Merge branch 'main' into brulee-two-layer

Author: topepo

.Rbuildignore

@@ -19,3 +19,4 @@ derby.log
 ^codecov\.yml$
 ^LICENSE\.md$
 ^man-roxygen$
+^vignettes/articles$

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: parsnip
 Title: A Common API to Modeling and Analysis Functions
-Version: 1.2.1.9003
+Version: 1.2.1.9004
 Authors@R: c(
     person("Max", "Kuhn", , "max@posit.co", role = c("aut", "cre")),
     person("Davis", "Vaughan", , "davis@posit.co", role = "aut"),
     person("Emil", "Hvitfeldt", , "emil.hvitfeldt@posit.co", role = "ctb"),
-    person("Posit Software, PBC", role = c("cph", "fnd"))
+    person("Posit Software, PBC", role = c("cph", "fnd"), comment = c(ROR = "03wc8by49"))
   )
 Maintainer: Max Kuhn <max@posit.co>
 Description: A common interface is provided to allow users to specify a
@@ -25,23 +25,23 @@ Imports:
     ggplot2,
     globals,
     glue,
-    hardhat (>= 1.4.0),
+    hardhat (>= 1.4.1),
     lifecycle,
     magrittr,
     pillar,
     prettyunits,
     purrr (>= 1.0.0),
     rlang (>= 1.1.0),
-    sparsevctrs (>= 0.1.0.9000),
+    sparsevctrs (>= 0.2.0),
     stats,
     tibble (>= 2.1.1),
     tidyr (>= 1.3.0),
     utils,
     vctrs (>= 0.6.0),
     withr
 Suggests: 
-    C50,
     bench,
+    C50,
     covr,
     dials (>= 1.1.0),
     earth,
@@ -71,14 +71,12 @@ VignetteBuilder:
     knitr
 ByteCompile: true
 Config/Needs/website: C50, dbarts, earth, glmnet, keras, kernlab, kknn,
-    LiblineaR, mgcv, nnet, parsnip, randomForest, ranger, rpart, rstanarm,
-    tidymodels/tidymodels, tidyverse/tidytemplate, rstudio/reticulate,
-    xgboost
+    LiblineaR, mgcv, nnet, parsnip, quantreg, randomForest, ranger, rpart, 
+    rstanarm, tidymodels/tidymodels, tidyverse/tidytemplate, rstudio/reticulate,
+    xgboost, rmarkdown
 Config/rcmdcheck/ignore-inconsequential-notes: true
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-Remotes:  
-    r-lib/sparsevctrs
 RoxygenNote: 7.3.2

NAMESPACE

@@ -185,6 +185,7 @@ export(.dat)
 export(.extract_surv_status)
 export(.extract_surv_time)
 export(.facts)
+export(.get_prediction_column_names)
 export(.lvls)
 export(.model_param_name_key)
 export(.obs)
@@ -202,7 +203,6 @@ export(bag_mars)
 export(bag_mlp)
 export(bag_tree)
 export(bart)
-export(bartMachine_interval_calc)
 export(boost_tree)
 export(case_weights_allowed)
 export(cforest_train)
@@ -221,6 +221,7 @@ export(discrim_flexible)
 export(discrim_linear)
 export(discrim_quad)
 export(discrim_regularized)
+export(ensure_parsnip_format)
 export(eval_args)
 export(extract_fit_engine)
 export(extract_fit_time)
@@ -253,6 +254,7 @@ export(glm_grouped)
 export(has_multi_predict)
 export(importance_weights)
 export(is_varying)
+export(keras_activations)
 export(keras_mlp)
 export(keras_predict_classes)
 export(knit_engine_docs)
@@ -264,6 +266,7 @@ export(make_classes)
 export(make_engine_list)
 export(make_seealso_list)
 export(mars)
+export(matrix_to_quantile_pred)
 export(max_mtry_formula)
 export(maybe_data_frame)
 export(maybe_matrix)
@@ -311,7 +314,6 @@ export(rand_forest)
 export(repair_call)
 export(req_pkgs)
 export(required_pkgs)
-export(rpart_train)
 export(rule_fit)
 export(set_args)
 export(set_dependency)
@@ -377,6 +379,7 @@ importFrom(generics,tune_args)
 importFrom(generics,varying_args)
 importFrom(ggplot2,autoplot)
 importFrom(glue,glue_collapse)
+importFrom(hardhat,contr_one_hot)
 importFrom(hardhat,extract_fit_engine)
 importFrom(hardhat,extract_fit_time)
 importFrom(hardhat,extract_parameter_dials)

NEWS.md

@@ -1,25 +1,53 @@
 # parsnip (development version)
 
+## New Features
+
+* A new model mode (`"quantile regression"`) was added. Including:
+  * A `linear_reg()` engine for `"quantreg"`. 
+  * Predictions are encoded via a custom vector type. See [hardhat::quantile_pred()].
+  * Predicted quantile levels are designated when the new mode is specified. See `?set_mode`.
+  
 * `fit_xy()` can now take dgCMatrix input for `x` argument (#1121).
 
