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clonecensorweighting

clonecensorweighting is an R package for building reproducible clone-censor-weighting workflows for target trial emulation.

This repository is meant to be easy to use from a fresh GitHub clone and easy to maintain as a shared collaboration project. The recommended setup uses:

  • rig to install and switch to the project R version
  • renv to restore the same package environment for every collaborator
  • GitHub Actions to check reproducibility and package health

Quick start

1. Clone the repository

git clone https://github.com/CausalInferenceLab/clonecensorweighting.git
cd clonecensorweighting

2. Use rig to install R 4.4.2

This project is pinned to R 4.4.2 for reproducibility.

rig add 4.4.2
rig default 4.4.2

If you already have R 4.4.2, you can skip rig add 4.4.2.

3. Restore the project package library with renv

Open R in the project directory and run:

install.packages("renv")
renv::restore()

renv::restore() installs the package versions recorded in renv.lock, so everyone works with the same dependency set.

Note: this repository includes a .Rprofile file that activates renv automatically when you open the project in R.

4. Install the package locally

From the project root:

R CMD INSTALL .

Then in R:

library(clonecensorweighting)

First example

library(clonecensorweighting)

trial_data <- tibble::tibble(
  id = c(1, 2),
  follow_up = c(10, 12),
  event = c(1, 0),
  treatment = c("A", "B")
)

clones <- clone_censor_weighting(
  data = trial_data,
  id = "id",
  follow_up = "follow_up",
  event = "event",
  treatment = "treatment",
  regimes = c("A", "B")
)

clones

make_surv_response(
  data = trial_data,
  follow_up = "follow_up",
  event = "event"
)

What the package currently provides

The package is still an early, lightweight foundation for future work. Right now it includes:

  • read_trial_data() to read trial-style CSV data into a tibble
  • clone_censor_weighting() to create a starter cloned dataset across regimes
  • make_surv_response() to build a survival::Surv() response object

Working together on this repository

For collaborative work, the safest pattern is:

  1. Clone the repository.
  2. Switch to R 4.4.2 with rig.
  3. Run renv::restore().
  4. Make your changes in a branch.
  5. Run checks before opening a pull request.

Useful commands:

R CMD INSTALL .
R CMD check --no-manual .

In R:

testthat::test_local()

If you add, remove, or upgrade dependencies, update the lockfile from R:

renv::settings$snapshot.type("explicit")
renv::status(dev = TRUE)
renv::snapshot(dev = TRUE)

Please commit both code changes and the updated renv.lock when dependency changes are intentional.

Continuous integration

This repository includes two GitHub Actions workflows:

  • check-reproducible.yaml runs R CMD check with pinned R 4.4.2 and renv
  • check-latest.yaml runs broader checks across operating systems and R versions

Together, these workflows help keep the project reproducible for collaborators and stable for future users.