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  "Title": "AvonCap Study Analysis",
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  "Description": "A WIP set of functions allowing data load, wrangling of\nthe AvonCap data set.",
  "License": "MIT + file LICENSE",
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  "BugReports": "https://github.com/bristol-vaccine-centre/avoncap/issues",
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  "Repository": "https://bristol-vaccine-centre.r-universe.dev",
  "Date/Publication": "2024-12-03 17:46:00 UTC",
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      ],
      "topics": [
        "derive_patient_identifier"
      ]
    },
    {
      "page": "derive_pcv_groupings",
      "title": "Group pneumo serotypes according to e.g. vaccine coverage",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_pcv_groupings"
      ]
    },
    {
      "page": "derive_phe_pcv_group",
      "title": "Get vaccine coverage group for known serotype",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_phe_pcv_group"
      ]
    },
    {
      "page": "derive_pneumo_clinical_syndrome",
      "title": "Add in clinical syndrome indicator",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_pneumo_clinical_syndrome"
      ]
    },
    {
      "page": "derive_pneumo_polyfill",
      "title": "Make pneumo data compatible with AvonCAP",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_pneumo_polyfill"
      ]
    },
    {
      "page": "derive_pneumo_uad_panel",
      "title": "Calculate UAD panel for test",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_pneumo_uad_panel"
      ]
    },
    {
      "page": "derive_pneumo_uad_status",
      "title": "Calculate summary status from UAD (or other serotype) panel results",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_pneumo_uad_status"
      ]
    },
    {
      "page": "derive_pneumococcal_categories",
      "title": "The pneumococcal incidence diagnostic classifications",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_pneumococcal_categories"
      ]
    },
    {
      "page": "derive_pneumococcal_high_risk",
      "title": "Determine if patient is in a high pneumococcal risk group",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_pneumococcal_high_risk"
      ]
    },
    {
      "page": "derive_pneumococcal_risk_category",
      "title": "Determine pneumococcal risk group",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_pneumococcal_risk_category"
      ]
    },
    {
      "page": "derive_polyfill_central",
      "title": "Polyfill data",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_polyfill_central"
      ]
    },
    {
      "page": "derive_polyfill_ed",
      "title": "Polyfill ED data",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_polyfill_ed"
      ]
    },
    {
      "page": "derive_presumed_diagnosis_categories",
      "title": "Create presumed diagnostic categories",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_presumed_diagnosis_categories"
      ]
    },
    {
      "page": "derive_qcovid",
      "title": "Calculate a QCOVID2 score from AvonCap data source",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_qcovid"
      ]
    },
    {
      "page": "derive_quintile_category",
      "title": "Split a continuous variable into quintiles",
      "topics": [
        "derive_quintile_category"
      ]
    },
    {
      "page": "derive_severe_disease_outcomes",
      "title": "Binary outcomes for severe disease",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_severe_disease_outcomes"
      ]
    },
    {
      "page": "derive_simpler_comorbidities",
      "title": "Rationalise some of the more detailed comorbidities",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_simpler_comorbidities"
      ]
    },
    {
      "page": "derive_survival_censoring",
      "title": "Survival outcomes",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_survival_censoring"
      ]
    },
    {
      "page": "derive_survival_times_avoncap",
      "title": "Survival analysis times",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_survival_times_avoncap"
      ]
    },
    {
      "page": "derive_survival_times_pneumo",
      "title": "Survival analysis times",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_survival_times_pneumo"
      ]
    },
    {
      "page": "derive_template",
      "title": "Derived data function template",
      "topics": [
        "derive_template"
      ]
    },
    {
      "page": "derive_vaccination_timings",
      "title": "Derive times from vaccination to symptom onset",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_vaccination_timings"
      ]
    },
    {
      "page": "derive_vaccine_combinations",
