Check in changes - DEVR-3489-fix-bugs-for-generating-title

Merck · Oct 29, 2024 · 34536ae · 34536ae
1 parent 5ec7885
commit 34536ae
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Showing 14 changed files with 39 additions and 6 deletions.
diff --git a/R/tlf_ae_exp_adj.R b/R/tlf_ae_exp_adj.R
@@ -20,6 +20,8 @@
 #'
 #' @inheritParams tlf_ae_specific
 #'
+#' @param analysis One of analysis name existing at `outdata$meta$analysis`
+#'
 #' @return RTF file and source dataset for exposure-adjusted AE summary table.
 #'
 #' @export
@@ -42,6 +44,7 @@
 #'   )
 tlf_ae_exp_adj <- function(outdata,
                            source,
+                           analysis,
                            col_rel_width = NULL,
                            text_font_size = 9,
                            orientation = "portrait",
@@ -65,7 +68,7 @@ tlf_ae_exp_adj <- function(outdata,
       outdata$population,
       outdata$observation,
       parameters[1],
-      analysis = "ae_exp_adj",
+      analysis = analysis,
       title_order = title
     )
   }

diff --git a/R/tlf_ae_listing.R b/R/tlf_ae_listing.R
@@ -21,6 +21,7 @@
 #' @param outdata An `outdata` object created by [prepare_ae_listing()].
 #' @param footnotes A character vector of table footnotes.
 #' @param source A character value of the data source.
+#' @param analysis One of analysis name existing at `outdata$meta$analysis`
 #' @inheritParams r2rtf::rtf_page
 #' @inheritParams r2rtf::rtf_body
 #' @param path_outdata A character string of the outdata path.
@@ -45,14 +46,15 @@
 tlf_ae_listing <- function(outdata,
                            footnotes = NULL,
                            source = NULL,
+                           analysis,
                            col_rel_width = NULL,
                            text_font_size = 9,
                            orientation = "landscape",
                            path_outdata = NULL,
                            path_outtable = NULL) {
   res <- outdata$tbl
 
-  mapping <- collect_adam_mapping(outdata$meta, "ae_listing")
+  mapping <- collect_adam_mapping(outdata$meta, analysis)
   var_name <- eval(mapping$var_name)
   subline <- eval(mapping$subline)
   subline_by <- eval(mapping$subline_by)
@@ -62,7 +64,7 @@ tlf_ae_listing <- function(outdata,
   col_name <- outdata$col_name
 
   # Define title
-  title <- collect_title(outdata$meta, outdata$population, outdata$observation, outdata$parameter, analysis = "ae_listing")
+  title <- collect_title(outdata$meta, outdata$population, outdata$observation, outdata$parameter, analysis = analysis)
 
   if (!nrow(res) == 0) {
     res <- as.data.frame(res)

diff --git a/R/tlf_ae_specific.R b/R/tlf_ae_specific.R
@@ -22,6 +22,7 @@
 #' @param meddra_version A character value of the MedDRA version
 #'   for this dataset.
 #' @param source A character value of the data source.
+#' @param analysis One of analysis name existing at `outdata$meta$analysis`
 #' @inheritParams r2rtf::rtf_page
 #' @inheritParams r2rtf::rtf_body
 #' @param footnotes A character vector of table footnotes.
@@ -53,6 +54,7 @@
 tlf_ae_specific <- function(outdata,
                             meddra_version,
                             source,
+                            analysis,
                             col_rel_width = NULL,
                             text_font_size = 9,
                             orientation = "portrait",
@@ -99,7 +101,7 @@ tlf_ae_specific <- function(outdata,
       outdata$population,
       outdata$observation,
       outdata$parameter,
-      analysis = "ae_specific",
+      analysis = analysis,
       title_order = title
     )
 

diff --git a/R/tlf_ae_specific_subgroup.R b/R/tlf_ae_specific_subgroup.R
@@ -20,6 +20,8 @@
 #'
 #' @inheritParams tlf_ae_specific
 #'
+#' @param analysis One of analysis name existing at `outdata$meta$analysis`
+#'
 #' @return RTF file and the source dataset for AE specific subgroup analysis table.
 #'
 #' @export
@@ -43,6 +45,7 @@ tlf_ae_specific_subgroup <- function(
     outdata,
     meddra_version,
     source,
+    analysis,
     col_rel_width = NULL,
     text_font_size = 9,
     orientation = "landscape",
@@ -94,7 +97,7 @@ tlf_ae_specific_subgroup <- function(
       outdata$population,
       outdata$observation,
       outdata$parameter,
-      analysis = "ae_specific"
+      analysis = analysis
     )
   }
 