-* `fit()` and `fit_xy()` can now take sparse tibbles as data values (#1165).
+* `fit_xy()` can now take sparse tibbles as data values (#1165).
 
 * `predict()` can now take dgCMatrix and sparse tibble input for `new_data` argument, and error informatively when model doesn't support it (#1167).
 
-* Transitioned package errors and warnings to use cli (#1147 and #1148 by
-  @shum461, #1153 by @RobLBaker and @wright13, #1154 by @JamesHWade, #1160, 
-  #1161, #1081).
+* New `extract_fit_time()` method has been added that returns the time it took to train the model (#853).
+
+* `mlp()` with `keras` engine now work for all activation functions currently supported by `keras` (#1127).
+
+## Other Changes
+
+* Transitioned package errors and warnings to use cli (#1147 and #1148 by @shum461, #1153 by @RobLBaker and @wright13, #1154 by @JamesHWade, #1160, #1161, #1081).
 
 * `fit_xy()` currently raises an error for `gen_additive_mod()` model specifications as the default engine (`"mgcv"`) specifies smoothing terms in model formulas. However, some engines specify smooths via additional arguments, in which case the restriction on `fit_xy()` is excessive. parsnip will now only raise an error when fitting a `gen_additive_mod()` with `fit_xy()` when using the `"mgcv"` engine (#775).
 
 * Aligned `null_model()` with other model types; the model type now has an engine argument that defaults to `"parsnip"` and is checked with the same machinery that checks other model types in the package (#1083).
 
-* New `extract_fit_time()` method has been added that returns the time it took to train the model (#853).
+* If linear regression is requested with a Poisson family, an error will occur and refer the user to `poisson_reg()` (#1219).
+
+* The deprecated function `rpart_train()` was removed after its deprecation period (#1044).
+
+## Bug Fixes
+
+* Make sure that parsnip does not convert ordered factor predictions to be unordered.
 
 * Ensure that `knit_engine_docs()` has the required packages installed (#1156).
 
 * Fixed bug where some models fit using `fit_xy()` couldn't predict (#1166).
 
+* Fixed bug related to using local (non-package) models (#1229)
+
+* `tunable()` now references a dials object for the `mixture` parameter (#1236)
+
+## Breaking Change
+
+* For quantile prediction, the `quantile` argument to `predict()` has been deprecate in facor of `quantile_levels`. This does not affect models with mode `"quantile regression"`. 
+
+* The quantile regression prediction type was disabled for the deprecated `surv_reg()` model. 
+
+
 # parsnip 1.2.1
 
 * Added a missing `tidy()` method for survival analysis glmnet models (#1086).

R/README.md

@@ -1,7 +1,3 @@
-# Standalone file: do not edit by hand
-# Source: <https://github.com/r-lib/rlang/blob/main/R/standalone-types-check.R>
-# ----------------------------------------------------------------------
-#
 # ---
 # repo: r-lib/rlang
 # file: standalone-types-check.R
@@ -13,6 +9,9 @@
 #
 # ## Changelog
 #
+# 2024-08-15:
+# - `check_character()` gains an `allow_na` argument (@martaalcalde, #1724)
+#
 # 2023-03-13:
 # - Improved error messages of number checkers (@teunbrand)
 # - Added `allow_infinite` argument to `check_number_whole()` (@mgirlich).
@@ -461,15 +460,28 @@ check_formula <- function(x,
 
 # Vectors -----------------------------------------------------------------
 
+# TODO: Figure out what to do with logical `NA` and `allow_na = TRUE`
+
 check_character <- function(x,
                             ...,
+                            allow_na = TRUE,
                             allow_null = FALSE,
                             arg = caller_arg(x),
                             call = caller_env()) {
+
   if (!missing(x)) {
     if (is_character(x)) {
+      if (!allow_na && any(is.na(x))) {
+        abort(
+          sprintf("`%s` can't contain NA values.", arg),
+          arg = arg,
+          call = call
+        )
+      }
+
       return(invisible(NULL))
     }
+
     if (allow_null && is_null(x)) {
       return(invisible(NULL))
     }
@@ -479,7 +491,6 @@ check_character <- function(x,
     x,
     "a character vector",
     ...,
-    allow_na = FALSE,
     allow_null = allow_null,
     arg = arg,
     call = call