easystats
Mislabelled output for `BayesFactor::regressionBF()` models?
With regressionBF, if I inspect a model directly I get
require(discovr)
require(BayesFactor)
album_tib <- discovr::album_sales
album_bf <- BayesFactor::regressionBF(sales ~ adverts + airplay + image, rscaleCont = "medium", data = album_tib)
album_bf
|==================================================================================================| 100%
Bayes factor analysis
--------------
[1] adverts : 1.320123e+16 ±0%
[2] airplay : 4.723817e+17 ±0.01%
[3] image : 6039.289 ±0%
[4] adverts + airplay : 5.65038e+39 ±0%
[5] adverts + image : 2.65494e+20 ±0%
[6] airplay + image : 1.034464e+20 ±0%
[7] adverts + airplay + image : 7.746101e+42 ±0%
Against denominator:
Intercept only
---
Bayes factor type: BFlinearModel, JZS
but with model_parameters(album_bf) I get:
model_parameters(album_bf)
Multiple `BFBayesFactor` models detected - posteriors are extracted from the first numerator
model.
See help("get_parameters", package = "insight").
# Extra Parameters
Parameter | Median | 95% CI | pd | BF
----------------------------------------------------------
mu | 193.03 | [ 183.63, 202.51] | 100% | 1.32e+16
adverts | 0.09 | [ 0.08, 0.11] | 100% | 4.72e+17
sig2 | 4389.28 | [3629.69, 5366.11] | 100% | 6.04e+03
g | 0.42 | [ 0.08, 12.32] | 100% | 5.65e+39
# Fixed Effects
Parameter | BF
--------------------
adverts | 2.65e+20
airplay | 1.03e+20
image | 7.75e+42
The values in column BF map onto the output of album_bf but the labels in Parameter do not. Am I misunderstanding the labels, or is model_parameters() mis-labelling? [For the record I'm using model_parameters() to get nice output and because I want students to learn a consistent workflow with all models.]
You mean, what about using them instead? I don't have space to properly talk about priors so I need something that has defaults comparable to BayesFactor (which I'm useing as a gateway drug for the reader!) I don't have space to get into stuff like brms or stan. If you can point me to something that shows how to mimic Bayesfactor functions using bayestestR then I'll take a look. I couldn't find anything obvious on the bayestestR website.
I should also add that @DominiqueMakowski is exerting considerable pressure to do everything with model-parameters() (and I think his point is quite compelling in terms of students having to learn a workflow that they can apply to almost any model).
What about the bayestestR functions?
Haha I literally said to andy "use parameters instead of bayestestR for that"
But regardless, same issue:
> bayestestR::describe_posterior(album_bf)
Multiple `BFBayesFactor` models detected - posteriors are extracted from
the first numerator model.
See help("get_parameters", package = "insight").
Summary of Posterior Distribution
Parameter | Median | 95% CI | pd | ROPE
---------------------------------------------------------------------
mu | 193.14 | [ 183.86, 202.58] | 100% | [-8.07, 8.07]
adverts | 0.09 | [ 0.08, 0.11] | 100% | [-8.07, 8.07]
sig2 | 4389.83 | [3631.90, 5373.08] | 100% | [-8.07, 8.07]
g | 0.44 | [ 0.08, 11.72] | 100% | [-8.07, 8.07]
adverts-adverts | | | |
airplay-airplay | | | |
image-image | | | |
Parameter | % in ROPE | BF | Prior
----------------------------------------------
mu | 0% | 1.32e+16 |
adverts | 100% | 1.32e+16 |
sig2 | 0% | 1.32e+16 |
g | 98.76% | 1.32e+16 |
adverts-adverts | | |
airplay-airplay | | |
image-image | | |
We probably never implemented full support for RegressionBF in insight:
> insight::find_parameters(album_bf)
$conditional
[1] "adverts-adverts" "airplay-airplay" "image-image"
$extra
[1] "mu" "adverts" "sig2" "g"
This is definitely wrong. I'll take a look.
