Merge pull request #247 from SciML/ordering_output

Ordering the elements in the output

src/ODE.jl

@@ -365,6 +365,8 @@ Here,
 macro ODEmodel(ex::Expr...)
     equations = [ex...]
     x_vars, y_vars, u_vars, all_symb = macrohelper_extract_vars(equations)
+    # ensures that the parameters will be ordered
+    all_symb = sort(all_symb)
 
     # creating the polynomial ring
     vars_list = :([$(all_symb...)])

src/StructuralIdentifiability.jl

@@ -93,7 +93,7 @@ Input:
 
 Assesses identifiability of a given ODE model. The result is guaranteed to be correct with the probability
 at least `p`.
-The function returns a dictionary from the functions to check to their identifiability properties 
+The function returns an (ordered) dictionary from the functions to check to their identifiability properties 
 (one of `:nonidentifiable`, `:locally`, `:globally`).
 """
 function assess_identifiability(
@@ -118,7 +118,7 @@ function _assess_identifiability(
     p_loc = 1 - (1 - p) * 0.1
 
     if isempty(funcs_to_check)
-        funcs_to_check = vcat(ode.parameters, ode.x_vars)
+        funcs_to_check = vcat(ode.x_vars, ode.parameters)
     end
 
     @info "Assessing local identifiability"
@@ -148,7 +148,7 @@ function _assess_identifiability(
     @info "Global identifiability assessed in $runtime seconds"
     _runtime_logger[:glob_time] = runtime
 
-    result = Dict{Any, Symbol}()
+    result = OrderedDict{Any, Symbol}()
     glob_ind = 1
     for i in 1:length(funcs_to_check)
         if !local_result[funcs_to_check[i]]
@@ -210,13 +210,13 @@ function _assess_identifiability(
     ode, conversion = mtk_to_si(ode, measured_quantities)
     conversion_back = Dict(v => k for (k, v) in conversion)
     if isempty(funcs_to_check)
-        funcs_to_check = [conversion_back[x] for x in [ode.parameters..., ode.x_vars...]]
+        funcs_to_check = [conversion_back[x] for x in [ode.x_vars..., ode.parameters...]]
     end
     funcs_to_check_ = [eval_at_nemo(each, conversion) for each in funcs_to_check]
 
     result = _assess_identifiability(ode, funcs_to_check = funcs_to_check_, p = p)
     nemo2mtk = Dict(funcs_to_check_ .=> funcs_to_check)
-    out_dict = Dict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
+    out_dict = OrderedDict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
     return out_dict
 end
 

src/discrete.jl

@@ -267,7 +267,7 @@ function _assess_local_identifiability_discrete(
 
     @debug "Computing the result"
     base_rank = LinearAlgebra.rank(Jac)
-    result = Dict{Any, Bool}()
+    result = OrderedDict{Any, Bool}()
     for i in 1:length(funcs_to_check)
         for (k, p) in enumerate(dds_ext.parameters)
             Jac[k, 1] =
@@ -280,7 +280,7 @@ function _assess_local_identifiability_discrete(
         result[funcs_to_check[i]] = LinearAlgebra.rank(Jac) == base_rank
     end
 
-    return Dict(result)
+    return result
 end
 
 # ------------------------------------------------------------------------------
@@ -301,7 +301,7 @@ Input:
 - `p` - probability of correctness
 
 Output:
-- the result is a dictionary from each function to to boolean;
+- the result is an (ordered) dictionary from each function to to boolean;
 
 The result is correct with probability at least `p`.
 """
@@ -331,16 +331,16 @@ function assess_local_identifiability(
     dds_aux, conversion = mtk_to_si(dds, measured_quantities)
     if length(funcs_to_check) == 0
         funcs_to_check = vcat(
-            parameters(dds),
             [x for x in states(dds) if conversion[x] in dds_aux.x_vars],
+            parameters(dds),
         )
     end
     funcs_to_check_ = [eval_at_nemo(x, conversion) for x in funcs_to_check]
     known_ic_ = [eval_at_nemo(x, conversion) for x in known_ic]
 
     result = _assess_local_identifiability_discrete(dds_aux, funcs_to_check_, known_ic_, p)
     nemo2mtk = Dict(funcs_to_check_ .=> funcs_to_check)
-    out_dict = Dict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
+    out_dict = OrderedDict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
     if length(known_ic) > 0
         @warn "Since known initial conditions were provided, identifiability of states (e.g., `x(t)`) is at t = 0 only !"
     end

src/local_identifiability.jl

@@ -154,7 +154,7 @@ Input:
 - `loglevel` - the minimal level of log messages to display (`Logging.Info` by default)
 
 Output:
-- for `type=:SE`, the result is a dictionary from each parameter to boolean;
+- for `type=:SE`, the result is an (ordered) dictionary from each parameter to boolean;
 - for `type=:ME`, the result is a tuple with the dictionary as in `:SE` case and array of number of experiments.
 
