parameters.json

[
  {
    "disease": "Adenovirus",
    "pathogen": "Adenovirus",
    "epi_name": "incubation period",
    "probability_distribution": {
        "prob_distribution": "lnorm",
        "parameters": { }
    },
    "summary_statistics": {
      "quantile_values": [4.8, 6.5],
      "quantile_names": ["25", "75"],
      "median": 5.6,
      "median_ci_limits": [4.8, 6.3],
      "median_ci": 95,
      "dispersion": 1.26,
      "dispersion_ci_limits": [1.13, 1.38],
      "dispersion_ci": 95
    },
    "citation": {
      "author": [
        {
          "given": "Justin",
          "family": "Lessler"
        },
        {
          "given": "Nicholas G.",
          "family": "Reich"
        },
        {
          "given": "Ron",
          "family": "Brookmeyer"
        },
        {
          "given": "Trish M.",
          "family": "Perl"
        },
        {
          "given": "Kenrad E.",
          "family": "Nelson"
        },
        {
          "given": "Derek A. T.",
          "family": "Cummings"
        }
      ],
      "title": "Incubation periods of acute respiratory viral infections: a systematic review",
      "journal": "The Lancet Infectious Diseases",
      "year": 2009,
      "pmid": 19393959,
      "doi": "10.1016/S1473-3099(09)70069-6"
    },
    "metadata": {
      "units": "days",
      "sample_size": 14,
      "region": "USA",
      "transmission_mode": "experimental",
      "extrinsic": false,
      "inference_method": "mle"
    },
    "method_assessment": {
      "truncation": null,
      "discretised": false,
      "censored": true,
      "right_truncated": false,
      "phase_bias_adjusted": false
    },
    "notes": "Analysis on data from Commission on Acute Respiratory Disease. Experimental transmission of minor respiratory illness to human volunteers by filter-passing agents. I. Demonstration of two types of illness characterized by long and short incubation periods and diff erent clinical features. J Clin Invest 1947; 26: 957–82."
  },
  {
    "disease": "Human Coronavirus",
    "pathogen": "Human_Cov",
    "epi_name": "incubation period",
    "probability_distribution": {
      "prob_distribution": "lnorm",
      "parameters": { }
    },
    "summary_statistics": {
      "quantile_values": [2.9, 3.5],
      "quantile_names": ["25", "75"],
      "median": 3.2,
      "median_ci_limits": [2.8, 3.7],
      "median_ci": 95,
      "dispersion": 1.15,
      "dispersion_ci_limits": [1.07, 1.34],
      "dispersion_ci": 95
    },
    "citation": {
      "author": [
        {
          "given": "Justin",
          "family": "Lessler"
        },
        {
          "given": "Nicholas G.",
          "family": "Reich"
        },
        {
          "given": "Ron",
          "family": "Brookmeyer"
        },
        {
          "given": "Trish M.",
          "family": "Perl"
        },
        {
          "given": "Kenrad E.",
          "family": "Nelson"
        },
        {
          "given": "Derek A. T.",
          "family": "Cummings"
        }
      ],
      "title": "Incubation periods of acute respiratory viral infections: a systematic review",
      "journal": "The Lancet Infectious Diseases",
      "year": 2009,
      "pmid": 19393959,
      "doi": "10.1016/S1473-3099(09)70069-7"
    },
    "metadata": {
      "units": "days",
      "sample_size": 13,
      "region": "UK",
      "transmission_mode": "experimental",
      "extrinsic": false,
      "inference_method": "bayesian"
    },
    "method_assessment": {
      "truncation": null,
      "discretised": false,
      "censored": true,
      "right_truncated": false,
      "phase_bias_adjusted": false
    },
    "notes": "Analysis on data from  Bradburne AF, Bynoe ML, Tyrrell DA. Eff ects of a “new” human respiratory virus in volunteers. Br Med J 1967; 3: 767–69."
  },
  {
  "disease": "SARS",
  "pathogen": "SARS-Cov-1",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [1.5, 2.7, 5.9, 10.6],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 4,
    "median_ci_limits": [3.6, 4.4],
    "median_ci": 95,
    "dispersion": 1.81,
    "dispersion_ci_limits": [1.67, 1.95],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given":  "Kenrad E.",
        "family": "Nelson"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of acute respiratory viral infections: a systematic review",
    "journal": "The Lancet Infectious Diseases",
    "year": 2009,
    "pmid": 19393959,
    "doi": "10.1016/S1473-3099(09)70069-8"
  },
  "metadata": {
    "units": "days",
    "sample_size": 157,
    "region": "Mixed",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets"
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [0.7, 1.1, 1.9, 2.8],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 1.4,
    "median_ci_limits": [1.3, 1.5],
    "median_ci": 95,
    "dispersion": 1.51,
    "dispersion_ci_limits": [1.43, 1.6],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Kenrad E.",
        "family": "Nelson"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of acute respiratory viral infections: a systematic review",
    "journal": "The Lancet Infectious Diseases",
    "year": 2009,
    "pmid": 19393959,
    "doi": "10.1016/S1473-3099(09)70069-9"
  },
  "metadata": {
    "units": "days",
    "sample_size": 151,
    "region": "Mixed",
    "transmission_mode": "mixed",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets"
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [1.4, 1.7, 2.2, 2.7],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 1.9,
    "median_ci_limits": [1.8, 2],
    "median_ci": 95,
    "dispersion": 1.23,
    "dispersion_ci_limits": [1.17, 1.29],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Kenrad E.",
        "family": "Nelson"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of acute respiratory viral infections: a systematic review",
    "journal": "The Lancet Infectious Diseases",
    "year": 2009,
    "pmid": 19393959,
    "doi": "10.1016/S1473-3099(09)70069-10"
  },
  "metadata": {
    "units": "days",
    "sample_size": 90,
    "region": "Mixed",
    "transmission_mode": "mixed",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "These estimates for the incubation period of influenza A from Lessler et al. 2009 are different from the estimates from the complete data, as they remove Henle et al. 1945 J Immunol, as it is an outlier in the dataset (n=61). Values found at the bottom Table 3."
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-B",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [0.3, 0.4, 0.7, 1.1],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 0.6,
    "median_ci_limits": [0.5, 0.6],
    "median_ci": 95,
    "dispersion": 1.51,
    "dispersion_ci_limits": [1.37, 1.64],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Kenrad E.",
        "family": "Nelson"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of acute respiratory viral infections: a systematic review",
    "journal": "The Lancet Infectious Diseases",
    "year": 2009,
    "pmid": 19393959,
    "doi": "10.1016/S1473-3099(09)70069-11"
  },
  "metadata": {
    "units": "days",
    "sample_size": 78,
    "region": "USA",
    "transmission_mode": "experimental",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets"
},
{
  "disease": "Measles",
  "pathogen": "Measles Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [8.9, 10.9, 14.4, 17.7],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 12.5,
    "median_ci_limits": [11.8, 13.3],
    "median_ci": 95,
    "dispersion": 1.23,
    "dispersion_ci_limits": [1.18, 1.28],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Kenrad E.",
        "family": "Nelson"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of acute respiratory viral infections: a systematic review",
    "journal": "The Lancet Infectious Diseases",
    "year": 2009,
    "pmid": 19393959,
    "doi": "10.1016/S1473-3099(09)70069-12"
  },
  "metadata": {
    "units": "days",
    "sample_size": 55,
    "region": "Mixed",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets"
},
{
  "disease": "Parainfluenza",
  "pathogen": "Parainfluenza Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [2.1, 3.2],
    "quantile_names": ["25", "75"],
    "median": 2.6,
    "median_ci_limits": [2.1, 3.1],
    "median_ci": 95,
    "dispersion": 1.35,
    "dispersion_ci_limits": [1.16, 1.55],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Kenrad E.",
        "family": "Nelson"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of acute respiratory viral infections: a systematic review",
    "journal": "The Lancet Infectious Diseases",
    "year": 2009,
    "pmid": 19393959,
    "doi": "10.1016/S1473-3099(09)70069-13"
  },
  "metadata": {
    "units": "days",
    "sample_size": 11,
    "region": "Mixed",
    "transmission_mode": "experimental",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets"
},
{
  "disease": "RSV",
  "pathogen": "RSV",
  "epi_name": "incubation period",
  "probability_distribution": {
      "prob_distribution": "lnorm",
      "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [3.1, 3.8, 5.1, 6.3],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 4.4,
    "median_ci_limits": [3.9, 4.9],
    "median_ci": 95,
    "dispersion": 1.24,
    "dispersion_ci_limits": [1.13, 1.35],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Kenrad E.",
        "family": "Nelson"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of acute respiratory viral infections: a systematic review",
    "journal": "The Lancet Infectious Diseases",
    "year": 2009,
    "pmid": 19393959,
    "doi": "10.1016/S1473-3099(09)70069-14"
  },
  "metadata": {
    "units": "days",
    "sample_size": 24,
    "region": "Mixed",
    "transmission_mode": "mixed",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets"
},
{
  "disease": "Rhinovirus",
  "pathogen": "Rhinovirus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [0.8, 1.3, 2.7, 4.5],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 1.9,
    "median_ci_limits": [1.4, 2.4],
    "median_ci": 95,
    "dispersion": 1.68,
    "dispersion_ci_limits": [1.36, 2.01],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Kenrad E.",
        "family": "Nelson"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of acute respiratory viral infections: a systematic review",
    "journal": "The Lancet Infectious Diseases",
    "year": 2009,
    "pmid": 19393959,
    "doi": "10.1016/S1473-3099(09)70069-15"
  },
  "metadata": {
    "units": "days",
    "sample_size": 28,
    "region": "USA",
    "transmission_mode": "experimental",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets"
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [0.73, 2.94],
    "quantile_names": ["5", "95"],
    "median": 1.46,
    "median_ci_limits": [1.35, 1.57],
    "median_ci": 95,
    "dispersion": 1.53,
    "dispersion_ci_limits": [1.44, 1.61],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      }
    ],
    "title": "Estimating incubation period distributions with coarse data",
    "journal": "Statistics in Medicine",
    "year": 2009,
    "pmid": 19598148,
    "doi": "10.1002/sim.3659"
  },
  "metadata": {
    "units": "days",
    "sample_size": 151,
    "region": "Mixed",
    "transmission_mode": "unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Data from Lessler et al 2009 using double interval-censored analysis. Not open source"
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [0.73, 2.83],
    "quantile_names": ["5", "95"],
    "median": 1.43,
    "median_ci_limits": [1.33, 1.54],
    "median_ci": 95,
    "dispersion": 1.51,
    "dispersion_ci_limits": [1.43, 1.6],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      }
    ],
    "title": "Estimating incubation period distributions with coarse data",
    "journal": "Statistics in Medicine",
    "year": 2009,
    "pmid": 19598148,
    "doi": "10.1002/sim.3659"
  },
  "metadata": {
    "units": "days",
    "sample_size": 151,
    "region": "Mixed",
    "transmission_mode": "unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Data from Lessler et al 2009 using single interval-censored analysis. Not open source"
},
{
  "disease": "RSV",
  "pathogen": "RSV",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [3.05, 6.39],
    "quantile_names": ["5", "95"],
    "median": 4.41,
    "median_ci_limits": [3.9, 4.92],
    "median_ci": 95,
    "dispersion": 1.25,
    "dispersion_ci_limits": [1.14, 1.36],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      }
    ],
    "title": "Estimating incubation period distributions with coarse data",
    "journal": "Statistics in Medicine",
    "year": 2009,
    "pmid": 19598148,
    "doi": "10.1002/sim.3659"
  },
  "metadata": {
    "units": "days",
    "sample_size": 24,
    "region": "Mixed",
    "transmission_mode": "unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
  "truncation": null,
  "discretised": false,
  "censored": true,
  "right_truncated": false,
  "phase_bias_adjusted": false
  },
  "notes": "Data from Lessler et al 2009 using double interval-censored analysis. Not open source"
},
{
  "disease": "RSV",
  "pathogen": "RSV",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [3.11, 6.26],
    "quantile_names": ["5", "95"],
    "median": 4.41,
    "median_ci_limits": [3.89, 4.94],
    "median_ci": 95,
    "dispersion": 1.24,
    "dispersion_ci_limits": [1.12, 1.35],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      },
      {
        "given": "Ron",
        "family": "Brookmeyer"
      }
    ],
    "title": "Estimating incubation period distributions with coarse data",
    "journal": "Statistics in Medicine",
    "year": 2009,
    "pmid": 19598148,
    "doi": "10.1002/sim.3659"
  },
  "metadata": {
    "units": "days",
    "sample_size": 24,
    "region": "Mixed",
    "transmission_mode": "unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Data from Lessler et al 2009 using single interval-censored analysis. Not open source"
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H1N1",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": {
      "shape": 3.27,
      "scale": 0.51
    }
  },
  "summary_statistics": {
    "quantile_values": [3.43],
    "quantile_names": ["95"],
    "median": 1.51,
    "median_ci_limits": [1.47, 1.55],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      },
      {
        "given": "Hisashi",
        "family": "Inaba"
      }
    ],
    "title": "Estimation of the incubation period of influenza A (H1N1-2009) among imported cases: addressing censoring using outbreak data at the origin of importation",
    "journal": "Journal of Theoretical Biology",
    "year": 2011,
    "pmid": 21168422,
    "doi": "10.1016/j.jtbi.2010.12.017"
  },
  "metadata": {
    "units": "days",
    "sample_size": 72,
    "region": "Japan",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": true
  },
  "notes": "Gamma and weibull distributions had equally good fit to the data. This entry is the gamma distribution. Gamma, exponential. Not open source."
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H1N1",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "weibull",
    "parameters": {
      "shape": 1.74,
      "scale": 1.83
    }
  },
  "summary_statistics": {
    "quantile_values": [3.18],
    "quantile_names": ["95"],
    "median": 1.43,
    "median_ci_limits": [1.21, 1.65],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      },
      {
        "given": "Hisashi",
        "family": "Inaba"
      }
    ],
    "title": "Estimation of the incubation period of influenza A (H1N1-2009) among imported cases: addressing censoring using outbreak data at the origin of importation",
    "journal": "Journal of Theoretical Biology",
    "year": 2011,
    "pmid": 21168422,
    "doi": "10.1016/j.jtbi.2010.12.017"
  },
  "metadata": {
    "units": "days",
    "sample_size": 72,
    "region": "Japan",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": true
  },
  "notes": "Gamma and weibull distributions had equally good fit to the data. This entry is the weibull distribution. Weibull, exponential"
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H7N9",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "weibull",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 3.4,
    "mean_ci_limits": [3, 3.7],
    "mean_ci": 95,
    "sd": 1.7,
    "quantile_values": [6.5],
    "quantile_names": ["95"]
  },
  "citation": {
    "author": [
      {
        "given": "Victor",
        "family": "Virlogeux"
      },
      {
        "given": "Ming",
        "family": "Li"
      },
      {
        "given":  "Tim K.",
        "family": "Tsang"
      },
      {
        "given": "Luzhao",
        "family": "Feng"
      },
      {
        "given": "Vicky J.",
        "family": "Fang"
      },
      {
        "given": "Hui",
        "family": "Jiang"
      },
      {
        "given": "Peng",
        "family": "Wu"
      },
      {
        "given": "Jiandong",
        "family": "Zheng"
      },
      {
        "given": "Eric H. Y.",
        "family": "Lau"
      },
      {
        "given": "Yu",
        "family": "Cao"
      },
      {
        "given": "Ying",
        "family": "Qin"
      },
      {
        "given": "Qiaohong",
        "family": "Liao"
      },
      {
        "given": "Hongjie",
        "family": "Yu"
      },
      {
        "given":  "Benjamin J.",
        "family": "Cowling"
      }
    ],
    "title": "Estimating the Distribution of the Incubation Periods of Human Avian Influenza A(H7N9) Virus Infections",
    "journal": "American Journal of Epidemiology",
    "year": 2015,
    "pmid": 26409239,
    "doi": "10.1093/aje/kwv115"
  },
  "metadata": {
    "units": "days",
    "sample_size": 229,
    "region": "China",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This study used an original data set and a modified data set. This weibull distribution was fitted to the modified data set and it is recommended to use this one."
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H7N9",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 4.5,
    "mean_ci_limits": [2.8, 16.2],
    "mean_ci": 95,
    "sd": 3.3,
    "quantile_values": [11],
    "quantile_names": ["95"]
  },
  "citation": {
    "author": [
      {
        "given": "Victor",
        "family": "Virlogeux"
      },
      {
        "given": "Ming",
        "family": "Li"
      },
      {
        "given": "Tim K.",
        "family": "Tsang"
      },
      {
        "given": "Luzhao",
        "family": "Feng"
      },
      {
        "given": "Vicky J.",
        "family": "Fang"
      },
      {
        "given": "Hui",
        "family": "Jiang"
      },
      {
        "given": "Peng",
        "family": "Wu"
      },
      {
        "given": "Jiandong",
        "family": "Zheng"
      },
      {
        "given": "Eric H. Y.",
        "family": "Lau"
      },
      {
        "given": "Yu",
        "family": "Cao"
      },
      {
        "given": "Ying",
        "family": "Qin"
      },
      {
        "given": "Qiaohong",
        "family": "Liao"
      },
      {
        "given": "Hongjie",
        "family": "Yu"
      },
      {
        "given": "Benjamin J.",
        "family": "Cowling"
      }
    ],
    "title": "Estimating the Distribution of the Incubation Periods of Human Avian Influenza A(H7N9) Virus Infections",
    "journal": "American Journal of Epidemiology",
    "year": 2015,
    "pmid": 26409239,
    "doi": "10.1093/aje/kwv115"
  },
  "metadata": {
    "units": "days",
    "sample_size": 229,
    "region": "China",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This study used an original data set and a modified data set. This gamma distribution was fitted to the original data set and it is recommended to use the weibull distribution that was fitted to the modified data set."
