rsh52 commented 3 months ago

Feature Request Description

It can be a common use case that multiple choice fields (i.e. checkbox fields) need to be consolidated into a single column, such as when powering Table 1s for manuscript reporting.

Proposed Solution

This function, placeholder name reduce_multi_to_single_column() will be the first REDCapTidieR analytic tool that users can implement on columns in their extracted tibbles.

It should:

Be capable of using tidyselect functions (i.e. starts_with("race"))
Supply users an option of what to change multiple selections to (i.e. "Multiple", "Other", etc.) per their specification

Additional Context

This was prompted by the request in #192 and should be a more generalizable solution.

Checklist

[x] The issue is atomic
[x] The issue description is documented
[x] The issue title describes the problem succinctly
[x] Developers are assigned to the issue
[x] Labels are assigned to the issue

ezraporter commented 2 months ago

The stuff in https://github.com/CHOP-CGTInformatics/REDCapTidieR/commit/96c3309959caa5d574ae192604ce86ceef04bea1 looks like a good start. I didn't look closely at the code and mainly focused on the API.

My biggest reaction is that the current API take a supertibble as input and returns a tibble and I'm not sure that's right. I think we want data manipulation functions like this to be pipe-friendly which requires that inputs and outputs are the same type of thing.

I think the best way of doing this is to have this function modify a tibble within the supertibble and return the whole thing. To get the current behavior you'd do need to do something like:

supertbl |>
  reduce_multi_to_single_column() |>
  extract_tibble()

but this buys us composability:

supertbl |>
  reduce_multi_to_single_column() |>
  reduce_multi_to_single_column() |>
  some_other_transformation() |>
  ...

Naming thoughts

Maybe we should call this unite_checkbox() in reference to tidyr::unite()?

For parameter names what about: cols_to -> values_to no_val -> values_fill multi_val -> multi_value_label

The first 2 are inspired by pivot_* naming conventions in tidyr

skadauke commented 2 months ago

Hi,

There isn't a general rule that says that the pipe should always have inputs and outputs that are the same type of thing. That's more of a dplyr-specific rule that's not shared by other tidy packages such as e.g. tidymodels.

That said, I agree with your point and actually think this function should take a tibble and return a modified tibble. So the workflow would be

supertbl |> extract_tibble(x) |> reduce_multi_to_single_column(...)

I think "unite" is much less specific than "reduce_multi_to_single_column".

My thoughts! S

From: Ezra Porter @.> Sent: Friday, July 12, 2024 2:43 PM To: CHOP-CGTInformatics/REDCapTidieR @.> Cc: Subscribed @.***> Subject: [External]Re: [CHOP-CGTInformatics/REDCapTidieR] [FEATURE] Multiple Choice to Single Column Function (Issue #194)

The stuff in 96c3309https://github.com/CHOP-CGTInformatics/REDCapTidieR/commit/96c3309959caa5d574ae192604ce86ceef04bea1 looks like a good start. I didn't look closely at the code and mainly focused on the API.

My biggest reaction is that the current API take a supertibble as input and returns a tibble and I'm not sure that's right. I think we want data manipulation functions like this to be pipe-friendly which requires that inputs and outputs are the same type of thing.

I think the best way of doing this is to have this function modify a tibble within the supertibble and return the whole thing. To get the current behavior you'd do need to do something like:

supertbl |> reduce_multi_to_single_column() |> extract_tibble()

but this buys us composability:

supertbl |> reduce_multi_to_single_column() |> reduce_multi_to_single_column() |> some_other_transformation() |> ...

Naming thoughts

Maybe we should call this unite_checkbox() in reference to tidyr::unite()?

For parameter names what about: cols_to -> values_to no_val -> values_fill multi_val -> multi_value_label

The first 2 are inspired by pivot_* naming conventions in tidyr

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rsh52 commented 2 months ago

My biggest reaction is that the current API take a supertibble as input and returns a tibble and I'm not sure that's right. I think we want data manipulation functions like this to be pipe-friendly which requires that inputs and outputs are the same type of thing.

For the API change, I think this is easily reworkable if we agree on what it should intake and output. I definitely see what you're saying. My concern with returning a supertibble is that you don't actually see the changes from the output of the function, it's sort of "masked" inside of the data tibbles. But maybe that's not a big issue here?

Either way the function needs access to the metadata raw/label values associated with the checkboxes to be united, so I don't see much way of not having users supply the supertibble. Otherwise they'd have to supply the data tibble and metadata tibble separately.

Naming thoughts

I like the naming much better, these all make sense to me.

rsh52 commented 2 months ago

That said, I agree with your point and actually think this function should take a tibble and return a modified tibble. So the workflow would be supertbl |> extract_tibble(x) |> reduce_multi_to_single_column(...)

@skadauke This also makes some sense, but then users would still need to supply the metadata separately. That's what led me to wrapping the extract_() internally.

skadauke commented 2 months ago

What metadata is needed for the transformation?

From: Rich Hanna @.> Sent: Friday, July 12, 2024 2:56 PM To: CHOP-CGTInformatics/REDCapTidieR @.> Cc: Stephan Kadauke @.>; Mention @.> Subject: [External]Re: [CHOP-CGTInformatics/REDCapTidieR] [FEATURE] Multiple Choice to Single Column Function (Issue #194)

That said, I agree with your point and actually think this function should take a tibble and return a modified tibble. So the workflow would be supertbl |> extract_tibble(x) |> reduce_multi_to_single_column(...)

@skadaukehttps://github.com/skadauke This also makes some sense, but then users would still need to supply the metadata separately. That's what led me to wrapping the extract_() internally.

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rsh52 commented 2 months ago

What metadata is needed for the transformation?

The general rule is to consolidate checkboxes under one column, showing the raw/label value associated with the checkbox if only one value is selected OR a custom value (i.e. "multiple" / "many") if multiple selected. There's no way to grab these values in the data tibble, they are either 1s and 0s or TRUEs and FALSEs. Ex:

> nonrepeat_data
# A tibble: 3 × 4
  study_id multi___1 multi___2 multi___3
     <dbl> <lgl>     <lgl>     <lgl>    
1        1 TRUE      FALSE     FALSE    
2        2 TRUE      TRUE      FALSE    
3        3 FALSE     FALSE     FALSE    
> nonrepeat_metadata
# A tibble: 4 × 2
  field_name select_choices_or_calculations
  <chr>      <chr>                         
1 study_id   NA                            
2 multi___1  1, Red | 2, Yellow | 3, Blue  
3 multi___2  1, Red | 2, Yellow | 3, Blue  
4 multi___3  1, Red | 2, Yellow | 3, Blue

CHOP-CGTInformatics / REDCapTidieR

[FEATURE] Multiple Choice to Single Column Function #194

Feature Request Description

Proposed Solution

Additional Context

Checklist

Naming thoughts