li><em>TSF<sub>l</sub> = (1/99.989)*(1/1)</em></li>
* <li><em>TSF<sub>l</sub> = 0.0100011</em></li>
* </ul>
* <ul>
* <li><em>&beta;<sup>*</sup> = &beta; TSF<sub>l</sub></em></li>
* <li><em>&beta;<sup>*</sup> = 0.1 * 0.0100011</em></li>
* <li><em>&beta;<sup>*</sup> = 0.00100011</em></li>
* </ul>
* <ul>
* <li><em>&Delta;B = &mu; * (S + I<sup>R</sup> + I<sup>F</sup> +R)</em></li>
* <li><em>&Delta;B = 0.01 * 99.989 </em> </li>
* <li><em>&Delta;B = 0.99989</em> </li>
* </ul>
* <ul>
* <li><em>&Delta;DD = &mu;<sub>i</sub> I<sup>F</sup> </em> </li>
* <li><em>&Delta;DD= 0.1 * 0.0099</em> </li>
* <li><em>&Delta;DD= 0.00099</em> </li>
* </ul>
* <ul>
* <li><em>&Delta;D = &mu; S + (&mu; + &mu;<sub>i</sub> )I<sup>F</sup> + &mu; I<sup>R</sup> + &mu; R </em>
* </li>
* <li><em>&Delta;D = 0.01 * 98.911 + (0.01 + 0.1) 0.0099 + 0.01 * 1.0691 + 0.01 * 0.01</em>
* </li>
* <li><em>&Delta;D= 1.00099</em> </li>
* </ul>
* <ul>
* <li><em>&Delta;S = &mu; (S + I + R) - &beta;<sup>*</sup> S I + &gamma;R - &mu; S</em></li>
* <li><em>&Delta;S = 0.01 * 99.989 - 0.00100011 * 98.911 * (1.0691+0.0099) + 0.01 * 0.01 - 0.01 * 98.911</em></li>
* <li><em>&Delta;S = 0.99989 - 0.106736709 + 0.0001 - 0.98911</em></li>
* <li><em>&Delta;S = -0.095856709</em></li>
* </ul>
* <ul>
* <li><em>&Delta;I<sup>R</sup> = (1-x)&beta;<sup>*</sup> S I - &sigma; I<sup>R</sup> - &mu; I<sup>R</sup></em></li>
* <li><em>&Delta;I<sup>R</sup> = 0.9 * 0.00100011 * 98.911 * (1.0691+0.0099) - 0.01 * 1.0691 - 0.01 * 1.0691</em></li>
* <li><em>&Delta;I<sup>R</sup> = 0.096063038 - .010691 - .010691</em></li>
* <li><em>&Delta;I<sup>R</sup> = 0.074681038</em></li>
* </ul>
* <ul>
* <li><em>&Delta;I<sup>F</sup> = x&beta;<sup>*</sup> S I - (&mu; + &mu;<sub>i</sub>) I<sup>F</sup></em></li>
* <li><em>&Delta;I<sup>F</sup> = 0.1 * 0.00100011 * 98.911 * (1.0691+0.0099) - (0.01 + 0.1) * 0.0099</em></li>
* <li><em>&Delta;I<sup>F</sup> = 0.010673671 - 0.001089</em></li>
* <li><em>&Delta;I<sup>F</sup> = .009584671</em></li>
* </ul>
* <ul>
* <li><em>&Delta;R = &sigma; I<sup>R</sup> - &gamma;R - &mu; R</em></li>
* <li><em>&Delta;R = 0.01 * 1.0691 - 0.01 * 0.01 - 0.01 * 0.01</em></li>
* <li><em>&Delta;R = .010491</em></li>
* </ul>
* <p>
* S= 98.81514329, I<sup>R</sup>=1.143781038, I<sup>F</sup>=0.019484671,
* R=0.020491, B=1.99989, D=2.00099, DD=0.00099
* </p>
*
*/
public class DeterministicSIRScenarioTest extends SIRDiseaseModelScenarioTest {
private static final String DISEASE_URI_PREFIX = "DeterministicSIR";
private static Map<String, Integer> expectedNumberOfLabelsToUpdate = new HashMap<String, Integer>();
private static Map<String, SIRLabelValue[][][]> expectedDiseaseModelStates = new HashMap<String, SIRLabelValue[][][]>();
static {
// 1x1
expectedDiseaseModelStates.put(TEST_SCENARIO1x1_KEY,
new SIRLabelValue[][][] {
// Step 0
{ {
// N[0,0]
new SIRLabelValueImpl(99.01, 0.98, 0.0, 0.01,
0.0) } },
// Step 1
{ {
// N[0,0]
new SIRLabelValueImpl(99.02, 0.96, 0.0, 0.02,
0.00) } } } // new
// SIRLabelValue
); // put(TEST_SCENARIO1x1_KEY)
// 1x2
expectedDiseaseModelStates
.put(TEST_SCENARIO1x2_KEY,
new SIRLabelValue[][][] {
// Step 0
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0) } },
// Step 1
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0
) } },
// Step 2
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0
),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0
) } } } // new
// SIRLabelValue
); // put(TEST_SCENARIO1x2_KEY)
// 1x3
expectedDiseaseModelStates.put(TEST_SCENARIO1x3_KEY,
new SIRLabelValue[][][] {
// Step 0
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
} },
// Step 1
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
} },
// Step 2
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
} } } // new SIRLabelValue