diff --git a/R/tlf_ae_summary.R b/R/tlf_ae_summary.R
@@ -20,6 +20,8 @@
 #'
 #' @inheritParams tlf_ae_specific
 #'
+#' @param analysis One of analysis name existing at `outdata$meta$analysis`
+#'
 #' @return RTF file and the source dataset for AE summary table.
 #'
 #' @export
@@ -40,6 +42,7 @@
 #'   )
 tlf_ae_summary <- function(outdata,
                            source,
+                           analysis,
                            col_rel_width = NULL,
                            text_font_size = 9,
                            orientation = "portrait",
@@ -63,7 +66,7 @@ tlf_ae_summary <- function(outdata,
       outdata$population,
       outdata$observation,
       parameters[1],
-      analysis = "ae_summary",
+      analysis = analysis,
       title_order = title
     )
   }

diff --git a/tests/testthat/test-independent-testing-tlf-ae-listing.R b/tests/testthat/test-independent-testing-tlf-ae-listing.R
@@ -15,6 +15,7 @@ tbl <- outdata |>
   tlf_ae_listing(
     footnotes = "footnote1",
     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+    analysis = "ae_listing",
     path_outdata = path_rdata,
     path_outtable = path_rtf
   )

diff --git a/tests/testthat/test-independent-testing-tlf_ae_exp_adj.R b/tests/testthat/test-independent-testing-tlf_ae_exp_adj.R
@@ -21,6 +21,7 @@ test_that("rtf output: n, total_exp, events, eaer, total", {
     ) |>
     tlf_ae_exp_adj(
       source = "Source: [CDISCpilot: adam-adsl]",
+      analysis = "ae_exp_adj",
       path_outdata = path_rdata,
       path_outtable = path_rtf
     )
@@ -51,6 +52,7 @@ test_that("rtf output: n, total_exp, events, eaer, total", {
     ) |>
     tlf_ae_exp_adj(
       source = "Source: [CDISCpilot: adam-adsl]",
+      analysis = "ae_exp_adj",
       path_outdata = path_rdata,
       path_outtable = path_rtf
     )

diff --git a/tests/testthat/test-independent-testing-tlf_ae_specific.R b/tests/testthat/test-independent-testing-tlf_ae_specific.R
@@ -20,6 +20,7 @@ test_that("rtf output: events, dur, n, and prop w/o total", {
     tlf_ae_specific(
       meddra_version = "24.0",
       source = "Source:  [CDISCpilot: adam-adsl; adae]",
+      analysis = "ae_specific",
       path_outdata = path_rdata,
       path_outtable = path_rtf
     )
@@ -41,6 +42,7 @@ test_that("rtf output: events, dur, n, and prop w/ total", {
     tlf_ae_specific(
       meddra_version = "24.0",
       source = "Source:  [CDISCpilot: adam-adsl; adae]",
+      analysis = "ae_specific",
       path_outdata = path_rdata,
       path_outtable = path_rtf
     )
@@ -64,6 +66,7 @@ test_that("rtf output: diff, events, dur, n, and prop w/o total", {
     tlf_ae_specific(
       meddra_version = "24.0",
       source = "Source:  [CDISCpilot: adam-adsl; adae]",
+      analysis = "ae_specific",
       path_outdata = path_rdata,
       path_outtable = path_rtf
     )
@@ -86,6 +89,7 @@ test_that("rtf output: diff, events, dur, n, and prop w/ total", {
     tlf_ae_specific(
       meddra_version = "24.0",
       source = "Source:  [CDISCpilot: adam-adsl; adae]",
+      analysis = "ae_specific",
       col_rel_width = c(5, rep(c(1, 2, 3, 3), 4), 1, 2, 3, 1, 2, 3),
       path_outdata = path_rdata,
       path_outtable = path_rtf
@@ -111,6 +115,7 @@ test_that("rtf output: events, dur, n, and prop w/ total", {
     tlf_ae_specific(
       meddra_version = "24.0",
       source = "Source:  [CDISCpilot: adam-adsl; adae]",
+      analysis = "ae_specific",
       path_outdata = path_rdata,
       path_outtable = path_rtf
     )
@@ -166,6 +171,7 @@ test_that("relative width 'works'", {
         tlf_ae_specific(
           meddra_version = "24.0",
           source = "Source:  [CDISCpilot: adam-adsl; adae]",
+          analysis = "ae_specific",
           path_outdata = path_rdata,
           path_outtable = path_rtf,
           col_rel_width = c(rep(1, 8))
@@ -181,6 +187,7 @@ test_that("relative width 'works'", {
         tlf_ae_specific(
           meddra_version = "24.0",
           source = "Source:  [CDISCpilot: adam-adsl; adae]",
+          analysis = "ae_specific",
           path_outdata = path_rdata,
           path_outtable = path_rtf,
           col_rel_width = c(rep(1, 7))

