Merge pull request #52 from mayer79/cran_050

prepare CRAN submission

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.4.1
-Date: 2023-01-11 17:58:30 UTC
-SHA: 68d9a2c4c60680dcd8df2ed5c5bfd01c395a6059
+Version: 0.5.0
+Date: 2023-02-03 11:14:39 UTC
+SHA: 097dce7331a12179ae5b45a869627f3d49efffc7

R/shapviz.R

@@ -100,7 +100,7 @@ shapviz.matrix = function(object, X, baseline = 0, collapse = NULL,
 #' @examples
 #' X_pred <- data.matrix(iris[, -1])
 #' dtrain <- xgboost::xgb.DMatrix(X_pred, label = iris[, 1])
-#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50)
+#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50, nthread = 1)
 #'
 #' # Will use numeric matrix "X_pred" as feature matrix
 #' x <- shapviz(fit, X_pred = X_pred)

R/sv_dependence.R

@@ -39,7 +39,7 @@
 #' @seealso \code{\link{potential_interactions}}
 #' @examples
 #' dtrain <- xgboost::xgb.DMatrix(data.matrix(iris[, -1]), label = iris[, 1])
-#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50)
+#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50, nthread = 1)
 #' x <- shapviz(fit, X_pred = dtrain, X = iris)
 #' sv_dependence(x, "Petal.Length")
 #' sv_dependence(x, "Petal.Length", color_var = "Species")

R/sv_force.R

@@ -31,7 +31,7 @@
 #' @seealso \code{\link{sv_waterfall}}
 #' @examples
 #' dtrain <- xgboost::xgb.DMatrix(data.matrix(iris[, -1]), label = iris[, 1])
-#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50)
+#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50, nthread = 1)
 #' x <- shapviz(fit, X_pred = dtrain, X = iris[, -1])
 #' sv_force(x)
 #' sv_force(x, row_id = 65, max_display = 3, size = 9, fill_colors = 4:5)

R/sv_importance.R

@@ -47,7 +47,7 @@
 #' @examples
 #' X_train <- data.matrix(iris[, -1])
 #' dtrain <- xgboost::xgb.DMatrix(X_train, label = iris[, 1])
-#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50)
+#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50, nthread = 1)
 #' x <- shapviz(fit, X_pred = X_train)
 #' sv_importance(x)
 #' sv_importance(x, kind = "beeswarm", show_numbers = TRUE)

R/sv_interaction.R

@@ -31,7 +31,7 @@
 #' @export
 #' @examples
 #' dtrain <- xgboost::xgb.DMatrix(data.matrix(iris[, -1]), label = iris[, 1])
-#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50)
+#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50, nthread = 1)
 #' x <- shapviz(fit, X_pred = dtrain, X = iris, interactions = TRUE)
 #' sv_interaction(x)
 #' sv_interaction(x, max_display = 2, size = 3, alpha = 0.1)
@@ -61,7 +61,10 @@ sv_interaction.shapviz <- function(object, kind = c("beeswarm", "no"),
   ord <- names(.get_imp(get_shap_values(object)))
 
   if (kind == "no") {
-    return(apply(abs(S_inter), 2:3, mean)[ord, ord])
+    mat <- apply(abs(S_inter), 2:3, mean)[ord, ord]
+    off_diag <- row(mat) != col(mat)
+    mat[off_diag] <- mat[off_diag] * 2  # compensate symmetry
+    return(mat)
   }
 
   if (ncol(S_inter) > max_display) {

R/sv_waterfall.R

@@ -36,7 +36,7 @@
 #' @seealso \code{\link{sv_force}}
 #' @examples
 #' dtrain <- xgboost::xgb.DMatrix(data.matrix(iris[, -1]), label = iris[, 1])
-#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50)
+#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 50, nthread = 1)
 #' x <- shapviz(fit, X_pred = dtrain, X = iris[, -1])
 #' sv_waterfall(x)
 #' sv_waterfall(x, row_id = 123, max_display = 2, size = 9, fill_colors = 4:5)

cran-comments.md

@@ -1,4 +1,17 @@
-# Submission of shapviz 0.5.0
+# Re-Submission of shapviz 0.5.0
+
+A pre-check failed:
+
+```
+Examples with CPU time > 2.5 times elapsed time
+               user system elapsed ratio
+sv_dependence 1.268  0.032   0.472 2.754
+```
+
+I have now set the parameter `nthread = 1` in fitting the XGBoost models in the
+examples, hoping to solve that issue.
+
+## Original message
 
 Dear CRAN team. "shapviz" now offers plots for SHAP interaction values - a feature that was on the wishlist for quite some time.
 
@@ -11,8 +24,6 @@ Dear CRAN team. "shapviz" now offers plots for SHAP interaction values - a featu
 
 ### check_rhub()
 
-Winbuilder: Status: OK
-
 rhub notes
 
 NOTES:
@@ -25,3 +36,4 @@ Found the following files/directories:
 
 ### check_win_devel()
 
+winbuilder: Status: OK