From 7f5d92870a71444858ef316fc2ba46b848d3a953 Mon Sep 17 00:00:00 2001
From: "James P. Fairbanks" <fairbanksj@ufl.edu>
Date: Tue, 2 Jan 2024 15:36:59 -0500
Subject: [PATCH 1/2] WIP: initial guess at regnet support

---
 src/regnets.jl | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 src/regnets.jl

diff --git a/src/regnets.jl b/src/regnets.jl
new file mode 100644
index 0000000..5ad82b8
--- /dev/null
+++ b/src/regnets.jl
@@ -0,0 +1,36 @@
+using SyntacticModels
+using SyntacticModels.SyntacticModelsBase
+using SyntacticModels.AMR
+using ACSets.ADTs
+using MLStyle
+
+@as_record Properties <: AbstractTerm
+  rate_constant::String
+end
+
+@as_record struct Edge <: AbstractTerm
+  id::String
+  source::String
+  target::String
+  properties::Properties
+  sign::Bool
+end
+
+@as_record struct Vertex <: AbstractTerm
+  id::String
+  name::String
+  grounding::Any
+  initial::String
+  rate_constant::String
+  sign::Bool
+end
+
+@data struct RegNet <: AbstractTerm
+  Edgelist(vertices::Vector{Vertex}, edges::Vector{Edge})
+end
+
+@as_record struct RegNetModel <: AbstractTerm
+  header::Header
+  model::RegNet
+  parameters::Vector{AMR.Parameter}
+end

From a4fa9616923c5089c064077f70e19d322200f1ca Mon Sep 17 00:00:00 2001
From: "James P. Fairbanks" <fairbanksj@ufl.edu>
Date: Tue, 2 Jan 2024 16:42:05 -0500
Subject: [PATCH 2/2] wip: writing lotka volterra example by hand

---
 src/regnets.jl | 89 ++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 86 insertions(+), 3 deletions(-)

diff --git a/src/regnets.jl b/src/regnets.jl
index 5ad82b8..c3f8ce8 100644
--- a/src/regnets.jl
+++ b/src/regnets.jl
@@ -1,10 +1,11 @@
 using SyntacticModels
 using SyntacticModels.SyntacticModelsBase
 using SyntacticModels.AMR
+import SyntacticModels.AMR: nounit
 using ACSets.ADTs
 using MLStyle
 
-@as_record Properties <: AbstractTerm
+@as_record struct Properties <: AbstractTerm
   rate_constant::String
 end
 
@@ -12,8 +13,8 @@ end
   id::String
   source::String
   target::String
-  properties::Properties
   sign::Bool
+  properties::Properties
 end
 
 @as_record struct Vertex <: AbstractTerm
@@ -25,7 +26,7 @@ end
   sign::Bool
 end
 
-@data struct RegNet <: AbstractTerm
+@data RegNet <: AbstractTerm begin
   Edgelist(vertices::Vector{Vertex}, edges::Vector{Edge})
 end
 
@@ -34,3 +35,85 @@ end
   model::RegNet
   parameters::Vector{AMR.Parameter}
 end
+
+
+vertices = [
+  Vertex("R",
+    "Rabbits",
+    nothing,
+    "R0",
+    "alpha",
+    true),
+  Vertex("W",
+    "Wolves",
+    nothing,
+    "W0",
+    "gamma",
+    false)
+]
+
+edges = [
+  Edge(
+    "wolf_eats_rabbit",
+    "W",
+    "R",
+    false,
+    Properties("beta")),
+  Edge(
+    "rabbit_feeds_wolf",
+    "R",
+    "W",
+    true,
+    Properties("delta"))
+]
+
+parameters = [
+  Parameter(
+    :R0,
+    "Initial rabbit population",
+    nounit,
+    2.,
+    PointMass(2)
+  ),
+  Parameter(
+    :W0,
+    "Initial wolf population",
+    nounit,
+    1.,
+    Uniform(.9,1.1)
+  ),
+  Parameter(
+    :alpha,
+    "Maximum per capita prey growth rate",
+    nounit,
+    0.667,
+    PointMass(.667)
+  ),
+  Parameter(
+    :beta,
+    "Effect of predators on prey",
+    nounit,
+    1.333,
+    PointMass(1.333)
+  ),
+  Parameter(
+    :gamma,
+    "Effect of prey on predators",
+    nounit,
+    1.,
+    PointMass(1)
+  ),
+  Parameter(
+    :delta,
+    "Maximum per capita predator death rate",
+    nounit,
+    1.,
+    PointMass(1.0)
+  )
+]
+
+rnm = RegNetModel(
+  Header("Lotka Volterra", "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", "regnet", "Lotka Volterra model", "0.1"),
+  Edgelist(vertices, edges),
+  parameters
+)