{ "_id": "6a33c7143efcd9bda43b1b81", "Package": "omopgenerics", "Title": "Methods and Classes for the OMOP Common Data Model", "Version": "1.4.0", "Authors@R": "c(\nperson(\n\"Martí\", \"Català\", email = \"marti.catalasabate@ndorms.ox.ac.uk\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3308-9905\")\n),\nperson(\n\"Edward\", \"Burn\", email = \"edward.burn@ndorms.ox.ac.uk\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9286-1128\")\n),\nperson(\n\"Mike\", \"Du\", email = \"mike.du@ndorms.ox.ac.uk\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-9517-8834\")\n),\nperson(\n\"Yuchen\", \"Guo\", email = \"yuchen.guo@ndorms.ox.ac.uk\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-0847-4855\")\n),\nperson(\n\"Adam\", \"Black\", email = \"black@ohdsi.org\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-5576-8701\")\n),\nperson(\n\"Marta\", \"Alcalde-Herraiz\",\nemail = \"marta.alcaldeherraiz@ndorms.ox.ac.uk\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0009-0002-4405-1814\")\n)\n)", "Description": "Provides definitions of core classes and methods used by\nanalytic pipelines that query the OMOP (Observational Medical\nOutcomes Partnership) common data model.", "License": "Apache License (>= 2)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://darwin-eu.github.io/omopgenerics/", "BugReports": "https://github.com/darwin-eu/omopgenerics/issues", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://darwin-eu.r-universe.dev", "Date/Publication": "2026-06-18 08:05:36 UTC", "RemoteUrl": "https://github.com/darwin-eu/omopgenerics", "RemoteRef": "HEAD", "RemoteSha": "d94fd7772d796ee003aa0779c1dfd8674c7c9055", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-18 10:18:57 UTC", "User": "root" }, "Author": "Martí Català [aut, cre] (ORCID:\n),\nEdward Burn [aut] (ORCID: ),\nMike Du [ctb] 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] }, { "page": "assertLogical", "title": "Assert that an object is a logical.", "topics": [ "assertLogical" ] }, { "page": "assertNumeric", "title": "Assert that an object is a numeric.", "topics": [ "assertNumeric" ] }, { "page": "assertTable", "title": "Assert that an object is a table.", "topics": [ "assertTable" ] }, { "page": "assertTrue", "title": "Assert that an expression is TRUE.", "topics": [ "assertTrue" ] }, { "page": "attrition", "title": "Get attrition from an object.", "topics": [ "attrition" ] }, { "page": "attrition.cohort_table", "title": "Get cohort attrition from a cohort_table object.", "topics": [ "attrition.cohort_table" ] }, { "page": "bind", "title": "Bind two or more objects of the same class.", "topics": [ "bind" ] }, { "page": "bind.cohort_table", "title": "Bind two or more cohort tables", "topics": [ "bind.cohort_table" ] }, { "page": "bind.summarised_result", "title": "Bind two or summarised_result objects", "topics": [ "bind.summarised_result" ] }, { "page": "cdmClasses", "title": "Separate the cdm tables in classes", "topics": [ "cdmClasses" ] }, { "page": "cdmDisconnect", "title": "Disconnect from a cdm object.", "topics": [ "cdmDisconnect" ] }, { "page": "cdmFromTables", "title": "Create a cdm object from local tables", "topics": [ "cdmFromTables" ] }, { "page": "cdmName", "title": "Get or set the name of a cdm_reference associated object", "topics": [ "cdmName", "cdmName<-" ] }, { "page": "cdmReference", "title": "Get the 'cdm_reference' of a 'cdm_table'.", "topics": [ "cdmReference" ] }, { "page": "cdmSelect", "title": "Restrict the cdm object to a subset of tables.", "topics": [ "cdmSelect" ] }, { "page": "cdmSource", "title": "Get the cdmSource of an object.", "topics": [ "cdmSource" ] }, { "page": "cdmSourceType", "title": "Get the source type of a cdm_reference object.", "topics": [ "cdmSourceType" ] }, { "page": "cdmTableFromSource", "title": "This is an internal developer