[R-sig-ME] glmmTMB syntax to brm() syntax

[Simon Harmel]

Ben, can I ask a similar question? Is there also a function similar to
glmmTMB::new_simulate() to easily simulate the following model?

nlme::lme(Y ~ condition + Cognitive_Rate, random= ~1 | subject, data = DATA,
weights = varIdent(form=~1|condition),
 correlation = corSymm(form = ~1| subject))

Thank you!
Simon

On Thu, Oct 24, 2024 at 9:11 PM Ben Bolker <bbolker using gmail.com> wrote:
>
>    Most of the time taken by the brms version is in compilation. It may
> be possible (I don't remember how) to cache the compiled model and
> re-use it for subsequent models, if you are going to be (for example)
> fitting the same model to many different data sets ...
>
> On 10/24/24 21:44, Simon Harmel wrote:
> > Thank you so very much, Ben! And wow, the brm() version is extremely slow.
> >
> > Simon
> >
> > On Thu, Oct 24, 2024 at 11:11 AM Ben Bolker <bbolker using gmail.com> wrote:
> >>
> >>     See below.  The two models (glmmTMB and brms) give sufficiently
> >> similar estimates that I'm confident that the specifications match.
> >>
> >> set.seed(101)
> >> library(glmmTMB)
> >> library(brms)
> >> library(broom.mixed)
> >> library(tidyverse)
> >>
> >> dd <- data.frame(ID = rep(1:100, each = 10),
> >>                    TRIAL_INDEX = rep(1:10, 100),
> >>                    con = rnorm(1000))
> >> dd$pic_percent <- simulate_new(
> >>       ~ con + (0+con | ID) +
> >>           (0+con | TRIAL_INDEX),
> >>       ziformula = ~1,
> >>       family = beta_family(),
> >>       newdata = dd,
> >>       newparams = list(beta = c(0, 0.5), theta = rep(-1,2),
> >>                        betadisp = 1, betazi = -2))[[1]]
> >>
> >>
> >> m1 <- glmmTMB(pic_percent ~ con + (0+con | ID) +
> >>       (0+con | TRIAL_INDEX),
> >>           data=dd,
> >>           family = beta_family(),
> >>           ziformula = ~1)
> >>
> >> ##
> >> https://mvuorre.github.io/posts/2019-02-18-analyze-analog-scale-ratings-with-zero-one-inflated-beta-models/
> >> m2 <- brm(
> >>       bf(pic_percent ~ con + (0+con | ID) +
> >>              (0+con | TRIAL_INDEX),
> >>       zi = ~ 1),
> >>       data=dd,
> >>       family = zero_inflated_beta()
> >> )
> >>
> >>
> >> (purrr::map_dfr(list(glmmTMB = m1, brms = m2), tidy, .id = "model")
> >>       |> select(model, effect, component, group, term, estimate)
> >>       |> pivot_wider(names_from = model, values_from = estimate)
> >> )
> >>
> >>
> >>
> >> On 10/23/24 19:13, Simon Harmel wrote:
> >>> Hello all,
> >>>
> >>> I was wondering what is the closest equivalent of my glmmTMB syntax below
> >>> in brms::brm() syntax?
> >>>
> >>> glmmTMBglmmTMB(pic_percent ~ con +
> >>>                         (0+con | ID) +
> >>>                         (0+con | TRIAL_INDEX),
> >>>                       data=DATA,
> >>>           family = beta_family(),
> >>>           ziformula = ~1)
> >>>
> >>>
> >>> Thank you,
> >>>
> >>> Simon
> >>>
> >>>        [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> R-sig-mixed-models using r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >>
> >> --
> >> Dr. Benjamin Bolker
> >> Professor, Mathematics & Statistics and Biology, McMaster University
> >> Director, School of Computational Science and Engineering
> >> * E-mail is sent at my convenience; I don't expect replies outside of
> >> working hours.
> >>
> >> _______________________________________________
> >> R-sig-mixed-models using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
> --
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> * E-mail is sent at my convenience; I don't expect replies outside of
> working hours.
>