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

[Ben Bolker]

   You should be getting version 1.1.10 from CRAN, unless you're using 
an outdated mirror, see 
https://cran.r-project.org/web/packages/glmmTMB/index.html ... you will 
need version 1.1.10 to avoid the error.

    If you want a dispersion parameter of 1.0 then you probably want 
betadisp = 0 (since the dispersion model uses a log link).

   You also need to provide only a vector of length 1 for theta, since 
you only have a single (scalar) random effect term.  And you need to 
provide two values for betadisp (since you are specifying ~con, and con 
is a two-level factor), i.e.

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



On 2024-10-28 1:39 p.m., Simon Harmel wrote:
> 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.
>>

-- 
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.