Merge pull request #132 from ModelOriented/cran-1

CRAN Release

Author: mayer79

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.9.2
-Date: 2023-10-14 16:44:29 UTC
-SHA: 1d239694c309c6b48168b2ca19b8fd5c8d6f1d2d
+Version: 0.9.3
+Date: 2024-01-12 11:21:47 UTC
+SHA: d2f329e540177df778e787a27dec50d34cb5ed5c

R/shapviz.R

@@ -111,7 +111,6 @@ shapviz.matrix = function(object, X, baseline = 0, collapse = NULL,
 #'   Creates a "shapviz" object from an XGBoost model.
 #' @export
 #' @examples
-#' \dontrun{
 #' # XGBoost models
 #' X_pred <- data.matrix(iris[, -1])
 #' dtrain <- xgboost::xgb.DMatrix(X_pred, label = iris[, 1], nthread = 1)
@@ -184,7 +183,6 @@ shapviz.matrix = function(object, X, baseline = 0, collapse = NULL,
 #'   mx
 #'   all.equal(mx[[3]], x)
 #' }
-#' }
 shapviz.xgb.Booster = function(object, X_pred, X = X_pred, which_class = NULL,
                                collapse = NULL, interactions = FALSE, ...) {
   stopifnot(

R/sv_dependence.R

@@ -39,7 +39,6 @@
 #' @param ... Arguments passed to [ggplot2::geom_jitter()].
 #' @returns An object of class "ggplot" (or "patchwork") representing a dependence plot.
 #' @examples
-#' \dontrun{
 #' dtrain <- xgboost::xgb.DMatrix(
 #'   data.matrix(iris[, -1]), label = iris[, 1], nthread = 1
 #' )
@@ -57,7 +56,6 @@
 #' sv_dependence(
 #'   x2, c("Petal.Length", "Species"), color_var = NULL, interactions = TRUE
 #' )
-#' }
 #' @export
 #' @seealso [potential_interactions()]
 sv_dependence <- function(object, ...) {

R/sv_dependence2D.R

@@ -29,7 +29,6 @@
 #' @param ... Arguments passed to [ggplot2::geom_jitter()].
 #' @returns An object of class "ggplot" (or "patchwork") representing a dependence plot.
 #' @examples
-#' \dontrun{
 #' dtrain <- xgboost::xgb.DMatrix(
 #'   data.matrix(iris[, -1]), label = iris[, 1], nthread = 1
 #' )
@@ -48,7 +47,6 @@
 #' # mshapviz object
 #' mx <- split(sv, f = iris$Species)
 #' sv_dependence2D(mx, x = "Petal.Length", y = "Sepal.Width")
-#' }
 #' @export
 #' @seealso [sv_dependence()]
 sv_dependence2D <- function(object, ...) {

R/sv_force.R

@@ -11,7 +11,6 @@
 #'   (via [ggrepel::geom_text_repel()]).
 #' @returns An object of class "ggplot" (or "patchwork") representing a force plot.
 #' @examples
-#' \dontrun{
 #' dtrain <- xgboost::xgb.DMatrix(
 #'   data.matrix(iris[, -1]), label = iris[, 1], nthread = 1
 #' )
@@ -22,7 +21,6 @@
 #'
 #' # Aggregate over all observations with Petal.Length == 1.4
 #' sv_force(x, row_id = x$X$Petal.Length == 1.4)
-#' }
 #' @export
 #' @seealso [sv_waterfall()]
 sv_force <- function(object, ...) {

R/sv_importance.R

@@ -46,16 +46,13 @@
 #'   `kind = "no"` - a named numeric vector of sorted SHAP feature importances
 #'   (or a matrix in case of an object of class "mshapviz").
 #' @examples
-#' \dontrun{
 #' X_train <- data.matrix(iris[, -1])
 #' dtrain <- xgboost::xgb.DMatrix(X_train, label = iris[, 1], nthread = 1)
 #' fit <- xgboost::xgb.train(data = dtrain, nrounds = 10, nthread = 1)
 #' x <- shapviz(fit, X_pred = X_train)
 #' sv_importance(x)
 #' sv_importance(x, kind = "no")
 #' sv_importance(x, kind = "beeswarm", show_numbers = TRUE)
-#' }
-#'
 #' @seealso \code{\link{sv_interaction}}
 #' @export
 sv_importance <- function(object, ...) {

