{
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  "Package": "epidist",
  "Title": "Estimate Epidemiological Delay Distributions with 'brms'",
  "Version": "1.0.0",
  "Authors@R": "c(person(given = \"Adam\",\nfamily = \"Howes\",\nrole = c(\"aut\"),\nemail = \"adamthowes@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2386-4031\")),\nperson(given = \"Sang Woo\",\nfamily = \"Park\",\nrole = c(\"aut\"),\nemail = \"swp2@princeton.edu\",\ncomment = c(ORCID = \"0000-0003-2202-3361\")),\nperson(given = \"Sam\",\nfamily = \"Abbott\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"contact@samabbott.co.uk\",\ncomment = c(ORCID = \"0000-0001-8057-8037\")),\nperson(given = \"Sebastian\",\nfamily = \"Funk\",\nrole = c(\"ctb\"),\nemail = \"sebastian.funk@lshtm.ac.uk\",\ncomment = c(ORCID = \"0000-0002-2842-3406\")))",
  "Description": "Understanding and accurately estimating epidemiological\ndelay distributions is important for public health policy.\nThese estimates influence epidemic situational awareness,\ncontrol strategies, and resource allocation. This package\nprovides methods to address the key challenges in estimating\nthese distributions, including truncation, interval censoring,\nand dynamical biases, following Park et al. (2024)\n<doi:10.1101/2024.01.12.24301247> and Charniga et al. (2024)\n<doi:10.1371/journal.pcbi.1012520>. These issues are frequently\noverlooked, resulting in biased conclusions. Built on top of\n'brms', it allows for flexible modelling including time-varying\nand spatial effects and partially pooled estimates of\ndemographic characteristics.",
  "License": "MIT + file LICENSE",
  "URL": "https://epidist.epinowcast.org/,\nhttps://github.com/epinowcast/epidist/",
  "BugReports": "https://github.com/epinowcast/epidist/issues/",
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  "Author": "Adam Howes [aut] (ORCID:\n<https://orcid.org/0000-0003-2386-4031>), Sang Woo Park [aut]\n(ORCID: <https://orcid.org/0000-0003-2202-3361>), Sam Abbott\n[aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-8057-8037>), Sebastian Funk [ctb]\n(ORCID: <https://orcid.org/0000-0002-2842-3406>)",
  "Maintainer": "Sam Abbott <contact@samabbott.co.uk>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-10-13 14:40:02 UTC",
  "RemoteUrl": "https://github.com/cran/epidist",
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  "_created": "2026-10-13T23:41:29.000Z",
  "_published": "2026-10-13T23:47:48.823Z",
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    "description": "Real-time infectious disease modelling. Developing tools and methods for outbreak response, routine surveillance, and pandemic preparedness.",
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  "_exports": [
    "add_delay_parameter_draws",
    "add_summaries",
    "as_epidist_aggregate_data",
    "as_epidist_estimates_data",
    "as_epidist_latent_model",
    "as_epidist_linelist_data",
    "as_epidist_marginal_model",
    "as_epidist_meta_model",
    "as_epidist_multivariate",
    "as_epidist_naive_model",
    "assert_epidist",
    "bf",
    "delay_parameter_draws",
    "delay_summary_draws",
    "epidist",
    "epidist_diagnostics",
    "epidist_estimates_epireview",
    "epidist_estimates_parameters",
    "epidist_estimates_summaries",
    "epidist_family",
    "epidist_family_model",
    "epidist_family_prior",
    "epidist_formula",
    "epidist_formula_model",
    "epidist_gen_log_lik",
    "epidist_gen_meta_log_lik",
    "epidist_gen_meta_predict",
    "epidist_gen_posterior_epred",
    "epidist_gen_posterior_predict",
    "epidist_meta_leave_one_out",
    "epidist_model_prior",
    "epidist_newdata",
    "epidist_prior",
    "epidist_stancode",
    "epidist_strata",
    "epidist_transform_data_model",
    "Gamma",
    "gengamma",
    "is_epidist_aggregate_data",
    "is_epidist_data",
    "is_epidist_estimates_data",
    "is_epidist_latent_model",
    "is_epidist_linelist_data",
    "is_epidist_marginal_model",
    "is_epidist_meta_model",
    "is_epidist_multivariate",
    "is_epidist_naive_model",
    "lognormal",
    "new_epidist_aggregate_data",
    "new_epidist_estimates_data",
    "new_epidist_latent_model",
    "new_epidist_linelist_data",
    "new_epidist_marginal_model",
    "new_epidist_meta_model",
    "new_epidist_multivariate",
    "new_epidist_naive_model",
    "plot_delays",
    "plot_events",
    "simulate_dates",
    "simulate_exponential_cases",
    "simulate_gillespie",
    "simulate_secondary",
    "simulate_study",
    "simulate_uniform_cases",
    "weibull"
  ],
  "_datasets": [
    {
      "name": "sierra_leone_ebola_data",
