This vignette describes how `galamm`

can be used to
estimate generalized linear mixed models with factor structures. Such
models are an instance of the generalized linear latent and mixed models
(GLLAMM) framework described by Rabe-Hesketh,
Skrondal, and Pickles (2004).
The R package PLmixed (Rockwood and Jeon
2019) estimates such models using a profile likelihood
algorithm initially proposed by Jeon and
Rabe-Hesketh (2012).
The models are also a special case of generalized additive latent and
mixed models (GALAMM), and in galamm these models are estimated using a
more direct algorithm described in Sørensen,
Fjell, and Walhovd (2023).

As for the vignette on linear mixed models, we thank Rockwood and Jeon (2019) for creating the PLmixed package, from which we take example datasets, and on which we have based the formula syntax of galamm.

We use a simulated dataset from the PLmixed package for this example. The observations are binomial responses representing an ability measurement. The first few lines are shown below.

```
library(PLmixed)
head(IRTsim)
#> sid school item y
#> 1.1 1 1 1 1
#> 1.2 1 1 2 1
#> 1.3 1 1 3 1
#> 1.4 1 1 4 0
#> 1.5 1 1 5 1
#> 2.1 2 1 1 1
```

Each student is identified by a student id `sid`

, and each
school with a school id given by the `school`

variable. For
each student, five item measurements have been made. We assume that the
student’s performance depends both on the students ability as well as on
the school the student attends. Having the outline of GALAMMs from the
introductory
vignette in mind, we assume a binomial response model with a logit
link, yielding for the \(i\)th
measurement of the \(j\)th student in
the \(k\)th school,

\[ \text{P}(y_{ijk} = 1 | \mathbf{x}_{ijk}, \boldsymbol{\eta}_{jk}) = \frac{\exp(\nu_{ijk})}{1 + \exp(\nu_{ijk})} \]

The latent variable vector is given by \(\boldsymbol{\eta}_{jk} = (\eta_{j}, \eta_{jk})^{T}\), where the last element is the effect of the school which the \(j\)th student attends. The nonlinear predictor is given by

\[ \nu_{ijk} = \mathbf{x}_{ijk}^{T} \boldsymbol{\beta} + \mathbf{x}_{ijk}^{T}\boldsymbol{\lambda} (\eta_{j} + \eta_{jk}) \]

where \(\mathbf{x}_{ij}\) is a vector containing dummy variables for items, \(\eta_{j}\) is a latent variable describing the underlying ability of student \(j\), and \(\eta_{k}\) is a latent variable describing the effect of school \(k\). The factor loading \(\lambda\) describes how the sum of the two latent variables impacts the nonlinear predictor, and hence the probability of correct response. We note that using a common \(\lambda\) for two latent variables like this is not necessarily a good model, but it makes this introductory example easier to follow. We will extend the model later.

The structural model is simply

\[ \boldsymbol{\eta}_{jk} = \boldsymbol{\zeta}_{jk} \sim N_{2}(\mathbf{0}, \boldsymbol{\Psi}), \]

where \(N(\mathbf{0}, \boldsymbol{\Psi})\) denotes a bivariate normal distribution with mean zero covariance matrix \(\boldsymbol{\Psi}\). The covariance matrix is assumed to be diagonal.

We confirm that `item`

has five levels. This means that
\(\boldsymbol{\lambda}\) is a vector
with five elements.

For identifiability, we fix the first element of \(\boldsymbol{\lambda}\) to one. The rest
will be freely estimated. We do this by defining the following matrix.
Any numeric value implies that the element is fixed, whereas
`NA`

implies that the element is unknown, and will be
estimated.

```
(loading_matrix <- matrix(c(1, NA, NA, NA, NA), ncol = 1))
#> [,1]
#> [1,] 1
#> [2,] NA
#> [3,] NA
#> [4,] NA
#> [5,] NA
```

We fit the model as follows:

```
mod <- galamm(
formula = y ~ item + (0 + ability | school / sid),
data = IRTsim,
family = binomial,
load.var = "item",
factor = "ability",
lambda = loading_matrix
)
```

