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Questions tagged [brms]

97 questions
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brms - understanding chains, iter and warmup

I am trying to use the brms package's brm function to fit bayesian mixed effect models. The documentation isnt very clear on what exactly is achieved by increasing the number of chains, number of iterations and warmup. It would be helpful if someone…
rAmAnA
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bayes_factor in brms causes R and Rstudio session abort

bayes_factor in brms causes R and Rstudio session abort. I deleted and reinstalled both R and Rstudio. At first it wouldn’t fit brm() models but after I tried remove.packages(c("StanHeaders", "rstan")) install.packages("StanHeaders", repos =…
Bommby
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Fixing parameters through prior selection in RStan

I often see analysts "fixing a parameter" to some value when using Stan by setting a prior on the parameter. For example, the Stan user's guide section on Item Response Models notes that in including alpha ~ std_normal() in the model{} block in a…
socialscientist
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Can I allow for two-level variance in brms

I'm considering a linear multilevel model. It seems that such a model with two-level coefficient can be estimated by brms. However, I'm wondering if it is possible to allow for a two-level structure in the variance of error term such as $\sigma_i^2…
user0131
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Problems with brms package in R Studio

I ran the following model in R studio with brms: model <- brm(bf(formula), data = df_region, prior = bpriors, warmup = 1000, iter = 5000, chains = 2, cores =…
Ozgur Alptekın
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modelsummary display output from lm and brms concurrently with statistics

models <- list( "Linear" = lm(outcome ~ week * food data = df ), "Bayesian" = brm(outcome ~ s(week, k = 4, fx = TRUE, by = food) + food, data = df, family = "zero_one_inflated_beta") ) The following code works when I run it modelsummary(models, …
nerd
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hi all . i am trying to run the bym2 model . at this stage, i have a problem.are you help me?

library(“rstan”) library(“rstudioapi”) library(“parallel”) library(“brms”) rstan_options(auto_write = TRUE) options(mc.cores = parallel::detectgores()) library(pkgbuild) # load packAge find_rtools() # should be TRUE, assuming you have Rtools…
shal
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Error when compiling R packages : Eigen/Core : new: no file or directory

This is my first question on stack ! Hope I follow correctly the guidelines... Device Thinkpad series Manjaro KDE (kernel 5.13) Fresh R install (4.2) Fresh Rstudio install Several packages installed yesterday evening, following approximately this…
user21048379
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Using savage dickey null point hypotheses for arms models

Lets say I have a brms model of y ~ a*b + (1|group) and I'd really like to compare it against an alternative model y ~ a + b + (1|group) (in my example a is time and b is experimental condition). Using hypothesis I could write: hypothesis(m1, c("a:b…
bjw
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Stan model not compiling with brms (only) in combination with Renv: 'omp.h' file not found

I have code to specify a stan model using the brms package. This code works well when using RStudio without a project open. However, when I open an RStudio project, I receive an error when trying to compile the stan model: Error in compileCode(f,…
Jasper
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modelsummary not reading columns from custom tidy and glance functions

Apologies for not having a full reproducible example here, but the models take a fairly long time to run and the model objects are fairly large. I have a chunk of code that to generate a table from three multilevel multinomial logit models run using…
Michael Flynn
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Bug in derivative calculation GI type GAM

I have many hierarchical GAMs fitted with the brm() function of the brms package. Some of my GAMs have a 'I type' structure : y ~ 1 + s(year, by = site, bs = "tp", m = 2) + s(level, bs = "tp") + (1|r|transect), zi ~ 1 + s(year, by = site, bs…
Julien Beaulieu
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Rendering a Quarto blog post trips an error when reading in a brms file object

First, I'll apologize for not having a fuller reproducable example, but I'm not entirely sure how to go about that given the various layers to the question/problem. I'm moving a blog over from Blogdown to a new Quarto-based website and blog. I have…
Michael Flynn
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Both bayes_R2 and loo_R2 get weird estimate 1

I ran a brms model on a dataset containing almost 11000 species using the following command. fit <- brm(formula =brl ~ LH + (1|species), data = data_, cov_ranef = list(species=phyloMat), family =…
Dong Zhang
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