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16.5 Solving DAEs

Stan provides a dae function for solving DAEs, so that the above chemical reaction equation can be solved in the following code.

data {
  int N;
  vector[3] yy0;
  vector[3] yp0;
  real t0;
  real alpha;
  real beta;
  array[N] real ts;
  array[N] vector[3] y;
}
parameters {
  real gamma;
}
transformed parameters {
  vector[3] y_hat[N] = dae(chem, yy0, yp0, t0, ts, alpha, beta, gamma);
}

Since gamma is a parameter, the DAE solver is called in the transformed parameters block.