108 add buncreatinine chart #153

Lovemore-Gakava · 2024-09-08T12:08:27Z

Added the graph of BUN/serum creatinine over time, with two threshold lines, one at 10 and one at 20.

feat:
save_adlb - add BUN/CREAT updates
meta_nepExplorer - add BUN/CREAT updates and tidy up ALB/CREAT ratio
patient_profile_mod - update for drawBunCreat use the BUN/CREAT ratio
patient_profile_charts - update for drawBunCreat use the BUN/CREAT ratio
create_nepexplorer_app - add BUN/CREAT mapping
examples/safetyGraphics_demo_app - add the ALB/CREAT and BUN/CREAT records and update units for associated tests
examples/standalone_app - add BUN/CREATE mapping
man/drawBunCreat - add documentation

Examples:

examples/standalone_app - should now show the additional plot

examples/safetyGraphics_demo_app - when the ISG is launched go to mapping tab

select the Albumin value from the dropdown Albumin (mg/dL) and and Unit column select STRESU.
Then under charts select: Nep Explorer - Module

…://github.com/SafetyGraphics/nepExplorer into 108-add-buncreatinine-chart

…tyGraphics/nepExplorer into 108-add-buncreatinine-chart

save_adlb - add BUN/CREAT updates meta_nepExplorer - add BUN/CREAT updates and tidy up ALB/CREAT ratio patient_profile_mod - update for drawBunCreat use the BUN/CREAT ratio patient_profile_charts - update for drawBunCreat use the BUN/CREAT ratio create_nepexplorer_app - add BUN/CREAT mapping examples/safetyGraphics_demo_app - add the ALB/CREAT and BUN/CREAT records and update units for associated tests examples/standalone_app - add BUN/CREATE mapping man/drawBunCreat - add documentation

- Warning: file=inst/examples/safetyGraphics_demo_app.R,line=14,col=3,[object_length_linter] Variable and function names should not be longer than 30 characters. Warning: file=R/patient_profile_charts.R,line=410,col=1,[trailing_blank_lines_linter] Trailing blank lines are superfluous. Warning: file=R/patient_profile_mod.R,line=104,col=51,[trailing_whitespace_linter] Trailing whitespace is superfluous.

Lovemore-Gakava · 2024-09-08T12:37:21Z

Currently we have pkgdown workflow failing because we have stored docs there which are not built by pkgdown - nepExplorer/docs' is non-empty and not built by pkgdown. Do we want to keep these documents here or move them outside the repo?

pburnsdata

@Lovemore-Gakava I can see the chart in standa lone app and it looks great - nice work on this! Got a few changes/questions in here for your review

pburnsdata · 2024-09-21T14:00:19Z

inst/examples/safetyGraphics_demo_app.R

+        PARAMCD == "ALB"   ~ convert_alb_to_mgdl(BASE),
+        TRUE               ~ BASE
+      ),
+      CHG = case_when(


Since the same changes are being applied to base and aval, i don't think you'd need a unit conversion on CHG, I think that'd stay the same number since it's same division - double check my thinking though @Lovemore-Gakava, it's the morning and my mind is still getting started

@pburnsdata - I appreciate your feedback. The update extends beyond the ratio calculation. It aims to maintain consistency across all variables derived from or associated with BASE or AVAL/LBSTRESN, including CHG, A1LO, A1HI, and others. This ensures that users have reliable data for other various uses outside the BUN/CREAT chart.

o I see, the is raw CHG, idk why I thought this was fold change - sounds good!

pburnsdata · 2024-09-21T14:09:52Z

data-raw/save_adlb.R

+  mutate(STRESN  = ifelse(TEST == "Creatinine" & STRESU == "μmol/L", STRESN / 88.4, # 1 mg/dL creatinine = 88.4 µmol/L
+                          ifelse(TEST == "Blood Urea Nitrogen" & STRESU == "mmol/L", STRESN * 2.86, STRESN) # 1 mmol/L BUN = 2.8 mg/dL BUN
+                          ), # Convert μmol/L to mg/dL and mmol/L to mg/dL
+         STRESU  = ifelse(TEST %in% c("Creatinine", "Blood Urea Nitrogen", "Albumin"), "mg/dL", 


wouldn't we need the albumin conversion to mg/dL that you have in the app example code here if we're changing it's unit to mg/dL?

Thanks - it's been updated. To be consistent with the ISG demo app.

pburnsdata · 2024-09-21T14:13:00Z

inst/examples/safetyGraphics_demo_app.R

+        PARAM == "Blood Urea Nitrogen (mmol/L)"       ~ "Blood Urea Nitrogen (mg/dL)",
+        PARAM == "Albumin (g/L)"                      ~ "Albumin (mg/dL)",
+        TRUE                                         ~ PARAM
+      ) # todo: consider removing the units from the PARAM column - if this is implemented also update meta_nepExplorer


yeah I don't think it affects the app in anyway, but could cause confusion in the documentation and examples if users see that and think "oh I need to have units in the param" when they don't. I created #155 for this

Thanks - lets discuss this further when we look at #155, as we might need to be consistent across the application such as what users see under filters and what is shown on the chart. For example Creatinine (mg/dL) vs Creatinine

pburnsdata · 2024-09-21T14:18:10Z

R/patient_profile_charts.R

+  adlb_norm <- adlb %>%
+    filter(.data[[settings$measure_col]] == settings$measure_values[["BUN/CREAT"]])
+
+  uacr_unit <- unique(adlb_norm[[settings$unit_col]])


