Drop pmx_integrate_ode_group_* functions

[kyleam]

Using the following functions in a Stan model triggers a "not a member of 'stan::math'" error:

• pmx_integrate_ode_group_adams
• pmx_integrate_ode_group_bdf
• pmx_integrate_ode_group_rk45

I think these fail because the pmx_integration_* pattern is not mapped to the torsten:: namespace at this spot in stanc3/src/stan_math_backend/Lower_expr.ml.

The conclusion on the call, as far as I understand, was that these will be removed.

References in user guide

as of current develop (b414a05)

• Torsten/docs/torsten_users_guide.org

  Line 974 in b414a05

  matrix pmx_integrate_ode_group_[adams || rk45 || bdf](ODE_system, real[ , ] y0, real t0, int[] len, real[] ts, real[ , ] theta, real[ , ] x_r, int[ , ] x_i, [ real rtol, real atol, int max_step ] );

• Torsten/docs/torsten_users_guide.org

  Line 1334 in b414a05

  Using =pmx_integrate_ode_group_rk45=, the following example fits

References in .stan files

as of current develop (b414a05)

$ git grep pmx_integrate_ode_group_adams b414a05ac4 -- '*.stan'
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group.stan:  y = pmx_integrate_ode_group_adams (ode, y0, t0, len, ts, theta, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group.stan:  yp = pmx_integrate_ode_group_adams (ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group_control.stan:  y = pmx_integrate_ode_group_adams (ode, y0, t0, len, ts, theta, x_r, x_i, rtol, atol, max_num_steps);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group_control.stan:  yp = pmx_integrate_ode_group_adams (ode, y0_p, t0, len, ts, theta_p, x_r, x_i, rtol, atol, max_num_steps);
b414a05ac4:example-models/harmonic_oscillator_ode_group_model/sho_simu_group.stan:  yp = pmx_integrate_ode_group_adams(sho, y0_p, t0, len, ts, theta_p, x_r_p, x_i_p);

$ git grep pmx_integrate_ode_group_bdf b414a05ac4 -- '*.stan'
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group/bdf_bad_functor.stan:  yp = pmx_integrate_ode_group_bdf(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group/bdf_bad_len.stan:  yp = pmx_integrate_ode_group_bdf(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group/bdf_bad_t0.stan:  yp = pmx_integrate_ode_group_bdf(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group/bdf_bad_theta.stan:  yp = pmx_integrate_ode_group_bdf(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group/bdf_bad_ts.stan:  yp = pmx_integrate_ode_group_bdf(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group/bdf_bad_x_i.stan:  yp = pmx_integrate_ode_group_bdf(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group/bdf_bad_x_r.stan:  yp = pmx_integrate_ode_group_bdf(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group/bdf_bad_y0.stan:  yp = pmx_integrate_ode_group_bdf(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group.stan:  y = pmx_integrate_ode_group_bdf   (ode, y0, t0, len, ts, theta, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group.stan:  yp = pmx_integrate_ode_group_bdf   (ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group_control.stan:  y = pmx_integrate_ode_group_bdf   (ode, y0, t0, len, ts, theta, x_r, x_i, rtol, atol, max_num_steps);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group_control.stan:  yp = pmx_integrate_ode_group_bdf   (ode, y0_p, t0, len, ts, theta_p, x_r, x_i, rtol, atol, max_num_steps);
b414a05ac4:example-models/chemical_reactions/chem_group.stan:  x = pmx_integrate_ode_group_bdf(reaction, y0_pop, t0, len, ts,
b414a05ac4:example-models/chemical_reactions_with_stiffness_diff/chem_group.stan:  x = pmx_integrate_ode_group_bdf(reaction, y0_pop, t0, len, ts, theta,
b414a05ac4:example-models/chemical_reactions_with_stiffness_diff/chem_group_nonstiff.stan:  x = pmx_integrate_ode_group_bdf(reaction, y0_pop, t0, len, ts,
b414a05ac4:example-models/chemical_reactions_with_stiffness_diff/chem_group_stiff.stan:  x = pmx_integrate_ode_group_bdf(reaction, y0_pop, t0, len, ts,
b414a05ac4:example-models/chemical_reactions_with_unbalance_load/chem_group.stan:  x = pmx_integrate_ode_group_bdf(reaction, y0_pop, t0, len, ts,
b414a05ac4:example-models/harmonic_oscillator_ode_group_model/sho_group.stan:  y = pmx_integrate_ode_group_bdf(sho, y0, 0.0, len, ts, theta, rep_array(rep_array(0.0, 0),N_subj), rep_array(rep_array(0, 0),N_subj));
b414a05ac4:example-models/harmonic_oscillator_ode_group_model/sho_simu_group.stan:/*   yp = pmx_integrate_ode_group_bdf(sho, y0_p, t0, len, ts, theta_p, x_r_p, x_i_p); */
b414a05ac4:tests/sho_group.stan:  y = pmx_integrate_ode_group_bdf(sho, y0, 0.0, len, ts, theta, rep_array(rep_array(0.0, 0),N_subj), rep_array(rep_array(0, 0),N_subj));

$ git grep pmx_integrate_ode_group_rk45 b414a05ac4 -- '*.stan'
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group_control/rk45_bad_functor.stan:  yp = pmx_integrate_ode_group_rk45(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group_control/rk45_bad_len.stan:  yp = pmx_integrate_ode_group_rk45(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group_control/rk45_bad_t0.stan:  yp = pmx_integrate_ode_group_rk45(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group_control/rk45_bad_theta.stan:  yp = pmx_integrate_ode_group_rk45(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group_control/rk45_bad_ts.stan:  yp = pmx_integrate_ode_group_rk45(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group_control/rk45_bad_x_i.stan:  yp = pmx_integrate_ode_group_rk45(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group_control/rk45_bad_x_r.stan:  yp = pmx_integrate_ode_group_rk45(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/bad/torsten/pmx_integrate_ode_group_control/rk45_bad_y0.stan:  yp = pmx_integrate_ode_group_rk45(ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group.stan:  y = pmx_integrate_ode_group_rk45  (ode, y0, t0, len, ts, theta, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group.stan:  yp = pmx_integrate_ode_group_rk45  (ode, y0_p, t0, len, ts, theta_p, x_r, x_i);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group_control.stan:  y = pmx_integrate_ode_group_rk45  (ode, y0, t0, len, ts, theta, x_r, x_i, rtol, atol, max_num_steps);
b414a05ac4:cmdstan/stan/src/test/test-models/good/torsten/pmx_integrate_ode_group_control.stan:  yp = pmx_integrate_ode_group_rk45  (ode, y0_p, t0, len, ts, theta_p, x_r, x_i, rtol, atol, max_num_steps);
b414a05ac4:example-models/lotka_volterra_ode_group_model/lv_group.stan:  z = pmx_integrate_ode_group_rk45(dz_dt, z_init, 0, len, ts, theta, rep_array(rep_array(0.0, 0), N_subj), rep_array(rep_array(0, 0),N_subj));

[yizhang-yiz]

Resolved in PR #63.