diff --git a/tests/testthat/test-independent-testing-tlf_ae_specific_subgroup.R b/tests/testthat/test-independent-testing-tlf_ae_specific_subgroup.R
@@ -18,6 +18,7 @@ test_that("rtf output: n, and prop w/o total", {
     tlf_ae_specific_subgroup(
       meddra_version = "24.0",
       source = "Source:  [CDISCpilot: adam-adsl; adae]",
+      analysis = "ae_specific",
       # path_outdata = path_rdata,
       path_outtable = path_rtf
     )

diff --git a/tests/testthat/test-independent-testing-tlf_ae_summary.R b/tests/testthat/test-independent-testing-tlf_ae_summary.R
@@ -14,6 +14,7 @@ tbl <- outdata |>
   format_ae_summary() |>
   tlf_ae_summary(
     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+    analysis = "ae_summary",
     path_outtable = path_rtf,
     path_outdata = path_rdata
   )

diff --git a/vignettes/ae-listing.Rmd b/vignettes/ae-listing.Rmd
@@ -101,6 +101,7 @@ tbl |> tlf_ae_listing(
   footnotes = footnote,
   orientation = "portrait",
   source = "Source:  [CDISCpilot: adam-adsl; adae]",
+  analysis = "ae_listing",
   path_outtable = "rtf/ae0listing0ser0wk12.rtf",
   path_outdata = NULL
 )

diff --git a/vignettes/ae-specific-subgroup.Rmd b/vignettes/ae-specific-subgroup.Rmd
@@ -161,6 +161,7 @@ outdata |>
   tlf_ae_specific_subgroup(
     meddra_version = "24.0",
     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+    analysis = "ae_specific",
     path_outtable = "rtf/ae0specific0sub0gender1.rtf"
   )
 ```

diff --git a/vignettes/ae-specific.Rmd b/vignettes/ae-specific.Rmd
@@ -255,6 +255,7 @@ outdata |>
   tlf_ae_specific(
     meddra_version = "24.0",
     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+    analysis = "ae_specific",
     path_outtable = "rtf/ae0specific1.rtf"
   )
 ```
@@ -272,6 +273,7 @@ outdata |>
   tlf_ae_specific(
     meddra_version = "24.0",
     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+    analysis = "ae_specific",
     col_rel_width = c(6, rep(1, 8)),
     text_font_size = 8,
     orientation = "landscape",
@@ -291,6 +293,7 @@ outdata |>
   tlf_ae_specific(
     meddra_version = "24.0",
     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+    analysis = "ae_specific",
     path_outtable = "rtf/mock_ae0specific1.rtf"
   )
 ```

diff --git a/vignettes/ae-summary.Rmd b/vignettes/ae-summary.Rmd
@@ -187,6 +187,7 @@ outdata |>
   format_ae_summary() |>
   tlf_ae_summary(
     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+    analysis = "ae_summary",
     path_outtable = "rtf/ae0summary1.rtf"
   )
 ```
@@ -202,6 +203,7 @@ outdata |>
   format_ae_summary() |>
   tlf_ae_summary(
     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+    analysis = "ae_summary",
     col_rel_width = c(6, rep(1, 8)),
     text_font_size = 8,
     orientation = "landscape",
@@ -228,6 +230,7 @@ outdata |>
   format_ae_summary(mock = TRUE) |>
   tlf_ae_summary(
     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+    analysis = "ae_summary",
     path_outtable = "rtf/mock_ae0summary1.rtf"
   )
 ```