emmeans (version 1.4.1)

CLD: Extract and display information on all pairwise comparisons of estimated marginal means.

Description

Extract and display information on all pairwise comparisons of estimated marginal means.

Usage

CLD(object, ...)

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

cld.emmGrid(object, ...)

Arguments

object

An object of class emmGrid

...

Arguments passed to contrast (for example, an adjust method)

This function 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.

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.

Value

When details == FALSE, an object of class summary.ref_grid (which inherits from data.frame) showing the summary of EMMs with an added column named .groups containing the CLD information. When details == TRUE, a list with the object just described, as well as the summary of the contrast results showing each comparison, its estimate, standard error, t ratio, and adjusted P value.

Deprecated

The CLD function and methods are deprecated. Compact-letter displays (CLDs) encourage a misleading interpretation of significance testing by visually grouping means whose comparisons have P > alpha as though they are equal. However, failing to prove two means are different does not prove that they are the same. In addition, CLDs make a hard distinction between P values nearly equal to alpha but on opposite sides.

Some users may find pwpp to be a useful alternative. It produces a plot showing all P values for all pairwise comparisons (or other set of comparisons), and can also show one-sided P values and tests of equivalence or noninferiority. Also, if you insist, cld is still available in the multcomp package, and multcomp::cld(emm) still works.

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.

See Also

cld in the multcomp package, for which a courtesy method is provided for emmGrid objects.