Bug: derive_param_tte() fails if dataset and by_vars is specified

[bundfussr]

What happened?

derive_param_tte() fails if dataset and by_vars is specified because the check on duplicate parameter codes fails.

Session Information

No response

Reproducible Example

library(dplyr)
library(lubridate)
library(admiral)
adsl <- tibble::tribble(
  ~USUBJID, ~TRTSDT,           ~TRTEDT,           ~EOSDT,
  "01",     ymd("2020-12-06"), ymd("2021-03-02"), ymd("2021-03-06"),
  "02",     ymd("2021-01-16"), ymd("2021-01-20"), ymd("2021-02-03")
) %>%
  mutate(STUDYID = "AB42")

ae <- tibble::tribble(
  ~USUBJID, ~AESTDTC,     ~AESEQ, ~AEDECOD,
  "01",     "2021-01-03",      1, "Flu",
  "01",     "2021-03-04",      2, "Cough",
  "01",     "2021-01-01",      3, "Flu"
) %>%
  mutate(
    STUDYID = "AB42",
    AESTDT = ymd(AESTDTC)
  )

ttae <- event_source(
  dataset_name = "ae",
  date = AESTDT,
  set_values_to = exprs(
    EVENTDESC = "AE",
    SRCDOM = "AE",
    SRCVAR = "AESTDTC",
    SRCSEQ = AESEQ
  )
)

eot <- censor_source(
  dataset_name = "adsl",
  date = pmin(TRTEDT + days(10), EOSDT),
  censor = 1,
  set_values_to = exprs(
    EVENTDESC = "END OF TRT",
    SRCDOM = "ADSL",
    SRCVAR = "TRTEDT"
  )
)

  derive_param_tte(
    dataset = adsl %>% select(STUDYID, USUBJID) %>% mutate(PARAMCD = "XYZ"),
    dataset_adsl = adsl,
    by_vars = exprs(AEDECOD),
    start_date = TRTSDT,
    event_conditions = list(ttae),
    censor_conditions = list(eot),
    source_datasets = list(adsl = adsl, ae = ae),
    set_values_to = exprs(
      PARAMCD = paste0("TTAE", as.numeric(as.factor(AEDECOD))),
      PARAM = paste("Time to First", AEDECOD, "Adverse Event"),
      PARCAT1 = "TTAE",
      PARCAT2 = AEDECOD
    )
  )

results in

Error in match(x, table, nomatch = 0L) : 
  'match' requires vector arguments

[bms63]

Is this a critical bug or one that we can wait on for a while?

[bundfussr]

As a work-around you could not specify the dataset argument, create separate datasets for each derive_param_tte() call, and bind them all together using bind_rows().
So it is not super-critical. However, I am not sure if we should wait until June.

[bms63]

I will add to agenda for next week's meeting.

[millerg23]

@bms63 I looked at the Hotfix release page, do you create the patch branch that I should take feature branch from to fix this?

[bms63]

I think we should create a patch branch off the latest release tag and then branch off the patch to make the fix. whew!! @zdz2101

[millerg23]

OK thanks, I have created a branch called patch from tag 1.0.1 on GItHub

[bundfussr]

Our documentation is inconsistent. On the one hand it requires that the patch branch is protected and updated after each release. On the other hand it suggests to create the patch branch from a release tag.

And the formatting of the "Hot Fix Release" section got mixed up:

[bms63]

Our documentation is inconsistent. On the one hand it requires that the patch branch is protected and updated after each release. On the other hand it suggests to create the patch branch from a release tag.

And the formatting of the "Hot Fix Release" section got mixed up:

Thanks Stefan I created a new issue pharmaverse/admiraldev#365