bug in tukey_hsd: wrong grouping labels when - present

[IndrajeetPatil]

The grouping levels here are a-0 and b-1, but that's not what is returned:

library(rstatix)

g <- c(rep("a-0", 50), rep("b-1", 50))
x <- rnorm(100)
(df <- tibble::as_tibble(cbind.data.frame(g, x)))
#> # A tibble: 100 x 2
#>    g          x
#>    <fct>  <dbl>
#>  1 a-0   -2.08 
#>  2 a-0   -0.527
#>  3 a-0    2.44 
#>  4 a-0   -0.556
#>  5 a-0    0.886
#>  6 a-0    0.655
#>  7 a-0    0.882
#>  8 a-0   -0.262
#>  9 a-0    0.223
#> 10 a-0    0.117
#> # ... with 90 more rows

rstatix::tukey_hsd(aov(x ~ g, data = df))
#> Warning: Expected 2 pieces. Additional pieces discarded in 1 rows [1].
#> # A tibble: 1 x 8
#>   term  group1 group2 estimate conf.low conf.high p.adj p.adj.signif
#> * <chr> <chr>  <chr>     <dbl>    <dbl>     <dbl> <dbl> <chr>       
#> 1 g     1      b        -0.127   -0.521     0.267 0.524 ns

^{Created on 2019-12-23 by the reprex package (v0.3.0)}

Session info

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[kassambara]

Internally, in the turkey_hsd() function, the following R code is used to separate comparisons into groups:

separate(comparison, into= c("group2", "group1"), sep = "-") 

Consequently, If group levels contain special chars, such as "-", a wrong result is returned.

A quick fix that appears in my mind is to systematically apply the function make.names() on the grouping variables before computing TukeyHSD().

Any better suggestion?

[IndrajeetPatil]

This is a super-hacky solution I have adopted in my workflow but I feel like there might be a smarter way to do this-

https://github.com/IndrajeetPatil/pairwiseComparisons/blob/7665dffdbde6354232febafdf7825d05a73b183e/R/pairwise_comparisons.R#L184-L224

I am not sure how make.names would work since I am not familiar with that function.

[kassambara]

With make.names(), all invalid characters are translated to "."

Examples:

make.names(c("a b", "a-b", "10", "a;b"))

Output:

[1] "a.b" "a.b" "X10" "a.b"

[IndrajeetPatil]

Hmm, that will solve the issue but, as a user, I will not be happy that the names were changed by the function. Rarely a good idea since people might want to rely on their names of choices downstream in a script where this function might be used.

[kassambara]

fixed now, thanks!