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

[Ben Bolker]

    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.