swh:1:snp:813359ba77493c9d5dd1abad9a1f53490a8abf57
Tip revision: 035df276b039349a91d92b6c5691fdeb05819f3a authored by Torsten Hothorn on 17 July 2017, 21:32:53 UTC
version 1.2-1
version 1.2-1
Tip revision: 035df27
mercuryfish.Rd
\name{mercuryfish}
\docType{data}
\alias{mercuryfish}
\title{Chromosomal Effects of Mercury-Contaminated Fish Consumption}
\description{
The mercury level in blood, the proportion of cells with abnormalities, and
the proportion of cells with chromosome aberrations in consumers of
mercury-contaminated fish and a control group.
}
\usage{mercuryfish}
\format{
A data frame with 39 observations on 4 variables.
\describe{
\item{\code{group}}{
a factor with levels \code{"control"} and \code{"exposed"}.
}
\item{\code{mercury}}{
mercury level in blood.
}
\item{\code{abnormal}}{
the proportion of cells with structural abnormalities.
}
\item{\code{ccells}}{
the proportion of \eqn{C_u} cells, i.e., cells with asymmetrical or
incomplete-symmetrical chromosome aberrations.
}
}
}
\details{
Control subjects (\code{"control"}) and subjects who ate contaminated fish for
more than three years (\code{"exposed"}) are under study.
Rosenbaum (1994) proposed a coherence criterion defining a partial ordering,
i.e., an observation is smaller than another when all responses are smaller,
and a score reflecting the \dQuote{ranking} is attached to each observation.
The corresponding partially ordered set (POSET) test can be used to test if
the distribution of the scores differ between the groups. Alternatively, a
multivariate test can be applied.
}
\source{
Skerfving, S., Hansson, K., Mangs, C., Lindsten, J. and Ryman, N. (1974).
Methylmercury-induced chromosome damage in men. \emph{Environmental Research}
\bold{7}(1), 83--98.
}
\references{
Hothorn, T., Hornik, K., van de Wiel, M. A. and Zeileis, A. (2006). A Lego
system for conditional inference. \emph{The American Statistician}
\bold{60}(3), 257--263.
Rosenbaum, P. R. (1994). Coherence in observational studies.
\emph{Biometrics} \bold{50}(2), 368--374.
}
\examples{
## Coherence criterion
coherence <- function(data) {
x <- as.matrix(data)
matrix(apply(x, 1, function(y)
sum(colSums(t(x) < y) == ncol(x)) -
sum(colSums(t(x) > y) == ncol(x))), ncol = 1)
}
## Asymptotic POSET test
poset <- independence_test(mercury + abnormal + ccells ~ group,
data = mercuryfish, ytrafo = coherence)
## Linear statistic (T in the notation of Rosenbaum, 1994)
statistic(poset, type = "linear")
## Expectation
expectation(poset)
## Variance
## Note: typo in Rosenbaum (1994, p. 371, Sec. 2, last paragraph)
variance(poset)
## Standardized statistic
statistic(poset)
## P-value
pvalue(poset)
## Exact POSET test
independence_test(mercury + abnormal + ccells ~ group,
data = mercuryfish, ytrafo = coherence,
distribution = "exact")
## Asymptotic multivariate test
mvtest <- independence_test(mercury + abnormal + ccells ~ group,
data = mercuryfish)
## Global p-value
pvalue(mvtest)
## Single-step adjusted p-values
pvalue(mvtest, method = "single-step")
## Step-down adjusted p-values
pvalue(mvtest, method = "step-down")
}
\keyword{datasets}