simpler ensemble demo

Project.toml

@@ -4,10 +4,17 @@ authors = ["SciML"]
 version = "0.1.9"
 
 [deps]
+AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
+Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
+CommonSolve = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 GlobalSensitivity = "af5da776-676b-467e-8baf-acd8249e4f0f"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MathML = "abcecc63-2b08-419c-80c4-c63dca6fa478"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
@@ -18,6 +25,7 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SciMLExpectations = "afe9f18d-7609-4d0e-b7b7-af0cb72b8ea8"
+Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 
 [compat]

data/amr_sir.json

@@ -0,0 +1,199 @@
+{
+  "name": "SIR Model",
+  "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.1/petrinet/petrinet_schema.json",
+  "description": "SIR model created by Ben, Micah, Brandon",
+  "model_version": "0.1",
+  "model": {
+    "states": [
+      {
+        "id": "S",
+        "name": "Susceptible",
+        "grounding": {
+          "identifiers": {
+            "ido": "0000514"
+          }
+        }
+      },
+      {
+        "id": "I",
+        "name": "Infected",
+        "grounding": {
+          "identifiers": {
+            "ido": "0000511"
+          }
+        }
+      },
+      {
+        "id": "R",
+        "name": "Recovered",
+        "grounding": {
+          "identifiers": {
+            "ido": "0000592"
+          }
+        }
+      }
+    ],
+    "transitions": [
+      {
+        "id": "inf",
+        "input": [
+          "S",
+          "I"
+        ],
+        "output": [
+          "I",
+          "I"
+        ],
+        "properties": {
+          "name": "Infection"
+        }
+      },
+      {
+        "id": "rec",
+        "input": [
+          "I"
+        ],
+        "output": [
+          "R"
+        ],
+        "properties": {
+          "name": "Recovery"
+        }
+      }
+    ]
+  },
+  "semantics": {
+    "ode": {
+      "rates": [
+        {
+          "target": "inf",
+          "expression": "S*I*beta",
+          "expression_mathml": "<apply><times/><ci>S</ci><ci>I</ci><ci>beta</ci></apply>"
+        },
+        {
+          "target": "rec",
+          "expression": "I*gamma",
+          "expression_mathml": "<apply><times/><ci>I</ci><ci>gamma</ci></apply>"
+        }
+      ],
+      "initials": [
+        {
+          "target": "S",
+          "expression": "S0",
+          "expression_mathml": "<ci>S0</ci>"
+        },
+        {
+          "target": "I",
+          "expression": "I0",
+          "expression_mathml": "<ci>I0</ci>"
+        },
+        {
+          "target": "R",
+          "expression": "R0",
+          "expression_mathml": "<ci>R0</ci>"
+        }
+      ],
+      "parameters": [
+        {
+          "id": "beta",
+          "description": "infection rate",
+          "value": 0.027,
+          "distribution": {
+            "type": "StandardUniform1",
+            "parameters": {
+              "minimum": 0.026,
+              "maximum": 0.028
+            }
+          }
+        },
+        {
+          "id": "gamma",
+          "description": "recovery rate",
+          "grounding": {
+            "identifiers": {
+              "askemo": "0000013"
+            }
+          },
+          "value": 0.14,
+          "distribution": {
+            "type": "StandardUniform1",
+            "parameters": {
+              "minimum": 0.1,
+              "maximum": 0.18
+            }
+          }
+        },
+        {
+          "id": "S0",
+          "description": "Total susceptible population at timestep 0",
+          "value": 1000
+        },
+        {
+          "id": "I0",
+          "description": "Total infected population at timestep 0",
+          "value": 1
+        },
+        {
+          "id": "R0",
+          "description": "Total recovered population at timestep 0",
+          "value": 0
+        }
+      ]
+    }
+  },
+  "metadata": {
+    "processed_at": 1682964953,
+    "processed_by": "mit:process-node1",
+    "variable_statements": [
+      {
+        "id": "v0",
+        "variable": {
+          "id": "v0",
+          "name": "VE",
+          "metadata": [
+            {
+              "type": "text_annotation",
+              "value": " Vaccine Effectiveness"
+            },
+            {
+              "type": "text_annotation",
+              "value": " Vaccine Effectiveness"
+            }
+          ],
+          "dkg_groundings": [],
+          "column": [
+            {
+              "id": "9-2",
+              "name": "new_persons_vaccinated",
+              "dataset": {
+                "id": "9",
+                "name": "usa-vaccinations.csv",
+                "metadata": "https://github.com/DARPA-ASKEM/program-milestones/blob/main/6-month-milestone/evaluation/scenario_3/ta_1/google-health-data/usa-vaccinations.csv"
+              }
+            },
+            {
+              "id": "9-3",
+              "name": "cumulative_persons_vaccinated",
+              "dataset": {
+                "id": "9",
+                "name": "usa-vaccinations.csv",
+                "metadata": "https://github.com/DARPA-ASKEM/program-milestones/blob/main/6-month-milestone/evaluation/scenario_3/ta_1/google-health-data/usa-vaccinations.csv"
+              }
+            }
+          ],
+          "paper": {
+            "id": "COVID-19 Vaccine Effectiveness by Product and Timing in New York State",
+            "file_directory": "https://www.medrxiv.org/content/10.1101/2021.10.08.21264595v1",
+            "doi": "10.1101/2021.10.08.21264595"
+          },
+          "equations": []
+        },
+        "metadata": [],
+        "provenance": {
+          "method": "MIT annotation",
+          "description": "text, dataset, formula annotation (chunwei@mit.edu)"
+        }
+      }
+    ]
+  }
+}

