Merge pull request #436 from tidymodels/xgboost-event-level

Set event level for xgboost

NEWS.md

@@ -22,6 +22,8 @@
 
 * Column names for `x` are now required when `fit_xy()` is used. (#398)
 
+* There is now an `event_level` argument for the `xgboost` engine. (#420)
+
 * New mode "censored regression" and new prediction types "linear_pred", "time", "survival", "hazard". (#396)
 
 * Censored regression models cannot use `fit_xy()` (use `fit()`). (#442)

R/boost_tree.R

@@ -305,6 +305,9 @@ check_args.boost_tree <- function(object) {
 #' @param objective A single string (or NULL) that defines the loss function that
 #' `xgboost` uses to create trees. See [xgboost::xgb.train()] for options. If left
 #' NULL, an appropriate loss function is chosen.
+#' @param event_level For binary classification, this is a single string of either
+#' `"first"` or `"second"` to pass along describing which level of the outcome
+#' should be considered the "event".
 #' @param ... Other options to pass to `xgb.train`.
 #' @return A fitted `xgboost` object.
 #' @keywords internal
@@ -313,8 +316,11 @@ xgb_train <- function(
   x, y,
   max_depth = 6, nrounds = 15, eta  = 0.3, colsample_bytree = 1,
   min_child_weight = 1, gamma = 0, subsample = 1, validation = 0,
-  early_stop = NULL, objective = NULL, ...) {
+  early_stop = NULL, objective = NULL,
+  event_level = c("first", "second"),
+  ...) {
 
+  event_level <- rlang::arg_match(event_level, c("first", "second"))
   others <- list(...)
 
   num_class <- length(levels(y))
@@ -347,7 +353,7 @@ xgb_train <- function(
   n <- nrow(x)
   p <- ncol(x)
 
-  x <- as_xgb_data(x, y, validation)
+  x <- as_xgb_data(x, y, validation, event_level)
 
   # translate `subsample` and `colsample_bytree` to be on (0, 1] if not
   if (subsample > 1) {
@@ -427,7 +433,7 @@ xgb_pred <- function(object, newdata, ...) {
 }
 
 
-as_xgb_data <- function(x, y, validation = 0, ...) {
+as_xgb_data <- function(x, y, validation = 0, event_level = "first", ...) {
   lvls <- levels(y)
   n <- nrow(x)
 
@@ -436,7 +442,16 @@ as_xgb_data <- function(x, y, validation = 0, ...) {
   }
 
   if (is.factor(y)) {
-    y <- as.numeric(y) - 1
+    if (length(lvls) < 3) {
+      if (event_level == "first") {
+        y <- -as.numeric(y) + 2
+      } else {
+        y <- as.numeric(y) - 1
+      }
+    } else {
+      if (event_level == "second") rlang::warn("`event_level` can only be set for binary variables.")
+      y <- as.numeric(y) - 1
+    }
   }
 
   if (!inherits(x, "xgb.DMatrix")) {

man/rmd/boost-tree.Rmd

@@ -41,7 +41,9 @@ mod_param <-
 For this engine, tuning over `trees` is very efficient since the same model 
 object can be used to make predictions over multiple values of `trees`.  
 
-Finally, note that `xgboost` models require that non-numeric predictors (e.g., factors) must be converted to dummy variables or some other numeric representation. By default, when using `fit()` with `xgboost`, a one-hot encoding is used to convert factor predictors to indicator variables. 
+Note that `xgboost` models require that non-numeric predictors (e.g., factors) must be converted to dummy variables or some other numeric representation. By default, when using `fit()` with `xgboost`, a one-hot encoding is used to convert factor predictors to indicator variables. 
+
+Finally, in the classification mode, non-numeric outcomes (i.e., factors) are converted to numeric. For binary classification, the `event_level` argument of `set_engine()` can be set to either `"first"` or `"second"` to specify which level should be used as the event. This can be helpful when a watchlist is used to monitor performance from with the xgboost training process. 
 
 
 ## C5.0

revdep/README.md

@@ -3,44 +3,67 @@
 |field    |value                        |
 |:--------|:----------------------------|
 |version  |R version 4.0.3 (2020-10-10) |
-|os       |macOS Catalina 10.15.5       |
-|system   |x86_64, darwin17.0           |
-|ui       |RStudio                      |
-|language |(EN)                         |
-|collate  |en_US.UTF-8                  |
-|ctype    |en_US.UTF-8                  |
-|tz       |America/New_York             |
-|date     |2021-01-19                   |
+|os       |Ubuntu 18.04.5 LTS           |
+|system   |x86_64, linux-gnu            |
+|ui       |X11                          |
+|language |en                           |
+|collate  |en_GB.UTF-8                  |
+|ctype    |en_GB.UTF-8                  |
+|tz       |Europe/London                |
+|date     |2021-02-23                   |
 
