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Merge pull request #580 from terrytangyuan/test

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Fixed most of the lint issues
This commit is contained in:
Yuan (Terry) Tang 2015-10-29 00:54:16 -04:00
commit b9a9cd9db8
15 changed files with 191 additions and 197 deletions
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2
R-package/R/predict.xgb.Booster.R
View File

@ -48,7 +48,7 @@ setMethod("predict", signature = "xgb.Booster",
stop("predict: ntreelimit must be equal to or greater than 1")
}
}
option = 0
option <- 0
if (outputmargin) {
option <- option + 1
}

4
R-package/R/slice.xgb.DMatrix.R
View File

@ -34,8 +34,8 @@ setMethod("slice", signature = "xgb.DMatrix",
attr_list <- attributes(object)
nr <- xgb.numrow(object)
len <- sapply(attr_list,length)
ind <- which(len==nr)
if (length(ind)>0) {
ind <- which(len == nr)
if (length(ind) > 0) {
nms <- names(attr_list)[ind]
for (i in 1:length(ind)) {
attr(ret,nms[i]) <- attr(object,nms[i])[idxset]

18
R-package/R/utils.R
View File

@ -1,4 +1,4 @@
#' @importClassesFrom Matrix dgCMatrix dgeMatrix
#' @importClassesFrom Matrix dgCMatrix dgeMatrix
#' @import methods
# depends on matrix
@ -15,14 +15,14 @@ xgb.setinfo <- function(dmat, name, info) {
stop("xgb.setinfo: first argument dtrain must be xgb.DMatrix")
}
if (name == "label") {
if (length(info)!=xgb.numrow(dmat))
if (length(info) != xgb.numrow(dmat))
stop("The length of labels must equal to the number of rows in the input data")
.Call("XGDMatrixSetInfo_R", dmat, name, as.numeric(info),
PACKAGE = "xgboost")
return(TRUE)
}
if (name == "weight") {
if (length(info)!=xgb.numrow(dmat))
if (length(info) != xgb.numrow(dmat))
stop("The length of weights must equal to the number of rows in the input data")
.Call("XGDMatrixSetInfo_R", dmat, name, as.numeric(info),
PACKAGE = "xgboost")
@ -36,7 +36,7 @@ xgb.setinfo <- function(dmat, name, info) {
return(TRUE)
}
if (name == "group") {
if (sum(info)!=xgb.numrow(dmat))
if (sum(info) != xgb.numrow(dmat))
stop("The sum of groups must equal to the number of rows in the input data")
.Call("XGDMatrixSetInfo_R", dmat, name, as.integer(info),
PACKAGE = "xgboost")
@ -251,7 +251,7 @@ xgb.cv.mknfold <- function(dall, nfold, param, stratified, folds) {
# make simple non-stratified folds
kstep <- length(randidx) %/% nfold
folds <- list()
for (i in 1:(nfold-1)) {
for (i in 1:(nfold - 1)) {
folds[[i]] <- randidx[1:kstep]
randidx <- setdiff(randidx, folds[[i]])
}
@ -261,7 +261,7 @@ xgb.cv.mknfold <- function(dall, nfold, param, stratified, folds) {
ret <- list()
for (k in 1:nfold) {
dtest <- slice(dall, folds[[k]])
didx = c()
didx <- c()
for (i in 1:nfold) {
if (i != k) {
didx <- append(didx, folds[[i]])
@ -310,9 +310,9 @@ xgb.createFolds <- function(y, k = 10)
## At most, we will use quantiles. If the sample
## is too small, we just do regular unstratified
## CV
cuts <- floor(length(y)/k)
if(cuts < 2) cuts <- 2
if(cuts > 5) cuts <- 5
cuts <- floor(length(y) / k)
if (cuts < 2) cuts <- 2
if (cuts > 5) cuts <- 5
y <- cut(y,
unique(stats::quantile(y, probs = seq(0, 1, length = cuts))),
include.lowest = TRUE)

