From e0ba2feda406eb424403dfce2d352b224076da4d Mon Sep 17 00:00:00 2001
From: "Zhao, Yujie" <yujie.zhao@merck.com>
Date: Wed, 21 Feb 2024 12:27:08 -0500
Subject: [PATCH] add milestone test

---
 NAMESPACE        |  1 +
 R/milestone.R    | 54 ++++++++++++++++++++++++++++++++++++++++++++++++
 _pkgdown.yml     |  1 +
 man/milestone.Rd | 25 ++++++++++++++++++++++
 4 files changed, 81 insertions(+)
 create mode 100644 R/milestone.R
 create mode 100644 man/milestone.Rd

diff --git a/NAMESPACE b/NAMESPACE
index c9d85999..20a05c2a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,6 +13,7 @@ export(get_cut_date_by_event)
 export(maxcombo)
 export(mb)
 export(mb_weight)
+export(milestone)
 export(pvalue_maxcombo)
 export(randomize_by_fixed_block)
 export(rmst)
diff --git a/R/milestone.R b/R/milestone.R
new file mode 100644
index 00000000..09365e88
--- /dev/null
+++ b/R/milestone.R
@@ -0,0 +1,54 @@
+#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  All rights reserved.
+#
+#  This file is part of the simtrial program.
+#
+#  simtrial is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+#' Milestone test for two survival curves
+#'
+#' @param data Dataset contains at least 3 columns: \code{tte} (time to event),
+#' \code{event} (event indicator), and \code{treatment} (grouping variable).
+#' @param ms_time Milestone analysis time
+#'
+#' @return A data frame containing the test statistics
+#' @export
+#'
+#' @examples
+#' sim_pw_surv(n = 200) |>
+#'   cut_data_by_event(150) |>
+#'   milestone(10)
+milestone <- function(data, ms_time) {
+  # Fit into KM curves
+  fit <- survfit(Surv(tte, event) ~ treatment, data = data)
+  fit_res <- summary(fit, time = ms_time, extend = TRUE)
+
+  # Survival difference
+  diff_survival <- fit_res$surv[2] - fit_res$surv[1]
+
+  # Indicator whether the std is NA or not
+  na_col <- is.na(fit_res$std.err[1])
+  na_exp <- is.na(fit_res$std.err[2])
+
+  # Calcualte the test statistcis
+  if(na_col + na_exp == 2){
+    z <- -Inf
+  }else{
+    var_survival <- ifelse(na_col, 0, fit_res$std.err[1])^2 + ifelse(na_exp, 0, fit_res$std.err[2])^2
+    z <-  diff_survival / sqrt(var_survival)
+  }
+
+  ans <- data.frame(z = z)
+  return(ans)
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index f649ee29..ba44cdad 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -49,6 +49,7 @@ reference:
     - counting_process
     - pvalue_maxcombo
     - rmst
+    - milestone
     - wlr
     - maxcombo
 
diff --git a/man/milestone.Rd b/man/milestone.Rd
new file mode 100644
index 00000000..ce7b6eb2
--- /dev/null
+++ b/man/milestone.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/milestone.R
+\name{milestone}
+\alias{milestone}
+\title{Milestone test for two survival curves}
+\usage{
+milestone(data, ms_time)
+}
+\arguments{
+\item{data}{Dataset contains at least 3 columns: \code{tte} (time to event),
+\code{event} (event indicator), and \code{treatment} (grouping variable).}
+
+\item{ms_time}{Milestone analysis time}
+}
+\value{
+A data frame containing the test statistics
+}
+\description{
+Milestone test for two survival curves
+}
+\examples{
+sim_pw_surv(n = 200) |>
+  cut_data_by_event(150) |>
+  milestone(10)
+}