focused function that creates a cdm_table from a table that shares the source but it is not a cdm_table. Please use insertTable if you want to insert a table to a cdm_reference object.", "topics": [ "cdmTableFromSource" ] }, { "page": "cdmVersion", "title": "Get the version of an object.", "topics": [ "cdmVersion" ] }, { "page": "checkCohortRequirements", "title": "Check whether a cohort table satisfies requirements", "topics": [ "checkCohortRequirements" ] }, { "page": "cohortCodelist", "title": "Get codelist from a cohort_table object.", "topics": [ "cohortCodelist" ] }, { "page": "cohortColumns", "title": "Required columns for a generated cohort set.", "topics": [ "cohortColumns" ] }, { "page": "cohortCount", "title": "Get cohort counts from a cohort_table object.", "topics": [ "cohortCount" ] }, { "page": "cohortTables", "title": "Cohort tables that a cdm reference can contain in the OMOP Common Data Model.", "topics": [ "cohortTables" ] }, { "page": "collect.cdm_reference", "title": "Retrieve the cdm reference into a local cdm.", "topics": [ "collect.cdm_reference" ] }, { "page": 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"emptyAchillesTable", "title": "Create an empty achilles table", "topics": [ "emptyAchillesTable" ] }, { "page": "emptyCdmReference", "title": "Create an empty cdm_reference", "topics": [ "emptyCdmReference" ] }, { "page": "emptyCodelist", "title": "Empty 'codelist' object.", "topics": [ "emptyCodelist" ] }, { "page": "emptyCodelistWithDetails", "title": "Empty 'codelist' object.", "topics": [ "emptyCodelistWithDetails" ] }, { "page": "emptyCodeSearch", "title": "Empty code search object", "topics": [ "emptyCodeSearch" ] }, { "page": "emptyCohortTable", "title": "Create an empty cohort_table object", "topics": [ "emptyCohortTable" ] }, { "page": "emptyConceptSetExpression", "title": "Empty 'concept_set_expression' object.", "topics": [ "emptyConceptSetExpression" ] }, { "page": "emptyOmopTable", "title": "Create an empty omop table", "topics": [ "emptyOmopTable" ] }, { "page": "emptySummarisedResult", "title": "Empty 'summarised_result' object.", "topics": [ "emptySummarisedResult" ] }, { "page": "estimateTypeChoices", "title": "Choices that can be present in 'estimate_type' column.", "topics": [ "estimateTypeChoices" ] }, { "page": "existingIndexes", "title": "Existing indexes in a cdm object", "topics": [ "existingIndexes" ] }, { "page": "expectedIndexes", "title": "Expected indexes in a cdm object", "topics": [ "expectedIndexes" ] }, { "page": "exportCodelist", "title": "Export a codelist object.", "topics": [ "exportCodelist" ] }, { "page": "exportCodelistWithDetails", "title": "Export a codelist with details object.", "topics": [ "exportCodelistWithDetails" ] }, { "page": "exportCodeSearch", "title": "Export a 'code_search' object into an Excel spreadsheet", "topics": [ "exportCodeSearch" ] }, { "page": "exportConceptSetExpression", "title": "Export a concept set expression.", "topics": [ "exportConceptSetExpression" ] }, { "page": "exportSummarisedResult", "title": "Export a summarised_result object to a CSV file.", "topics": [ "exportSummarisedResult" ] }, { "page": "filterAdditional", "title": "Filter the additional_name-additional_level pair in a summarised_result", "topics": [ "filterAdditional" ] }, { "page": "filterGroup", "title": "Filter the group_name-group_level pair in a summarised_result", "topics": [ "filterGroup" ] }, { "page": "filterResult", "title": "Filter a automatically", "topics": [ "filterResult" ] }, { "page": "filterSettings", "title": "Filter a using the settings", "topics": [ "filterSettings" ] }, { "page": "filterStrata", "title": "Filter the strata_name-strata_level pair in a summarised_result", "topics": [ "filterStrata" ] }, { "page": "getCohortId", "title": "Get the cohort definition id of a certain