Contains the code for a model to estimate trends in chlamydia incidence in Australia. The original code was developed for the paper:
Hammad Ali, Ewan Cameron, Christopher C Drovandi, James M McCaw, Rebecca J Guy, Melanie Middleton, Carol El-Hayek, et al. “A New Approach to Estimating Trends in Chlamydia Incidence.” Sexually Transmitted Infections, 2015;91:513–519. doi:10.1136/sextrans-2014-051631
For the paper, estimates were generated for the 2001-2013 period. The original code has been modified slightly to produce annual estimates since 2013 for the HIV, viral hepatitis and sexually transmissible infections in Australia Annual Surveillance Report produced annually by the The Kirby Institute.
This version contains the code, input data and outputs for the year 2016 associated with a manuscript on the Australian Chlamydia Cascade.