{
  "_id": "6a169144acfb0bcc41d7899a",
  "Package": "vigicaen",
  "Title": "'VigiBase' Pharmacovigilance Database Toolbox",
  "Version": "1.0.0.9000",
  "Authors@R": "c(\nperson(\"Charles\", \"Dolladille\", email = \"cdolladille@hotmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0449-6261\")),\nperson(\"Basile\", \"Chrétien\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-7483-2489\")),\nperson(\"Universite de Caen Normandie\", role = c(\"cph\"), comment = \"Caen, France\"),\nperson(\"Unite de pharmaco-epidemiologie\", role = c(\"cph\") , comment = \"Service de pharmacologie, Centre Hospitalier Universitaire de Caen, Caen, France\")\n)",
  "Description": "Perform the analysis of the World Health Organization\n(WHO) Pharmacovigilance database 'VigiBase' (Extract Case Level\nversion), <https://who-umc.org/> e.g., load data, perform data\nmanagement, disproportionality analysis, and descriptive\nstatistics. Intended for pharmacovigilance routine use or\nstudies. This package is NOT supported nor reflect the opinion\nof the WHO, or the Uppsala Monitoring Centre.\nDisproportionality methods are described by Norén et al (2013)\n<doi:10.1177/0962280211403604>.",
  "License": "CeCILL-2.1",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "LazyDataCompression": "xz",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/pharmacologie-caen/vigicaen,\nhttps://pharmacologie-caen.github.io/vigicaen/",
  "BugReports": "https://github.com/pharmacologie-caen/vigicaen/issues",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libicu-dev libssl-dev",
  "Repository": "https://pharmacologie-caen.r-universe.dev",
  "Date/Publication": "2026-03-26 02:22:25 UTC",
  "RemoteUrl": "https://github.com/pharmacologie-caen/vigicaen",
  "RemoteRef": "HEAD",
  "RemoteSha": "97a72724d069fc5ed7da838c8a3f9c56d9426b9f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 06:33:16 UTC",
    "User": "root"
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  "Author": "Charles Dolladille [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0449-6261>),\nBasile Chrétien [aut] (ORCID: <https://orcid.org/0000-0002-7483-2489>),\nUniversite de Caen Normandie [cph] (Caen, France),\nUnite de pharmaco-epidemiologie [cph] (Service de pharmacologie, Centre\nHospitalier Universitaire de Caen, Caen, France)",
  "Maintainer": "Charles Dolladille <cdolladille@hotmail.com>",
  "MD5sum": "fd85065888ef0588f07813df8528acad",
  "_user": "pharmacologie-caen",
  "_type": "src",
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  "_created": "2026-05-27T06:33:16.000Z",
  "_published": "2026-05-27T06:37:56.476Z",
  "_distro": "noble",
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    "author": "Basile <150671964+BasileChretien@users.noreply.github.com>",
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    "message": "Merge pull request #165 from pharmacologie-caen/csv_input\n\nswitch to csv input and rename MedicinalProd_Id to Record_Id",
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    "add_dose",
    "add_drug",
    "add_ind",
    "cff",
    "check_dm",
    "compute_dispro",
    "compute_interaction",
    "compute_or_mod",
    "create_ex_main_csv",
    "create_ex_main_pq",
    "create_ex_meddra_asc",
    "create_ex_sub_csv",
    "create_ex_sub_pq",
    "create_ex_who_csv",
    "desc_cont",
    "desc_dch",
    "desc_facvar",
    "desc_outcome",
    "desc_rch",
    "desc_tto",
    "dt_parquet",
    "extract_tto",
    "get_atc_code",
    "get_drecno",
    "get_llt_smq",
    "get_llt_soc",
    "ic_tail",
    "nice_p",
    "screen_adr",
    "screen_drug",
    "tb_meddra",
    "tb_subset",
    "tb_vigibase",
    "tb_who",
    "vigi_routine"
  ],
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      "title": "Data of immune checkpoint inhibitors.",
      "object": "adr_",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "UMCReportId",
        "Adr_Id",
        "MedDRA_Id",
        "Outcome"
      ],
      "rows": 2133,
      "table": true,
      "tojson": true
    },
    {
      "name": "demo_",
      "title": "Data of immune checkpoint inhibitors.",
      "object": "demo_",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "UMCReportId",
        "AgeGroup",
        "Gender",
        "DateDatabase",
        "Type",
        "Region",
        "FirstDateDatabase"
      ],
      "rows": 750,
      "table": true,
      "tojson": true
    },
    {
