fix plenty of small bugs

R-package/NAMESPACE

@@ -25,6 +25,7 @@ importFrom(data.table,copy)
 importFrom(data.table,data.table)
 importFrom(data.table,rbindlist)
 importFrom(data.table,set)
+importFrom(data.table,setnames)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,add)
 importFrom(magrittr,not)

R-package/R/xgb.dump.R

@@ -47,7 +47,7 @@ xgb.dump <- function(model = NULL, fname = NULL, fmap = "", with.stats=FALSE) {
   if(is.null(fname)) {
     return(str_split(result, "\n") %>% unlist %>% str_replace("^\t+","") %>% Filter(function(x) x != "", .))
   } else {
-    writeLines(result, fname)
+    result %>% str_split("\n") %>% unlist %>% Filter(function(x) x != "", .) %>% writeLines(fname)
     return(TRUE)
   }
 }

R-package/R/xgb.importance.R

@@ -4,8 +4,9 @@
 #' Can be tree or linear model (text dump of linear model are only supported in dev version of \code{Xgboost} for now).
 #' 
 #' @importFrom data.table data.table
-#' @importFrom magrittr %>%
+#' @importFrom data.table setnames
 #' @importFrom data.table :=
+#' @importFrom magrittr %>%
 #' @param feature_names names of each feature as a character vector. Can be extracted from a sparse matrix (see example). If model dump already contains feature names, this argument should be \code{NULL}.
 #' @param filename_dump the path to the text file storing the model. Model dump must include the gain per feature and per tree (\code{with.stats = T} in function \code{xgb.dump}).
 #'

R-package/R/xgb.model.dt.tree.R

@@ -5,6 +5,7 @@
 #' @importFrom data.table data.table
 #' @importFrom data.table set
 #' @importFrom data.table rbindlist
+#' @importFrom data.table copy
 #' @importFrom data.table :=
 #' @importFrom magrittr %>%
 #' @importFrom magrittr not
@@ -88,11 +89,13 @@ xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, text =
     
     tree <- text[(position[i]+1):(position[i+1]-1)]
     
+    treeID <- i-1
+    
     notLeaf <- str_match(tree, "leaf") %>% is.na
     leaf <- notLeaf %>% not %>% tree[.]
     branch <- notLeaf %>% tree[.]
-    idBranch <- str_extract(branch, "\\d*:") %>% str_replace(":", "") %>% addTreeId(i)
-    idLeaf <- str_extract(leaf, "\\d*:") %>% str_replace(":", "") %>% addTreeId(i)
+    idBranch <- str_extract(branch, "\\d*:") %>% str_replace(":", "") %>% addTreeId(treeID)
+    idLeaf <- str_extract(leaf, "\\d*:") %>% str_replace(":", "") %>% addTreeId(treeID)
     featureBranch <- str_extract(branch, "f\\d*<") %>% str_replace("<", "") %>% str_replace("f", "") %>% as.numeric 
     if(!is.null(feature_names)){
       featureBranch <- feature_names[featureBranch + 1]
@@ -100,20 +103,48 @@ xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, text =
     featureLeaf <- rep("Leaf", length(leaf))
     splitBranch <- str_extract(branch, "<\\d*\\.*\\d*\\]") %>% str_replace("<", "") %>% str_replace("\\]", "") 
     splitLeaf <- rep(NA, length(leaf)) 
-    yesBranch <- extract(branch, "yes=\\d*") %>% addTreeId(i)
+    yesBranch <- extract(branch, "yes=\\d*") %>% addTreeId(treeID)
     yesLeaf <- rep(NA, length(leaf)) 
-    noBranch <- extract(branch, "no=\\d*") %>% addTreeId(i)
+    noBranch <- extract(branch, "no=\\d*") %>% addTreeId(treeID)
     noLeaf <- rep(NA, length(leaf))
-    missingBranch <- extract(branch, "missing=\\d+") %>% addTreeId(i)
+    missingBranch <- extract(branch, "missing=\\d+") %>% addTreeId(treeID)
     missingLeaf <- rep(NA, length(leaf))
     qualityBranch <- extract(branch, "gain=\\d*\\.*\\d*")
     qualityLeaf <- extract(leaf, "leaf=\\-*\\d*\\.*\\d*")
     coverBranch <- extract(branch, "cover=\\d*\\.*\\d*")
     coverLeaf <- extract(leaf, "cover=\\d*\\.*\\d*")
-    dt <- data.table(ID = c(idBranch, idLeaf), Feature = c(featureBranch, featureLeaf), Split = c(splitBranch, splitLeaf), Yes = c(yesBranch, yesLeaf), No = c(noBranch, noLeaf), Missing = c(missingBranch, missingLeaf), Quality = c(qualityBranch, qualityLeaf), Cover = c(coverBranch, coverLeaf))[order(ID)][,Tree:=i]
+    dt <- data.table(ID = c(idBranch, idLeaf), Feature = c(featureBranch, featureLeaf), Split = c(splitBranch, splitLeaf), Yes = c(yesBranch, yesLeaf), No = c(noBranch, noLeaf), Missing = c(missingBranch, missingLeaf), Quality = c(qualityBranch, qualityLeaf), Cover = c(coverBranch, coverLeaf))[order(ID)][,Tree:=treeID]
         
