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How to make t.test handle "NA" and "essentially constant values" ?

9 messages · Ng Stanley, PIKAL Petr, ONKELINX, Thierry +3 more

Original
PIKAL Petr
# 
Hi

r-help-bounces at r-project.org napsal dne 12.02.2008 09:09:23:
make your data not constant
increase number of observations
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.

Regards
Petr
http://www.R-project.org/posting-guide.html
ONKELINX, Thierry
# 
Have a look at ?try 

try(t.test(x))

HTH,

Thierry


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx op inbo.be 
www.inbo.be 

Do not put your faith in what statistics say until you have carefully
considered what they do not say.  ~William W. Watt
A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney

-----Oorspronkelijk bericht-----
Van: r-help-bounces op r-project.org [mailto:r-help-bounces op r-project.org]
Namens Ng Stanley
Verzonden: dinsdag 12 februari 2008 11:56
Aan: r-help
Onderwerp: Re: [R] How to make t.test handle "NA" and "essentially
constantvalues" ?

Thanks. Someone please help to make t.test go through all the data and
not
to be disrupted by the two problems.
On 2/12/08, Petr PIKAL <petr.pikal op precheza.cz> wrote:
data.
making
or
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and provide commented, minimal, self-contained, reproducible code.
Richard Pearson
# 
Do you mean to deal with the situation where you're doing many t-tests 
in a loop? If so there was a post very recently on this list about this:

https://stat.ethz.ch/pipermail/r-help/2008-February/153254.html

Richard.
Ng Stanley wrote:
Tony Plate
#
Petr PIKAL wrote:
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
Hadley Wickham
# 
I've written the following functions to make these tasks a little easier:

try_default <- function (expr, default = NA) {
  result <- default
  tryCatch(result <- expr, error = function(e) {})
  result
}

failwith <- function(default = NULL, f, ...) {
  function(...) try_default(f(...), default)
}

so my.t.test.p.value could be created as:

my.t.test.p.value <- function(...) failwith(NA, t.test(...))


Hadley