Examples with LogisticGrowthN0 dr.evomodel.epidemiology.LogisticGrowthN0 used on opensource projects

Example 1 with LogisticGrowthN0

use of dr.evomodel.epidemiology.LogisticGrowthN0 in project beast-mcmc by beast-dev.

the class TransmissionTreeToVirusTree method main.

public static void main(String[] args) {
    ModelType model = ModelType.CONSTANT;
    double startNe = 1;
    double growthRate = 0;
    double t50 = 0;
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.StringOption(DEMOGRAPHIC_MODEL, demographics, false, "The type of within-host" + " demographic function to use, default = constant"), new Arguments.RealOption(STARTING_POPULATION_SIZE, "The effective population size at time zero" + " (used in all models), default = 1"), new Arguments.RealOption(GROWTH_RATE, "The effective population size growth rate (used in" + " exponential and logistic models), default = 0"), new Arguments.RealOption(T50, "The time point, relative to the time of infection in backwards " + "time, at which the population is equal to half its final asymptotic value, in the " + "logistic model default = 0") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        System.out.println(ae);
        printUsage(arguments);
        System.exit(1);
    }
    if (arguments.hasOption(HELP)) {
        printUsage(arguments);
        System.exit(0);
    }
    if (arguments.hasOption(DEMOGRAPHIC_MODEL)) {
        String modelString = arguments.getStringOption(DEMOGRAPHIC_MODEL);
        if (modelString.toLowerCase().startsWith("c")) {
            model = ModelType.CONSTANT;
        } else if (modelString.toLowerCase().startsWith("e")) {
            model = ModelType.EXPONENTIAL;
        } else if (modelString.toLowerCase().startsWith("l")) {
            model = ModelType.LOGISTIC;
        } else {
            progressStream.print("Unrecognised demographic model type");
            System.exit(1);
        }
    }
    if (arguments.hasOption(STARTING_POPULATION_SIZE)) {
        startNe = arguments.getRealOption(STARTING_POPULATION_SIZE);
    }
    if (arguments.hasOption(GROWTH_RATE) && model != ModelType.CONSTANT) {
        growthRate = arguments.getRealOption(GROWTH_RATE);
    }
    if (arguments.hasOption(T50) && model == ModelType.LOGISTIC) {
        t50 = arguments.getRealOption(T50);
    }
    DemographicFunction demoFunction = null;
    switch(model) {
        case CONSTANT:
            {
                demoFunction = new ConstantPopulation(Units.Type.YEARS);
                ((ConstantPopulation) demoFunction).setN0(startNe);
            }
        case EXPONENTIAL:
            {
                demoFunction = new ExponentialGrowth(Units.Type.YEARS);
                ((ExponentialGrowth) demoFunction).setN0(startNe);
                ((ExponentialGrowth) demoFunction).setGrowthRate(growthRate);
            }
        case LOGISTIC:
            {
                demoFunction = new LogisticGrowthN0(Units.Type.YEARS);
                ((LogisticGrowthN0) demoFunction).setN0(startNe);
                ((LogisticGrowthN0) demoFunction).setGrowthRate(growthRate);
                ((LogisticGrowthN0) demoFunction).setT50(t50);
            }
    }
    final String[] args2 = arguments.getLeftoverArguments();
    if (args2.length != 3) {
        printUsage(arguments);
        System.exit(1);
    }
    String infectionsFileName = args2[0];
    String samplesFileName = args2[1];
    String outputFileRoot = args2[2];
    TransmissionTreeToVirusTree instance = new TransmissionTreeToVirusTree(samplesFileName, infectionsFileName, demoFunction, outputFileRoot);
    try {
        instance.run();
    } catch (IOException e) {
        e.printStackTrace();
    }
}