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  "Title": "Bayesian Estimation of the Force of Infection from Serological\nData",
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  "Authors@R": "c(\nperson(\"Zulma M.\", \"Cucunubá\", , \"zulma.cucunuba@javeriana.edu.co\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8165-3198\")),\nperson(\"Nicolás\", \"T. Domínguez\", , \"ex-ntorres@javeriana.edu.co\", role = \"aut\",\ncomment = c(ORCID = \"0009-0002-8484-1298\")),\nperson(\"Ben\", \"Lambert\", role = \"aut\"),\nperson(\"Pierre\", \"Nouvellet\", role = \"aut\"),\nperson(\"Geraldine\", \"Gómez\", role = \"ctb\",\ncomment = c(ORCID = \"0009-0007-8701-0568\")),\nperson(\"Jaime A.\", \"Pavlich-Mariscal\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-3892-6680\")),\nperson(\"Hugo\", \"Gruson\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4094-1476\")),\nperson(\"David Santiago\", \"Quevedo\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-1583-4262\")),\nperson(\"Miguel\", \"Gámez\", role = \"ctb\"),\nperson(\"Sumali\", \"Bajaj\", role = \"ctb\"),\nperson(\"Everlyn\", \"Kamau\", role = \"ctb\"),\nperson(\"Richard\", \"Creswell\", role = \"ctb\"),\nperson(\"International Development Research Center (IDRC)\", role = \"fnd\"),\nperson(\"Pontificia Universidad Javeriana\", role = \"cph\")\n)",
  "Description": "Estimating the force of infection from time varying, age\nvarying, or constant serocatalytic models from population based\nseroprevalence studies using a Bayesian framework, including\ndata simulation functions enabling the generation of\nserological surveys based on this models. This tool also\nprovides a flexible prior specification syntax for the force of\ninfection and the seroreversion rate, as well as methods to\nassess model convergence and comparison criteria along with\nuseful visualisation functions.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/epiverse-trace/serofoi,\nhttps://epiverse-trace.github.io/serofoi/",
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  "Author": "Zulma M. Cucunubá [aut, cre]\n(<https://orcid.org/0000-0002-8165-3198>), Nicolás T. Domínguez\n[aut] (<https://orcid.org/0009-0002-8484-1298>), Ben Lambert\n[aut], Pierre Nouvellet [aut], Geraldine Gómez [ctb]\n(<https://orcid.org/0009-0007-8701-0568>), Jaime A.\nPavlich-Mariscal [ctb]\n(<https://orcid.org/0000-0002-3892-6680>), Hugo Gruson [ctb]\n(<https://orcid.org/0000-0002-4094-1476>), David Santiago\nQuevedo [ctb] (<https://orcid.org/0000-0003-1583-4262>), Miguel\nGámez [ctb], Sumali Bajaj [ctb], Everlyn Kamau [ctb], Richard\nCreswell [ctb], International Development Research Center\n(IDRC) [fnd], Pontificia Universidad Javeriana [cph]",
  "Maintainer": "Zulma M. Cucunubá <zulma.cucunuba@javeriana.edu.co>",
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  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2025-03-31 10:40:55 UTC",
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  "_created": "2026-10-29T11:11:49.000Z",
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    "add_age_group_to_serosurvey",
    "build_stan_data",
    "extract_central_estimates",
    "fit_seromodel",
    "get_foi_index",
    "plot_foi_estimates",
    "plot_rhats",
    "plot_seromodel",
    "plot_seroprev_estimates",
    "plot_serosurvey",
    "plot_summary",
    "prepare_serosurvey_for_plot",
    "prob_seroprev_age_by_age",
    "prob_seroprev_age_time_by_age",
    "prob_seroprev_by_age",
    "prob_seroprev_gen_by_age",
    "prob_seroprev_time_by_age",
    "probability_exact_age_varying",
    "probability_exact_time_varying",
    "set_foi_init",
    "set_stan_data_defaults",
    "sf_cauchy",
    "sf_none",
    "sf_normal",
    "sf_uniform",
    "simulate_serosurvey",
    "simulate_serosurvey_age",
    "simulate_serosurvey_age_time",
    "simulate_serosurvey_general",
    "simulate_serosurvey_time",
    "summarise_central_estimate",
    "summarise_loo_estimate",
    "summarise_seromodel"
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      "title": "Chagas seroprevalence data in serofoi",
      "object": "chagas2012",
      "class": [
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      ],
      "fields": [
        "survey_year",
        "n_sample",
        "n_seropositive",
        "age_min",
        "age_max"
      ],
      "rows": 72,
      "table": true,
      "tojson": true
    },
    {
      "name": "chik2015",
      "title": "Chikungunya seroprevalence data in serofoi",
      "object": "chik2015",
      "class": [
        "data.frame"
      ],
      "fields": [
        "survey_year",
        "n_sample",
        "n_seropositive",
        "age_min",
        "age_max"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "veev2012",
      "title": "Venezuelan Equine Encephalitis Virus (VEEV) seroprevalence data in serofoi",
      "object": "veev2012",
      "class": [
        "data.frame"
      ],
      "fields": [
        "survey_year",
        "n_sample",
        "n_seropositive",
        "age_min",
        "age_max"
      ],
      "rows": 6,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "serofoi-package",
      "title": "The 'serofoi' package.",
      "topics": [
        "serofoi-package",
        "serofoi"
      ]
    },
    {
      "page": "add_age_group_to_serosurvey",
      "title": "Adds age group marker to serosurvey",
      "topics": [
        "add_age_group_to_serosurvey"
      ]
    },
    {
      "page": "build_stan_data",
      "title": "Builds stan data for sampling depending on the selected model",
      "topics": [
        "build_stan_data"
      ]
    },
    {
      "page": "chagas2012",
      "title": "Chagas seroprevalence data in serofoi",
      "topics": [
        "chagas2012"
      ]
    },
    {
      "page": "chik2015",
      "title": "Chikungunya seroprevalence data in serofoi",
      "topics": [
        "chik2015"
