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.
createTable1(
covariateData1,
covariateData2 = NULL,
cohortId1 = NULL,
cohortId2 = NULL,
specifications = getDefaultTable1Specifications(),
output = "two columns",
showCounts = FALSE,
showPercent = TRUE,
percentDigits = 1,
valueDigits = 1,
stdDiffDigits = 2
)
The covariate data of the cohort to be included in the table.
The covariate data of the cohort to also be included, when comparing two cohorts.
If provided, covariateData1
will be restricted to this cohort. If not
provided, covariateData1
is assumed to contain data on only 1 cohort.
If provided, covariateData2
will be restricted to this cohort. If not
provided, covariateData2
is assumed to contain data on only 1 cohort.
Specifications of which covariates to display, and how.
The output format for the table. Options are output = "two columns"
,
output = "one column"
, or output = "list"
.
Show the number of cohort entries having the binary covariate?
Show the percentage of cohort entries having the binary covariate?
Number of digits to be used for percentages.
Number of digits to be used for the values of continuous variables.
Number of digits to be used for the standardized differences.
A data frame, or, when output = "list"
a list of two data frames.
if (FALSE) {
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
)
}