complete.cases() -> vec_detect_complete()

tidymodels · Sep 9, 2024 · c67e83e · c67e83e
1 parent dd2e0d5
commit c67e83e
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Showing 13 changed files with 22 additions and 22 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -765,7 +765,6 @@ importFrom(purrr,map_dbl)
 importFrom(purrr,map_lgl)
 importFrom(stats,as.formula)
 importFrom(stats,binomial)
-importFrom(stats,complete.cases)
 importFrom(stats,cov)
 importFrom(stats,cov.wt)
 importFrom(stats,lm)
@@ -794,4 +793,5 @@ importFrom(utils,install.packages)
 importFrom(utils,object.size)
 importFrom(vctrs,vec_cast)
 importFrom(vctrs,vec_cbind)
+importFrom(vctrs,vec_detect_complete)
 importFrom(vctrs,vec_slice)
diff --git a/R/case_weights.R b/R/case_weights.R
@@ -131,7 +131,7 @@ wt_calcs <- function(x, wts, statistic = "mean") {
     wts <- rep(1L, nrow(x))
   }
 
-  complete <- stats::complete.cases(x) & !is.na(wts)
+  complete <- vec_detect_complete(x) & !is.na(wts)
   wts <- wts[complete]
   x <- x[complete,,drop = FALSE]
   res <- stats::cov.wt(x, wt = wts, cor = statistic == "cor")

diff --git a/R/classdist.R b/R/classdist.R
@@ -58,7 +58,7 @@
 #'
 #' @examplesIf rlang::is_installed(c("modeldata"))
 #' data(penguins, package = "modeldata")
-#' penguins <- penguins[complete.cases(penguins), ]
+#' penguins <- penguins[vctrs::vec_detect_complete(penguins), ]
 #' penguins$island <- NULL
 #' penguins$sex <- NULL
 #'

diff --git a/R/classdist_shrunken.R b/R/classdist_shrunken.R
@@ -62,7 +62,7 @@
 #' of the National Academy of Sciences_, 99(10), 6567-6572.
 #' @examplesIf rlang::is_installed(c("modeldata"))
 #' data(penguins, package = "modeldata")
-#' penguins <- penguins[complete.cases(penguins), ]
+#' penguins <- penguins[vctrs::vec_detect_complete(penguins), ]
 #' penguins$island <- NULL
 #' penguins$sex <- NULL
 #'

diff --git a/R/corr.R b/R/corr.R
@@ -185,7 +185,7 @@ corr_filter <-
            method = "pearson") {
     x <- correlations(x, wts = wts, use = use, method = method)
 
-    if (any(!complete.cases(x))) {
+    if (any(!vec_detect_complete(x))) {
       all_na <- apply(x, 2, function(x) all(is.na(x)))
       if (sum(all_na) >= nrow(x) - 1) {
         cli::cli_warn(

diff --git a/R/impute_bag.R b/R/impute_bag.R
@@ -248,14 +248,14 @@ bake.step_impute_bag <- function(object, new_data, ...) {
   col_names <- names(object$models)
   check_new_data(col_names, object, new_data)
 
-  missing_rows <- !complete.cases(new_data)
+  missing_rows <- !vec_detect_complete(new_data)
   if (!any(missing_rows)) {
     return(new_data)
   }
 
   old_data <- new_data
   for (col_name in col_names) {
-    missing_rows <- !complete.cases(new_data[[col_name]])
+    missing_rows <- !vec_detect_complete(new_data[[col_name]])
     if (!any(missing_rows)) {
       next
     }

diff --git a/R/impute_knn.R b/R/impute_knn.R
@@ -221,7 +221,7 @@ bake.step_impute_knn <- function(object, new_data, ...) {
   all_cols <- unique(unlist(object$columns, recursive = TRUE))
   check_new_data(all_cols, object, new_data)
 