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H7N9",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "weibull",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 3.5,
    "mean_ci_limits": [3.2, 3.8],
    "mean_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Victor",
        "family": "Virlogeux"
      },
      {
        "given": "Juan",
        "family": "Yang"
      },
      {
        "given": "Vicky J.",
        "family": "Fang"
      },
      {
        "given": "Luzhao",
        "family": "Feng"
      },
      {
        "given": "Tim K.",
        "family": "Tsang"
      },
      {
        "given": "Hui",
        "family": "Jiang"
      },
      {
        "given": "Peng",
        "family": "Wu"
      },
      {
        "given": "Jiandong",
        "family": "Zheng"
      },
      {
        "given": "Eric H. Y.",
        "family": "Lau"
      },
      {
        "given": "Ying",
        "family": "Qin"
      },
      {
        "given": "Zhibin",
        "family": "Peng"
      },
      {
        "given": "J. S. Malik",
        "family": "Peiris"
      },
      {
        "given": "Hongjie",
        "family": "Yu"
      },
      {
        "given": "Benjamin J.",
        "family": "Cowling"
      }
    ],
    "title": "Association between the Severity of Influenza A(H7N9) Virus Infections and Length of the Incubation Period",
    "journal": "PLoS One",
    "year": 2016,
    "pmid": 26885816,
    "doi": "10.1371/journal.pone.0148506"
  },
  "metadata": {
    "units": "days",
    "sample_size": 395,
    "region": "China",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This study fit the weibull distribution to estimate the parameters for the complete data set, those who had a fatal outcome and those with a non-fatal outcome. This is the distribution fit to the complete unpartitioned data."
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H7N9",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "weibull",
    "parameters": {
      "shape": 2.3,
      "shape_ci_limits": [1.8, 2.89],
      "shape_ci": 95,
      "scale": 4.21,
      "scale_ci_limits": [3.62, 4.85],
      "scale_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 3.7,
    "mean_ci_limits": [3.4, 4.1],
    "mean_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Victor",
        "family": "Virlogeux"
      },
      {
        "given": "Juan",
        "family": "Yang"
      },
      {
        "given": "Vicky J.",
        "family": "Fang"
      },
      {
        "given": "Luzhao",
        "family": "Feng"
      },
      {
        "given": "Tim K.",
        "family": "Tsang"
      },
      {
        "given": "Hui",
        "family": "Jiang"
      },
      {
        "given": "Peng",
        "family": "Wu"
      },
      {
        "given": "Jiandong",
        "family": "Zheng"
      },
      {
        "given": "Eric H. Y.",
        "family": "Lau"
      },
      {
        "given": "Ying",
        "family": "Qin"
      },
      {
        "given": "Zhibin",
        "family": "Peng"
      },
      {
        "given": "J. S. Malik",
        "family": "Peiris"
      },
      {
        "given": "Hongjie",
        "family": "Yu"
      },
      {
        "given": "Benjamin J.",
        "family": "Cowling"
      }
    ],
    "title": "Association between the Severity of Influenza A(H7N9) Virus Infections and Length of the Incubation Period",
    "journal": "PLoS One",
    "year": 2016,
    "pmid": 26885816,
    "doi": "10.1371/journal.pone.0148506"
  },
  "metadata": {
    "units": "days",
    "sample_size": 173,
    "region": "China",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This study fit the weibull distribution to estimate the parameters for the complete data set, those who had a fatal outcome and those with a non-fatal outcome. This is the distribution fit to the fatal outcome data."
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H7N9",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "weibull",
    "parameters": {
      "shape": 2.03,
      "shape_ci_limits": [1.62, 2.52],
      "shape_ci": 95,
      "scale": 3.74,
      "scale_ci_limits": [3.2, 4.36],
      "scale_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 3.3,
    "mean_ci_limits": [2.9, 3.6],
    "mean_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Victor",
        "family": "Virlogeux"
      },
      {
        "given": "Juan",
        "family": "Yang"
      },
      {
        "given":"Vicky J.",
        "family": "Fang"
      },
      {
        "given": "Luzhao",
        "family": "Feng"
      },
      {
        "given": "Tim K.",
        "family": "Tsang"
      },
      {
        "given": "Hui",
        "family": "Jiang"
      },
      {
        "given": "Peng",
        "family": "Wu"
      },
      {
        "given": "Jiandong",
        "family": "Zheng"
      },
      {
        "given": "Eric H. Y.",
        "family": "Lau"
      },
      {
        "given": "Ying",
        "family": "Qin"
      },
      {
        "given": "Zhibin",
        "family": "Peng"
      },
      {
        "given": "J. S. Malik",
        "family": "Peiris"
      },
      {
        "given": "Hongjie",
        "family": "Yu"
      },
      {
        "given": "Benjamin J.",
        "family": "Cowling"
      }
    ],
    "title": "Association between the Severity of Influenza A(H7N9) Virus Infections and Length of the Incubation Period",
    "journal": "PLoS One",
    "year": 2016,
    "pmid": 26885816,
    "doi": "10.1371/journal.pone.0148506"
  },
  "metadata": {
    "units": "days",
    "sample_size": 222,
    "region": "China",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This study fit the weibull distribution to estimate the parameters for the complete data set, those who had a fatal outcome and those with a non-fatal outcome. This is the distribution fit to the non-fatal outcome data."
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H1N1",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 4.3,
    "mean_ci_limits": [2.6, 6.6],
    "mean_ci": 95,
    "median": 4
  },
  "citation": {
    "author": [
      {
        "given": "Ashleigh R.",
        "family": "Tuite"
      },
      {
        "given": "Amy L.",
        "family": "Greer"
      },
      {
        "given": "Michael",
        "family": "Whelan"
      },
      {
        "given": "Anne-Luise",
        "family": "Winter"
      },
      {
        "given": "Brenda",
        "family": "Lee"
      },
      {
        "given": "Ping",
        "family": "Yan"
      },
      {
        "given": "Jianhong",
        "family": "Wu"
      },
      {
        "given": "Seyed",
        "family": "Moghadas"
      },
      {
        "given": "David",
        "family": "Buckeridge"
      },
      {
        "given": "Babak",
        "family": "Pourbohloul"
      },
      {
        "given": "David N.",
        "family": "Fisman"
      }
    ],
    "title": "Estimated epidemiologic parameters and morbidity associated with pandemic H1N1 influenza",
    "journal": "Canadian Medical Association Journal",
    "year": 2010,
    "pmid": 19959592,
    "doi": "10.1503/cmaj.091807"
  },
  "metadata": {
    "units": "days",
    "sample_size": 316,
    "region": "Canada",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "The mid-point of the exposure time was used to approximate an exact exposure time instead of interval-censoring. This can lead to a possible bias (overestimation) in incubation times. It was ambiguously reported whether the mean is the mean of the distribution or the meanlog parameter of the lognormal distribution."
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H1N1Pdm",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 2.05,
    "sd": 0.49
  },
  "citation": {
    "author": [
      {
        "given": "Azra",
        "family": "Ghani"
      },
      {
        "given": "Marc",
        "family": "Baguelin"
      },
      {
        "given": "Jamie",
        "family": "Griffin"
      },
      {
        "given": "Stefan",
        "family": "Flasche"
      },
      {
        "given": "Albert Jan",
        "family": "van Hoek"
      },
      {
        "given": "Simon",
        "family": "Cauchemez"
      },
      {
        "given": "Christl",
        "family": "Donnelly"
      },
      {
        "given": "Chris",
        "family": "Robertson"
      },
      {
        "given": "Michael",
        "family": "White"
      },
      {
        "given": "James",
        "family": "Truscott"
      },
      {
        "given": "Christophe",
        "family": "Fraser"
      },
      {
        "given": "Tini",
        "family": "Garske"
      },
      {
        "given": "Peter",
        "family": "White"
      },
      {
        "given": "Steve",
        "family": "Leach"
      },
      {
        "given": "Ian",
        "family": "Hall"
      },
      {
        "given": "Helen",
        "family": "Jenkins"
      },
      {
        "given": "Neil",
        "family": "Ferguson"
      },
      {
        "given": "Ben",
        "family": "Cooper"
      }
    ],
    "title": "The Early Transmission Dynamics of H1N1pdm Influenza in the United Kingdom",
    "journal": "PLoS Currents",
    "year": 2009,
    "pmid": 20029668,
    "doi": "10.1371/currents.RRN1130"
  },
  "metadata": {
    "units": "days",
    "sample_size": 16,
    "region": "UK",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H1N1Pdm",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 2.51,
    "sd": 1.55
  },
  "citation": {
    "author": [
      {
        "given": "Azra",
        "family": "Ghani"
      },
      {
        "given": "Marc",
        "family": "Baguelin"
      },
      {
        "given": "Jamie",
        "family": "Griffin"
      },
      {
        "given": "Stefan",
        "family": "Flasche"
      },
      {
        "given": "Albert Jan",
        "family": "van Hoek"
      },
      {
        "given": "Simon",
        "family": "Cauchemez"
      },
      {
        "given": "Christl",
        "family": "Donnelly"
      },
      {
        "given": "Chris",
        "family": "Robertson"
      },
      {
        "given": "Michael",
        "family": "White"
      },
      {
        "given": "James",
        "family": "Truscott"
      },
      {
        "given": "Christophe",
        "family": "Fraser"
      },
      {
        "given": "Tini",
        "family": "Garske"
      },
      {
        "given": "Peter",
        "family": "White"
      },
      {
        "given": "Steve",
        "family": "Leach"
      },
      {
        "given": "Ian",
        "family": "Hall"
      },
      {
        "given": "Helen",
        "family": "Jenkins"
      },
      {
        "given": "Neil",
        "family": "Ferguson"
      },
      {
        "given": "Ben",
        "family": "Cooper"
      }
    ],
    "title": "The Early Transmission Dynamics of H1N1pdm Influenza in the United Kingdom",
    "journal": "PLoS Currents",
    "year": 2009,
    "pmid": 20029668,
    "doi": "10.1371/currents.RRN1130"
  },
  "metadata": {
    "units": "days",
    "sample_size": 58,
    "region": "UK",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H1N1",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [0.9, 2.2],
    "quantile_names": ["5", "95"],
    "median": 1.4,
    "median_ci_limits": [1, 1.8],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Derek A.T.",
        "family": "Cummings"
      },
      {
        "given": "New York City Department of Health and Mental Hygiene Swine Influenza Investigation Team",
        "family": null
      }
    ],
    "title": "Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School",
    "journal": "The New England Journal of Medicine",
    "year": 2009,
    "pmid": 20042754,
    "doi": "10.1056/NEJMoa0906089"
  },
  "metadata": {
    "units": "days",
    "sample_size": 124,
    "region": "New York, USA",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes."
},
{
  "disease": "Influenza",
  "pathogen": "Influenza-A-H1N1",
  "epi_name": "generation time",
  "probability_distribution": {
      "prob_distribution": "weibull",
      "parameters": {
        "shape": 2.36,
        "scale": 3.18
      }
  },
  "summary_statistics": {
    "quantile_values": [0.9, 5.1],
    "quantile_names": ["5", "95"],
    "median": 2.7,
    "median_ci_limits": [2, 3.5],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Derek A.T.",
        "family": "Cummings"
      },
      {
        "given": "New York City Department of Health and Mental Hygiene Swine Influenza Investigation Team",
        "family": null
      }
    ],
    "title": "Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School",
    "journal": "The New England Journal of Medicine",
    "year": 2009,
    "pmid": 20042754,
    "doi": "10.1056/NEJMoa0906089"
  },
  "metadata": {
    "units": "days",
    "sample_size": 16,
    "region": "New York, USA",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "The parameters of the weibull are stated without reporting the uncertainty around them. The parameter estimates and sample size is reported in the supplementary appendix."
},
{
  "disease": "Marburg Virus Disease",
  "pathogen": "Marburg Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "lower_range": 2,
    "upper_range": 26
  },
  "citation": {
    "author": [
      {
        "given": "Boris I.",
        "family": "Pavlin"
      }
    ],
    "title": "Calculation of incubation period and serial interval from multiple outbreaks of Marburg virus disease",
    "journal": "BMC Research Notes",
    "year": 2014,
    "pmid": 25495697,
    "doi": "10.1186/1756-0500-7-906"
  },
  "metadata": {
    "units": "days",
    "sample_size": 76,
    "region": "Mixed",
    "transmission_mode": "mixed",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This paper did not fit a distribution to the incubation period data and only reported a lower and upper range of the data. This is present in the database as there are no other studies that report the incubation period for Marburg virus. There is another incubation period reported from the same paper for a subset of the data which report the median and interquartile range but again do not fit a distribution to the data."
},
{
  "disease": "Marburg Virus Disease",
  "pathogen": "Marburg Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "median": 7,
    "lower_range": 2,
    "upper_range": 13
  },
  "citation": {
    "author": [
      {
        "given": "Boris I.",
        "family": "Pavlin"
      }
    ],
    "title": "Calculation of incubation period and serial interval from multiple outbreaks of Marburg virus disease",
    "journal": "BMC Research Notes",
    "year": 2014,
    "pmid": 25495697,
    "doi": "10.1186/1756-0500-7-906"
  },
  "metadata": {
    "units": "days",
    "sample_size": 18,
    "region": "Mixed",
    "transmission_mode": "mixed",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This paper did not fit a distribution to the incubation period data and only reported a median and range for a subset of the data. This is present in the database as there are no other studies that report the incubation period for Marburg virus. This paper also reports the maximum and minimum for the complete data set."
},
{
  "disease": "Marburg Virus Disease",
  "pathogen": "Marburg Virus",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [8, 15],
    "quantile_names": ["25", "75"],
    "median": 11
  },
  "citation": {
    "author": [
      {
        "given": "Boris I.",
        "family": "Pavlin"
      }
    ],
    "title": "Calculation of incubation period and serial interval from multiple outbreaks of Marburg virus disease",
    "journal": "BMC Research Notes",
    "year": 2014,
    "pmid": 25495697,
    "doi": "10.1186/1756-0500-7-906"
  },
  "metadata": {
    "units": "days",
    "sample_size": 38,
    "region": "Mixed",
    "transmission_mode": "mixed",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This paper did not fit a distribution to the serial interval data and only reported a median and interquartile range. This is present in the database as there are no other studies that report the serial interval for Marburg virus."
},
{
  "disease": "Marburg Virus Disease",
  "pathogen": "Marburg Virus",
  "epi_name": "onset to death",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "median": 8,
    "lower_range": 2,
    "upper_range": 16
  },
  "citation": {
    "author": [
      {
        "given": "Robert",
        "family": "Colebunders"
      },
      {
        "given": "Antoine",
        "family": "Tshomba"
      },
      {
        "given": "Maria D.",
        "family": "Van Kerkhove"
      },
      {
        "given": "Daniel G.",
        "family": "Bausch"
      },
      {
        "given": "Pat",
        "family": "Campbell"
      },
      {
        "given": "Modeste",
        "family": "Libande"
      },
      {
        "given": "Patricia",
        "family": "Pirard"
      },
      {
        "given": "Florimond",
        "family": "Tshioko"
      },
      {
        "given": "Simon",
        "family": "Mardel"
      },
      {
        "given": "Sabue",
        "family": "Mulangu"
      },
      {
        "given": "Hilde",
        "family": "Sleurs"
      },
      {
        "given": "Pierre E.",
        "family": "Rollin"
      },
      {
        "given": "Jean-Jacques",
        "family": "Muyembe-Tamfum"
      },
      {
        "given": "Benjamin",
        "family": "Jeffs"
      },
      {
        "given": "Matthias",
        "family": "Borchert"
      },
      {
        "given": "International Scientific and Technical Committee 'DRC Watsa/Durba 1999 Marburg Outbreak Investigation Group'",
        "family": null
      }
    ],
    "title": "Marburg hemorrhagic fever in Durba and Watsa, Democratic Republic of the Congo: clinical documentation, features of illness, and treatment",
    "journal": "The Journal of Infectious Diseases",
    "year": 2007,
    "pmid": 17940943,
    "doi": "10.1086/520543"
  },
  "metadata": {
    "units": "days",
    "sample_size": 77,
    "region": "DR Congo",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This paper reports the median and range of the symptom onset to death delay but did not fit a parametric distribution to the data. This is included in the database as it is the only reported symptom onset to death reported in the literature"
},
{
  "disease": "Marburg Virus Disease",
  "pathogen": "Marburg Virus",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 9,
    "mean_ci_limits": [8.2, 10],
    "mean_ci": 95,
    "sd": 5.4,
    "sd_ci_limits": [3.9, 8.6],
    "sd_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Marco",
        "family": "Ajelli"
      },
      {
        "given": "Stefano",
        "family": "Merler"
      }
    ],
    "title": "Transmission Potential and Design of Adequate Control Measures for Marburg Hemorrhagic Fever",
    "journal": "PLoS One",
    "year": 2012,
    "pmid": 23251407,
    "doi": "10.1371/journal.pone.0050948"
  },
  "metadata": {
    "units": "days",
    "sample_size": 374,
    "region": "Angola",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "The generation time is estimated from non-human viral load data. This paper reports the generation time but assumes the generation time and serial interval are the same it is classified as serial interval here based on Van Kerkove et al. 2015 <10.1038/sdata.2015.19>. The sample size is take from Van Kerkove et al. 2015."
},
{
  "disease": "SARS",
  "pathogen": "SARS-Cov-1",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 1.63,
      "mean_ci_limits": [0.54, 2.65],
      "mean_ci": 90,
      "dispersion": 0.16,
      "dispersion_ci_limits": [0.11, 0.64],
      "dispersion_ci": 90
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 57,
    "region": "Singapore",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Parameter estimates are retrieved from the supplementary tables."
