In dth2/EpiModelHIV_SHAMP: Epidemic Modeling of HIV Transmission among MSM, MSMF and Heterosexual Populations

knitr::opts_chunk$set(echo = TRUE)

############################################################################
# Packages
library(EpiModelHIV)
library(EpiModelHPC)
library(ergm.ego)
library(tergmLite)

Run sim

############################################################################
# Run new sim or load from previous run

runNow <- FALSE

############################################################################
# Data: ergm.ego model and parameters

load(file = "~/EpiModelHIV_shamp_modeling/scenarios/est/fitsmall.rda")
load(file = "~/EpiModelHIV_shamp_modeling/scenarios/est/data.params.rda")
source(file= "~/EpiModelHIV_SHAMP2/tests/age_mort.R")

############################################################################
# Model setup
param <- param_shamp(data.params)
init <- init_shamp()
control <- control_shamp(nsteps = 1040)

############################################################################
# Run now and save outside of package, or load

if (runNow) {
  test_baseline<-netsim(est, param, init, control)
  save(test_baseline, file = "~/EpiModelHIV_shamp_modeling/scenarios/test_baseline.rda")
} else {
  load(file = "~/EpiModelHIV_shamp_modeling/scenarios/test_baseline.rda")
}

Check outcomes

Prevalence plot

# Plot code - move to package
plotprev <- function(netobj, 
                     maxtime=1040, 
                     groups=c('i.prev.B', 'i.prev.BI', 'i.prev.H', 'i.prev.HI', 'i.prev.W'), 
                     labels=c('B', 'BI', 'H', 'HI', 'W'),
                     prevcolors=c('deeppink2', 'red4', 'darkviolet', 'blue3', 
                              'dodgerblue3', 'darkgreen', 'gold4', 'grey39')) {
  time <- 1:maxtime
  plot(time, netobj$epi$i.prev[,1], type='l', lwd=4, ylab='Prevalence')
  for (i in 1:length(groups)) {
    lines(netobj$epi[[groups[i]]][,1], col=prevcolors[i], lwd=1.5)
  }
  legend('topright', bty='n', fill=c('black', prevcolors[1:length(groups)]),
         legend=c('Total', labels))
}


# Plot
plotprev(test_baseline)

plotprev(test_baseline, 
         groups=c('i.prev.m', 'i.prev.f', 'i.prev.msmf'),
         labels=c('M', 'F', 'MSMF'))

dth2/EpiModelHIV_SHAMP documentation built on May 15, 2019, 4:56 p.m.