      "title": "Deprecated - Vaccine combinations are less relevant now",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_vaccine_combinations"
      ]
    },
    {
      "page": "derive_WHO_outcome_score",
      "title": "determine WHO outcome score",
      "concept": [
        "derived"
      ],
      "topics": [
        "derive_WHO_outcome_score"
      ]
    },
    {
      "page": "extract_dependencies",
      "title": "Get provenance of data column",
      "topics": [
        "extract_dependencies"
      ]
    },
    {
      "page": "find_new_field_names",
      "title": "Get the transformed columns from original field names",
      "topics": [
        "find_new_field_names"
      ]
    },
    {
      "page": "frameworks",
      "title": "Frameworks",
      "topics": [
        "frameworks"
      ]
    },
    {
      "page": "get_value_sets",
      "title": "Get a value set list of a dataframe",
      "topics": [
        "get_value_sets"
      ]
    },
    {
      "page": "icb_surgeries",
      "title": "GP surgeries in the Bristol ICB area",
      "topics": [
        "icb_surgeries"
      ]
    },
    {
      "page": "imd_to_townsend",
      "title": "High level IMD to Townsend score map",
      "topics": [
        "imd_to_townsend"
      ]
    },
    {
      "page": "input",
      "title": "Locate the input directory",
      "topics": [
        "input"
      ]
    },
    {
      "page": "key_dates",
      "title": "Key dates:",
      "topics": [
        "key_dates"
      ]
    },
    {
      "page": "km_plot",
      "title": "Faceted Kaplan-Meier plot",
      "topics": [
        "km_plot"
      ]
    },
    {
      "page": "load_data",
      "title": "Load data and check structure",
      "topics": [
        "load_data"
      ]
    },
    {
      "page": "map_avoncap_central",
      "title": "Core avoncap normalisation",
      "concept": [
        "map"
      ],
      "topics": [
        "map_avoncap_central"
      ]
    },
    {
      "page": "map_avoncap_consent",
      "title": "Core avoncap consent",
      "concept": [
        "map"
      ],
      "topics": [
        "map_avoncap_consent"
      ]
    },
    {
      "page": "map_avoncap_ed",
      "title": "Avoncap ED normalisation",
      "concept": [
        "map"
      ],
      "topics": [
        "map_avoncap_ed"
      ]
    },
    {
      "page": "map_avoncap_ed_consent",
      "title": "ED consent",
      "concept": [
        "map"
      ],
      "topics": [
        "map_avoncap_ed_consent"
      ]
    },
    {
      "page": "map_avoncap_haem",
      "title": "Normalise the avoncap data haematology data",
      "concept": [
        "map"
      ],
      "topics": [
        "map_avoncap_haem"
      ]
    },
    {
      "page": "map_avoncap_micro",
      "title": "Normalise the avoncap data microbiology data",
      "concept": [
        "map"
      ],
      "topics": [
        "map_avoncap_micro"
      ]
    },
    {
      "page": "map_avoncap_pneumococcal",
      "title": "Normalise the avoncap pneumococcal data",
      "concept": [
        "map"
      ],
      "topics": [
        "map_avoncap_pneumococcal"
      ]
    },
    {
      "page": "map_avoncap_radio",
      "title": "Normalise the avoncap data radiology data",
      "concept": [
        "map"
      ],
      "topics": [
        "map_avoncap_radio"
      ]
    },
    {
      "page": "map_avoncap_virol",
      "title": "Normalise the avoncap data virology data",
      "concept": [
        "map"
      ],
      "topics": [
        "map_avoncap_virol"
      ]
    },
    {
      "page": "map_urine_antigens",
      "title": "Normalise the urinary antigen data",
      "concept": [
        "map"
      ],
      "topics": [
        "map_urine_antigens"
      ]
    },
    {
      "page": "map_urine_binax",
      "title": "Normalise the urinary antigen data (binax results)",
      "concept": [
        "map"
      ],
      "topics": [
        "map_urine_binax"
      ]
    },
    {
      "page": "most_recent_files",
      "title": "find most recent files of a specific type",
      "topics": [
        "most_recent_files"
      ]
    },
    {
      "page": "normalise_data",
      "title": "Sanitise AvonCap data columns",
      "topics": [
        "normalise_data"
      ]
    },
    {
      "page": "original_field_names",
      "title": "Get the mapping of transformed columns back to original",
      "topics": [
        "original_field_names"
      ]
    },
    {
      "page": "phe_serotypes",
      "title": "Pneumococcal UAD serotypes",
      "topics": [
        "phe_serotypes"
      ]
    },
    {
      "page": "readable_label",
      "title": "Get a label for a column",
      "topics": [
        "readable_label"
      ]
    },
    {
      "page": "readable_label_mapping",
      "title": "Get a readable label for the AvonCap data as a named list (for ggplot)",
      "topics": [
        "readable_label_mapping",
