knitr::opts_chunk$set(echo = TRUE) ############################################################################ # Packages library(EpiModelHIV) library(EpiModelHPC) library(ergm.ego) library(tergmLite)
############################################################################ # Run new sim or load from previous run runNow <- FALSE ############################################################################ # Data: ergm.ego model and parameters load(file = "~/EpiModelHIV_shamp_modeling/scenarios/est/fitsmall.rda") load(file = "~/EpiModelHIV_shamp_modeling/scenarios/est/data.params.rda") source(file= "~/EpiModelHIV_SHAMP2/tests/age_mort.R") ############################################################################ # Model setup param <- param_shamp(data.params) init <- init_shamp() control <- control_shamp(nsteps = 1040) ############################################################################ # Run now and save outside of package, or load if (runNow) { test_baseline<-netsim(est, param, init, control) save(test_baseline, file = "~/EpiModelHIV_shamp_modeling/scenarios/test_baseline.rda") } else { load(file = "~/EpiModelHIV_shamp_modeling/scenarios/test_baseline.rda") }
# Plot code - move to package plotprev <- function(netobj, maxtime=1040, groups=c('i.prev.B', 'i.prev.BI', 'i.prev.H', 'i.prev.HI', 'i.prev.W'), labels=c('B', 'BI', 'H', 'HI', 'W'), prevcolors=c('deeppink2', 'red4', 'darkviolet', 'blue3', 'dodgerblue3', 'darkgreen', 'gold4', 'grey39')) { time <- 1:maxtime plot(time, netobj$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'))
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