Changes for #71

tidymodels · Feb 13, 2024 · 2dd7bff · 2dd7bff
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Showing 13 changed files with 20 additions and 28 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,7 +22,6 @@ Imports:
     C50,
     dials,
     dplyr,
-    earth,
     furrr,
     generics,
     hardhat (>= 1.1.0),
@@ -38,6 +37,7 @@ Imports:
 Suggests: 
     AmesHousing,
     covr,
+    earth,    
     modeldata,
     nnet,
     recipes,
@@ -50,4 +50,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -23,8 +23,6 @@ importFrom(C50,C5.0Control)
 importFrom(C50,C5imp)
 importFrom(C50,as.party.C5.0)
 importFrom(dials,new_quant_param)
-importFrom(earth,earth)
-importFrom(earth,evimp)
 importFrom(furrr,future_map)
 importFrom(furrr,future_map2)
 importFrom(generics,var_imp)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,7 @@
 # baguette (development version)
 
+* Move the earth package to Suggests due to CRAN note about the TeachingDemos (#71).
+
 # baguette 1.0.1
 
 * Added a `"nnet"` method for `bagger()`. 

diff --git a/R/aaa.R b/R/aaa.R
@@ -7,7 +7,6 @@
 #' @importFrom parsnip new_model_spec null_value update_main_parameters
 #' @importFrom parsnip check_final_param model_printer show_call
 #' @importFrom utils globalVariables
-#' @importFrom earth earth evimp
 #' @importFrom rsample analysis bootstraps assessment
 #' @importFrom purrr map map2 map_df map_dfr map_lgl
 #' @importFrom tibble tibble as_tibble is_tibble

diff --git a/R/bagger.R b/R/bagger.R
@@ -67,11 +67,6 @@
 #'
 #' # `times` is low to make the examples run faster
 #'
-#' set.seed(7687)
-#' mars_bag <- bagger(x = biomass_tr[, -6], y = biomass_tr$HHV,
-#'                    base_model = "MARS", times = 5, control = ctrl)
-#' mars_bag
-#' var_imp(mars_bag)
 #'
 #' set.seed(7687)
 #' cart_bag <- bagger(x = biomass_tr[, -6], y = biomass_tr$HHV,
@@ -92,10 +87,6 @@
 #'
 #' cart_pca_bag
 #'
-#' # Using formulas
-#' mars_bag <- bagger(HHV ~ ., data = biomass_tr, base_model = "MARS", times = 5,
-#'                    control = ctrl)
-#' mars_bag
 #' @export
 bagger <- function(x, ...) {
   UseMethod("bagger")

diff --git a/R/mars.R b/R/mars.R
@@ -100,7 +100,10 @@ mars_fit  <- function(split, spec, control = control_bag()) {
 }
 
 mars_imp <- function(x) {
-  imps <- earth::evimp(x$fit)
+  # see issue 71
+  rlang::check_installed("earth")
+  cl <- rlang::call2("evimp", .ns = "earth", object = quote(x$fit))
+  imps <- rlang::eval_tidy(cl)
   imps <- imps[, "gcv", drop = FALSE]
   x <- tibble::tibble(predictor = rownames(imps), importance = unname(imps[, "gcv"]))
   x <- x[x$importance > 0,]

diff --git a/R/predict.R b/R/predict.R
@@ -15,8 +15,8 @@
 #' data(airquality)
 #'
 #' set.seed(7687)
-#' mars_bag <- bagger(Ozone ~ ., data = airquality, base_model = "MARS", times = 5)
-#' predict(mars_bag, new_data = airquality[, -1])
+#' cart_bag <- bagger(Ozone ~ ., data = airquality, base_model = "CART", times = 5)
+#' predict(cart_bag, new_data = airquality[, -1])
 #' @export
 predict.bagger <- function(object, new_data, type = NULL, ...) {
   type <- check_type(object, type)

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -8,6 +8,7 @@ Lifecycle
 Modelling
 ORCID
 PBC
+TeachingDemos
 al
 doi
 et

diff --git a/man/bagger.Rd b/man/bagger.Rd
diff --git a/man/predict.bagger.Rd b/man/predict.bagger.Rd
diff --git a/tests/testthat/test-interfaces.R b/tests/testthat/test-interfaces.R
@@ -28,6 +28,7 @@ test_that('recipe execution', {
 # ------------------------------------------------------------------------------
 
 test_that('var_imp', {
+  skip_if_not_installed("earth")
   mod <- bagger(mpg ~ ., data = mtcars, base_model = "MARS", times = 2)
   expect_true(tibble::is_tibble(var_imp(mod)))
   expect_equal(names(var_imp(mod)), c("term", "value", "std.error", "used"))

diff --git a/tests/testthat/test-mars.R b/tests/testthat/test-mars.R
@@ -1,4 +1,5 @@
 test_that('check mars opt', {
+  skip_if_not_installed("earth")
   set.seed(36323)
   check_pruning <- function(x, ...) {
     rlang::eval_tidy(x$call$pmethod) == "backward"
@@ -57,6 +58,7 @@ test_that('check mars opt', {
 # ------------------------------------------------------------------------------
 
 test_that('check model reduction', {
+  skip_if_not_installed("earth")
   set.seed(36323)
   reduced <-
     bagger(
@@ -88,6 +90,7 @@ test_that('check model reduction', {
 # ------------------------------------------------------------------------------
 
 test_that('check MARS parsnip interface', {
+  skip_if_not_installed("earth")
   set.seed(4779)
   expect_error(
     reg_mod <- bag_mars(num_terms = 5, prod_degree = 2) %>%
@@ -149,6 +152,7 @@ test_that('check MARS parsnip interface', {
 })
 
 test_that('mode specific package dependencies', {
+  skip_if_not_installed("earth")
   expect_identical(
     get_from_env(paste0("bag_mars", "_pkgs")) %>%
       dplyr::filter(engine == "earth", mode == "classification") %>%
@@ -167,6 +171,7 @@ test_that('mode specific package dependencies', {
 
 
 test_that('case weights', {
+  skip_if_not_installed("earth")
   set.seed(1)
   wts <- runif(nrow(mtcars))
 

diff --git a/tests/testthat/test-validation.R b/tests/testthat/test-validation.R
@@ -87,6 +87,7 @@ test_that('validate imps', {
 # ------------------------------------------------------------------------------
 
 test_that('bad inputs', {
+  skip_if_not_installed("earth")
   expect_error(
     bagger(mpg ~ ., data = mtcars, base_model = letters[1:2]),
     "should be a single character value."
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,6 +8,7 @@ Lifecycle @@
     Modelling
     ORCID
     PBC
+    TeachingDemos
     al
     doi
     et
@@ Expand Down @@