tests/age_mort.R

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

#Create additional required elements for est
# Time unit for simulation, relative to 1 day
time.unit <- 7
method<-1

#Simulation size.
sim.size<-38145


#Mortality
ages <- 18:59
age.unit <- 52

asmr.B.f <- c(rep(0, 17),
            1-(1-c(rep(0.000405376, 12),
                   rep(0.000661066, 10),
                   rep(0.001378053, 10),
                   rep(0.003065837, 10)))^(1 / age.unit),
            1)
asmr.BI.f <- c(rep(0, 17),
             1-(1-c(rep(0.000405376, 12),
                    rep(0.000661066, 10),
                    rep(0.001378053, 10),
                    rep(0.003065837, 10)))^(1 / age.unit),
             1)

asmr.H.f <- c(rep(0, 17),
            1-(1-c(rep(0.000405376, 12),
                   rep(0.000661066, 10),
                   rep(0.001378053, 10),
                   rep(0.003065837, 10)))^(1/age.unit),
            1)
asmr.HI.f <- c(rep(0, 17),
             1-(1-c(rep(0.000405376, 12),
                    rep(0.000661066, 10),
                    rep(0.001378053, 10),
                    rep(0.003065837, 10)))^(1/age.unit),
             1)
asmr.W.f <- c(rep(0, 17),
            1-(1-c(rep(0.000405376, 12),
                   rep(0.000661066, 10),
                   rep(0.001378053, 10),
                   rep(0.003065837, 10)))^(1/age.unit),
            1)


asmr.B.m <- c(rep(0, 17),
              1-(1-c(rep(0.000853417, 12),
                     rep(0.001084014, 10),
                     rep(0.001982864, 10),
                     rep(0.005400669, 10)))^(1 / age.unit),
              1)
asmr.BI.m <- c(rep(0, 17),
               1-(1-c(rep(0.000853417, 12),
                      rep(0.001084014, 10),
                      rep(0.001982864, 10),
                      rep(0.005400669, 10)))^(1 / age.unit),
               1)

asmr.H.m <- c(rep(0, 17),
              1-(1-c(rep(0.000853417, 12),
                     rep(0.001084014, 10),
                     rep(0.001982864, 10),
                     rep(0.005400669, 10)))^(1/age.unit),
              1)
asmr.HI.m <- c(rep(0, 17),
               1-(1-c(rep(0.000853417, 12),
                      rep(0.001084014, 10),
                      rep(0.001982864, 10),
                      rep(0.005400669, 10)))^(1/age.unit),
               1)
asmr.W.m <- c(rep(0, 17),
              1-(1-c(rep(0.000853417, 12),
                     rep(0.001084014, 10),
                     rep(0.001982864, 10),
                     rep(0.005400669, 10)))^(1/age.unit),
              1)




exp.mort <- (mean(asmr.B.f[ages]) + mean(asmr.BI.f[ages]) + mean(asmr.H.f[ages])
             + mean(asmr.HI.f[ages]) + mean(asmr.W.f[ages]) + mean(asmr.B.m[ages]) 
             + mean(asmr.BI.m[ages]) + mean(asmr.H.m[ages])
             + mean(asmr.HI.m[ages]) + mean(asmr.W.m[ages]) ) / 10