Generate a Self-Rendering Reproducibility Appendix (E2)
Source:R/nested_survival_run.R
repro_appendix.RdCollects and renders a standardized reproducibility record for Quarto and R Markdown reports, including:
Package versions and R session platform metadata
Git commit SHA and working tree status
RNG seed and task `seed_scheme` version (`"v0.5.6"`)
Active `future::plan()` and worker count
SHA-256 content hashes of input datasets or pipeline hash manifests
Pre-flight [validate_start_stop()] summary
Checkpoint directory fingerprints and `seed_scheme` audit
Render manifest (`render_manifest.json`) summary
Usage
repro_appendix(
run = NULL,
data = NULL,
validation = NULL,
run_dir = NULL,
manifest_path = NULL,
seed = NULL,
id = "id",
start = "tstart",
stop = "tstop",
status = "status",
packages = c("TempleCBE", "survival", "glmnet", "recipes", "rsample", "yardstick",
"furrr", "future", "quarto", "rmarkdown", "renv"),
title = "Reproducibility Appendix",
heading_level = 2L,
format = c("markdown", "list")
)Arguments
- run
Optional [nested_survival_run()] object (or list of such objects across domains). When supplied, `data`, `validation`, `run_dir`, `seed`, and `checkpoint_fingerprints` are extracted from `run` automatically.
- data
Optional data frame or named list of data frames to hash with SHA-256 (and validate with [validate_start_stop()] if `validation` is not supplied).
- validation
Optional [validate_start_stop()] result.
- run_dir
Optional directory path containing checkpoints and/or `render_manifest.json`.
- manifest_path
Optional explicit path to `render_manifest.json`.
- seed
Optional integer seed used for the report or run.
- id, start, stop, status
Column names passed to [validate_start_stop()] when `data` is a survival data frame and `validation` is `NULL`.
- packages
Character vector of packages whose versions should be recorded.
- title
Section heading for the appendix (default `"Reproducibility Appendix"`).
- heading_level
Integer Markdown heading level (default `2L`, i.e. `##`).
- format
Output representation: `"markdown"` (default; returns a character object of class `c("cbe_repro_appendix", "knit_asis")` with all structured metadata attached in attributes and `$` accessors) or `"list"` (returns the structured list directly).
Value
An object of class `cbe_repro_appendix` containing the rendered Markdown string and structured fields `package_versions`, `git`, `seed`, `seed_scheme`, `future_plan`, `data_hashes`, `validation`, `checkpoint_fingerprints`, `render_manifest`, and `markdown`.