data/sir.json

@@ -0,0 +1,49 @@
+{
+    "T": [
+        {
+            "tname": "inf"
+        },
+        {
+            "tname": "rec"
+        }
+    ],
+    "S": [
+        {
+            "sname": "S"
+        },
+        {
+            "sname": "I"
+        },
+        {
+            "sname": "R"
+        }
+    ],
+    "I": [
+        {
+            "it": 1,
+            "is": 1
+        },
+        {
+            "it": 1,
+            "is": 2
+        },
+        {
+            "it": 2,
+            "is": 2
+        }
+    ],
+    "O": [
+        {
+            "ot": 1,
+            "os": 2
+        },
+        {
+            "ot": 1,
+            "os": 2
+        },
+        {
+            "ot": 2,
+            "os": 3
+        }
+    ]
+}

data/sird.json

@@ -0,0 +1 @@
+{"T":[{"tname":"inf"},{"tname":"rec"},{"tname":"death"}],"S":[{"sname":"S"},{"sname":"I"},{"sname":"R"},{"sname":"D"}],"I":[{"it":1,"is":1},{"it":1,"is":2},{"it":2,"is":2},{"it":3,"is":2}],"O":[{"ot":1,"os":2},{"ot":1,"os":2},{"ot":2,"os":3},{"ot":3,"os":4}]}

data/sirh.json

@@ -0,0 +1 @@
+{"T":[{"tname":"inf"},{"tname":"rec"},{"tname":"hosp"},{"tname":"hrec"}],"S":[{"sname":"S"},{"sname":"I"},{"sname":"R"},{"sname":"H"}],"I":[{"it":1,"is":1},{"it":1,"is":2},{"it":2,"is":2},{"it":3,"is":2},{"it":4,"is":4}],"O":[{"ot":1,"os":2},{"ot":1,"os":2},{"ot":2,"os":3},{"ot":3,"os":4},{"ot":4,"os":3}]}

data/sirhd.json

@@ -0,0 +1,99 @@
+{
+    "T": [
+        {
+            "tname": "inf"
+        },
+        {
+            "tname": "rec"
+        },
+        {
+            "tname": "hosp"
+        },
+        {
+            "tname": "ideath"
+        },
+        {
+            "tname": "hrec"
+        },
+        {
+            "tname": "death"
+        }
+    ],
+    "S": [
+        {
+            "sname": "S"
+        },
+        {
+            "sname": "I"
+        },
+        {
+            "sname": "R"
+        },
+        {
+            "sname": "H"
+        },
+        {
+            "sname": "D"
+        }
+    ],
+    "I": [
+        {
+            "it": 1,
+            "is": 1
+        },
+        {
+            "it": 1,
+            "is": 2
+        },
+        {
+            "it": 2,
+            "is": 2
+        },
+        {
+            "it": 3,
+            "is": 2
+        },
+        {
+            "it": 4,
+            "is": 2
+        },
+        {
+            "it": 5,
+            "is": 4
+        },
+        {
+            "it": 6,
+            "is": 4
+        }
+    ],
+    "O": [
+        {
+            "ot": 1,
+            "os": 2
+        },
+        {
+            "ot": 1,
+            "os": 2
+        },
+        {
+            "ot": 2,
+            "os": 3
+        },
+        {
+            "ot": 3,
+            "os": 4
+        },
+        {
+            "ot": 4,
+            "os": 5
+        },
+        {
+            "ot": 5,
+            "os": 3
+        },
+        {
+            "ot": 6,
+            "os": 5
+        }
+    ]
+}

docs/make.jl

@@ -46,6 +46,7 @@ makedocs(sitename = "EasyModelAnalysis.jl",
                  "tutorials/datafitting.md",
                  "tutorials/threshold_interventions.md",
                  "tutorials/probabilistic_thresholds.md",
+                 "tutorials/ensemble.md",
              ],
              "Examples" => [
                  "examples/petri.md",