Methods and Classes for the OMOP Common Data Model


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Documentation for package ‘omopgenerics’ version 0.0.3

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$.cdm_reference Subset a cdm reference object.
$<-.cdm_reference Assign an table to a cdm reference.
achillesColumns Required columns for achilles result tables
achillesTables Tables containing 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 cohort_table
cdmFromTables Create a cdm object from local tables
cdmName Get the name of a cdm_reference.
cdmReference Get the 'cdm_reference' of a 'cdm_table'.
cdmSource Get the source of a cdm_reference.
cdmVersion Get the version of a cdm_reference.
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.
dropTable Drop a table from a cdm object.
emptyAchillesTable Create an empty achilles table
emptyCdmReference Create an empty cdm_reference
emptyCohortTable Create an empty cohort_table object
emptyComparedResult Empty 'compared_result' object.
emptyOmopTable Create an empty omop table
emptySummarisedResult Empty 'summarised_result' object.
estimateTypeChoices Choices that can be present in 'estimate_type' column.
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.
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
newCohortTable 'cohort_table' objects constructor.
newComparedResult 'compared_results' object constructor
newConceptSetExpression 'conceptSetExpression' object constructor
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
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.
sourceType Get the source type of a cdm_source.
subsetResult Subset a summarised_result or compared_result object to a certain result_type.
summary.cdm_reference Summary a cdm reference
summary.cohort_table Summary a generated cohort set
suppress 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.
uniqueTableName Create a unique table name
[[.cdm_reference Subset a cdm reference object.
[[<-.cdm_reference Assign an table to a cdm reference.