Output from preprocess_ode generates erro when given to e.g. assess_identifiability

[TorkelE]

Minimal example:

# Fetch packages.
using ModelingToolkit, StructuralIdentifiability

# Create model
@parameters p1 p2
@variables t x1(t) x2(t) y(t)
D = Differential(t)
eqs = [D(x1) ~ p1* x2 - x1,
       D(x2) ~ p2 - p1* x2]
@named osys = ODESystem(eqs)

# Create StructuralIdentifiability ODE.
known_parameter = [p1]
measured_quantities = [y ~ x1]
si_ode_1 = preprocess_ode(osys, known_parameter)
si_ode_2 = preprocess_ode(osys, measured_quantities)

assess_identifiability(si_ode_1)
assess_identifiability(si_ode_2)
assess_local_identifiability(si_ode_1)
assess_local_identifiability(si_ode_2)

All the ones at the end give errors like:

ERROR: MethodError: no method matching assess_local_identifiability(::Tuple{ODE{Nemo.QQMPolyRingElem}, Dict{SymbolicUtils.BasicSymbolic{Real}, Nemo.QQMPolyRingElem}})

Closest candidates are:
  assess_local_identifiability(::ODE{P}; funcs_to_check, p, type, trbasis) where P<:AbstractAlgebra.MPolyRingElem{Nemo.QQFieldElem}
   @ StructuralIdentifiability ~/.julia/packages/StructuralIdentifiability/JIDUk/src/local_identifiability.jl:231
  assess_local_identifiability(::ODESystem; measured_quantities, funcs_to_check, p, type)
   @ StructuralIdentifiability ~/.julia/packages/StructuralIdentifiability/JIDUk/src/local_identifiability.jl:166
  assess_local_identifiability(::DiscreteSystem; measured_quantities, funcs_to_check, known_ic, p)
   @ StructuralIdentifiability ~/.julia/packages/StructuralIdentifiability/JIDUk/src/discrete.jl:308

Stacktrace:
 [1] top-level scope
   @ ~/Desktop/Julia Playground/StructuralIdentifiabiltiyExtension tests/playground.jl:21

[pogudingleb]

The reason is that preprocess_ode returns not only ODE object but also a dictionary to do conversion between the variables in the ODE object and the symbols from ModelingToolit (this is also mentioned in the docstring, perhaps I should have emphasized this).

So, to make this code work, one should just insert , _ at a couple of places:

# Fetch packages.
using ModelingToolkit, StructuralIdentifiability

# Create model
@parameters p1 p2
@variables t x1(t) x2(t) y(t)
D = Differential(t)
eqs = [D(x1) ~ p1* x2 - x1,
       D(x2) ~ p2 - p1* x2]
@named osys = ODESystem(eqs)

# Create StructuralIdentifiability ODE.
known_parameter = [p1]
measured_quantities = [y ~ x1]
si_ode_1, _ = preprocess_ode(osys, known_parameter)
si_ode_2, _ = preprocess_ode(osys, measured_quantities)

assess_identifiability(si_ode_1)
assess_identifiability(si_ode_2)
assess_local_identifiability(si_ode_1)
assess_local_identifiability(si_ode_2)

[TorkelE]

Thanks a lot! Yes, I should have checked the doc string properly, that's on me.