Example model failures

[kyleam]

run time init dimension error

The neutropeniaPopulation.stan model fails with a dimension mismatch.

Running example-models/neutropeniaPopulation/neutropeniaPopulation.stan fails with

Exception: mismatch in number dimensions declared and found in context; processing stage=data initialization; variable name=ii; dims declared=(445); dims found=() (in '[...]/Torsten/example-models/neutropeniaPopulation/neutropeniaPopulation.stan', line 64, column 2 to column 31)

This is perhaps related to stanc3 v2.32.1 starting to check the shapes of initial values against what's specified in the model: stanc3#1316.

array syntax failures

The following models in example-models/ fail to compile due to using outdated array syntax:

• chemical_reactions_with_stiffness_diff/chem_group_nonstiff.stan
• chemical_reactions_with_stiffness_diff/chem_group_stiff.stan
• chemical_reactions_with_unbalance_load/chem_group.stan
• harmonic_oscillator_ode_group_model/sho_group.stan
• harmonic_oscillator_ode_group_model/sho_loop.stan
• harmonic_oscillator_ode_group_model/sho_simu_group.stan
• lotka_volterra_ode_group_model/lv.stan
• lotka_volterra_ode_group_model/lv_group.stan
• multiDoseME2PK1/multiDoseME2PK1.stan

These should of course be straightforward to update. However, at least some of these array errors mask other errors (e.g., lv_group.stan hits into the "not a stan math member" error).

failures due to "unregistered" stanc3 issues

The following example models fail to compile due to "not a stan math member" errors (related to gh-56):

• chemical_reactions/chem_group.stan
• chemical_reactions_with_stiffness_diff/chem_group.stan

The following examples fail to compile due to "undeclared identifier" errors (related to gh-53 and gh-54):

• chemical_reactions_with_unbalance_load/chem.stan
• harmonic_oscillator_ode_group_model/sho_pmx_loop.stan
• lotka_volterra_ode_group_model/lv_pmx.stan
• ttpn2/ttpn2.stan
• ttpn2/ttpn2Sim.stan

Similarly, the following example models use old Torsten function names:

• harmonic_oscillator_ode_group_model/sho_loop.stan (integrate_ode_bdf)
• lotka_volterra_ode_group_model/lv.stan (integrate_ode_rk45)
• ttpn2/ttpn2.stan (generalOdeModel_rk45)