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Validating an FDA study-data package

What this package is

openstudyval is an independent R validator for a study-data folder prepared for an FDA submission. It covers:

SAS v5 transport constraints from the FDA Study Data Technical Conformance Guide (8-character names, 40-character labels, 200-character values)
eCTD technical-rejection criteria 1734, 1735, 1736, and 1738 where they can be evaluated from the study folder
structural SDTM, SEND, and ADaM checks, plus a CSV rule catalog you can extend

It is not Pinnacle 21, and a clean report is not an FDA certification.

Run the bundled example

library(openstudyval)
report <- validate_submission(example_study("sdtm"), standard = "SDTM")
summary(report)
#> Issue summary (SDTM)
#>   rule_id severity     domains records
#>   SDTM003   Reject          TS       1
#>   SDTM010    Error          DM       1
#>   SDTM011    Error          DM       1
#>   SDTM012    Error          AE       1
#>   SDTM013    Error          AE       1
#>   SDTM022    Error          DM       1
#>   SDTM024    Error          AE       1
#>   SDTM025    Error          AE       1
#>  TRC1736D    Error  define.xml       1
#>   FDAB008  Warning          EX       1
#>   SDTM002  Warning TA,TE,TI,TV       4
#>   SDTM033  Warning          AE       1
#>                                                                                                        message
#>     TS does not contain TSPARMCD = SSTDTC. FDA technical-rejection criterion 1734 requires a study start date.
#>                                                                  DOMAIN value does not match the dataset name.
#>                                                                             USUBJID should begin with STUDYID.
#>                                                                                  USUBJID is not present in DM.
#>                                                                            AESEQ is not unique within USUBJID.
#>                                               SEX is not in the core controlled terminology. Allowed: M, F, U.
#>                                                            AESER must be Y or N when populated. Allowed: Y, N.
#>                                        AESEV is not MILD / MODERATE / SEVERE. Allowed: MILD, MODERATE, SEVERE.
#>            define.xml was not found beside the datasets. FDA expects a define.xml for standardized study data.
#>  Exposure date/time falls outside the DM reference start/end window (public FDA business-rule intent FDAB008).
#>                          Trial Design dataset missing. FDA TCG expects TA, TE, TI, TS, and TV when applicable.
#>                                                Date/time variable is not a complete or partial ISO 8601 value.

Write the HTML report next to your study:

write_validation_report(report, "validation-report.html")

Add a study-specific rule

extra <- data.frame(
  rule_id = "CUST_ARM",
  publisher = "sponsor",
  standard = "SDTM",
  domains = "DM",
  severity = "Error",
  check = "codelist",
  argument = "ARMCD=A|B",
  message = "ARMCD is not in the study arm codelist.",
  guidance = "Protocol section 6",
  stringsAsFactors = FALSE
)
study <- read_study_data(example_study("sdtm"))
custom <- validate_datasets(study, standard = "SDTM", rules = extra)
"CUST_ARM" %in% custom$issues$rule_id
#> [1] FALSE

Full MedDRA and WHODrug dictionaries are licensed and are not bundled. Pass permitted terms in ct or as the right-hand side of a codelist rule.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.