From dc0b2f0e75e4e5ccbc45dce62539dcda6b8683ae Mon Sep 17 00:00:00 2001
From: niup0 <poyao.niu@merck.com>
Date: Tue, 9 Jul 2024 09:11:26 -0400
Subject: [PATCH] Create prepare function and example for exposure duration

---
 R/meta_sl_example.R      | 61 ++++++++++++++++++++++++++++++++++++++++
 R/prepare_exp_duration.R | 52 ++++++++++++++++++++++++++++++++++
 2 files changed, 113 insertions(+)
 create mode 100644 R/prepare_exp_duration.R

diff --git a/R/meta_sl_example.R b/R/meta_sl_example.R
index 59bbd4f..59dbc96 100644
--- a/R/meta_sl_example.R
+++ b/R/meta_sl_example.R
@@ -126,3 +126,64 @@ meta_sl_example <- function() {
     ) |>
     metalite::meta_build()
 }
+
+#' Create an example `meta_sl_exposure_example` object
+#'
+#' This function is only for illustration purpose.
+#' r2rtf is required.
+#'
+#' @return A metadata object.
+#'
+#' @export
+#'
+#' @examples
+#' meta_sl_exposure_example()
+meta_sl_exposure_example <- function() {
+  adsl <- r2rtf::r2rtf_adsl
+  
+  # Create ADEXSUM dataset
+  adexsum <- data.frame(USUBJID=adsl$USUBJID)
+  adexsum$TRTA <- factor(adsl$TRT01A,
+                         levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"),
+                         labels = c("Placebo", "Low Dose", "High Dose")
+  )
+  
+  adexsum$APERIODC <- "Base"
+  adexsum$APERIOD <- 1
+  adexsum$AVAL <- sample(x = 0:(24*7), size = length(adexsum$USUBJID), replace = TRUE)
+  adexsum$EXDURGR <- "not treated"
+  adexsum$EXDURGR[adexsum$AVAL>=1] <- ">=1 day"
+  adexsum$EXDURGR[adexsum$AVAL>=7] <- ">=7 days"
+  adexsum$EXDURGR[adexsum$AVAL>=28] <- ">=28 days"
+  adexsum$EXDURGR[adexsum$AVAL>=12*7] <- ">=12 weeks"
+  adexsum$EXDURGR[adexsum$AVAL>=24*7] <- ">=24 weeks"
+  
+  plan <- metalite::plan(
+    analysis = "exp_dur", population = "apat",
+    observation = "apat", parameter = "expdur"
+  ) 
+  
+  meta <- metalite::meta_adam(
+    population = adexsum,
+    observation = adexsum
+  ) |>
+    metalite::define_plan(plan) |>
+    metalite::define_population(
+      name = "apat",
+      group = "TRTA",
+      subset = quote(APERIOD==1 & AVAL>0),
+      var = c("USUBJID", "TRTA", "EXDURGR", "AVAL"),
+    ) |>
+    metalite::define_parameter(
+      name = "expdur",
+      var = "AVAL",
+      label = "Exposure Duration (Days)",
+      vargroup = "EXDURGR"
+    )|>
+    metalite::define_analysis(
+      name = "exp_dur",
+      title = "Summary of Exposure Duration",
+      label = "exposure duration table"
+    ) |>
+    metalite::meta_build()
+}
\ No newline at end of file
diff --git a/R/prepare_exp_duration.R b/R/prepare_exp_duration.R
new file mode 100644
index 0000000..e308e9c
--- /dev/null
+++ b/R/prepare_exp_duration.R
@@ -0,0 +1,52 @@
+# Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+# All rights reserved.
+#
+# This file is part of the metalite.sl program.
+#
+# metalite.sl 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/>.
+
+#' Prepare data for exposure duration table
+#'
+#' @param meta A metadata object created by metalite.
+#' @param population A character value of population term name.
+#'   The term name is used as key to link information.
+# @param observation A character value of observation term name.
+#   The term name is used as key to link information.
+#' @param analysis A character value of analysis term name.
+#'   The term name is used as key to link information.
+#' @param parameter A character value of parameter term name.
+#'   The term name is used as key to link information.
+# @param display_total A logic value of displaying the total group.
+#'
+#' @return A list of analysis raw datasets.
+#'
+#' @export
+#'
+#' @examples
+#' meta <- meta_sl_exposure_example()
+#' meta |> prepare_exp_duration()
+prepare_exp_duration <- function(meta,
+                                analysis = "exp_dur",
+                                population = meta$plan[meta$plan$analysis==analysis,]$population,
+                                parameter = paste(meta$plan[meta$plan$analysis==analysis,]$parameter, collapse = ";") 
+) {
+  return(
+    prepare_sl_summary(meta,
+                       analysis = analysis,
+                       population = population,
+                       parameter = parameter
+    )
+  )
+  
+}
\ No newline at end of file