# Demystifying Item Response Theory (3/4)

Improving Estimation through Partial Pooling

## Fixed, Random and Mixed

Statistics is confusing enough through its massive terminology. Psychology, which is largely experiment-oriented, further confuses people by adding in its own flavor. A peek at the definitions of fixed, random, and mixed effects in the APA Dictionary of Psychology exemplifies this:

[A mixed-effect model is] any statistical procedure or experimental design that uses one or more independent variables whose levels are

specifically selected by the researcher(fixed effects; e.g., gender) and one or more additional independent variables whose levels arechosen randomlyfrom a wide range of possible values (random effects; e.g., age).

—Definition of “mixed-effect model” in the APA Dictionary of Psychology

The definitions for random and fixed effects above are not only
confusing but also misleading. In principle, whether a categorical
variable is “fixed” or “random” has nothing to do with the nature of the
variable (e.g., *gender* doesn’t have to be fixed) or how the levels
within a variable are selected (randomly drawn or chosen by
researchers). Whether a variable is modeled as fixed or random is a
decision to be made by the modeler. And the modeler **should
model variables as random** if there are no justifiable prohibitive
reasons. Let me explain.

## Multilevel Instead of Mixed

A better way to understand fixed and random effects is to think
**hierarchically**. The levels of a random-effect variable are treated
as **related** by the model, meaning that the effect of each level is
estimated by also considering information from other levels in the
variable. This is known as **partial pooling**, and it has several
desirable properties. On the other hand, the levels within a
fixed-effect variable are treated as independent: during parameter
estimation, the model considers only information within each level. This
is the **no-pooling** case. So how does the model incorporate
information from the other levels during estimation in the
partial-pooling case? To explain this, let me start with the no-pooling
case.

As an example, suppose we have a categorical variable with $n$ levels.
Our goal is to obtain an estimate for each of these levels (and the
variability in the estimates), labeled as
$\alpha_1, \alpha_2, …, \alpha_n$. To provide some context, we can
think of the categorical variable here as *nationality*, and for each
nation (a level), we want to estimate the average height (the parameter)
of its citizens. When we are **not pooling information across the
levels**, the structure of the data-generating process assumed by the
statistical model is shown in the figure below. Here, the model assumes
that there is a parameter associated with each level that generates the
observations. However, the parameters here are assumed to be
independent. Therefore, the model utilizes only the observations under
each level to estimate its parameter. What has been learned about a
nation is uninformative about another nation for the **no-pooling**
model.

But there actually is some information, right? Take the perspective of an alien, for instance. Knowing the average height of the Americans, say 5′9″, provides quite much information about the heights of the Japanese—they are unlikely to be 60 feet or 6 inches, agree? This is why we prefer to partial pool. Partial pooling allows the sharing of information across different levels, which, as elucidated below, leads to several desirable properties.

When we want to incorporate—or partial pool—information from other levels during estimation, we can utilize models that assume a hierarchical structure on the levels within a variable. Such a hierarchical structure is exemplified in the figure below. This hierarchical structure assumes that all levels, or more precisely all parameters underlying the levels, come from a common distribution. Here, this common distribution is assumed to be a normal distribution with mean $\mu$ and variance $\sigma^2$. The mean and the variance are to be estimated from the data. When this structure is imposed, the observations under different levels will be naturally linked since now, the observations under every level all provide information for estimating the common distribution.

What can be gained from partial pooling information across levels? As
mentioned above, when we partial-pool, the information of the
observations across all levels is shared. This means that the model
considers **more information** for estimating the parameter of each
level. As a direct result of this, the model uses the data
(observations) more efficiently by squeezing out more information.
Secondly, it reduces overfitting and thus provides better
(out-of-sample) estimation. The model is less likely to overfit because
it is more “objective” by considering information across different
levels. Overfitting occurs when data are scarce, which is the case in
the no-pooling case since only data within each level are considered. In
such cases, the model bases the estimations on fewer observations and
hence tends to be overly sensitive to idiosyncratic patterns in the
local data. Another great thing about partial pooling is that it
automatically adjusts according to the sample sizes under each level.
For levels with fewer observations (e.g, North Korea, in which the alien
managed to collect only heights from three of its citizens), the model
places more weight on the overall information provided by other levels,
resulting in larger adjustments of the levels’ estimates. For levels
with abundant data, their estimates are only slightly affected by the
observations from other levels.