-  missing_rows <- !complete.cases(new_data)
+  missing_rows <- !vec_detect_complete(new_data)
   if (!any(missing_rows)) {
     return(new_data)
   }
@@ -230,7 +230,7 @@ bake.step_impute_knn <- function(object, new_data, ...) {
 
   old_data <- new_data
   for (col_name in col_names) {
-    missing_rows <- !complete.cases(new_data[, col_name])
+    missing_rows <- !vec_detect_complete(new_data[, col_name])
     if (!any(missing_rows)) {
       next
     }

diff --git a/R/impute_linear.R b/R/impute_linear.R
@@ -115,7 +115,7 @@ step_impute_linear_new <-
 
 lm_wrap <- function(vars, dat, wts = NULL, call = caller_env(2)) {
   dat <- as.data.frame(dat[, c(vars$y, vars$x)])
-  complete <- stats::complete.cases(dat)
+  complete <- vec_detect_complete(dat)
   dat <- dat[complete, ]
   wts <- wts[complete]
   if (nrow(dat) == 0) {
@@ -200,14 +200,14 @@ bake.step_impute_linear <- function(object, new_data, ...) {
   col_names <- names(object$models)
   check_new_data(col_names, object, new_data)
 
-  missing_rows <- !complete.cases(new_data)
+  missing_rows <- !vec_detect_complete(new_data)
   if (!any(missing_rows)) {
     return(new_data)
   }
 
   old_data <- new_data
   for (col_name in col_names) {
-    missing_rows <- !complete.cases(new_data[[col_name]])
+    missing_rows <- !vec_detect_complete(new_data[[col_name]])
     if (!any(missing_rows)) {
       next
     }

diff --git a/R/misc.R b/R/misc.R
@@ -206,7 +206,7 @@ strings2factors <- function(x, info) {
 
 # ------------------------------------------------------------------------------
 
-# `complete.cases` fails on list columns. This version counts a list column
+# `vec_detect_complete` fails on list columns. This version counts a list column
 # as missing if _all_ values are missing. For if a list vector element is a
 # data frame with one missing value, that element of the list column will
 # be counted as complete.
@@ -218,7 +218,7 @@ n_complete_rows <- function(x) {
     x[[pos_list_col]] <- purrr::map_lgl(x[[pos_list_col]], flatten_na)
   }
 
-  sum(complete.cases(x))
+  sum(vec_detect_complete(x))
 }
 
 flatten_na <- function(x) {

diff --git a/R/recipes-package.R b/R/recipes-package.R
@@ -71,7 +71,6 @@
 #' @importFrom purrr map_lgl
 #' @importFrom stats as.formula
 #' @importFrom stats binomial
-#' @importFrom stats complete.cases
 #' @importFrom stats cov
 #' @importFrom stats cov.wt
 #' @importFrom stats lm
@@ -99,6 +98,7 @@
 #' @importFrom utils object.size
 #' @importFrom vctrs vec_cast
 #' @importFrom vctrs vec_cbind
+#' @importFrom vctrs vec_detect_complete
 #' @importFrom vctrs vec_slice
 ## usethis namespace: end
 NULL
diff --git a/man/step_classdist.Rd b/man/step_classdist.Rd
diff --git a/man/step_classdist_shrunken.Rd b/man/step_classdist_shrunken.Rd
diff --git a/tests/testthat/test-dummy.R b/tests/testthat/test-dummy.R
@@ -15,7 +15,7 @@ sacr$city[sample(1:nrow(sacr), 20)] <- NA_character_
 sacr_missing <- sacr
 
 sacr$city[is.na(sacr$city)] <- "missing"
-sacr <- sacr[complete.cases(sacr), -3]
+sacr <- sacr[vec_detect_complete(sacr), -3]
 
 sacr_fac <- sacr
 sacr_fac$city <- factor(sacr_fac$city)
@@ -167,10 +167,10 @@ test_that("tests for NA values in factor", {
   )
 
   expect_true(
-    all(complete.cases(factors_data_0) == complete.cases(sacr_missing[, "city"]))
+    all(vec_detect_complete(factors_data_0) == vec_detect_complete(sacr_missing[, "city"]))
   )
   expect_true(
-    all(complete.cases(factors_data_1) == complete.cases(sacr_missing[, "city"]))
+    all(vec_detect_complete(factors_data_1) == vec_detect_complete(sacr_missing[, "city"]))
   )
 })
 
@@ -189,10 +189,10 @@ test_that("tests for NA values in ordered factor", {
   )
 
   expect_true(
-    all(complete.cases(factors_data_0) == complete.cases(sacr_ordered[, "city"]))
+    all(vec_detect_complete(factors_data_0) == vec_detect_complete(sacr_ordered[, "city"]))
   )
   expect_true(
-    all(complete.cases(factors_data_1) == complete.cases(sacr_ordered[, "city"]))
+    all(vec_detect_complete(factors_data_1) == vec_detect_complete(sacr_ordered[, "city"]))
   )
 })