change function name of base_char

NAMESPACE

@@ -4,6 +4,7 @@ export(collect_baseline)
 export(defmt_pct)
 export(format_base_char)
 export(meta_sl_example)
-export(prepare_base_char)
+export(prepare_sl_summary)
+export(prepare_trt_compliance)
 export(react_base_char)
 export(rtf_base_char)

R/format_base_char.R

@@ -18,7 +18,7 @@
 
 #' Prepare data for baseline characteristic table
 #'
-#' @param outdata A metadata object created by [prepare_base_char()].
+#' @param outdata A metadata object created by [prepare_sl_summary()].
 #' @param display_col Column wants to display on the table.
 #'   The term could be selected from `c("n", "prop", "total")`.
 #' @param digits_prop Number of digits for proportion columns.
@@ -34,7 +34,7 @@
 #' meta <- meta_sl_example()
 #'
 #' meta |>
-#'   prepare_base_char(parameter = "age;gender") |>
+#'   prepare_sl_summary(parameter = "age;gender") |>
 #'   format_base_char()
 format_base_char <- function(
     outdata,

R/meta_sl_example.R

@@ -34,27 +34,46 @@ meta_sl_example <- function() {
     levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"),
     labels = c("Placebo", "Low Dose", "High Dose")
   )
-
+
+  plan <- metalite::plan(
+    analysis = "base_char", population = "apr",
+    observation = "apr", parameter = "age;gender;race"
+    ) |>
+    metalite::add_plan(
+      analysis = "trt_compliance", population = "apat",
+      observation = "apat", parameter = "comp8;comp16;comp24"
+    )
+
   meta <- metalite::meta_adam(
     population = adsl,
     observation = adsl
   ) |>
-    metalite::define_plan(plan = metalite::plan(
-      analysis = "base_char", population = "apat",
-      observation = "apat", parameter = "age;gender;race"
-    )) |>
+    metalite::define_plan(plan) |>
     metalite::define_population(
       name = "apat",
       group = "TRTA",
       subset = quote(SAFFL == "Y"),
       var = c("USUBJID", "TRTA", "SAFFL", "AGEGR1", "SEX", "RACE")
     ) |>
+    metalite::define_population(
+      name = "apr",
+      group = "TRTA",
+      subset = quote(ITTFL == "Y"),
+      label = "All Participants Randomized"
+    ) |>
     metalite::define_observation(
       name = "apat",
       group = "TRTA",
       subset = quote(SAFFL == "Y"),
       var = c("USUBJID", "TRTA", "SAFFL", "AGEGR1", "SEX", "RACE")
     ) |>
+    metalite::define_observation(
+      name = "apr",
+      group = "TRTA",
+      subset = quote(ITTFL == "Y"),
+      label = "All Participants Randomized"
+    ) |>
+    # For Baseline Characteristic
     metalite::define_parameter(
       name = "age",
       var = "AGE",
@@ -77,5 +96,26 @@ meta_sl_example <- function() {
       label = "baseline characteristic table",
       var_name = c("AGEGR1", "SEX")
     ) |>
+    # For compliance
+    metalite::define_parameter(
+      name = "comp8",
+      var = "COMP8FL",
+      label = "Compliance (Week 8)",
+    ) |>
+    metalite::define_parameter(
+      name = "comp16",
+      var = "COMP16FL",
+      label = "Compliance (Week 16)",
+    ) |>
+    metalite::define_parameter(
+      name = "comp24",
+      var = "COMP24FL",
+      label = "Compliance (Week 24)",
+    ) |>
+    metalite::define_analysis(
+      name = "trt_compliance",
+      title = "Summary of Treatment Compliance",
+      label = "treatment compliance table"
+    ) |>
     metalite::meta_build()
 }

R/prepare_base_char.R

@@ -34,8 +34,8 @@
 #'
 #' @examples
 #' meta <- meta_sl_example()
-#' meta |> prepare_base_char()
-prepare_base_char <- function(
+#' meta |> prepare_sl_summary()
+prepare_sl_summary <- function(
     meta,
     population = "apat",
     observation = "wk12",