     allTrees <- rbindlist(list(allTrees, dt), use.names = T, fill = F)
   }
   
+  yes <- allTrees[!is.na(Yes),Yes]
+  
+  set(allTrees, i = which(allTrees[,Feature]!= "Leaf"), 
+      j = "Yes.Feature", 
+      value = allTrees[ID == yes,Feature])
+
+  set(allTrees, i = which(allTrees[,Feature]!= "Leaf"), 
+      j = "Yes.Cover", 
+      value = allTrees[ID == yes,Cover])
+
+  set(allTrees, i = which(allTrees[,Feature]!= "Leaf"), 
+    j = "Yes.Quality", 
+    value = allTrees[ID == yes,Quality])
+  
+  no <- allTrees[!is.na(No),No]
+  
+  set(allTrees, i = which(allTrees[,Feature]!= "Leaf"), 
+      j = "No.Feature", 
+      value = allTrees[ID == no,Feature])
+  
+  set(allTrees, i = which(allTrees[,Feature]!= "Leaf"), 
+      j = "No.Cover", 
+      value = allTrees[ID == no,Cover])
+  
+  set(allTrees, i = which(allTrees[,Feature]!= "Leaf"), 
+      j = "No.Quality", 
+      value = allTrees[ID == no,Quality])
+      
   allTrees
 }

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

@@ -59,13 +59,9 @@ xgb.plot.tree <- function(feature_names = NULL, filename_dump = NULL, n_first_tr
     
   allTrees <- xgb.model.dt.tree(feature_names, filename_dump, n_first_tree)
   
-  set(allTrees, i = which(allTrees[,Feature]!= "Leaf"), j = "YesFeature", value = merge(copy(allTrees)[,ID:=Yes][, .(ID)], allTrees[,.(ID, Feature, Quality, Cover)], by = "ID")[,paste(Feature, "<br/>Cover: ", Cover, sep = "")])
+  allTrees[Feature!="Leaf" ,yesPath:= paste(ID,"(", Feature, "<br/>Cover: ", Cover, "<br/>Gain: ", Quality, ")-->|< ", Split, "|", Yes, ">", Yes.Feature, "]", sep = "")]
   
-  set(allTrees, i = which(allTrees[,Feature]!= "Leaf"), j = "NoFeature", value = merge(copy(allTrees)[,ID:=No][, .(ID)], allTrees[,.(ID, Feature, Quality, Cover)], by = "ID")[,paste(Feature, "<br/>Cover: ", Cover, sep = "")])
-  
-  allTrees[Feature!="Leaf" ,yesPath:= paste(ID,"(", Feature, "<br/>Cover: ", Cover, "<br/>Gain: ", Quality, ")-->|< ", Split, "|", Yes, ">", YesFeature, "]", sep = "")]
-  
-  allTrees[Feature!="Leaf" ,noPath:= paste(ID,"(", Feature, ")-->|>= ", Split, "|", No, ">", NoFeature, "]", sep = "")]
+  allTrees[Feature!="Leaf" ,noPath:= paste(ID,"(", Feature, ")-->|>= ", Split, "|", No, ">", No.Feature, "]", sep = "")]
   
   
   if(is.null(styles)){