Description Usage Arguments Details
View source: R/CohortDiagnostics.R
Execute the cohort diagnostics
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | runCohortDiagnostics(
connectionDetails,
cdmDatabaseSchema,
cohortDatabaseSchema = cdmDatabaseSchema,
cohortTable = "cohort",
oracleTempSchema = cohortDatabaseSchema,
outputFolder,
databaseId = "Unknown",
databaseName = "Unknown",
databaseDescription = "Unknown",
createCohorts = TRUE,
runInclusionStatistics = TRUE,
runIncludedSourceConcepts = TRUE,
runOrphanConcepts = TRUE,
runTimeDistributions = TRUE,
runBreakdownIndexEvents = TRUE,
runIncidenceRates = TRUE,
runCohortOverlap = TRUE,
runCohortCharacterization = TRUE,
minCellCount = 5
)
|
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'. |
cohortDatabaseSchema |
Schema name where intermediate data can be stored. You will need to have write priviliges in this schema. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'. |
cohortTable |
The name of the table that will be created in the work database schema. This table will hold the exposure and outcome cohorts used in this study. |
oracleTempSchema |
Should be used in Oracle to specify a schema where the user has write priviliges for storing temporary tables. |
outputFolder |
Name of local folder to place results; make sure to use forward slashes (/). Do not use a folder on a network drive since this greatly impacts performance. |
databaseId |
A short string for identifying the database (e.g. 'Synpuf'). |
databaseName |
The full name of the database (e.g. 'Medicare Claims Synthetic Public Use Files (SynPUFs)'). |
databaseDescription |
A short description (several sentences) of the database. |
createCohorts |
Create the cohortTable table with the exposure and outcome cohorts? |
runInclusionStatistics |
Generate and export statistic on the cohort incusion rules? |
runIncludedSourceConcepts |
Generate and export the source concepts included in the cohorts? |
runOrphanConcepts |
Generate and export potential orphan concepts? |
runTimeDistributions |
Generate and export cohort time distributions? |
runBreakdownIndexEvents |
Generate and export the breakdown of index events? |
runIncidenceRates |
Generate and export the cohort incidence rates? |
runCohortOverlap |
Generate and export the cohort overlap? |
runCohortCharacterization |
Generate and export the cohort characterization? |
minCellCount |
The minimum number of subjects contributing to a count before it can be included in packaged results. |
This function executes the cohort diagnostics.
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