emmeans: CLD.emmGrid – R documentation

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CLD.emmGrid

Compact letter displays

Description

A method for multicomp::cld() is provided for users desiring to produce compact-letter displays (CLDs). This method uses the Piepho (2004) algorithm (as implemented in the multcompView package) to generate a compact letter display of all pairwise comparisons of estimated marginal means. The function obtains (possibly adjusted) P values for all pairwise comparisons of means, using the contrast function with method = "pairwise". When a P value exceeds alpha, then the two means have at least one letter in common.

Usage

## S3 method for class 'emmGrid'
cld(object, details = FALSE, sort = TRUE, by,
  alpha = 0.05, Letters = c("1234567890", LETTERS, letters),
  reversed = FALSE, ...)

Arguments

`object`	An object of class `emmGrid`
`details`	Logical value determining whether detailed information on tests of pairwise comparisons is displayed
`sort`	Logical value determining whether the EMMs are sorted before the comparisons are produced. When `TRUE`, the results are displayed according to `reversed`.
`by`	Character value giving the name or names of variables by which separate families of comparisons are tested. If NULL, all means are compared. If missing, the object's `by.vars` setting, if any, is used.
`alpha`	Numeric value giving the significance level for the comparisons
`Letters`	Character vector of letters to use in the display. Any strings of length greater than 1 are expanded into individual characters
`reversed`	Logical value (passed to `multcompView::multcompLetters`.) If `TRUE`, the order of use of the letters is reversed. In addition, if both `sort` and `reversed` are TRUE, the sort order of results is reversed.
`...`	Arguments passed to `contrast` (for example, an `adjust` method)

Note

We warn that such displays encourage a poor practice in interpreting significance tests. CLDs are misleading because they visually group means with comparisons P > alpha as though they are equal, when in fact we have only failed to prove that they differ. As alternatives, consider pwpp (graphical display of P values) or pwpm (matrix display).

References

Piepho, Hans-Peter (2004) An algorithm for a letter-based representation of all pairwise comparisons, Journal of Computational and Graphical Statistics, 13(2), 456-466.

Examples

if(requireNamespace("multcomp")) {
    pigs.lm <- lm(log(conc) ~ source + factor(percent), data = pigs)
    pigs.emm <- emmeans(pigs.lm, "percent", type = "response")
    multcomp::cld(pigs.emm, alpha = 0.10, Letters = LETTERS)
}

emmeans

Estimated Marginal Means, aka Least-Squares Means

v1.6.0

GPL-2 | GPL-3

Authors

Russell V. Lenth [aut, cre, cph], Paul Buerkner [ctb], Maxime Herve [ctb], Jonathon Love [ctb], Hannes Riebl [ctb], Henrik Singmann [ctb]

Initial release

2021-04-25