      "title": "Ebola linelist data from Fang et al. (2016)",
      "object": "sierra_leone_ebola_data",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "id",
        "age",
        "sex",
        "date_of_symptom_onset",
        "date_of_sample_tested",
        "district",
        "chiefdom"
      ],
      "rows": 8358,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_summaries",
      "title": "Add natural scale summaries of the delay distribution",
      "concept": [
        "postprocess"
      ],
      "topics": [
        "add_summaries"
      ]
    },
    {
      "page": "as_dist_spec.epidist_fit",
      "title": "Export a fitted delay distribution as a 'distspec' distribution",
      "concept": [
        "postprocess"
      ],
      "topics": [
        "as_dist_spec.epidist_fit"
      ]
    },
    {
      "page": "as_epidist_aggregate_data",
      "title": "Create an epidist_aggregate_data object",
      "concept": [
        "aggregate_data"
      ],
      "topics": [
        "as_epidist_aggregate_data"
      ]
    },
    {
      "page": "as_epidist_aggregate_data.data.frame",
      "title": "Create an epidist_aggregate_data object from a data.frame",
      "concept": [
        "aggregate_data"
      ],
      "topics": [
        "as_epidist_aggregate_data.data.frame"
      ]
    },
    {
      "page": "as_epidist_aggregate_data.default",
      "title": "Create an epidist_aggregate_data object from vectors of event times",
      "concept": [
        "aggregate_data"
      ],
      "topics": [
        "as_epidist_aggregate_data.default"
      ]
    },
    {
      "page": "as_epidist_aggregate_data.epidist_linelist_data",
      "title": "Convert linelist data to aggregate format",
      "concept": [
        "aggregate_data"
      ],
      "topics": [
        "as_epidist_aggregate_data.epidist_linelist_data"
      ]
    },
    {
      "page": "as_epidist_estimates_data",
      "title": "Create an 'epidist_estimates_data' object",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "as_epidist_estimates_data"
      ]
    },
    {
      "page": "as_epidist_estimates_data.data.frame",
      "title": "Create an 'epidist_estimates_data' object from a data frame",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "as_epidist_estimates_data.data.frame"
      ]
    },
    {
      "page": "as_epidist_estimates_data.epidist_estimates_data",
      "title": "Return an 'epidist_estimates_data' object unchanged",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "as_epidist_estimates_data.epidist_estimates_data"
      ]
    },
    {
      "page": "as_epidist_estimates_data.epidist_multivariate",
      "title": "Create an 'epidist_estimates_data' object from a multivariate representation",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "as_epidist_estimates_data.epidist_multivariate"
      ]
    },
    {
      "page": "as_epidist_estimates_data.list",
      "title": "Combine 'epidist_estimates_data' objects from several studies",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "as_epidist_estimates_data.list"
      ]
    },
    {
      "page": "as_epidist_latent_model",
      "title": "Convert an object to an 'epidist_latent_model' object",
      "concept": [
        "latent_model"
      ],
      "topics": [
        "as_epidist_latent_model"
      ]
    },
    {
      "page": "as_epidist_latent_model.epidist_aggregate_data",
      "title": "The latent model method for 'epidist_aggregate_data' objects",
      "concept": [
        "latent_model"
      ],
      "topics": [
        "as_epidist_latent_model.epidist_aggregate_data"
      ]
    },
    {
      "page": "as_epidist_latent_model.epidist_linelist_data",
      "title": "The latent model method for 'epidist_linelist_data' objects",
      "concept": [
        "latent_model"
      ],
      "topics": [
        "as_epidist_latent_model.epidist_linelist_data"
      ]
    },
    {
      "page": "as_epidist_linelist_data",
      "title": "Create an epidist_linelist_data object",
      "concept": [
        "linelist_data"
      ],
      "topics": [
        "as_epidist_linelist_data"
      ]
    },
    {
      "page": "as_epidist_linelist_data.data.frame",
      "title": "Create an epidist_linelist_data object from a data frame with event dates",
      "concept": [
        "linelist_data"
      ],
      "topics": [
        "as_epidist_linelist_data.data.frame"
      ]
    },
    {
      "page": "as_epidist_linelist_data.default",
      "title": "Create an epidist_linelist_data object from vectors of event times",
      "concept": [
        "linelist_data"
      ],
      "topics": [
