# Chapter 11 Complex models and reparameterization

Now that we know how to fit simple regression models using Stan syntax, we can now turn to more complex cases, such as the hierarchical models that we fit in brms in chapter 5. Fitting such models in Stan allows us a great deal of flexibility. However, a price to be paid when using Stan is that we need to think about how exactly we code the model. In some cases, two pieces of computer code that are mathematically equivalent might behave differently due to the computer’s limitations; in this chapter, we will learn some of the more common techniques needed to optimize the model’s behavior. In particular, we will learn how to deal with convergence problems using what is called the non-centered reparameterization.

## 11.1 Hierarchical models with Stan

In the following sections, we will revisit and expand on some of the examples from chapter 5.

### 11.1.1 Varying intercept model with Stan

Recall that in section 5.2, we fit models to investigate the effect of cloze probability on EEG averages in the N400 spatiotemporal time window. For our first model, we’ll make the (implausible) assumption that only the average signal varies across subjects, but all subjects share the same effect of cloze probability. This means that the likelihood incorporates the assumption that the intercept, $$\alpha$$, is adjusted with the term $$u_i$$ for each subject.

$\begin{equation} signal_n \sim \mathit{Normal}(\alpha + u_{subj[n]} + c\_cloze_n \cdot \beta,\sigma) \end{equation}$

\begin{equation} \begin{aligned} \alpha &\sim \mathit{Normal}(0,10)\\ \beta &\sim \mathit{Normal}(0,10)\\ u &\sim \mathit{Normal}(0,\tau_u)\\ \tau_{u} &\sim \mathit{Normal}_+(0,20) \\ \sigma &\sim \mathit{Normal}_+(0,50) \end{aligned} \end{equation}

Here $$n$$ represents each observation, the $$n$$th row in the data frame and $$subj[n]$$ is the subject that corresponds to observation $$n$$. We present the mathematical notation of the likelihood with “multiple indexing” [see the Stan users guide, available from mc-stan.org]: the index of $$u$$ is provided by the vector $$subj$$.

Before we discuss the Stan implementation, let’s see what the vector $$\mu$$, the location of the normal likelihood, looks like. There are 2863 observations; that means that $$\boldsymbol{\mu}=\{\mu_1,\mu_2, \ldots, \mu_{2863}\}$$. We have 37 subjects which means that $$\boldsymbol{u}=\{u_1,u_2, \ldots, u_{37}\}$$. The following equation shows that the use of multiple indexing allows us to have a vector of adjustments with only 37 different elements, with a total length of 2863. In the equation below, the multiplication operator $$\circ$$ is the Hadamard product (Fieller 2016): when we write $$X\circ B$$, both $$X$$ and $$B$$ have the same dimensions $$m\times n$$, and each cell in location $$[i,j]$$ (where $$i=1,\dots,m$$, and $$j=1,\dots,n$$) in $$X$$ and $$B$$ are multiplied to give a matrix that also has dimensions $$m\times n$$.

\begin{equation} \begin{aligned} \boldsymbol{\mu} &= \begin{bmatrix} \mu_1 \\ \mu_2 \\ \ldots \\ \mu_{101} \\ \mu_{102} \\ \ldots \\ \mu_{215} \\ \mu_{216} \\ \mu_{217} \\ \ldots \\ \mu_{1000} \\ \ldots \\ \mu_{2863} \end{bmatrix} = \begin{bmatrix} \alpha \\ \alpha \\ \ldots \\ \alpha \\ \alpha \\ \ldots \\ \alpha \\ \alpha \\ \alpha \\ \ldots \\ \alpha \\ \ldots \\ \alpha \end{bmatrix} + \begin{bmatrix} u_{subj} \\ u_{subj} \\ \ldots \\ u_{subj} \\ u_{subj} \\ \ldots \\ u_{subj} \\ u_{subj} \\ u_{subj} \\ \ldots \\ u_{subj} \\ \ldots \\ u_{i} \end{bmatrix} + \begin{bmatrix} ccloze_1 \\ ccloze_2 \\ \ldots \\ ccloze_{101} \\ ccloze_{102} \\ \ldots \\ ccloze_{215} \\ ccloze_{216} \\ ccloze_{217} \\ \ldots \\ ccloze_{1000} \\ \ldots \\ ccloze_{2863} \end{bmatrix} \circ \begin{bmatrix} \beta \\ \beta \\ \ldots \\ \beta \\ \beta \\ \ldots \\ \beta \\ \beta \\ \beta \\ \ldots \\ \beta \\ \ldots \\ \beta \end{bmatrix} \\ & = \begin{bmatrix} \alpha \\ \alpha \\ \ldots \\ \alpha \\ \alpha \\ \ldots \\ \alpha \\ \alpha \\ \alpha \\ \ldots \\ \alpha \\ \ldots \\ \alpha \end{bmatrix} + \begin{bmatrix} u_{1} \\ u_{1} \\ \ldots \\ u_{2} \\ u_{2} \\ \ldots \\ u_{3} \\ u_{3} \\ u_{3} \\ \ldots \\ u_{13} \\ \ldots \\ u_{37 } \end{bmatrix} + \begin{bmatrix} {-0.476} \\ {-0.446} \\ \ldots \\ {-0.206} \\ {0.494} \\ \ldots \\ {-0.136} \\ {0.094} \\ {0.294} \\ \ldots \\ {0.524} \\ \ldots \\ {0.494 } \end{bmatrix} \circ \begin{bmatrix} \beta \\ \beta \\ \ldots \\ \beta \\ \beta \\ \ldots \\ \beta \\ \beta \\ \beta \\ \ldots \\ \beta \\ \ldots \\ \beta \end{bmatrix} \end{aligned} \end{equation}

In this model, each subject has their own intercept adjustment $$u_i$$, with $$i$$ indexing the subjects. If $$u_i$$ is positive, the subject has a more positive EEG signal than the average over all the subjects; if $$u_i$$ is negative, then the subject has a more negative EEG signal than the average; and if $$u_i$$ is $$0$$, then the subject has the same EEG signal as the average. As we discussed in section 5.2.3, since we are estimating $$\alpha$$ and $$u$$ at the same time and we assume that the average of the $$u$$’s is $$0$$ (since it is assumed to be normally distributed with a mean of $$0$$), whatever the subjects have in common “goes” to $$\alpha$$, and $$u$$ only “absorbs” the differences between subjects through the variance component $$\tau_u$$.

