updates to resolve styler errors

pharmaverse · Jul 3, 2024 · 7f6c9f9 · 7f6c9f9
1 parent 1e722f9
commit 7f6c9f9
Show file tree

Hide file tree

Showing 4 changed files with 25 additions and 22 deletions.
diff --git a/R/date_cut.R b/R/date_cut.R
@@ -74,8 +74,8 @@ date_cut <- function(dataset_sdtm,
     mutate(TEMP_DCUT_KEEP = "Y")
 
   ifelse(!is.na(dcut$DCUT_TEMP_DCUTDTM), assert_that(is.POSIXt(dcut$DCUT_TEMP_DCUTDTM),
-           msg = "cut_var is expected to be of date type POSIXt"
-         ), NA)
+    msg = "cut_var is expected to be of date type POSIXt"
+  ), NA)
 
   attributes(dcut$USUBJID)$label <- attributes(dataset_sdtm$USUBJID)$label
 
@@ -90,7 +90,7 @@ date_cut <- function(dataset_sdtm,
   # Flag records to be removed - those occurring after cut date and patients not in dcut dataset
   dataset <- dataset_sdtm_pt %>%
     mutate(DCUT_TEMP_REMOVE = ifelse((DCUT_TEMP_SDTM_DATE > DCUT_TEMP_DCUTDTM) |
-                                       is.na(TEMP_DCUT_KEEP), "Y", NA_character_))
+      is.na(TEMP_DCUT_KEEP), "Y", NA_character_))
 
   # Ensure variable is character
   dataset$DCUT_TEMP_REMOVE <- as.character(dataset$DCUT_TEMP_REMOVE)

diff --git a/R/special_dm_cut.R b/R/special_dm_cut.R
@@ -68,8 +68,8 @@ special_dm_cut <- function(dataset_dm,
     )
 
   ifelse(!is.na(dm_temp$DCUT_TEMP_DCUTDTM), assert_that(is.POSIXt(dm_temp$DCUT_TEMP_DCUTDTM),
-           msg = "cut_var is expected to be of date type POSIXt"
-         ), NA)
+    msg = "cut_var is expected to be of date type POSIXt"
+  ), NA)
 
   # Flag records with Death Date after Cut date
   dataset_updatedth <- dm_temp %>%

diff --git a/inst/read-out/read_out.Rmd b/inst/read-out/read_out.Rmd
@@ -39,8 +39,8 @@ data_review <- function(pt_data, dt_data, dm_data, no_cut) {
   is_all_null <- all(sapply(objects, is.null))
   if (is_all_null) {
     cat("No data has been inputted into the read-out function.", " \n",
-      "If you would like to view a summary of the datacut, please double check you have filled in 
-      all the parameters in the read_out() function (or process_cut() when using the wrapped 
+      "If you would like to view a summary of the datacut, please double check you have filled in
+      all the parameters in the read_out() function (or process_cut() when using the wrapped
       approach.)", " \n",
       fill = TRUE
     )
@@ -125,7 +125,8 @@ data_review <- function(pt_data, dt_data, dm_data, no_cut) {
   reactable(sum_t,
     columnGroups = list(
       colGroup("Total Number of Records",
-               columns = c("Before Cut", "After Cut", "Removed", "Modified"))
+        columns = c("Before Cut", "After Cut", "Removed", "Modified")
+      )
     ),
     bordered = TRUE, filterable = TRUE, searchable = TRUE, pagination = TRUE,
     showPageSizeOptions = TRUE, striped = TRUE, showSortable = TRUE
@@ -173,10 +174,10 @@ df_tabs <- function(data) {
         cat(paste("Number of records removed in ", toupper(name), ": ", x, " \n", " \n"))
         removed <- df %>% filter(df$DCUT_TEMP_REMOVE == "Y")
         print(htmltools::tagList(reactable(removed,
-                bordered = TRUE, filterable = TRUE, searchable = TRUE, pagination = TRUE,
-                showPageSizeOptions = TRUE, showSortable = TRUE,
-                striped = TRUE, wrap = FALSE, resizable = TRUE
-              )))
+          bordered = TRUE, filterable = TRUE, searchable = TRUE, pagination = TRUE,
+          showPageSizeOptions = TRUE, showSortable = TRUE,
+          striped = TRUE, wrap = FALSE, resizable = TRUE
+        )))
         cat(" \n\n")
         cyc_num <- cyc_num + 1
       }
@@ -197,8 +198,8 @@ sum_test <- function(data) {
   # case when data = NULL
   if (is.null(data)) {
     cat("No data has been cut with this cut type.", " \n")
-    cat("If you would like to apply this cut, please double check you have ran this cut / filled in 
-        all the parameters in process_cut() - for the wrapped approach - or read_out() - modular 
+    cat("If you would like to apply this cut, please double check you have ran this cut / filled in
+        all the parameters in process_cut() - for the wrapped approach - or read_out() - modular
         approach.")
     cat(" \n\n")
   } else {
@@ -216,12 +217,14 @@ sum_test <- function(data) {
         Modified = numeric()
       ) %>%
         add_row(Dataset = "DM", `Before Cut` = uncut, `After Cut` = cut, Removed = x, Modified = y)
-      print(htmltools::tagList(reactable(sum_t, columnGroups = list(
-        colGroup("Total Number of Records",
-                 columns = c("Before Cut", "After Cut", "Removed", "Modified"))
-      ),
-      bordered = TRUE, filterable = TRUE, searchable = TRUE, pagination = TRUE,
-      showPageSizeOptions = TRUE, striped = TRUE, showSortable = TRUE
+      print(htmltools::tagList(reactable(sum_t,
+        columnGroups = list(
+          colGroup("Total Number of Records",
+            columns = c("Before Cut", "After Cut", "Removed", "Modified")
+          )
+        ),
+        bordered = TRUE, filterable = TRUE, searchable = TRUE, pagination = TRUE,
+        showPageSizeOptions = TRUE, striped = TRUE, showSortable = TRUE
       )))
       cat(" \n\n")
     } else {

diff --git a/vignettes/variable_cut.Rmd b/vignettes/variable_cut.Rmd
@@ -81,8 +81,8 @@ sv <- tibble::tribble(
 
 dcut <- dcut %>%
   left_join(sv %>%
-              filter(VISIT == "WEEK24") %>%
-              select(USUBJID, SVSTDTC)) %>%
+    filter(VISIT == "WEEK24") %>%
+    select(USUBJID, SVSTDTC)) %>%
   mutate(DCUTDTC = as.character(ifelse(!is.na(SVSTDTC), SVSTDTC, as.character(DCUTDTC)))) %>%
   impute_dcutdtc(dsin = ., varin = DCUTDTC, varout = DCUTDTM)
 ```