Dealing with TRUE, FALSE, NA and NaN

You don't need to wrap anything in a function - the following works

a = c(T,F,NA)a %in% TRUE[1]  TRUE FALSE FALSE

To answer your questions in order:

1) The == operator does indeed not treat NA's as you would expect it to. A very useful function is this compareNA function from r-cookbook.com:

  compareNA <- function(v1,v2) {    # This function returns TRUE wherever elements are the same, including NA's,    # and false everywhere else.    same <- (v1 == v2)  |  (is.na(v1) & is.na(v2))    same[is.na(same)] <- FALSE    return(same)   }

2) NA stands for "Not available", and is not the same as the general NaN ("not a number"). NA is generally used for a default value for a number to stand in for missing data; NaN's are normally generated because a numerical issue (taking log of -1 or similar).

3) I'm not really sure what you mean by "logical things"--many different data types, including numeric vectors, can be used as input to logical operators. You might want to try reading the R logical operators page: http://stat.ethz.ch/R-manual/R-patched/library/base/html/Logic.html.

Hope this helps!

So you want TRUE to remain TRUE and FALSE to remain FALSE, the only real change is that NA needs to become FALSE, so just do this change like:

a[ is.na(a) ] <- FALSE

Or you could rephrase to say it is only TRUE if it is TRUE and not missing:

a <- a & !is.na(a)