ERROR IN STAN CODE

[abqozeem]

I have the below code:

functions {
  real[] RPubSIR(real t, real[] y, real[] theta, 
             real[] x_r, int[] x_i) {

      real S = y[1];
      real I = y[2];
      real R = y[3];
      real N = x_i[1];
      
      real beta = theta[1];
      real sigma = theta[2];
      
      #TODO: fill it in.
      real dS_dt = -beta * S * I / N;
      real dI_dt = beta * S * I / N - sigma * I;
      real dR_dt = sigma * I;

      
      return {dS_dt, dI_dt, dR_dt};
  }
}

data {
  int<lower=1> n_days;
  real y0[3];
  real t0;
  real ts[n_days];
  int N;
  int cases[n_days];
}

transformed data {
  real x_r[0];
  int x_i[1] = {N};
}

parameters {
  real<lower=0> sigma;
  real<lower=0> beta;
  real<lower=0> phi_inv;
}

transformed parameters{
  real y[n_days, 3];
  real phi = 1. / phi_inv;
  {
    real theta[2]; // model parameters
    theta[1] = beta;
    theta[2] = sigma;

    y = integrate_ode_rk45(RPubSIR, y0, t0, ts, theta, x_r, x_i);
  }
}

model {
  //priors
  beta ~ normal(2, 1); //truncated at 0
  sigma ~ normal(0.4, 0.25); //truncated at 0
  phi_inv ~ exponential(5);
  
  //likelihood
  //col(matrix x, int n) - The n-th column of matrix x. Here the number of infected people
  cases ~ neg_binomial_2(col(to_matrix(y), 2), phi);
}

generated quantities {
  real recovery_time = 1 / sigma;
  real pred_cases[n_days];
  pred_cases = neg_binomial_2_rng(col(to_matrix(y), 2) + 1e-5, phi);
}

and when I tried to save it and further to the Rscript to compile, an error popped up and is:

> rstan:::rstudio_stanc("RPubSIR.stan")
Error in stanc(filename, allow_undefined = TRUE) : 0
Internal compiler error:
TypeError: not a function

Kindly respond by helping to debug.

[WardBrian]

@abqozeem this sounds like a duplicate of #1446

We've seen some reports suggesting this goes away if you can install the V8 package

@andrjohns -- another one