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  "Package": "nbTransmission",
  "Title": "Naive Bayes Transmission Analysis",
  "Version": "1.2.0",
  "Date": "2025-05-14",
  "Authors@R": "c(\nperson(\"Sarah V\", \"Leavitt\", email = \"sv1205@bu.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Anne\", \"Shapiro\", email = \"anshap@bu.edu\", role = \"aut\"))",
  "Maintainer": "Sarah V Leavitt <sv1205@bu.edu>",
  "Description": "Estimates the relative transmission probabilities between\ncases in an infectious disease outbreak or cluster using naive\nBayes. Included are various functions to use these\nprobabilities to estimate transmission parameters such as the\ngeneration/serial interval and reproductive number as well as\nfinding the contribution of covariates to the probabilities and\nvisualizing results. The ideal use is for an infectious disease\ndataset with metadata on the majority of cases but more\ninformative data such as contact tracing or pathogen whole\ngenome sequencing on only a subset of cases. For a detailed\ndescription of the methods see Leavitt et al. (2020)\n<doi:10.1093/ije/dyaa031>.",
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        "infector",
        "infectionDate",
        "sampleDate",
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        "X2",
        "X3",
        "X4"
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        "individualID.2",
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        "sampleDate.2",
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    },
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      ],
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        "individualID.2",
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        "infectionDate.2",
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        "sampleDate.2",
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      "page": "clusterInfectors",
      "title": "Clusters the infectors based on their transmission probabilities",
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      "title": "Estimates the effective reproductive number",
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      ]
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    {
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      "title": "Estimates individual-level reproductive numbers",
      "topics": [
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      ]
    },
    {
      "page": "estimateRt",
      "title": "Estimates time-level reproductive numbers",
      "topics": [
        "estimateRt"
      ]
    },
    {
      "page": "estimateRtAvg",
      "title": "Estimates the average effective reproductive number",
      "topics": [
        "estimateRtAvg"
      ]
    },
    {
      "page": "estimateSI",
      "title": "Estimates the generation/serial interval distribution",
      "topics": [
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      ]
    },
    {
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      "title": "Individual-level simulated outbreak dataset",
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      ]
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    },
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      "title": "Plots a heatmap of the relative transmission probabilities",
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    },
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      "title": "Plots a network of the relative transmission probabilities",
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      "title": "Estimates relative transmission probabilities",
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    },
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