This model is implemented in the file hierarchical1.stan, available in the bcosci package:

data {
int<lower=1> N;
vector[N] signal;
int<lower = 1> N_subj;
vector[N] c_cloze;
// The following line creates an array of integers;
array[N] int<lower = 1, upper = N_subj> subj;
}
parameters {
real<lower = 0> sigma;
real<lower = 0>  tau_u;
real alpha;
real beta;
vector[N_subj] u;
}
model {
target += normal_lpdf(alpha| 0,10);
target += normal_lpdf(beta | 0,10);
target += normal_lpdf(sigma | 0, 50)  -
normal_lccdf(0 | 0, 50);
target += normal_lpdf(tau_u | 0, 20)  -
normal_lccdf(0 | 0, 20);
target += normal_lpdf(u | 0, tau_u);
target += normal_lpdf(signal | alpha + u[subj] +
c_cloze * beta, sigma);
}


In the Stan code above, we use

array [N] int<lower = 1, upper = N_subj> subj;

to define a one-dimensional array of N elements that contains integers (bounded between 1 and N_subj). As explained in Box 10.4, the difference between vectors and one-dimensional arrays is that vectors can only contain real numbers and can be used with matrix algebra functions, and arrays can contain any type but can’t be used with matrix algebra functions. We use normal_lpdf rather than normal_glm_lpdf since at the moment there is no efficient likelihood implementation of hierarchical generalized linear models.

The following code centers the predictor cloze and stores the data required by the Stan model in a list. Because we are using subj as a vector of indices, we need to be careful to have integers starting from 1 and ending in N_subj without skipping any number (but the order of the subject ids won’t matter).36

data("df_eeg")
df_eeg <- df_eeg %>%
mutate(c_cloze = cloze - mean(cloze))
ls_eeg <- list(
N = nrow(df_eeg),
signal = df_eeg$n400, c_cloze = df_eeg$c_cloze,
subj = df_eeg$subj, N_subj = max(df_eeg$subj)
)

Fit the model:

hierarchical1 <- system.file("stan_models",
"hierarchical1.stan",
package = "bcogsci"
)
fit_eeg1 <- stan(hierarchical1, data = ls_eeg)

Summary of the model:

print(fit_eeg1, pars = c("alpha", "beta", "sigma", "tau_u"))
##        mean  2.5% 97.5% n_eff Rhat
## alpha  3.66  2.85  4.53  1683    1
## beta   2.31  1.26  3.34  5614    1
## sigma 11.64 11.33 11.94  4651    1
## tau_u  2.18  1.52  3.06  2101    1

### 11.1.2 Uncorrelated varying intercept and slopes model with Stan

In the following model, we relax the strong assumption that every subject will be affected equally by the manipulation. For ease of exposition, we start by assuming that (as we did in section 5.2.3) the adjustments for the intercept and slope are not correlated.

$\begin{equation} signal_n \sim \mathit{Normal}(\alpha + u_{subj[n],1} + c\_cloze_n \cdot (\beta+ u_{subj[n],2}),\sigma) \tag{11.1} \end{equation}$

\begin{equation} \begin{aligned} \alpha &\sim \mathit{Normal}(0,10)\\ \beta &\sim \mathit{Normal}(0,10)\\ u_1 &\sim \mathit{Normal}(0,\tau_{u_1})\\ u_2 &\sim \mathit{Normal}(0,\tau_{u_2})\\ \tau_{u_1} &\sim \mathit{Normal}_+(0,20) \\ \tau_{u_2} &\sim \mathit{Normal}_+(0,20) \\ \sigma &\sim \mathit{Normal}_+(0,50) \end{aligned} \tag{11.2} \end{equation}

We implement this in Stan in hierarchical2.stan:

data {
int<lower=1> N;
vector[N] signal;
int<lower = 1> N_subj;
vector[N] c_cloze;
array[N] int<lower = 1, upper = N_subj> subj;
}
parameters {
real<lower = 0> sigma;
vector<lower = 0>  tau_u;
real alpha;
real beta;
matrix[N_subj, 2] u;
}
model {
target += normal_lpdf(alpha| 0,10);
target += normal_lpdf(beta | 0,10);
target += normal_lpdf(sigma | 0, 50)  -
normal_lccdf(0 | 0, 50);
target += normal_lpdf(tau_u | 0, 20)  -
normal_lccdf(0 | 0, 20);
target += normal_lpdf(tau_u | 0, 20)  -
normal_lccdf(0 | 0, 20);
target += normal_lpdf(u[, 1]| 0, tau_u);
target += normal_lpdf(u[, 2]| 0, tau_u);
target += normal_lpdf(signal | alpha + u[subj, 1] +
c_cloze .* (beta + u[subj, 2]), sigma);
}


In the previous model, we assign the same prior distribution to both tau_u and tau_u, and thus in principle we could have written the two statements in one (we multiply by 2 because there are two PDFs that need to be corrected for the truncation):

  target += normal_lpdf(tau_u | 0, 20)  -
2 * normal_lccdf(0 | 0, 20);

Fit the model as follows:

hierarchical2 <- system.file("stan_models",
"hierarchical2.stan",
package = "bcogsci")
fit_eeg2 <- stan(hierarchical2, data = ls_eeg)
 ## Warning: There were 3 chains where the estimated
## Bayesian Fraction of Missing Information was low. See
## https://mc-stan.org/misc/warnings.html#bfmi-low 
 ## Warning: Examine the pairs() plot to diagnose sampling
## problems 
 ## Warning: Bulk Effective Samples Size (ESS) is too low,
## indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess 
 ## Warning: Tail Effective Samples Size (ESS) is too low,
## indicating posterior variances and tail quantiles may be
## unreliable. Running the chains for more iterations may
## help. See
## https://mc-stan.org/misc/warnings.html#tail-ess 

We see that there are warnings. As we increase the complexity and the number of parameters, the sampler has a harder time exploring the parameter space.

Show the summary of the model below:

print(fit_eeg2, pars = c("alpha", "beta", "tau_u", "sigma"))
##           mean  2.5% 97.5% n_eff Rhat
## alpha     3.66  2.81  4.50  1601 1.00
## beta      2.34  1.09  3.55  4734 1.00
## tau_u  2.19  1.56  3.04  3371 1.00
## tau_u  1.77  0.32  3.47   187 1.01
## sigma    11.62 11.32 11.93  7954 1.00

We see that tau_u has a low number of effective samples (n_eff).

The traceplots are displayed in Figure 11.1:

traceplot(fit_eeg2, pars = c("alpha", "beta", "tau_u", "sigma")) FIGURE 11.1: Traceplots of alpha, beta, tau_u, and sigma from the model fit_eeg2.

Figure 11.1 shows that the chains of the parameter tau_u are not mixing properly. This parameter is specially problematic because there are not enough data from each subject to estimate this parameter accurately, its estimated mean is quite small (in comparison with sigma), it’s bounded by zero, and there is a dependency between this parameter and u[, 2]. This makes the exploration by the sampler quite hard.

Pairs plots can be useful to uncover pathologies in the sampling, since we can visualize correlations between samples, which are in general problematic. The following code creates a pair plot where we see the samples of tau_u against some of the adjustments to the slope u; see Figure 11.2.

pairs(fit_eeg2, pars = c("tau_u", "u[1,2]", "u[2,2]", "u[3,2]")) FIGURE 11.2: Pair plots showing a relatively strong correlations (funnel-shaped clouds of samples) between the samples of $$\tau_2$$ and some of the by-subject adjustments to the slope.