        "readable_label_mapping.character",
        "readable_label_mapping.data.frame",
        "readable_label_mapping.default",
        "readable_label_mapping.list"
      ]
    },
    {
      "page": "relevel_serotypes",
      "title": "Relevel serotype data into an factor based on PCV group status and serotype name.",
      "topics": [
        "relevel_serotypes"
      ]
    },
    {
      "page": "save_data_source_info",
      "title": "Write file source information out to a text files",
      "topics": [
        "save_data_source_info"
      ]
    },
    {
      "page": "scale_fill_serotype",
      "title": "A ggplot scale for pneumococcal serotypes that keeps PCV groups together",
      "topics": [
        "scale_fill_serotype"
      ]
    },
    {
      "page": "serotype_data",
      "title": "Pneumococcal UAD serotype groups and crossmaps",
      "topics": [
        "serotype_data"
      ]
    },
    {
      "page": "serotype_pcv_map",
      "title": "Pneumococcal serotype PCV groups",
      "topics": [
        "serotype_pcv_map"
      ]
    },
    {
      "page": "serotype_uad_map",
      "title": "Serotype UAD mappings",
      "topics": [
        "serotype_uad_map"
      ]
    },
    {
      "page": "set_input",
      "title": "Sets the location of data for an analysis",
      "topics": [
        "set_input"
      ]
    },
    {
      "page": "spline_term_plot",
      "title": "Spline term marginal effects plot",
      "topics": [
        "spline_term_plot"
      ]
    },
    {
      "page": "stacked_barplot",
      "title": "Stacked bar plot",
      "topics": [
        "stacked_barplot"
      ]
    },
    {
      "page": "start_date_of_week",
      "title": "Convert a study week back into a date",
      "topics": [
        "start_date_of_week"
      ]
    },
    {
      "page": "start_date_of_week_legacy",
      "title": "Convert a study week back into a date",
      "topics": [
        "start_date_of_week_legacy"
      ]
    },
    {
      "page": "study_week",
      "title": "Convert a date to a study week",
      "topics": [
        "study_week"
      ]
    },
    {
      "page": "study_week_legacy",
      "title": "Convert a date to a study week",
      "topics": [
        "study_week_legacy"
      ]
    },
    {
      "page": "uad_groups",
      "title": "UAD serotype groups",
      "topics": [
        "uad_groups"
      ]
    },
    {
      "page": "uad_pcv_map",
      "title": "UAD PCV map",
      "topics": [
        "uad_pcv_map"
      ]
    },
    {
      "page": "upset_plot",
      "title": "Upset plot with counts stratified by a categorical column",
      "topics": [
        "upset_plot"
      ]
    },
    {
      "page": "valid_inputs",
      "title": "A valid set of types of file that can be loaded by 'load_data(...)'",
      "topics": [
        "valid_inputs"
      ]
    },
    {
      "page": "validate_data",
      "title": "Validate AvonCap raw data",
      "topics": [
        "validate_data"
      ]
    },
    {
      "page": "write_issues",
      "title": "Write out data quality issues",
      "topics": [
        "write_issues"
      ]
    },
    {
      "page": "xglimpse",
      "title": "Wrapper around 'table'",
      "topics": [
        "xglimpse"
      ]
    },
    {
      "page": "year_week_number_lookup",
      "title": "Year and week number lookup table",
      "topics": [
        "year_week_number_lookup"
      ]
    }
  ],
  "_readme": "https://github.com/bristol-vaccine-centre/avoncap/raw/HEAD/README.md",
  "_rundeps": [
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    "base64enc",
    "binom",
    "bit",
    "bit64",
    "cli",
    "clipr",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "data.tree",
    "digest",
    "dplyr",
    "dtrackr",
    "farver",
    "fastmap",
    "forcats",
    "fs",
    "generics",
    "ggplot2",
    "ggstance",
    "glue",
    "gtable",
    "hms",
    "htmltools",
    "isoband",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "lubridate",
    "magrittr",
    "Matrix",
    "nplyr",
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    "pdftools",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "qpdf",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "readr",
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    "scales",
    "stringi",
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    "survival",
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    "tibble",
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    "timechange",
    "tzdb",
    "utf8",
    "V8",
    "vctrs",
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    "vroom",
    "withr",
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  "_score": 1.740362689494244,
  "_indexed": true,
  "_nocasepkg": "avoncap",
  "_universes": [
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}