Partial pooling essentially arises from the hierarchical structure
assumed in the models. Therefore, these models are known as
**hierarchical** or **multilevel** models. **Mixed (effect)** models are
another common label for these models, though, as explained above, the
name is quite uninformative. To understand how these models work, it is
better to start with their hierarchical structuring. I will use the term
**multilevel models** from now on to save ourselves from confusion. This
name is also nice in that it coincides in abbreviation with the mixed
model—both of them are abbreviated as GLMM for Generalized Linear
Multilevel/Mixed Models.

## Back to IRT

Now, we are acquainted with the concept of partial pooling and multilevel models, let’s apply them to the IRT context to improve our previous model, which is fitted without partial pooling across levels. To warm up, let me rephrase the structure of the simulated IRT dataset in terms of the multilevel terminologies.

There are two variables at work here—the item variable and the person
(or subject) variable. Within the item variable, there are several
items. In other words, each item acts as a level within the item
variable. Similarly, each person corresponds to a level within the
person variable. For each item, we want to estimate a parameter, the
item’s difficulty. Likewise, for each person, we also want to estimate a
parameter, the person’s ability. To improve our model in estimating the
item/person parameters, we can partial pool information across the
levels **within** the item and/or the person variable.

The chunk below copies the data simulation code from the previous post,
with two minor changes. The first is the renaming of the variables for
the item and subject ID as `Iid`

(originally `I`

) and `Sid`

(originally
`S`

). The second is that, instead of item difficulty (`D`

in the
previous post), we conceptualize the effect of items as **easiness**
(`E`

) here. Item easiness is simply the negative of item difficulty.
This simple switch would allow us to skip the step of reversing the item
effects’ signs returned by the regression model.

```
1logistic = function(x) 1 / (1 + exp(-x))
2logit = function( p ) log( p/(1-p) )
3rbern = function( p, n=length(p) ) rbinom( n=n, size=1, prob=p )
4
5set.seed(12)
6n_item = 30 # number of items
7n_subj = 60 # number of subjects
8n_resp = n_item * n_subj
9n_param = n_item + n_subj
10A = rnorm( n_subj ) # Person ability
11E = seq( -1.6, 1, length=n_item ) # Item easiness
12
13# The data
14d = expand.grid( Sid=1:n_subj, Iid=1:n_item, KEEP.OUT.ATTRS = F )
15d$mu = A[d$Sid] + E[d$Iid]
16d$R = rbern( logistic( d$mu ) )
17d$Sid = factor(d$Sid)
18d$Iid = factor(d$Iid)
```

### Unpooled Model

With the data prepared, let’s refit model
`m1.2`

from the
previous post. Later, I will fit another model that partial pools the
subject variable (`m2`

) and compare it to the unpooled model here
(`m1`

).

The code below for fitting `m1`

is identical to those in the previous
post, except that I adopt another method (starting from line 5) to
reconstruct the dropped estimate (forced by the sum-to-zero constraint).
This change is necessary, as it also allows us to reconstruct the
standard errors of the dropped estimate. We will need the standard
errors later to quantify the *uncertainty* in the estimates, which are
used for comparing the unpooled and partial-pooled models. In addition,
the method adopted here is more principled and general, which further
consolidates our understanding of contrasts and dummy coding. However,
it takes up some space for the explanation since a little matrix algebra
is involved. I thus leave the details in the box at
the end of the post.

```
1d1 = d
2contrasts(d1$Sid) = contr.sum( n_subj )
3m1 = glm( R ~ -1 + Iid + Sid, data=d1, family=binomial("logit") )
4
5# Construct contrast matrix
6Cmat = diag(0, nrow=n_item+n_subj)[, -1]
7diag(Cmat)[1:n_item] = 1
8idxS = 1:n_subj + n_item
9Cmat[idxS, idxS[-length(idxS)]] = contr.sum( n_subj )
10
11# Reconstruct estimates with the constrast matrix
12m1_eff = (Cmat %*% coef(m1))[, 1]
13# Reconstruct std. error of the estimates with the constrast matrix
14Vmat = Cmat %*% vcov(m1) %*% t(Cmat)
15m1_se = sqrt(diag(Vmat))
```

