First of all I apologize as some might see this a stupid question, but I cannot manage to find the answer.

I am using brms package in R. I have two models, an interaction and a simple model, that roughly have similar distributions of data by a factor of 3 levels (TrialRep) model1 <- brm(Inter_div_abs~TrialRep + (1|ID/AbsSuj), data=totaldf1, family=student), and an interaction with grouping factor in the second model (TrialRep*Group) model2 <- brm(Inter_div_abs~TrialRep*Group + (1|ID/AbsSuj), data=totaldf2, family=student). I would expect the population-effect estimates in both models to be around the same scale, but this is not the case. When I plot the conditional_effects I have the following results:

conditional_effects plot composite

In the y axis scale it is obvious something is not well. I post also the summary of both models:

This is population effects for model1 (only TrialRep)

Population-Level Effects: 
          Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
Intercept     1.46      0.13     1.20     1.73 1.00    11034    21440
TrialRep2    -1.03      0.07    -1.18    -0.90 1.00    57843    51081
TrialRep3    -1.15      0.07    -1.29    -1.01 1.00    56529    50206

And this is population effects for model2 (interaction TrialRep*Group)

Population-Level Effects: 
                 Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
Intercept            3.77      0.20     3.39     4.16 1.00    11466    20753
TrialRep2           -1.83      0.06    -1.94    -1.72 1.00    58790    57464
TrialRep3           -2.21      0.06    -2.33    -2.10 1.00    58552    56927
GroupI              -0.08      0.28    -0.63     0.46 1.00    10058    18532
TrialRep2:GroupI     0.98      0.08     0.82     1.14 1.00    60255    58130
TrialRep3:GroupI     1.04      0.08     0.88     1.20 1.00    60912    57605

Given that the datasets are based on a repetition of the same experiment I would expect them to be at the same scale as well, but this is not the case. I understand what I am modeling with this specification is Trial repetition 1 as Intercept and then model calculates the estimated differences in the next 2 levels, but I cannot figure out how to specify this simple model in order to have uncentered results and therefore, have a straightforward reading of the results.

Even if they come from different samples, in a sanity check calculating means from these two samples I obtain these results, which are clearly inside the scale I would expect, that is captured by the interaction model or model2.

#Simple Model: Group*TrialRep

> mean(totaldf1[totaldf1$TrialRep =="1",]$Inter_div_abs, na.rm=TRUE)
[1] 5.866142
> mean(totaldf1[totaldf1$TrialRep =="2",]$Inter_div_abs, na.rm=TRUE)
[1] 2.410974
> mean(totaldf1[totaldf1$TrialRep =="3",]$Inter_div_abs, na.rm=TRUE)
[1] 1.306225

#Interaction Model: Group*TrialRep

> mean(totaldf2[totaldf2$TrialRep =="1",]$Inter_div_abs, na.rm=TRUE)
[1] 5.607245
> mean(totaldf2[totaldf2$TrialRep =="2",]$Inter_div_abs, na.rm=TRUE)
[1] 3.41219
> mean(totaldf2[totaldf2$TrialRep =="3",]$Inter_div_abs, na.rm=TRUE)
[1] 2.906711

Final test, doing it in a frequentist approach, I get the fixed effects estimators close to what I would be expecting according to previous sanity check.

> m <- lmer(Inter_div_abs~ TrialRep + (1|ID/AbsSuj), data=totaldf)
boundary (singular) fit: see help('isSingular')
> m
Linear mixed model fit by REML ['lmerModLmerTest']
Formula: Inter_div_abs ~ TrialRep + (1 | ID/AbsSuj)
   Data: totaldf
REML criterion at convergence: 63112.62
Random effects:
 Groups    Name        Std.Dev.
 AbsSuj:ID (Intercept) 0.0000  
 ID        (Intercept) 0.9875  
 Residual              4.6132  
Number of obs: 10694, groups:  AbsSuj:ID, 36; ID, 18
Fixed Effects:
(Intercept)    TrialRep2    TrialRep3  
      5.872       -3.458       -4.570  

I am posting the complete code for modeling I am using and I also upload the dataset and can be accessed from this link.

totaldf <- read.csv("totaldata2reduced.csv")

#Make sure this columns are factors
totaldf[,names] <- lapply(totaldf[,names],factor)

#Control of outliers
q <- quantile(totaldf$Inter_div_abs, probs = 0.99)
for(i in 1:nrow(totaldf)){#if outlier, p50=0
  tmp <- totaldf$Inter_div_abs[i]
  totaldf$Inter_div_abs[i] <- ifelse(totaldf$Inter_div_abs[i]>q,NA,tmp)

#Specify prior
bprior2 <- get_prior(Inter_div_abs~ (1|TrialRep) + (1|ID/AbsSuj), data=totaldf)
#Edit prior
bprior2$prior[1] <- "student_t(3, 2, 3)"
bprior2$prior[2] <- "student_t(3, 0, 3)"

#Specify the model
total_bayesian_mlm2 <- brm(Inter_div_abs~ TrialRep + (1|ID/AbsSuj), data=totaldf, family=student,prior=bprior2, chains=4, cores=4, iter=20000, warmup=2000, init='0', control=list(adapt_delta=0.9, max_treedepth = 10))

Thanks in advance!

  • $\begingroup$ This question seems hard to answer without the data. Can you provide us with the data? Or a dataset which reproduces the issue and is okay to share even if it's not the "actual" data? $\endgroup$
    – dipetkov
    Feb 11, 2023 at 10:09
  • $\begingroup$ You can also consider asking the question on the Stan forum: discourse.mc-stan.org. $\endgroup$
    – dipetkov
    Feb 11, 2023 at 10:19
  • $\begingroup$ Thank you! I thought it could be a specification problem, not a programming problem, that's why I asked here. $\endgroup$ Feb 13, 2023 at 9:52
  • $\begingroup$ That may be the case. But then you provide few details about your data, variables, statistical problem formulation and no minimal reproducible example. $\endgroup$
    – dipetkov
    Feb 13, 2023 at 9:58
  • $\begingroup$ I understand, I also could have edited that, but the question was closed. Anyhow I am taking your advice and asking the question in Stan forum. Thanks again. $\endgroup$ Feb 13, 2023 at 10:11

1 Answer 1


I finally understood the family=student was not appropriate in this case. The distribution was closer to family=gaussian or even family="skew_normal" and this was specially important in the model with a single predictor. I finally decided to compare the models through pp_check() and other model comparators like loo_compare() for instance.

So takeaway message, probably obvious for most of you (but a learning for me), we need to always take account of different diagnostics to specify appropriately the model.


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