        "as_epidist_linelist_data.default"
      ]
    },
    {
      "page": "as_epidist_linelist_data.epidist_aggregate_data",
      "title": "Convert aggregate data to linelist format",
      "concept": [
        "linelist_data"
      ],
      "topics": [
        "as_epidist_linelist_data.epidist_aggregate_data"
      ]
    },
    {
      "page": "as_epidist_marginal_model",
      "title": "Convert an object to an 'epidist_marginal_model' object",
      "concept": [
        "marginal_model"
      ],
      "topics": [
        "as_epidist_marginal_model"
      ]
    },
    {
      "page": "as_epidist_marginal_model.epidist_aggregate_data",
      "title": "The marginal model method for 'epidist_aggregate_data' objects",
      "concept": [
        "marginal_model"
      ],
      "topics": [
        "as_epidist_marginal_model.epidist_aggregate_data"
      ]
    },
    {
      "page": "as_epidist_marginal_model.epidist_linelist_data",
      "title": "The marginal model method for 'epidist_linelist_data' objects",
      "concept": [
        "marginal_model"
      ],
      "topics": [
        "as_epidist_marginal_model.epidist_linelist_data"
      ]
    },
    {
      "page": "as_epidist_meta_model",
      "title": "Convert an object to an 'epidist_meta_model' object",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "as_epidist_meta_model"
      ]
    },
    {
      "page": "as_epidist_meta_model.epidist_aggregate_data",
      "title": "The meta model method for 'epidist_aggregate_data' objects",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "as_epidist_meta_model.epidist_aggregate_data"
      ]
    },
    {
      "page": "as_epidist_meta_model.epidist_estimates_data",
      "title": "The meta model method for 'epidist_estimates_data' objects",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "as_epidist_meta_model.epidist_estimates_data"
      ]
    },
    {
      "page": "as_epidist_meta_model.epidist_linelist_data",
      "title": "The meta model method for 'epidist_linelist_data' objects",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "as_epidist_meta_model.epidist_linelist_data"
      ]
    },
    {
      "page": "as_epidist_meta_model.NULL",
      "title": "The meta model method for summary estimates only",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "as_epidist_meta_model.NULL"
      ]
    },
    {
      "page": "as_epidist_multivariate",
      "title": "Create an 'epidist_multivariate' object",
      "concept": [
        "multivariate"
      ],
      "topics": [
        "as_epidist_multivariate"
      ]
    },
    {
      "page": "as_epidist_multivariate.data.frame",
      "title": "Create an 'epidist_multivariate' object from a data frame of draws",
      "concept": [
        "multivariate"
      ],
      "topics": [
        "as_epidist_multivariate.data.frame"
      ]
    },
    {
      "page": "as_epidist_multivariate.matrix",
      "title": "Create an 'epidist_multivariate' object from a matrix of draws",
      "concept": [
        "multivariate"
      ],
      "topics": [
        "as_epidist_multivariate.matrix"
      ]
    },
    {
      "page": "as_epidist_naive_model",
      "title": "Convert an object to an 'epidist_naive_model' object",
      "concept": [
        "naive_model"
      ],
      "topics": [
        "as_epidist_naive_model"
      ]
    },
    {
      "page": "as_epidist_naive_model.epidist_aggregate_data",
      "title": "The naive model method for 'epidist_aggregate_data' objects",
      "concept": [
        "naive_model"
      ],
      "topics": [
        "as_epidist_naive_model.epidist_aggregate_data"
      ]
    },
    {
      "page": "as_epidist_naive_model.epidist_linelist_data",
      "title": "The naive model method for 'epidist_linelist_data' objects",
      "concept": [
        "naive_model"
      ],
      "topics": [
        "as_epidist_naive_model.epidist_linelist_data"
      ]
    },
    {
      "page": "assert_epidist",
      "title": "Validation for epidist objects",
      "concept": [
        "assert"
      ],
      "topics": [
        "assert_epidist"
      ]
    },
    {
      "page": "assert_epidist.epidist_aggregate_data",
      "title": "Assert validity of 'epidist_aggregate_data' objects",
      "concept": [
        "aggregate_data"
      ],
      "topics": [
        "assert_epidist.epidist_aggregate_data"
      ]
    },
    {
      "page": "assert_epidist.epidist_estimates_data",
      "title": "Assert validity of 'epidist_estimates_data' objects",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "assert_epidist.epidist_estimates_data"
      ]
    },
    {