### Partial-pooled Model

To fit the partial-pooled model, `glmer()`

from the `lme4`

package is
used.

```
1library(lme4)
2m2 = glmer( R ~ -1 + Iid + (1|Sid), data=d, family=binomial('logit') )
```

`lme4`

provides a syntax for expressing multilevel models of different
structures. For our model here, which is one of the simplest multilevel
models (known as the varying intercept models), we express the partial
pooling of persons with the syntax `(1|Sid)`

, as shown in the last term
of the model formula. When such a partial pooling structure is
specified, `glmer()`

automatically imposes a constraint of **zero-meaned
normal distribution** on the partial-pooled variable. In the case here,
this means that the ability of each person is modeled as being drawn
from a normal distribution with a mean of zero and an unknown standard
deviation to be estimated from the data. This constraint on the
distribution of the person ability naturally resolves the identification
issue of the IRT model. Hence, there is no need to impose an additional
sum-to-zero constraint as we did in `m1`

. We are only partial-pooling
the person variable here, so except for `(1|Sid)`

, everything else in
`glmer()`

is identical to those in `m1`

.

After fitting the model, the estimates from `m2`

can be obtained with
the code below. Unpooled and partial-pooled estimates are extracted
differently in `lme4`

. To extract the unpooled estimates, one uses the
`fixef()`

function. These unpooled estimates, along with their standard
errors and other information, are also found in the model summary table
returned by `summary()`

. The partial-pooled estimates, however, are not
found in the table. To extract them, we need the `ranef()`

function as
shown below.

```
1m2_eff.item = fixef(m2)
2m2_eff.subj = ranef(m2)$Sid[, 1]
```

In addition to the estimates, we would also like to retrieve their
standard errors. Similar to the estimates, the standard errors of the
estimates are extracted differently according to whether they are
unpooled (fixed) or partial-pooled (random). We can utilize `se.fixef()`

and `se.ranef()`

from the `arm`

package to extract these standard
errors:

```
1m2_se.item = arm::se.fixef(m2)
2m2_se.subj = arm::se.ranef(m2)$Sid[, 1]
```

Finally, to compare the estimates of `m1`

and `m2`

, I plot them together
in the same figure. I also plot the uncertainty—calculated as
$\pm 2 \times Standard~error$—around each estimate. Estimates and
uncertainties from `m1`

are plotted as blue, whereas those from `m2`

are
plotted as pink. The true effects for generating the simulated data are
plotted as solid black points.

```
1# Concatenate item & subj effect/std to match m1_eff/m1_se
2m2_eff = c( m2_eff.item, m2_eff.subj )
3m2_se = c( m2_se.item, m2_se.subj )
4
5#' Function stolen from `rethinking::col.alpha()`
6col.alpha = function (acol, alpha = 0.5) {
7 acol = col2rgb(acol)
8 acol = rgb(acol[1]/255, acol[2]/255, acol[3]/255, alpha)
9 acol
10}
11
12# Plot for comparing `m1` & `m2`
13plot( 1, type="n", ylim = c(-4.8, 4.8), xlim=c( 0, n_subj+n_item + 1 ),
14 ylab="Effect", xlab="Item Index" )
15abline( v=n_item + .5, lty=2, col="grey" )
16segments( -5, mean(m2_eff.item), n_item+.5, lty=2, col="grey" )
17segments( n_item+.5, 0, 1000, lty=2, col="grey" )
18points( c(E, A), pch=19 )
19# Uncertainty bars
20for (i in seq_along(m2_se)) {
21 lines( c(i,i), m1_eff[i] + c(-2,2)*m1_se[i], col=col.alpha(4), lwd=6 )
22 lines( c(i,i), m2_eff[i] + c(-2,2)*m2_se[i], col=col.alpha(2,.7), lwd=3 )
23}
24points( m1_eff, col=4 )
25points( m2_eff, col=2 )
```