I'm thinking this unit variabel name should be different since no uacr involved, also I think on safetygraphics app example it gives an error for this chart because there's no unit, we may want to cahnge this to check for units because the if(length) statement below crashes it. I think albumin/creat chart needs the same change

Thanks Preston - uacr_unit references updated.

pburnsdata · 2024-09-21T14:22:41Z

@Lovemore-Gakava good point on the docs, they look like legacy reference material from back when Spencer was working on this, please delete them as part of your PR here to clear up the docs folder. I've palced them here for now: https://github.com/SafetyGraphics/nepExplorer/wiki/Clinical-Reference-Material

pburnsdata · 2024-09-21T14:34:24Z

data-raw/save_adlb.R

+  tidyr::spread(TEST, STRESN) %>%
+  mutate(STRESN = `Blood Urea Nitrogen` / Creatinine,
+         TEST = "Blood Urea Nitrogen/Creatinine",
+         STRESU = "Ratio") %>%


I'm wodnering if we need to say anything beyond 'ratio', like i could see users asking "ratio of what". For example, how by looking at the chart can you know the units of the creatinine and BUN? Idk what best practice is, may can ask Jim - could be a separate issue we can make if that makes sense to you

Agreed - I've opened a new issue #157 and lets ask Jim for best practice.

- uuppdated adlb and related files to include alb converted from g/L to mg/dl - removed documents from doc folder - added comment s to explain conversions in safetyGraphics demo app.

Merge branch '108-add-buncreatinine-chart' of https://github.com/SafetyGraphics/nepExplorer into 108-add-buncreatinine-chart # Conflicts: # R/patient_profile_charts.R

…tyGraphics/nepExplorer into 108-add-buncreatinine-chart

pburnsdata · 2024-09-24T01:22:58Z

R/patient_profile_charts.R

-  uacr_unit <- unique(adlb_norm[[settings$unit_col]])
-
+  if (is.null(adlb_norm[[settings$unit_col]]) || all(adlb_norm[[settings$unit_col]] == "")) {
+    uacr_unit <- "Ratio"


pburnsdata

Great work @Lovemore-Gakava !

Lovemore-Gakava added 9 commits June 14, 2024 23:02

feat: Initial.

40cfe12

feat: Initial.

70b91d6

Resolve conflicts.Merge branch '108-add-buncreatinine-chart' of https…

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…://github.com/SafetyGraphics/nepExplorer into 108-add-buncreatinine-chart

Resolve conflicts.Merge branch '108-add-buncreatinine-chart' of https…

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…://github.com/SafetyGraphics/nepExplorer into 108-add-buncreatinine-chart

Merge branch '108-add-buncreatinine-chart' of https://github.com/Safe…

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…tyGraphics/nepExplorer into 108-add-buncreatinine-chart

Merge branch '108-add-buncreatinine-chart' of https://github.com/Safe…

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…tyGraphics/nepExplorer into 108-add-buncreatinine-chart

Merge branch '108-add-buncreatinine-chart' of https://github.com/Safe…

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…tyGraphics/nepExplorer into 108-add-buncreatinine-chart

fix: Malformed Title field: should not end in a period

9f5545c

Lovemore-Gakava requested review from pburnsdata and jwoolfolk September 8, 2024 12:08

Lovemore-Gakava marked this pull request as ready for review September 8, 2024 12:37

pburnsdata requested a review from elimillera September 21, 2024 13:34

pburnsdata requested changes Sep 21, 2024

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pburnsdata reviewed Sep 21, 2024

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Lovemore-Gakava added 6 commits September 21, 2024 22:16

fix: Removed uacr_unit references

245b1ff

- uuppdated adlb and related files to include alb converted from g/L to mg/dl - removed documents from doc folder - added comment s to explain conversions in safetyGraphics demo app.

fix: Removed uacr_unit references

005b925

- uuppdated adlb and related files to include alb converted from g/L to mg/dl - removed documents from doc folder - added comment s to explain conversions in safetyGraphics demo app.

Fix: add check if unit variable exists or is empty.

2178f38

Merge branch '108-add-buncreatinine-chart' of https://github.com/SafetyGraphics/nepExplorer into 108-add-buncreatinine-chart # Conflicts: # R/patient_profile_charts.R

Fix: add check if unit variable exists or is empty.

ba28fe5

Merge branch '108-add-buncreatinine-chart' of https://github.com/SafetyGraphics/nepExplorer into 108-add-buncreatinine-chart # Conflicts: # R/patient_profile_charts.R

Merge branch '108-add-buncreatinine-chart' of https://github.com/Safe…

613a05d

…tyGraphics/nepExplorer into 108-add-buncreatinine-chart

fix: ensure albumin/creat chart doesn't crash when unit is missing/blank

7ef8f93

pburnsdata reviewed Sep 24, 2024

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pburnsdata approved these changes Sep 24, 2024

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pburnsdata merged commit b9099f7 into dev Sep 24, 2024
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pburnsdata deleted the 108-add-buncreatinine-chart branch September 24, 2024 01:27

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108 add buncreatinine chart #153

108 add buncreatinine chart #153

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108 add buncreatinine chart #153

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