      "page": "assert_epidist.epidist_linelist_data",
      "title": "Assert validity of 'epidist_linelist_data' objects",
      "concept": [
        "linelist_data"
      ],
      "topics": [
        "assert_epidist.epidist_linelist_data"
      ]
    },
    {
      "page": "assert_epidist.epidist_meta_model",
      "title": "Assert validity of 'epidist_meta_model' objects",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "assert_epidist.epidist_meta_model"
      ]
    },
    {
      "page": "assert_epidist.epidist_multivariate",
      "title": "Assert validity of 'epidist_multivariate' objects",
      "concept": [
        "multivariate"
      ],
      "topics": [
        "assert_epidist.epidist_multivariate"
      ]
    },
    {
      "page": "delay_parameter_draws",
      "title": "Posterior draws of the delay distribution parameters",
      "concept": [
        "postprocess"
      ],
      "topics": [
        "add_delay_parameter_draws",
        "delay_parameter_draws"
      ]
    },
    {
      "page": "delay_summary_draws",
      "title": "Posterior draws of the delay distribution, summarised",
      "concept": [
        "postprocess"
      ],
      "topics": [
        "delay_summary_draws"
      ]
    },
    {
      "page": "epidist",
      "title": "Fit epidemiological delay distributions using a 'brms' interface",
      "concept": [
        "fit"
      ],
      "topics": [
        "epidist"
      ]
    },
    {
      "page": "epidist_data",
      "title": "Keep 'epidist' objects in their class",
      "concept": [
        "epidist_data"
      ],
      "topics": [
        "$<-.epidist_data",
        "dplyr_col_modify.epidist_data",
        "dplyr_reconstruct.epidist_data",
        "dplyr_row_slice.epidist_data",
        "epidist_data",
        "group_by.epidist_data",
        "names<-.epidist_data",
        "rbind.epidist_data",
        "ungroup.epidist_data",
        "[.epidist_data",
        "[<-.epidist_data",
        "[[<-.epidist_data"
      ]
    },
    {
      "page": "epidist_delay_draws",
      "title": "Keep the 'epidist_delay_draws' class through 'dplyr' verbs",
      "concept": [
        "postprocess"
      ],
      "topics": [
        "dplyr_col_modify.epidist_delay_draws",
        "dplyr_reconstruct.epidist_delay_draws",
        "dplyr_row_slice.epidist_delay_draws",
        "epidist_delay_draws",
        "group_by.epidist_delay_draws",
        "names<-.epidist_delay_draws",
        "ungroup.epidist_delay_draws",
        "[.epidist_delay_draws"
      ]
    },
    {
      "page": "epidist_diagnostics",
      "title": "Diagnostics for 'epidist_fit' models",
      "concept": [
        "diagnostics"
      ],
      "topics": [
        "epidist_diagnostics"
      ]
    },
    {
      "page": "epidist_estimates_epireview",
      "title": "Report studies from an 'epireview' parameter table",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "epidist_estimates_epireview"
      ]
    },
    {
      "page": "epidist_estimates_parameters",
      "title": "Report a study that published the parameters of a distribution it fitted",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "epidist_estimates_parameters"
      ]
    },
    {
      "page": "epidist_estimates_summaries",
      "title": "Report a study that published summaries of its delays",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "epidist_estimates_summaries"
      ]
    },
    {
      "page": "epidist_family",
      "title": "Define 'epidist' family",
      "concept": [
        "family"
      ],
      "topics": [
        "epidist_family"
      ]
    },
    {
      "page": "epidist_family_model",
      "title": "The model-specific parts of an 'epidist_family()' call",
      "concept": [
        "family"
      ],
      "topics": [
        "epidist_family_model"
      ]
    },
    {
      "page": "epidist_family_model.default",
      "title": "Default method for defining a model specific family",
      "concept": [
        "family"
      ],
      "topics": [
        "epidist_family_model.default"
      ]
    },
    {
      "page": "epidist_family_model.epidist_latent_model",
      "title": "Create the model-specific component of an 'epidist' custom family",
      "concept": [
        "latent_model"
      ],
      "topics": [
        "epidist_family_model.epidist_latent_model"
      ]
    },
    {
      "page": "epidist_family_model.epidist_marginal_model",
      "title": "Create the model-specific component of an 'epidist' custom family",
      "concept": [
        "marginal_model"
      ],
      "topics": [
        "epidist_family_model.epidist_marginal_model"