### Shrinkage

Some of the benefits of partial pooling discussed
earlier are visualized in the comparison
plot above. The most drastic changes from the unpooled to the
partial-pooled model are seen in the ability estimates, which are
exactly the levels that get partially pooled. Two things to notice here.
First, there is less uncertainty in the partial-pooled estimates than in
the unpooled ones (pink bars tend to be shorter than their blue
counterparts). This follows naturally because, through partial pooling,
the model has access to more information (hence less uncertainty) for
each level. Secondly, the partial-pooled estimates tend to get “pulled”
towards the center (i.e., the grand mean of the subject estimates). In
addition, more extreme estimates are further pulled toward the center.
Essentially, this means that the model behaves in a way that is robust
against observations that result in extreme estimates. This is known as
**shrinkage** and is also a feature that naturally arises from partial
pooling.

From the figure, we can see that partial pooling improves the estimation
of the person abilities, as most pink circles are found to be much
closer to the solid black dots (true effects) than the blue ones. For
item easiness, which are not partial-pooled, the estimates also improve
slightly. This results from the improvement in estimating abilities.
Since ability and easiness are jointly estimated by the model, the
improvement from ability estimation carries on to easiness estimation.
Given the large improvement in ability estimates, one might consider
also pooling the items. Indeed, there is no reason to not pool.
**Partial pooling should be the default**.

### Partial Pool Items and Subjects

To specify the partial pooling of items in the model, we again utilize
the “bar” syntax: `(1|Iid)`

. This allows `glmer()`

to also model the
items as coming from a normal distribution with zero mean and unknown
variance. Now, since both the items and the subjects are centered at
zeros, an additional step is needed to reconstruct the zero-centered
item estimates back to their original locations^{1}. This is why the
model formula in `m2.2`

uses `1`

instead of `-1`

. By specifying `1`

,
`glmer()`

estimates an independent global intercept. In the case here,
this intercept is identical to the amount subtracted from the item
effects for centering. Hence, to reconstruct the original non-centered
item estimates, we add the global intercept back to the item estimates,
as shown in line 4 in the code below.

```
1m2.2 = glmer( R ~ 1 + (1|Iid) + (1|Sid), data=d, family=binomial('logit') )
2
3m2.2_eff.subj = ranef(m2.2)$Sid[, 1]
4m2.2_eff.item = ranef(m2.2)$Iid[, 1] + fixef(m2.2)[["(Intercept)"]]
5m2.2_eff = c( m2.2_eff.item, m2.2_eff.subj )
6m2.2_se = arm::se.ranef( m2.2 )
7m2.2_se = c( m2.2_se$Iid, m2.2_se$Sid )
```

You can compare `m2.2`

to `m2`

by plotting their estimates with the
plotting code previously shown and see that `m2.2`

further improves the
estimation (though not large). In the psychometric/measurement
literature, partial pooling both item and person is uncommon. But as
seen in our simulate-and-fit approach, partial pooling results in better
estimation. This approach also refutes the unjustified belief that
“*fixed* effects should be used when the levels are **specifically
selected by the researcher**”. In our simulation, values of the item
easiness are specifically “picked out”. They are deliberately set to be
equally-spaced values. And still, we saw that modeling the item effects
as *random* is not only benign but even improves estimation. This is
true in general, and you can change the values of the item easiness in
the simulation to see that partial pooling mostly, if not always, gives
better estimates.

## What’s next

So far, we have been dealing with item response models with dichotomous
item responses. That is, a response can only either be correct (`1`

) or
wrong (`0`

). In Part 4, we move on to item response models for
rating responses. These models are extremely useful since rating scales
are common in the social sciences. The models also allow us to model the
so-called “rater effect”, which quantifies the leniency of the raters.
By incorporating such rater effects, the model corrects for potential
biases introduced by subjective ratings, thereby giving more accurate
person and item estimates.

Don’t be intimidated by matrix algebra. It’s simply arithmetics in a fancy manner, and it looks scary only because it does many things at once. With some patience, you will be able to break down and understand the steps involved.

