Code for PMTCT models and data

Repository to model PMTCT.

Statnet packages and versions

The following packages need to be installed:

tergm_3.1.1.tar.gz
ergm_3.1-0.tar.gz
network_1.9.0.tar.gz
networkDynamic_0.4.1.tar.gz

Main Directories

/Development

• Contains the engine

  • /common.functions_fieldingmortality_d9.R
  • /update.vital.dynamics_newinfected_entryage18_d13a.R
  • /assign.pregnancy_d8d1.R
  • /update.treatment_d11.R
  • /compute.cd4.count_d3.R
  • /compute.viral.load_d7_d3.R
  • /assign.infectivity_d4.R
  • /transmission_d10.R

• Contains files with country-specific parameters

  • Uganda: /params_uganda_d3.R
  • South Africa: /params_za_d2.R

/Development/Uganda_Runs

• Estimation file
• Burnin file
• Output RData file: contains network data
• Example of intervention (Option A, Current coverage)

/Development/South_Africa_Development_Runs

• Estimation file
• Burnin file
• Output RData file: contains network data
• Example of intervention (Option A, Current coverage)

Instructions to run burnin and simulation models are here.

/Development/Simulation_Graphics

• Output: plot_pdfs.zip
  Incidence: hiv_incidence_plot.pdf
  Prevalence: hiv_prevalence_plot.pdf
  Incidence and Viral Suppression vs Coverage: coverage_scenarios_plot.pdf
  Per cent Virally Suppressed: viral_suppression_plot.pdf

• Data: data.zip
  Incidence: hiv_prevalence.RData
  Prevalence: hiv_incidence.RData
  Viral Suppression: viral_suppression.RData
  Incidence and Viral Suppression vs Coverage: coverage_scenarios_data.RData

• Code: plotfiles.zip
  Incidence: hiv_prevalence.RData
  Prevalence: hiv_prevalence_plot.R
  Viral Suppression: viral_suppression_plot.R
  Incidence and Viral Suppression vs Coverage: coverage_scenarios_plot.R