Man pages for omopgenerics
Methods and Classes for the OMOP Common Data Model
| achillesColumns | Required columns for each of the achilles result tables |
| achillesTables | Names of the tables that contain the results of achilles... |
| additionalColumns | Identify variables in additional_name column |
| addSettings | Add settings columns to a <summarised_result> object |
| assertCharacter | Assert that an object is a character and satisfies certain... |
| assertChoice | Assert that an object is one of a set of options. |
| assertClass | Assert that an object has a certain class. |
| assertDate | Assert Date |
| assertDoc | Helper for consistent documentation of assertion functions. |
| assertList | Assert that an object is a list. |
| assertLogical | Assert that an object is a logical. |
| assertNumeric | Assert that an object is a numeric. |
| assertTable | Assert that an object is a table. |
| assertTrue | Assert that an expression is TRUE. |
| attrition | Get attrition from an object. |
| attrition.cohort_table | Get cohort attrition from a cohort_table object. |
| bind | Bind two or more objects of the same class. |
| bind.cohort_table | Bind two or more cohort tables |
| bind.summarised_result | Bind two or summarised_result objects |
| cash-.cdm_reference | Subset a cdm reference object. |
| cash-set-.cdm_reference | Assign a table to a cdm reference. |
| castDoc | Helper for consistent documentation of cast arguments. |
| cdmAssignTableDoc | Helper for consistent documentation of assigning tables to a... |
| cdmClasses | Separate the cdm tables in classes |
| cdmDisconnect | Disconnect from a cdm object. |
| cdmDoc | Helper for consistent documentation of 'cdm'. |
| cdmFromTables | Create a cdm object from local tables |
| cdmIndexDoc | Helper for consistent documentation of CDM index functions. |
| cdmName | Get or set the name of a cdm_reference associated object |
| cdmNameDoc | Helper for consistent documentation of CDM names. |
| cdmOrTableDoc | Helper for consistent documentation of cdm reference or table... |
| cdmReference | Get the 'cdm_reference' of a 'cdm_table'. |
| cdmSelect | Restrict the cdm object to a subset of tables. |
| cdmSource | Get the cdmSource of an object. |
| cdmSourceType | Get the source type of a cdm_reference object. |
| cdmTableDoc | Helper for consistent documentation of 'cdm_table' objects. |
| cdmTableFromSource | This is an internal developer focused function that creates a... |
| cdmVersion | Get the version of an object. |
| cdmVersionArgumentDoc | Helper for consistent documentation of CDM version arguments. |
| checkCohortRequirements | Check whether a cohort table satisfies requirements |
| cliCallDoc | Helper for consistent documentation of call arguments. |
| codelistDoc | Helper for consistent documentation of 'codelist' objects. |
| codelistWithDetailsDoc | Helper for consistent documentation of... |
| cohortCodelist | Get codelist from a cohort_table object. |
| cohortColumns | Required columns for a generated cohort set. |
| cohortCount | Get cohort counts from a cohort_table object. |
| cohortDoc | Helper for consistent documentation of 'cohort_table'... |
| cohortTables | Cohort tables that a cdm reference can contain in the OMOP... |
| cohortValidationChecksDoc | Helper for consistent documentation of cohort validation... |
| collect.cdm_reference | Retrieve the cdm reference into a local cdm. |
| collect.cohort_table | To collect a 'cohort_table' object. |
| combineStrata | Provide all combinations of strata levels. |
| compareOmopTableFields | Compare the fields of two different OMOP CDM versions |
| compute.cdm_table | Store results in a table. |
| conceptCdmDoc | Helper for consistent documentation of 'cdm' concept... |
| conceptSetExpressionDoc | Helper for consistent documentation of... |
| createIndexes | Create the missing indexes |
| createLogFile | Create a log file |
| createTableIndex | Create a table index |
| dropSourceTable | Drop a table from a cdm object. |
| dropTable | Drop a table from a cdm object. *[Deprecated]* |
| emptyAchillesTable | Create an empty achilles table |
| emptyCdmReference | Create an empty cdm_reference |
| emptyCodelist | Empty 'codelist' object. |
| emptyCodelistWithDetails | Empty 'codelist' object. |
