It is common to fit a model where a variable (or variables) has an effect on the expected mean. You may also want to fit a model where a variable has an effect on the variance, that is a model with heteroskedastic errors. One example is a hierarchical model where the error variance is not constant over some categorical variable (e.g., gender). Another example is a longitudinal model where you might want to allow the errors to vary across time. This page describes how to fit such a model and demonstrates with an example.

## Example 1: Heteroskedastic errors by group

It may be useful to note that a multi-level model (or a single level model) that allows different error terms between groups is similar to a multi-group structural equation model in which all parameters in the model are constrained to equality except for the error terms.

The dataset for this example includes data on 7185 students in 160
school. This dataset and model come from the HLM manual. The variable **mathach** is a measure of each student’s
math achievement, the variable **female** is a binary variable equal to one if the student is
female and zero otherwise, and the variable **id** contains the school
identifier.

Below we run a model that uses **female** to predict **mathach**. This
model assumes equal error variances for males and females.

use http://www.ats.ucla.edu/stat/stata/faq/hsb, clear mixed mathach female || id:, var mle nologMixed-effects ML regression Number of obs = 7185 Group variable: id Number of groups = 160 Obs per group: min = 14 avg = 44.9 max = 67 Wald chi2(1) = 62.89 Log likelihood = -23526.66 Prob > chi2 = 0.0000 ------------------------------------------------------------------------------ mathach | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- female | -1.35939 .1714111 -7.93 0.000 -1.69535 -1.02343 _cons | 13.34526 .253935 52.55 0.000 12.84756 13.84297 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Random-effects Parameters | Estimate Std. Err. [95% Conf. Interval] -----------------------------+------------------------------------------------ id: Identity | var(_cons) | 8.108982 1.018274 6.339834 10.37181 -----------------------------+------------------------------------------------ var(Residual) | 38.84481 .6555316 37.58101 40.15112 ------------------------------------------------------------------------------ LR test vs. linear regression: chibar2(01) = 936.66 Prob >= chibar2 = 0.0000

In order to fit a model with heteroskedastic errors, we must modify the above model. The model shown above can be written as:

mathach_ij = b0 + b1*female_ij + u_i + e_ij (1)

This model assumes:

e_ij ~ N(0,s2) u_i ~ N(0,t2)

Where **e_ij** is the level 1 errors (i.e., residuals)**, ** and** u_i** is the random intercept across classrooms (i.e., the level 2
variance). We want to allow
the variance of **e_ij** (i.e., **s2**) to be different
for male and female students. One way to think about this would be to replace the single
**e_ij**
term, with
separate terms for males and females, in equation form:

e_ij = e(m)_ij*male + e(f)_ij*female (2)

Where **male** is a dummy variable equal to one if the student is male and
equal to zero otherwise, and **e(m)_ij** is the error term for males. The
variable **female** and the term **e(f)_ij** are the same except that they
are for females. Another way to write this is:

e_ij ~ N(0,s2_1) males N(0,s2_2) females

Another way to think about this is to use one group as the reference group, and estimate the difference between the variance of the two groups. In equation form this would be:

e_ij = e(m)_ij + e(f)_ij*female (3)

Where **e(m)_ij** is the error term for males, and **e(f)_ij** is the
difference between the errors for males and females. This can also be written:

e_ij ~ N(0,s2 + s2_2*female)

This second way of looking at the error structure is part of how we will restructure our model to allow for heteroskedastic error terms.

Equation 3 says that the residual variance is a function of gender. So we can write it as r_ijk, where i is the group, j is the subject, and k is the gender.

mathach_ij = b0 + b1*female + u_i + r_ijk (4)

To model this, we add a level to our model. Now the third level will be classrooms (previously level 2), the second level will be students (previously level 1), and level 1 will be a single case within each student. The only random effect at level 1 is gender (even the intercept is fixed). The new model can be written as:

mathach_ij = b0 + b1*female_ij + u_i + e_ij*female + r_ij0 r_ijk = r_ij0 male r_ij1 female=e_ij+r_ij0

Where the level one error
is represented by **r_ij0**. Because males are the omitted category in the
random portion of the model, the variance of **r_ij0** is the variance of the
errors males (i.e., **female**=0). This is similar to the interpretation of
the intercept in the fixed portion of the mode, where **b0** represents the
intercept for males, since they are the omitted category. The difference between
the error terms for males and females is **e_ij** so the error term for females is
**r_ij** + **e1_ij**.

