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Code: Lint fixes on trailing spaces

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This commit is contained in:
terrytangyuan 2015-10-24 16:50:03 -04:00
parent 537b34dc6f
commit 139feaf97a
7 changed files with 86 additions and 86 deletions
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14
R-package/R/xgb.DMatrix.R
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@ -20,26 +20,26 @@
#'
xgb.DMatrix <- function(data, info = list(), missing = NA, ...) {
if (typeof(data) == "character") {
handle <- .Call("XGDMatrixCreateFromFile_R", data, as.integer(FALSE),
handle <- .Call("XGDMatrixCreateFromFile_R", data, as.integer(FALSE),
PACKAGE = "xgboost")
} else if (is.matrix(data)) {
handle <- .Call("XGDMatrixCreateFromMat_R", data, missing,
handle <- .Call("XGDMatrixCreateFromMat_R", data, missing,
PACKAGE = "xgboost")
} else if (class(data) == "dgCMatrix") {
handle <- .Call("XGDMatrixCreateFromCSC_R", data@p, data@i, data@x,
handle <- .Call("XGDMatrixCreateFromCSC_R", data@p, data@i, data@x,
PACKAGE = "xgboost")
} else {
stop(paste("xgb.DMatrix: does not support to construct from ",
stop(paste("xgb.DMatrix: does not support to construct from ",
typeof(data)))
}
dmat <- structure(handle, class = "xgb.DMatrix")
info <- append(info, list(...))
if (length(info) == 0)
if (length(info) == 0)
return(dmat)
for (i in 1:length(info)) {
p <- info[i]
xgb.setinfo(dmat, names(p), p[[1]])
}
return(dmat)
}
}

4
R-package/R/xgb.DMatrix.save.R
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@ -18,10 +18,10 @@ xgb.DMatrix.save <- function(DMatrix, fname) {
stop("xgb.save: fname must be character")
}
if (class(DMatrix) == "xgb.DMatrix") {
.Call("XGDMatrixSaveBinary_R", DMatrix, fname, as.integer(FALSE),
.Call("XGDMatrixSaveBinary_R", DMatrix, fname, as.integer(FALSE),
PACKAGE = "xgboost")
return(TRUE)
}
stop("xgb.DMatrix.save: the input must be xgb.DMatrix")
return(FALSE)
}
}

58
R-package/R/xgb.cv.R
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@ -151,21 +151,21 @@ xgb.cv <- function(params=list(), data, nrounds, nfold, label = NULL, missing =
}
if (maximize) {
bestScore = 0
bestScore <- 0
} else {
bestScore = Inf
bestScore <- Inf
}
bestInd = 0
earlyStopflag = FALSE
bestInd <- 0
earlyStopflag <- FALSE
if (length(metrics)>1)
warning('Only the first metric is used for early stopping process.')
}
xgb_folds <- xgb.cv.mknfold(dtrain, nfold, params, stratified, folds)
obj_type = params[['objective']]
mat_pred = FALSE
if (!is.null(obj_type) && obj_type=='multi:softprob')
obj_type <- params[['objective']]
mat_pred <- FALSE
if (!is.null(obj_type) && obj_type == 'multi:softprob')
{
num_class = params[['num_class']]
if (is.null(num_class))
@ -187,20 +187,20 @@ xgb.cv <- function(params=list(), data, nrounds, nfold, label = NULL, missing =
ret <- xgb.cv.aggcv(msg, showsd)
history <- c(history, ret)
if(verbose)
if (0==(i-1L)%%print.every.n)
if (0 == (i-1L)%%print.every.n)
cat(ret, "\n", sep="")
# early_Stopping
if (!is.null(early.stop.round)){
score = strsplit(ret,'\\s+')[[1]][1+length(metrics)+2]
score = strsplit(score,'\\+|:')[[1]][[2]]
score = as.numeric(score)
if ((maximize && score>bestScore) || (!maximize && score<bestScore)) {
bestScore = score
bestInd = i
score <- strsplit(ret,'\\s+')[[1]][1+length(metrics)+2]
score <- strsplit(score,'\\+|:')[[1]][[2]]
score <- as.numeric(score)
if ((maximize && score > bestScore) || (!maximize && score < bestScore)) {
bestScore <- score
bestInd <- i
} else {
if (i-bestInd>=early.stop.round) {
earlyStopflag = TRUE
if (i-bestInd >= early.stop.round) {
earlyStopflag <- TRUE
cat('Stopping. Best iteration:',bestInd)
break
}
@ -211,36 +211,36 @@ xgb.cv <- function(params=list(), data, nrounds, nfold, label = NULL, missing =
if (prediction) {
for (k in 1:nfold) {
fd = xgb_folds[[k]]
fd <- xgb_folds[[k]]
if (!is.null(early.stop.round) && earlyStopflag) {
res = xgb.iter.eval(fd$booster, fd$watchlist, bestInd - 1, feval, prediction)
res <- xgb.iter.eval(fd$booster, fd$watchlist, bestInd - 1, feval, prediction)
} else {
res = xgb.iter.eval(fd$booster, fd$watchlist, nrounds - 1, feval, prediction)
res <- xgb.iter.eval(fd$booster, fd$watchlist, nrounds - 1, feval, prediction)
}
if (mat_pred) {
pred_mat = matrix(res[[2]],num_class,length(fd$index))
predictValues[fd$index,] = t(pred_mat)
pred_mat <- matrix(res[[2]],num_class,length(fd$index))
predictValues[fd$index,] <- t(pred_mat)
} else {
predictValues[fd$index] = res[[2]]
predictValues[fd$index] <- res[[2]]
}
}
}
colnames <- str_split(string = history[1], pattern = "\t")[[1]] %>% .[2:length(.)] %>% str_extract(".*:") %>% str_replace(":","") %>% str_replace("-", ".")
colnamesMean <- paste(colnames, "mean")
if(showsd) colnamesStd <- paste(colnames, "std")
colnames <- c()
if(showsd) for(i in 1:length(colnamesMean)) colnames <- c(colnames, colnamesMean[i], colnamesStd[i])
else colnames <- colnamesMean
type <- rep(x = "numeric", times = length(colnames))
dt <- utils::read.table(text = "", colClasses = type, col.names = colnames) %>% as.data.table
split <- str_split(string = history, pattern = "\t")
for(line in split) dt <- line[2:length(line)] %>% str_extract_all(pattern = "\\d*\\.+\\d*") %>% unlist %>% as.numeric %>% as.list %>% {rbindlist(list(dt, .), use.names = F, fill = F)}
if (prediction) {
return(list(dt = dt,pred = predictValues))
}

