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assets/literate/DCM.md

@@ -88,7 +88,7 @@ end
 finally we compose the simulation model
 
 ````julia:ex5
-@named simmodel = system_from_graph(g, split=false)
+@named simmodel = system_from_graph(g, split=false);
 ````
 
 ## Run the simulation and plot the results
@@ -226,7 +226,7 @@ for (i, idx) in enumerate(CartesianIndices(A_prior))
     end
 end
 # Avoid simplification of the model in order to be able to exclude some parameters from fitting
-@named fitmodel = system_from_graph(g, simplify=false)
+@named fitmodel = system_from_graph(g, simplify=false);
 ````
 
 With the function `changetune` we can provide a dictionary of parameters whose tunable flag should be changed, for instance set to false to exclude them from the optimization procedure.

assets/literate/DCM_script.jl

@@ -31,7 +31,7 @@ for idx in CartesianIndices(A_true)
     add_edge!(g, regions[idx[1]] => regions[idx[2]], weight=A_true[idx[1], idx[2]])
 end
 
-@named simmodel = system_from_graph(g, split=false)
+@named simmodel = system_from_graph(g, split=false);
 
 tspan = (0.0, 512.0)
 prob = SDEProblem(simmodel, [], tspan)
@@ -104,7 +104,7 @@ for (i, idx) in enumerate(CartesianIndices(A_prior))
     end
 end
 # Avoid simplification of the model in order to be able to exclude some parameters from fitting
-@named fitmodel = system_from_graph(g, simplify=false)
+@named fitmodel = system_from_graph(g, simplify=false);
 
 untune = Dict(A[3] => false, A[7] => false)
 fitmodel = changetune(fitmodel, untune)                 # 3 and 7 are not present in the simulation model

assets/pages/DCM/code/ex17.jl

@@ -13,4 +13,4 @@ for (i, idx) in enumerate(CartesianIndices(A_prior))
     end
 end
 # Avoid simplification of the model in order to be able to exclude some parameters from fitting
-@named fitmodel = system_from_graph(g, simplify=false)
+@named fitmodel = system_from_graph(g, simplify=false);

assets/pages/DCM/code/ex5.jl

@@ -1,2 +1,2 @@
 # This file was generated, do not modify it. # hide
-@named simmodel = system_from_graph(g, split=false)
+@named simmodel = system_from_graph(g, split=false);

assets/pages/DCM/code/output/ex17.res

@@ -1,58 +1 @@
-Model fitmodel:
-Subsystems (9): see hierarchy(fitmodel)
-  r1₊ei
-  r1₊lm
-  r1₊bm
-  r2₊ei
-  r2₊lm
-  r2₊bm
-  r3₊ei
-  r3₊lm
-  r3₊bm
-Equations (27):
-  27 standard: see equations(r3₊bm)
-Unknowns (27): see unknowns(r3₊bm)
-  r1₊ei₊u(t): ext_input
-  r1₊lm₊x(t) [defaults to 0.0]
-  r1₊lm₊jcn(t)
-  r1₊bm₊s(t) [defaults to 1.0]
-  r1₊bm₊lnu(t) [defaults to 0.0]
-  r1₊bm₊lnν(t) [defaults to 0.0]
-  r1₊bm₊lnq(t) [defaults to 0.0]
