R: Compact letter display of pairwise comparisons

cld {lsmeans} | R Documentation

## Compact letter display of pairwise comparisons

### Description

Extract and display information on all pairwise comparisons of least-squares means.

### Usage

    ## S3 method for class 'ref.grid'
    cld(object, details = FALSE, sort = TRUE, by, alpha = 0.05,
        Letters = c("1234567890", LETTERS, letters), reversed = FALSE, ...)
    ## S3 method for class 'lsm.list'
    cld(object, ..., which = 1)

### Arguments

`object` | An object of class `ref.grid`
`details` | Logical value determining whether detailed information on tests of pairwise comparisons is displayed
`sort` | Logical value determining whether the LS means are sorted before the comparisons are produced. When `sort` is `TRUE`, the results are displayed in increasing order if `reversed` is `FALSE` (the default), or in decreasing order if `reversed` is `TRUE`.
`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, and a `by` variable was used in creating `object`, it is used as the `by` variable in `cld`.
`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 `multcompLetters` in the multcompView package.) 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)
`which` | When `object` is a list, this determines which element is analyzed.

### Details

This function uses the Piepho (2004) algorithm (as implemented in the multcompView package) to generate a compact letter display of all pairwise comparisons of least-squares 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.

### Value

When `details == FALSE`, an object of class `summary.ref.grid` (which inherits from `data.frame`) showing the summary of LS means with an added column named `.groups` with the cld information. When `details == TRUE`, a list 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.

### Note

This function requires the multcompView package to be installed. Otherwise an error message is produced.

### Author(s)

Russell V. Lenth

### References

Hans-Peter Piepho (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

### Examples

    warp.lm <- lm(breaks ~ wool * tension, data = warpbreaks)
    warp.lsm <- lsmeans(warp.lm, ~ tension | wool)
    cld(warp.lsm)                  # implicitly uses by = "wool"
    cld(warp.lsm, by = "tension")  # overrides implicit 'by'

    # Mimic grouping bars and compare all 6 means
    cld(warp.lsm, by = NULL, Letters = "||||||||", alpha = .01)

[Package lsmeans version 2.25-5 Index]