Is run_check() looking for dataset "ae" and not "AE" ?

[jimrothstein]

Problem:   sdtmchecks::run_check()  does not appear to work with dummy data only for AE 
To run properly, "ae" dataset must be populated.  Most other checks require "AE" be populated.


 suspect code?   in line containing parse
  
## fxn_in="AE=ae"
## parse(text = paste0(check, "(", fxn_in, ")"))
  
library(sdtmchecks)

### Pick a check (check_ae_aeacnoth):
metads = sdtmchecksmeta[sdtmchecksmeta$check == "check_ae_aeacnoth", ]
metads$check
#> [1] "check_ae_aeacnoth"

### Populate dummy AE
### "Assuming sdtm datasets are in your global environment"
   AE <- data.frame(
    USUBJID = 1:7,
    AETERM = 1:7,
    AESTDTC = 1:7,
    AEACNOTH = 1:7,
    AEACNOT1 = 1:7,
    AEACNOT2 = 1:7,
    AESPID = "FORMNAME-R:13/L:13XXXX"
   )

### check: pass
check_ae_aeacnoth(AE)
#> [1] TRUE

run 2 ways, (1) ae not in environment (2) ae=AE

rec1 <- run_check(
check = metads$check,
fxn_in = metads$fxn_in,
xls_title = metads$xls_title,
pdf_title = metads$pdf_title,
pdf_subtitle = metads$pdf_subtitle,
pdf_return = metads$pdf_return,
verbose = T
)

ae=AE

rec2 <- run_check(
check = metads$check,
fxn_in = metads$fxn_in,
xls_title = metads$xls_title,
pdf_title = metads$pdf_title,
pdf_subtitle = metads$pdf_subtitle,
pdf_return = metads$pdf_return,
verbose = T
)
identical(rec1, rec2)
#> [1] FALSE

rec1$notes
#> [1] "ATTENTION! Check was not run: AE does not exist or failed to read"
rec2$notes
#> [1] " "

rec1
#> $xls_title
#> [1] "AE AEACNOTH multiple"
#>
#> $pdf_title
#> [1] "Check for null AEACNOT[1/2] when AEACNOTH = 'MULTIPLE'"
#>
#> $pdf_subtitle
#> [1] "* This check looks for null AEACNOT[1/2] when AEACNOTH = 'MULTIPLE', which indicates a possible SDTMv mapping issue\n* NOTE: not all ongoing studies are adopting this approach for AE resolution and this may not be appropriate to query"
#>
#> $nrec
#> [1] 0
#>
#> $notes
#> [1] "ATTENTION! Check was not run: AE does not exist or failed to read"
#>
#> $msg
#> character(0)
#>
#> $data
#> data frame with 0 columns and 0 rows
rec2
#> $xls_title
#> [1] "AE AEACNOTH multiple"
#>
#> $pdf_title
#> [1] "Check for null AEACNOT[1/2] when AEACNOTH = 'MULTIPLE'"
#>
#> $pdf_subtitle
#> [1] "* This check looks for null AEACNOT[1/2] when AEACNOTH = 'MULTIPLE', which indicates a possible SDTMv mapping issue\n* NOTE: not all ongoing studies are adopting this approach for AE resolution and this may not be appropriate to query"
#>
#> $nrec
#> [1] 0
#>
#> $notes
#> [1] " "
#>
#> $msg
#> character(0)
#>
#> $data
#> data frame with 0 columns and 0 rows
Created on 2024-06-19 with reprex v2.1.0

Standard output and standard error