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I need to create a plot from a glmer model, and I tried to use EMMIP function for this:

model<-glmer(Accuracy ~ day, dataframe, family = 'binomial')
emmip(model, ~ day, xlab = "day", ylab = "Accuracy", main = "XXX")

Although it produces a seemingly accurate plot, it has a strange y-axis labelling. It is strange because I want it to be mean percentage of accuracy, but it shows definitely something else. It is interesting that when I use emmip() with an ANOVA model I don't have this problem. Does anybody know if there is anything I could do to have accurate information on y-axis?

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  • $\begingroup$ can you tell us what kind of plot this is supposed to be, and what package the emmip() function comes from? $\endgroup$ – Ben Bolker Aug 25 '18 at 23:36
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You probably need type="response"; the default is to make predictions on the linear predictor scale, which for a binomial model is the logit or log-odds scale.

From ?emmeans:emmip:

type: As in ‘predict.emmGrid’, this determines whether we want to inverse-transform the predictions (‘type = "response"’) or not (any other choice). The default is ‘"link"’, unless the ‘"predict.type"’ option is in force; see ‘emm_options’.

By the way, if we're being picky, this will be a proportion response (0-1), not a percentage (0-100); I don't know offhand if there's a way to multiply the prediction by 100.

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  • $\begingroup$ Ben Bolker, thank you very much - the problem is solved!! $\endgroup$ – Tasha Aug 26 '18 at 9:25

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