8000 Add lab abnormality KRI by samussiah · Pull Request #617 · Gilead-BioStats/gsm · GitHub
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Add lab abnormality KRI #617

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Merged
merged 38 commits into from
Aug 5, 2022
Merged

Add lab abnormality KRI #617

merged 38 commits into from
Aug 5, 2022

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samussiah
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Overview

Adds a lab abnormality KRI that models the number of abnormal lab results out of the total number of lab results.

Test Notes/Sample Code

output <- LB_Map_Raw() %>% LB_Assess()

# stratified by lab category
output_stratified <- MakeAssessmentList() %>%
    pluck('lbCategory') %>%
    MakeStratifiedAssessment(
        yaml::read_yaml(system.file('mappings', 'mapping_rawplus.yaml', package = 'gsm')),
        list(dfSUBJ = clindata::rawplus_subj, dfLB = clindata::rawplus_lb)
    ) %>%
    map(~.x %>%
        RunAssessment(
            list(dfSUBJ = clindata::rawplus_subj, dfLB = clindata::rawplus_lb),
            system.file('mappings', 'mapping_rawplus.yaml', package = 'gsm')
        )
    )

Notes:
The stratified assessment is bombing somewhere, but the standalone is good to go. It'd be useful to directly visualize the rate of abnormal labs - perhaps the standard KRI viz will handle this use case - but the KRI is the count, not the proportion. It's also be nice to flag on that proportion (>5% abnormal labs for instance)...

mattroumaya
mattroumaya reviewed Jul 26, 2022
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@samussiah - Haven't pulled this to review in more detail, but at first glance it looks like there are some .rda files in here. Did they sneak in from clindata or are they needed for labs?

@samussiah
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@mattroumaya yeah, I attached the mappings as R data to avoid typing yaml::read_yaml(system.file('mappings', 'mapping_rawplus.yaml', package = 'gsm')) all the time.

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Ahhh cool! Got it.

mattroumaya
mattroumaya requested changes Jul 26, 2022
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Looks great @samussiah!

Left some comments/suggestions, mostly just for passing all possible grouping columns in mapping, and adding the ability to group in assess.

@mattroumaya
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Forgot to mention that clindata was released with rawplus_lb updates - feel free to update to v0.6.2 in workflows.

samussiah and others added 12 commits July 26, 2022 18:56
@samussiah @mattroumaya
Update DESCRIPTION
9e2d37f 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah @mattroumaya
Update R/LB_Map_Raw.R
22d688d 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah @mattroumaya
Update R/LB_Map_Raw.R
f1049f5 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah @mattroumaya
Update R/LB_Assess.R
37ca067 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah @mattroumaya
Update R/LB_Assess.R
b61808d 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah @mattroumaya
Update R/LB_Assess.R
7d2b221 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah @mattroumaya
Update R/LB_Assess.R
7590592 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah @mattroumaya
Update inst/mappings/LB_Assess.yaml
4398c47 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah @mattroumaya
Update inst/mappings/LB_Map_Raw.yaml
a6812ea 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah @mattroumaya
Update inst/specs/LB_Assess.yaml
25179f6 
Co-authored-by: Matt Roumaya <40671730+mattroumaya@users.noreply.github.com>
@samussiah
Build Markdown
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...
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@samussiah - note to add Analyze_Identity() to the assess function

@mattroumaya mattroumaya mentioned this pull request Aug 4, 2022
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@samussiah samussiah requested a review from mattroumaya August 5, 2022 17:11
mattroumaya
mattroumaya approved these changes Aug 5, 2022
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Awesome - great work @samussiah!

@mattroumaya mattroumaya merged commit ee633a1 into dev Aug 5, 2022
@mattroumaya mattroumaya deleted the fix-541 branch August 5, 2022 17:23
@samussiah samussiah mentioned this pull request Aug 5, 2022
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@mattroumaya mattroumaya mentioned this pull request Aug 8, 2022
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@mattroumaya mattroumaya mattroumaya approved these changes

@jwildfire jwildfire Awaiting requested review from jwildfire

@gwu05 gwu05 Awaiting requested review from gwu05

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