| emptyCodeSearch | Empty code search object |
| emptyCohortTable | Create an empty cohort_table object |
| emptyConceptSetExpression | Empty 'concept_set_expression' object. |
| emptyDoc | Helper for consistent documentation of empty arguments. |
| emptyOmopTable | Create an empty omop table |
| emptySummarisedResult | Empty 'summarised_result' object. |
| emptyTableNameDoc | Helper for consistent documentation of empty table names. |
| estimateTypeChoices | Choices that can be present in 'estimate_type' column. |
| existingIndexes | Existing indexes in a cdm object |
| expectedIndexes | Expected indexes in a cdm object |
| exportCodelist | Export a codelist object. |
| exportCodelistWithDetails | Export a codelist with details object. |
| exportCodeSearch | Export a 'code_search' object into an Excel spreadsheet |
| exportConceptSetExpression | Export a concept set expression. |
| exportFileDoc | Helper for consistent documentation of exported files. |
| exportSummarisedResult | Export a summarised_result object to a CSV file. |
| filterAdditional | Filter the additional_name-additional_level pair in a... |
| filterGroup | Filter the group_name-group_level pair in a summarised_result |
| filterResult | Filter a <summarised_result> automatically |
| filterSettings | Filter a <summarised_result> using the settings |
| filterStrata | Filter the strata_name-strata_level pair in a... |
| getCohortId | Get the cohort definition id of a certain name |
| getCohortName | Get the cohort name of a certain cohort definition id |
| getPersonIdentifier | Get the column name with the person identifier from a table... |
| groupColumns | Identify variables in group_name column |
| importCodelist | Import a codelist. |
| importCodelistWithDetails | Import a codelist with details. |
| importCodeSearch | Import a 'code_search' object from an Excel spreadsheet |
| importConceptSetExpression | Import a concept set expression. |
| importFileDoc | Helper for consistent documentation of imported files. |
| importSummarisedResult | Import a set of summarised results. |
| insertCdmTo | Insert a cdm_reference object to a different source. |
| insertFromSource | Convert a table that is not a cdm_table but have the same... |
| insertTable | Insert a table into a cdm object. |
| isResultSuppressed | To check whether an object is already suppressed to a certain... |
| isTableEmpty | Check if a table is empty or not |
| listSourceTables | List tables that can be accessed through a cdm object. |
| logMessage | Log a message to a logFile |
| newAchillesTable | Create an achilles table from a cdm_table. |
| newCdmReference | 'cdm_reference' objects constructor |
| newCdmSource | Create a cdm source object. |
| newCdmTable | Create an cdm table. |
| newCodelist | 'codelist' object constructor |
| newCodelistWithDetails | 'codelist' object constructor |
| newCodeSearch | Create a new 'code_search' object |
| newCohortTable | 'cohort_table' objects constructor. |
| newConceptSetExpression | 'concept_set_expression' object constructor |
| newLocalSource | A new local source for the cdm |
| newOmopTable | Create an omop table from a cdm table. |
| newReadOnlySource | A new read-only source for the cdm |
| newSummarisedResult | 'summarised_result' object constructor |
| numberRecords | Count the number of records that a 'cdm_table' has. |
| numberSubjects | Count the number of subjects that a 'cdm_table' has. |
| omopCdmVersionDoc | Helper for consistent documentation of OMOP CDM versions. |
| omopColumns | Required columns that the standard tables in the OMOP Common... |
| omopDataFolder | Check or set the OMOP_DATA_FOLDER where the OMOP related data... |
| omopgenerics-package | omopgenerics: Methods and Classes for the OMOP Common Data... |
| omopTableFields | Return a table of omop cdm field information |
| omopTables | Standard tables that a cdm reference can contain in the OMOP... |
| overwriteDoc | Helper for consistent documentation of overwrite arguments. |
| pivotEstimates | Set estimates as columns |
| print.cdm_reference | Print a CDM reference object |
| print.codelist | Print a codelist |
| print.codelist_with_details | Print a codelist with details |
| print.code_search | Print a code search |
