Merge pull request #128 from neonWhiteout/SemanticDomainsNoZero

Causal Loop with Polarities

Project.toml

@@ -2,7 +2,7 @@ name = "StockFlow"
 uuid = "58c4a0e8-2944-4d18-9fa2-e17726aee9e5"
 license = "MIT"
 authors = ["Xiaoyan Li <[email protected]>"]
-version = "0.2.2"
+version = "0.2.3"
 
 [deps]
 AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"

docs/literate/full_fledged_schema_examples_new/CasualLoopDiagrams/Causal_Loop_Operations.jl

@@ -0,0 +1,174 @@
+# # Causal Loop Operations
+
+using StockFlow
+using StockFlow.Syntax
+using StockFlow.PremadeModels
+
+GraphCL(convertToCausalLoop(seir()))
+
+C2 = CausalLoopPM([:C2], [:C2 => :C2 for _ in 1:5], [POL_NEGATIVE, POL_POSITIVE, POL_NEGATIVE, POL_POSITIVE, POL_NEGATIVE])
+
+C2′ = @causal_loop begin
+    :nodes
+    C2
+    :edges
+    C2 => -C2
+    C2 => +C2
+    C2 => -C2
+    C2 => +C2
+    C2 => -C2
+end;
+
+C2′′ = (@cl C2 => -C2, C2 => +C2, C2 => -C2, C2 => +C2, C2 => -C2);
+
+C2 == C2′ == C2′′
+
+GraphCL(C2)
+
+GraphRB(C2)
+
+CL_ABC = @cl A => +B, B => +C, C => -A, D
+
+GraphCL(CL_ABC)
+
+GraphRB(CL_ABC)
+
+nvert(CL_ABC)
+
+nedges(CL_ABC)
+
+np(CL_ABC)
+
+nm(CL_ABC)
+
+sedge(CL_ABC, 3) # Source node for edge 3, which is C => A, is C, which is index 3
+
+tedge(CL_ABC, 3) # C => A, target is A, with index 1
+
+vnames(CL_ABC)
+
+epol(CL_ABC, 1) # Polarity of edge 1, A => B, is positive
+
+epols(CL_ABC)
+
+outgoing_edges(CL_ABC, 1) # indices of all edges with src 1 (in this case, A)
+
+outgoing_edges(CL_ABC, 4) # D
+
+incoming_edges(CL_ABC, 1) # indices of all edges with src 1
+
+cl_cycles(CL_ABC)
+
+extract_loops(CL_ABC)
+
+is_walk(CL_ABC, [1,2,3,1,2])
+
+is_walk(CL_ABC, [3,2])
+
+is_walk(CL_ABC, Vector{Int}())
+
+is_circuit(CL_ABC, [1,2,3])
+
+is_circuit(CL_ABC, [1,2])
+
+walk_polarity(CL_ABC, [1,2,3,1,2,3])
+
+extract_all_nonduplicate_paths(CL_ABC)
+
+num_loops_var_on(CL_ABC, :D)
+
+num_loops_var_on(CL_ABC, :A)
+
+num_loops_var_on(C2, :C2)
+
+num_indep_loops_var_on(C2, :C2) # Treating each pair of nodes as if there is at most one edge between them
+
+to_graphs_graph(CL_ABC)
+
+betweenness(CL_ABC)
+
+to_graphs_graph(C2) # eliminates duplicate edges!
+
+betweenness(C2)
+
+num_inputs_outputs(C2) # in, out
+
+num_inputs_outputs_pols(C2) # pos in, pos out, neg in, neg out
+
+all_shortest_paths(C2) 
+
+ all_shortest_paths(@cl((A => B, B => C, C => D, A => B′, B′ => C′, C′ => D)))
+
+shortest_paths( (@cl A => B, B => C, C => D, A => B′, B′ => C′, C′ => D), :A, :D )
+
+ betweenness(@cl((A => B, B => C, C => D, A => B′, B′ => C′, C′ => D)))
+
+all_shortest_paths(convertToCausalLoop(seir()))
+
+all_shortest_paths(CL_ABC)
+
+GraphCL(CL_ABC)
+
+shortest_paths(CL_ABC, :A, :C)
+
+cl = @causal_loop begin
+        :nodes
+        A
+        B
+        C
+        D
+        E
+        :edges
+        A => B
+        B => C
+        B => C
+        B => D
+        D => C
+    end;
+
+cl2 = @causal_loop begin
+        :nodes
+        A
+        B
+        C
+        D
+        E
+        :edges
+        A => B
+        B => C
+        B => D
+        D => C
+    end;
+
+GraphCL(cl)
+
+betweenness(cl)
+
+betweenness(cl2)
+
+# ### Note, negative polarities always come after positive!
+
+cl_small = @cl A => -B, B => +C 
+
+epols(cl_small)
+
+to_simple_cl(cl_small) == (@cl A, B => C, A => B) # Note the order!
+
+to_simple_cl(cl_small)
+
+using StockFlow.Syntax.Composition
+
+ABC = (@cl A => B, B => C)
+BCD = (@cl B => C, C => D)
+@compose ABC BCD begin
+    (ABC, BCD)
+    (ABC, BCD) ^ B => C
+end
+
+ABC_pol = (@cl A => +B, B => -C)
+BCD_pol = (@cl B => -C, C => +D)
+@compose ABC_pol BCD_pol begin
+    (ABC, BCD)
+    (ABC, BCD) ^ B => -C
+end
+

docs/literate/full_fledged_schema_examples_new/CasualLoopDiagrams/convert_from_SEIR_stockFlowDiagram.jl

@@ -50,6 +50,6 @@ GraphF(seir)
 
 seir_causalLoop = convertToCausalLoop(seir)
 
