createTable1 {FeatureExtraction}

Create a table 1

Description

Creates a formatted table of cohort characteristics, to be included in publications or reports. Allows for creating a table describing a single cohort, or a table comparing two cohorts.

Usage

createTable1(
  covariateData1,
  covariateData2 = NULL,
  cohortId1 = NULL,
  cohortId2 = NULL,
  specifications = getDefaultTable1Specifications(),
  output = "two columns",
  showCounts = FALSE,
  showPercent = TRUE,
  percentDigits = 1,
  valueDigits = 1,
  stdDiffDigits = 2
)

Arguments

covariateData1

The covariate data of the cohort to be included in the table.

covariateData2

The covariate data of the cohort to also be included, when comparing two cohorts.

cohortId1

If provided, covariateData1 will be restricted to this cohort. If not provided, covariateData1 is assumed to contain data on only 1 cohort.

cohortId2

If provided, covariateData2 will be restricted to this cohort. If not provided, covariateData2 is assumed to contain data on only 1 cohort.

specifications

Specifications of which covariates to display, and how.

output

The output format for the table. Options are output = "two columns", output = "one column", or output = "list".

showCounts

Show the number of cohort entries having the binary covariate?

showPercent

Show the percentage of cohort entries having the binary covariate?

percentDigits

Number of digits to be used for percentages.

valueDigits

Number of digits to be used for the values of continuous variables.

stdDiffDigits

Number of digits to be used for the standardized differences.

Value

A data frame, or, when output = "list" a list of two data frames.

Examples

eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails()
covSettings <- createDefaultCovariateSettings()
Eunomia::createCohorts(
  connectionDetails = eunomiaConnectionDetails,
  cdmDatabaseSchema = "main",
  cohortDatabaseSchema = "main",
  cohortTable = "cohort"
)
covData1 <- getDbCovariateData(
  connectionDetails = eunomiaConnectionDetails,
  oracleTempSchema = NULL,
  cdmDatabaseSchema = "main",
  cdmVersion = "5",
  cohortTable = "cohort",
  cohortDatabaseSchema = "main",
  cohortTableIsTemp = FALSE,
  cohortId = 1,
  rowIdField = "subject_id",
  covariateSettings = covSettings,
  aggregated = TRUE
)
covData2 <- getDbCovariateData(
  connectionDetails = eunomiaConnectionDetails,
  oracleTempSchema = NULL,
  cdmDatabaseSchema = "main",
  cdmVersion = "5",
  cohortTable = "cohort",
  cohortDatabaseSchema = "main",
  cohortTableIsTemp = FALSE,
  cohortId = 2,
  rowIdField = "subject_id",
  covariateSettings = covSettings,
  aggregated = TRUE
)
table1 <- createTable1(
  covariateData1 = covData1,
  covariateData2 = covData2,
  cohortId1 = 1,
  cohortId2 = 2,
  specifications = getDefaultTable1Specifications(),
  output = "one column",
  showCounts = FALSE,
  showPercent = TRUE,
  percentDigits = 1,
  valueDigits = 1,
  stdDiffDigits = 2
)