Questions tagged [brms]
brms is an R package interfacing stan for Bayesian analysis
86 questions
3
votes
1
answer
46
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Calculate marginal effects for random effects model with two crossed random effects
I am trying to get effects marginal of two crossed random effects (using STAN or brms). I understand how to do it for a single random effect following McElreath's book and Kurtz's brms version of the ...
3
votes
0
answers
45
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Fitting models with known and unknown nonlinear shapes in R
I am trying to fit a model for hypothesis-testing in R using mgcv.
The response, Y is hypothesized to be a linear function of <...
- 141
0
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0
answers
13
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Multivariate vs Univariate models in brms: Equivalence and computational efficacy
In R's brms package, I am analyzing multiple response variables. I understand that setting set_rescor(FALSE) in a multivariate ...
- 613
1
vote
1
answer
37
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Is a random intercept necessary for multivariate models?
I’m modeling height and weight as joint outcomes in a Bayesian multivariate model with brms, ...
- 613
1
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0
answers
26
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Bootstrapping spline construction
I wonder if we should bootstrap the construction of smoothing splines?
I am modelling a logistic model with smoothing term in brms (and mgcv). When performing Bootstrap, a normal replaced resampling ...
- 11
0
votes
0
answers
33
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Extracting continuous effects from a brms model after weighting using the marginaleffects package - avg_slopes() or slopes()?
I'd like to estimate the causal effect of the continuous variable perc_quality_plus_palms on the number of counts of different bird species for each combination of Forest.dependency (3 categories) and ...
- 31
4
votes
1
answer
88
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Priors in brms are not working as I expect
I'm new to Bayesian Statistics, and I'm trying to fit a simple Linear Regression using brms and setting priors manually to each parameter, but it does not work as I ...
- 43
2
votes
1
answer
53
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Inflated fixed effects in mixed-effects logistic regression model
I have a dataset with multiple observations per ID and a binary outcome. I am trying to fit a mixed-effects logistic regression, however, the fixed effect estimate of the intercept is extremely large ...
- 123
0
votes
0
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7
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Sparse adjacency matrix for CAR in brms?
I want to fit a model in the R package brms. My data consists of spatial polygons and I want to use conditional autoregression to account for autocorrelation. This is possible in brms but requires a ...
- 119
0
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0
answers
20
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Is forcing correlation between parameter values allowed in bayesian regression
I am using bayesian nonlinear regression in brms to fit some model parameters, and I'm running into some issues getting MCMC chains to converge. I know this is ...
- 358
0
votes
0
answers
11
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Fitting nonlinear Bayesian regression with a summation term in brms
I'm trying to fit parameters for a Holling type II curve for multiple prey items. This takes the form:
$$
\frac{dP_i}{dt} = \frac{a_iP_i}{1 +\sum_j{a_jh_jP_j}}
$$
where $P_i$ is density of prey ...
- 358
0
votes
0
answers
19
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Bayesian model missing outliers at cutoff in data
I am having trouble getting the model to fit. I have ED50 values of chlorophyll in corals during a heating experiment. I have 4 reef sites and 4 species of coral with ~14 corals per site-species group....
- 11
0
votes
0
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46
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2-way interaction with emtrends or emmeans for a continues and categorical variable
I have a dataset with a continuous outcome variable (curiosity) and three independent variables: age and accuracy (both categorical with two levels), and confidence that has a linear and quadratic ...
- 1
1
vote
1
answer
32
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Propagating measurement uncertainty with posterior predictions as data in another model
I'm working on a modeling approach that incorporated estimates of measurement uncertainty trying to use brms in R. I'm working from the example in chapter 14 of ...
- 358
1
vote
0
answers
38
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Multilevel model where skew of random effect depends on an independent variable
I am trying to construct a model where the skew of the distribution of a random effect changes with an independent variable. I'd eventually like to fit this using ...
- 358
2
votes
1
answer
46
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Is it okay to have two separate interactions with the same variable in one model?
My main model is this:
...
- 375
1
vote
1
answer
47
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How to plot posterior marginal means for categorical variables?
I ran this model. Each categorical variable has three levels. How can I plot the results such as posterior marginal means for each six levels by country?
...
- 375
0
votes
0
answers
72
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How to use posterior predictions from one model (standard curve) as an outcome variable in another model?