 # Dependencies
 
 |package     |old    |new        |Δ  |
 |:-----------|:------|:----------|:--|
-|parsnip     |0.1.4  |0.1.4.9000 |*  |
+|parsnip     |0.1.5  |0.1.5.9000 |*  |
 |assertthat  |0.2.1  |0.2.1      |   |
-|cli         |2.2.0  |2.2.0      |   |
-|cpp11       |0.2.5  |0.2.5      |   |
-|crayon      |1.3.4  |1.3.4      |   |
+|cli         |2.3.1  |2.3.1      |   |
+|cpp11       |0.2.6  |0.2.6      |   |
+|crayon      |1.4.1  |1.4.1      |   |
 |digest      |0.6.27 |0.6.27     |   |
-|dplyr       |1.0.3  |1.0.3      |   |
+|dplyr       |1.0.4  |1.0.4      |   |
 |ellipsis    |0.3.1  |0.3.1      |   |
 |fansi       |0.4.2  |0.4.2      |   |
 |generics    |0.1.0  |0.1.0      |   |
 |globals     |0.14.0 |0.14.0     |   |
 |glue        |1.4.2  |1.4.2      |   |
-|lifecycle   |0.2.0  |0.2.0      |   |
+|lifecycle   |1.0.0  |1.0.0      |   |
 |magrittr    |2.0.1  |2.0.1      |   |
-|pillar      |1.4.7  |1.4.7      |   |
+|pillar      |1.5.0  |1.5.0      |   |
 |pkgconfig   |2.0.3  |2.0.3      |   |
 |prettyunits |1.1.1  |1.1.1      |   |
 |purrr       |0.3.4  |0.3.4      |   |
 |R6          |2.5.0  |2.5.0      |   |
 |rlang       |0.4.10 |0.4.10     |   |
-|tibble      |3.0.5  |3.0.5      |   |
+|tibble      |3.0.6  |3.0.6      |   |
 |tidyr       |1.1.2  |1.1.2      |   |
 |tidyselect  |1.1.0  |1.1.0      |   |
 |utf8        |1.1.4  |1.1.4      |   |
 |vctrs       |0.3.6  |0.3.6      |   |
 
 # Revdeps
 
+## Failed to check (18)
+
+|package            |version |error |warning |note |
+|:------------------|:-------|:-----|:-------|:----|
+|baguette           |?       |      |        |     |
+|bayesian           |?       |      |        |     |
+|butcher            |?       |      |        |     |
+|coefplot           |?       |      |        |     |
+|condvis2           |?       |      |        |     |
+|discrim            |?       |      |        |     |
+|easyalluvial       |?       |      |        |     |
+|finetune           |?       |      |        |     |
+|insight            |?       |      |        |     |
+|modeltime          |?       |      |        |     |
+|modeltime.ensemble |?       |      |        |     |
+|modeltime.gluonts  |?       |      |        |     |
+|modeltime.resample |?       |      |        |     |
+|plsmod             |?       |      |        |     |
+|SSLR               |?       |      |        |     |
+|tabnet             |?       |      |        |     |
+|timetk             |?       |      |        |     |
+|vip                |?       |      |        |     |
+

tests/testthat/test_boost_tree_xgboost.R

@@ -350,6 +350,18 @@ test_that('xgboost data conversion', {
   expect_true(inherits(from_mat$watchlist$validation, "xgb.DMatrix"))
   expect_true(nrow(from_sparse$data) > nrow(from_sparse$watchlist$validation))
 
+  # set event_level for factors
+
+  mtcars_y <- factor(mtcars$mpg < 15, levels = c(TRUE, FALSE), labels = c("low", "high"))
+  expect_error(from_df <- parsnip:::as_xgb_data(mtcar_x, mtcars_y), regexp = NA)
+  expect_equal(xgboost::getinfo(from_df$data, name = "label")[1:5],  rep(0, 5))
+  expect_error(from_df <- parsnip:::as_xgb_data(mtcar_x, mtcars_y, event_level = "second"), regexp = NA)
+  expect_equal(xgboost::getinfo(from_df$data, name = "label")[1:5],  rep(1, 5))
+
+  mtcars_y <- factor(mtcars$mpg < 15, levels = c(TRUE, FALSE, "na"), labels = c("low", "high", "missing"))
+  expect_warning(from_df <- parsnip:::as_xgb_data(mtcar_x, mtcars_y, event_level = "second"),
+                 regexp = "`event_level` can only be set for binary variables.")
+
 })
 
 
@@ -410,4 +422,43 @@ test_that('argument checks for data dimensions', {
 
 })
 
+test_that("set `event_level` as engine-specific argument", {
+
+  skip_if_not_installed("xgboost")
+
+  data(penguins, package = "modeldata")
+  penguins <- na.omit(penguins[, -c(1:2)])
 
+  spec <-
+    boost_tree(trees = 10, tree_depth = 3) %>%
+    set_engine(
+      "xgboost",
+      eval_metric = "aucpr",
+      event_level = "second",
+      verbose = 1
+    ) %>%
+    set_mode("classification")
+
+  set.seed(24)
+  fit_p <- spec %>% fit(sex ~ ., data = penguins)
+
+  penguins_x <- as.matrix(penguins[, -5])
+  penguins_y <- as.numeric(penguins$sex) - 1
+  xgbmat <- xgb.DMatrix(data = penguins_x, label = penguins_y)
+
+  set.seed(24)
+  fit_xgb <- xgboost::xgb.train(data = xgbmat,
+                                params = list(eta = 0.3, max_depth = 3,
+                                              gamma = 0, colsample_bytree = 1,
+                                              min_child_weight = 1,
+                                              subsample = 1),
+                                nrounds = 10,
+                                watchlist = list("training" = xgbmat),
+                                objective = "binary:logistic",
+                                verbose = 1,
+                                eval_metric = "aucpr",
+                                nthread = 1)
+
+  expect_equal(fit_p$fit$evaluation_log, fit_xgb$evaluation_log)
+
+})