#### Reconstructing Dropped Estimates

Let’s first see how the contrast matrix reconstructs the dropped
estimate from the sum-to-zero constrained model. I’ll start with a toy
example with only three subjects, $S_1, S_2, S_3$. The contrast matrix
for imposing a sum-to-zero constraint on the subjects is shown below.
Recall that the sum-to-zero constraint is coded through the dropping of
the last subject, $S_3$ (hence two columns left in the contrast matrix),
and implicit coding of $S_3$’s information into $S_1$ and $S_2$ by the
`-1`

s on the third row. Given this coding, the effect of $S_3$ can be
reconstructed from the effects of $S_1$ and $S_2$ by taking the negative
of their sum. This can be done through the code
`c(subj_eff.m1.2, -sum(subj_eff.m1.2) )`

from the previous post.

$S_1$ | $S_2$ | |
---|---|---|

$S_1$ | 1 | 0 |

$S_2$ | 0 | 1 |

$S_3$ | -1 | -1 |

The same thing can be done through **matrix multiplication**. Simply
take the above 3-by-2 contrast matrix and multiply the 2-by-1 column
vector of the estimated effects for $S_1$ and $S_2$, which I abbreviate
as $E_1$ and $E_2$ here. The last entry of the resulting column vector
would then give what we want.

$$ \begin{bmatrix} 1 & 0 \\ 0 & 1 \\ -1 & -1 \end{bmatrix} \begin{bmatrix} E_1 \\ E_2 \end{bmatrix} = \begin{bmatrix} E_1 \\ E_2 \\ -E_1 - E_2 \end{bmatrix} $$

Here’s the R code version of the above matrix multiplication:

```
1Cmat = contr.sum(3) # Contrast matrix coding sum-to-zero constraint
2eff = c( E1=1.5, E2=1.7 ) # Made-up effect of S1 and S2
3Cmat %*% eff
```

```
[,1]
1 1.5
2 1.7
3 -3.2
```

#### Reconstructing Standard Error of Dropped Estimates

The contrast matrix can similarly be applied to reconstruct the variance
( hence the standard error) of the dropped subject’s estimate. The
reconstruction is based on the **variance sum law**,
$Var(X+Y) = Var(X) + Var(Y) + 2~Cov(X,Y)$, which has a natural
generalization through matrix notations. Hence, given the variance of
the estimates for $S_1$ and $S_2$ and their covariance, we will be able
to reconstruct the variance of $E_3$ as

$$ \begin{equation} Var(E_3) = Var(E_1) + Var(E_2) + 2~Cov(E_1,E_2) \tag{1} \end{equation} $$

The variances and covariances of the estimates are given by the (variance-)covariance matrix of the fitted model. The formula below shows the matrix generalization to the variance sum law. Note that through the matrix generalization, we also get the reconstructed covariances, as shown in the off-diagonal entries in the reconstructed covariance matrix (the right-most matrix). The variance of $E_1$, $E_2$, and $E_3$ are found on the diagonal. The standard errors of the estimates are then obtained by taking the square roots of these diagonal entries.

In R, the same calculation is done with the code below.

```
1Cmat = contr.sum(3) # Contrast matrix for coding sum-to-zero constraint
2# Made-up variances-covariances matrix of the estimates
3Vmat = matrix(c( 0.3, -0.01,
4 0.0, 0.4 ),
5 byrow=T, nrow=2 )
6Cmat %*% Vmat %*% t(Cmat) # Reconstructed variance-covariance matrix
```

```
1 2 3
1 0.3 -0.01 -0.29
2 0.0 0.40 -0.40
3 -0.3 -0.39 0.69
```

#### Back to the Code

```
1d1 = d
2contrasts(d1$Sid) = contr.sum( n_subj )
3m1 = glm( R ~ -1 + Iid + Sid, data=d1, family=binomial("logit") )
4
5# Construct contrast matrix
6Cmat = diag(0, nrow=n_item+n_subj)[, -1]
7diag(Cmat)[1:n_item] = 1
8idxS = 1:n_subj + n_item
9Cmat[idxS, idxS[-length(idxS)]] = contr.sum( n_subj )
10
11# Reconstruct estimates with the constrast matrix
12m1_eff = (Cmat %*% coef(m1))[, 1]
13# Reconstruct std. error of the estimates with the constrast matrix
14Vmat = Cmat %*% vcov(m1) %*% t(Cmat)
15m1_se = sqrt(diag(Vmat))
```

