$.cdm_reference |
Subset a cdm reference object. |
$<-.cdm_reference |
Assign an table to a cdm reference. |
achillesColumns |
Required columns for each of the achilles result tables |
achillesTables |
Names of the tables that contain the results of achilles analyses |
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 |
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 source of a cdm_reference. |
cdmSourceType |
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 a cdm_reference. |
checkCohortRequirements |
Check whether a cohort table satisfies requirements |
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.cdm_reference |
Retrieves the cdm reference into a local cdm. |
collect.cohort_table |
To collect a 'cohort_table' object. |
compute.cdm_table |
Store results in a table. |
dropSourceTable |
Drop a table from a cdm object. |
dropTable |
Drop a table from a cdm object. |
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. |
estimateTypeChoices |
Choices that can be present in 'estimate_type' column. |
exportSummarisedResult |
Export a summarised_result object to a csv file. |
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 (either subject_id or person_id), it will throw an error if it contains both or neither. |
insertFromSource |
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. |
insertTable |
Insert a table to a cdm object. |
listSourceTables |
List tables that can be accessed though a cdm object. |
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 |
omopColumns |
Required columns that the standard tables in the OMOP Common Data Model must have. |
omopTables |
Standard tables that a cdm reference can contain in the OMOP Common Data Model. |
participants |
It returns the participants that contributed to a particular analysis |
print.cdm_reference |
Print a CDM reference object |
print.codelist |
Print a codelist |
print.codelist_with_details |
Print a codelist with details |
print.conceptSetExpression |
Print a concept set expression |
readSourceTable |
Read a table from the cdm_source and add it to to the cdm. |
recordCohortAttrition |
Update cohort attrition. |
resultColumns |
Required columns that the result tables must have. |
settings |
Get settings from an object. |
settings.cohort_table |
Get cohort settings from a cohort_table object. |
settings.summarised_result |
Get settings from a summarised_result object. |
sourceType |
Get the source type of a cdm_source. |
summary.cdm_reference |
Summary a cdm reference |
summary.cohort_table |
Summary a generated cohort set |
summary.summarised_result |
Summary 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'. |
tmpPrefix |
Create a temporary prefix for tables, that contains a unique prefix that starts with tmp. |
toSnakeCase |
Convert a character vector to snake case |
uniqueId |
Get a unique Identifier with a certain number of characters and a prefix. |
uniqueTableName |
Create a unique table name |
validateNameLevel |
Validate if two columns are valid Name-Level pair. |
[[.cdm_reference |
Subset a cdm reference object. |
[[<-.cdm_reference |
Assign a table to a cdm reference. |