name", "topics": [ "getCohortId" ] }, { "page": "getCohortName", "title": "Get the cohort name of a certain cohort definition id", "topics": [ "getCohortName" ] }, { "page": "getPersonIdentifier", "title": "Get the column name with the person identifier from a table (either subject_id or person_id), it will throw an error if it contains both or neither.", "topics": [ "getPersonIdentifier" ] }, { "page": "groupColumns", "title": "Identify variables in group_name column", "topics": [ "groupColumns" ] }, { "page": "importCodelist", "title": "Import a codelist.", "topics": [ "importCodelist" ] }, { "page": "importCodelistWithDetails", "title": "Import a codelist with details.", "topics": [ "importCodelistWithDetails" ] }, { "page": "importCodeSearch", "title": "Import a 'code_search' object from an Excel spreadsheet", "topics": [ "importCodeSearch" ] }, { "page": "importConceptSetExpression", "title": "Import a concept set expression.", "topics": [ "importConceptSetExpression" ] }, { "page": "importSummarisedResult", "title": "Import a set of summarised results.", "topics": [ "importSummarisedResult" ] }, { "page": "insertCdmTo", "title": "Insert a cdm_reference object to a different source.", "topics": [ "insertCdmTo" ] }, { "page": "insertFromSource", "title": "Convert a table that is not a cdm_table but have the same original source to a cdm_table. This Table is not meant to be used to insert tables in the cdm, please use insertTable instead.", "topics": [ "insertFromSource" ] }, { "page": "insertTable", "title": "Insert a table into a cdm object.", "topics": [ "insertTable" ] }, { "page": "isResultSuppressed", "title": "To check whether an object is already suppressed to a certain min cell count.", "topics": [ "isResultSuppressed" ] }, { "page": "isTableEmpty", "title": "Check if a table is empty or not", "topics": [ "isTableEmpty" ] }, { "page": "listSourceTables", "title": "List tables that can be accessed through a cdm object.", "topics": [ "listSourceTables" ] }, { "page": "logMessage", "title": "Log a message to a logFile", "topics": [ "logMessage" ] }, { "page": "newAchillesTable", "title": "Create an achilles table from a cdm_table.", "topics": [ "newAchillesTable" ] }, { "page": "newCdmReference", "title": "'cdm_reference' objects constructor", "topics": [ "newCdmReference" ] }, { "page": "newCdmSource", "title": "Create a cdm source object.", "topics": [ "newCdmSource" ] }, { "page": "newCdmTable", "title": "Create an cdm table.", "topics": [ "newCdmTable" ] }, { "page": "newCodelist", "title": "'codelist' object constructor", "topics": [ "newCodelist" ] }, { "page": "newCodelistWithDetails", "title": "'codelist' object constructor", "topics": [ "newCodelistWithDetails" ] }, { "page": "newCodeSearch", "title": "Create a new 'code_search' object", "topics": [ "newCodeSearch" ] }, { "page": "newCohortTable", "title": "'cohort_table' objects constructor.", "topics": [ "newCohortTable" ] }, { "page": "newConceptSetExpression", "title": "'concept_set_expression' object constructor", "topics": [ "newConceptSetExpression" ] }, { "page": "newLocalSource", "title": "A new local source for the cdm", "topics": [ "newLocalSource" ] }, { "page": "newOmopTable", "title": "Create an omop table from a cdm table.", "topics": [ "newOmopTable" ] }, { "page": "newReadOnlySource", "title": "A new read-only source for the cdm", "topics": [ "newReadOnlySource" ] }, { "page": "newSummarisedResult", "title": "'summarised_result' object constructor", "topics": [ "newSummarisedResult" ] }, { "page": "numberRecords", "title": "Count the number of records that a 'cdm_table' has.", "topics": [ "numberRecords" ] }, { "page": "numberSubjects", "title": "Count the number of subjects that a 'cdm_table' has.", "topics": [ "numberSubjects" ] }, { "page": "omopColumns", "title": "Required columns that