R/sv_interaction.R

@@ -18,15 +18,13 @@
 #'   numeric matrix of average absolute SHAP interactions sorted by the average
 #'   absolute SHAP values (or a list of such matrices in case of "mshapviz" object).
 #' @examples
-#' \dontrun{
 #' dtrain <- xgboost::xgb.DMatrix(
 #'   data.matrix(iris[, -1]), label = iris[, 1], nthread = 1
 #' )
 #' fit <- xgboost::xgb.train(data = dtrain, nrounds = 10, nthread = 1)
 #' x <- shapviz(fit, X_pred = dtrain, X = iris, interactions = TRUE)
 #' sv_interaction(x, kind = "no")
 #' sv_interaction(x, max_display = 2, size = 3)
-#' }
 #' @seealso [sv_importance()]
 #' @export
 sv_interaction <- function(object, ...) {

R/sv_waterfall.R

@@ -35,7 +35,6 @@
 #'   will altogether suppress adding text to the bars.
 #' @returns An object of class "ggplot" (or "patchwork") representing a waterfall plot.
 #' @examples
-#' \dontrun{
 #' dtrain <- xgboost::xgb.DMatrix(
 #'   data.matrix(iris[, -1]), label = iris[, 1], nthread = 1
 #' )
@@ -51,7 +50,6 @@
 #'
 #' # Aggregate over all observations with Petal.Length == 1.4
 #' sv_waterfall(x, row_id = x$X$Petal.Length == 1.4)
-#' }
 #' @export
 #' @seealso [sv_force()]
 sv_waterfall <- function(object, ...) {

cran-comments.md

@@ -1,61 +1,29 @@
-# shapviz 0.9.2
+# shapviz 0.9.3
 
-## Resubmission 7
+Hi CRAN team
 
-No effect of setDTthreads(2). Commenting out now all tests with xgboost.
-
-## Resubmission 6
-
-Test timing not fixed, still. Now testing to import {data.table} and setDTthreads(2) pre checks.
-
-## Resubmission 5
-
-Now trying 
-
-Sys.setenv(DT_NUM_THREADS = 1)
-Sys.setenv("TESTTHAT_CPUS" = 1)
-options(Ncpus = 1)
-
-
-## Resubmission 4
-
-Trying to set Sys.setenv(DT_NUM_THREADS = 2) in the unit tests to fix the crazy Debian behaviour.
-
-## Resubmission 3
-
-Moving one single nthread = 1 into param = list(). Setting nrounds = 1 in all tests. If this does not help, I will need to delete most unit tests.
-
-## Resubmission 2
-
-Setting nthread = 1 in unit tests and vignettes. Hope this fixes the problems.
-
-## Resubmission 1
-
-Fixing problems with curly braces in .rd files.
-
-### Original message
-
-Hello CRAN team
-
-{shapviz} already got 2 reverse dependencies, which look okay.
-
-The update has mainly added more flexibility of the importance plots for multi-output models.
+This is a relatively small update, but offers much more flexibility in the interaction heuristic.
 
 ## Checks look good
 
 ### check(manual = TRUE, cran = TRUE)
 
-- checking HTML version of manual ... NOTE
-  Skipping checking HTML validation: no command 'tidy' found
+Ok
 
 ### RHub (usual notes)
 
 * checking package dependencies ... NOTE
 Packages which this enhances but not available for checking:
   'fastshap', 'h2o', 'lightgbm'
 * checking HTML version of manual ... NOTE
-Skipping checking HTML validation: no command 'tidy' found
 Skipping checking math rendering: package 'V8' unavailable
+* checking for non-standard things in the check directory ... NOTE
+Found the following files/directories:
+  ''NULL''
+* checking for detritus in the temp directory ... NOTE
+Found the following files/directories:
+  'lastMiKTeXException'
+  
 
 ### Winbuilder()