36
R-package/R/xgb.cv.R
View File

@ -124,15 +124,15 @@ xgb.cv <- function(params=list(), data, nrounds, nfold, label = NULL, missing =
stop("xgb.cv: cannot assign two different objectives")
if (!is.null(params$objective))
if (class(params$objective) == 'function') {
obj = params$objective
params[['objective']] = NULL
obj <- params$objective
params[['objective']] <- NULL
}
# if (!is.null(params$eval_metric) && !is.null(feval))
# stop("xgb.cv: cannot assign two different evaluation metrics")
if (!is.null(params$eval_metric))
if (class(params$eval_metric)=='function') {
feval = params$eval_metric
params[['eval_metric']] = NULL
if (class(params$eval_metric) == 'function') {
feval <- params$eval_metric
params[['eval_metric']] <- NULL
}
# Early Stopping
@ -144,9 +144,9 @@ xgb.cv <- function(params=list(), data, nrounds, nfold, label = NULL, missing =
if (is.null(maximize))
{
if (params$eval_metric %in% c('rmse','logloss','error','merror','mlogloss')) {
maximize = FALSE
maximize <- FALSE
} else {
maximize = TRUE
maximize <- TRUE
}
}
@ -158,7 +158,7 @@ xgb.cv <- function(params=list(), data, nrounds, nfold, label = NULL, missing =
bestInd <- 0
earlyStopflag <- FALSE
if (length(metrics)>1)
if (length(metrics) > 1)
warning('Only the first metric is used for early stopping process.')
}
@ -167,16 +167,16 @@ xgb.cv <- function(params=list(), data, nrounds, nfold, label = NULL, missing =
mat_pred <- FALSE
if (!is.null(obj_type) && obj_type == 'multi:softprob')
{
num_class = params[['num_class']]
num_class <- params[['num_class']]
if (is.null(num_class))
stop('must set num_class to use softmax')
predictValues <- matrix(0,xgb.numrow(dtrain),num_class)
mat_pred = TRUE
mat_pred <- TRUE
}
else
predictValues <- rep(0,xgb.numrow(dtrain))
history <- c()
print.every.n = max(as.integer(print.every.n), 1L)
print.every.n <- max(as.integer(print.every.n), 1L)
for (i in 1:nrounds) {
msg <- list()
for (k in 1:nfold) {
@ -187,26 +187,25 @@ 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(ret,'\\s+')[[1]][1 + length(metrics) + 2]
score <- strsplit(score,'\\+|:')[[1]][[2]]
score <- as.numeric(score)
if ((maximize && score > bestScore) || (!maximize && score < bestScore)) {
if ( (maximize && score > bestScore) || (!maximize && score < bestScore)) {
bestScore <- score
bestInd <- i
} else {
if (i-bestInd >= early.stop.round) {
if (i - bestInd >= early.stop.round) {
earlyStopflag <- TRUE
cat('Stopping. Best iteration:',bestInd)
break
}
}
}
}
if (prediction) {
@ -226,7 +225,6 @@ xgb.cv <- function(params=list(), data, nrounds, nfold, label = NULL, missing =
}
}
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")
@ -239,10 +237,10 @@ xgb.cv <- function(params=list(), data, nrounds, nfold, label = NULL, missing =
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)}
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))
return( list( dt = dt,pred = predictValues))
}
return(dt)
}

10
R-package/R/xgb.importance.R
View File

@ -66,7 +66,7 @@
#' 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)){
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.")
}
@ -79,7 +79,7 @@ xgb.importance <- function(feature_names = NULL, filename_dump = NULL, model = N
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))) {
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.")
}
@ -110,7 +110,7 @@ xgb.importance <- function(feature_names = NULL, filename_dump = NULL, model = N
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 <- result[, "RealCover" := as.numeric(vec), with = F][, "RealCover %" := RealCover / sum(label)][,MissingNo := NULL]
}
}
result
@ -119,13 +119,13 @@ xgb.importance <- function(feature_names = NULL, filename_dump = NULL, model = N
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 <- 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
}
linearDump <- function(feature_names, text){
which(text == "weight:") %>% {a=.+1;text[a:length(text)]} %>% as.numeric %>% data.table(Feature = feature_names, Weight = .)
which(text == "weight:") %>% {a =. + 1; text[a:length(text)]} %>% as.numeric %>% data.table(Feature = feature_names, Weight = .)
}
# Avoid error messages during CRAN check.

