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
)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,
covariateData1will be restricted to this cohort. If not provided,covariateData1is assumed to contain data on only 1 cohort.- cohortId2
If provided,
covariateData2will be restricted to this cohort. If not provided,covariateData2is 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", oroutput = "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
# \donttest{
eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails()
covSettings <- createDefaultCovariateSettings()
Eunomia::createCohorts(
connectionDetails = eunomiaConnectionDetails,
cdmDatabaseSchema = "main",
cohortDatabaseSchema = "main",
cohortTable = "cohort"
)
#> Cohorts created in table main.cohort
#> cohortId name
#> 1 1 Celecoxib
#> 2 2 Diclofenac
#> 3 3 GiBleed
#> 4 4 NSAIDs
#> description
#> 1 A simplified cohort definition for new users of celecoxib, designed specifically for Eunomia.
#> 2 A simplified cohort definition for new users ofdiclofenac, designed specifically for Eunomia.
#> 3 A simplified cohort definition for gastrointestinal bleeding, designed specifically for Eunomia.
#> 4 A simplified cohort definition for new users of NSAIDs, designed specifically for Eunomia.
#> count
#> 1 1844
#> 2 850
#> 3 479
#> 4 2694
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
)
#> Warning: cohortId argument has been deprecated, please use cohortIds
#> Connecting using SQLite driver
#> Constructing features on server
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#> Executing SQL took 1.15 secs
#> Fetching data from server
#> Fetching data took 0.0696 secs
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
)
#> Warning: cohortId argument has been deprecated, please use cohortIds
#> Connecting using SQLite driver
#> Constructing features on server
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#> Executing SQL took 0.912 secs
#> Fetching data from server
#> Fetching data took 0.0623 secs
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
)
# }