A couple of things in the model formula are worth pointing out. First
the part `(0 + ability | school / sid)`

in the model formula
specifies that student ability varies between students within schools.
It corresponds to the term \(\mathbf{x}_{ijk}^{T}\boldsymbol{\lambda} (\eta_{j}
+ \eta_{jk})\) in the mathematical specification of the model.
The variable `ability`

is not part of the `IRTsim`

dataframe, but is instead specified in the argument
`factor = "ability"`

. The argument
`load.var = "item"`

specifies that all rows in the dataframe
with the same value of “item” should get the same element of \(\boldsymbol{\lambda}\), and hence it
defines the dummy variable \(\mathbf{x}_{ijk}\). Finally,
`lambda = loading_matrix`

provides the matrix of factor
loadings. Note that we must explicitly add a zero in
`(0 + ability | school / sid)`

to avoid having a random
intercept estimated in addition to the effect for each value of “item”;
such a model would not be identified. The fixed effect part of the model
formula, which is simply `item`

, specifies the term \(\mathbf{x}_{ijk}^{T}
\boldsymbol{\beta}\).

We can start by inspecting the fitted model:

```
summary(mod)
#> GALAMM fit by maximum marginal likelihood.
#> Formula: y ~ item + (0 + ability | school/sid)
#> Data: IRTsim
#>
#> AIC BIC logLik deviance df.resid
#> 2966.4 3030.5 -1472.2 2372.3 2489
#>
#> Scaled residuals:
#> Min 1Q Median 3Q Max
#> -2.8884 -0.7335 0.4266 0.6235 3.0410
#>
#> Lambda:
#> ability SE
#> lambda1 1.0000 .
#> lambda2 0.7370 0.1456
#> lambda3 0.9351 0.1872
#> lambda4 0.6069 0.1261
#> lambda5 0.5860 0.1163
#>
#> Random effects:
#> Groups Name Variance Std.Dev.
#> sid:school ability 1.466 1.211
#> school ability 1.300 1.140
#> Number of obs: 2500, groups: sid:school, 500; school, 26
#>
#> Fixed effects:
#> Estimate Std. Error z value Pr(>|z|)
#> (Intercept) 0.5112 0.2617 1.953 0.050777
#> item2 0.3256 0.1791 1.818 0.069068
#> item3 -0.4491 0.1623 -2.768 0.005644
#> item4 0.4930 0.1924 2.562 0.010402
#> item5 0.4585 0.1922 2.385 0.017067
```

The `fixef`

method lets us consider the fixed effects:

```
fixef(mod)
#> (Intercept) item2 item3 item4 item5
#> 0.5112006 0.3255941 -0.4491070 0.4929827 0.4584897
```

We can also get Wald type confidence intervals for the fixed effects.

```
confint(mod, parm = "beta")
#> 2.5 % 97.5 %
#> (Intercept) -0.001727334 1.0241286
#> item2 -0.025430062 0.6766183
#> item3 -0.767138526 -0.1310755
#> item4 0.115869898 0.8700955
#> item5 0.081749228 0.8352303
```

We can similarly extract the factor loadings.

```
factor_loadings(mod)
#> ability SE
#> lambda1 1.0000000 NA
#> lambda2 0.7370254 0.1455782
#> lambda3 0.9351105 0.1872049
#> lambda4 0.6069065 0.1260943
#> lambda5 0.5859914 0.1162977
```

And we can find confidence intervals for them. Currently, only Wald type confidence intervals are available. Be aware that such intervals may have poor coverage properties.

```
confint(mod, parm = "lambda")
#> 2.5 % 97.5 %
#> lambda1 0.4516974 1.0223534
#> lambda2 0.5681956 1.3020254
#> lambda3 0.3597662 0.8540468
#> lambda4 0.3580520 0.8139307
```

We can also show a diagnostic plot, although for a binomial model like this it is not very informative.

