Update funcs

DESCRIPTION

@@ -25,7 +25,7 @@ RoxygenNote: 7.1.0
 Depends:
     R (>= 3.5.0),
     mice (>= 3.9.0),
-    ranger (>= 0.12.3)
+    ranger (>= 0.12.1)
 Suggests: 
     testthat (>= 2.1.0),
     knitr,

NEWS.md

@@ -1,4 +1,6 @@
 ## RfEmpImp 2.1.5
+* Add new wrapper function to recover dependency on `ranger (>= 0.12.1)` and
+to fix parameter passing
 * New independent `mice.impute.rfpred.norm` function, and thus simplified
 `mice.impute.rfpred.emp` function
 * Bypass collinearity and constant checks in `mice` for `imp.*` functions
@@ -11,7 +13,6 @@ with the terminal nodes
 * Add new function `conv.factor` for converting variables
 * Update dependency for `mice (>= 3.9.0)` to avoid collinearity checks during
 imputation
-* Update dependency for `ranger (>= 0.12.3)` to fix parameter passing
 * Update documentations
 
 ## RfEmpImp 2.0.3

R/mice.impute.rfnode.R

@@ -122,13 +122,19 @@ mice.impute.rfnode <- function(
     }
     xMis <- x[wy, , drop = FALSE]
     # Output in-bag list when using conditional distribution
-    # Let ranger handle unused arguments after v0.12.3
-    rfObj <- suppressWarnings(ranger(x = xObs,
+    # TODO: Let ranger handle unused arguments after v0.12.3
+    # rfObj <- suppressWarnings(ranger(x = xObs,
+    #                 y = yObs,
+    #                 num.trees = num.trees.node,
+    #                 keep.inbag = use.node.cond.dist,
+    #                 num.threads = num.threads,
+    #                 ...))
+    rfObj <- rangerCallerSafe(x = xObs,
                     y = yObs,
                     num.trees = num.trees.node,
                     keep.inbag = use.node.cond.dist,
                     num.threads = num.threads,
-                    ...))
+                    ...)
     # Get Nodes for training and test set
     nodeObjMis <- predict(rfObj, data = xMis, type = "terminalNodes")
     nodeObjObs <- predict(rfObj, data = xObs, type = "terminalNodes")

R/mice.impute.rfpred.cate.R

@@ -117,27 +117,43 @@ mice.impute.rfpred.cate <- function(
     xMis <- x[wy, , drop = FALSE]
     if (isTRUE(forest.vote.cate)) {
         # Construct predictions based on major votes, less variant
-        rangerObj <- suppressWarnings(ranger(
+        # TODO: Let ranger handle unused arguments after v0.12.3
+        # rangerObj <- suppressWarnings(ranger(
+        #     x = xObs,
+        #     y = yObs,
+        #     oob.error = FALSE,
+        #     num.trees = num.trees.cate,
+        #     num.threads = num.threads,
+        #     ...))
+        rangerObj <- rangerCallerSafe(
             x = xObs,
             y = yObs,
             oob.error = FALSE,
             num.trees = num.trees.cate,
             num.threads = num.threads,
-            ...))
+            ...)
         impVal <- predictions(predict(rangerObj, xMis))
     } else if (isTRUE(use.pred.prob.cate)) {
         # Construct predictions based on probabilities
         # Suppress warnings like:
         # "Dropped unused factor level(s) in dependent variable"
-        # Let ranger handle unused arguments after v0.12.3
-        rangerObjProb <- suppressWarnings(ranger(
+        # TODO: Let ranger handle unused arguments after v0.12.3
+        # rangerObjProb <- suppressWarnings(ranger(
+        #     x = xObs,
+        #     y = yObs,
+        #     probability = TRUE,
+        #     oob.error = FALSE,
+        #     num.trees = num.trees.cate,
+        #     num.threads = num.threads,
+        #     ...))
+        rangerObjProb <- rangerCallerSafe(
             x = xObs,
             y = yObs,
             probability = TRUE,
             oob.error = FALSE,
             num.trees = num.trees.cate,
             num.threads = num.threads,
-            ...))
+            ...)
         misPredMat <- predictions(predict(rangerObjProb, xMis))
         yLevels <- colnames(misPredMat)
         impValChar <- apply(
@@ -149,7 +165,15 @@ mice.impute.rfpred.cate <- function(
         impVal <- factor(x = impValChar, levels = levels(y))
     } else {
         # Imputation using random draws from predictions of trees
-        rangerObj <- ranger(
+        # TODO: Let ranger handle unused arguments after v0.12.3
+        # rangerObj <- suppressWarnings(ranger(
+        #     x = xObs,
+        #     y = yObs,
+        #     oob.error = FALSE,
+        #     num.trees = num.trees.cate,
+        #     num.threads = num.threads,
+        #     ...))
+        rangerObj <- rangerCallerSafe(
             x = xObs,
             y = yObs,
             oob.error = FALSE,

