. 2017 Apr 8;34(8):2065–2084. doi: 10.1093/molbev/msx124

Table 1.

Parameters of the Transmission Model Used in Simulation of Datasets.

Parameter	Interpretation	Value
$ɛ_{I_{1}}$	Infectiousness of undiagnosed chronic stage individuals	0.25 year^–1
$ɛ_{I_{2}}$	Infectiousness of undiagnosed AIDS individuals	0 year^–1
$ɛ_{J_{0}}$	Infectiousness of diagnosed acute stage individuals	0.125 year^–1
$ɛ_{J_{1}}$	Infectiousness of diagnosed chronic stage individuals	0.025 year^–1
$ɛ_{J_{2}}$	Infectiousness of diagnosed AIDS individuals	0 year^–1
$μ_{I_{0}}$	Death rate+aging rate of undiagnosed acute stage individuals	1/3 year^–1
$μ_{I_{1}}$	Death rate+aging rate of undiagnosed chronic stage individuals	1/3 year^–1
$μ_{I_{2}}$	Death rate+aging rate of undiagnosed AIDS individuals	5/6 year^–1
$μ_{J_{0}}$	Death rate+aging rate of diagnosed acute stage individuals	1/3 year^–1
$μ_{J_{1}}$	Death rate+aging rate of diagnosed chronic stage individuals	1/3 year^–1
$μ_{J_{2}}$	Death rate+aging rate of diagnosed AIDS individuals	2/3 year^–1
$γ_{I_{0}}$	Progression rate from undiagnosed acute to undiagnosed chronic	1 year^–1
$γ_{I_{1}}$	Progression rate from undiagnosed chronic to undiagnosed AIDS	1/6.3 year^–1
$γ_{J_{0}}$	Progression rate from diagnosed acute to diagnosed chronic	1 year^–1
$γ_{J_{1}}$	Progression rate from diagnosed chronic to diagnosed AIDS	1/6.3 year^–1
ρ₀	Diagnosis rate of acute stage individuals	0.5 year^–1
ρ₁	Diagnosis rate of chronic stage individuals	0.225 year^–1
ρ₂	Diagnosis rate of AIDS individuals	50 year^–1
ψ	Immigration rate of infected individuals	0 year^–1
$ϕ$	Emigration rate of infected individuals	0 year^–1
t_root	Root (polytomy) time	0 year
t₀	Time to begin simulation of the transmission model	2 year
t_end	Time to end simulation of the transmission model	10 year
n_loci	Length of the sequences to simulate	100 base pairs
p_G	Probability of a sequence given diagnosis	0.48
$N_{I_{0}} (t_{0})$	Number of undiagnosed early-stage individuals at t₀	11
$N_{I_{1}} (t_{0})$	Number of undiagnosed chronic-stage individuals at t₀	15
$N_{I_{2}} (t_{0})$	Number of undiagnosed AIDS individuals at t₀	0
$N_{J_{0}} (t_{0})$	Number of diagnosed early-stage individuals at t₀	4
$N_{J_{1}} (t_{0})$	Number of diagnosed chronic-stage individuals at t₀	8
$N_{J_{2}} (t_{0})$	Number of diagnosed AIDS individuals at t₀	6