I'm analysing the results of a M BACI experiment. When trying to estimate means using emmeans, I'm getting this message:
NOTE: A nesting structure was detected in the fitted model: BurnType %in% (SiteClass*Period)
My model is:
result.all.lmer <- lmer(logBatAct ~ BurnType+SiteClass+Period+SiteClass:Period+BurnType:SiteClass:Period + (1|Site) + (1|Site:Period), data=bats) anova(result.all.lmer, ddf="Kenward-Roger")
and to estimate the means:
result.lmer.emmo.B <- emmeans::emmeans(result.all.lmer, ~BurnType) summary(result.lmer.emmo.B)
Have I created the model incorrectly? How can I address this? Should I just try lsmeans instead?