Hi all,

I have some issues in evaluating the log probability at the initial value.

```
rt[] nt[] rc[] nc[]
10 595.2 21 640.2
2 762.0 0 756.0
54 5635.0 70 5600.0
47 5135.0 63 4960.0
53 3760.0 62 4210.0
10 2233.0 9 2084.5
25 7056.1 35 6824.0
47 8099.0 31 8267.0
43 5810.0 39 5922.0
25 5397.0 45 5173.0
157 22162.7 182 22172.5
92 20885.0 72 20645.0
")
names(dat) <- gsub(".", "", names(dat), fixed = TRUE)
dataList = list(
Ntotal = 12,
nt=log(dat$nt/1000),
rt=dat$rt,
nc=log(dat$nc/1000),
rc=dat$rc
)
################Stan###############
modelString1 = "
data{
int<lower=0> Ntotal;
real nt[Ntotal];
int<lower=0> rt[Ntotal];
real nc[Ntotal];
int<lower=0> rc[Ntotal];
}
parameters {
real<lower=-10,upper=10> mu;
real<lower=0,upper=10> tau2;
real<lower=0,upper=10> tauphi;
real<lower=-10,upper=10> muphi;
real<lower=-10,upper=10> beta;
real phi[Ntotal];
real thetaadjpred[10];
}
transformed parameters {
real mt[Ntotal];
real mc[Ntotal];
real <lower=0> mtt[Ntotal];
real <lower=0> mcc[Ntotal];
real theta[Ntotal];
real thetaadj[Ntotal];
for(i in 1:12){
theta[i] = thetaadj[i] + beta*(phi[i]-mean(phi[1:12]));
mt[i] = nt[i] + phi[i] + theta[i];
mc[i] = nc[i] + phi[i];
mtt[i] = exp(mt[i]);//+ (1e-10)
mcc[i] = exp(mc[i]);//+ (1e-10)
}
}
model
{
for(j in 1:10){
thetaadjpred[j] ~ normal(mu,tau2);
}
for(i in 1:12){
target += normal_lpdf(thetaadj[i] | mu,tau2);
phi[i] ~ normal(muphi, tauphi);
rt[i]~poisson(mtt[i]);
rc[i]~poisson(mcc[i]);
}
}
generated quantities {
real phi0;
real <lower=0> invph0;
real thetapred[10];
real <lower=0> rr[Ntotal];
real <lower=0> rbase[Ntotal];
phi0 = -mu/beta + mean(phi[1:12]);
invph0=exp(phi0);
for(j in 1:10){
thetapred[j] = thetaadjpred[j] + beta*( (j-3)/2.0 -mean(phi[1:12]));
}
for(i in 1:10){
rr[i]= exp( theta[i]);
rbase[i]=exp(phi[i]);
}
}
"
writeLines( modelString1 , con="TEMPmodel.stan" )
stanModel <- stan(
data = dataList ,
file = "TEMPmodel.stan",
chains = 4,
warmup = 5000,
iter = 25000,
control = list(adapt_delta = 0.99)
)
stanModel
```

When I try to debug, I try to swith the order of the code, but it never work.

here are the issues I have:

Chain 1: Rejecting initial value:

Chain 1: Error evaluating the log probability at the initial value.

Chain 1: Exception: validate transformed params: mtt[i_0__] is nan, but must be greater than or equal to 0 (in ‘model27e02255220e_TEMPmodel’ at line 24)

Thanks for helping to look into this.