| print.concept_set_expression | Print a concept set expression |
| readSourceTable | Read a table from the cdm_source and add it to the cdm. |
| recordCohortAttrition | Update cohort attrition. |
| recursiveDoc | Helper for consistent documentation of recursive file... |
| reexports | Objects exported from other packages |
| resultColumns | Required columns that the result tables must have. |
| resultPackageVersion | Check if different package versions are used for a... |
| resultType | Get the 'result_type(s)' defined in a certain package |
| searchStrategy | Get the search strategy used to create a 'code_search' |
| settings | Get settings from an object. |
| settings.cohort_table | Get cohort settings from a cohort_table object. |
| settingsColumns | Identify settings columns of a <summarised_result> |
| settings.summarised_result | Get settings from a summarised_result object. |
| sourceType | Get the source type of an object. |
| splitAdditional | Split additional_name and additional_level columns |
| splitAll | Split all pairs name-level into columns. |
| splitGroup | Split group_name and group_level columns |
| splitStrata | Split strata_name and strata_level columns |
| statusIndexes | Status of the indexes |
| strataColumns | Identify variables in strata_name column |
| sub-sub-.cdm_reference | Subset a cdm reference object. |
| sub-subset-.cdm_reference | Assign a table to a cdm reference. |
| summarisedResultDoc | Helper for consistent documentation of 'summarised_result'... |
| summariseLogFile | Summarise and extract the information of a log file into a... |
| summary.cdm_reference | Summarise a cdm reference |
| summary.cdm_source | Summarise a 'cdm_source' object |
| summary.cohort_table | Summarise a generated cohort set |
| summary.summarised_result | Summarise a summarised_result |
| suppress | Function to suppress counts in result objects |
| suppress.summarised_result | Function to suppress counts in result objects |
| tableName | Get the table name of a 'cdm_table'. |
| tableSource | Get the table source of a 'cdm_table'. |
| tidyColumns | Identify tidy columns of a <summarised_result> |
| tidy.summarised_result | Turn a <summarised_result> object into a tidy tibble |
| tmpPrefix | Create a temporary prefix for tables that contains a unique... |
| toSnakeCase | Convert a character vector to snake case |
| transformToSummarisedResult | Create a <summarised_result> object from a data.frame, given... |
| uniqueId | Get a unique Identifier with a certain number of characters... |
| uniqueTableName | Create a unique table name |
| uniteAdditional | Unite one or more columns in additional_name-additional_level... |
| uniteGroup | Unite one or more columns in group_name-group_level format |
| uniteStrata | Unite one or more columns in strata_name-strata_level format |
| unusedDotsDoc | Helper for consistent documentation of unused dots. |
| validateAchillesTable | Validate if a cdm_table is a valid achilles table. |
| validateAgeGroupArgument | Validate the ageGroup argument. It must be a list of two... |
| validateCdmArgument | Validate if an object in a valid cdm_reference. |
| validateCdmTable | Validate if a table is a valid cdm_table object. |
| validateCohortArgument | Validate a cohort table input. |
| validateCohortIdArgument | Validate cohortId argument. CohortId can either be a... |
| validateColumn | Validate whether a variable points to a certain existing... |
| validateConceptSetArgument | Validate conceptSet argument. It can either be a list, a... |
| validateNameArgument | Validate name argument. It must be a snake_case character... |
| validateNameLevel | Validate if two columns are valid Name-Level pair. |
| validateNameStyle | Validate 'nameStyle' argument. If any of the element in '...'... |
| validateNewColumn | Validate a new column of a table |
| validateOmopTable | Validate an omop_table |
| validateResultArgument | Validate whether an object is a valid 'summarised_result'... |
| validateStrataArgument | To validate a strata list. It makes sure that elements are... |
| validateWindowArgument | Validate a window argument. It must be a list of two elements... |
| validationDoc | Helper for consistent documentation of validation mode. |