A final consideration before we can actually fit the model is that Stata restricts the estimates of the error variances to be greater than zero. As a result, we must use the group with the smallest variance as the omitted category, since this will result in the values of the error variances for the group(s) being positive. To establish which group has the lowest variance you can examine the residuals from a model without heteroskedastic errors. In this example, examination of the residuals shows that the residual variance is smaller for females than males.

The code below creates two new variables, **male**, and **nid**. The variable **nid**
will be the identifier for the students.

recode female (0=1) (1=0), gen(male) gen nid = _n

The resulting data set should look something like the one shown below. Where each classroom
(identified by the variable **id**) has multiple rows in the dataset, but each case
(i.e., each student, identified by the variable **nid**) has only one row.

id nid 1224 1 1224 2 1224 3 ... 1288 48 1288 49 1288 50 ... 1296 73 1296 74 1296 75

Once the necessary variables are created, we can run the model as shown
below, which allows for a difference in the variance of the errors for males and
females. It is necessary to specify the **nocons**
option suppresses the random intercept at level 2, so that the only random
effect at level 2 is gender (i.e., **male**).

mixed mathach female || id: || nid: male, nocons var mle nologMixed-effects ML regression Number of obs = 7185 ----------------------------------------------------------- | No. of Observations per Group Group Variable | Groups Minimum Average Maximum ----------------+------------------------------------------ id | 160 14 44.9 67 nid | 7185 1 1.0 1 ----------------------------------------------------------- Wald chi2(1) = 63.03 Log likelihood = -23522.932 Prob > chi2 = 0.0000 ------------------------------------------------------------------------------ mathach | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- female | -1.363969 .1718025 -7.94 0.000 -1.700695 -1.027242 _cons | 13.34707 .2548619 52.37 0.000 12.84755 13.84659 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Random-effects Parameters | Estimate Std. Err. [95% Conf. Interval] -----------------------------+------------------------------------------------ id: Identity | var(_cons) | 8.090527 1.016457 6.324639 10.34946 -----------------------------+------------------------------------------------ nid: Identity | var(male) | 3.622413 1.333432 1.76062 7.452988 -----------------------------+------------------------------------------------ var(Residual) | 37.13827 .8657943 35.47953 38.87456 ------------------------------------------------------------------------------ LR test vs. linear regression: chi2(2) = 944.12 Prob > chi2 = 0.0000 Note: LR test is conservative and provided only for reference.

The second table in the output shows the estimated random effects. The residual variance for females is equal to **var(Residuals)** = 37.138,
while the variance for males is **var(Residuals)** + **var(male)** =
37.1383 + 3.622 = 40.7607. Since the 95% confidence interval for **var(male)**
does not include zero, we can say that the difference between the variances is
statistically significant at the p<0.05 level.

Traditionally, and in some other packages (e.g., HLM), the variances in models with heteroskedastic errors have been parameterized as:

s2_ij = exp(a_0 + a_1*x_ij)

Where **s2_ij** is the variance of the residuals, **x_ij** is a
dichotomous variable equal to one for one group and zero for the other, and **a_0** and **a_1** are estimated parameters for the
variance. **a_0** is the variance in the group where **x_ij**
= 0, and **a_1** is the difference in the variances between the two groups.
If you want to compare the results of your analysis in Stata to those from another
package, it is possible to translate between the two. As a first step, let’s
think about what Stata is estimating a little more. One way to write what Stata models
is:

s2_ij = var(Residuals) + var(x_ij)*x_ij

Where **var(Residuals)** is the variance of the level 1 errors, and **
var(x_ij)** is the random effect of the dummy variable **x_ij**. Because Stata models the natural log of the standard deviation of the error term,
the above is visually clear, but not quite correct. The actual model is:

s2_ij = exp(2*lnsd_0 ) + exp(2*lnsd_1)*x_ij

Where **lnsd_0** is the natural log of the standard deviation of the level
1 errors, and **lnsd_1** is the natural log of the standard deviation of
the level 2 random effect. We can convert the estimates Stata gives us to **a_0**
and **a_1** using the formulas below (each formula is written twice, the
first for visual clarity, the second to reflect what is actually modeled by
Stata):

a_0 = ln(var(Residuals)) a_0 = ln(exp(2*lnsd_0)) a_1 = ln(var(Residuals)+var(x_ij)) - ln(var(Residuals)) a_1 = ln[exp(2*lnsd_0) + exp(2*lnsd_1)] - ln[exp(2*lnsd_0)]

