[R-package] remove dependency on {magrittr} (#6928)

Co-authored-by: Hyunsu Cho <chohyu01@cs.washington.edu>

R-package/R/callbacks.R

@@ -642,8 +642,13 @@ cb.gblinear.history <- function(sparse=FALSE) {
       coefs <<- list2mat(coefs)
     } else { # xgb.cv:
       # first lapply transposes the list
-      coefs <<- lapply(seq_along(coefs[[1]]), function(i) lapply(coefs, "[[", i)) %>%
-                lapply(function(x) list2mat(x))
+      coefs <<- lapply(
+        X = lapply(
+          X = seq_along(coefs[[1]]),
+          FUN = function(i) lapply(coefs, "[[", i)
+        ),
+        FUN = function(x) list2mat(x)
+      )
     }
   }
 

R-package/R/xgb.Booster.R

@@ -372,8 +372,14 @@ predict.xgb.Booster <- function(object, newdata, missing = NA, outputmargin = FA
     } else if (n_group == 1) {
       matrix(ret, nrow = n_row, byrow = TRUE, dimnames = list(NULL, cnames))
     } else {
-      arr <- array(ret, c(n_col1, n_group, n_row),
-                   dimnames = list(cnames, NULL, NULL)) %>% aperm(c(2, 3, 1)) # [group, row, col]
+      arr <- aperm(
+        a = array(
+          data = ret,
+          dim = c(n_col1, n_group, n_row),
+          dimnames = list(cnames, NULL, NULL)
+        ),
+        perm = c(2, 3, 1)  # [group, row, col]
+      )
       lapply(seq_len(n_group), function(g) arr[g, , ])
     }
   } else if (predinteraction) {
@@ -383,10 +389,23 @@ predict.xgb.Booster <- function(object, newdata, missing = NA, outputmargin = FA
     ret <- if (n_ret == n_row) {
       matrix(ret, ncol = 1, dimnames = list(NULL, cnames))
     } else if (n_group == 1) {
-      array(ret, c(n_col1, n_col1, n_row), dimnames = list(cnames, cnames, NULL)) %>% aperm(c(3, 1, 2))
+      aperm(
+        a = array(
+          data = ret,
+          dim = c(n_col1, n_col1, n_row),
+          dimnames = list(cnames, cnames, NULL)
+        ),
+        perm = c(3, 1, 2)
+      )
     } else {
-      arr <- array(ret, c(n_col1, n_col1, n_group, n_row),
-                   dimnames = list(cnames, cnames, NULL, NULL)) %>% aperm(c(3, 4, 1, 2)) # [group, row, col1, col2]
+      arr <- aperm(
+        a = array(
+          data = ret,
+          dim = c(n_col1, n_col1, n_group, n_row),
+          dimnames = list(cnames, cnames, NULL, NULL)
+        ),
+        perm = c(3, 4, 1, 2)  # [group, row, col1, col2]
+      )
       lapply(seq_len(n_group), function(g) arr[g, , , ])
     }
   } else if (reshape && npred_per_case > 1) {

R-package/R/xgb.importance.R

@@ -100,9 +100,10 @@ xgb.importance <- function(feature_names = NULL, model = NULL, trees = NULL,
 
   # linear model
   if (model_text_dump[2] == "bias:"){
-    weights <- which(model_text_dump == "weight:") %>%
-               {model_text_dump[(. + 1):length(model_text_dump)]} %>%
-               as.numeric
+    weight_index <- which(model_text_dump == "weight:") + 1
+    weights <- as.numeric(
+      model_text_dump[weight_index:length(model_text_dump)]
+    )
 
     num_class <- NVL(model$params$num_class, 1)
     if (is.null(feature_names))

R-package/R/xgb.plot.multi.trees.R

@@ -75,8 +75,8 @@ xgb.plot.multi.trees <- function(model, feature_names = NULL, features_keep = 5,
   while (tree.matrix[, sum(is.na(abs.node.position))] > 0) {
     yes.row.nodes <- tree.matrix[abs.node.position %in% precedent.nodes & !is.na(Yes)]
     no.row.nodes <- tree.matrix[abs.node.position %in% precedent.nodes & !is.na(No)]
-    yes.nodes.abs.pos <- yes.row.nodes[, abs.node.position] %>% paste0("_0")
-    no.nodes.abs.pos <- no.row.nodes[, abs.node.position] %>% paste0("_1")
+    yes.nodes.abs.pos <- paste0(yes.row.nodes[, abs.node.position], "_0")
+    no.nodes.abs.pos <- paste0(no.row.nodes[, abs.node.position], "_1")
 
     tree.matrix[ID %in% yes.row.nodes[, Yes], abs.node.position := yes.nodes.abs.pos]
     tree.matrix[ID %in% no.row.nodes[, No], abs.node.position := no.nodes.abs.pos]
@@ -92,19 +92,28 @@ xgb.plot.multi.trees <- function(model, feature_names = NULL, features_keep = 5,
   nodes.dt <- tree.matrix[
         , .(Quality = sum(Quality))
         , by = .(abs.node.position, Feature)
-      ][, .(Text = paste0(Feature[1:min(length(Feature), features_keep)],
-                          " (",
-                          format(Quality[1:min(length(Quality), features_keep)], digits = 5),
-                          ")") %>%
-                   paste0(collapse = "\n"))
-        , by = abs.node.position]
+      ][, .(Text = paste0(
+              paste0(
+                Feature[1:min(length(Feature), features_keep)],
+                " (",
+                format(Quality[1:min(length(Quality), features_keep)], digits = 5),
+                ")"
+              ),
+              collapse = "\n"
+            )
+          )
+        , by = abs.node.position
+      ]
 
