Merge pull request #142 from koalaverse/devel

tweak headers

.Rbuildignore

@@ -5,8 +5,10 @@
 ^codecov\.yml$
 ^data-raw$
 ^docs$
+^lightgbm\.model$
 ^README\.Rmd$
 ^README_cache
+^revdep
 ^rjournal$
 ^slowtests
 ^tools$

DESCRIPTION

@@ -10,11 +10,7 @@ Authors@R: c(
   person("Brad", "Boehmke",
          email = "bradleyboehmke@gmail.com",
          role = c("aut"),
-         comment = c(ORCID = "0000-0002-3611-8516")),
-  person("Bernie", "Gray",
-         email = "bfgray3@gmail.com",
-         role = c("aut"),
-         comment = c(ORCID = "0000-0001-9190-6032"))
+         comment = c(ORCID = "0000-0002-3611-8516"))
   )
 Description: A general framework for constructing variable importance plots from 
   various types of machine learning models in R. Aside from some standard model-
@@ -32,57 +28,54 @@ URL: https://github.com/koalaverse/vip/,
 BugReports: https://github.com/koalaverse/vip/issues
 Encoding: UTF-8
 VignetteBuilder: knitr
-Depends: R (>= 2.10)
+Depends: R (>= 4.1.0)
 Imports: 
     foreach,
     ggplot2 (>= 0.9.0),
-    magrittr,
     stats,
     tibble,
-    yardstick,
-    utils
+    utils,
+    yardstick
 Suggests: 
     bookdown,
     DT,
-    C50,
-    caret,
-    Ckmeans.1d.dp,
     covr,
-    Cubist,
     doParallel,
     dplyr,
+    fastshap (>= 0.1.0),
+    knitr,
+    lattice,
+    mlbench,
+    modeldata,
+    NeuralNetTools,
+    pdp,
+    rmarkdown,
+    tinytest (>= 1.4.1),
+    varImp
+Enhances: 
+    C50,
+    caret,
+    Cubist,
     earth,
-    fastshap,
     gbm,
     glmnet,
     h2o,
-    htmlwidgets,
-    keras,
-    knitr,
-    lattice,
+    lightgbm,
     mixOmics,
-    mlbench,
     mlr,
     mlr3,
-    modeldata,
     neuralnet,
-    NeuralNetTools,
     nnet,
     parsnip (>= 0.1.7),
     party,
     partykit,
-    pdp,
     pls,
     randomForest,
     ranger,
-    rmarkdown,
     rpart,
     RSNNS,
-    sparkline,
     sparklyr (>= 0.8.0),
     tidymodels,
-    tinytest (>= 1.4.1),
-    varImp,
     workflows (>= 0.2.3),
     xgboost
 LazyData: true

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(add_sparklines,vi)
 S3method(vi,default)
 S3method(vi_firm,default)
 S3method(vi_model,C5.0)
@@ -18,6 +17,7 @@ S3method(vi_model,default)
 S3method(vi_model,earth)
 S3method(vi_model,gbm)
 S3method(vi_model,glmnet)
+S3method(vi_model,lgb.Booster)
 S3method(vi_model,lm)
 S3method(vi_model,mixo_pls)
 S3method(vi_model,mixo_spls)
@@ -47,9 +47,6 @@ S3method(vip,WrappedModel)
 S3method(vip,default)
 S3method(vip,model_fit)
 S3method(vip,workflow)
-export("%>%")
-export("%T>%")
-export(add_sparklines)
 export(gen_friedman)
 export(list_metrics)
 export(vi)
@@ -61,5 +58,3 @@ export(vip)
 importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
-importFrom(magrittr,"%>%")
-importFrom(magrittr,"%T>%")

NEWS.md

@@ -1,24 +1,18 @@
-# vip 0.3.3
+# vip 0.4.0
 
-## Breaking changes
-
-* The `var_fun` argument in `vi_firm()` has been deprecated; use the new `var_continuous` and `var_categorical` instead.
-
-* The explicit `ice` argument in `vi_firm()` has been removed; it was not really needed since it can be passed via the `...` argument. 
-
-## Enhancements
+## Changed
 