},
{
  "disease": "SARS",
  "pathogen": "SARS-Cov-1",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 0.94,
      "mean_ci_limits": [0.27, 1.51],
      "mean_ci": 90,
      "dispersion": 0.17,
      "dispersion_ci_limits": [0.1, 0.64],
      "dispersion_ci": 90
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 33,
    "region": "Beijing",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "Smallpox",
  "pathogen": "Smallpox-Variola-Major",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 3.19,
      "mean_ci_limits": [1.66, 4.62],
      "mean_ci": 90,
      "dispersion": 0.37,
      "dispersion_ci_limits": [0.26, 0.69],
      "dispersion_ci": 90
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 32,
    "region": "Europe",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "Smallpox",
  "pathogen": "Smallpox-Variola-Major",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 0.8,
      "mean_ci_limits": [0.32, 1.2],
      "mean_ci": 90,
      "dispersion": 0.32,
      "dispersion_ci_limits": [0.16, 1.76],
      "dispersion_ci": 90
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 25,
    "region": "Benin",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "Smallpox",
  "pathogen": "Smallpox-Variola-Minor",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 1.6,
      "mean_ci_limits": [0.88, 2.16],
      "mean_ci": 90,
      "dispersion": 0.65,
      "dispersion_ci_limits": [0.34, 2.32],
      "dispersion_ci": 90
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 25,
    "region": "England",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "Smallpox",
  "pathogen": "Smallpox-Variola-Minor",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 1.49,
      "dispersion": 0.72,
      "dispersion_ci_limits": [0.44, 2.05],
      "dispersion_ci": 90
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 47,
    "region": "Pakistan",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Estimate of R0 taken from original study and CI of dispersion calculated mean of Z and proportion of zeros known "
},
{
  "disease": "Mpox",
  "pathogen": "Monkeypox Virus",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 0.32,
      "mean_ci_limits": [0.22, 0.40],
      "mean_ci": 90,
      "dispersion": 0.58,
      "dispersion_ci_limits": [0.32, 3.57],
      "dispersion_ci": 90
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 147,
    "region": "Zaire",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "In the model comparison the geometric model was the better fit to the monkeypox data, however, only the parameters of the negative binomial were reported as so are stored in the database."
},
{
  "disease": "Pneumonic Plague",
  "pathogen": "Yersinia Pestis",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 1.32,
      "mean_ci_limits": [1.01, 1.61],
      "mean_ci": 90,
      "dispersion": 1.37,
      "dispersion_ci_limits": [0.88, 3.53],
      "dispersion_ci": 90
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 74,
    "region": "Mixed",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "In the model comparison the geometric model was the better fit to the Pneumonic Plague data, however, only the parameters of the negative binomial were reported as so are stored in the database."
},
{
  "disease": "Hantavirus Pulmonary Syndrome",
  "pathogen": "Hantavirus (Andes Virus)",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 0.7,
      "mean_ci_limits": [0.20, 1.05],
      "mean_ci": 90,
      "dispersion": 1.66
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 20,
    "region": "Argentina",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "In the model comparison the geometric model was the better fit to the Hantavirus data, however, only the parameters of the negative binomial were reported as so are stored in the database. The uncertainty for the dispersion parameter is currently not stored in the database as the upper bound for the confidence interval is infinite, and currently infinite values are not supported."
},
{
  "disease": "Ebola Virus Disease",
  "pathogen": "Ebola Virus",
  "epi_name": "offspring distribution",
  "probability_distribution": {
    "prob_distribution": "nbinom",
    "parameters": {
      "mean": 1.5,
      "mean_ci_limits": [0.85, 2.08],
      "mean_ci": 90,
      "dispersion": 5.10
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "J. O.",
        "family": "Lloyd-Smith"
      },
      {
        "given": "S. J.",
        "family": "Schreiber"
      },
      {
        "given": "P. E.",
        "family": "Kopp"
      },
      {
        "given": "W. M.",
        "family": "Getz"
      }
    ],
    "title": "Superspreading and the effect of individual variation on disease emergence",
    "journal": "Nature",
    "year": 2005,
    "pmid": 16292310,
    "doi": "10.1038/nature04153"
  },
  "metadata": {
    "units": "No units",
    "sample_size": 13,
    "region": "Uganda",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "In the model comparison the poisson model was the better fit to the Ebola data, however, only the parameters of the negative binomial were reported as so are stored in the database. The uncertainty for the dispersion parameter is currently not stored in the database as the upper bound for the confidence interval is infinite, and currently infinite values are not supported."
},
{
  "disease": "Dengue",
  "pathogen": "Dengue Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 15,
    "mean_ci_limits": [10, 20],
    "mean_ci": 95,
    "quantile_values": [5, 33],
    "quantile_names": ["2.5", "97.5"]
  },
  "citation": {
    "author": [
      {
        "given": "Miranda",
        "family": "Chan"
      },
      {
        "given": "Michael A.",
        "family": "Johansson"
      }
    ],
    "title": "The Incubation Periods of Dengue Viruses",
    "journal": "PLoS One",
    "year": 2012,
    "pmid": 23226436,
    "doi": "10.1371/journal.pone.0050972"
  },
  "metadata": {
    "units": "days",
    "sample_size": 146,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "Aedes aegypti and Aedes albopictus",
    "extrinsic": true,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Extrinsic incubation period for data at 25 degrees celcius"
},
{
  "disease": "Dengue",
  "pathogen": "Dengue Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": {
      "precision": 4.9,
      "precision_ci_limits": [2.8, 7.5],
      "precision_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 6.5,
    "mean_ci_limits": [4.8, 8.8],
    "mean_ci": 95,
    "quantile_values": [2.4, 15],
    "quantile_names": ["2.5" ,"97.5"]
  },
  "citation": {
    "author": [
      {
        "given": "Miranda",
        "family": "Chan"
      },
      {
        "given": "Michael A.",
        "family": "Johansson"
      }
    ],
    "title": "The Incubation Periods of Dengue Viruses",
    "journal": "PLoS One",
    "year": 2012,
    "pmid": 23226436,
    "doi": "10.1371/journal.pone.0050972"
  },
  "metadata": {
    "units": "days",
    "sample_size": 146,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "Aedes aegypti and Aedes albopictus",
    "extrinsic": true,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Extrinsic incubation period for data at 30 degrees celcius"
},
{
  "disease": "Dengue",
  "pathogen": "Dengue Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": {
      "meanlog": 1.75,
      "sdlog": 0.27,
      "precision": 13.7,
      "precision_ci_limits": [10.9, 16.9],
      "precision_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 5.97,
    "mean_ci_limits": [5.5, 6.4],
    "mean_ci": 95,
    "sd": 1.64,
    "quantile_values": [3.4, 10],
    "quantile_names": ["2.5", "97.5"]
  },
  "citation": {
    "author": [
      {
        "given": "Miranda",
        "family": "Chan"
      },
      {
        "given": "Michael A.",
        "family": "Johansson"
      }
    ],
    "title": "The Incubation Periods of Dengue Viruses",
    "journal": "PLoS One",
    "year": 2012,
    "pmid": 23226436,
    "doi": "10.1371/journal.pone.0050972"
  },
  "metadata": {
    "units": "days",
    "sample_size": 153,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "Aedes aegypti and Aedes albopictus",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Standard deviation, meanlog and sdlog is taken from Siraj et al. 2017 <10.1371/journal.pntd.0005797>"
},
{
  "disease": "Zika Virus Disease",
  "pathogen": "Zika Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [3.2, 4.6, 7.6, 11.2],
    "quantile_names": ["5" ,"25", "75", "95"],
    "median": 5.9,
    "median_ci_limits": [4.4, 7.6],
    "median_ci": 95,
    "dispersion": 1.5,
    "dispersion_ci_limits": [1.2, 1.9],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Cassandra T.",
        "family": "Ott"
      },
      {
        "given": "Andrea C.",
        "family": "Carcelen"
      },
      {
        "given": "Jacob M.",
        "family": "Konikoff"
      },
      {
        "given": "Joe",
        "family": "Williamson"
      },
      {
        "given": "Qifang",
        "family": "Bi"
      },
      {
        "given": "Lauren M.",
        "family": "Kucirka"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Lelia H.",
        "family": "Chaisson"
      }
    ],
    "title": "Times to key events in Zika virus infection and implications for blood donation: a systematic review",
    "journal": "Bulletin of the World Health Organization",
    "year": 2016,
    "pmid": 27821887,
    "doi": "10.2471/BLT.16.174540"
  },
  "metadata": {
    "units": "days",
    "sample_size": 25,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "Aedes aegypti and Aedes albopictus",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Lessler et al. 2016 for references of datasets"
},
{
  "disease": "Chikungunya",
  "pathogen": "Chikungunya Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [2.9, 3],
    "quantile_names": ["25", "75"],
    "median": 3,
    "median_ci_limits": [0.5, 3.1],
    "median_ci": 95,
    "dispersion": 1.04,
    "dispersion_ci_limits": [1.04, 1.08],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 21,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "Aedes albopictus",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets"
},
{
  "disease": "Dengue",
  "pathogen": "Dengue Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [4.5, 7.1],
    "quantile_names": ["25", "75"],
    "median": 5.6,
    "median_ci_limits": [5.3, 6],
    "median_ci": 95,
    "dispersion": 1.41,
    "dispersion_ci_limits": [1.34, 1.5],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 169,
    "region": "Mixed",
    "transmission_mode": "multiple",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets"
},
{
  "disease": "Dengue",
  "pathogen": "Dengue Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [4.3, 6.6],
    "quantile_names": ["25", "75"],
    "median": 5.3,
    "median_ci_limits": [5, 5.7],
    "median_ci": 95,
    "dispersion": 1.37,
    "dispersion_ci_limits": [1.27, 1.52],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 124,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "Aedes aegypti and Aedes albopictus",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets. This is a subset of data containing only mosquito-transmitted infections"
},
{
  "disease": "Japanese Encephalitis",
  "pathogen": "Japanese Encephalitis Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [8.1, 8.6],
    "quantile_names": ["25", "75"],
    "median": 8.4,
    "median_ci_limits": [5.1, 9.4],
    "median_ci": 95,
    "dispersion": 1.04,
    "dispersion_ci_limits": [1.04, 1.05],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 6,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "mosquito",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets"
},
{
  "disease": "Rift Valley Fever",
  "pathogen": "Rift Valley Fever Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [3.1, 5.3],
    "quantile_names": ["25", "75"],
    "median": 4,
    "median_ci_limits": [3.4, 4.9],
    "median_ci": 95,
    "dispersion": 1.5,
    "dispersion_ci_limits": [1.22, 1.82],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 23,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "mosquito",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets. Of the 18 samples at least 17 of them are not trasmitted by mosquitoes"
},
{
  "disease": "West Nile Fever",
  "pathogen": "West Nile Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [1, 1.7, 3.8, 7],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 2.6,
    "median_ci_limits": [1.6, 3.5],
    "median_ci": 95,
    "dispersion": 1.82,
    "dispersion_ci_limits": [1.27, 2.67],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 18,
    "region": "Mixed",
    "transmission_mode": "multiple",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets"
},
{
  "disease": "West Nile Fever",
  "pathogen": "West Nile Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [2.8, 3],
    "quantile_names": ["25", "75"],
    "median": 2.9,
    "median_ci_limits": [0.5, 3.1],
    "median_ci": 95,
    "dispersion": 1.04,
    "dispersion_ci_limits": [1.04, 1.29],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 8,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "mosquito",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets. This is a subset of data containing only mosquito-transmitted infections"
},
{
  "disease": "West Nile Fever",
  "pathogen": "West Nile Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [8.7, 13.3],
    "quantile_names": ["25", "75"],
    "median": 10.8,
    "median_ci_limits": [8.4, 14.2],
    "median_ci": 95,
    "dispersion": 1.35,
    "dispersion_ci_limits": [1.12, 1.47],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 6,
    "region": "Mixed",
    "transmission_mode": "organ_transplant",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets. This is a subset of data containing only tramsission by transplant or transfusion. "
},
{
  "disease": "Yellow Fever",
  "pathogen": "Yellow Fever Viruses",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [1.9, 3.2, 6.3, 10.3],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 4.4,
    "median_ci_limits": [4, 5],
    "median_ci": 95,
    "dispersion": 1.66,
    "dispersion_ci_limits": [1.48, 1.82],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 91,
    "region": "Mixed",
    "transmission_mode": "multiple",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets"
},
{
  "disease": "Yellow Fever",
  "pathogen": "Yellow Fever Viruses",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [1.9, 3.1, 6.2, 10.3],
    "quantile_names": ["5", "25", "75", "95"],
    "median": 4.4,
    "median_ci_limits": [3.9, 5],
    "median_ci": 95,
    "dispersion": 1.67,
    "dispersion_ci_limits": [1.47, 1.84],
    "dispersion_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kara E.",
        "family": "Rudolph"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      },
      {
        "given": "Rachael M.",
        "family": "Moloney"
      },
      {
        "given": "Brittany",
        "family": "Kmush"
      },
      {
        "given": "Derek A. T.",
        "family": "Cummings"
      }
    ],
    "title": "Incubation periods of mosquito-borne viral infections: a systematic review",
    "journal": "The American Journal of Tropical Medicine and Hygiene",
    "year": 2014,
    "pmid": 24639305,
    "doi": "10.4269/ajtmh.13-0403"
  },
  "metadata": {
    "units": "days",
    "sample_size": 80,
    "region": "Mixed",
    "transmission_mode": "vector_borne",
    "vector": "mosquito",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Pooled analysis on several data sets, see Rudolph et al 2014 for references of datasets. This is a subset of data containing only mosquito-transmitted infections"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 9,
    "mean_ci_limits": [6.6, 10.9],
    "mean_ci": 95,
    "quantile_values": [3.6, 4.2, 17.3, 19.9],
    "quantile_names": ["2.5", "5", "95", "97.5"],
    "median": 8.5,
    "median_ci_limits": [6.6, 10.9],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Fuminari",
        "family": "Miura"
      },
      {
        "given": "Catharina E.",
        "family": "van Ewijk"
      },
      {
        "given": "Jantien A.",
        "family": "Backer"
      },
      {
        "given": "Maria",
        "family": "Xiridou"
      },
      {
        "given": "Eelco",
        "family": "Franz"
      },
      {
        "given": "Eline",
        "family": "Op de Coul"
      },
      {
        "given": "Diederik",
        "family": "Brandwagt"
      },
      {
        "given": "Brigitte",
        "family": "van Cleef"
      },
      {
        "given": "Gini",
        "family": "van Rijckevorsel"
      },
      {
        "given": "Corien",
        "family": "Swaan"
      },
      {
        "given": "Susan",
        "family": "van den Hof"
      },
      {
        "given": "Jacco",
        "family": "Wallinga"
      }
    ],
    "title": "Estimated incubation period for monkeypox cases confirmed in the Netherlands, May 2022",
    "journal": "Eurosurveillance",
    "year": 2022,
    "pmid": 35713026,
    "doi": "10.2807/1560-7917.ES.2022.27.24.2200448"
  },
  "metadata": {
    "units": "days",
    "sample_size": 18,
    "region": "Netherlands",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 7.6,
    "mean_ci_limits": [6.2, 9.7],
    "mean_ci": 95,
    "sd": 1.8,
    "sd_ci_limits": [1.6, 2.2],
    "sd_ci": 95,
    "quantile_values": [17.1],
    "quantile_names": ["95"],
    "median": 6.4,
    "median_ci_limits": [5.1, 7.9],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Kelly",
        "family": "Charniga"
      },
      {
        "given": "Nina B.",
        "family": "Masters"
      },
      {
        "given": "Rachel B.",
        "family": "Slayton"
      },
      {
        "given": "Lucas",
        "family": "Gosdin"
      },
      {
        "given": "Faisal S.",
        "family": "Minhaj"
      },
      {
        "given": "David",
        "family": "Philpott"
      },
      {
        "given": "Dallas",
        "family": "Smith"
      },
      {
        "given": "Shannon",
        "family": "Gearhart"
      },
      {
        "given": "Francisco",
        "family": "Alvarado-Ramy"
      },
      {
        "given": "Clive",
        "family": "Brown"
      },
      {
        "given": "Michelle A.",
        "family": "Waltenburg"
      },
      {
        "given": "Christine M.",
        "family": "Hughes"
      },
      {
        "given": "Yoshinori",
        "family": "Nakazawa"
      }
    ],
    "title": "Estimating the incubation period of monkeypox virus during the 2022 multi-national outbreak",
    "journal": "medRxiv",
    "year": 2022,
    "pmid": null,
    "doi": "10.1101/2022.06.22.22276713"
  },
  "metadata": {
    "units": "days",
    "sample_size": 22,
    "region": "USA",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Uses the methods described by Lessler (10.2471/BLT.16.174540) and Reich (10.1002/sim.3659). Estimated from time from exposure to first symptom onset"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": {
       "shape": 2.42,
      "shape_ci_limits": [1.26, 3.62],
      "shape_ci": 95,
      "scale": 3.75 ,
      "scale_ci_limits": [2.17, 7.13],
      "scale_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 9.1,
    "mean_ci_limits": [6.5, 10.9],
    "mean_ci": 95,
    "quantile_values": [2, 20],
    "quantile_names": ["5", "95"]
  },
  "citation": {
    "author": [
      {
        "given": "Giorgio",
        "family": "Guzzetta"
      },
      {
        "given": "Alessia",
        "family": "Mammone"
      },
      {
        "given": "Federica",
        "family": "Ferraro"
      },
      {
        "given": "Anna",
        "family": "Caraglia"
      },
      {
        "given": "Alessia",
        "family": "Rapiti"
      },
      {
        "given": "Valentina",
        "family": "Marziano"
      },
      {
        "given": "Piero",
        "family": "Poletti"
      },
      {
        "given": "Danilo",
        "family": "Cereda"
      },
      {
        "given": "Francesco",
        "family": "Vairo"
      },
      {
        "given": "Giovanna",
        "family": "Mattei"
      },
      {
        "given": "Francesco",
        "family": "Maraglino"
      },
      {
        "given": "Giovanni",
        "family": "Rezza"
      },
      {
        "given": "Stefano",
        "family": "Merler"
      }
    ],
    "title": "Early Estimates of Monkeypox Incubation Period, Generation Time, and Reproduction Number, Italy, May-June 2022",
    "journal": "Emerging Infectious Diseases",
    "year": 2022,
    "pmid": 35994726,
    "doi": "10.3201/eid2810.221126"
  },
  "metadata": {
    "units": "days",
    "sample_size": 30,
    "region": "Italy",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": {
      "meanlog": 1.8,
      "meanlog_ci_limits": [1.6, 2.1],
      "meanlog_ci": 95,
      "sdlog": 0.6,
      "sdlog_ci_limits": [0.4, 0.8],
      "sdlog_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 7.5,
    "mean_ci_limits": [6, 9.8],
    "mean_ci": 95,
    "sd": 4.9,
    "sd_ci_limits": [3.2, 8.8],
    "sd_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Zachary J.",
        "family": "Madewell"
      },
      {
        "given": "Kelly",
        "family": "Charniga"
      },
      {
        "given": "Nina B.",
        "family": "Masters"
      },
      {
        "given": "Jason",
        "family": "Asher"
      },
      {
        "given": "Lily",
        "family": "Fahrenwald"
      },
      {
        "given": "William",
        "family": "Still"
      },
      {
        "given": "Judy",
        "family": "Chen"
      },
      {
        "given": "Naama",
        "family": "Kipperman"
      },
      {
        "given": "David",
        "family": "Bui"
      },
      {
        "given": "Meghan",
        "family": "Shea"
      },
      {
        "given": "Lori",
        "family": "Saathoff-Huber"
      },
      {
        "given": "Shannon",
        "family": "Johnson"
      },
      {
        "given": "Khalil",
        "family": "Harbi"
      },
      {
        "given": "Abby L.",
        "family": "Berns"
      },
      {
        "given": "Taidy",
        "family": "Perez"
      },
      {
        "given": "Emily",
        "family": "Gateley"
      },
      {
        "given": "Ian H.",
        "family": "Spicknall"
      },
      {
        "given": "Yoshinori",
        "family": "Nakazawa"
      },
      {
        "given": "Thomas L.",
        "family": "Gift"
      },
      {
        "given": "2022 Monkeypox Outbreak Response Team",
        "family": null
      }
    ],
    "title": "Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May – August 2022",
    "journal": "medRxiv",
    "year": 2022,
    "pmid": null,
    "doi": "10.1101/2022.10.26.22281516"
  },
  "metadata": {
    "units": "days",
    "sample_size": 35,
    "region": "USA",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Meanlog, sdlog, and fitted distribution from supplementary material. Uses cases from Charniga 2022 + extra cases. Incubation period as exposure to rash onset."