Compare with tau_u plotted against the by-subject adjustments to the intercept. In Figure 11.3, instead of funnels we see blobs, indicating no strong correlation between the parameters.

pairs(fit_eeg2, pars = c("tau_u", "u[1,1]", "u[2,1]", "u[3,1]")) FIGURE 11.3: Pair plots showing no strong correlation (blob-shaped clouds of samples) between the samples of $$\tau_1$$ and some of the by-subject adjustments to the intercept.

In contrast to Figure 11.3, which shows blob-shaped clouds of samples, Figure 11.2 shows a relatively strong correlation between the samples of some of the parameters of the model, in particular $$\tau_2$$ and the samples of $$u_{i,2}$$. This strong correlation is hindering the exploration of the sampler leading to the warnings we saw in Stan. However, the problem that the sampler faces is, in fact, more serious than what our initial plots show. Stan samples in an unconstrained space where all the parameters can range from minus infinity to plus infinity, and then transforms back the parameters to the constrained space that we specified where, for example, a standard deviation parameter is restricted to be positive. This means that Stan is actually sampling from an auxiliary parameter equivalent to log(tau_u) rather than from tau_u. We can use mcmc_pairs to see the actual funnel; see Figure 11.4.

mcmc_pairs(as.array(fit_eeg2),
pars = c("tau_u", "u[1,2]"),
transform = list(tau_u = "log")
) FIGURE 11.4: Pair plots showing a strong correlation (funnel-shaped clouds of samples) between the samples of $$\tau_2$$ and one of the by-subject adjustments to the intercept ($$u_{1,2}$$).

At the neck of the funnel, tau_u is close to zero (and log(tau_u) is a negative number) and thus the adjustment u is constrained to be near $$0$$. This is a problem because a step size that’s optimized to work well in the broad part of the funnel will fail to work appropriately in the neck of the funnel and vice versa; see also Neal’s funnel (Neal 2003) and the optimization chapter of Stan’s manual (Stan Development Team 2021, sec. 22.7). There are two options, we might just remove the by-subject varying slope since it’s not giving us much information anyway, or we can alleviate this problem by reparameterizing the model. In general, this is the trickiest and probably most annoying part of modeling. A model can be theoretically and mathematically sound, but still fail to converge. The best advice to solve this type of problem is to start small with simulated data where we know the true values of the parameters, and increase the complexity of the models gradually. Although in this example the problem was clearly in the parameterization of tau_u, in many cases the biggest hurdle is to identify where the problem lies. Fortunately, the issue with tau_u is a common problem which is easy to solve by using a non-centered parameterization (Papaspiliopoulos, Roberts, and Sköld 2007). The following Box explains the specific reparameterization we use for the improved version of our Stan code.

Box 11.1 A simple non-centered parameterization

The sampler can explore the parameter space more easily if its step size is appropriate for all the parameters. This is achieved when there are no strong correlations between parameters. We want to assume the following.

$\begin{equation} \mathbf{u}_{2} \sim \mathit{Normal}(0, \tau_{u_2}) \end{equation}$

where $$\mathbf{u}_{2}$$ is the column vector of $$u_{i,2}$$’s. The index $$i$$ refers to the subject id.

We can transform $$u_2$$ to z-scores as follows. This amounts to centering the parameter, so we can call this centered parameterization.

$\begin{equation} \mathbf{z}_{u_2} =\frac{\mathbf{u}_{2} - 0}{\tau_{u_2}} \end{equation}$

where $\begin{equation} \mathbf{z}_{u_2} \sim \mathit{Normal}(0, 1) \end{equation}$

Now $$\mathbf{z}_{u_2}$$ is easier to sample because it doesn’t depend on other parameters (in particular, it is no longer conditional on $$\tau$$) and its scale is $$1$$. Once we have sampled this centered parameter, we can derive the actual parameter we care about by carrying out the reverse operation, which is called a non-centered parameterization:

$\begin{equation} \mathbf{u}_{2} = \mathbf{z}_{u_2} \cdot \tau_{u_2} \end{equation}$

A question that might be raised here is whether using a non-centered parameterization is always a good idea. Betancourt and Girolami (2013) point out that the extremeness of the correlation depends on the amount of data, and the efficacy of the parameterization depends on the relative strength of the data. When there is enough data, this parameterization is unnecessary and it may be more efficient to use the centered parameterization. However, cases where there is enough data to render this parameterization useless are also cases where the partial pooling of the hierarchical models isn’t needed in the first place. Although data from conventional lab experiments in psychology, psycholinguistics, and related areas seem to benefit from the non-centered parameterization, the jury is still out for larger data sets with thousands of subjects from crowdsourcing websites.

From a mathematical point of view, the following model is equivalent to the one described in Equations (11.1) and (11.2). However, as discussed previously, the computational implementation of the “new” model is more efficient. The following model includes the reparameterization of both adjustments $$u_1$$ and $$u_2$$, although the reparameterization of $$u_1$$ is not strictly necessary (we didn’t see any problems in the trace plots), it won’t hurt either and the Stan code will be simpler.

$\begin{equation} signal_n \sim \mathit{Normal}(\alpha + u_{subj[n],1} + c\_cloze_n \cdot (\beta+ u_{subj[n],2}),\sigma) \tag{11.3} \end{equation}$

\begin{equation} \begin{aligned} \alpha &\sim \mathit{Normal}(0,10)\\ \beta &\sim \mathit{Normal}(0,10)\\ z_{u_1} &\sim \mathit{Normal}(0, 1)\\ z_{u_2} &\sim \mathit{Normal}(0, 1)\\ \tau_{u_1} &\sim \mathit{Normal}_+(0,20) \\ \tau_{u_2} &\sim \mathit{Normal}_+(0,20) \\ \sigma &\sim \mathit{Normal}_+(0,50)\\ u_1 &= z_{u_1} \cdot \tau_{u_1}\\ u_2 &= z_{u_2} \cdot \tau_{u_2} \end{aligned} \tag{11.4} \end{equation}

The following Stan code (hierarchical3.stan) uses the previous parameterization, and introduces some new Stan functions: to_vector() converts a matrix into a long column vector (in column-major order, that is, concatenating the columns from left to right); and std_normal_lpdf() implements the log PDF of a standard normal distribution, a normal distribution with location 0 and scale 1. This function is just a more efficient version of normal_lpdf(... | 0, 1). We also introduce a new optional block called transformed parameters. With each iteration of the sampler, the values of the parameters (i.e., alpha, beta, sigma, and z) are available at the transformed parameters block, and we can derive new auxiliary variables based on them. In this case, we use z_u and tau_u to obtain u, that then becomes available in the model block.

