Update documentation on R package warnings

[parmsam-pfizer]

Document warning messages from datasetjson and metacore R packages when reading JSON and dataset spec files.

[github-actions]

Dataset QC Check Complete!

Date: 2026-01-13
Run by: parmsam-pfizer
Git Ref: refs/pull/139/merge
BASE: Pilot 5 Datasets
COMPARE: Pilot 3 Datasets

✅ Dataset: adadas

No issues were found!

✅ Dataset: adae

No issues were found!

✅ Dataset: adlbc

No issues were found!

✅ Dataset: adsl

No issues were found!

✅ Dataset: adtte

No issues were found!

[github-actions]

TLF QC Check Complete!

Date: 2026-01-13
Run by: parmsam-pfizer
Git Ref: refs/pull/139/merge
BASE: Pilot 5 Datasets
COMPARE: Pilot 3 Datasets

✅ Dataset: tlf-demographic-pilot5.out

old[36:40] vs new[36:40]
  "—————————————————————————————————————————————————————————————————————————————————————————————————"
  ""
  "Program: tlf-demographic.r "
- "2026-01-08 02:22:28.583663"
+ "2024-04-18 20:17:25"
  ""

✅ TLF: tlf-kmplot-pilot5.pdf - Score: 78

[1] "1. Title format: First image has 'KM plot for Time to First Dermatologic Event: Safety population' while second has 'KM plot for Time to First Dermatologic Event-Safety population' (hyphen vs colon difference)\n\n2. Y-axis label: First image shows 'Survival Event' while second image shows 'Probability of event'\n\n3. Y-axis scale: First image ranges from 0.00 to 1.00, second image ranges from 0.00 to 1.00 but with different tick mark intervals\n\n4. X-axis label: First image shows 'Time to First Dermatologic Event (Days)' while second shows 'Time to First Dermatologic Event (Days)' - same text but different formatting\n\n5. X-axis range: First image extends to approximately 210 days, second image clearly shows 200 days maximum\n\n6. Grid lines: First image has no visible grid lines, second image has prominent grid lines throughout\n\n7. Legend position: First image has legend on right side labeled 'TRT01A', second image has legend on right side also labeled 'TRT01A' but slightly different positioning\n\n8. Legend text: Both show Placebo, Xanomeline Low Dose, and Xanomeline High Dose, but with slightly different formatting\n\n9. Reference line: First image shows a dotted horizontal line at approximately 0.50, second image shows a dashed horizontal line at 0.50\n\n10. Confidence interval shading: Both show confidence intervals but the shading appears slightly different in transparency\n\n11. Risk table formatting: First image has 'At Risk' and 'Number at risk' rows with data, second image has 'At risk' label with data formatted differently\n\n12. Risk table values: The numbers in the risk tables appear similar but may have minor differences in specific values\n\n13. Footer text: First image shows 'Program ID: Excerpt | 2024-01-07 18:07:04|242' while second shows 'Program: tflkmplo1.r | 202404~18 20:17:28]' - completely different program information\n\n14. Overall styling: Second image appears to have a cleaner, more modern appearance with the grid lines and slightly different color scheme"

✅ TLF: tlf-efficacy-pilot5.rtf - Score: 99

[1] "After careful examination of both images, I found the following differences:\n\n1. Footer timestamp: The first image shows 'SNAPSHOT: 2024-01-18 20:17' while the second image shows 'SNAPSHOT: 2024-01-18 20:18' - a one-minute difference in the timestamp.\n\nAside from this single timestamp difference in the footer, the two images appear to be identical in all other aspects:\n- Same title: 'ANCOVA of Change from Baseline at Week 20'\n- Same table structure with identical columns and rows\n- Same data values across all cells\n- Same statistical values (Mean, SD, N values)\n- Same CI values (confidence intervals)\n- Same footnote text and formatting\n- Same overall layout and positioning"

✅ TLF: tlf-primary-pilot5.rtf - Score: 99

[1] "After careful examination of both images, I found only one difference:\n\n1. In the footnote text at the bottom of both tables (the text starting with 'CI = confidence interval'), there is a slight text difference. The first image appears to have slightly different spacing or formatting in the footnote text compared to the second image, though the actual content and wording are identical.\n\nAll other elements appear to be identical:\n- Both tables show 'Protocol: CDISCO1/Phase 1+2' and 'Population: {ADS}'\n- Both have the same title 'Table 14.3.1' and 'Table 14.3.2'\n- Both show 'Primary Endpoint Analysis: ARDS Low-Titer Flow Cytom Studies at Week 28 - LOCF'\n- All numerical values in both tables are identical (e.g., Mean(SD), Median Range values)\n- Column headers (Placebo, Low-Dose, High-Dose, Xanomeline Combined) are the same\n- All sample sizes (N values) match\n- Statistical values and confidence intervals are identical\n- Table structure and layout are the same\n- Footer information matches"

[bms63]

fingers crossed!!