Once familiar with the matrix algebra discussed, the above code for
reconstructing the dropped subject’s effect should become
self-explaining. The only complication here is that instead of using the
contrast matrix of the subjects, a larger matrix encompassing the coding
of **all levels of both the item and the subject variables** is used to
match the covariance matrix given by the model (which also contains all
levels from all variables). This large contrast matrix can be thought of
as the concatenation of two contrast matrices along the diagonal, with
the remaining off-diagonal entries filled in with zeros. To better
explain this, let me go back to our previous example with three
subjects.

To keep things simple, let’s assume additionally that there are only three items. Since in the model, the sum-to-zero constraint is only imposed on the subjects, the contrast matrix for the coding of items would be a 3-by-3 identity matrix. Concatenating the item and subject contrast matrices in the way mentioned above results in the matrix:

`$$ \begin{bmatrix} \begin{bmatrix} 1 & 0 & 0 \\ 0 & 1 & 0 \\ 0 & 0 & 1 \end{bmatrix}_{3 \times 3} & 0~~~~~ \\ 0 & \begin{bmatrix} 1 & 0 \\ 0 & 1 \\ -1 & -1 \end{bmatrix}_{3 \times 2} \end{bmatrix}_{6 \times 5} $$`

In general, with $n_I$ items and $n_S$ subjects, this concatenated contrast matrix has the form:

`$$ \begin{bmatrix} ~~\mathrm{I}_{n_I \times n_I}~~~ & 0 ~~~~~~~~~~~~~~ \\ \\ 0 & \begin{bmatrix} 1 & 0 & \cdots & 0 \\ 0 & 1 & & 0 \\ \vdots & & \ddots & \vdots \\ 0 & 0 & \cdots & 1 \\ -1 & -1 & \cdots & -1 \end{bmatrix}_{n_S \times (n_S - 1)} \end{bmatrix}_{ (n_I + n_S) \times (n_I + n_S - 1) } $$`

This is what the second part of the above code (reproduced below) is
doing. It first sets up the correct shape of this large contrast matrix
according to the number of items and subjects. The trick here is to use
the `diag()`

function to initialize a square matrix of zeros and drop
one of the columns to match the correct number of dimensions. Then, line
3 of the code sets the upper-left portion of this matrix (the item
sub-matrix) as an identity matrix by filling in the diagonal with ones.
Finally, the lower-right portion of the matrix (the subject sub-matrix)
is replaced with the subject contrast matrix constructed by the
`contr.sum()`

function.

```
1# Construct contrast matrix
2Cmat = diag(0, nrow=n_item+n_subj)[, -1]
3diag(Cmat)[1:n_item] = 1
4idxS = 1:n_subj + n_item
5Cmat[idxS, idxS[-length(idxS)]] = contr.sum( n_subj )
```

With the contrast matrix `Cmat`

prepared, we can construct what we need
through matrix algebra. The estimates for all levels, including the
dropped one, are reconstructed by multiplying `Cmat`

with the estimates
returned by the model. This is illustrated in the line below. The
estimates are given by `coef(m1)`

, and the `[, 1]`

at the end of the
line forces the resulting one-column matrix into vector form.

```
1m1_eff = ( Cmat %*% coef(m1) )[, 1]
```

The full covariance matrix is similarly reconstructed through `Cmat`

and
the covariance matrix extracted from the model (`vcov(m1)`

):

```
1Vmat = Cmat %*% vcov(m1) %*% t(Cmat)
```

Since the final products we need are the standard errors, we extract the
diagonal entries of `Vmat`

and take the square root:

```
1m1_se = sqrt( diag(Vmat) )
```

We don’t touch the subject estimates, though, since we assume them to be centered at zero in the simulation, remember? ↩︎