[R] Odp: How to make t.test handle "NA" and "essentially constant values" ?

[Tony Plate]

Petr PIKAL wrote:
> Hi
> 
> r-help-bounces at r-project.org napsal dne 12.02.2008 09:09:23:
> 
>> Hi,
>>
>> First problem:
>>> test <- matrix(c(1,1,2,1), 2,2)
>>> apply(test, 1, function(x) { t.test(x) $p.value })
>> Error in t.test.default(x) : data are essentially constant
> 
> make your data not constant
> 
>> Second problem:
>>> test <- matrix(c(1,0,NA,1), 2,2)
>>> apply(test, 1, function(x) { t.test(x) $p.value })
>> Error in t.test.default(x) : not enough 'x' observations
> 
> increase number of observations
> 
> 
>> How to make t-test ignores this errors ?
> 
> Well, the procedure is complaining that you do not give it correct data. 
> You shall be gratefull for a great software which prevent you from making 
> silly things as try to compute t.test when data have zero variantion or 
> number of observations is 1.

It's nice that the software recognizes situations in which a sensible 
answer can't be computed.  At that point, there are two possible actions: 
(1) stop with an informative error, and (2) silently return NA.  Option (1) 
is wonderful for interactive use, but option (2) is easier to handle in 
programs where one is making many calls to the function as part of some 
automated procedure (e.g., as part of a bootstrap procedure).

Speaking from personal experience, it can be quite a drag when one has set 
up and mostly-debugged a long computation only to have it stop with an 
error like "data are essentially constant" right near the end because of 
some condition for which the function author thought it better to stop with 
an error rather than return NA (or some other indication that there was no 
sensible answer) (didn't happen with t.test, but I've experienced it with a 
few other functions.)

So, I don't think it's at all unreasonable for the OP to request a way to 
make t.test() return NA instead of stopping with an error.

Looking at the code for t.test, it doesn't look like there's any argument 
to specify such behavior, so the options are to write one's own version of 
t.test, or use try() as other posters have suggested.  Here's an example 
using try():

 > my.t.test.p.value <- function(...) {
+    obj<-try(t.test(...), silent=TRUE)
+    if (is(obj, "try-error")) return(NA) else return(obj$p.value)
+ }
 > my.t.test.p.value(numeric(0))
[1] NA
 > my.t.test.p.value(1:10)
[1] 0.000278196
 > my.t.test.p.value(1)
[1] NA
 > my.t.test.p.value(c(1,1,1))
[1] NA
 > my.t.test.p.value(c(1,2,NA))
[1] 0.2048328
 > my.t.test.p.value(c(1,2))
[1] 0.2048328
 >

hope this helps,

Tony Plate

> 
> Regards
> Petr
> 
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>>
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