ready set go
This commit is contained in:
@@ -0,0 +1,117 @@
|
||||
# Target Trial Emulation Learning Project
|
||||
|
||||
This project is for learning how to code and understand target trial emulation in R.
|
||||
|
||||
The main teaching example is an ICU septic shock study:
|
||||
|
||||
> Among ICU patients with suspected septic shock at ICU admission, what is the effect of initiating vasopressors early versus not initiating vasopressors early on 28-day mortality?
|
||||
|
||||
## How To Work With The User
|
||||
|
||||
- Teach by showing small code chunks that the user can type in manually.
|
||||
- Explain each meaningful line of code before moving on.
|
||||
- Teach the base R mechanics when a concept is new, then prefer readable tidyverse-style code for routine analysis.
|
||||
- Make the smallest correct change when editing project files.
|
||||
- Keep scripts and notebooks numbered so the learning sequence is obvious.
|
||||
- Avoid over-abstraction early; build reusable primitives only after the concept is clear.
|
||||
- When adding reusable code, explain what future project need it supports.
|
||||
- When using external dependencies, prefer wrapping them behind project functions so the user learns stable primitives.
|
||||
|
||||
## Code Style
|
||||
|
||||
- Use the native pipe `|>`, not `%>%`
|
||||
- snake_case for all names
|
||||
- Prefer `vapply` over `sapply`; explicit return types
|
||||
- Use `cli::cli_*` for messages, not `message()`/`cat()`
|
||||
- Prefer `dplyr` verbs for data manipulation when external dependencies are allowed.
|
||||
- Prefer `skimr` for quick data summaries.
|
||||
- Prefer `gt` and `gtsummary` for clear analytic tables in notebooks and reports.
|
||||
- Style with `styler::style_pkg()` before commits
|
||||
|
||||
## Don'ts
|
||||
|
||||
- Don't modify `renv.lock` by hand
|
||||
- Don't `setwd()` — rely on the project root (`here::here()`)
|
||||
- Don't introduce new dependencies beyond the approved stack without asking
|
||||
|
||||
## Stack
|
||||
|
||||
- R 4.4 managed by rig
|
||||
- renv for dependency management; lockfile is source of truth
|
||||
- targets for pipeline orchestration
|
||||
- tidyverse, especially `dplyr`, for routine data manipulation
|
||||
- data.table for performance-oriented data manipulation when needed
|
||||
- skimr for quick data summaries
|
||||
- gt for presentation tables
|
||||
- gtsummary for descriptive and model summary tables
|
||||
- Quarto for reports
|
||||
|
||||
## Dependency Preference
|
||||
|
||||
- The first scripts may remain base R to teach the underlying mechanics.
|
||||
- Going forward, use `dplyr`, `tidyverse`, `skimr`, `gt`, and `gtsummary` where they make the code clearer.
|
||||
- Keep base R explanations available when they help the user understand what the package code is doing.
|
||||
- Do not add packages outside the approved stack without asking first.
|
||||
|
||||
## Learning Roadmap
|
||||
|
||||
- [x] Choose ICU teaching scenario: early vasopressor strategy in septic shock.
|
||||
- [x] Simulate a simple ICU observational cohort.
|
||||
- [x] Define the target trial protocol explicitly.
|
||||
- [x] Estimate a naive observational association.
|
||||
- [ ] Show why naive comparison can be biased.
|
||||
- [ ] Align time zero and eligibility criteria.
|
||||
- [ ] Introduce treatment assignment windows.
|
||||
- [ ] Add censoring logic.
|
||||
- [ ] Add inverse probability weighting from first principles.
|
||||
- [x] Refactor repeated logic into reusable project functions.
|
||||
- [ ] Re-implement selected steps with external dependencies.
|
||||
- [ ] Build wrapper functions around external dependency workflows.
|
||||
- [ ] Add a targets pipeline.
|
||||
- [x] Add initial Quarto report for reproducible analysis.
|
||||
|
||||
## Initial Target Trial Protocol
|
||||
|
||||
Clinical question:
|
||||
|
||||
Among ICU patients with suspected septic shock at ICU admission, what is the effect of starting vasopressors within 2 hours compared with not starting vasopressors within 2 hours on 28-day mortality?
|
||||
|
||||
Eligibility criteria:
|
||||
|
||||
- ICU admission.
|
||||
- Suspected sepsis.
|
||||
- Hypotension at baseline.
|
||||
- Elevated lactate at baseline.
|
||||
|
||||
Time zero:
|
||||
|
||||
- ICU admission.
|
||||
|
||||
Treatment strategies:
|
||||
|
||||
- Early vasopressor strategy: start vasopressors within 2 hours of ICU admission.
|
||||
- No early vasopressor strategy: do not start vasopressors within 2 hours of ICU admission.
|
||||
|
||||
Outcome:
|
||||
|
||||
- Death within 28 days.
|
||||
|
||||
Baseline confounders in the first simulated dataset:
|
||||
|
||||
- Age.
|
||||
- Sex.
|
||||
- SOFA score.
|
||||
- Lactate.
|
||||
- Mean arterial pressure.
|
||||
|
||||
Initial causal contrast:
|
||||
|
||||
- Risk difference in 28-day mortality.
|
||||
- Risk ratio for 28-day mortality.
|
||||
|
||||
## File Sequence
|
||||
|
||||
- `scripts/01_simulate_icu_data_base_r.R`: generate synthetic ICU cohort data from the reusable simulation primitive.
|
||||
- `scripts/02_naive_analysis_base_r.R`: compute an initial naive comparison with readable tidyverse-style code.
|
||||
- `R/simulate_icu_cohort.R`: first reusable simulation primitive.
|
||||
- `notebooks/01_target_trial_basics.qmd`: conceptual walkthrough of the target trial protocol with `skimr`, `gt`, and `gtsummary` examples.
|
||||
Reference in New Issue
Block a user