runCohortGeneration {CohortGenerator} | R Documentation |
Run a cohort generation and export results
Description
Run a cohort generation and export results
Usage
runCohortGeneration(
connectionDetails,
cdmDatabaseSchema,
tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
cohortDatabaseSchema = cdmDatabaseSchema,
cohortTableNames = getCohortTableNames(),
cohortDefinitionSet = NULL,
negativeControlOutcomeCohortSet = NULL,
occurrenceType = "all",
detectOnDescendants = FALSE,
stopOnError = TRUE,
outputFolder,
databaseId = 1,
minCellCount = 5,
incremental = FALSE,
incrementalFolder = NULL
)
Arguments
connectionDetails |
An object of type |
cdmDatabaseSchema |
Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'. |
tempEmulationSchema |
Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created. |
cohortDatabaseSchema |
Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'. |
cohortTableNames |
The names of the cohort tables. See |
cohortDefinitionSet |
The
Optionally, this data frame may contain:
|
negativeControlOutcomeCohortSet |
The
|
occurrenceType |
For negative controls outcomes, the occurrenceType will detect either: the first time an outcomeConceptId occurs or all times the outcomeConceptId occurs for a person. Values accepted: 'all' or 'first'. |
detectOnDescendants |
For negative controls outcomes, when set to TRUE, detectOnDescendants will use the vocabulary to find negative control outcomes using the outcomeConceptId and all descendants via the concept_ancestor table. When FALSE, only the exact outcomeConceptId will be used to detect the outcome. |
stopOnError |
If an error happens while generating one of the cohorts in the cohortDefinitionSet, should we stop processing the other cohorts? The default is TRUE; when set to FALSE, failures will be identified in the return value from this function. |
outputFolder |
Name of the folder where all the outputs will written to. |
databaseId |
A unique ID for the database. This will be appended to most tables. |
minCellCount |
To preserve privacy: the minimum number of subjects contributing to a count before it can be included in the results. If the count is below this threshold, it will be set to '-minCellCount'. |
incremental |
Create only cohorts that haven't been created before? |
incrementalFolder |
If |
Details
Run a cohort generation for a set of cohorts and negative control outcomes. This function will also export the results of the run to the 'outputFolder'.