-  r1₊bm₊jcn(t)
-  r1₊bm₊bold(t) [defaults to 0.0]: measurement
-  r2₊ei₊u(t): ext_input
-  r2₊lm₊x(t) [defaults to 0.0]
-  r2₊lm₊jcn(t)
-  r2₊bm₊s(t) [defaults to 1.0]
-  r2₊bm₊lnu(t) [defaults to 0.0]
-  r2₊bm₊lnν(t) [defaults to 0.0]
-  r2₊bm₊lnq(t) [defaults to 0.0]
-  r2₊bm₊jcn(t)
-  r2₊bm₊bold(t) [defaults to 0.0]: measurement
-  r3₊ei₊u(t): ext_input
-  r3₊lm₊x(t) [defaults to 0.0]
-  r3₊lm₊jcn(t)
-  r3₊bm₊s(t) [defaults to 1.0]
-  r3₊bm₊lnu(t) [defaults to 0.0]
-  r3₊bm₊lnν(t) [defaults to 0.0]
-  r3₊bm₊lnq(t) [defaults to 0.0]
-  r3₊bm₊jcn(t)
-  r3₊bm₊bold(t) [defaults to 0.0]: measurement
-Parameters (16): see parameters(r3₊bm)
-  C [defaults to 0.0625]
-  A1 [defaults to 0.0]
-  w_r1₊lm_r1₊bm [defaults to 1.0]
-  A2 [defaults to 0.0148102]
-  A3 [defaults to -0.00716553]
-  A4 [defaults to 0.00345049]
-  A5 [defaults to 0.0]
-  w_r2₊lm_r2₊bm [defaults to 1.0]
-  A6 [defaults to 0.00429191]
-  A7 [defaults to -0.0122152]
-  A8 [defaults to 0.00437472]
-  A9 [defaults to 0.0]
-  w_r3₊lm_r3₊bm [defaults to 1.0]
-  lnκ
-  lnτ
-  lnϵ
+nothing

assets/pages/DCM/code/output/ex5.res

@@ -1,60 +1 @@
-Model simmodel:
-Equations (21):
-  21 standard: see equations(simmodel)
-Unknowns (21): see unknowns(simmodel)
-  r1₊ou₊x(t) [defaults to 0.0]
-  r1₊lm₊x(t) [defaults to 0.0]
-  r1₊bm₊s(t) [defaults to 1.0]
-  r1₊bm₊lnu(t) [defaults to 0.0]
-  r1₊bm₊lnν(t) [defaults to 0.0]
-  r1₊bm₊lnq(t) [defaults to 0.0]
-  r2₊ou₊x(t) [defaults to 0.0]
-  r2₊lm₊x(t) [defaults to 0.0]
-  r2₊bm₊s(t) [defaults to 1.0]
-  r2₊bm₊lnu(t) [defaults to 0.0]
-  r2₊bm₊lnν(t) [defaults to 0.0]
-  r2₊bm₊lnq(t) [defaults to 0.0]
-  r3₊ou₊x(t) [defaults to 0.0]
-  r3₊lm₊x(t) [defaults to 0.0]
-  r3₊bm₊s(t) [defaults to 1.0]
-  r3₊bm₊lnu(t) [defaults to 0.0]
-  r3₊bm₊lnν(t) [defaults to 0.0]
-  r3₊bm₊lnq(t) [defaults to 0.0]
-  r1₊bm₊bold(t) [defaults to 0.0]: measurement
-  r2₊bm₊bold(t) [defaults to 0.0]: measurement
-  r3₊bm₊bold(t) [defaults to 0.0]: measurement
-Parameters (33): see parameters(simmodel)
-  r3₊bm₊lnτ [defaults to 0.0]
-  r1₊ou₊τ [defaults to 1.0]
-  r2₊ou₊μ [defaults to 0.0]
-  r2₊bm₊lnτ [defaults to 0.0]
-  r3₊ou₊μ [defaults to 0.0]
-  r3₊bm₊lnκ [defaults to 0.0]
-  r2₊bm₊lnκ [defaults to 0.0]
-  r2₊ou₊σ [defaults to 0.1]
-  r3₊ou₊τ [defaults to 1.0]
-  r3₊bm₊lnϵ [defaults to 0.0]
-  r2₊bm₊lnϵ [defaults to 0.0]
-  r1₊ou₊μ [defaults to 0.0]
-  r2₊ou₊τ [defaults to 1.0]
-  r1₊bm₊lnϵ [defaults to 0.0]
-  r1₊bm₊lnκ [defaults to 0.0]
-  r1₊bm₊lnτ [defaults to 0.0]
-  r3₊ou₊σ [defaults to 0.1]
-  r1₊ou₊σ [defaults to 0.1]
-  w_r1₊ou_r1₊lm [defaults to 0.0625]