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": {
      "meanlog": 1.5,
      "meanlog_ci_limits": [1.2, 1.8],
      "meanlog_ci": 95,
      "sdlog": 0.7,
      "sdlog_ci_limits": [0.5, 1],
      "sdlog_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 5.6,
    "mean_ci_limits": [4.3, 7.8],
    "mean_ci": 95,
    "sd": 4.4,
    "sd_ci_limits": [2.8, 8.7],
    "sd_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Zachary J.",
        "family": "Madewell"
      },
      {
        "given": "Kelly",
        "family": "Charniga"
      },
      {
        "given": "Nina B.",
        "family": "Masters"
      },
      {
        "given": "Jason",
        "family": "Asher"
      },
      {
        "given": "Lily",
        "family": "Fahrenwald"
      },
      {
        "given": "William",
        "family": "Still"
      },
      {
        "given": "Judy",
        "family": "Chen"
      },
      {
        "given": "Naama",
        "family": "Kipperman"
      },
      {
        "given": "David",
        "family": "Bui"
      },
      {
        "given": "Meghan",
        "family": "Shea"
      },
      {
        "given": "Lori",
        "family": "Saathoff-Huber"
      },
      {
        "given": "Shannon",
        "family": "Johnson"
      },
      {
        "given": "Khalil",
        "family": "Harbi"
      },
      {
        "given": "Abby L.",
        "family": "Berns"
      },
      {
        "given": "Taidy",
        "family": "Perez"
      },
      {
        "given": "Emily",
        "family": "Gateley"
      },
      {
        "given": "Ian H.",
        "family": "Spicknall"
      },
      {
        "given": "Yoshinori",
        "family": "Nakazawa"
      },
      {
        "given": "Thomas L.",
        "family": "Gift"
      },
      {
        "given": "2022 Monkeypox Outbreak Response Team",
        "family": null
      }
    ],
    "title": "Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May – August 2023",
    "journal": "medRxiv",
    "year": 2022,
    "pmid": null,
    "doi": "10.1101/2022.10.26.22281516"
  },
  "metadata": {
    "units": "days",
    "sample_size": 36,
    "region": "USA",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Meanlog, sdlog, and fitted distribution from supplementary material. Uses cases from Charniga 2022 + extra cases. Incubation period as exposure to symptom onset."
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": {
      "shape": 2.9,
      "shape_ci_limits": [2, 4.1],
      "shape_ci": 95,
      "scale": 2.9,
      "scale_ci_limits": [2, 4.4],
      "scale_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 8.5,
    "mean_ci_limits": [7.3, 9.9],
    "mean_ci": 95,
    "sd": 5,
    "sd_ci_limits": [4, 6.4],
    "sd_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Zachary J.",
        "family": "Madewell"
      },
      {
        "given": "Kelly",
        "family": "Charniga"
      },
      {
        "given": "Nina B.",
        "family": "Masters"
      },
      {
        "given": "Jason",
        "family": "Asher"
      },
      {
        "given": "Lily",
        "family": "Fahrenwald"
      },
      {
        "given": "William",
        "family": "Still"
      },
      {
        "given": "Judy",
        "family": "Chen"
      },
      {
        "given": "Naama",
        "family": "Kipperman"
      },
      {
        "given": "David",
        "family": "Bui"
      },
      {
        "given": "Meghan",
        "family": "Shea"
      },
      {
        "given": "Lori",
        "family": "Saathoff-Huber"
      },
      {
        "given": "Shannon",
        "family": "Johnson"
      },
      {
        "given": "Khalil",
        "family": "Harbi"
      },
      {
        "given": "Abby L.",
        "family": "Berns"
      },
      {
        "given": "Taidy",
        "family": "Perez"
      },
      {
        "given": "Emily",
        "family": "Gateley"
      },
      {
        "given": "Ian H.",
        "family": "Spicknall"
      },
      {
        "given": "Yoshinori",
        "family": "Nakazawa"
      },
      {
        "given": "Thomas L.",
        "family": "Gift"
      },
      {
        "given": "2022 Monkeypox Outbreak Response Team",
        "family": null
      }
    ],
    "title": "Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May – August 2024",
    "journal": "medRxiv",
    "year": 2022,
    "pmid": null,
    "doi": "10.1101/2022.10.26.22281516"
  },
  "metadata": {
    "units": "days",
    "sample_size": 57,
    "region": "USA",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Shape and scale from supp. material. Serial interval as exposure to symptom onset"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": {
      "shape": 2.8,
      "shape_ci_limits": [1.8, 4.2],
      "shape_ci": 95,
      "scale": 2.5,
      "scale_ci_limits": [2.5, 4],
      "scale_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 7,
    "mean_ci_limits": [5.8, 8.4],
    "mean_ci": 95,
    "sd": 4.2,
    "sd_ci_limits": [3.2, 5.6],
    "sd_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Zachary J.",
        "family": "Madewell"
      },
      {
        "given": "Kelly",
        "family": "Charniga"
      },
      {
        "given": "Nina B.",
        "family": "Masters"
      },
      {
        "given": "Jason",
        "family": "Asher"
      },
      {
        "given": "Lily",
        "family": "Fahrenwald"
      },
      {
        "given": "William",
        "family": "Still"
      },
      {
        "given": "Judy",
        "family": "Chen"
      },
      {
        "given": "Naama",
        "family": "Kipperman"
      },
      {
        "given": "David",
        "family": "Bui"
      },
      {
        "given": "Meghan",
        "family": "Shea"
      },
      {
        "given": "Lori",
        "family": "Saathoff-Huber"
      },
      {
        "given": "Shannon",
        "family": "Johnson"
      },
      {
        "given": "Khalil",
        "family": "Harbi"
      },
      {
        "given": "Abby L.",
        "family": "Berns"
      },
      {
        "given": "Taidy",
        "family": "Perez"
      },
      {
        "given": "Emily",
        "family": "Gateley"
      },
      {
        "given": "Ian H.",
        "family": "Spicknall"
      },
      {
        "given": "Yoshinori",
        "family": "Nakazawa"
      },
      {
        "given": "Thomas L.",
        "family": "Gift"
      },
      {
        "given": "2022 Monkeypox Outbreak Response Team",
        "family": null
      }
    ],
    "title": "Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May – August 2025",
    "journal": "medRxiv",
    "year": 2022,
    "pmid": null,
    "doi": "10.1101/2022.10.26.22281516"
  },
  "metadata": {
    "units": "days",
    "sample_size": 40,
    "region": "USA",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Shape and scale from supp. material. Serial interval as exposure to rash onset"
},
{
  "disease": "Ebola Virus Disease",
  "pathogen": "Ebola Virus-Zaire Subtype",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 12.7,
    "sd": 4.31
  },
  "citation": {
    "author": [
      {
        "given": "Martin",
        "family": "Eichner"
      },
      {
        "given": "Scott F.",
        "family": "Dowell"
      },
      {
        "given": "Nina",
        "family": "Firese"
      }
    ],
    "title": "Incubation period of ebola hemorrhagic virus subtype zaire",
    "journal": "Osong Public Health and Research Perspectives",
    "year": 2011,
    "pmid": 24159443,
    "doi": "10.1016/j.phrp.2011.04.001"
  },
  "metadata": {
    "units": "days",
    "sample_size": 196,
    "region": "Kikwit, Democratic Republic of Congo",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "The paper reports lower and upper supported ranges for the mean and standard deviation but it is not clear if these are confidence intervals or not so are not included in the database"
},
{
  "disease": "Ebola Virus Disease",
  "pathogen": "Ebola Virus-Zaire Subtype",
  "epi_name": "onset to death",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": {
      "shape": 2.4,
      "shape_ci_limits": [1.1, 4.5],
      "shape_ci": 95,
      "scale": 3.3333,
      "scale_ci_limits": [2, 10],
      "scale_ci": 95
    }
  },
  "summary_statistics": {
    "mean": 9.3,
    "mean_ci_limits": [6.6, 13.6],
    "mean_ci": 95,
    "sd": 6,
    "sd_ci_limits": [4, 11],
    "sd_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "The Ebola Outbreak Epidemiology Team",
        "family": null
      },
      {
        "given": "Ahmadou",
        "family": "Barry"
      },
      {
        "given": "Steve",
        "family": "Ahuka-Mundeke"
      },
      {
        "given":  "Yahaya",
        "family": "Ali Ahmed"
      },
      {
        "given": "Yokouide",
        "family": "Allarangar"
      },
      {
        "given": "Julienne",
        "family": "Anoko"
      },
      {
        "given": "Brett Nicholas",
        "family": "Archer"
      },
      {
        "given": "Aaron Aruna",
        "family": "Abedi"
      },
      {
        "given": "Jayshree",
        "family": "Bagaria"
      },
      {
        "given": "Marie Roseline Darnycka",
        "family": "Belizaire"
      },
      {
        "given": "Sangeeta",
        "family": "Bhatia"
      },
      {
        "given": "Théophile",
        "family": "Bokenge"
      },
      {
        "given": "Emanuele",
        "family": "Bruni"
      },
      {
        "given": "Anne",
        "family": "Cori"
      },
      {
        "given": "Ernest",
        "family": "Dabire"
      },
      {
        "given": "Amadou Mouctar",
        "family": "Diallo"
      },
      {
        "given": "Boubacar",
        "family": "Diallo"
      },
      {
        "given": "Christl Ann",
        "family": "Donnelly"
      },
      {
        "given": "Ilaria",
        "family": "Dorigatti"
      },
      {
        "given": "Tshewang Choden",
        "family": "Dorji"
      },
      {
        "given": "Aura Rocio Escobar Corado",
        "family": "Waeber"
      },
      {
        "given": "Ibrahima Socé",
        "family": "Fall"
      },
      {
        "given": "Neil M.",
        "family": "Ferguson"
      },
      {
        "given": "Richard Gareth",
        "family": "FitzJohn"
      },
      {
        "given": "Gervais Leon Folefack",
        "family": "Tengomo"
      },
      {
        "given": "Pierre Bernard Henri",
        "family": "Formenty"
      },
      {
        "given": "Alpha",
        "family": "Forna"
      },
      {
        "given": "Anne",
        "family": "Fortin"
      },
      {
        "given": "Tini",
        "family": "Garske"
      },
      {
        "given": "Katy A. M.",
        "family": "Gaythorpe"
      },
      {
        "given": "Celine",
        "family": "Gurry"
      },
      {
        "given": "Esther",
        "family": "Hamblion"
      },
      {
        "given": "Mamoudou Harouna",
        "family": "Djingarey"
      },
      {
        "given": "Christopher",
        "family": "Haskew"
      },
      {
        "given": "Stéphane Alexandre Louis",
        "family": "Hugonnet"
      },
      {
        "given": "Natsuko",
        "family": "Imai"
      },
      {
        "given": "Benido",
        "family": "Impouma"
      },
      {
        "given": "Guylain",
        "family": "Kabongo"
      },
      {
        "given": "Oly Ilunga",
        "family": "Kalenga"
      },
      {
        "given": "Emerencienne",
        "family": "Kibangou"
      },
      {
        "given": "Theresa Min-Hyung",
        "family": "Lee"
      },
      {
        "given": "Charles Okot",
        "family": "Lukoya"
      },
      {
        "given": "Ousmane",
        "family": "Ly"
      },
      {
        "given": "Sheila",
        "family": "Makiala-Mandanda"
      },
      {
        "given": "Augustin",
        "family": "Mamba"
      },
      {
        "given": "Placide",
        "family": "Mbala-Kingebeni"
      },
      {
        "given": "Franck Fortune Roland",
        "family": "Mboussou"
      },
      {
        "given": "Tamayi",
        "family": "Mlanda"
      },
      {
        "given": "Vital Mondonge",
        "family": "Makuma"
      },
      {
        "given": "Oliver",
        "family": "Morgan"
      },
      {
        "given": "Anastasie Mujinga",
        "family": "Mulumba"
      },
      {
        "given": "Patrick Mukadi",
        "family": "Kakoni"
      },
      {
        "given": "Daniel",
        "family": "Mukadi-Bamuleka"
      },
      {
        "given": "Jean-Jaques",
        "family": "Muyembe"
      },
      {
        "given": "Ndjoloko Tambwe",
        "family": "Bathé"
      },
      {
        "given": "Patricia",
        "family": "Ndumbi Ngamala"
      },
      {
        "given": "Roland",
        "family": "Ngom"
      },
      {
        "given": "Guillaume",
        "family": "Ngoy"
      },
      {
        "given": "Pierre",
        "family": "Nouvellet"
      },
      {
        "given": "Justus",
        "family": "Nsio"
      },
      {
        "given": "Kevin Babila",
        "family": "Ousman"
      },
      {
        "given": "Emilie",
        "family": "Peron"
      },
      {
        "given": "Jonathan Aaron",
        "family": "Polonsky"
      },
      {
        "given": "Michael J.",
        "family": "Ryan"
      },
      {
        "given": "Alhassane",
        "family": "Touré"
      },
      {
        "given": "Rodney",
        "family": "Towner"
      },
      {
        "given": "Gaston",
        "family": "Tshapenda"
      },
      {
        "given": "Reinhilde",
        "family": "Van De Weerdt"
      },
      {
        "given": "Maria",
        "family": "Van Kerkhove"
      },
      {
        "given": "Annika",
        "family": "Wendland"
      },
      {
        "given": "N'Da Konan Michel",
        "family": "Yao"
      },
      {
        "given": "Zabulon",
        "family": "Yoti"
      },
      {
        "given": "Etienne",
        "family": "Yuma"
      },
      {
        "given": "Guy",
        "family": "Kalambayi Kabamba"
      },
      {
        "given": "Jean de Dieu Lukwesa",
        "family": "Mwati"
      },
      {
        "given": "Gisele",
        "family": "Mbuy"
      },
      {
        "given": "Leopold",
        "family": "Lubula"
      },
      {
        "given": "Anny",
        "family": "Mutombo"
      },
      {
        "given": "Oscar",
        "family": "Mavila"
      },
      {
        "given": "Yyonne",
        "family": "Lay"
      },
      {
        "given": "Emma",
        "family": "Kitenge"
      }
    ],
    "title": "Outbreak of Ebola virus disease in the Democratic Republic of the Congo, April–May, 2018: an epidemiological study",
    "journal": "The Lancet",
    "year": 2018,
    "pmid": 30047375,
    "doi": "10.1016/S0140-6736(18)31387-4"
  },
  "metadata": {
    "units": "days",
    "sample_size": 14,
    "region": "DR Congo",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Data extracted from Appendix. The mean, sd, shape and scale are taken from the paper, the conversion between the two does not match exactly. The data used to estimate the onset-to-death distribution is not from the DRC outbreak but from the west african outbreak."
