Merge pull request #57 from mayer79/CRAN-release

CRAN release

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.3.0
-Date: 2023-10-20 17:47:38 UTC
-SHA: 1c965edd764059432feee32e5be994bcd633bde6
+Version: 2.4.0
+Date: 2023-11-19 09:02:12 UTC
+SHA: b030db7e573dc6f6739fcd13dc3b213e28357655

NEWS.md

@@ -1,9 +1,12 @@
 # missRanger 2.4.0
 
+## Future Output API
+
+- New argument `data_only = TRUE` to control if only the imputed data should be returned (default), or an object of class "missRanger". This object contains the imputed data and infos like OOB prediction errors, fixing [#28](https://github.com/mayer79/missRanger/issues/28). The value `FALSE` will later becoming the default in {missRanger 3.0.0}. This will be announced via deprecation cycle.
+
 ## Enhancements
 
-- New argument `data_only = TRUE` to control if only the imputed data should returned (default), or an object of class "missRanger". This object contains the imputed data and infos like OOB prediction errors. This fixes [28](https://github.com/mayer79/missRanger/issues/28). The value `FALSE` will become the default in {missRanger 3.0.0}. This will be announced via deprecation cycle.
-- New argument `keep_forests = FALSE`. Should the random forests of the best iteration (the one that generated the final imputed data) be added to the "missRanger" object? Note that this will use a lot of memory. Only relevant if `data_only = FALSE`. This solves [54](https://github.com/mayer79/missRanger/issues/54)
+- New argument `keep_forests = FALSE`. Should the random forests of the best iteration (the one that generated the final imputed data) be added to the "missRanger" object? Note that this will use a lot of memory. Only relevant if `data_only = FALSE`. This solves [#54](https://github.com/mayer79/missRanger/issues/54).
 
 ## Bug fixes
 

R/methods.R

@@ -8,7 +8,7 @@
 #' @export
 #' @examples
 #' CO2_ <- generateNA(CO2, seed = 1)
-#' imp <- missRanger(CO2_, pmm.k = 5, data_only = FALSE)
+#' imp <- missRanger(CO2_, pmm.k = 5, data_only = FALSE, num.threads = 1)
 #' imp
 print.missRanger <- function(x, ...) {
  b <- x$best_iter
@@ -28,7 +28,7 @@ print.missRanger <- function(x, ...) {
 #' @export
 #' @examples
 #' CO2_ <- generateNA(CO2, seed = 1)
-#' imp <- missRanger(CO2_, pmm.k = 5, data_only = FALSE)
+#' imp <- missRanger(CO2_, pmm.k = 5, data_only = FALSE, num.threads = 1)
 #' summary(imp)
 summary.missRanger <- function(object, ...) {
  print(object)

R/missRanger.R

@@ -91,6 +91,7 @@
 #' head(irisImputed)
 #' head(irisWithNA)
 #' 
+#' \dontrun{
 #' # Extended output
 #' imp <- missRanger(irisWithNA, pmm.k = 3, num.trees = 100, data_only = FALSE)
 #' head(imp$data)
@@ -100,9 +101,9 @@
 #' imp <- missRanger(
 #' irisWithNA, pmm.k = 3, num.trees = 100, data_only = FALSE, keep_forests = TRUE
 #' )
-#' imp$forests$Species
 #' imp$forests$Sepal.Width
 #' imp$pred_errors[imp$best_iter, "Sepal.Width"] # 1 - R-squared
+#' }
 missRanger <- function(data, formula = . ~ ., pmm.k = 0L, maxiter = 10L, 
  seed = NULL, verbose = 1, returnOOB = FALSE, case.weights = NULL, 
  data_only = TRUE, keep_forests = FALSE, ...) {

cran-comments.md

@@ -1,31 +1,28 @@
-# missRanger 2.3.0
+# missRanger 2.4.0
 
-Dear CRAN team
+Hello CRAN team
 
-This update fixes two issues: non-syntactic column names, and too many features.
+This update introduces the future API of missRanger.
 
-I have checked reverse dependencies, without finding.
-
-## R CMD check
+## R CMD check (local)
 
 - WARNING: 'qpdf' is needed for checks on size reduction of PDFs
-- NOTE: no command 'tidy' found
+- NOTE: Skipping checking HTML validation: no command 'tidy' found
 
 ## RHub 
 
-* checking HTML version of manual ... NOTE
-Skipping checking HTML validation: no command 'tidy' found
+* 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
 
-Status: 1 NOTE
-R Under development (unstable) (2023-10-18 r85349 ucrt)
+Status: OK
 
 ## revdepcheck results
 
-We checked 7 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
-
- * We saw 0 new problems
- * We failed to check 0 packages
-
-
+OK: 7 
+BROKEN: 0

revdep/README.md

@@ -10,19 +10,19 @@
 |collate |German_Switzerland.utf8 |
 |ctype |German_Switzerland.utf8 |
 |tz |Europe/Zurich |
-|date |2023-10-20 |
+|date |2023-11-19 |
 |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 |
 |:----------|:---------|:---------|:--|
-|missRanger |2.2.1 |2.3.0 |* |
+|missRanger |2.3.0 |2.4.0 |* |
 |FNN |1.1.3.2 |1.1.3.2 | |
-|ranger |0.15.1 |0.15.1 | |
+|ranger |0.16.0 |0.16.0 | |
 |Rcpp |1.0.11 |1.0.11 | |
-|RcppEigen |0.3.3.9.3 |0.3.3.9.3 | |
+|RcppEigen |0.3.3.9.4 |0.3.3.9.4 | |
 
 # Revdeps