16
R-package/R/xgb.model.dt.tree.R
View File

@ -81,12 +81,12 @@ xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, model
}
if(!is.null(model)){
text = xgb.dump(model = model, with.stats = T)
text <- xgb.dump(model = model, with.stats = T)
} else if(!is.null(filename_dump)){
text <- readLines(filename_dump) %>% str_trim(side = "both")
}
position <- str_match(text, "booster") %>% is.na %>% not %>% which %>% c(length(text)+1)
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
@ -96,15 +96,15 @@ xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, model
allTrees <- data.table()
anynumber_regex<-"[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?"
for(i in 1:n_round){
anynumber_regex <- "[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?"
for (i in 1:n_round){
tree <- text[(position[i]+1):(position[i+1]-1)]
tree <- text[(position[i] + 1):(position[i + 1] - 1)]
# avoid tree made of a leaf only (no split)
if(length(tree) <2) next
if(length(tree) < 2) next
treeID <- i-1
treeID <- i - 1
notLeaf <- str_match(tree, "leaf") %>% is.na
leaf <- notLeaf %>% not %>% tree[.]
@ -128,7 +128,7 @@ xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, model
qualityLeaf <- extract(leaf, paste0("leaf=",anynumber_regex))
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]
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)
}

4
R-package/R/xgb.plot.importance.R
View File

@ -44,9 +44,9 @@ xgb.plot.importance <- function(importance_matrix = NULL, numberOfClusters = c(1
importance_matrix <- importance_matrix[, .(Gain = sum(Gain)), by = Feature]
clusters <- suppressWarnings(Ckmeans.1d.dp::Ckmeans.1d.dp(importance_matrix[,Gain], numberOfClusters))
importance_matrix[,"Cluster":=clusters$cluster %>% as.character]
importance_matrix[,"Cluster" := clusters$cluster %>% as.character]
plot <- ggplot2::ggplot(importance_matrix, ggplot2::aes(x=stats::reorder(Feature, Gain), y = Gain, width= 0.05), environment = environment())+ ggplot2::geom_bar(ggplot2::aes(fill=Cluster), stat="identity", position="identity") + ggplot2::coord_flip() + ggplot2::xlab("Features") + ggplot2::ylab("Gain") + ggplot2::ggtitle("Feature importance") + ggplot2::theme(plot.title = ggplot2::element_text(lineheight=.9, face="bold"), panel.grid.major.y = ggplot2::element_blank() )
plot <- ggplot2::ggplot(importance_matrix, ggplot2::aes(x=stats::reorder(Feature, Gain), y = Gain, width = 0.05), environment = environment()) + ggplot2::geom_bar(ggplot2::aes(fill=Cluster), stat="identity", position="identity") + ggplot2::coord_flip() + ggplot2::xlab("Features") + ggplot2::ylab("Gain") + ggplot2::ggtitle("Feature importance") + ggplot2::theme(plot.title = ggplot2::element_text(lineheight=.9, face="bold"), panel.grid.major.y = ggplot2::element_blank() )
return(plot)
}

