run_all_checks {sdtmchecks}

Run all data checks in sdtmchecks package using parallel processing

Description

This function runs all checks in the sdtmchecks package. It expects SDTM domains saved as dataframe objects in your global environment. These dataframes should have lowercase names, e.g., dm.

Usage

run_all_checks(
  metads = sdtmchecksmeta,
  priority = c("High", "Medium", "Low"),
  type = c("ALL", "ONC", "COVID", "PRO", "OPHTH"),
  verbose = TRUE,
  ncores = 1
)

Arguments

metads

Metadata to use to execute the checks. The default is the sdtmchecksmeta dataframe available in the package. This object could easily be customized, subset, etc.

priority

Priority level of data checks, i.e., c("High", "Medium", "Low"). NULL runs all priority levels.

type

Type of data checks, i.e., c("ALL", "ONC", "COV", "PRO", "OPHTH"). NULL runs all type.

verbose

Whether to display messages while running

ncores

Number of cores for parallel processing, with default set to 1 (sequential)

Details

To look up documentation for the data checks in package, please use command ??sdtmchecks

Value

list with results from individual data check functions

See Also

Example programs for running data checks diff_reports(), report_to_xlsx(), run_check()

Examples

# Assuming sdtm datasets are in your global environment
# Note we are only specifying AE and DS here so all unrelated checks wont be run

ae <- data.frame(
    STUDYID = 1,
    USUBJID = c(1,2,3,1,2,3),
    AESTDTC = '2020-05-05',
    AETERM  = c("abc Covid-19", "covid TEST POSITIVE",rep("other AE",4)),
    AEDECOD = c("COVID-19", "CORONAVIRUS POSITIVE", rep("OTHER AE",4)),
    AEACN = c("DRUG WITHDRAWN", rep("DOSE NOT CHANGED",5)),
    AESPID = "FORMNAME-R:13/L:13XXXX",
    stringsAsFactors = FALSE
)

ds <- data.frame(
 USUBJID = c(1,1,2,3,4),
 DSSPID  = 'XXX-DISCTX-XXX',
 DSCAT   = "DISPOSITION EVENT",
 DSDECOD = "OTHER REASON",
 DSSEQ = c(1,2,1,1,1),
 stringsAsFactors = FALSE
)

all_rec<-run_all_checks(metads=sdtmchecksmeta, 
                        verbose=FALSE)