These datasets include the sexual network at the last time step, biomarker data with detailed trajectories, infection, death and partnership events, and counts of various quantities at each time step.

Results

Demography

We first compute the annual growth rate.

The average final population size, across the 5 is 1467.2, corresponding to a growth rate of -4.38%. (The rate of entry of new individuals is a free parameter, and will be adjusted to reflect data form the three cities).

The age distribution at the end of the simulation is below.

# gg net%v%"age"
# plot(
#   qplot(age, geom="histogram", binwidth=5, 
#        col=I("red"), 
#        alpha=I(.2))
#   )

Prevalence

The overall prevalence at the end of the simulation was about 0.7, 0.8, 0.7, 0.7, 0.8%. HIV prevalence as a function of time is shown below.

Incidence

The annual incidence rates over the course of the simulation are shown below.

   ## No id variables; using all as measure variables

Main Partnerships

Mean degree.

The target main mean degree is 0.46 and a plot of the simulated mean degree, over the course of the simulations, is below.

## Warning: Removed 33 rows containing missing values (geom_path).

Degree Distribution

## degree0 degree1 degree2 degree3 
##     793     516      24       2 
## degree0 degree1 degree2 degree3 
##     852     617      26       1 
## degree0 degree1 degree2 degree3 
##     891     557      19       1 
## degree0 degree1 degree2 
##     900     536      19 
## degree0 degree1 degree2 
##     928     630      24

## Warning in unlist(sim_deg_dist_in_num)/unlist(final.vcount): longer object
## length is not a multiple of shorter object length

## Warning in matrix(sim_deg_dist_prop, ncol = 4, byrow = TRUE): data length
## [18] is not a sub-multiple or multiple of the number of rows [5]

Partnership duration.

## Don't know how to automatically pick scale for object of type data.frame. Defaulting to continuous.

Casual Partnerships

Mean degree.

The target main mean degree is 0.59 and a plot of the simulated mean degree, over the course of the simulations, is below.

## degree0 degree1 degree2 degree3 
##     799     511      24       1 
## degree0 degree1 degree2 degree3 
##     862     607      26       1 
## degree0 degree1 degree2 degree3 
##     870     574      22       2 
## degree0 degree1 degree2 degree3 
##     818     603      31       3 
## degree0 degree1 degree2 degree3 
##     973     578      29       2