Changed multinomial distribution to Dirichlet multinomial distrbution…

… for readcount model #56

phylonco-lphy/examples/gt16CoalErrModel.lphy

@@ -1,9 +1,9 @@
 Θ ~ LogNormal(meanlog=-2.0, sdlog=1.0);
-ψ ~ Coalescent(n=16, theta=Θ);
+ψ ~ Coalescent(n=4, theta=Θ);
 π ~ Dirichlet(conc=[3.0,3.0,3.0,3.0,3.0,3.0,3.0,3.0,3.0,3.0,3.0,3.0,3.0,3.0,3.0,3.0]);
 rates ~ Dirichlet(conc=[1.0, 2.0, 1.0, 1.0, 2.0, 1.0]);
 Q = gt16(freq=π, rates=rates); // construct the GT16 instantaneous rate matrix
-A ~ PhyloCTMC(L=200, Q=Q, tree=ψ, dataType=phasedGenotype());
+A ~ PhyloCTMC(L=5, Q=Q, tree=ψ, dataType=phasedGenotype());
 epsilon ~ Beta(alpha=2, beta=18);
 delta ~ Beta(alpha=1.5, beta=4.5);
 E ~ GT16ErrorModel(delta=delta, epsilon=epsilon, alignment=A);

phylonco-lphy/examples/gt16ReadCountModel.lphy

@@ -9,7 +9,7 @@ Q = gt16(freq=π, rates=rates); // construct the GT16 instantaneous rate matrix
 A ~ PhyloCTMC(L=l, Q=Q, tree=ψ, dataType=phasedGenotype());
 //epsilon ~ Beta(alpha=2, beta=18);
 //delta ~ Beta(alpha=1.5, beta=4.5);
-epsilon = 0.01;
+epsilon = 0.1;
 delta = 0.24;
 // cov = [rep(1, 5), rep(2, 5), rep(3, 5), rep(4, 5)];
 meanT = 2.3; // average coverage = lognormal(meanT, sdT)
@@ -24,5 +24,6 @@ s ~ LogNormal(meanlog= meanS, sdlog= sdS, replicates=n);
 alpha ~ Ploidy(l= l, n= n, delta= delta);
 cov ~ CoverageModel(alpha= alpha, t= t, v= v, s= s);
 
+w1 = 100.0;
 
-r ~ ReadCountModel(D=A, epsilon=epsilon, alpha=alpha, coverage=cov);
+r1 ~ ReadCountModel(D=A, epsilon=epsilon, alpha=alpha, coverage=cov, w=w1);