Functions / Examples / Tests

DESCRIPTION

@@ -1,8 +1,13 @@
 Package: clonecensorweighting
 Title: Infrastructure for Clone-Censor-Weighting Analyses
 Version: 0.0.0.9000
-Authors@R:
-    person("Sang Ho", "Park", email = "shstat1729@gmail.com", role = c("aut", "cre"))
+Authors@R: c(
+    person("Sang Ho", "Park", email = "shstat1729@gmail.com", role = c("aut", "cre")),
+    person("Youngrok", "Lee", role = "aut")
+    )
+Author: Sang Ho Park [aut, cre],
+    Youngrok Lee [aut]
+Maintainer: Sang Ho Park <shstat1729@gmail.com>
 Description: Provides a starter package for clone-censor-weighting workflows
     used in target trial emulation. The package currently includes data
     ingestion helpers, a minimal data cloning routine, and utilities for

NAMESPACE

@@ -6,9 +6,12 @@ export(clone_censor_weighting)
 export(create_censoring_logics_A)
 export(create_final_data)
 export(create_policy_A)
-export(create_timestamp_table)
+export(emul_estimate)
+export(emul_estimate_bootstrap)
+export(estimate_censoring)
 export(make_surv_response)
 export(read_trial_data)
-export(split_at_timestamp)
+export(weight_cases)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
+importFrom(rlang,.env)

NEWS.md

@@ -0,0 +1,49 @@
+# 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.

R/apply_logics.R

@@ -13,6 +13,20 @@
 #'
 #' @export
 #' @examples
+#' data(lungcancer)
+#' arms <- c("Control", "Surgery")
+#' clones <- clone_arms(lungcancer, arms)
+#' policies <- create_policy_A(
+#'   arms,
+#'   treatment = "surgery",
+#'   time_to_treatment = "timetosurgery",
+#'   grace_period = 182.62,
+#'   outcome = "death",
+#'   followup = "fup_obs",
+#'   clone_outcome = "outcome",
+#'   clone_followup = "fup"
+#' )
+#' clones_policy <- apply_logics(clones, policies)
 apply_logics <- function(
   clones,
   logics
@@ -91,6 +105,17 @@ apply_logics <- function(
 #'
 #' @export
 #' @examples
+#' arms <- c("Control", "Surgery")
+#' policies <- create_policy_A(
+#'   arms,
+#'   treatment = "surgery",
+#'   time_to_treatment = "timetosurgery",
+#'   grace_period = 182.62,
+#'   outcome = "death",
+#'   followup = "fup_obs",
+#'   clone_outcome = "outcome",
+#'   clone_followup = "fup"
+#' )
 create_policy_A <- function(
   arms,
   treatment,
@@ -203,6 +228,16 @@ create_policy_A <- function(
 #'
 #' @export
 #' @examples
+#' arms <- c("Control", "Surgery")
+#' censoring_logics <- create_censoring_logics_A(
+#'   arms,
+#'   treatment = "surgery",
+#'   time_to_treatment = "timetosurgery",
+#'   grace_period = 182.62,
+#'   followup = "fup_obs",
+#'   clone_censoring = "censoring",
+#'   clone_uncensored_followup = "fup_uncensored"
+#' )
 create_censoring_logics_A <- function(
   arms,
   treatment,