I've been trying to bootstrap a linear mixed model with three 2-level categorical fixed factors (and all two-way interactions), and one random factor.
I can get the linear mixed model to run, I can bootstrap the linear mixed model, and I can get the type 3 fixed effects of the linear mixed model. The problem is combining those last two. I'm looking to get bootstrapped type 3 fixed effects of the linear mixed model, and I can't figure out how to get those.
The linear mixed model seems to provide the estimates of fixed effects (which compare fixed effects to a reference category), but not the type 3 fixed effects. To get those, I run an ANOVA on the linear mixed model. I understand how to bootstrap the linear mixed model itself (or a regular ANOVA), but I'm struggling with how to run an bootstrap on an the ANOVA of the linear mixed model, which is what I need to get bootstrapped type 3 fixed effects of the linear mixed model.
I'm using the libraries lme4, lmerTest, and lmeresampler.
Here is the relevant part of my code:
#Run the linear mixed model:
lmm=lmer(unlist(DV) ~ unlist(IV1) + unlist(IV2) + unlist(IV3) + unlist(IV1):unlist(IV2) + unlist(IV1):unlist(IV3) + unlist(IV2):unlist(IV3) + (1 | unlist(randomfactor)), data = table)
#Bootstrap the linear mixed model:
lmm.boot=bootstrap(lmm, type = "residual", B = 5000, resample = c(TRUE, TRUE))
#Get type 3 fixed effects of the linear mixed model:
anova.lmm=anova(lmm)
The output running the ANOVA on the linear mixed model looks like this:
Type III Analysis of Variance Table with Satterthwaite's method
Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
unlist(sex) 44.03 44.03 1 109.041 0.1831 0.6696
unlist(f0groupfemale) 611.01 611.01 1 16.435 2.5406 0.1300
unlist(f0groupmale) 10.37 10.37 1 16.431 0.0431 0.8381
unlist(sex):unlist(f0groupfemale) 149.70 149.70 1 108.462 0.6225 0.4319
unlist(sex):unlist(f0groupmale) 89.36 89.36 1 109.708 0.3716 0.5434
unlist(f0groupfemale):unlist(f0groupmale) 66.19 66.19 1 16.419 0.2752 0.6069
Question: Is there a way to bootstrap the type 3 ANOVA here? I know ANOVA.boot can be used to bootstrap a regular ANOVA, but I can't get it to work with the ANOVA of the linear mixed model.