      ]
    },
    {
      "page": "epidist_family_model.epidist_meta_model",
      "title": "Create the model-specific component of an 'epidist' custom family",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "epidist_family_model.epidist_meta_model"
      ]
    },
    {
      "page": "epidist_family_param.default",
      "title": "Default method for families which do not require a reparameterisation",
      "concept": [
        "family"
      ],
      "topics": [
        "epidist_family_param.default"
      ]
    },
    {
      "page": "epidist_family_param.gengamma",
      "title": "Method for the 'gengamma()' family",
      "concept": [
        "family"
      ],
      "topics": [
        "epidist_family_param.gengamma"
      ]
    },
    {
      "page": "epidist_family_prior",
      "title": "Family specific prior distributions",
      "concept": [
        "prior"
      ],
      "topics": [
        "epidist_family_prior"
      ]
    },
    {
      "page": "epidist_family_prior.default",
      "title": "Default family specific prior distributions",
      "concept": [
        "prior"
      ],
      "topics": [
        "epidist_family_prior.default"
      ]
    },
    {
      "page": "epidist_family_prior.gengamma",
      "title": "Family specific prior distributions for the generalised gamma family",
      "concept": [
        "prior"
      ],
      "topics": [
        "epidist_family_prior.gengamma"
      ]
    },
    {
      "page": "epidist_family_prior.lognormal",
      "title": "Family specific prior distributions for the lognormal family",
      "concept": [
        "prior"
      ],
      "topics": [
        "epidist_family_prior.lognormal"
      ]
    },
    {
      "page": "epidist_formula",
      "title": "Define a model specific formula",
      "concept": [
        "formula"
      ],
      "topics": [
        "epidist_formula"
      ]
    },
    {
      "page": "epidist_formula_model",
      "title": "The model-specific parts of an 'epidist_formula()' call",
      "concept": [
        "formula"
      ],
      "topics": [
        "epidist_formula_model"
      ]
    },
    {
      "page": "epidist_formula_model.default",
      "title": "Default method for defining a model specific formula",
      "concept": [
        "formula"
      ],
      "topics": [
        "epidist_formula_model.default"
      ]
    },
    {
      "page": "epidist_formula_model.epidist_latent_model",
      "title": "Define the model-specific component of an 'epidist' custom formula for the latent model",
      "concept": [
        "latent_model"
      ],
      "topics": [
        "epidist_formula_model.epidist_latent_model"
      ]
    },
    {
      "page": "epidist_formula_model.epidist_marginal_model",
      "title": "Define the model-specific component of an 'epidist' custom formula for the marginal model",
      "concept": [
        "marginal_model"
      ],
      "topics": [
        "epidist_formula_model.epidist_marginal_model"
      ]
    },
    {
      "page": "epidist_formula_model.epidist_meta_model",
      "title": "Define the model-specific component of an 'epidist' custom formula for the meta model",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "epidist_formula_model.epidist_meta_model"
      ]
    },
    {
      "page": "epidist_formula_model.epidist_naive_model",
      "title": "Define the model-specific component of an 'epidist' custom formula for the naive model",
      "concept": [
        "naive_model"
      ],
      "topics": [
        "epidist_formula_model.epidist_naive_model"
      ]
    },
    {
      "page": "epidist_gen_log_lik",
      "title": "Create a function to calculate the marginalised log likelihood for double censored and truncated delay distributions",
      "concept": [
        "gen"
      ],
      "topics": [
        "epidist_gen_log_lik"
      ]
    },
    {
      "page": "epidist_gen_meta_log_lik",
      "title": "Create a function to calculate the meta model log likelihood",
      "concept": [
        "gen"
      ],
      "topics": [
        "epidist_gen_meta_log_lik"
      ]
    },
    {
      "page": "epidist_gen_meta_predict",
      "title": "Create a function to draw from the meta model posterior predictive distribution",
      "concept": [
        "gen"
      ],
      "topics": [
        "epidist_gen_meta_predict"
      ]
    },
    {
      "page": "epidist_gen_posterior_epred",
      "title": "Create a function to draw from the expected value of the posterior predictive distribution for a model",
      "concept": [
        "gen"
      ],
      "topics": [
        "epidist_gen_posterior_epred"
