99 create var from codelist bugfix #102
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
LiamHobby
added
0.3.0
Collaborator
Author
|
@bms63 Could you take a look at this one please |
added 2 commits
December 19, 2025 14:25
Merge branch '99-create-var-from-codelist-bugfix' of github.com:pharmaverse/metatools into 99-create-var-from-codelist-bugfix # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit.
bms63
reviewed
Dec 19, 2025
Comment on lines
+88
to
+97
| create_var_from_codelist( | ||
| data = data, | ||
| metacore = adlb_spec, | ||
| input_var = PARAMCD, | ||
| out_var = PARAM, | ||
| codelist = get_control_term(adlb_spec, PARAMCD), | ||
| decode_to_code = FALSE, | ||
| strict = TRUE | ||
| ) |> | ||
| expect_warning() |
Collaborator
There was a problem hiding this comment.
when i run this as standalone I am not getting a warning
> load(metacore::metacore_example("pilot_ADaM.rda"))
> adlb_spec <- metacore::select_dataset(metacore, "ADLBC", quiet = TRUE)
✔ ADLBC dataset successfully selected
ℹ Dataset metadata specification subsetted with suppressed warnings
> data <- tibble::tibble(
+ PARAMCD = c("ALB", "ALP", "ALT", "DUMMY", "DUMMY2")
+ )
> compare <- tibble::tibble(
+ PARAMCD = c("ALB", "ALP", "ALT", "DUMMY", "DUMMY2"),
+ PARAM = c("Albumin (g/L)", "Alkaline Phosphatase (U/L)", "Alanine Aminotransferase (U/L)", NA, NA)
+ )
>
> create_var_from_codelist(
+ data = data,
+ metacore = adlb_spec,
+ input_var = PARAMCD,
+ out_var = PARAM,
+ codelist = get_control_term(adlb_spec, PARAMCD),
+ decode_to_code = FALSE,
+ strict = FALSE
+ )
# A tibble: 5 × 2
PARAMCD PARAM
<chr> <chr>
1 ALB Albumin (g/L)
2 ALP Alkaline Phosphatase (U/L)
3 ALT Alanine Aminotransferase (U/L)
4 DUMMY NA
5 DUMMY2 NA
>
Collaborator
There was a problem hiding this comment.
however the tests run fine - but im a bit suspicious
bms63
reviewed
Dec 19, 2025
| metacore = adlb_spec, | ||
| input_var = PARAMCD, | ||
| out_var = PARAM, | ||
| codelist = get_control_term(adlb_spec, PARAMCD), |
Collaborator
There was a problem hiding this comment.
Suggested change
| codelist = get_control_term(adlb_spec, PARAMCD), | |
| codelist = metacore::get_control_term(adlb_spec, PARAMCD), |
I thought this was from metatools at first and got confused...maybe be more explicit here with the :: for those who come later?
bms63
reviewed
Dec 19, 2025
Comment on lines
+149
to
+161
| data3 <- tibble::tibble( | ||
| PARAMN = c(18, 19, 20, 99, 999) | ||
| ) | ||
|
|
||
| create_var_from_codelist( | ||
| data = data3, | ||
| metacore = adlb_spec, | ||
| input_var = PARAMN, | ||
| out_var = PARAM, | ||
| codelist = get_control_term(adlb_spec, PARAMN), | ||
| decode_to_code = FALSE, | ||
| strict = TRUE | ||
| ) |> |
Collaborator
There was a problem hiding this comment.
This one produced the warning when I fired off in the console
> # Test numeric variable used as input_var / multiple issue case (strict == TRUE)
> data3 <- tibble::tibble(
+ PARAMN = c(18, 19, 20, 99, 999)
+ )
>
> create_var_from_codelist(
+ data = data3,
+ metacore = adlb_spec,
+ input_var = PARAMN,
+ out_var = PARAM,
+ codelist = get_control_term(adlb_spec, PARAMN),
+ decode_to_code = FALSE,
+ strict = TRUE
+ )
# A tibble: 5 × 2
PARAMN PARAM
<dbl> <chr>
1 18 Sodium (mmol/L)
2 19 Potassium (mmol/L)
3 20 Chloride (mmol/L)
4 99 NA
5 999 NA
Warning message:
In `create_var_from_codelist()`: The following values present in the input dataset are not present in the
codelist: 99 and 999
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Closes #99
This bug occurred only when there were multiple values from a numeric type input column that were not present in the codelist i.e., values of 99 and 999 in the dataset but no appropriate record in the CT.
The fix just required placing a
cli::qty()check prior to the glue substitution that uses pluralization.This wasn't caught in testing because the test case only had a single value of wrong CT in the test dataset. I have expanded the test cases to include both single and multiple bad CT for both character and numeric input.