I am trying to calculate the estimated marginal means (aka least squared means) in R in order to do statistical analysis for a univariate dataset and am struggling as all the examples are from multivariate datasets.

My design is count data (wallaby scats from fixed quadrats) with repeated measures (samples taken once a year over three years). *I am interested in the mean changes of scat counts over the three years*. A reduced sample of my data looke like:

My mixed effects model looks like:

scatcount ~ year + (1|plot)

the random effect of plot is included to account for the repeated measures.

I was advised to calculate the estimated marginal means and am using the "emmeans" package in R. However I am struggling to get the code and process right for this. All the examples I can find are comparing two or more fixed and/or random variables so I'm struggling to apply it to my data. I am also unsure how to include the random effect of plot in the EMM calculation, or if I even need to? Any suggestions on how to do this in R would be much appreciate!

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#### Best Answer

You need to do something like this:

`library(lme4) model <- lmer(scatcount ~ year + (1|plot), data = scatdata) library(emmeans) emmeans(model, "year") # display the EMMs pairs(.Last.value) # pairwise comparisons `

I'll consider adding a simple one-factor example somewhere in the documentation.

Note: The *model* is what accounts for the random effect. `emmeans`

just summarizes results from a model; so if the model accounts properly for the random effect(s), you don't need to do anything extra in `emmeans`

.

PS — For that particular response variable, I'm guessing you will have pretty heterogeneous errors (evidenced, e.g., by a horn-shaped scatterplot of residuals versus fitted values). You probably should consider either a transformed response (e.g., `sqrt(scatcount) ~ ...`

) or a generalized linear mixed model for a Poisson response (using, e.g., `lme4::glmer()`

). Such models are also supported by the **emmeans** package but you may want to do additional things to obtain results back on the `scatcount`

scale; see the vignette on transformations and link functions.

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