      ]
    },
    {
      "page": "epidist_gen_posterior_predict",
      "title": "Create a function to draw from the posterior predictive distribution for a double censored and truncated delay distribution",
      "concept": [
        "gen"
      ],
      "topics": [
        "epidist_gen_posterior_predict"
      ]
    },
    {
      "page": "epidist_meta_leave_one_out",
      "title": "Refit a meta model leaving each study out in turn",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "epidist_meta_leave_one_out"
      ]
    },
    {
      "page": "epidist_model_prior",
      "title": "Model specific prior distributions",
      "concept": [
        "prior"
      ],
      "topics": [
        "epidist_model_prior"
      ]
    },
    {
      "page": "epidist_model_prior.default",
      "title": "Default model specific prior distributions",
      "concept": [
        "prior"
      ],
      "topics": [
        "epidist_model_prior.default"
      ]
    },
    {
      "page": "epidist_model_prior.epidist_latent_model",
      "title": "Model specific prior distributions for latent models",
      "concept": [
        "latent_model"
      ],
      "topics": [
        "epidist_model_prior.epidist_latent_model"
      ]
    },
    {
      "page": "epidist_model_prior.epidist_meta_model",
      "title": "Model specific prior distributions for the meta model",
      "concept": [
        "meta_model",
        "prior"
      ],
      "topics": [
        "epidist_model_prior.epidist_meta_model"
      ]
    },
    {
      "page": "epidist_newdata",
      "title": "Build 'newdata' for prediction from an 'epidist' data object",
      "concept": [
        "newdata"
      ],
      "topics": [
        "epidist_newdata"
      ]
    },
    {
      "page": "epidist_newdata.default",
      "title": "Default method for building 'newdata'",
      "concept": [
        "newdata"
      ],
      "topics": [
        "epidist_newdata.default"
      ]
    },
    {
      "page": "epidist_newdata.epidist_latent_model",
      "title": "Build 'newdata' for the latent model",
      "concept": [
        "latent_model",
        "newdata"
      ],
      "topics": [
        "epidist_newdata.epidist_latent_model"
      ]
    },
    {
      "page": "epidist_newdata.epidist_marginal_model",
      "title": "Build 'newdata' for the marginal model",
      "concept": [
        "marginal_model",
        "newdata"
      ],
      "topics": [
        "epidist_newdata.epidist_marginal_model"
      ]
    },
    {
      "page": "epidist_newdata.epidist_meta_model",
      "title": "Build 'newdata' for the meta model",
      "concept": [
        "meta_model",
        "newdata"
      ],
      "topics": [
        "epidist_newdata.epidist_meta_model"
      ]
    },
    {
      "page": "epidist_newdata.epidist_naive_model",
      "title": "Build 'newdata' for the naive model",
      "concept": [
        "naive_model",
        "newdata"
      ],
      "topics": [
        "epidist_newdata.epidist_naive_model"
      ]
    },
    {
      "page": "epidist_prior",
      "title": "Define custom prior distributions for epidist models",
      "concept": [
        "prior"
      ],
      "topics": [
        "epidist_prior"
      ]
    },
    {
      "page": "epidist_stancode",
      "title": "Define model specific Stan code",
      "concept": [
        "stan"
      ],
      "topics": [
        "epidist_stancode"
      ]
    },
    {
      "page": "epidist_stancode.default",
      "title": "Default method for defining model specific Stan code",
      "concept": [
        "stan"
      ],
      "topics": [
        "epidist_stancode.default"
      ]
    },
    {
      "page": "epidist_stancode.epidist_naive_model",
      "title": "Define the Stan code of the naive model",
      "concept": [
        "naive_model"
      ],
      "topics": [
        "epidist_stancode.epidist_naive_model"
      ]
    },
    {
      "page": "epidist_strata",
      "title": "Unique combinations of the predictors in a model",
      "concept": [
        "postprocess"
      ],
      "topics": [
        "epidist_strata"
      ]
    },
    {
      "page": "epidist_transform_data_model",
      "title": "The model-specific parts of an 'epidist_transform_data()' call",
      "concept": [
        "transform_data"
      ],
      "topics": [
        "epidist_transform_data_model"
      ]
    },
    {
      "page": "epidist_transform_data_model.default",
      "title": "Default method for transforming data for a model",
      "concept": [
        "transform_data"
      ],
      "topics": [
        "epidist_transform_data_model.default"
      ]
    },
