Two-compartment model as a linear ODE model for single patient

Using pmx_solve_linode, the following example fits a two-compartment model with first order absorption. We omit data and model block as they are identical to Two-compartment model for single patient Example.

transformed data{
  row_vector[nObs] logCObs = log(cObs);
  int nCmt = 3;
  real biovar[nCmt];
  real tlag[nCmt];

  for (i in 1:nCmt) {
    biovar[i] = 1;
    tlag[i] = 0;
  }
}

parameters{
  real<lower = 0> CL;
  real<lower = 0> Q;
  real<lower = 0> V1;
  real<lower = 0> V2;
  real<lower = 0> ka;
  real<lower = 0> sigma;
}

transformed parameters{
  matrix[3, 3] K;
  real k10 = CL / V1;
  real k12 = Q / V1;
  real k21 = Q / V2;
  row_vector<lower = 0>[nt] cHat;
  row_vector<lower = 0>[nObs] cHatObs;
  matrix<lower = 0>[3, nt] x;

  K = rep_matrix(0, 3, 3);

  K[1, 1] = -ka;
  K[2, 1] = ka;
  K[2, 2] = -(k10 + k12);
  K[2, 3] = k21;
  K[3, 2] = k12;
  K[3, 3] = -k21;

  x = pmx_solve_linode(time, amt, rate, ii, evid, cmt, addl, ss, K, biovar, tlag);

  cHat = row(x, 2) ./ V1;

  for(i in 1:nObs){
    cHatObs[i] = cHat[iObs[i]];  // predictions for observed data records
  }
}