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[R] Keep row names in predictions #10727

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Aug 20, 2024
Merged

[R] Keep row names in predictions #10727

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18 changes: 18 additions & 0 deletions R-package/R/xgb.Booster.R
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Original file line number Diff line number Diff line change
Expand Up @@ -354,6 +354,11 @@ predict.xgb.Booster <- function(object, newdata, missing = NA, outputmargin = FA
" Should be passed as argument to 'xgb.DMatrix' constructor."
)
}
if (is_dmatrix) {
rnames <- NULL
} else {
rnames <- row.names(newdata)
}

use_as_df <- FALSE
use_as_dense_matrix <- FALSE
Expand Down Expand Up @@ -501,6 +506,19 @@ predict.xgb.Booster <- function(object, newdata, missing = NA, outputmargin = FA
.Call(XGSetArrayDimNamesInplace_R, arr, dim_names)
}

if (NROW(rnames)) {
if (is.null(dim(arr))) {
.Call(XGSetVectorNamesInplace_R, arr, rnames)
} else {
dim_names <- dimnames(arr)
if (is.null(dim_names)) {
dim_names <- vector(mode = "list", length = length(dim(arr)))
}
dim_names[[length(dim_names)]] <- rnames
.Call(XGSetArrayDimNamesInplace_R, arr, dim_names)
}
}

if (!avoid_transpose && is.array(arr)) {
arr <- aperm(arr)
}
Expand Down
2 changes: 2 additions & 0 deletions R-package/src/init.c
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Expand Up @@ -46,6 +46,7 @@ extern SEXP XGBoosterSetParam_R(SEXP, SEXP, SEXP);
extern SEXP XGBoosterUpdateOneIter_R(SEXP, SEXP, SEXP);
extern SEXP XGCheckNullPtr_R(SEXP);
extern SEXP XGSetArrayDimNamesInplace_R(SEXP, SEXP);
extern SEXP XGSetVectorNamesInplace_R(SEXP, SEXP);
extern SEXP XGDMatrixCreateFromCSC_R(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
extern SEXP XGDMatrixCreateFromCSR_R(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
extern SEXP XGDMatrixCreateFromURI_R(SEXP, SEXP, SEXP);
Expand Down Expand Up @@ -108,6 +109,7 @@ static const R_CallMethodDef CallEntries[] = {
{"XGBoosterUpdateOneIter_R", (DL_FUNC) &XGBoosterUpdateOneIter_R, 3},
{"XGCheckNullPtr_R", (DL_FUNC) &XGCheckNullPtr_R, 1},
{"XGSetArrayDimNamesInplace_R", (DL_FUNC) &XGSetArrayDimNamesInplace_R, 2},
{"XGSetVectorNamesInplace_R", (DL_FUNC) &XGSetVectorNamesInplace_R, 2},
{"XGDMatrixCreateFromCSC_R", (DL_FUNC) &XGDMatrixCreateFromCSC_R, 6},
{"XGDMatrixCreateFromCSR_R", (DL_FUNC) &XGDMatrixCreateFromCSR_R, 6},
{"XGDMatrixCreateFromURI_R", (DL_FUNC) &XGDMatrixCreateFromURI_R, 3},
Expand Down
5 changes: 5 additions & 0 deletions R-package/src/xgboost_R.cc
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Expand Up @@ -335,6 +335,11 @@ XGB_DLL SEXP XGSetArrayDimNamesInplace_R(SEXP arr, SEXP dim_names) {
return R_NilValue;
}

XGB_DLL SEXP XGSetVectorNamesInplace_R(SEXP arr, SEXP names) {
Rf_setAttrib(arr, R_NamesSymbol, names);
return R_NilValue;
}

namespace {
void _DMatrixFinalizer(SEXP ext) {
R_API_BEGIN();
Expand Down
8 changes: 8 additions & 0 deletions R-package/src/xgboost_R.h
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Expand Up @@ -34,6 +34,14 @@ XGB_DLL SEXP XGCheckNullPtr_R(SEXP handle);
*/
XGB_DLL SEXP XGSetArrayDimNamesInplace_R(SEXP arr, SEXP dim_names);

/*!
* \brief set the names of a vector in-place
* \param arr
* \param names names for the dimensions to set
* \return NULL value
*/
XGB_DLL SEXP XGSetVectorNamesInplace_R(SEXP arr, SEXP names);

