add function extend_ae_summary_eaer

NAMESPACE

@@ -3,6 +3,8 @@
 export(extend_ae_specific_duration)
 export(extend_ae_specific_events)
 export(extend_ae_specific_inference)
+export(extend_ae_specific_subgroup)
+export(extend_ae_summary_eaer)
 export(fmt_ci)
 export(fmt_est)
 export(fmt_pct)

R/extend_ae_summary_eaer.R

@@ -1,7 +1,45 @@
+# Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+# All rights reserved.
+#
+# This file is part of the metalite.ae program.
+#
+# metalite.ae 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/>.
+
+#' Add exposure-adjusted rate information for AE summary analysis
+#'
+#' @param outdata  An `outdata` object created by [prepare_ae_summary()].
+#' @param duration_var A character value of duration variable name.
+#'   By default, `"TRTDUR"` is used.
+#' @param adj_unit A character value of exposure adjusted unit.
+#'   It could be select from `"year"`, `"month"`, `"week"`, and `"day"`.
+#'
+#' @return A list of analysis raw datasets.
+#'
+#' @export
+#'
+#' @examples
+#' meta <- meta_ae_example()
+#' prepare_ae_summary(
+#'   meta,
+#'   population = "apat",
+#'   observation = "wk12",
+#'   parameter = "any;rel;ser"
+#' ) |>
+#' extend_ae_summary_eaer()
 extend_ae_summary_eaer <- function(outdata,
                                    duration_var = "TRTDUR",
-                                   adj_unit = c("year", "month", "week", "day"),
-                                   ...) {
+                                   adj_unit = c("year", "month", "week", "day")) {
   time_unit <- list("year" = 365.24, "month" = 30.4367, "week" = 7, "day" = 1)
   adj_unit <- match.arg(adj_unit)
   exp_factor <- 100 * time_unit[[adj_unit]]
@@ -25,19 +63,10 @@ extend_ae_summary_eaer <- function(outdata,
   })
 
   adj_rate_table <- do.call(rbind, res)
+  outdata$total_exp <- total_exposure
+  outdata$eaer <- adj_rate_table
 
-  metalite::outdata(meta, population, observation, parameter,
-    n = rbind(n_pop, tbl_num),
-    order = c(1, seq_len(nrow(tbl_num)) * 100),
-    group = res[[1]]$group,
-    reference_group = res[[1]]$reference_group,
-    prop = rbind(pop_prop, tbl_prop),
-    diff = rbind(pop_diff, tbl_diff),
-    n_pop = n_pop,
-    name = c(pop_name, name),
-    prepare_call = match.call(),
-    eaer = eaer
-  )
+  outdata
 }
 
 

_pkgdown.yml

@@ -41,6 +41,7 @@ reference:
     - prepare_ae_summary
     - format_ae_summary
     - tlf_ae_summary
+    - extend_ae_summary_eaer
 - title: AE specification
   contents:
     - prepare_ae_specific