},
{
  "disease": "Ebola Virus Disease",
  "pathogen": "Ebola Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 10.3,
    "mean_ci_limits": [9.9, 10.7],
    "mean_ci": 95,
    "sd": 8.2,
    "sd_ci_limits": [7.8, 8.6],
    "sd_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "WHO Ebola Response Team",
        "family": null
      },
      {
        "given": "Junerlyn",
        "family": "Agua-Agum"
      },
      {
        "given": "Archchun",
        "family": "Ariyarajah"
      },
      {
        "given": "Bruce",
        "family": "Aylward"
      },
      {
        "given": "Isobel M.",
        "family": "Blake"
      },
      {
        "given": "Richard",
        "family": "Brennan"
      },
      {
        "given": "Anne",
        "family": "Cori"
      },
      {
        "given": "Christl A.",
        "family": "Donnelly"
      },
      {
        "given": "Ilaria",
        "family": "Dorigatti"
      },
      {
        "given": "Christopher",
        "family": "Dye"
      },
      {
        "given": "Tim",
        "family": "Eckmanns"
      },
      {
        "given": "Neil M.",
        "family": "Ferguson"
      },
      {
        "given": "Pierre",
        "family": "Formenty"
      },
      {
        "given": "Christophe",
        "family": "Fraser"
      },
      {
        "given": "Erika",
        "family": "Garcia"
      },
      {
        "given": "Tini",
        "family": "Garske"
      },
      {
        "given": "Wes",
        "family": "Hinsley"
      },
      {
        "given": "David",
        "family": "Holmes"
      },
      {
        "given": "Stéphane",
        "family": "Hugonnet"
      },
      {
        "given": "Swathi",
        "family": "Iyengar"
      },
      {
        "given": "Thibaut",
        "family": "Jombart"
      },
      {
        "given": "Ravi",
        "family": "Krishnan"
      },
      {
        "given": "Sascha",
        "family": "Meijers"
      },
      {
        "given": "Harriet L.",
        "family": "Mills"
      },
      {
        "given": "Yasmine",
        "family": "Mohamed"
      },
      {
        "given": "Gemma",
        "family": "Nedjati-Gilani"
      },
      {
        "given": "Emily",
        "family": "Newton"
      },
      {
        "given": "Pierre",
        "family": "Nouvellet"
      },
      {
        "given": "Louise",
        "family": "Pelletier"
      },
      {
        "given": "Devin",
        "family": "Perkins"
      },
      {
        "given": "Steven",
        "family": "Riley"
      },
      {
        "given": "Maria",
        "family": "Sagrado"
      },
      {
        "given": "Johannes",
        "family": "Schnitzler"
      },
      {
        "given": "Dirk",
        "family": "Schumacher"
      },
      {
        "given": "Anita",
        "family": "Shah"
      },
      {
        "given": "Maria D.",
        "family": "Van Kerkhove"
      },
      {
        "given": "Olivia",
        "family": "Varsaneux"
      },
      {
        "given": "Niluka Wijekoon",
        "family": "Kannangarage"
      }
    ],
    "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control",
    "journal": "The New England Journal of Medicine",
    "year": 2015,
    "pmid": 25539446,
    "doi": "10.1056/NEJMc1414992"
  },
  "metadata": {
    "units": "days",
    "sample_size": 1798,
    "region": "West Africa",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Data extracted from Appendix. This data comes from the entire period of the west africa ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100"
},
{
  "disease": "Ebola Virus Disease",
  "pathogen": "Ebola Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 12.6,
    "mean_ci_limits": [9.1, 17.1],
    "mean_ci": 95,
    "sd": 13.1,
    "sd_ci_limits": [9.6, 19.6],
    "sd_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "WHO Ebola Response Team",
        "family": null
      },
      {
        "given": "Junerlyn",
        "family": "Agua-Agum"
      },
      {
        "given": "Archchun",
        "family": "Ariyarajah"
      },
      {
        "given": "Bruce",
        "family": "Aylward"
      },
      {
        "given": "Isobel M.",
        "family": "Blake"
      },
      {
        "given": "Richard",
        "family": "Brennan"
      },
      {
        "given": "Anne",
        "family": "Cori"
      },
      {
        "given": "Christl A.",
        "family": "Donnelly"
      },
      {
        "given": "Ilaria",
        "family": "Dorigatti"
      },
      {
        "given": "Christopher",
        "family": "Dye"
      },
      {
        "given": "Tim",
        "family": "Eckmanns"
      },
      {
        "given": "Neil M.",
        "family": "Ferguson"
      },
      {
        "given": "Pierre",
        "family": "Formenty"
      },
      {
        "given": "Christophe",
        "family": "Fraser"
      },
      {
        "given": "Erika",
        "family": "Garcia"
      },
      {
        "given": "Tini",
        "family": "Garske"
      },
      {
        "given": "Wes",
        "family": "Hinsley"
      },
      {
        "given": "David",
        "family": "Holmes"
      },
      {
        "given": "Stéphane",
        "family": "Hugonnet"
      },
      {
        "given": "Swathi",
        "family": "Iyengar"
      },
      {
        "given": "Thibaut",
        "family": "Jombart"
      },
      {
        "given": "Ravi",
        "family": "Krishnan"
      },
      {
        "given": "Sascha",
        "family": "Meijers"
      },
      {
        "given": "Harriet L.",
        "family": "Mills"
      },
      {
        "given": "Yasmine",
        "family": "Mohamed"
      },
      {
        "given": "Gemma",
        "family": "Nedjati-Gilani"
      },
      {
        "given": "Emily",
        "family": "Newton"
      },
      {
        "given": "Pierre",
        "family": "Nouvellet"
      },
      {
        "given": "Louise",
        "family": "Pelletier"
      },
      {
        "given": "Devin",
        "family": "Perkins"
      },
      {
        "given": "Steven",
        "family": "Riley"
      },
      {
        "given": "Maria",
        "family": "Sagrado"
      },
      {
        "given": "Johannes",
        "family": "Schnitzler"
      },
      {
        "given": "Dirk",
        "family": "Schumacher"
      },
      {
        "given": "Anita",
        "family": "Shah"
      },
      {
        "given": "Maria D.",
        "family": "Van Kerkhove"
      },
      {
        "given": "Olivia",
        "family": "Varsaneux"
      },
      {
        "given": "Niluka Wijekoon",
        "family": "Kannangarage"
      }
    ],
    "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control",
    "journal": "The New England Journal of Medicine",
    "year": 2015,
    "pmid": 25539446,
    "doi": "10.1056/NEJMc1414992"
  },
  "metadata": {
    "units": "days",
    "sample_size": 49,
    "region": "Guinea",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This data comes from the entire period of the Guinea ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100"
},
{
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      {
        "given": "Archchun",
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      {
        "given": "Bruce",
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      {
        "given": "Isobel M.",
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      {
        "given": "Richard",
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      {
        "given": "Anne",
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        "given": "Christl A.",
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        "given": "Neil M.",
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      {
        "given": "Pierre",
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      {
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      {
        "given": "Erika",
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      {
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        "given": "Wes",
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        "given": "David",
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      {
        "given": "Harriet L.",
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      {
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      {
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      {
        "given": "Emily",
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      {
        "given": "Pierre",
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      {
        "given": "Louise",
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      {
        "given": "Devin",
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      {
        "given": "Steven",
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      {
        "given": "Maria",
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      },
      {
        "given": "Johannes",
        "family": "Schnitzler"
      },
      {
        "given": "Dirk",
        "family": "Schumacher"
      },
      {
        "given": "Anita",
        "family": "Shah"
      },
      {
        "given": "Maria D.",
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      },
      {
        "given": "Olivia",
        "family": "Varsaneux"
      },
      {
        "given": "Niluka Wijekoon",
        "family": "Kannangarage"
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    ],
    "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control",
    "journal": "The New England Journal of Medicine",
    "year": 2015,
    "pmid": 25539446,
    "doi": "10.1056/NEJMc1414992"
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        "given": "Erika",
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      {
        "given": "David",
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      {
        "given": "Harriet L.",
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        "given": "Emily",
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        "given": "Pierre",
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        "given": "Devin",
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      {
        "given": "Maria",
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      {
        "given": "Johannes",
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      {
        "given": "Dirk",
        "family": "Schumacher"
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      {
        "given": "Anita",
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      {
        "given": "Maria D.",
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      {
        "given": "Olivia",
        "family": "Varsaneux"
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      {
        "given": "Niluka Wijekoon",
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    ],
    "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control",
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{
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      {
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      {
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      {
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      {
        "given": "Emily",
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      {
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      {
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      {
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      {
        "given": "Anita",
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      {
        "given": "Maria D.",
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      {
        "given": "Olivia",
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      {
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{
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      {
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      {
        "given": "Christl A.",
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        "given": "Ilaria",
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      {
        "given": "Christopher",
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        "given": "Neil M.",
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        "given": "Christophe",
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      {
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      {
        "given": "Sascha",
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      {
        "given": "Harriet L.",
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      {
        "given": "Yasmine",
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      {
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      {
        "given": "Emily",
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      {
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      {
        "given": "Louise",
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        "given": "Dirk",
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      {
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      {
        "given": "Maria D.",
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      {
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      {
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},
{
  "disease": "Ebola Virus Disease",
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        "given": "Johannes",
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      {
        "given": "Dirk",
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      {
        "given": "Anita",
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      {
        "given": "Maria D.",
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        "given": "Olivia",
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      {
        "given": "Niluka Wijekoon",
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      {
        "given": "Anne",
        "family": "Cori"
      },
      {
        "given": "Christl A.",
        "family": "Donnelly"
      },
      {
        "given": "Ilaria",
        "family": "Dorigatti"
      },
      {
        "given": "Christopher",
        "family": "Dye"
      },
      {
        "given": "Tim",
        "family": "Eckmanns"
      },
      {
        "given": "Neil M.",
        "family": "Ferguson"
      },
      {
        "given": "Pierre",
        "family": "Formenty"
      },
      {
        "given": "Christophe",
        "family": "Fraser"
      },
      {
        "given": "Erika",
        "family": "Garcia"
      },
      {
        "given": "Tini",
        "family": "Garske"
      },
      {
        "given": "Wes",
        "family": "Hinsley"
      },
      {
        "given": "David",
        "family": "Holmes"
      },
      {
        "given": "Stéphane",
        "family": "Hugonnet"
      },
      {
        "given": "Swathi",
        "family": "Iyengar"
      },
      {
        "given": "Thibaut",
        "family": "Jombart"
      },
      {
        "given": "Ravi",
        "family": "Krishnan"
      },
      {
        "given": "Sascha",
        "family": "Meijers"
      },
      {
        "given": "Harriet L.",
        "family": "Mills"
      },
      {
        "given": "Yasmine",
        "family": "Mohamed"
      },
      {
        "given": "Gemma",
        "family": "Nedjati-Gilani"
      },
      {
        "given": "Emily",
        "family": "Newton"
      },
      {
        "given": "Pierre",
        "family": "Nouvellet"
      },
      {
        "given": "Louise",
        "family": "Pelletier"
      },
      {
        "given": "Devin",
        "family": "Perkins"
      },
      {
        "given": "Steven",
        "family": "Riley"
      },
      {
        "given": "Maria",
        "family": "Sagrado"
      },
      {
        "given": "Johannes",
        "family": "Schnitzler"
      },
      {
        "given": "Dirk",
        "family": "Schumacher"
      },
      {
        "given": "Anita",
        "family": "Shah"
      },
      {
        "given": "Maria D.",
        "family": "Van Kerkhove"
      },
      {
        "given": "Olivia",
        "family": "Varsaneux"
      },
      {
        "given": "Niluka Wijekoon",
        "family": "Kannangarage"
      }
    ],
    "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control",
    "journal": "The New England Journal of Medicine",
    "year": 2015,
    "pmid": 25539446,
    "doi": "10.1056/NEJMc1414992"
  },
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    "sample_size": 2741,
    "region": "West Africa",
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  "notes": "This data comes from the entire period of the west africa ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100"
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{
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    "prob_distribution": "gamma",
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    "mean_ci_limits": [14.6, 15.6],
    "mean_ci": 95,
    "sd": 8.9,
    "sd_ci_limits": [8.5, 9.3],
    "sd_ci": 95
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    "author": [
      {
        "given": "WHO Ebola Response Team",
        "family": null
      },
      {
        "given": "Junerlyn",
        "family": "Agua-Agum"
      },
      {
        "given": "Archchun",
        "family": "Ariyarajah"
      },
      {
        "given": "Bruce",
        "family": "Aylward"
      },
      {
        "given": "Isobel M.",
        "family": "Blake"
      },
      {
        "given": "Richard",
        "family": "Brennan"
      },
      {
        "given": "Anne",
        "family": "Cori"
      },
      {
        "given": "Christl A.",
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      },
      {
        "given": "Ilaria",
        "family": "Dorigatti"
      },
      {
        "given": "Christopher",
        "family": "Dye"
      },
      {
        "given": "Tim",
        "family": "Eckmanns"
      },
      {
        "given": "Neil M.",
        "family": "Ferguson"
      },
      {
        "given": "Pierre",
        "family": "Formenty"
      },
      {
        "given": "Christophe",
        "family": "Fraser"
      },
      {
        "given": "Erika",
        "family": "Garcia"
      },
      {
        "given": "Tini",
        "family": "Garske"
      },
      {
        "given": "Wes",
        "family": "Hinsley"
      },
      {
        "given": "David",
        "family": "Holmes"
      },
      {
        "given": "Stéphane",
        "family": "Hugonnet"
      },
      {
        "given": "Swathi",
        "family": "Iyengar"
      },
      {
        "given": "Thibaut",
        "family": "Jombart"
      },
      {
        "given": "Ravi",
        "family": "Krishnan"
      },
      {
        "given": "Sascha",
        "family": "Meijers"
      },
      {
        "given": "Harriet L.",
        "family": "Mills"
      },
      {
        "given": "Yasmine",
        "family": "Mohamed"
      },
      {
        "given": "Gemma",
        "family": "Nedjati-Gilani"
      },
      {
        "given": "Emily",
        "family": "Newton"
      },
      {
        "given": "Pierre",
        "family": "Nouvellet"
      },
      {
        "given": "Louise",
        "family": "Pelletier"
      },
      {
        "given": "Devin",
        "family": "Perkins"
      },
      {
        "given": "Steven",
        "family": "Riley"
      },
      {
        "given": "Maria",
        "family": "Sagrado"
      },
      {
        "given": "Johannes",
        "family": "Schnitzler"
      },
      {
        "given": "Dirk",
        "family": "Schumacher"
      },
      {
        "given": "Anita",
        "family": "Shah"
      },
      {
        "given": "Maria D.",
        "family": "Van Kerkhove"
      },
      {
        "given": "Olivia",
        "family": "Varsaneux"
      },
      {
        "given": "Niluka Wijekoon",
        "family": "Kannangarage"
      }
    ],
    "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control",
    "journal": "The New England Journal of Medicine",
    "year": 2015,
    "pmid": 25539446,
    "doi": "10.1056/NEJMc1414992"
  },
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    "units": "days",
    "sample_size": 1335,
    "region": "West Africa",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
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    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
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  "notes": "This data comes from the entire period of the west africa ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100"
},
{
  "disease": "MERS",
  "pathogen": "MERS-Cov",
  "epi_name": "incubation period",
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    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [2.2, 12.4],
    "quantile_names": ["5", "95"],
    "median": 5.2,
    "median_ci_limits": [1.9, 14.7],
    "median_ci": null
  },
  "citation": {
    "author": [
      {
        "given": "Abdullah",
        "family": "Assiri"
      },
      {
        "given": "Allison",
        "family": "McGeer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Connie S.",
        "family": "Price"
      },
      {
        "given": "Abdullah A.",
        "family": "Al Rabeeah"
      },
      {
        "given": "Derek A.T.",
        "family": "Cummings"
      },
      {
        "given": "Zaki N.",
        "family": "Alabdullatif"
      },
      {
        "given": "Maher",
        "family": "Assad"
      },
      {
        "given": "Abdulmohsen",
        "family": "Almulhim"
      },
      {
        "given": "Hatem",
        "family": "Makhdoom"
      },
      {
        "given": "Hossam",
        "family": "Madani"
      },
      {
        "given": "Rafat",
        "family": "Alhakeem"
      },
      {
        "given": "Jaffar A.",
        "family": "Al-Tawfiq"
      },
      {
        "given": "Matthew",
        "family": "Cotten"
      },
      {
        "given": "Simon J.",
        "family": "Watson"
      },
      {
        "given": "Paul",
        "family": "Kellam"
      },
      {
        "given": "Alimuddin I.",
        "family": "Zumla"
      },
      {
        "given": "Ziad A.",
        "family": "Memish"
      },
      {
        "given": "KSA MERSCOV Investigation Team",
        "family": null
      }
    ],
    "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus",
    "journal": "The New England Journal of Medicine",
    "year": 2013,
    "pmid": 23782161,
    "doi": "10.1056/NEJMoa1306742"
  },
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    "units": "days",
    "sample_size": 23,
    "region": "Saudi Arabia",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
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    "discretised": false,
    "censored": true,
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    "phase_bias_adjusted": false
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  "notes": "The sample size is not explicitly stated. The number of confirmed cases is 23 and there are 2 suspected cases, therefore it is not clear whether the 2 suspected cases were included in the estimation, the sample size is assumed to be 23."
