[R] p values for polychor

From: andrew collier <digitalpenis_at_bluebottle.com>
Date: Wed, 07 May 2008 07:25:38 -0700


i have been using cor.test() for calculating the correlation coefficient and p values for some data. however, since the data consist of two dichotomous sequences (actually just binary data), i understand that simply using the pearson correlation is not sufficient. however, having done a bit of research i found that the tetrachoric correlation is what i am after. found the polycor package and the polychor routine, which seem to do precisely what i want. however, i don't get p values out of polychor, just the standard deviation.

so, in a rather naive way i have tried to write a function which will return a list with similar fields as what one gets from cor.test(). not being terribly strong with statistics though, i am not sure whether this is entirely correct. could someone tell me if i am on the right track... or point out where i am going wrong?

tetrachoric.test <- function(x, y) {

	p <- polychor(x, y, std.err = TRUE)
	p$statistic <- p$rho / sqrt(c(p$var))
	p$estimate <- p$rho
	p$p.value = 2 * (1 - pnorm(abs(p$statistic)))


the assumption is that the p value is the integration of the two tails of the distribution?

> x <- as.integer(runif(20) > 0.5)
> y <- as.integer(runif(20) > 0.5)
> p <- tetrachoric.test(x, y)
> p$statistic

[1] -0.2616866
> p$p.value

[1] 0.7935631
> p$var

[1,] 0.1452105

thanks for any help!

best regards,

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