[MAINT] Deal with global variable notes via globalVariables()

DESCRIPTION

@@ -29,7 +29,7 @@ Suggests:
     MASS (>= 7.3.47),
     testthat
 VignetteBuilder: knitr
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 URL: https://github.com/ModelOriented/randomForestExplainer, https://modeloriented.github.io/randomForestExplainer/
 Config/testthat/edition: 3
 Config/Needs/website: ModelOriented/DrWhyTemplate

R/measure_importance.R

@@ -323,7 +323,6 @@ plot_multi_way_importance <- function(importance_frame, x_measure = "mean_min_de
                                       y_measure = "times_a_root", size_measure = NULL,
                                       min_no_of_trees = 0, no_of_labels = 10,
                                       main = "Multi-way importance plot"){
-  variable <- NULL
   if(any(c("randomForest", "ranger") %in% class(importance_frame))){
     importance_frame <- measure_importance(importance_frame)
   }

R/min_depth_distribution.R

@@ -64,7 +64,6 @@ min_depth_distribution <- function(forest){
 #' @importFrom data.table rbindlist
 #' @export
 min_depth_distribution.randomForest <- function(forest){
-  tree <- NULL; `split var` <- NULL; depth <- NULL
   forest_table <- lapply(
     1:forest$ntree,
     function(i)
@@ -85,7 +84,6 @@ min_depth_distribution.randomForest <- function(forest){
 #' @importFrom data.table rbindlist
 #' @export
 min_depth_distribution.ranger <- function(forest){
-  tree <- NULL; splitvarName <- NULL; depth <- NULL
   forest_table <- lapply(
     1:forest$num.trees,
     function(i)
@@ -103,7 +101,6 @@ min_depth_distribution.ranger <- function(forest){
 
 # Count the trees in which each variable had a given minimal depth
 min_depth_count <- function(min_depth_frame){
-  tree <- NULL; minimal_depth <- NULL; variable <- NULL
   mean_tree_depth <- dplyr::group_by(min_depth_frame, tree) %>%
     dplyr::summarize(depth = max(minimal_depth) + 1) %>% as.data.frame()
   mean_tree_depth <- mean(mean_tree_depth$depth)
@@ -122,7 +119,6 @@ min_depth_count <- function(min_depth_frame){
 
 # Get a data frame with means of minimal depth calculated using sample = c("all_trees", "top_trees", "relevant_trees")
 get_min_depth_means <- function(min_depth_frame, min_depth_count_list, mean_sample){
-  .SD <- NULL; variable <- NULL
   if(mean_sample == "all_trees"){
     min_depth_count_list[[1]][is.na(min_depth_count_list[[1]]$minimal_depth), "minimal_depth"] <- min_depth_count_list[[3]]
     min_depth_means <-
@@ -166,7 +162,6 @@ get_min_depth_means <- function(min_depth_frame, min_depth_count_list, mean_samp
 plot_min_depth_distribution <- function(min_depth_frame, k = 10, min_no_of_trees = 0,
                                         mean_sample = "top_trees", mean_scale = FALSE, mean_round = 2,
                                         main = "Distribution of minimal depth and its mean"){
-  minimal_depth <- NULL; mean_minimal_depth_label <- NULL; mean_minimal_depth <- NULL
   if(any(c("randomForest", "ranger") %in% class(min_depth_frame))){
     min_depth_frame <- min_depth_distribution(min_depth_frame)
   }

