Nothing
require(xgboost)
require(Matrix)
context("testing xgb.DMatrix functionality")
data(agaricus.test, package = 'xgboost')
test_data <- agaricus.test$data[1:100, ]
test_label <- agaricus.test$label[1:100]
n_threads <- 2
test_that("xgb.DMatrix: basic construction", {
# from sparse matrix
dtest1 <- xgb.DMatrix(test_data, label = test_label, nthread = n_threads)
# from dense matrix
dtest2 <- xgb.DMatrix(as.matrix(test_data), label = test_label, nthread = n_threads)
expect_equal(getinfo(dtest1, "label"), getinfo(dtest2, "label"))
expect_equal(dim(dtest1), dim(dtest2))
#from dense integer matrix
int_data <- as.matrix(test_data)
storage.mode(int_data) <- "integer"
dtest3 <- xgb.DMatrix(int_data, label = test_label, nthread = n_threads)
expect_equal(dim(dtest1), dim(dtest3))
})
test_that("xgb.DMatrix: NA", {
n_samples <- 3
x <- cbind(
x1 = sample(x = 4, size = n_samples, replace = TRUE),
x2 = sample(x = 4, size = n_samples, replace = TRUE)
)
x[1, "x1"] <- NA
m <- xgb.DMatrix(x, nthread = n_threads)
xgb.DMatrix.save(m, "int.dmatrix")
x <- matrix(as.numeric(x), nrow = n_samples, ncol = 2)
colnames(x) <- c("x1", "x2")
m <- xgb.DMatrix(x, nthread = n_threads)
xgb.DMatrix.save(m, "float.dmatrix")
iconn <- file("int.dmatrix", "rb")
fconn <- file("float.dmatrix", "rb")
expect_equal(file.size("int.dmatrix"), file.size("float.dmatrix"))
bytes <- file.size("int.dmatrix")
idmatrix <- readBin(iconn, "raw", n = bytes)
fdmatrix <- readBin(fconn, "raw", n = bytes)
expect_equal(length(idmatrix), length(fdmatrix))
expect_equal(idmatrix, fdmatrix)
close(iconn)
close(fconn)
file.remove("int.dmatrix")
file.remove("float.dmatrix")
})
test_that("xgb.DMatrix: saving, loading", {
# save to a local file
dtest1 <- xgb.DMatrix(test_data, label = test_label, nthread = n_threads)
tmp_file <- tempfile('xgb.DMatrix_')
on.exit(unlink(tmp_file))
expect_true(xgb.DMatrix.save(dtest1, tmp_file))
# read from a local file
expect_output(dtest3 <- xgb.DMatrix(tmp_file), "entries loaded from")
expect_output(dtest3 <- xgb.DMatrix(tmp_file, silent = TRUE), NA)
unlink(tmp_file)
expect_equal(getinfo(dtest1, 'label'), getinfo(dtest3, 'label'))
# from a libsvm text file
tmp <- c("0 1:1 2:1", "1 3:1", "0 1:1")
tmp_file <- 'tmp.libsvm'
writeLines(tmp, tmp_file)
expect_true(file.exists(tmp_file))
dtest4 <- xgb.DMatrix(
paste(tmp_file, "?format=libsvm", sep = ""), silent = TRUE, nthread = n_threads
)
expect_equal(dim(dtest4), c(3, 4))
expect_equal(getinfo(dtest4, 'label'), c(0, 1, 0))
# check that feature info is saved
data(agaricus.train, package = 'xgboost')
dtrain <- xgb.DMatrix(
data = agaricus.train$data, label = agaricus.train$label, nthread = n_threads
)
cnames <- colnames(dtrain)
expect_equal(length(cnames), 126)
tmp_file <- tempfile('xgb.DMatrix_')
xgb.DMatrix.save(dtrain, tmp_file)
dtrain <- xgb.DMatrix(tmp_file)
expect_equal(colnames(dtrain), cnames)
ft <- rep(c("c", "q"), each=length(cnames)/2)
setinfo(dtrain, "feature_type", ft)
expect_equal(ft, getinfo(dtrain, "feature_type"))
})
test_that("xgb.DMatrix: getinfo & setinfo", {
dtest <- xgb.DMatrix(test_data, nthread = n_threads)
expect_true(setinfo(dtest, 'label', test_label))
labels <- getinfo(dtest, 'label')
expect_equal(test_label, getinfo(dtest, 'label'))
expect_true(setinfo(dtest, 'label_lower_bound', test_label))
expect_equal(test_label, getinfo(dtest, 'label_lower_bound'))
expect_true(setinfo(dtest, 'label_upper_bound', test_label))
expect_equal(test_label, getinfo(dtest, 'label_upper_bound'))
expect_true(length(getinfo(dtest, 'weight')) == 0)
expect_true(length(getinfo(dtest, 'base_margin')) == 0)
expect_true(setinfo(dtest, 'weight', test_label))
expect_true(setinfo(dtest, 'base_margin', test_label))
expect_true(setinfo(dtest, 'group', c(50, 50)))
expect_error(setinfo(dtest, 'group', test_label))
# providing character values will give an error
expect_error(setinfo(dtest, 'weight', rep('a', nrow(test_data))))
# any other label should error
expect_error(setinfo(dtest, 'asdf', test_label))
})
test_that("xgb.DMatrix: slice, dim", {
dtest <- xgb.DMatrix(test_data, label = test_label, nthread = n_threads)
expect_equal(dim(dtest), dim(test_data))
dsub1 <- slice(dtest, 1:42)
expect_equal(nrow(dsub1), 42)
expect_equal(ncol(dsub1), ncol(test_data))
dsub2 <- dtest[1:42, ]
expect_equal(dim(dtest), dim(test_data))
expect_equal(getinfo(dsub1, 'label'), getinfo(dsub2, 'label'))
})
test_that("xgb.DMatrix: slice, trailing empty rows", {
data(agaricus.train, package = 'xgboost')
train_data <- agaricus.train$data
train_label <- agaricus.train$label
dtrain <- xgb.DMatrix(
data = train_data, label = train_label, nthread = n_threads
)
slice(dtrain, 6513L)
train_data[6513, ] <- 0
dtrain <- xgb.DMatrix(
data = train_data, label = train_label, nthread = n_threads
)
slice(dtrain, 6513L)
expect_equal(nrow(dtrain), 6513)
})
test_that("xgb.DMatrix: colnames", {
dtest <- xgb.DMatrix(test_data, label = test_label, nthread = n_threads)
expect_equal(colnames(dtest), colnames(test_data))
expect_error(colnames(dtest) <- 'asdf')
new_names <- make.names(seq_len(ncol(test_data)))
expect_silent(colnames(dtest) <- new_names)
expect_equal(colnames(dtest), new_names)
expect_silent(colnames(dtest) <- NULL)
expect_null(colnames(dtest))
})
test_that("xgb.DMatrix: nrow is correct for a very sparse matrix", {
set.seed(123)
nr <- 1000
x <- rsparsematrix(nr, 100, density = 0.0005)
# we want it very sparse, so that last rows are empty
expect_lt(max(x@i), nr)
dtest <- xgb.DMatrix(x, nthread = n_threads)
expect_equal(dim(dtest), dim(x))
})
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