r - Is it possible to set na.rm to TRUE globally?

Question

For commands like max the option na.rm is set by default to FALSE. I understand why this is a good idea in general, but I'd like to turn it off reversibly for a while -- i.e. during a session.

How can I require R to set na.rm = TRUE whenever it is an option? I found

options(na.action = na.omit)

but this doesn't work. I know that I can set a na.rm=TRUE option for each and every function I write.

my.max <- function(x) {max(x, na.rm=TRUE)}

But that's not what I am looking for. I'm wondering if there's something I could do more globally/universally instead of doing it for each function.

Answer 1

One workaround (dangerous), is to do the following :

1. List all functions that have na.rm as argument. Here I limited my search to the base package.
2. Fetch each function and add this line at the beginning of its body: na.rm = TRUE
3. Assign the function back to the base package.

So first I store in a list (ll) all functions having na.rm as argument:

uses_arg <- function(x,arg) 
  is.function(fx <- get(x)) && 
  arg %in% names(formals(fx))
basevals <- ls(pos="package:base")      
na.rm.f <- basevals[sapply(basevals,uses_arg,'na.rm')]

EDIT better method to get all na.rm's argument functions (thanks to mnel comment)

Funs <- Filter(is.function,sapply(ls(baseenv()),get,baseenv()))
na.rm.f <- names(Filter(function(x) any(names(formals(args(x)))%in% 'na.rm'),Funs))

So na.rm.f list looks like:

 [1] "all"                     "any"                     "colMeans"                "colSums"                
 [5] "is.unsorted"             "max"                     "mean.default"            "min"                    
 [9] "pmax"                    "pmax.int"                "pmin"                    "pmin.int"               
[13] "prod"                    "range"                   "range.default"           "rowMeans"               
[17] "rowsum.data.frame"       "rowsum.default"          "rowSums"                 "sum"                    
[21] "Summary.data.frame"      "Summary.Date"            "Summary.difftime"        "Summary.factor"         
[25] "Summary.numeric_version" "Summary.ordered"         "Summary.POSIXct"         "Summary.POSIXlt" 

Then for each function I change the body, the code is inspired from data.table package (FAQ 2.23) that add one line to the start of rbind.data.frame and cbind.data.frame.

ll <- lapply(na.rm.f,function(x)
  {
  tt <- get(x)
  ss = body(tt)
  if (class(ss)!="{") ss = as.call(c(as.name("{"), ss))
  if(length(ss) < 2) print(x)
  else{
    if (!length(grep("na.rm = TRUE",ss[[2]],fixed=TRUE))) {
      ss = ss[c(1,NA,2:length(ss))]
      ss[[2]] = parse(text="na.rm = TRUE")[[1]]
      body(tt)=ss
      (unlockBinding)(x,baseenv())
      assign(x,tt,envir=asNamespace("base"),inherits=FALSE)
      lockBinding(x,baseenv())
      }
    }
  })

No if you check , the first line of each function of our list :

unique(lapply(na.rm.f,function(x) body(get(x))[[2]]))
[[1]]
na.rm = TRUE