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  "Title": "Estimating Infection Rates from Serological Data",
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  "Description": "Translates antibody levels measured in cross-sectional\npopulation samples into estimates of the frequency with which\nseroconversions (infections) occur in the sampled populations.\nReplaces the previous `seroincidence` package.",
  "License": "GPL-3",
  "URL": "https://ucd-serg.github.io/serocalculator/,\nhttps://github.com/UCD-SERG/serocalculator",
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  "Date/Publication": "2026-10-09 00:52:53 UTC",
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  "Author": "Kristina Lai [aut, cre],\nChris Orwa [aut],\nKwan Ho Lee [ctb],\nPeter Teunis [aut, cph] (Author of the method and original code.),\nKristen Aiemjoy [aut],\nDouglas Ezra Morrison [aut]",
  "Maintainer": "Kristina Lai <kwlai@ucdavis.edu>",
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  "_created": "2026-10-09T02:46:39.000Z",
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  "_exports": [
    "ab_5p",
    "analyze_sims",
    "antibody_decay_curve",
    "as_curve_params",
    "as_noise_params",
    "as_pop_data",
    "as_sr_params",
    "autoplot",
    "check_pop_data",
    "compare_seroincidence",
    "count_strata",
    "curve_app",
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    "est_seroincidence_by",
    "est_seroincidence_by_cached",
    "est.incidence",
    "est.incidence.by",
    "expect_snapshot_data",
    "f_dev",
    "f_dev0",
    "fdev",
    "get_biomarker_levels",
    "get_biomarker_names",
    "get_biomarker_names_var",
    "get_values",
    "get_values_var",
    "graph_loglik",
    "graph_seroresponse_model_1",
    "graph.curve.params",
    "ids",
    "ids_varname",
    "llik",
    "load_curve_params",
    "load_noise_params",
    "load_pop_data",
    "load_sr_params",
    "log_likelihood",
    "pathogen_decay_curve",
    "plot_decay_curve",
    "refit_strata",
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    "set_id_var",
    "sim_pop_data",
    "sim_pop_data_2",
    "sim_pop_data_multi",
    "sim_pop_data_multi_cached",
    "sim.cs",
    "sim.cs.multi",
    "strat_ests_barplot",
    "strat_ests_scatterplot",
    "strata",
    "t1f",
    "y1f"
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    {
      "name": "example_noise_params_pk",
      "title": "Small example of noise parameters for typhoid",
      "object": "example_noise_params_pk",
      "class": [
        "noise_params",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "antigen_iso",
        "Country",
        "y.low",
        "eps",
        "nu",
        "y.high",
        "Lab"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_noise_params_sees",
      "title": "Small example of noise parameters for typhoid",
      "object": "example_noise_params_sees",
      "class": [
        "noise_params",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
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        "Country",
        "y.low",
        "eps",
        "nu",
        "y.high",
        "Lab"
      ],
      "rows": 16,
      "table": true,
      "tojson": true
    },
    {
      "name": "sees_pop_data_100",
      "title": "Small example cross-sectional data set",
      "object": "sees_pop_data_100",
      "class": [
        "pop_data",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "id",
        "Country",
        "cluster",
        "catchment",
        "age",
        "ageCat",
        "antigen_iso",
        "value"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "sees_pop_data_pk_100",
      "title": "Small example cross-sectional data set",
      "object": "sees_pop_data_pk_100",
      "class": [
        "pop_data",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
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        "id",
        "Country",
        "cluster",
        "catchment",
        "age",
        "ageCat",
        "antigen_iso",
        "value"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    },
    {
      "name": "sees_pop_data_pk_100_old_names",
      "title": "Small example cross-sectional data set",
      "object": "sees_pop_data_pk_100_old_names",
      "class": [
        "pop_data",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
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        "Country",
        "cluster",
        "catchment",
        "Age",
        "ageCat",
        "antigen_iso",
        "result"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    },
    {
      "name": "sees_typhoid_ests_strat",
      "title": "Example '\"seroincidence.by\"' object",
      "object": "sees_typhoid_ests_strat",
      "class": [
        "seroincidence.by",
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "typhoid_curves_nostrat_100",
      "title": "Small example of antibody response curve parameters for typhoid",
      "object": "typhoid_curves_nostrat_100",
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        "curve_params",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
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        "iter",
        "y0",
        "y1",
        "t1",
        "alpha",
        "r"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "analyze_sims",
      "title": "Analyze simulation results",
      "topics": [
        "analyze_sims"
      ]
    },
    {
      "page": "antibody_decay_curve",
      "title": "Antibody decay curve with natural parameters",
      "topics": [
        "antibody_decay_curve"
      ]
    },
    {
      "page": "as_noise_params",
      "title": "Load noise parameters",
      "topics": [
        "as_noise_params"
      ]
    },
    {
      "page": "as_pop_data",
      "title": "Load a cross-sectional antibody survey data set",
      "topics": [
        "as_pop_data"
      ]
    },
    {
      "page": "as_sr_params",
      "title": "Load longitudinal seroresponse parameters",
      "topics": [
        "as_sr_params"
      ]
    },
    {
      "page": "autoplot.curve_params",
      "title": "Graph antibody decay curves by antigen isotype",
      "topics": [
        "autoplot.curve_params"
      ]
    },
    {
      "page": "autoplot.pop_data",
      "title": "Plot distribution of antibodies",
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