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  "Title": "Simulation-Based Inference Methods for Infectious Disease Models",
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      "commit": "3fce6d8b31314565ddfd2f516ffe696024ec69f8",
      "fileid": "4269db2e6926920d6c2ffa2561fd332b95dabcf3f442347ad153d17433ba57ca",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tjmckinley/actions/runs/26325944879"
    }
  ]
}