6
R-package/R/xgb.dump.R
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@ -49,13 +49,13 @@ xgb.dump <- function(model = NULL, fname = NULL, fmap = "", with.stats=FALSE) {
if (!(class(fmap) %in% c("character", "NULL") && length(fname) <= 1)) {
stop("fmap: argument must be type character (when provided)")
}
longString <- .Call("XGBoosterDumpModel_R", model$handle, fmap, as.integer(with.stats), PACKAGE = "xgboost")
dt <- fread(paste(longString, collapse = ""), sep = "\n", header = F)
setnames(dt, "Lines")
if(is.null(fname)) {
result <- dt[Lines != "0"][, Lines := str_replace(Lines, "^\t+", "")][Lines != ""][, paste(Lines)]
return(result)

34
R-package/R/xgb.importance.R
View File

@ -66,42 +66,42 @@
#' xgb.importance(train$data@@Dimnames[[2]], model = bst, data = train$data, label = train$label)
#'
#' @export
xgb.importance <- function(feature_names = NULL, filename_dump = NULL, model = NULL, data = NULL, label = NULL, target = function(x) ((x + label) == 2)){
if (!class(feature_names) %in% c("character", "NULL")) {
xgb.importance <- function(feature_names = NULL, filename_dump = NULL, model = NULL, data = NULL, label = NULL, target = function(x) ((x + label) == 2)){
if (!class(feature_names) %in% c("character", "NULL")) {
stop("feature_names: Has to be a vector of character or NULL if the model dump already contains feature name. Look at this function documentation to see where to get feature names.")
}
if (!(class(filename_dump) %in% c("character", "NULL") && length(filename_dump) <= 1)) {
stop("filename_dump: Has to be a path to the model dump file.")
}
if (!class(model) %in% c("xgb.Booster", "NULL")) {
stop("model: Has to be an object of class xgb.Booster model generaged by the xgb.train function.")
}
if((is.null(data) & !is.null(label)) |(!is.null(data) & is.null(label))) {
stop("data/label: Provide the two arguments if you want co-occurence computation or none of them if you are not interested but not one of them only.")
}
if(class(label) == "numeric"){
if(sum(label == 0) / length(label) > 0.5) label <- as(label, "sparseVector")
}
if(is.null(model)){
text <- readLines(filename_dump)
text <- readLines(filename_dump)
} else {
text <- xgb.dump(model = model, with.stats = T)
}
}
if(text[2] == "bias:"){
result <- readLines(filename_dump) %>% linearDump(feature_names, .)
if(!is.null(data) | !is.null(label)) warning("data/label: these parameters should only be provided with decision tree based models.")
} else {
result <- treeDump(feature_names, text = text, keepDetail = !is.null(data))
# Co-occurence computation
if(!is.null(data) & !is.null(label) & nrow(result) > 0) {
# Take care of missing column
# Take care of missing column
a <- data[, result[MissingNo == T,Feature], drop=FALSE] != 0
# Bind the two Matrix and reorder columns
c <- data[, result[MissingNo == F,Feature], drop=FALSE] %>% cBind(a,.) %>% .[,result[,Feature]]
@ -109,19 +109,19 @@ xgb.importance <- function(feature_names = NULL, filename_dump = NULL, model = N
# Apply split
d <- data[, result[,Feature], drop=FALSE] < as.numeric(result[,Split])
apply(c & d, 2, . %>% target %>% sum) -> vec
result <- result[, "RealCover":= as.numeric(vec), with = F][, "RealCover %" := RealCover / sum(label)][,MissingNo:=NULL]
}
}
}
result
}
treeDump <- function(feature_names, text, keepDetail){
if(keepDetail) groupBy <- c("Feature", "Split", "MissingNo") else groupBy <- "Feature"
result <- xgb.model.dt.tree(feature_names = feature_names, text = text)[,"MissingNo":= Missing == No ][Feature!="Leaf",.(Gain = sum(Quality), Cover = sum(Cover), Frequence = .N), by = groupBy, with = T][,`:=`(Gain = Gain/sum(Gain), Cover = Cover/sum(Cover), Frequence = Frequence/sum(Frequence))][order(Gain, decreasing = T)]
result
result
}
linearDump <- function(feature_names, text){

