Question

I have a data.frame like this:

(t=structure(list(count = c(NA, 2, NA, NA, NA, 8, NA, NA, NA)), .Names = "count", row.names = c(NA,-9L), class = "data.frame"))
  count
1    NA
2     2
3    NA
4    NA
5    NA
6     8
7    NA
8    NA
9    NA

It is great that R has the NA value but sometimes it bites me. I often forget about it and try to do subsetting like this

> t[t$count>=1,]
[1] NA  2 NA NA NA  8 NA NA NA

And the output includes all NA rows. (which I don’t like)

After an hour of bug searching I change the code to this and that is what I want (imagine large dataframe a lots of non-NA resuls and only few “well-hidden” NAs):

> t[t$count>=1&!is.na(t$count),]
[1] 2 8

1.
Is there a feature of the “as.integer” function so that I could do something like this:

t[as.integer.EXCLUDE.NA(t$count)>=1,]

I would want to use such feature in other as.xxxx functions as well. Basically force R to stop think like a statistician and treat NA differently (e.g., like NULL (I am not sure NULL would solve my issue) (this did not work: t$count[3]<-NULL for some reason)

2.
or how would I run

transform(t, replace all NAs from count columns with 0)

or even better

transform(t, replace all NA from all numeric columns with 0 in t)

3.
any generic comments on making R forget about NAs are welcomed?

Answer 1

I do not like the choices that were made at the time of designing how “[” handles NA values either. The approach I take when I want to extract values using a logical test is to wrap the logical expression in which. This converts the result to a set of numbers and indexing succeeds without dragging along the unwanted NA’s:

> t[ which(t$count >= 1), ]
[1] 2 8
# Or if you still want a dataframe result
> t[ which(t$count >= 1), , drop=FALSE]
  count
2     2
6     8

I also use subset since it handles NA’s in the same manner as which(logical). The one gotcha is when which is used with a “-” sign to retrieve the complement set. If there are no elements in the set satisfying the logical-condition, there will also be no elements in the -which(logical)-form. So I just do not use the -which combo:

> t[ -which(t$count < 1), , drop=FALSE]
[1] count
<0 rows> (or 0-length row.names)
> t[ which(t$count < 1), , drop=FALSE]
[1] count
<0 rows> (or 0-length row.names)