Merge pull request #132 from ModelOriented/cran-1

CRAN Release
ModelOriented · Jan 12, 2024 · 8e4c726 · 8e4c726
2 parents 1e39218 + b97d7a9
commit 8e4c726
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diff --git a/CRAN-SUBMISSION b/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
diff --git a/R/shapviz.R b/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(

diff --git a/R/sv_dependence.R b/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, ...) {

diff --git a/R/sv_dependence2D.R b/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, ...) {

diff --git a/R/sv_force.R b/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, ...) {

diff --git a/R/sv_importance.R b/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, ...) {

diff --git a/R/sv_interaction.R b/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, ...) {

diff --git a/R/sv_waterfall.R b/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, ...) {

diff --git a/cran-comments.md b/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()
 

diff --git a/man/shapviz.Rd b/man/shapviz.Rd
diff --git a/man/sv_dependence.Rd b/man/sv_dependence.Rd
diff --git a/man/sv_dependence2D.Rd b/man/sv_dependence2D.Rd
diff --git a/man/sv_force.Rd b/man/sv_force.Rd
diff --git a/man/sv_importance.Rd b/man/sv_importance.Rd
diff --git a/man/sv_interaction.Rd b/man/sv_interaction.Rd
diff --git a/man/sv_waterfall.Rd b/man/sv_waterfall.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -10,57 +10,57 @@
 |collate  |German_Switzerland.utf8                                  |
 |ctype    |German_Switzerland.utf8                                  |
 |tz       |Europe/Zurich                                            |
-|date     |2023-10-13                                               |
+|date     |2024-01-12                                               |
 |rstudio  |2023.06.1+524 Mountain Hydrangea (desktop)               |
 |pandoc   |3.1.6 @ C:\Users\Michael\AppData\Local\Pandoc\pandoc.exe |
 
 # Dependencies
 
 |package      |old     |new     |Δ  |
 |:------------|:-------|:-------|:--|
-|shapviz      |0.9.1   |0.9.2   |*  |
-|cli          |3.6.1   |3.6.1   |   |
+|shapviz      |0.9.2   |0.9.3   |*  |
+|cli          |3.6.2   |3.6.2   |   |
 |colorspace   |2.1-0   |2.1-0   |   |
 |commonmark   |1.9.0   |1.9.0   |   |
-|curl         |5.1.0   |5.1.0   |   |
-|data.table   |1.14.8  |1.14.8  |   |
-|fansi        |1.0.5   |1.0.5   |   |
+|curl         |5.2.0   |5.2.0   |   |
+|data.table   |1.14.10 |1.14.10 |   |
+|fansi        |1.0.6   |1.0.6   |   |
 |farver       |2.1.1   |2.1.1   |   |
 |ggfittext    |0.10.1  |0.10.1  |   |
 |gggenes      |0.5.1   |0.5.1   |   |
 |ggplot2      |3.4.4   |3.4.4   |   |
-|ggrepel      |0.9.3   |0.9.3   |   |
-|glue         |1.6.2   |1.6.2   |   |
+|ggrepel      |0.9.5   |0.9.5   |   |
+|glue         |1.7.0   |1.7.0   |   |
 |gridtext     |0.1.5   |0.1.5   |   |
 |gtable       |0.3.4   |0.3.4   |   |
 |isoband      |0.2.7   |0.2.7   |   |
 |jpeg         |0.1-10  |0.1-10  |   |
-|jsonlite     |1.8.7   |1.8.7   |   |
+|jsonlite     |1.8.8   |1.8.8   |   |
 |labeling     |0.4.3   |0.4.3   |   |
-|lifecycle    |1.0.3   |1.0.3   |   |
+|lifecycle    |1.0.4   |1.0.4   |   |
 |magrittr     |2.0.3   |2.0.3   |   |
-|markdown     |1.10    |1.10    |   |
+|markdown     |1.12    |1.12    |   |
 |munsell      |0.5.0   |0.5.0   |   |
-|patchwork    |1.1.3   |1.1.3   |   |
+|patchwork    |1.2.0   |1.2.0   |   |
 |pillar       |1.9.0   |1.9.0   |   |
 |pkgconfig    |2.0.3   |2.0.3   |   |
 |png          |0.1-8   |0.1-8   |   |
 |R6           |2.5.1   |2.5.1   |   |
 |RColorBrewer |1.1-3   |1.1-3   |   |
-|Rcpp         |1.0.11  |1.0.11  |   |
-|rlang        |1.1.1   |1.1.1   |   |
-|scales       |1.2.1   |1.2.1   |   |
+|Rcpp         |1.0.12  |1.0.12  |   |
+|rlang        |1.1.3   |1.1.3   |   |
+|scales       |1.3.0   |1.3.0   |   |
 |shades       |1.4.0   |1.4.0   |   |
-|stringi      |1.7.12  |1.7.12  |   |
-|stringr      |1.5.0   |1.5.0   |   |
+|stringi      |1.8.3   |1.8.3   |   |
+|stringr      |1.5.1   |1.5.1   |   |
 |tibble       |3.2.1   |3.2.1   |   |
-|utf8         |1.2.3   |1.2.3   |   |
-|vctrs        |0.6.3   |0.6.3   |   |
+|utf8         |1.2.4   |1.2.4   |   |
+|vctrs        |0.6.5   |0.6.5   |   |
 |viridisLite  |0.4.2   |0.4.2   |   |
-|withr        |2.5.1   |2.5.1   |   |
-|xfun         |0.40    |0.40    |   |
-|xgboost      |1.7.5.1 |1.7.5.1 |   |
-|xml2         |1.3.5   |1.3.5   |   |
+|withr        |2.5.2   |2.5.2   |   |
+|xfun         |0.41    |0.41    |   |
+|xgboost      |1.7.6.1 |1.7.6.1 |   |
+|xml2         |1.3.6   |1.3.6   |   |
 
 # Revdeps
 
diff --git a/vignettes/basic_use.Rmd b/vignettes/basic_use.Rmd
@@ -68,8 +68,10 @@ set.seed(1)
 
 # Build model
 x <- c("carat", "cut", "color", "clarity")
-dtrain <- xgb.DMatrix(data.matrix(diamonds[x]), label = diamonds$price)
-fit <- xgb.train(params = list(learning_rate = 0.1), data = dtrain, nrounds = 65)
+dtrain <- xgb.DMatrix(data.matrix(diamonds[x]), label = diamonds$price, nthread = 1)
+fit <- xgb.train(
+  params = list(learning_rate = 0.1, nthread = 1), data = dtrain, nrounds = 65
+)
 
 # SHAP analysis: X can even contain factors
 dia_2000 <- diamonds[sample(nrow(diamonds), 2000), x]