Compact letter display for lists of comparisons

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

Value

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

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".

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.

References

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

Author

Salvatore Mangiafico, mangiafico@njaes.rutgers.edu

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
#>                        Comparison      diff       lwr     lwr.1        p.adj
#> 1   Jason Penopolis-Brendon Small  52.11111 -72.56724 -72.56724 7.548594e-01
#> 2    Melissa Robins-Brendon Small 221.55556  96.87720  96.87720 8.753993e-05
#> 3       Paula Small-Brendon Small 289.44444 164.76609 164.76609 5.990211e-07
#> 4     Coach McGuirk-Brendon Small 391.22222 266.54387 266.54387 4.084650e-10
#> 5  Melissa Robins-Jason Penopolis 169.44444  44.76609  44.76609 3.304461e-03
#> 6     Paula Small-Jason Penopolis 237.33333 112.65498 112.65498 2.777130e-05
#> 7   Coach McGuirk-Jason Penopolis 339.11111 214.43276 214.43276 1.606650e-08
#> 8      Paula Small-Melissa Robins  67.88889 -56.78946 -56.78946 5.339451e-01
#> 9    Coach McGuirk-Melissa Robins 169.66667  44.98832  44.98832 3.256342e-03
#> 10      Coach McGuirk-Paula Small 101.77778 -22.90057 -22.90057 1.562254e-01

cldList(p.adj ~ Comparison, data = HSD,
        threshold = 0.05,
        remove.space=FALSE)
#>             Group Letter MonoLetter
#> 1 Jason Penopolis      a        a  
#> 2  Melissa Robins      b         b 
#> 3     Paula Small     bc         bc
#> 4   Coach McGuirk      c          c
#> 5   Brendon Small      a        a