/*!
* \brief Set global configuration
* \param json_str a JSON string representing the list of key-value pairs
Expand Down
50 changes: 47 additions & 3 deletions R-package/tests/testthat/test_basic.R
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Expand Up @@ -678,7 +678,7 @@ test_that("Can predict on data.frame objects", {

pred_mat <- predict(model, xgb.DMatrix(x_mat))
pred_df <- predict(model, x_df)
expect_equal(pred_mat, pred_df)
expect_equal(pred_mat, unname(pred_df))
})

test_that("'base_margin' gives the same result in DMatrix as in inplace_predict", {
Expand All @@ -702,7 +702,7 @@ test_that("'base_margin' gives the same result in DMatrix as in inplace_predict"
pred_from_dm <- predict(model, dm_w_base)
pred_from_mat <- predict(model, x, base_margin = base_margin)

expect_equal(pred_from_dm, pred_from_mat)
expect_equal(pred_from_dm, unname(pred_from_mat))
})

test_that("Coefficients from gblinear have the expected shape and names", {
Expand All @@ -725,7 +725,7 @@ test_that("Coefficients from gblinear have the expected shape and names", {
expect_equal(names(coefs), c("(Intercept)", colnames(x)))
pred_auto <- predict(model, x)
pred_manual <- as.numeric(mm %*% coefs)
expect_equal(pred_manual, pred_auto, tolerance = 1e-5)
expect_equal(pred_manual, unname(pred_auto), tolerance = 1e-5)

# Multi-column coefficients
data(iris)
Expand Down Expand Up @@ -949,3 +949,47 @@ test_that("xgb.cv works for ranking", {
)
expect_equal(length(res$folds), 2L)
})

test_that("Row names are preserved in outputs", {
data(iris)
x <- iris[, -5]
y <- as.numeric(iris$Species) - 1
dm <- xgb.DMatrix(x, label = y, nthread = 1)
model <- xgb.train(
data = dm,
params = list(
objective = "multi:softprob",
num_class = 3,
max_depth = 2,
nthread = 1
),
nrounds = 3
)
row.names(x) <- paste0("r", seq(1, nrow(x)))
pred <- predict(model, x)
expect_equal(row.names(pred), row.names(x))
pred <- predict(model, x, avoid_transpose = TRUE)
expect_equal(colnames(pred), row.names(x))

data(mtcars)
y <- mtcars[, 1]
x <- as.matrix(mtcars[, -1])
dm <- xgb.DMatrix(data = x, label = y)
model <- xgb.train(
data = dm,
params = list(
max_depth = 2,
nthread = 1
),
nrounds = 3
)
row.names(x) <- paste0("r", seq(1, nrow(x)))
pred <- predict(model, x)
expect_equal(names(pred), row.names(x))
pred <- predict(model, x, avoid_transpose = TRUE)
expect_equal(names(pred), row.names(x))
pred <- predict(model, x, predleaf = TRUE)
expect_equal(row.names(pred), row.names(x))
pred <- predict(model, x, predleaf = TRUE, avoid_transpose = TRUE)
expect_equal(colnames(pred), row.names(x))
})
6 changes: 4 additions & 2 deletions R-package/tests/testthat/test_dmatrix.R
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Expand Up @@ -493,6 +493,7 @@ test_that("xgb.DMatrix: ExternalDMatrix produces the same results as regular DMa
nrounds = 5
)
pred <- predict(model, x)
pred <- unname(pred)

iterator_env <- as.environment(
list(
Expand Down Expand Up @@ -538,7 +539,7 @@ test_that("xgb.DMatrix: ExternalDMatrix produces the same results as regular DMa
)

pred_model1_edm <- predict(model, edm)
pred_model2_mat <- predict(model_ext, x)
pred_model2_mat <- predict(model_ext, x) |> unname()
pred_model2_edm <- predict(model_ext, edm)

expect_equal(pred_model1_edm, pred)
Expand Down Expand Up @@ -567,6 +568,7 @@ test_that("xgb.DMatrix: External QDM produces same results as regular QDM", {
nrounds = 5
)
pred <- predict(model, x)
pred <- unname(pred)

iterator_env <- as.environment(
list(
Expand Down Expand Up @@ -616,7 +618,7 @@ test_that("xgb.DMatrix: External QDM produces same results as regular QDM", {
)

pred_model1_qdm <- predict(model, qdm)
pred_model2_mat <- predict(model_ext, x)
pred_model2_mat <- predict(model_ext, x) |> unname()
pred_model2_qdm <- predict(model_ext, qdm)

expect_equal(pred_model1_qdm, pred)
Expand Down
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