11
R-package/R/xgb.plot.tree.R
View File

@ -74,20 +74,19 @@ xgb.plot.tree <- function(feature_names = NULL, filename_dump = NULL, model = NU
allTrees <- xgb.model.dt.tree(feature_names = feature_names, model = model, n_first_tree = n_first_tree)
}
allTrees[Feature!="Leaf" ,yesPath:= paste(ID,"(", Feature, "<br/>Cover: ", Cover, "<br/>Gain: ", Quality, ")-->|< ", Split, "|", Yes, ">", Yes.Feature, "]", sep = "")]
allTrees[Feature!="Leaf" ,noPath:= paste(ID,"(", Feature, ")-->|>= ", Split, "|", No, ">", No.Feature, "]", sep = "")]
allTrees[Feature != "Leaf" ,yesPath := paste(ID,"(", Feature, "<br/>Cover: ", Cover, "<br/>Gain: ", Quality, ")-->|< ", Split, "|", Yes, ">", Yes.Feature, "]", sep = "")]
allTrees[Feature != "Leaf" ,noPath := paste(ID,"(", Feature, ")-->|>= ", Split, "|", No, ">", No.Feature, "]", sep = "")]
if(is.null(CSSstyle)){
CSSstyle <- "classDef greenNode fill:#A2EB86, stroke:#04C4AB, stroke-width:2px;classDef redNode fill:#FFA070, stroke:#FF5E5E, stroke-width:2px"
}
yes <- allTrees[Feature!="Leaf", c(Yes)] %>% paste(collapse = ",") %>% paste("class ", ., " greenNode", sep = "")
yes <- allTrees[Feature != "Leaf", c(Yes)] %>% paste(collapse = ",") %>% paste("class ", ., " greenNode", sep = "")
no <- allTrees[Feature!="Leaf", c(No)] %>% paste(collapse = ",") %>% paste("class ", ., " redNode", sep = "")
no <- allTrees[Feature != "Leaf", c(No)] %>% paste(collapse = ",") %>% paste("class ", ., " redNode", sep = "")
path <- allTrees[Feature!="Leaf", c(yesPath, noPath)] %>% .[order(.)] %>% paste(sep = "", collapse = ";") %>% paste("graph LR", .,collapse = "", sep = ";") %>% paste(CSSstyle, yes, no, sep = ";")
path <- allTrees[Feature != "Leaf", c(yesPath, noPath)] %>% .[order(.)] %>% paste(sep = "", collapse = ";") %>% paste("graph LR", .,collapse = "", sep = ";") %>% paste(CSSstyle, yes, no, sep = ";")
DiagrammeR::mermaid(path, width, height)
}

