scripts/DA.R

[jenna-a2ai]

Data Assembly

Note: Please modify the checklist items to insert relevant QC context.

Reproducibility and Organization

• [ ] Script is a quarto document.
• [ ] Script renders free of error within the Rproject space.
• [ ] renv::status() present at beginning of script and passes.
• [ ] Relative paths are used.
• [ ] .Rprofile is present in same directory as final script.
• [ ] :red_circle: Parquet files are used where available.
  • files that should be parquet: [INSERT]
• [x] :red_circle: Data hash codes are printed and match source and output data.
  • expected hash files: [INSERT]
• [x] :red_circle: Correct source data files are read in.
  • correct source data: [INSERT]
• [ ] Final dataset outputs to expected location as a csv, converts all NA values to a period, and outputs a hash.
• [ ] All code chunks are labeled.
• [ ] session.info() included at the conclusion of script.

yspec

• [ ] All yspec files can be found in <project>/data/derived and are excluded from gitignore.
• [ ] All variables have descriptions. All descriptions are easy to read and understand. All variables have units where applicable.
• [ ] All categorical variables have all options outlined and a 1:1 numerical decoded value. All categorical variables match the decoding present in the yspec.
• [ ] :red_circle: All continuous variables specify units and all units match those of the final dataset. If multiple analytes are included in a single column, units are clear for each analyte.
• [ ] :red_circle: The yspec file contains all necessary variables for analysis, including both project specific variables and NONMEM required variables.

Dataset Assumptions - Automated

:red_circle: These can be done using pointblank and QCer can just confirm these pass!

• [ ] :red_circle: LIST POINTBLANK ASSUMPTIONS.
• [ ] The final dataset includes both a numeric (ID) and character (e.g. USUBJID) version of the unique subject identifier.
• [ ] The final dataset includes all columns listed in the corresponding yspec file.
• [ ] Any missing columns or observations are confirmed to be missing in source data and marked as -999.
• [ ] Missing data is documented appropriately in dataset.

Data Assumptions - Manual

:red_circle: These CAN’T be done using pointblank and QCer must look closely at specific sections of code.

• [ ] :red_circle: All manual conversions are accurate and consistent.
• [ ] :red_circle: All manual imputations are well documented to outside sources or sufficiently justified.
• [ ] :red_circle: All manual imputations are accurate according to their specified source.
• [ ] :red_circle: All assumptions are well justified (e.g. by the protocol, project lead decision, client decision, etc.), documented, and reasonable.
• [ ] :red_circle: All records to be excluded (e.g. for all analyses, for sensitivity analysis only) are properly identified, justified, and documented (i.e., CFLAG or other flag column).

Misc

• [ ] Code is easily readable and follows general coding guidelines (link to code hub).
• [ ] Helper functions are well documented, make sense, make reasonable assumptions, and follow good coding practices.
• [ ] :red_circle: Helper function arguments match as stated in yspec (e.g. SEX variable in Cockcroft-Gault equation matches decoding in yspec).

Metadata

• author: jenna-a2ai jenna@a2-ai.com
• qc type: Data Assembly
• script hash: a187afdc5feb87577baef97a1c0a0a84
• git sha: 3bacb8150e08e60d8fd61485e8e065a2139d4b66
• file history: https://github.com/A2-ai/gilead_ghqc_demo/commits/main/scripts/DA.R

[jenna-a2ai]

context on scripts...

[jenna-a2ai]

@wes-a2ai

thanks! this is the right study, right?

File Difference

reference commit (older version): 3bacb8150e08e60d8fd61485e8e065a2139d4b66

comparator commit (newer version): 0d256c0adbd1be1ca4440bc45ac64fe395d2a0bd

@@ - reference:  lines 12-16 @@
@@ + comparator: lines 12-16 @@
  12                     EVID == 0 & ATFD > 0 & is.na(DV) ~ 1),      
  13     LLOQ = NA,                                                  
- 14     STUDY = "STUDY-NAME-CHANGED",                               
+ 14     STUDY = "NEW_STUDY_NAME", # changing this per Wes's feedback
  15     IMPDOS = 0,                                                 
  16     DOSEA = AMT[first(which(EVID == 1))],                       

Metadata

• reference commit: 3bacb8150e08e60d8fd61485e8e065a2139d4b66
• reference script hash: 05c92a0662bfbcddd38d1ef3404f8715
• comparator commit: 0d256c0adbd1be1ca4440bc45ac64fe395d2a0bd
• comparator script hash: dbc02fb8c5ea0f6ab909fc0bdd68eb42