{ "_id": "6a17e78aacfb0bcc41da1a6a", "Package": "omopgenerics", "Title": "Methods and Classes for the OMOP Common Data Model", "Version": "1.3.6", "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": "2026-01-28 17:42:47 UTC", "RemoteUrl": "https://github.com/darwin-eu/omopgenerics", "RemoteRef": "HEAD", "RemoteSha": "241d8917b7742c028820c4ce2eafafb0c88ef01f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 06:50:27 UTC", "User": "root" }, "Author": "Martí Català [aut, cre] (ORCID:\n),\nEdward Burn [aut] (ORCID: ),\nMike Du [ctb] 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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": "Retrieves the cdm reference into a local cdm.", "topics": [ "collect.cdm_reference" ] }, { "page": 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"page": "expectedIndexes", "title": "Expected indexes in a cdm object", "topics": [ "expectedIndexes" ] }, { "page": "exportCodelist", "title": "Export a codelist object.", "topics": [ "exportCodelist" ] }, { "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": "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" ] }, { 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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 to 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 though 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": "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": "newSummarisedResult", "title": "'summarised_results' 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 fields informations", "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.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 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 packages version are used for summarise_results object", "topics": [ "resultPackageVersion" ] }, { "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": "Summary 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": "Summary a generated cohort set", "topics": [ "summary.cohort_table" ] }, { "page": "summary.summarised_result", "title": "Summary 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 referinc 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 exiting 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 the a cdm object to check '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 if a an object is a valid 'summarised_result' object.", "topics": [ "validateResultArgument" ] }, { "page": "validateStrataArgument", "title": "To validate a strata list. 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