data {
int<lower=1> N;
vector[N] signal;
int<lower = 1> N_subj;
vector[N] c_cloze;
array[N] int<lower = 1, upper = N_subj> subj;
}
parameters {
real<lower = 0> sigma;
vector<lower = 0>  tau_u;
real alpha;
real beta;
matrix[N_subj, 2] z_u;
}
transformed parameters {
matrix[N_subj, 2] u;
u[, 1] = z_u[, 1] * tau_u;
u[, 2] = z_u[, 2] * tau_u;
}
model {
target += normal_lpdf(alpha| 0,10);
target += normal_lpdf(beta | 0,10);
target += normal_lpdf(sigma | 0, 50)  -
normal_lccdf(0 | 0, 50);
target += normal_lpdf(tau_u | 0, 20)  -
normal_lccdf(0 | 0, 20);
target += normal_lpdf(tau_u | 0, 20)  -
normal_lccdf(0 | 0, 20);
target += std_normal_lpdf(to_vector(z_u));
target += normal_lpdf(signal | alpha + u[subj, 1] +
c_cloze .* (beta + u[subj, 2]), sigma);
}


By reparameterizing the model we can also optimize it more, we can convert the matrix z_u into a long column vector allowing us to use a single call of std_normal_lpdf. Fit the model named hierarchical3.stan.

hierarchical3 <- system.file("stan_models",
"hierarchical3.stan",
package = "bcogsci"
)
fit_eeg3 <- stan(hierarchical3, data = ls_eeg) 

Verify that the model worked as expected by printing its summary and traceplots; see Figure 11.5.

print(fit_eeg3, pars = c("alpha", "beta", "tau_u", "sigma"))
##           mean  2.5% 97.5% n_eff Rhat
## alpha     3.64  2.83  4.48  1234    1
## beta      2.31  1.06  3.54  3334    1
## tau_u  2.19  1.54  3.01  1226    1
## tau_u  1.76  0.17  3.55  1019    1
## sigma    11.62 11.32 11.92  4924    1
traceplot(fit_eeg3, pars = c("alpha", "beta", "tau_u", "sigma")) FIGURE 11.5: Traceplots of alpha, beta, tau_u, and sigma from the model fit_eeg3.

Although the samples of tau_u are still correlated with the adjustments for the slope, u[,2], these latter parameters are not the ones explored by the model, the auxiliary parameters, z_u, are the relevant ones for the sampler. The plots in Figures 11.6 and 11.7 show that although log(tau_u) and u[1,2] are still correlated, log(tau_u) and z_u[1,2] are not.


mcmc_pairs(as.array(fit_eeg3),
pars = c("tau_u", "u[1,2]"),
transform = list(tau_u = "log")
) FIGURE 11.6: Pair plots showing a clear correlations (funnel-shaped clouds of samples) between the samples of $$\tau_2$$ and some of the by-subject adjustments to the slope.


mcmc_pairs(as.array(fit_eeg3),
pars = c("tau_u", "z_u[1,2]"),
transform = list(tau_u = "log")
) FIGURE 11.7: Pair plots showing no clear correlation between the samples of $$\tau_2$$ and some of the by-subject auxiliary parameters (z_u) used to build the adjustments to the slope.

### 11.1.3 Correlated varying intercept varying slopes model

For the model with correlated varying intercepts and slopes, the likelihood remains identical to the model without a correlation between group-level intercepts and slopes. Priors and hyperpriors change to reflect the potential correlation between by-subject adjustments to intercepts and slopes:

$\begin{equation} signal_n \sim \mathit{Normal}(\alpha + u_{subj[n],1} + c\_cloze_n \cdot (\beta + u_{subj[n],2}),\sigma) \end{equation}$

The correlation is indicated in the priors on the adjustments for vector of by-subject intercepts $$u_{1}$$ and the vector of by-subject slopes $$u_{2}$$.

• Priors: \begin{equation} \begin{aligned} \alpha & \sim \mathit{Normal}(0,10) \\ \beta & \sim \mathit{Normal}(0,10) \\ \sigma &\sim \mathit{Normal}_+(0,50)\\ {\begin{pmatrix} u_{i,1} \\ u_{i,2} \end{pmatrix}} &\sim {\mathcal {N}} \left( {\begin{pmatrix} 0\\ 0 \end{pmatrix}} ,\boldsymbol{\Sigma_u} \right) \end{aligned} \end{equation}

where $$i = \{1, .., N_{subj} \}$$

$\begin{equation} \boldsymbol{\Sigma_u} = {\begin{pmatrix} \tau_{u_1}^2 & \rho_u \tau_{u_1} \tau_{u_2} \\ \rho_u \tau_{u_1} \tau_{u_2} & \tau_{u_2}^2 \end{pmatrix}} \end{equation}$

\begin{equation} \begin{aligned} \tau_{u_1} &\sim \mathit{Normal}_+(0,20)\\ \tau_{u_2} &\sim \mathit{Normal}_+(0,20)\\ \rho_u &\sim \mathit{LKJcorr}(2) \end{aligned} \end{equation}

As a first attempt, we write this model following the mathematical notation as closely as possible. We’ll see that this will be problematic in terms of efficient sampling and convergence. In this Stan model (hierarchical_corr.stan), we use some new functions and types:

• corr_matrix[n] M; defines a (square) matrix of $$n$$ rows and $$n$$ columns called $$M$$, symmetrical around a diagonal of ones.
• rep_row_vector(X, n) creates a row vector with $$n$$ columns filled with $$X$$.
• quad_form_diag(M, V) creates a quadratic form using the column vector $$V$$ as a diagonal matrix (a matrix with all zeros except for its diagonal), this function corresponds in Stan to: diag_matrix(V) * M * diag_matrix(V) and in R to diag(V) %*% M %*% diag(V). This computes a variance-covariance matrix from the vector of standard deviations, $$V$$, and the correlation matrix, $$M$$ (recall the generation of multivariate data in section 1.6.3).
data {
int<lower=1> N;
vector[N] signal;
int<lower = 1> N_subj;
vector[N] c_cloze;
array[N] int<lower = 1, upper = N_subj> subj;
}
parameters {
real<lower = 0> sigma;
vector<lower = 0>  tau_u;
real alpha;
real beta;
matrix[N_subj, 2] u;
corr_matrix rho_u;
}
model {
target += normal_lpdf(alpha| 0,10);
target += normal_lpdf(beta | 0,10);
target += normal_lpdf(sigma | 0, 50)  -
normal_lccdf(0 | 0, 50);
target += normal_lpdf(tau_u | 0, 20)  -
normal_lccdf(0 | 0, 20);
target += normal_lpdf(tau_u | 0, 20)  -
normal_lccdf(0 | 0, 20);
target += lkj_corr_lpdf(rho_u | 2);
for(i in 1:N_subj)
target +=  multi_normal_lpdf(u[i,] |
rep_row_vector(0, 2),
target += normal_lpdf(signal | alpha + u[subj, 1] +
c_cloze .* (beta + u[subj, 2]), sigma);
}