    {
      "page": "epidist_transform_data_model.epidist_marginal_model",
      "title": "Transform data for the marginal model",
      "concept": [
        "marginal_model"
      ],
      "topics": [
        "epidist_transform_data_model.epidist_marginal_model"
      ]
    },
    {
      "page": "epidist_transform_data_model.epidist_meta_model",
      "title": "Transform data for the meta model",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "epidist_transform_data_model.epidist_meta_model"
      ]
    },
    {
      "page": "epidist_transform_data_model.epidist_naive_model",
      "title": "Transform data for the naive model",
      "concept": [
        "naive_model"
      ],
      "topics": [
        "epidist_transform_data_model.epidist_naive_model"
      ]
    },
    {
      "page": "gengamma",
      "title": "Generalised gamma delay distribution family",
      "concept": [
        "family"
      ],
      "topics": [
        "gengamma"
      ]
    },
    {
      "page": "is_epidist_aggregate_data",
      "title": "Check if data has the 'epidist_aggregate_data' class",
      "concept": [
        "aggregate_data"
      ],
      "topics": [
        "is_epidist_aggregate_data"
      ]
    },
    {
      "page": "is_epidist_data",
      "title": "Check if data has the 'epidist_data' class",
      "concept": [
        "epidist_data"
      ],
      "topics": [
        "is_epidist_data"
      ]
    },
    {
      "page": "is_epidist_estimates_data",
      "title": "Check if data has the 'epidist_estimates_data' class",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "is_epidist_estimates_data"
      ]
    },
    {
      "page": "is_epidist_latent_model",
      "title": "Check if data has the 'epidist_latent_model' class",
      "concept": [
        "latent_model"
      ],
      "topics": [
        "is_epidist_latent_model"
      ]
    },
    {
      "page": "is_epidist_linelist_data",
      "title": "Check if data has the 'epidist_linelist_data' class",
      "concept": [
        "linelist_data"
      ],
      "topics": [
        "is_epidist_linelist_data"
      ]
    },
    {
      "page": "is_epidist_marginal_model",
      "title": "Check if data has the 'epidist_marginal_model' class",
      "concept": [
        "marginal_model"
      ],
      "topics": [
        "is_epidist_marginal_model"
      ]
    },
    {
      "page": "is_epidist_meta_model",
      "title": "Check if data has the 'epidist_meta_model' class",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "is_epidist_meta_model"
      ]
    },
    {
      "page": "is_epidist_multivariate",
      "title": "Check if an object has the 'epidist_multivariate' class",
      "concept": [
        "multivariate"
      ],
      "topics": [
        "is_epidist_multivariate"
      ]
    },
    {
      "page": "is_epidist_naive_model",
      "title": "Check if data has the 'epidist_naive_model' class",
      "concept": [
        "naive_model"
      ],
      "topics": [
        "is_epidist_naive_model"
      ]
    },
    {
      "page": "new_epidist_aggregate_data",
      "title": "Class constructor for 'epidist_aggregate_data' objects",
      "concept": [
        "aggregate_data"
      ],
      "topics": [
        "new_epidist_aggregate_data"
      ]
    },
    {
      "page": "new_epidist_estimates_data",
      "title": "Class constructor for 'epidist_estimates_data' objects",
      "concept": [
        "estimates_data"
      ],
      "topics": [
        "new_epidist_estimates_data"
      ]
    },
    {
      "page": "new_epidist_latent_model",
      "title": "Class constructor for 'epidist_latent_model' objects",
      "concept": [
        "latent_model"
      ],
      "topics": [
        "new_epidist_latent_model"
      ]
    },
    {
      "page": "new_epidist_linelist_data",
      "title": "Class constructor for 'epidist_linelist_data' objects",
      "concept": [
        "linelist_data"
      ],
      "topics": [
        "new_epidist_linelist_data"
      ]
    },
    {
      "page": "new_epidist_marginal_model",
      "title": "Class constructor for 'epidist_marginal_model' objects",
      "concept": [
        "marginal_model"
      ],
      "topics": [
        "new_epidist_marginal_model"
      ]
    },
    {
      "page": "new_epidist_meta_model",
      "title": "Class constructor for 'epidist_meta_model' objects",
      "concept": [
        "meta_model"
      ],
      "topics": [
        "new_epidist_meta_model"
      ]
    },
    {
      "page": "new_epidist_multivariate",
      "title": "Class constructor for 'epidist_multivariate' objects",
      "concept": [