(However, @profandyfield might I suggest not teaching the {BayesFactor} package for inference anything more complex than a correlation/contingency table/t test 📛)
I think the only context - other rthan those you list - that I use it is comparing linear models (as in the example above). For this case what would you suggest instead? (Bearing in mind the aim is as a gateway to more sophisticated approaches should the user be convinced to find out more about Bayesian methods.)
The bf_*() functions in bayestestR should work. But testing parameters only works for Bayesian models
Sidetracking the original issue, but I also only use {BayesFactor} exclusively for t-tests & correlations, and find BayesFactor::regressionBF confusing: you would expect that it would be consistent with other "regression" functions (lm, glm) and return parameters of the specified model, but it does something quite different and the output is quite confusing
I would also just not use BFs for anything else than simple tests, and simply signpost that doing Bayesian regressions requires a bit more thought / different approach and is outside the scope of the module...
I just saw that the BF function does a combined all variables and indeed tests models.
In this case, you could fit the single models and use bf_models().
(and that might be the reason why parameters or insight fail, because of the dynamic output which we haven't taken into consideration yet)
album_tib <- discovr::album_sales
lm0 <- lm(sales ~ 1, data = album_tib)
lm1 <- lm(sales ~ adverts, data = album_tib)
lm2 <- lm(sales ~ airplay, data = album_tib)
lm3 <- lm(sales ~ image, data = album_tib)
lm4 <- lm(sales ~ adverts + airplay, data = album_tib)
lm5 <- lm(sales ~ adverts + image, data = album_tib)
lm6 <- lm(sales ~ airplay + image, data = album_tib)
lm7 <- lm(sales ~ adverts + airplay + image, data = album_tib)
bayestestR::bf_models(lm0, lm1, lm2, lm3, lm4, lm5, lm6, lm7, denominator = 1)
#> Bayes Factors for Model Comparison
#>
#> Model BF
#> [lm1] adverts 3.50e+16
#> [lm2] airplay 1.39e+18
#> [lm3] image 5.40e+03
#> [lm4] adverts + airplay 6.24e+40
#> [lm5] adverts + image 7.11e+20
#> [lm6] airplay + image 2.67e+20
#> [lm7] adverts + airplay + image 1.00e+44
#>
#> * Against Denominator: [lm0] (Intercept only)
#> * Bayes Factor Type: BIC approximation
Created on 2025-04-18 with reprex v2.1.1
@profandyfield For a soft entry into Bayesian estimation, I would avoid {BayesFactor} because the parameterization there is non-standard, and it has very little support (plotting, emmeans/marginaleffects, etc...) - instead I would teach {rstanarm} (though I typically skip straight to {brms}).
For Bayesian model comparisons, I would also avoid {BayesFactor} because it is limited only to linear models (and also there is much debate regarding the validity of "default priors" for testing in complex models). A very soft entry would be the BIC approximations, as demonstrated above by @strengejacke - it is easy to already do if you know how to fit models, and widely applicable. For BFs for specific hypothesis, I would also switch to {rstanarm}/{brms} + {bridgesampling} (which we wrap in bayestestR with bayesfactor_models()).
Regarding your issue, parameters::model_parameters() and bayestestR::describe_posterior() both have a BF column, but it is not the same - in bayestestR::describe_posterior() it is repreating the BF of the selected (first) model compared to the null, while in parameters::model_parameters() it is the BF table.
I think we discussed this elsewhere, but I think in both cases the BF column is inappropriate as it implies these are parameter-specific Bayes factors (such as those given by bayesfactor_parameters()), which they are not.
We should be returning information by all the parameters provided by BayesFactor::posterior() other than g or those starting with g_.
Thanks for the useful comments @mattansb. Given my time constraints, I will use the BIC approximations in the first instance but have made a note-to-self to look at rstanarm (which I haven't used but looks interesting) in more detail and come back to it later in the writing cycle if there's time.
@profandyfield I used the Regression and Other Stories textbook when I taught intro regression. It uses rstanarm for all of its code examples and I think it's a great text for folks new to modeling in general or to Bayesian modeling in particular.