Problematic aspects of the first model presented in section 11.1.2 (before the reparameterization), that is, dependencies between parameters, are also present here. Fit the model as follows:

hierarchical_corr <- system.file("stan_models",
"hierarchical_corr.stan",
package = "bcogsci"
)
fit_eeg_corr <- stan(hierarchical_corr, data = ls_eeg)
 ## Warning: There were 37 divergent transitions after
## warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate
## them. 
 ## Warning: There were 1 chains where the estimated
## Bayesian Fraction of Missing Information was low. See
## https://mc-stan.org/misc/warnings.html#bfmi-low 
 ## Warning: Examine the pairs() plot to diagnose sampling
## problems 
 ## Warning: Bulk Effective Samples Size (ESS) is too low,
## indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess 
 ## Warning: Tail Effective Samples Size (ESS) is too low,
## indicating posterior variances and tail quantiles may be
## unreliable. Running the chains for more iterations may
## help. See
## https://mc-stan.org/misc/warnings.html#tail-ess 

As we expected, there are warnings and bad mixing of the chains for tau_u; see also the traceplots in Figure 11.8.

print(fit_eeg_corr, pars = c("alpha", "beta", "tau_u", "sigma"))
##           mean  2.5% 97.5% n_eff Rhat
## alpha     3.65  2.79  4.53   867 1.00
## beta      2.32  1.14  3.55  1972 1.00
## tau_u  2.19  1.56  2.96  1914 1.00
## tau_u  1.78  0.46  3.49   138 1.02
## sigma    11.62 11.33 11.92  4853 1.00

traceplot(fit_eeg_corr, pars = c("alpha", "beta", "tau_u", "sigma")) FIGURE 11.8: Traceplots of alpha, beta, tau_u, and sigma from the model fit_eeg_corr.

The problem (which can also be discovered in a pairs plot) is the same one that we saw before: There is a strong correlation between tau_u (in fact, log(tau_u), which is the parameter dimension that the sampler considers) and u, creating a funnel.

The solution to this problem is the reparameterization of this model. The non-centered parameterization for this type of model is called the Cholesky factorization (Fieller 2016). The mathematics and the intuition behind this parameterization are explained in Box 11.2.

Box 11.2 Cholesky factorization

First, some definitions that we will need below. A matrix is square if the number of rows and columns is identical. A square matrix $$A$$ is symmetric if $$A^T = A$$, i.e., if transposing the matrix gives the matrix back. Suppose that $$A$$ is a known matrix with real numbers. If $$\boldsymbol{x}$$ is a vector of variables with length $$p$$ (a $$p\times 1$$ matrix), then $$x^T A x$$ is called a quadratic form in $$x$$ ($$x^T A x$$ will be a scalar, $$1\times 1$$). If $$x^TAx>0$$ for all $$x$$, then $$A$$ is a positive definite matrix. If $$x^TAx\geq 0$$ for all $$x$$, then $$A$$ is positive semi-definite.

We encountered correlation matrices first in section 1.6.3. A correlation matrix is always symmetric, has ones along the diagonal, and real values ranging between $$-1$$ and $$1$$ on the off-diagonals. Given a correlation matrix $$\boldsymbol{\rho_u}$$ that is positive definite or semi-definite, we can decompose it into a lower triangular matrix $$\mathbf{L_u}$$ such that $$\mathbf{L_u}\mathbf{L_u}^T=\boldsymbol{\rho_u}$$. The matrix $$\mathbf{L_u}$$ is called the Cholesky factor of $$\boldsymbol{\rho_u}$$. Intuitively, you can think of $$L_u$$ as the matrix equivalent of the square root of $$\boldsymbol{\rho_u}$$. More details on the Cholesky factorization can be found in Gentle (2007).

$\begin{equation} \mathbf{L_u} = {\begin{pmatrix} l_{11} & 0 \\ l_{21} & l_{22} \end{pmatrix}} \end{equation}$

For a model without a correlation between adjustments for the intercept and slope, we assumed that adjustments $$u_{1}$$ and $$u_{2}$$ were generated by two independent normal distributions. But now we want to allow the possibility that the adjustments can have a non-zero correlation. We can use the Cholesky factorization to generate correlated random variables in the following way.

1. Generate uncorrelated vectors, $$z_{u_1}$$ and $$z_{u_2}$$, for each vector of adjustments $$u_1$$ and $$u_2$$, as sampled from $$\mathit{Normal}(0,1)$$:

$z_{u_1} \sim \mathit{Normal}(0,1)$ $z_{u_2} \sim \mathit{Normal}(0,1)$

1. By multiplying the Cholesky factor with the $$z$$’s, generate a matrix that contains two row vectors of correlated variables (with standard deviation $$1$$).

$\mathbf{L_u}\cdot \mathbf{z_u} = {\begin{pmatrix} l_{11} & 0 \\ l_{21} & l_{22} \end{pmatrix}} {\begin{pmatrix} z_{u_{1,subj=1}} & z_{u_{1,subj=2}} & ... & z_{u_{1,subj=N_{subj}}} \\ z_{u_{2,subj=1}} & z_{u_{2,subj=2}} & ... & z_{u_{2,subj=N_{subj}}} \end{pmatrix}}$

$\mathbf{L_u}\cdot \mathbf{z_u} = {\begin{pmatrix} l_{11} \cdot z_{u_{1,1}} + 0 \cdot z_{u_{2,1}} & ... & l_{11} \cdot z_{u_{1,N_{subj}}} \\ l_{21} \cdot z_{u_{1,1}} + l_{22} \cdot z_{u_{2,1}} & ... & l_{11} \cdot z_{u_{1,N_{subj}}} + l_{22} \cdot z_{u_{2,N_{subj}}} \end{pmatrix}}$

A very informal explanation of why this works is that we are making the variable that corresponds to the slope to be a function of a scaled version of the intercept.

1. The last step is to scale the previous matrix to the desired standard deviation. We define the diagonalized matrix $$diag\_matrix(\tau_u)$$ as before:

${\begin{pmatrix} \tau_{u_1} & 0 \\ 0 & \tau_{u_2} \end{pmatrix}}$

Then pre-multiply it by the correlated variables with standard deviation 1 from before:

$\mathbf{u} = diag\_matrix(\tau_u) \cdot \mathbf{L_u}\cdot \mathbf{z_u} =$

${\begin{pmatrix} \tau_{u_1} & 0 \\ 0 & \tau_{u_2} \end{pmatrix}} {\begin{pmatrix} l_{11} \cdot z_{u_{1,1}} & ... \\ l_{21} \cdot z_{u_{1,1}} + l_{22} \cdot z_{u_{2,1}} & ... \end{pmatrix}}$

${\begin{pmatrix} \tau_{u_1} \cdot l_{11} \cdot z_{u_{1,1}} & \tau_{u_1} \cdot l_{11} \cdot z_{u_{1,2}} & ... \\ \tau_{u_2} \cdot (l_{21} \cdot z_{u_{1,1}} + l_{22} \cdot z_{u_{2,1}}) & \tau_{u_2} \cdot (l_{21} \cdot z_{u_{1,2}} + l_{22} \cdot z_{u_{2,2}}) & ... \end{pmatrix}}$

It might be helpful to see how one would implement this in R:

Let’s assume a correlation of $$0.8$$.