R/mice.impute.rfpred.emp.R

@@ -117,13 +117,20 @@ mice.impute.rfpred.emp <- function(
     }
     xMis <- x[wy, , drop = FALSE]
     # Let ranger handle unused arguments after v0.12.3
-    rfObj <- suppressWarnings(ranger(
+    # rfObj <- suppressWarnings(ranger(
+    #     x = xObs,
+    #     y = yObs,
+    #     oob.error = TRUE,
+    #     num.trees = num.trees.cont,
+    #     num.threads = num.threads,
+    #     ...))
+    rfObj <- rangerCallerSafe(
         x = xObs,
         y = yObs,
         oob.error = TRUE,
         num.trees = num.trees.cont,
         num.threads = num.threads,
-        ...))
+        ...)
     misPredVal <- predictions(predict(rfObj, xMis))
     # Get empirical OOB prediction errors
     oobErrEmp <-  yObs - rfObj[["predictions"]]

R/mice.impute.rfpred.norm.R

@@ -105,16 +105,20 @@ mice.impute.rfpred.norm <- function(
     }
     xMis <- x[wy, , drop = FALSE]
     # Let ranger handle unused arguments after v0.12.3
-    rfObj <- suppressWarnings(
-        ranger(
-            x = xObs,
-            y = yObs,
-            oob.error = TRUE,
-            num.trees = num.trees.cont,
-            num.threads = num.threads,
-            ...
-        )
-    )
+    # rfObj <- suppressWarnings(ranger(
+    #     x = xObs,
+    #     y = yObs,
+    #     oob.error = TRUE,
+    #     num.trees = num.trees.cont,
+    #     num.threads = num.threads,
+    #     ...))
+    rfObj <- rangerCallerSafe(
+        x = xObs,
+        y = yObs,
+        oob.error = TRUE,
+        num.trees = num.trees.cont,
+        num.threads = num.threads,
+        ...)
     misPredVal <- predictions(predict(rfObj, xMis))
     if (norm.err.cont) {
         oobMse <- NULL

R/rangerCallerSafe.R

@@ -0,0 +1,14 @@
+#' Remove unnecessary arguments for \code{ranger} function
+#'
+#' This function serves as an workaround for ranger function.
+#  Will let ranger handle unused arguments after v0.12.3.
+#'
+#' @param ... Parameters to pass down.
+#'
+#' @return Constructed \code{ranger} object.
+rangerCallerSafe <- function(...) {
+    params <- list(...)
+    validName <- setdiff(names(formals(ranger)), "...")
+    params <- params[names(params) %in% validName]
+    return(suppressWarnings(do.call(what = ranger, args = params)))
+}

tests/testthat/test-Imp-Pred-Continuous.R

@@ -139,3 +139,4 @@ test_that("mice.impute.rfpred.norm works for continuous variables", {
         }
     }
 })
+