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

Table 3.

Parameters Fixed in the Data Analysis.

Parameter	Interpretation	Value
$μ_{I_{0}}$	Death rate of undiagnosed acute stage individuals	1/70 year⁻¹
$μ_{I_{1}}$	Death rate of undiagnosed chronic stage individuals	1/70 year⁻¹
$μ_{I_{2}}$	Death rate of undiagnosed AIDS individuals	1/2 year⁻¹
$μ_{J_{0}}$	Death rate of diagnosed acute stage individuals	1/70 year⁻¹
$μ_{J_{1}}$	Death rate of diagnosed chronic stage individuals	1/70 year⁻¹
$μ_{J_{2}}$	Death rate of diagnosed AIDS individuals	1/70 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	0.225 year⁻¹
ρ₁	Diagnosis rate of chronic stage individuals	0.225 year⁻¹
ρ₂	Diagnosis rate of AIDS individuals	50 year⁻¹
$φ$	Emigration rate of infected individuals	0 year⁻¹
$N_{I_{0}} (t_{0})$	Number of undiagnosed early-stage individuals at t₀	20
$N_{I_{1}} (t_{0})$	Number of undiagnosed chronic-stage individuals at t₀	36
$N_{I_{2}} (t_{0})$	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	22
$N_{J_{2}} (t_{0})$	Number of diagnosed AIDS individuals at t₀	16
σ_site	Relaxation of molecular clock with respect to sites	0 year
t₀	Time to start filtering	January 1, 2004