rho <- .8
# Correlation matrix
(rho_u <- matrix(c(1, rho, rho, 1), ncol = 2))
##      [,1] [,2]
## [1,]  1.0  0.8
## [2,]  0.8  1.0
# Cholesky factor:
# (Transpose it so that it looks the same as in Stan)
(L_u <- t(chol(rho_u)))
##      [,1] [,2]
## [1,]  1.0  0.0
## [2,]  0.8  0.6
# Verify that we recover rho_u,
# Recall that %*% indicates matrix multiplication
L_u %*% t(L_u)
##      [,1] [,2]
## [1,]  1.0  0.8
## [2,]  0.8  1.0
1. Generate uncorrelated z from a standard normal distribution assuming only 10 subjects.
N_subj <- 10
(z_u1 <- rnorm(N_subj, 0, 1))
##    0.21876 -1.70185  1.12707  0.27846  0.83054  0.52538
##   -0.00591 -0.20405 -0.52281 -0.59610
(z_u2 <- rnorm(N_subj, 0, 1))
##   -0.755  1.409 -0.639  0.160  0.442 -2.245 -0.822 -0.996
##    0.292 -0.237
1. Create matrix of correlated parameters.

First, create a matrix with the uncorrelated parameters:

# matrix z_u
(z_u <- matrix(c(z_u1, z_u2), ncol = N_subj, byrow = TRUE))
##        [,1]  [,2]   [,3]  [,4]  [,5]   [,6]     [,7]   [,8]
## [1,]  0.219 -1.70  1.127 0.278 0.831  0.525 -0.00591 -0.204
## [2,] -0.755  1.41 -0.639 0.160 0.442 -2.245 -0.82191 -0.996
##        [,9]  [,10]
## [1,] -0.523 -0.596
## [2,]  0.292 -0.237

Then, generate correlated parameters by pre-multiplying the $$\mathbf{z}_u$$ matrix with $$\mathbf{L}_u$$.

L_u %*% z_u
##        [,1]   [,2]  [,3]  [,4]  [,5]   [,6]     [,7]   [,8]   [,9]
## [1,]  0.219 -1.702 1.127 0.278 0.831  0.525 -0.00591 -0.204 -0.523
## [2,] -0.278 -0.516 0.518 0.319 0.930 -0.927 -0.49788 -0.761 -0.243
##       [,10]
## [1,] -0.596
## [2,] -0.619
1. Use the following diagonal matrix to scale the z_u.
tau_u1 <- 0.2
tau_u2 <- 0.01
(diag_matrix_tau <- diag(c(tau_u1,  tau_u2)))
##      [,1] [,2]
## [1,]  0.2 0.00
## [2,]  0.0 0.01
1. Finally, generate the adjustments for each subject u:
(u <- diag_matrix_tau %*% L_u %*% z_u)
##          [,1]     [,2]    [,3]    [,4]   [,5]     [,6]
## [1,]  0.04375 -0.34037 0.22541 0.05569 0.1661  0.10508
## [2,] -0.00278 -0.00516 0.00518 0.00319 0.0093 -0.00927
##          [,7]     [,8]     [,9]    [,10]
## [1,] -0.00118 -0.04081 -0.10456 -0.11922
## [2,] -0.00498 -0.00761 -0.00243 -0.00619
# The rows are correlated ~.8
cor(u[1, ], u[2, ])
##  0.549
# The variance components can be recovered as well:
sd(u[1, ])
##  0.162
sd(u[2, ])
##  0.00603

The reparameterization of the model, which allows for a correlation between adjustments for the intercepts and slopes, in hierarchical_corr2.stan is shown below. The code implements the following new types and functions:

• cholesky_factor_corr L_u, which defines L_u as a lower triangular ($$2 \times 2$$) matrix which has to be the Cholesky factor of a correlation.
• diag_pre_multiply(tau_u,L_u) which makes a diagonal matrix out of the vector tau_u and multiplies it by L_u.
• to_vector(z_u) makes a long vector out the matrix z_u.
• L_u ~ lkj_corr_cholesky(2) is the Cholesky factor associated with the LKJ correlation distribution. It implies that L_u * L_u' = rho_u ~ lkj_corr(2.0). The symbol ' indicates transposition (in R, this corresponds to the function t()).
data {
int<lower=1> N;
vector[N] signal;
int<lower = 1> N_subj;
vector[N] c_cloze;
array[N] int<lower = 1, upper = N_subj> subj;
}
parameters {
real<lower = 0> sigma;
vector<lower = 0>  tau_u;
real alpha;
real beta;
matrix[2, N_subj] z_u;
cholesky_factor_corr L_u;
}
transformed parameters {
matrix[N_subj, 2] u;
u = (diag_pre_multiply(tau_u, L_u) * z_u)';
}
model {
target += normal_lpdf(alpha| 0,10);
target += normal_lpdf(beta | 0,10);
target += normal_lpdf(sigma | 0, 50)  -
normal_lccdf(0 | 0, 50);
target += normal_lpdf(tau_u | 0, 20)  -
normal_lccdf(0 | 0, 20);
target += normal_lpdf(tau_u | 0, 20)  -
normal_lccdf(0 | 0, 20);
target += lkj_corr_cholesky_lpdf(L_u | 2);
target += std_normal_lpdf(to_vector(z_u));
target += normal_lpdf(signal | alpha + u[subj, 1] +
c_cloze .* (beta + u[subj, 2]), sigma);
}
generated quantities {
corr_matrix rho_u= L_u * L_u';
vector[N_subj] effect_by_subj;
for(i in 1:N_subj)
effect_by_subj[i] = beta + u[i, 2];
}

In this Stan model, we also created an effect_by_subject in the generated quantities. This would allow us to plot or to summarize by-subject effects of cloze probability.

One can recover the correlation parameter by adding in the generated quantities section a $$2 \times 2$$ matrix rho_u, defined as rho_u = L_u * L_u';.

Fit the new model:

hierarchical_corr2 <- system.file("stan_models",
"hierarchical_corr2.stan",
package = "bcogsci"
)
fit_eeg_corr2 <- stan(hierarchical_corr2, data = ls_eeg)

The Cholesky matrix has some elements which are always zero or one, and thus the variance within and between chains (and therefore Rhat) are not defined. However, the rest of the parameters of the model have an appropriate number of effective sample size (more than 10% of the total number of post-warmup samples), Rhats are close to one, and the chains are mixing well; see also the traceplots in Figure 11.9.

print(fit_eeg_corr2,
pars =
c("alpha", "beta", "tau_u", "rho_u", "sigma", "L_u"))
##             mean  2.5% 97.5% n_eff Rhat
## alpha       3.65  2.78  4.43  1282    1
## beta        2.33  1.12  3.58  4331    1
## tau_u    2.18  1.52  2.96  1563    1
## tau_u    1.65  0.10  3.48  1095    1
## rho_u[1,1]  1.00  1.00  1.00   NaN  NaN
## rho_u[1,2]  0.16 -0.57  0.75  3535    1
## rho_u[2,1]  0.16 -0.57  0.75  3535    1
## rho_u[2,2]  1.00  1.00  1.00   133    1
## sigma      11.62 11.31 11.94  5090    1
## L_u[1,1]    1.00  1.00  1.00   NaN  NaN
## L_u[1,2]    0.00  0.00  0.00   NaN  NaN
## L_u[2,1]    0.16 -0.57  0.75  3535    1
## L_u[2,2]    0.92  0.64  1.00  2041    1

traceplot(fit_eeg_corr2,
pars = c("alpha", "beta", "tau_u", "L_u[2,1]", "L_u[2,2]", "sigma")) FIGURE 11.9: Traceplots of alpha, beta, tau_u, L_u, and sigma from the model fit_eeg_corr.