the standard tables in the OMOP Common Data Model must have.", "topics": [ "omopColumns" ] }, { "page": "omopDataFolder", "title": "Check or set the OMOP_DATA_FOLDER where the OMOP related data is stored.", "topics": [ "omopDataFolder" ] }, { "page": "omopTableFields", "title": "Return a table of omop cdm field information", "topics": [ "omopTableFields" ] }, { "page": "omopTables", "title": "Standard tables that a cdm reference can contain in the OMOP Common Data Model.", "topics": [ "omopTables" ] }, { "page": "pivotEstimates", "title": "Set estimates as columns", "topics": [ "pivotEstimates" ] }, { "page": "print.cdm_reference", "title": "Print a CDM reference object", "topics": [ "print.cdm_reference" ] }, { "page": "print.code_search", "title": "Print a code search", "topics": [ "print.code_search" ] }, { "page": "print.codelist", "title": "Print a codelist", "topics": [ "print.codelist" ] }, { "page": "print.codelist_with_details", "title": "Print a codelist with details", "topics": [ "print.codelist_with_details" ] }, { "page": "print.concept_set_expression", "title": "Print a concept set expression", "topics": [ "print.concept_set_expression" ] }, { "page": "readSourceTable", "title": "Read a table from the cdm_source and add it to the cdm.", "topics": [ "readSourceTable" ] }, { "page": "recordCohortAttrition", "title": "Update cohort attrition.", "topics": [ "recordCohortAttrition" ] }, { "page": "resultColumns", "title": "Required columns that the result tables must have.", "topics": [ "resultColumns" ] }, { "page": "resultPackageVersion", "title": "Check if different package versions are used for a summarised_result object", "topics": [ "resultPackageVersion" ] }, { "page": "resultType", "title": "Get the 'result_type(s)' defined in a certain package", "topics": [ "resultType" ] }, { "page": "searchStrategy", "title": "Get the search strategy used to create a 'code_search'", "topics": [ "searchStrategy" ] }, { "page": "settings", "title": "Get settings from an object.", "topics": [ "settings" ] }, { "page": "settings.cohort_table", "title": "Get cohort settings from a cohort_table object.", "topics": [ "settings.cohort_table" ] }, { "page": "settings.summarised_result", "title": "Get settings from a summarised_result object.", "topics": [ "settings.summarised_result" ] }, { "page": "settingsColumns", "title": "Identify settings columns of a ", "topics": [ "settingsColumns" ] }, { "page": "sourceType", "title": "Get the source type of an object.", "topics": [ "sourceType" ] }, { "page": "splitAdditional", "title": "Split additional_name and additional_level columns", "topics": [ "splitAdditional" ] }, { "page": "splitAll", "title": "Split all pairs name-level into columns.", "topics": [ "splitAll" ] }, { "page": "splitGroup", "title": "Split group_name and group_level columns", "topics": [ "splitGroup" ] }, { "page": "splitStrata", "title": "Split strata_name and strata_level columns", "topics": [ "splitStrata" ] }, { "page": "statusIndexes", "title": "Status of the indexes", "topics": [ "statusIndexes" ] }, { "page": "strataColumns", "title": "Identify variables in strata_name column", "topics": [ "strataColumns" ] }, { "page": "summariseLogFile", "title": "Summarise and extract the information of a log file into a 'summarised_result' object.", "topics": [ "summariseLogFile" ] }, { "page": "summary.cdm_reference", "title": "Summarise a cdm reference", "topics": [ "summary.cdm_reference" ] }, { "page": "summary.cdm_source", "title": "Summarise a 'cdm_source' object", "topics": [ "summary.cdm_source" ] }, { "page": "summary.cohort_table", "title": "Summarise a generated cohort set", "topics": [ "summary.cohort_table" ] }, { "page": "summary.summarised_result", "title": "Summarise a summarised_result", "topics": [ "summary.summarised_result" ] }, { "page": "suppress", "title": "Function