      "name": "drug_",
      "title": "Data of immune checkpoint inhibitors.",
      "object": "drug_",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "UMCReportId",
        "Drug_Id",
        "Record_Id",
        "DrecNo",
        "Seq1",
        "Seq2",
        "Route",
        "Basis",
        "Amount",
        "AmountU",
        "Frequency",
        "FrequencyU"
      ],
      "rows": 3514,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_",
      "title": "Data for the immune checkpoint inhibitors example",
      "object": "ex_",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
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      "title": "Data of immune checkpoint inhibitors.",
      "object": "followup_",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "UMCReportId",
        "ReplacedUMCReportId"
      ],
      "rows": 902,
      "table": true,
      "tojson": true
    },
    {
      "name": "ind_",
      "title": "Data of immune checkpoint inhibitors.",
      "object": "ind_",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "Drug_Id",
        "Indication"
      ],
      "rows": 2426,
      "table": true,
      "tojson": true
    },
    {
      "name": "link_",
      "title": "Data of immune checkpoint inhibitors.",
      "object": "link_",
      "class": [
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        "data.frame"
      ],
      "fields": [
        "Drug_Id",
        "Adr_Id",
        "Dechallenge1",
        "Dechallenge2",
        "Rechallenge1",
        "Rechallenge2",
        "TimeToOnsetMin",
        "TimeToOnsetMax",
        "tto_mean",
        "range",
        "UMCReportId"
      ],
      "rows": 5136,
      "table": true,
      "tojson": true
    },
    {
      "name": "meddra_",
      "title": "Sample of MedDRA",
      "object": "meddra_",
      "class": [
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        "data.frame"
      ],
      "fields": [
        "llt_code",
        "llt_name",
        "pt_code",
        "hlt_code",
        "hlgt_code",
        "soc_code",
        "pt_name",
        "hlt_name",
        "hlgt_name",
        "soc_name",
        "soc_abbrev",
        "null_field",
        "pt_soc_code",
        "primary_soc_fg",
        "empty_col"
      ],
      "rows": 677,
      "table": true,
      "tojson": true
    },
    {
      "name": "mp_",
      "title": "Sample of WHODrug",
      "object": "mp_",
      "class": [
        "data.table",
        "data.frame"
      ],
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        "Record_Id",
        "Sequence.number.1",
        "Sequence.number.2",
        "DrecNo",
        "drug_name_t",
        "Create.date",
        "Date.changed",
        "Country"
      ],
      "rows": 14147,
      "table": true,
      "tojson": true
    },
    {
      "name": "out_",
      "title": "Data of immune checkpoint inhibitors.",
      "object": "out_",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "UMCReportId",
        "Seriousness",
        "Serious"
      ],
      "rows": 747,
      "table": true,
      "tojson": true
    },
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        "data.frame"
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        "term_code",
        "term_level",
        "term_scope",
        "term_category",
        "term_weight",
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        "term_addition_version",
        "term_last_modified_version"
      ],
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      "table": true,
      "tojson": true
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      "object": "smq_list_",
      "class": [
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        "data.frame"
      ],
      "fields": [
        "smq_code",
        "smq_name",
        "smq_level",
        "smq_description",
        "smq_source",
        "smq_note",
        "MedDRA_version",
        "status",
        "smq_algorithm"
      ],
      "rows": 11,
      "table": true,
      "tojson": true
    },
    {
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      "title": "Sample of MedDRA",
      "object": "smq_list_content_",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "smq_code",
        "smq_name",
        "smq_level",
        "smq_description",
        "smq_source",
        "smq_note",
        "MedDRA_version",
        "status",
        "smq_algorithm",