},
{
  "disease": "MERS",
  "pathogen": "MERS-Cov",
  "epi_name": "serial interval",
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    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [3, 19.4],
    "quantile_names": ["5", "95"],
    "median": 7.6,
    "median_ci_limits": [2.5, 23.1],
    "median_ci": null
  },
  "citation": {
    "author": [
      {
        "given": "Abdullah",
        "family": "Assiri"
      },
      {
        "given": "Allison",
        "family": "McGeer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Connie S.",
        "family": "Price"
      },
      {
        "given": "Abdullah A.",
        "family": "Al Rabeeah"
      },
      {
        "given": "Derek A.T.",
        "family": "Cummings"
      },
      {
        "given": "Zaki N.",
        "family": "Alabdullatif"
      },
      {
        "given": "Maher",
        "family": "Assad"
      },
      {
        "given": "Abdulmohsen",
        "family": "Almulhim"
      },
      {
        "given": "Hatem",
        "family": "Makhdoom"
      },
      {
        "given": "Hossam",
        "family": "Madani"
      },
      {
        "given": "Rafat",
        "family": "Alhakeem"
      },
      {
        "given": "Jaffar A.",
        "family": "Al-Tawfiq"
      },
      {
        "given": "Matthew",
        "family": "Cotten"
      },
      {
        "given": "Simon J.",
        "family": "Watson"
      },
      {
        "given": "Paul",
        "family": "Kellam"
      },
      {
        "given": "Alimuddin I.",
        "family": "Zumla"
      },
      {
        "given": "Ziad A.",
        "family": "Memish"
      },
      {
        "given": "KSA MERSCOV Investigation Team",
        "family": null
      }
    ],
    "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus",
    "journal": "The New England Journal of Medicine",
    "year": 2013,
    "pmid": 23782161,
    "doi": "10.1056/NEJMoa1306742"
  },
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    "sample_size": 23,
    "region": "Saudi Arabia",
    "transmission_mode": "natural_natural_human_to_human",
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    "censored": true,
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    "phase_bias_adjusted": false
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  "notes": "The sample size is not explicitly stated. The number of confirmed cases is 23 and there are 2 suspected cases, therefore it is not clear whether the 2 suspected cases were included in the estimation, the sample size is assumed to be 23."
},
{
  "disease": "MERS",
  "pathogen": "MERS-Cov",
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    "prob_distribution": null,
    "parameters": { }
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    "lower_range": 1,
    "upper_range": 10
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        "given": "Abdullah",
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      {
        "given": "Allison",
        "family": "McGeer"
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      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Connie S.",
        "family": "Price"
      },
      {
        "given": "Abdullah A.",
        "family": "Al Rabeeah"
      },
      {
        "given": "Derek A.T.",
        "family": "Cummings"
      },
      {
        "given": "Zaki N.",
        "family": "Alabdullatif"
      },
      {
        "given": "Maher",
        "family": "Assad"
      },
      {
        "given": "Abdulmohsen",
        "family": "Almulhim"
      },
      {
        "given": "Hatem",
        "family": "Makhdoom"
      },
      {
        "given": "Hossam",
        "family": "Madani"
      },
      {
        "given": "Rafat",
        "family": "Alhakeem"
      },
      {
        "given": "Jaffar A.",
        "family": "Al-Tawfiq"
      },
      {
        "given": "Matthew",
        "family": "Cotten"
      },
      {
        "given": "Simon J.",
        "family": "Watson"
      },
      {
        "given": "Paul",
        "family": "Kellam"
      },
      {
        "given": "Alimuddin I.",
        "family": "Zumla"
      },
      {
        "given": "Ziad A.",
        "family": "Memish"
      },
      {
        "given": "KSA MERSCOV Investigation Team",
        "family": null
      }
    ],
    "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus",
    "journal": "The New England Journal of Medicine",
    "year": 2013,
    "pmid": 23782161,
    "doi": "10.1056/NEJMoa1306742"
  },
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    "phase_bias_adjusted": false
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},
{
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  "pathogen": "MERS-Cov",
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    "parameters": { }
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      {
        "given": "Allison",
        "family": "McGeer"
      },
      {
        "given": "Trish M.",
        "family": "Perl"
      },
      {
        "given": "Connie S.",
        "family": "Price"
      },
      {
        "given": "Abdullah A.",
        "family": "Al Rabeeah"
      },
      {
        "given": "Derek A.T.",
        "family": "Cummings"
      },
      {
        "given": "Zaki N.",
        "family": "Alabdullatif"
      },
      {
        "given": "Maher",
        "family": "Assad"
      },
      {
        "given": "Abdulmohsen",
        "family": "Almulhim"
      },
      {
        "given": "Hatem",
        "family": "Makhdoom"
      },
      {
        "given": "Hossam",
        "family": "Madani"
      },
      {
        "given": "Rafat",
        "family": "Alhakeem"
      },
      {
        "given": "Jaffar A.",
        "family": "Al-Tawfiq"
      },
      {
        "given": "Matthew",
        "family": "Cotten"
      },
      {
        "given": "Simon J.",
        "family": "Watson"
      },
      {
        "given": "Paul",
        "family": "Kellam"
      },
      {
        "given": "Alimuddin I.",
        "family": "Zumla"
      },
      {
        "given": "Ziad A.",
        "family": "Memish"
      },
      {
        "given": "KSA MERSCOV Investigation Team",
        "family": null
      }
    ],
    "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus",
    "journal": "The New England Journal of Medicine",
    "year": 2013,
    "pmid": 23782161,
    "doi": "10.1056/NEJMoa1306742"
  },
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},
{
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    "parameters": { }
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      {
        "given": "Allison",
        "family": "McGeer"
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      {
        "given": "Trish M.",
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      },
      {
        "given": "Connie S.",
        "family": "Price"
      },
      {
        "given": "Abdullah A.",
        "family": "Al Rabeeah"
      },
      {
        "given": "Derek A.T.",
        "family": "Cummings"
      },
      {
        "given": "Zaki N.",
        "family": "Alabdullatif"
      },
      {
        "given": "Maher",
        "family": "Assad"
      },
      {
        "given": "Abdulmohsen",
        "family": "Almulhim"
      },
      {
        "given": "Hatem",
        "family": "Makhdoom"
      },
      {
        "given": "Hossam",
        "family": "Madani"
      },
      {
        "given": "Rafat",
        "family": "Alhakeem"
      },
      {
        "given": "Jaffar A.",
        "family": "Al-Tawfiq"
      },
      {
        "given": "Matthew",
        "family": "Cotten"
      },
      {
        "given": "Simon J.",
        "family": "Watson"
      },
      {
        "given": "Paul",
        "family": "Kellam"
      },
      {
        "given": "Alimuddin I.",
        "family": "Zumla"
      },
      {
        "given": "Ziad A.",
        "family": "Memish"
      },
      {
        "given": "KSA MERSCOV Investigation Team",
        "family": null
      }
    ],
    "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus",
    "journal": "The New England Journal of Medicine",
    "year": 2013,
    "pmid": 23782161,
    "doi": "10.1056/NEJMoa1306742"
  },
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    "transmission_mode": "natural_natural_human_to_human",
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    "phase_bias_adjusted": false
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},
{
  "disease": "MERS",
  "pathogen": "MERS-Cov",
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    "parameters": { }
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        "family": "Mizumoto"
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      {
        "given": "Akira",
        "family": "Endo"
      },
      {
        "given": "Gerardo",
        "family": "Chowell"
      },
      {
        "given": "Yuichiro",
        "family": "Miyamatsu"
      },
      {
        "given": "Masaya",
        "family": "Saitoh"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Real-time characterization of risks of death associated with the Middle East respiratory syndrome (MERS) in the Republic of Korea, 2015",
    "journal": "BMC Medicine",
    "year": 2015,
    "pmid": 26420593,
    "doi": "10.1186/s12916-015-0468-3"
  },
  "metadata": {
    "units": "days",
    "sample_size": 185,
    "region": "South Korea",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "The distribution parameters were jointly inferred with the risk factors of mortality."
},
{
  "disease": "MERS",
  "pathogen": "MERS-Cov",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 6.7,
    "mean_ci_limits": [6.1, 7.3],
    "mean_ci": 95,
    "median": 6.3,
    "median_ci_limits": [5.7, 6.8],
    "median_ci": 95,
    "quantile_values": [12.1],
    "quantile_names": ["95"]
  },
  "citation": {
    "author": [
      {
        "given": "B. J.",
        "family": "Cowling"
      },
      {
        "given": "M.",
        "family": "Park"
      },
      {
        "given": "V. J.",
        "family": "Fang"
      },
      {
        "given": "P.",
        "family": "Wu"
      },
      {
        "given": "G. M.",
        "family": "Leung"
      },
      {
        "given": "J. T.",
        "family": "Wu"
      }
    ],
    "title": "Preliminary epidemiological assessment of MERS-CoV outbreak in South Korea, May to June 2015",
    "journal": "Eurosurveillance",
    "year": 2015,
    "pmid": 26132767,
    "doi": "10.2807/1560-7917.es2015.20.25.21163"
  },
  "metadata": {
    "units": "days",
    "sample_size": 166,
    "region": "South Korea",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "MERS",
  "pathogen": "MERS-Cov",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 12.6,
    "mean_ci_limits": [12.1, 13.1],
    "mean_ci": 95,
    "sd": 2.8,
    "sd_ci_limits": [2.4, 3.1],
    "sd_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "B. J.",
        "family": "Cowling"
      },
      {
        "given": "M.",
        "family": "Park"
      },
      {
        "given": "V. J.",
        "family": "Fang"
      },
      {
        "given": "P.",
        "family": "Wu"
      },
      {
        "given": "G. M.",
        "family": "Leung"
      },
      {
        "given": "J. T.",
        "family": "Wu"
      }
    ],
    "title": "Preliminary epidemiological assessment of MERS-CoV outbreak in South Korea, May to June 2016",
    "journal": "Eurosurveillance",
    "year": 2015,
    "pmid": 26132767,
    "doi": "10.2807/1560-7917.es2015.20.25.21163"
  },
  "metadata": {
    "units": "days",
    "sample_size": 99,
    "region": "South Korea",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 5.84,
    "mean_ci_limits": [5.07, 6.55],
    "mean_ci": 95,
    "sd": 2.98,
    "sd_ci_limits": [2.31, 3.72],
    "sd_ci": 95,
    "quantile_values": [2.69, 12.89],
    "quantile_names": ["2.5", "97.5"],
    "median": 5.01,
    "median_ci_limits": [4, 6],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Ke",
        "family": "Men"
      },
      {
        "given": "Xia",
        "family": "Wang"
      },
      {
        "given": "Li",
        "family": "Yihao"
      },
      {
        "given": "Guangwei",
        "family": "Zhang"
      },
      {
        "given": "Jingjing",
        "family": "Hu"
      },
      {
        "given": "Yanyan",
        "family": "Gao"
      },
      {
        "given": "Henry",
        "family": "Han"
      }
    ],
    "title": "Estimate the incubation period of coronavirus 2019 (COVID-19)",
    "journal": "medRxiv",
    "year": 2020,
    "pmid": null,
    "doi": "10.1101/2020.02.24.20027474"
  },
  "metadata": {
    "units": "days",
    "sample_size": 59,
    "region": "China",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "The estimate of the incubation period is from a non-parametric bootstrap approach that does not fit a parametric distribution."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 5.74,
    "mean_ci_limits": [5.18, 6.3],
    "mean_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Balram",
        "family": "Rai"
      },
      {
        "given": "Anandi",
        "family": "Shukla"
      },
      {
        "given": "Laxmi Kant",
        "family": "Dwivedi"
      }
    ],
    "title": "Incubation period for COVID-19: a systematic review and meta-analysis",
    "journal": "Zeitschrift fur Gesundheitswissenschaften",
    "year": 2022,
    "pmid": 33643779,
    "doi": "10.1007/s10389-021-01478-1"
  },
  "metadata": {
    "units": "days",
    "sample_size": 6241,
    "region": "Mixed",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This estimated mean incubation period is from a meta-analysis of 15 other incubation period estimates. Only the mean is reported and a distribution cannot be specified as the meta-mean is estimated from a random-effects model."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 6.5,
    "mean_ci_limits": [5.9, 7.1],
    "mean_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Muluneh",
        "family": "Alene"
      },
      {
        "given": "Leltework",
        "family": "Yismaw"
      },
      {
        "given": "Moges Agazhe",
        "family": "Assemie"
      },
      {
        "given": "Daniel Bekele",
        "family": "Ketema"
      },
      {
        "given": "Wodaje",
        "family": "Gietaneh"
      },
      {
        "given": "Tilahun Yemanu",
        "family": "Birhan"
      }
    ],
    "title": "Serial interval and incubation period of COVID-19: a systematic review and meta-analysis",
    "journal": "BMC Infectious Diseases",
    "year": 2021,
    "pmid": 33706702,
    "doi": "10.1186/s12879-021-05950-x"
  },
  "metadata": {
    "units": "days",
    "sample_size": 1453,
    "region": "Mixed",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This estimated mean incubation period is from a meta-analysis of 14 other incubation period estimates. Only the mean is reported and a distribution cannot be specified as the meta-mean is estimated from a random-effects model."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 5.2,
    "mean_ci_limits": [4.9, 5.5],
    "mean_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Muluneh",
        "family": "Alene"
      },
      {
        "given": "Leltework",
        "family": "Yismaw"
      },
      {
        "given": "Moges Agazhe",
        "family": "Assemie"
      },
      {
        "given": "Daniel Bekele",
        "family": "Ketema"
      },
      {
        "given": "Wodaje",
        "family": "Gietaneh"
      },
      {
        "given": "Tilahun Yemanu",
        "family": "Birhan"
      }
    ],
    "title": "Serial interval and incubation period of COVID-19: a systematic review and meta-analysis",
    "journal": "BMC Infectious Diseases",
    "year": 2021,
    "pmid": 33706702,
    "doi": "10.1186/s12879-021-05950-x"
  },
  "metadata": {
    "units": "days",
    "sample_size": 3924,
    "region": "Mixed",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This estimated mean serial interval is from a meta-analysis of 23 other serial interval estimates. Only the mean is reported and a distribution cannot be specified as the meta-mean is estimated from a random-effects model."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 4.7,
    "mean_ci_limits": [3.7, 6.0],
    "mean_ci": 95,
    "sd": 2.9,
    "sd_ci_limits": [1.9, 4.9],
    "sd_ci": 95,
    "median": 4.0,
    "median_ci_limits": [3.1, 4.9],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      },
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      }
    ],
    "title": "Serial interval of novel coronavirus (COVID-19) infections",
    "journal": "International Journal of Infectious Diseases",
    "year": 2020,
    "pmid": 32145466,
    "doi": "10.1016/j.ijid.2020.02.060"
  },
  "metadata": {
    "units": "days",
    "sample_size": 28,
    "region": "Mixed",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": true,
    "phase_bias_adjusted": false
  },
  "notes": "These estimates are from fitting to the entire dataset of contact pairs, including pairs that are uncertain."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": "weibull",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 4.8,
    "mean_ci_limits": [3.8, 6.1],
    "mean_ci": 95,
    "sd": 2.3,
    "sd_ci_limits": [1.6, 3.5],
    "sd_ci": 95,
    "median": 4.6,
    "median_ci_limits": [3.5, 5.9],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      },
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      }
    ],
    "title": "Serial interval of novel coronavirus (COVID-19) infections",
    "journal": "International Journal of Infectious Diseases",
    "year": 2020,
    "pmid": 32145466,
    "doi": "10.1016/j.ijid.2020.02.060"
  },
  "metadata": {
    "units": "days",
    "sample_size": 18,
    "region": "Mixed",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": true,
    "phase_bias_adjusted": false
  },
  "notes": "These estimates are from fitting to a subset of the dataset of contact pairs, only including pairs that are the most certain."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "weibull",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [1, 1.1, 13.7, 15, 17.8],
    "quantile_names": ["2.5", "5", "95", "97.5", "99"],
    "median": 5.4,
    "median_ci_limits": [4.8, 6.0],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Lin",
        "family": "Yang"
      },
      {
        "given": "Jingyi",
        "family": "Dai"
      },
      {
        "given": "Jun",
        "family": "Zhao"
      },
      {
        "given": "Yunfu",
        "family": "Wang"
      },
      {
        "given": "Pingji",
        "family": "Deng"
      },
      {
        "given": "Jing",
        "family": "Wang"
      }
    ],
    "title": "Estimation of incubation period and serial interval of COVID-19: analysis of 178 cases and 131 transmission chains in Hubei province, China",
    "journal": "Epidemiology and Infection",
    "year": 2020,
    "pmid": 32594928,
    "doi": "10.1017/S0950268820001338"
  },
  "metadata": {
    "units": "days",
    "sample_size": 178,
    "region": "Hubei province, China",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": "norm",
    "parameters": {
      "mean": 4.6,
      "mean_ci_limits": [3.7, 5.5],
      "mean_ci": 95,
       "sd": 4.4,
       "sd_ci_limits": [3.8, 5.0],
       "sd_ci": 95
    }
  },
  "summary_statistics": {
    "quantile_values": [11.8, 14.8],
    "quantile_names": ["95", "99"],
    "median": 4.6
  },
  "citation": {
    "author": [
      {
        "given": "Lin",
        "family": "Yang"
      },
      {
        "given": "Jingyi",
        "family": "Dai"
      },
      {
        "given": "Jun",
        "family": "Zhao"
      },
      {
        "given": "Yunfu",
        "family": "Wang"
      },
      {
        "given": "Pingji",
        "family": "Deng"
      },
      {
        "given": "Jing",
        "family": "Wang"
      }
    ],
    "title": "Estimation of incubation period and serial interval of COVID-19: analysis of 178 cases and 131 transmission chains in Hubei province, China",
    "journal": "Epidemiology and Infection",
    "year": 2020,
    "pmid": 32594928,
    "doi": "10.1017/S0950268820001338"
  },
  "metadata": {
    "units": "days",
    "sample_size": 131,
    "region": "Hubei province, China",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 6.38,
    "mean_ci_limits": [5.79, 6.97],
    "mean_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Christelle",
        "family": "Elias"
      },
      {
        "given": "Abel",
        "family": "Sekri"
      },
      {
        "given": "Pierre",
        "family": "Leblanc"
      },
      {
        "given": "Michel",
        "family": "Cucherat"
      },
      {
        "given": "Philippe",
        "family": "Vanhems"
      }
    ],
    "title": "The incubation period of COVID-19: A meta-analysis",
    "journal": "International Journal of Infectious Diseases",
    "year": 2021,
    "pmid": 33548553,
    "doi": "10.1016/j.ijid.2021.01.069"
  },
  "metadata": {
    "units": "days",
    "sample_size": 28675,
    "region": "Mixed",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This estimated mean incubation period is from a meta-analysis of 99 other incubation period estimates. Only the mean is reported and a distribution cannot be specified as the meta-mean is estimated from a random-effects model."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "weibull",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 6.4,
    "mean_ci_limits": [4.89, 8.5],
    "mean_ci": 95,
    "sd": 3.05,
    "sd_ci_limits": [3.05, 5.3],
    "sd_ci": 95,
    "quantile_values": [1.35, 1.9, 11.9, 13.04],
    "quantile_names": ["2.5", "5", "95", "97.5"],
    "median": 6.1
  },
  "citation": {
    "author": [
      {
        "given": "Long V.",
        "family": "Bui"
      },
      {
        "given": "Ha T.",
        "family": "Nguyen"
      },
      {
        "given": "Hagai",
        "family": "Levine"
      },
      {
        "given": "Ha N.",
        "family": "Nguyen"
      },
      {
        "given": "Thu-Anh",
        "family": "Nguyen"
      },
      {
        "given": "Thuy P.",
        "family": "Nguyen"
      },
      {
        "given": "Truong T.",
        "family": "Nguyen"
      },
      {
        "given": "Toan T. T.",
        "family": "Do"
      },
      {
        "given": "Ngoc T.",
        "family": "Pham"
      },
      {
        "given": "My Hanh",
        "family": "Bui"
      }
    ],
    "title": "Estimation of the incubation period of COVID-19 in Vietnam",
    "journal": "PLoS One",
    "year": 2020,
    "pmid": 33362233,
    "doi": "10.1371/journal.pone.0243889"
  },
  "metadata": {
    "units": "days",
    "sample_size": 19,
    "region": "Vietnam",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes"
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": {
      "meanlog": 1.66,
      "meanlog_ci_limits": [1.55, 1.76],
      "meanlog_ci": 95,
      "sdlog": 0.48,
      "sdlog_ci_limits": [0.42, 0.54],
      "sdlog_ci": 95
    }
  },
  "summary_statistics": { },
  "citation": {
    "author": [
      {
        "given": "Conor",
        "family": "McAloon"
      },
      {
        "given": "Áine",
        "family": "Collins"
      },
      {
        "given": "Kevin",
        "family": "Hunt"
      },
      {
        "given": "Ann",
        "family": "Barber"
      },
      {
        "given": "Andrew W.",
        "family": "Byrne"
      },
      {
        "given": "Francis",
        "family": "Butler"
      },
      {
        "given": "Miriam",
        "family": "Casey"
      },
      {
        "given": "John",
        "family": "Griffin"
      },
      {
        "given": "Elizabeth",
        "family": "Lane"
      },
      {
        "given": "David",
        "family": "McEvoy"
      },
      {
        "given": "Patrick",
        "family": "Wall"
      },
      {
        "given": "Martin",
        "family": "Green"
      },
      {
        "given": "Luke",
        "family": "O'Grady"
      },
      {
        "given": "Simon J.",
        "family": "More"
      }
    ],
    "title": "Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research",
    "journal": "BMJ Open",
    "year": 2020,
    "pmid": 32801208,
    "doi": "10.1136/bmjopen-2020-039652"
  },
  "metadata": {
    "units": "days",
    "sample_size": 1357,
    "region": "Mixed",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
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  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "The incubation period parameters are estimated from a meta-analysis of other studies that estimated the incubation period using a lognormal distribution. This is the full set of data (N=9)."
