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Improve error messaging for derive_param_tte() #2519

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rossfarrugia opened this issue Oct 2, 2024 · 5 comments · May be fixed by #2530
Open

Improve error messaging for derive_param_tte() #2519

rossfarrugia opened this issue Oct 2, 2024 · 5 comments · May be fixed by #2530
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@bundfussr
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programming

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@rossfarrugia
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rossfarrugia commented Oct 2, 2024 •
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What happened?

Any reason why derive_param_tte() argument source_datasets doesn't like underscores?

Session Information

Using {admiral} 1.1.1

Reproducible Example

This code works (assuming I have a valid adsl_death dataset and I've set rand_censor):

death <- event_source(
  dataset_name = "adsl",
  filter = DTHFL == "Y",
  date = DTHDT
)

test_os <- derive_param_tte(
  dataset_adsl = adsl_death,
  start_date = RANDDT,
  event_conditions = list(death),
  censor_conditions = list(rand_censor),
  source_datasets = list(adsl = adsl_death),
  set_values_to = exprs(
    PARAMCD = "OS"
  )
)

This code errors:

death <- event_source(
  dataset_name = "adsl_death",
  filter = DTHFL == "Y",
  date = DTHDT
)

test_os <- derive_param_tte(
  dataset_adsl = adsl_death,
  start_date = RANDDT,
  event_conditions = list(death),
  censor_conditions = list(rand_censor),
  source_datasets = list(adsl_death = adsl_death),
  set_values_to = exprs(
    PARAMCD = "OS"
  )
)

The error given is:

Error in `fun(..., .envir = .envir)`:
! Could not evaluate cli `{}` expression: `source_names`.
Caused by error in `eval(expr, envir = envir)`:
! object 'source_names' not found
Type .Last.error to see the more details.
@rossfarrugia rossfarrugia added bug Something isn't working programming labels Oct 2, 2024
@bundfussr bundfussr self-assigned this Oct 2, 2024
@bundfussr bundfussr mentioned this issue Oct 10, 2024
Open
bundfussr added a commit that referenced this issue Oct 10, 2024
@bundfussr
#2519 fix_param_tte: add test
a07fe27
bundfussr added a commit that referenced this issue Oct 10, 2024
@bundfussr
#2519 fix_param_tte: style file
ecd417f
@bundfussr bundfussr linked a pull request Oct 10, 2024 that will close this issue
Closes #2519 fix_param_tte: add test #2530
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@bundfussr
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@rossfarrugia , I think the issue is not related to underscores but an issue in the error message. The correct error message should be:

Error in `derive_param_tte()`:
! The dataset names must be included in the list specified for the `source_datasets` argument.
ℹ Following names were provided by `source_datasets`: "adsl_death"
ℹ But, `censor_conditions[[1]]$dataset_name = adsl`

I assume in your example rand_censor is referring to adsl instead of adsl_death. Could you check?

@rossfarrugia
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Yes! That's it @bundfussr - great spot. It was an error on my side but the error message could definitely be improved, as I'd have spent hours trying to figure that out.

@rossfarrugia rossfarrugia changed the title Bug: Any reason why derive_param_tte() argument source_datasets doesn't like underscores Improve error messaging for derive_param_tte() Oct 11, 2024
@rossfarrugia rossfarrugia removed the bug Something isn't working label Oct 11, 2024
@bundfussr
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Yes! That's it @bundfussr - great spot. It was an error on my side but the error message could definitely be improved, as I'd have spent hours trying to figure that out.

@rossfarrugia , I have fixed the bug in the error message. If you want to try it out, you need to call remotes::install_github("pharmaverse/admiraldev", ref = "469_fix_assert_list_element") to install the admiraldev version where the bug is fixed.

@rossfarrugia
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yes, works now by giving better error message when re-running the same code 👍

@bms63
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bms63 commented Oct 11, 2024

Yes! That's it @bundfussr - great spot. It was an error on my side but the error message could definitely be improved, as I'd have spent hours trying to figure that out.

hours!! oh no!!

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@bundfussr bundfussr

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programming
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admiral (sdtm/adam, dev, ci, template, core)
Status: In Review
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Closes #2519 fix_param_tte: add test pharmaverse/admiral
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@bms63 @bundfussr @rossfarrugia