57
R-package/R/xgb.train.R
View File

@ -140,27 +140,27 @@ xgb.train <- function(params=list(), data, nrounds, watchlist = list(),
warning('watchlist is provided but verbose=0, no evaluation information will be printed')
}
dot.params = list(...)
nms.params = names(params)
nms.dot.params = names(dot.params)
if (length(intersect(nms.params,nms.dot.params))>0)
dot.params <- list(...)
nms.params <- names(params)
nms.dot.params <- names(dot.params)
if (length(intersect(nms.params,nms.dot.params)) > 0)
stop("Duplicated term in parameters. Please check your list of params.")
params = append(params, dot.params)
params <- append(params, dot.params)
# customized objective and evaluation metric interface
if (!is.null(params$objective) && !is.null(obj))
stop("xgb.train: cannot assign two different objectives")
if (!is.null(params$objective))
if (class(params$objective)=='function') {
obj = params$objective
params$objective = NULL
if (class(params$objective) == 'function') {
obj <- params$objective
params$objective <- NULL
}
if (!is.null(params$eval_metric) && !is.null(feval))
stop("xgb.train: cannot assign two different evaluation metrics")
if (!is.null(params$eval_metric))
if (class(params$eval_metric)=='function') {
feval = params$eval_metric
params$eval_metric = NULL
if (class(params$eval_metric) == 'function') {
feval <- params$eval_metric
params$eval_metric <- NULL
}
# Early stopping
@ -174,44 +174,43 @@ xgb.train <- function(params=list(), data, nrounds, watchlist = list(),
if (is.null(maximize))
{
if (params$eval_metric %in% c('rmse','logloss','error','merror','mlogloss')) {
maximize = FALSE
maximize <- FALSE
} else {
maximize = TRUE
maximize <- TRUE
}
}
if (maximize) {
bestScore = 0
bestScore <- 0
} else {
bestScore = Inf
bestScore <- Inf
}
bestInd = 0
bestInd <- 0
earlyStopflag = FALSE
if (length(watchlist)>1)
if (length(watchlist) > 1)
warning('Only the first data set in watchlist is used for early stopping process.')
}
handle <- xgb.Booster(params, append(watchlist, dtrain))
bst <- xgb.handleToBooster(handle)
print.every.n=max( as.integer(print.every.n), 1L)
print.every.n <- max( as.integer(print.every.n), 1L)
for (i in 1:nrounds) {
succ <- xgb.iter.update(bst$handle, dtrain, i - 1, obj)
if (length(watchlist) != 0) {
msg <- xgb.iter.eval(bst$handle, watchlist, i - 1, feval)
if (0== ( (i-1) %% print.every.n))
cat(paste(msg, "\n", sep=""))
if (0 == ( (i - 1) %% print.every.n))
cat(paste(msg, "\n", sep = ""))
if (!is.null(early.stop.round))
{
score = strsplit(msg,':|\\s+')[[1]][3]
score = as.numeric(score)
if ((maximize && score>bestScore) || (!maximize && score<bestScore)) {
bestScore = score
bestInd = i
score <- strsplit(msg,':|\\s+')[[1]][3]
score <- as.numeric(score)
if ( (maximize && score > bestScore) || (!maximize && score < bestScore)) {
bestScore <- score
bestInd <- i
} else {
if (i-bestInd>=early.stop.round) {
earlyStopflag = TRUE
if (i - bestInd >= early.stop.round) {
cat('Stopping. Best iteration:',bestInd)
break
}
@ -226,8 +225,8 @@ xgb.train <- function(params=list(), data, nrounds, watchlist = list(),
}
bst <- xgb.Booster.check(bst)
if (!is.null(early.stop.round)) {
bst$bestScore = bestScore
bst$bestInd = bestInd
bst$bestScore <- bestScore
bst$bestInd <- bestInd
}
return(bst)
}

2
R-package/R/xgboost.R
View File

@ -79,8 +79,6 @@ xgboost <- function(data = NULL, label = NULL, missing = NA, weight = NULL,
return(bst)
}
#' Training part from Mushroom Data Set
#'
#' This data set is originally from the Mushroom data set,

20
R-package/tests/testthat/test_basic.R
View File

@ -4,30 +4,30 @@ context("basic functions")
data(agaricus.train, package='xgboost')
data(agaricus.test, package='xgboost')
train = agaricus.train
test = agaricus.test
train <- agaricus.train
test <- agaricus.test
test_that("train and predict", {
bst = xgboost(data = train$data, label = train$label, max.depth = 2,
bst <- xgboost(data = train$data, label = train$label, max.depth = 2,
eta = 1, nthread = 2, nround = 2, objective = "binary:logistic")
pred = predict(bst, test$data)
pred <- predict(bst, test$data)
})
test_that("early stopping", {
res = xgb.cv(data = train$data, label = train$label, max.depth = 2, nfold = 5,
res <- xgb.cv(data = train$data, label = train$label, max.depth = 2, nfold = 5,
eta = 0.3, nthread = 2, nround = 20, objective = "binary:logistic",
early.stop.round = 3, maximize = FALSE)
expect_true(nrow(res)<20)
bst = xgboost(data = train$data, label = train$label, max.depth = 2,
expect_true(nrow(res) < 20)
bst <- xgboost(data = train$data, label = train$label, max.depth = 2,
eta = 0.3, nthread = 2, nround = 20, objective = "binary:logistic",
early.stop.round = 3, maximize = FALSE)
pred = predict(bst, test$data)
pred <- predict(bst, test$data)
})
test_that("save_period", {
bst = xgboost(data = train$data, label = train$label, max.depth = 2,
bst <- xgboost(data = train$data, label = train$label, max.depth = 2,
eta = 0.3, nthread = 2, nround = 20, objective = "binary:logistic",
save_period = 10, save_name = "xgb.model")
pred = predict(bst, test$data)
pred <- predict(bst, test$data)
})

