createTable1: Create a table 1

In FeatureExtraction: Generating Features for a Cohort

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,
  tempEmulationSchema = NULL,
  cdmDatabaseSchema = "main",
  cdmVersion = "5",
  cohortTable = "cohort",
  cohortDatabaseSchema = "main",
  cohortTableIsTemp = FALSE,
  cohortId = 1,
  rowIdField = "subject_id",
  covariateSettings = covSettings,
  aggregated = TRUE
)
covData2 <- getDbCovariateData(
  connectionDetails = eunomiaConnectionDetails,
  tempEmulationSchema = 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
)

FeatureExtraction documentation built on Oct. 18, 2024, 9:06 a.m.