Like in OLS / ML or other frequentists methods of model parameter estimation, standardizing the parameters of Bayesian (generalized) linear regression models can allow for the comparison of so-called “effects” within and between models, variables and studies.

As with frequentists methods, standardizing parameters should not be the only method of examining the role different predictors play in a particular Bayesian model, and this vignette generally assumes that the issues of model convergence, goodness of fit and model selection have already been taken care of. (Learn more about how to become a Bayesian master with the `bayestestR`

package.)

We will examine the predictive role of overtime (`xtra_hours`

), number of compliments given to the boss (`n_comps`

) and seniority in predicting workers salaries. Let’s fit the model:

```
library(rstanarm)
data("hardlyworking", package = "effectsize")
head(hardlyworking)
```

```
> salary xtra_hours n_comps age seniority
> 1 19745 4.2 1 32 3
> 2 11302 1.6 0 34 3
> 3 20636 1.2 3 33 5
> 4 23047 7.2 1 35 3
> 5 27342 11.3 0 33 4
> 6 25657 3.6 2 30 5
```

```
<- stan_glm(salary ~ xtra_hours + n_comps + seniority,
mod data = hardlyworking,
prior = normal(0, scale = c(1, 0.5, 0.5), autoscale = TRUE), # set some priors
refresh = 0)
::model_parameters(mod, test = NULL) parameters
```

```
> # Fixed effects
>
> Parameter | Median | 89% CI | Rhat | ESS | Prior
> ----------------------------------------------------------------------------------------
> (Intercept) | 10023.20 | [9365.61, 10724.72] | 0.999 | 5405 | Normal (20000 +- 15495.02)
> xtra_hours | 1236.25 | [1189.92, 1285.99] | 1.000 | 4756 | Normal (0 +- 1587.80)
> n_comps | 2964.35 | [2754.07, 3165.00] | 1.000 | 5032 | Normal (0 +- 3755.71)
> seniority | 439.46 | [ 286.51, 605.06] | 0.999 | 4283 | Normal (0 +- 2702.93)
>
> Using highest density intervals as credible intervals.
```

Looking at the un-standardized (“raw”) parameters, it looks like all predictors positively predict workers’ salaries, but which has the highest predictive power? Unfortunately, the predictors are not on the same scale (hours, compliments, years), so comparing them is hard when looking at the raw data. This is where standardization comes in.

Like with frequentists models we can choose from the same standardization methods. Let’s use the (slow) `"refit"`

method.

```
library(effectsize)
standardize_parameters(mod, method = "refit", ci = 0.89)
```

```
> # Standardization method: refit
>
> Parameter | Median (std.) | 89% CI
> -------------------------------------------
> (Intercept) | -2.63e-04 | [-0.03, 0.03]
> xtra_hours | 0.78 | [ 0.75, 0.81]
> n_comps | 0.39 | [ 0.37, 0.42]
> seniority | 0.08 | [ 0.05, 0.11]
```

Note that the central tendency of the posterior distribution is still the *median* - the median of the standardized posterior distribution. We can easily change this, of the type of credible interval used:

```
library(effectsize)
standardize_parameters(mod, method = "basic", ci = 0.89,
centrality = "MAP", ci_method = "eti")
```

```
> # Standardization method: basic
>
> Parameter | MAP (std.) | 89% CI
> ---------------------------------------
> (Intercept) | 0.00 | [0.00, 0.00]
> xtra_hours | 0.78 | [0.75, 0.81]
> n_comps | 0.39 | [0.37, 0.42]
> seniority | 0.08 | [0.05, 0.11]
```

As we can see, working harder (or at least for longer hours) has stronger predictive power than complementing or seniority. (Do note, however, that this does not mean that if you wish to have a higher salary you should work overtime - the raw parameters seem to suggest that complementing your boss is the way to go, with one compliment worth almost 3.5 times **more** than a full hours’ work!)

