[R] keep row names in predictions (#10727)

R-package/R/xgb.Booster.R

@@ -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
@@ -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)
   }

R-package/src/init.c

@@ -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);
@@ -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},

R-package/src/xgboost_R.cc

@@ -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();

R-package/src/xgboost_R.h

@@ -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

R-package/tests/testthat/test_basic.R

@@ -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", {
@@ -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", {
@@ -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)
@@ -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))
+})

R-package/tests/testthat/test_dmatrix.R

@@ -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(
@@ -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)
@@ -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(
@@ -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)