-Graph(seir_causalLoop)
+GraphCL(seir_causalLoop)
 
 

docs/make.jl

@@ -53,6 +53,7 @@ makedocs(
     "Example" => Any[
       "generated/Covid19_composition_model_in_paper.md",
       "generated/full_fledged_schema_examples_new/CasualLoopDiagrams/convert_from_SEIR_stockFlowDiagram.md",
+      "generated/full_fledged_schema_examples_new/CasualLoopDiagrams/Causal_Loop_Operations.md",
       "generated/full_fledged_schema_examples_new/composition/composed_open_population_SIRV_model.md",
       "generated/full_fledged_schema_examples_new/composition/COVID_full_model.md",
       "generated/full_fledged_schema_examples_new/composition/curable_sexually_transmitted_diseases_model.md",

docs/src/DSLs.md

@@ -124,6 +124,100 @@ end) == ([StockAndFlow0([:A, :AA],[:B],[:A => :B, :AA => :B]),
     StockAndFlow0([:X, :Z],[:Y, :B],[:X => :Y, :X => :B])])
 ```
 
+---
+
+---
+
+## @causal_loop
+
+Create a causal loop, with or without polarities.  X => +Y indicates a positive
+polarity, X => -Y indicates a negative polarity, and if there are any edges
+X => Y without polarities, the ultimate causal loop diagram will be without
+polarities.
+
+Use :nodes to indicate nodes, and :edges to indicate edges.
+
+If there are no edges, will default to a causal loop with polarities.
+
+Note, for functions which return indices for edges, negative edges come
+after positive edges.
+
+Avoid using nodes with the same name.
+
+```julia
+
+# Triangle, without polarities.
+@causal_loop begin
+    :nodes
+    A
+    B
+    C
+
+    :edges
+    A => B
+    B => C
+    C => A
+end
+
+# Triangle, with polarities, creating a balancing loop.
+@causal_loop begin
+    :nodes
+    A
+    B
+    C
+
+    :edges
+    A => -B
+    B => +C
+    C => +A
+end
+
+# Causal loop with two nodes and three edges;
+# A has a positive self edge, and A has two edges to B, one positive, one negative.
+@causal_loop begin
+    :nodes
+    A
+    B
+
+    :edges
+    A => +A
+    A => +B
+    A => -B
+end
+
+# Empty causal loop, treated with polarities.
+@causal_loop begin end 
+
+```
+
+---
+
+## @cl
+
+Compressed syntax for creating a causal loop diagram.  Similar to above.
+
+Separate statements with commas, and use a symbol on its own to indicate a
+node without an edge.  Nodes will be ordered in the order they're encountered.
+
+```julia
+# Triangle, without polarities.
+(@cl A => B, B => C, C => A)
+# Triangle, with polarities, creating a balancing loop.
+(@cl A => -B, B => +C C => +A)
+
+# No edges between nodes, treated as a causal loop with polarities.
+(@cl A, B, C)
+
+# Same as first, but now C is node 1, B is node 2, and A is node 3.
+(@cl C, B, A => B, B => C, C => A)
+
+# Empty causal loop, treated as with polarities.
+(@cl)
+
+```
+
+
+
 ---
 
 # Stratification
@@ -261,6 +355,10 @@ and sums which are in the corresponding foot.
 
 Composition with no stockflows given as argument returns an empty stockflow.
 
+Composition also works with causal loop diagrams.  If using causal loop with
+polarities, the edges you compose on must have the same polarities; you
+cannot compose A => +B with A => -B.
+
 ```julia
 (@compose begin 
     ()
@@ -287,6 +385,15 @@ Diabetes_Model = @compose Model_Normoglycemic Model_Hyperglycemic Model_Norm_Hyp
     (Hyper, NH) ^ Prediabetic_U => N
     (Hyper, NH) ^ Prediabetic_D => N
 end
+
+ABC = (@cl A => B, B => C)
+BCD = (@cl B => C, C => D)
+
+ABCD = @compose ABC BCD begin
+    (ABC, BCD)
+    (ABC, BCD) ^ B => C
+end
+
 ```
 
 ---
@@ -306,10 +413,10 @@ Rewrite has 8 headers, :stocks, :flows, :sums, :dynamic\_variables, :redefs, :re
 and :dyvar\_swaps
 
 The first five are used to indicate if an instance of that type is being
-added.  Use the same definition syntax as in @stock_and_flow.
+added.  Use the same definition syntax as in @stock\_and\_flow.
 
 :redefs is used to change the definition of a dynamic variable, flow or
-sum.  Again, use the same syntax as in @stock_and_flow.
+sum.  Again, use the same syntax as in @stock\_and\_flow.
 
 :removes indicates that an object should be deleted.  You just need the name of it in the original.
 
@@ -370,39 +477,8 @@ end
 
 ---
 
-# Homomorphism
 
-## @hom
 
-Using two stockflows and a block with the same headers as @stratify, define an ACSetTransformation from the first stockflow to another.
 
-Half of a stratify.  Rather than creating two homomorphisms and taking the pullback, creates one homomorphism.
 
-```julia
-@hom WeightModel l_type begin
-  :stocks
-  NormalWeight => pop
-  OverWeight => pop
-  Obese => pop
-
-  :parameters
-  μ => μ
-  ~δ => δ
-  rage => rage
-  _ => rFstOrder
-
-  :dynamic_variables
-  v_NewBorn => v_birth
-  ~Becoming => v_fstOrder
-  ~Death => v_death
-  _ => v_aging
-
-  :flows
-  f_NewBorn => f_birth
-  ~Becoming => f_fstOrder
-  ~Death => f_death
-  ~id => f_aging
-  _ => f_death
 
-end
-```