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The standard library of LPhy, which contains the required generative distributions and basic functions.

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package lphy.base.evolution.sitemodel;

import lphy.core.model.MultiDimensional;
import lphy.core.model.annotation.GeneratorCategory;
import lphy.core.model.annotation.MethodInfo;
import lphy.core.model.annotation.TypeInfo;

@TypeInfo(description = "A composited model containing instantaneous rate matrix, " +
        "rate per site before accounting for proportion invariable, and the proportion of invariable sites.",
        examples = {"simpleBModelTest.lphy"})
public class SiteModel implements MultiDimensional {

    // instantaneous rate matrix
    Double[][] Q;

    // rate per site before accounting for proportion invariable.
    Double[] siteRates;

    // the proportion of invariable sites
    // this should be used to mask a binomial random fraction of the site rates to zero.
    Double proportionInvariable;

    int nchar;

    public SiteModel(Double[][] Q, Double[] siteRates, Double proportionInvariable) {
        this.Q = Q;
        this.siteRates = siteRates;
        this.proportionInvariable = proportionInvariable;
    }

    @MethodInfo(description = "the Q matrix for this site model",
            category = GeneratorCategory.SITE_MODEL, examples = {"simpleBModelTest.lphy"})
    public Double[][] getQ() {
        return Q;
    }

    public boolean hasSiteRates() {
        return siteRates != null;
    }

    @MethodInfo(description = "the raw site rates for this site model")
    public Double[] siteRates() {
        return siteRates;
    }

    public Integer stateCount() {
        return Q.length;
    }

    @MethodInfo(description = "the proportion of invariable sites")
    public Double getProportionInvariable() {
        return proportionInvariable;
    }

    @Override
    public int getDimension() {
        return 1 + Q.length * Q.length + siteRates.length;
    }
}