to suppress counts in result objects", "topics": [ "suppress" ] }, { "page": "suppress.summarised_result", "title": "Function to suppress counts in result objects", "topics": [ "suppress.summarised_result" ] }, { "page": "tableName", "title": "Get the table name of a 'cdm_table'.", "topics": [ "tableName" ] }, { "page": "tableSource", "title": "Get the table source of a 'cdm_table'.", "topics": [ "tableSource" ] }, { "page": "tidy.summarised_result", "title": "Turn a object into a tidy tibble", "topics": [ "tidy.summarised_result" ] }, { "page": "tidyColumns", "title": "Identify tidy columns of a ", "topics": [ "tidyColumns" ] }, { "page": "tmpPrefix", "title": "Create a temporary prefix for tables that contains a unique prefix that starts with tmp.", "topics": [ "tmpPrefix" ] }, { "page": "toSnakeCase", "title": "Convert a character vector to snake case", "topics": [ "toSnakeCase" ] }, { "page": "transformToSummarisedResult", "title": "Create a object from a data.frame, given a set of specifications.", "topics": [ "transformToSummarisedResult" ] }, { "page": "uniqueId", "title": "Get a unique Identifier with a certain number of characters and a prefix.", "topics": [ "uniqueId" ] }, { "page": "uniqueTableName", "title": "Create a unique table name", "topics": [ "uniqueTableName" ] }, { "page": "uniteAdditional", "title": "Unite one or more columns in additional_name-additional_level format", "topics": [ "uniteAdditional" ] }, { "page": "uniteGroup", "title": "Unite one or more columns in group_name-group_level format", "topics": [ "uniteGroup" ] }, { "page": "uniteStrata", "title": "Unite one or more columns in strata_name-strata_level format", "topics": [ "uniteStrata" ] }, { "page": "validateAchillesTable", "title": "Validate if a cdm_table is a valid achilles table.", "topics": [ "validateAchillesTable" ] }, { "page": "validateAgeGroupArgument", "title": "Validate the ageGroup argument. It must be a list of two integerish numbers lower age and upper age, both of the must be greater or equal to 0 and lower age must be lower or equal to the upper age. If not named automatic names will be given in the output list.", "topics": [ "validateAgeGroupArgument" ] }, { "page": "validateCdmArgument", "title": "Validate if an object in a valid cdm_reference.", "topics": [ "validateCdmArgument" ] }, { "page": "validateCdmTable", "title": "Validate if a table is a valid cdm_table object.", "topics": [ "validateCdmTable" ] }, { "page": "validateCohortArgument", "title": "Validate a cohort table input.", "topics": [ "validateCohortArgument" ] }, { "page": "validateCohortIdArgument", "title": "Validate cohortId argument. CohortId can either be a cohort_definition_id value, a cohort_name or a tidyselect expression referring to cohort_names. If you want to support tidyselect expressions please use the function as: 'validateCohortIdArgument({{cohortId}}, cohort)'.", "topics": [ "validateCohortIdArgument" ] }, { "page": "validateColumn", "title": "Validate whether a variable points to a certain existing column in a table.", "topics": [ "validateColumn" ] }, { "page": "validateConceptSetArgument", "title": "Validate conceptSet argument. It can either be a list, a codelist, a concept set expression or a codelist with details. The output will always be a codelist.", "topics": [ "validateConceptSetArgument" ] }, { "page": "validateNameArgument", "title": "Validate name argument. It must be a snake_case character vector. You can add a cdm object to check that 'name' is not already used in that cdm.", "topics": [ "validateNameArgument" ] }, { "page": "validateNameLevel", "title": "Validate if two columns are valid Name-Level pair.", "topics": [ "validateNameLevel" ] }, { "page": "validateNameStyle", "title": "Validate 'nameStyle' argument. If any of the element in '...' has