I'm working with a dataset concerning the concentration of a large number of different chemical compounds in a mixture, using a Bayesian approach (with brms in R). The instrument that measures the ...
- 358
4
votes
3
answers
141
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How to fit a Bayesian model to a mixture of Beta and One-Zero inflated data?
I have very noisy data, which I believe is created through interactions of multiple physical processes. In the mapping $Y = f(X),$ $Y$ is a ratio $[0, 1]$ and $X \ge 0.$ While $Y$ is a function of $X,$...
- 145
0
votes
0
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87
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post-hoc test for multinomial logistic regression brm model (categorical response)
I apologise as I am very new to this package and I really appreciate any help I can get.
I have a brms model with a categorical response variable (Species) with the ...
Leo
3
votes
1
answer
94
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The default covariance structure implicitly assumed in the brms formula
Background: The brms official page provides the following example code to illustrate the usage of the package:
...
- 133
0
votes
0
answers
20
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Estimating markov transition matrix using total elevator "ups" and "downs" by floor
I have data on elevator presses and I am hoping to use them to estimate a Markov transition matrix, so I can ultimately estimate how frequently people go to different floors.
For each floor from 1-4, ...
- 156
1
vote
0
answers
32
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Inconsistent posterior from hierarchical survival model
I asked about this question on Stan forum but no one replied so dual posting here. I'd really appreciate some insight, as I'm completely stuck.
I’m trying to do hierarchical survival modeling using ...
- 81
3
votes
1
answer
91
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Calculating contrasts of marginal effects with marginaleffects for brms model
I have fitted a logistic model with brms and want to calculate the average marginal effects (AMEs).
...
- 97
0
votes
1
answer
53
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Interaction: Posterior comparison brms, difference between as_draws, and posterior_predict. Is it correct to interpret posterior_predict instead?
I have an interaction effect in my model, and I want to extract the posterior of each of my parameter in order to compare them and make inference about them. I couldn't simply use the as_draws() ...
0
votes
0
answers
32
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Likert scale study - ordinal regression model
My linguistics rating experiment contains 36 stimuli in total for rating. There are 6 themes (e.g. doctor, farm, etc), and each theme has 3 conditions (good, bad, mixed), and each condition has 2 ...
Joy Fu
4
votes
1
answer
552
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Setting priors for categorical variables in bayesian multilevel model analysis with BRMS package (repost)
I am reposting the same question that I made on Stack Overflow. I am new with Bayesian analysis methods and I am still struggling understanding some concepts regarding priors. I am running a model ...
- 41
0
votes
0
answers
26
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Include error on the predictor from mean and asymetric credible interval
I am doing non-linear models with brms. My model is :
...
Julien Beaulieu
0
votes
0
answers
24
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How to select a proper prior to control the time dependent structure of variable?
I am new in analyzing RCT data and not familiar with the techniques that are always used in RCT analysis.
I am analyzing a dataset of a study: An RCT study with 50 participants; the data was collected ...
- 364
0
votes
0
answers
42
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Results dirichlet regression - brms vs DirichelReg comparison
I am new to Dirichlet regression, but I am trying to understand why model outputs are potentially different when I use two different R packages, and how I could interpret the slope and intercept ...
- 1
3
votes
1
answer
276
views
Bayesian linear regression: How to enforce constraint on the sum of coefficients?
I have a linear regression problem in which my $X$ matrix is not full rank. Here is a small example:
$$X =
\left[\begin{array}{rrrr}
-1 & 0 & 0 & 1 \\
1 & 0 & -1 & 0 \\
0 &...
- 471
1
vote
0
answers
69
views
How to improve bayesian logistic regression model with priors
I'm trying to fit a bayesian logistic regression model to calculate the expected goals (xG) of certain shootings data in football. My model has some simple features where I first fit a model with ...
- 389
1
vote
0
answers
32
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Is it possible to estimate effects using Bayesian modelling after matching?
I am following [Greifer 2023][1] to estimate the effect size after (genetic) matching, where I am using bootstrapping to estimate the confidence intervals. Since I have a hierarchical setup with ...
- 51
0
votes
1
answer
238
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Interpreting Coefficients of brms Bernoulli family model
I am struggling with interpreting model results from a brm() model. The first result uses scaled and centered data with command scale(df$column, scale = TRUE, center = TRUE).
