Introduction to Multilevel Models and MLwiN

Practical 5: Introduction to Multilevel Models and MLwiN
In this short practical you will have your first experience of using MLwiN. You will fit
the variance components model discussed in the lecture to an educational dataset and
look at certain features of this model. We will firstly give a little background on the
The tutorial data set
The data in the worksheet we use have been selected from a very much larger data set of
examination results from six inner London Education Authorities (school boards). A key
aim of the original analysis was to establish whether some schools were more ‘effective’
than others in promoting students’ learning and development, taking account of variations
in the characteristics of students when they started Secondary school. Below are a list of
all the variables in the dataset. We will here however only focus on fitting models to the
normexam variable and consider the standlrt variable as a predictor.
The data set contains the following variables:
Numeric school identifier
Numeric student identifier
Student’s exam score at age 16, normalised to have approximately
a standard Normal distribution. (Note that the normalisation was
carried out on a larger sample, so the mean in this sample is not
exactly equal to 0 and the variance is not exactly equal to 1.)
A column of one’s. If included as an explanatory variable in a
regression model, its coefficient is the intercept. See Chapter 7.
Student’s score at age 11 on the London Reading Test,
standardised using Z-scores.
1=girl, 0=boy
School’s gender (1=mixed school, 2=boys’ school, 3=girls’ school)
Average LRT score in school
Average LRT score in school, coded into 3 categories (1=bottom
25%, 2=middle 50%, 3=top 25%)
Student’s score in test of verbal reasoning at age 11, coded into 3
categories (1=top 25%, 2=middle 50%, 3=bottom 25%)
Opening the worksheet and looking at the data
When you start MLwiN the main window appears. Immediately below the MLwiN title
bar are the menu bar and below it the tool bar as shown:
Below the tool bar is a blank workspace into which you will open windows. These
windows form the rest of the ‘graphical user interface’ which you use to specify tasks in
MLwiN. Below the workspace is the status bar, which monitors the progress of the
iterative estimation procedure. Open the tutorial worksheet as follows:
Select Open worksheet from the File menu.
Select from the list of files.
Click on the Open button.
When this operation is complete the filename will appear in the title bar of the main
window and the status bar will be initialised. The Names window will also appear,
giving a summary of the data in the worksheet:
The MLwiN worksheet holds the data and other information in a series of columns, as on
a spreadsheet. These are initially named c1, c2, …, but we recommend that they be given
meaningful names to show what their contents relate to. This has already been done in the
tutorial worksheet that you have loaded.
Each line in the body of the Names window summarises a column of data. In the present
case only the first 10 of the 400 columns of the worksheet contain data. Each column
contains 4059 values, one for each student represented in the data set. There are no
missing values, and the minimum and maximum value in each column are shown. Note
the Help button on the Windows tool bar. The remaining items on the tool bar of this
window are for attaching a name to a column. We shall use these later.
You can view individual values in the data using the Data window as follows:
Select View or edit data from the Data Manipulation menu.
When this window is first opened it always shows the first three columns in the
worksheet. The exact number of values shown depends on the space available on your
screen. You can view any selection of columns, spreadsheet fashion, as follows:
Click the View button
Select columns to view
Click OK
You can select a block of adjacent columns either by pointing and dragging or by
selecting the column at one end of the block and holding down ‘Shift’ while you select
the column at the other end. You can add to an existing selection by holding down ‘Ctrl’
while you select new columns or blocks. Use the scroll bars of the Data window to move
horizontally and vertically through the data, and move or resize the window if you wish.
You can go straight to line 1035, for example, by typing 1035 in the goto line box, and
you can highlight a particular cell by pointing and clicking. This provides a means to edit
data: see the Help system for more details.
Having viewed your data you will typically wish to tabulate and plot selected variables,
and derive other summary statistics, before proceeding to actual modelling. Tabulation
and other basic statistical operations are available on the Basic Statistics menu. These
operations are described in the Help system.
We will here consider a plot of our response normexam variable against the standlrt
predictor variable.