-  w_r2₊lm_r1₊lm [defaults to 0.4]
-  w_r3₊ou_r3₊lm [defaults to 0.0625]
-  w_r1₊lm_r1₊lm [defaults to -0.5]
-  w_r2₊lm_r3₊lm [defaults to -0.3]
-  w_r1₊lm_r3₊lm [defaults to 0.0]
-  w_r1₊lm_r2₊lm [defaults to -2.0]
-  w_r1₊lm_r1₊bm [defaults to 1.0]
-  w_r2₊ou_r2₊lm [defaults to 0.0625]
-  w_r2₊lm_r2₊bm [defaults to 1.0]
-  w_r3₊lm_r3₊lm [defaults to -0.5]
-  w_r3₊lm_r1₊lm [defaults to 0.0]
-  w_r3₊lm_r3₊bm [defaults to 1.0]
-  w_r2₊lm_r2₊lm [defaults to -0.5]
-  w_r3₊lm_r2₊lm [defaults to 0.2]
-Observed (9): see observed(simmodel)
+nothing

assets/pages/blox_connections/code/output/ex6.res

@@ -1,4 +1,4 @@
-Main.FD_SANDBOX_15604780526313532720.IzhNeuron(ModelingToolkit.ODESystem(0x0000000000001ffd, Symbolics.Equation[Differential(t)(V(t)) ~ 145 + jcn - u(t) + 5V(t) + 0.04(V(t)^2), Differential(t)(u(t)) ~ a*(-u(t) + b*V(t))], t, SymbolicUtils.BasicSymbolic{Real}[V(t), u(t), jcn], SymbolicUtils.BasicSymbolic{Real}[a, b, V_reset, d, θ], nothing, Dict{Any, Any}(:a => a, :b => b, :d => d, :V => V(t), :jcn => jcn, :u => u(t), :θ => θ, :V_reset => V_reset), Any[], Symbolics.Equation[], Base.RefValue{Vector{Symbolics.Num}}(Symbolics.Num[]), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), :izh, "", ModelingToolkit.ODESystem[], Dict{Any, Any}(a => 0.02, V_reset => -50, d => 2, u(t) => -13, V(t) => -65.0, b => 0.2, θ => 30), Dict{Any, Any}(), nothing, nothing, Symbolics.Equation[], nothing, nothing, nothing, ModelingToolkit.SymbolicContinuousCallback[], ModelingToolkit.SymbolicDiscreteCallback[condition: V(t) > θ
+Main.FD_SANDBOX_15604780526313532720.IzhNeuron(ModelingToolkit.ODESystem(0x0000000000001fe9, Symbolics.Equation[Differential(t)(V(t)) ~ 145 + jcn - u(t) + 5V(t) + 0.04(V(t)^2), Differential(t)(u(t)) ~ a*(-u(t) + b*V(t))], t, SymbolicUtils.BasicSymbolic{Real}[V(t), u(t), jcn], SymbolicUtils.BasicSymbolic{Real}[a, b, V_reset, d, θ], nothing, Dict{Any, Any}(:a => a, :b => b, :d => d, :V => V(t), :jcn => jcn, :u => u(t), :θ => θ, :V_reset => V_reset), Any[], Symbolics.Equation[], Base.RefValue{Vector{Symbolics.Num}}(Symbolics.Num[]), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Any}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), Base.RefValue{Matrix{Symbolics.Num}}(Matrix{Symbolics.Num}(undef, 0, 0)), :izh, "", ModelingToolkit.ODESystem[], Dict{Any, Any}(a => 0.02, V_reset => -50, d => 2, u(t) => -13, V(t) => -65.0, b => 0.2, θ => 30), Dict{Any, Any}(), nothing, nothing, Symbolics.Equation[], nothing, nothing, nothing, ModelingToolkit.SymbolicContinuousCallback[], ModelingToolkit.SymbolicDiscreteCallback[condition: V(t) > θ
 affects:
   u(t) ~ d + u(t)
   V(t) ~ V_reset