[R-sig-ME] Mixed models with a dichotomous outcome, random slopes, and accounting for autocorrelation

[Ben Bolker]

  This seems to have slipped through the cracks, sorry about that.

  lme4 doesn't do correlation structures, but glmmTMB does. The closest 
analogue would be something like

## this should be observation number within group
dat$times <- numFactor(dat$times)

model2 <- glmmTMB(continuous_outcome ~ 1 + Predictor_X + Day +
    (1 + Day | Team / Year) + ar1(times + 0 | Team:Year)

  (your random effect has two | in it; was the second meant to be a / ?)

See https://glmmtmb.github.io/glmmTMB/articles/covstruct.html

On 2023-01-25 5:13 p.m., Adam Roebuck wrote:
> Hello,
> 
> I am attempting to set up a multilevel model with two grouping variables
> (team and year), random slopes for day of the year, and accounting for
> autocorrelation. I have a number of different outcome variables I can use.
> When the outcome variable is continuous, I can set up a simple growth model
> using the nlme package that looks something like the following:
> 
> model1 <- lme(continuous_outcome ~ 1 + Predictor_X + Day,
> 
> random = ~1 + Day | Team | Year, data = dat, method = "REML",
> 
> control=list(opt="optim"), correlation = corAR1()
> 
> However, I now want to build a model with a dichotomous outcome variable.
> As far as I know, nlme cannot account for all of the above and a
> dichotomous outcome. I have, however, seen a few references to glmer (in
> the lme4 package) and glmmTMB being capable of such. I've gone back through
> the archives, though, and am not seeing any clear explanations on how to
> set up such a model.
> 
> Using the parameters above and the variables I specified, could someone
> please help specify what that model might look like in R or at least point
> me in the right direction?
> 
> Thanks,
> Adam
> 




-- 
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
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