Changes for #71 (#72)

Co-authored-by: ‘topepo’ <‘[email protected]’>

Author: topepo

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

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)

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()`. 

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

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")

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,]

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)

inst/WORDLIST

@@ -8,6 +8,7 @@ Lifecycle
 Modelling
 ORCID
 PBC
+TeachingDemos
 al
 doi
 et

man/bagger.Rd

@@ -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"))

man/predict.bagger.Rd

@@ -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))
 

tests/testthat/test-interfaces.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."