10
R-package/tests/testthat/test_custom_objective.R
View File

@ -13,14 +13,14 @@ test_that("custom objective works", {
logregobj <- function(preds, dtrain) {
labels <- getinfo(dtrain, "label")
preds <- 1/(1 + exp(-preds))
preds <- 1 / (1 + exp(-preds))
grad <- preds - labels
hess <- preds * (1 - preds)
return(list(grad = grad, hess = hess))
}
evalerror <- function(preds, dtrain) {
labels <- getinfo(dtrain, "label")
err <- as.numeric(sum(labels != (preds > 0)))/length(labels)
err <- as.numeric(sum(labels != (preds > 0))) / length(labels)
return(list(metric = "error", value = err))
}
@ -34,13 +34,13 @@ test_that("custom objective works", {
logregobjattr <- function(preds, dtrain) {
labels <- attr(dtrain, 'label')
preds <- 1/(1 + exp(-preds))
preds <- 1 / (1 + exp(-preds))
grad <- preds - labels
hess <- preds * (1 - preds)
return(list(grad = grad, hess = hess))
}
param <- list(max.depth=2, eta=1, nthread = 2, silent=1,
objective=logregobjattr, eval_metric=evalerror)
param <- list(max.depth=2, eta=1, nthread = 2, silent = 1,
objective = logregobjattr, eval_metric = evalerror)
bst <- xgb.train(param, dtrain, num_round, watchlist)
expect_equal(class(bst), "xgb.Booster")
expect_equal(length(bst$raw), 1064)

10
R-package/tests/testthat/test_helpers.R
View File

@ -8,11 +8,11 @@ require(vcd)
data(Arthritis)
data(agaricus.train, package='xgboost')
df <- data.table(Arthritis, keep.rownames = F)
df[,AgeDiscret:= as.factor(round(Age/10,0))]
df[,AgeCat:= as.factor(ifelse(Age > 30, "Old", "Young"))]
df[,ID:=NULL]
sparse_matrix = sparse.model.matrix(Improved~.-1, data = df)
output_vector = df[,Y:=0][Improved == "Marked",Y:=1][,Y]
df[,AgeDiscret := as.factor(round(Age / 10,0))]
df[,AgeCat := as.factor(ifelse(Age > 30, "Old", "Young"))]
df[,ID := NULL]
sparse_matrix <- sparse.model.matrix(Improved~.-1, data = df)
output_vector <- df[,Y := 0][Improved == "Marked",Y := 1][,Y]
bst <- xgboost(data = sparse_matrix, label = output_vector, max.depth = 9,
eta = 1, nthread = 2, nround = 10,objective = "binary:logistic")

8
R-package/tests/testthat/test_poisson_regression.R
View File

@ -4,10 +4,10 @@ require(xgboost)
test_that("poisson regression works", {
data(mtcars)
bst = xgboost(data=as.matrix(mtcars[,-11]),label=mtcars[,11],
objective='count:poisson',nrounds=5)
bst <- xgboost(data = as.matrix(mtcars[,-11]),label = mtcars[,11],
objective = 'count:poisson', nrounds=5)
expect_equal(class(bst), "xgb.Booster")
pred = predict(bst,as.matrix(mtcars[,-11]))
pred <- predict(bst,as.matrix(mtcars[, -11]))
expect_equal(length(pred), 32)
sqrt(mean((pred-mtcars[,11])^2))
sqrt(mean( (pred - mtcars[,11]) ^ 2))
})