11 Pipeline Reference
Complete reference for all Makefile targets, R package dependencies, configuration files, and troubleshooting.
11.1 All Makefile Targets
| Target | Description | Dependencies |
|---|---|---|
help |
Show available targets | None |
setup |
One-time environment bootstrap | None |
verify |
Check environment health | None |
init |
Create new project directory tree | Python (uv) |
simulate |
Generate simulated data (single scenario) | R |
simulate-all |
Generate all 7 simulated datasets | R |
validate-data |
Validate TTE data structure | R |
profile-data |
Generate data profile report | R |
diagnose |
Run all 6 diagnostic checks + report | R, validate-data, profile-data |
route |
Diagnose and recommend analysis path | R, Python, diagnose |
analyze-standard |
Standard KM + Cox (6 scripts) | R |
analyze-competing |
Competing risks (5 scripts) | R |
analyze-recurrent |
Recurrent/multi-state (8 scripts) | R |
analyze-time-varying |
Time-varying exposure (5 scripts) | R |
analyze-advanced |
Advanced adjustments (5 scripts) | R |
analyze-auto |
Auto-select and run analysis | R, Python, route |
figures |
Generate publication figures | R |
manuscript |
Build Table 1 and results section | R |
render |
Render Quarto to PDF + DOCX | Quarto, LaTeX |
qa |
Run QA validation | Python |
checkpoint |
Create pipeline checkpoint | Python |
all |
Full pipeline end-to-end | All above |
demo-all |
Run all demo scenarios | All above |
clean |
Remove generated outputs (keeps raw data) | rip |
11.2 R Package Dependencies
| Package | Purpose |
|---|---|
survival |
Core survival analysis (Surv, coxph, survfit) |
survminer |
KM curve visualisation (ggsurvplot) |
cmprsk |
Competing risks (cuminc, crr) |
mstate |
Multi-state models |
frailtypack |
Frailty models |
gtsummary |
Table 1 and regression tables |
ggplot2 |
Grammar of graphics |
patchwork |
Multi-panel figure assembly |
ggsci |
Journal colour palettes |
dplyr / tidyr |
Data wrangling |
renv |
Package version management |
11.3 Configuration Files
| File | Location | Purpose |
|---|---|---|
Makefile |
Project root | All pipeline targets |
setup.sh |
Project root | Environment bootstrap |
verify_environment.sh |
Project root | Health check |
renv.lock |
Project root | R package versions |
.python-version |
Project root | Python version pin |
_quarto.yml |
Per-project manuscript dir | Quarto render settings |
11.4 Simulation Scenarios
| Scenario | Description | Routed To |
|---|---|---|
| 1 | Standard single-endpoint | sa-standard-km |
| 2 | Competing risks (2 event types) | sa-competing-risks |
| 3 | Recurrent events | sa-recurrent-multistate |
| 4 | Multi-state transitions | sa-recurrent-multistate |
| 5 | Time-varying exposure | sa-time-varying |
| 6 | Complex (multiple flags) | Multiple modules |
| 7 | Combined adjustments needed | Primary + sa-advanced-adjustments |
11.5 Troubleshooting
WarningCommon Issues
frailtypack fails to install — Install gfortran first: brew install gcc on macOS.
Quarto PDF rendering fails — Install TinyTeX: quarto install tinytex.
renv::restore() hangs — Delete renv/library/ and re-run bash setup.sh.
Diagnostic router returns “unknown path” — Ensure make diagnose completed successfully and check 02_diagnostics/diagnostic_report.json.
Figures are low resolution — Verify dpi = 300 in ggsave() calls; check the units argument matches your width/height.