Merge pull request #405 from SciML/typo

Fix a typo in reparametrization.md

Author: pogudingleb

benchmarking/IdentifiableFunctions/benchmark_result_04-07-23.md

@@ -214,93 +214,3 @@ new_vector_field, new_outputs, new_vars =
 =#
 
 # 2.
-#! format: off
-ode = StructuralIdentifiability.@ODEmodel(
-    x1'(t) = a * x1, 
-    x2'(t) = b * x2, 
-    y(t) = x1*x2
-)
-
-id_funcs = StructuralIdentifiability.find_identifiable_functions(
-    ode,
-    with_states = true,
-    strategy = (:hybrid,),
-)
-@info "" id_funcs
-#=
-┌ Info: 
-│   id_funcs =
-│    2-element Vector{AbstractAlgebra.Generic.Frac{QQMPolyRingElem}}:
-│     x2*x1
-└     a + b
-=#
-
-new_states = [x1 * x2]
-new_params = [a + b]
-
-new_vector_field, new_outputs, new_vars = reparametrize_with_respect_to(ode, new_states, new_params)
-@info "" new_vector_field new_outputs new_vars
-#=
-┌ Info: 
-│   new_vector_field =
-│    Dict{Any, Any} with 1 entry:
-│      T1 => T1*T2
-│   new_outputs =
-│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 1 entry:
-│      y => T1
-│   new_vars =
-│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 2 entries:
-│      T2 => a + b
-└      T1 => x2*x1
-=#
-
-# 3.
-#! format: off
-ode = StructuralIdentifiability.@ODEmodel(
-    x1'(t) = a * x1, 
-    x2'(t) = b * x2, 
-    y(t) = x1 + x2
-)
-
-id_funcs = StructuralIdentifiability.find_identifiable_functions(
-    ode,
-    with_states = true,
-    strategy = (:hybrid,),
-)
-@info "" id_funcs
-#=
-┌ Info: 
-│   id_funcs =
-│    5-element Vector{AbstractAlgebra.Generic.Frac{QQMPolyRingElem}}:
-│     x2*x1
-│     a*b
-│     x2 + x1
-│     a + b
-└     a*x2 - a*x1 - b*x2 + b*x1
-=#
-
-new_states = [x1 * x2, x1 + x2, a*x2 - a*x1 - b*x2 + b*x1]
-new_params = [a + b, a*b]
-
-new_vector_field, new_iutputs, new_vars = reparametrize_with_respect_to(ode, new_states, new_params)
-@info "" new_vector_field new_outputs new_vars
-#=
-┌ Info: 
-│   new_vector_field =
-│    Dict{Any, Any} with 3 entries:
-│      T1 => 1//2*T1*T4 - 1//2*T3
-│      T2 => T2*T4
-│      T3 => -1//2*T1*T4^2 + 2*T1*T5 + 1//2*T3*T4
-│   new_outputs =
-│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 1 entry:
-│      y => T1
-│   new_vars =
-│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 5 entries:
-│      T1 => x2 + x1
-│      T2 => x2*x1
-│      T3 => a*x2 - a*x1 - b*x2 + b*x1
-│      T4 => a + b
-└      T5 => a*b
-=#
-#! format: on
-#####################

benchmarking/IdentifiableFunctions/param.jl

@@ -68,7 +68,7 @@ reparam[:new_ode]
 
 In order to analyze this result, let us give more interpretable names to the new variables and parameters:
 
-$I := I, \; \widetilde{E} := \alpha E, \widetilde{S} := \alpha, \; \widetilde{I} := \alpha (I + U), \; \gamma := \gamma,\;\delta := \delta,\;\widetilde{N} := \frac{\alpha N}{\beta}$
+$I := I, \; \widetilde{E} := \alpha E, \widetilde{S} := \alpha S, \; \widetilde{I} := \alpha (I + U), \; \gamma := \gamma,\;\delta := \delta,\;\widetilde{N} := \frac{\alpha N}{\beta}$
 
 Then the reparametrize system becomes
 

docs/src/tutorials/reparametrization.md

@@ -231,9 +231,9 @@ function __mtk_to_si(
             filter(
                 s ->
                     !iscall(s) &&
-                        !(string(s) in string.(state_vars)) &&
-                        !(string(s) * "(t)" in string.(state_vars)) &&
-                        (string(s) != string(t)),
+                    !(string(s) in string.(state_vars)) &&
+                    !(string(s) * "(t)" in string.(state_vars)) &&
+                    (string(s) != string(t)),
                 get_variables(y[2]),
             ) for y in measured_quantities
         ]...,

ext/ModelingToolkitSIExt.jl

@@ -65,8 +65,8 @@ function differentiate_solution(
     return (
         ps_sol,
         Dict(
-            (vars[i], vars[j]) => sol_var_system[i, j] for i in 1:length(ode.x_vars),
-            j in 1:length(vars)
+            (vars[i], vars[j]) => sol_var_system[i, j] for
+            i in 1:length(ode.x_vars), j in 1:length(vars)
         ),
     )
 end

src/local_identifiability.jl

@@ -30,7 +30,7 @@ struct PBRepresentation
         new_varnames = filter(
             v ->
                 (v in param_names) ||
-                    decompose_derivative(v, vcat(y_names, u_names)) != nothing,
+                decompose_derivative(v, vcat(y_names, u_names)) != nothing,
             map(var_to_str, gens(old_ring)),
         )
         newring, _ = Nemo.polynomial_ring(base_ring(old_ring), new_varnames)

src/pb_representation.jl

@@ -87,23 +87,21 @@ if GROUP == "All" || GROUP == "Core"
         R, (a, b, y, x2, c, x1) = polynomial_ring(Nemo.QQ, ["a", "b", "y", "x2", "c", "x1"])
         append!(
             cases,
-            [
-                (
-                    generators = [
-                        x1 // one(R),
-                        a // one(R),
-                        (a * c + c^2) // one(R),
-                        c // x2,
-                        x2 // (a + b),
-                    ],
-                    to_be_reduced = [
-                        (a * c + c^2 + x1) // (a * c + c^2),
-                        (a * c + c^2 + x1) // (a^2 + a * b + a * c + b * c),
-                        (a * x2 + a * x1 + b * x1) // x2,
-                    ],
-                    memberships = Bool[1, 1, 1],
-                ),
-            ],
+            [(
+                generators = [
+                    x1 // one(R),
+                    a // one(R),
+                    (a * c + c^2) // one(R),
+                    c // x2,
+                    x2 // (a + b),
+                ],
+                to_be_reduced = [
+                    (a * c + c^2 + x1) // (a * c + c^2),
+                    (a * c + c^2 + x1) // (a^2 + a * b + a * c + b * c),
+                    (a * x2 + a * x1 + b * x1) // x2,
+                ],
+                memberships = Bool[1, 1, 1],
+            ),],
         )
 
         for case in cases