# R/xchisq.test.R In ProjectMOSAIC/mosaic: Project MOSAIC Statistics and Mathematics Teaching Utilities

#### Documented in xchisq.test

```#' Augmented Chi-squared test
#'
#' This augmented version of [chisq.test()] provides more verbose
#' output.
#'
#' @param x,y,correct,p,rescale.p,simulate.p.value,B as in [chisq.test()], but
#' `x` may also be a formula, in which case `x` is replaced by `tally(x, data)`
#' prior to the call to [chisq.test()].
#' @param data a data frame for use when `x` is a formula.
#'
#' @seealso [chisq.test()]
#'
#' @examples
#' # Physicians' Health Study data
#' phs <- cbind(c(104,189),c(10933,10845))
#' rownames(phs) <- c("aspirin","placebo")
#' colnames(phs) <- c("heart attack","no heart attack")
#' phs
#' xchisq.test(phs)
#' xchisq.test(sex ~ substance, data = HELPrct)
#' @export

xchisq.test <-
function (x, y=NULL, correct=TRUE, p = rep(1/length(x), length(x)),
rescale.p=FALSE, simulate.p.value=FALSE, B=2000, data = environment(x))
{
if (inherits(x, "formula")) {
x <- tally(x, data = data)
orig <- chisq.test(x, correct = correct, p = p,
rescale.p = rescale.p,
simulate.p.value = simulate.p.value, B = B)
} else {
orig <- chisq.test(x = x, y = y, correct = correct, p = p,
rescale.p = rescale.p,
simulate.p.value=simulate.p.value, B=B)
}
if (is.matrix(orig\$observed)) {
dd <- dim(orig\$observed)
}
else {
dd <- c(1, length(orig\$observed))
}
obs <- surround(orig\$observed, " ", " ", digits = 2, nsmall = 2)
exp <- surround(orig\$expected, "(", ")", digits = 2, nsmall = 2)
contribution <- (orig\$observed - orig\$expected) ^ 2 / orig\$expected
if (correct && all(dd == c(2,2)) && ! simulate.p.value) {
# use continuity correction
contrib2 <- (abs(orig\$observed - orig\$expected) - .5)^2 / orig\$expected
contribution <- pmin(contribution, contrib2)
}
contrib <- surround(contribution, "[", "]", digits = 2, nsmall = 2)
resid <- surround(orig\$residuals, "<", ">", digits = 2, nsmall = 2)
blank <- rep(" ", prod(dd))
result <- c(obs, exp, contrib, resid, blank)
dim(result) <- c(dd, 5)
print(orig)
for (i in 1:dd[1]) {
for (j in 1:5) {
cat(result[i, , j])
cat("\n")
}
}
cat("key:\n")
cat("\tobserved\n")
cat("\t(expected)\n")
cat("\t[contribution to X-squared]\n")
cat("\t<Pearson residual>\n")
orig\$contribution <- contribution
return(invisible(orig))
}
```
ProjectMOSAIC/mosaic documentation built on Aug. 19, 2018, 9:14 a.m.