Check in changes (2nd time) - DEVR-3489-fix-bugs-for-generating-title

Merck · Nov 4, 2024 · 710c7cd · 710c7cd
1 parent 34536ae
commit 710c7cd
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Showing 17 changed files with 82 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -47,4 +47,4 @@ Suggests:
     tidyr
 Config/testthat/edition: 3
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/R/tlf_ae_exp_adj.R b/R/tlf_ae_exp_adj.R
@@ -39,6 +39,7 @@
 #'   format_ae_exp_adj() |>
 #'   tlf_ae_exp_adj(
 #'     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+#'     analysis = "ae_exp_adj",
 #'     path_outdata = tempfile(fileext = ".Rdata"),
 #'     path_outtable = tempfile(fileext = ".rtf")
 #'   )
@@ -59,6 +60,15 @@ tlf_ae_exp_adj <- function(outdata,
   n_row <- nrow(tbl)
   n_col <- ncol(tbl)
 
+  # Check if the parameter analysis contains the correct analysis that should exist in "outdata$meta$analysis"
+  analysis_name <- names(outdata$meta$analysis)
+  if (!(analysis %in% analysis_name))  {
+    stop(
+      "Please provide a valid analysis that matches with what being defined in 'outdata$meta$analysis'",
+      call. = FALSE
+    )
+  }
+
   parameters <- unlist(strsplit(outdata$parameter, ";"))
 
   # Title

diff --git a/R/tlf_ae_listing.R b/R/tlf_ae_listing.R
@@ -40,6 +40,7 @@
 #'   tlf_ae_listing(
 #'     footnotes = "footnote1",
 #'     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+#'     analysis = "ae_listing",
 #'     path_outdata = tempfile(fileext = ".Rdata"),
 #'     path_outtable = tempfile(fileext = ".rtf")
 #'   )
@@ -54,6 +55,15 @@ tlf_ae_listing <- function(outdata,
                            path_outtable = NULL) {
   res <- outdata$tbl
 
+  # Check if the parameter analysis contains the correct analysis that should exist in "outdata$meta$analysis"
+  analysis_name <- names(outdata$meta$analysis)
+  if (!(analysis %in% analysis_name))  {
+    stop(
+      "Please provide a valid analysis that matches with what being defined in 'outdata$meta$analysis'",
+      call. = FALSE
+    )
+  }
+
   mapping <- collect_adam_mapping(outdata$meta, analysis)
   var_name <- eval(mapping$var_name)
   subline <- eval(mapping$subline)

diff --git a/R/tlf_ae_specific.R b/R/tlf_ae_specific.R
@@ -47,6 +47,7 @@
 #'   format_ae_specific() |>
 #'   tlf_ae_specific(
 #'     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+#'     analysis = "ae_specific",
 #'     meddra_version = "24.0",
 #'     path_outdata = tempfile(fileext = ".Rdata"),
 #'     path_outtable = tempfile(fileext = ".rtf")
@@ -94,6 +95,15 @@ tlf_ae_specific <- function(outdata,
     )
   }
 
+  # Check if the parameter analysis contains the correct analysis that should exist in "outdata$meta$analysis"
+  analysis_name <- names(outdata$meta$analysis)
+  if (!(analysis %in% analysis_name))  {
+    stop(
+      "Please provide a valid analysis that matches with what being defined in 'outdata$meta$analysis'",
+      call. = FALSE
+    )
+  }
+
   # Define title
   if ("analysis" %in% title | "observation" %in% title | "population" %in% title) {
     title_key <- title

diff --git a/R/tlf_ae_specific_subgroup.R b/R/tlf_ae_specific_subgroup.R
@@ -39,6 +39,7 @@
 #'   tlf_ae_specific_subgroup(
 #'     meddra_version = "24.0",
 #'     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+#'     analysis = "ae_specific",
 #'     path_outtable = tempfile(fileext = ".rtf")
 #'   )
 tlf_ae_specific_subgroup <- function(
@@ -91,6 +92,15 @@ tlf_ae_specific_subgroup <- function(
     )
   }
 
+  # Check if the parameter analysis contains the correct analysis that should exist in "outdata$meta$analysis"
+  analysis_name <- names(outdata$meta$analysis)
+  if (!(analysis %in% analysis_name))  {
+    stop(
+      "Please provide a valid analysis that matches with what being defined in 'outdata$meta$analysis'",
+      call. = FALSE
+    )
+  }
+
   # Define title
   if (is.null(title)) {
     title <- collect_title(outdata$meta,

diff --git a/R/tlf_ae_summary.R b/R/tlf_ae_summary.R
@@ -37,6 +37,7 @@
 #'   format_ae_summary() |>
 #'   tlf_ae_summary(
 #'     source = "Source:  [CDISCpilot: adam-adsl; adae]",
+#'     analysis = "ae_summary",
 #'     path_outdata = tempfile(fileext = ".Rdata"),
 #'     path_outtable = tempfile(fileext = ".rtf")
 #'   )
@@ -57,6 +58,15 @@ tlf_ae_summary <- function(outdata,
   n_row <- nrow(tbl)
   n_col <- ncol(tbl)
 
+  # Check if the parameter analysis contains the correct analysis that should exist in "outdata$meta$analysis"
+  analysis_name <- names(outdata$meta$analysis)
+  if (!(analysis %in% analysis_name))  {
+    stop(
+      "Please provide a valid analysis that matches with what being defined in 'outdata$meta$analysis'",
+      call. = FALSE
+    )
+  }
+
   parameters <- unlist(strsplit(outdata$parameter, ";"))
 
   # Title

diff --git a/man/tlf_ae_exp_adj.Rd b/man/tlf_ae_exp_adj.Rd
diff --git a/man/tlf_ae_listing.Rd b/man/tlf_ae_listing.Rd
diff --git a/man/tlf_ae_specific.Rd b/man/tlf_ae_specific.Rd
diff --git a/man/tlf_ae_specific_subgroup.Rd b/man/tlf_ae_specific_subgroup.Rd
diff --git a/man/tlf_ae_summary.Rd b/man/tlf_ae_summary.Rd
diff --git a/tests/testthat/test-independent-testing-empty_table.R b/tests/testthat/test-independent-testing-empty_table.R
@@ -39,6 +39,7 @@ generate_analysis_or_empty <- function(meta, outdata) {
       ) |>
       tlf_ae_specific(
         source = "Source: [CDISCpilot: adam-adsl; adae]",
+        analysis = "ae_specific",
         meddra_version = "24.0",
         path_outdata = path_rdata,
         path_outtable = path_rtf
@@ -74,6 +75,7 @@ test_that("RTF output: empty table or analysis table.", {
       ) |>
       tlf_ae_specific(
         source = "Source: [CDISCpilot: adam-adsl; adae]",
+        analysis = "ae_specific",
         meddra_version = "24.0",
         path_outdata = path_rdata,
         path_outtable = path_rtf

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

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

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

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

diff --git a/vignettes/metalite-ae.Rmd b/vignettes/metalite-ae.Rmd
@@ -89,6 +89,7 @@ meta_ae_example() |> # Example AE data created using metalite
   format_ae_summary() |>
   tlf_ae_summary(
     source = "Source:  [CDISCpilot: adam-adsl; adae]", # Define data source
+    analysis = "ae_specific", # Provide analysis type defined in meta$analysis
     path_outtable = "ae0summary.rtf" # Define output
   )
 ```