Is there a correlation between the by-subject intercept and slope?

Let’s visualize some of the posteriors with the following code (see Figure 11.10):

mcmc_hist(as.data.frame(fit_eeg_corr2),
pars = c("beta", "rho_u[1,2]")) FIGURE 11.10: Histograms of the samples of the posteriors of beta and rho_u[1,2] from the model fit_eeg_corr2.

Figure 11.10 shows that the posterior distribution is widely spread out between $$-1$$ and $$+1$$. One can’t really learn from these data whether the by-subject intercepts and slopes are correlated. The broad spread of the posterior indicates that we don’t have enough data to estimate this parameter with high enough precision: the posterior is basically just reflecting the prior specification (the LKJcorr prior with parameter $$\eta = 2$$).

### 11.1.4 By-subject and by-items correlated varying intercept varying slopes model

We extend the previous model by adding by-items intercepts and slopes, and priors and hyperpriors that reflect the potential correlation between by-items adjustments to intercepts and slopes:

$\begin{multline} signal_n \sim \mathit{Normal}(\alpha + u_{subj[n], 1} + w_{item[n], 1} + \\ c\_cloze_n \cdot (\beta + u_{subj[n],2} + w_{item[n], 2}),\sigma) \end{multline}$

The correlation is indicated in the priors on the adjustments for the vectors representing the varying intercepts $$u_{1}$$ and varying slopes $$u_{2}$$ for subjects, and the varying intercepts $$w_{1}$$ and varying slopes $$w_{2}$$ for items.

• Priors: \begin{equation} \begin{aligned} \alpha & \sim \mathit{Normal}(0,10) \\ \beta & \sim \mathit{Normal}(0,10) \\ \sigma &\sim \mathit{Normal}_+(0, 50)\\ {\begin{pmatrix} u_{i,1} \\ u_{i,2} \end{pmatrix}} &\sim {\mathcal {N}} \left( {\begin{pmatrix} 0\\ 0 \end{pmatrix}} ,\boldsymbol{\Sigma_u} \right) \\ {\begin{pmatrix} w_{i,1} \\ w_{i,2} \end{pmatrix}} &\sim {\mathcal {N}} \left( {\begin{pmatrix} 0\\ 0 \end{pmatrix}} ,\boldsymbol{\Sigma_w} \right) \end{aligned} \end{equation}

$\begin{equation} \boldsymbol{\Sigma_u} = {\begin{pmatrix} \tau_{u_1}^2 & \rho_u \tau_{u_1} \tau_{u_2} \\ \rho_u \tau_{u_1} \tau_{u_1} & \tau_{u_2}^2 \end{pmatrix}} \end{equation}$

$\begin{equation} \boldsymbol{\Sigma_w} = {\begin{pmatrix} \tau_{w_1}^2 & \rho_w \tau_{w_1} \tau_{w_2} \\ \rho_w \tau_{w_1} \tau_{w_1} & \tau_{w_2}^2 \end{pmatrix}} \end{equation}$

\begin{equation} \begin{aligned} \tau_{u_1} &\sim \mathit{Normal}_+(0,20)\\ \tau_{u_2} &\sim \mathit{Normal}_+(0,20)\\ \rho_u &\sim \mathit{LKJcorr}(2) \end{aligned} \end{equation}

\begin{equation} \begin{aligned} \tau_{w_1} &\sim \mathit{Normal}_+(0,20)\\ \tau_{w_2} &\sim \mathit{Normal}_+(0,20)\\ \rho_w &\sim \mathit{LKJcorr}(2) \end{aligned} \end{equation}

The translation to Stan (hierarchical_corr_by.stan) looks as follows:

data {
int<lower=1> N;
vector[N] signal;
int<lower = 1> N_subj;
int<lower = 1> N_item;
vector[N] c_cloze;
array[N] int<lower = 1, upper = N_subj> subj;
array[N] int<lower = 1, upper = N_item> item;
}
parameters {
real<lower = 0> sigma;
vector<lower = 0>  tau_u;
vector<lower = 0>  tau_w;
real alpha;
real beta;
matrix[2, N_subj] z_u;
matrix[2, N_item] z_w;
cholesky_factor_corr L_u;
cholesky_factor_corr L_w;
}
transformed parameters {
matrix[N_subj, 2] u;
matrix[N_item, 2] w;
u = (diag_pre_multiply(tau_u, L_u) * z_u)';
w = (diag_pre_multiply(tau_w, L_w) * z_w)';
}
model {
target += normal_lpdf(alpha| 0,10);
target += normal_lpdf(beta | 0,10);
target += normal_lpdf(sigma | 0, 50)  -
normal_lccdf(0 | 0, 50);
target += normal_lpdf(tau_u | 0, 20) -
2 * normal_lccdf(0 | 0, 20);
target += normal_lpdf(tau_w | 0, 20) -
2* normal_lccdf(0 | 0, 20);
target += lkj_corr_cholesky_lpdf(L_u | 2);
target += lkj_corr_cholesky_lpdf(L_w | 2);
target += std_normal_lpdf(to_vector(z_u));
target += std_normal_lpdf(to_vector(z_w));
target += normal_lpdf(signal | alpha + u[subj, 1] + w[item, 1]+
c_cloze .* (beta + u[subj, 2] + w[item, 2]), sigma);
}
generated quantities {
corr_matrix rho_u = L_u * L_u';
corr_matrix rho_w = L_w * L_w';
}

Add item as a number to the data and store it in a list:

df_eeg <- df_eeg %>%
mutate(item = as.numeric(as.factor(item)))
ls_eeg <- list(
N = nrow(df_eeg),
signal = df_eeg$n400, c_cloze = df_eeg$c_cloze,
subj = df_eeg$subj, item = df_eeg$item,
N_subj = max(df_eeg$subj), N_item = max(df_eeg$item))

Fit the model:

hierarchical_corr_by <- system.file("stan_models",
"hierarchical_corr_by.stan",
package = "bcogsci")
fit_eeg_corr_by <- stan(hierarchical_corr_by, data = ls_eeg)