      ]
    },
    {
      "page": "extract_central_estimates",
      "title": "Extracts central estimates from stan_fit object for specified parameter",
      "topics": [
        "extract_central_estimates"
      ]
    },
    {
      "page": "fit_seromodel",
      "title": "Runs specified stan model for the Force-of-Infection (FoI)",
      "topics": [
        "fit_seromodel"
      ]
    },
    {
      "page": "get_foi_index",
      "title": "Generates Force-of-Infection indexes for heterogeneous age groups",
      "topics": [
        "get_foi_index"
      ]
    },
    {
      "page": "plot_foi_estimates",
      "title": "Plots Force-of-Infection central estimates",
      "topics": [
        "plot_foi_estimates"
      ]
    },
    {
      "page": "plot_rhats",
      "title": "Plot r-hats convergence criteria for the specified model",
      "topics": [
        "plot_rhats"
      ]
    },
    {
      "page": "plot_seromodel",
      "title": "Visualise results of the provided model",
      "topics": [
        "plot_seromodel"
      ]
    },
    {
      "page": "plot_seroprev_estimates",
      "title": "Plot seroprevalence estimates on top of the serosurvey",
      "topics": [
        "plot_seroprev_estimates"
      ]
    },
    {
      "page": "plot_serosurvey",
      "title": "Plots seroprevalence from the given serosurvey",
      "topics": [
        "plot_serosurvey"
      ]
    },
    {
      "page": "plot_summary",
      "title": "Plots model summary",
      "topics": [
        "plot_summary"
      ]
    },
    {
      "page": "prepare_serosurvey_for_plot",
      "title": "Prepares serosurvey for plotting",
      "topics": [
        "prepare_serosurvey_for_plot"
      ]
    },
    {
      "page": "prob_seroprev_age_by_age",
      "title": "Generate probabilities of seropositivity by age based on an age-varying Force-of-Infection (FoI) model.",
      "topics": [
        "prob_seroprev_age_by_age"
      ]
    },
    {
      "page": "prob_seroprev_age_time_by_age",
      "title": "Generate probabilities of seropositivity by age based on an age-and-time varying Force-of-Infection (FoI) model.",
      "topics": [
        "prob_seroprev_age_time_by_age"
      ]
    },
    {
      "page": "prob_seroprev_by_age",
      "title": "Generate probabilities of seropositivity by age based on model choice.",
      "topics": [
        "prob_seroprev_by_age"
      ]
    },
    {
      "page": "prob_seroprev_gen_by_age",
      "title": "Generate probabilities of seropositivity by age based on a general Force-of-Infection (FoI) model.",
      "topics": [
        "prob_seroprev_gen_by_age"
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    },
    {
      "page": "prob_seroprev_time_by_age",
      "title": "Generate probabilities of seropositivity by age based on a time-varying Force-of-Infection (FoI) model.",
      "topics": [
        "prob_seroprev_time_by_age"
      ]
    },
    {
      "page": "probability_exact_age_varying",
      "title": "Computes the probability of being seropositive when Forces-of-Infection (FoIs) vary by age",
      "topics": [
        "probability_exact_age_varying"
      ]
    },
    {
      "page": "probability_exact_time_varying",
      "title": "Computes the probability of being seropositive when Forces-of-Infection (FoIs) vary by time",
      "topics": [
        "probability_exact_time_varying"
      ]
    },
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    },
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      "title": "Set stan data defaults for sampling",
      "topics": [
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      ]
    },
    {
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      "title": "Sets Cauchy distribution parameters for sampling",
      "topics": [
        "sf_cauchy"
      ]
    },
    {
      "page": "sf_none",
      "title": "Sets empty prior distribution",
      "topics": [
        "sf_none"
      ]
    },
    {
      "page": "sf_normal",
      "title": "Sets normal distribution parameters for sampling",
      "topics": [
        "sf_normal"
      ]
    },
    {
      "page": "sf_uniform",
      "title": "Sets uniform distribution parameters for sampling",
      "topics": [
        "sf_uniform"
      ]
    },
    {
      "page": "simulate_serosurvey",
      "title": "Simulate serosurvey data based on various Force-of-Infection (FoI) models.",
      "topics": [
        "simulate_serosurvey"
      ]
    },
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      "page": "simulate_serosurvey_age",
      "title": "Simulate serosurvey data based on an age-varying Force-of-Infection (FoI) model.",
      "topics": [
        "simulate_serosurvey_age"
      ]
    },
    {
      "page": "simulate_serosurvey_age_time",
      "title": "Simulate serosurvey data based on an age-and-time-varying Force-of-Infection (FoI) model.",
      "topics": [
        "simulate_serosurvey_age_time"
      ]
    },
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      "page": "simulate_serosurvey_general",
      "title": "Simulate serosurvey data based on general serocatalytic model.",
      "topics": [
        "simulate_serosurvey_general"
      ]
    },
    {
      "page": "simulate_serosurvey_time",
      "title": "Simulate serosurvey data based on a time-varying Force-of-Infection (FoI) model.",
      "topics": [
        "simulate_serosurvey_time"
      ]
    },
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      "title": "Summarise central estimate",
      "topics": [
        "summarise_central_estimate"
      ]
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      "title": "Summarise specified model",
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      "title": "Venezuelan Equine Encephalitis Virus (VEEV) seroprevalence data in serofoi",
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