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

Table 4.

Parameters Fit in the Data Analysis.

Parameter	Interpretation	Diagnosis data	Diagnosis data and genetic sequences	Diagnosis data, with ψ fixed at 0
ψ	Immigration rate of infected individuals	120 (104, 134) year^–1	5.82 (2.55, 11.2) year^–1	0 year^–1
$ɛ_{I_{0}}$	Infectiousness of undiagnosed acute stage individuals	0 (0, 0.413)	0.257 (0.0399, 0.623)	0 (0, 0.192)
$ɛ_{I_{1}}$	Infectiousness of undiagnosed chronic stage individuals	0.0042	0.00048	0.0056
$ɛ_{I_{2}}$	Infectiousness of undiagnosed AIDS individuals	0	0	0
$ɛ_{J_{0}}$	Infectiousness of diagnosed acute stage individuals	0.0675 (0, 1.17)	3.36 (3.13, 4.2)	7.34 (5.78, 9.25)
$ɛ_{J_{1}}$	Infectiousness of diagnosed chronic stage individuals	0.0089	0.17	0.032
$ɛ_{J_{2}}$	Infectiousness of diagnosed AIDS individuals	0	0	0
β	Rate of transversions	—	0.0042 year^–1	—
α_Y	Rate of transitions between purines	—	0.047 year^–1	—
α_R	Rate of transitions between pyrimidines	—	0.043 year^–1	—
π_A	Equilibrium frequency of adenine	—	0.37	—
π_G	Equilibrium frequency of guanine	—	0.24	—
π_C	Equilibrium frequency of cytosine	—	0.18	—
π_T	Equilibrium frequency of thymine	—	0.21	—
σ	Relaxation of molecular clock with respect to edges	—	2 year	—
δ_prop	Proportion of time since infection to use for diagnosis edge	—	0.064	—
δ_fixed	Amount of calendar time to add on to diagnosis edge	—	0.00049 year	—
t_root	Time of the polytomy that joins all genetic lineages	—	August 27, 2000	—

We present confidences intervals for parameters for which we computed likelihood profiles. For all other parameters, we present only the point estimate.