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Tukey Honest Significant Differences

Source: R/tukey_hsd.R
tukey_hsd.Rd

[Experimental]

Helper function to perform Tukey post-hoc tests. It is used in gafem.

Usage

tukey_hsd(model, ..., out = "long")

Arguments

model

an object of class aov or lm.

...

other arguments passed to the function stats::TukeyHSD(). These include:

  • which: A character vector listing terms in the fitted model for which the intervals should be calculated. Defaults to all the terms.

  • ordered: A logical value indicating if the levels of the factor should be ordered according to increasing average in the sample before taking differences. If ordered is true then the calculated differences in the means will all be positive. The significant differences will be those for which the lwr end point is positive.

out

The format of outputs. If out = "long" a 'long' format (tibble) is returned. If out = "wide", a matrix with the adjusted p-values for each term is returned.

Value

A tibble data frame containing the results of the pairwise comparisons (if out = "long") or a "list-columns" with p-values for each term (if out = "wide").

Examples

# \donttest{
library(metan)
mod <- lm(PH ~ GEN + REP, data = data_g)
tukey_hsd(mod)
#> # A tibble: 81 × 8
#>    term  group1 group2 estimate conf.low conf.high p.adj sign 
#>    <chr> <chr>  <chr>     <dbl>    <dbl>     <dbl> <dbl> <chr>
#>  1 GEN   H1     H10     -0.159    -0.700     0.382 0.995 ns   
#>  2 GEN   H1     H11     -0.0960   -0.637     0.445 1.00  ns   
#>  3 GEN   H1     H12      0.233    -0.308     0.774 0.921 ns   
#>  4 GEN   H1     H13      0.401    -0.140     0.942 0.303 ns   
#>  5 GEN   H1     H2      -0.0433   -0.584     0.498 1.00  ns   
#>  6 GEN   H1     H3      -0.154    -0.695     0.387 0.997 ns   
#>  7 GEN   H1     H4      -0.148    -0.689     0.393 0.998 ns   
#>  8 GEN   H1     H5      -0.103    -0.644     0.438 1.00  ns   
#>  9 GEN   H1     H6      -0.0440   -0.585     0.497 1.00  ns   
#> 10 GEN   H1     H7      -0.0200   -0.561     0.521 1     ns   
#> # … with 71 more rows
tukey_hsd(mod, out = "wide")
#> # A tibble: 14 × 15
#>    term     H10   H11    H12     H13     H2      H3      H4      H5     H6
#>    <chr>  <dbl> <dbl>  <dbl>   <dbl>  <dbl>   <dbl>   <dbl>   <dbl>  <dbl>
#>  1 GEN    0.995  1.00  0.921  0.303   1.00   0.997   0.998   1.00    1.00 
#>  2 GEN   NA      1.00  0.334  0.0375  1.00   1       1       1.00    1.00 
#>  3 GEN   NA     NA     0.585  0.0928  1.00   1.00    1.00    1       1.00 
#>  4 GEN   NA     NA    NA      0.993   0.797  0.352   0.374   0.556   0.795
#>  5 GEN   NA     NA    NA     NA       0.184  0.0406  0.0443  0.0847  0.182
#>  6 GEN   NA     NA    NA     NA      NA      1.00    1.00    1.00    1    
#>  7 GEN   NA     NA    NA     NA      NA     NA       1       1.00    1.00 
#>  8 GEN   NA     NA    NA     NA      NA     NA      NA       1.00    1.00 
#>  9 GEN   NA     NA    NA     NA      NA     NA      NA      NA       1.00 
#> 10 GEN   NA     NA    NA     NA      NA     NA      NA      NA      NA    
#> 11 GEN   NA     NA    NA     NA      NA     NA      NA      NA      NA    
#> 12 GEN   NA     NA    NA     NA      NA     NA      NA      NA      NA    
#> 13 REP   NA     NA    NA     NA      NA     NA      NA      NA      NA    
#> 14 REP   NA     NA    NA     NA      NA     NA      NA      NA      NA    
#> # … with 5 more variables: H7 <dbl>, H8 <dbl>, H9 <dbl>, `2` <dbl>, `3` <dbl>
# }