context('Test preProcess')
# Helper function
check.medianImpute <- function(x) {
# Reference column medians for checks
med <- apply(x, 2, median, na.rm=TRUE)
anyEmptyColumn <- any(is.na(med))
med[is.na(med)] <- 0
if(anyEmptyColumn) {
expect_warning(
pp <- preProcess(x, method = "medianImpute"),
"never filled"
)
} else {
pp <- preProcess(x, method = "medianImpute")
}
expect_equal(pp$median, med)
x.filled <- predict(pp, newdata=x)
expect_false(any(is.na(x.filled)))
expect_equal(x[!is.na(x)], x.filled[!is.na(x)])
med.filled <- apply(x.filled, 2, median)
expect_equal(med.filled, med)
}
# Tested data matrix
set.seed(1)
x <- matrix(rnorm(20, mean=10,sd=5), nrow=4)
x[2,1] <- x[3,4] <- x[2,5] <- x[4,5] <- NA
x[,3] <- NA
colnames(x) <- paste0("Var.",1:ncol(x))
test_that("median Impute works for matrix with named columns", {
check.medianImpute(x)
})
test_that("median Impute works for data.frames", {
check.medianImpute(as.data.frame(x, stringsAsFactors = TRUE))
})
test_that("correlation filter", {
expect_equal(
preProcess(iris, "corr")$method,
list(ignore = "Species", remove = "Petal.Length")
)
})
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