R/prepare_trt_compliance.R

@@ -0,0 +1,53 @@
+# 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 treatment compliance 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_example()
+#' meta |> prepare_trt_compliance()
+prepare_trt_compliance <- function(meta,
+                                   analysis = "trt_compliance",
+                                   population = meta$plan[meta$plan$analysis==analysis,]$population,
+                                   parameter = paste(meta$plan[meta$plan$analysis==analysis,]$parameter, collapse = ";") #, display_total = TRUE
+                                   ) {
+  return(
+    prepare_sl_summary(meta,
+                      analysis = analysis,
+                      population = population,
+                      observation = population,
+                      parameter = parameter #, display_total = display_total
+                      )
+  )
+
+}   

R/react_base_char.R

@@ -78,7 +78,7 @@ react_base_char <- function(
   #   prepare the baseline char table numbers #
   # ----------------------------------------- #
   x_sl <- metadata_sl |>
-    prepare_base_char(
+    prepare_sl_summary(
       population = population,
       observation = population,
       analysis = "base_char",

R/rtf_base_char.R

@@ -18,7 +18,7 @@
 
 #' Baseline characteristic table
 #'
-#' @param outdata An `outdata` object created by [prepare_base_char()].
+#' @param outdata An `outdata` object created by [prepare_sl_summary()].
 #' @param source A character value of the data source.
 #' @inheritParams r2rtf::rtf_page
 #' @inheritParams r2rtf::rtf_body
@@ -35,7 +35,7 @@
 #' meta <- meta_sl_example()
 #'
 #' meta |>
-#'   prepare_base_char(
+#'   prepare_sl_summary(
 #'     population = "apat",
 #'     observation = "apat",
 #'     parameter = "age;gender"

README.md

@@ -16,7 +16,7 @@ inputs and outputs.
 The general workflow is:
 
 1. Define metadata information using metalite.
-2. `prepare_base_char()` prepares datasets for summary of baseline characteristics.
+2. `prepare_sl_summary()` prepares datasets for summary of baseline characteristics.
 3. `format_base_char()` formats output layout.
 4. `rtf_base_char()` creates TLFs.
 
@@ -26,7 +26,7 @@ Here is a quick example
 library("metalite.sl")
 
 meta_sl_example() |>
-  prepare_base_char(
+  prepare_sl_summary(
     population = "apat",
     observation = "apat",
     parameter = "age;gender"

tests/testthat/test-independent-testing-format_base_char.R

@@ -61,7 +61,7 @@ test_meta_base_char <- meta_adam(
     title = "Participant Baseline Characteristics by Treatment Group",
     var_name = c("AGEGR1", "AGE", "RACE", "SEX")
   ) |>
-  prepare_base_char(
+  prepare_sl_summary(
     population = "apat",
     observation = "apat",
     analysis = "base_char",

tests/testthat/test-independent-testing-prepare_base_char.R

@@ -65,7 +65,7 @@ meta_test <- meta_adam(
   )
 
 # Prepare test data by the tested function
-test_meta_base_char <- prepare_base_char(
+test_meta_base_char <- prepare_sl_summary(
   meta_test,
   population = "apat",
   observation = "apat",
@@ -344,6 +344,6 @@ test_that("Parameter matching", {
   expect_equal(test_meta_base_char$parameter, "age;agen;gender;race")
 })
 
-test_that("Output from prepare_base_char is a list", {
+test_that("Output from prepare_sl_summary is a list", {
   expect_true("outdata" %in% class(test_meta_base_char))
 })

tests/testthat/test-independent-testing-rtf_base_char.R

@@ -1,7 +1,7 @@
 # library(metalite)
 # 
 # meta <- meta_sl_example()
-# outdata <- prepare_base_char(meta,
+# outdata <- prepare_sl_summary(meta,
 #   population = "apat",
 #   observation = "apat",
 #   parameter = "age;gender"

vignettes/metalite-sl.Rmd

@@ -75,7 +75,7 @@ meta <- meta_adam(
 
 ```{r}
 outdata <- meta |>
-  prepare_base_char(
+  prepare_sl_summary(
     population = "apat",
     observation = "wk12",
     analysis = "base_char",