| Subset a cdm reference object. | [[.cdm_reference |
| Assign a table to a cdm reference. | [[<-.cdm_reference |
| Subset a cdm reference object. | $.cdm_reference |
| Assign an table to a cdm reference. | $<-.cdm_reference |
| Required columns for each of the achilles result tables | achillesColumns |
| Names of the tables that contain the results of achilles analyses | achillesTables |
| Identify variables in additional_name column | additionalColumns |
| Add settings columns to a <summarised_result> object | addSettings |
| Assert that an object is a character and fulfill certain conditions. | assertCharacter |
| Assert that an object is within a certain oprtions. | assertChoice |
| Assert that an object has a certain class. | assertClass |
| Assert Date | assertDate |
| Assert that an object is a list. | assertList |
| Assert that an object is a logical. | assertLogical |
| Assert that an object is a numeric. | assertNumeric |
| Assert that an object is a table. | assertTable |
| Assert that an expression is TRUE. | assertTrue |
| Get attrition from an object. | attrition |
| Get cohort attrition from a cohort_table object. | attrition.cohort_table |
| Bind two or more objects of the same class. | bind |
| Bind two or more cohort tables | bind.cohort_table |
| Bind two or summarised_result objects | bind.summarised_result |
| Separate the cdm tables in classes | cdmClasses |
| Disconnect from a cdm object. | cdmDisconnect |
| Create a cdm object from local tables | cdmFromTables |
| Get the name of a cdm_reference associated object | cdmName |
| Get the 'cdm_reference' of a 'cdm_table'. | cdmReference |
| Restrict the cdm object to a subset of tables. | cdmSelect |
| Get the cdmSource of an object. | cdmSource |
| Get the source type of a cdm_reference object. | cdmSourceType |
| 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. | cdmTableFromSource |
| Get the version of an object. | cdmVersion |
| Check whether a cohort table satisfies requirements | checkCohortRequirements |
| Get codelist from a cohort_table object. | cohortCodelist |
| Required columns for a generated cohort set. | cohortColumns |
| Get cohort counts from a cohort_table object. | cohortCount |
| Cohort tables that a cdm reference can contain in the OMOP Common Data Model. | cohortTables |
| Retrieves the cdm reference into a local cdm. | collect.cdm_reference |
| To collect a 'cohort_table' object. | collect.cohort_table |
| Provide all combinations of strata levels. | combineStrata |
| Store results in a table. | compute.cdm_table |
| Create the missing indexes | createIndexes |
| Create a log file | createLogFile |
| Create a table index | createTableIndex |
| Drop a table from a cdm object. | dropSourceTable |
| Drop a table from a cdm object. *[Deprecated]* | dropTable |
| Create an empty achilles table | emptyAchillesTable |
| Create an empty cdm_reference | emptyCdmReference |
| Empty 'codelist' object. | emptyCodelist |
| Empty 'codelist' object. | emptyCodelistWithDetails |
| Create an empty cohort_table object | emptyCohortTable |
| Empty 'concept_set_expression' object. | emptyConceptSetExpression |
| Create an empty omop table | emptyOmopTable |
| Empty 'summarised_result' object. | emptySummarisedResult |
| Choices that can be present in 'estimate_type' column. | estimateTypeChoices |
| Existing indexes in a cdm object | existingIndexes |
| Expected indexes in a cdm object | expectedIndexes |
| Export a codelist object. | exportCodelist |
| Export a concept set expression. | exportConceptSetExpression |
| Export a summarised_result object to a csv file. | exportSummarisedResult |
| Filter the additional_name-additional_level pair in a summarised_result | filterAdditional |
| Filter the group_name-group_level pair in a summarised_result | filterGroup |
| Filter a <summarised_result> using the settings | filterSettings |
| Filter the strata_name-strata_level pair in a summarised_result | filterStrata |
| Get the cohort definition id of a certain name | getCohortId |
| Get the cohort name of a certain cohort definition id | getCohortName |
| 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. | getPersonIdentifier |
| Identify variables in group_name column | groupColumns |
| Import a codelist. | importCodelist |
| Import a concept set expression. | importConceptSetExpression |
| Import a set of summarised results. | importSummarisedResult |
| Insert a cdm_reference object to a different source. | insertCdmTo |
| 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. | insertFromSource |
| Insert a table to a cdm object. | insertTable |
| To check whether an object is already suppressed to a certain min cell count. | isResultSuppressed |
| Check if a table is empty or not | isTableEmpty |
| List tables that can be accessed though a cdm object. | listSourceTables |
| Log a message to a logFile | logMessage |
| Create an achilles table from a cdm_table. | newAchillesTable |
| 'cdm_reference' objects constructor | newCdmReference |
