Fortify methods for objects produced by multcomp

This function is deprecated because using broom::tidy() is a better solution to convert model objects.

Usage

# S3 method for class 'glht'
fortify(model, data, ...)

# S3 method for class 'confint.glht'
fortify(model, data, ...)

# S3 method for class 'summary.glht'
fortify(model, data, ...)

# S3 method for class 'cld'
fortify(model, data, ...)

Arguments

model

an object of class glht, confint.glht, summary.glht or multcomp::cld()

data, ...

other arguments to the generic ignored in this method.

Examples

amod <- aov(breaks ~ wool + tension, data = warpbreaks)
wht <- multcomp::glht(amod, linfct = multcomp::mcp(tension = "Tukey"))

tidy(wht) # recommended
#> # A tibble: 3 × 7
#>   term    contrast null.value estimate std.error statistic adj.p.value
#>   <chr>   <chr>         <dbl>    <dbl>     <dbl>     <dbl>       <dbl>
#> 1 tension M - L             0   -10         3.87     -2.58     0.0336 
#> 2 tension H - L             0   -14.7       3.87     -3.80     0.00111
#> 3 tension H - M             0    -4.72      3.87     -1.22     0.447  
fortify(wht)
#> Warning: `fortify(<glht>)` was deprecated in ggplot2 3.6.0.
#> ℹ Please use `broom::tidy(<glht>)` instead.
#>            lhs rhs   estimate
#> tension1 M - L   0 -10.000000
#> tension2 H - L   0 -14.722222
#> tension3 H - M   0  -4.722222

ggplot(tidy(wht), aes(contrast, estimate)) + geom_point()


ci <- confint(wht)
tidy(ci) # recommended
#> # A tibble: 3 × 5
#>   term    contrast estimate conf.low conf.high
#>   <chr>   <chr>       <dbl>    <dbl>     <dbl>
#> 1 tension M - L      -10       -19.4    -0.648
#> 2 tension H - L      -14.7     -24.1    -5.37 
#> 3 tension H - M       -4.72    -14.1     4.63 
fortify(ci)
#> Warning: `fortify(<confint.glht>)` was deprecated in ggplot2 3.6.0.
#> ℹ Please use `broom::tidy(<confint.glht>)` instead.
#>         lhs rhs   estimate       lwr        upr
#> M - L M - L   0 -10.000000 -19.35230 -0.6476956
#> H - L H - L   0 -14.722222 -24.07453 -5.3699178
#> H - M H - M   0  -4.722222 -14.07453  4.6300822

ggplot(tidy(confint(wht)),
       aes(contrast, estimate, ymin = conf.low, ymax = conf.high)) +
   geom_pointrange()


smry <- summary(wht)
tidy(smry) # recommended
#> # A tibble: 3 × 7
#>   term    contrast null.value estimate std.error statistic adj.p.value
#>   <chr>   <chr>         <dbl>    <dbl>     <dbl>     <dbl>       <dbl>
#> 1 tension M - L             0   -10         3.87     -2.58     0.0335 
#> 2 tension H - L             0   -14.7       3.87     -3.80     0.00114
#> 3 tension H - M             0    -4.72      3.87     -1.22     0.447  
fortify(smry)
#> Warning: `fortify(<summary.glht>)` was deprecated in ggplot2 3.6.0.
#> ℹ Please use `broom::tidy(<summary.glht>)` instead.
#>         lhs rhs   estimate       se         t          p
#> M - L M - L   0 -10.000000 3.872378 -2.582393 0.03353428
#> H - L H - L   0 -14.722222 3.872378 -3.801856 0.00114445
#> H - M H - M   0  -4.722222 3.872378 -1.219463 0.44739006

ggplot(mapping = aes(contrast, estimate)) +
   geom_linerange(aes(ymin = conf.low, ymax = conf.high), data = tidy(ci)) +
   geom_point(aes(size = adj.p.value), data = tidy(smry)) +
   scale_size(transform = "reverse")


cld <- multcomp::cld(wht)
tidy(cld) # recommended
#> # A tibble: 3 × 2
#>   tension letters
#>   <chr>   <chr>  
#> 1 L       a      
#> 2 M       b      
#> 3 H       b      
fortify(cld)
#>   lhs letters
#> L   L       a
#> M   M       b
#> H   H       b