        "multivariate"
      ],
      "topics": [
        "new_epidist_multivariate"
      ]
    },
    {
      "page": "new_epidist_naive_model",
      "title": "Class constructor for 'epidist_naive_model' objects",
      "concept": [
        "naive_model"
      ],
      "topics": [
        "new_epidist_naive_model"
      ]
    },
    {
      "page": "plot_delays",
      "title": "Plot the observed delay distribution",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_delays"
      ]
    },
    {
      "page": "plot_delays.default",
      "title": "Default method for plotting observed delays",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_delays.default"
      ]
    },
    {
      "page": "plot_delays.epidist_fit",
      "title": "Plot the delays a fitted model predicts over the delays it was fitted to",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_delays.epidist_fit"
      ]
    },
    {
      "page": "plot_delays.epidist_linelist_data",
      "title": "Plot the observed delays of a dataset",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_delays.epidist_linelist_data"
      ]
    },
    {
      "page": "plot_delays.list",
      "title": "Compare the observed delays of several datasets",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_delays.list"
      ]
    },
    {
      "page": "plot_events",
      "title": "Plot the primary and secondary event windows of each case",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_events"
      ]
    },
    {
      "page": "plot.epidist_delay_draws",
      "title": "Plot posterior draws of the delay distribution",
      "concept": [
        "plot"
      ],
      "topics": [
        "autoplot.epidist_delay_draws",
        "plot.epidist_delay_draws"
      ]
    },
    {
      "page": "print.epidist_multivariate",
      "title": "Print an 'epidist_multivariate' object",
      "concept": [
        "multivariate"
      ],
      "topics": [
        "print.epidist_multivariate"
      ]
    },
    {
      "page": "sierra_leone_ebola_data",
      "title": "Ebola linelist data from Fang et al. (2016)",
      "concept": [
        "data"
      ],
      "topics": [
        "sierra_leone_ebola_data"
      ]
    },
    {
      "page": "simulate_dates",
      "title": "Convert simulated event times to dates",
      "concept": [
        "simulate"
      ],
      "topics": [
        "simulate_dates"
      ]
    },
    {
      "page": "simulate_exponential_cases",
      "title": "Simulate exponential cases",
      "concept": [
        "simulate"
      ],
      "topics": [
        "simulate_exponential_cases"
      ]
    },
    {
      "page": "simulate_gillespie",
      "title": "Simulate cases from a stochastic SIR model",
      "concept": [
        "simulate"
      ],
      "topics": [
        "simulate_gillespie"
      ]
    },
    {
      "page": "simulate_secondary",
      "title": "Simulate secondary events based on a delay distribution",
      "concept": [
        "simulate"
      ],
      "topics": [
        "simulate_secondary"
      ]
    },
    {
      "page": "simulate_study",
      "title": "Simulate the summaries a published study would have reported",
      "concept": [
        "simulate"
      ],
      "topics": [
        "simulate_study"
      ]
    },
    {
      "page": "simulate_uniform_cases",
      "title": "Simulate cases from a uniform distribution",
      "concept": [
        "simulate"
      ],
      "topics": [
        "simulate_uniform_cases"
      ]
    },
    {
      "page": "vcov.epidist_multivariate",
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        "Comparing the fits",
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        "The population level delay and the size of the phase bias",
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        "Interval censoring",
        "The naive model",
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        "A non-uniform primary event",
        "The marginal model",
        "The meta model",
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        "A reported standard deviation",
        "A reported quantile",
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        "A vector of summaries with a covariance",
        "Reported distribution parameters",
        "Individual level records",
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        "Censoring adjustment",
        "An estimated growth rate",
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        "Identifying the growth rate",
        "Summary",
        "References"
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