| Create a cdm source object. | newCdmSource |
| Create an cdm table. | newCdmTable |
| 'codelist' object constructor | newCodelist |
| 'codelist' object constructor | newCodelistWithDetails |
| 'cohort_table' objects constructor. | newCohortTable |
| 'concept_set_expression' object constructor | newConceptSetExpression |
| A new local source for the cdm | newLocalSource |
| Create an omop table from a cdm table. | newOmopTable |
| 'summarised_results' object constructor | newSummarisedResult |
| Count the number of records that a 'cdm_table' has. | numberRecords |
| Count the number of subjects that a 'cdm_table' has. | numberSubjects |
| Required columns that the standard tables in the OMOP Common Data Model must have. | omopColumns |
| Check or set the OMOP_DATA_FOLDER where the OMOP related data is stored. | omopDataFolder |
| Return a table of omop cdm fields informations | omopTableFields |
| Standard tables that a cdm reference can contain in the OMOP Common Data Model. | omopTables |
| Set estimates as columns | pivotEstimates |
| Print a CDM reference object | print.cdm_reference |
| Print a codelist | print.codelist |
| Print a codelist with details | print.codelist_with_details |
| Print a concept set expression | print.concept_set_expression |
| Read a table from the cdm_source and add it to to the cdm. | readSourceTable |
| Update cohort attrition. | recordCohortAttrition |
| Required columns that the result tables must have. | resultColumns |
| Check if different packages version are used for summarise_results object | resultPackageVersion |
| Get settings from an object. | settings |
| Get cohort settings from a cohort_table object. | settings.cohort_table |
| Get settings from a summarised_result object. | settings.summarised_result |
| Identify settings columns of a <summarised_result> | settingsColumns |
| Get the source type of an object. | sourceType |
| Split additional_name and additional_level columns | splitAdditional |
| Split all pairs name-level into columns. | splitAll |
| Split group_name and group_level columns | splitGroup |
| Split strata_name and strata_level columns | splitStrata |
| Status of the indexes | statusIndexes |
| Identify variables in strata_name column | strataColumns |
| Summarise and extract the information of a log file into a 'summarised_result' object. | summariseLogFile |
| Summary a cdm reference | summary.cdm_reference |
| Summarise a 'cdm_source' object | summary.cdm_source |
| Summary a generated cohort set | summary.cohort_table |
| Summary a summarised_result | summary.summarised_result |
| Function to suppress counts in result objects | suppress |
| Function to suppress counts in result objects | suppress.summarised_result |
| Get the table name of a 'cdm_table'. | tableName |
| Get the table source of a 'cdm_table'. | tableSource |
| Turn a <summarised_result> object into a tidy tibble | tidy.summarised_result |
| Identify tidy columns of a <summarised_result> | tidyColumns |
| Create a temporary prefix for tables, that contains a unique prefix that starts with tmp. | tmpPrefix |
| Convert a character vector to snake case | toSnakeCase |
| Create a <summarised_result> object from a data.frame, given a set of specifications. | transformToSummarisedResult |
| Get a unique Identifier with a certain number of characters and a prefix. | uniqueId |
| Create a unique table name | uniqueTableName |
| Unite one or more columns in additional_name-additional_level format | uniteAdditional |
| Unite one or more columns in group_name-group_level format | uniteGroup |
| Unite one or more columns in strata_name-strata_level format | uniteStrata |
| Validate if a cdm_table is a valid achilles table. | validateAchillesTable |
| 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. | validateAgeGroupArgument |
| Validate if an object in a valid cdm_reference. | validateCdmArgument |
| Validate if a table is a valid cdm_table object. | validateCdmTable |
| Validate a cohort table input. | validateCohortArgument |
| 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)'. | validateCohortIdArgument |
| Validate whether a variable points to a certain exiting column in a table. | validateColumn |
| 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. | validateConceptSetArgument |
| 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. | validateNameArgument |
| Validate if two columns are valid Name-Level pair. | validateNameLevel |
| 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. | validateNameStyle |
| Validate a new column of a table | validateNewColumn |
| Validate an omop_table | validateOmopTable |
| Validate if a an object is a valid 'summarised_result' object. | validateResultArgument |
| To validate a strata list. It makes sure that elements are unique and point to columns in table. | validateStrataArgument |
| Validate a window argument. It must be a list of two elements (window start and window end), both must be integerish and window start must be lower or equal than window end. | validateWindowArgument |