Print the summary:

print(fit_eeg_corr_by,
pars = c("alpha", "beta", "sigma", "tau_u", "tau_w",
"rho_u", "rho_w"))
##             mean  2.5% 97.5% n_eff Rhat
## alpha       3.67  2.79  4.55  1974    1
## beta        2.29  0.90  3.63  4030    1
## sigma      11.49 11.19 11.80  5975    1
## tau_u    2.19  1.55  3.01  1601    1
## tau_u    1.49  0.09  3.34  1067    1
## tau_w    1.51  0.83  2.18  1663    1
## tau_w    2.27  0.26  4.21   935    1
## rho_u[1,1]  1.00  1.00  1.00   NaN  NaN
## rho_u[1,2]  0.14 -0.60  0.77  3872    1
## rho_u[2,1]  0.14 -0.60  0.77  3872    1
## rho_u[2,2]  1.00  1.00  1.00   629    1
## rho_w[1,1]  1.00  1.00  1.00   NaN  NaN
## rho_w[1,2] -0.41 -0.89  0.31  2143    1
## rho_w[2,1] -0.41 -0.89  0.31  2143    1
## rho_w[2,2]  1.00  1.00  1.00   180    1

The correlations of interest are rho_u[1,2] and rho_w[1,2]; the summary above shows that the data are far too sparse to get tight estimates of these parameters: both posteriors are widely spread out.

This completes our review of hierarchical models and their implementation in Stan. The importance of coding a hierarchical model directly in Stan rather than using brms is that this increases the flexibility of the type of models that we can fit. In fact, we will see in chapters 17-20 that the same “machinery” can be used to have hierarchical parameters in cognitive models.

## 11.2 Summary

In this chapter, we learned to fit the four standard types of hierarchical models that we encountered in earlier chapters:

• The by-subjects varying intercepts model.
• The by-subjects varying intercepts and varying slopes model without any correlation.
• The by-subjects varying intercepts and varying slopes model with correlation.
• The hierarchical model, with a full variance covariance matrix for both subjects and items.

We also learned about some important and powerful tools for making the Stan models more efficient at sampling: the non-centered parameterization and the Cholesky factorization. One important takeaway was that if data are sparse, the posteriors will just reflect the priors. We saw examples of this situation when investigating the posteriors of the correlation parameters.

Gelman and Hill (2007) provides a comprehensive introduction to Bayesian hierarchical models, although that edition does not use Stan but rather WinBUGS. Sorensen, Hohenstein, and Vasishth (2016) is a short tutorial on hierarchical modeling using Stan, especially tailored for psychologists and linguists.

## 11.4 Exercises

Exercise 11.1 A log-normal model in Stan.

Refit the Stroop example from section 5.3 in Stan (df_stroop).

Assume the following likelihood and priors:

$\begin{equation} rt_n \sim \mathit{LogNormal}(\alpha + u_{subj[n],1} + c\_cond_n \cdot (\beta + u_{subj[n],2}), \sigma) \end{equation}$

\begin{equation} \begin{aligned} \alpha & \sim \mathit{Normal}(6, 1.5) \\ \beta & \sim \mathit{Normal}(0, .1) \\ \sigma &\sim \mathit{Normal}_+(0, 1) \end{aligned} \end{equation}

\begin{equation} \begin{aligned} \tau_{u_1} &\sim \mathit{Normal}_+(0,1)\\ \tau_{u_2} &\sim \mathit{Normal}_+(0,1)\\ \rho_u &\sim \mathit{LKJcorr}(2) \end{aligned} \end{equation}

Exercise 11.2 A by-subjects and by-items hierarchical model with a log-normal likelihood.

Revisit the question “Are subject relatives easier to process than object relatives?” Fit the model from the exercise 5.2 using Stan.

Exercise 11.3 A hierarchical logistic regression with Stan.

Revisit the question “Is there a Stroop effect in accuracy?” Fit the model the exercise 5.6 using Stan.

Exercise 11.4 A distributional regression model of the effect of cloze probability on the N400.

In section 5.2.6, we saw how to fit a distributional regression model. We might want to extend this approach to Stan. Fit the EEG data to a hierarchical model with by-subject and by-items varying intercept and slopes, and in addition assume that the residual standard deviation (the scale of the normal likelihood) can vary by subject.

\begin{equation} \begin{aligned} signal_n &\sim \mathit{Normal}(\alpha + u_{subj[n],1} + w_{item[n],1} + \\ & c\_cloze_n \cdot (\beta + u_{subj[n],2}+ w_{item[n],2}), \sigma_n)\\ \sigma_n &= \exp(\alpha_{\sigma} + u_{\sigma_{subj[n]}}) \end{aligned} \end{equation}

\begin{equation} \begin{aligned} \alpha_\alpha &\sim \mathit{Normal}(0,log(50))\\ u_\sigma &\sim \mathit{Normal}(0, \tau_{u_\sigma}) \\ \tau_{u_\sigma} &\sim \mathit{Normal}_+(0, 5) \end{aligned} \end{equation}

To fit this model, take into account that sigma is now a vector, and it is a transformed parameter which depends on two parameters: alpha_sigma and the vector with N_subj elements u_sigma. In addition, u_sigma depends on the hyperparameter tau_u_sigma ($$\tau_{u_\sigma}$$). (Using non-centered parameterization for u_sigma speeds up the model fit considerably).

### References

Betancourt, Michael J., and Mark Girolami. 2013. “Hamiltonian Monte Carlo for Hierarchical Models.”

Fieller, Nick. 2016. Basics of Matrix Algebra for Statistics with R. Boca Raton, FL: CRC Press.

Gelman, Andrew, and Jennifer Hill. 2007. Data Analysis Using Regression and Multilevel/Hierarchical Models. Cambridge University Press.

Gentle, James E. 2007. “Matrix Algebra: Theory, Computations, and Applications in Statistics.” Springer Texts in Statistics 10. New York, NY: Springer.

Neal, Radford M. 2003. “Slice Sampling.” Annals of Statistics 31 (3). The Institute of Mathematical Statistics: 705–67. https://doi.org/10.1214/aos/1056562461.

Papaspiliopoulos, Omiros, Gareth O. Roberts, and Martin Sköld. 2007. “A General Framework for the Parametrization of Hierarchical Models.” Statistical Science 22 (1). The Institute of Mathematical Statistics: 59–73. https://doi.org/10.1214/088342307000000014.

Sorensen, Tanner, Sven Hohenstein, and Shravan Vasishth. 2016. “Bayesian Linear Mixed Models Using Stan: A Tutorial for Psychologists, Linguists, and Cognitive Scientists.” Quantitative Methods for Psychology 12 (3): 175–200.

Stan Development Team. 2021. “Stan Modeling Language Users Guide and Reference Manual, Version 2.27.” https://mc-stan.org.

1. If this is not the case, we can do as.numeric(as.factor(df_eeg\$subj)) to transform a vector where some numbers are skipped into a vector with consecutive numbers. For example, both as.numeric(as.factor(c(1, 3, 4, 7, 9))) and as.numeric(as.factor(paste0("subj", c(1, 3, 4, 7, 9)))) will give as output 1 2 3 4 5.