We can use the **display** command to calculate these values. Stata stores the ln(sd) for the
level 1 residuals as **[lnsig_e]_cons**, and the ln(sd) of the random effect
of male in **[lns2_1_1]_cons**. Below we use these values to calculate **a_0** and **a_1**.

di "a_0=" ln(exp(2 * [lnsig_e]_cons))a_0=3.6147746di "a_1=" ln(exp(2 * [lnsig_e]_cons)+exp(2 * [lns2_1_1]_cons)) - ln(exp(2 * [lnsig_e]_cons))a_1=.09308814

## Example 2: A growth curve model

When you run a growth curve model in the structural equation modeling framework, it is not uncommon to allow the error variance to be different across time points, or at least to test whether such differences exist. A longitudinal model that allows different error variances across time points is similar to a growth model in the structural equation modeling setting, where all parameters except for the error terms across time points are constrained to equality. Below we show how to allow for different error variances across time points, and how to test whether the error variances are significantly different from each other.

The example dataset contains data on 239 subjects. The dataset includes
observations at up to five time points per subject, for a total of 1079 observations.
The variable **id** uniquely identifies subjects. The time at which an
observation was taken is indicated by the variable **time**, which takes on
the values 0 to 4.

Below we use **mixed** to fit a model where
the variables **x** and **time**
predict the variable **attit**. This model assumes the variance is the same
across time points.

use http://www.ats.ucla.edu/stat/stata/faq/nys2, clear mixed attit x time ||id:, var mle nologMixed-effects ML regression Number of obs = 1079 Group variable: id Number of groups = 239 Obs per group: min = 1 avg = 4.5 max = 5 Wald chi2(2) = 324.65 Log likelihood = 140.31043 Prob > chi2 = 0.0000 ------------------------------------------------------------------------------ attit | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- x | .0241245 .0033107 7.29 0.000 .0176357 .0306134 time | .0600884 .0039557 15.19 0.000 .0523353 .0678415 _cons | .1191882 .0184893 6.45 0.000 .0829498 .1554267 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Random-effects Parameters | Estimate Std. Err. [95% Conf. Interval] -----------------------------+------------------------------------------------ id: Identity | var(_cons) | .0308536 .003533 .0246511 .0386167 -----------------------------+------------------------------------------------ var(Residual) | .0311131 .0015204 .0282714 .0342405 ------------------------------------------------------------------------------ LR test vs. linear regression: chibar2(01) = 324.66 Prob >= chibar2 = 0.0000

The model above can be written as:

attit_it = b0 + b1*x_it + b2*time_it + u_i + e_it (4)

It is assumed that:

e_it ~ N(0,s2) u_i ~ N(0,t2)

Where u_i is the random intercept across individuals (i.e., the level 2
variance), and e_it represents the level 1 errors (i.e., residuals). We want to allow
the variance of e_it to be different
at each time point. One way to think about this would be to replace the single
**e_ij**
term, with
separate terms for each time point, in equation form:

e_it = e_i0*t0 + e_i1*t1 + e_i2*t2 + e_i3*t3 + e_i4*t4

Where **t0** is a dummy variable equal to one if **time** = 0 (i.e. the
first time point) and equal to zero otherwise, and **e_i0** is the error for
the first measurement occasion (time=0). The variables **t1** to **t4**, are dummy variables for time
points 1 to 4. The terms
**e_i1** to **e_i4** are the error terms for time points 1 to 4.

In order to model the heteroskedastic errors, we add a third level to our model. In this new model, the third level will be individuals (previously level 2), the second level will be time points (previously level 1), and level 1 will be a single case within each time point. Since the effect of time is in the level at model 2, only random effects for time are included at level 1. The new model can be written as:

attit_itk = b0 + b1*x_it + b2*time_it + e_i1*t1 + e_i2*t2 + e_i3*t3 + e_i4*t4 + r_ij0

Where the level one error
is represented by **r_it0**. Because the **time**=0 is the omitted category, the variance of **
r_it0** is the variance of the
errors at **time**=0. The
random effects **e_i1** to **e_i4** represent the difference between the variance
of the errors and the variance of the errors at **time**=0 for each time
point.

A final consideration before we can actually fit the model is
that Stata restricts the estimates of the error variances to be greater than zero. As a result, we must use the time point (or other
category/group) with the smallest variance as the omitted category, since this will result in the values of the error variances for the other time points
being positive. To establish which time point or group has the lowest variance
you can examine the residuals from a model without heteroskedastic errors. In
this example, the residual variance is smallest when **time**=0.

