ABSTRACT
This chapter presents some of the datasets used in this text together with samples of using the mentioned software packages. In addition to providing sample code for fitting the GEE models discussed in this text, we also provide sample code for fitting alternative likelihood-based models where appropriate. This section will not teach the reader how to use a particular software package, but will provide samples from which other analyses can be produced. We pay particular attention to the various options available in each package to highlight the relatively minor differences between them. Samples are presented by means of input files which can be run in “batch”
mode. Readers can then interactively enter the commands; however, we suggest first running the programs in their entirety and then reading the results. The PA-GEE model has the best support across packages. There are some
minor differences in the default behavior for the packages that we highlight in the following programs. We include comments to assist the reader in understanding the choices of both the analysis and the selected options. The datasets listed in this chapter are available in tab-delimited plain text
format from:
5.1 Programs
The following pages include programs for fitting various models and calculating various diagnostic statistics. These programs can be run in batch mode and illustrate each of the software packages used in this text.
