update

docs/src/inverse_problems/structural_identifiability.md

@@ -73,11 +73,11 @@ nothing # hide
 ### Assessing identifiability for specified quantities only
 By default, StructuralIdentifiability assesses identifiability for all parameters and variables. It is, however, possible to designate precisely which quantities you want to check using the `funcs_to_check` option. This both includes selecting a smaller subset of parameters and variables to check, or defining customised expressions. Let us consider the Goodwind from previously, and say that we would like to check whether the production parameters ($pₘ$, $pₑ$, and $pₚ$) and the total amount of the three species ($P + M + E$) are identifiable quantities. Here, we would first unpack these (allowing us to form algebraic expressions) and then use the following code:
 ```example si1
-@unpack pₘ, pₑ, and pₚ, M, E, P = goodwind_oscillator
-assess_identifiability(goodwind_oscillator; funcs_to_check=[pₘ, pₑ, pₚ, M + E + P], loglevel=Logging.Error)
+@unpack pₘ, pₑ, pₚ, M, E, P = goodwind_oscillator
+assess_identifiability(goodwind_oscillator; measured_quantities=[:M], funcs_to_check=[pₘ, pₑ, pₚ, M + E + P], loglevel=Logging.Error)
+nothing # hide
 ```
 
-
 ### Probability of correctness
 The identifiability methods used can, in theory, produce erroneous results. However, it is possible to adjust the lower bound for the probability of correctness using the argument `p` (by default set to `0.99`, that is, at least a $99%$ chance of correctness). We can e.g. increase the bound through:
 ```example si2

ext/CatalystStructuralIdentifiabilityExtension/structural_identifiability_extension.jl

@@ -21,6 +21,7 @@ si_ode(rs; measured_quantities = [:X], known_p = [:p])
 ```
 """
 function Catalyst.make_si_ode(rs::ReactionSystem; measured_quantities = [], known_p = [], ignore_no_measured_warn=false)
+    rs = Catalyst.expand_registered_functions(rs)
     known_quantities = make_measured_quantities(rs, measured_quantities, known_p; ignore_no_measured_warn)
     return StructuralIdentifiability.preprocess_ode(convert(ODESystem, rs), known_quantities)[1]
 end
@@ -38,20 +39,23 @@ end
 
 # Local identifiability.
 function StructuralIdentifiability.assess_local_identifiability(rs::ReactionSystem, args...; measured_quantities = Num[], known_p = Num[], ignore_no_measured_warn=false, kwargs...)
+    rs = Catalyst.expand_registered_functions(rs)
     known_quantities = make_measured_quantities(rs, measured_quantities, known_p; ignore_no_measured_warn)
     osys = convert(ODESystem, rs)
     return StructuralIdentifiability.assess_local_identifiability(osys, args...; measured_quantities=known_quantities, kwargs...)
 end
 
 # Global identifiability.
 function StructuralIdentifiability.assess_identifiability(rs::ReactionSystem, args...; measured_quantities = Num[], known_p = Num[], ignore_no_measured_warn=false, kwargs...)
+    rs = Catalyst.expand_registered_functions(rs)
     known_quantities = make_measured_quantities(rs, measured_quantities, known_p; ignore_no_measured_warn)
     osys = convert(ODESystem, rs)
     return StructuralIdentifiability.assess_identifiability(osys, args...; measured_quantities=known_quantities, kwargs...)
 end
 
 # Identifiable functions.
 function StructuralIdentifiability.find_identifiable_functions(rs::ReactionSystem, args...; measured_quantities = Num[], known_p = Num[], ignore_no_measured_warn=false, kwargs...)
+    rs = Catalyst.expand_registered_functions(rs)
     known_quantities = make_measured_quantities(rs, measured_quantities, known_p; ignore_no_measured_warn)
     osys = convert(ODESystem, rs)
     return StructuralIdentifiability.find_identifiable_functions(osys, args...; measured_quantities=known_quantities, kwargs...)

test/extensions/structural_identifiability.jl

@@ -7,11 +7,14 @@ using StructuralIdentifiability
 ### Helper Function ###
 
 # Converts the output dicts from StructuralIdentifiability functions from "weird symbol => stuff" to "symbol => stuff" (the output have some strange meta data which prevents equality checks, this enables this).
+# Structural identifiability also provides variables like x (rather than x(t)). This is a bug, but we have to convert to make it work (now just remove any (t) to make them all equal).
 function sym_dict(dict_in)
     dict_out = Dict{Symbol,Any}()
     for key in keys(dict_in)
-        dict_out[Symbol(key)] = dict_in[key]
-    end
+        sym_key = Symbol(key)
+        sym_key = Symbol(replace(String(sym_key), "(t)" => ""))
+        dict_out[sym_key] = dict_in[key]
+    end    
     return dict_out
 end