R: Prints PMCMR objects

get.pvalues {PMCMR} | R Documentation

## Prints PMCMR objects

### Description

Returns a vector of pvalues that includes the names of the pairwise groups (i.e. the null hypothesis). The output can be used by `multcompLetters` to find homogeneous groups.

### Usage

    get.pvalues(object, ...)

### Arguments

`object` | either an object of class `"PMCMR"`, usually, a result of a call to any of the posthoc-tests included in the package PMCMR. Or an object of class `"pairwise.htest"`, a result of a call to `pairwise.prop.test`, `pairwise.t.test` or `pairwise.wilcox.test`.
`...` | further arguments, currently ignored.

### Value

`out` | a named vector with p-values

### See Also

`multcompLetters`, `xtable`, `pairwise.prop.test`, `pairwise.t.test`, `pairwise.wilcox.test`

### Examples

    data(InsectSprays)
    attach(InsectSprays)
    out <- posthoc.kruskal.dunn.test(count ~ spray, p.adjust="bonf")
    out.p <- get.pvalues(out)
    out.p

    ### a barplot, significant level at p < 0.05
    require(multcompView)
    out.mcV <- multcompLetters(out.p, threshold=0.05)
    Rij <- rank(count)
    Rj.mean <- tapply(Rij, spray, mean)
    ti <- paste(out$method, "\nP-adjustment method:", out$p.adjust.method)
    xx <- barplot(Rj.mean, ylim=c(0, 1.2* max(Rj.mean)),
    xlab="Spray", ylab="Mean rank", main=ti)
    yy <- Rj.mean + 3
    text(xx, yy, lab=out.mcV$Letters)

    ## table format
    dat <- data.frame(Group = names(Rj.mean),
                      meanRj = Rj.mean,
                      M = out.mcV$Letters)
    dat

    ## LaTeX table
    require(xtable)
    xtable(dat, caption=ti, digits=1)

    detach(InsectSprays)

[Package PMCMR version 4.2 Index]