R/min_depth_interactions.R

@@ -1,7 +1,6 @@
 # Calculate conditional depth in a tree with respect to all variables from vector vars
 # randomForest
 conditional_depth <- function(frame, vars){
-  `.SD` <- NULL; depth <- NULL; `split var` <- NULL
   index <- data.table::as.data.table(frame)[, .SD[which.min(depth), "number"], by = `split var`]
   index <- index[!is.na(index$`split var`), ]
   if(any(index$`split var` %in% vars)){
@@ -29,7 +28,6 @@ conditional_depth <- function(frame, vars){
 # Calculate conditional depth in a tree with respect to all variables from vector vars
 # ranger
 conditional_depth_ranger <- function(frame, vars){
-  `.SD` <- NULL; depth <- NULL; splitvarName <- NULL
   index <- data.table::as.data.table(frame)[, .SD[which.min(depth), "number"], by = splitvarName]
   index <- index[!is.na(index$splitvarName), ]
   if(any(index$splitvarName %in% vars)){
@@ -57,7 +55,6 @@ conditional_depth_ranger <- function(frame, vars){
 # Get a data frame with values of minimal depth conditional on selected variables for the whole forest
 # randomForest
 min_depth_interactions_values <- function(forest, vars){
-  `.` <- NULL; .SD <- NULL; tree <- NULL; `split var` <- NULL
   interactions_frame <- lapply(
     1:forest$ntree,
     function(i)
@@ -93,7 +90,6 @@ min_depth_interactions_values <- function(forest, vars){
 # Get a data frame with values of minimal depth conditional on selected variables for the whole forest
 # ranger
 min_depth_interactions_values_ranger <- function(forest, vars){
-  `.` <- NULL; .SD <- NULL; tree <- NULL; splitvarName <- NULL
   interactions_frame <- lapply(
     1:forest$num.trees,
     function(i)
@@ -149,7 +145,6 @@ min_depth_interactions <- function(forest, vars = important_variables(measure_im
 #' @export
 min_depth_interactions.randomForest <- function(forest, vars = important_variables(measure_importance(forest)),
                                                 mean_sample = "top_trees", uncond_mean_sample = mean_sample){
-  variable <- NULL; `.` <- NULL; tree <- NULL; `split var` <- NULL; depth <- NULL
   min_depth_interactions_frame <- min_depth_interactions_values(forest, vars)
   mean_tree_depth <- min_depth_interactions_frame[[2]]
   min_depth_interactions_frame <- min_depth_interactions_frame[[1]]
@@ -217,7 +212,6 @@ min_depth_interactions.randomForest <- function(forest, vars = important_variabl
 #' @export
 min_depth_interactions.ranger <- function(forest, vars = important_variables(measure_importance(forest)),
                                           mean_sample = "top_trees", uncond_mean_sample = mean_sample){
-  variable <- NULL; `.` <- NULL; tree <- NULL; splitvarName <- NULL; depth <- NULL
   min_depth_interactions_frame <- min_depth_interactions_values_ranger(forest, vars)
   mean_tree_depth <- min_depth_interactions_frame[[2]]
   min_depth_interactions_frame <- min_depth_interactions_frame[[1]]
@@ -287,7 +281,6 @@ min_depth_interactions.ranger <- function(forest, vars = important_variables(mea
 plot_min_depth_interactions <- function(interactions_frame, k = 30,
                                         main = paste0("Mean minimal depth for ",
                                                       paste0(k, " most frequent interactions"))){
-  mean_min_depth <- NULL; occurrences <- NULL; uncond_mean_min_depth <- NULL
   if(any(c("randomForest", "ranger") %in% class(interactions_frame))){
     interactions_frame <- min_depth_interactions(interactions_frame)
   }

R/utils.R

@@ -21,5 +21,25 @@ max_na <- function(x) {
   max(x, na.rm = TRUE)
 }
 
-utils::globalVariables(c("prediction", "variable"))
+# Deal with the global variable note
+utils::globalVariables(
+  c(
+    ".",
+    ".SD",
+    "depth",
+    "mean_min_depth",
+    "mean_minimal_depth",
+    "mean_minimal_depth_label",
+    "minimal_depth",
+    "occurrences",
+    "prediction",
+    "split var",
+    "splitvarName",
+    "tree",
+    "uncond_mean_min_depth",
+    "variable"
+  )
+)
+
+