some more small fixes

.coderabbit.yaml

@@ -12,4 +12,4 @@ reviews:
     enabled: true
     drafts: false
 chat:
-  auto_reply: false
+  auto_reply: false

R/caretList.R

@@ -153,10 +153,10 @@ extractCaretTarget.formula <- function(form, data, ...) {
 }
 
 #' Create a list of several train models from the caret package
-# "
+#'
 #' Build a list of train objects suitable for ensembling using the \code{\link{caretEnsemble}}
 #' function.
-# "
+#'
 #' @param ... arguments to pass to \code{\link{train}}.  These arguments will determine which train method gets dispatched.
 #' @param trControl a \code{\link{trainControl}} object.  We are going to intercept this object check that it has the "index" slot defined, and define the indexes if they are not.
 #' @param methodList optional, a character vector of caret models to ensemble.  One of methodList or tuneList must be specified.
@@ -306,7 +306,7 @@ as.caretList.list <- function(object) {
 
 #' @title Create a matrix of predictions for each of the models in a caretList
 #' @description Make a matrix of predictions from a list of caret models
-# "
+#'
 #' @param object an object of class caretList
 #' @param verbose Logical. If FALSE no progress bar is printed if TRUE a progress
 #' bar is shown. Default FALSE.

tests/testthat/test-caretList.R

@@ -77,13 +77,13 @@ test_that("caretList errors for bad models", {
     bad = caretModelSpec(method = "glm", tuneLength = 1)
   )
   suppressWarnings({
-    sink <- capture.output({
+    invisible(capture.output({
       expect_error(caretList(iris[, 1:4], iris[, 5], tuneList = bad_bad, trControl = my_control))
       expect_error(caretList(iris[, 1:4], iris[, 5], tuneList = good_bad, trControl = my_control))
       expect_error(caretList(iris[, 1:4], iris[, 5], tuneList = bad_bad, trControl = my_control, continue_on_fail = TRUE))
       working <- caretList(iris[, 1:4], iris[, 5], tuneList = good_bad, trControl = my_control, continue_on_fail = TRUE)
       expect_is(working, "caretList")
-    })
+    }))
   })
 })
 
@@ -213,7 +213,7 @@ test_that("We can handle different CV methods", {
         )
       })
     })
-    sink <- sapply(models, expect_is, class = "train")
+    invisible(sapply(models, expect_is, class = "train"))
 
     suppressWarnings({
       suppressMessages({

tests/testthat/test-caretStack.R

@@ -20,7 +20,7 @@ test_that("We can stack regression models", {
   )
   expect_that(ens.reg, is_a("caretStack"))
   expect_is(summary(ens.reg), "summary.lm")
-  sink <- capture.output(print(ens.reg))
+  invisible(capture.output(print(ens.reg)))
   suppressWarnings(pred.reg <- predict(ens.reg, newdata = X.reg))
   expect_true(is.numeric(pred.reg))
   expect_true(length(pred.reg) == 150)
@@ -35,7 +35,7 @@ test_that("We can stack classification models", {
   )
   expect_that(ens.class, is_a("caretStack"))
   expect_is(summary(ens.class), "summary.glm")
-  sink <- capture.output(print(ens.class))
+  invisible(capture.output(print(ens.class)))
   suppressWarnings(pred.class <- predict(ens.class, X.class, type = "prob"))
   expect_true(is.numeric(pred.class))
   expect_true(length(pred.class) == 150)

tests/testthat/test-helper_functions.R

@@ -84,7 +84,7 @@ test_that("We can predict", {
 })
 
 test_that("predict results same regardless of verbose option", {
-  sink <- capture.output({
+  invisible(capture.output({
     suppressWarnings({
       expect_is(predict(models.class, "Classification", newdata = X.class), "matrix")
       out1 <- predict(models.class, "Classification", newdata = X.class)
@@ -97,7 +97,7 @@ test_that("predict results same regardless of verbose option", {
       out2 <- predict(models.reg, "Regression", verbose = TRUE, newdata = X.reg)
       expect_identical(out1, out2)
     })
-  })
+  }))
 })
 
 context("Test weighted standard deviations")