Bug: AUC start 0 (which also needs Feature: C0 imputation) #138
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Jan 17, 2025 in 0s
16 / 16 tasks completed
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Required Tasks
| Task | Status |
|---|---|
| Doses times are being considered at the first measure, instead of at the real dose time | Incomplete |
| No imputed measure at dose time is consdiered | Incomplete |
| At "NCA">"NCA Results", when C0 is imputed it is expected that start=AFRLT-ARRLT (being AFRLT-ARRLT= 0 in DOSNO=1) | Completed |
| At "NCA">"NCA Results", when C0 is not imputed it is expected that start={time of 1st observation} | Completed |
| AUC values (auclast, aucinf...) from start=AFRLT-ARRLT are calculated when C0 is imputed | Completed |
| All variables that should only be based on observed data (cmax, tmax...) are not considering C0 imputations | Completed |
| Test that PKNCA also deals well with predoses as duplicates for the NCA | Completed |
| Check slope selector plots and NCA results remain well after running NCA | Completed |
| Check if in general C0 imputation logic works well (NCA experts): | |
if C0 exists ~ C0=C0 |
|
if DOSNO=1 & IV bolus (ADOSEDUR=0, ROUTE=intravascular) ~ C0=0 |
|
if DOSNO>1 & not IV bolus ~ C0=predose |
|
if IV bolus and monoexponential data ~ logslope |
|
if IV bolus and not monoexponential data ~ C0=C1 |
Completed |
| Code passes lintr checks | Completed |
| Code passes all unit tests | Completed |
| New logic covered by unit tests | Completed |
| New logic is documented | Completed |
Please do not any files that solely generate UI to the /R folder - this is a folder for our logic. File partial_auc_input belongs in the inst/shiny folder, either in /modules (if there is any server logic attached, here it isnt, but might be added) or folder like functions. We can also create a new folder for UI elements, called ui or elements or widgets or whatever you find suitable. |
Incomplete |
If you are creating new files or adding new functions in the /R folder, please make sure that this logic is testable and do take some effort to write at least basic unit tests. Adding tests back to existing logic is tough and time consuming, so we should at least make sure that our testing suite keeps up with any new features or major changes to the old ones. |
Incomplete |
Deleted the extra UI function from \R |
Incomplete |
Added tests for all functions called in format_data,R, create_start_impute and PKNCA_impute_method_additions |
Incomplete |
| In the data selection, after you select analyte and dose number, the table shown does not represent the selections, as I can still see all the dose numbers. We want this table for the user to see exactly the data that will be used for NCA, so either we need to filter the dose number here, or move the dose number selectInput. I will let you decide. | Incomplete |
| For the dummy data, Doseno >3 does not work and the app crashes. I get the following error: Error in if: argument is of length zero. I double checked and I do not get this issue in main, so it is related to something in this branch. Also, for DOSNO = 2, USUBJID 11102 has empty cells for lambda z calculation, but no explanation why and because of this the slope selection crashes. This could be created as a separate bug issue to fix later or you can see if its something to fix now. | Incomplete |
| App crashes if AUC rule sets are selected | Completed |
| Slope selector not working- i tested an exclusion and the app crashed. Haven't tried selections. | Completed |
| Data table in Data selection tab is not sorted- needs to be sorted by USUBJID for better visualisation. | Completed |
| It would be good if the user can see an updated data table after the imputations, so they know what the data being used looks like. If this is too complex then maybe you can add an explanation of what the imputation is doing. But it would be good if they can see what data is being created. | Completed |
| Some clarification/relabelling is required in terms of what the imputation does. 'C0 missing' is not always accurate, for example if the predose value is present in the data set but ATime is <0, it gets excluded, but its not technically missing. Some more clarification on this would be good for the user so they know that imputation is also for predose samples. | Completed |
| Predose samples/ duplicates are not being included. Need to figure out a way to ensure they are- by creating duplicates manually or making sure PKNCA includes them. | Incomplete |
Please do not any files that solely generate UI to the /R folder - this is a folder for our logic. File partial_auc_input belongs in the inst/shiny folder, either in /modules (if there is any server logic attached, here it isnt, but might be added) or folder like functions. We can also create a new folder for UI elements, called ui or elements or widgets or whatever you find suitable. |
Incomplete |
If you are creating new files or adding new functions in the /R folder, please make sure that this logic is testable and do take some effort to write at least basic unit tests. Adding tests back to existing logic is tough and time consuming, so we should at least make sure that our testing suite keeps up with any new features or major changes to the old ones. |
Incomplete |
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