R: Chromosomal Effects of Mercury-Contaminated Fish Consumption
mercuryfish
R Documentation
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.
group
a factor with levels "control" and "exposed".
mercury
mercury level in blood.
abnormal
the proportion of cells with structural abnormalities.
ccells
the proportion of C_u cells, i.e., cells with asymmetrical or
incomplete-symmetrical chromosome aberrations.
Details
Control subjects ("control") and subjects who ate contaminated fish for
more than three years ("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 “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. Environmental Research7(1), 83–98.
References
Hothorn, T., Hornik, K., van de Wiel, M. A. and Zeileis, A. (2006). A Lego
system for conditional inference. The American Statistician60(3), 257–263.
Rosenbaum, P. R. (1994). Coherence in observational studies.
Biometrics50(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")