Merge pull request #152 from koalaverse/devel

update vignette examples

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: vip
 Type: Package
 Title: Variable Importance Plots
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: c(
   person(c("Brandon", "M."), family = "Greenwell", 
          email = "greenwell.brandon@gmail.com",

NEWS.md

@@ -1,14 +1,23 @@
+# vip 0.4.1
+
+## Changed
+
+* Minor tweaks to URLs and tests to pass CRAN checks.
+
+
 # vip 0.4.0
 
 ## Changed
 
 * This NEWS file now follows the [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-* The training data has to be explicitly passed in more cases.
+* Removed lifecycle badge from `README` file.
+
+* The training data has to be explicitly passed in more cases when using `vi_permute()`, `vi_shap()`, and `vi_firm()`.
 
 * Raised R version dependency to >= 4.1.0 (the introduction of the native piper operator `|>`).
 
-* The `vi_permute` function now uses [yardstick](https://cran.r-project.org/package=yardstick); consequently, metric functions now conform to [yardstick](https://cran.r-project.org/package=yardstick) metric argument names.
+* The `vi_permute` function now relies on the [yardstick](https://cran.r-project.org/package=yardstick) package for compouting performance measures (e.g., RMSE and log loss); consequently, user-supplied metric functions now nned to conform to [yardstick](https://cran.r-project.org/package=yardstick) metric argument names.
 
 * The `var_fun` argument in `vi_firm()` has been deprecated; use the new `var_continuous` and `var_categorical` instead.
 

R/vi_shap.R

@@ -30,7 +30,7 @@
 #'
 #' @details This approach to computing VI scores is based on the mean absolute
 #' value of the SHAP values for each feature; see, for example,
-#' <https://github.com/slundberg/shap> and the references therein.
+#' <https://github.com/shap/shap> and the references therein.
 #'
 #' Strumbelj, E., and Kononenko, I. Explaining prediction models and individual
 #' predictions with feature contributions. Knowledge and information systems

R/vip.R

@@ -27,8 +27,9 @@
 #'  only for the permutation-based importance method with \code{nsim > 1} and
 #'  `keep = TRUE`; see [vi_permute][vip::vi_permute] for details.
 #'
-#' @param mapping Set of aesthetic mappings created by [aes][ggplot2::aes]
-#' or [aes_][ggplot2::aes_]. See example usage below.
+#' @param mapping Set of aesthetic mappings created by
+#' [aes][ggplot2::aes]-related functions and/or tidy eval helpers. See example
+#' usage below.
 #'
 #' @param aesthetics List specifying additional arguments passed on to
 #' [layer][ggplot2::layer]. These are often aesthetics, used to set an aesthetic
@@ -79,9 +80,10 @@
 #' vip(vis, geom = "point", horiz = FALSE, aesthetics = list(size = 3))
 #'
 #' # Plot unaggregated permutation scores (boxplot colored by feature)
-#' library(ggplot2)  # for `aes_string()` function
+#' library(ggplot2)  # for `aes()`-related functions and tidy eval helpers
 #' vip(vis, geom = "boxplot", all_permutations = TRUE, jitter = TRUE,
-#'     mapping = aes_string(fill = "Variable"),
+#'     #mapping = aes_string(fill = "Variable"),   # for ggplot2 (< 3.0.0)
+#'     mapping = aes(fill = .data[["Variable"]]),  # for ggplot2 (>= 3.0.0)
 #'     aesthetics = list(color = "grey35", size = 0.8))
 #'
 #' #
@@ -161,7 +163,7 @@ vip.default <- function(
   }
   imp <- sort_importance_scores(imp, decreasing = TRUE)  # make sure these are sorted first!
   imp <- imp[seq_len(num_features), ]  # only retain num_features variable importance scores
-  x.string <- "reorder(Variable, Importance)"
+  # x.string <- "reorder(Variable, Importance)"
 
   # Clean up raw scores for permutation-based VI scores
   if (!is.null(attr(imp, which = "raw_scores"))) {
@@ -178,7 +180,11 @@ vip.default <- function(
   }
 
   # Initialize plot
-  p <- ggplot2::ggplot(imp, ggplot2::aes_string(x = x.string, y = "Importance"))
+  # p <- ggplot2::ggplot(imp, ggplot2::aes_string(x = x.string, y = "Importance"))
+  p <- ggplot2::ggplot(imp, ggplot2::aes(
+    x = reorder(Variable, Importance),
+    y = Importance
+  ))
 
   # Construct a barplot
   if (geom == "col") {

README.Rmd

@@ -17,7 +17,6 @@ knitr::opts_chunk$set(
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/vip)](https://cran.r-project.org/package=vip)
 [![R-CMD-check](https://github.com/koalaverse/vip/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/koalaverse/vip/actions/workflows/R-CMD-check.yaml)
 [![Coverage Status](https://codecov.io/gh/koalaverse/vip/graph/badge.svg)](https://app.codecov.io/github/koalaverse/vip?branch=master)
-[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Downloads](https://cranlogs.r-pkg.org/badges/vip)](https://cran.r-project.org/package=vip/)
 [![The R Journal](https://img.shields.io/badge/The%20R%20Journal-10.32614%2FRJ--2020--013-brightgreen)](https://doi.org/10.32614/RJ-2020-013)
 <!-- badges: end -->

README.md

@@ -7,8 +7,6 @@
 [![R-CMD-check](https://github.com/koalaverse/vip/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/koalaverse/vip/actions/workflows/R-CMD-check.yaml)
 [![Coverage
 Status](https://codecov.io/gh/koalaverse/vip/graph/badge.svg)](https://app.codecov.io/github/koalaverse/vip?branch=master)
-[![Lifecycle:
-stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Downloads](https://cranlogs.r-pkg.org/badges/vip)](https://cran.r-project.org/package=vip/)
 [![The R
 Journal](https://img.shields.io/badge/The%20R%20Journal-10.32614%2FRJ--2020--013-brightgreen)](https://doi.org/10.32614/RJ-2020-013)

inst/tinytest/test_pkg_partykit.R

@@ -36,18 +36,6 @@ expect_identical(
   target = unname(vis4)
 )
 
-# Expectations for `get_training_data()`
-expect_equal(
-  current = vip:::get_training_data.default(fit1),
-  target = friedman1,
-  check.attributes = FALSE
-)
-expect_equal(
-  current = vip:::get_training_data.default(fit2),
-  target = friedman1,
-  check.attributes = FALSE
-)
-
 # Expectations for `get_feature_names()`
 expect_identical(
   current = vip:::get_feature_names.constparty(fit1),

inst/tinytest/test_pkg_pls.R

@@ -27,12 +27,6 @@ expect_identical(
   target = caret::varImp(fit)$Overall
 )
 
-# Expectations for `get_training_data()`
-expect_identical(
-  current = vip:::get_training_data.default(fit),
-  target = friedman1
-)
-
 # Expectations for `get_feature_names()`
 expect_identical(
   current = vip:::get_feature_names.mvr(fit),