# How to address a detected nesting structure using emmeans

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?

with(bats, table(BurnType, SiteClass, Period))

If that is not the case, you can avoid invoking the separate analyses of each nesting level by specifying nesting = NULL in the emmeans call.