},
{
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  "pathogen": "SARS-CoV-2",
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      "meanlog_ci_limits": [1.51, 1.75],
      "meanlog_ci": 95,
      "sdlog": 0.5,
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      "sdlog_ci": 95
    }
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    "mean_ci_limits": [5, 6.7],
    "mean_ci": 95,
    "median": 5.1,
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    "median_ci": 95,
    "quantile_values": [11.7],
    "quantile_names": ["95"]
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  "citation": {
    "author": [
      {
        "given": "Conor",
        "family": "McAloon"
      },
      {
        "given": "Áine",
        "family": "Collins"
      },
      {
        "given": "Kevin",
        "family": "Hunt"
      },
      {
        "given": "Ann",
        "family": "Barber"
      },
      {
        "given": "Andrew W.",
        "family": "Byrne"
      },
      {
        "given": "Francis",
        "family": "Butler"
      },
      {
        "given": "Miriam",
        "family": "Casey"
      },
      {
        "given": "John",
        "family": "Griffin"
      },
      {
        "given": "Elizabeth",
        "family": "Lane"
      },
      {
        "given": "David",
        "family": "McEvoy"
      },
      {
        "given": "Patrick",
        "family": "Wall"
      },
      {
        "given": "Martin",
        "family": "Green"
      },
      {
        "given": "Luke",
        "family": "O'Grady"
      },
      {
        "given": "Simon J.",
        "family": "More"
      }
    ],
    "title": "Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research",
    "journal": "BMJ Open",
    "year": 2020,
    "pmid": 32801208,
    "doi": "10.1136/bmjopen-2020-039652"
  },
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    "sample_size": 1269,
    "region": "Mixed",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "The incubation period parameters are estimated from a meta-analysis of other studies that estimated the incubation period using a lognormal distribution. This is the data set with Backer removed as they did not have a defined exposure window (N=8)."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
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    "prob_distribution": "lnorm",
    "parameters": { }
  },
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    "mean": 5,
    "mean_ci_limits": [4.2, 6],
    "mean_ci": 95,
    "sd": 3,
    "sd_ci_limits": [2.1, 4.5],
    "sd_ci": 95,
    "quantile_values": [1.7, 10.6],
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    "median_ci": 95
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  "citation": {
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      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Tetsuro",
        "family": "Kobayashi"
      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
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    "units": "days",
    "sample_size": 52,
    "region": "China",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This dataset excludes Wuhan residents (to have a more precise exposure interval). This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions."
},
{
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  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
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    "mean_ci_limits": [5, 6.3],
    "mean_ci": 95,
    "sd": 2.8,
    "sd_ci_limits": [2.2, 3.6],
    "sd_ci": 95,
    "quantile_values": [2.3, 10.8],
    "quantile_names": ["5", "95"],
    "median": 5,
    "median_ci_limits": [4.4, 5.6],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Tetsuro",
        "family": "Kobayashi"
      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
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    "units": "days",
    "sample_size": 158,
    "region": "China",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This dataset includes Wuhan residents (which have a less precise exposure interval). This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "onset to hospitalisation",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 3.3,
    "mean_ci_limits": [2.7, 4],
    "mean_ci": 95,
    "sd": 4.2,
    "sd_ci_limits": [3.3, 5.4],
    "sd_ci": 95,
    "quantile_values": [0, 11.6],
    "quantile_names": ["5", "95"],
    "median": 1.7,
    "median_ci_limits": [1.2, 2.2],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Tetsuro",
        "family": "Kobayashi"
      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
  "metadata": {
    "units": "days",
    "sample_size": 155,
    "region": "China",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "onset to hospitalisation",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 6.5,
    "mean_ci_limits": [5.2, 8],
    "mean_ci": 95,
    "sd": 4.3,
    "sd_ci_limits": [2.9, 5.6],
    "sd_ci": 95,
    "quantile_values": [1.9, 13.9],
    "quantile_names": ["5", "95"],
    "median": 5.1,
    "median_ci_limits": [4.1, 6.3],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Tetsuro",
        "family": "Kobayashi"
      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
  "metadata": {
    "units": "days",
    "sample_size": 34,
    "region": "China",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "onset to death",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 14.5,
    "mean_ci_limits": [12.5, 17],
    "mean_ci": 95,
    "sd": 6.7,
    "sd_ci_limits": [4.9, 9.4],
    "sd_ci": 95,
    "quantile_values": [6.5, 26.8],
    "quantile_names": ["5", "95"],
    "median": 13.2,
    "median_ci_limits": [11.3, 15.3],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Tetsuro",
        "family": "Kobayashi"
      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
  "metadata": {
    "units": "days",
    "sample_size": 34,
    "region": "China",
    "transmission_mode": "natural_natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "hospitalisation to death",
  "probability_distribution": {
    "prob_distribution": "weibull",
    "parameters": { }
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  "summary_statistics": {
    "mean": 8.9,
    "mean_ci_limits": [7.3, 10.4],
    "mean_ci": 95,
    "sd": 5.7,
    "sd_ci_limits": [4.3, 7.8],
    "sd_ci": 95,
    "quantile_values": [1.7, 18.8],
    "quantile_names": ["5", "95"],
    "median": 8,
    "median_ci_limits": [6.2, 9.8],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Tetsuro",
        "family": "Kobayashi"
      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
  "metadata": {
    "units": "days",
    "sample_size": 39,
    "region": "China",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 5.6,
    "mean_ci_limits": [4.4, 4.8],
    "mean_ci": 95,
    "sd": 3.9,
    "sd_ci_limits": [2.4, 6.9],
    "sd_ci": 95,
    "quantile_values": [1.7, 12.3],
    "quantile_names": ["5", "95"],
    "median": 4.6,
    "median_ci_limits": [3.7, 5.7],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Tetsuro",
        "family": "Kobayashi"
      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
  "metadata": {
    "units": "days",
    "sample_size": 52,
    "region": "China",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": true,
    "phase_bias_adjusted": true
  },
  "notes": "This is excluding Wuhan residents from the dataset as this provides a more precise exposure interval. This method applies right-truncation but only fits a lognormal distribution."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "onset to hospitalisation",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
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    "mean_ci_limits": [5.4, 17],
    "mean_ci": 95,
    "sd": 35.2,
    "sd_ci_limits": [12.9, 84.5],
    "sd_ci": 95,
    "quantile_values": [0.2, 35.1],
    "quantile_names": ["5", "95"],
    "median": 2.6,
    "median_ci_limits": [1.9, 3.8],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Tetsuro",
        "family": "Kobayashi"
      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
  "metadata": {
    "units": "days",
    "sample_size": 155,
    "region": "China",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
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  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": true,
    "phase_bias_adjusted": true
  },
  "notes": "This dataset includes only surviving patients. This method applies right-truncation but only fits a lognormal distribution."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "onset to hospitalisation",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
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    "mean_ci_limits": [5.2, 8.8],
    "mean_ci": 95,
    "sd": 4.9,
    "sd_ci_limits": [3, 8.6],
    "sd_ci": 95,
    "quantile_values": [1.9, 15],
    "quantile_names": ["5", "95"],
    "median": 5.3,
    "median_ci_limits": [4.2, 6.8],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
      },
      {
        "given": "Tetsuro",
        "family": "Kobayashi"
      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
      }
    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
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    "sample_size": 34,
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    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
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    "phase_bias_adjusted": true
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  "notes": "This dataset includes only deceased patients. This method applies right-truncation but only fits a lognormal distribution."
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{
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    "sd_ci_limits": [6.6, 21.8],
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    "quantile_names": ["5", "95"],
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    "median_ci_limits": [13.5, 24.1],
    "median_ci": 95
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  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
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      {
        "given": "Tetsuro",
        "family": "Kobayashi"
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      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
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    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
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    "units": "days",
    "sample_size": 34,
    "region": "China",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
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    "discretised": false,
    "censored": true,
    "right_truncated": true,
    "phase_bias_adjusted": true
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  "notes": "This method applies right-truncation but only fits a lognormal distribution."
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{
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    "prob_distribution": "lnorm",
    "parameters": { }
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    "mean_ci_limits": [8.7, 20.9],
    "mean_ci": 95,
    "sd": 12.7,
    "sd_ci_limits": [6.4, 26],
    "sd_ci": 95,
    "quantile_values": [2.5, 33.1],
    "quantile_names": ["5", "95"],
    "median": 9.1,
    "median_ci_limits": [6.7, 13.7],
    "median_ci": 95
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  "citation": {
    "author": [
      {
        "given": "Natalie M.",
        "family": "Linton"
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      {
        "given": "Tetsuro",
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      },
      {
        "given": "Yichi",
        "family": "Yang"
      },
      {
        "given": "Katsuma",
        "family": "Hayashi"
      },
      {
        "given": "Andrei R.",
        "family": "Akhmetzhanov"
      },
      {
        "given": "Sung-mok",
        "family": "Jung"
      },
      {
        "given": "Baoyin",
        "family": "Yuan"
      },
      {
        "given": "Ryo",
        "family": "Kinoshita"
      },
      {
        "given": "Hiroshi",
        "family": "Nishiura"
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    ],
    "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data",
    "journal": "Journal of Clinical Medicine",
    "year": 2020,
    "pmid": 32079150,
    "doi": "10.3390/jcm9020538"
  },
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    "units": "days",
    "sample_size": 39,
    "region": "China",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "bayesian"
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  "method_assessment": {
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    "discretised": false,
    "censored": true,
    "right_truncated": true,
    "phase_bias_adjusted": true
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  "notes": "This method applies right-truncation but only fits a lognormal distribution."
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{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
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    "quantile_values": [2.2, 11.5],
    "quantile_names": ["2.5", "97.5"],
    "median": 5.1,
    "median_ci_limits": [4.5, 5.8],
    "median_ci": 95,
    "dispersion": 1.52,
    "dispersion_ci_limits": [1.32, 1.72],
    "dispersion_ci": 95
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  "citation": {
    "author": [
      {
        "given": "Stephen A.",
        "family": "Lauer"
      },
      {
        "given": "Kyra H.",
        "family": "Grantz"
      },
      {
        "given": "Qifang",
        "family": "Bi"
      },
      {
        "given": "Forrest K.",
        "family": "Jones"
      },
      {
        "given": "Qulu",
        "family": "Zheng"
      },
      {
        "given": "Hannah R.",
        "family": "Meredith"
      },
      {
        "given": "Andrew S.",
        "family": "Azman"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      }
    ],
    "title": "The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application",
    "journal": "Annals of Internal Medicine",
    "year": 2020,
    "pmid": 32150748,
    "doi": "10.7326/M20-0504"
  },
  "metadata": {
    "units": "days",
    "sample_size": 181,
    "region": "Mixed",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": true
  },
  "notes": "This is the complete data set."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [2.6, 12.5],
    "quantile_names": ["2.5", "97.5"],
    "median": 5.7,
    "median_ci_limits": [4.9, 6.8],
    "median_ci": 95
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  "citation": {
    "author": [
      {
        "given": "Stephen A.",
        "family": "Lauer"
      },
      {
        "given": "Kyra H.",
        "family": "Grantz"
      },
      {
        "given": "Qifang",
        "family": "Bi"
      },
      {
        "given": "Forrest K.",
        "family": "Jones"
      },
      {
        "given": "Qulu",
        "family": "Zheng"
      },
      {
        "given": "Hannah R.",
        "family": "Meredith"
      },
      {
        "given": "Andrew S.",
        "family": "Azman"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      }
    ],
    "title": "The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application",
    "journal": "Annals of Internal Medicine",
    "year": 2020,
    "pmid": 32150748,
    "doi": "10.7326/M20-0504"
  },
  "metadata": {
    "units": "days",
    "sample_size": 99,
    "region": "Mixed",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": true
  },
  "notes": "This is a subset of the data, including only those cases with a known onset of fever to be sure that the onset of symptoms is not from another pathogen."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
    "quantile_values": [2.1, 14.7],
    "quantile_names": ["2.5", "97.5"],
    "median": 5.5,
    "median_ci_limits": [4.4, 7],
    "median_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Stephen A.",
        "family": "Lauer"
      },
      {
        "given": "Kyra H.",
        "family": "Grantz"
      },
      {
        "given": "Qifang",
        "family": "Bi"
      },
      {
        "given": "Forrest K.",
        "family": "Jones"
      },
      {
        "given": "Qulu",
        "family": "Zheng"
      },
      {
        "given": "Hannah R.",
        "family": "Meredith"
      },
      {
        "given": "Andrew S.",
        "family": "Azman"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      }
    ],
    "title": "The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application",
    "journal": "Annals of Internal Medicine",
    "year": 2020,
    "pmid": 32150748,
    "doi": "10.7326/M20-0504"
  },
  "metadata": {
    "units": "days",
    "sample_size": 108,
    "region": "Mixed",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": true
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  "notes": "This is a subset of the data, including only cases that are detected outside of mainland China."
},
{
  "disease": "COVID-19",
  "pathogen": "SARS-CoV-2",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": "lnorm",
    "parameters": { }
  },
  "summary_statistics": {
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    "quantile_names": ["2.5", "97.5"],
    "median": 4.8,
    "median_ci_limits": [4.2, 5.6],
    "median_ci": 95
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  "citation": {
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      {
        "given": "Stephen A.",
        "family": "Lauer"
      },
      {
        "given": "Kyra H.",
        "family": "Grantz"
      },
      {
        "given": "Qifang",
        "family": "Bi"
      },
      {
        "given": "Forrest K.",
        "family": "Jones"
      },
      {
        "given": "Qulu",
        "family": "Zheng"
      },
      {
        "given": "Hannah R.",
        "family": "Meredith"
      },
      {
        "given": "Andrew S.",
        "family": "Azman"
      },
      {
        "given": "Nicholas G.",
        "family": "Reich"
      },
      {
        "given": "Justin",
        "family": "Lessler"
      }
    ],
    "title": "The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application",
    "journal": "Annals of Internal Medicine",
    "year": 2020,
    "pmid": 32150748,
    "doi": "10.7326/M20-0504"
  },
  "metadata": {
    "units": "days",
    "sample_size": 73,
    "region": "China",
    "transmission_mode": "natural_human_to_human",
    "extrinsic": false,
    "inference_method": "mle"
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  "method_assessment": {
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    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": true
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  "notes": "This is a subset of the data, including only cases that are detected inside mainland China."
