change function name of base_char

NAMESPACE

@@ -3,8 +3,15 @@
 export(collect_baseline)
 export(defmt_pct)
 export(format_base_char)
+export(format_disposition)
+export(format_trt_compliance)
 export(meta_sl)
 export(meta_sl_example)
 export(prepare_base_char)
+export(prepare_disposition)
+export(prepare_sl_summary)
+export(prepare_trt_compliance)
 export(react_base_char)
 export(rtf_base_char)
+export(rtf_disposition)
+export(rtf_trt_compliance)

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.
@@ -119,3 +119,38 @@ format_base_char <- function(
 
   return(outdata)
 }
+
+#' Format Treatment Compliance Analysis
+#'
+#' @inheritParams format_base_char
+#'
+#' @return A list of analysis raw datasets.
+#'
+#' @export
+#'
+#' @examples
+#' meta <- meta_sl_example()
+#'
+#' meta |>
+#'   prepare_trt_compliance(parameter = "comp8;comp16") |>
+#'   format_trt_compliance()
+format_trt_compliance <- format_base_char
+
+
+#' Format Disposition Analysis
+#'
+#' @inheritParams format_base_char
+#'
+#' @return A list of analysis raw datasets.
+#'
+#' @export
+#'
+#' @examples
+#' meta <- meta_sl_example()
+#'
+#' meta |>
+#'   prepare_disposition(parameter = "disposition;medical-disposition") |>
+#'   format_disposition()
+format_disposition <- format_base_char
+
+

R/meta_sl_example.R

@@ -34,26 +34,39 @@ meta_sl_example <- function() {
     levels = c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"),
     labels = c("Placebo", "Low Dose", "High Dose")
   )
-
+
+  # Create a variable EOSSTT indicating the end of end of study status
+  adsl$EOSSTT <- sample(x = c("Participants Ongoing", "Discontinued"),
+                        size = length(adsl$USUBJID), 
+                        prob = c(0.8, 0.2), replace = TRUE)
+  # Create a variable EOTSTT1 indicating the end of treatment status part 1
+  adsl$EOTSTT1 <- sample(x = c("Completed", "Discontinued"),
+                         size = length(adsl$USUBJID), 
+                         prob = c(0.85, 0.15), replace = TRUE)
+
+  plan <- metalite::plan(
+    analysis = "base_char", population = "apat",
+    observation = "apat", parameter = "age;gender;race"
+    ) |>
+    metalite::add_plan(
+      analysis = "trt_compliance", population = "apat",
+      observation = "apat", parameter = "comp8;comp16;comp24"
+    ) |>
+    metalite::add_plan(
+      analysis = "disp", population = "apat",
+      observation = "apat", parameter = "disposition;medical-disposition"    
+    )
+
   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_observation(
-      name = "apat",
-      group = "TRTA",
-      subset = quote(SAFFL == "Y"),
-      var = c("USUBJID", "TRTA", "SAFFL", "AGEGR1", "SEX", "RACE")
+      var = c("USUBJID", "TRTA", "SAFFL", "AGEGR1", "SEX", "RACE", "EOSSTT", "EOTSTT1", "COMP8FL", "COMP16FL", "COMP24FL")
     ) |>
     metalite::define_parameter(
       name = "age",
@@ -71,11 +84,45 @@ meta_sl_example <- function() {
       var = "RACE",
       label = "Race"
     ) |>
+    metalite::define_parameter(
+      name = "disposition",
+      var = "EOSSTT",
+      label = "Trial Disposition"
+    ) |>
+    metalite::define_parameter(
+      name = "medical-disposition",
+      var = "EOTSTT1",
+      label = "Participant Study Medication Disposition"
+    ) |>
+    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 = "base_char",
       title = "Participant Baseline Characteristics by Treatment Group",
-      label = "baseline characteristic table",
-      var_name = c("AGEGR1", "SEX")
+      label = "baseline characteristic table"
+    ) |>
+    metalite::define_analysis(
+      name = "trt_compliance",
+      title = "Summary of Treatment Compliance",
+      label = "treatment compliance table"
+    ) |>
+    metalite::define_analysis(
+      name = "disp",
+      title = "Disposition of Participant",
+      label = "disposition table"
     ) |>
     metalite::meta_build()
 }

R/prepare_base_char.R

@@ -16,17 +16,18 @@
 # 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 baseline characteristic table
+#' 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 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.
 #'
@@ -35,78 +36,16 @@
 #' @examples
 #' meta <- meta_sl_example()
 #' meta |> prepare_base_char()
-prepare_base_char <- function(
-    meta,
-    population = "apat",
-    observation = "wk12",
-    analysis = "base_char",
-    parameter = paste(names(meta$parameter), collapse = ";")) {
-  parameters <- unlist(strsplit(parameter, ";"))
-
-  # obtain variables
-  pop_var <- metalite::collect_adam_mapping(meta, population)$var
-  obs_var <- metalite::collect_adam_mapping(meta, observation)$var
-  par_var <- metalite::collect_adam_mapping(meta, parameter)$var
-
-  pop_group <- metalite::collect_adam_mapping(meta, population)$group
-  obs_group <- metalite::collect_adam_mapping(meta, observation)$group
-
-  pop_id <- metalite::collect_adam_mapping(meta, population)$id
-  obs_id <- metalite::collect_adam_mapping(meta, observation)$id
-
-  # obtain data
-  pop <- metalite::collect_population_record(meta, population, var = pop_var)
-
-  # obtain group names
-  group <- unique(pop[[pop_group]])
-
-  # count the number of subjects in each arms
-  n_pop <- metalite::n_subject(id = pop[[pop_id]], group = pop[[pop_group]])
-  names(n_pop) <- do.call(
-    c,
-    lapply(
-      factor(names(n_pop), levels = levels(pop[[pop_group]])) |> as.numeric(),
-      function(x) {
-        paste0("n_", x)
-      }
+prepare_base_char <- function(meta,
+                              analysis = "base_char",
+                              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
     )
   )
-  n_pop$n_9999 <- sum(n_pop[1, ])
-  n_pop$name <- "Participants in population"
-  n_pop <- n_pop[, c(length(group) + 2, 1:(length(group) + 1))]
-  n_pop$var_label <- "-----"
-
-  # Get the baseline characteristics variables in adsl
-  # char_var <- collect_adam_mapping(meta, analysis)$var_name
-  char_var <- do.call(c, lapply(parameters, function(x) {
-    metalite::collect_adam_mapping(meta, x)$var
-  }))
-
-  # Get the baseline characteristics counts
-  char_n <- lapply(parameters, function(x) {
-    collect_baseline(meta, population, x)[[2]]
-  })
-
-  # Get the baseline characteristics propositions
-  char_prop <- lapply(parameters, function(x) {
-    collect_baseline(meta, population, x)[[3]]
-  })
-
-  # Get the variable date type
-  var_type <- lapply(parameters, function(x) {
-    collect_baseline(meta, population, x)[[4]]
-  })
-
-  ans <- metalite::outdata(
-    meta, population, observation, parameter,
-    n = n_pop,
-    order = NULL, group = pop_group, reference_group = NULL,
-    char_n = char_n,
-    char_var = char_var,
-    char_prop = char_prop,
-    var_type = var_type,
-    group_label = unique(pop[[pop_group]])
-  )
-
-  return(ans)
-}
+}   

R/prepare_disposition.R

@@ -0,0 +1,51 @@
+# 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_base_char()
+prepare_disposition <- function(meta,
+                              analysis = "disp",
+                              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
+    )
+  )
+}