new extract functions (#518)

* new extract functions

* missing hardhat remote

* extract_parsnip_spec -> extract_spec_parsnip

* notes about model extraction

* small text adjustments

* Update R/extract.R

Co-authored-by: Hannah Frick <[email protected]>

* extract test cases

* less specific remote

Co-authored-by: Hannah Frick <[email protected]>

Author: topepo

DESCRIPTION

@@ -31,7 +31,8 @@ Imports:
     tidyr (>= 1.0.0),
     globals,
     prettyunits,
-    vctrs (>= 0.2.0)
+    vctrs (>= 0.2.0),
+    hardhat (>= 0.1.5.9000)
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1.9001
 Suggests: 
@@ -59,4 +60,6 @@ Suggests:
     dials (>= 0.0.9.9000)
 Remotes:  
     tidymodels/dials,
-    topepo/C5.0
+    topepo/C5.0,
+    tidymodels/hardhat
+

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(augment,model_fit)
+S3method(extract_fit_engine,model_fit)
+S3method(extract_spec_parsnip,model_fit)
 S3method(fit,model_spec)
 S3method(fit_xy,gen_additive_mod)
 S3method(fit_xy,model_spec)
@@ -138,6 +140,8 @@ export(control_parsnip)
 export(convert_stan_interval)
 export(decision_tree)
 export(eval_args)
+export(extract_fit_engine)
+export(extract_spec_parsnip)
 export(find_engine_files)
 export(fit)
 export(fit.model_spec)
@@ -259,6 +263,8 @@ importFrom(generics,required_pkgs)
 importFrom(generics,tidy)
 importFrom(generics,varying_args)
 importFrom(glue,glue_collapse)
+importFrom(hardhat,extract_fit_engine)
+importFrom(hardhat,extract_spec_parsnip)
 importFrom(magrittr,"%>%")
 importFrom(purrr,as_vector)
 importFrom(purrr,imap)

R/extract.R

@@ -0,0 +1,67 @@
+#' Extract elements of a parsnip model object
+#'
+#' @description
+#' These functions extract various elements from a parsnip object. If they do
+#' not exist yet, an error is thrown.
+#'
+#' - `extract_spec_parsnip()` returns the parsnip model specification.
+#'
+#' - `extract_fit_engine()` returns the engine specific fit embedded within
+#'   a parsnip model fit. For example, when using [parsnip::linear_reg()]
+#'   with the `"lm"` engine, this returns the underlying `lm` object.
+#'
+#' @param x A parsnip `model_fit` object.
+#' @param ... Not currently used.
+#' @details
+#' Extracting the underlying engine fit can be helpful for describing the
+#'  model (via `print()`, `summary()`, `plot()`, etc.) or for variable
+#'  importance/explainers.
+#'
+#' However, users should not invoke the `predict()` method on an extracted
+#'  model. There may be preprocessing operations that `parsnip` has executed on
+#'  the data prior to giving it to the model. Bypassing these can lead to errors
+#'  or silently generating incorrect predictions.
+#'
+#' **Good**:
+#' ```r
+#'    parsnip_fit %>% predict(new_data)
+#' ```
+#'
+#' **Bad**:
+#' ```r
+#'    parsnip_fit %>% extract_fit_engine() %>% predict(new_data)
+#' ```
+#' @return
+#' The extracted value from the parsnip object, `x`, as described in the description
+#' section.
+#'
+#' @name extract-parsnip
+#' @examples
+#' lm_spec <- linear_reg() %>% set_engine("lm")
+#' lm_fit <- fit(lm_spec, mpg ~ ., data = mtcars)
+#'
+#' lm_spec
+#' extract_spec_parsnip(lm_fit)
+#'
+#' extract_fit_engine(lm_fit)
+#' lm(mpg ~ ., data = mtcars)
+NULL
+
+#' @export
+#' @rdname extract-parsnip
+extract_spec_parsnip.model_fit <- function(x, ...) {
+  if (any(names(x) == "spec")) {
+    return(x$spec)
+  }
+  rlang::abort("Internal error: The model fit does not have a model spec.")
+}
+
+
+#' @export
+#' @rdname extract-parsnip
+extract_fit_engine.model_fit <- function(x, ...) {
+  if (any(names(x) == "fit")) {
+    return(x$fit)
+  }
+  rlang::abort("Internal error: The model fit does not have an engine fit.")
+}

R/reexports.R

@@ -26,3 +26,11 @@ generics::augment
 #' @importFrom generics required_pkgs
 #' @export
 generics::required_pkgs
+
+#' @importFrom hardhat extract_spec_parsnip
+#' @export
+hardhat::extract_spec_parsnip
+
+#' @importFrom hardhat extract_fit_engine
+#' @export
+hardhat::extract_fit_engine

man/extract-parsnip.Rd

@@ -0,0 +1,19 @@
+
+context("model extraction")
+
+# ------------------------------------------------------------------------------
+
+test_that('extract', {
+  x <- linear_reg() %>% set_engine("lm") %>% fit(mpg ~ ., data = mtcars)
+  x_no_spec <- x
+  x_no_spec$spec <- NULL
+  x_no_fit <- x
+  x_no_fit$fit <- NULL
+
+  expect_true(inherits(extract_spec_parsnip(x), "model_spec"))
+  expect_true(inherits(extract_fit_engine(x), "lm"))
+
+  expect_error(extract_spec_parsnip(x_no_spec), "Internal error")
+  expect_error(extract_fit_engine(x_no_fit), "Internal error")
+})
+