cldList: 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,
  ...
)

Value

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

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

Author

Salvatore Mangiafico, mangiafico@njaes.rutgers.edu

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".

References

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

Examples

Run this code

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)

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