The current version of the tutorial SIR2 Treelikelihood cannot be followed properly due to:
sir2Master.xml is missing from the repository
Modifying the provided sir2TrajectoryFinal0.xml using it together with sir2Master.nwk generates the following problem (tested with BEAST 2.5.0 in Mac and 2.5.2 in Linux. In both cases I am using the latest version of PhyDyn installed using BEAST2's packagemanager)
`File: sir2Trajectory_final.xml seed: 1554771653242 threads: 1
Generating Likelihood test xml
output xml file = sir2Likelihood.xml
--- tree file: sir2Master.nwk
root height: 13.225650562640002
num tips = 200
-- Population model
model-name = twodeme;
definitions = {
k0 = beta0S;
k1 = beta1S;
}
equations = {
F(I0,I0) = k0I0;
F(I1,I0) = k1I1;
G(I0,I1) = gamma0I0;
D(I0) = 0;
D(I1) = gamma1I1;
dot(S) = bS-(beta0I0+beta1I1)S;
}
model-parameters = {
beta0 = 0.001;
beta1 = 1.0E-4;
gamma0 = 1.0;
gamma1 = 0.1111;
b = 0.01;
}
trajectory-parameters = {
t0 = 0.0 t1 = 20.0
method=classicrk; integrationSteps=1001;
initial-vales = {
I0 = 1.0;
I1 = 0.0;
S = 999.0;
};
}
Fatal exception: null
java.lang.NullPointerException
at phydyn.model.ModelParameters.writeXML(Unknown Source)
at phydyn.model.PopModelODE.writeXML(Unknown Source)
at phydyn.run.XMLGenerator.writeLikelihood(Unknown Source)
at phydyn.run.XMLGenerator.run(Unknown Source)
at beast.app.BeastMCMC.run(Unknown Source)
at beast.app.beastapp.BeastMain.(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
Fatal exception: null
java.lang.RuntimeException: An error was encounted. Terminating BEAST
at beast.app.util.ErrorLogHandler.publish(Unknown Source)
at java.util.logging.Logger.log(Logger.java:738)
at java.util.logging.Logger.doLog(Logger.java:765)
at java.util.logging.Logger.log(Logger.java:788)
at java.util.logging.Logger.severe(Logger.java:1463)
at beast.app.beastapp.BeastMain.(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
igococha
commented
4 years ago
The current version of the tutorial SIR2 Treelikelihood cannot be followed properly due to:
`File: sir2Trajectory_final.xml seed: 1554771653242 threads: 1 Generating Likelihood test xml output xml file = sir2Likelihood.xml --- tree file: sir2Master.nwk root height: 13.225650562640002 num tips = 200 -- Population model model-name = twodeme; definitions = { k0 = beta0S; k1 = beta1S; } equations = { F(I0,I0) = k0I0; F(I1,I0) = k1I1; G(I0,I1) = gamma0I0; D(I0) = 0; D(I1) = gamma1I1; dot(S) = bS-(beta0I0+beta1I1)S; } model-parameters = { beta0 = 0.001; beta1 = 1.0E-4; gamma0 = 1.0; gamma1 = 0.1111; b = 0.01; } trajectory-parameters = { t0 = 0.0 t1 = 20.0 method=classicrk; integrationSteps=1001; initial-vales = { I0 = 1.0; I1 = 0.0; S = 999.0; }; } Fatal exception: null java.lang.NullPointerException at phydyn.model.ModelParameters.writeXML(Unknown Source) at phydyn.model.PopModelODE.writeXML(Unknown Source) at phydyn.run.XMLGenerator.writeLikelihood(Unknown Source) at phydyn.run.XMLGenerator.run(Unknown Source) at beast.app.BeastMCMC.run(Unknown Source) at beast.app.beastapp.BeastMain.(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
Fatal exception: null
java.lang.RuntimeException: An error was encounted. Terminating BEAST
at beast.app.util.ErrorLogHandler.publish(Unknown Source)
at java.util.logging.Logger.log(Logger.java:738)
at java.util.logging.Logger.doLog(Logger.java:765)
at java.util.logging.Logger.log(Logger.java:788)
at java.util.logging.Logger.severe(Logger.java:1463)
at beast.app.beastapp.BeastMain.(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
`