); // put(TEST_SCENARIO1x3_KEY)
// 2x2
expectedDiseaseModelStates.put(TEST_SCENARIO2x2_KEY,
new SIRLabelValue[][][] {
// Step 0
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
}, {
// N[1,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[1,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
} },
// Step 1
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
}, {
// N[1,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[1,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
} },
// Step 2
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
}, {
// N[1,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[1,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
} } } // new SIRLabelValue
); // put(TEST_SCENARIO2x2_KEY)
// 3x3
expectedDiseaseModelStates.put(TEST_SCENARIO3x3_KEY,
new SIRLabelValue[][][] {
// Step 0
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
}, {
// N[1,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[1,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[1,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
}, {
// N[2,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[2,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[2,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
} },
// Step 1
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
}, {
// N[1,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[1,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[1,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
}, {
// N[2,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[2,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[2,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
} },
// Step 2
{ {
// N[0,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[0,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
}, {
// N[1,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[1,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[1,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
}, {
// N[2,0]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[2,1]
new SIRLabelValueImpl(100, 0, 0, 0, 0),
// N[2,2]
new SIRLabelValueImpl(100, 0, 0, 0, 0)
} } } // new SIRLabelValue
); // put(TEST_SCENARIO3x3_KEY)
// Fill out the map that specifies how many labels should be updated by
// a disease model for each test.
for (TestSpec testSpec : testSpecifications) {
expectedNumberOfLabelsToUpdate
.put(
testSpec.scenarioDiseaseKey,
new Integer(
computeExpectedNumberOfLabels(expectedDiseaseModelStates
.get(testSpec.scenarioDiseaseKey))));
} // for each test specification
} // static
/**
* @see org.eclipse.stem.diseasemodels.standard.tests.DiseaseModelScenarioTest#getDiseaseModelsToTest()
*/
@Override
public List<NodeDecorator> getDiseaseModelsToTest() {
final List<NodeDecorator> retValue = new ArrayList<NodeDecorator>();
retValue.add(DeterministicSIRDiseaseModelTest.createFixture());
return retValue;
} // getDiseaseModelsToTest
@Override
protected int getNumberOfSteps(final String diseaseScenarioKey) {
SIRLabelValue[][][] temp = expectedDiseaseModelStates
.get(diseaseScenarioKey);
return temp.length;
} // getNumberOfSteps
@Override
protected int getExpectedNumberOfLabelsToUpdate(
final String diseaseScenarioKey) {
Integer temp = expectedNumberOfLabelsToUpdate.get(diseaseScenarioKey);
return temp.intValue();
} // getExpectedNumberOfLabelsToUpdate
@Override
protected LabelValue[][] getExpectedDiseaseModelState(
final String diseaseScenarioKey, final int step) {
final SIRLabelValue[][][] sirLabelValue = expectedDiseaseModelStates
.get(diseaseScenarioKey);
return sirLabelValue[step];
} // getExpectedDiseaseModelState
protected String getDiseaseURIPrefix() {
return DISEASE_URI_PREFIX;
} // getDiseaseURIPrefix
} // DeterministicSIRScenarioTest