6
R-package/R/xgb.load.R
View File

@ -17,9 +17,9 @@
#' @export
#'
xgb.load <- function(modelfile) {
if (is.null(modelfile))
if (is.null(modelfile))
stop("xgb.load: modelfile cannot be NULL")
handle <- xgb.Booster(modelfile = modelfile)
# re-use modelfile if it is raw so we donot need to serialize
if (typeof(modelfile) == "raw") {
@ -29,4 +29,4 @@ xgb.load <- function(modelfile) {
}
bst <- xgb.Booster.check(bst)
return(bst)
}
}

50
R-package/R/xgb.model.dt.tree.R
View File

@ -56,8 +56,8 @@
#'
#' @export
xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, model = NULL, text = NULL, n_first_tree = NULL){
if (!class(feature_names) %in% c("character", "NULL")) {
if (!class(feature_names) %in% c("character", "NULL")) {
stop("feature_names: Has to be a vector of character or NULL if the model dump already contains feature name. Look at this function documentation to see where to get feature names.")
}
if (!(class(filename_dump) %in% c("character", "NULL") && length(filename_dump) <= 1)) {
@ -67,59 +67,59 @@ xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, model
} else if(is.null(filename_dump) && is.null(model) && is.null(text)){
stop("filename_dump & model & text: no path to dump model, no model, no text dump, have been provided.")
}
if (!class(model) %in% c("xgb.Booster", "NULL")) {
stop("model: Has to be an object of class xgb.Booster model generaged by the xgb.train function.")
}
if (!class(text) %in% c("character", "NULL")) {
if (!class(text) %in% c("character", "NULL")) {
stop("text: Has to be a vector of character or NULL if a path to the model dump has already been provided.")
}
if (!class(n_first_tree) %in% c("numeric", "NULL") | length(n_first_tree) > 1) {
stop("n_first_tree: Has to be a numeric vector of size 1.")
}
if(!is.null(model)){
text = xgb.dump(model = model, with.stats = T)
} else if(!is.null(filename_dump)){
text <- readLines(filename_dump) %>% str_trim(side = "both")
text <- readLines(filename_dump) %>% str_trim(side = "both")
}
position <- str_match(text, "booster") %>% is.na %>% not %>% which %>% c(length(text)+1)
extract <- function(x, pattern) str_extract(x, pattern) %>% str_split("=") %>% lapply(function(x) x[2] %>% as.numeric) %>% unlist
n_round <- min(length(position) - 1, n_first_tree)
addTreeId <- function(x, i) paste(i,x,sep = "-")
allTrees <- data.table()
anynumber_regex<-"[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?"
anynumber_regex<-"[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?"
for(i in 1:n_round){
tree <- text[(position[i]+1):(position[i+1]-1)]
# avoid tree made of a leaf only (no split)
if(length(tree) <2) next
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(treeID)
idLeaf <- str_extract(leaf, "\\d*:") %>% str_replace(":", "") %>% addTreeId(treeID)
featureBranch <- str_extract(branch, "f\\d*<") %>% str_replace("<", "") %>% str_replace("f", "") %>% as.numeric
featureBranch <- str_extract(branch, "f\\d*<") %>% str_replace("<", "") %>% str_replace("f", "") %>% as.numeric
if(!is.null(feature_names)){
featureBranch <- feature_names[featureBranch + 1]
}
featureLeaf <- rep("Leaf", length(leaf))
splitBranch <- str_extract(branch, paste0("<",anynumber_regex,"\\]")) %>% str_replace("<", "") %>% str_replace("\\]", "")
splitLeaf <- rep(NA, length(leaf))
splitBranch <- str_extract(branch, paste0("<",anynumber_regex,"\\]")) %>% str_replace("<", "") %>% str_replace("\\]", "")
splitLeaf <- rep(NA, length(leaf))
yesBranch <- extract(branch, "yes=\\d*") %>% addTreeId(treeID)
yesLeaf <- rep(NA, length(leaf))
yesLeaf <- rep(NA, length(leaf))
noBranch <- extract(branch, "no=\\d*") %>% addTreeId(treeID)
noLeaf <- rep(NA, length(leaf))
missingBranch <- extract(branch, "missing=\\d+") %>% addTreeId(treeID)
@ -129,10 +129,10 @@ xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, model
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:=treeID]
allTrees <- rbindlist(list(allTrees, dt), use.names = T, fill = F)
}
yes <- allTrees[!is.na(Yes), Yes]
set(allTrees, i = which(allTrees[, Feature] != "Leaf"),