In classical frequentists models, the computation of *η*^{2} or *η*_{p}^{2} is straightforward: based on the right combinations of sums-of-squares (*SS*s), we get the correct proportion of variance accounted for by some predictor term. However such a computation is not as straightforward for Bayesian models, for various reasons (e.g., the model-*SS* and the residual-*SS* don’t necessarily sum to the total-*SS*). Although some have proposed Bayesian methods of estimating explained variance in ANOVA designs (Marsman et al. 2019), these are not yet easy to implement with `stan`

-based models.

An alternative route to obtaining effect sizes of explained variance, is via the use of the * posterior predictive distribution* (

By sampling from the PPD, we can decompose the sample to the various *SS*s needed for the computation of explained variance measures. By repeatedly sampling from the PPD, we can generate a posterior distribution of explained variance estimates. But note that **these estimates are conditioned not only on the location-parameters of the model, but also on the scale-parameters of the model!** So it is vital to validate the PPD before using it to estimate explained variance measures.

Let’s factorize out data from above:

```
$age_f <- cut(hardlyworking$age,
hardlyworkingbreaks = c(25,35,45), right = FALSE,
labels = c("Young", "Less_young"))
$comps_f <- cut(hardlyworking$n_comps,
hardlyworkingbreaks = c(0,1,2,3),
include.lowest = TRUE,
right = FALSE)
table(hardlyworking$age_f,hardlyworking$comps_f)
```

```
>
> [0,1) [1,2) [2,3]
> Young 124 188 114
> Less_young 13 34 27
```

And fit our model:

```
# use (special) effects coding
contrasts(hardlyworking$age_f) <- bayestestR::contr.bayes
contrasts(hardlyworking$comps_f) <- bayestestR::contr.bayes
<- stan_glm(salary ~ age_f * comps_f,
modAOV data = hardlyworking, family = gaussian(),
refresh = 0)
```

We can use `eta_squared_posterior()`

to get the posterior distribution of *e ta*

```
<- eta_squared_posterior(modAOV,
pes_posterior draws = 500, # how many samples from the PPD?
partial = TRUE, # partial eta squared
# type 3 SS
ss_function = car::Anova, type = 3)
```

`> Simulating effect size... This can take a while...`

`head(pes_posterior)`

```
> age_f comps_f age_f:comps_f
> 1 0.028 0.161 0.0024
> 2 0.030 0.117 0.0252
> 3 0.014 0.091 0.0078
> 4 0.035 0.112 0.0118
> 5 0.017 0.100 0.0054
> 6 0.126 0.058 0.0013
```

`::describe_posterior(pes_posterior, rope_range = c(0, 0.1), test = "rope") bayestestR`

```
> # Description of Posterior Distributions
>
> Parameter | Median | 89% CI | 89% ROPE | % in ROPE
> --------------------------------------------------------------------
> age_f | 0.027 | [0.000, 0.060] | [0.000, 0.100] | 100.000
> comps_f | 0.135 | [0.068, 0.192] | [0.000, 0.100] | 14.350
> age_f:comps_f | 0.010 | [0.000, 0.031] | [0.000, 0.100] | 100.000
```

Compare to:

```
<- lm(salary ~ age_f * comps_f,
modAOV_f data = hardlyworking)
eta_squared(car::Anova(modAOV_f, type = 3))
```

```
> Parameter | Eta2 (partial) | 90% CI
> ---------------------------------------------
> age_f | 0.03 | [0.01, 0.05]
> comps_f | 0.13 | [0.09, 0.18]
> age_f:comps_f | 6.65e-03 | [0.00, 0.02]
```

Gelman, Andrew, John B Carlin, Hal S Stern, and Donald B Rubin. 2014. “Bayesian Data Analysis (Vol. 2).” *Boca Raton, FL: Chapman*.

Marsman, Maarten, Lourens Waldorp, Fabian Dablander, and Eric-Jan Wagenmakers. 2019. “Bayesian Estimation of Explained Variance in ANOVA Designs.” *Statistica Neerlandica* 73 (3): 351–72.