-  edges.dt <- tree.matrix[Feature != "Leaf", .(abs.node.position, Yes)] %>%
-    list(tree.matrix[Feature != "Leaf", .(abs.node.position, No)]) %>%
-    rbindlist() %>%
-    setnames(c("From", "To")) %>%
-    .[, .N, .(From, To)] %>%
-    .[, N := NULL]
+  edges.dt <- data.table::rbindlist(
+    l = list(
+      tree.matrix[Feature != "Leaf", .(abs.node.position, Yes)],
+      tree.matrix[Feature != "Leaf", .(abs.node.position, No)]
+    )
+  )
+  data.table::setnames(edges.dt, c("From", "To"))
+  edges.dt <- edges.dt[, .N, .(From, To)]
+  edges.dt[, N := NULL]
 
   nodes <- DiagrammeR::create_node_df(
     n = nrow(nodes.dt),
@@ -120,21 +129,25 @@ xgb.plot.multi.trees <- function(model, feature_names = NULL, features_keep = 5,
       nodes_df = nodes,
       edges_df = edges,
       attr_theme = NULL
-      ) %>%
-    DiagrammeR::add_global_graph_attrs(
+  )
+  graph <- DiagrammeR::add_global_graph_attrs(
+      graph = graph,
       attr_type = "graph",
       attr  = c("layout", "rankdir"),
       value = c("dot", "LR")
-      ) %>%
-    DiagrammeR::add_global_graph_attrs(
+  )
+  graph <- DiagrammeR::add_global_graph_attrs(
+      graph = graph,
       attr_type = "node",
       attr  = c("color", "fillcolor", "style", "shape", "fontname"),
       value = c("DimGray", "beige", "filled", "rectangle", "Helvetica")
-      ) %>%
-    DiagrammeR::add_global_graph_attrs(
+  )
+  graph <- DiagrammeR::add_global_graph_attrs(
+      graph = graph,
       attr_type = "edge",
       attr  = c("color", "arrowsize", "arrowhead", "fontname"),
-      value = c("DimGray", "1.5", "vee", "Helvetica"))
+      value = c("DimGray", "1.5", "vee", "Helvetica")
+  )
 
   if (!render) return(invisible(graph))
 

R-package/R/xgb.plot.tree.R

@@ -99,33 +99,41 @@ xgb.plot.tree <- function(feature_names = NULL, model = NULL, trees = NULL, plot
     fontcolor = "black")
 
   edges <- DiagrammeR::create_edge_df(
-    from  = match(dt[Feature != "Leaf", c(ID)] %>% rep(2), dt$ID),
+    from  = match(rep(dt[Feature != "Leaf", c(ID)], 2), dt$ID),
     to    = match(dt[Feature != "Leaf", c(Yes, No)], dt$ID),
-    label = dt[Feature != "Leaf", paste("<", Split)] %>%
-            c(rep("", nrow(dt[Feature != "Leaf"]))),
-    style = dt[Feature != "Leaf", ifelse(Missing == Yes, "bold", "solid")] %>%
-            c(dt[Feature != "Leaf", ifelse(Missing == No, "bold", "solid")]),
+    label = c(
+      dt[Feature != "Leaf", paste("<", Split)],
+      rep("", nrow(dt[Feature != "Leaf"]))
+    ),
+    style = c(
+      dt[Feature != "Leaf", ifelse(Missing == Yes, "bold", "solid")],
+      dt[Feature != "Leaf", ifelse(Missing == No, "bold", "solid")]
+    ),
     rel   = "leading_to")
 
   graph <- DiagrammeR::create_graph(
       nodes_df = nodes,
       edges_df = edges,
       attr_theme = NULL
-      ) %>%
-    DiagrammeR::add_global_graph_attrs(
+  )
+  graph <- DiagrammeR::add_global_graph_attrs(
+      graph = graph,
       attr_type = "graph",
       attr  = c("layout", "rankdir"),
       value = c("dot", "LR")
-      ) %>%
-    DiagrammeR::add_global_graph_attrs(
+  )
+  graph <- DiagrammeR::add_global_graph_attrs(
+      graph = graph,
       attr_type = "node",
       attr  = c("color", "style", "fontname"),
       value = c("DimGray", "filled", "Helvetica")
-      ) %>%
-    DiagrammeR::add_global_graph_attrs(
+  )
+  graph <- DiagrammeR::add_global_graph_attrs(
+      graph = graph,
       attr_type = "edge",
       attr  = c("color", "arrowsize", "arrowhead", "fontname"),
-      value = c("DimGray", "1.5", "vee", "Helvetica"))
+      value = c("DimGray", "1.5", "vee", "Helvetica")
+  )
 
   if (!render) return(invisible(graph))
 

R-package/R/xgboost.R

@@ -90,7 +90,6 @@ NULL
 #' @importFrom data.table setkey
 #' @importFrom data.table setkeyv
 #' @importFrom data.table setnames
-#' @importFrom magrittr %>%
 #' @importFrom jsonlite fromJSON
 #' @importFrom jsonlite toJSON
 #' @importFrom utils object.size str tail