glmmTMB syntax to brm() syntax
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 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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_______________________________________________ R-sig-mixed-models at 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.