length greater than 1 it must be contained in nameStyle. Note that snake case notation is used.", "topics": [ "validateNameStyle" ] }, { "page": "validateNewColumn", "title": "Validate a new column of a table", "topics": [ "validateNewColumn" ] }, { "page": "validateOmopTable", "title": "Validate an omop_table", "topics": [ "validateOmopTable" ] }, { "page": "validateResultArgument", "title": "Validate whether an object is a valid 'summarised_result' object.", "topics": [ "validateResultArgument" ] }, { "page": "validateStrataArgument", "title": "To validate a strata list. It makes sure that elements are unique and point to columns in table.", "topics": [ "validateStrataArgument" ] }, { "page": "validateWindowArgument", "title": "Validate a window argument. It must be a list of two elements (window start and window end), both must be numeric, integerish by default, and window start must be lower or equal than window end.", "topics": [ "validateWindowArgument" ] } ], "_readme": "https://github.com/darwin-eu/omopgenerics/raw/HEAD/README.md", "_rundeps": [ "blob", "cli", "cpp11", "DBI", "dbplyr", "dplyr", "generics", "glue", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "rlang", "snakecase", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "cdm_reference.Rmd", "filename": "cdm_reference.html", "title": "The cdm reference", "engine": "knitr::rmarkdown", "headings": [ "1) Standard OMOP CDM tables", "2) Cohort tables", "3) Achilles result tables", "4) Other tables", "General rules for a cdm reference", "Export metadata about the cdm reference" ], "created": "2024-07-04 17:21:26", "modified": "2026-06-18 08:05:36", "commits": 3 }, { "source": "cohorts.Rmd", "filename": "cohorts.html", "title": "Cohort tables", "engine": "knitr::rmarkdown", "headings": [ "Cohort table", "Cohort Set", "Cohort Attrition", "Cohort Codelist", "Cohort Table", "Combining generated cohort sets", "Export metadata about a cohort table" ], "created": "2024-07-04 17:21:26", "modified": "2026-06-18 08:05:36", "commits": 7 }, { "source": "codelists.Rmd", "filename": "codelists.html", "title": "Concept sets", "engine": "knitr::rmarkdown", "headings": [ "Codelist", "Concept set expression" ], "created": "2024-07-04 17:21:26", "modified": "2026-06-18 08:05:36", "commits": 4 }, { "source": "expanding_omopgenerics.Rmd", "filename": "expanding_omopgenerics.html", "title": "Expanding omopgenerics", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The source object", "Methods", "insertTable", "listSourceTables", "readSourceTable", "dropSourceTable", "insertCdmTo", "summary", "compute", "The cdm reference object" ], "created": "2025-07-15 18:46:36", "modified": "2026-06-18 08:05:36", "commits": 2 }, { "source": "logging.Rmd", "filename": "logging.html", "title": "Logging with omopgenerics", "engine": "knitr::rmarkdown", "headings": [ "Logging", "Logging with omopgenerics", "Example", "exportSummarisedResult" ], "created": "2025-05-21 17:35:16", "modified": "2026-06-18 08:05:36", "commits": 2 }, { "source": "reexport.Rmd", "filename": "reexport.html", "title": "Re-exporting functions from omopgenerics", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Methods", "CDM reference", "Cohorts", "Summarised result" ], "created": "2024-02-16 16:25:52", "modified": "2026-06-18 08:05:36", "commits": 8 }, { "source": "summarised_result.Rmd", "filename": "summarised_result.html", "title": "A summarised result", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Results table", "Settings", "newSummarisedResult", "Combining summarised results", "Minimum cell count suppression", "Export and import summarised results", "Tidy a ", "Tidy method", "1. Split group, strata, and additional pairs into separate columns:", "2. Add settings of the object as columns:", "3. 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