Log variables not being saved correctly

[zjzxiaohei]

I am using LPhy with the phylonco package and the saved logged variables file has negative numbers where the result is not negative.

My LPhy script is:

n = 2;
l = 2;

Θ ~ LogNormal(meanlog=-2.0, sdlog=1.0);
ψ ~ Coalescent(n=n, 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=l, Q=Q, tree=ψ, dataType=phasedGenotype());
epsilon = 0.06; // try 0.5
delta = 0.5;
meanT = 2.3; // average coverage = lognormal(meanT, sdT)
sdT = 0.1;
meanV = 0.1; // variance coverage = lognormal(meanV, sdV)
sdV = 0.05;
meanS = 0.04; // cell-specific scaling
sdS = 0.001;
t ~ LogNormal(meanlog= meanT, sdlog= sdT);
v ~ LogNormal(meanlog= meanV, sdlog= sdV);
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 = 10.0;

r1 ~ ReadCountModel(D=A, epsilon=epsilon, alpha=alpha, coverage=cov, w=w1);
[readCountVars.txt](https://github.com/user-attachments/files/16405540/readCountVars.txt)
[readCountVarsTrue.txt](https://github.com/user-attachments/files/16405541/readCountVarsTrue.txt)

Variables files saved from the LPhyStudio Menu is attached as "readCountVars.txt"

The true variables as shown in the Variable Summary panel in LPhyStudio is attached as "readCountVarsTrue.txt"

[walterxie]

1. can you reload your file?
2. look at any lphy examples that have data and model block, and tidy up your code. It is difficult to read.

[zjzxiaohei]

readCountVars.txt readCountVarsTrue.txt

[zjzxiaohei]

n = 2;
l = 2;
w1 = 10.0;
epsilon = 0.6; // try 0.5
delta = 0.5;
meanT = 2.3; // average coverage = lognormal(meanT, sdT)
sdT = 0.1;
meanV = 0.1; // variance coverage = lognormal(meanV, sdV)
sdV = 0.05;
meanS = 0.04; // cell-specific scaling
sdS = 0.001;

Θ ~ LogNormal(meanlog=-2.0, sdlog=1.0);
ψ ~ Coalescent(n=n, 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=l, Q=Q, tree=ψ, dataType=phasedGenotype());
t ~ LogNormal(meanlog= meanT, sdlog= sdT);
v ~ LogNormal(meanlog= meanV, sdlog= sdV);
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);
r1 ~ ReadCountModel(D=A, epsilon=epsilon, alpha=alpha, coverage=cov, w=w1);

[walterxie]

I still do not understand your problem. After asking Kylie, I found few problems in your code:

1. PloidyModel missing setter;
2. why using Multinomial, not Binomial,

Value<Integer[]> alpha1 = multinomialAlpha.sample();
if (alpha1.value()[0] == 1) {
     alp[i][j] = 1;
} else alp[i][j] = 2;

The above code seems suspicious to put inside a nested loop.

In addition, few more minor issues:

i. too many empty lines above RandomVariable<Integer[][]> sample(); ii. no comment, difficult to read; iii. you still did not put the lphy script into data and model block.

I have explained all these details to Kylie.