R: Chromosomal Effects of Mercury-Contaminated Fish Consumption

mercuryfish {coin} | 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 Research 7(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 Statistician 60(3), 257–263.

Rosenbaum, P. R. (1994). Coherence in observational studies. Biometrics 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")

[Package coin version 1.1-3 Index]