Simulates 120 compartment ODE model for London MSM HIV epidemic. Population categorized by 
age (4 quantiles, based on avail data)
X care continuum (undiagnosed, diagnosed, treated)
X natural history (5 CD4 stages, based on Cori et al. )
X risk variation (2 levels of risk behaviour, not correlated with susceptibility)

There is assortativity within age groups. 

Default parameters match incidence from Phillips PLoS One et al. & match cumulative diagnoses reported by PHE for London MSM. 

Also simulates coalescent trees using rcolgem package. Trees are matched to sample times and sample states of available sequence data. 

Many parameters can be tuned to adjust the relative infectiousness by age X care X clinical stage X risk level.