complete.cases() working outside but not inside an R function? - r

Question

I'm wondering why when I run: iris[complete.cases(iris), ] it works perfectly fine. But when I do the same thing from the function below, it gives me the error: colMeans(x, na.rm = TRUE) : 'x' must be numeric?
p.s. scale() works well with data.frames ==> scale(mtcars).
Can this be fixed?
Here is the function:
standard <- function(data, scale = TRUE, center = TRUE, na.rm = TRUE){
data <- if(na.rm) data[complete.cases(data), ]
data[paste0(names(data), ".s")] <- scale(data, center = center, scale = scale)
return(data)
}
# EXAMPLE:
standard(iris)

Answer 1

EDIT:
Yes, the error is thrown by scale(), and not earlier. If you want to scale all the numeric columns and leave the other columns as is, you'll need to add a step that extracts the numeric columns, scales them, and then puts them back in. Incidentally, scale can handle NA values, so you can put the complete.cases() call after the scale.
Original Answer:
You can step through this by adding a call to browser() inside your function, but I suspect you'll find the error is thrown here:
scale(data, center = center, scale = scale)
Note from the documentation on scale()
Arguments
x a numeric matrix(like object).
Here's how you'd debug this:
make your function this:
standard <- function(data, scale = TRUE, center = TRUE, na.rm = TRUE){
browser()
data <- if(na.rm) data[complete.cases(data), ]
data[paste0(names(data), ".s")] <- scale(data, center = center, scale = scale)
return(data)
}
Then try to call it with standard(immer)
It will open a browser for you to step through each statement in the function. If you do this in RStudio you can see the environment changes in the Environment tab in the upper right window. Use the command help to see how to navigate the browser, but in general, you'll use n and/or s to step through each statement. Q gets you out of the browser, and removing the browser() call from your function lets you run it as you would usually.