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Extract the self controlled case series (sccs) results

Source: R/EstimationQueries.R
getSccsEstimation.Rd

This function extracts the single database sccs estimates

Usage

getSccsEstimation(
  connectionHandler,
  schema,
  sccsTablePrefix = "sccs_",
  cgTablePrefix = "cg_",
  databaseTable = "database_meta_data",
  targetIds = NULL,
  outcomeIds = NULL
)

Arguments

connectionHandler

A connection handler that connects to the database and extracts sql queries. Create a connection handler via `ResultModelManager::ConnectionHandler$new()`.

schema

The result database schema (e.g., 'main' for sqlite)

sccsTablePrefix

The prefix used for the cohort generator results tables

cgTablePrefix

The prefix used for the cohort generator results tables

databaseTable

The name of the table with the database details (default 'database_meta_data')

targetIds

A vector of integers corresponding to the target cohort IDs

outcomeIds

A vector of integers corresponding to the outcome cohort IDs

Value

Returns a data.frame with the columns:

  • databaseName the database name

  • analysisId the analysis unique identifier

  • description an analysis description

  • targetName the target name

  • targetId the target cohort id

  • outcomeName the outcome name

  • outcomeId the outcome cohort id

  • covariateName whether main or secondary analysis

  • outcomeSubjects The number of subjects with at least one outcome.

  • outcomeEvents The number of outcome events.

  • outcomeObservationPeriods The number of observation periods containing at least one outcome.

  • covariateSubjects The number of subjects having the covariate.

  • covariateDays The total covariate time in days.

  • covariateEras The number of continuous eras of the covariate.

  • covariateOutcomes The number of outcomes observed during the covariate time.

  • observedDays The number of days subjects were observed.

  • rr the relative risk

  • ci95Lb the lower bound of the 95 percent confidence interval for the relative risk

  • ci95Ub the upper bound of the 95 percent confidence interval for the relative risk

  • p the p-value for the relative risk

  • logRr the log of the relative risk

  • seLogRr the standard error or the log of the relative risk

  • calibratedRr the calibrated relative risk

  • calibratedCi95Lb the lower bound of the 95 percent confidence interval for the calibrated relative risk

  • calibratedCi95Ub the upper bound of the 95 percent confidence interval for the calibrated relative risk

  • calibratedP the calibrated p-value

  • calibratedLogRr the calibrated log of the relative risk

  • calibratedSeLogRr the calibrated log of the relative risk standard error

  • llr The log of the likelihood ratio (of the MLE vs the null hypothesis of no effect).

  • mdrr The minimum detectable relative risk.

  • unblind Whether the results can be unblinded

Details

Specify the connectionHandler, the schema and the target/outcome cohort IDs

See also

Other Estimation: getCMEstimation(), getCmDiagnosticsData(), getCmMetaEstimation(), getSccsDiagnosticsData(), getSccsMetaEstimation(), plotCmEstimates(), plotSccsEstimates()

Examples

conDet <- getExampleConnectionDetails()

connectionHandler <- ResultModelManager::ConnectionHandler$new(conDet)
#> Connecting using SQLite driver

sccsEst <- getSccsEstimation(
  connectionHandler = connectionHandler, 
  schema = 'main',
  targetIds = 1,
  outcomeIds = 3
)