In order to fit the model we will need dummy variables for each of the other time points.

gen t1 = (time==1) gen t2 = (time==2) gen t3 = (time==3) gen t4 = (time==4)

Now we are ready to fit our model using **mixed**. The **nocons** option
suppresses the random intercept at level 2.

mixed attit x time ||id: ||time: t1 t2 t3 t4, nocons var mle nologMixed-effects ML regression Number of obs = 1079 ----------------------------------------------------------- | No. of Observations per Group Group Variable | Groups Minimum Average Maximum ----------------+------------------------------------------ id | 239 1 4.5 5 time | 1079 1 1.0 1 ----------------------------------------------------------- Wald chi2(2) = 319.37 Log likelihood = 143.67787 Prob > chi2 = 0.0000 ------------------------------------------------------------------------------ attit | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- x | .0238029 .0033059 7.20 0.000 .0173235 .0302823 time | .0597567 .0039638 15.08 0.000 .0519878 .0675256 _cons | .1208 .0178047 6.78 0.000 .0859035 .1556965 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Random-effects Parameters | Estimate Std. Err. [95% Conf. Interval] -----------------------------+------------------------------------------------ id: Identity | var(_cons) | .0280981 .0034551 .0220805 .0357557 -----------------------------+------------------------------------------------ time: Independent | var(t1) | .0027798 .0046901 .0001018 .0758888 var(t2) | .0058393 .0053178 .0009799 .0347972 var(t3) | .0125841 .0060606 .0048964 .0323421 var(t4) | .01354 .0059784 .0056988 .0321702 -----------------------------+------------------------------------------------ var(Residual) | .0247609 .0033388 .0190103 .032251 ------------------------------------------------------------------------------ LR test vs. linear regression: chi2(5) = 331.40 Prob > chi2 = 0.0000 Note: LR test is conservative and provided only for reference.

Once we have run the model, we may want to test whether the estimated
variances are different either from zero or different from each other. Below **nlcom** is used to
get the estimated variance at each time point.

nlcom (time0: exp(2 * [lnsig_e]_cons)) /// (time1: exp(2 * [lnsig_e]_cons) + exp(2 * [lns2_1_1]_cons)) /// (time2: exp(2 * [lnsig_e]_cons) + exp(2 * [lns2_1_2]_cons)) /// (time3: exp(2 * [lnsig_e]_cons) + exp(2 * [lns2_1_3]_cons)) /// (time4: exp(2 * [lnsig_e]_cons) + exp(2 * [lns2_1_4]_cons))time0: exp(2 * [lnsig_e]_cons) time1: exp(2 * [lnsig_e]_cons) + exp(2 * [lns2_1_1]_cons) time2: exp(2 * [lnsig_e]_cons) + exp(2 * [lns2_1_2]_cons) time3: exp(2 * [lnsig_e]_cons) + exp(2 * [lns2_1_3]_cons) time4: exp(2 * [lnsig_e]_cons) + exp(2 * [lns2_1_4]_cons) ------------------------------------------------------------------------------ attit | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- time0 | .0247609 .0033388 7.42 0.000 .018217 .0313048 time1 | .0275406 .0034705 7.94 0.000 .0207385 .0343427 time2 | .0306002 .0035976 8.51 0.000 .0235491 .0376513 time3 | .037345 .0044345 8.42 0.000 .0286536 .0460364 time4 | .0383009 .0044824 8.54 0.000 .0295155 .0470862 ------------------------------------------------------------------------------

We can also use **nlcom** to estimate the difference in the variance between time points,
in this case, the difference between the variance at time = 1 and time = 4.

nlcom (t4_t1: exp(2 * [lns2_1_4]_cons) - exp(2 * [lns2_1_1]_cons))t4_t1: exp(2 * [lns2_1_4]_cons) - exp(2 * [lns2_1_1]_cons) ------------------------------------------------------------------------------ attit | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- t4_t1 | .0107602 .0060541 1.78 0.076 -.0011055 .0226259 ------------------------------------------------------------------------------

## References

Gutierrez, Roberto G. (2008) Tricks of the Trade: Getting the most out of xtmixed. 2008 Fall North American Stata Users Group Meeting, San Francisco, CA.

Raudenbush, Stephen, Anthony Bryk, Yuk Fai Cheong, and Richard Congdon (2001) HLM 5: Hierarchical Linear and Nonlinear Modeling. Scientific Software International. Lincolnwood, IL.