Select Customised graph from the Graphs menu
In the dropdown list labelled y select normexam
In the drop down list labelled x select standlrt
Click on the Apply button
The following graph will appear:
The plot shows, as might be expected, a positive correlation where pupils with higher
intake scores tend to have higher outcome scores. This suggests a regression relationship
between normexam and standlrt and we can fit a linear regression model in MLwiN but
we will here go straight into fitting a random intercept model.
Setting up a random intercepts model in the Equations window
In MLwiN we set up models in the Equations window.
Select Equations from the Model menu.
The Equations window will then appear:
We now have to tell the program the structure of our model and which columns hold the
data for our response and predictor variables. We will firstly define our response (y)
variable to do this:
Click on y (either of the y symbols shown will do).
In the y list, select ‘normexam’.
We will next set up the structure of the model. The model is set up as follows
In the N levels list, select ‘2-ij’.
In the level 2 (j) list, select ‘school’.
In the level 1 (i) list, select ‘student’.
Click on the Done button.
In the Equations window the red y has changed to a black yij to indicate that the response
and the first and second level indicators have been defined. We now need to set up the
predictors for the linear regression model.
Click on the red x0.
In the drop-down list, select ‘cons’.
Note that ‘cons’ is a column containing the value 1 for every student and will hence be
used for the intercept term. The fixed parameter tick box is checked by default and so
we have added to our model a fixed intercept term. We also need to set up residuals and
school effects so that the two sides of the equation balance. To do this:
Check the box labelled ‘i(student)’.
Check the box labelled ‘j(school)’.
Click on the Done button.
We have now set up our intercept and residual terms but to produce the random intercepts
regression model we also need to include the fixed slope (‘standlrt’) term. To do this we
need to add a term to our model as follows:
Click the Add Term button on the tool bar.
Select ‘standlrt’ from the variable list.
Click on the Done button.
Click on the Estimates button on the tool bar.
Note that this adds a fixed effect only for the ‘standlrt’ variable. The equations window
should now look as follows:
We now need to run this model using the IGLS algorithm and so to do this and see the
estimates we do the following
Click on the Start button.
Click on the Estimates button on the tool bar.
Having run the model the estimates will turn from blue to green to denote convergence of
the IGLS method. The Equations window should now look as follows:
Here we see from the coefficient β1 that there is a strong positive effect of prior
attainment (as measured by the London reading test) on the exam performance at age 16.
We also see that the unexplained variance has been split into two parts, the between
schools variance σ2u and the residual variance σ2e. It is often of interest to find how
important the schools are in explaining the variation and this is captured by a statistic
called the Variance Partition Coefficient (VPC) which measures the percentage of
variation explained by a classification.
Here the VPC = 0.092/(0.566+0.092)= 0.140, in other words after accounting for prior
attainment schools explain 14% of the remaining variation.
Note that you can calculate the VPC in MLwiN yourself by doing the following:
Select Command Interface window from the Data Manipulation menu.
Type calc 0.092/(0.566+0.092) in the Command Interface window
We will probably also be interested in seeing a picture of the fitted school lines for our
random intercepts model. This can be done via the predictions and graph windows.
Select the Predictions window from the Model menu.
At the bottom of the window click on variable and from the options that appear
Select Include all explanatory variables.
Click on the e0ij to remove level 1 residuals from the prediction.
column c11
from should
the dropnow
to output from prediction to
If you click on the Calc button then the fitted predictions will be stored in the column
c11. We now wish to see these displayed graphically so we need to do the following:
Select Customised graph(s) from the Graphs menu.
Select D1 from the drop down list in the top left of this window.
Select ‘c11’ from the y drop down list.
Select ‘standlrt’ from the x drop down list.
Select ‘school’ from the group drop down list.
Select ‘line’ from the plot type drop down list.
The window should be as follows:
If we now click on the Apply button we will see the 65 parallel school lines that we have
What you should have learnt from this exercise
How to set up variance components models in MLwiN
How to calculate the VPC for a multilevel model
How to graph predictions in MLwiN.
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