glmmTMB syntax to brm() syntax

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 at 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 at 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

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--
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.

--
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.