I can't get marginaleffects to return all the pairwise comparisons of a three level variable.
Consider this model
library(tidyverse)
library(palmerpenguins)
library(marginaleffects)
library(emmeans)
lm1 <- lm(
bill_length_mm ~ species,
data = penguins
)
If you want the pairwise contrasts of species from emmeans you write
lm1 %>%
emmeans(
pairwise ~ species
)
which returns
$emmeans
species emmean SE df lower.CL upper.CL
Adelie 38.8 0.241 339 38.3 39.3
Chinstrap 48.8 0.359 339 48.1 49.5
Gentoo 47.5 0.267 339 47.0 48.0
Confidence level used: 0.95
$contrasts
contrast estimate SE df t.ratio p.value
Adelie - Chinstrap -10.04 0.432 339 -23.232 <.0001
Adelie - Gentoo -8.71 0.360 339 -24.237 <.0001
Chinstrap - Gentoo 1.33 0.447 339 2.971 0.0089
P value adjustment: tukey method for comparing a family of 3 estimates
However, this, from marginaleffects::avg_comparisons()
avg_comparisons(
lm1,
variables = "species"
)
only reports the first two contrasts:
Contrast Estimate Std. Error z Pr(>|z|) S 2.5 % 97.5 %
Chinstrap - Adelie 10.04 0.432 23.2 <0.001 394.2 9.20 10.89
Gentoo - Adelie 8.71 0.360 24.2 <0.001 428.7 8.01 9.42
Term: species
Type: response
How do I get marginaleffects to report all three contrasts, for all pairwise comparisons of the three levels of species?
If you type ?avg_comparisons or visit the marginaleffects.com website, you will see that this option is clearly documented under the variables argument:
library(palmerpenguins)
library(marginaleffects)
lm1 <- lm(
bill_length_mm ~ species,
data = penguins
)
avg_comparisons(
lm1,
variables = list("species" = "pairwise")
)
#>
#> Contrast Estimate Std. Error z Pr(>|z|) S 2.5 % 97.5 %
#> Chinstrap - Adelie 10.04 0.432 23.23 < 0.001 394.2 9.20 10.890
#> Gentoo - Adelie 8.71 0.360 24.24 < 0.001 428.7 8.01 9.418
#> Gentoo - Chinstrap -1.33 0.447 -2.97 0.00297 8.4 -2.21 -0.452
#>
#> Term: species
#> Type: response