Writing functions for log-likelihoods in rstan

Interfaces RStan
, ,
1

Hi all,
I’m writing the functions for the log-likelihood of my hierarchical model in RSTAN. But, I got the below error in stan. Here, the county is a vector with dim= num_elements(t) that shows the residence place of patients (N=34750, county = 1, … , 31). Can anyone help me to solve this error?
Stan Error:
SYNTAX ERROR, MESSAGE(S) FROM PARSER:
Container index must be integer; found type=real
error in ‘model52ad62e48c9e_Onicesco_dependency_model_right_interval_weibull34744’ at line 21, column 20
19: spdf = a (p,kernel, exp_x);
20: for (i in 1:num_elements(t)){
21: log_S[i] = log(spdf[county[i]]) + weibull_lccdf(t[i]|shape,scale[i]);

^

22: }

PARSER EXPECTED: <one or more container indexes followed by ‘]’>
Error in stanc(filename, allow_undefined = TRUE) :

Thank you

My stan codes are as follows:

functions{
  // defines the log new pdf
vector a (vector p,matrix kernel, vector exp_x){
vector[num_elements(p)] a; 
vector[num_elements(p)] landa;
for (k in 1 : num_elements(p)) {
landa[k] = kernel[k] * exp_x * p[k];
    }
a = landa / sum(landa); // assign `a`
return a;
    }
// defines the log survival
vector log_S (vector t,vector p, matrix kernel, vector exp_x, vector county, real shape,vector scale){
vector[num_elements(t)] log_S;
vector[num_elements(p)] spdf;
spdf = a (p,kernel, exp_x);
for (i in 1:num_elements(t)){
log_S[i] = log(spdf[county[i]]) + weibull_lccdf(t[i]|shape,scale[i]); // county is a vector that shows the location of patients with dim = num_elements(t) 
}
return log_S;
}
//defines the log pdf
vector log_h (vector t,vector p, matrix kernel, vector exp_x, vector county, real shape,vector scale){
vector[num_elements(t)] log_f ;
vector[num_elements(p)] spdf;
spdf = a (p,kernel, exp_x);
for (i in 1:num_elements(t)){
log_f[i] = log(spdf[county[i]]) + (weibull_lpdf(t[i]|shape,scale[i]));
}
return log_h;
}
//defines the log-likelihood for right censored data
real surv_weibull_lpdf(vector t,vector d,real shape,
vector scale){
vector[num_elements(t)] log_lik;
real prob;
log_lik = d .* log_h(t,shape,scale)+
log_S(t,shape,scale);
prob = sum(log_lik);
return prob;
}
}
.```
2

My guess is it’s this indexing statement: spdf[county[i]]). The Stan language reference manual section 5.4 says

Vectors and matrices cannot be typed to return integer values. They are restricted to real values

Maybe you could declare county as an integer array?

3

Thank you much for your reply and assistance.