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

[Simon Harmel]

Thank you, Ben. I deleted and installed glmmTMB from CRAN and it is
still version 1.1.9 on my machine with that same error showing up.

I love the 'covstruct' vignette. But I, for example, don't know what
to use in my simulate_new() call below to define the dispersion,
would that be 'sigmadisp'?

dd <- data.frame(ID = rep(1:100, each = 2),
                 con = rep(c("simple","complex"), 100)) %>%
  group_by(ID) %>% mutate(obs=row_number())

dd$VOCD <- simulate_new(
  ~ 0+con + (1|ID),
  dispformula = ~ con,
  newdata = dd,
  newparams = list(beta = c(0, 0.5), theta = rep(-1,2),
                   disp = 1))[[1]]

On Mon, Oct 28, 2024 at 12:10 PM Ben Bolker <bbolker using gmail.com> wrote:
>
>     That's quite old, by R standards (1.1.8 came out a year ago, latest
> version is 1.1.10 -- there's a note in the NEWS for 1.1.10
> <https://cran.r-project.org/web/packages/glmmTMB/news.html> about fixing
> a simulate bug for the beta family
>
>    (It's simulate_new(), not new_simulate())
>
>    The docs say "(‘beta’, ‘betazi’, ‘betadisp’, ‘theta’, etc.)"; in this
> case "etc." includes thetazi (random-effects parameters for ZI terms, if
> any) and thetadisp (ditto, dispersion terms).
>
>   The 'covstruct' vignette is the best place to read about
> parameterization of random-effects components.
>
> On 2024-10-28 1:05 p.m., Simon Harmel wrote:
> > Ben, when I run your code below, I get the following error message: y
> > values must be 0 <= y < 1. My glmmTMB version is: ‘1.1.7’.
> >
> > Also, is there any good documentation explaining all possible names
> > used in argument `newparams=` in glmmTMB::new_simulate()?
> >
> > Thank you!
> > 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.
>