We now show how the model studied above can be extended to handle binomially distributed data with multiple trials. We simulate such data by computing predictions from the model fitted above, and drawing binomial samples with multiple trials.

```
set.seed(1234)
dat <- IRTsim
dat$trials <- sample(1:10, nrow(dat), replace = TRUE)
dat$y <- rbinom(
n = nrow(dat), size = dat$trials,
prob = plogis(fitted(mod))
)
head(dat)
#> sid school item y trials
#> 1.1 1 1 1 8 10
#> 1.2 1 1 2 5 6
#> 1.3 1 1 3 5 5
#> 1.4 1 1 4 5 9
#> 1.5 1 1 5 3 5
#> 2.1 2 1 1 5 6
```

For binomial models with more than one trial, the response should be
specified `cbind(successes, failures)`

.

```
galamm_mod_trials <- galamm(
formula = cbind(y, trials - y) ~ item + (0 + ability | school / sid),
data = dat,
family = binomial,
load.var = "item",
factor = "ability",
lambda = loading_matrix
)
```

All the utility functions apply to this model as well. We simply post its summary output here.

```
summary(galamm_mod_trials)
#> GALAMM fit by maximum marginal likelihood.
#> Formula: cbind(y, trials - y) ~ item + (0 + ability | school/sid)
#> Data: dat
#>
#> AIC BIC logLik deviance df.resid
#> 7149.8 7213.9 -3563.9 2974.8 2489
#>
#> Scaled residuals:
#> Min 1Q Median 3Q Max
#> -1.573 2.830 5.003 9.183 20.222
#>
#> Lambda:
#> ability SE
#> lambda1 1.0000 .
#> lambda2 0.7013 0.2123
#> lambda3 0.5007 0.1899
#> lambda4 0.4265 0.1869
#> lambda5 0.6326 0.2121
#>
#> Random effects:
#> Groups Name Variance Std.Dev.
#> sid:school ability 0.00000 0.0000
#> school ability 0.06048 0.2459
#> Number of obs: 2500, groups: sid:school, 500; school, 26
#>
#> Fixed effects:
#> Estimate Std. Error z value Pr(>|z|)
#> (Intercept) 0.57682 0.06436 8.962 3.191e-19
#> item2 0.07417 0.05930 1.251 2.110e-01
#> item3 -0.09932 0.06205 -1.601 1.095e-01
#> item4 0.07328 0.06469 1.133 2.573e-01
#> item5 0.19302 0.06098 3.165 1.548e-03
```

To illustrate the model for counts, we consider an example from Chapter 11.3 in Skrondal and Rabe-Hesketh (2004). The model does not contain factor loadings, but we use it to demonstrate how to fit GLMMs with Poisson distributed responses.

```
count_mod <- galamm(
formula = y ~ lbas * treat + lage + v4 + (1 | subj),
data = epilep,
family = poisson
)
```

We can look at the summary output.

```
summary(count_mod)
#> GALAMM fit by maximum marginal likelihood.
#> Formula: y ~ lbas * treat + lage + v4 + (1 | subj)
#> Data: epilep
#>
#> AIC BIC logLik deviance df.resid
#> 1344.7 1369.0 -665.4 407.0 229
#>
#> Scaled residuals:
#> Min 1Q Median 3Q Max
#> -3.1918 -0.8456 -0.0917 0.5839 6.6303
#>
#> Random effects:
#> Groups Name Variance Std.Dev.
#> subj (Intercept) 0.2516 0.5016
#> Number of obs: 236, groups: subj, 59
#>
#> Fixed effects:
#> Estimate Std. Error z value Pr(>|z|)
#> (Intercept) 1.7936 0.10468 17.134 8.230e-66
#> lbas 0.8845 0.13096 6.754 1.436e-11
#> treat -0.3350 0.14775 -2.267 2.339e-02
#> lage 0.4846 0.34658 1.398 1.621e-01
#> v4 -0.1611 0.05458 -2.952 3.161e-03
#> lbas:treat 0.3384 0.20293 1.668 9.541e-02
```

In this case there are no factor loadings to return:

We can again look at a diagnostic plot, which in this case looks much more reasonable.

