Package index • omopgenerics

Methods

General methods deffined by omopgenerics

attrition(): Get attrition from an object.

bind(): Bind two or more objects of the same class.

settings(): Get settings from an object.

suppress(): Function to suppress counts in result objects

Create new objects

To create new omopgenerics S3 classes objects

combineStrata(): Provide all combinations of strata levels.

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

newCohortTable(): cohort_table objects constructor.

newConceptSetExpression(): 'conceptSetExpression' object constructor

newLocalSource(): A new local source for the cdm

newOmopTable(): Create an omop table from a cdm table.

newSummarisedResult(): 'summarised_results' object constructor

Creates empty objects

To create empty omopgenerics S3 classes objects

emptyAchillesTable(): Create an empty achilles table

emptyCdmReference(): Create an empty cdm_reference

emptyCodelist(): Empty codelist object.

emptyCodelistWithDetails(): Empty codelist object.

emptyCohortTable(): Create an empty cohort_table object

emptyOmopTable(): Create an empty omop table

emptySummarisedResult(): Empty summarised_result object.

cdm_reference utility functions

Utility functions for cdm_reference objects

`$`(<cdm_reference>): Subset a cdm reference object.

`$<-`(<cdm_reference>): Assign an table to a cdm reference.

cdmFromTables(): Create a cdm object from local tables

cdmName(): Get the name of a cdm_reference associated object

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() deprecated: Get the source type of a cdm_reference object.

cdmTableFromSource(): 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.

cdmVersion(): Get the version of an object.

collect(<cdm_reference>): Retrieves the cdm reference into a local cdm.

compute(<cdm_table>): Store results in a table.

print(<cdm_reference>): Print a CDM reference object

`[[`(<cdm_reference>): Subset a cdm reference object.

`[[<-`(<cdm_reference>): Assign a table to a cdm reference.

summary(<cdm_reference>): Summary a cdm reference

listSourceTables(): List tables that can be accessed though a cdm object.

dropSourceTable(): Drop a table from a cdm object.

insertTable(): Insert a table to a cdm object.

readSourceTable(): Read a table from the cdm_source and add it to to the cdm.

getPersonIdentifier(): 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.

cdm_table utility functions

Utility functions for cdm_table objects

tableName(): Get the table name of a cdm_table.

tableSource(): Get the table source of a cdm_table.

omop_table utility functions

Utility functions for omop_table objects

omopColumns(): Required columns that the standard tables in the OMOP Common Data Model must have.

omopTableFields(): Return a table of omop cdm fields informations

omopTables(): Standard tables that a cdm reference can contain in the OMOP Common Data Model.

achilles_table utility functions

Utility functions for achilles_table objects

achillesColumns(): Required columns for each of the achilles result tables

achillesTables(): Names of the tables that contain the results of achilles analyses

cohort_table utility functions

Utility functions for cohort_table objects

attrition(<cohort_table>): Get cohort attrition from a cohort_table object.

bind(<cohort_table>): Bind two or more cohort tables

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.

cohortTables(): Cohort tables that a cdm reference can contain in the OMOP Common Data Model.

collect(<cohort_table>): To collect a cohort_table object.

getCohortId(): Get the cohort definition id of a certain name

getCohortName(): Get the cohort name of a certain cohort definition id

recordCohortAttrition(): Update cohort attrition.

settings(<cohort_table>): Get cohort settings from a cohort_table object.

summary(<cohort_table>): Summary a generated cohort set

summarised_result utility functions

Utility functions for summarised_result objects

addSettings(): Add settings columns to a <summarised_result> object

additionalColumns(): Identify variables in additional_name column

bind(<summarised_result>): Bind two or summarised_result objects

estimateTypeChoices(): Choices that can be present in estimate_type column.

exportSummarisedResult(): Export a summarised_result object to a csv file.

filterAdditional(): Filter the additional_name-additional_level pair in a summarised_result

filterGroup(): Filter the group_name-group_level pair in a summarised_result

filterSettings(): Filter a <summarised_result> using the settings

filterStrata(): Filter the strata_name-strata_level pair in a summarised_result

groupColumns(): Identify variables in group_name column

importSummarisedResult(): Import a set of summarised results.

pivotEstimates(): Set estimates as columns

resultColumns(): Required columns that the result tables must have.

settings(<summarised_result>): Get settings from a summarised_result object.

settingsColumns(): Identify settings columns of a <summarised_result>

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

strataColumns(): Identify variables in strata_name column

summary(<summarised_result>): Summary a summarised_result

suppress(<summarised_result>): Function to suppress counts in result objects

tidy(<summarised_result>) experimental: Turn a <summarised_result> object into a tidy tibble

tidyColumns(): Identify tidy columns of a <summarised_result>

uniteAdditional(): Unite one or more columns in additional_name-additional_level format

uniteGroup(): Unite one or more columns in group_name-group_level format

uniteStrata(): Unite one or more columns in strata_name-strata_level format

codelist utility functions

Utility functions for codelist objects

exportCodelist(): Export a codelist object.

exportConceptSetExpression(): Export a concept set expression.

importCodelist(): Import a codelist.

importConceptSetExpression(): Import a concept set expression.

print(<codelist>): Print a codelist

print(<codelist_with_details>): Print a codelist with details

print(<conceptSetExpression>): Print a concept set expression

resultPackageVersion(): Check if different packages version are used for summarise_results object

Argument validation

To validate input arguments of the functions

validateAgeGroupArgument(): validateAgeGroupArgument

validateCdmArgument(): validateCdmArgument

validateCohortArgument(): Validate a cohort table input.

validateCohortIdArgument(): 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).

validateConceptSetArgument(): Validate conceptSet argument.

validateNameArgument(): Validate name argument.

validateNameLevel(): Validate if two columns are valid Name-Level pair.

validateNewColumn(): Validate a new column of a table

validateResultArguemnt(): validateResultArgument

validateResultArgument(): validateResultArgument

validateWindowArgument(): validateWindowArgument

isResultSuppressed(): isResultSuppressed

General assertions

To assert that an object fulfills certain criteria

assertCharacter(): Assert that an object is a character and fulfill certain conditions.

assertChoice(): Assert that an object is within a certain oprtions.

assertClass(): Assert that an object has a certain class.

assertDate(): Assert Date

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.

Utility functions

To be used internally by other packages, not meant to be user focused functions

insertFromSource() deprecated: 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.

isTableEmpty(): Check if a table is empty or not

omopTableFields(): Return a table of omop cdm fields informations

sourceType(): Get the source type of an object.

tmpPrefix(): Create a temporary prefix for tables, that contains a unique prefix that starts with tmp.

uniqueId(): Get a unique Identifier with a certain number of characters and a prefix.

uniqueTableName(): Create a unique table name

Deprecated

Deprecated function that will be eliminated in future releases of the package

checkCohortRequirements() deprecated: Check whether a cohort table satisfies requirements

dropTable(): Drop a table from a cdm object.

toSnakeCase(): Convert a character vector to snake case