Hierachical Model Specification- Array Issue

Modeling
#1

Hi!

I’m currently running into an issue with model specification as part of an ODE system I’m trying to solve- I’m doing the following:


transformed parameters {
   real params[nStudies, 9];
   real y0[nStudies, 3];
   for(i in 1:nStudies){
     params[i, 1] = epsilon; 
     params[i, 2] = muMF_0;
     params[i, 3] = muW;
     params[i, 4] = foi[i];
     params[i, 5] = muMF_1_max[i];
     params[i, 6] = rho[i];
     params[i, 7] = beta_1_max[i];
     params[i, 8] = lambda[i];
     params[i, 9] = treatment_time;
     y0[i, 1] = fertile_worms_equilibrium(foi[i], muW);
     y0[i, 2] = 0;
     y0[i, 3] = mf_equilibrium(epsilon, y0[1, i], muMF_0);
   }
}

model{
  real y_hat[nStudies, K, 3];
  for(i in 1:nStudies){
    y_hat[i] = integrate_ode_rk45(LoaModel, to_array_1d(y0[i]), t0, time, to_array_1d(params[i]), x_r, x_i);
  }
- some other code underneath-
}

And I’m getting this error message:

stan second argument to integrate_ode_rk45 must have type real[] for intial system state; found type=real[,]. fifth argument to integrate_ode_rk45 must have type real[] for parameters; found type=real[,].

Does anyone have any idea what’s going on? I was expecting to_array_1d to give me real[] but evidently not! Any and all help would be massively appreciated!

#2

It helps if you include your whole program so we can test it.

I’m not sure how you’re getting that result, as the only output types of to_array_1d are indeed real[] (or int[], but your y is real).

To solve the problem, you should be able to use just y0[i] instead of to_array_1d and same for params[i]. But it should work as written, which is why I’d like to see the whole program to determine if it’s a parser bug…

Also, you can simplify syntax with:

for (i in 1:nStudies) {
  params[i] = { epsilon, muMF_0, ..., treatment_time };
  y0[i] = { fertile_worms_equilibrium( ), 0, mf_equilibrium(...) };
}

You might want to just define params and y0 as local variables in the model block—I can’t imagine you want to save params in that form.