[R] warning message in hand-made function

[Prof Brian Ripley]

The problem is that that you have asserted your result is of class 
"htest", and it is not like the format given in e.g. ?t.test. 
Specifically, print.htest contains

     if (!is.null(x$p.value)) {
         fp <- format.pval(x$p.value, digits = digits)
         out <- c(out, paste("p-value", if (substr(fp, 1, 1) ==
             "<") fp else paste("=", fp)))
     }

and this assumes x$p.value is of length one, not two.

On Thu, 30 Mar 2006, Matthieu Dubois wrote:

> Dear Rusers,
>
> I  tried to implement a function comparing mean scores between one
> subject (the patient) and a group a control subjects. The function
> returns attended results, but  I also obtained the following warning :
>
> Warning message:
> the condition has length > 1 and only the first element will be used
> in: if (substr(fp, 1, 1) == "<") fp else paste("=", fp)
>
> Maybe the cause of the message is obvious, but I don't understand. I
> am newbie in R  and certainly I missed something. Any help would be
> greatly appreciated.
>
> The aim of the function was to :
> 1. compute a modified t-test with either raw data (controls and
> patient) in vectors or only summaries for the control group (mean,
> standard deviation, size of the group :  mean.c, sd.c, n) as inputs ;
> 2. estimate the rarity of the  difference observed between patient
> and controls and computing confidence intervals
>
> The function was the following:
>
> crawford.t.test <- function(patient, controls, mean.c=0, sd.c=0, n=0,
> na.rm=F) {
> 	#from Crawford et al. (1998, Clinical Neuropsychologist ; 2002,
> Neuropsychologia)
>
> 	na<-na.rm
>
> 	#if no summaries are entered, they are computed
> 	if(missing(n)) {
> 		n <- length(controls)
> 		mean.c <- mean(controls, na.rm=na)
> 		sd.c <- sd(controls, na.rm=na)
> 		}
> 	dl <- n-1	#degrees of freedom of the  test
>
> 	#t.test computation
> 	t.obs <- (patient-mean.c) / (sd.c*(((n+1)/n)^0.5))
> 	proba.onetailed <- 1-pt(abs(t.obs), df=dl)
> 	rar <- pt(t.obs, df=dl) #point estimate of the rarity
>
> 	#confidence intervals computation on the rarity (Crawford &
> Garthwaite, 2002, Neuropsychologia)
> 	c <- (patient-mean.c)/sd.c
> 	#finding the non central parameter of t distributions
> 	f <- function(delta, pr, x, df) pt(x, df = df, ncp = delta) - pr
> 	deltaL <- uniroot(f, lower=-37.62, upper=37.62, pr = 0.025, x = c*
> (n^0.5), df = dl)
> 	deltaU <- uniroot(f, lower=-37.62, upper=37.62, pr = 0.975, x = c*
> (n^0.5), df = dl)
> 	CI.U <- pnorm(deltaL$root/(n^0.5)) * 100 #upper bound of the
> confidence interval
> 	CI.L <- pnorm(deltaU$root/(n^0.5)) * 100 #lower bound of the
> confidence interval
>
> 	#output
> 	output <- list(statistic=t.obs, p.value=c
> (one.tailed=proba.onetailed, twotailed=2*proba.onetailed), rarity=c
> (rarity=rar, lower.boud=CI.L, upper.bound=CI.U), df=dl, method=paste
> ("Crawford modified t test with", dl, "degrees of freedom", sep=" "))
> 	class(output)<-"htest"
> 	return(output)
> 	}
>
>
>
> Matthieu Dubois, PH.D. Student
> Cognitive Neuroscience Unit
> Université catholique de Louvain
> 10, Place cardinal Mercier - 1348 Louvain-la-Neuve - BELGIUM
>
> Matthieu.Dubois at psp.ucl.ac.be
>
>
>
>
> 	[[alternative HTML version deleted]]
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595