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clonecensorweighting 0.0.0.9000

Refactoring

  • Split the final censoring-probability training data workflow into focused functions.
  • Kept create_final_data() as the public interface for constructing long-form clone data.
  • Moved create_timestamp_table() and split_at_timestamp() to internal helper status and removed them from the package exports.
  • Removed duplicated reshape code and script-style execution leftovers from the package R files.
  • Added clone-list and clone-column validation helpers for clearer errors when required variables are missing.
  • Updated create_final_data() internals to use explicit character-vector column selection and joins.
  • Added estimate_censoring() as the public interface for Cox, pooled-logit, and stabilized pooled-logit censoring probability estimation.
  • Added weight_cases() as the public interface for unstabilized and stabilized inverse probability of censoring weights.
  • Added emul_estimate() as the public interface for Cox, logistic, and Kaplan-Meier analyses of the emulated trial.
  • Added emul_estimate_bootstrap() as the public interface for bootstrap confidence intervals for two-arm Cox and logistic analyses.
  • Kept formula construction, cumulative uncensoring, baseline predictor extraction, predictor/weight normalization, arm binding, and coefficient extraction as internal helpers.

Documentation

  • Removed generated help pages for internal timestamp and splitting helpers.
  • Regenerated the create_final_data() help source reference after moving the function to its own file.
  • Added generated help pages for censoring estimation, case weighting, emulated-trial estimation, and bootstrap estimation.
  • Added runnable examples for public workflow functions using the bundled lungcancer data where appropriate.
  • Updated the README with a full lungcancer clone-censor-weighting workflow.

Testing

  • Added focused tests for timestamp table creation, interval splitting, final data construction, internal helper export status, and missing-column errors.
  • Added focused tests for censoring probability estimation, IPC weighting, emulated-trial model fitting, bootstrap output, and internal helper export status.
  • Added an integration test that runs the bundled lungcancer data through cloning, censoring, interval expansion, censoring probability estimation, weighting, emulated-trial estimation, and bootstrap estimation.