 The function determines local identifiability of parameters in `funcs_to_check` or all possible parameters if `funcs_to_check` is empty
@@ -208,8 +208,8 @@ end
     end
     if length(funcs_to_check) == 0
         funcs_to_check = vcat(
-            ModelingToolkit.parameters(ode),
             [e for e in ModelingToolkit.states(ode) if !ModelingToolkit.isoutput(e)],
+            ModelingToolkit.parameters(ode),
         )
     end
     ode, conversion = mtk_to_si(ode, measured_quantities)
@@ -223,7 +223,8 @@ end
             type = type,
         )
         nemo2mtk = Dict(funcs_to_check_ .=> funcs_to_check)
-        out_dict = Dict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
+        out_dict =
+            OrderedDict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
         return out_dict
     elseif isequal(type, :ME)
         result, bd = _assess_local_identifiability(
@@ -233,7 +234,8 @@ end
             type = type,
         )
         nemo2mtk = Dict(funcs_to_check_ .=> funcs_to_check)
-        out_dict = Dict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
+        out_dict =
+            OrderedDict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
         return (out_dict, bd)
     end
 end
@@ -280,7 +282,7 @@ function _assess_local_identifiability(
     if isempty(funcs_to_check)
         funcs_to_check = ode.parameters
         if type == :SE
-            funcs_to_check = vcat(funcs_to_check, ode.x_vars)
+            funcs_to_check = vcat(ode.x_vars, ode.parameters)
         end
     end
 
@@ -440,7 +442,7 @@ function _assess_local_identifiability(
 
     @debug "Computing the result"
     base_rank = LinearAlgebra.rank(Jac)
-    result = Dict{Any, Bool}()
+    result = OrderedDict{Any, Bool}()
     for i in 1:length(funcs_to_check)
         for (k, p) in enumerate(ode_red.parameters)
             Jac[k, 1] =
@@ -459,9 +461,9 @@ function _assess_local_identifiability(
     # NB: the Jac contains now the derivatives of the last from `funcs_to_check`
 
     if type == :SE
-        return Dict(result)
+        return result
     end
-    return (Dict(result), num_exp)
+    return (result, num_exp)
 end
 
 # ------------------------------------------------------------------------------

test/identifiability.jl

@@ -23,7 +23,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -38,13 +38,13 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
     # Also test when `funcs_to_test` is empty!
     funcs_to_test = Vector{typeof(x1)}()
-    correct = Dict(x1 => :nonidentifiable, x2 => :nonidentifiable)
+    correct = OrderedDict(x1 => :nonidentifiable, x2 => :nonidentifiable)
     push!(test_cases, Dict(:ode => ode, :funcs => funcs_to_test, :correct => correct))
 
     #--------------------------------------------------------------------------
@@ -69,7 +69,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -89,7 +89,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -118,7 +118,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -137,7 +137,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -155,7 +155,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -173,7 +173,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -192,7 +192,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -222,7 +222,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 

test/local_identifiability.jl

@@ -24,7 +24,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -42,7 +42,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -62,7 +62,7 @@
         Dict(
             :ode => ode,
             :funcs => funcs_to_test,
-            :correct => Dict(funcs_to_test .=> correct),
+            :correct => OrderedDict(funcs_to_test .=> correct),
         ),
     )
 
@@ -76,7 +76,7 @@
         y(t) = x1(t)
     )
     funcs_to_test = [b, c, alpha, beta, delta, gama, beta + delta, beta * delta]
-    correct = Dict([
+    correct = OrderedDict([
         b => true,
         c => true,
         alpha => false,
@@ -96,7 +96,7 @@
         y(t) = x1(t) * x2(t)
     )
     funcs_to_test = [a1, a2, a3, a4, a5, a6, a7, a8]
-    correct = Dict(a => false for a in funcs_to_test)
+    correct = OrderedDict(a => false for a in funcs_to_test)
     push!(test_cases, Dict(:ode => ode, :funcs => funcs_to_test, :correct => correct))
 
     #--------------------------------------------------------------------------
@@ -109,7 +109,7 @@
         y2(t) = x3(t)
     )
     funcs_to_test = [x1, x2, x1 + x2]
-    correct = Dict(x1 => false, x2 => false, x1 + x2 => true)
+    correct = OrderedDict(x1 => false, x2 => false, x1 + x2 => true)
     push!(test_cases, Dict(:ode => ode, :funcs => funcs_to_test, :correct => correct))
 
     #--------------------------------------------------------------------------