        "empty_col.x",
        "term_code",
        "term_level",
        "term_scope",
        "term_category",
        "term_weight",
        "term_status",
        "term_addition_version",
        "term_last_modified_version",
        "empty_col.y"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "srce_",
      "title": "Data of immune checkpoint inhibitors.",
      "object": "srce_",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "UMCReportId",
        "Type"
      ],
      "rows": 729,
      "table": true,
      "tojson": true
    },
    {
      "name": "thg_",
      "title": "Sample of WHODrug",
      "object": "thg_",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "Therapgroup_Id",
        "ATC.code",
        "Create.date",
        "Official.ATC.code",
        "Record_Id"
      ],
      "rows": 4079,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_adr",
      "title": "Add adverse drug reaction column(s) to a dataset",
      "topics": [
        "add_adr"
      ]
    },
    {
      "page": "add_dose",
      "title": "Add drug dose column(s) to a dataset, in milligram per day",
      "topics": [
        "add_dose"
      ]
    },
    {
      "page": "add_drug",
      "title": "Add drug column(s) to a dataset",
      "topics": [
        "add_drug"
      ]
    },
    {
      "page": "add_ind",
      "title": "Add indication column(s) to a dataset",
      "topics": [
        "add_ind"
      ]
    },
    {
      "page": "cff",
      "title": "Fast formatting of numbers",
      "topics": [
        "cff"
      ]
    },
    {
      "page": "check_dm",
      "title": "Check binary variables",
      "topics": [
        "check_dm"
      ]
    },
    {
      "page": "compute_dispro",
      "title": "Compute disproportionality",
      "topics": [
        "compute_dispro"
      ]
    },
    {
      "page": "compute_interaction",
      "title": "Compute interaction disproportionality",
      "topics": [
        "compute_interaction"
      ]
    },
    {
      "page": "compute_or_mod",
      "title": "Compute (r)OR from a model summary",
      "topics": [
        "compute_or_mod"
      ]
    },
    {
      "page": "create_example_tables",
      "title": "Example source tables for VigiBase and MedDRA",
      "topics": [
        "create_example_tables",
        "create_ex_main_csv",
        "create_ex_main_pq",
        "create_ex_meddra_asc",
        "create_ex_sub_csv",
        "create_ex_sub_pq",
        "create_ex_who_csv"
      ]
    },
    {
      "page": "demo_",
      "title": "Data of immune checkpoint inhibitors.",
      "topics": [
        "adr_",
        "demo_",
        "drug_",
        "followup_",
        "ind_",
        "link_",
        "out_",
        "srce_"
      ]
    },
    {
      "page": "desc_cont",
      "title": "Summarise continuous variables",
      "topics": [
        "desc_cont"
      ]
    },
    {
      "page": "desc_dch",
      "title": "Dechallenge descriptive",
      "topics": [
        "desc_dch"
      ]
    },
    {
      "page": "desc_facvar",
      "title": "Summarise categorical variables",
      "topics": [
        "desc_facvar"
      ]
    },
    {
      "page": "desc_outcome",
      "title": "Outcome descriptive",
      "topics": [
        "desc_outcome"
      ]
    },
    {
      "page": "desc_rch",
      "title": "Rechallenge descriptive",
      "topics": [
        "desc_rch"
      ]
    },
    {
      "page": "desc_tto",
      "title": "Time to onset descriptive",
      "topics": [
        "desc_tto"
      ]
    },
    {
      "page": "dt_parquet",
      "title": "Read parquet and convert to data.table",
      "topics": [
        "dt_parquet"
      ]
    },
    {
      "page": "ex_",
      "title": "Data for the immune checkpoint inhibitors example",
      "topics": [
        "ex_"
      ]
    },
    {
      "page": "extract_tto",
      "title": "Time to onset extraction",
      "topics": [
        "extract_tto"
      ]
    },
    {
      "page": "get_atc_code",
      "title": "Get ATC codes (DrecNos or MPIs)",
      "topics": [
        "get_atc_code"
      ]
    },
    {
      "page": "get_drecno",
      "title": "Get DrecNo from drug names or Record_Id",
      "topics": [
        "get_drecno"
      ]
    },
    {
      "page": "get_llt_smq",
      "title": "Get low level term codes from SMQs",
      "topics": [
        "get_llt_smq"
      ]
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