mercuryfish {coin}R Documentation

Chromosomal Effects of Mercury Contaminated Fish Consumption

Description

The mercury level in the blood, the proportion of cells with abnormalities and the proportion of cells with chromosome aberrations for a group of consuments of mercury contaminated fish and a control group.

Usage

data("mercuryfish")

Format

A data frame with 39 observations on the following 4 variables.

group

a factor with levels control and exposed.

mercury

the level of mercury in the blood.

abnormal

the proportion of cells with structural abnormalities.

ccells

the proportion of cells with asymmetrical or incomplete-symmetrical chromosome aberrations called C_u cells.

Details

Subjects who ate contaminated fish for more than three years in the exposed group and subjects of a control group are to be compared. Instead of a multivariate comparison, Rosenbaum (1994) applied a coherence criterion. The observations are partially ordered: an observation is smaller than another when all three variables (mercury, abnormal and ccells) are smaller and a score reflecting the ‘ranking’ is attached to each observation. The distribution of the scores in both groups is to be compared and the corresponding test is called ‘POSET-test’ (partially ordered sets).

Source

S. Skerfving, K. Hansson, C. Mangs, J. Lindsten, N. Ryman (1974), Methylmercury-induced chromosome damage in men. Environmental Research 7, 83–98.

References

P. R. Rosenbaum (1994). Coherence in observational studies. Biometrics 50, 368–374.

Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel \& Achim Zeileis (2006). A Lego system for conditional inference, The American Statistician, 60(3), 257–263.

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)
  }

  ### POSET-test
  poset <- independence_test(mercury + abnormal + ccells ~ group, data =
                             mercuryfish, ytrafo = coherence)

  ### linear statistic (T in Rosenbaum's, 1994, notation)
  statistic(poset, "linear")

  ### expectation
  expectation(poset)

  ### variance (there is a typo in Rosenbaum, 1994, page 371, 
  ### last paragraph Section 2)
  covariance(poset)

  ### the standardized statistic
  statistic(poset)

  ### and asymptotic p-value
  pvalue(poset)

  ### exact p-value
  independence_test(mercury + abnormal + ccells ~ group, data =
                    mercuryfish, ytrafo = coherence, distribution = "exact")

  ### multivariate analysis
  mvtest <- independence_test(mercury + abnormal + ccells ~ group, 
                              data = mercuryfish)

  ### global p-value
  pvalue(mvtest)

  ### adjusted univariate p-value
  pvalue(mvtest, method = "single-step")


[Package coin version 1.0-20 Index]