-* The permutation importance method (i.e., function `vi_permute()`) now integrates with and uses [yardstick](https://cran.r-project.org/package=yardstick) performance metrics.
+* This NEWS file now follows the [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-* `list_metrics()` gained an additional `smaller_is_better` column indicating whether or not the corresponding metric should be minimized (`smaller_is_better = TRUE`) or maximized (`smaller_is_better = FALSE`); thanks to @topedo. Additionally, all the column names are now in lower case. 
+* Raised R version dependency to >= 4.1.0 (the introduction of the native piper operator `|>`).
 
-* Added support for partial least squares via the [mixOmics](https://bioconductor.org/packages/mixOmics/) package [(PR #129)](https://github.com/koalaverse/vip/pull/129); thanks to @topedo.
+* 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.
 
-* Added support for the [workflows](https://cran.r-project.org/package=workflows) and [parsnip](https://cran.r-project.org/package=parsnip) packages from the [tidymodels](https://www.tidymodels.org/) ecosystem [(PR #128)](https://github.com/koalaverse/vip/pull/128); thanks to @topedo.
+* The `var_fun` argument in `vi_firm()` has been deprecated; use the new `var_continuous` and `var_categorical` instead.
 
-* New [pkgdown](https://cran.r-project.org/package=pkgdown) site and vignette based on our original R Journal article.
+* The explicit `ice` argument in `vi_firm()` has been removed; it was not really needed since it can be passed via the `...` argument. 
 
-## Miscellaneous
+* Removed [magrittr](https://cran.r-project.org/package=magrittr) from imports; it's easy enough to just laod the package if you need it or use R's newer internal pipe operator.
 
 * Tweaked examples.
 
@@ -34,7 +28,27 @@
 
 * Switched to using markdown syntax in `roxygen2` comments.
 
-## Bug fixes
+## Added
+
+* `vi_model()` now supports [lightgbm](https://cran.r-project.org/package=lightgbm) models. Thanks to @nipnipj for the suggestion [(#146)](https://github.com/koalaverse/vip/issues/146).
+
+* The permutation importance method (i.e., function `vi_permute()`) now integrates with and uses [yardstick](https://cran.r-project.org/package=yardstick) performance metrics.
+
+* `list_metrics()` gained an additional `smaller_is_better` column indicating whether or not the corresponding metric should be minimized (`smaller_is_better = TRUE`) or maximized (`smaller_is_better = FALSE`); thanks to @topedo. Additionally, all the column names are now in lower case. 
+
+* Added support for partial least squares via the [mixOmics](https://bioconductor.org/packages/mixOmics/) package [(PR #129)](https://github.com/koalaverse/vip/pull/129); thanks to @topedo.
+
+* Added support for the [workflows](https://cran.r-project.org/package=workflows) and [parsnip](https://cran.r-project.org/package=parsnip) packages from the [tidymodels](https://www.tidymodels.org/) ecosystem [(PR #128)](https://github.com/koalaverse/vip/pull/128); thanks to @topedo.
+
+* New [pkgdown](https://cran.r-project.org/package=pkgdown) site and vignette based on our original R Journal article.
+
+## Removed
+
+* Function `add_sparklines()` seems out of scope and has been removed.
+* Function `vint()` also seems out of scope and is too slow to implement for most practical problems; for now, the function will likely live on in the [moreparty](https://cran.r-project.org/package=moreparty) package.
+
+
+## Fixed
 
 * Fix model-based VI support for [mlr](https://cran.r-project.org/package=mlr), [mlr3](https://cran.r-project.org/package=mlr3), [parsnip](https://cran.r-project.org/package=parsnip), and [workflows](https://cran.r-project.org/package=workflows) model fits.