improved noise scaling

src/networkapi.jl

@@ -504,7 +504,9 @@ end
 
 # convert symbol of the form :sys.a.b.c to a symbolic a.b.c
 function _symbol_to_var(sys, sym)
-    if hasproperty(sys, sym)
+    if sym isa Num
+        return sym
+    elseif hasproperty(sys, sym)
         var = getproperty(sys, sym, namespace = false)
     else
         strs = split(String(sym), "₊")   # need to check if this should be split of not!!!
@@ -563,25 +565,39 @@ pmap   = symmap_to_varmap(sys, [:β => 1.0, :ν => 1.0, :subsys₊k => 1.0])
 Notes:
 - Any `Symbol`, `sym`, within `symmap` must be a valid field of `sys`. i.e.
   `sys.sym` must be defined.
+- The function works even if symbols and symbolics are mixed, e.g.
+```julia
+sir = @reaction_network sir begin
+    β, S + I --> 2I
+    ν, I --> R
+end
+@unpack S = sir
+mixed_u0map = [S => 1.0, :I => 1.0, :R => 1.0]
+u0map  = symmap_to_varmap(sir, mixed_u0map)
+```
+
 """
 function symmap_to_varmap(sys, symmap::Tuple)
     if all(p -> p isa Pair{Symbol}, symmap)
         return ((_symbol_to_var(sys, sym) => val for (sym, val) in symmap)...,)
     else  # if not all entries map a symbol to value pass through
-        return symmap
+        return symmapAny
     end
 end
 
-function symmap_to_varmap(sys, symmap::AbstractArray{Pair{Symbol, T}}) where {T}
+function symmap_to_varmap(sys, symmap::AbstractArray{Pair{Any, T}}) where {T}
     [_symbol_to_var(sys, sym) => val for (sym, val) in symmap]
 end
 
-function symmap_to_varmap(sys, symmap::Dict{Symbol, T}) where {T}
+function symmap_to_varmap(sys, symmap::Dict{Any, T}) where {T}
     Dict(_symbol_to_var(sys, sym) => val for (sym, val) in symmap)
 end
 
-# don't permute any other types and let varmap_to_vars handle erroring
+# don't permute any other types and let varmap_to_vars handle erroring.
+# If all keys are `Num`, conversion not needed.
 symmap_to_varmap(sys, symmap) = symmap
+symmap_to_varmap(sys, symmap::AbstractArray{Pair{Num, T}}) where {T} = symmap
+symmap_to_varmap(sys, symmap::Dict{Num, T}) where {T} = symmap
 #error("symmap_to_varmap requires a Dict, AbstractArray or Tuple to map Symbols to values.")
 
 ######################## reaction complexes and reaction rates ###############################

src/reaction_network.jl

@@ -123,7 +123,7 @@ const forbidden_variables_error = let
 end
 
 # Declares the keys used for various options.
-const option_keys = (:species, :parameters, :variables, :ivs)
+const option_keys = (:species, :parameters, :variables, :ivs, :noise_scaling_parameters)
 
 ### The @species macro, basically a copy of the @variables macro. ###
 macro species(ex...)
@@ -364,6 +364,9 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
     parameters_declared = extract_syms(options, :parameters)
     variables = extract_syms(options, :variables)
 
+    # Handles a (potential) noise scaling parameter.
+    #nosie_scaling_p_args = handle_noise_scaling_ps!(parameters_declared, options)
+
     # handle independent variables
     if haskey(options, :ivs)
         ivs = Tuple(extract_syms(options, :ivs))
@@ -382,7 +385,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
                                                                               declared_syms)
     species = vcat(species_declared, species_extracted)
     parameters = vcat(parameters_declared, parameters_extracted)
-
+    
     # Checks for input errors.
     (sum(length.([reaction_lines, option_lines])) != length(ex.args)) &&
         error("@reaction_network input contain $(length(ex.args) - sum(length.([reaction_lines,option_lines]))) malformed lines.")
@@ -404,6 +407,9 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
         push!(rxexprs.args, get_rxexprs(reaction))
     end
 
+    # Adds potentital nosie scaling parameters.
+    #append!(ps.args, nosie_scaling_p_args)
+
     # Returns the rephrased expression.
     quote
         $ps
@@ -531,8 +537,22 @@ function get_pexpr(parameters_extracted, options)
     pexprs = (haskey(options, :parameters) ? options[:parameters] :
               (isempty(parameters_extracted) ? :() : :(@parameters)))
     foreach(p -> push!(pexprs.args, p), parameters_extracted)
+    append!(pexprs.args, get_noise_scaling_pexpr(options))
     pexprs
 end
+# Extracts any decalred nosie scaling parameters.
+function get_noise_scaling_pexpr(options)
+    haskey(options, :noise_scaling_parameters) || return []
+    ns_expr = options[:noise_scaling_parameters]
+    for idx = length(ns_expr.args):-1:3
+        if ns_expr.args[idx] isa Symbol
+            insert!(ns_expr.args, idx+1, :([noisescalingparameter=true]))
+        elseif (ns_expr.args[idx] isa Expr) && (ns_expr.args[idx].head == :ref)
+            insert!(ns_expr.args, idx+1, :([noisescalingparameter=true]))
+        end
+    end
+    return ns_expr.args[3:end]
+end
 
 # Creates the reaction vector declaration statement.
 function get_rxexprs(rxstruct)
@@ -676,6 +696,21 @@ function recursive_expand_functions!(expr::ExprValues)
     expr
 end
 
+### Option Handling ###
+
+# Extracts any potential nosie scaling parameters and add them to teh decalred parameters.
+function add_noise_scaling_ps!(parameters_declared, options)
+    haskey(options, :noise_scaling_parameters) || return
+    for arg in options[:noise_scaling_parameters].args[end:-1:3]
+        if arg isa Symbol
+            push!(parameters_declared, arg)
+        elseif arg isa Expr
+            push!(parameters_declared, arg.args[1])
+        end
+    end
+end
+
+
 # ### Old functions (for deleting).
 
 # function get_rx_species_deletethis(rxs, ps)

src/reactionsystem.jl

@@ -58,7 +58,7 @@ drop_dynamics(s) = isconstant(s) || isbc(s) || (!isspecies(s))
 
 # Denotes that a parameter controls the scaling of noise in the CLE.
 struct NoiseScalingParameter end
-Symbolics.option_to_metadata_type(::Val{:isnoisescalingparameter}) = NoiseScalingParameter
+Symbolics.option_to_metadata_type(::Val{:noisescalingparameter}) = NoiseScalingParameter
 
 isnoisescalingparameter(s::Num) = isnoisescalingparameter(MT.value(s))
 function isnoisescalingparameter(s)
@@ -1427,7 +1427,16 @@ end
 
 # Extracts any noise scaling parameters from a reaction system.
 function get_noise_scaling(rs::ReactionSystem)
-    return nothing
+    ns_params = filter(p -> isnoisescalingparameter(p), parameters(rs))
+    if isempty(ns_params)
+        return nothing
+    elseif length(ns_params) == 1
+        return Num(ns_params[1])
+    elseif length(ns_params) == length(reactions(rs)) 
+        return ns_params
+    else
+        error("The system have $(length(ns_params)) noise scaling parameters. This number should be equal to 0, 1, or the number of reactions ($(length(reactions(rs)))).")
+    end
 end
 
 """