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
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  "summary_statistics": {
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    "sd": 1.5,
    "sd_ci_limits": [0.4, 2.4],
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    "quantile_values": [8.3],
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    "median_ci_limits": [1.4, 10.4],
    "median_ci": 95
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  "citation": {
    "author": [
      {
        "given": "Zihao",
        "family": "Guo"
      },
      {
        "given": "Shi",
        "family": "Zhao"
      },
      {
        "given": "Shengzhi",
        "family": "Sun"
      },
      {
        "given": "Daihai",
        "family": "He"
      },
      {
        "given": "Ka Chun",
        "family": "Chong"
      },
      {
        "given": "Eng Kiong",
        "family": "Yeoh"
      }
    ],
    "title": "Estimation of the serial interval of monkeypox during the early outbreak in 2022",
    "journal": "Journal of Medical Virology",
    "year": 2022,
    "pmid": 36271480,
    "doi": "10.1002/jmv.28248"
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  "metadata": {
    "units": "days",
    "sample_size": 42,
    "region": "Mixed",
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    "inference_method": "bayesian"
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    "discretised": false,
    "censored": false,
    "right_truncated": true,
    "phase_bias_adjusted": true
  },
  "notes": "Data from Kraemer et al 10.1016/S1473-3099(22)00359-0"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus Clade I",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
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  "summary_statistics": {
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    "quantile_names": ["25", "75"],
    "median": 9.67
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  "citation": {
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      {
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      {
        "given": "Fengdi",
        "family": "Zhang"
      },
      {
        "given": "Zhilu",
        "family": "Yuan"
      },
      {
        "given": "Mingda",
        "family": "Xu"
      },
      {
        "given": "Zhen",
        "family": "Wang"
      },
      {
        "given": "Chao",
        "family": "Gao"
      },
      {
        "given": "Renzhong",
        "family": "Guo"
      },
      {
        "given": "Zhanwei",
        "family": "Du"
      }
    ],
    "title": "Serial intervals and incubation periods of the monkeypox virus clades",
    "journal": "Journal of Travel Medicine",
    "year": 2022,
    "pmid": 36130210,
    "doi": "10.1093/jtm/taac105"
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  "metadata": {
    "units": "days",
    "sample_size": 16,
    "region": "Congo",
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    "inference_method": null
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    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Systematic review"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "serial interval",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
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    "quantile_names": ["25", "75"],
    "median": 9.78
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  "citation": {
    "author": [
      {
        "given": "Shuqi",
        "family": "Wang"
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      {
        "given": "Fengdi",
        "family": "Zhang"
      },
      {
        "given": "Zhilu",
        "family": "Yuan"
      },
      {
        "given": "Mingda",
        "family": "Xu"
      },
      {
        "given": "Zhen",
        "family": "Wang"
      },
      {
        "given": "Chao",
        "family": "Gao"
      },
      {
        "given": "Renzhong",
        "family": "Guo"
      },
      {
        "given": "Zhanwei",
        "family": "Du"
      }
    ],
    "title": "Serial intervals and incubation periods of the monkeypox virus clades",
    "journal": "Journal of Travel Medicine",
    "year": 2022,
    "pmid": 36130210,
    "doi": "10.1093/jtm/taac105"
  },
  "metadata": {
    "units": "days",
    "sample_size": 34,
    "region": "Mixed",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": null
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  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Systematic review"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus Clade I",
  "epi_name": "incubation period",
  "probability_distribution": {
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    "parameters": { }
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  "citation": {
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      {
        "given": "Shuqi",
        "family": "Wang"
      },
      {
        "given": "Fengdi",
        "family": "Zhang"
      },
      {
        "given": "Zhilu",
        "family": "Yuan"
      },
      {
        "given": "Mingda",
        "family": "Xu"
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      {
        "given": "Zhen",
        "family": "Wang"
      },
      {
        "given": "Chao",
        "family": "Gao"
      },
      {
        "given": "Renzhong",
        "family": "Guo"
      },
      {
        "given": "Zhanwei",
        "family": "Du"
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    "title": "Serial intervals and incubation periods of the monkeypox virus clades",
    "journal": "Journal of Travel Medicine",
    "year": 2022,
    "pmid": 36130210,
    "doi": "10.1093/jtm/taac105"
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    "discretised": false,
    "censored": false,
    "right_truncated": false,
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  "notes": "Systematic review"
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{
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    "parameters": { }
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  "citation": {
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        "given": "Fengdi",
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        "given": "Zhilu",
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      {
        "given": "Mingda",
        "family": "Xu"
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      {
        "given": "Zhen",
        "family": "Wang"
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      {
        "given": "Chao",
        "family": "Gao"
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      {
        "given": "Renzhong",
        "family": "Guo"
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      {
        "given": "Zhanwei",
        "family": "Du"
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    ],
    "title": "Serial intervals and incubation periods of the monkeypox virus clades",
    "journal": "Journal of Travel Medicine",
    "year": 2022,
    "pmid": 36130210,
    "doi": "10.1093/jtm/taac105"
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  "metadata": {
    "units": "days",
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    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
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  "notes": "Systematic review"
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{
  "disease": "Mpox",
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    "prob_distribution": null,
    "parameters": { }
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  "citation": {
    "author": [
      {
        "given": "Shuqi",
        "family": "Wang"
      },
      {
        "given": "Fengdi",
        "family": "Zhang"
      },
      {
        "given": "Zhilu",
        "family": "Yuan"
      },
      {
        "given": "Mingda",
        "family": "Xu"
      },
      {
        "given": "Zhen",
        "family": "Wang"
      },
      {
        "given": "Chao",
        "family": "Gao"
      },
      {
        "given": "Renzhong",
        "family": "Guo"
      },
      {
        "given": "Zhanwei",
        "family": "Du"
      }
    ],
    "title": "Serial intervals and incubation periods of the monkeypox virus clades",
    "journal": "Journal of Travel Medicine",
    "year": 2022,
    "pmid": 36130210,
    "doi": "10.1093/jtm/taac105"
  },
  "metadata": {
    "units": "days",
    "sample_size": 114,
    "region": "mixed",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Systematic review"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 8.13,
    "mean_ci_limits": [4.9, 19.5],
    "mean_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Fengying",
        "family": "Wei"
      },
      {
        "given": "Zhihang",
        "family": "Peng"
      },
      {
        "given": "Zhen",
        "family": "Jin"
      },
      {
        "given": "Jinjie",
        "family": "Wang"
      },
      {
        "given": "Ximing",
        "family": "Xu"
      },
      {
        "given": "Xinyan",
        "family": "Zhang"
      },
      {
        "given": "Jun",
        "family": "Xu"
      },
      {
        "given": "Zixiong",
        "family": "Ren"
      },
      {
        "given": "Yao",
        "family": "Bai"
      },
      {
        "given": "Xiaoli",
        "family": "Wang"
      },
      {
        "given": "Bulai",
        "family": "Lu"
      },
      {
        "given": "Zhaojun",
        "family": "Wang"
      },
      {
        "given": "Jianguo",
        "family": "Xu"
      },
      {
        "given": "Senzhong",
        "family": "Huang"
      }
    ],
    "title": "Study and prediction of the 2022 global monkeypox epidemic",
    "journal": "Journal of Biosafety and Biosecurity",
    "year": 2022,
    "pmid": 36573222,
    "doi": "10.1016/j.jobb.2022.12.001"
  },
  "metadata": {
    "units": "days",
    "sample_size": null,
    "region": "USA",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "SEIR model from 10.1016/j.mbs.2008.06.005 where the IP is assumed to follow a gamma distribution"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 8.08,
    "mean_ci_limits": [4.8, 21],
    "mean_ci": 95
  },
  "citation": {
    "author": [
      {
        "given": "Fengying",
        "family": "Wei"
      },
      {
        "given": "Zhihang",
        "family": "Peng"
      },
      {
        "given": "Zhen",
        "family": "Jin"
      },
      {
        "given": "Jinjie",
        "family": "Wang"
      },
      {
        "given": "Ximing",
        "family": "Xu"
      },
      {
        "given": "Xinyan",
        "family": "Zhang"
      },
      {
        "given": "Jun",
        "family": "Xu"
      },
      {
        "given": "Zixiong",
        "family": "Ren"
      },
      {
        "given": "Yao",
        "family": "Bai"
      },
      {
        "given": "Xiaoli",
        "family": "Wang"
      },
      {
        "given": "Bulai",
        "family": "Lu"
      },
      {
        "given": "Zhaojun",
        "family": "Wang"
      },
      {
        "given": "Jianguo",
        "family": "Xu"
      },
      {
        "given": "Senzhong",
        "family": "Huang"
      }
    ],
    "title": "Study and prediction of the 2022 global monkeypox epidemic",
    "journal": "Journal of Biosafety and Biosecurity",
    "year": 2022,
    "pmid": 36573222,
    "doi": "10.1016/j.jobb.2022.12.001"
  },
  "metadata": {
    "units": "days",
    "sample_size": null,
    "region": "Europe",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "SEIR model from 10.1016/j.mbs.2008.06.005 where the IP is assumed to follow a gamma distribution"
},
{
  "disease": "Mpox",
  "pathogen": "Mpox Virus",
  "epi_name": "incubation period",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 8.23,
    "mean_ci_limits": [4.9, 21.4],
    "mean_ci": 95,
    "quantile_values": [20],
    "quantile_names": ["95"]
  },
  "citation": {
    "author": [
      {
        "given": "Fengying",
        "family": "Wei"
      },
      {
        "given": "Zhihang",
        "family": "Peng"
      },
      {
        "given": "Zhen",
        "family": "Jin"
      },
      {
        "given": "Jinjie",
        "family": "Wang"
      },
      {
        "given": "Ximing",
        "family": "Xu"
      },
      {
        "given": "Xinyan",
        "family": "Zhang"
      },
      {
        "given": "Jun",
        "family": "Xu"
      },
      {
        "given": "Zixiong",
        "family": "Ren"
      },
      {
        "given": "Yao",
        "family": "Bai"
      },
      {
        "given": "Xiaoli",
        "family": "Wang"
      },
      {
        "given": "Bulai",
        "family": "Lu"
      },
      {
        "given": "Zhaojun",
        "family": "Wang"
      },
      {
        "given": "Jianguo",
        "family": "Xu"
      },
      {
        "given": "Senzhong",
        "family": "Huang"
      }
    ],
    "title": "Study and prediction of the 2022 global monkeypox epidemic",
    "journal": "Journal of Biosafety and Biosecurity",
    "year": 2022,
    "pmid": 36573222,
    "doi": "10.1016/j.jobb.2022.12.001"
  },
  "metadata": {
    "units": "days",
    "sample_size": null,
    "region": "Global",
    "transmission_mode": "natural_unknown",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "SEIR model from 10.1016/j.mbs.2008.06.005 where the IP is assumed to follow a gamma distribution"
},
{
  "disease": "Chikungunya",
  "pathogen": "Chikungunya Virus",
  "epi_name": "generation time",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 14,
    "sd": 6.2
  },
  "citation": {
    "author": [
      {
        "given": "Henrik",
        "family": "Salje"
      },
      {
        "given": "Simon",
        "family": "Cauchemez"
      },
      {
        "given": "Maria Theresa",
        "family": "Alera"
      },
      {
        "given": "Isabel",
        "family": "Rodriguez-Barraquer"
      },
      {
        "given": "Butsaya",
        "family": "Thaisomboonsuk"
      },
      {
        "given": "Anon",
        "family": "Srikiatkhachorn"
      },
      {
        "given": "Catherine B.",
        "family": "Lago"
      },
      {
        "given": "Daisy",
        "family": "Villa"
      },
      {
        "given": "Chonticha",
        "family": "Klungthong"
      },
      {
        "given": "Ilya A.",
        "family": "Tac-An"
      },
      {
        "given": "Stefan",
        "family": "Fernandez"
      },
      {
        "given": "John Mark",
        "family": "Velasco"
      },
      {
        "given": "Vito G.",
        "family": "Roque Jr"
      },
      {
        "given": "Ananda",
        "family": "Nisalak"
      },
      {
        "given": "Louis R.",
        "family": "Macareo"
      },
      {
        "given": "Jens W.",
        "family": "Levy"
      },
      {
        "given": "Derek",
        "family": "Cummings"
      },
      {
        "given": "In-Kyu",
        "family": "Yoon"
      }
    ],
     "title": "Reconstruction of 60 Years of Chikungunya Epidemiology in the Philippines Demonstrates Episodic and Focal Transmission",
    "journal": "The Journal of Infectious Diseases",
    "year": 2015,
    "pmid": 26410592,
    "doi": "10.1093/infdis/jiv470"
  },
  "metadata": {
    "units": "days",
    "sample_size": null,
    "region": "Philippines",
    "transmission_mode": "vector_borne",
    "vector": "mosquito",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Database entry per communication K. Charniga, Z. Cucunubá & Laura Gomez Bermeo."
},
{
    "disease": "Chikungunya",
  "pathogen": "Chikungunya Virus",
  "epi_name": "generation time",
  "probability_distribution": {
    "prob_distribution": "gamma",
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 12.4,
    "mean_ci_limits": [11.7, 13.3],
    "mean_ci": 95,
    "quantile_values": [5.6, 22.1],
    "quantile_names": ["2.5", "97.5"]
  },
  "citation": {
    "author": [
      {
        "given": "Giorgio",
        "family": "Guzzetta"
      },
      {
        "given": "Francesco",
        "family": "Vairo"
      },
      {
        "given": "Alessia",
        "family": "Mammone"
      },
      {
        "given": "Simone",
        "family": "Lanini"
      },
      {
        "given": "Piero",
        "family": "Poletti"
      },
      {
        "given": "Mattia",
        "family": "Manica"
      },
      {
        "given": "Roberto",
        "family": "Rosa"
      },
      {
        "given": "Beniamino",
        "family": "Caputo"
      },
      {
        "given": "Angelo",
        "family": "Solimini"
      },
      {
        "given": "Alessandra",
        "family": "della Torre"
      },
      {
        "given": "Paola",
        "family": "Scognamiglio"
      },
      {
        "given": "Alimuddin",
        "family": "Zumla"
      },
      {
        "given": "Giuseppe",
        "family": "Ippolito"
      },
      {
        "given": "Stefano",
        "family": "Merler"
      }
    ],
     "title": "Spatial modes for transmission of chikungunya virus during a large chikungunya outbreak in Italy: a modeling analysis",
    "journal": "BMC Medicine",
    "year": 2020,
    "pmid": 32762750,
    "doi": "10.1186/s12916-020-01674-y"
  },
  "metadata": {
    "units": "days",
    "sample_size": 412,
    "region": "Italy",
    "transmission_mode": "vector_borne",
    "vector": "Aedes albopictus",
    "extrinsic": false,
    "inference_method": "bayesian"
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": false,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "No additional notes."
},
{
  "disease": "Chikungunya",
  "pathogen": "Chikungunya Virus",
  "epi_name": "case fatality risk",
  "probability_distribution": {
    "prob_distribution": null,
    "parameters": { }
  },
  "summary_statistics": {
    "mean": 1.3
  },
  "citation": {
    "author": [
      {
        "given": "William M",
        "family": "de Souza"
      },
      {
        "given": "Shirlene T. S.",
        "family": "de Lima"
      },
      {
        "given": "Leda M Simões",
        "family": "Mello"
      },
      {
        "given": "Darlan S.",
        "family": "Candido"
      },
      {
        "given": "Lewis",
        "family": "Buss"
      },
      {
        "given": "Charles",
        "family": "Whittaker"
      },
      {
        "given": "Ingra M",
        "family": "Claro"
      },
      {
        "given": "Nilani",
        "family": "Chandradeva"
      },
      {
        "given": "Fabiana",
        "family": "Granja"
      },
      {
        "given": "Ronaldo",
        "family": "de Jesus"
      },
      {
        "given": "Poliana S.",
        "family": "Lemos"
      },
      {
        "given": "Daniel A.",
        "family": "Toledo-Teixeira"
      },
      {
        "given": "Priscilla P.",
        "family": "Barbosa"
      },
      {
        "given": "Antonio Carlos L.",
        "family": "Firmino"
      },
      {
        "given": "Mariene R.",
        "family": "Amorim"
      },
      {
        "given": "Larissa M. F.",
        "family": "Duarte"
      },
      {
        "given": "Ivan B.",
        "family": "Pessoa Jr"
      },
      {
        "given": "Julia",
        "family": "Forato"
      },
      {
        "given": "Irihane L.",
        "family": "Vasconcelos"
      },
      {
        "given": "Ana Carolina B. M.",
        "family": "Maximo"
      },
      {
        "given": "Emerson L. L.",
        "family": "Araújo"
      },
      {
        "given": "Liana Perdigão",
        "family": "Mello"
      },
      {
        "given": "Ester C.",
        "family": "Sabino"
      },
      {
        "given": "José Luiz",
        "family": "Proença-Módena"
      },
      {
        "given": "Nuno R.",
        "family": "Faria"
      },
      {
        "given": "Scott C.",
        "family": "Weaver"
      }
    ],
    "title": "Spatiotemporal dynamics and recurrence of chikungunya virus in Brazil: an epidemiological study",
    "journal": "The Lancet Microbe",
    "year": 2023,
    "pmid": 37031687,
    "doi": "10.1016/S2666-5247(23)00033-2"
  },
  "metadata": {
    "units": "deaths per 1000 cases",
    "sample_size": 253545,
    "region": "Brazil",
    "transmission_mode": "vector_borne",
    "vector": "Aedes aegypti and Aedes albopictus",
    "extrinsic": false,
    "inference_method": null
  },
  "method_assessment": {
    "truncation": null,
    "discretised": false,
    "censored": true,
    "right_truncated": false,
    "phase_bias_adjusted": false
  },
  "notes": "Case fatality risk is given in deaths per 1,000 cases. It was calculated as a cumulative case fatality ratio. CFR is a population-wide estimate. Odds of chikungunya-related death were not significantly different between males and females. Odds of chikungunya-related death were significantly higher for 55-74 years old, and >75 years old compared to <18."
}
]