cldList: Compact letter display for lists of comparisons

In rcompanion: Functions to Support Extension Education Program Evaluation

Compact letter display for lists of comparisons

Description

Produces a compact letter display (cld) from pairwise comparisons that were summarized in a table of comparisons

Usage

cldList(
  formula = NULL,
  data = NULL,
  comparison = NULL,
  p.value = NULL,
  threshold = 0.05,
  print.comp = FALSE,
  remove.space = TRUE,
  remove.equal = TRUE,
  remove.zero = TRUE,
  swap.colon = TRUE,
  swap.vs = FALSE,
  ...
)

Arguments

formula	A formula indicating the variable holding p-values and the variable holding the comparisons. e.g. P.adj ~ Comparison.
data	The data frame to use.
comparison	A vector of text describing comparisons, with each element in a form similar to "Treat.A - Treat.B = 0". Spaces and "=" and "0" are removed by default
p.value	A vector of p-values corresponding to the comparisons in the comparison argument
threshold	The alpha value. That is, the p-value below which the comparison will be considered significant
print.comp	If TRUE, prints out a data frame of the modified text of the comparisons. Useful for debugging
remove.space	If TRUE, removes spaces from the text of the comparisons
remove.equal	If TRUE, removes "=" from the text of the comparisons
remove.zero	If TRUE, removes "0" from the text of the comparisons
swap.colon	If TRUE, swaps ":" with "-" in the text of the comparisons
swap.vs	If TRUE, swaps "vs" with "-" in the text of the comparisons
...	Additional arguments passed to multcompLetters

Details

The input should include either formula and data; or comparison and p.value.

This function relies upon the multcompLetters function in the multcompView package. The text for the comparisons passed to multcompLetters should be in the form "Treat.A-Treat.B". Currently by default cldList removes spaces, equal signs, and zeros, by default, and so can use text in the form e.g. "Treat.A - Treat.B = 0". It also changes ":" to "-", and so can use text in the form e.g. "Treat.A : Treat.B".

Value

A data frame of group names, group separation letters, and monospaced separtions letters

Note

The parsing of the formula is simplistic. The first variable on the left side is used as the measurement variable. The first variable on the right side is used for the grouping variable.

It is often helpful to reorder the factor levels in the data set so that the group with the largest e.g. mean or median is first, and so on.

Author(s)

Salvatore Mangiafico, [e-mail]

References

https://rcompanion.org/handbook/G_06.html

See Also

fullPTable

Examples

data(BrendonSmall)

model = aov(Calories ~ Instructor, data=BrendonSmall)

TUK = TukeyHSD(model, "Instructor", ordered = TRUE)

### Convert the TukeyHSD output to a standard data frame

TUK = as.data.frame(TUK$Instructor)
names(TUK) = gsub(" ", ".", names(TUK))

HSD = data.frame(Comparison=row.names(TUK), 
                 diff=TUK$diff, lwr=TUK$lwr, lwr=TUK$lwr, p.adj=TUK$p.adj)

HSD

cldList(p.adj ~ Comparison, data = HSD,
        threshold = 0.05,
        remove.space=FALSE)

rcompanion documentation built on Sept. 17, 2023, 5:07 p.m.