In this case we can confirm that the `galamm`

function is
correctly implemented by comparing it to the output of
`lme4::glmer`

. For a model like this, it would also be best
to use `lme4`

, but with factor structures or other
nonlinearities, `lme4`

no longer provides the flexibility we
need.

```
library(lme4)
#> Loading required package: Matrix
#>
#> Attaching package: 'lme4'
#> The following object is masked from 'package:galamm':
#>
#> llikAIC
count_mod_lme4 <- glmer(
formula = y ~ lbas * treat + lage + v4 + (1 | subj),
data = epilep,
family = poisson
)
```

We can confirm that the diagnostic plot has the same values as for galamm:

And we can do the same for the summary output.

```
summary(count_mod_lme4)
#> Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod']
#> Family: poisson ( log )
#> Formula: y ~ lbas * treat + lage + v4 + (1 | subj)
#> Data: epilep
#>
#> AIC BIC logLik deviance df.resid
#> 1344.7 1369.0 -665.4 1330.7 229
#>
#> Scaled residuals:
#> Min 1Q Median 3Q Max
#> -3.1918 -0.8456 -0.0918 0.5837 6.6303
#>
#> Random effects:
#> Groups Name Variance Std.Dev.
#> subj (Intercept) 0.2515 0.5015
#> Number of obs: 236, groups: subj, 59
#>
#> Fixed effects:
#> Estimate Std. Error z value Pr(>|z|)
#> (Intercept) 1.7937 0.1045 17.165 < 2e-16 ***
#> lbas 0.8844 0.1308 6.764 1.34e-11 ***
#> treat -0.3349 0.1474 -2.272 0.02311 *
#> lage 0.4845 0.3458 1.401 0.16122
#> v4 -0.1611 0.0543 -2.966 0.00301 **
#> lbas:treat 0.3382 0.2025 1.671 0.09479 .
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#>
#> Correlation of Fixed Effects:
#> (Intr) lbas treat lage v4
#> lbas -0.035
#> treat -0.708 0.024
#> lage -0.092 -0.037 0.099
#> v4 0.015 0.000 0.000 0.000
#> lbas:treat 0.001 -0.654 -0.087 0.252 0.000
```

You might note that the deviance in the summary output of the model fitted by lme4 is different from the deviance of the model fitted by galamm. This is because in the summary output, lme4 shows the deviance as minus two times the log likelihood. In contrast, calling the deviance function on a model object fitted by glmer gives the same output as galamm.

For details on deviance calculation in lme4, see
`help(deviance.merMod, "lme4")`

.

Jeon, Minjeong, and Sophia Rabe-Hesketh. 2012.
“Profile-Likelihood Approach for Estimating
Generalized Linear Mixed Models With Factor Structures.”
*Journal of Educational and Behavioral Statistics* 37 (4):
518–42. https://doi.org/10.3102/1076998611417628.

Rabe-Hesketh, Sophia, Anders Skrondal, and Andrew Pickles. 2004.
“Generalized Multilevel Structural Equation Modeling.”
*Psychometrika* 69 (2): 167–90. https://doi.org/10.1007/BF02295939.

Rockwood, Nicholas J., and Minjeong Jeon. 2019. “Estimating
Complex Measurement and Growth Models Using
the R Package PLmixed.” *Multivariate Behavioral
Research* 54 (2): 288–306. https://doi.org/10.1080/00273171.2018.1516541.

Skrondal, Anders, and Sophia Rabe-Hesketh. 2004. *Generalized Latent
Variable Modeling*. Interdisciplinary Statistics
Series. Boca Raton, Florida: Chapman and Hall/CRC.

Sørensen, Øystein, Anders M. Fjell, and Kristine B. Walhovd. 2023.
“Longitudinal Modeling of Age-Dependent Latent
Traits with Generalized Additive Latent and
Mixed Models.” *Psychometrika* 88 (2):
456–86. https://doi.org/10.1007/s11336-023-09910-z.