ssm/examples/tutorial/ssm.json

Inference for State Space Model (SSM)

{
  "data": [
    { 
      "name": "cases", 
      "require": { "path": "data/data.csv", "fields": ["date", "cases"] }
    }
  ],
  
  "inputs": [
    {
      "name": "r0", 
      "description": "Basic reproduction number", 
      "require": { "name": "r0", "path": "data/r0.json" } 
    },
    { 
      "name": "v",
      "description": "Recovery rate",
      "require": { "name":  "pr_v", "path": "data/pr_v.json" },
      "transformation": "1/pr_v",
      "to_resource": "1/v" 
    },
    {
      "name": "S", 
      "description": "Number of susceptible",
      "require": { "name": "S", "path": "data/S.json" } 
    },
    { 
      "name": "I",
      "description": "Number of infectious", 
      "require": { "name": "I", "path": "data/I.json" } 
    },
    { 
      "name": "R", 
      "description": "Number of recovered",
      "require": { "name": "R", "path": "data/R.json" } 
    },
    { 
      "name": "rep",
      "description": "Reporting rate",
      "require": { "name": "rep", "path": "data/rep.json" } 
    }
  ],

  "populations": [
    {"name": "NYC", "composition": ["S", "I", "R"]}
  ],

  "reactions": [
    {"from": "S", "to": "I", "rate": "r0/(S+I+R)*v*I", "description": "infection", "accumulators": ["Inc"]},
    {"from": "I", "to": "R", "rate": "v", "description":"recovery"}
  ],

  "observations": [
    {
      "name": "cases",
      "start": "2012-07-26",
      "distribution": "discretized_normal",
      "mean": "rep * Inc",
      "sd": "sqrt(rep * ( 1.0 - rep ) * Inc )"
    }
  ]
}