...
blake.struthers
2
votes
1
answer
294
views
How to Compute Mean Ratios and Their 95% Confidence Intervals in a Bayesian Model
I am working on a Bayesian model using the brm function from the brms package in R, and I am interested in comparing mean responses of different groups. Specifically, I would like to calculate the ...
- 613
1
vote
0
answers
40
views
Proper analysis of completely crossed design with subjects and items as random effects (brms)
I have the following study design:
stimuli: 240 pictures:
6 pictures of 40 students each
(each student fixated one of six points and during each fixation one picture was taken)
each stimulus was ...
- 11
1
vote
1
answer
197
views
Calculating percentage change from emmeans
A related question was asked on this thread How to calculate percentage difference of geometric means with emmeans?, but I still need some help.
Instead of calculating the absolute difference between ...
- 11
1
vote
2
answers
32
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Incorporating neighboring years in multilevel model, estimated in Stan using brms
I am estimating a multilevel model in Stan, using the brms package. Specifically, I am estimating a model of the following form:
m1 <- brm(y ~ 1 + (1 | year))
...
- 23
4
votes
1
answer
154
views
Is it possible to use smooth functions as part of a nonlinear regression?
Background
I am fitting nonlinear regressions with a single response and two predictors. I know the relationship between the response and each of the predictors, but I do not know how they interact. I ...
- 20.4k
1
vote
1
answer
55
views
Why do you always need to interact the covariates with the slope in mutlilevel models?
On a number of occassions, I have seen people remark that you should always interact your covariates with the with your slope when running multilevel models. That is, for example, you should not run ...
1
vote
0
answers
34
views
Sourcing Informative Priors from an already conducted Empirical Study in brms package in R
I am conducting two studies (with 15 participants) and my study is based on two already conducted studies with a very similar objective and method. One of the studies contain only the results, and one ...
0
votes
1
answer
36
views
Access to the interaction of two three level factors on a mixed model
Using a mixed model (either frequentist lmer or bayesian brms) I have an issue regarding an interaction in my model.
I have two factor variable of three level : condition (0-1-2) and Tps_real (0-300-...
1
vote
0
answers
104
views
Bounded uniform prior in R
I have been fitting a bayesian GLM using brms. The code works well but when I loop this over several data and make it a bit more complex, R encounters a fatal error and crashes. This seems to be ...
0
votes
1
answer
83
views
Non-linear formulas in mgcv
in brms (which is heavily based on mgcv) there is a possibility to define non-linear formulas (meaning not linear in parameters). However, for different reasons I need to use mgcv.
E.g. the model
<...
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1
vote
0
answers
40
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Measuring uncertainty in edge weights using Bayesian modeling and brms in R
I'm interested in using Bayesian models to measure uncertainty in edge weights within social networks. Specifically, I have been trying to replicate how this package works but using brms: https://...
- 11
2
votes
1
answer
603
views
brms model specification with 3 (crossed or nested?) levels
I have a data set that looks like this toy data
...
- 43
2
votes
1
answer
416
views
Is it possible to specify a nested autocorrelation term when working with a hierarchical structure (GAM)?
I am modelling the occurrence of a species at 5 different sites on an hourly basis (presence/absence), based on a range of temporal predictors (e.g. time of the year, day/night cycle, tides ...). ...
- 309
0
votes
1
answer
64
views
Title: How to fit a Frequentist Equivalent of Bayesian mixed-effects model with nlme or lme4 and obtain category-specific variances and intercepts?
I am interested in fitting a Bayesian mixed-effects model to my data using the brms package. My data includes three grouping variables (Category, BioRep, and TechRep), and I want to estimate category-...
- 165
1
vote
0
answers
132
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bayesian problem using inverse gamma: negative initial values
My study involves a dependent variable measuring reading times (minimum value = 0.3) and two categorical variables (y = "quick" or "slow"; t = "cute" or "ugly") ...
- 375
5
votes
1
answer
1k
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How to interpret elpd_diff of Bayesian LOO estimate in Bayesian Logistic Regression
I have conducted a Bayesian Logistic regression, and I would like to compare 2 models : one model with one continuous predictor (M1) and one model without predictor (M0). The outcome is a binary ...
- 61