lintrs

Author: zsigmas

.lintr.R

@@ -3,8 +3,7 @@ linters <- lintr::modify_defaults(
   linters
   , line_length_linter = NULL                 # we see how long lines are when we write them
   , indentation_linter = NULL
-  , trailing_whitespace_linter = NULL
-  , cyclocomp_linter = NULL                   # prevents trivial amount of nesting and long but straightforward functions
+  , trailing_whitespace_linter = NULL  
   , object_name_linter = NULL                 # we have reasons to capitalize. nobody in our team CamelCase. shiny does
   , object_length_linter = NULL               # we don't type long var names just because
   , pipe_continuation_linter = NULL           # wickham being overly prescriptive

R/mod_bsafe.R

@@ -407,10 +407,10 @@ mod_bsafe <- function(module_id, dataset_name) {
       d <- afmm[["unfiltered_plus_filter_info"]]()
       df <- d[["unfiltered_dataset_list"]][[dataset_name]]
       df_mask <- d[["filter_info"]][["result"]][["filter_info"]][[dataset_name]][["mask"]]
-      df <- df[df_mask, , drop=FALSE]
+      df <- df[df_mask, , drop = FALSE]
       df
     })
-    bsafe_server("bsafe",dataset = dataset)
+    bsafe_server("bsafe", dataset = dataset)
 
     },
     module_id = module_id

inst/template_ae_summary_table.Rmd

@@ -146,7 +146,7 @@ for (g in groups) {
   )
 
 
-  list_table_1_1[[g]] <- cbind(as.data.frame(array_inci[, , 1, g, drop = F]), as.data.frame(array_inci[, , 2, g, drop = F]))
+  list_table_1_1[[g]] <- cbind(as.data.frame(array_inci[, , 1, g, drop = FALSE]), as.data.frame(array_inci[, , 2, g, drop = FALSE]))  
   # list_table_1_1[[g]] <- list_table_1_1[[g]] |> na.omit()
   list_table_1_1[[g]][, c(3, 10)] <- round(list_table_1_1[[g]][, c(3, 10)] * 100, 1)
   list_table_1_1[[g]][, c(3, 10)] <- round(list_table_1_1[[g]][, c(3, 10)] * 100, 1)
@@ -182,7 +182,7 @@ for (g in groups) {
     " vs. Arm B: ",
     ARMS_ARM_B
   )
-  list_table_1_2[[g]] <- cbind(as.data.frame(array_inci_comp[, , 1, g, drop = F]), as.data.frame(array_inci_comp[, , 2, g, drop = F]))
+  list_table_1_2[[g]] <- cbind(as.data.frame(array_inci_comp[, , 1, g, drop = FALSE]), as.data.frame(array_inci_comp[, , 2, g, drop = FALSE]))
   # list_table_1_2[[g]] <- as.data.frame(cbind(array_inci_comp[, , 1, g], array_inci_comp[, , 2, g]))
   # list_table_1_2[[g]] <- list_table_1_2[[g]] |> na.omit()
   table_display_2 <- kableExtra::kable(list_table_1_2[[g]][, -6],
@@ -223,7 +223,7 @@ for (g in groups) {
     ARMS_ARM_B
   )
   # list_table_2_1[[g]] <- as.data.frame(cbind(array_er[, , 1, g], array_er[, , 2, g]))
-  list_table_2_1[[g]] <- cbind(as.data.frame(array_er[, , 1, g, drop = F]), as.data.frame(array_er[, , 2, g, drop = F]))
+  list_table_2_1[[g]] <- cbind(as.data.frame(array_er[, , 1, g, drop = FALSE]), as.data.frame(array_er[, , 2, g, drop = FALSE]))
   # list_table_2_1[[g]] <- list_table_2_1[[g]] |> na.omit()
   table_display_3 <- kableExtra::kable(list_table_2_1[[g]],
     format = "latex",
@@ -260,7 +260,7 @@ for (g in groups) {
     " vs. Arm B: ",
     ARMS_ARM_B
   )
-  list_table_2_2[[g]] <- cbind(as.data.frame(array_er_comp[, , 1, g, drop = F]), as.data.frame(array_er_comp[, , 2, g, drop = F]))
+  list_table_2_2[[g]] <- cbind(as.data.frame(array_er_comp[, , 1, g, drop = FALSE]), as.data.frame(array_er_comp[, , 2, g, drop = FALSE]))
   # list_table_2_2[[g]] <- as.data.frame(cbind(array_er_comp[, , 1, g], array_er_comp[, , 2, g]))
   # list_table_2_2[[g]] <- list_table_2_2[[g]] |> na.omit()
   if (length(list_table_2_2[[g]]) == 0) {